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Sample records for chain rotamer sampling

  1. A protein-dependent side-chain rotamer library.

    KAUST Repository

    Bhuyan, M.S.

    2011-12-14

    Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.

  2. Beyond rotamers: a generative, probabilistic model of side chains in proteins

    DEFF Research Database (Denmark)

    Harder, Tim; Boomsma, Wouter; Paluszewski, Martin;

    2010-01-01

    Background: Accurately covering the conformational space of amino acid side chains is essential for important applications such as protein design, docking and high resolution structure prediction. Today, the most common way to capture this conformational space is through rotamer libraries discrete...... for certain applications. For example, rigorously combining rotamers with physical force fields is associated with numerous problems. Results: In this work we present BASILISK: a generative, probabilistic model of the conformational space of side chains that makes it possible to sample in continuous space...... model of side chain conformational space. We also illustrate how the model can be used for rigorous, unbiased sampling with a physical force field, and how it improves side chain prediction when used as a pseudo-energy term. In conclusion, BASILISK is an important step forward on the way to a rigorous...

  3. Protein design using continuous rotamers.

    Directory of Open Access Journals (Sweden)

    Pablo Gainza

    2012-01-01

    Full Text Available Optimizing amino acid conformation and identity is a central problem in computational protein design. Protein design algorithms must allow realistic protein flexibility to occur during this optimization, or they may fail to find the best sequence with the lowest energy. Most design algorithms implement side-chain flexibility by allowing the side chains to move between a small set of discrete, low-energy states, which we call rigid rotamers. In this work we show that allowing continuous side-chain flexibility (which we call continuous rotamers greatly improves protein flexibility modeling. We present a large-scale study that compares the sequences and best energy conformations in 69 protein-core redesigns using a rigid-rotamer model versus a continuous-rotamer model. We show that in nearly all of our redesigns the sequence found by the continuous-rotamer model is different and has a lower energy than the one found by the rigid-rotamer model. Moreover, the sequences found by the continuous-rotamer model are more similar to the native sequences. We then show that the seemingly easy solution of sampling more rigid rotamers within the continuous region is not a practical alternative to a continuous-rotamer model: at computationally feasible resolutions, using more rigid rotamers was never better than a continuous-rotamer model and almost always resulted in higher energies. Finally, we present a new protein design algorithm based on the dead-end elimination (DEE algorithm, which we call iMinDEE, that makes the use of continuous rotamers feasible in larger systems. iMinDEE guarantees finding the optimal answer while pruning the search space with close to the same efficiency of DEE.Software is available under the Lesser GNU Public License v3. Contact the authors for source code.

  4. Using quantum mechanics to improve estimates of amino acid side chain rotamer energies.

    Science.gov (United States)

    Renfrew, P Douglas; Butterfoss, Glenn L; Kuhlman, Brian

    2008-06-01

    Amino acid side chains adopt a discrete set of favorable conformations typically referred to as rotamers. The relative energies of rotamers partially determine which side chain conformations are more often observed in protein structures and accurate estimates of these energies are important for predicting protein structure and designing new proteins. Protein modelers typically calculate side chain rotamer energies by using molecular mechanics (MM) potentials or by converting rotamer probabilities from the protein database (PDB) into relative free energies. One limitation of the knowledge-based energies is that rotamer preferences observed in the PDB can reflect internal side chain energies as well as longer-range interactions with the rest of the protein. Here, we test an alternative approach for calculating rotamer energies. We use three different quantum mechanics (QM) methods (second order Møller-Plesset (MP2), density functional theory (DFT) energy calculation using the B3LYP functional, and Hartree-Fock) to calculate the energy of amino acid rotamers in a dipeptide model system, and then use these pre-calculated values in side chain placement simulations. Energies were calculated for over 36,000 different conformations of leucine, isoleucine, and valine dipeptides with backbone torsion angles from the helical and strand regions of the Ramachandran plot. In a subset of cases these energies differ significantly from those calculated with standard molecular mechanics potentials or those derived from PDB statistics. We find that in these cases the energies from the QM methods result in more accurate placement of amino acid side chains in structure prediction tests.

  5. The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M

    2011-01-01

    and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the ¿-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation...... of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...

  6. A rotamer library to enable modeling and design of peptoid foldamers.

    Science.gov (United States)

    Renfrew, P Douglas; Craven, Timothy W; Butterfoss, Glenn L; Kirshenbaum, Kent; Bonneau, Richard

    2014-06-18

    Peptoids are a family of synthetic oligomers composed of N-substituted glycine units. Along with other "foldamer" systems, peptoid oligomer sequences can be predictably designed to form a variety of stable secondary structures. It is not yet evident if foldamer design can be extended to reliably create tertiary structure features that mimic more complex biomolecular folds and functions. Computational modeling and prediction of peptoid conformations will likely play a critical role in enabling complex biomimetic designs. We introduce a computational approach to provide accurate conformational and energetic parameters for peptoid side chains needed for successful modeling and design. We find that peptoids can be described by a "rotamer" treatment, similar to that established for proteins, in which the peptoid side chains display rotational isomerism to populate discrete regions of the conformational landscape. Because of the insufficient number of solved peptoid structures, we have calculated the relative energies of side-chain conformational states to provide a backbone-dependent (BBD) rotamer library for a set of 54 different peptoid side chains. We evaluated two rotamer library development methods that employ quantum mechanics (QM) and/or molecular mechanics (MM) energy calculations to identify side-chain rotamers. We show by comparison to experimental peptoid structures that both methods provide an accurate prediction of peptoid side chain placements in folded peptoid oligomers and at protein interfaces. We have incorporated our peptoid rotamer libraries into ROSETTA, a molecular design package previously validated in the context of protein design and structure prediction.

  7. Correlation of tryptophan fluorescence intensity decay parameters with sup 1 H NMR-determined rotamer conformations: (tryptophan sup 2 )oxytocin

    Energy Technology Data Exchange (ETDEWEB)

    Ross, J.B.A.; Schwartz, G.P.; Laws, W.R. (Mount Sinai, New York, NY (United States)); Wyssbrod, H.R.; Porter, R.A. (Univ. of Louisville, KY (United States)); Michaels, C.A. (Swarthmore Coll., PA (United States))

    1992-02-18

    While the fluorescence decay kinetics of tyrosine model compounds can be explained in terms of heterogeneity derived from the three ground-state {chi}{sup 1} rotamers, a similar correlation has yet to be directly observed for a tryptophan residue. In addition, the asymmetric indole ring might also lead to heterogeneity from {chi}{sup 2} rotations. In this paper, the time-resolved and steady-state fluorescence properties of (tryptophan{sup 2})oxytocin at pH 3 are presented and compared with {sup 1}H NMR results. According to the unrestricted analyses of individual fluorescence decay curves taken as a function of emission wavelength-independent decay constants, only three exponential terms are required. In addition, the preexponential weighting factors (amplitudes) have the same relative relationship (weights) as the {sup 1}H NMR-determined {chi}{sup 1} rotamer populations of the indole side chain. {sup 15}N was used in heteronuclear coupling experiments to confirm the rotamer assignments. Inclusion of a linked function restricting the decay amplitudes to the {chi}{sup 1} rotamer populations in the individual decay curve analyses and in the global analysis confirms this correlation. According to qualitative nuclear Overhauser data, there are two {chi}{sup 2} populations.

  8. Compressed classification learning with Markov chain samples.

    Science.gov (United States)

    Cao, Feilong; Dai, Tenghui; Zhang, Yongquan; Tan, Yuanpeng

    2014-02-01

    In this article, we address the problem of compressed classification learning. A generalization bound of the support vector machines (SVMs) compressed classification algorithm with uniformly ergodic Markov chain samples is established. This bound indicates that the accuracy of the SVM classifier in the compressed domain is close to that of the best classifier in the data domain. In a sense, the fact that the compressed learning can avoid the curse of dimensionality in the learning process is shown. In addition, we show that compressed classification learning reduces the learning time at the price of decreasing the classification accuracy, but the decrement can be controlled. The numerical experiments further verify the results claimed in this article.

  9. Cis–Trans Amide Bond Rotamers in β-Peptoids and Peptoids: Evaluation of Stereoelectronic

    DEFF Research Database (Denmark)

    Laursen, Jonas Striegler; Engel-Andreasen, Jens; Fristrup, Peter;

    2013-01-01

    to folding propensity. Thus, we here report an investigation of the effect of structural variations on the cis–trans amide bond rotamer equilibria in a selection of monomer model systems. In addition to various side chain effects, which correlated well with previous studies of α-peptoids, we present...... the synthesis and investigation of cis–trans isomerism in the first examples of peptoids and β-peptoids containing thioamide bonds as well as trifluoroacetylated peptoids and β-peptoids. These systems revealed an increase in the preference for cis-amides as compared to their parent compounds, and thus provide...

  10. Side Chain Conformational Distributions of a Small Protein Derived from Model-Free Analysis of a Large Set of Residual Dipolar Couplings.

    Science.gov (United States)

    Li, Fang; Grishaev, Alexander; Ying, Jinfa; Bax, Ad

    2015-11-25

    Accurate quantitative measurement of structural dispersion in proteins remains a prime challenge to both X-ray crystallography and NMR spectroscopy. Here we use a model-free approach based on measurement of many residual dipolar couplings (RDCs) in differentially orienting aqueous liquid crystalline solutions to obtain the side chain χ1 distribution sampled by each residue in solution. Applied to the small well-ordered model protein GB3, our approach reveals that the RDC data are compatible with a single narrow distribution of side chain χ1 angles for only about 40% of the residues. For more than half of the residues, populations greater than 10% for a second rotamer are observed, and four residues require sampling of three rotameric states to fit the RDC data. In virtually all cases, sampled χ1 values are found to center closely around ideal g(-), g(+) and t rotameric angles, even though no rotamer restraint is used when deriving the sampled angles. The root-mean-square difference between experimental (3)JHαHβ couplings and those predicted by the Haasnoot-parametrized, motion-adjusted Karplus equation reduces from 2.05 to 0.75 Hz when using the new rotamer analysis instead of the 1.1-Å X-ray structure as input for the dihedral angles. A comparison between observed and predicted (3)JHαHβ values suggests that the root-mean-square amplitude of χ1 angle fluctuations within a given rotamer well is ca. 20°. The quantitatively defined side chain rotamer equilibria obtained from our study set new benchmarks for evaluating improved molecular dynamics force fields, and also will enable further development of quantitative relations between side chain chemical shift and structure.

  11. Perfect Sampling of Markov Chains with Piecewise Homogeneous Events

    CERN Document Server

    Bušić, Ana; Pin, Furcy

    2010-01-01

    Perfect sampling is a technique that uses coupling arguments to provide a sample from the stationary distribution of a Markov chain in a finite time without ever computing the distribution. This technique is very efficient if all the events in the system have monotonicity property. However, in the general (non-monotone) case, this technique needs to consider the whole state space, which limits its application only to chains with a state space of small cardinality. We propose here a new approach for the general case that only needs to consider two trajectories. Instead of the original chain, we use two bounding processes (envelopes) and we show that, whenever they couple, one obtains a sample under the stationary distribution of the original chain. We show that this new approach is particularly effective when the state space can be partitioned into pieces where envelopes can be easily computed. We further show that most Markovian queueing networks have this property and we propose efficient algorithms for some...

  12. Automated microdroplet platform for sample manipulation and polymerase chain reaction.

    Science.gov (United States)

    Chabert, Max; Dorfman, Kevin D; de Cremoux, Patricia; Roeraade, Johan; Viovy, Jean-Louis

    2006-11-15

    We present a fully automated system performing continuous sampling, reagent mixing, and polymerase chain reaction (PCR) in microdroplets transported in immiscible oil. Sample preparation and analysis are totally automated, using an original injection method from a modified 96-well plate layered with three superimposed liquid layers and in-capillary laser-induced fluorescence endpoint detection. The process is continuous, allowing sample droplets to be carried uninterruptedly into the reaction zone while new drops are aspirated from the sample plate. Reproducible amplification, negligible cross-contamination, and detection of low sample concentrations were demonstrated on numerous consecutive sample drops. The system, which opens the route to strong reagents and labor savings in high-throughput applications, was validated on the clinically relevant quantification of progesterone receptor gene expression in human breast cancer cell lines.

  13. Optimized nested Markov chain Monte Carlo sampling: theory

    Energy Technology Data Exchange (ETDEWEB)

    Coe, Joshua D [Los Alamos National Laboratory; Shaw, M Sam [Los Alamos National Laboratory; Sewell, Thomas D [U. MISSOURI

    2009-01-01

    Metropolis Monte Carlo sampling of a reference potential is used to build a Markov chain in the isothermal-isobaric ensemble. At the endpoints of the chain, the energy is reevaluated at a different level of approximation (the 'full' energy) and a composite move encompassing all of the intervening steps is accepted on the basis of a modified Metropolis criterion. By manipulating the thermodynamic variables characterizing the reference system we maximize the average acceptance probability of composite moves, lengthening significantly the random walk made between consecutive evaluations of the full energy at a fixed acceptance probability. This provides maximally decorrelated samples of the full potential, thereby lowering the total number required to build ensemble averages of a given variance. The efficiency of the method is illustrated using model potentials appropriate to molecular fluids at high pressure. Implications for ab initio or density functional theory (DFT) treatment are discussed.

  14. Organic cleanliness of the Mars Science Laboratory sample transfer chain.

    Science.gov (United States)

    Blakkolb, B; Logan, C; Jandura, L; Okon, A; Anderson, M; Katz, I; Aveni, G; Brown, K; Chung, S; Ferraro, N; Limonadi, D; Melko, J; Mennella, J; Yavrouian, A

    2014-07-01

    One of the primary science goals of the Mars Science Laboratory (MSL) Rover, Curiosity, is the detection of organics in Mars rock and regolith. To achieve this, the Curiosity rover includes a robotic sampling system that acquires rock and regolith samples and delivers it to the Sample Analysis at Mars (SAM) instrument on board the rover. In order to provide confidence that any significant organics detection result was Martian and not terrestrial in origin, a requirement was levied on the flight system (i.e., all sources minus the SAM instrument) to impart no more than 36 parts per billion (ppb by weight) of total reduced carbon terrestrial contamination to any sample transferred to the SAM instrument. This very clean level was achieved by a combination of a rigorous contamination control program on the project, and then using the first collected samples for a "dilution cleaning" campaign of the sample chain prior to delivering a sample to the SAM instrument. Direct cleanliness assays of the sample-contacting and other Flight System surfaces during pre-launch processing were used as inputs to determine the number of dilution cleaning samples needed once on Mars, to enable delivery of suitably clean samples to the SAM experiment. Taking into account contaminant redistribution during launch thorough landing of the MSL on Mars, the amount of residue present on the sampling hardware prior to the time of first dilution cleaning sample acquisition was estimated to be 60 ng/cm(2) on exposed outer surfaces of the sampling hardware and 20 ng/cm(2) on internal sample contacting surfaces; residues consisting mainly of aliphatic hydrocarbons and esters. After three dilution cleaning samples, estimated in-sample contamination level for the first regolith sample delivered to the SAM instrument at the Gale Crater "Rocknest" site was bounded at ≤10 ppb total organic carbon. A Project decision to forego ejecting the dilution cleaning sample and instead transfer the first drill

  15. Toxoplasma polymerase chain reaction on experimental blood samples.

    Science.gov (United States)

    Joss, A W; Chatterton, J M; Evans, R; Ho-Yen, D O

    1993-01-01

    A two-stage polymerase chain reaction (PCR) assay employing oligonucleotide primers from the B1 gene of Toxoplasma gondii was developed and assessed for sensitivity and specificity. It was able to detect T. gondii DNA from as little as one parasite/sample in mock-infected rat or mouse leucocyte preparations. Parasitaemia was also identified in animals at five stages between 16 and 66 h after infection with the virulent RH strain, and at 12 stages between 2 and 38 days after infection with the cyst-forming Beverley strain. In the latter case, PCR was more sensitive than animal culture. No cross-reactions were observed in samples containing various opportunist pathogens which may also be found in the blood of immunocompromised patients.

  16. Thermodynamic properties of rod-like chains: Entropic sampling simulations

    Science.gov (United States)

    Ferreira, L. S.; Jorge, L. N.; Caparica, A. A.; Nascimento, D. A.; Neto, Minos A.; Sousa, J. R.

    2016-11-01

    In this work, we apply entropic sampling simulations to a three-state model which has exact solutions in the microcanonical and grand-canonical ensembles. We consider N chains placed on an unidimensional lattice, such that each site may assume one of the three states: empty (state 1), with a single molecule energetically null (state 2), and with a single molecule with energy 𝜀 (state 3). Each molecule, which we will treat here as dimers, consists of two monomers connected one to each other by a rod. The thermodynamic properties such as internal energy, densities of dimers and specific heat were obtained as functions of temperature, where the analytic results in the microcanonical and grand-canonical ensembles were successfully confirmed by the entropic sampling simulations.

  17. Flat versus twisted rotamers of 2,4-disubstituted thiazoles: the effect of intermolecular hydrogen bonds.

    Science.gov (United States)

    Bernès, Sylvain; Berros, Martha I; Rodríguez de Barbarín, Cecilia; Sánchez-Viesca, Francisco

    2002-03-01

    In the title compounds, 2-amino-4-(2-chloro-4,5-dimethoxyphenyl)-1,3-thiazole, C(11)H(11)ClN(2)O(2)S, (I), and 4-(2-chloro-4,5-dimethoxyphenyl)-2-methyl-1,3-thiazole, C(12)H(12)ClNO(2)S, (II), the dihedral angles between the thiazole moiety and the chloroaryl group are 51.61 (10) and 8.44 (14), respectively. This difference is a consequence of intermolecular hydrogen bonds forcing the stabilization of a twisted rotamer in (I). Substitution of the amino function by a methyl group precludes these contacts, giving a flat rotamer in (II).

  18. Exploring the activity space of peptides binding to diverse SH3 domains using principal property descriptors derived from amino acid rotamers.

    Science.gov (United States)

    He, Ping; Wu, Wei; Yang, Kang; Jing, Tao; Liao, Ke-Long; Zhang, Wei; Wang, Hai-Dong; Hua, Xing

    2011-01-01

    Although there were intensive works addressed on multivariate extraction of the informative components from numerous physicochemical parameters of amino acids in isolated state, the various conformational behaviors of amino acids in complicated biological context have long been underappreciated in the field of quantitative structure-activity relationship (QSAR). In this work, the amino acid rotamers, which were derived from statistical survey of protein crystal structures, were used to reproduce the conformational variety of amino acid side-chains in real condition. In this procedure, these rotamers were superposed into a nx x ny x nz lattice and an artificial probe was employed to detect four kinds of nonbonding field potentials (i.e., electrostatic, steric, hydrophobic, and hydrogen bonds) at each lattice point using a Gaussian-type potential function; the generated massive data were then subjected to a principal component analysis (PCA) treatment to obtain a set of few, informative amino acid descriptors. We used this set of descriptors, that we named principal property descriptors derived from amino acid rotamers (PDAR), to characterize over 13,000 peptides with known binding affinities to 10 types of SH3 domains. Genetic algorithm/ partial least square regression (GA/PLS) modeling and Monte Carlo cross-validation (MCCV) demonstrated that the correlation between the PDAR descriptors and the binding affinities of peptides are comparable with or even better than previously published models. Furthermore, from the PDAR-based QSAR models we concluded that the core motif of peptides, particularly the electrostatic property, hydrophobicity, and hydrogen bond at residue positions P3, P2, and/or P0, contribute significantly to the hAmph SH3 domain-peptide binding, whereas two ends of the peptides, such as P6, P4, P-4, and P5, only play a secondary role in the binding.

  19. Maintaining solvent accessible surface area under rotamer substitution for protein design.

    Science.gov (United States)

    Leaver-Fay, Andrew; Butterfoss, Glenn L; Snoeyink, Jack; Kuhlman, Brian

    2007-06-01

    Although quantities derived from solvent accessible surface areas (SASA) are useful in many applications in protein design and structural biology, the computational cost of accurate SASA calculation makes SASA-based scores difficult to integrate into commonly used protein design methodologies. We demonstrate a method for maintaining accurate SASA during a Monte Carlo search of sequence and rotamer space for a fixed protein backbone. We extend the fast Le Grand and Merz algorithm (Le Grand and Merz, J Comput Chem, 14, 349), which discretizes the solvent accessible surface for each atom by placing dots on a sphere and combines Boolean masks to determine which dots are exposed. By replacing semigroup operations with group operations (from Boolean logic to counting dot coverage) we support SASA updates. Our algorithm takes time proportional to the number of atoms affected by rotamer substitution, rather than the number of atoms in the protein. For design simulations with a one hundred residue protein our approach is approximately 145 times faster than performing a Le Grand and Merz SASA calculation from scratch following each rotamer substitution. To demonstrate practical effectiveness, we optimize a SASA-based measure of protein packing in the complete redesign of a large set of proteins and protein-protein interfaces.

  20. Investigating the ground-state rotamers of n-propylperoxy radical

    Science.gov (United States)

    Hoobler, Preston R.; Turney, Justin M.; Schaefer, Henry F.

    2016-11-01

    The n-propylperoxy radical has been described as a molecule of critical importance to studies of low temperature combustion. Ab initio methods were used to study this three-carbon alkylperoxy radical, normal propylperoxy. Reliable CCSD(T) (coupled-cluster theory, incorporating single, double, and perturbative triple)/ANO0 geometries were predicted for the molecule's five rotamers. For each rotamer, energetic predictions were made using basis sets as large as the cc-pV5Z in conjunction with coupled cluster levels of theory up to CCSDT(Q). Along with the extrapolations, corrections for relativistic effects, zero-point vibrational energies, and diagonal Born-Oppenheimer corrections were used to further refine energies. The results indicate that the lowest conformer is the gauche-gauche (GG) rotamer followed by the gauche-trans (0.12 kcal mol-1 above GG), trans-gauche (0.44 kcal mol-1), gauche'-gauche (0.47 kcal mol-1), and trans-trans (0.57 kcal mol-1). Fundamental vibrational frequencies were obtained using second-order vibrational perturbation theory. This is the first time anharmonic frequencies have been computed for this system. The most intense IR features include all but one of the C-H stretches. The O-O fundamental (1063 cm-1 for the GG structure) also has a significant IR intensity, 19.6 km mol-1. The anharmonicity effects on the potential energy surface were also used to compute vibrationally averaged rg,0K bond lengths, accounting for zero-point vibrations present within the molecule.

  1. Vibrational spectra, NMR and theoretical studies of the enantiomers and rotamers of alpha-cypermethrin

    Science.gov (United States)

    Jubert, Alicia H.; Alegre, María L.; Diez, Reinaldo Pis; Pomilio, Alicia B.; Szewczuk, Víctor D.

    2007-04-01

    NMR, infrared and Raman vibrational spectra of alpha-cypermethrin have been measured at room temperature. Infrared spectra were also recorded to low temperature. The spectra were analyzed by means of ab initio calculations. The conformational space of both enantiomers and some rotamers A, B and C of alpha-cypermethrin has been scanned using molecular dynamics and complemented with functional density calculations that optimize the geometry of the lowest-energy conformers of each species as obtained in the simulations. The vibrational frequencies and the 1H and 13C NMR chemical shifts were assigned using functional density calculations. The molecular electrostatic potential maps were obtained and analyzed.

  2. Unique structural properties of 2,4,6-tri-tert-butylanilide: isomerization and switching between separable amide rotamers through the reaction of anilide enolates.

    Science.gov (United States)

    Tsukagoshi, Shiori; Ototake, Nobutaka; Ohnishi, Yusuke; Shimizu, Mayu; Kitagawa, Osamu

    2013-05-17

    Herein, we report a unique structural property of 2,4,6-tri-tert-butylanilide, which can be separated into its amide rotamers at room temperature. Interconversion between the rotamers of anilide enolates occurs readily at room temperature and their reaction with electrophiles gives mixtures of the rotamers in a ratio that depends on the reactivity of the corresponding electrophile. That is, the reaction of the 2,4,6-tri-tert-butylacetanilide enolate with reactive electrophiles, such as allyl bromide or protic acids, gives mixtures of the anilide rotamers in which the E rotamer is the major component, whereas less-reactive electrophiles, such as 1-bromopropane and 2-iodopropane, yield mixtures of the rotamers in which the Z rotamer is the major component. The rotameric ratio of the product is also strongly dependent on the reactivity of the anilide enolate. Switching between the anilide rotamers can be achieved through protonation of a less-reactive enolate by a less-reactive protic acid and thermal isomerization of the anilide.

  3. Adapting chain referral methods to sample new migrants: Possibilities and limitations

    Directory of Open Access Journals (Sweden)

    Lucinda Platt

    2015-09-01

    Full Text Available Background: Demographic research on migration requires representative samples of migrant populations. Yet recent immigrants, who are particularly informative about current migrant flows, are difficult to capture even in specialist surveys. Respondent-driven sampling (RDS, a chain referral sampling and analysis technique, potentially offers the opportunity to achieve population-level inference of recently arrived migrant populations. Objective: We evaluate the attempt to use RDS to sample two groups of migrants, from Pakistan and Poland, who had arrived in the UK within the previous 18 months, and we present an alternative approach adapted to recent migrants. Methods: We discuss how connectedness, privacy, clustering, and motivation are expected to differ among recently arrived migrants, compared to typical applications of RDS. We develop a researcher-led chain referral approach, and compare success in recruitment and indicators of representativeness to standard RDS recruitment. Results: Our researcher-led approach led to higher rates of chain-referral, and enabled us to reach population members with smaller network sizes. The researcher-led approach resulted in similar recruiter-recruit transition probabilities to traditional RDS across many demographic and social characteristics. However, we did not succeed in building up long referral chains, largely due to the lack of connectedness of our target populations and some reluctance to refer. There were some differences between the two migrant groups, with less mobile and less hidden Pakistani men producing longer referral chains. Conclusions: Chain referral is difficult to implement for sampling newly arrived migrants. However, our researcher-led adaptation shows promise for less hidden and more stable recent immigrant populations. Contribution: The paper offers an evaluation of RDS for surveying recent immigrants and an adaptation that may be effective under certain conditions.

  4. On-Chip integration of sample pretreatment and Multiplex polymerase chain reaction (PCR) for DNA analysis

    DEFF Research Database (Denmark)

    Brivio, Monica; Snakenborg, Detlef; Søgaard, E.;

    2008-01-01

    In this paper we present a modular lab-on-a-chip system for integrated sample pre-treatment (PT) by magnetophoresis and DNA amplification by polymerase chain reaction (PCR). It consists of a polymer-based microfluidic chip mounted on a custom-made thermocycler (Figure 1) and includes a simple...

  5. Contamination profiles of short-chain polychlorinated n-alkanes in foodstuff samples from Japan

    Energy Technology Data Exchange (ETDEWEB)

    Matsukami, Hidenori; Kurunthachalam, S.; Ohi, Etsumasa; Takasuga, Takumi [Shimadzu Techno Research, Inc., Kyoto (Japan); Iino, Fukuya; Nakanishi, Junko [National Inst. of Advanced Industrial Science and Technology, Tsukuba (Japan)

    2004-09-15

    Polychlorinated n-alkanes (PCAs) are group of chemicals manufactured by chlorination of liquid n-paraffin or paraffin wax that contain 30 to 70% chlorine by weight. Large amounts of PCAs are widely used as plasticizers for vinyl chloride, lubricants, paints, and flame retardants and number of other industrial applications. Annual global production of PCAs is approximately 300 kilo tones, with a majority having medium-carbon-chain (C14-C19) length. According to the investigation made by Kagaku Kogyo Nippon-Sha, the annual consumption of PCAs in Japan was about 83,000 tons in between 1986-2001. Short-carbon-chain (C10-C13) has been placed on the Priority Substance List under Canadian Environmental Protection Act and on the Environmental Protection Agency Toxic Release Inventory in the USA due to its potential to act as tumor promoters in mammals. Data on environment levels of PCAs is meager, nevertheless, PCAs have been measured at relatively high concentrations in biota from Sweden, biota, sediment from Canada and marine biota and human milk from the Canadian Arctic. In our earlier study, we reported concentrations of short-chain PCAs from sewage treatment plant (STP) collected from Tama River, Tokyo and river water and sediment from Tokyo and Osaka. STP influent water contained greater shortchain PCAs concentrations than STP effluent. In addition, some river water and sediment samples contained detectable concentrations of short-chain PCAs, which was similar to other industrial countries. However, there is no study conducted to explore the contamination profiles of short-chain PCAs in human foodstuff samples. In the present study, we analyzed eleven foodstuff samples that were purchased from various supermarkets in order to know the short-chain PCAs concentrations in the foodstuff and possible human total daily intake (TDI) amounts.

  6. RosettaEPR: rotamer library for spin label structure and dynamics.

    Directory of Open Access Journals (Sweden)

    Nathan S Alexander

    Full Text Available An increasingly used parameter in structural biology is the measurement of distances between spin labels bound to a protein. One limitation to these measurements is the unknown position of the spin label relative to the protein backbone. To overcome this drawback, we introduce a rotamer library of the methanethiosulfonate spin label (MTSSL into the protein modeling program Rosetta. Spin label rotamers were derived from conformations observed in crystal structures of spin labeled T4 lysozyme and previously published molecular dynamics simulations. Rosetta's ability to accurately recover spin label conformations and EPR measured distance distributions was evaluated against 19 experimentally determined MTSSL labeled structures of T4 lysozyme and the membrane protein LeuT and 73 distance distributions from T4 lysozyme and the membrane protein MsbA. For a site in the core of T4 lysozyme, the correct spin label conformation (Χ1 and Χ2 is recovered in 99.8% of trials. In surface positions 53% of the trajectories agree with crystallized conformations in Χ1 and Χ2. This level of recovery is on par with Rosetta performance for the 20 natural amino acids. In addition, Rosetta predicts the distance between two spin labels with a mean error of 4.4 Å. The width of the experimental distance distribution, which reflects the flexibility of the two spin labels, is predicted with a mean error of 1.3 Å. RosettaEPR makes full-atom spin label modeling available to a wide scientific community in conjunction with the powerful suite of modeling methods within Rosetta.

  7. Detection of Helicobactor pylori by polymerase chain reaction: A comparison in sample preparation

    Directory of Open Access Journals (Sweden)

    Murugesan R

    2005-01-01

    Full Text Available Gastric biopsy samples obtained from 14 patients with upper abdominal pain, clinically diagnosed as acid peptic disease, were analysed for the presence of Helicobacter pylori (H. pylori by Polymerase Chain Reaction (PCR using partially (template A and completely purified DNA (template B. Antigen specific primer was used to analyse the sample by PCR method. The presence of H. pylori in the samples was confirmed by running a positive control. The presence of H. pylori was also detected by urease method using standard protocol. Among the 14 samples studied, 8 showed the presence of H. pylori with both templates A and B. Among these 8 samples only 3 showed positive for the presence of H. pylori with urease method. The present work discusses the results obtained in the detection of H. pylori in template A and B by PCR method.

  8. Use of pooled samples for the detection of Salmonella in feces by polymerase chain reaction.

    Science.gov (United States)

    Singer, Randall S; Cooke, Cara L; Maddox, Carol W; Isaacson, Richard E; Wallace, Richard L

    2006-07-01

    Many epidemiological studies of Salmonella rely on conventional bacteriological culture methods to detect Salmonella in fecal samples. These culture-based methods are inefficient for epidemiological studies in populations with a low prevalence of Salmonella. The objective of this study was to optimize a protocol that uses pooled Salmonella enrichment broth cultures of bovine feces and polymerase chain reaction (PCR) for the detection of the invA gene of Salmonella in feces. In one field trial, 196 animals were sampled, and all samples were tested by culture, invA PCR on individual samples, invA PCR on pools of 5 samples, and BAX PCR on individual samples. All assays showed a high agreement on individual samples (kappa > or = 0.75). The invA PCR was run on each of 40 pools and detected 19 of 22 culture-positive pools. In another field trial, 152 samples were taken from 4 dairies, and the invA PCR was performed on pools of 5 samples in addition to bacteriological culture of individual samples. Salmonella was detected in 5 of the 32 pools (7 total positive samples) by both PCR and culture. One pool was PCR-positive but culture-negative. Pooling did not dramatically affect the performance of the invA PCR; most of the culture-positive samples were detected, including all of the samples when there were 4 or more Salmonella colonies on the agar plate. Based on these field trials, invA PCR on pooled samples appears to be an efficient method of Salmonella detection as long as Salmonella loads are not extremely low.

  9. Use of polymerase chain reaction (PCR for detection of Chlamydia trachomatis infection in cervical swab samples

    Directory of Open Access Journals (Sweden)

    Mania-Pramanik Jayanti

    2001-09-01

    Full Text Available A polymerase chain reaction (PCR based method has been set up for detection of Chlamydia trachomatis (C. trachomatis infection in single cervical swab samples. A primer pair specific to the major outer membrane protein (MOMP gene common to all serotypes of C. trachomatis was used. This method was validated for its sensitivity as well as specificity. A minimum Ing of DNA could be used for detection of the infection. Specificity of the method was confirmed by carrying out a sample dilution curve. The cervical swab samples analysed in the present study were in coded form for validation of the PCR with an established commercial ELISA (Chlamydiazyme. Both the sensitivity and specificity of PCR was 100% when the ELISA results of these samples were decoded. Thus, this PCR technique could be used for better diagnosis of C. trachomatis infection in comparison to the commercially available ELISA technique.

  10. Rapid Detection of Salmonella in Food and Beverage Samples by Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Radji, M.

    2010-01-01

    Full Text Available Polymerase chain reaction (PCR assay had been used to detect Salmonella in food and beverage samples using suitable primers which are based on specific invA gene of Salmonella. Twenty nine samples were collected from street food counters and some canteens in Margonda Street, Depok, West Java, Indonesia. It was found that five of twenty nine samples were detected to contain Salmonella and showed the presence of the amplified product of the size 244 bp. The method of PCR demonstrated the specificity of invA primers for detection of Salmonella as confirmed by biochemical and serological assay. The results of this study revealed that PCR was a rapid and useful tool for detection of Salmonella in food and beverage samples.

  11. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    Science.gov (United States)

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

  12. Mitochondrial Respiration Chain Enzymatic Activities in the Human Brain: Methodological Implications for Tissue Sampling and Storage.

    Science.gov (United States)

    Ronsoni, Marcelo Fernando; Remor, Aline Pertile; Lopes, Mark William; Hohl, Alexandre; Troncoso, Iris H Z; Leal, Rodrigo Bainy; Boos, Gustavo Luchi; Kondageski, Charles; Nunes, Jean Costa; Linhares, Marcelo Neves; Lin, Kátia; Latini, Alexandra Susana; Walz, Roger

    2016-04-01

    Mitochondrial respiratory chain complexes enzymatic (MRCCE) activities were successfully evaluated in frozen brain samples. Epilepsy surgery offers an ethical opportunity to study human brain tissue surgically removed to treat drug resistant epilepsies. Epilepsy surgeries are done with hemodynamic and laboratory parameters to maintain physiology, but there are no studies analyzing the association among these parameters and MRCCE activities in the human brain tissue. We determined the intra-operative parameters independently associated with MRCCE activities in middle temporal neocortex (Cx), amygdala (AMY) and head of hippocampus (HIP) samples of patients (n = 23) who underwent temporal lobectomy using multiple linear regressions. MRCCE activities in Cx, AMY and HIP are differentially associated to trans-operative mean arterial blood pressure, O2 saturation, hemoglobin, and anesthesia duration to time of tissue sampling. The time-course between the last seizure occurrence and tissue sampling as well as the sample storage to biochemical assessments were also associated with enzyme activities. Linear regression models including these variables explain 13-17 % of MRCCE activities and show a moderate to strong effect (r = 0.37-0.82). Intraoperative hemodynamic and laboratory parameters as well as the time from last seizure to tissue sampling and storage time are associated with MRCCE activities in human samples from the Cx, AMYG and HIP. Careful control of these parameters is required to minimize confounding biases in studies using human brain samples collected from elective neurosurgery.

  13. Uncertainty assessment of integrated distributed hydrological models using GLUE with Markov chain Monte Carlo sampling

    DEFF Research Database (Denmark)

    Blasone, Roberta-Serena; Madsen, Henrik; Rosbjerg, Dan

    2008-01-01

    uncertainty estimation (GLUE) procedure based on Markov chain Monte Carlo sampling is applied in order to improve the performance of the methodology in estimating parameters and posterior output distributions. The description of the spatial variations of the hydrological processes is accounted for by defining...... the identifiability of the parameters and results in satisfactory multi-variable simulations and uncertainty estimates. However, the parameter uncertainty alone cannot explain the total uncertainty at all the sites, due to limitations in the distributed data included in the model calibration. The study also indicates...

  14. Sampling based motion planning with reachable volumes: Application to manipulators and closed chain systems

    KAUST Repository

    McMahon, Troy

    2014-09-01

    © 2014 IEEE. Reachable volumes are a geometric representation of the regions the joints of a robot can reach. They can be used to generate constraint satisfying samples for problems including complicated linkage robots (e.g. closed chains and graspers). They can also be used to assist robot operators and to help in robot design.We show that reachable volumes have an O(1) complexity in unconstrained problems as well as in many constrained problems. We also show that reachable volumes can be computed in linear time and that reachable volume samples can be generated in linear time in problems without constraints. We experimentally validate reachable volume sampling, both with and without constraints on end effectors and/or internal joints. We show that reachable volume samples are less likely to be invalid due to self-collisions, making reachable volume sampling significantly more efficient for higher dimensional problems. We also show that these samples are easier to connect than others, resulting in better connected roadmaps. We demonstrate that our method can be applied to 262-dof, multi-loop, and tree-like linkages including combinations of planar, prismatic and spherical joints. In contrast, existing methods either cannot be used for these problems or do not produce good quality solutions.

  15. Pooling of porcine fecal samples for quantification of Lawsonia intracellularis by real-time polymerase chain reaction

    DEFF Research Database (Denmark)

    Pedersen, Ken Steen; Johansen, Markku; Jorsal, Sven Erik Lind;

    2014-01-01

    obtained by averaging test results from individual fecal samples in relation to a quantitative polymerase chain reaction (qPCR) test for Lawsonia intracellularis. Ten diarrheic and 10 normal fecal samples were submitted from each of 43 Danish swine herds (n = 860 fecal samples). Pools (n = 43), each...

  16. Statistical geometry of lattice chain polymers with voids of defined shapes: Sampling with strong constraints

    Science.gov (United States)

    Lin, Ming; Chen, Rong; Liang, Jie

    2008-02-01

    Proteins contain many voids, which are unfilled spaces enclosed in the interior. A few of them have shapes compatible to ligands and substrates and are important for protein functions. An important general question is how the need for maintaining functional voids is influenced by, and affects other aspects of proteins structures and properties (e.g., protein folding stability, kinetic accessibility, and evolution selection pressure). In this paper, we examine in detail the effects of maintaining voids of different shapes and sizes using two-dimensional lattice models. We study the propensity for conformations to form a void of specific shape, which is related to the entropic cost of void maintenance. We also study the location that voids of a specific shape and size tend to form, and the influence of compactness on the formation of such voids. As enumeration is infeasible for long chain polymer, a key development in this work is the design of a novel sequential Monte Carlo strategy for generating large number of sample conformations under very constraining restrictions. Our method is validated by comparing results obtained from sampling and from enumeration for short polymer chains. We succeeded in accurate estimation of entropic cost of void maintenance, with and without an increasing number of restrictive conditions, such as loops forming the wall of void with fixed length, with additionally fixed starting position in the sequence. Additionally, we have identified the key structural properties of voids that are important in determining the entropic cost of void formation. We have further developed a parametric model to predict quantitatively void entropy. Our model is highly effective, and these results indicate that voids representing functional sites can be used as an improved model for studying the evolution of protein functions and how protein function relates to protein stability.

  17. Solid-phase microextraction for the analysis of short-chain chlorinated paraffins in water samples.

    Science.gov (United States)

    Castells, P; Santos, F J; Galceran, M T

    2003-01-10

    A novel solid-phase microextraction (SPME) method coupled to gas chromatography with electron capture detection (GC-ECD) was developed as an alternative to liquid-liquid and solid-phase extraction for the analysis of short-chain chlorinated paraffins (SCCPs) in water samples. The extraction efficiency of five different commercially available fibres was evaluated and the 100-microm polydimethylsiloxane coating was the most suitable for the absorption of the SCCPs. Optimisation of several SPME parameters, such as extraction time and temperature, ionic strength and desorption time, was performed. Quality parameters were established using Milli-Q, tap water and river water. Linearity ranged between 0.06 and 6 microg l(-1) for spiked Milli-Q water and between 0.6 and 6 microg l(-1) for natural waters. The precision of the SPME-GC-ECD method for the three aqueous matrices was similar and gave relative standard deviations (RSD) between 12 and 14%. The limit of detection (LOD) was 0.02 microg l(-1) for Milli-Q water and 0.3 microg l(-1) for both tap water and river water. The optimised SPME-GC-ECD method was successfully applied to the determination of SCCPs in river water samples.

  18. Development of a sampling method for the simultaneous monitoring of straight-chain alkanes, straight-chain saturated carbonyl compounds and monoterpenes in remote areas.

    Science.gov (United States)

    Detournay, Anaïs; Sauvage, Stéphane; Locoge, Nadine; Gaudion, Vincent; Leonardis, Thierry; Fronval, Isabelle; Kaluzny, Pascal; Galloo, Jean-Claude

    2011-04-01

    Studies have shown that biogenic compounds, long chain secondary compounds and long lifetime anthropogenic compounds are involved in the formation of organic aerosols in both polluted areas and remote places. This work aims at developing an active sampling method to monitor these compounds (i.e. 6 straight-chain saturated aldehydes from C6 to C11; 8 straight-chain alkanes from C9 to C16; 6 monoterpenes: α-pinene, β-pinene, camphene, limonene, α-terpinene, & γ-terpinene; and 5 aromatic compounds: toluene, ethylbenzene, meta-, para- and ortho-xylenes) in remote areas. Samples are collected onto multi-bed sorbent cartridges at 200 mL min(-1) flow rate, using the automatic sampler SyPAC (TERA-Environnement, Crolles, France). No breakthrough was observed for sampling volumes up to 120 L (standard mixture at ambient temperature, with a relative humidity of 75%). As ozone has been shown to alter the samples (losses of 90% of aldehydes and up to 95% of terpenes were observed), the addition of a conditioned manganese dioxide (MnO(2)) scrubber to the system has been validated (full recovery of the affected compounds for a standard mixture at 50% relative humidity--RH). Samples are first thermodesorbed and then analysed by GC/FID/MS. This method allows suitable detection limits (from 2 ppt for camphene to 13 ppt for octanal--36 L sampled), and reproducibility (from 1% for toluene to 22% for heptanal). It has been successfully used to determine the diurnal variation of the target compounds (six 3 h samples a day) during winter and summer measurement campaigns at a remote site in the south of France.

  19. Connectivity patterns and rotamer states of nucleobases determine acid-base properties of metalated purine quartets.

    Science.gov (United States)

    Lüth, Marc Sven; Freisinger, Eva; Kampf, Gunnar; Garijo Anorbe, Marta; Griesser, Rolf; Operschall, Bert P; Sigel, Helmut; Lippert, Bernhard

    2015-07-01

    Potentiometric pH titrations and pD dependent (1)H NMR spectroscopy have been applied to study the acidification of the exocyclic amino group of adenine (A) model nucleobases (N9 position blocked by alkyl groups) when carrying trans-a2Pt(II) (with a=NH3 or CH3NH2) entities both at N1 and N7 positions. As demonstrated, in trinuclear complexes containing central A-Pt-A units, it depends on the connectivity pattern of the adenine bases (N7/N7 or N1/N1) and their rotamer states (head-head or head-tail), how large the acidifying effect is. Specifically, a series of trinuclear complexes with (A-N7)-Pt-(N7-A) and (A-N1)-Pt-(N1-A) cross-linking patterns and terminal 9-alkylguanine ligands (9MeGH, 9EtGH) have been analyzed in this respect, and it is shown that, for example, the 9MeA ligands in trans-,trans-,trans-[Pt(NH3)2(N7-9MeA-N1)2{Pt(NH3)2(9EtGH-N7)}2](ClO4)6·6H2O (4a) and trans-,trans-,trans-[Pt(NH3)2(N7-9EtA-N1)2{Pt(CH3NH2)2(9-MeGH-N7)}2](ClO4)6·3H2O (4b) are more acidic, by ca. 1.3 units (first pKa), than the linkage isomer trans-,trans-,trans-[Pt(CH3NH2)2(N1-9MeA-N7)2{Pt(NH3)2(9MeGH-N7)}2](NO3)6·6.25H2O (1b). Overall, acidifications in these types of complexes amount to 7-9 units, bringing the pKa values of such adenine ligands in the best case close to the physiological pH range. Comparison with pKa values of related trinuclear Pt(II) complexes having different co-ligands at the Pt ions, confirms this picture and supports our earlier proposal that the close proximity of the exocyclic amino groups in a head-head arrangement of (A-N7)-Pt-(N7-A), and the stabilization of the resulting N6H(-)⋯H2N6 unit, is key to this difference.

  20. BORRELIA BURGDORFERI DNA IN BIOLOGICAL SAMPLES FROM PATIENTS WITH SARCOIDOSIS USING THE POLYMERASE CHAIN REACTION TECHNIQUE

    Institute of Scientific and Technical Information of China (English)

    连伟; 罗慰慈

    1995-01-01

    Polymerase chain reaction (PCR) was used to detect the presence of Borretia burgdoferi DNA in biological samples from patients with sarcoidcsis. The target DNA sequence was of chromosomal origin. The amplified DNA sequence was analyzed by agarose gel electrophoresis, PAGE with silver staining, and the identity of amplified DNA was confirmed by restriction enzyme cleavage and DNA-DNA hybridlzation with a 32P-labelled probe. The assay was sensitive to fewer than two copies of B. burgdor feri genome, even in the presence of a 104-fold excess of human eukaryotic DNA, and was also specific to different B. burgdorferl strains tested. Sera seroiogieally positive to B. burgdorferi (n=26), broncbemlveolar lavage fluid and supematant of BALF (n=26) and peripheral blood (n=9) from sarcoidosis patients were tested. The positive rate was low (4/26, 2/26, and 0/9, respectively). It was considered that DNA from B. bur gdor feri may be identified in a minority of patients with s,arcoidosis, and it may play a pathogenetic rote in such cases. More studies need to be done before advancing the hypothesis of an etiologic role of B. burgdorferi in sarcoidosis.

  1. How to get an exact sample from a generic Markov chain and sample a random spanning tree from a directed graph, both within the cover time

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, D.B.; Propp, J.G.

    1996-12-31

    This paper shows how to obtain unbiased samples from an unknown Markov chain by observing it for O(T{sub c}) steps, where T{sub c} is the cover time. This algorithm improves on several previous algorithms, and there is a matching lower bound. Using the techniques from the sampling algorithm, we also show how to sample random directed spanning trees from a weighted directed graph, with arcs directed to a root, and probability proportional to the product of the edge weights. This tree sampling algorithm runs within 18 cover times of the associated random walk, and is more generally applicable than the algorithm of Broder and Aldous.

  2. A Markov chain Monte Carlo with Gibbs sampling approach to anisotropic receiver function forward modeling

    Science.gov (United States)

    Wirth, Erin A.; Long, Maureen D.; Moriarty, John C.

    2017-01-01

    Teleseismic receiver functions contain information regarding Earth structure beneath a seismic station. P-to-SV converted phases are often used to characterize crustal and upper-mantle discontinuities and isotropic velocity structures. More recently, P-to-SH converted energy has been used to interrogate the orientation of anisotropy at depth, as well as the geometry of dipping interfaces. Many studies use a trial-and-error forward modeling approach for the interpretation of receiver functions, generating synthetic receiver functions from a user-defined input model of Earth structure and amending this model until it matches major features in the actual data. While often successful, such an approach makes it impossible to explore model space in a systematic and robust manner, which is especially important given that solutions are likely non-unique. Here, we present a Markov chain Monte Carlo algorithm with Gibbs sampling for the interpretation of anisotropic receiver functions. Synthetic examples are used to test the viability of the algorithm, suggesting that it works well for models with a reasonable number of free parameters (<˜20). Additionally, the synthetic tests illustrate that certain parameters are well constrained by receiver function data, while others are subject to severe trade-offs-an important implication for studies that attempt to interpret Earth structure based on receiver function data. Finally, we apply our algorithm to receiver function data from station WCI in the central United States. We find evidence for a change in anisotropic structure at mid-lithospheric depths, consistent with previous work that used a grid search approach to model receiver function data at this station. Forward modeling of receiver functions using model space search algorithms, such as the one presented here, provide a meaningful framework for interrogating Earth structure from receiver function data.

  3. A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers.

    Science.gov (United States)

    Hansen, Halvor S; Hünenberger, Philippe H

    2011-04-30

    This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A(CARBO) (nearly equivalent to 53A6 for non-carbohydrate systems). This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the force field to properties that had not been included previously into the parameterization procedure. The new 56A(CARBO) force field is characterized by: (i) the formulation of systematic build-up rules for the automatic generation of force-field topologies over a large class of compounds including (but not restricted to) unfunctionalized polyhexopyranoses with arbritrary connectivities; (ii) the systematic use of enhanced sampling methods for inclusion of experimental thermodynamic data concerning slow or unphysical processes into the parameterization procedure; and (iii) an extensive validation against available experimental data in solution and, to a limited extent, theoretical (quantum-mechanical) data in the gas phase. At present, the 56A(CARBO) force field is restricted to compounds of the elements C, O, and H presenting single bonds only, no oxygen functions other than alcohol, ether, hemiacetal, or acetal, and no cyclic segments other than six-membered rings (separated by at least one intermediate atom). After calibration, this force field is shown to reproduce well the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. As a result, the 56A(CARBO) force field should be suitable for: (i) the characterization of the dynamics of pyranose ring conformational transitions (in simulations on the microsecond timescale); (ii) the investigation of systems where alternative ring conformations become significantly populated; (iii) the investigation of anomerization or epimerization in terms of free-energy differences

  4. Fitting a distribution to censored contamination data using Markov Chain Monte Carlo methods and samples selected with unequal probabilities.

    Science.gov (United States)

    Williams, Michael S; Ebel, Eric D

    2014-11-18

    The fitting of statistical distributions to chemical and microbial contamination data is a common application in risk assessment. These distributions are used to make inferences regarding even the most pedestrian of statistics, such as the population mean. The reason for the heavy reliance on a fitted distribution is the presence of left-, right-, and interval-censored observations in the data sets, with censored observations being the result of nondetects in an assay, the use of screening tests, and other practical limitations. Considerable effort has been expended to develop statistical distributions and fitting techniques for a wide variety of applications. Of the various fitting methods, Markov Chain Monte Carlo methods are common. An underlying assumption for many of the proposed Markov Chain Monte Carlo methods is that the data represent independent and identically distributed (iid) observations from an assumed distribution. This condition is satisfied when samples are collected using a simple random sampling design. Unfortunately, samples of food commodities are generally not collected in accordance with a strict probability design. Nevertheless, pseudosystematic sampling efforts (e.g., collection of a sample hourly or weekly) from a single location in the farm-to-table continuum are reasonable approximations of a simple random sample. The assumption that the data represent an iid sample from a single distribution is more difficult to defend if samples are collected at multiple locations in the farm-to-table continuum or risk-based sampling methods are employed to preferentially select samples that are more likely to be contaminated. This paper develops a weighted bootstrap estimation framework that is appropriate for fitting a distribution to microbiological samples that are collected with unequal probabilities of selection. An example based on microbial data, derived by the Most Probable Number technique, demonstrates the method and highlights the

  5. Accelerating Markov chain Monte Carlo simulation by differential evolution with self-adaptive randomized subspace sampling

    NARCIS (Netherlands)

    Vrugt, J.A.; Braak, ter C.J.F.; Diks, C.G.H.; Robinson, B.A.; Hyman, J.M.; Higdon, D.

    2009-01-01

    Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well-constructed MCMC schemes to the appropriate

  6. Accelerating Markov chain Monte Carlo simulation by differential evolution with self-adaptive randomized subspace sampling

    NARCIS (Netherlands)

    Vrugt, J.A.; Braak, C.J.F.; Diks, C.G.H.; Robinson, B.A.; Hyman, J.M.; Higdon, D.

    2009-01-01

    Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate

  7. Rapid Detection/pathotyping of Newcastle disease virus isolates in clinical samples using real time polymerase chain reaction assay

    OpenAIRE

    sprotocols

    2014-01-01

    Authors: Abdul Wajid, Muhammad Wasim, Tahir Yaqub, Shafqat F Rehmani, Tasra Bibi, Nadia Mukhtar, Javed Muhammad, Umar Bacha, Suliman Qadir Afridi, Muhammad Nauman Zahid, Zia u ddin, Muhammad Zubair Shabbir, Kamran Abbas & Muneer Ahmad ### Abstract In the present protocol we describe the real time reverse transcription polymerase chain reaction (rRT-PCR) assay for the rapid detection/pathotyping of Newcastle disease virus (NDV) isoaltes in clinical samples. Fusion gene and matrix ...

  8. Comparison of Nested Polymerase Chain Reaction and Real-Time Polymerase Chain Reaction with Parasitological Methods for Detection of Strongyloides stercoralis in Human Fecal Samples.

    Science.gov (United States)

    Sharifdini, Meysam; Mirhendi, Hossein; Ashrafi, Keyhan; Hosseini, Mostafa; Mohebali, Mehdi; Khodadadi, Hossein; Kia, Eshrat Beigom

    2015-12-01

    This study was performed to evaluate nested polymerase chain reaction (PCR) and real-time PCR methods for detection of Strongyloides stercoralis in fecal samples compared with parasitological methods. A total of 466 stool samples were examined by conventional parasitological methods (formalin ether concentration [FEC] and agar plate culture [APC]). DNA was extracted using an in-house method, and mitochondrial cytochrome c oxidase subunit 1 and 18S ribosomal genes were amplified by nested PCR and real-time PCR, respectively. Among 466 samples, 12.7% and 18.2% were found infected with S. stercoralis by FEC and APC, respectively. DNA of S. stercoralis was detected in 18.9% and 25.1% of samples by real-time PCR and nested PCR, respectively. Considering parasitological methods as the diagnostic gold standard, the sensitivity and specificity of nested PCR were 100% and 91.6%, respectively, and that of real-time PCR were 84.7% and 95.8%, respectively. However, considering sequence analyzes of the selected nested PCR products, the specificity of nested PCR is increased. In general, molecular methods were superior to parasitological methods. They were more sensitive and more reliable in detection of S. stercoralis in comparison with parasitological methods. Between the two molecular methods, the sensitivity of nested PCR was higher than real-time PCR.

  9. Development of a polymerase chain reaction assay for the detection of pseudorabies virus in clinical samples

    OpenAIRE

    Lester J Pérez; Heidy Díaz de Arce

    2009-01-01

    Aujeszky's disease, also known as pseudorabies causes severe economic losses in swine industry and affects the pig husbandry all over the world. The conventional diagnostic procedure is time-consuming and false-negative results may occur in submissions from latently infected animals. The development, optimization and evaluation of a polymerase chain reaction (PCR) assay are presented for the diagnosis of pseudorabies infection. This assay was based on the amplification of a highly conserved v...

  10. Branched-Chain in situ Hybridization for κ and λ Light Chains: A Powerful Ancillary Technique for Determining B-Cell Clonality in Cytology Samples

    Science.gov (United States)

    Arora, Kshitij; Chebib, Ivan; Zukerberg, Lawrence; Gandhi, Manoj; Rivera, Miguel; Ting, David; Deshpande, Vikram

    2017-01-01

    BACKGROUND Current immunohistochemical and in situ hybridization (ISH) assays are generally inconclusive for clonality unless plasmacytic differentiation is present. This study examined a series of cytology specimens and explored the ability of a branched-chain RNA (bRNA) ISH assay for immunoglobulin κ constant (IGKC) and immunoglobulin λ constant (IGLC) to detect a clonal population of B lymphocytes. METHODS Pathology databases were used to identify fine-needle aspiration biopsies (n = 28) and exfoliative cytology samples (n = 20). Demographic, flow cytometry, and excision biopsy results were recorded. bRNA ISH was performed on the Leica Bond platform with the following probes: IGKC, IGLC, immunoglobulin λ-like polypeptide 5 (IGLL5), and a housekeeping gene (HKG). RESULTS The bRNA ISH assay was validated with 30 surgical biopsies. On bRNA ISH, a clonal B-cell population (light-chain ratio > 10:1) was detected in 22 of 28 cases with a final diagnosis of lymphoma. In 2 cases, a κ predominance was present, although the ratio was <10:1. Eleven of the 17 κ-clonal lymphomas also expressed IGLL5, the latter recognized by the presence of an intranuclear signal. Two B-cell lymphomas lacked IGKC and IGLC, whereas 2 cases were negative for the HKG. In 12 of the 20 cases with reactive lymphoid tissue, bRNA ISH identified a polyclonal lymphoid population. No light-chain messenger RNA was detected in 6 cases (typically those associated with very few B cells). CONCLUSIONS The automated bRNA ISH platform is a robust technique for detecting a clonal B-cell population in cytology material. PMID:26524200

  11. Comparison of a conventional polymerase chain reaction with real-time polymerase chain reaction for the detection of neurotropic viruses in cerebrospinal fluid samples

    Directory of Open Access Journals (Sweden)

    M Ramamurthy

    2011-01-01

    Full Text Available Purpose : To compare a conventional polymerase chain reaction (PCR and real-time PCR for the detection of neurotropic DNA viruses. Materials and Methods : A total of 147 cerebrospinal fluid (CSF samples was collected from patients attending a tertiary care hospital in South India for a period from 2005 to 2008. All these samples were tested using a conventional multiplex/uniplex PCR and a real-time multiplex/uniplex PCR. This technique was used to detect a large number of herpes viruses responsible for central nervous system infections, including HSV-1, HSV-2, VZV, CMV and EBV and the polyoma virus JCV. Results : Overall, in the entire set of samples, the real-time PCR yielded 88 (59.9% positives and conventional PCR had six (4.1% positives. Conclusion : Our results suggest that the real-time PCR assay was more sensitive compared with the conventional PCR. The advantage of real-time PCR is that it can be performed much faster than conventional PCR. Real-time PCR is less time-consuming, less labour-intensive and also reduces the chance of contamination as there is no post-amplification procedure. In the entire study population, the major viruses detected using real-time PCR were EBV (34%, HSV-2 (10.8% and VZV (6.8%.

  12. Histoplasmosis diagnosis using a polymerase chain reaction method. Application on human samples in French Guiana, South America.

    Science.gov (United States)

    Maubon, Danièle; Simon, Stéphane; Aznar, Christine

    2007-08-01

    Untreated histoplasmosis is life threatening, especially in immunosuppressed patients. In French Guiana, South America, it is one of the most common opportunistic infections in AIDS patients. Twenty-one cases of disseminated histoplasmosis were diagnosed in 2004 in the mycology laboratory of Cayenne hospital. Culture samples for histoplasmosis diagnosis is simple, sensitive, and specific, but it is a lengthy process. Management of the disease is then dangerously delayed. In this work, we tested a polymerase chain reaction (PCR) method on 40 samples from patients with suspected disseminated histoplasmosis. The recently described Hcp100 nested PCR method was used to detect Histoplasma capsulatum DNA in these samples. All of the positive cultures for H. capsulatum were also positive with PCR method. Tested on other fungi or negative culture, it also showed high specificity. Furthermore, it allows treating patients more rapidly. Culture remains necessary, but histoplasmosis PCR offers great prospects, on a clinical point of view.

  13. Leptospira spp detection by Polymerase Chain Reaction (PCR in clinical samples of captive black-capped Capuchin monkey (Cebus apella

    Directory of Open Access Journals (Sweden)

    Scarcelli Eliana

    2003-01-01

    Full Text Available Leptospirosis is a widely distributed zoonosis that affects domestic and wild animals, and that has the man as the end point of its epidemiological chain. Leptospirosis diagnosis in primates is more difficult than in other animal species, as clinical signs and lesions are less evident and antibody response is detected only for short periods. The aim of this article was to describe the detection of Leptospira spp using polymerase chain reaction (PCR, in clinical samples from one captive black-capped Capuchin monkey (Cebus apella, which presented characteristics compatible with leptospirosis (jaundice and haemorrhagic kdney in the macroscopic post-mortem examination. A friable kidney fragment and urine sample were cultured and submitted to experimental inoculation in guinea pigs and PCR using genus specific primer pair targeting the 16S rRNA region from Leptospira interrogans serovar canicola. Isolation of the agent was negative both in culture and experimental inoculation. The PCR amplification of the clinical samples showed a 330 pb amplified fragment that corresponds to the Leptospira genus. Based on these results PCR was considered an important tool for leptospira detection in nonhumam primates, more sensitive and specific than other techniques, especially considering that the viability of the pathogen was not possible. These advantages enable the detection of the leptospiras in urine and kidney, even when autolysed, frozen or badly conserved, which prevented the isolation and experimental inoculation from positive results.

  14. Detection and Enumeration of Streptococcus agalactiae from Bovine Milk Samples by Real-Time Polymerase Chain Reaction.

    Science.gov (United States)

    de Carvalho, Nara Ladeira; Gonçalves, Juliano Leonel; Botaro, Bruno Garcia; Silva, Luis Felipe de Prada E; dos Santos, Marcos Veiga

    2015-09-01

    The aim of this study was to evaluate the use of real-time polymerase chain reaction (qPCR) combined with DNA extraction directly from composite milk and bulk tank samples for detection and enumeration of Streptococcus agalactiae (SAG) causing subclinical mastitis. Dilutions of sterile reconstituted skim milk inoculated with SAG ATCC 13813 were used to establish a standard curve (cfu/mL) for the qPCR assay targeting SAG. The analytical sensitivity and repeatability of the qPCR assay were determined. Bulk tank (BTM; n = 38) and composite milk samples (CM; n = 26) collected from lactating cows with positive isolation of SAG were submitted to the qPCR protocol and SAG plate counting, with results from both methods compared. Amplification of DNA was not possible in two out of 64 samples, indicating that qPCR was able to detect SAG in 96 and 97% of BTM and CM samples, respectively. The inter-assay coefficient of variation was <5%, showing that the technique had adequate repeatability. The qPCR protocol can be a high-throughput and rapid diagnostic assay to accurately detect SAG from BTM and CM samples compared with conventional microbiological culture method. However, the evaluated qPCR protocol is not accurate for enumerating SAG in milk samples, probably due to quantification of DNA of non-viable cells.

  15. Optimized nested Markov chain Monte Carlo sampling: application to the liquid nitrogen Hugoniot using density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, Milton Sam [Los Alamos National Laboratory; Coe, Joshua D [Los Alamos National Laboratory; Sewell, Thomas D [UNIV OF MISSOURI-COLUMBIA

    2009-01-01

    An optimized version of the Nested Markov Chain Monte Carlo sampling method is applied to the calculation of the Hugoniot for liquid nitrogen. The 'full' system of interest is calculated using density functional theory (DFT) with a 6-31 G* basis set for the configurational energies. The 'reference' system is given by a model potential fit to the anisotropic pair interaction of two nitrogen molecules from DFT calculations. The EOS is sampled in the isobaric-isothermal (NPT) ensemble with a trial move constructed from many Monte Carlo steps in the reference system. The trial move is then accepted with a probability chosen to give the full system distribution. The P's and T's of the reference and full systems are chosen separately to optimize the computational time required to produce the full system EOS. The method is numerically very efficient and predicts a Hugoniot in excellent agreement with experimental data.

  16. Feline coronavirus quantitative reverse transcriptase polymerase chain reaction on effusion samples in cats with and without feline infectious peritonitis.

    Science.gov (United States)

    Longstaff, Louise; Porter, Emily; Crossley, Victoria J; Hayhow, Sophie E; Helps, Christopher R; Tasker, Séverine

    2017-02-01

    Objectives The aim of the study was to determine whether feline coronavirus (FCoV) RNA in effusion samples can be used as a diagnostic marker of feline infectious peritonitis (FIP); and in FCoV RNA-positive samples to examine amino acid codons in the FCoV spike protein at positions 1058 and 1060 where leucine and alanine, respectively, have been associated with systemic or virulent (FIP) FCoV infection. Methods Total RNA was extracted from effusion samples from 20 cats with confirmed FIP and 23 cats with other diseases. Feline coronavirus RNA was detected using a reverse transcriptase quantitative polymerase chain reaction assay (qRT-PCR), and positive samples underwent pyrosequencing of position 1058 with or without Sanger sequencing of position 1060 in the FCoV spike protein. Results Seventeen (85%) of the effusion samples from 20 cats with FIP were positive for FCoV RNA, whereas none of the 23 cats with other diseases were positive. Pyrosequencing of the 17 FCoV-positive samples showed that 11 (65%) of the cats had leucine and two (12%) had methionine at position 1058. Of the latter two samples with methionine, one had alanine at position 1060. Conclusions and relevance A positive FCoV qRT-PCR result on effusions appears specific for FIP and may be a useful diagnostic marker for FIP in cats with effusions. The majority of FCoVs contained amino acid changes previously associated with systemic spread or virulence (FIP) of the virus.

  17. Hierarchical Bayesian modeling and Markov chain Monte Carlo sampling for tuning-curve analysis.

    Science.gov (United States)

    Cronin, Beau; Stevenson, Ian H; Sur, Mriganka; Körding, Konrad P

    2010-01-01

    A central theme of systems neuroscience is to characterize the tuning of neural responses to sensory stimuli or the production of movement. Statistically, we often want to estimate the parameters of the tuning curve, such as preferred direction, as well as the associated degree of uncertainty, characterized by error bars. Here we present a new sampling-based, Bayesian method that allows the estimation of tuning-curve parameters, the estimation of error bars, and hypothesis testing. This method also provides a useful way of visualizing which tuning curves are compatible with the recorded data. We demonstrate the utility of this approach using recordings of orientation and direction tuning in primary visual cortex, direction of motion tuning in primary motor cortex, and simulated data.

  18. Nested Markov chain Monte Carlo sampling of a density functional theory potential: equilibrium thermodynamics of dense fluid nitrogen.

    Science.gov (United States)

    Coe, Joshua D; Sewell, Thomas D; Shaw, M Sam

    2009-08-21

    An optimized variant of the nested Markov chain Monte Carlo [n(MC)(2)] method [J. Chem. Phys. 130, 164104 (2009)] is applied to fluid N(2). In this implementation of n(MC)(2), isothermal-isobaric (NPT) ensemble sampling on the basis of a pair potential (the "reference" system) is used to enhance the efficiency of sampling based on Perdew-Burke-Ernzerhof density functional theory with a 6-31G(*) basis set (PBE6-31G(*), the "full" system). A long sequence of Monte Carlo steps taken in the reference system is converted into a trial step taken in the full system; for a good choice of reference potential, these trial steps have a high probability of acceptance. Using decorrelated samples drawn from the reference distribution, the pressure and temperature of the full system are varied such that its distribution overlaps maximally with that of the reference system. Optimized pressures and temperatures then serve as input parameters for n(MC)(2) sampling of dense fluid N(2) over a wide range of thermodynamic conditions. The simulation results are combined to construct the Hugoniot of nitrogen fluid, yielding predictions in excellent agreement with experiment.

  19. High-throughput multiplex quantitative polymerase chain reaction method for Giardia lamblia and Cryptosporidium species detection in stool samples.

    Science.gov (United States)

    Nurminen, Noora; Juuti, Rosa; Oikarinen, Sami; Fan, Yue-Mei; Lehto, Kirsi-Maarit; Mangani, Charles; Maleta, Kenneth; Ashorn, Per; Hyöty, Heikki

    2015-06-01

    Giardia lamblia and Cryptosporidium species belong to a complex group of pathogens that cause diseases hampering development and socioeconomic improvements in the developing countries. Both pathogens are recognized as significant causes of diarrhea and nutritional disorders. However, further studies are needed to clarify the role of parasitic infections, especially asymptomatic infections in malnutrition and stunting. We developed a high-throughput multiplex quantitative polymerase chain reaction (qPCR) method for G. lamblia and Cryptosporidium spp. detection in stool samples. The sensitivity and specificity of the method were ensured by analyzing confirmed positive samples acquired from diagnostics laboratories and participating in an external quality control round. Its capability to detect asymptomatic G. lamblia and Cryptosporidium spp. infections was confirmed by analyzing stool samples collected from 44 asymptomatic 6-month-old infants living in an endemic region in Malawi. Of these, five samples were found to be positive for G. lamblia and two for Cryptosporidium spp. In conclusion, the developed method is suitable for large-scale studies evaluating the occurrence of G. lamblia and Cryptosporidium spp. in endemic regions and for clinical diagnostics of these infections.

  20. Detection of Wuchereria bancrofti DNA in paired serum and urine samples using polymerase chain reaction-based systems

    Directory of Open Access Journals (Sweden)

    Camila Ximenes

    2014-12-01

    Full Text Available The Global Program for the Elimination of Lymphatic Filariasis (GPELF aims to eliminate this disease by the year 2020. However, the development of more specific and sensitive tests is important for the success of the GPELF. The present study aimed to standardise polymerase chain reaction (PCR-based systems for the diagnosis of filariasis in serum and urine. Twenty paired biological urine and serum samples from individuals already known to be positive for Wuchereria bancrofti were collected during the day. Conventional PCR and semi-nested PCR assays were optimised. The detection limit of the technique for purified W. bancrofti DNA extracted from adult worms was 10 fg for the internal systems (WbF/Wb2 and 0.1 fg by using semi-nested PCR. The specificity of the primers was confirmed experimentally by amplification of 1 ng of purified genomic DNA from other species of parasites. Evaluation of the paired urine and serum samples by the semi-nested PCR technique indicated only two of the 20 tested individuals were positive, whereas the simple internal PCR system (WbF/Wb2, which has highly promising performance, revealed that all the patients were positive using both samples. This study successfully demonstrated the possibility of using the PCR technique on urine for the diagnosis of W. bancrofti infection.

  1. Side chain conformational averaging in human dihydrofolate reductase.

    Science.gov (United States)

    Tuttle, Lisa M; Dyson, H Jane; Wright, Peter E

    2014-02-25

    The three-dimensional structures of the dihydrofolate reductase enzymes from Escherichia coli (ecDHFR or ecE) and Homo sapiens (hDHFR or hE) are very similar, despite a rather low level of sequence identity. Whereas the active site loops of ecDHFR undergo major conformational rearrangements during progression through the reaction cycle, hDHFR remains fixed in a closed loop conformation in all of its catalytic intermediates. To elucidate the structural and dynamic differences between the human and E. coli enzymes, we conducted a comprehensive analysis of side chain flexibility and dynamics in complexes of hDHFR that represent intermediates in the major catalytic cycle. Nuclear magnetic resonance relaxation dispersion experiments show that, in marked contrast to the functionally important motions that feature prominently in the catalytic intermediates of ecDHFR, millisecond time scale fluctuations cannot be detected for hDHFR side chains. Ligand flux in hDHFR is thought to be mediated by conformational changes between a hinge-open state when the substrate/product-binding pocket is vacant and a hinge-closed state when this pocket is occupied. Comparison of X-ray structures of hinge-open and hinge-closed states shows that helix αF changes position by sliding between the two states. Analysis of χ1 rotamer populations derived from measurements of (3)JCγCO and (3)JCγN couplings indicates that many of the side chains that contact helix αF exhibit rotamer averaging that may facilitate the conformational change. The χ1 rotamer adopted by the Phe31 side chain depends upon whether the active site contains the substrate or product. In the holoenzyme (the binary complex of hDHFR with reduced nicotinamide adenine dinucleotide phosphate), a combination of hinge opening and a change in the Phe31 χ1 rotamer opens the active site to facilitate entry of the substrate. Overall, the data suggest that, unlike ecDHFR, hDHFR requires minimal backbone conformational rearrangement as

  2. Detection of hblA and bal Genes in Bacillus cereus Isolates From Cheese Samples Using the Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Molayi Kohneshahri

    2016-03-01

    Full Text Available Background Bacillus cereus is a Gram-positive spore-forming bacterium, which causes food poisoning. Spores enable the persistence of B. cereus in the environment, and B. cereus strains can tolerate adverse environmental conditions, such as temperature and insufficient nutrients. B. cereus causes food poisoning via the production of two enterotoxins. Most isolates produce toxins leading to diarrhea (enterotoxins and vomiting (emetic forms. Diarrhea is caused by the production of three different heat-labile enterotoxins: HBL, NHE, and cytotoxin K. A heat-stable toxin, cereulide, is responsible for emesis. Objectives This study aimed to detect enterotoxigenic B. cereus isolates in cheese samples using the polymerase chain reaction (PCR. Materials and Methods Two-hundred pasteurized (n = 100 and nonpasteurized (n = 100 cheese samples were collected. The initial isolation was performed on PEMBA specific medium. Antibiotic susceptibility testing was performed using several antibiotic disks, according to the guidelines of the Clinical Laboratory and Standards Institute. Specific primers amplifying the hblA enterotoxin-encoding gene and bal hemolysin-encoding gene were used for the molecular detection of the toxins. Results Ten samples were positive for the presence of B. cereus, with both Gram staining and biochemical reactions. All the isolates were resistant to penicillin and ampicillin but susceptible to vancomycin, erythromycin, and ciprofloxacin. Six and three isolates were resistant to tetracycline and trimethoprim-sulfamethoxazole, respectively. The hblA and bal genes were amplified in all the B. cereus isolates. Conclusions The prevalence of B. cereus among the cheese samples was low. All the isolates were positive for genes encoding the hblA enterotoxin and bal toxin.

  3. Comparison of DNA extraction methods for polymerase chain reaction amplification of guanaco (Lama guanicoe) fecal DNA samples.

    Science.gov (United States)

    Espinosa, M I; Bertin, A; Squeo, F A; Cortés, A; Gouin, N

    2015-01-23

    Feces-based population genetic studies have become increasingly popular. However, polymerase chain reaction (PCR) amplification rates from fecal material vary depending on the species, populations, loci, and extraction protocols. Here, we assessed the PCR amplification success of three microsatellite markers and a segment of the mitochondrial control region of DNA extracted from field-collected feces of guanaco (Lama guanicoe) using two protocols - Qiagen DNA Stool Kit and 2 cetyltrimethylammonium bromide/phenol:chloroform:isoamyl alcohol (2CTAB/PCI) method. Chelex resin treatment to remove inhibitors was also tested. Our results show that the mitochondrial locus was the most difficult to amplify. PCR success rates improved for all markers after Chelex treatment of extracted DNA, and 2CTAB/PCI method (95.83%) appeared to perform slightly better than stool kit (91.67%) for the nuclear markers. Amplification success was significantly influenced by the extraction method, Chelex treatment, and locus (P 0.89), but they decreased slightly after treatment for amplification of nuclear markers and markedly after treatment for amplification of the mitochondrial control region. Thus, we showed that Chelex treatment gives high PCR success, especially for nuclear markers, and adequate DNA extraction rates can be achieved from L. guanicoe feces even from non-fresh fecal material. Although not significant, 2CTAB/PCI method tended to provide higher successful amplification rates on a whole set of samples, suggesting that the method could be particularly useful when using small sample sizes.

  4. PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure.

    Science.gov (United States)

    Boomsma, Wouter; Frellsen, Jes; Harder, Tim; Bottaro, Sandro; Johansson, Kristoffer E; Tian, Pengfei; Stovgaard, Kasper; Andreetta, Christian; Olsson, Simon; Valentin, Jan B; Antonov, Lubomir D; Christensen, Anders S; Borg, Mikael; Jensen, Jan H; Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas

    2013-07-15

    We present a new software framework for Markov chain Monte Carlo sampling for simulation, prediction, and inference of protein structure. The software package contains implementations of recent advances in Monte Carlo methodology, such as efficient local updates and sampling from probabilistic models of local protein structure. These models form a probabilistic alternative to the widely used fragment and rotamer libraries. Combined with an easily extendible software architecture, this makes PHAISTOS well suited for Bayesian inference of protein structure from sequence and/or experimental data. Currently, two force-fields are available within the framework: PROFASI and OPLS-AA/L, the latter including the generalized Born surface area solvent model. A flexible command-line and configuration-file interface allows users quickly to set up simulations with the desired configuration. PHAISTOS is released under the GNU General Public License v3.0. Source code and documentation are freely available from http://phaistos.sourceforge.net. The software is implemented in C++ and has been tested on Linux and OSX platforms.

  5. Diagnosis of visceral leishmaniasis by the polymerase chain reaction using blood, bone marrow and lymph node samples from patients from the Sudan

    DEFF Research Database (Denmark)

    Andresen, K; Gasim, S; Elhassan, A M

    1997-01-01

    We have evaluated the sensitivity of the polymerase chain reaction (PCR) as a diagnostic tool for Leishmania donovani using blood, bone marrow and lymph node samples from Sudanese patients with a confirmed infection. Forty patients were diagnosed by microscopic examination of bone marrow or lymph...

  6. Comprehensive and sensitive quantification of long-chain and very long-chain polyunsaturated fatty acids in small samples of human and mouse retina.

    Science.gov (United States)

    Liu, Aihua; Terry, Ryan; Lin, Yanhua; Nelson, Kelly; Bernstein, Paul S

    2013-09-13

    Fatty acids (FAs), including long-chain and very long-chain polyunsaturated fatty acids (LC-PUFAs, C12-22; VLC-PUFAs, C24-38), play an important role in retinal function and health. Deficiencies in LC-PUFAs and VLC-PUFAs, as well as mutations in the enzyme responsible for elongation of very long-chain fatty acids (ELOVL4), have been associated with macular dystrophies and degenerations. Published analytical methods, including high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS) and gas chromatography-MS (GC-MS), can quantify VLC-PUFAs but require at least an entire human retina which limits the ability to understand physiologically relevant variations in lipids that can occur at a regional level within the retina. Until now, quantification of VLC-PUFAs in just the human macula, the cone-rich region of the central retina responsible for high acuity vision, has not been feasible due to its small size (4-5mm in diameter). In this study, we have developed a sensitive GC-MS method using newer generation enhanced GC-MS detector sensitivity which for the first time quantifies not only 14 VLC-PUFAs and 26 LC-FAs but also n-3/n-6 ratios of PUFAs in 4mm punches of human retina or a single pair of mouse retinas. Our results showed that saturated LC-FAs are higher in the human peripheral retina than in the macula, while unsaturated LC-FAs are higher in the macula than in the peripheral retina. On the other hand, the VLC-PUFAs are higher in the peripheral retina compared to macula. There is no difference in n-3/n-6 ratios of PUFAs observed between human macula and peripheral retina, while mouse retina has almost ten times more VLC-PUFAs than human macula and peripheral retina (2.27% versus 0.25% and 0.32%, respectively) and much higher n-3/n-6 ratios compared to human retina (9:1 versus ∼0.9:1). This high sensitivity analytical technique provides a valuable new tool for studies on the role of FAs in the pathological processes of macular

  7. Detection and genotyping of vancomycin-resistant Enterococcus spp. by multiplex polymerase chain reaction in Korean aquatic environmental samples.

    Science.gov (United States)

    Nam, Sehee; Kim, Min-jeong; Park, Chulmin; Park, Jong-Geun; Maeng, Pil Jae; Lee, Gyu-Cheol

    2013-07-01

    The distribution characteristics of Enterococcus spp., which are indicators of fecal pollution, were investigated at 33 sites within the 3 major water systems of Korea. Enterococci were detected at concentrations ranging from 1 to 37 CFU/100mL in 41 of 132 samples (31.1%) from the 3 major water systems. The overall average detected concentration was 1.2 CFU/100mL, while the average concentration for all detection sites was 5.3 CFU/100mL. After optimized multiplex polymerase chain reaction (PCR) was performed with newly developed VanA, VanB, VanC-1, and VanC-2/3 primers, concentrations of vancomycin-resistant Enterococcus spp. (VRE) ranging from 1 to 23 CFU/100mL were detected in 17 of 132 samples (12.9%). Of 216 individual enterococcal colonies, 64 (29.6%) displayed the VanC genotype. The results of a susceptibility test to vancomycin showed that the range of the minimal inhibitory concentration (MIC), an indicator of bacterial resistance, was 4 to 24μg/mL, with the average MIC at 9.2±4.5μg/mL. Of the bacterial isolates, 1 colony with the VanC-1 genotype was identified as E. gallinarum by 16S rDNA sequencing, whereas the other 63 colonies had the VanC-2/3 genotype and were identified as E. casseliflavus. Although these results imply that the major head bays of Korea are not contaminated with the highly vancomycin-resistant VanA- or VanB-type VREs, the misuse of antibiotics should be prohibited to minimize the presence of VREs and to maintain a safe water supply for protecting the health of the general population. Based on the study results, we also recommend the implementation of a continuous, broad-spectrum inspection program for Enterococcus spp. and VRE contamination in the major head bays. Furthermore, the multiplex PCR method described in this study can be used effectively for this purpose.

  8. Effects of Holding Time, Storage, and the Preservation of Samples on Sample Integrity for the Detection of Fecal Indicator Bacteria by Quantitative Polymerase Chain Reaction (qPCR)-based assays.

    Science.gov (United States)

    The purpose of this project was to answer questions related to storage of samples to be analyzed by the quantitative polymerase chain reaction (qPCR)-based assays for fecal indicator bacteria. The project was divided into two parts. The first part was to determine if filters th...

  9. Excited State s-cis Rotamers Produced by Extreme Red Edge Excitation of all-trans-1,4-Diphenyl-1,3-butadiene

    DEFF Research Database (Denmark)

    Wallace-Williams, Stacie E.; Møller, Søren; Goldbeck, Robert A.;

    1993-01-01

    The shapes of the fluorescence emission and lowest excited singlet-state absorption spectra of all-trans-1,4- diphenylbutadiene (DPB) in hydrocarbon solvents vary with excitation wavelength when exciting on the extreme red edge of the ground-state absorption spectrum. This contrasts with the wave......The shapes of the fluorescence emission and lowest excited singlet-state absorption spectra of all-trans-1,4- diphenylbutadiene (DPB) in hydrocarbon solvents vary with excitation wavelength when exciting on the extreme red edge of the ground-state absorption spectrum. This contrasts...... changes in DPB can be explained in terms of an excitation wavelength-dependent production of s-cis and s-trans rotamer populations in the excited state. The DPB fluorescence emission spectrum was resolved into s-cis and s-trans components. The vibronic structure of the s-cis fluorescence spectrum...

  10. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  11. Diagnosis of visceral leishmaniasis by the polymerase chain reaction using blood, bone marrow and lymph node samples from patients from the Sudan

    DEFF Research Database (Denmark)

    Andresen, K; Gasim, S; Elhassan, A M;

    1997-01-01

    We have evaluated the sensitivity of the polymerase chain reaction (PCR) as a diagnostic tool for Leishmania donovani using blood, bone marrow and lymph node samples from Sudanese patients with a confirmed infection. Forty patients were diagnosed by microscopic examination of bone marrow or lymph...... node samples. The PCR was able to detect parasite DNA in 37 out of 40 blood samples. In bone marrow and lymph node samples, the PCR was able to detect parasite DNA in all 7 and 6 samples, respectively. We suggest that the PCR should be considered as a valuable and sensitive tool for the diagnosis of L....... donovani infection. However, if PCR diagnosis is to supplement or even replace microscopic diagnosis in developing countries, a large number of patients with no apparent signs of infection and patients with other diseases have to be tested in order to evaluate its true potential....

  12. A rapid DNA extraction method from culture and clinical samples. Suitable for the detection of human cytomegalovirus by the polymerase chain reaction.

    Science.gov (United States)

    Zandotti, C; De Lamballerie, X; Guignole-Vignoli, C; Bollet, C; De Micco, P

    1993-02-01

    We propose an one-step DNA extraction method suitable for the polymerase chain reaction. This procedure utilizes Chelex 100, a chelating in exchange resin. This technique was compared with a traditional technique (proteinase K lysis, phenol-chloroform extraction and ethanol precipitation) for isolation of human cytomegalovirus DNA from clinical samples. The procedure using Chelex 100 appeared to be a simple and fast extraction method for human cytomegalovirus DNA.

  13. Comparison of direct fecal smear microscopy, culture, and polymerase chain reaction for the detection ofBlastocystis sp. in human stool samples

    Institute of Scientific and Technical Information of China (English)

    Herbert J Santos; Windell L Rivera

    2013-01-01

    Objective:To compare the sensitivity and specificity of direct fecal smear microscopy, culture, and polymerase chain reaction in the detection ofBlastocystis sp. in human stool. Methods:Human stool samples were collected from a community inSanIsidro,Rodriguez, Rizal,Philippines.These samples were subjected to direct fecal smear microscopy, culture and polymerase chain reaction to detect the presence of Blastocystissp.Results:Of the110 stool samples collected,28(25%) were detected positive for the presence ofBlastocystis sp. by two or more tests.Culture method detected the highest number ofBlastocystis-positive stool samples (n=36), followed byPCR ofDNA extracted from culture(n=26),PCR ofDNA extracted from stool (n=10), and direct fecal smear(n=9).Compared to culture, the sensitivity of the other detection methods were66.7% forPCR from culture and19.4% for bothPCR from stool and direct fecal smear.Specificity of the methods was high, withPCR from culture and direct fecal smear having 97.3%, whilePCR from stool at95.9%.Conclusions:In this study,in vitroculture is the best method for detectingBlastocystis sp. in human stool samples.

  14. The quantification of short-chain chlorinated paraffins in sediment samples using comprehensive two-dimensional gas chromatography with μECD detection.

    Science.gov (United States)

    Muscalu, Alina M; Morse, Dave; Reiner, Eric J; Górecki, Tadeusz

    2017-03-01

    The analysis of persistent organic pollutants in environmental samples is a challenge due to the very large number of compounds with varying chemical and physical properties. Chlorinated paraffins (CPs) are complex mixtures of chlorinated n-alkanes with varying chain lengths (C10 to C30) and degree of chlorination (30 to 70% by weight). Their physical-chemical properties make these compounds persistent in the environment and able to bioaccumulate in living organisms. Comprehensive two-dimensional gas chromatography (GC × GC) coupled with micro-electron capture detection (μECD) was used to separate and quantify short-chain chlorinated paraffins (SCCP) in sediment samples. Distinct ordered bands were observed in the GC × GC chromatograms pointing to group separation. Using the Classification function of the ChromaTOF software, summary tables were generated to determine total area counts to set up multilevel-calibration curves for different technical mixes. Fortified sediment samples were analyzed by GC × GC-μECD with minimal extraction and cleanup. Recoveries ranged from 120 to 130%. To further validate the proposed method for the analysis of SCCPs, the laboratory participated in interlaboratory studies for the analysis of standards and sediment samples. The results showed recoveries between 75 and 95% and z-score values <2, demonstrating that the method is suitable for the analysis of SCCPs in soil/sediment samples. Graphical abstract Quantification of SCCPs by 2D-GC-μECD.

  15. Distance-Guided Forward and Backward Chain-Growth Monte Carlo Method for Conformational Sampling and Structural Prediction of Antibody CDR-H3 Loops.

    Science.gov (United States)

    Tang, Ke; Zhang, Jinfeng; Liang, Jie

    2017-01-10

    Antibodies recognize antigens through the complementary determining regions (CDR) formed by six-loop hypervariable regions crucial for the diversity of antigen specificities. Among the six CDR loops, the H3 loop is the most challenging to predict because of its much higher variation in sequence length and identity, resulting in much larger and complex structural space, compared to the other five loops. We developed a novel method based on a chain-growth sequential Monte Carlo method, called distance-guided sequential chain-growth Monte Carlo for H3 loops (DiSGro-H3). The new method samples protein chains in both forward and backward directions. It can efficiently generate low energy, near-native H3 loop structures using the conformation types predicted from the sequences of H3 loops. DiSGro-H3 performs significantly better than another ab initio method, RosettaAntibody, in both sampling and prediction, while taking less computational time. It performs comparably to template-based methods. As an ab initio method, DiSGro-H3 offers satisfactory accuracy while being able to predict any H3 loops without templates.

  16. Rapid detection of avian influenza virus in chicken fecal samples by immunomagnetic capture reverse transcriptase–polymerase chain reaction assay

    DEFF Research Database (Denmark)

    Dhumpa, Raghuram; Handberg, Kurt; Jørgensen, Poul Henrik;

    2011-01-01

    Avian influenza virus (AIV) causes great economic losses for the poultry industry worldwide and threatens the human population with a pandemic. The conventional detection method for AIV involves sample preparation of viral RNA extraction and purification from raw sample such as bird droppings. In...

  17. Effect of Genital Sampling Site on the Detection and Quantification of Ureaplasma Species with Quantitative Polymerase Chain Reaction during Pregnancy

    Science.gov (United States)

    Vancutsem, Ellen; Buyl, Ronald; Gucciardo, Leonardo; Foulon, Walter

    2017-01-01

    Objective. This study aimed to compare the qualitative and quantitative reproducibility of quantitative PCR (qPCR) for Ureaplasma species (Ureaplasma spp.) throughout pregnancy and according to the genital sampling site. Study Design. Between 5 and 14 weeks of gestation (T1), vaginal, fornix, and two cervical samples were taken. Sampling was repeated during the 2nd (T2) and 3rd (T3) trimester in randomly selected T1 positive and negative women. Qualitative and quantitative reproducibility were evaluated using, respectively, Cohen's kappa (κ) and interclass correlation coefficients (ICC) and repeated measures ANOVA on the log-transformed mean number of DNA copies for each sampling site. Results. During T1, 51/127 women were positive for U. parvum and 8 for U. urealyticum (4 patients for both). Sampling was repeated for 44/55 women at T2 and/or T3; 43 (97.7%) remained positive at the three timepoints. κ ranged between 0.83 and 0.95 and the ICC for cervical samples was 0.86. Conclusions. Colonization by Ureaplasma spp. seems to be very constant during pregnancy and vaginal samples have the highest detection rate.

  18. A conventional polymerase chain reaction-based method for the diagnosis of human schistosomiasis in stool samples from individuals in a low-endemicity area

    Directory of Open Access Journals (Sweden)

    Teiliane Rodrigues Carneiro

    2013-12-01

    Full Text Available The aim of this study was to evaluate the efficacy of a polymerase chain reaction (PCR-based method to detect Schistosoma mansoni DNA in stool samples from individuals living in a low-endemicity area in Brazil. Of the 125 initial stool samples, 80 were ELISA reactive and eggs were identified in 19 of the samples by parasitological examination. For the PCR evaluations, 56 stool samples were selected and divided into five groups. Groups I-IV were scored negative for S. mansoni eggs by parasitological examination. Groups I and II were ELISA reactive, whereas Groups III and IV were ELISA nonreactive. Groups II and III were positive for other intestinal parasites. PCR testing scored eight samples as positive from these four groups. Group V represented the S. mansoni -positive group and it included ELISA-reactive samples that were scored positive for S. mansoni by one or more parasitological examinations (6/19 were positive by Kato-Katz method, 9/17 by saline gradient and 10/13 by Helmintex®. PCR scored 13 of these 19 samples as positive for S. mansoni . We conclude that while none of these methods yielded 100% sensitivity, a combination of techniques should be effective for improving the detection of S. mansoni infection in low-endemicity areas.

  19. A conventional polymerase chain reaction-based method for the diagnosis of human schistosomiasis in stool samples from individuals in a low-endemicity area

    Science.gov (United States)

    Carneiro, Teiliane Rodrigues; Peralta, Regina Helena Saramago; Pinheiro, Marta Cristhiany Cunha; de Oliveira, Sara Menezes; Peralta, José Mauro; Bezerra, Fernando Schemelzer Moraes

    2013-01-01

    The aim of this study was to evaluate the efficacy of a polymerase chain reaction (PCR)-based method to detect Schistosoma mansoni DNA in stool samples from individuals living in a low-endemicity area in Brazil. Of the 125 initial stool samples, 80 were ELISA reactive and eggs were identified in 19 of the samples by parasitological examination. For the PCR evaluations, 56 stool samples were selected and divided into five groups. Groups I-IV were scored negative for S. mansoni eggs by parasitological examination. Groups I and II were ELISA reactive, whereas Groups III and IV were ELISA nonreactive. Groups II and III were positive for other intestinal parasites. PCR testing scored eight samples as positive from these four groups. Group V represented the S. mansoni -positive group and it included ELISA-reactive samples that were scored positive for S. mansoni by one or more parasitological examinations (6/19 were positive by Kato-Katz method, 9/17 by saline gradient and 10/13 by Helmintex®). PCR scored 13 of these 19 samples as positive for S. mansoni . We conclude that while none of these methods yielded 100% sensitivity, a combination of techniques should be effective for improving the detection of S. mansoni infection in low-endemicity areas. PMID:24402156

  20. Polymerase chain reaction and bacteriological comparative analysis of raw milk samples and buffalo mozzarella produced and marketed in Caserta in the Campania region of Italy

    Directory of Open Access Journals (Sweden)

    Elisabetta Di Giannatale

    2009-09-01

    Full Text Available To help identify an epidemiological link between the consumption of buffalo mozzarella prepared with raw milk (not heat-treated and cases of human brucellosis, 80 samples of raw buffalo milk and 315 samples of mozzarella were tested for the presence of Brucella spp. Samples originated from Caserta, the province with the highest number of Brucella-positive buffalo herds in Campania, the region in which 96.02% of all cases of human brucellosis reported in 2000-2005 were recorded. To take into account possible seasonal variations, between February 2006 and March 2007, samples were purchased directly from 72 dairy outlets that were representative of the province. Samples were tested for Brucella spp. using the polymerase chain reaction (PCR and bacterial isolation. Samples tested negative for Brucella using both methods. Spiked samples were then prepared and tested by PCR and bacterial isolation and the sensitivity, specificity, repeatability, reproducibility and limit of detection were determined. The PCR limit of detection was below 1 colony-forming unit (cfu/g. The repeatability and reproducibility of the method were 100% (p = 0.95, the sensitivity was 96.7% (p = 0.95 and the specificity was 100% (p = 0.95.

  1. Separation and screening of short-chain chlorinated paraffins in environmental samples using comprehensive two-dimensional gas chromatography with micro electron capture detection.

    Science.gov (United States)

    Xia, Dan; Gao, Lirong; Zhu, Shuai; Zheng, Minghui

    2014-11-01

    Short-chain chlorinated paraffins (SCCPs) are highly complex technical mixtures with thousands of isomers and numerous homologs. They are classified as priority candidate persistent organic pollutants under the Stockholm Convention for their persistence, bioaccumulation, and toxicity. Analyzing SCCPs is challenging because of the complexity of the mixtures. Chromatograms of SCCPs acquired using one-dimensional (1D) gas chromatography (GC) contain a large characteristic "peak" with a broad and unresolved profile. Comprehensive two-dimensional GC (GC×GC) shows excellent potential for separating complex mixtures. In this study, GC×GC coupled with micro electron capture detection (μECD) was used to separate and screen SCCPs. The chromatographic parameters, including the GC column types, oven temperature program, and modulation period, were systematically optimized. The SCCP congeners were separated into groups using a DM-1 column connected to a BPX-50 column. The SCCP congeners in technical mixtures were separated according to the number of chlorine substituents for a given carbon chain length and according to the number of carbon atoms plus chlorine atoms for different carbon chain lengths. A fish tissue sample was analyzed to illustrate the feasibility of the GC×GC-μECD method in analyzing biological samples. Over 1,500 compounds were identified in the fish extract, significantly more than were identified using 1D GC. The detection limits for five selected SCCP congeners were between 1 and 5 pg/L using the GC×GC method, and these were significantly lower than those achieved using 1D GC. This method is a good choice for analysis of SCCPs in environmental samples, exhibiting good separation and good sensitivity.

  2. Polymerase chain reaction detection of Leishmania DNA in skin biopsy samples in Sri Lanka where the causative agent of cutaneous leishmaniasis is Leishmania donovani.

    Science.gov (United States)

    Ranasinghe, Shalindra; Wickremasinghe, Renu; Hulangamuwa, Sanjeeva; Sirimanna, Ganga; Opathella, Nandimithra; Maingon, Rhaiza D C; Chandrasekharan, Vishvanath

    2015-12-01

    Leishmania donovani is the known causative agent of both cutaneous (CL) and visceral leishmaniasis in Sri Lanka. CL is considered to be under-reported partly due to relatively poor sensitivity and specificity of microscopic diagnosis. We compared robustness of three previously described polymerase chain reaction (PCR) based methods to detect Leishmania DNA in 38 punch biopsy samples from patients presented with suspected lesions in 2010. Both, Leishmania genus-specific JW11/JW12 KDNA and LITSR/L5.8S internal transcribed spacer (ITS)1 PCR assays detected 92% (35/38) of the samples whereas a KDNA assay specific forL. donovani (LdF/LdR) detected only 71% (27/38) of samples. All positive samples showed a L. donovani banding pattern upon HaeIII ITS1 PCR-restriction fragment length polymorphism analysis. PCR assay specificity was evaluated in samples containing Mycobacterium tuberculosis, Mycobacterium leprae, and human DNA, and there was no cross-amplification in JW11/JW12 and LITSR/L5.8S PCR assays. The LdF/LdR PCR assay did not amplify M. leprae or human DNA although 500 bp and 700 bp bands were observed in M. tuberculosis samples. In conclusion, it was successfully shown in this study that it is possible to diagnose Sri Lankan CL with high accuracy, to genus and species identification, using Leishmania DNA PCR assays.

  3. Pooling of cultured samples and comparison of multistate laboratory workflows with the MagMAX sample preparation system and VetMAX quantitative polymerase chain reaction reagents for detection of Tritrichomonas foetus-colonized bulls.

    Science.gov (United States)

    Effinger, Lee; Peddireddi, Lalitha; Simunich, Marilyn; Oberst, Richard; O'Connell, Catherine; Leyva-Baca, Ivan

    2014-01-01

    The objectives of the current study were 1) to compare sample preparation workflows and quantitative real-time polymerase chain reaction assays (qPCR) as currently used in veterinary diagnostic laboratories with a study protocol utilizing commercially available reagents for individual Tritrichomonas foetus testing, 2) to assess the accuracy of pooling cultured smegma samples followed by extraction and qPCR testing as used in the study laboratory, and 3) to assess the specificity of the currently used primers and probes by sequencing all positive and presumptive positive samples identified in the study laboratory in an attempt to capture any nucleotide variability between T. foetus isolates and to rule out false-positive results possibly due to Simplicimonas moskowitzi. Eight hundred three cultured smegma samples were collected from different regions of the United States with the collaboration of 5 veterinary testing laboratories. The samples were processed individually by the respective laboratories, and then sent to the study laboratory and retested using the study protocol. Comparison testing showed an overall agreement of 95.89% between the veterinary testing laboratories and the study laboratory. One hundred seventy-six positive or presumptive positive samples plus 625 negative qPCR samples were combined and retested using a pooling protocol. Pools consisted of 1 positive sample and 4 negative samples (1/5). These pools were processed using the same study laboratory protocols, and 96% of the positive samples were detected in these pools. Nested PCR followed by sequencing confirmed 175 of the 178 samples classified as positive or presumptive positive in the study laboratory as containing T. foetus-specific DNA.

  4. Rapid and accurate detection of Arcobacter contamination in commercial chicken products and wastewater samples by real-time polymerase chain reaction.

    Science.gov (United States)

    González, Ana; Suski, Jan; Ferrús, Maria A

    2010-03-01

    An SYBR Green real-time polymerase chain reaction (PCR) assay was developed for Arcobacter detection in food and wastewater samples. The assay was applied to 36 chicken and 33 wastewater samples, and the results were compared with those obtained for conventional PCR, multiplex PCR, and culture isolation. Isolates were identified by multiplex PCR and restriction fragment length polymorphism analysis of PCR-amplified DNA fragment, and typed by randomly amplified polymorphic DNA. Arcobacter sp. was detected in 25 of the 26 chicken carcasses (96%) and in 4 of the 10 liver samples (40%) by real-time PCR. Twenty-five chicken samples were positive also by conventional PCR, but in most of them the detection was only possible after 48-h enrichment. Arcobacter butzleri was the most frequently detected species. Twenty-four Arcobacter isolates were obtained from chicken samples, where A. butzleri is the only identified species. All the wastewater samples (100%) were positive for Arcobacter sp. by real-time PCR without enrichment. A. butzleri and Arcobacter cryaerophilus were detected by multiplex PCR. Fifteen samples were found to be positive by culture. Thirty-six isolates were obtained; all of them were identified as A. butzleri by multiplex PCR. However, by PCR-restriction fragment length polymorphism, 34 were identified as A. butzleri, 1 as A. cryaerophilus, and another 1 as Arcobacter skirrowii. A great genetic heterogeneity was observed by randomly amplified polymorphic DNA-PCR profiling. The real-time PCR assay developed in this work showed better detection levels than conventional PCR, together with shorter times of testing samples. Therefore, it could be used as a rapid and accurate instrument for monitoring Arcobacter contamination levels in food and water samples.

  5. An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees.

    Science.gov (United States)

    Aberer, Andre J; Stamatakis, Alexandros; Ronquist, Fredrik

    2016-01-01

    Sampling tree space is the most challenging aspect of Bayesian phylogenetic inference. The sheer number of alternative topologies is problematic by itself. In addition, the complex dependency between branch lengths and topology increases the difficulty of moving efficiently among topologies. Current tree proposals are fast but sample new trees using primitive transformations or re-mappings of old branch lengths. This reduces acceptance rates and presumably slows down convergence and mixing. Here, we explore branch proposals that do not rely on old branch lengths but instead are based on approximations of the conditional posterior. Using a diverse set of empirical data sets, we show that most conditional branch posteriors can be accurately approximated via a [Formula: see text] distribution. We empirically determine the relationship between the logarithmic conditional posterior density, its derivatives, and the characteristics of the branch posterior. We use these relationships to derive an independence sampler for proposing branches with an acceptance ratio of ~90% on most data sets. This proposal samples branches between 2× and 3× more efficiently than traditional proposals with respect to the effective sample size per unit of runtime. We also compare the performance of standard topology proposals with hybrid proposals that use the new independence sampler to update those branches that are most affected by the topological change. Our results show that hybrid proposals can sometimes noticeably decrease the number of generations necessary for topological convergence. Inconsistent performance gains indicate that branch updates are not the limiting factor in improving topological convergence for the currently employed set of proposals. However, our independence sampler might be essential for the construction of novel tree proposals that apply more radical topology changes.

  6. [Analysis of short-chain chlorinated paraffins in sediment samples from the mouth of the Daliao River by HRGC/ECNI-LRMS].

    Science.gov (United States)

    Gao, Yuan; Wang, Cheng; Zhang, Hai-jun; Zou, Li-li; Tian, Yu-zeng; Chen, Ji-ping

    2010-08-01

    An analytical method for quantifying short-chain chlorinated paraffins (SCCPs) by high-resolution gas chromatography/electron capture negative ion low-resolution mass spectrometry (HRGC/ECNI-LRMS) was presented. The cleanup procedure with an acid silica gel column and activated neutral alumina column was optimized to remove the interferences. As illustration of the application of the method to environmental samples, it is found that lower chlorinated C10 and C11 compounds were the main SCCPs compounds in six sediment samples from the mouth of the Daliao River. The concentrations of SCCPs in sediments were determined to be in the range of 64.9-407.0 ng/g and showed a decreasing tendency from the shore to the remote location.

  7. GC/MS method for determining carbon isotope enrichment and concentration of underivatized short-chain fatty acids by direct aqueous solution injection of biogas digester samples.

    Science.gov (United States)

    Mulat, Daniel Girma; Feilberg, Anders

    2015-10-01

    In anaerobic digestion of organic matter, several metabolic pathways are involved during the simultaneous production and consumption of short-chain fatty acids (SCFA) in general and acetate in particular. Understanding the role of each pathway requires both the determination of the concentration and isotope enrichment of intermediates in conjunction with isotope labeled substrates. The objective of this study was to establish a rapid and simple GC/MS method for determining the isotope enrichment of acetate and concentration of underivatized short-chain fatty acids (SCFA) in biogas digester samples by direct liquid injection of acidified aqueous samples. Sample preparation involves only acidification, centrifugation and filtration of the aqueous solution followed by direct injection of the aqueous supernatant solution onto a polar column. With the sample preparation and GC/MS conditions employed, well-resolved and sharp peaks of underivatized SCFA were obtained in a reasonably short time. Good recovery (96.6-102.3%) as well as low detection (4-7 µmol/L) and quantification limits (14-22 µmol/L) were obtained for all the 6 SCFA studied. Good linearity was achieved for both concentration and isotope enrichment measurement with regression coefficients higher than 0.9978 and 0.9996, respectively. The method has a good intra- and inter-day precision with a relative standard deviation (RSD) below 6% for determining the tracer-to-tracee ratio (TTR) of both [2-(13)C]acetate and [U-(13)C]acetate. It has also a good intra- and inter-day precision with a RSD below 6% and 5% for determining the concentration of standard solution and biogas digester samples, respectively. Acidification of biogas digester samples with oxalic acid provided the low pH required for the protonation of SCFA and thus, allows the extraction of SCFA from the complex sample matrix. Moreover, oxalic acid was the source of formic acid which was produced in the injector set at high temperature. The produced

  8. Quantitative real-time polymerase chain reaction is an alternative method for the detection of HER-2 amplification in formalin-fixed paraffin-embedded breast cancer samples.

    Science.gov (United States)

    Pu, Tianjie; Guo, Peng; Qiu, Yan; Chen, Shinan; Yang, Libo; Sun, Linyong; Ye, Feng; Bu, Hong

    2015-01-01

    Fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC) are the most common methods that are used to quantify HER-2 gene and protein levels, respectively, in human breast cancer. However, due to bad sample quality, some samples are unable to be subjected to a FISH assay. We evaluated 71 formalin-fixed paraffin-embedded (FFPE) breast carcinoma specimens by quantitative real-time polymerase chain reaction (qPCR), IHC, and FISH. We also performed qPCR and FISH assays on delayed formalin-fixed (DDF) samples. The qPCR results were in complete concordance with the results of IHC and FISH. In regards to the DDF samples, the HER-2 fluorescent signal seemed decayed compared with that of the DDF samples after 1 h. However, the qPCR method still works well up to 12 hours. Our results indicated that qPCR was obviously superior to FISH in cases that were not fixed in a reasonable amount of time. However, qPCR can be an alternative method by which to perform HER2 amplification assays in breast cancer.

  9. Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples

    Science.gov (United States)

    Stelzer, Erin A.; Strickler, Kriston M.; Schill, William B.

    2012-01-01

    During summer and early fall 2010, 15 river samples and 6 fecal-source samples were collected in West Virginia. These samples were analyzed by three laboratories for three microbial source tracking (MST) markers: AllBac, a general fecal indicator; BacHum, a human-associated fecal indicator; and BoBac, a ruminant-associated fecal indicator. MST markers were analyzed by means of the quantitative polymerase chain reaction (qPCR) method. The aim was to assess interlaboratory precision when the three laboratories used the same MST marker and shared deoxyribonucleic acid (DNA) extracts of the samples, but different equipment, reagents, and analyst experience levels. The term assay refers to both the markers and the procedure differences listed above. Interlaboratory precision was best for all three MST assays when using the geometric mean absolute relative percent difference (ARPD) and Friedman's statistical test as a measure of interlaboratory precision. Adjustment factors (one for each MST assay) were calculated using results from fecal-source samples analyzed by all three laboratories and applied retrospectively to sample concentrations to account for differences in qPCR results among labs using different standards and procedures. Following the application of adjustment factors to qPCR results, ARPDs were lower; however, statistically significant differences between labs were still observed for the BacHum and BoBac assays. This was a small study and two of the MST assays had 52 percent of samples with concentrations at or below the limit of accurate quantification; hence, more testing could be done to determine if the adjustment factors would work better if the majority of sample concentrations were above the quantification limit.

  10. Differential Diagnosis of Entamoeba spp. in Clinical Stool Samples Using SYBR Green Real-Time Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Thiago dos Santos Gomes

    2014-01-01

    Full Text Available Amoebiasis, a disease caused by Entamoeba histolytica, is usually diagnosed by microscopic examination, which does not differentiate the morphologically identical species of the E. histolytica/E. dispar complex. Furthermore, morphologically similar species such as Entamoeba hartmanni contribute to misidentification. Therefore, there is a need for more sensitive and specific methods. This study standardized a multiplex real-time PCR system for E. histolytica and E. dispar and a single real-time PCR for E. hartmanni. The multiplex protocol detected up to 0.0143 pg of E. histolytica DNA and 0.5156 pg of E. dispar DNA, and the average melting temperature (Tm was 73°C and 70°C, respectively. For E. hartmanni, the Tm was 73°C and the amplification was successful down to 0.03 fg of plasmid DNA. Negative controls and other intestinal parasites presented no amplification. Among the 48 samples tested, E. dispar DNA was detected in 37; none exhibited E. histolytica DNA and 11 were negative in the multiplex protocol. In 4 of these 11 samples, however, E. hartmanni DNA was amplified. SYBR Green is demonstrated to be an interesting option and these combined PCR reactions can improve laboratory diagnosis of amoebiasis in developing countries.

  11. Differential diagnosis of Entamoeba spp. in clinical stool samples using SYBR green real-time polymerase chain reaction.

    Science.gov (United States)

    Gomes, Thiago Dos Santos; Garcia, Mariana Coimbra; de Souza Cunha, Flavia; Werneck de Macedo, Heloisa; Peralta, José Mauro; Peralta, Regina Helena Saramago

    2014-01-01

    Amoebiasis, a disease caused by Entamoeba histolytica, is usually diagnosed by microscopic examination, which does not differentiate the morphologically identical species of the E. histolytica/E. dispar complex. Furthermore, morphologically similar species such as Entamoeba hartmanni contribute to misidentification. Therefore, there is a need for more sensitive and specific methods. This study standardized a multiplex real-time PCR system for E. histolytica and E. dispar and a single real-time PCR for E. hartmanni. The multiplex protocol detected up to 0.0143 pg of E. histolytica DNA and 0.5156 pg of E. dispar DNA, and the average melting temperature (T(m)) was 73 °C and 70 °C, respectively. For E. hartmanni, the T(m) was 73 °C and the amplification was successful down to 0.03 fg of plasmid DNA. Negative controls and other intestinal parasites presented no amplification. Among the 48 samples tested, E. dispar DNA was detected in 37; none exhibited E. histolytica DNA and 11 were negative in the multiplex protocol. In 4 of these 11 samples, however, E. hartmanni DNA was amplified. SYBR Green is demonstrated to be an interesting option and these combined PCR reactions can improve laboratory diagnosis of amoebiasis in developing countries.

  12. Specific detection of Neospora caninum oocysts in fecal samples from experimentally-infected dogs using the polymerase chain reaction.

    Science.gov (United States)

    Hill, D E; Liddell, S; Jenkins, M C; Dubey, J P

    2001-04-01

    Neospora caninum oocysts, passed in the feces of a definitive host (dog), were isolated, and genomic DNA was extracted. A polymerase cahin reaction (PCR) targeting the N. caninum-specific Nc 5 genomic sequence was performed using the isolated DNA. A synthesized competitor molecule containing part of the Nc 5 sequence was included in the assay as a check against false-negative PCR results and to quantify N. caninum oocyst DNA in fecal samples. A standard curve of the ratio of fluorescence intensity of PCR-amplified competitor to that of oocyst DNA was constructed to compare oocyst equivalents from fecal samples containing unknown numbers of N. caninum oocysts and to assess the sensitivity of the assay. The specificity of the assay was determined using the Nc 5-specific primers in PCR assays against other parasites likely to be found in canine feces. Genomic DNA sequences from the canine coccidians Hammondia heydorni, Cryptosporidium parvum, Sarcocystis cruzi, S. tenella, and Isospora ohioensis and the canine helminth parasites Strongyloides stercoralis, Toxocara canis, Dipylidium caninum, and Ancylostoma caninum were not amplified. In addition, genomic DNA sequences from oocysts of coccidian parasites that might contaminate dog feces, such as Hammondia hammondi, Toxoplasma gondii, or Eimeria tenella, were not amplified in the PCR assay. The assay should be useful in epidemiological surveys of both domestic and wild canine hosts and in investigations of oocyst biology in experimental infections.

  13. Differential Diagnosis of Entamoeba spp. in Clinical Stool Samples Using SYBR Green Real-Time Polymerase Chain Reaction

    Science.gov (United States)

    Gomes, Thiago dos Santos; Garcia, Mariana Coimbra; de Souza Cunha, Flavia; Peralta, José Mauro; Peralta, Regina Helena Saramago

    2014-01-01

    Amoebiasis, a disease caused by Entamoeba histolytica, is usually diagnosed by microscopic examination, which does not differentiate the morphologically identical species of the E. histolytica/E. dispar complex. Furthermore, morphologically similar species such as Entamoeba hartmanni contribute to misidentification. Therefore, there is a need for more sensitive and specific methods. This study standardized a multiplex real-time PCR system for E. histolytica and E. dispar and a single real-time PCR for E. hartmanni. The multiplex protocol detected up to 0.0143 pg of E. histolytica DNA and 0.5156 pg of E. dispar DNA, and the average melting temperature (Tm) was 73°C and 70°C, respectively. For E. hartmanni, the Tm was 73°C and the amplification was successful down to 0.03 fg of plasmid DNA. Negative controls and other intestinal parasites presented no amplification. Among the 48 samples tested, E. dispar DNA was detected in 37; none exhibited E. histolytica DNA and 11 were negative in the multiplex protocol. In 4 of these 11 samples, however, E. hartmanni DNA was amplified. SYBR Green is demonstrated to be an interesting option and these combined PCR reactions can improve laboratory diagnosis of amoebiasis in developing countries. PMID:24693242

  14. Comparison of sample types and analytical methods for the detection of highly campylobacter-colonized broiler flocks at different stages in the poultry meat production chain.

    Science.gov (United States)

    Seliwiorstow, Tomasz; Duarte, Alexandra; Baré, Julie; Botteldoorn, Nadine; Dierick, Katelijne; Uyttendaele, Mieke; De Zutter, Lieven

    2015-05-01

    Exclusion of broiler batches, highly colonized with Campylobacter (>7.5 log10 colony-forming units/g), from the fresh poultry meat market might decrease the risk of human campylobacteriosis. The objective of this study was to compare different sample types (both at the farm and the slaughterhouse) and methods (direct culture, quantitative real-time polymerase chain reaction [qPCR], propidium monoazide [PMA]-qPCR) applied for the quantification of the Campylobacter colonization level. In addition, the applicability of the lateral flow-based immunoassay, Singlepath(®) Direct Campy Poultry test (Singlepath(®) test), was evaluated as a rapid method for the qualitative detection of Campylobacter in highly colonized broiler batches. Campylobacter counts differed significantly between sample types collected at farm level (cecal droppings, feces, boot swabs) and at slaughterhouse level (cecal content, fecal material from crates). Furthermore, comparison of Campylobacter counts obtained by different methods (direct culture, qPCR, PMA-qPCR) in cecal droppings revealed significant differences, although this was not observed for cecal-content samples. Evaluation of the Singlepath(®) test on cecal droppings and cecal-content samples revealed an acceptable level of sensitivity and specificity. In conclusion, cecal droppings and cecal content are proposed as the most representative sample types for quantification of Campylobacter colonization level of broilers at farm and slaughterhouse, respectively. Direct culture and qPCR are equally sensitive for quantification of Campylobacter in fresh cecal-content samples. PMA treatment before qPCR inhibits the signal from dead Campylobacter cells. Consequently, when samples are extensively stored and/or transported, qPCR is preferred to direct culture and PMA-qPCR. Furthermore, the Singlepath(®) test offers a convenient alternative method for rapid detection of Campylobacter in highly colonized broiler batches.

  15. Nonlinear calibration transfer based on hierarchical Bayesian models and Lagrange Multipliers: Error bounds of estimates via Monte Carlo - Markov Chain sampling.

    Science.gov (United States)

    Seichter, Felicia; Vogt, Josef; Radermacher, Peter; Mizaikoff, Boris

    2017-01-25

    The calibration of analytical systems is time-consuming and the effort for daily calibration routines should therefore be minimized, while maintaining the analytical accuracy and precision. The 'calibration transfer' approach proposes to combine calibration data already recorded with actual calibrations measurements. However, this strategy was developed for the multivariate, linear analysis of spectroscopic data, and thus, cannot be applied to sensors with a single response channel and/or a non-linear relationship between signal and desired analytical concentration. To fill this gap for a non-linear calibration equation, we assume that the coefficients for the equation, collected over several calibration runs, are normally distributed. Considering that coefficients of an actual calibration are a sample of this distribution, only a few standards are needed for a complete calibration data set. The resulting calibration transfer approach is demonstrated for a fluorescence oxygen sensor and implemented as a hierarchical Bayesian model, combined with a Lagrange Multipliers technique and Monte-Carlo Markov-Chain sampling. The latter provides realistic estimates for coefficients and prediction together with accurate error bounds by simulating known measurement errors and system fluctuations. Performance criteria for validation and optimal selection of a reduced set of calibration samples were developed and lead to a setup which maintains the analytical performance of a full calibration. Strategies for a rapid determination of problems occurring in a daily calibration routine, are proposed, thereby opening the possibility of correcting the problem just in time.

  16. Toxoplasma gondii and pre-treatment protocols for polymerase chain reaction analysis of milk samples: a field trial in sheep from Southern Italy

    Directory of Open Access Journals (Sweden)

    Alice Vismarra

    2017-02-01

    Full Text Available Toxoplasmosis is a zoonotic disease caused by the protozoan Toxoplasma gondii. Ingestion of raw milk has been suggested as a risk for transmission to humans. Here the authors evaluated pre-treatment protocols for DNA extraction on T. gondii tachyzoite-spiked sheep milk with the aim of identifying the method that resulted in the most rapid and reliable polymerase chain reaction (PCR positivity. This protocol was then used to analyse milk samples from sheep of three different farms in Southern Italy, including real time PCR for DNA quantification and PCR-restriction fragment length polymorphism for genotyping. The pre-treatment protocol using ethylenediaminetetraacetic acid and Tris-HCl to remove casein gave the best results in the least amount of time compared to the others on spiked milk samples. One sample of 21 collected from sheep farms was positive on one-step PCR, real time PCR and resulted in a Type I genotype at one locus (SAG3. Milk usually contains a low number of tachyzoites and this could be a limiting factor for molecular identification. Our preliminary data has evaluated a rapid, cost-effective and sensitive protocol to treat milk before DNA extraction. The results of the present study also confirm the possibility of T. gondii transmission through consumption of raw milk and its unpasteurised derivatives.

  17. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence.

    Science.gov (United States)

    Alfaro, Michael E; Zoller, Stefan; Lutzoni, François

    2003-02-01

    Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.

  18. The use of epifluorescent microscopy and quantitative polymerase chain reaction to determine the presence/absence and identification of microorganisms associated with domestic and foreign wallboard samples

    Science.gov (United States)

    Griffin, Dale W.

    2011-01-01

    Epifluorescent microscopy and quantitative polymerase chain reaction (qPCR) were utilized to determine the presence, concentration and identification of bacteria, and more specifically sulfate reducing bacteria (SRB) in subsamples of Chinese and North American wallboard, and wallboard-mine rock. Bacteria were visible in most subsamples, which included wallboard-lining paper from each side of the wallboard, wallboard filler, wallboard tape and fragments of mined wallboard rock via microscopy. Observed bacteria occurred as single or small clusters of cells and no mass aggregates indicating colonization were noted. Universal 16S qPCR was utilized to directly examine samples and detected bacteria at concentrations ranging from 1.4 x 103 to 6.4 x 104 genomic equivalents per mm2 of paper or per gram of wallboard filler or mined rock, in 12 of 41 subsamples. Subsamples were incubated in sulfate reducing broth for ~30 to 60 days (enrichment assay) and then analyzed by universal 16S and SRB qPCR. Enrichment universal 16S qPCR detected bacteria in 32 of 41 subsamples at concentrations ranging from 1.5 x 104 to 4.2 x 107 genomic equivalents per ml of culture broth. Evaluation of enriched subsamples by SRB qPCR demonstrated that SRB were not detectable in most of the samples and if they were detected, detection was not reproducible (an indication of low concentrations, if present). Enrichment universal 16S and SRB qPCR demonstrated that viable bacteria were present in subsamples (as expected given exposure of the samples following manufacture, transport and use) but that SRB were either not present or present at very low numbers. Further, no differences in trends were noted between the various Chinese and North American wallboard samples. In all, the microscopy and qPCR data indicated that the suspected ‘sulfur emissions’ emanating from suspect wallboard samples is not due to microbial activity.

  19. Detection of Salmonella enteritidis in pooled poultry environmental samples using a serotype-specific real-time-polymerase chain reaction assay.

    Science.gov (United States)

    Adams, Derek R; Stensland, Wendy R; Wang, Chong H; O'Connor, Annette M; Trampel, Darrell W; Harmon, Karen M; Strait, Erin L; Frana, Timothy S

    2013-03-01

    While real-time-polymerase chain reaction (RT PCR) has been used as a rapid test for detection of Salmonella Enteritidis in recent years, little research has been done to assess the feasibility of pooling poultry environmental samples with a Salmonella Enteritidis-specific RT PCR assay. Therefore the objective of this study was to compare RT PCR Salmonella Enteritidis detection in individual and pooled (in groups of two, three, and four) poultry environmental drag swab samples to traditional cultural methods. The drag swabs were collected from poultry facilities previously confirmed positive for Salmonella Enteritidis and were cultured according to National Poultry Improvement Plan guidelines. Initial, Salmonella Enteritidis-specific RT PCR assay threshold cycle cutoff values of Salmonella Enteritidis was cultured in 7 of 208 environmental samples (3.4%). Individual samples were 99.0%, 100%, and 100% in agreement with the RT PCR at threshold cycle (C(t)) cutoff values of < or = 36, < or = 30, and < or = 28 respectively. The agreement for pooled samples also followed the same trend with highest agreement at C(t) < or = 28 (pool of 2 = 100.0%, pool of 3 = 100.0%, pool of 4 = 100.0%), midrange agreement at C(t) < or = 30 (pool of 2 = 99.0%, pool of 3 = 100.0%, pool of 4 = 100.0%), and lowest agreement at C(t) < or = 36 (pool of 2 = 98.1%, pool of 3 = 97.1%, pool of 4 = 98.1%). In conclusion, regardless of the level of pooling after tetrathionate enrichment, sensitivity was very good, and results would be comparable to what would have been found with individual culture or individual RT PCR at C(t) < or = 36.

  20. Sampling the conformation of protein surface residues for flexible protein docking

    Directory of Open Access Journals (Sweden)

    Amenta Nina

    2010-11-01

    Full Text Available Abstract Background The problem of determining the physical conformation of a protein dimer, given the structures of the two interacting proteins in their unbound state, is a difficult one. The location of the docking interface is determined largely by geometric complementarity, but finding complementary geometry is complicated by the flexibility of the backbone and side-chains of both proteins. We seek to generate candidates for docking that approximate the bound state well, even in cases where there is backbone and/or side-chain difference from unbound to bound states. Results We divide the surfaces of each protein into local patches and describe the effect of side-chain flexibility on each patch by sampling the space of conformations of its side-chains. Likely positions of individual side-chains are given by a rotamer library; this library is used to derive a sample of possible mutual conformations within the patch. We enforce broad coverage of torsion space. We control the size of the sample by using energy criteria to eliminate unlikely configurations, and by clustering similar configurations, resulting in 50 candidates for a patch, a manageable number for docking. Conclusions Using a database of protein dimers for which the bound and unbound structures of the monomers are known, we show that from the unbound patch we are able to generate candidates for docking that approximate the bound structure. In patches where backbone change is small (within 1 Å RMSD of bound, we are able to account for flexibility and generate candidates that are good approximations of the bound state (82% are within 1 Å and 98% are within 1.4 Å RMSD of the bound conformation. We also find that even in cases of moderate backbone flexibility our candidates are able to capture some of the overall shape change. Overall, in 650 of 700 test patches we produce a candidate that is either within 1 Å RMSD of the bound conformation or is closer to the bound state than the

  1. Entropy and enthalpy of interaction between amino acid side chains in nanopores

    CERN Document Server

    Vaitheeswaran, S

    2014-01-01

    Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientations between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by e...

  2. Development of a diagnostic real-time polymerase chain reaction assay for the detection of invasive Haemophilus influenzae in clinical samples.

    LENUS (Irish Health Repository)

    Meyler, Kenneth L

    2012-12-01

    Since the introduction of the Haemophilus influenzae serotype b vaccine, invasive H. influenzae disease has become dominated by nontypeable (NT) strains. Several widely used molecular diagnostic methods have been shown to lack sensitivity or specificity in the detection of some of these strains. Novel real-time assays targeting the fucK, licA, and ompP2 genes were developed and evaluated. The fucK assay detected all strains of H. influenzae tested (n = 116) and had an analytical sensitivity of 10 genome copies\\/polymerase chain reaction (PCR). This assay detected both serotype b and NT H. influenzae in 12 previously positive specimens (culture and\\/or bexA PCR) and also detected H. influenzae in a further 5 of 883 culture-negative blood and cerebrospinal fluid (CSF) samples. The fucK assay has excellent potential as a diagnostic test for detection of typeable and nontypeable strains of invasive H. influenzae in clinical samples of blood and CSF.

  3. Determining short chain fatty acids in sewage sludge hydrolysate: a comparison of three analytical methods and investigation of sample storage effects.

    Science.gov (United States)

    Ibrahim, Victor; Hey, Tobias; Jönsson, Karin

    2014-04-01

    In anaerobic digestion, the production of short-chain fatty acids (SCFAs) can be beneficial or harmful to the overall process, depending on the concentration of accumulated acids. Therefore, the accurate determination of the SCFA concentration in both fresh and stored sludge hydrolysates is important. To select a suitable method for monitoring SCFAs during the anaerobic digestion of sewage sludge, the accuracy of three available analytical methods, including 5 pH point acid titration (TITRA5), gas chromatography (GC), and spectrophotometry, were compared in the present study. The results revealed that TITRA5 and GC displayed better agreement in the achieved measurements and higher precision and accuracy than the spectrophotometric assay, as supported by the application of different statistical models. TITRA5 excelled in titrating unfiltered hydrolysate while simultaneously measuring the alkalinity, whereas the GC method provided detailed information on the contribution of different fatty acids to the total acidity. In contrast, the spectrophotometric assay suffered from many forms of interference, depending on the sample's matrix. SCFA production followed the pattern of enzymatic reactions and fitted the Michaelis-Menten model. In addition to promoting TITRA5 as an accurate and robust analytical tool for routine SCFA analyses, this comparative study also demonstrated the possibility of storing hydrolysate samples at different temperatures and durations without altering the SCFA measurements.

  4. Giardia duodenalis in Damascus, Syria: Identification of Giardia genotypes in a sample of human fecal isolates using polymerase chain reaction and restriction fragment length polymorphism analyzing method.

    Science.gov (United States)

    Skhal, Dania; Aboualchamat, Ghalia; Al Nahhas, Samar

    2016-02-01

    Giardia duodenalis is a common gastrointestinal parasite that infects humans and many other mammals. It is most prevalent in many developing and industrialized countries. G. duodenalis is considered to be a complex species. While no morphological distinction among different assemblages exist, it can be genetically differentiated into eight major assemblages: A to H. The aim of this study was to determine the genetic heterogeneity of G. duodenalis in human isolates (a study conducted for the first time in Syria). 40 fecal samples were collected from three different hospitals during the hot summer season of 2014. Extraction of genomic DNA from all Giardia positive samples (based on a microscopic examination) was performed using QIAamp DNA Stool Mini Kit. β-giardin gene was used to differentiate between different Giardia assemblages. The 514 bp fragment was amplified using the Polymerase Chain Reaction method, followed by digestion in HaeIII restriction enzyme. Our result showed that genotype A was more frequent than genotype B, 27/40 (67.5%); 4/40 (10%) respectively. A mixed genotype of A+B was only detected in 9 isolates (22.5%). This is the first molecular study performed on G. duodenalis isolates in Syria in order to discriminate among the different genotypes. Further expanded studies using more genes are needed to detect and identify the Giardia parasite at the level of assemblage and sub-assemblage.

  5. Variation in Bluetongue virus real-time reverse transcription polymerase chain reaction assay results in blood samples of sheep, cattle, and alpaca.

    Science.gov (United States)

    Brito, Barbara P; Gardner, Ian A; Hietala, Sharon K; Crossley, Beate M

    2011-07-01

    Bluetongue is a vector-borne viral disease that affects domestic and wild ruminants. The epidemiology of this disease has recently changed, with occurrence in new geographic areas. Various real-time quantitative reverse transcription polymerase chain reaction (real-time qRT-PCR) assays are used to detect Bluetongue virus (BTV); however, the impact of biologic differences between New World camelids and domestic ruminant samples on PCR efficiency, for which the BTV real-time qRT-PCR was initially validated are unknown. New world camelids are known to have important biologic differences in whole blood composition, including hemoglobin concentration, which can alter PCR performance. In the present study, sheep, cattle, and alpaca blood were spiked with BTV serotypes 10, 11, 13, and 17 and analyzed in 10-fold dilutions by real-time qRT-PCR to determine if species affected nucleic acid recovery and assay performance. A separate experiment was performed using spiked alpaca blood subsequently diluted in 10-fold series in sheep blood to assess the influence of alpaca blood on performance efficiency of the BTV real-time qRT-PCR assay. Results showed that BTV-specific nucleic acid detection from alpaca blood was consistently 1-2 logs lower than from sheep and cattle blood, and results were similar for each of the 4 BTV serotypes analyzed.

  6. Detection and differentiation of Cryptosporidium by real-time polymerase chain reaction in stool samples from patients in Rio de Janeiro, Brazil

    Directory of Open Access Journals (Sweden)

    Roberta Flávia Ribeiro Rolando

    2012-06-01

    Full Text Available This study reports the first genetic characterisation of Cryptosporidium isolates in Brazil using real-time polymerase chain reaction (RT-PCR. A total of 1,197 faecal specimens from children and 10 specimens from human immunodeficiency virus-infected patients were collected between 1999-2010 and screened using microscopy. Forty-eight Cryptosporidium oocyst-positive isolates were identified and analysed using a generic TaqMan assay targeting the 18S rRNA to detect Cryptosporidium species and two other TaqMan assays to identify Cryptosporidium hominis and Cryptosporidium parvum. The 18S rRNA assay detected Cryptosporidium species in all 48 of the stool specimens. The C. parvum TaqMan assay correctly identified five/48 stool samples, while 37/48 stool specimens were correctly amplified in the C. hominis TaqMan assay. The results obtained in this study support previous findings showing that C. hominis infections are more prevalent than C. parvum infections in Brazil and they demonstrate that the TaqMan RT-PCR procedure is a simple, fast and valuable tool for the detection and differentiation of Cryptosporidium species.

  7. Detection of KPC Carbapenemase in Pseudomonas aeruginosa Isolated From Clinical Samples Using Modified Hodge Test and Boronic Acid Phenotypic Methods and Their Comparison With the Polymerase Chain Reaction

    Science.gov (United States)

    Falahat, Saeed; Shojapour, Mana; Sadeghi, Abdorrahim

    2016-01-01

    Background Bacterial resistance to antibiotics has become a major source of concern for public health. Pseudomonas aeruginosa strains are important opportunistic pathogens. These bacteria have a high resistance to a wide range of existing antimicrobials and antibiotics. Objectives The present study was performed to evaluate the frequency of KPC in P. aeruginosa isolated from clinical samples of educational hospitals of Arak University of Medical Sciences, using the mentioned phenotypic and genotypic methods. Materials and Methods One hundred and eight non-duplicate clinical isolates of P. aeruginosa were collected from hospitals of Arak University of Medical Sciences, Arak, Iran. Antibacterial susceptibility was determined by the disk diffusion method. KPC production was confirmed by the Modified Hodge Test (MHT), which is a phenotypic test, and combined-disk test with boronic acid and the Polymerase Chain Reaction (PCR). Results In the present study, 13 isolates (12%) of P. aeruginosa were positive for KPC, using PCR. Comparison of the two phenotypic methods used in this study showed that boronic acid is more sensitive than MHT in identification of KPC-producing strains (84.6% vs. 77%). Conclusions Utilization of reliable methods for identifying carbapenemase-producing strains and determining their antibiotic resistance pattern could have a very important role in treatment of infections caused by these strains. A substantial amount of P. aeruginosa isolated from clinical samples of hospitals in Arak (Iran) produce KPC carbapenemase. Due to their low specificity, MHT and boronic acid phenotypic methods could not completely identify KPC-producing P. aeruginosa. However, the sensitivity of boronic acid phenotypic method in detection of KPC was higher than MHT.

  8. [Detection of Echinococcus granulosus and Echinococcus multilocularis in cyst samples using a novel single tube multiplex real-time polymerase chain reaction].

    Science.gov (United States)

    Can, Hüseyin; İnceboz, Tonay; Caner, Ayşe; Atalay Şahar, Esra; Karakavuk, Muhammet; Döşkaya, Mert; Çelebi, Fehmi; Değirmenci Döşkaya, Aysu; Gülçe İz, Sultan; Gürüz, Yüksel; Korkmaz, Metin

    2016-04-01

    Cystic echinococcosis (CE) and alveolar echinococcosis (AE) caused by Echinococcus granulosus and Echinococcus multilocularis, respectively, are important helminthic diseases worldwide as well as in our country. Epidemiological studies conducted in Turkey showed that the prevalence of CE is 291-585/100.000. It has also been showed that the seroprevalence of AE is 3.5%. For the diagnosis of CE and AE, radiological (ultrasonography, computed tomography, magnetic resonance) and serological methods, in addition to clinical findings, are being used. The definitive diagnosis relies on pathological examination When the hydatid cysts are sterile or does not contain protoscolex, problems may occur during pathological discrimination of E.granulosus and E.multilocularis species. In this study, we aimed to develop a novel multiplex real-time polymerase chain reaction (M-RT-PCR) targeting mitochondrial 12S rRNA gene of E.granulosus and E.multilocularis using Echi S (5'-TTTATGAATATTGTGACCCTGAGAT-3') and Echi A (5'-GGTCTTAACTCAACTCATGGAG-3') primers and three different probes; Anchor Ech (5'-GTTTGCCACCTCGATGTTGACTTAG-fluoroscein-3'), Granulosus (5'-LC640-CTAAGGTTTTGGTGTAGTAATTGATATTTT-phosphate-3') and Multilocularis (5'-LC705-CTGTGATCTTGGTGTAGTAGTTGAGATT-phosphate-3') that will enable the diagnosis of CE and AE in same assay. During M-RTR-PCR, plasmids containing E.granulosus (GenBank: AF297617.1) and E.multilocularis (GenBank: NC_000928.2) mitochondrial 12S rRNA regions were used as positive controls. Cysts samples of patients which were pathologically confirmed to be CE (n: 10) and AE (n: 15) and healthy human DNA samples (n: 25) as negative control as well as DNA samples of 12 different parasites (Taenia saginata, Hymenolepis nana, Trichuris trichiura, Fasciola hepatica, Enterobius vermicularis, Toxoplasma gondii, Pneumocystis jirovecii, Trichomonas vaginalis, Cryptosporidium hominis, Strongyloides stercoralis, Plasmodium falciparum, Plasmodium vivax) were used to develop M

  9. Stochastic Engine Final Report: Applying Markov Chain Monte Carlo Methods with Importance Sampling to Large-Scale Data-Driven Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Glaser, R E; Johannesson, G; Sengupta, S; Kosovic, B; Carle, S; Franz, G A; Aines, R D; Nitao, J J; Hanley, W G; Ramirez, A L; Newmark, R L; Johnson, V M; Dyer, K M; Henderson, K A; Sugiyama, G A; Hickling, T L; Pasyanos, M E; Jones, D A; Grimm, R J; Levine, R A

    2004-03-11

    Accurate prediction of complex phenomena can be greatly enhanced through the use of data and observations to update simulations. The ability to create these data-driven simulations is limited by error and uncertainty in both the data and the simulation. The stochastic engine project addressed this problem through the development and application of a family of Markov Chain Monte Carlo methods utilizing importance sampling driven by forward simulators to minimize time spent search very large state spaces. The stochastic engine rapidly chooses among a very large number of hypothesized states and selects those that are consistent (within error) with all the information at hand. Predicted measurements from the simulator are used to estimate the likelihood of actual measurements, which in turn reduces the uncertainty in the original sample space via a conditional probability method called Bayesian inferencing. This highly efficient, staged Metropolis-type search algorithm allows us to address extremely complex problems and opens the door to solving many data-driven, nonlinear, multidimensional problems. A key challenge has been developing representation methods that integrate the local details of real data with the global physics of the simulations, enabling supercomputers to efficiently solve the problem. Development focused on large-scale problems, and on examining the mathematical robustness of the approach in diverse applications. Multiple data types were combined with large-scale simulations to evaluate systems with {approx}{sup 10}20,000 possible states (detecting underground leaks at the Hanford waste tanks). The probable uses of chemical process facilities were assessed using an evidence-tree representation and in-process updating. Other applications included contaminant flow paths at the Savannah River Site, locating structural flaws in buildings, improving models for seismic travel times systems used to monitor nuclear proliferation, characterizing the source

  10. Determine the prevalence of Brucella spp. and Leptospira spp. in blood samples by multiplex polymerase chain reaction collected from cattle, sheep and goats in herds located in provinces of Iran

    OpenAIRE

    Faham Khamesipour; Shahin Nejat Dehkordi; Taghi Taktaz Hafshejani; Elahe Tajbakhsh; Shahrzad Azizi

    2014-01-01

    Leptospirosis and brucellosis are common zoonosis that affect many species of mammals mostly causing economical losses. Further, very important fact is huge danger for human and animal health around the world. The purpose of the study is to determine the prevalence of Brucella spp. and Leptospira spp. using multiplex polymerase chain reaction (mPCR) method, in blood samples collected from cattle, sheep and goats. In this study, a total number of 250 blood samples (5 cc of blood with ethilen d...

  11. Slice Sampling

    CERN Document Server

    Neal, R M

    2000-01-01

    Markov chain sampling methods that automatically adapt to characteristics of the distribution being sampled can be constructed by exploiting the principle that one can sample from a distribution by sampling uniformly from the region under the plot of its density function. A Markov chain that converges to this uniform distribution can be constructed by alternating uniform sampling in the vertical direction with uniform sampling from the horizontal `slice' defined by the current vertical position, or more generally, with some update that leaves the uniform distribution over this slice invariant. Variations on such `slice sampling' methods are easily implemented for univariate distributions, and can be used to sample from a multivariate distribution by updating each variable in turn. This approach is often easier to implement than Gibbs sampling, and more efficient than simple Metropolis updates, due to the ability of slice sampling to adaptively choose the magnitude of changes made. It is therefore attractive f...

  12. Comparison of Enterococcus quantitative polymerase chain reaction analysis results from midwest U.S. river samples using EPA Method 1611 and Method 1609 PCR reagents

    Science.gov (United States)

    The U.S. Environmental Protection Agency (EPA) has provided recommended beach advisory values in its 2012 recreational water quality criteria (RWQC) for states wishing to use quantitative polymerase chain reaction (qPCR) for the monitoring of Enterococcus fecal indicator bacteria...

  13. Using a bank of predatory fish samples for bioindication of radioactive contamination of aquatic food chains in the area affected by the Chernobyl accident.

    Science.gov (United States)

    Kryshev, I I; Ryabov, I N; Sazykina, T G

    1993-11-01

    From the analysis of experimental data on radioactive contamination of various fish, it is suggested that predatory fish specimens can be used as bioindicators of radionuclide accumulation in reservoir food chains of the Chernobyl emergency area. The increased content of cesium radionuclides were detected in the muscle tissue of predatory fish collected in various regions of the Chernobyl emergency area. In most of the water bodies studied, maximum contamination levels of predatory fish by radionuclides of cesium occurred in 1987-1988, whereas in 'nonpredatory' fish the concentration of cesium was maximum, as a rule, in the first year following the accident. The exposure doses of fish of various ecological groups and ages are estimated. The exposure doses of various population groups, using fish from contaminated water bodies, are also estimated. When forming the environmental data bank for the Chernobyl accident zone it is suggested that perch, pike-perch and pike be used as bioindicators of radioactive contamination of food chains.

  14. Falling chains

    Science.gov (United States)

    Wong, Chun Wa; Yasui, Kosuke

    2006-06-01

    The one-dimensional fall of a folded chain with one end suspended from a rigid support and a chain falling from a resting heap on a table is studied. Because their Lagrangians contain no explicit time dependence, the falling chains are conservative systems. Their equations of motion are shown to contain a term that enforces energy conservation when masses are transferred between subchains. We show that Cayley's 1857 energy nonconserving solution for a chain falling from a resting heap is incorrect because it neglects the energy gained when a link leaves a subchain. The maximum chain tension measured by Calkin and March for the falling folded chain is given a simple if rough interpretation. Other aspects of the falling folded chain are briefly discussed.

  15. Inhibition of the polymerase chain reaction by sputum samples from tuberculosis patients after processing using a silica-guanidiniumthiocyanate DNA isolation procedure

    Directory of Open Access Journals (Sweden)

    Philip Suffys

    2001-11-01

    Full Text Available With the objective to evaluate PCR-mediated detection of Mycobacterium tuberculosis DNA as a diagnostic procedure for diagnosis of tuberculosis in individuals attending ambulatory services in Primary Health Units of the City Tuberculosis Program in Rio de Janeiro, Brazil, their sputum samples were collected and treated with a DNA extraction procedure using silica-guanidiniumthiocyanate. This procedure has been described to be highly efficient for extraction of different kind of nucleic acids from bacteria and clinical samples. Upon comparing PCR results with the number of acid-fast bacilli, no direct relation was observed between the number of bacilli present in the sample and PCR positivity. Part of the processed samples was therefore spiked with pure DNA of M. tuberculosis and inhibition of the PCR reaction was verified in 22 out of 36 (61% of the samples, demonstrating that the extraction procedure as originally described should not be used for PCR analysis of sputum samples.

  16. Unwrapping Chains

    CERN Document Server

    Cambou, A D; Hamm, E; Hanna, J A; Menon, N; Santangelo, C D; Walsh, L

    2012-01-01

    A loop of chain can move along its own tangents, maintaining a steady shape. An open-ended chain undergoing a nontrivial motion must change its shape. One consequence is that chains pulled around objects will fail to follow the contours of the objects, unwrapping themselves instead. This short note accompanies a fluid dynamics video submission (83068) to the APS DFD Gallery of Fluid Motion 2012.

  17. Falling chains

    CERN Document Server

    Wong, C W; Wong, Chun Wa; Yasui, Kosuke

    2006-01-01

    The one-dimensional falling motion of a bungee chain suspended from a rigid support and of a chain falling from a resting heap on a table is studied. Their Lagrangians are found to contain no explicit time dependence. As a result, these falling chains are conservative systems. Each of their Lagrange's equations of motion is shown to contain a term that enforces energy conservation when masses are transferred between subchains. We show in particular that Cayley's 1857 energy nonconserving solution for a chain falling from a resting heap is incorrect because it neglects the energy gained when the transferred link is emitted by the emitting subchain. The maximum chain tension measured by Calkin and March for the falling bungee chain is given a simple if rough interpretation. In the simplified one-dimensional treatment, the kinetic energy of the center of mass of the falling bungee chain is found to be converted by the chain tension at the rigid support into the internal kinetic energy of the chain. However, as t...

  18. Real-time polymerase chain reaction-based identification of bacteria in milk samples from bovine clinical mastitis with no growth in conventional culturing.

    Science.gov (United States)

    Taponen, S; Salmikivi, L; Simojoki, H; Koskinen, M T; Pyörälä, S

    2009-06-01

    In more than 30% of milk samples from clinical and subclinical bovine mastitis, bacteria fail to grow even after 48 h of conventional culture. The "no-growth" samples are problematic for mastitis laboratories, veterinarians, and dairy producers. This study provides the first investigation of the bacteriological etiology of such samples, using a real-time PCR-based commercial reagent kit. The assay targets the DNA of the 11 most common bacterial species or groups in mastitis and the staphylococcal blaZ gene (responsible for penicillin resistance) and can identify and quantify bacterial cells even if dead or growth-inhibited. A study was made of 79 mastitic milk samples with no-growth bacteria in conventional culture, originating from cows with clinical mastitis. Of the 79 samples, 34 (43%) were positive for 1 (32 samples) or 2 (2 samples) of the target bacteria. The positive findings included 11 Staphylococcus spp. (staphylococci other than Staphylococcus aureus), 10 Streptococcus uberis, 2 Streptococcus dysgalactiae, 6 Corynebacterium bovis, 3 Staph. aureus, 1 Escherichia coli, 1 Enterococcus, and 1 Arcanobacterium pyogenes. The positive samples contained as many as 10(3) to 10(7) bacterial genome copies per milliliter of milk. This study demonstrates that in nearly half of the clinical mastitis cases in which conventional culture failed to detect bacteria, mastitis pathogens were still present, often in substantial quantities. The clearly elevated N-acetyl-beta-d-glucosaminidase activity values of the milk samples, together with clinical signs of the infected cows and quarters, confirmed the diagnosis of clinical mastitis and indicated that real-time, PCR-based bacterial findings are able to reveal bacteriological etiology. We conclude that all common mastitis bacteria can occur in large quantities in clinical mastitis samples that exhibit no growth in conventional culture, and that the real-time PCR assay is a useful tool for bacteriological diagnosis of such

  19. Development of a locked nucleic acid real-time polymerase chain reaction assay for the detection of Pinus armandii in mixed species pine nut samples associated with dysgeusia.

    Science.gov (United States)

    Handy, Sara M; Timme, Ruth E; Jacob, Salena M; Deeds, Jonathan R

    2013-02-01

    Recent work has shown that the presence of the species Pinus armandii , even when occurring as species mixtures of pine nuts, is correlated with taste disturbance (dysgeusia), also referred to as "pine mouth". Because of this known possibility of pine nut mixtures, a need was identified for a rapid streamlined assay to detect the presence of this species in the presence of other types of pine nuts. A locked nucleic acid probe was employed in a real-time polymerase chain reaction (RT-PCR) format to detect a single nucleotide polymorphism (SNP) unique to this species. This assay was able to detect P. armandii in homogenates down to ∼1% concentration (the lowest level tested) in the presence of several commonly co-occurring and closely related species of pine and should prove to be a useful tool for the detection of this species in food products.

  20. Application of cinchona-sulfonate-based chiral zwitterionic ion exchangers for the separation of proline-containing dipeptide rotamers and determination of on-column isomerization parameters from dynamic elution profiles

    Energy Technology Data Exchange (ETDEWEB)

    Wernisch, Stefanie, E-mail: stefanie.wernisch@univie.ac.at [Institute for Analytical Chemistry, University of Vienna, Währinger Straße 38, A-1090 Vienna (Austria); Trapp, Oliver, E-mail: trapp@oci.uni-heidelberg.de [Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg (Germany); Lindner, Wolfgang, E-mail: wolfgang.lindner@univie.ac.at [Institute for Analytical Chemistry, University of Vienna, Währinger Straße 38, A-1090 Vienna (Austria)

    2013-09-17

    Graphical abstract: -- Highlights: •X-Pro peptides produce interconverting elution profiles on zwitterionic stationary phases. •The cis–trans isomerization rate in solution is lower than in the chromatographic system. •Cinchona-based zwitterionic selectors apparently lower the isomerization barrier. •Rotamer separation is feasible <0 °C, enantiomer separation above room temperature. -- Abstract: The interconversion of cis and trans isomers of dipeptides containing C-terminal proline was studied by dynamic chromatography on zwitterionic chiral stationary phases at temperatures ranging from −15 °C to +45 °C The cis–trans isomers could be separated below 0 °C and above 0–10 °C plateau formation and peak coalescence phenomena occurred, which is characteristic for a dynamic process at the time-scale of partitioning. At and above room temperature, full coalescence was observed, which allowed separations of enantiomers without interference from interconversion effects. Analysis of the dynamic elution profiles of the interconverting peptides allowed the determination of isomerization rate constants and thermodynamic activation parameters (isomerization enthalpy, entropy and activation energy). In accordance with established results, isomerization rates and thermodynamic parameters were found to depend on the nature of the N-terminal amino acid. Isomerization barriers were only slightly lower than values determined with other methods but significant differences in the relative contributions of the activation enthalpy and entropy as well as isomerization rates pointed toward selector-moderated isomerization dynamics.

  1. Impact of the multiplex polymerase chain reaction in culture-positive samples on appropriate antibiotic use in patients with staphylococcal bacteremia.

    Science.gov (United States)

    Na, Sun Hee; Kim, Chung-Jong; Kim, Moonsuk; Park, Jeong Su; Song, Kyoung-Ho; Choe, Pyoeng Gyun; Park, Wan Beom; Bang, Ji-Hwan; Kim, Eu Suk; Park, Sang Won; Park, Kyoung Un; Kim, Nam Joong; Oh, Myoung-Don; Kim, Hong Bin

    2016-04-01

    Rapid identification of the microorganisms in patients with bacteremia may be useful in clinical practice. We evaluated the impact of the multiplex polymerase chain reaction (PCR) on appropriate antibiotic use for patients with gram-positive cocci cluster (GPCC) bacteremia. We divided the GPCC bacteremia cases into a pre-PCR group (2010-2011) and a post-PCR group (2012-2013). A total 664 cases were included in the pre-PCR group; and 570, in the post-PCR group. In methicillin-susceptible Staphylococcus aureus (MSSA) cases, optimal antibiotics were administered earlier in the post-PCR group (77.4h versus 42.6h, P=0.035). Although the proportions of glycopeptide exposure did not differ (54.7% versus 56.7%, P=0.799), the duration of exposure decreased (69.6h versus 30.7h, P=0.004). In methicillin-resistant S. aureus cases, the time to optimal antibiotics administration did not differ (45.4h versus 43.7h, P=0.275). Multiplex PCR test significantly improved the early initiation of optimal antibiotics in MSSA bacteremia and reduced the unnecessary glycopeptide exposure.

  2. Quality of bulk tank milk samples from Danish dairy herds based on real-time polymerase chain reaction identification of mastitis pathogens

    DEFF Research Database (Denmark)

    Katholm, Jørgen; Bennedsgaard, T.W.; Koskinen, M.T.;

    2012-01-01

    Results of a commercial real-time PCR analysis for 11 mastitis pathogens from bulk tank milk (BTM) samples from all 4,258 Danish dairy herds in November 2009 to January 2010 were compared with somatic cell count (SCC) and total bacteria count (TBC) estimates in BTM. For Streptococcus agalactiae, ...

  3. Polymerase chain reaction genotyping of Epstein-Barr virus in scraping samples of the tongue lateral border in HIV-1 seropositive patients

    Directory of Open Access Journals (Sweden)

    TF Robaina

    2008-06-01

    Full Text Available The Epstein-Barr virus (EBV is the etiological agent of oral hairy leukoplakia (OHL, an oral lesion with important diagnostic and prognostic value in acquired immunodeficiency disease syndrome. The two EBV genotypes, EBV-1 and EBV-2, can be distinguished by divergent gene sequences encoding the EBNA-2, 3A, 3B, and 3C proteins. The purpose of this study was to identify the EBV genotype prevalent in 53 samples of scrapings from the lateral border of the tongue of HIV-1 seropositive patients, with and without OHL, and to correlate the genotypes with presence of clinical or subclinical OHL with the clinic data collected. EBV-1 and EBV-2 were identified through PCR and Nested-PCR based on sequence differences of the EBNA-2 gene. EBV-1 was identified in the 31 samples (15 without OHL, 7 with clinical OHL and 9 with subclinical OHL, EBV-2 in 12 samples (10 without OHL, 1 with clinical and 1 subclinical OHL, and a mixed infection in 10 samples (2 without OHL, 3 with clinical and 5 with subclinical OHL. The presence of EBV-1 was higher in women, but a significant statistical result relating one the EBV genotypes to the development of OHL was not found. We conclude that the oral epithelium in HIV-1 seropositive patients can be infected by EBV-1, EBV-2 or by a mixed viral population.

  4. A novel nested multiplex polymerase chain reaction (PCR assay for differential detection of Entamoeba histolytica, E. moshkovskii and E. dispar DNA in stool samples

    Directory of Open Access Journals (Sweden)

    Parija Subhash C

    2007-05-01

    Full Text Available Abstract Background E. histolytica, a pathogenic amoeba, is indistinguishable in its cyst and trophozoite stages from those of non-pathogenic E. moshkovskii and E. dispar by light microscopy. We have developed a nested multiplex PCR targeting a 16S-like rRNA gene for differential detection of all the three morphologically similar forms of E. histolytica, E. moshkovskii and E. dispar simultaneously in stool samples. Results The species specific product size for E. histolytica, E. moshkovskii and E. dispar was 439, 553 and 174 bp respectively, which was clearly different for all the three Entamoeba species. The nested multiplex PCR showed a sensitivity of 94% and specificity of 100% for the demonstration of E. histolytica, E. moshkovskii and E. dispar DNA in stool samples. The PCR was positive for E. histolytica, E. moshkovskii and E. dispar in a total of 190 out of 202 stool specimens (94% sensitive that were positive for E. histolytica/E. dispar/E. moshkovskii by examination of stool by microscopy and/or culture. All the 35 negative control stool samples that were negative for E. histolytica/E. dispar/E. moshkovskii by microscopy and culture were also found negative by the nested multiplex PCR (100% specific. The result from the study shows that only 34.6% of the patient stool samples that were positive for E. histolytica/E. dispar/E. moshkovskii by examination of stool by microscopy and/or culture, were actually positive for pathogenic E. histolytica and the remaining majority of the stool samples were positive for non-pathogenic E. dispar or E. moshkovskii as demonstrated by the use of nested multiplex PCR. Conclusion The present study reports a new nested multiplex PCR strategy for species specific detection and differentiation of E. histolytica, E. dispar and E. moshkovskii DNA in stool specimens. The test is highly specific, sensitive and also rapid, providing the results within 12 hours of receiving stool specimens.

  5. Identifying the major bacteria causing intramammary infections in individual milk samples of sheep and goats using traditional bacteria culturing and real-time polymerase chain reaction.

    Science.gov (United States)

    Rovai, M; Caja, G; Salama, A A K; Jubert, A; Lázaro, B; Lázaro, M; Leitner, G

    2014-09-01

    Use of DNA-based methods, such as real-time PCR, has increased the sensitivity and shortened the time for bacterial identification, compared with traditional bacteriology; however, results should be interpreted carefully because a positive PCR result does not necessarily mean that an infection exists. One hundred eight lactating dairy ewes (56 Manchega and 52 Lacaune) and 24 Murciano-Granadina dairy goats were used for identifying the main bacteria causing intramammary infections (IMI) using traditional bacterial culturing and real-time PCR and their effects on milk performance. Udder-half milk samples were taken for bacterial culturing and somatic cell count (SCC) 3 times throughout lactation. Intramammary infections were assessed based on bacteria isolated in ≥2 samplings accompanied by increased SCC. Prevalence of subclinical IMI was 42.9% in Manchega and 50.0% in Lacaune ewes and 41.7% in goats, with the estimated milk yield loss being 13.1, 17.9, and 18.0%, respectively. According to bacteriology results, 87% of the identified single bacteria species (with more than 3 colonies/plate) or culture-negative growth were identical throughout samplings, which agreed 98.9% with the PCR results. Nevertheless, the study emphasized that 1 sampling may not be sufficient to determine IMI and, therefore, other inflammatory responses such as increased SCC should be monitored to identify true infections. Moreover, when PCR methodology is used, aseptic and precise milk sampling procedures are key for avoiding false-positive amplifications. In conclusion, both PCR and bacterial culture methods proved to have similar accuracy for identifying infective bacteria in sheep and goats. The final choice will depend on their response time and cost analysis, according to the requirements and farm management strategy.

  6. Triplex polymerase chain reaction assay for detection of major soil-transmitted helminths, Ascaris lumbricoides, Trichuris trichiura, Necator americanus, in fecal samples.

    Science.gov (United States)

    Phuphisut, Orawan; Yoonuan, Tippayarat; Sanguankiat, Surapol; Chaisiri, Kittipong; Maipanich, Wanna; Pubampen, Somchit; Komalamisra, Chalit; Adisakwattana, Poom

    2014-03-01

    Ascaris lumbricoides, Trichuris trichiura, and Necator americanus are medically important soil-transmitted helminths (STHs) occurring frequently worldwide including Thailand. Fecal examination using a microscope has been recommended as the gold standard for diagnosis of STH infections, but suffers from low sensitivity. Recently, highly sensitive and specific assays, such as multiplex quantitative PCR, has been established, but the high cost and need for special instruments are still barriers limiting their applications in routine diagnosis. Therefore, a conventional multiplex PCR assay, with its lower cost and greater simplicity, was developed, for the simultaneous detection of STHs in fecal samples. The multiplex PCR assay was species-specific to the three STHs, and could detect one copy of DNA target. Compared with microscopic examination of fecal samples, sensitivity and specificity of the multiplex PCR was 87% and 83%, respectively. This multiplex PCR assay provides an alternative method for routine diagnosis of STHs infection, and might be applied for epidemiological studies of STHs in endemic areas.

  7. Pressure-driven one-step solid phase-based on-chip sample preparation on a microfabricated plastic device and integration with flow-through polymerase chain reaction (PCR).

    Science.gov (United States)

    Tran, Hong Hanh; Trinh, Kieu The Loan; Lee, Nae Yoon

    2013-10-01

    In this study, we fabricate a monolithic poly(methylmethacrylate) (PMMA) microdevice on which solid phase-based DNA preparation and flow-through polymerase chain reaction (PCR) units were functionally integrated for one-step sample preparation and amplification operated by pressure. Chelex resin, which is used as a solid support for DNA preparation, can capture denatured proteins but releases DNA, and the purified DNA can then be used as a template in a subsequent amplification process. Using the PMMA microdevices, DNA was successfully purified from both Escherichia coli and human hair sample, and the plasmid vector inserted in E. coli and the D1S80 locus in human genomic DNA were successfully amplified from on-chip purified E. coli and human hair samples. Furthermore, the integration potential of the proposed sample preparation and flow-through PCR units was successfully demonstrate on a monolithic PMMA microdevice with a seamless flow, which could pave the way for a pressure-driven, simple one-step sample preparation and amplification with greatly decreased manufacture cost and enhanced device disposability.

  8. Comparison of real-time polymerase chain reaction with the COBAS Amplicor test for quantitation of hepatitis B virus DNA in serum samples

    Institute of Scientific and Technical Information of China (English)

    Ming Shi; Yong Zhang; Ying-Hua Zhu; Jing Zhang; Wei-Jia Xu

    2008-01-01

    AIM: To compare the clinical performance of a real-time PCR assay with the COBAS Amplicor Hepatitis B Virus (HBV) Monitor test for quantitation of HBV DNA in serum samples. METHODS: The reference sera of the Chinese National Institute for the Control of Pharmaceutical and Biological Products and the National Center for Clinical Laboratories of China, and 158 clinical serum samples were used in this study. The linearity, accuracy, reproducibility, assay time, and costs of the real-time PCR were evaluated and compared with those of the Cobas Amplicor test. RESULTS: The intra-assay and inter-assay variations of the real-time PCR ranged from 0.3% to 3.8% and 1.4% to 8.1%, respectively. The HBV DNA levels measured by the real-time PCR correlated very well with those obtained with the COBAS Amplicor test (r = 0.948). The real-time PCR HBV DNA kit was much cheaper and had a wider dynamic range. CONCLUSION: The real-time PCR assay is an excellent tool for monitoring of HBV DNA levels in patients with chronic hepatitis B.

  9. Detection and quantitation of infectious pancreatic necrosis virus by real-time reverse transcriptase-polymerase chain reaction using lethal and non-lethal tissue sampling.

    Science.gov (United States)

    Bowers, Robert M; Lapatra, Scott E; Dhar, Arun K

    2008-02-01

    Infectious pancreatic necrosis virus (IPNV) is a bisegmented double-stranded RNA virus belonging to the family Birnaviridae, genus Aquabirnavirus, which is a major viral pathogen of salmonid fish. The virus infects wild and cultured salmonids, causing high mortality in juvenile trout and salmon. A highly sensitive and specific real-time RT-PCR assay using the fluorogenic dye SYBR((R)) Green I was developed for the detection and quantitation of IPNV in rainbow trout (Oncorhynchus mykiss). Rainbow trout were infected experimentally with IPNV in the laboratory by injection or immersion and then pectoral fin, spleen, and head kidney samples were collected for analysis. The corresponding cDNA was synthesized using DNase I-treated total RNA and then real-time RT-PCR was performed using primers based on the IPNV non-structural protein gene, designated as either NS or VP4. Rainbow trout beta-actin and elongation factor 1alpha (EF-1alpha) genes were used as internal controls. Using real-time RT-PCR, the virus was successfully detected in pectoral fin, spleen, and head kidney tissue samples. The dissociation curves for each amplicon showed a single melting peak at 83, 81.5, and 84 degrees C for IPNV NS, trout beta-actin, and EF-1alpha genes, respectively. The amplicon size and nucleotide sequence was used to confirm the specificity of the products. Using a dilution series of in vitro transcribed RNA, IPNV was reliably detected down to 10 RNA copies and had a dynamic range up to 10(7) RNA copies. A time course assay, using immersion challenged samples, revealed that the virus could be detected in pectoral fin, spleen, and head kidney as early as 24h post-challenge. The average viral load in all three tissues increased over time, reaching its highest level at 21 days post-challenge, which was followed by a slight decrease at 28 days post-challenge. IPNV load in pectoral fin tissue was comparable to the viral load in spleen and head kidney tissues, indicating that pectoral fin

  10. Diagnostic potential of IS6110, 38kDa, 65kDa and 85B sequence-based polymerase chain reaction in the diagnosis of Mycobacterium tuberculosis in clinical samples

    Directory of Open Access Journals (Sweden)

    Negi S

    2007-01-01

    Full Text Available Purpose: The correlation between the presence of specific gene sequence of M. tuberculosis and specific diagnosis of clinical tuberculosis is not known. This study compared the results of polymerase chain reaction (PCR amplification of M . tuberculosis specific DNA sequences (IS6110, 65kDa, 38kDa and mRNA coding for 85 B protein from different clinical samples of pulmonary and extrapulmonary tuberculosis. Methods: One hundred and seventy-two clinical samples from suspected tuberculosis patients were tested for smear examination, culture (LJ and rapid BACTEC 460 TB system and PCR. PCR was performed with specific primers for the targets: IS6110, 65kDa, 38kDa and 85B. Results: Each PCR test was found to have a much higher positivity than conventional test and BACTEC culture ( P < 0.05. Smear positive samples (56 and the samples (36 showing positive results by conventional methods (smear and LJ medium culture and BACTEC were found to be positive by all PCR protocols. No significant difference was found between the four PCR protocols ( P >0.05. The primer specific for amplifying the 123bp IS6110 fragment gave the highest positivity (83%, followed by 65kDa, 38kDa and 85B RT-PCR in descending order. Conclusions: These data suggest that the presence of IS6110 correlates more closely with the diagnosis of clinical tuberculosis than that of 65kDa, 38kDa and 85B proteins.

  11. Development and evaluation of a reverse transcription-insulated isothermal polymerase chain reaction (RT-iiPCR) assay for detection of equine arteritis virus in equine semen and tissue samples using the POCKIT™ system.

    Science.gov (United States)

    Carossino, Mariano; Lee, Pei-Yu A; Nam, Bora; Skillman, Ashley; Shuck, Kathleen M; Timoney, Peter J; Tsai, Yun-Long; Ma, Li-Juan; Chang, Hsiao-Fen G; Wang, Hwa-Tang T; Balasuriya, Udeni B R

    2016-08-01

    Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory and reproductive disease of horses. Most importantly, EAV induces abortion in pregnant mares and can establish persistent infection in up to 10-70% of the infected stallions, which will continue to shed the virus in their semen. The objective of this study was to develop and evaluate a reverse transcription insulated isothermal polymerase chain reaction (RT-iiPCR) for the detection of EAV in semen and tissue samples. The newly developed assay had a limit of detection of 10 RNA copies and a 10-fold higher sensitivity than a previously described real-time RT-PCR (RT-qPCR). Evaluation of 125 semen samples revealed a sensitivity and specificity of 98.46% and 100.00%, respectively for the RT-qPCR assay, and 100.00% and 98.33%, respectively for the RT-iiPCR assay. Both assays had the same accuracy (99.2%, k=0.98) compared to virus isolation. Corresponding values derived from testing various tissue samples (n=122) collected from aborted fetuses, foals, and EAV carrier stallions are as follows: relative sensitivity, specificity, and accuracy of 88.14%, 96.83%, and 92.62% (k=0.85), respectively for the RT-qPCR assay, and 98.31%, 92.06%, and 95.08% (k=0.90), respectively for the RT-iiPCR assay. These results indicate that RT-iiPCR is a sensitive, specific, and a robust test enabling detection of EAV in semen and tissue samples with very considerable accuracy. Even though the RT-qPCR assay showed a sensitivity and specificity equal to virus isolation for semen samples, its diagnostic performance was somewhat limited for tissue samples. Thus, this new RT-iiPCR could be considered as an alternative tool in the implementation of EAV control and prevention strategies.

  12. Chain Gang

    Science.gov (United States)

    2006-01-01

    6 August 2006 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a chain of clustered and battered craters. These were formed by secondary impact. That is, somewhere to the south (beyond the bottom of this image), a large impact crater formed. When this occurred, material ejected from the crater was thrown tens to hundreds of kilometers away. This material then impacted the martian surface, forming clusters and chains of smaller craters. Location near: 15.8oN, 35.6oW Image width: 3 km (1.9 mi) Illumination from: upper left Season: Northern Spring

  13. Rapid detection of cytomegalovirus in bronchoalveolar lavage fluid and serum samples by polymerase chain reaction: correlation of virus isolation and clinical outcome for patients with human immunodeficiency virus infection

    DEFF Research Database (Denmark)

    Hansen, K K; Vestbo, Jørgen; Benfield, T;

    1997-01-01

    Bronchoalveolar lavage (BAL) fluids and serum samples from 153 patients with pulmonary symptoms who were infected with human immunodeficiency virus (HIV) and underwent BAL were examined for the presence of cytomegalovirus (CMV) by conventional culture and by polymerase chain reaction (PCR.......0; confidence interval [CI], 3.8-16.8) or the finding of CMV DNA in serum (RR, 7.4; CI, 3.2-17.3) or BAL fluid (RR, 8.0; CI, 3.1-20.7) by PCR. Mortality was found to be similar for patients who did or did not have CMV detected by either culture or PCR. Detection of CMV DNA by PCR was a more rapid and sensitive...

  14. [Determination of short-chain chlorinated paraffins in ambient air using high-volume sampling combined with high resolutimi gas chromatography-electron capture negative ion-low resolution mass spectrometry].

    Science.gov (United States)

    Shi, Loimeng; Gao, Yuan; Hou, Xiaohong; Zhang, Haijun; Zhang, Yichi; Chen, Jiping

    2016-02-01

    An analytical method for quantifying short-chain chlorinated paraffins (SCCPs) in ambient air using high-volume sampling combined with high resolution gas chromatography-electron capture negative ion-low resolution mass spectrometry ( HRGC-ECNI-LRMS) was developed. An acidified silica gel column and a basic alumina column were used to optimize the cleanup procedures. The results showed a good linearity (R2>0. 99) between the total response factors and the degree of chlorination of SCCPs in the content range of 58. 1%-63. 3%. The limits of detection (S/N ≥3) and the limits of quantification (S/N ≥ 10) were 4. 2 and 12 µg, respectively. The method detection limit (MDL) for SCCPs was 0. 34 ng/m3 (n = 7). The recoveries of SCCPs in air samples were in the range of 81. 9% to 94. 2%. It is demonstrated that the method is suitable for the quantitative analysis of SCCPs in air samples.

  15. Determine the prevalence of Brucella spp. and Leptospira spp. in blood samples by multiplex polymerase chain reaction collected from cattle, sheep and goats in herds located in provinces of Iran

    Directory of Open Access Journals (Sweden)

    Faham Khamesipour

    2014-05-01

    Full Text Available Leptospirosis and brucellosis are common zoonosis that affect many species of mammals mostly causing economical losses. Further, very important fact is huge danger for human and animal health around the world. The purpose of the study is to determine the prevalence of Brucella spp. and Leptospira spp. using multiplex polymerase chain reaction (mPCR method, in blood samples collected from cattle, sheep and goats. In this study, a total number of 250 blood samples (5 cc of blood with ethilen diamin tetra asetic acid were collected randomly from 100 cattle, 80 sheep and 70 goats located on 6 herds in Chaharmahal Va Bakhtiari and Esfahan provinces, Iran. After DNA extraction and setting of mPCR for Brucella spp. and Leptospira spp. mPCR products were screened. The DNA of these microorganisms was detected by multiplex PCR from 31 and 21 out of 100 cattle, respectively. Four of 70 goat’s blood samples from goat breeding farms were positive for Leptospira spp. and 11 were positive for Brucella spp. Out of 80 sheep blood samples 23 were positive for Brucella spp. and 14 for Leptospira spp. The results of the present study show ruminant as an important reservoir for transmission of these zoonotic diseases to humans in Iran. mPCR has the ability to concurrently detect both Brucella and Leptospira species from blood samples of ruminants. The convenience and the possibility of detection of both bacteria at a time, strongly support the use of this mPCR for routine diagnostics.

  16. Detection of Echinoderm Microtubule Associated Protein Like 4-Anaplastic Lymphoma Kinase Fusion Genes in Non-small Cell Lung Cancer Clinical Samples by a Real-time Quantitative Reverse Transcription Polymerase Chain Reaction Method.

    Science.gov (United States)

    Zhao, Jing; Zhao, Jin-Yin; Chen, Zhi-Xia; Zhong, Wei; Li, Long-Yun; Liu, Li-Cheng; Hu, Xiao-Xu; Chen, Wei-Jun; Wang, Meng-Zhao

    2016-12-20

    Objective To establish a real-time quantitative reverse transcription polymerase chain reaction assay (qRT-PCR) for the rapid, sensitive, and specific detection of echinoderm microtubule associated protein like 4-anaplastic lymphoma kinase (EML4-ALK) fusion genes in non-small cell lung cancer. Methods The specific primers for the four variants of EML4-ALK fusion genes (V1, V2, V3a, and V3b) and Taqman fluorescence probes for the detection of the target sequences were carefully designed by the Primer Premier 5.0 software. Then, using pseudovirus containing EML4-ALK fusion genes variants (V1, V2, V3a, and V3b) as the study objects, we further analyzed the lower limit, sensitivity, and specificity of this method. Finally, 50 clinical samples, including 3 ALK-fluorescence in situ hybridization (FISH) positive specimens, were collected and used to detect EML4-ALK fusion genes using this method. Results The lower limit of this method for the detection of EML4-ALK fusion genes was 10 copies/μl if no interference of background RNA existed. Regarding the method's sensitivity, the detection resolution was as high as 1% and 0.5% in the background of 500 and 5000 copies/μl wild-type ALK gene, respectively. Regarding the method's specificity, no non-specific amplification was found when it was used to detect EML4-ALK fusion genes in leukocyte and plasma RNA samples from healthy volunteers. Among the 50 clinical samples, 47 ALK-FISH negative samples were also negative. Among 3 ALK-FISH positive samples, 2 cases were detected positive using this method, but another was not detected because of the failure of RNA extraction. Conclusion The proposed qRT-PCR assay for the detection of EML4-ALK fusion genes is rapid, simple, sensitive, and specific, which is deserved to be validated and widely used in clinical settings.

  17. Evaluation and application of a one-step duplex real-time reverse transcription polymerase chain reaction assay for the rapid detection of influenza A (H7N9) virus from poultry samples.

    Science.gov (United States)

    Bao, Hongmei; Ma, Yong; Shi, Jianzhong; Zeng, Xianying; Zhao, Yuhui; Wang, Xiurong; Chen, Hualan

    2015-10-01

    In China, a novel reassortant influenza A (H7N9) virus, which has caused 435 cases of human infection, has recently emerged. Most cases of human infections with the H7N9 virus are known to be associated with a poultry farm and live-poultry markets. In this study, a one-step duplex real-time reverse transcription polymerase chain reaction (RRT-PCR) assay was developed for the simultaneous detection of the hemagglutinin (HA) and neuraminidase (NA) genes of the H7N9 virus for effective surveillance and early diagnosis of cases from clinical samples collected from live-poultry markets or poultry farms. The detection limit of this assay was as low as 0.1 EID50 of H7N9 viruses, which is similar to the detection limit of the real-time RT-PCR assay released by the Word Health Organization. The coefficients of variation (CVs) of both inter-assay and intra-assay reproducibility were less than 1.55 %, showing good reproducibility. No cross-reactivity was observed with RNA of other subtypes of influenza virus or other avian respiratory viruses. The assay can effectively detect H7N9 influenza virus RNA from multiple sources, including chickens, pigeons, ducks, humans, and the environment. Furthermore, the RRT-PCR assay was evaluated with more than 700 clinical samples collected from live-poultry markets and 120 experimentally infected chicken samples. Together, these results indicate that the duplex RRT-PCR assay is a specific, sensitive, and efficient diagnostic method for the epidemiological surveillance and diagnosis of H7N9 virus from different sources, particularly poultry samples.

  18. Comparative evaluation of a competitive polymerase chain reaction (PCR) and a SYBR Green-based real-time PCR to quantify Porcine circovirus-2 DNA in swine tissue samples.

    Science.gov (United States)

    Dezen, Diogenes; Rijsewijk, Franciscus A M; Teixeira, Thais F; Holz, Carine L; Varela, Ana P; Cibulski, Samuel P; Gregianini, Tatiane Shäffer; Batista, Helena B C R; Franco, Ana C; Roehe, Paulo M

    2011-11-01

    Porcine circovirus-2 (PCV-2) is considered the major etiological agent of post-weaning multisystemic wasting syndrome (PMWS) in pigs. The clinical manifestations of the disease are correlated with moderate to high amounts of PCV-2 DNA in biological samples of affected pigs. A threshold of 10(7) DNA copies/ml is suggested as the trigger factor for symptoms. A comparative study was conducted to determine which quantitative method would be more suitable to estimate the PCV-2 DNA load. Two polymerase chain reaction (PCR) assays were developed: a competitive PCR (cPCR) and a SYBR Green-based real-time PCR. The assays were compared for their capacity to detect PCV-2 in DNA samples extracted from liver, lung, spleen, mesenteric lymph nodes, and kidney of PMWS-affected (n = 23) or non-PMWS-affected pigs (n = 9). Both assays could successfully quantify PCV-2 DNA in all tissue samples and were able to detect significant differences between the numbers of PCV-2 DNA copies found in tissues of PMWS-affected and non-PMWS-affected pigs (≥ 10(2.5)). The highest mean viral loads were detected by the SYBR Green real-time PCR, up to 10(7.0 ± 1.5) copies/100 ng of total DNA sample, while the cPCR detected up to 10(4.8 ± 1.5). A mean difference of 10(1.8) was found between the amounts of PCV-2 DNA detected, using the SYBR Green real-time PCR and the cPCR, suggesting that the viral load threshold for PMWS should be determined for each particular assay.

  19. A Rapid and Sensitive UPLC-MS/MS-Method for the Separation and Quantification of Branched-Chain Amino Acids from Dried Blood Samples of Patients with Maple Syrup Urine Disease (MSUD

    Directory of Open Access Journals (Sweden)

    Ralph Fingerhut

    2016-06-01

    Full Text Available Newborn screening for MSUD is a special challenge since patients with MSUD can metabolically decompensate rapidly without adequate treatment within the first two weeks of life. However, the screening method does not detect the actual marker metabolite (alloisoleucine specifically, but only as part of the group of the other isobaric amino acids leucine, isoleucine and hydroxyproline. We describe a sensitive and rapid second-tier UPLC-MS/MS method to determine branched-chain amino acids from the initial extraction of the screening sample. Quantification is based on a seven-point calibration curve. Reference ranges (mean ± SD in µmol/L were determined from 179 normal, not pre-selected samples from the newborn screening: leucine: 72 ± 27; isoleucine: 37 ± 19; valine: 98 ± 46; hydroxyproline: 23 ± 13. The concentration of alloisoleucine was below the detection limit in about 55% of the cases, and the highest concentration was 1.9 µmol/L. In all 30 retrospectively studied screening samples from patients with confirmed MSUD the concentration of alloisoleucine was significantly increased. In 238 samples with false-positive newborn screening due to a significant increase in the combined concentration of leucine + isoleucine + alloisoleucine + hydroxyproline (400 to >4000 µmol/L, alloisoleucine was below 6.5 µmol/L (n = 57 or not detectable (n = 181. The application of this assay markedly reduces the false-positive rate and the associated anxiety and costs. It is also suitable for routinely monitoring blood spots of patients with MSUD.

  20. Detection of Streptococcus pneumoniae and identification of pneumococcal serotypes by real-time polymerase chain reaction using blood samples from Italian children ≤ 5 years of age with community-acquired pneumonia.

    Science.gov (United States)

    Marchese, Anna; Esposito, Susanna; Coppo, Erika; Rossi, Giovanni A; Tozzi, Alberto; Romano, Mariateresa; Da Dalt, Liviana; Schito, Gian Carlo; Principi, Nicola

    2011-09-01

    Streptococcus pneumoniae is a leading cause of severe life-threatening infections. Laboratory identification and serotyping of this pathogens is desirable to monitor vaccine impact and coverage; however, especially in pediatric patients, the yield of traditional microbiological diagnostic procedures can be very low. The aim of this study was to develop real-time polymerase chain reaction (PCR)-based assays to be performed directly on blood samples to identify the most common capsular serotypes causing pneumonia in Italian children (≤ 5 years of ages) after the introduction of the 7-valent conjugate vaccine. Our real-time PCR-based assays showed high sensitivity (at least 35 fg of pneumococcal DNA), and they were validated with 49 well-characterized pneumococcal isolates, 8 nonpneumococcal isolates, 13 simulated blood clinical samples loaded with S. pneumoniae of known serotypes, and 46 blood clinical samples. All the strains tested and the simulated blood clinical samples were correctly typed by the technique. Real-time PCR allowed serotyping in 37/46 children ≤ 5 years of age (80.4%) in whom pneumonia was diagnosed in four Italian hospitals. Non-PCV7 serotypes accounted for at least 47.8% (22/46) of cases, serotype 19A being the most common (34.7%, 16/46). Although, it is not known at present whether the incidence of 19A serotype is attributable to the use of PCV7 only, expanding pneumococcal serotype coverage has clearly the potential to prevent a larger number of pneumonias in Italian children less than ≤ 5 years of age. Molecular methods are of increasing importance in the diagnosis of pneumococcal pneumonia and in monitoring serotype distribution and replacement.

  1. Reverse transcription polymerase chain reaction (RT-PCR based detection and serotyping of FMD Virus from field samples of Gazipur, Bangladesh, and adaptation of the virus in BHK-21 cell

    Directory of Open Access Journals (Sweden)

    Mohammad Ashraful Alam

    2015-09-01

    Full Text Available The study aimed for the detection and serotyping of Foot and Mouth Disease virus (FMDV circulating in Kapasia Upazila, Gazipur district of Bangladesh during 2013. Twelve samples comprising of tongue epithelium (n=8 and inter digital tissue (n=4 were collected from suspected cattle, and inocula were prepared. The inocula were inoculated into confluent BHK-21 cell line for virus propagation. After 3 subsequent passages; progressive cytopathic effects (CPE specific for FMDV i.e., rounding and flattening of cells, breaking down of the intercellular bridge and finally cell death (almost 100% were observed; these were indicative of successful virus propagation in the cells. Viral RNA was extracted, and Reverse Transcription Polymerase Chain Reaction (RT-PCR was performed using three sets of primers corresponding to the serotype and lsquo;O', and lsquo;Asia-1' and and lsquo;A', respectively. Out of the 12 samples, 10 (83.33% were found to be positive for FMDV, and all of those were of serotype and lsquo;O'. It is concluded that FMDV serotype and lsquo;O' is circulating among the cattle of Gazipur district, Bangladesh. [J Adv Vet Anim Res 2015; 2(3.000: 291-295

  2. Markov chain Monte Carlo and importance sampling for multiple targets tracking%马尔可夫链蒙特卡洛重要度采样与多目标跟踪

    Institute of Scientific and Technical Information of China (English)

    龙云利; 徐晖; 安玮

    2011-01-01

    针对强杂波环境下的多目标跟踪问题,提出一种基于马尔可夫链蒙特卡洛重要度采样的跟踪方法.通过马尔可夫链蒙特卡洛实现对联合关联事件的采样,据此计算目标可关联量测数据的边缘关联概率.在联合关联事件求解中利用单目标量测的概率密度进行重要度采样,提高采样效率.马尔可夫链蒙特卡洛重要度采样方法克服了联合概率数据关联中的“组合爆炸”问题,能够在强杂波干扰下较好地实现多目标实时跟踪.通过仿真实验对比分析了算法的跟踪精度和处理的时效性,验证了方法的有效性.%This paper presents an algorithm based on Markov chain Monte Carlo and importance sampling(MCMCIS) for tracking multi-target in a dense environment. The joint associated events are sampled by the Markov chain Monte Carlo and the marginal association probability of the measurement to the target is calculated. The probabilistic density is utilized when sampling the associated events as to improve the efficiency. Although the joint probabilistic data association(JPDA) is NP-hard, the MCMCIS provides the ability to track multi-target timely in a dense environment. The simulation experiments are implemented to analyze the tracking precision and processing time, which shows the effectiveness of the algorithm.

  3. Rapid detection of cytomegalovirus in bronchoalveolar lavage fluid and serum samples by polymerase chain reaction: correlation of virus isolation and clinical outcome for patients with human immunodeficiency virus infection

    DEFF Research Database (Denmark)

    Hansen, K K; Vestbo, Jørgen; Benfield, T;

    1997-01-01

    Bronchoalveolar lavage (BAL) fluids and serum samples from 153 patients with pulmonary symptoms who were infected with human immunodeficiency virus (HIV) and underwent BAL were examined for the presence of cytomegalovirus (CMV) by conventional culture and by polymerase chain reaction (PCR......) for detection of CMV DNA. PCR detected CMV more frequently than did cultures of BAL fluid (PCR of BAL fluid, 53%; PCR of serum, 40%; and culture, 30%). In a multivariate model, development of extrapulmonary CMV disease was predicted by the finding of CMV in BAL fluid by culture (relative risk [RR], 8.......0; confidence interval [CI], 3.8-16.8) or the finding of CMV DNA in serum (RR, 7.4; CI, 3.2-17.3) or BAL fluid (RR, 8.0; CI, 3.1-20.7) by PCR. Mortality was found to be similar for patients who did or did not have CMV detected by either culture or PCR. Detection of CMV DNA by PCR was a more rapid and sensitive...

  4. Graphs: Associated Markov Chains

    OpenAIRE

    2012-01-01

    In this research paper, weighted / unweighted, directed / undirected graphs are associated with interesting Discrete Time Markov Chains (DTMCs) as well as Continuous Time Markov Chains (CTMCs). The equilibrium / transient behaviour of such Markov chains is studied. Also entropy dynamics (Shannon entropy) of certain structured Markov chains is investigated. Finally certain structured graphs and the associated Markov chains are studied.

  5. Elastic Behavior of Polymer Chains

    Institute of Scientific and Technical Information of China (English)

    Teng Lu; Tao Chen; Hao-jun Liang

    2008-01-01

    The elastic behavior of the polymer chain was investigated in a three-dimensional off-lattice model. We sample more than 109 conformations of each kind of polymer chain by using a Monte Carlo algorithm, then analyze them with the non-Gaussian theory of rubberlike elasticity, and end with a statistical study. Through observing the effect of the chain flexibility and the stretching ratio on the mean-square end-to-end distance,the average energy, the average Helmholtz free energy, the elastic force, the contribution of energy to the elastic force, and the entropy contribution to elastic force of the polymer chain, we find that a rigid polymer chain is much easier to stretch than a flexible polymer chain. Also, a rigid polymer chain will become difficult to stretch only at a quite high stretching ratio because of the effect of the entropy contribution.These results of our simulation calculation may explain some of the macroscopic phenomena of polymer and biomacromolecular elasticity.

  6. qPCR (quantitative polymerase chain reaction) for the quantification of bacteriophages in stream water samples to investigate hydrological processes: a proof-of-concept study in the Huewelerbach experimental catchment (Luxembourg)

    Science.gov (United States)

    Antonelli, Marta; Narayanan Balasubramanian, Mukundh; Ogorzaly, Leslie; Pfister, Laurent

    2016-04-01

    Albeit recent technological developments (e.g. field deployable instruments operating at high temporal frequencies), experimental hydrology is a discipline that remains measurement limited. From this perspective, trans-disciplinary approaches may create valuable opportunities to enlarge the amount of tools available for investigating hydrological processes. Bacteriophages have been widely used in hydrology as biological tracer for investigating colloid transport and contamination of ground water systems. However, there are only a few studies focusing on the employability of bacteriophages as surface water tracers (i.e. phage transport, system functioning). Here, we present a proof-of-concept study carried out in the Huewelerbach catchment in Luxembourg in December 2015. The aim of this study was to investigate how viral particles can be used to detect hydrological connectivity between the riparian zone/river bank and the stream during rainfall events. Moreover, this study is one of the first attempts for applying the qPCR (quantitative polymerase chain reaction) technique for the quantification of bacteriophages in stream water samples to investigate hydrological processes. This technique is very sensitive and has a large dynamic range - enhancing ease and speed of phage detection. We used two different male-specific coliphages (GA phage, genogroup II and SP phage, genogroup IV). Two litres of GA phage were injected directly in the stream as a slug injection and two litres of SP phage were poured next to the river bank (alluvial deposition) close to the injection point. We also added NaCl (200 g) to both phage suspensions. We collected stream water samples 100 m and 500 m downstream (i.e. catchment outlet) of the injection point for one week. Phages were concentrated through ultracentrifugation of 100 ml of water sample followed by quantification via qPCR. Conductivity in stream water was monitored for the entire duration of the experiment. Discharge was monitored

  7. Structure-activity study on the Phe side chain arrangement of endomorphins using conformationally constrained analogues.

    Science.gov (United States)

    Tömböly, Csaba; Kövér, Katalin E; Péter, Antal; Tourwé, Dirk; Biyashev, Dauren; Benyhe, Sándor; Borsodi, Anna; Al-Khrasani, Mahmoud; Rónai, András Z; Tóth, Géza

    2004-01-29

    Endomorphins-1 and -2 were substituted with all the beta-MePhe stereoisomers in their Phe residues to generate a conformationally constrained peptide set. This series of molecules was subjected to biological assays, and for beta-MePhe(4)-endomorphins-2, a conformational analysis was performed. Incorporation of (2S,3S)-beta-MePhe(4) resulted in the most potent analogues of both endomorphins with enhanced enzymatic stability. Their micro opioid affinities were 4-times higher than the parent peptides, they stimulated [(35)S]GTPgammaS binding, and they were found to be full agonists. NMR experiments revealed that C-terminal (2S,3S)-beta-MePhe in endomorphin-2 strongly favored the gauche (-) spatial orientation which implies the presence of the chi(1) = -60 degrees rotamer of Phe(4) in the binding conformer of endomorphins. Our results emphasize that the appropriate orientation of the C-terminal aromatic side chain of endomorphins is substantial for binding to the micro opioid receptor.

  8. Parallel Computing Properties of Tail Copolymer Chain

    Directory of Open Access Journals (Sweden)

    Hong Li

    2013-08-01

    Full Text Available The properties of a AB diblock copolymer chain are calculated by Monte Carlo methods. Monomer A contacting to the surface has an adsorption energy E=-1 and monomer B E= 0. The polymer chain is simulated by self-avoiding walk in simple cubic lattice. The adsorption properties and the conformation properties of the polymer chain are computed by using message passing interface (MPI. The speedup is close to linear speedup by parallel computing independent samples.    

  9. Logistic chain modelling

    NARCIS (Netherlands)

    Slats, P.A.; Bhola, B.; Evers, J.J.M.; Dijkhuizen, G.

    1995-01-01

    Logistic chain modelling is very important in improving the overall performance of the total logistic chain. Logistic models provide support for a large range of applications, such as analysing bottlenecks, improving customer service, configuring new logistic chains and adapting existing chains to n

  10. Health supply chain management.

    Science.gov (United States)

    Zimmerman, Rolf; Gallagher, Pat

    2010-01-01

    This chapter gives an educational overview of: * The actual application of supply chain practice and disciplines required for service delivery improvement within the current health environment. * A rationale for the application of Supply Chain Management (SCM) approaches to the Health sector. * The tools and methods available for supply chain analysis and benchmarking. * Key supply chain success factors.

  11. Sustainable Supply Chain Design

    DEFF Research Database (Denmark)

    Bals, Lydia; Tate, Wendy

    to implement TBL goals across the supply chain. In supply chain design, the classic economic perspective still dominates, although the idea of the TBL is more widely disseminated. The purpose of this research is to add to the sustainable supply chain management literature (SSCM) research agenda......A significant conceptual and practical challenge is how to integrate triple bottom line (TBL; including economic, social and environmental) sustainability into global supply chains. Although this integration is necessary to slow down global resource depletion, understanding is limited of how...... by incorporating the physical chain, and the (information and financial) support chains into supply chain design. This manuscript tackles issues of what the chains are designed for and how they are designed structurally. Four sustainable businesses are used as illustrative case examples of innovative supply chain...

  12. The Global Value Chain

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull

    The conference paper aims to develop the global value chain concept by including corporate internal value adding activities and competition to the basic framework in order to turn the global value chain into a strategic management tool......The conference paper aims to develop the global value chain concept by including corporate internal value adding activities and competition to the basic framework in order to turn the global value chain into a strategic management tool...

  13. Serum Free Light Chains

    Science.gov (United States)

    ... or of one of its component parts – a kappa or lambda light chain, or rarely, a heavy chain. Traditionally, plasma cell ... protein (M-protein) production and to calculate a kappa/lambda free light chain ratio. If the protein electrophoresis test is abnormal, ...

  14. Gushing metal chain

    Science.gov (United States)

    Belyaev, Alexander; Sukhanov, Alexander; Tsvetkov, Alexander

    2016-03-01

    This article addresses the problem in which a chain falls from a glass from some height. This phenomenon demonstrates a paradoxical rise of the chain over the glass. To explain this effect, an initial hypothesis and an appropriate theory are proposed for calculating the steady fall parameters of the chain. For this purpose, the modified Cayley's problem of falling chain given its rise due to the centrifugal force of upward inertia is solved. Results show that the lift caused by an increase in linear density at the part of chain where it is being bent (the upper part) is due to the convergence of the chain balls to one another. The experiments confirm the obtained estimates of the lifting chain.

  15. Ligand pose and orientational sampling in molecular docking.

    Directory of Open Access Journals (Sweden)

    Ryan G Coleman

    Full Text Available Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys-Enhanced (DUD-E benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20,000 molecular orientations in the binding site (and so from about 1×10(10 to 4×10(10 to 1×10(11 to 2×10(11 to 5×10(11 mean atoms scored per target, since multiple conformations are sampled per orientation, the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field.

  16. Electric Power Supply Chain Management Addressing Climate Change

    DEFF Research Database (Denmark)

    Wang, Xiao-Hui; Cong, Ronggang

    2012-01-01

    change. The study compared the difference between electric power supply chain management and traditional supply chain management. Furthermore, some possible research topics are addressed. The aim of this paper was to promote the application of supply chain management in the China electricity sector......Supply chain management played a critical role in the electric power industrial chain optimization. The purpose of this paper was to review a sample of the literature relating to supply chain management and its possible applications in electricity power system, especially in the context of climate...... optimizations and brought a change in the related government policy options....

  17. Venous Sampling

    Science.gov (United States)

    ... Physician Resources Professions Site Index A-Z Venous sampling Venous sampling is a diagnostic procedure that uses ... the limitations of venous sampling? What is venous sampling? Venous sampling is a diagnostic procedure that involves ...

  18. Supply Chain Management og Supply Chain costing

    DEFF Research Database (Denmark)

    Nielsen, Steen; Mortensen, Ole

    2002-01-01

    Formålet med denne artikel er at belyse de muligheder som ligger i at integrere virksomhedens økonomiske styring med begrebet Supply Chain Management (SCM). Dette søges belyst ved først at beskrive den teoretiske ramme, hvori SCM indgår. Herefter analyseres begrebet Supply Chain Costing (SCC) som...... Århus. Et resultat er, at via begrebet Supply Chain Costing skabes der mulighed for at måle logistikkædens aktiviteter i kr./øre. Anvendelsen af denne information har også strategisk betydning for at kunne vælge kunde og leverandør. Ved hjælp af integrationen skabes der også helt nye mulighed...

  19. Understanding the Chain Fountain

    CERN Document Server

    Biggins, John Simeon

    2013-01-01

    If a chain is initially at rest in a beaker at a height h1 above the ground, and the end of the chain is pulled over the rim of the beaker and down towards the ground and then released, the chain will spontaneously "flow" out of the beaker under gravity. Furthermore, if h1 is sufficient, the beads do not simply drag over the edge of the beaker but form a fountain reaching a height h2 above it. We show that the formation of a fountain requires that the beads come into motion not only by being pulled upwards by the part of the chain immediately above the pile, but also by being pushed upwards by an anomalous reaction force from the pile of stationary chain. We propose possible origins for this force, argue that its magnitude will be proportional to the square of the chain velocity, and predict and verify experimentally that h2 is proportional to h1.

  20. Food supply chains

    OpenAIRE

    Zhou, Qian

    2011-01-01

    The dissertation analyses food waste in global supply chain. From the related managerial literature, the process of supply chain operation, from agriculture, manufacturing, warehouses, retailers to customers are explained clearly. Then the reasons and characteristics of food wastes in any point of food supply chain are analyzed. From some case studies and questionnaire investigation, some corresponding methods to reduce food waste are put forward in the following. Lastly, in terms of method s...

  1. Supply chain components

    Directory of Open Access Journals (Sweden)

    Vieraşu, T.

    2011-01-01

    Full Text Available In this article I will go through three main logistics components, which are represented by: transportation, inventory and facilities, and the three secondary logistical components: information, production location, price and how they determine performance of any supply chain. I will discuss then how these components are used in the design, planning and operation of a supply chain. I will also talk about some obstacles a supply chain manager may encounter.

  2. Supply chain planning classification

    Science.gov (United States)

    Hvolby, Hans-Henrik; Trienekens, Jacques; Bonde, Hans

    2001-10-01

    Industry experience a need to shift in focus from internal production planning towards planning in the supply network. In this respect customer oriented thinking becomes almost a common good amongst companies in the supply network. An increase in the use of information technology is needed to enable companies to better tune their production planning with customers and suppliers. Information technology opportunities and supply chain planning systems facilitate companies to monitor and control their supplier network. In spite if these developments, most links in today's supply chains make individual plans, because the real demand information is not available throughout the chain. The current systems and processes of the supply chains are not designed to meet the requirements now placed upon them. For long term relationships with suppliers and customers, an integrated decision-making process is needed in order to obtain a satisfactory result for all parties. Especially when customized production and short lead-time is in focus. An effective value chain makes inventory available and visible among the value chain members, minimizes response time and optimizes total inventory value held throughout the chain. In this paper a supply chain planning classification grid is presented based current manufacturing classifications and supply chain planning initiatives.

  3. Lifting—A nonreversible Markov chain Monte Carlo algorithm

    Science.gov (United States)

    Vucelja, Marija

    2016-12-01

    Markov chain Monte Carlo algorithms are invaluable tools for exploring stationary properties of physical systems, especially in situations where direct sampling is unfeasible. Common implementations of Monte Carlo algorithms employ reversible Markov chains. Reversible chains obey detailed balance and thus ensure that the system will eventually relax to equilibrium, though detailed balance is not necessary for convergence to equilibrium. We review nonreversible Markov chains, which violate detailed balance and yet still relax to a given target stationary distribution. In particular cases, nonreversible Markov chains are substantially better at sampling than the conventional reversible Markov chains with up to a square root improvement in the convergence time to the steady state. One kind of nonreversible Markov chain is constructed from the reversible ones by enlarging the state space and by modifying and adding extra transition rates to create non-reversible moves. Because of the augmentation of the state space, such chains are often referred to as lifted Markov Chains. We illustrate the use of lifted Markov chains for efficient sampling on several examples. The examples include sampling on a ring, sampling on a torus, the Ising model on a complete graph, and the one-dimensional Ising model. We also provide a pseudocode implementation, review related work, and discuss the applicability of such methods.

  4. Formation of helical ion chains

    CERN Document Server

    Nigmatullin, Ramil; De Chiara, Gabriele; Morigi, Giovanna; Plenio, Martin B; Retzker, Alex

    2011-01-01

    We study the nonequilibrium dynamics of the linear to zigzag structural phase transition exhibited by an ion chain confined in a trap with periodic boundary conditions. The transition is driven by reducing the transverse confinement at a finite quench rate, which can be accurately controlled. This results in the formation of zigzag domains oriented along different transverse planes. The twists between different domains can be stabilized by the topology of the trap and under laser cooling the system relaxes to a helical chain with possibly nonzero winding number. Molecular dynamics simulations are used to obtain a large sample of possible trajectories for different quench rates. The scaling of the average winding number with different quench rates is compared to the prediction of the Kibble-Zurek theory, and a good quantitative agreement is found.

  5. Independent sets in chain cacti

    CERN Document Server

    Sedlar, Jelena

    2011-01-01

    In this paper chain cacti are considered. First, for two specific classes of chain cacti (orto-chains and meta-chains of cycles with h vertices) the recurrence relation for independence polynomial is derived. That recurrence relation is then used in deriving explicit expressions for independence number and number of maximum independent sets for such chains. Also, the recurrence relation for total number of independent sets for such graphs is derived. Finaly, the proof is provided that orto-chains and meta-chains are the only extremal chain cacti with respect to total number of independent sets (orto-chains minimal and meta-chains maximal).

  6. Decisive Markov Chains

    CERN Document Server

    Abdulla, Parosh Aziz; Mayr, Richard

    2007-01-01

    We consider qualitative and quantitative verification problems for infinite-state Markov chains. We call a Markov chain decisive w.r.t. a given set of target states F if it almost certainly eventually reaches either F or a state from which F can no longer be reached. While all finite Markov chains are trivially decisive (for every set F), this also holds for many classes of infinite Markov chains. Infinite Markov chains which contain a finite attractor are decisive w.r.t. every set F. In particular, this holds for probabilistic lossy channel systems (PLCS). Furthermore, all globally coarse Markov chains are decisive. This class includes probabilistic vector addition systems (PVASS) and probabilistic noisy Turing machines (PNTM). We consider both safety and liveness problems for decisive Markov chains, i.e., the probabilities that a given set of states F is eventually reached or reached infinitely often, respectively. 1. We express the qualitative problems in abstract terms for decisive Markov chains, and show...

  7. Fields From Markov Chains

    DEFF Research Database (Denmark)

    Justesen, Jørn

    2005-01-01

    A simple construction of two-dimensional (2-D) fields is presented. Rows and columns are outcomes of the same Markov chain. The entropy can be calculated explicitly.......A simple construction of two-dimensional (2-D) fields is presented. Rows and columns are outcomes of the same Markov chain. The entropy can be calculated explicitly....

  8. REVERSE SUPPLY CHAIN

    Directory of Open Access Journals (Sweden)

    Tomasz DOMAGAŁA

    2013-10-01

    Full Text Available The paper focuses on the presentation of the reverse supply chain, of which the role in the modern business grows along with the increasing number of environmental regulations and possibilities of reducing an operating cost. The paper also describes main problems in developing the profitable chain and possibilities to take an action in order to overcome them.

  9. Value Chain Engineering

    DEFF Research Database (Denmark)

    Wæhrens, Brian Vejrum; Slepniov, Dmitrij

    2015-01-01

    This workbook is recommended for the attention of students of and managers in Danish small and medium sized enterprises (SMEs). Danish SMEs are currently facing a number of key challenges related to their position in global value chains. This book provides an insight into value chain management...

  10. Supply Chain Management

    DEFF Research Database (Denmark)

    Wieland, Andreas; Handfield, Robert B.

    Supply chain management has made great strides in becoming a discipline with a standalone body of theories. As part of this evolution, researchers have sought to embed and integrate observed supply chain management phenomena into theoretical statements. In our review, we explore where we have been...

  11. Supply Chain Connectivity: Enhancing Participation in the Global Supply Chain

    OpenAIRE

    Epictetus E. Patalinghug

    2015-01-01

    Supply chain connectivity is vital for the efficient flow of trade among APEC economies. This paper reviews the literature and supply chain management, describes the barriers to enhancing participation in global supply chain, analyzes the various measures of supply chain performance, and suggests steps for the Philippines to fully reap the benefits of the global value chain.

  12. Project Decision Chain

    DEFF Research Database (Denmark)

    Rolstadås, Asbjørn; Pinto, Jeffrey K.; Falster, Peter

    2015-01-01

    To add value to project performance and help obtain project success, a new framework for decision making in projects is defined. It introduces the project decision chain inspired by the supply chain thinking in the manufacturing sector and uses three types of decisions: authorization, selection......, and plan decision. A primitive decision element is defined where all the three decision types can be accommodated. Each task in the primitive element can in itself contain subtasks that in turn will comprise new primitive elements. The primitive elements are nested together in a project decision chain....

  13. Plastic value chains

    DEFF Research Database (Denmark)

    Baxter, John; Wahlstrom, Margareta; Zu Castell-Rüdenhausen, Malin

    2014-01-01

    Optimizing plastic value chains is regarded as an important measure in order to increase recycling of plastics in an efficient way. This can also lead to improved awareness of the hazardous substances contained in plastic waste, and how to avoid that these substances are recycled. As an example......, plastics from WEEE is chosen as a Nordic case study. The project aims to propose a number of improvements for this value chain together with representatives from Nordic stakeholders. Based on the experiences made, a guide for other plastic value chains shall be developed....

  14. The short-chain oxidoreductase Q9HYA2 from Pseudomonas aeruginosa PAO1 contains an atypical catalytic center.

    Science.gov (United States)

    Huether, Robert; Mao, Qilong; Duax, William L; Umland, Timothy C

    2010-05-01

    The characteristic oxidation or reduction reaction mechanisms of short-chain oxidoreductase (SCOR) enzymes involve a highly conserved Asp-Ser-Tyr-Lys catalytic tetrad. The SCOR enzyme Q9HYA2 from the pathogenic bacterium Pseudomonas aeruginosa was recognized to possess an atypical catalytic tetrad composed of Lys118-Ser146-Thr159-Arg163. Orthologs of Q9HYA2 containing the unusual catalytic tetrad along with conserved substrate and cofactor recognition residues were identified in 27 additional species, the majority of which are bacterial pathogens. However, this atypical catalytic tetrad was not represented within the Protein Data Bank. The crystal structures of unligated and NADPH-complexed Q9HYA2 were determined at 2.3 A resolution. Structural alignment to a polyketide ketoreductase (KR), a typical SCOR, demonstrated that Q9HYA2's Lys118, Ser146, and Arg163 superimposed upon the KR's catalytic Asp114, Ser144, and Lys161, respectively. However, only the backbone of Q9HYA2's Thr159 overlapped KR's catalytic Tyr157. The Thr159 hydroxyl in apo Q9HYA2 is poorly positioned for participating in catalysis. In the Q9HYA2-NADPH complex, the Thr159 side chain was modeled in two alternate rotamers, one of which is positioned to interact with other members of the tetrad and the bound cofactor. A chloride ion is bound at the position normally occupied by the catalytic tyrosine hydroxyl. The putative active site of Q9HYA2 contains a chemical moiety at each catalytically important position of a typical SCOR enzyme. This is the first observation of a SCOR protein with this alternate catalytic center that includes threonine replacing the catalytic tyrosine and an ion replacing the hydroxyl moiety of the catalytic tyrosine.

  15. Supply chain risk management

    Directory of Open Access Journals (Sweden)

    Christian Hollstein

    2013-03-01

    Full Text Available Background: Supply chain risk management increasingly gains prominence in many international industries. In order to strengthen supply chain structures, processes, and networks, adequate potentials for risk management need to be built (focus on effective logistics and to be utilized (focus on efficient logistics. Natural-based disasters, such as the case of Fukushima, illustrate how crucial risk management is. Method: By aligning a theoretical-conceptual framework with empirical-inductive findings, it may be hypothesized that logistical systems do have a positive effect on supply chain risk management activities.  Result/conclusion:  Flexibility and capacity, as well as redundancy and standardization, are often viewed as being conflictionary. It shows, however, that in the light of supply chain risk management, those factors may yield a common benefit if proper logistics systems are applied.  

  16. Editorial: Supply Chain Management

    Directory of Open Access Journals (Sweden)

    Aidonis, D.

    2012-01-01

    Full Text Available This special issue has followed up the 2nd Olympus International Conference on Supply Chains held on October 5-6, 2012, in Katerini, Greece. The Conference was organized by the Department of Logistics of Alexander Technological Educational Institution (ATEI of Thessaloniki, in collaboration with the Laboratory of Quantitative Analysis, Logistics and Supply Chain Management of the Department of Mechanical Engineering, Aristotle University of Thessaloniki (AUTH. During the 2-Days Conference more than 50 research papers were presented covering the following thematic areas: (i Business Logistics, (ii Transportation, Telematics and Distribution Networks, (iii Green Logistics, (iv Information and Communication Technologies in Supply Chain Management, and (v Services and Quality. Three keynote invited speakers addressed interesting issues for the Humanitarian Logistics, Green Supply Chains of the Agrifood Sector and the Opportunities and Prospects of Greek Ports chaired Round Tables with other Greek and Foreign Scientists and Specialists.

  17. Moldova - Value Chain Training

    Data.gov (United States)

    Millennium Challenge Corporation — The evaluation of the GHS value chain training subactivity wwas designed to measure the extent, if any, to which the training activities improved the productivity...

  18. Light chain nephropathy

    Directory of Open Access Journals (Sweden)

    Sihem Darouich

    2015-01-01

    Full Text Available Light chain deposition disease (LCDD is characterized by the tissue deposition of monotypic immunoglobulin light chains of either kappa or lambda isotype. It is the archetypal systemic disease that is most frequently diagnosed on a kidney biopsy, although the deposits may involve several other organs. This brief review focuses on the clinicopathological features of LCDD-associated nephropathy with an emphasis on the diagnostic and therapeutic difficulties related to this elusive condition.

  19. Supply Chain Interoperability Measurement

    Science.gov (United States)

    2015-06-19

    Base, Ohio DISTRIBUTION STATEMENT A. APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED. The views expressed in this thesis ...chain connections are often hindered by inconsistent vocabularies , terms, ontologies, and semantics utilized by various supply chain members (Ye et...eg.COOPERATION PROCESS)-Don’t address synergies between SC X X X X X X X X Don’t track effectiveness over time-lack of learning by experience Loss of SC

  20. Supply chain quality management

    OpenAIRE

    Hannan Amoozad Mahdiraji; Meysam Arabzadeh; Reza Ghaffari

    2012-01-01

    In recent years, there are several methods introduced for the improvement of operational performances. Total quality management and supply chain management are two methods recommended for this purpose. These two approaches have been studied in most researches separately, while they have objectives in common, and this makes them a strategic means, which can be used, simultaneously. Total quality management and supply chain management play significant roles to increase the organizational compet...

  1. Innovation Across the Supply Chain

    DEFF Research Database (Denmark)

    Druehl, Cheryl; Carrillo, Janice; Hsuan, Juliana

    Innovation is an integral part of every firm’s ongoing operations. Beyond product innovation, supply chain innovations offer a unique source of competitive advantage. We synthesize recent research on innovation in the supply chain, specifically, innovative supply chain processes...

  2. MASTERING SUPPLY CHAIN RISKS

    Directory of Open Access Journals (Sweden)

    Borut Jereb

    2012-11-01

    Full Text Available Risks in supply chains represent one of the major business issues today. Since every organizationstrives for success and uninterrupted operations, efficient supply chain risk management is crucial.During supply chain risk research at the Faculty of Logistics in Maribor (Slovenia some keyissues in the field were identified, the major being the lack of instruments which can make riskmanagement in an organization easier and more efficient. Consequently, a model which captures anddescribes risks in an organization and its supply chain was developed. It is in accordance with thegeneral risk management and supply chain security standards, the ISO 31000 and ISO 28000families. It also incorporates recent finding from the risk management field, especially from theviewpoint of segmenting of the public.The model described in this paper focuses on the risks itself by defining them by different keydimensions, so that risk management is simplified and can be undertaken in every supply chain andorganizations within them. Based on our mode and consequent practical research in actualorganizations, a freely accessible risk catalog has been assembled and published online from the risksthat have been identified so far. This catalog can serve as a checklist and a starting point in supplychain risk management in organizations. It also incorporates experts from the field into a community,in order to assemble an ever growing list of possible risks and to provide insight into the model andits value in practice.

  3. Issues on Supply Chain Management

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Although supply chain is regarded as an integrated pr ocess, actually, researchers and practitioners have primarily investigated the v arious processes of the supply chain individually. The competitive field in most markets requires well-designed integrated supply chain instead of individual o perations. In this paper, some traditional thinking of supply chain is given fir st, then SCM (Supply Chain Management) is introduced, which views the entire sup ply chain as a whole rather than individual process a...

  4. Sample Design.

    Science.gov (United States)

    Ross, Kenneth N.

    1987-01-01

    This article considers various kinds of probability and non-probability samples in both experimental and survey studies. Throughout, how a sample is chosen is stressed. Size alone is not the determining consideration in sample selection. Good samples do not occur by accident; they are the result of a careful design. (Author/JAZ)

  5. Balanced sampling

    NARCIS (Netherlands)

    Brus, D.J.

    2015-01-01

    In balanced sampling a linear relation between the soil property of interest and one or more covariates with known means is exploited in selecting the sampling locations. Recent developments make this sampling design attractive for statistical soil surveys. This paper introduces balanced sampling

  6. Phasic Triplet Markov Chains.

    Science.gov (United States)

    El Yazid Boudaren, Mohamed; Monfrini, Emmanuel; Pieczynski, Wojciech; Aïssani, Amar

    2014-11-01

    Hidden Markov chains have been shown to be inadequate for data modeling under some complex conditions. In this work, we address the problem of statistical modeling of phenomena involving two heterogeneous system states. Such phenomena may arise in biology or communications, among other fields. Namely, we consider that a sequence of meaningful words is to be searched within a whole observation that also contains arbitrary one-by-one symbols. Moreover, a word may be interrupted at some site to be carried on later. Applying plain hidden Markov chains to such data, while ignoring their specificity, yields unsatisfactory results. The Phasic triplet Markov chain, proposed in this paper, overcomes this difficulty by means of an auxiliary underlying process in accordance with the triplet Markov chains theory. Related Bayesian restoration techniques and parameters estimation procedures according to the new model are then described. Finally, to assess the performance of the proposed model against the conventional hidden Markov chain model, experiments are conducted on synthetic and real data.

  7. Spatial Data Supply Chains

    Science.gov (United States)

    Varadharajulu, P.; Azeem Saqiq, M.; Yu, F.; McMeekin, D. A.; West, G.; Arnold, L.; Moncrieff, S.

    2015-06-01

    This paper describes current research into the supply of spatial data to the end user in as close to real time as possible via the World Wide Web. The Spatial Data Infrastructure paradigm has been discussed since the early 1990s. The concept has evolved significantly since then but has almost always examined data from the perspective of the supplier. It has been a supplier driven focus rather than a user driven focus. The current research being conducted is making a paradigm shift and looking at the supply of spatial data as a supply chain, similar to a manufacturing supply chain in which users play a significant part. A comprehensive consultation process took place within Australia and New Zealand incorporating a large number of stakeholders. Three research projects that have arisen from this consultation process are examining Spatial Data Supply Chains within Australia and New Zealand and are discussed within this paper.

  8. Environmental Retail Supply Chains

    DEFF Research Database (Denmark)

    Kotzab, Herbert; Munch, Hilde; de Faultrier, Birgitte;

    2011-01-01

    Purpose – The purpose of this paper is to develop a scale that evaluates the environmental elements in retail supply chains and to examine the environmental supply chain management initiatives of the world's largest 100 retailing companies. Design/methodology/approach – The empirical evaluation has...... short-term oriented (green operations). Long-term oriented green design initiatives were hardly observed. Furthermore, the specific environmental activities of three retailers from Denmark, France and the UK were compared. Research limitations/implications – The empirical study investigates supply chain...... operations of retailers and excludes other areas of retail management. The results are based on material that is published by the respective companies and thus do not include internal reports. Originality/value – The main contribution of this paper is to test the proposition that global retailers follow...

  9. Fuzzy Markov chains: uncertain probabilities

    OpenAIRE

    2002-01-01

    We consider finite Markov chains where there are uncertainties in some of the transition probabilities. These uncertainties are modeled by fuzzy numbers. Using a restricted fuzzy matrix multiplication we investigate the properties of regular, and absorbing, fuzzy Markov chains and show that the basic properties of these classical Markov chains generalize to fuzzy Markov chains.

  10. Essentials of supply chain management

    CERN Document Server

    Hugos, Michael H

    2011-01-01

    The latest thinking, strategies, developments, and technologies to stay current in supply chain management Presenting the core concepts and techniques of supply chain management in a clear, concise and easily readable style, the Third Edition of Essentials of Supply Chain Management outlines the most crucial tenets and concepts of supply chain management.

  11. Supply-Chain Optimization Template

    Science.gov (United States)

    Quiett, William F.; Sealing, Scott L.

    2009-01-01

    The Supply-Chain Optimization Template (SCOT) is an instructional guide for identifying, evaluating, and optimizing (including re-engineering) aerospace- oriented supply chains. The SCOT was derived from the Supply Chain Council s Supply-Chain Operations Reference (SCC SCOR) Model, which is more generic and more oriented toward achieving a competitive advantage in business.

  12. Electron Transfer Chain Catalysis

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Electron-transfer chain (ETC) catalysis belongs to the family of chain reactions where the electron is the catalyst. The ETC mechanism could be initiated by chemical activation, electrochemistry, or photolysis. If this pathway is applied to the preparation of organometallic complexes, it utilizes the greatly enhanced reactivity of organometallic 17e and 19e radicals. The chemical propagation is followed by the cross electron-transfer while the electron-transfer step is also followed by the chemical propagation, creating a loop in which reactants are facilely transformed into products. Interestingly the overall reaction is without any net redox change.

  13. Electron Transfer Chain Catalysis

    Institute of Scientific and Technical Information of China (English)

    LIU; LingKang

    2001-01-01

    Electron-transfer chain (ETC) catalysis belongs to the family of chain reactions where the electron is the catalyst. The ETC mechanism could be initiated by chemical activation, electrochemistry, or photolysis. If this pathway is applied to the preparation of organometallic complexes, it utilizes the greatly enhanced reactivity of organometallic 17e and 19e radicals. The chemical propagation is followed by the cross electron-transfer while the electron-transfer step is also followed by the chemical propagation, creating a loop in which reactants are facilely transformed into products. Interestingly the overall reaction is without any net redox change.  ……

  14. METRODOS: Meteorological preprocessor chain

    DEFF Research Database (Denmark)

    Astrup, P.; Mikkelsen, T.; Deme, S.

    2001-01-01

    The METRODOS meteorological preprocessor chain combines measured tower data and coarse grid numerical weather prediction (NWP) data with local scale flow models and similarity scaling to give high resolution approximations of the meteorological situation. Based on available wind velocity...... - heat flux related measurement, e.g. a temperature gradient, are used to give local values of friction velocity and Monin-Obukhov length plus an estimate of the mixing height. The METRODOS meteorological preprocessor chain is an integral part of the RODOS - Real Time On Line Decision Support - program...

  15. Modelling the coal chain

    Energy Technology Data Exchange (ETDEWEB)

    Gertenbach, J.-D.; Varendorff, R. von [Knowledge Based Engineering, Sandton (South Africa)

    1999-03-01

    Managing the supply chain in an integrated coal operation involves many operation and control options often too complex for the human mind to comprehend and react to. By integrating all the knowledge of a supply chain into an expert system, both off-line and on-line real time decisions are possible. Knowledge Based Engineering based in South Africa, has gained valuable experience in modelling such mining operations. The article discusses the methodologies that the company has implemented. KBE uses Gensym`s G2 Real Time Expert System as the foundation of the system and the knowledge base is developed modularly.

  16. Effect of gamma radiation on the growth of Aspergillus Flavus aflatoxins producer and on the use of polymerase chain reaction technique (PCR) in samples of maize grains artificially inoculated; Efeitos da radiacao gama no crescimento de Aspergillus flavus produtor de aflatoxinas e no emprego da tecnica da Reacao em Cadeia da Polimerase (RCP) em amostras de graos de milho inoculadas artificialmente

    Energy Technology Data Exchange (ETDEWEB)

    Aquino, Simone

    2003-07-01

    The aim of this present study was to verify the effects of gamma radiation on the growth of Aspergillus flavus Link aflatoxins producer; to demonstrate the application of Polymerase Chain Reaction (PCR) technique in the diagnostic of A. Flavus, as well to verify the effect of radiation in the profile of DNA bands. Twenty samples of grains maize with 200 g each were individually irradiated with 20 kGy, to eliminate the microbial contamination. In following, the samples were inoculated with an toxigenic A. flavus (1x10{sup 6} spores/ml), incubated for 15 days at 25 deg C with a relative humidity of around 97,5% and irradiated with 0, 2; 5 and 10 kGy. The samples, 5 to each dose of irradiation, were individually analyzed for the number of fungal cells, water activity, viability test (fluorescein diacetate and ethidium bromide), PCR and aflatoxins (AFB) detection. The results showed that the doses used were effective in reducing the number of Colony Forming Units (CFU/g) mainly the doses of 5 and 10 kGy. In addition, the viability test showed a decrease of viable cells with increase of irradiation doses. The reduction of AFB{sub 1} and AFB-2, was more efficient with the use of 2 kGy in comparison with the dose of 5 kGy, while the dose of 10 kGy, degraded the aflatoxins. Thereby, it was observed that AFB2 showed to be more radiosensitive. The use of PCR technique showed the presence of DNA bands, in all samples. (author)

  17. Integrated supply chain risk management

    Directory of Open Access Journals (Sweden)

    Riaan Bredell

    2007-11-01

    Full Text Available Integrated supply chain risk management (ISCRM has become indispensable to the theory and practice of supply chain management. The economic and political realities of the modern world require not only a different approach to supply chain management, but also bold steps to secure supply chain performance and sustainable wealth creation. Integrated supply chain risk management provides supply chain organisations with a level of insight into their supply chains yet to be achieved. If correctly applied, this process may optimise management decision-making and assist in the protection and enhancement of shareholder value.

  18. Capillary sample

    Science.gov (United States)

    ... several times a day using capillary blood sampling. Disadvantages to capillary blood sampling include: Only a limited ... do not constitute endorsements of those other sites. Copyright 1997-2017, A.D.A.M., Inc. Duplication ...

  19. Independent sets in chain cacti

    OpenAIRE

    Sedlar, Jelena

    2011-01-01

    In this paper chain cacti are considered. First, for two specific classes of chain cacti (orto-chains and meta-chains of cycles with h vertices) the recurrence relation for independence polynomial is derived. That recurrence relation is then used in deriving explicit expressions for independence number and number of maximum independent sets for such chains. Also, the recurrence relation for total number of independent sets for such graphs is derived. Finaly, the proof is provided that orto-ch...

  20. Ensemble Bayesian model averaging using Markov Chain Monte Carlo sampling

    NARCIS (Netherlands)

    Vrugt, J.A.; Diks, C.G.H.; Clark, M.

    2008-01-01

    Bayesian model averaging (BMA) has recently been proposed as a statistical method to calibrate forecast ensembles from numerical weather models. Successful implementation of BMA however, requires accurate estimates of the weights and variances of the individual competing models in the ensemble. In t

  1. Standard handbook of chains chains for power transmission and material handling

    CERN Document Server

    Chain Association, American

    2005-01-01

    A BRIEF HISTORY OF THE DEVELOPMENT OF CHAINEarly DevelopmentsCog ChainCast Detachable ChainCast Pintle ChainPrecision Roller ChainEngineering Steel ChainSilent ChainFlat-Top ChainTerminologyA CHAIN OVERVIEW: USES AND ADVANTAGESGeneralTypes of ChainScope of Chains CoveredStyles and Forms of ChainsStraight and Offset Link ChainsChains With and Without RollersUses of ChainStandard Chains and Their UsesThe Advantages of Chains in ApplicationsAdvantages of Roller Chains in DrivesAdvantages of Silent Chain Drives

  2. Development Value Chains meet Business Supply Chains : The concept of Global Value Chains unraveled

    NARCIS (Netherlands)

    S. Drost (Sarah); J.C.A.C. van Wijk (Jeroen); S. Vellema (Sietze)

    2011-01-01

    textabstractValue chain promotion is considered a key element of private sector development strategies and pro-poor growth. However, (value) chain concepts are rather complex and unclear. This paper unravels the concept of global value chains and studies the diversity of key value chain-related (sup

  3. Nodal-chain metals

    Science.gov (United States)

    Bzdušek, Tomáš; Wu, Quansheng; Rüegg, Andreas; Sigrist, Manfred; Soluyanov, Alexey A.

    2016-10-01

    The band theory of solids is arguably the most successful theory of condensed-matter physics, providing a description of the electronic energy levels in various materials. Electronic wavefunctions obtained from the band theory enable a topological characterization of metals for which the electronic spectrum may host robust, topologically protected, fermionic quasiparticles. Many of these quasiparticles are analogues of the elementary particles of the Standard Model, but others do not have a counterpart in relativistic high-energy theories. A complete list of possible quasiparticles in solids is lacking, even in the non-interacting case. Here we describe the possible existence of a hitherto unrecognized type of fermionic excitation in metals. This excitation forms a nodal chain—a chain of connected loops in momentum space—along which conduction and valence bands touch. We prove that the nodal chain is topologically distinct from previously reported excitations. We discuss the symmetry requirements for the appearance of this excitation and predict that it is realized in an existing material, iridium tetrafluoride (IrF4), as well as in other compounds of this class of materials. Using IrF4 as an example, we provide a discussion of the topological surface states associated with the nodal chain. We argue that the presence of the nodal-chain fermions will result in anomalous magnetotransport properties, distinct from those of materials exhibiting previously known excitations.

  4. CHAINE DES ROTISSEUR @ HILTON

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The annual gala dinner of Chaine des Rotisseurs was hosted by Hilton Beijing. The “Ballet Dinner” - a great creation for both art and fine dining lovers was taken place in varies places within the hotel, including hotel lobby, 3rd floor and lobby lounge.

  5. Exploration Supply Chain Simulation

    Science.gov (United States)

    2008-01-01

    The Exploration Supply Chain Simulation project was chartered by the NASA Exploration Systems Mission Directorate to develop a software tool, with proper data, to quantitatively analyze supply chains for future program planning. This tool is a discrete-event simulation that uses the basic supply chain concepts of planning, sourcing, making, delivering, and returning. This supply chain perspective is combined with other discrete or continuous simulation factors. Discrete resource events (such as launch or delivery reviews) are represented as organizational functional units. Continuous resources (such as civil service or contractor program functions) are defined as enabling functional units. Concepts of fixed and variable costs are included in the model to allow the discrete events to interact with cost calculations. The definition file is intrinsic to the model, but a blank start can be initiated at any time. The current definition file is an Orion Ares I crew launch vehicle. Parameters stretch from Kennedy Space Center across and into other program entities (Michaud Assembly Facility, Aliant Techsystems, Stennis Space Center, Johnson Space Center, etc.) though these will only gain detail as the file continues to evolve. The Orion Ares I file definition in the tool continues to evolve, and analysis from this tool is expected in 2008. This is the first application of such business-driven modeling to a NASA/government-- aerospace contractor endeavor.

  6. Innovation in Supply Chains

    DEFF Research Database (Denmark)

    Maier, Maximilian; Korbel, Jakob; Brem, Alexander

    2015-01-01

    . Moreover, along with the fourth industrial revolution – industry 4.0 – new technologies such as cyber physical systems are fast gaining popularity. Hence, based on the analysis of relevant literature, we further develop the supply chain committee model, developed by Kaluza et al. (2003) to demonstrate how...

  7. Supply chain reliability modelling

    Directory of Open Access Journals (Sweden)

    Eugen Zaitsev

    2012-03-01

    Full Text Available Background: Today it is virtually impossible to operate alone on the international level in the logistics business. This promotes the establishment and development of new integrated business entities - logistic operators. However, such cooperation within a supply chain creates also many problems related to the supply chain reliability as well as the optimization of the supplies planning. The aim of this paper was to develop and formulate the mathematical model and algorithms to find the optimum plan of supplies by using economic criterion and the model for the probability evaluating of non-failure operation of supply chain. Methods: The mathematical model and algorithms to find the optimum plan of supplies were developed and formulated by using economic criterion and the model for the probability evaluating of non-failure operation of supply chain. Results and conclusions: The problem of ensuring failure-free performance of goods supply channel analyzed in the paper is characteristic of distributed network systems that make active use of business process outsourcing technologies. The complex planning problem occurring in such systems that requires taking into account the consumer's requirements for failure-free performance in terms of supply volumes and correctness can be reduced to a relatively simple linear programming problem through logical analysis of the structures. The sequence of the operations, which should be taken into account during the process of the supply planning with the supplier's functional reliability, was presented.

  8. Chain binomial models and binomial autoregressive processes.

    Science.gov (United States)

    Weiss, Christian H; Pollett, Philip K

    2012-09-01

    We establish a connection between a class of chain-binomial models of use in ecology and epidemiology and binomial autoregressive (AR) processes. New results are obtained for the latter, including expressions for the lag-conditional distribution and related quantities. We focus on two types of chain-binomial model, extinction-colonization and colonization-extinction models, and present two approaches to parameter estimation. The asymptotic distributions of the resulting estimators are studied, as well as their finite-sample performance, and we give an application to real data. A connection is made with standard AR models, which also has implications for parameter estimation.

  9. A protrusion can "eclipse" looping of a long self-avoiding chain

    CERN Document Server

    Pollak, Yaroslav; Amit, Roee

    2016-01-01

    We simulate long self-avoiding chains using a weighted-biased sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain's termini reduces the probability of looping, even for chains much longer than the protrusion-chain-terminus distance. This effect increases with protrusion size, and decreases with protrusion-terminus distance. We model the simulated results theoretically by considering how the protrusion "eclipses" the chain terminus closer to the protrusion from the more distant chain terminus. This eclipse mechanism has implications for understanding the regulatory role of proteins bound to DNA.

  10. Structural Origins of Nitroxide Side Chain Dynamics on Membrane Protein [alpha]-Helical Sites

    Energy Technology Data Exchange (ETDEWEB)

    Kroncke, Brett M.; Horanyi, Peter S.; Columbus, Linda (UV)

    2010-12-07

    Understanding the structure and dynamics of membrane proteins in their native, hydrophobic environment is important to understanding how these proteins function. EPR spectroscopy in combination with site-directed spin labeling (SDSL) can measure dynamics and structure of membrane proteins in their native lipid environment; however, until now the dynamics measured have been qualitative due to limited knowledge of the nitroxide spin label's intramolecular motion in the hydrophobic environment. Although several studies have elucidated the structural origins of EPR line shapes of water-soluble proteins, EPR spectra of nitroxide spin-labeled proteins in detergents or lipids have characteristic differences from their water-soluble counterparts, suggesting significant differences in the underlying molecular motion of the spin label between the two environments. To elucidate these differences, membrane-exposed {alpha}-helical sites of the leucine transporter, LeuT, from Aquifex aeolicus, were investigated using X-ray crystallography, mutational analysis, nitroxide side chain derivatives, and spectral simulations in order to obtain a motional model of the nitroxide. For each crystal structure, the nitroxide ring of a disulfide-linked spin label side chain (R1) is resolved and makes contacts with hydrophobic residues on the protein surface. The spin label at site I204 on LeuT makes a nontraditional hydrogen bond with the ortho-hydrogen on its nearest neighbor F208, whereas the spin label at site F177 makes multiple van der Waals contacts with a hydrophobic pocket formed with an adjacent helix. These results coupled with the spectral effect of mutating the i {+-} 3, 4 residues suggest that the spin label has a greater affinity for its local protein environment in the low dielectric than on a water-soluble protein surface. The simulations of the EPR spectra presented here suggest the spin label oscillates about the terminal bond nearest the ring while maintaining weak

  11. Performance Metrics in Supply Chain Management. Evidence from Romanian Economy

    Directory of Open Access Journals (Sweden)

    Alexandru Constăngioară

    2013-02-01

    Full Text Available The proposed empirical research uses a national sample of 19 Romanian companies from various industries to estimate de utilities for financial and non-financial performance measures used in Romanian supply chains. Empirical findings show that national supply chain measurement systems are balanced, using both financial and non-financial performance measures. The high estimated utility corresponding to indicators measuring logistic costs provides evidence that inter-functional and inter-organization integration in supply chains at national level are realized through operational excellence. Achieving the full potential of supply chain integration requires that management fosters both integration of operations and integration of customers.

  12. On the Markov Chain Monte Carlo (MCMC) method

    Indian Academy of Sciences (India)

    Rajeeva L Karandikar

    2006-04-01

    Markov Chain Monte Carlo (MCMC) is a popular method used to generate samples from arbitrary distributions, which may be specified indirectly. In this article, we give an introduction to this method along with some examples.

  13. Language sampling

    DEFF Research Database (Denmark)

    Rijkhoff, Jan; Bakker, Dik

    1998-01-01

    This article has two aims: [1] to present a revised version of the sampling method that was originally proposed in 1993 by Rijkhoff, Bakker, Hengeveld and Kahrel, and [2] to discuss a number of other approaches to language sampling in the light of our own method. We will also demonstrate how our...... sampling method is used with different genetic classifications (Voegelin & Voegelin 1977, Ruhlen 1987, Grimes ed. 1997) and argue that —on the whole— our sampling technique compares favourably with other methods, especially in the case of exploratory research....

  14. Iron modulates the alpha chain of fibrinogen.

    Science.gov (United States)

    Nielsen, Vance G; Jacobsen, Wayne K

    2016-04-01

    Iron-bound fibrinogen has been noted to accelerate plasmatic coagulation in patients with divergent conditions involving upregulation of heme oxygenase activity, including hemodialysis, Alzheimer's disease, sickle cell anemia, and chronic migraine. Our goal was to determine if a site of iron-fibrinogen interaction was on the alpha chain. Using thrombelastography, we compared the coagulation kinetic profiles of plasma exposed to 0-10 µM ferric chloride after activation of coagulation with thrombin generated by contact activation of plasma with the plastic sample cup or by exposure to 1 µg/ml of Calloselasma rhodostoma venom (rich in ancrod activity), which causes coagulation via polymerization of alpha chain monomers. Venom mediated coagulation always occurred before thrombin activated thrombus formation, and ferric chloride always diminished the time of onset of coagulation and increased the velocity of clot growth. Iron enhances plasmatic coagulation kinetics by modulating the alpha chain of fibrinogen.

  15. The design of supply chains

    DEFF Research Database (Denmark)

    Bøge Sørensen, Lars

    2004-01-01

    Keywords Supply Chain Management, Supply Chain Design, Literature studyAbstract Argues stability is a design objective for supply chain design alongside cost, leadtime and responsiveness. Performs an extensive literature study on supply chain design,identifies methods, theories and objectives...... in the existing literature. Describes the conceptexternal specificity and how it's used to design supply chains. Using the concept upstream,archetypes of risk minimal and maximal design are identified. Downstream the conceptdescribes two viable scenarios, one minimizing the impact, the other minimizing...... theprobability of (intended) departure of a supply chain partner. Finally, principles for supplychain design are described and managerial outlined....

  16. Decision-Making for Supply Chain Integration Supply Chain Integration

    CERN Document Server

    Lettice, Fiona; Durowoju, Olatunde

    2012-01-01

    Effective supply chain integration, and the tight co-ordination it creates, is an essential pre-requisite for successful supply chain management.  Decision-Making for Supply Chain Integration is a practical reference on recent research in the area of supply chain integration focusing on distributed decision-making problems. Recent applications of various decision-making tools for integrating supply chains are covered including chapters focusing on: •Supplier selection, pricing strategy and inventory decisions in multi-level supply chains, •RFID-enabled distributed decision-making, •Operational risk issues and time-critical decision-making for sensitive logistics nodes, Modelling end to end processes to improve supply chain integration, and •Integrated systems to improve service delivery and optimize resource use. Decision-Making for Supply Chain Integration provides an insight into the tools and methodologies of this field with support from real-life case studies demonstrating successful application ...

  17. Towards Intelligent Supply Chains

    DEFF Research Database (Denmark)

    Siurdyban, Artur; Møller, Charles

    2012-01-01

    applied to the context of organizational processes can increase the success rate of business operations. The framework is created using a set of theoretical based constructs grounded in a discussion across several streams of research including psychology, pedagogy, artificial intelligence, learning...... of deploying inapt operations leading to deterioration of profits. To address this problem, we propose a unified business process design framework based on the paradigm of intelligence. Intelligence allows humans and human-designed systems cope with environmental volatility, and we argue that its principles......, business process management and supply chain management. It outlines a number of system tasks combined in four integrated management perspectives: build, execute, grow and innovate, put forward as business process design propositions for Intelligent Supply Chains....

  18. Perioperative supply chain management.

    Science.gov (United States)

    Feistritzer, N R; Keck, B R

    2000-09-01

    Faced with declining revenues and increasing operating expenses, hospitals are evaluating numerous mechanisms designed to reduce costs while simultaneously maintaining quality care. Many facilities have targeted initial cost reduction efforts in the reduction of labor expenses. Once labor expenses have been "right sized," facilities have continued to focus on service delivery improvements by the optimization of the "supply chain" process. This report presents a case study of the efforts of Vanderbilt University Medical Center in the redesign of its supply chain management process in the department of Perioperative Services. Utilizing a multidisciplinary project management structure, 3 work teams were established to complete the redesign process. To date, the project has reduced costs by $2.3 million and enhanced quality patient care by enhancing the delivery of appropriate clinical supplies during the perioperative experience.

  19. Volumes of chain links

    CERN Document Server

    Kaiser, James; Rollins, Clint

    2011-01-01

    Agol has conjectured that minimally twisted n-chain links are the smallest volume hyperbolic manifolds with n cusps, for n at most 10. In his thesis, Venzke mentions that these cannot be smallest volume for n at least 11, but does not provide a proof. In this paper, we give a proof of Venzke's statement. The proof for n at least 60 is completely rigorous. The proof for n between 11 and 59 uses a computer calculation, and can be made rigorous for manifolds of small enough complexity, using methods of Moser and Milley. Finally, we prove that the n-chain link with 2m or 2m+1 half-twists cannot be the minimal volume hyperbolic manifold with n cusps, provided n is at least 60 or |m| is at least 8, and we give computational data indicating this remains true for smaller n and |m|.

  20. Extended linear chain compounds

    CERN Document Server

    Linear chain substances span a large cross section of contemporary chemistry ranging from covalent polymers, to organic charge transfer com­ plexes to nonstoichiometric transition metal coordination complexes. Their commonality, which coalesced intense interest in the theoretical and exper­ imental solid state physics/chemistry communities, was based on the obser­ vation that these inorganic and organic polymeric substrates exhibit striking metal-like electrical and optical properties. Exploitation and extension of these systems has led to the systematic study of both the chemistry and physics of highly and poorly conducting linear chain substances. To gain a salient understanding of these complex materials rich in anomalous aniso­ tropic electrical, optical, magnetic, and mechanical properties, the conver­ gence of diverse skills and talents was required. The constructive blending of traditionally segregated disciplines such as synthetic and physical organic, inorganic, and polymer chemistry, crystallog...

  1. Sampling Development

    Science.gov (United States)

    Adolph, Karen E.; Robinson, Scott R.

    2011-01-01

    Research in developmental psychology requires sampling at different time points. Accurate depictions of developmental change provide a foundation for further empirical studies and theories about developmental mechanisms. However, overreliance on widely spaced sampling intervals in cross-sectional and longitudinal designs threatens the validity of…

  2. The innovation value chain.

    Science.gov (United States)

    Hansen, Morten T; Birkinshaw, Julian

    2007-06-01

    The challenges of coming up with fresh ideas and realizing profits from them are different for every company. One firm may excel at finding good ideas but may have weak systems for bringing them to market. Another organization may have a terrific process for funding and rolling out new products and services but a shortage of concepts to develop. In this article, Hansen and Birkinshaw caution executives against using the latest and greatest innovation approaches and tools without understanding the unique deficiencies in their companies' innovation systems. They offer a framework for evaluating innovation performance: the innovation value chain. It comprises the three main phases of innovation (idea generation, conversion, and diffusion) as well as the critical activities performed during those phases (looking for ideas inside your unit; looking for them in other units; looking for them externally; selecting ideas; funding them; and promoting and spreading ideas companywide). Using this framework, managers get an end-to-end view of their innovation efforts. They can pinpoint their weakest links and tailor innovation best practices appropriately to strengthen those links. Companies typically succumb to one of three broad "weakest-link" scenarios. They are idea poor, conversion poor, or diffusion poor. The article looks at the ways smart companies - including Intuit, P&G, Sara Lee, Shell, and Siemens- modify the best innovation practices and apply them to address those organizations' individual needs and flaws. The authors warn that adopting the chain-based view of innovation requires new measures of what can be delivered by each link in the chain. The approach also entails new roles for employees "external scouts" and "internal evangelists," for example. Indeed, in their search for new hires, companies should seek out those candidates who can help address particular weaknesses in the innovation value chain.

  3. Monitoring Global Supply Chains

    OpenAIRE

    2014-01-01

    Firms reliant on supply chains to manufacture their goods risk reputational harm if the working conditions in those factories are revealed to be dangerous, illegal, or otherwise problematic. While firms are increasingly relying on private-sector "social auditors" to assess factory conditions, little had been known about the accuracy of those assessments. We analyzed nearly 17,000 code-of-conduct audits conducted at nearly 6,000 suppliers around the world. We found that audits yield fewer viol...

  4. Port supply chain integration : analyzing biofuel supply chains

    NARCIS (Netherlands)

    Stevens, Leonie C. E.; Vis, Iris F. A.

    2016-01-01

    This paper focuses on port supply chain integration to strengthen operational and business performance. We provide a structured and comprehensive method to enable port supply chain integration and demonstrate its applicability to the biofuel supply chain. We define the value proposition, role, activ

  5. Rotamers and Migration: Investigating the Dissociative Photoionization of Ethylenediamine.

    Science.gov (United States)

    Muller, Giel; Voronova, Krisztina; Sztáray, Bálint; Meloni, Giovanni

    2016-06-09

    The unimolecular dissociation of energy-selected ethylenediamine cations was studied by threshold photoelectron photoion coincidence spectroscopy (TPEPICO) in the photon energy range of 8.60-12.50 eV. Modeling the breakdown diagram and time-of-flight distributions with rigid activated complex RRKM theory yielded 0 K appearance energies for eight dissociation channels, leading to NH2CHCH2(+)(•) at 9.120 ± 0.010 eV, CH3C(NH2)2(+) at 9.200 ± 0.012 eV, NH2CHCH3(+) at 9.34 ± 0.08 eV, CH2NH2(+) at 9.449 ± 0.025 eV, CH2NH3(+) at 9.8 ± 0.1 eV, c-C2H4NH2(+) at 10.1 ± 0.1 eV, CH3NHCHCH2(+) at 10.2 ± 0.1 eV, and the reappearance of CH2NH2(+) at 10.2 ± 0.1 eV. The CBS-QB3-calculated pathways highlighted the influence of intramolecular hydrogen attractions on the dissociation processes, presenting novel isomers and low-energy van der Waals intermediates that led to fragments in good agreement with experimental results. While most of the dissociation channels take place through reverse barriers, the 0 K heat of formation of (•)CH2NH2 was determined to be 147.6 ± 3.7 kJ mol(-1), in excellent agreement with literature, and the 0 K heat of formation of CH2NH3(+) at 844 ± 10 kJ mol(-1) is the first experimentally measured value available and is in good agreement with theory.

  6. Adjustable chain trees for proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Fonseca, Rasmus

    2012-01-01

    A chain tree is a data structure for changing protein conformations. It enables very fast detection of clashes and free energy potential calculations. A modified version of chain trees that adjust themselves to the changing conformations of folding proteins is introduced. This results in much...... tighter bounding volume hierarchies and therefore fewer intersection checks. Computational results indicate that the efficiency of the adjustable chain trees is significantly improved compared to the traditional chain trees....

  7. Supply chain dynamics in Asia

    OpenAIRE

    Banomyong, Ruth

    2010-01-01

    Supply chain management in Asia is a relatively novel topic but a key challenge for all Asian based manufacturers and traders when trying to integrate into the "global market". The purpose of the paper is to describe key supply chain issues faced in Asia. These issues are related to supply chain security that forces Asian firms to comply with numerous requirements as well as the importance of a properly managed supply chain in enhancing firms' competitiveness. The critical role played by Asia...

  8. Requirements of supply chain management in differentiating European pork chains.

    Science.gov (United States)

    Trienekens, Jacques; Wognum, Nel

    2013-11-01

    This paper summarizes results obtained by research into pork chain management in the EU Integrated Project Q-Porkchains. Changing demands for intrinsic and extrinsic quality attributes of pork products impact the way supply chain management should be organized from the farmer down to the consumer. The paper shows the importance of Quality Management Systems for integrating supply chains and enhancing consumer confidence. The paper also presents innovations in information system integration for aligning information exchange in the supply chain and logistics concepts based on innovative measurement technologies at the slaughterhouse stage. In the final section research challenges towards sustainable pork supply chains satisfying current consumer demands are presented.

  9. On chains of centered valuations

    Directory of Open Access Journals (Sweden)

    Rachid Chibloun

    2003-01-01

    Full Text Available We study chains of centered valuations of a domain A and chains of centered valuations of A [X1,…,Xn] corresponding to valuations of A. Finally, we make some applications to chains of valuations centered on the same ideal of A [X1,…,Xn] and extending the same valuation of A.

  10. Designing structural supply chain flexibility

    NARCIS (Netherlands)

    Mulinski, Ksawery Jan

    2012-01-01

    In a continuously changing business environment the role of supply chain flexibility is constantly increasing. A flexible supply chain can ensure survival in quickly changing market conditions as well as enable sustainable growth. This thesis explores the topic of supply chain flexibility with focus

  11. Radiology's value chain.

    Science.gov (United States)

    Enzmann, Dieter R

    2012-04-01

    A diagnostic radiology value chain is constructed to define its main components, all of which are vulnerable to change, because digitization has caused disaggregation of the chain. Some components afford opportunities to improve productivity, some add value, while some face outsourcing to lower labor cost and to information technology substitutes, raising commoditization risks. Digital image information, because it can be competitive at smaller economies of scale, allows faster, differential rates of technological innovation of components, initiating a centralization-to-decentralization technology trend. Digitization, having triggered disaggregation of radiology's professional service model, may soon usher in an information business model. This means moving from a mind-set of "reading images" to an orientation of creating and organizing information for greater accuracy, faster speed, and lower cost in medical decision making. Information businesses view value chain investments differently than do small professional services. In the former model, producing a better business product will extend image interpretation beyond a radiologist's personal fund of knowledge to encompass expanding external imaging databases. A follow-on expansion with integration of image and molecular information into a report will offer new value in medical decision making. Improved interpretation plus new integration will enrich and diversify radiology's key service products, the report and consultation. A more robust, information-rich report derived from a "systems" and "computational" radiology approach will be facilitated by a transition from a professional service to an information business. Under health care reform, radiology will transition its emphasis from volume to greater value. Radiology's future brightens with the adoption of a philosophy of offering information rather than "reads" for decision making. Staunchly defending the status quo via turf wars is unlikely to constitute a

  12. Supply Chain Costing

    DEFF Research Database (Denmark)

    Asmussen, Jesper Normann; Kristensen, Jesper; Wæhrens, Brian Vejrum

    2016-01-01

    Based Costing (ABC) på et forsyningskædeniveau – heri benævnt Supply Chain Costing (SCC). Udoverdefordelederfindesved ABCtilføjerSCCogså et økonomisk grundlag til det strategiske rationale, der ofte ligger bag opbygningen af virksomhedens forsyningskæde, og kan dermed medvirke til konkret....... Virksomhedens evne til at udarbejde relevantinformation fremstår derfor som en vigtig parameter, såfremt virksomheden skal forblive konkurrencedygtig i en stadig mere kompleks verden, hvor udviklingen foregår stadig hurtigere. Denne arbejdsboggiverindsigtidemuligheder,der eksisterer ved at anvende Activity...

  13. Stochastic seismic tomography by interacting Markov chains

    Science.gov (United States)

    Bottero, Alexis; Gesret, Alexandrine; Romary, Thomas; Noble, Mark; Maisons, Christophe

    2016-10-01

    Markov chain Monte Carlo sampling methods are widely used for non-linear Bayesian inversion where no analytical expression for the forward relation between data and model parameters is available. Contrary to the linear(ized) approaches, they naturally allow to evaluate the uncertainties on the model found. Nevertheless their use is problematic in high-dimensional model spaces especially when the computational cost of the forward problem is significant and/or the a posteriori distribution is multimodal. In this case, the chain can stay stuck in one of the modes and hence not provide an exhaustive sampling of the distribution of interest. We present here a still relatively unknown algorithm that allows interaction between several Markov chains at different temperatures. These interactions (based on importance resampling) ensure a robust sampling of any posterior distribution and thus provide a way to efficiently tackle complex fully non-linear inverse problems. The algorithm is easy to implement and is well adapted to run on parallel supercomputers. In this paper, the algorithm is first introduced and applied to a synthetic multimodal distribution in order to demonstrate its robustness and efficiency compared to a simulated annealing method. It is then applied in the framework of first arrival traveltime seismic tomography on real data recorded in the context of hydraulic fracturing. To carry out this study a wavelet-based adaptive model parametrization has been used. This allows to integrate the a priori information provided by sonic logs and to reduce optimally the dimension of the problem.

  14. Stochastic seismic tomography by interacting Markov chains

    Science.gov (United States)

    Bottero, Alexis; Gesret, Alexandrine; Romary, Thomas; Noble, Mark; Maisons, Christophe

    2016-07-01

    Markov chain Monte Carlo sampling methods are widely used for non-linear Bayesian inversion where no analytical expression for the forward relation between data and model parameters is available. Contrary to the linear(ized) approaches they naturally allow to evaluate the uncertainties on the model found. Nevertheless their use is problematic in high dimensional model spaces especially when the computational cost of the forward problem is significant and/or the a posteriori distribution is multimodal. In this case the chain can stay stuck in one of the modes and hence not provide an exhaustive sampling of the distribution of interest. We present here a still relatively unknown algorithm that allows interaction between several Markov chains at different temperatures. These interactions (based on Importance Resampling) ensure a robust sampling of any posterior distribution and thus provide a way to efficiently tackle complex fully non linear inverse problems. The algorithm is easy to implement and is well adapted to run on parallel supercomputers. In this paper the algorithm is first introduced and applied to a synthetic multimodal distribution in order to demonstrate its robustness and efficiency compared to a Simulated Annealing method. It is then applied in the framework of first arrival traveltime seismic tomography on real data recorded in the context of hydraulic fracturing. To carry out this study a wavelet based adaptive model parametrization has been used. This allows to integrate the a priori information provided by sonic logs and to reduce optimally the dimension of the problem.

  15. [Trophic chains in soil].

    Science.gov (United States)

    Goncharov, A A; Tiunov, A V

    2013-01-01

    Trophic links of soil animals are extensively diverse but also flexible. Moreover, feeding activity of large soil saprotrophs often cascades into a range of ecosystem-level consequences via the ecological engineering. Better knowledge on the main sources of energy utilized by soil animals is needed for understanding functional structure of soil animal communities and their participation in the global carbon cycling. Using published and original data, we consider the relative importance of dead organic matter and saprotrophic microorganisms as a basal energy source in the detritus-based food chains, the feeding of endogeic macrofauna on the stabilized soil organic matter, and the role of recent photosynthate in the energy budget of soil communities. Soil food webs are spatially and functionally compartmentalized, though the separation of food chains into bacteria- and fungi-based channels seems to be an over-simplification. The regulation of the litter decomposition rates via top-down trophic interactions across more than one trophic level is only partly supported by experimental data, but mobile litter-dwelling predators play a crucial role in integrating local food webs within and across neighboring ecosystems.

  16. Work sampling

    OpenAIRE

    Salas Bacalla, julio; FII-UNMSM

    2014-01-01

    Work sampling is a method of indirect measurement, which means instantaneous observations, to determine the amount of uptime or downtime in a production process El muestreo de trabajo es un método de medición indirecto, que mediante observaciones instantaneas, permite determinar la cantidad de tiempo en actividad o inactividad en un proceso productivo

  17. Polyketide chain length control by chain length factor.

    Science.gov (United States)

    Tang, Yi; Tsai, Shiou-Chuan; Khosla, Chaitan

    2003-10-22

    Bacterial aromatic polyketides are pharmacologically important natural products. A critical parameter that dictates product structure is the carbon chain length of the polyketide backbone. Systematic manipulation of polyketide chain length represents a major unmet challenge in natural product biosynthesis. Polyketide chain elongation is catalyzed by a heterodimeric ketosynthase. In contrast to homodimeric ketosynthases found in fatty acid synthases, the active site cysteine is absent from the one subunit of this heterodimer. The precise role of this catalytically silent subunit has been debated over the past decade. We demonstrate here that this subunit is the primary determinant of polyketide chain length, thereby validating its designation as chain length factor. Using structure-based mutagenesis, we identified key residues in the chain length factor that could be manipulated to convert an octaketide synthase into a decaketide synthase and vice versa. These results should lead to novel strategies for the engineered biosynthesis of hitherto unidentified polyketide scaffolds.

  18. Information in the supply chain: measuring supply chain performance

    OpenAIRE

    Bytheway, Andrew

    1995-01-01

    Information is one of many factors in the development of supply chain operations. It is a key factor in a number of new initiatives, such as: business process management. partnership development, efficient customer response, tighter integration of supply chain operations and outsourcing of ancillary operations. Improvement of the supply chain takes place at different levels: simple efficiency (the Improvement of existing processes), improved quality of service (the redesign of ...

  19. Doping of Semiconducting Atomic Chains

    Science.gov (United States)

    Toshishige, Yamada; Kutler, Paul (Technical Monitor)

    1997-01-01

    Due to the rapid progress in atom manipulation technology, atomic chain electronics would not be a dream, where foreign atoms are placed on a substrate to form a chain, and its electronic properties are designed by controlling the lattice constant d. It has been shown theoretically that a Si atomic chain is metallic regardless of d and that a Mg atomic chain is semiconducting or insulating with a band gap modified with d. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along the chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome this dilemma, we may place a dopant atom beside the chain at every N lattice periods (N > 1). Because of the periodic arrangement of dopant atoms, we can avoid the unwanted Anderson localization. Moreover, since the dopant atoms do not constitute the chain, the overlap interaction between them is minimized, and the band structure modification can be made smallest. Some tight-binding results will be discussed to demonstrate the present idea.

  20. Dynamics of Polymer Chains.

    Science.gov (United States)

    Hong, Tzay-Ming

    A major objective of this research is to establish at a more fundamental level some of the qualitative or semi-quantitative treatments in use at the present time, such as the Doi-Edwards tube picture, the switch from non -ideal to ideal behavior, and dynamical aspects of the reptation model. The main topics are: (I) An attempt was made to determine the order of magnitude of the elastic time interval of a viscoelastic polymer melt, defining it as the reciprocal of the average rate at which the total entanglement (clockwise plus anticlockwise) passes through zero due to thermal agitation. We calculated the case of a free chain winding about a straight rod both in friction-independent regime and in high friction regime. (II) By successively coarse -graining and rescaling the monomer-monomer interaction (using a modified Wilson recursion formula) we found that the interaction is driven to a very strong but short-ranged one. This verifies the observation that polymers in dilute solutions tend to curl up and behave like hard spheres. (III) We studied the case of chemical equilibrium of i-mers with their nucleating monomers and on the basis of a Flory-Huggins -type mean field theory find that in the dilute limit the swelling of the i-mers takes on the traditional N ^{3over5} law only for sufficiently small monomer chemical potential. When that potential is large enough, then, assuming a Flory law of chain propagation, the law seems to become N^{1over3 }. This is distinct from the problem of changeover from dilute to semidilute polymer system, which we also studied by imposing total polymer density as a constraint equation. (IV) Another item examined concerns the form of the space curve that a very long polymer must assume in order to minimize its free energy (we found that a family of helices with a definite functional relation between pitch and radius renders the free energy stationary). Because a chain is a one-dimensional object, this does not mean that helical shapes

  1. Quivers via anomaly chains

    Energy Technology Data Exchange (ETDEWEB)

    Casero, Roberto [Dipartimento di Fisica, Universita di Milano-Bicocca, Piazza della Scienza, 3, 20126 Milan (Italy)]. E-mail: roberto.casero@mib.infn.it; Trincherini, Enrico [Dipartimento di Fisica, Universita di Milano-Bicocca, Piazza della Scienza, 3, 20126 Milan (Italy)

    2003-09-01

    We study quivers in the context of matrix models. We introduce chains of generalized Konishi anomalies to write the quadratic and cubic equations that constrain the resolvents of general affine A-circumflex{sub n-1} and non-affine A{sub n} quiver gauge theories, and give a procedure to calculate all higher-order relations. For these theories we also evaluate, as functions of the resolvents, VEV's of chiral operators with two and four bi-fundamental insertions. As an example of the general procedure we explicitly consider the two simplest quivers A{sub 2} and A-circumflex{sub 1}, obtaining in the first case a cubic algebraic curve, and for the affine theory the same equation as that of U(N) theories with adjoint matter, successfully reproducing the RG cascade result. (author)

  2. Quivers via anomaly chains

    CERN Document Server

    Casero, R; Casero, Roberto; Trincherini, Enrico

    2003-01-01

    We study quivers in the context of matrix models. We introduce chains of generalized Konishi anomalies to write the quadratic and cubic equations that constrain the resolvents of general affine and non-affine quiver gauge theories, and give a procedure to calculate all higher-order relations. For these theories we also evaluate, as functions of the resolvents, VEV's of chiral operators with two and four bifundamental insertions. As an example of the general procedure we explicitly consider the two simplest quivers A2 and A1(affine), obtaining in the first case a cubic algebraic curve, and for the affine theory the same equation as that of U(N) theories with adjoint matter, successfully reproducing the RG cascade result.

  3. NNSA TRITIUM SUPPLY CHAIN

    Energy Technology Data Exchange (ETDEWEB)

    Wyrick, Steven [Savannah River National Laboratory, Aiken, SC, USA; Cordaro, Joseph [Savannah River National Laboratory, Aiken, SC, USA; Founds, Nanette [National Nuclear Security Administration, Albuquerque, NM, USA; Chambellan, Curtis [National Nuclear Security Administration, Albuquerque, NM, USA

    2013-08-21

    Savannah River Site plays a critical role in the Tritium Production Supply Chain for the National Nuclear Security Administration (NNSA). The entire process includes: • Production of Tritium Producing Burnable Absorber Rods (TPBARs) at the Westinghouse WesDyne Nuclear Fuels Plant in Columbia, South Carolina • Production of unobligated Low Enriched Uranium (LEU) at the United States Enrichment Corporation (USEC) in Portsmouth, Ohio • Irradiation of TPBARs with the LEU at the Tennessee Valley Authority (TVA) Watts Bar Reactor • Extraction of tritium from the irradiated TPBARs at the Tritium Extraction Facility (TEF) at Savannah River Site • Processing the tritium at the Savannah River Site, which includes removal of nonhydrogen species and separation of the hydrogen isotopes of protium, deuterium and tritium.

  4. PHONONS IN POLYACENIC CHAINS

    Institute of Scientific and Technical Information of China (English)

    O. Rafil; M. Tamine; B. Bourahla; R. Tigrine; S. Amoudache; A. Khater

    2006-01-01

    We have theoretically resolved phonon excitations in quasi-two-dimensional organic crystals of polyacenic semiconductor material which may be obtained by the pyrolytic treatment of phenol-formaldehyde resin. A model for studying the dynamical properties using three polyacene chains is proposed with the aim to present the vibrational properties of this structure. It employs the formalism of solid states in two dimensions which admit phonons. A simulation process of the two-dimensional lattice structure shows that elastic waves may explain the existence of vibrational modes in the frequency range 100-400 cm-1. The presence of acoustic and optical like phonons is discussed in terms of the elastic force constants. A hyperfine resonance structure is obtained. It allows the analysis of the dynamical evolution in thin films of polyacene. It is found that the behavior of the phonon density of states exhibits resonance between modes in the structure.

  5. Sampling Strategy

    Science.gov (United States)

    2008-01-01

    Three locations to the right of the test dig area are identified for the first samples to be delivered to the Thermal and Evolved Gas Analyzer (TEGA), the Wet Chemistry Lab (WCL), and the Optical Microscope (OM) on NASA's Phoenix Mars Lander. These sampling areas are informally labeled 'Baby Bear', 'Mama Bear', and 'Papa Bear' respectively. This image was taken on the seventh day of the Mars mission, or Sol 7 (June 1, 2008) by the Surface Stereo Imager aboard NASA's Phoenix Mars Lander. The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  6. Importance Sampling for the Infinite Sites Model*

    OpenAIRE

    Hobolth, Asger; Uyenoyama, Marcy K; Wiuf, Carsten

    2008-01-01

    Importance sampling or Markov Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics data. The applicability of these sampling-based inference techniques depends crucially on the proposal distribution. In this paper, we discuss importance sampling for the infinite sites model. The infinite sites assumption is attractive because it constraints the number of possible genealogies, thereby allowing for the analysis of larger data sets. We recall th...

  7. Chains, bombs, potrzebies and slugs

    Science.gov (United States)

    Jewess, Mike; McDowell, Alex; Maxfield, Stephen; Hunt, A. G.; Hicks, Bruce

    2010-03-01

    I read with pleasure Robert Crease's article on unusual units (February pp17-19). However, the article stated that an acre is 10×10 chains, when it is in fact 10×1 chains. Incidentally, a distance of 10 chains (220 yards) is known as a furlong, a word that suggests the length of a ploughed furrow and that is still used in horse-racing.

  8. DOS cones along atomic chains

    Science.gov (United States)

    Kwapiński, Tomasz

    2017-03-01

    The electron transport properties of a linear atomic chain are studied theoretically within the tight-binding Hamiltonian and the Green’s function method. Variations of the local density of states (DOS) along the chain are investigated. They are crucial in scanning tunnelling experiments and give important insight into the electron transport mechanism and charge distribution inside chains. It is found that depending on the chain parity the local DOS at the Fermi level can form cone-like structures (DOS cones) along the chain. The general condition for the local DOS oscillations is obtained and the linear behaviour of the local density function is confirmed analytically. DOS cones are characterized by a linear decay towards the chain which is in contrast to the propagation properties of charge density waves, end states and Friedel oscillations in one-dimensional systems. We find that DOS cones can appear due to non-resonant electron transport, the spin–orbit scattering or for chains fabricated on a substrate with localized electrons. It is also shown that for imperfect chains (e.g. with a reduced coupling strength between two neighboring sites) a diamond-like structure of the local DOS along the chain appears.

  9. Risikobasiertes Supply-Chain-Management

    DEFF Research Database (Denmark)

    Wieland, Andreas; Schinz, Philipp

    2015-01-01

    Das Management erlebt seit einigen Jahren dahingehend einen Paradigmenwechsel, dass nicht mehr Unternehmen als einzelne autonome Einheiten im Wettbewerb zueinander stehen, sondern die Supply Chains, in denen diese Unternehmen eingebunden sind. Ursachen hierfür sind beispielsweise die Auslagerung...... von Nicht-Kernprozessen auf vorgelagerte Stufen der Supply Chain oder auf Supply-Chain-Dienstleister sowie die Internationalisierung der Beschaffung. Dieser Paradigmenwechsel hat traditionelles Denken in den Schranken des Systems „Unternehmen“ abgelöst und zum Supply- Chain-Denken geführt, das vor......- und nachgelagerte Stufen des Systems „End-to-End-Supply-Chain“ einbezieht, etwa auch die Lieferanten von Lieferanten....

  10. Social Media and Supply Chain

    Directory of Open Access Journals (Sweden)

    Sonja Markova

    2013-02-01

    Full Text Available Web 2.0, also referred to as social media, is the use of the World Wide Web to increase creativity, information sharing, and collaboration among users. Social media is driving the rethinking of many of the principles of economics. The use of social media within supply chains is lagging behind their usage for other operational functions, however supply chain management is evolving into supply chain management 2.0.The purpose of this article is to provide researches of the supply chain management a reference with the main concepts of social media: social profiles, social applications, brand outposts and communities, and the social ecosystem.

  11. Integrating the healthcare supply chain.

    Science.gov (United States)

    Brennan, C D

    1998-01-01

    Today's integrated delivery systems (IDSs) require efficient supply chain processes to speed products to users at the lowest possible cost. Most excess costs within the supply chain are a result of inefficient and redundant processes involved in the transport and delivery of supplies from suppliers to healthcare providers. By integrating and assuming control of these supply chain processes, improving supply chain management practices, and organizing and implementing a disciplined redesign plan, IDSs can achieve substantial savings and better focus their organizations on their core patient care mission.

  12. Requirements of supply chain management in differentiating European pork chains

    NARCIS (Netherlands)

    Trienekens, J.H.; Wognum, P.M.

    2013-01-01

    This paper summarizes results obtained by research into pork chain management in the EU Integrated Project Q-Porkchains. Changing demands for intrinsic and extrinsic quality attributes of pork products impact the way supply chain management should be organized from the farmer down to the consumer. T

  13. Sustainable Supply Chain Engagement in a Retail Environment

    Directory of Open Access Journals (Sweden)

    Anika Berning

    2015-05-01

    Full Text Available Sustainability is a key requirement for business success and is often regarded a competitive advantage if strategically managed. Sustainability-mature organisations look to their value chains where the retailer-supplier collaboration becomes critical in embedding sustainability. With this in mind, it is important to monitor retailer-supplier collaboration to determine whether it is effective. To facilitate this monitoring, the UN Global Compact Supply Chain Sustainability: A Guide for Continuous Improvement was consulted. The research question aimed to determine the progress of a prominent South African retailer regarding their sustainable supply chain management (SSCM and collaboration with suppliers. Therefore, this study attempts to apply the Supplier Engagement Continuum, extracted from the UN Global Compact Supply Chain Sustainability: A Guide for Continuous Improvement, in order to determine how the retailer is progressing in sustainable supply chain management. The qualitative and exploratory nature of the study necessitated a case study research design, while the technique of purposive sampling was used to select the sample of three suppliers. Data was collected by means of semi-structured interviews facilitated by an interview guide, and data analysis was conducted with Atlas.ti software. It was found that the retailer’s sustainable supply chain management can only be located on level one of the continuum. Supply chain sustainability in organisations lack the theoretical foundation of what sustainability really is. Therefore, the model was amended and an additional level was added to incorporate the education of sustainability.

  14. Force-Degradation Pattern of Six Different Orthodontic Elastomeric Chains

    Directory of Open Access Journals (Sweden)

    AH Mirhashemi

    2012-01-01

    Full Text Available Objective: An ideal orthodontic force system should exert continuous light force. Thus, many efforts have been made to improve the memory characteristics of elastomeric chains. The aim of this study was to compare elastomeric chains (ECs claimed by their manufacturers to offer high memory with traditional ones according to their force-extension diagrams.Materials and Methods: In this in-vitro study, ECs were divided into six groups, each containing 40 pieces of chain, from three brands (American Orthodontics, GAC and Ortho-Technology. Each brand was divided into two groups with respect to their claimed characteristics (with or without memory. Each sample was stretched to twice its original length and kept constant in 37°C distilled water. Force-extension diagrams were drawn by universal testing machine at 0,1,8,24,72 hours and 1, 2, 4-week intervals. Additionally, the amounts of elongation required to deliver 200 g force were calculated. To compare the results, ANOVA and Tukey tests were performed.Results: Force-decay rate was significantly different between traditional and memory chains (p<0.05. For traditional chains, there was a substantial decay in force in the first hour and 30-40% of the force was retained at 4 weeeks. The memory chains demonstrated more constant force and retained 60% of the force. The maximum amount of elongation required to deliver 200 g force belonged to American Orthodontics memory chains (61.9% after 24hr and the minimum to Ortho-Technology ECs (23.4% initially.Conclusion: Memory chains exhibited superior mechanical properties compared to traditional ones. For delivering the same force, memory chains required more elongation. Memory chains of GAC and American Orthodontics showed better characteristics among all chains.

  15. INTERNATIONALIZATION OF BRAZILIAN FRANCHISE CHAINS: A COMPARATIVE STUDY

    OpenAIRE

    Pedro Lucas de Resende Melo; Felipe Mendes Borini; Moacir de Miranda Oliveira Junior; Ronaldo Couto Parente

    2015-01-01

    The primary goal of this paper is to comprehend the fundamental organizational differences between Brazilian franchise chains that only operate in the home market and Brazilian franchise chains that operate internationally. The sample chosen for this study comprehends 96 Brazilian franchises operating in the home market and 67 franchises with international operations; logistic regression was used to analyze data obtained from these sources. Our findings suggest that the development of a brand...

  16. Supply chain integration in the retail sector in South Africa

    OpenAIRE

    2010-01-01

    M.Comm. A positive relationship exists between supply chain integration and the creation of customer value. With globalization increasing, companies need to explore this as a way to stay competitive and deliver exceptional value in an environment where the customer is more informed and more demanding. The main objective of this study was to determine the level of supply chain integration in the selected sample of retailers in South Africa. The findings indicated that high levels of supply ...

  17. The Fast Simulation Chain for ATLAS

    CERN Document Server

    Basalaev, Artem; The ATLAS collaboration

    2016-01-01

    In order to generate the huge number of Monte Carlo events that will be required by the ATLAS experiment over the next several runs, a very fast simulation is critical. Fast detector simulation alone, however, is insufficient: with very high numbers of simultaneous proton-proton collisions expected in Run 3 and beyond, the digitization (detector response emulation) and event reconstruction time quickly become comparable to the time required for detector simulation. The ATLAS Fast Chain simulation has been developed to solve this problem. Modules are implemented for fast simulation, fast digitization, and fast track reconstruction. The application is sufficiently fast -- several orders of magnitude faster than the standard simulation -- that the simultaneous proton-proton collisions can be generated during the simulation job, so Pythia8 also runs concurrently with the rest of the algorithms. The Fast Chain has been built to be extremely modular and flexible, so that each sample can be custom-tailored to match ...

  18. The Fast Simulation Chain for ATLAS

    CERN Document Server

    Basalaev, Artem; The ATLAS collaboration

    2017-01-01

    In order to generate the huge number of Monte Carlo events that will be required by the ATLAS experiment over the next several runs, a very fast simulation is critical. Fast detector simulation alone, however, is insufficient: with very high numbers of simultaneous proton-proton collisions expected in Run 3 and beyond, the digitization (detector response emulation) and event reconstruction time quickly become comparable to the time required for detector simulation. The ATLAS Fast Chain simulation has been developed to solve this problem. Modules are implemented for fast simulation, fast digitization, and fast track reconstruction. The application is sufficiently fast - several orders of magnitude faster than the standard simulation - that the simultaneous proton-proton collisions can be generated during the simulation job, so Pythia8 also runs concurrently with the rest of the algorithms. The Fast Chain has been built to be extremely modular and flexible, so that each sample can be custom-tailored to match th...

  19. Analysing the differences between theoretical and implemented supply chain strategies in selected organisations

    Directory of Open Access Journals (Sweden)

    Danie J. Nel

    2011-11-01

    Full Text Available Organisations can use supply chain strategies to gain a competitive advantage for the supply chain. A competitive advantage can be achieved by means of low cost or by means of differentiation. However, organisations have to implement the correct supply chain strategy. Returns on investment can be compromised if organisations implement an incorrect supply chain strategy. The objective of the article is to analyse the differences between theoretically implied and implemented supply chain strategies within selected organisations. The differences between supply chain strategies implied by literature and those implemented by selected organisations are analysed by determining how the organisations are managing their supply chain drivers. Organisations with lean supply chains should manage their supply chain drivers to achieve efficiency, while organisations with agile supply chains should manage their supply chain drivers with responsiveness towards customers' needs in mind. Non-probability sampling was used to include 13 organisations in the research. Six organisations are implementing different supply chain strategies to what literature principles are suggesting to them based on specific supply chain characteristics. An analysis is done on how these six organisations are managing their supply chain drivers.

  20. SUPPLY CHAIN STRATEGIES IN THE CONTEXT OF AN E-COMMERCE CHAIN (E-CHAIN

    Directory of Open Access Journals (Sweden)

    João Gilberto Mendes do Reis

    2014-05-01

    Full Text Available This paper purpose to explore the relationships between supply chain strategies and product performance in retail e-commerce. In this case, we concern that in current, in order to bear up under competition, organizations have to manage their supply chains so that they meet the needs of their final customers. With this concept in mind, the research presented in this study focuses on establishing the right strategy for supply chains according to their product segment. Thus, after a Literature Review, the paper explain a methodology based in different authors studies. Finally the article focuses on a pratical case in e-commerce retail that describes its application in this field. The research shows that it is possible to use a methodology for classifying supply chains using chain strategies and product features. The use of the right strategy for supply chains will improve the competitive advantage of businesses. One limitation is that the methodology study focuses on only two e-commerce segment; future studies may go further in refining the proposed framework for other segments. The aim of this research is to offer businesses a model for evaluating supply chains, allowing them to improve the performance of their products and services by using the right strategy for supply chains. The classification proposal of this paper presents an original model for classification of supply chains based on different studies on the theme.

  1. Academic Education Chain Operation Model

    NARCIS (Netherlands)

    Ruskov, Petko; Ruskov, Andrey

    2007-01-01

    This paper presents an approach for modelling the educational processes as a value added chain. It is an attempt to use a business approach to interpret and compile existing business and educational processes towards reference models and suggest an Academic Education Chain Operation Model. The model

  2. Spectral Analysis of Markov Chains

    OpenAIRE

    2007-01-01

    The paper deals with the problem of a statistical analysis of Markov chains connected with the spectral density. We present the expressions for the function of spectral density. These expressions may be used to estimate the parameter of the Markov chain.

  3. LEAN SUPPLY CHAIN DESIGN PRINCIPLES

    OpenAIRE

    Kozlov, Aleksandr

    2015-01-01

    The article presents a set of principles, which can guide the design of lean supply chains. The author divides design principles into 3 main categories. The first two sets describe internal production processes while the 3-rd set relates to the entire supply chain.

  4. Negotiations in Supply Chain Management

    DEFF Research Database (Denmark)

    Zachariassen, Frederik

    2008-01-01

    negotiation literature. Subsequently, an empirical case study is presented, which explicitly aims at exploring the role of negotiations between members of a supply chain. Based on the findings, the paper concludes on specific, normative guidelines for negotiations for improved supply chain competitiveness...

  5. Chain formation of metal atoms

    DEFF Research Database (Denmark)

    Bahn, Sune Rastad; Jacobsen, Karsten Wedel

    2001-01-01

    The possibility of formation of single-atomic chains by manipulation of nanocontacts is studied for a selection of metals (Ni, Pd, Pt, Cu, Ag, Au). Molecular dynamics simulations show that the tendency for chain formation is strongest for Au and Pt. Density functional theory calculations indicate...

  6. Verifying the Hanging Chain Model

    Science.gov (United States)

    Karls, Michael A.

    2013-01-01

    The wave equation with variable tension is a classic partial differential equation that can be used to describe the horizontal displacements of a vertical hanging chain with one end fixed and the other end free to move. Using a web camera and TRACKER software to record displacement data from a vibrating hanging chain, we verify a modified version…

  7. Developing sustainable food supply chains.

    Science.gov (United States)

    Smith, B Gail

    2008-02-27

    This paper reviews the opportunities available for food businesses to encourage consumers to eat healthier and more nutritious diets, to invest in more sustainable manufacturing and distribution systems and to develop procurement systems based on more sustainable forms of agriculture. The important factors in developing more sustainable supply chains are identified as the type of supply chain involved and the individual business attitude to extending responsibility for product quality into social and environmental performance within their own supply chains. Interpersonal trust and working to standards are both important to build more sustainable local and many conserved food supply chains, but inadequate to transform mainstream agriculture and raw material supplies to the manufactured and commodity food markets. Cooperation among food manufacturers, retailers, NGOs, governmental and farmers' organizations is vital in order to raise standards for some supply chains and to enable farmers to adopt more sustainable agricultural practices.

  8. Managing the Global Supply Chain

    DEFF Research Database (Denmark)

    Hsuan, Juliana; Skjøtt-Larsen, Tage; Kinra, Aseem

    edition has been fully updated with recent changes in concepts, technology and practice. Integration and collaboration are keywords in future competition. Firms must be agile and lean at the same time. The book gives an insightful overview of the conceptual foundations of the global supply chain, as......The world today faces global competition. The supply chain is vital part of the globalization process. Presenting a global view of the scope and complexity of supply chain management, this book reflects the rapid change that has taken place within the supply chain and its environment. This new...... well as current examples of best practice of managing supply chains in a global context....

  9. Environmental Management in Product Chains

    DEFF Research Database (Denmark)

    Jørgensen, Michael Søgaard; Forman, Marianne

    2009-01-01

    ). An overview of examples from our own research and from literature of the type and the role of environmental issues and initiatives in product chains (fourth section). A typology for characterizing corporate strategies as part of environmental management in product chains and characterizing those competencies......The chapter aims at giving background to companies, consultants, governmental regulators, NGOs etc. for the analysis and planning of environmental management in specific product chains through: A framework for understanding environmental management in product chains as shaped by the interaction...... between existing resources, norms and values and external pressures for environmental management (second section). A model for the types of corporate network relations that need to be mapped and understood in order to analyze and/or develop environmental management in a product chain (third section...

  10. The Service-Profit Chain

    DEFF Research Database (Denmark)

    Grønholdt, Lars; Martensen, Anne

    2016-01-01

    evidence of the employee-customer-profit chain. As it is possible to estimate the links, we have demonstrated their effect on company profitability. The research findings provide a better understanding of the service-profit chain and may help practitioners in improving company financial performance.......This paper examines the links between employee attitudes, customer loyalty and company profitability. From a conceptual point of view, this employee-customer-profit chain, also known as the service-profit chain, is well founded and generally accepted. But for many companies, it seems difficult...... to demonstrate such links, and several issues must be addressed to uncover the links. To investigate these links empirically, a hotel chain provided data matching employee and customer measures with measures of profitability. We have successfully employed a modeling approach, and the paper reports empirical...

  11. Managing the Global Supply Chain

    DEFF Research Database (Denmark)

    Skjøtt-Larsen, Tage; Schary, Philip B.; Mikkola, Juliana Hsuan

    The world today faces global competition. The supply chain is vital part of the globalization process. Presenting a global view of the scope and complexity of supply chain management, this book reflects the rapid change that has taken place within the supply chain and its environment. This new...... edition has been fully updated with recent changes in concepts, technology and practice. Integration and collaboration are keywords in future competition. Firms must be agile and lean at the same time. The book gives an insightful overview of the conceptual foundations of the global supply chain, as...... well as current examples of best practice of managing supply chains in a global context....

  12. Maximum Likelihood TDOA-FDOA Estimator Using Markov Chain Monte Carlo Sampling%基于马尔科夫键蒙特卡洛抽样的最大似然时差-频差联合估计算法

    Institute of Scientific and Technical Information of China (English)

    赵拥军; 赵勇胜; 赵闯

    2016-01-01

    This paper investigates the joint estimation of Time Difference Of Arrival (TDOA) and Frequency Difference Of Arrival (FDOA) in passive location system, where the true value of the reference signal is unknown. A novel Maximum Likelihood (ML) estimator of TDOA and FDOA is constructed, and Markov Chain Monte Carlo (MCMC) method is applied to finding the global maximum of likelihood function by generating the realizations of TDOA and FDOA. Unlike the Cross Ambiguity Function (CAF) algorithm or the Expectation Maximization (EM) algorithm, the proposed algorithm can also estimate the TDOA and FDOA of non-integer multiple of the sampling interval and has no dependence on the initial estimate. The Cramer Rao Lower Bound (CRLB) is also derived. Simulation results show that, the proposed algorithm outperforms the CAF and EM algorithm for different SNR conditions with higher accuracy and lower computational complexity.%该文针对无源定位中参考信号真实值未知的时差-频差联合估计问题,构建了一种新的时差-频差最大似然估计模型,并采用马尔科夫链蒙特卡洛(MCMC)方法求解似然函数的全局极大值,得到时差-频差联合估计.算法通过生成时差-频差样本,并统计样本均值得到估计值,克服了传统互模糊函数(CAF)算法只能得到时域和频域采样间隔整数倍估计值的问题,且不存在期望最大化(EM)等迭代算法的初值依赖和收敛问题.推导了时差-频差联合估计的克拉美罗界,并通过仿真实验表明,算法在不同信噪比条件下的估计精度优于CAF算法和EM算法,且计算复杂度较低.

  13. DNest3: Diffusive Nested Sampling

    Science.gov (United States)

    Brewer, Brendon

    2016-04-01

    DNest3 is a C++ implementation of Diffusive Nested Sampling (ascl:1010.029), a Markov Chain Monte Carlo (MCMC) algorithm for Bayesian Inference and Statistical Mechanics. Relative to older DNest versions, DNest3 has improved performance (in terms of the sampling overhead, likelihood evaluations still dominate in general) and is cleaner code: implementing new models should be easier than it was before. In addition, DNest3 is multi-threaded, so one can run multiple MCMC walkers at the same time, and the results will be combined together.

  14. Digital Microfluidics Sample Analyzer

    Science.gov (United States)

    Pollack, Michael G.; Srinivasan, Vijay; Eckhardt, Allen; Paik, Philip Y.; Sudarsan, Arjun; Shenderov, Alex; Hua, Zhishan; Pamula, Vamsee K.

    2010-01-01

    Three innovations address the needs of the medical world with regard to microfluidic manipulation and testing of physiological samples in ways that can benefit point-of-care needs for patients such as premature infants, for which drawing of blood for continuous tests can be life-threatening in their own right, and for expedited results. A chip with sample injection elements, reservoirs (and waste), droplet formation structures, fluidic pathways, mixing areas, and optical detection sites, was fabricated to test the various components of the microfluidic platform, both individually and in integrated fashion. The droplet control system permits a user to control droplet microactuator system functions, such as droplet operations and detector operations. Also, the programming system allows a user to develop software routines for controlling droplet microactuator system functions, such as droplet operations and detector operations. A chip is incorporated into the system with a controller, a detector, input and output devices, and software. A novel filler fluid formulation is used for the transport of droplets with high protein concentrations. Novel assemblies for detection of photons from an on-chip droplet are present, as well as novel systems for conducting various assays, such as immunoassays and PCR (polymerase chain reaction). The lab-on-a-chip (a.k.a., lab-on-a-printed-circuit board) processes physiological samples and comprises a system for automated, multi-analyte measurements using sub-microliter samples of human serum. The invention also relates to a diagnostic chip and system including the chip that performs many of the routine operations of a central labbased chemistry analyzer, integrating, for example, colorimetric assays (e.g., for proteins), chemiluminescence/fluorescence assays (e.g., for enzymes, electrolytes, and gases), and/or conductometric assays (e.g., for hematocrit on plasma and whole blood) on a single chip platform.

  15. Development of a polymerase chain reaction assay for the detection of pseudorabies virus in clinical samples Desenvolvimento de um ensaio de reação de polimerase em cadeia para detecção do vírus da pseudo-raiva em amostras clínicas

    Directory of Open Access Journals (Sweden)

    Lester J. Pérez

    2009-09-01

    Full Text Available Aujeszky's disease, also known as pseudorabies causes severe economic losses in swine industry and affects the pig husbandry all over the world. The conventional diagnostic procedure is time-consuming and false-negative results may occur in submissions from latently infected animals. The development, optimization and evaluation of a polymerase chain reaction (PCR assay are presented for the diagnosis of pseudorabies infection. This assay was based on the amplification of a highly conserved viral gD gene fragment. PCR products of the expected size were obtained from PRV strains. Non-specific reactions were not observed when a related herpesvirus, other porcine DNA genome viruses and uninfected cells were used to assess PCR. The analytical sensitivity of the test was estimated to be 1.34 TCID50/50 uL. The analysis of tissue homogenate samples from naturally infected animals proved the potential usefulness of the method for a rapid disease diagnosis from field cases. A rapid, sensitive and specific PCR-based diagnostic assay to detect pseudorabies virus in clinical samples is provided.A doença de Aujeszky, também conhecida como pseudo-raiva, causa perdas econômicas graves na indústria suína e afeta a criação de suínos em todo o mundo. O procedimento de diagnóstico convencional é demorado, podendo ocorrer resultados falso-negativos em animais infectados de forma latente. Este estudo apresenta o desenvolvimento, otimização e avaliação de um ensaio de Reação de Polimerase em Cadeia para o diagnóstico da pseudo-raiva. O ensaio baseou-se na amplificação do fragmento genético viral gD altamente conservado. Os produtos da PCR de tamanho esperado foram obtidos a partir de isolados de PRV. Não foram observadas reações inespecíficas quando foram testados herpes-vírus relacionados, outros vírus DNA de suínos e células não infectadas. A sensibilidade analítica estimada do teste foi 1,34 TCID50/50 uL. A análise de homogenatos

  16. Traceability in food supply chain:: Towards the synchronised supply chain

    OpenAIRE

    Lindh, Helena; Skjöldebrand, Christina; Olsson, Annika

    2008-01-01

    Today, food products are distributed all over the world. This has led to advantages in terms of availability but disadvantages in terms of more complex food supply chains. Global food competition is intense and therefore actors have started to adapt their mindsets toward a more holistic view and a supply chain perspective. In addition, food scares during recent years have turned focus towards food safety and traceability in a “farm-to-fork” perspective. The aim of this study is to explore...

  17. Markov chains theory and applications

    CERN Document Server

    Sericola, Bruno

    2013-01-01

    Markov chains are a fundamental class of stochastic processes. They are widely used to solve problems in a large number of domains such as operational research, computer science, communication networks and manufacturing systems. The success of Markov chains is mainly due to their simplicity of use, the large number of available theoretical results and the quality of algorithms developed for the numerical evaluation of many metrics of interest.The author presents the theory of both discrete-time and continuous-time homogeneous Markov chains. He carefully examines the explosion phenomenon, the

  18. Markov Chains and Markov Processes

    OpenAIRE

    2016-01-01

    Markov chain, which was named after Andrew Markov is a mathematical system that transfers a state to another state. Many real world systems contain uncertainty. This study helps us to understand the basic idea of a Markov chain and how is been useful in our daily lives. For some times there had been suspense on distinct predictions and future existences. Also in different games there had been different expectations or results involved. That is the reason why we need Markov chains to predict o...

  19. New sensors and processing chain

    CERN Document Server

    Yaakoubi, Nourdin

    2014-01-01

    A vital tool for researchers, engineers, and students, New Sensors and Processing Chain focuses on the processing chain to set up in order to extract relevant information on various systems. Highlighting the design of new microsensors and various applications, the authors present recent progress in instrumentation and microsystem design, providing insight to the modification of the sensor itself as well as its environment. Various applications illustrate the presentations, which show how a processing chain is organized from the data acquired by a specific sensor.

  20. Influence of chain topology and bond potential on the glass transition of polymer chains simulated with the bond fluctuation model

    Energy Technology Data Exchange (ETDEWEB)

    Freire, J J [Departamento de Ciencias y Tecnicas FisicoquImicas, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia (UNED), Senda del Rey 9, 28040 Madrid (Spain)], E-mail: jfreire@invi.uned.es

    2008-07-16

    The bond fluctuation model with a bond potential has been applied to investigation of the glass transition of linear chains and chains with a regular disposition of small branches. Cooling and subsequent heating curves are obtained for the chain energies and also for the mean acceptance probability of a bead jump. In order to mimic different trends to vitrification, a factor B gauging the strength of the bond potential with respect to the long-range potential (i.e. the intramolecular or intermolecular potential between indirectly bonded beads) has been introduced. (A higher value of B leads to a preference for the highest bond lengths and a higher total energy, implying a greater tendency to vitrify.) Different cases have been considered for linear chains: no long-range potential, no bond potential and several choices for B. Furthermore, two distinct values of B have been considered for alternate bonds in linear chains. In the case of the branched chains, mixed models with different values of B for bonds in the main chain and in the branches have also been investigated. The possible presence of ordering or crystallization has been characterized by calculating the collective light scattering function of the different samples after annealing at a convenient temperature below the onset of the abrupt change in the curves associated with a thermodynamic transition. It is concluded that ordering is inherited more efficiently in the systems with branched chains and also for higher values of B. The branched molecules with the highest B values in the main chain bonds exhibit two distinct transitions in the heating curves, which may be associated with two glass transitions. This behavior has been detected experimentally for chains with relatively long flexible branches.

  1. Salmonella serotype distribution in the Dutch broiler supply chain.

    Science.gov (United States)

    van Asselt, E D; Thissen, J T N M; van der Fels-Klerx, H J

    2009-12-01

    Salmonella serotype distribution can give insight in contamination routes and persistence along a production chain. Therefore, it is important to determine not only Salmonella prevalence but also to specify the serotypes involved at the different stages of the supply chain. For this purpose, data from a national monitoring program in the Netherlands were used to estimate the serotype distribution and to determine whether this distribution differs for the available sampling points in the broiler supply chain. Data covered the period from 2002 to 2005, all slaughterhouses (n = 22), and the following 6 sampling points: departure from hatchery, arrival at the farm, departure from the farm, arrival at the slaughterhouse, departure from the slaughterhouse, and end of processing. Furthermore, retail data for 2005 were used for comparison with slaughterhouse data. The following serotypes were followed throughout the chain: Salmonella Enteritidis, Salmonella Typhimurium, Salmonella Paratyphi B var. Java (Salmonella Java), Salmonella Infantis, Salmonella Virchow, and Salmonella Mbandaka. Results showed that serotype distribution varied significantly throughout the supply chain (P supply chain up to the retail phase.

  2. Bayesian posterior distributions without Markov chains.

    Science.gov (United States)

    Cole, Stephen R; Chu, Haitao; Greenland, Sander; Hamra, Ghassan; Richardson, David B

    2012-03-01

    Bayesian posterior parameter distributions are often simulated using Markov chain Monte Carlo (MCMC) methods. However, MCMC methods are not always necessary and do not help the uninitiated understand Bayesian inference. As a bridge to understanding Bayesian inference, the authors illustrate a transparent rejection sampling method. In example 1, they illustrate rejection sampling using 36 cases and 198 controls from a case-control study (1976-1983) assessing the relation between residential exposure to magnetic fields and the development of childhood cancer. Results from rejection sampling (odds ratio (OR) = 1.69, 95% posterior interval (PI): 0.57, 5.00) were similar to MCMC results (OR = 1.69, 95% PI: 0.58, 4.95) and approximations from data-augmentation priors (OR = 1.74, 95% PI: 0.60, 5.06). In example 2, the authors apply rejection sampling to a cohort study of 315 human immunodeficiency virus seroconverters (1984-1998) to assess the relation between viral load after infection and 5-year incidence of acquired immunodeficiency syndrome, adjusting for (continuous) age at seroconversion and race. In this more complex example, rejection sampling required a notably longer run time than MCMC sampling but remained feasible and again yielded similar results. The transparency of the proposed approach comes at a price of being less broadly applicable than MCMC.

  3. Supply Chain Shipment Pricing Data

    Data.gov (United States)

    US Agency for International Development — This data set provides supply chain health commodity shipment and pricing data. Specifically, the data set identifies Antiretroviral (ARV) and HIV lab shipments to...

  4. Environmental management in product chains

    DEFF Research Database (Denmark)

    Jørgensen, Michael Søgaard; Forman, Marianne; Hansen, Anne Grethe

    of environmental initiatives, a number of recommendations for governmental regulation, which can support the further diffusion of environmental management in product chains, are developed. Furthermore, the report describes a number of theoretical perspectives from sociology of technology, organisation theory...

  5. Bibliometric Application of Markov Chains.

    Science.gov (United States)

    Pao, Miranda Lee; McCreery, Laurie

    1986-01-01

    A rudimentary description of Markov Chains is presented in order to introduce its use to describe and to predict authors' movements among subareas of the discipline of ethnomusicology. Other possible applications are suggested. (Author)

  6. Gravity Waves from Chain Inflation

    CERN Document Server

    Ashoorioon, Amjad

    2008-01-01

    Chain inflation proceeds through a series of first order phase transitions, which can release considerable gravitational waves (GW). We demonstrate that bubble collisions can leave an observable signature for future high-frequency probes of GWs, such as advanced LIGO, LISA and BBO. A "smoking gun" for chain inflation would be wiggles in the spectrum (and consequently in the tensor spectral index) due to the multiple phase transitions. The spectrum could also be distinguished from a single first order phase transition by a small difference in the amplitude at low frequency. A second origin of GWs in chain inflation are tensor modes from quantum fluctuations; these GW can dominate and be observed on large scales. The consistency relation between scalar and tensor modes is different for chain inflation than for standard rolling models and is testable by Cosmic Microwave Background experiments. If inflation happened through a series of rapid tunnelings in the string landscape, future high frequency probes of GW c...

  7. Markov Chains and Chemical Processes

    Science.gov (United States)

    Miller, P. J.

    1972-01-01

    Views as important the relating of abstract ideas of modern mathematics now being taught in the schools to situations encountered in the sciences. Describes use of matrices and Markov chains to study first-order processes. (Author/DF)

  8. The chain re-action

    CERN Multimedia

    2009-01-01

    On 18 March, beam commissioning started in the first ‘link’ of the accelerator chain – LINAC 2. This marks the start of what will be the longest period of beam operations in CERN’s history, with the accelerator complex remaining operational throughout the winter to supply the LHC. The Bulletin finds out what is being done to make sure the whole chain is ready for this historic run.

  9. [The contamination under polymerase chain reaction studies: problems and solutions].

    Science.gov (United States)

    Titov, V N; Ameliushkina, V A; Rozhkova, T A

    2015-01-01

    The study was carried out to determine risk factors of false positive and false negative results under polymerase chain reaction-analysis of clinical material. The samples with high viral load can be the source of false positive results. The contamination with nucleic acids can occur at any section of polymerase chain reaction analysis. The study data permitted to establish that the most sensitive stage is isolation and purification of nucleic acids especially under manual mode of operation. The detection of positive signal in most samples of one setting indicates total contamination. The cases when only several samples are polluted are special challenge. The presence of sample with high concentration of viral nucleic acid and several samples with low concentration in one setting means necessity of repeated analysis beginning with stage of isolation of nucleic acid. The analysis of curves of accumulation of products of amplification, their forms and positioning on chart is the obligatory stage of polymerase chain reaction study in real time regimen. These actions permit to exclude the readouts of false negative testing results to departments. The study conclusions are equipotent for polymerase chain reaction testing of any nucleic acid targets.

  10. "Bullwhip Effect" in Supply Chains

    Directory of Open Access Journals (Sweden)

    Anđelko Ščukanec

    2007-09-01

    Full Text Available The system which connects all the elements between theproducer and the consumer is called the supply chain. This definitionof the supply chain shows its complexity, dynamics anduncertainty. Successful operation of supply chains requires thebest possible coordination of its elements, which obviously indicatesthe utmost importance of the information flow alongthem. The operation of supply chains on the whole has to bemore successful than the operation of their individual elements.It should be noted that such a complex process may give rise toa series of problems, unwanted events, as well as substantial reductionin profits and the level of service. One of such unwantedphenomena which may occur in the supply chain is the"bullwhip effect". This is a possible increase in the diversity oforders which occurs when we move along the elements of thesupply chain (from the customers' orders to the producers' orders.The work analyses the processes within the supply chainsand the occurrence of the bullwhip effect. The main causes ofthe bullwhip effect that we encounter daily in the supply chainshave been clearly defined. The paper also presents the mainnegative consequences of such a disturbance within the supplychains, and provides possible solutions for avoiding the bullwhipeffect.

  11. Reinforcement learning in supply chains.

    Science.gov (United States)

    Valluri, Annapurna; North, Michael J; Macal, Charles M

    2009-10-01

    Effective management of supply chains creates value and can strategically position companies. In practice, human beings have been found to be both surprisingly successful and disappointingly inept at managing supply chains. The related fields of cognitive psychology and artificial intelligence have postulated a variety of potential mechanisms to explain this behavior. One of the leading candidates is reinforcement learning. This paper applies agent-based modeling to investigate the comparative behavioral consequences of three simple reinforcement learning algorithms in a multi-stage supply chain. For the first time, our findings show that the specific algorithm that is employed can have dramatic effects on the results obtained. Reinforcement learning is found to be valuable in multi-stage supply chains with several learning agents, as independent agents can learn to coordinate their behavior. However, learning in multi-stage supply chains using these postulated approaches from cognitive psychology and artificial intelligence take extremely long time periods to achieve stability which raises questions about their ability to explain behavior in real supply chains. The fact that it takes thousands of periods for agents to learn in this simple multi-agent setting provides new evidence that real world decision makers are unlikely to be using strict reinforcement learning in practice.

  12. Sports Nutrition Food Industry Chain Development Research

    OpenAIRE

    Jie Yin

    2015-01-01

    Through the study of Henan sports nutrition food industry chain optimization, the study analyses development advantage and competitive advantage of Henan in sports nutrition food industry chain and existing problems and challenges in Henan sports nutrition food industry chain and at the same time introduces the theory of supply chain management to the development of sports nutrition food industry chain, clearly optimizes countermeasures of sports nutrition food industry chain. Pointing out sp...

  13. A demand chain design for Chinese oatmeal companies

    Directory of Open Access Journals (Sweden)

    Haitao Wen

    2015-04-01

    Full Text Available Purpose: The purpose of this paper is to provide a demand chain design framework for Chinese small and medium enterprises in the oatmeal industry, to help them blaze a new trail in China's oatmeal market. Design/methodology/approach: The approach using in the demand chain design is extended Quality Function Development (QFD, which provides a communication tool so that designers can find a way to integrate customers’ needs into design chain. Findings: This paper illustrates an investigation of oatmeal consumed in China, and the result shows 9 factors influencing consumer’s purchasing decisions mostly. Then use these factors to design the demand chain, and the most important processes and tasks for the enterprises are come out from the fist and the second House of Quality (HOQ, which are the main part of the design. Finally, a demand chain design is completed. Research limitations/implications: It is an application of a demand chain design framework in real Chinese oatmeal market, but the data sample is limited. Consumption surveys should have more data sources with more detailed consumer groups. And the design model needs more real-life examples to verify Practical implications: Since oatmeal products industry develops rapidly in China, oatmeal market is becoming a vast bright market. And due to the low customer satisfaction of Chinese oatmeal market, it is crucial that companies can find a way to design their demand chain, so they can completely meet the needs. Originality/value: A demand chain design framework is presented with being specific to Chinese oatmeal market. It shows a real-life example of demand chain design, and provides the domestic oatmeal companies with an approach to compete in the market.

  14. Demand chain management - The evolution

    Directory of Open Access Journals (Sweden)

    D Ericsson

    2011-06-01

    Full Text Available The concepts of Supply Chain Management (SCM and Demand Chain Management (DCM are among the new and debated topics concerning logistics in the literature. The question considered in this paper is: “Are these concepts needed or will they just add to the confusion?” Lasting business concepts have always evolved in close interaction between business and academia. Different approaches start out in business and they are then, more or less si- multaneously, aligned, integrated, systemised and structured in academia. In this way a terminology (or language is provided that helps in further diffusion of the concepts. There is a lack of consensus on the definition of the concept of SCM. This may be one of the major reasons for the difficulty in advancing the science and measuring the results of implementation in business. Relationships in SCM span from rather loose coalitions to highly structured virtual network integrations. DCM is a highly organised chain in which the key is mutual interdependence and partnership. The purpose is to create a distinctive competence for the chain as a whole that helps to identify and satisfy customer needs and wishes. The classical research concerning vertical marketing systems is very helpful in systemising the rather unstructured discussions in current SCM research. The trend lies in increasing competition between channels rather than between companies, which in turn leads to the creation of channels with a high degree of partnership and mutual interdependence between members. These types of channels are known as organised vertical marketing systems in the classic marketing channel research. The behaviour in these types of channels, as well as the formal and informal structures, roles in the network, power and dependence relations, etc. are well covered topics in the literature. The concept of vertical marketing systems lies behind the definition of demand chains and demand chain management proposed in this paper. A

  15. Evaluation of the Detection of Borrelia burgdorferi DNA in Urine Samples by Polymerase ChainReaction for Diagnosing Lyme Disease%聚合酶链法检测莱姆病患者尿液中伯氏疏螺旋体DNA(附17例报道)

    Institute of Scientific and Technical Information of China (English)

    谭毓绘; 朱沂; 刘勇; 孙荷; 龙江; 牛晓珊; 于鲁海; 莫合塔尔; 阿斯亚; 李红燕

    2012-01-01

    目的:评估聚合酶链反应(PCR)检测莱姆病患者尿液中伯氏疏螺旋体DNA的诊断价值.方法:2004至2006年来自新疆莱姆病自然疫源地临床疑似莱姆病患者17例(均有蜱暴露史和莱姆病临床证据者)和6例以前确诊并治疗后完全恢复的莱姆病患者,共23例为病例组;另选择25例非疑似莱姆病患者为对照组.应用PCR方法检测尿液中伯氏疏螺旋体DNA,采用间接免疫荧光(IFA)检测血清伯氏疏螺旋体抗体.结果:①17例莱姆病患者临床表现呈多系统损害.12/17例(70.59%)为神经型(周围神经病3例,其中1例合并下肢瘀积性皮炎;游走性红斑并发莱姆脑病2例;脑膜脑炎2例;脑炎2例;脑膜炎、脑干炎和脊髓炎各1例);流感样症状2例,其中伴皮疹1例;余心脏型、精神障碍和肝病型各1例.②PCR伯氏疏螺旋体DNA检测阳性17/17例(总阳性率100%).4例血清IFA试验伯氏疏螺旋体抗体阳性.以前确诊并治疗者6例及对照组25例尿PCR伯氏疏螺旋体DNA和血清IFA试验伯氏疏螺旋体抗体均阴性.③10例完成抗生素治疗后3个月复查,9例PCR伯氏疏螺旋体DNA检测阴性(包括3例晚期莱姆病患者),1例2年复查时仍阳性;4例血清伯氏疏螺旋体抗体阳性者复查均阴性.④早期莱姆病多采用几周的抗生素治疗方案.结论:PCR检测尿液中伯氏疏螺旋体DNA是莱姆病一个有价值的诊断工具.%Aim: To estimate the value of detecting Borrelia bugdorferi DNA in urine samples by polymerase chain reaction (PCR) for diagnosing Lyme disease. Methods: 17 patients suspected of Lyme disease come from nature foci and 25 cases with Non-Lyme disease evidence were enrolled from 2004 to 2006. Lyme serology was performed by IF A. Urine samples were examined by PCR. Results: 17 patients with Lyme disease showed sings of multisystem damage. The majority of them, accounting for 70.59%, was nervous system diseases called neuroborreliosis, which were

  16. Observation uncertainty in reversible Markov chains.

    Science.gov (United States)

    Metzner, Philipp; Weber, Marcus; Schütte, Christof

    2010-09-01

    In many applications one is interested in finding a simplified model which captures the essential dynamical behavior of a real life process. If the essential dynamics can be assumed to be (approximately) memoryless then a reasonable choice for a model is a Markov model whose parameters are estimated by means of Bayesian inference from an observed time series. We propose an efficient Monte Carlo Markov chain framework to assess the uncertainty of the Markov model and related observables. The derived Gibbs sampler allows for sampling distributions of transition matrices subject to reversibility and/or sparsity constraints. The performance of the suggested sampling scheme is demonstrated and discussed for a variety of model examples. The uncertainty analysis of functions of the Markov model under investigation is discussed in application to the identification of conformations of the trialanine molecule via Robust Perron Cluster Analysis (PCCA+) .

  17. A traceability study on the Moscato wine chain.

    Science.gov (United States)

    Aceto, Maurizio; Robotti, Elisa; Oddone, Matteo; Baldizzone, Massimo; Bonifacino, Gabriella; Bezzo, Guido; Di Stefano, Rocco; Gosetti, Fabio; Mazzucco, Eleonora; Manfredi, Marcello; Marengo, Emilio

    2013-06-01

    To address the growing interest of consumers for information on the provenance of foodstuffs, the production chain of world renowned Moscato d'Asti white wine has been studied using the distribution of lanthanides as chemical markers. From soil to must, upon every stage of the chain, samples have been taken and analysed with ICP-MS in order to verify whether the original fingerprint of soil is maintained or not along the chain. Results of this traceability study show clearly that lanthanides fingerprint is kept unaltered in the passage soil-grapes-must, while fractionation occurs upon wine clarifying with bentonites. The second part of the work involves a study on 102 samples of Moscato d'Asti musts in order to verify how they reflect the features of the different geographical zones where they come from, and to build a basis to be able to identify possible adulterations performed by addition of foreign musts.

  18. Magnetic Relaxation and Coercivity of Finite-size Single Chain Magnets

    Science.gov (United States)

    Gredig, Thomas; Byrne, Matthew; Vindigni, Alessandro

    2015-03-01

    The magnetic coercivity of hysteresis loops for iron phthalocyanine thin films depends on the iron chain length and the measurement sweep speed below 5 K. The average one-dimensional (1D) iron chain length in samples is controlled during deposition. These 1D iron chains can be tuned over one order of magnitude with the shortest chain having 100 elements. We show that the coercivity strongly increases with the average length of the iron chains, which self-assemble parallel to the substrate surface. Magnetic relaxation and sweep speed data suggest spin dynamics play an important role. Implementing Glauber dynamics with a finite-sized 1D Ising model provides qualitative agreement with experimental data. This suggests that iron phthalocyanine thin films act as single chain magnets and provide a solid test system for tunable finite-sized magnetic chains. This research has been supported with the NSF-DMR 0847552 grant.

  19. Campylobacter Prevalence in the Broiler Supply Chain in the Netherlands

    NARCIS (Netherlands)

    Asselt, van E.D.; Jacobs-Reitsma, W.F.; Brakel, van R.P.; Voet, van der H.; Fels-Klerx, van der H.J.

    2008-01-01

    After a national control program, data on Campylobacter prevalence in the broiler supply chain in the Netherlands were gathered for 3 sampling points: departure of broiler farm and arrival and departure of the slaughterhouse. Monitoring data from this control program for 2002 to 2005 were analyzed t

  20. Exploring Mass Perception with Markov Chain Monte Carlo

    Science.gov (United States)

    Cohen, Andrew L.; Ross, Michael G.

    2009-01-01

    Several previous studies have examined the ability to judge the relative mass of objects in idealized collisions. With a newly developed technique of psychological Markov chain Monte Carlo sampling (A. N. Sanborn & T. L. Griffiths, 2008), this work explores participants; perceptions of different collision mass ratios. The results reveal…

  1. Tunneling magnetoresistance of silicon chains

    Science.gov (United States)

    Matsuura, Yukihito

    2016-05-01

    The tunneling magnetoresistance (TMR) of a silicon chain sandwiched between nickel electrodes was examined by using first-principles density functional theory. The relative orientation of the magnetization in a parallel-alignment (PA) configuration of two nickel electrodes enhanced the current with a bias less than 0.4 V compared with that in an antiparallel-alignment configuration. Consequently, the silicon chain-nickel electrodes yielded good TMR characteristics. In addition, there was polarized spin current in the PA configuration. The spin polarization of sulfur atoms functioning as a linking bridge between the chain and nickel electrode played an important role in the magnetic effects of the electric current. Moreover, the hybridization of the sulfur 3p orbital and σ-conjugated silicon 3p orbital contributed to increasing the total current.

  2. MODELING SUPPLY CHAIN PERFORMANCE VARIABLES

    Directory of Open Access Journals (Sweden)

    Ashish Agarwal

    2005-01-01

    Full Text Available In order to understand the dynamic behavior of the variables that can play a major role in the performance improvement in a supply chain, a System Dynamics-based model is proposed. The model provides an effective framework for analyzing different variables affecting supply chain performance. Among different variables, a causal relationship among different variables has been identified. Variables emanating from performance measures such as gaps in customer satisfaction, cost minimization, lead-time reduction, service level improvement and quality improvement have been identified as goal-seeking loops. The proposed System Dynamics-based model analyzes the affect of dynamic behavior of variables for a period of 10 years on performance of case supply chain in auto business.

  3. Who Manages Our Supply Chains?

    DEFF Research Database (Denmark)

    Flöthmann, Christoph

    to manage the manifold tasks they face on a daily basis. Unfortunately, as globalization has simultaneously increased the complexity of supply chains and the demand for highly qualified personnel, companies are facing a significant undersupply of talent (Cottrill, 2010). Moreover, organizations appear......While managers in traditional management functions focus on developing strong expertise to become “specialists” in their own discipline, supply chain managers are a different species: They have to combine a cross-functional understanding of various business fields and multi-faceted competencies...... to lack understanding of supply chain personnel and how to support their recruitment, succession planning, and training and development (John, 2015). Surprisingly, at the same time, scientific research on that topic is relatively scarce. In response, the overarching purpose of this paper...

  4. Designing the Reverse Supply Chain

    DEFF Research Database (Denmark)

    Gobbi, Chiara

    2011-01-01

    for the reverse supply chain. Design/methodology/approach – In order to identify the relevance of the Fisher model, the model needs to be recast in terms of PRV, which, in this context, is considered the independent variable in the reverse logistics arena. Products defined as innovative in Fisher's taxonomy......Purpose – The purpose of this paper is to explore the impact of the product residual value (PRV) and the loss of value over time of returned products in the reverse supply chain configuration. It also examines whether or not the distinction of Fisher's functional and innovative products holds...... correspond to disposed products with high residual value, whereas functional products correspond to disposed products with low residual value. Furthermore, the PRV and the speed at which returned products lose their value are considered in order to determine the configuration of the reverse supply chain...

  5. Markov chains and mixing times

    CERN Document Server

    Levin, David A; Wilmer, Elizabeth L

    2009-01-01

    This book is an introduction to the modern approach to the theory of Markov chains. The main goal of this approach is to determine the rate of convergence of a Markov chain to the stationary distribution as a function of the size and geometry of the state space. The authors develop the key tools for estimating convergence times, including coupling, strong stationary times, and spectral methods. Whenever possible, probabilistic methods are emphasized. The book includes many examples and provides brief introductions to some central models of statistical mechanics. Also provided are accounts of r

  6. Quantum crystals and spin chains

    Energy Technology Data Exchange (ETDEWEB)

    Dijkgraaf, Robbert [KdV Institute for Mathematics, University of Amsterdam, Plantage Muidergracht 24, 1018 TV Amsterdam (Netherlands); Institute for Theoretical Physics, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands); Orlando, Domenico [Institut de Physique, Universite de Neuchatel, Rue Breguet 1, CH-2000 Neuchatel (Switzerland); Reffert, Susanne [Institute for Theoretical Physics, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands)], E-mail: sreffert@gmail.com

    2009-04-21

    In this article, we discuss the quantum version of the melting crystal corner in one, two, and three dimensions, generalizing the treatment for the quantum dimer model. Using a mapping to spin chains we find that the two-dimensional case (growth of random partitions) is integrable and leads directly to the Hamiltonian of the Heisenberg XXZ ferromagnet. The three-dimensional case of the melting crystal corner is described in terms of a system of coupled XXZ spin chains. We give a conjecture for its mass gap and analyze the system numerically.

  7. Quantum crystals and spin chains

    Science.gov (United States)

    Dijkgraaf, Robbert; Orlando, Domenico; Reffert, Susanne

    2009-04-01

    In this article, we discuss the quantum version of the melting crystal corner in one, two, and three dimensions, generalizing the treatment for the quantum dimer model. Using a mapping to spin chains we find that the two-dimensional case (growth of random partitions) is integrable and leads directly to the Hamiltonian of the Heisenberg XXZ ferromagnet. The three-dimensional case of the melting crystal corner is described in terms of a system of coupled XXZ spin chains. We give a conjecture for its mass gap and analyze the system numerically.

  8. Thermodynamics of Dipolar Chain Systems

    DEFF Research Database (Denmark)

    R. Armstrong, J.; Zinner, Nikolaj Thomas; V. Fedorov, D.

    2012-01-01

    The thermodynamics of a quantum system of layers containing perpendicularly oriented dipolar molecules is studied within an oscillator approximation for both bosonic and fermionic species. The system is assumed to be built from chains with one molecule in each layer. We consider the effects...... numerically. Our findings indicate that thermodynamic observables, such as the heat capacity, can be used to probe the signatures of the intralayer interaction between chains. This should be relevant for near future experiments on polar molecules with strong dipole moments....

  9. Thermal stability in exchange-spring chains of spins

    Science.gov (United States)

    Pellicelli, Raffaele; Solzi, Massimo

    2016-02-01

    Thermal stability and switching behaviour have been compared in pure-hard and soft-hard Heisenberg linear spin chains of the same total length and equal magnetic parameters (except for magnetic anisotropy) with the anisotropy axis and external magnetic field parallel to the chain direction. The zero-temperature energy barriers and finite-temperature transition rates between remanent equilibrium states have been calculated by utilizing the string method and the forward flux sampling (FFS) method, respectively. Depending on the assumed interfaces, the FFS method could in fact fail to correctly sample the characteristic transition paths at interfaces at which these paths have probabilities much lower than those associated with other non-characteristic transition paths. This can especially occur in the case of the asymmetric energy landscapes and multiple asymmetric minimum energy paths (MEPs) of soft-hard systems. Therefore, a proper interface definition is needed in order to deduce the correct transition rates. In particular, we show that the thermal switching of soft-hard chains starting in the soft or in the hard part turns out to occur with an equal rate provided that the interfaces of the FFS method are defined on the basis of the corresponding zero-temperature MEPs. The thermal stability of a soft-hard chain in the remanent equilibrium state could be to some extent lower with respect to that of a pure-hard chain, due to the shorter hard-part length crossed by the domain wall formed in the chain and also to the related slightly smaller energy barrier. However, its switching field at zero temperature is verified to be widely lower than that of the pure-hard chain. Analytical expressions of switching fields and energy barriers have been deduced in various cases.

  10. Reseach of Supply Chain Modeling Technology

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The supply chain modeling technology is research. Firstly, the concept of supply chain and supply chain management is introduced. Secondly, enterprise-modeling methods, such as CIM-OSA, GIM-GRAI, PERA and ARIS, are analyzed and compared. The supply chain modeling technology is studied. Then the ARIS-based supply chain modeling method is proposed and the supply chain operation reference model is set up. Finally, the applications of ARIS-based supply chain modeling method in Shanghai Turbine Generator Co. Ltd. (STGC) is described in detail.

  11. Population Education in Science: Some Sample Lessons.

    Science.gov (United States)

    United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and Oceania.

    This science teacher's manual contains nine sample population education lessons adapted from materials produced in several countries in Asia and Oceania. Activities are designed for lower primary through high school students. Included are class discussions, small group activities, and a role-playing situation. Food chains, human dependence upon…

  12. Adapting transport modes to supply chains classified by the uncertainty supply chain model: A case study at Manaus Industrial Pole

    Directory of Open Access Journals (Sweden)

    Fabiana Lucena Oliveira

    2017-01-01

    Full Text Available This paper discusses transport modes supporting Uncertainty Supply Chain Model (USCM in the case of Manaus Industrial Pole (PIM, an industrial cluster in the Brazilian Amazon that hosts six hundred factories with diverse logistics and supply chain managerial strategies. USCM (Lee, 2002; Fisher, 1997develops a dot matrix classification of the supply chains considering several attributes (e.g., agility, cost, security, responsiveness and argues that emergent economies industrial clusters, in the effort to keep attractiveness for technological frontier firms, need to adapt supply chain strategies according to USCM attributes. The paper takes a further step, discussing which transport modes are suitable to each supply chain classified at the USCM in PIM´s case. The research´s methods covered the use of PIM´s statistical official database (secondary data, interviews with the main logistical services providers of PIM and phone survey with a sample of firms (primary data. Findings confirm the theoretical argument that different supply chains will demand different transport modes running at the same time in the same industrial cluster (Oliveira, 2009. In the case of PIM, this implies investments on port and airport infrastructure and a strategic focus on air transport mode, due to (1 short life cycle of products, (2 distance from suppliers, (3 quick response to demand and (4 the fact that even PIM´s standard products use, in average, forty per cent of air transport at inbound logistics.

  13. Supply chain management and optimization in manufacturing

    CERN Document Server

    Pirim, Harun; Yilbas, Bekir Sami

    2014-01-01

    This book introduces general supply chain terminology particularly for novice readers, state of the art supply chain management and optimization issues and problems in manufacturing. The book provides insights for making supply chain decisions, planning and scheduling through supply chain network. It introduces optimization problems, i.e. transportation of raw materials, products and location, inventory of plants, warehouses and retailers, faced throughout the supply chain network.

  14. Precise low cost chain gears for heliostats

    Science.gov (United States)

    Liedke, Phillip; Lewandowski, Arkadiusz; Pfahl, Andreas; Hölle, Erwin

    2016-05-01

    This work investigates the potential of chain gears as precise and low cost driving systems for rim drive heliostats. After explaining chain gear basics the polygon effect and chain lengthening are investigated. The polygon effect could be measured by a heliostat with chain rim gear and the chain lengthening with an accordant test set up. Two gear stages are scope of this work: a rim gear and an intermediate gear. Dimensioning, pretensioning and designing for both stages are explained.

  15. Social Value Propagation for Supply Chain Formation

    OpenAIRE

    2013-01-01

    Supply Chain Formation is the process of determining the participants in a supply chain, who will exchange what with whom, and the terms of the exchanges. Decentralized supply chain formation appears as a highly intricate task because agents only possess local information, have limited knowledge about the capabilities of other agents, and prefer to preserve privacy. State-of-the-art decentralized supply chain formation approaches can either: (i) #12;find supply chains of high value at the ...

  16. Information system for the supply chain management

    OpenAIRE

    Delia Adriana Marincas

    2008-01-01

    Supply chain management SCM is the integration and management of supply chain organizations and activities through collaboration, effective business processes and high levels of information sharing. The supply chain concept has become a concern due to global competition and increasing customer demand for value. Thus, the information must be available in real time across the supply chain and this can not be achieved without an integrated software system for supply chain management. Supply chai...

  17. OVERVIEW OF CHINESE CHAIN CATERING MARKET

    OpenAIRE

    2012-01-01

    This thesis is a market overview for chain catering business situation in China. Chinese chain catering market is developing rapidly in recent years, it is a business where everybody can become a customer, but the business is highly competitive. The subject of this thesis is to give an overview of the market situation and strategies for market expansion of Chinese chain catering industry. It contains knowledge of chain management and introduction of Chinese chain catering ma...

  18. SUPPLY CHAIN MANAGEMENT – KEY FACTORS

    OpenAIRE

    Magdalena Daniela DINU

    2014-01-01

    This paper exposes Supply Chain Management by its key factors. Briefly, where the Supply Chain Management is treated as strategic part of a company then maintaining both control and influence throughout the entire supply chain are key factors and critical to success. On the other hand, finding the right partner to manage the non-strategic Supply Chains would be another key factor too. To define the most important key factors within Supply Chain Management means a deeply understanding of bot...

  19. Research on Integrated Green Supply Chain Management

    Institute of Scientific and Technical Information of China (English)

    DENG Lei; WANG Xu

    2006-01-01

    On the basis of the analyzing product life cycle and value chain management in green supply chain, integrated green supply chain is put forward and constructed which involve lean production, agile manufacturing and green supply chain. This integrated structure provides an effective method for resolving some questions such as cost, market, environment, etc. in enterprise. A case study is presented at the end of paper to demonstrate how integrated supply chain implemented successfully in enterprise.

  20. A Markov Chain Estimator of Multivariate Volatility from High Frequency Data

    DEFF Research Database (Denmark)

    Hansen, Peter Reinhard; Horel, Guillaume; Lunde, Asger;

    We introduce a multivariate estimator of financial volatility that is based on the theory of Markov chains. The Markov chain framework takes advantage of the discreteness of high-frequency returns. We study the finite sample properties of the estimation in a simulation study and apply...

  1. Quadratic Variation by Markov Chains

    DEFF Research Database (Denmark)

    Hansen, Peter Reinhard; Horel, Guillaume

    We introduce a novel estimator of the quadratic variation that is based on the the- ory of Markov chains. The estimator is motivated by some general results concerning filtering contaminated semimartingales. Specifically, we show that filtering can in prin- ciple remove the effects of market...

  2. Spin Chains and Gustafson's Integrals

    CERN Document Server

    Derkachov, S E

    2016-01-01

    The Gustafson's integrals are the multidimensional generalization of the classical Mellin--Barnes integrals. We show that some of these integrals arise from relations between matrix elements in the Sklyanin's representation of Separated Variables in the spin chain models. We also present several new integrals.

  3. Concurrent Product & Supply Chain Creation

    DEFF Research Database (Denmark)

    Gubi, Ebbe

    it is a structural premise. We also know that logistics costs generally are estimated 15-20% of total product costs. Accordingly, it stands to reason that a company can reduce costs, and thereby gain an edge on its competitors, by tailoring the supply chain in question to an individual product or product family; i...

  4. Replicator dynamics in value chains

    DEFF Research Database (Denmark)

    Cantner, Uwe; Savin, Ivan; Vannuccini, Simone

    2016-01-01

    dynamics may revert its effect. In these regressive developments of market selection, firms with low fitness expand because of being integrated with highly fit partners, and the other way around; ii) allowing partner's switching within a value chain illustrates that periods of instability in the early...

  5. Maximal right smooth extension chains

    CERN Document Server

    Huang, Yun Bao

    2010-01-01

    If $w=u\\alpha$ for $\\alpha\\in \\Sigma=\\{1,2\\}$ and $u\\in \\Sigma^*$, then $w$ is said to be a \\textit{simple right extension}of $u$ and denoted by $u\\prec w$. Let $k$ be a positive integer and $P^k(\\epsilon)$ denote the set of all $C^\\infty$-words of height $k$. Set $u_{1},\\,u_{2},..., u_{m}\\in P^{k}(\\epsilon)$, if $u_{1}\\prec u_{2}\\prec ...\\prec u_{m}$ and there is no element $v$ of $P^{k}(\\epsilon)$ such that $v\\prec u_{1}\\text{or} u_{m}\\prec v$, then $u_{1}\\prec u_{2}\\prec...\\prec u_{m}$ is said to be a \\textit{maximal right smooth extension (MRSE) chains}of height $k$. In this paper, we show that \\textit{MRSE} chains of height $k$ constitutes a partition of smooth words of height $k$ and give the formula of the number of \\textit{MRSE} chains of height $k$ for each positive integer $k$. Moreover, since there exist the minimal height $h_1$ and maximal height $h_2$ of smooth words of length $n$ for each positive integer $n$, we find that \\textit{MRSE} chains of heights $h_1-1$ and $h_2+1$ are good candidates t...

  6. Towards biotracing in food chains

    DEFF Research Database (Denmark)

    Hoorfar, Jeffrey; Wagner, Martin; Jordan, Kieran

    2011-01-01

    , and 21 cross-disciplinary work packages that cover tracing and tracking of contamination in feed, meat and dairy chains, in addition to accidental and deliberate contamination of bottled water. The BIOTRACER Consortium consists of 46 partners, including Europe's largest food/feed industries, several SMEs...

  7. Supply Chain Simulation : A Survey

    NARCIS (Netherlands)

    Kleijnen, J.P.C.

    2003-01-01

    This paper provides a survey of simulation in supply chain management.It reviews four types of simulation, namely spreadsheet simulation, system dynamics, discreteevent simulation, and business games.Which simulation type should be applied, depends on the type of managerial question to be answered b

  8. Labour in Global Value Chains

    DEFF Research Database (Denmark)

    Lund-Thomsen, Peter; Nadvi, Khalid; Chan, Anita

    2012-01-01

    A critical challenge facing developing country producers is to meet international labour standards and codes of conduct in order to engage in global value chains. Evidence of gains for workers from compliance with such standards and codes remains limited and patchy. This article focuses on the gl......A critical challenge facing developing country producers is to meet international labour standards and codes of conduct in order to engage in global value chains. Evidence of gains for workers from compliance with such standards and codes remains limited and patchy. This article focuses...... on the global football industry, a sector dominated by leading global brands that manage dispersed global value chains. It assesses the working conditions for football stitchers engaged in different forms of work organization, factories, stitching centres and home-based settings in Pakistan, India and China...... production contexts that influence work conditions. In doing so, it argues that current debates on the role of labour in global value chains have to go beyond a narrow focus on labour standards and corporate social responsibility compliance and engage with economic, technological and social upgrading...

  9. Efficient FPGA Hardware Reuse in a Multiplierless Decimation Chain

    Directory of Open Access Journals (Sweden)

    Guillermo A. Jaquenod

    2014-01-01

    Full Text Available In digital communications, an usual reception chain requires many stages of digital signal processing for filtering and sample rate reduction. For satellite on board applications, this need is hardly constrained by the very limited hardware resources available in space qualified FPGAs. This short paper focuses on the implementation of a dual chain of 14 stages of cascaded half band filters plus 2 : 1 decimators for complex signals (in-phase and quadrature with minimal hardware resources, using a small portion of an UT6325 Aeroflex FPGA, as a part of a receiver designed for a low data rate command and telemetry channel.

  10. Supply chain challenges. building relationships.

    Science.gov (United States)

    Beth, Scott; Burt, David N; Copacino, William; Gopal, Chris; Lee, Hau L; Lynch, Robert Porter; Morris, Sandra

    2003-07-01

    Supply chain management is all about software and systems, right? Put in the best technology, sit back, and watch as your processes run smoothly and the savings roll in? Apparently not. When HBR convened a panel of leading thinkers in the field of supply chain management, technology was not top of mind. People and relationships were the dominant issues of the day. The opportunities and problems created by globalization, for example, are requiring companies to establish relationships with new types of suppliers. The ever-present pressure for speed and cost containment is making it even more important to break down stubbornly high internal barriers and establish more effective cross-functional relationships. The costs of failure have never been higher. The leading supply chain performers are applying new technology, new innovations, and process thinking to far greater advantage than the laggards, reaping tremendous gains in all the variables that affect shareholder value: cost, customer service, asset productivity, and revenue generation. And the gap between the leaders and the losers is growing in almost every industry. This roundtable gathered many of the leading thinkers and doers in the field of supply chain management, including practitioners Scott Beth of Intuit, Sandra Morris of Intel, and Chris Gopal of Unisys. David Burt of the University of San Diego and Stanford's Hau Lee bring the latest research from academia. Accenture's William Copacino and the Warren Company's Robert Porter Lynch offer the consultant's perspectives. Together, they take a wide-ranging view of such topics as developing talent, the role of the chief executive, and the latest technologies, exploring both the tactical and the strategic in the current state of supply chain management.

  11. Improved Sampling for Diagnostic Reasoning in Bayesian Networks

    OpenAIRE

    Hulme, Mark

    2013-01-01

    Bayesian networks offer great potential for use in automating large scale diagnostic reasoning tasks. Gibbs sampling is the main technique used to perform diagnostic reasoning in large richly interconnected Bayesian networks. Unfortunately Gibbs sampling can take an excessive time to generate a representative sample. In this paper we describe and test a number of heuristic strategies for improving sampling in noisy-or Bayesian networks. The strategies include Monte Carlo Markov chain sampling...

  12. Supply Chain Management Practices in Toy Supply Chains

    DEFF Research Database (Denmark)

    Wong, Chee Yew; Arlbjørn, Jan Stentoft; Johansen, John

    2005-01-01

    qualitative semi-structured interviews and questionnaire with 11 main European toy retailers. Findings - The study concludes that there are three main SCM practices for toy retailers in terms of ordering behaviours (one-off, JIT, and mixed model), and one dominated SCM practice for toy manufacturers...... are required for such extreme volatility and seasonality are proposed. Originality/value - It reveals actual SCM practices in a volatile and seasonal supply chain, such that theoretical and practical gaps are identified. Also, it proposes a model to match manufacturing SCM-practices with retailer SCM-practices.......Purpose - Innovative products usually experience highly unpredictable and variable demand. This is especially valid for the volatile and seasonal toy industry, which produces high obsolete inventory, lost sales and markdown. In such a volatile industry, what supply chain management (SCM) practices...

  13. Supply Chain Management Performance in Tourism. Continental Hotels Chain Case

    OpenAIRE

    Gabriela Ţigu; Bogdan Călăreţu

    2013-01-01

    With its origins in logistics, Supply Chain Management (SCM) concept is covering all managerial aspects of the flow of materials and information from source to customer, across the entire range of materials handling and movement functions, and throughout an organization and its supply channels. In tourism, these issues relate to the whole process of providing tourism services from sourcing of raw materials, products or different services) to supply and distribution, and SCM performance can ul...

  14. Random sampling of lattice paths with constraints, via transportation

    CERN Document Server

    Gerin, Lucas

    2010-01-01

    We discuss a Monte Carlo Markov Chain (MCMC) procedure for the random sampling of some one-dimensional lattice paths with constraints, for various constraints. We show that an approach inspired by optimal transport allows us to bound efficiently the mixing time of the associated Markov chain. The algorithm is robust and easy to implement, and samples an "almost" uniform path of length $n$ in $n^{3+\\eps}$ steps. This bound makes use of a certain contraction property of the Markov chain, and is also used to derive a bound for the running time of Propp-Wilson's CFTP algorithm.

  15. chains

    Directory of Open Access Journals (Sweden)

    Gabriel Pérez-Salas

    2015-01-01

    Full Text Available Las barreras y aranceles al comercio exterior han disminuido significativamente gracias a los acuerdos multilaterales y los mecanismos de integración entre las naciones. Los costos logísticos representan una proporción significativa del precio final de los artículos, especialmente de los commodities. Por esta razón, minimizar los costos logísticos es un desafío importante para las naciones para fomentar la competitividad del comercio exterior y en particular para aprovechar la renta de los recursos naturales. En este artículo, proponemos un marco de referencia integral para la medición de costos logísticos, enfocado en determinar los extra-costos que resultan por procedimientos ineficientes y la falta de políticas públicas y regulaciones de las entidades públicas. Estos elementos no han sido considerados en la literatura, y este artículo aborda esta brecha. Como caso de estudio, presentamos la aplicación del marco de referencia para estimar los extra-costos en algunas cadenas logísticas de recursos naturales en Bolivia. Se presenta una discusión de los resultados encontrados, así como recomendaciones para trabajo futuro.

  16. INTERNATIONALIZATION OF BRAZILIAN FRANCHISE CHAINS: A COMPARATIVE STUDY

    Directory of Open Access Journals (Sweden)

    Pedro Lucas de Resende Melo

    2015-04-01

    Full Text Available The primary goal of this paper is to comprehend the fundamental organizational differences between Brazilian franchise chains that only operate in the home market and Brazilian franchise chains that operate internationally. The sample chosen for this study comprehends 96 Brazilian franchises operating in the home market and 67 franchises with international operations; logistic regression was used to analyze data obtained from these sources. Our findings suggest that the development of a brand in international operations can be strategic for certain Brazilian franchise chains; this seems to be, however, a scarce resource for many franchises and it could be developed through international operations. With regard to the fees charged, the outcomes demonstrate that Brazilian franchises with international operations tend to charge lower fees from its franchisees to install new units. Regarding the monitoring and control of franchises, there is evidence that the monitoring capability is one of the determining factors in the development of Brazilian franchises international operations.

  17. Actinobaculum suis Detection Using Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Cristina Román Amigo

    2012-01-01

    Full Text Available Actinobaculum suis is an important agent related to urinary infection in swine females. Due to its fastidious growth characteristics, the isolation of this anaerobic bacterium is difficult, thus impairing the estimation of its prevalence. The purpose of this study was to develop and test a polymerase chain reaction (PCR for the detection and identification of A. suis and then compare these results with traditional isolation methods. Bacterial isolation and PCR were performed on one hundred and ninety-two urine samples from sows and forty-five preputial swabs from boars. The results indicate that this PCR was specific for A. suis, presenting a detection limit between 1.0×101 CFU/mL and 1.0×102 CFU/mL. A. suis frequencies, as measured by PCR, were 8.9% (17/192 in sow urine samples and 82.2% (37/45 in preputial swabs. Assessed using conventional culturing techniques, none of the urine samples were positive for A. suis; however, A. suis was detected in 31.1% (14/45 of the swabs. This PCR technique was shown to be an efficient method for the detection of A. suis in urine and preputial swabs.

  18. The fishing industry - toward supply chain modelling

    DEFF Research Database (Denmark)

    Jensen, Toke Koldborg; Nielsen, Jette; Larsen, Erling P.

    Mathematical models for simulating and optimizing supply chain aspects such as distribution planning and optimal use of raw materials are widely used. However, modelling based on a holistic chain view is less studied, and food-related aspects such as quality and shelf life issues enforce additional...... requirements onto the chains. In this paper, we consider the supply chain structure of the Danish fishing industry and illustrate the potential of using mathematical models to identify quality and value-adding activities. This is a first step toward innovative supply chain modelling aimed to identify benefits...... for actors along chains in the fishing industry....

  19. The chain relation in sofic subshifts

    CERN Document Server

    Kazda, Alexandr

    2009-01-01

    The paper gives a characterisation of the chain relation of a sofic subshift. Every sofic subshift $\\Sigma$ can be described by a labelled graph $G$. Factorising $G$ in a suitable way we obtain the graph $G/_\\approx$ that offers insight into some properties of the original subshift. Using $G/_\\approx$ we describe first the chain relation in $\\Sigma$, then characterise chain-transitive sofic subshifts, chain-mixing sofic subshifts and finally the attractors of the subshift dynamic system. At the end we present (straightforward) algorithms deciding chain-transitivity and chain-mixing properties of a sofic subshift and listing all the attractors of the subshift system.

  20. Detection of adenovirus hexon sequence in a cat by polymerase chain reaction(short communication)

    NARCIS (Netherlands)

    Horzinek, M.C.; Lakatos, B.; Farkas, J.; Egberink, H.F.; Vennema, H.; Benko, M.

    1999-01-01

    Adenoviral nucleic acid was detected by polymerase chain reaction (PCR) in pharyngeal and rectal swab samples of a cat seropositive for adenovirus and suffering from transient hepatic failure. The samples were taken at a one-year interval, and both faecal samples as well as the second pharyngeal sam

  1. The Impact of Risks in Supply Chain on Organizational Performances: Evidence from Romania

    Directory of Open Access Journals (Sweden)

    Gyula Laszlo FLORIAN

    2014-12-01

    Full Text Available The proposed empirical research uses a national sample of 64 Romanian companies from various industries to document the relationship between organizational performances and risks in the context of Romanian supply chains. Empirical findings show that a supply chain risk management strategy successfully mitigates the negative consequences of risks. Our research underlines the changes necessary to maximize the benefits of supply chain integration. To extend the knowledge in this area our research is interdisciplinary, using a structural approach to model the determinants of organizational performances in supply chains and to measure the complex relationships among risks in supply chains and different facets of organizational performances in the context of Romanian supply chains.

  2. VALUE CHAINS IN EMERGING MARKETS

    Directory of Open Access Journals (Sweden)

    Abdyramanova, Z.

    2016-11-01

    Full Text Available The textiles sector is one of the main industry sectors in Kyrgyzstan in terms of output, employment and increasingly exports. Textile clusters are developing and patterns in cluster formations are emerging that reflect the differing economic conditions of the regions, demonstrating particular influences on the value chain. These differences are both depicted in the two regions of Kyrgyzstan-south and north. In the north of the Republic the infrastructure is more developed, there is greater facility to access international markets (exports. In the south the infrastructure is less developed, and garment producers in the region serve mainly local niche and near-neighbour markets. The research objective is to assess the key drivers of the value chain and profitability in the textiles sector in Kyrgyzstan, by comparing the garment sewing sector in the two contrasting regions of south and north Kyrgyzstan.

  3. Supply Chain Reorganization and Coordination

    Institute of Scientific and Technical Information of China (English)

    WANG Feng-bin

    2001-01-01

    Three generic forms of governance--hierarchy, hybrid and market are proposed in the newinstitutional economics, giving an abstract description of alternative coordination and control mechanisms forgeneral use. While this theory is known as far away from being operational and specified, a few researchersin the management and organization area are trying to extend Galbraith and/or Mintzberg's organizationaldesign theories into the application of logistical coordination for obtaining a smooth flow of products along thesupply chain within and without the focal organization. In this paper, we present an explorative case study onthe design of various organizational architectures of logistics activities and their relevant coordinationmechanisms, especially internal and external contracts as one new kind of hybrid mechanisms forcoordinating effective supply chains.

  4. Mobilizing Sustainable Bioenergy Supply Chains

    OpenAIRE

    Baxter, David; Cowie, Annette; BERNDES Goran; Junginger, Martin; MCMILLAN James D; Saddler, J N; VAN REE Rene

    2015-01-01

    Analysis of the five globally significant supply chains conducted by IEA Bioenergy inter-Task teams – boreal and temperate forests, agricultural crop residues, biogas, lignocellulosic crops, and cultivated grasslands and pastures in Brazil – has confirmed that feedstocks produced using logistically efficient production systems can be mobilized to make significant contributions to achieving global targets for bioenergy. However, the very significant challenges identified in this report indi...

  5. China's Role in Purchasing Chain

    Institute of Scientific and Technical Information of China (English)

    Eva; Alice

    2007-01-01

    @@ In current world market,"Made-in-China"often means good price and competitive quality.In terms of China's trade pattern,more than half of Chinese exporting products belong to processing trade industry according to the demands and requirements of international orders.On the purchasing chain,China is learning from its international partners.Safety and quality always tops all issues.

  6. The dynamic chain event graph

    OpenAIRE

    2015-01-01

    In this paper we develop a formal dynamic version of Chain Event Graphs (CEGs), a particularly expressive family of discrete graphical models. We demonstrate how this class links to semi-Markov models and provides a convenient generalization of the Dynamic Bayesian Network (DBN). In particular we develop a repeating time-slice Dynamic CEG providing a useful and simpler model in this family. We demonstrate how the Dynamic CEG’s graphical formulation exhibits asymmetric conditional independence...

  7. On Markov Chains and Filtrations

    OpenAIRE

    1997-01-01

    In this paper we rederive some well known results for continuous time Markov processes that live on a finite state space.Martingale techniques are used throughout the paper. Special attention is paid to the construction of a continuous timeMarkov process, when we start from a discrete time Markov chain. The Markov property here holds with respect tofiltrations that need not be minimal.

  8. Modeling Continuous IED Supply Chains

    Science.gov (United States)

    2014-03-27

    criminals, pirates, drug traffickers and terrorists. Moreover, JIEDDO has pointed out the spread of IED use to places such as Thailand and Norway. U.S... human networks that place IEDs. Dekker categorizes two main human aspects of IED placement. The first is motivation which 8 affects the number of...methods provided in this thesis and apply them to combat other threats. For example, drug trafficking supply chains. IED and drug trafficking supply

  9. Supply-Chain Risk Analysis

    Science.gov (United States)

    2016-06-07

    Classic Buffer Overflow 1. http://cwe.mitre.org/top25/ SANS (SysAdmin, Audit, Network , Security ) Institute 23 Veracode: State of Software Security ...Approved for public release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17...supply-chain risks. He participated in the design and development of the DHS Build- Security -In Web site and continues to contribute articles to it

  10. Synchronization Algorithms on Oriented Chains

    Directory of Open Access Journals (Sweden)

    D. Bein

    2008-01-01

    Full Text Available We present a space- and time-optimal self-stabilizing algorithm, SSDS, for a given synchronization problem on asynchronous oriented chains. SSDS is uniform and works under the unfair distributed daemon. From SSDS we derive solutions for the local mutual exclusion and distributed sorting. Algorithm SSDS can also be used to obtain optimal space solutions for other problems such as broadcasting, leader election, and mutual exclusion.

  11. Supply Chain Performance Evaluation: Trends and Challenges

    Directory of Open Access Journals (Sweden)

    Ezutah U. Olugu

    2009-01-01

    Full Text Available Problem statement: In today’s manufacturing world, globalization policies and rejuvenation have created a more intensive competition amongst manufacturers. On the other hand, manufacturers have turned to the option of adopting innovative technologies, process re-engineering and strategies such as efficient supply chain management to achieve a sustainable competitive advantage. Effective supply chain performance measurement has been identified as a key issue towards efficient supply chain management. To explore the extent of research in supply chain performance measurement and establish the gap in knowledge in supply chain performance measurement using fuzzy logic operation. Approach: Literatures in the area of supply chain performance measurement had been extensively reviewed. Both traditional and fuzzy logic approaches to supply chain performance measurement were scrutinized. Further scrutiny was carried out to establish potential research areas in the application of fuzzy logic operations in supply chain performance measurement. Results: The supply chain performance measurement using fuzzy logic operation was identified as a new direction in measuring the uncertainty and ambiguity surrounding supply chain performance measurement. Direction for further studies in the application of fuzzy logic operation in supply chain management and its performance measurement were also identified. Conclusion: Result of this study implied that there is still a gap in knowledge in the area of supply chain performance measurement. This new direction of studies involved extending the existing supply chains to incorporate product recovery after the useful life.

  12. ARCHITECTURAL CONCEPTS FOR VALUE CHAINS

    Directory of Open Access Journals (Sweden)

    A.C. Janse van Rensburg

    2012-01-01

    Full Text Available

    ENGLISH ABSTRACT:The Porter Value Chain has been widely adopted by the business community as a mechanism to understand and comprehend complexity in business environments, with the ultimate goal of structuring the business to maximize its competitive advantage. Implementing the Value Chain is not easy: a number of organizations can testify to their failure to derive any benefits at all from this concept. To overcome this problem, an approach is presented to assist the organization in creating a Value Chain reference model within the broader context of the organization’s enterprise architecture.

    AFRIKAANSE OPSOMMING: Die “Porter Waardeketting” is ’n algemene aanvaarde praktyk wat deur maatskappye gebruik word om die kompleksiteit van besigheidsomgewings mee te verstaan. Die uiteindelike doel hiervan is om die besigheid se mededings voordele te optimiseer. Om die Waardekettingkonsep te implementeer, is nie ’n maklike taak nie – verskeie organisasies kan getuig van mislukte implementeringspogings. Hierdie artikel beskryf ’n benadering beskryf wat gebruik kan word om die organisasie te help om ’n Waardekettingmodel te skep in die bree konteks van die organisasie se besigheidsargitektuur.

  13. Towards biotracing in food chains.

    Science.gov (United States)

    Hoorfar, Jeffrey; Wagner, Martin; Jordan, Kieran; Bouquin, Solveig Lind; Skiby, Jeffrey

    2011-03-01

    Biotracing is tracing (backward)/tracking (forward) biological contamination in the food/feed chain. Advances in detection technologies, improvements in molecular marker identification, clearer understanding of pathogenicity markers, improved modelling methodologies and, more importantly, the integration of these disciplines will lead to better capability in full-chain tracing and tracking biological contaminations (biotracing). The advantages of improved biotraceability are faster intervention, limited recalls and more targeted remedial action. The project is not dealing with risk assessments but developing tools that can be used in "second-generation" risk assessments involving quantitative microbiology. This concept is the core activity of BIOTRACER, which is an Integrated Project (2007-2011) funded by the EU 6th Framework Programme. The research in biotracing is organised into five Research Areas, and 21 cross-disciplinary work packages that cover tracing and tracking of contamination in feed, meat and dairy chains, in addition to accidental and deliberate contamination of bottled water. The BIOTRACER Consortium consists of 46 partners, including Europe's largest food/feed industries, several SMEs, and relevant International Cooperation (INCO) countries. The Consortium includes experts in predictive microbiology, database developers, software companies, risk assessors, risk managers, system biologists, food and molecular microbiologists, legislative officers, standardization and validation members and food retailers. The outcomes will ensure a more reliable and rapid response to a microbial contamination event.

  14. Monte Carlo properties of the hydrocarbon chains of phospholipid molecules

    Science.gov (United States)

    Zhurkin, D. V.; Rabinovich, A. L.

    2015-02-01

    Properties of 65 chain hydrocarbon molecules in the unperturbed state are investigated using the Monte Carlo method at temperatures of 293, 303, and 313 K. Chains with the general structure CH3-(CH2) a -(CH=CH-CH2) d -(CH2) b -CH3 are considered. The number of carbon atoms in a skeleton N = 16, 18, 20, and 22; the number of cis-double bonds d = 0, 1, ..., 6. Conformations are generated with continuous varying of the angles of internal rotation around simple C-C bonds in the range of 0°-360°, the interdependence of each three angles along the chain is allowed for, and essential sampling is performed. Different properties of molecules are considered: the average maximum projections of hydrocarbon chains on their main axes of inertia, average squares of the radii of inertia, and relative fluctuations in the squares of the radii of inertia. The dependence of the calculated characteristics on the structural parameters of the chains is investigated.

  15. Sterilizing elastomeric chains without losing mechanical properties. Is it possible?

    Science.gov (United States)

    Pithon, Matheus Melo; Ferraz, Caio Souza; Rosa, Francine Cristina Silva; Rosa, Luciano Pereira

    2015-01-01

    OBJECTIVE: To investigate the effects of different sterilization/disinfection methods on the mechanical properties of orthodontic elastomeric chains. METHODS: Segments of elastomeric chains with 5 links each were sent for sterilization by cobalt 60 (Co60) (20 KGy) gamma ray technology. After the procedure, the elastomeric chains were contaminated with clinical samples of Streptococcus mutans. Subsequently, the elastomeric chains were submitted to sterilization/disinfection tests carried out by means of different methods, forming six study groups, as follows: Group 1 (control - without contamination), Group 2 (70°GL alcohol), Group 3 (autoclave), Group 4 (ultraviolet), Group 5 (peracetic acid) and Group 6 (glutaraldehyde). After sterilization/disinfection, the effectiveness of these methods, by Colony forming units per mL (CFU/mL), and the mechanical properties of the material were assessed. Student's t-test was used to assess the number of CFUs while ANOVA and Tukey's test were used to assess elastic strength. RESULTS: Ultraviolet treatment was not completely effective for sterilization. No loss of mechanical properties occurred with the use of the different sterilization methods (p > 0.05). CONCLUSION: Biological control of elastomeric chains does not affect their mechanical properties. PMID:26154462

  16. Sterilizing elastomeric chains without losing mechanical properties. Is it possible?

    Directory of Open Access Journals (Sweden)

    Matheus Melo Pithon

    2015-06-01

    Full Text Available OBJECTIVE: To investigate the effects of different sterilization/disinfection methods on the mechanical properties of orthodontic elastomeric chains. METHODS: Segments of elastomeric chains with 5 links each were sent for sterilization by cobalt 60 (Co60 (20 KGy gamma ray technology. After the procedure, the elastomeric chains were contaminated with clinical samples of Streptococcus mutans. Subsequently, the elastomeric chains were submitted to sterilization/disinfection tests carried out by means of different methods, forming six study groups, as follows: Group 1 (control - without contamination, Group 2 (70°GL alcohol, Group 3 (autoclave, Group 4 (ultraviolet, Group 5 (peracetic acid and Group 6 (glutaraldehyde. After sterilization/disinfection, the effectiveness of these methods, by Colony forming units per mL (CFU/mL, and the mechanical properties of the material were assessed. Student's t-test was used to assess the number of CFUs while ANOVA and Tukey's test were used to assess elastic strength. RESULTS: Ultraviolet treatment was not completely effective for sterilization. No loss of mechanical properties occurred with the use of the different sterilization methods (p > 0.05. CONCLUSION: Biological control of elastomeric chains does not affect their mechanical properties.

  17. Molecular exchange in block copolymer micelles: when corona chains overlap

    Science.gov (United States)

    Lu, Jie; Lodge, Timothy; Bates, Frank; Choi, Soohyung

    2013-03-01

    The chain exchange kinetics of poly(styrene-b-ethylenepropylene) (PS-PEP) diblock copolymer micelles in squalane (C30H62) was investigated using time-resolved small angle neutron scattering (TR-SANS). The solvent is a mixture of h-squalane and d-squalane that contrast-matches a mixed 50/50 h/d PS micelle core. As isotope labeled chains exchange, the core contrast decreases, leading to a reduction in scattering intensity. This strategy therefore allows direct probing of the chain exchange rate. Separate copolymer micellar solutions containing either deuterium labeled (dPS) or normal (hPS) poly(styrene) core blocks were prepared and mixed at room temperature, below the core glass transition temperature. The samples were heated to several temperatures (around 100 °C) and monitored by TR-SANS every 5 min. As polymer concentration was increased from 1% to 15% by volume, we observed a significant slowing down of chain exchange rate. Similar retarded kinetics was found when part of the solvent in the 1% solution was replaced by homopolymer PEP (comparable size as corona block). Furthermore, if all the solvent is replaced with PEP, no exchange was detected for up to 3hr at 200 °C. These results will be discussed in terms of a molecular model for chain exchange Infineum, Iprime, NIST, ORNL

  18. Implicit Sampling, with Application to Data Assimilation

    Institute of Scientific and Technical Information of China (English)

    Alexandre J.CHORIN; Matthias MORZFELD; Xuemin TU

    2013-01-01

    There are many computational tasks,in which it is necessary to sample a given probability density function (or pdf for short),i.e.,to use a computer to construct a sequence of independent random vectors xi (i =1,2,...),whose histogram converges to the given pdf.This can be difficult because the sample space can be huge,and more importantly,because the portion of the space,where the density is significant,can be very small,so that one may miss it by an ill-designed sampling scheme.Indeed,Markovchain Monte Carlo,the most widely used sampling scheme,can be thought of as a search algorithm,where one starts at an arbitrary point and one advances step-by-step towards the high probability region of the space.This can be expensive,in particular because one is typically interested in independent samples,while the chain has a memory.The authors present an alternative,in which samples are found by solving an algebraic equation with a random right-hand side rather than by following a chain; each sample is independent of the previous samples.The construction in the context of numerical integration is explained,and then it is applied to data assimilation.

  19. Chain Networks as a Leverage for Innovation Capacity: The Case of Food SMEs

    Directory of Open Access Journals (Sweden)

    Bianka Kühne

    2011-02-01

    Full Text Available  Nowadays, innovation is no longer limited to the individual firm but involves increasingly the chain network in which the firm is embedded. The chain network is considered as the place where the internal and external resources of a firm are combined and transformed, leading to innovation capacity. In the increasingly globalizing market, innovation is an important strategic tool for small and medium sized enterprises (SMEs to achieve competitive advantage. However, SMEs are often confronted with barriers for developing and introducing innovations, such as the lack of economies of scale. Our paper investigates how the chain network is contributing to the enhancement of the innovation capacity and which chain network characteristics are crucial in this process. In contrast to previous studies at chain network level, in our research specific chain networks are investigated and compared to each other. Hence, data collection took place at different chain network levels, being the supplier, the food manufacturer and the customer, working together and consequently belonging to one specific and unique chain network.The analysis of innovation capacity at the chain network level is realized by means of cluster analysis. This results in a three-cluster solution dividing the sample into Non-innovator chain networks, Customer-driven innovator chain networks and food manufacturer-supplier-driven innovator chain networks. Next, the influence of the chain network on the innovation capacity is examined. Thereby, the three achieved clusters differ significantly related to certain chain network characteristics. The following characteristics form an important leverage for the innovation capacity: firm size, profitability and business growth of the chain network members, as well as higher dependency, and lower levels of integration, rewarding power, social satisfaction and collaboration. The distinction of Customer-driven and food manufacturer

  20. Polymerization as a Model Chain Reaction

    Science.gov (United States)

    Morton, Maurice

    1973-01-01

    Describes the features of the free radical, anionic, and cationic mechanisms of chain addition polymerization. Indicates that the nature of chain reactions can be best taught through the study of macromolecules. (CC)

  1. Supply chain strategies, issues and models

    CERN Document Server

    Ramanathan, Ramakrishnan

    2014-01-01

    In the 21st century, supply chain operations and relationships among supply chain partners have become highly challenging, necessitating new approaches, e.g., the development of new models. Supply Chain Strategies, Issues and Models discusses supply chain issues and models with examples from actual industrial cases. Expert authors with a wide spectrum of knowledge working in various areas of supply chain management from various geographical locations offer refreshing, novel and insightful ideas and address possible solutions using established theories and models. Supply Chain Strategies, Issues and Models features studies that have used mathematical modeling, statistical analyses and also descriptive qualitative studies. The chapters cover many relevant themes related to supply chains and logistics including supply chain complexity, information sharing, quality (six sigma), electronic Kanbans, inventory models, scheduling, purchasing and contracts. To facilitate easy reading, the chapters that deal with suppl...

  2. SUPPLY CHAIN MANAGEMENT – KEY FACTORS

    Directory of Open Access Journals (Sweden)

    Magdalena Daniela DINU

    2014-06-01

    Full Text Available This paper exposes Supply Chain Management by its key factors. Briefly, where the Supply Chain Management is treated as strategic part of a company then maintaining both control and influence throughout the entire supply chain are key factors and critical to success. On the other hand, finding the right partner to manage the non-strategic Supply Chains would be another key factor too. To define the most important key factors within Supply Chain Management means a deeply understanding of both Supply Chain’ s components, procedures, workflow, processes and the importance of Supply Chain Management into maximizing company's value. SCORE model able to provide solid information about measuring performance and identifying priorities within Supply Chain Management will help us to understand the key factors by analyzing its elements: Plan, Source, Make, Deliver,Return, Enable. These elements covers all the challenging areas from first to third tier of Supply Chain Management.

  3. Information flow in the pharmaceutical supply chain.

    Science.gov (United States)

    Yousefi, Nazila; Alibabaei, Ahmad

    2015-01-01

    Managing the supply chain plays an important role in creating competitive advantages for companies. Adequate information flow in supply chain is one of the most important issues in SCM. Therefore, using certain Information Systems can have a significant role in managing and integrating data and information within the supply chain. Pharmaceutical supply chain is more complex than many other supply chains, in the sense that it can affect social and political perspectives. On the other hand, managing the pharmaceutical supply chain is difficult because of its complexity and also government regulations in this field. Although, Iran has progressed a lot in pharmaceutical manufacturing, still there are many unsolved issues in managing the information flow in the pharmaceutical supply chain. In this study, we reviewed the benefits of using different levels of an integrated information system in the supply chain and the possible challenges ahead.

  4. Probability Sampling Method for a Hidden Population Using Respondent-Driven Sampling: Simulation for Cancer Survivors.

    Science.gov (United States)

    Jung, Minsoo

    2015-01-01

    When there is no sampling frame within a certain group or the group is concerned that making its population public would bring social stigma, we say the population is hidden. It is difficult to approach this kind of population survey-methodologically because the response rate is low and its members are not quite honest with their responses when probability sampling is used. The only alternative known to address the problems caused by previous methods such as snowball sampling is respondent-driven sampling (RDS), which was developed by Heckathorn and his colleagues. RDS is based on a Markov chain, and uses the social network information of the respondent. This characteristic allows for probability sampling when we survey a hidden population. We verified through computer simulation whether RDS can be used on a hidden population of cancer survivors. According to the simulation results of this thesis, the chain-referral sampling of RDS tends to minimize as the sample gets bigger, and it becomes stabilized as the wave progresses. Therefore, it shows that the final sample information can be completely independent from the initial seeds if a certain level of sample size is secured even if the initial seeds were selected through convenient sampling. Thus, RDS can be considered as an alternative which can improve upon both key informant sampling and ethnographic surveys, and it needs to be utilized for various cases domestically as well.

  5. Systematic sampling with errors in sample locations

    DEFF Research Database (Denmark)

    Ziegel, Johanna; Baddeley, Adrian; Dorph-Petersen, Karl-Anton

    2010-01-01

    Systematic sampling of points in continuous space is widely used in microscopy and spatial surveys. Classical theory provides asymptotic expressions for the variance of estimators based on systematic sampling as the grid spacing decreases. However, the classical theory assumes that the sample grid...... is exactly periodic; real physical sampling procedures may introduce errors in the placement of the sample points. This paper studies the effect of errors in sample positioning on the variance of estimators in the case of one-dimensional systematic sampling. First we sketch a general approach to variance...... analysis using point process methods. We then analyze three different models for the error process, calculate exact expressions for the variances, and derive asymptotic variances. Errors in the placement of sample points can lead to substantial inflation of the variance, dampening of zitterbewegung...

  6. BUSINESS TENDENCIES IN SERVICES WITHIN SUPPLY CHAIN

    OpenAIRE

    Beata Skowron-Grabowska

    2008-01-01

    Supply chain management has been a major component of competitive strategy to enhance organizational productivity and profitability. Client satisfaction and improvement in profitability are two basic goals while organizing supply chain. In the paper author tried to prove that there is a correlation between organization of supply chain and subjective evaluation of economic situation by enterprises. Logistics integration helps enterprises to find their place in the supply chain.

  7. Supply Chain Integration: Challenges and Solutions

    OpenAIRE

    Sweeney, Edward

    2011-01-01

    Rapid changes in technological development are forcing businesses to continuously innovate to improve their competitiveness, which is particularly evident in logistics and supply chain management (SCM), where innovation impacts both the strategic and operational levels. Supply Chain Innovation for Competing in Highly Dynamic Markets: Challenges and Solutions investigates the role of innovation in the management of supply chains of today. This book focuses on supply chain integration from both...

  8. Australian Lamb Supply Chain: A Conceptual Framework

    OpenAIRE

    Jie, Ferry

    2011-01-01

    In the last decade, supply chain management has played an important role to lead agribusiness today to succeed in their business goals, to gain competitive advantages, and to improve business performance. As the result of that, there has been extensive studying in a popular topic of strategic supply chain management in order to improve business performance as well as along supply chain performance under the real situation. This is because in current business world, supply chain practices are ...

  9. Lunar Sample Atlas

    Data.gov (United States)

    National Aeronautics and Space Administration — The Lunar Sample Atlas provides pictures of the Apollo samples taken in the Lunar Sample Laboratory, full-color views of the samples in microscopic thin-sections,...

  10. Visualisation for System Learning in Supply Chains

    Science.gov (United States)

    Lindskog, Magnus; Abrahamsson, Mats; Aronsson, Hakan

    2007-01-01

    Contemporary supply chains are vastly complex, and decisions made by actors have system-wide consequences that these might not be able to foresee. There are gaps between "best practice"-founded theory and actual practice in supply chains. To remedy this, we argue, the supply chain actors need to enhance systems knowledge. There is a need to…

  11. Learning to Integrate: Supply Chains Reconceptualised

    Science.gov (United States)

    Sense, Andrew J.; Clements, Michael D. J.

    2007-01-01

    This paper introduces and explains a conception of supply chains from a situated learning perspective. This non-conventional supply chain perspective invites the reader to consider supply chain scenarios as "situated learning opportunities involving multiple communities of practice" interacting and participating together. It is argued that by…

  12. Cellular chain formation in Escherichia coli biofilms

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk; Klemm, Per

    2009-01-01

    In this study we report on a novel structural phenotype in Escherichia coli biofilms: cellular chain formation. Biofilm chaining in E. coli K-12 was found to occur primarily by clonal expansion, but was not due to filamentous growth. Rather, chain formation was the result of intercellular...

  13. A concept for collaborative supply chain planning

    DEFF Research Database (Denmark)

    Alfnes, E.; Dreyer, H.C.; Hvolby, Hans-Henrik

    2012-01-01

    vendors such as Oracle, SAP and I2 offer supply chain planning systems. This limits the ability for SMEs to exploit the supply chain planning options. This paper is part of a research project carried out to develop a new supply chain add-on for Microsoft AX, a very common system for SMEs. The paper...

  14. The Advancement Value Chain: An Exploratory Model

    Science.gov (United States)

    Leonard, Edward F., III

    2005-01-01

    Since the introduction of the value chain concept in 1985, several varying, yet virtually similar, value chains have been developed for the business enterprise. Shifting to higher education, can a value chain be found that links together the various activities of advancement so that an institution's leaders can actually look at the philanthropic…

  15. Secure Supply Chains: Design Restrictions & Organizational Boundaries

    NARCIS (Netherlands)

    Ludema, M.W.

    2009-01-01

    An important issue in the design of secure supply chains is the understanding of the relation between supply chains and the organizational responsibility of specific parts of these supply chains. Organizational boundaries change over time by means of vertical and/or horizontal (des)-integration and

  16. On a Result for Finite Markov Chains

    Science.gov (United States)

    Kulathinal, Sangita; Ghosh, Lagnojita

    2006-01-01

    In an undergraduate course on stochastic processes, Markov chains are discussed in great detail. Textbooks on stochastic processes provide interesting properties of finite Markov chains. This note discusses one such property regarding the number of steps in which a state is reachable or accessible from another state in a finite Markov chain with M…

  17. Compressing redundant information in Markov chains

    OpenAIRE

    2006-01-01

    Given a strongly stationary Markov chain and a finite set of stopping rules, we prove the existence of a polynomial algorithm which projects the Markov chain onto a minimal Markov chain without redundant information. Markov complexity is hence defined and tested on some classical problems.

  18. STATISTICS OF A CLASS OF MARKOV CHAINS

    Institute of Scientific and Technical Information of China (English)

    DENG Yingchun; CAO Xianbing

    2004-01-01

    In this paper we prove that the distributions of their sojourn time and hitting time at one special state for random walks which are allowed to be finite or infinite and Markov chains on star-graphs with discrete time can uniquely determine the probability distribution of the whole chains. This result also suggests a new statistical method for Markov chains.

  19. Consistency and Refinement for Interval Markov Chains

    DEFF Research Database (Denmark)

    Delahaye, Benoit; Larsen, Kim Guldstrand; Legay, Axel;

    2012-01-01

    Interval Markov Chains (IMC), or Markov Chains with probability intervals in the transition matrix, are the base of a classic specification theory for probabilistic systems [18]. The standard semantics of IMCs assigns to a specification the set of all Markov Chains that satisfy its interval...

  20. Chains versus Independents: Newspaper and Market Characteristics.

    Science.gov (United States)

    Hale, F. Dennis

    A study examined the marketing differences between large chain newspapers and small chain and independent newspapers by analyzing differences in characteristics of the newspapers, patterns of circulation, economic and social conditions of the market, and competition from other print media. The 200 newspapers studied--113 large chain and 87 small…

  1. Principles in Halal Supply Chain Management

    NARCIS (Netherlands)

    Tieman, H.; Vorst, van der J.G.A.J.; Maznah Che Ghazali,

    2012-01-01

    Purpose – The purpose of this paper is to introduce a new framework to optimise the design of halal food supply chains, called the “Halal Supply Chain Model”. In this research the main logistics business processes are defined, which are the determinants for the halal supply chain performance. Design

  2. Systematic Methodology of Integrated Supply Chain Management

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Supply chain management (SCM) is a strategy for global competition. Th e characteristics of SCM are integration, systematic and coordination. Using sys tematic, coordination thoughts and integration theory, a new model of enterprise integration based on supply chain management is put forward and an implementing paradigm for systematic methodology of supply chain management is developed.

  3. Experiences with the Mango Chain Game

    NARCIS (Netherlands)

    Meijer, S.A.; Zuñiga-Arias, G.; Sterrenburg, S.

    2005-01-01

    The mango chain game is a simulation game used for research purposes. It facilitated studying the bargaining power of Costa Rican mango producers in international supply chains of mango. The game simulates a simplified mango export chain in which real world local producers can play the role of produ

  4. Review of Published Chain Information System Research

    NARCIS (Netherlands)

    Storer, C.E.; Trienekens, J.H.; Beulens, A.J.M.; Quaddus, M.A.

    2006-01-01

    This paper provides a review of the literature on chains and networks that examine interorganisational information systems used to manage chains of organisations. Difficulty was found in finding out how organisations exchanged information to manage relationships with customers and suppliers in chain

  5. 大体积采样结合高分辨气相色谱-电子捕获负化学源-低分辨质谱法测定空气中的短链氯化石蜡%Determination of short-chain chlorinated paraffins in ambient air using high-volume sampling combined with high resolution gas chromatography-electron capture negative ion-low resolution mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    史蕾蒙; 高媛; 侯晓虹; 张海军; 张亦弛; 陈吉平

    2016-01-01

    建立了大体积采样结合高分辨气相色谱-电子捕获负化学源-低分辨质谱( HRGC-ECNI-LRMS)测定空气中短链氯化石蜡( SCCPs)的定量分析方法.联合使用酸化硅胶复合层析柱和碱性氧化铝层析柱净化处理空气样品中的 SCCPs,并对净化条件进行优化.使用该方法计算得到氯含量为58. 1%~63. 3%的 SCCPs系列标准储备溶液的总响应因子与氯含量线性相关,相关系数(R2)大于 0. 99.该方法的仪器检出限(S/N≥3)为 4. 2 pg,定量限(S/N≥10)为12 pg.SCCPs的方法检出限(MDL)为0. 34 ng/m3(n=7),实际样品加标回收率均达 80%以上.该方法灵敏度高、选择性好,能满足空气样品中 SCCPs的监测和分析需求.%An analytical method for quantifying short-chain chlorinated paraffins( SCCPs)in ambient air using high-volume sampling combined with high resolution gas chromatography-electron capture negative ion-low resolution mass spectrometry ( HRGC-ECNI-LRMS ) was developed. An acidified silica gel column and a basic alumina column were used to optimize the cleanup procedures. The results showed a good linearity(R2>0. 99)between the total response factors and the degree of chlorination of SCCPs in the content range of 58. 1%-63. 3%. The lim-its of detection( S/N≥3 ) and the limits of quantification( S/N≥10 ) were 4. 2 and 12 pg, respectively. The method detection limit( MDL)for SCCPs was 0. 34 ng/m 3( n=7). The recov-eries of SCCPs in air samples were in the range of 81. 9% to 94. 2%. It is demonstrated that the method is suitable for the quantitative analysis of SCCPs in air samples.

  6. The parallel reaction monitoring method contributes to a highly sensitive polyubiquitin chain quantification

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchiya, Hikaru; Tanaka, Keiji, E-mail: tanaka-kj@igakuken.or.jp; Saeki, Yasushi, E-mail: saeki-ys@igakuken.or.jp

    2013-06-28

    Highlights: •The parallel reaction monitoring method was applied to ubiquitin quantification. •The ubiquitin PRM method is highly sensitive even in biological samples. •Using the method, we revealed that Ufd4 assembles the K29-linked ubiquitin chain. -- Abstract: Ubiquitylation is an essential posttranslational protein modification that is implicated in a diverse array of cellular functions. Although cells contain eight structurally distinct types of polyubiquitin chains, detailed function of several chain types including K29-linked chains has remained largely unclear. Current mass spectrometry (MS)-based quantification methods are highly inefficient for low abundant atypical chains, such as K29- and M1-linked chains, in complex mixtures that typically contain highly abundant proteins. In this study, we applied parallel reaction monitoring (PRM), a quantitative, high-resolution MS method, to quantify ubiquitin chains. The ubiquitin PRM method allows us to quantify 100 attomole amounts of all possible ubiquitin chains in cell extracts. Furthermore, we quantified ubiquitylation levels of ubiquitin-proline-β-galactosidase (Ub-P-βgal), a historically known model substrate of the ubiquitin fusion degradation (UFD) pathway. In wild-type cells, Ub-P-βgal is modified with ubiquitin chains consisting of 21% K29- and 78% K48-linked chains. In contrast, K29-linked chains are not detected in UFD4 knockout cells, suggesting that Ufd4 assembles the K29-linked ubiquitin chain(s) on Ub-P-βgal in vivo. Thus, the ubiquitin PRM is a novel, useful, quantitative method for analyzing the highly complicated ubiquitin system.

  7. Coring Sample Acquisition Tool

    Science.gov (United States)

    Haddad, Nicolas E.; Murray, Saben D.; Walkemeyer, Phillip E.; Badescu, Mircea; Sherrit, Stewart; Bao, Xiaoqi; Kriechbaum, Kristopher L.; Richardson, Megan; Klein, Kerry J.

    2012-01-01

    A sample acquisition tool (SAT) has been developed that can be used autonomously to sample drill and capture rock cores. The tool is designed to accommodate core transfer using a sample tube to the IMSAH (integrated Mars sample acquisition and handling) SHEC (sample handling, encapsulation, and containerization) without ever touching the pristine core sample in the transfer process.

  8. Signal sampling circuit

    NARCIS (Netherlands)

    Louwsma, Simon Minze; Vertregt, Maarten

    2011-01-01

    A sampling circuit for sampling a signal is disclosed. The sampling circuit comprises a plurality of sampling channels adapted to sample the signal in time-multiplexed fashion, each sampling channel comprising a respective track-and-hold circuit connected to a respective analogue to digital converte

  9. Signal sampling circuit

    NARCIS (Netherlands)

    Louwsma, Simon Minze; Vertregt, Maarten

    2010-01-01

    A sampling circuit for sampling a signal is disclosed. The sampling circuit comprises a plurality of sampling channels adapted to sample the signal in time-multiplexed fashion, each sampling channel comprising a respective track-and-hold circuit connected to a respective analogue to digital converte

  10. Supply Chain Management Performance in Tourism. Continental Hotels Chain Case

    Directory of Open Access Journals (Sweden)

    Gabriela Ţigu

    2013-02-01

    Full Text Available With its origins in logistics, Supply Chain Management (SCM concept is covering all managerial aspects of the flow of materials and information from source to customer, across the entire range of materials handling and movement functions, and throughout an organization and its supply channels. In tourism, these issues relate to the whole process of providing tourism services from sourcing of raw materials, products or different services to supply and distribution, and SCM performance can ultimately be measured by customer satisfaction. Thus, an important component of tourism SCM is the demand management. Therefore, this study aims to highlight the features of the concept of SCM and demand management in tourism, with an emphasis on a hotel chain in Romania, based on research and analysis of tourist traffic indicators as well as assessment of customers satisfaction. The sources of information are the internal company statistics, as well as various hotels booking websites that offer customers’ feedback. The results of the study provide a snapshot of how the hotel demand management can influence SCM performance in tourism.

  11. Sampling informative/complex a priori probability distributions using Gibbs sampling assisted by sequential simulation

    DEFF Research Database (Denmark)

    Hansen, Thomas Mejer; Mosegaard, Klaus; Cordua, Knud Skou

    2010-01-01

    Markov chain Monte Carlo methods such as the Gibbs sampler and the Metropolis algorithm can be used to sample the solutions to non-linear inverse problems. In principle these methods allow incorporation of arbitrarily complex a priori information, but current methods allow only relatively simple...... this algorithm with the Metropolis algorithm to obtain an efficient method for sampling posterior probability densities for nonlinear inverse problems....

  12. Activated aluminum oxide selectively retaining long chain n-alkanes: Part II. Integration into an on-line high performance liquid chromatography-liquid chromatography-gas chromatography-flame ionization detection method to remove plant paraffins for the determination of mineral paraffins in foods and environmental samples

    Energy Technology Data Exchange (ETDEWEB)

    Fiselier, Katell [Official Food Control Authority of the Canton of Zurich, P.O. Box, CH-8032 Zurich (Switzerland); Fiorini, Dennis [Department of Chemical Sciences, University of Camerino, V.S. Agostino 1, I-62032, Camerino (Italy); Grob, Koni [Official Food Control Authority of the Canton of Zurich, P.O. Box, CH-8032 Zurich (Switzerland)], E-mail: koni@grob.org

    2009-02-16

    Aluminum oxide activated by heating to 300-400 deg. C retains n-alkanes with more than about 20 carbon atoms, whereas iso-alkanes largely pass non-retained (with characteristics described in more detail in Part I). This property is useful for the analysis of mineral oil contamination of foods and other matrices: it enables the removal of plant n-alkanes, typically ranging from C{sub 23} to C{sub 33}, when they disturb the analysis of mineral paraffins (usually almost exclusively consisting of iso-alkanes). An on-line HPLC-LC-GC-FID method is proposed in which a first silica gel HPLC column isolates the paraffins from the bulk of edible oils or extracts and is backflushed with dichloromethane. In a second separation step, a 10 cm x 2 mm i.d. column packed with activated aluminum oxide separates the long chain n-alkanes from the fraction of the iso-alkanes which is transferred to GC-FID by the on-column interface and the retention gap technique. The retained n-alkanes are removed by flushing with iso-octane.

  13. The influence of power in supply chain innovation; a case study of the Dutch wheat chain

    NARCIS (Netherlands)

    Pol, Hanneke; Visscher, Klaasjan

    2010-01-01

    The purpose of this article is to clarify the relation between the power structure of a supply chain and the possibilities to realize supply chain innovations. In an in-depth case study of the faltering start of an innovation trajectory in the Dutch wheat supply chain, we show that supply chain inno

  14. Supply chain management - safety aspects

    Directory of Open Access Journals (Sweden)

    2010-12-01

    Full Text Available Developing economy, growing customer requirements and competition make the service level higher. Delivery safety - as the highest priority - has to be maintained at the same time. Customers more and more often require transport to be very flexible, fast, and complex in terms of carrying every quantity of goods of different sizes, from and to different countries, through customs clearance, storing and distribution of shipments. Meeting these requirements depends on complex information on transport processes and their safety. The article presents safety foundations and institution Authorized Economic Operator - AEO in supply chains.

  15. TBA for the Toda chain

    Energy Technology Data Exchange (ETDEWEB)

    Kozlowski, K.K.; Teschner, J.

    2010-06-15

    We give a direct derivation of a proposal of Nekrasov-Shatashvili concerning the quantization conditions of the Toda chain. The quantization conditions are formulated in terms of solutions to a nonlinear integral equation similar to the ones coming from the thermodynamic Bethe ansatz. This is equivalent to extremizing a certain function called Yang's potential. It is shown that the Nekrasov-Shatashvili formulation of the quantization conditions follows from the solution theory of the Baxter equation, suggesting that this way of formulating the quantization conditions should indeed be applicable to large classes of quantized algebraically integrable models. (orig.)

  16. MODELING SUPPLY CHAIN WITH SIMULATION

    OpenAIRE

    János Benkõ

    2010-01-01

    Supply Chain Management faces a lot of challenging issues involving difficult decisions which can be company-oriented and customer-oriented issues. In this study we deal with customeroriented issues. For example, a customer’s demand may not be fully satisfied from stock on hand and the shortage may be backordered or the sale may be lost. Either way, it is desirable to balance the holding cost which depends on the magnitude of inventory against the cost of not fully satisfying customer demand....

  17. Heat transport in coupled inhomogeneous chains

    Institute of Scientific and Technical Information of China (English)

    Hu Tao; Bai Meng; Hu Ke; Tang Yi

    2011-01-01

    We first investigate the heat transport in a network model consisting of two coupled dimerized chains. Results indicate that the thermal resistance of each chain increases with the decrease of the mass ratio γ of the two types of atoms. Then, we find, when a light impurity or a heavy one is added in the two coupled homogeneous chains and coupled with a particle of another chain, the interface thermal resistances Rlint andRγint present different dependences on the mass ratio γ'. Finally, a persistent circulation of energy current is observed in coupled inhomogeneous chains with two pairs of interchain coupling.

  18. Integration of Forestry Industrial Chain in China

    Institute of Scientific and Technical Information of China (English)

    Zhanzhan; LAN; Liqun; WANG

    2013-01-01

    Based on the Smile Curve and Michael E. Porter’ value chain model,this paper points out that China’s forestry industry stays at the low end of the value chain for a long time. Raw materials are imported from foreign countries and also sold in foreign countries. Then,the authors analyze characteristics and existing problems of China’s forestry industrial chain. They put forward the development direction of China’s forestry industrial chain with reference to International Paper Company. Finally,they present their recommendations for integration of China’s forestry industrial chain.

  19. Uncertainty quantification for Markov chain models.

    Science.gov (United States)

    Meidani, Hadi; Ghanem, Roger

    2012-12-01

    Transition probabilities serve to parameterize Markov chains and control their evolution and associated decisions and controls. Uncertainties in these parameters can be associated with inherent fluctuations in the medium through which a chain evolves, or with insufficient data such that the inferential value of the chain is jeopardized. The behavior of Markov chains associated with such uncertainties is described using a probabilistic model for the transition matrices. The principle of maximum entropy is used to characterize the probability measure of the transition rates. The formalism is demonstrated on a Markov chain describing the spread of disease, and a number of quantities of interest, pertaining to different aspects of decision-making, are investigated.

  20. Chain store management through private labels strategy

    Directory of Open Access Journals (Sweden)

    Martina Sopta

    2007-07-01

    Full Text Available The purpose of this paper is to examine the market shares of private labels in the European Union and on the global market, and to compare the results of the analysis with the level of presence of private labels on the Croatian market. Moreover, through the application of macro and microeconomic tools, the author tried to estimate the future trends of private labels in Croatia.For the purpose of the paper secondary and primary data was used in the research. Relevant scientific and professional literature of local and foreign authors was analyzed. In addition, a few recent research studies were analyzed and their results compared. Field research has been conducted by the survey method, with 225 respondents included in the intentional sample.The main hypothesis of the paper based on research is that, in total sales, private labels are gaining a growing share in all markets, regardless of the development level of those markets. Alongside the main hypothesis of the work, three supporting hypotheses were tested to see which private labels are a good alternative to other brands on the world market. Private labels are generally developed on generic products. The third supporting hypothesis starts from the assumption that the investments in the promotion of private labels are negligible, resulting in lower prices of thoseproducts. The results of research and analyses in the work indicate that the position of private labels will strengthen internationally, as part of the process of liberalization and globalization of trade flows. In the process of purchase of private labels the positioning of the point of sale and price have an increasing contribution. With the concentration of commerce in chain stores, the share of private labels grows, approaching a half of the total sales in some countries. Considering the Croatian market, according to the international product life cycle theory, the share of private labels in the total sales will grow in the future

  1. Adaptive Rate Sampling and Filtering Based on Level Crossing Sampling

    Directory of Open Access Journals (Sweden)

    Saeed Mian Qaisar

    2009-01-01

    Full Text Available The recent sophistications in areas of mobile systems and sensor networks demand more and more processing resources. In order to maintain the system autonomy, energy saving is becoming one of the most difficult industrial challenges, in mobile computing. Most of efforts to achieve this goal are focused on improving the embedded systems design and the battery technology, but very few studies target to exploit the input signal time-varying nature. This paper aims to achieve power efficiency by intelligently adapting the processing activity to the input signal local characteristics. It is done by completely rethinking the processing chain, by adopting a non conventional sampling scheme and adaptive rate filtering. The proposed approach, based on the LCSS (Level Crossing Sampling Scheme presents two filtering techniques, able to adapt their sampling rate and filter order by online analyzing the input signal variations. Indeed, the principle is to intelligently exploit the signal local characteristics—which is usually never considered—to filter only the relevant signal parts, by employing the relevant order filters. This idea leads towards a drastic gain in the computational efficiency and hence in the processing power when compared to the classical techniques.

  2. The fish industry - toward supply chain modelling

    DEFF Research Database (Denmark)

    Jensen, Toke Koldborg; Nielsen, Jette; Larsen, Erling

    2010-01-01

    Mathematical models for simulating and optimizing aspects of supply chains such as distribution, planning, and optimal handling of raw materials are widely used. However, modeling based on a holistic chain view including several or all supply chain agents is less studied, and food-related aspects...... such as quality and shelf-life issues enforce additional requirements onto the chains. In this article, we consider the supply chain structure of the fish industry. We discuss and illustrate the potential of using mathematical models to identify quality and value-adding activities. The article provides a first...... step toward innovative supply chain modeling aimed to identify benefits for all agents along chains in the fish industry....

  3. Sustainability Analysis for Gayo Coffee Supply Chain

    Directory of Open Access Journals (Sweden)

    Rachman Jaya

    2013-01-01

    Full Text Available Sustainable supply chain is a development of the conventional supply chains that discuses trade-off among economic, social and environmental dimensions in order to achieve better responsiveness in terms of quality, quantity and time-delivery in the supply chain structure. The objective of this research was to determine the Gayo coffee supply chain sustainability. The research was conducted at Bener Meriah and Aceh Tengah Districts, Aceh Province, Indonesia. Key actors in the supply chain considered were farmers, collectors, agro-industry and exporter. Sustainability dimensions considered in this research were the economic, social, environmental and material resources. The performance of each aspect was analyzed by using Multi-dimensional scaling and leverage analysis. The result of the research showed that the composite of Gayo coffee supply chain sustainability index was 33.53 which mean less sustainable level. Therefore it is recommended to reengineering the Gayo coffee supply chain by considering all of the four sustainability dimensions above.

  4. Determining an optimal supply chain strategy

    Directory of Open Access Journals (Sweden)

    Intaher M. Ambe

    2012-11-01

    Full Text Available In today’s business environment, many companies want to become efficient and flexible, but have struggled, in part, because they have not been able to formulate optimal supply chain strategies. Often this is as a result of insufficient knowledge about the costs involved in maintaining supply chains and the impact of the supply chain on their operations. Hence, these companies find it difficult to manufacture at a competitive cost and respond quickly and reliably to market demand. Mismatched strategies are the root cause of the problems that plague supply chains, and supply-chain strategies based on a one-size-fits-all strategy often fail. The purpose of this article is to suggest instruments to determine an optimal supply chain strategy. This article, which is conceptual in nature, provides a review of current supply chain strategies and suggests a framework for determining an optimal strategy.

  5. Large deviations of Rouse polymer chain: First passage problem

    Science.gov (United States)

    Cao, Jing; Zhu, Jian; Wang, Zuowei; Likhtman, Alexei E.

    2015-11-01

    The purpose of this paper is to investigate several analytical methods of solving first passage (FP) problem for the Rouse model, a simplest model of a polymer chain. We show that this problem has to be treated as a multi-dimensional Kramers' problem, which presents rich and unexpected behavior. We first perform direct and forward-flux sampling (FFS) simulations and measure the mean first-passage time τ(z) for the free end to reach a certain distance z away from the origin. The results show that the mean FP time is getting faster if the Rouse chain is represented by more beads. Two scaling regimes of τ(z) are observed, with transition between them varying as a function of chain length. We use these simulation results to test two theoretical approaches. One is a well known asymptotic theory valid in the limit of zero temperature. We show that this limit corresponds to fully extended chain when each chain segment is stretched, which is not particularly realistic. A new theory based on the well known Freidlin-Wentzell theory is proposed, where dynamics is projected onto the minimal action path. The new theory predicts both scaling regimes correctly, but fails to get the correct numerical prefactor in the first regime. Combining our theory with the FFS simulations leads us to a simple analytical expression valid for all extensions and chain lengths. One of the applications of polymer FP problem occurs in the context of branched polymer rheology. In this paper, we consider the arm-retraction mechanism in the tube model, which maps exactly on the model we have solved. The results are compared to the Milner-McLeish theory without constraint release, which is found to overestimate FP time by a factor of 10 or more.

  6. Challenges of locally manufactured vehicle supply chains in South Africa

    Directory of Open Access Journals (Sweden)

    Intaher M. Ambe

    2013-05-01

    Full Text Available Locally manufactured vehicles are destined (partly for the export market and thus, global competitiveness  is  important.  This  article  explores  the  challenges  facing  supply  chains  of locally manufactured vehicles in South Africa. The automotive industry is perceived to be the most advanced in supply chain management practices in South Africa. It has embraced technology and management practices that have transformed the manufacturing environment by using cutting-edge design and visualisation tools. However, the industry has fragilities and faces new and emerging supply chain challenges. A survey research design was employed and  the  data  was  collected  through  face-to-face  semi-structured  interview  questionnaires based on the purposive sampling technique. Data analysis and interpretation was based on descriptive  statistics  using  SPSS  software.  The  findings  revealed  that  there  are  challenges hindering  best  supply  chain  practices  of  local  vehicle  manufacturers.  The  research  also revealed that there is a perceived difference in supply chain challenges between the different manufacturers of different origins in South Africa. Asian manufacturers felt much stronger about the adequacy of their information systems compared to the European manufacturers. Asian  manufacturers  tended  to  agree  more  than  their  European  counterparts  that  labour problems were a challenge. European manufacturers, on the other hand, tended to agree more that rail transport is unreliable. This article contributes to the body of knowledge on supply chain practices in South Africa. 

  7. Configurational statistics of confined polymer chains

    Energy Technology Data Exchange (ETDEWEB)

    Lohse, David John

    1978-01-01

    The work on confined chain statistics is reviewed. The work on the general statistics is discussed first, and then some of the theories for the applications of statistics are considered. Two methods for determining the general statistics of a confined chain are discussed. The first is the method of images. The second method involves the use of differential equations. In a specific case the statistics of the unconfined chain are chosen to be defined by the Gaussian real chain distribution. The confinement is provided by two parallel walls. The distribution for the four possible types of chains, bridges (tie chains), loops, cilia (dangling chain ends), and floating (unattached) chains, are derived. These statistics are then applied to two polymer systems in which the confinement is due to internal surfaces, semicrystalline polymers and block copolymers. Both systems are modelled by chains between two walls for a number of morphologies. Mechanical properties are calculated for both systems and for block copolymers swelling is also considered. The main result of this work is that there are two effects which determine the behavior of the chains in these systems. The first is the effect of the confinement which operates on all the chains, since the mode of attachment is not important. The confinement reduces the number of configurations available to the chains. This effect is larger the closer the walls are, relative to the length and stiffness of the chains. The second effect operates only on bridges, since it requires that the ends of the chain be attached to different walls. This is the inherent elastic nature of the bridge, which means that the number of configurations is reduced when it is stretched beyond its equilibrium length. All the behavior calculated here can be explained by these two effects.

  8. MODELING A VALUE CHAIN IN PUBLIC SECTOR

    Directory of Open Access Journals (Sweden)

    Daiva Rapcevičienė

    2014-08-01

    Full Text Available Purpose – Over the past three decades comprehensive insights were made in order to design and manage the value chain. A lot of scholars discuss differences between private sector value chain – creation profit for the business and public sector value chain, the approach that public sector creates value through the services that it provides. However, there is a lack of a common understanding of what public sector value chain is in general. This paper reviews the literature on how the private value chain was transformed into public value chain and reviews a determination and architecture of a value chain in public sector which gives a structural approach to greater picture of how all structure works. It reviews an approach that the value chain for the public sector shows how the public sector organizes itself to ensure it is of value to the citizens. Design/methodology/approach – descriptive method, analysis of scientific literature. Findings – The public sector value chain is an adaptation of the private sector value chain. The difference between the two is that the customer is the focus of the public sector context, versus the profit focus in the private sector context. There are significant similarities between the two chain models. Each of the chain models are founded on a series of core components. For the public sector context, the core components are people, service and trust. Research limitations/implications – this paper based on presenting value chain for both private and public sectors and giving deeper knowledge for public sector value chain model. Practical implications – comprehension of general value chain model concept and public sector value chain model helps to see multiple connections throughout the entire process: from the beginning to the end. The paper presents the theoretical framework for further study of the value chain model for waste management creation. Originality/Value – The paper reveals the systematic

  9. Understanding for convergence monitoring for probabilistic risk assessment based on Markov Chain Monte Carlo Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Joo Yeon; Jang, Han Ki; Jang, Sol Ah; Park, Tae Jin [Korean Association for Radiation Application, Seoul (Korea, Republic of)

    2014-04-15

    There is a question that the simulation actually leads to draws from its target distribution and the most basic one is whether such Markov chains can always be constructed and all chain values sampled from them. The problem to be solved is the determination of how large this iteration should be to achieve the target distribution. This problem can be answered as convergence monitoring. In this paper, two widely used methods, such as autocorrelation and potential scale reduction factor (PSRF) in MCMC are characterized. There is no general agreement on the subject of the convergence. Although it is generally agreed that running n parallel chains in practice is computationally inefficient and unnecessary, running multiple parallel chains is generally applied for the convergence monitoring due to easy implementation. The main debate is the number of parallel chains needed. If the convergence properties of the chain are well understood then clearly a single chain suffices. Therefore, autocorrelation using single chain and multiple parallel ones are tried and their results then compared with each other in this study. And, the following question is answered from the two convergence results: Have the Markov chain realizations for achieved the target distribution?.

  10. A sampling algorithm for segregation analysis

    Directory of Open Access Journals (Sweden)

    Henshall John

    2001-11-01

    Full Text Available Abstract Methods for detecting Quantitative Trait Loci (QTL without markers have generally used iterative peeling algorithms for determining genotype probabilities. These algorithms have considerable shortcomings in complex pedigrees. A Monte Carlo Markov chain (MCMC method which samples the pedigree of the whole population jointly is described. Simultaneous sampling of the pedigree was achieved by sampling descent graphs using the Metropolis-Hastings algorithm. A descent graph describes the inheritance state of each allele and provides pedigrees guaranteed to be consistent with Mendelian sampling. Sampling descent graphs overcomes most, if not all, of the limitations incurred by iterative peeling algorithms. The algorithm was able to find the QTL in most of the simulated populations. However, when the QTL was not modeled or found then its effect was ascribed to the polygenic component. No QTL were detected when they were not simulated.

  11. Detection of TTV DNA from high background nuclear acid samples using specific nuclear acid captured polymerase chain reaction%特异核酸捕获-PCR技术在从高背景标本中检测TT病毒DNA的应用

    Institute of Scientific and Technical Information of China (English)

    彭晓谋; 邓练贤; 陈文思; 高志良; 姚集鲁

    2001-01-01

    Objective To improve the amplification of non-specificity of TTV DNA detection using PCR from high background nuclear acids because of its low level in samples. Methods Specific nuclear acid captured PCR(SNAC-PCR) was established through capturing TTV DNA onto microplate with specific nuclear acid by means of avidin-biotin system, then amplifying captured TTV DNA as usual. Its specificity was evaluated by comparing with the detection of routine extraction samples using nested-PCR with or without subsequent DNA sequencing in 10 samples of sera and liver tissues in pairs. Results Positive results were obtained using routine protocol in 4 and 9 out of 10 samples of the sera and the liver tissues respectivly. The PCR products were proved to be specific using RFLP analysis with Kpn I . However,positive results were found in only 2/10 and 3/10 of samples of sera and liver tissue using DNA sequencing. The results of SNAC-PCR were the same as those of routine protocol with subsequent DNA sequencing. Furthermore, sharper electrophoreais bands were obtained. Conclusion SNAC-PCR could dramatically increase the specificity of the detection of TTV DNA,especially in high background nuclear acid samples. It can be widely used in the detection of other pathogens with low seral level or in high background nuclear acid samples. The level of TTV infection might be over-evaluated by currently used TTV DNA detection when the PCR products were not confirmed by DNA sequencing.%目的解决因TTV在样本中的水平极低而导致从高背景核酸样本中检测TTV DNA存在非特异性扩增的问题。方法采用亲和素生物素系统将TTV特异的核酸片段包被在微孔板上,利用特异核酸捕获样本中的TTV DNA,从而建立特异核酸捕获-PCR检测TTV DNA方法,并以10份血清(4份TTV DNA阳性)和肝组织配对标本为对象与抽提法进行比较,阳性产物进行DNA序列分析,最后评价特异核酸捕获-PCR的特异性。结果抽提法在

  12. Light chain immunofluorescence in various nephropathies

    Directory of Open Access Journals (Sweden)

    Megha S Uppin

    2011-01-01

    Full Text Available Context: Light chain immunofluoresence (IF in renal biopsy is routinely used in the diagnosis of light chain deposition disease (LCDD, amyloidosis and cast nephropathy. Light chain predominance has also been reported in certain glomerulopathies like IgA nephropathy. However, pathogenesis of this pattern of deposition in various glomerulopathies is uncertain. Aim: To discuss the pathogenesis and utility of light chain IF in nephropathies. Setting and Design: Retrospective study. Materials and Methods: The pattern of light chain IF and light microscopic diagnosis in 306 cases of various nephropathies was reviewed. Direct IF was done in all these cases with commercial fluorescence (Fluoresciene Isothiocynate conjugated polyclonal rabbit anti-human antisera against IgM, IgG, IgA, C3, C1q, kappa and lambda light chains. Results: Light chain deposits were seen in 240 (78.43% cases. In IgA nephropathy, lupus nephritis and post-infectious glomerulonephritis (PIGN, lambda positivity was more as compared to kappa. Light chain deposits in LCDD and membranous nephropathy were more kappa type. The IF pattern in amyloidosis was not consistent. Conclusion: The pathogenesis of light chain predominance in glomerulopathies is not clear and it depends on isoelectric point and size of the immune complex. Light chain IF should be performed routinely in all the renal biopsies.

  13. Structure of polymer chains under confinement

    Indian Academy of Sciences (India)

    Jyotsana Lal

    2008-11-01

    We observe by SANS the structure of neutral polystyrene and charged polystyrene sulphonate chains in semi-dilute solutions confined in a model nanoporous glass, Vycor. The size of the free chains in solution is always larger than the pore diameter, 70. The use of a suitable mixture of hydrogenated and deuterated solvents and polymers enables us to measure directly the form factor of one single chain among the others. Single chain form factor was observed both for bulk and confined chains using the condition of zero average contrast. Our measurements on neutral polymer chains are in agreement with the theoretical predictions established by Daoud and de Gennes for chains confined in a cylindrical pore when the chains are entangled and laterally squeezed but remain ideal at large scale along the cylinder axis because of the screening of the excluded volume interactions (so-called regime of ``semi-dilute cigars"). For confined charged polymers, a peak is observed whose intensity increases with molecular weight and the asymptotic 1/ scattering region is extended compared to the bulk. We infer that the chains are sufficiently extended, under the influence of confinement, to highlight the large scale disordered structure of Vycor even under contrast matched conditions. The asymptotic behaviour of the observed interchain structure factor is ≈ 1/2 and ≈ 1/ for free and confined chains respectively.

  14. Phase behaviour of polyethylene knotted ring chains

    Institute of Scientific and Technical Information of China (English)

    Wen Xiao-Hui; Zhang Lin-Xi; Xia A-Gen; Chen Hong-Ping

    2011-01-01

    The phase behaviour of polyethylene knotted ring chains is investigated by using molecular dynamics simulations.In this paper, we focus on the collapse of the polyethylene knotted ring chain, and also present the results of linear and ring chains for comparison. At high temperatures, a fully extensive knot structure is observed. The mean-square radius of gyration per bond〈S2〉/(Nb2)and the shape factor(δ*)depend on not only the chain length but also the knot type.With temperature decreasing, chain collapse is observed, and the collapse temperature decreases with the chain length increasing. The actual collapse transition can be determined by the specific heat capacity Cv, and the knotted ring chain undergoes gas-liquid-solid-like transition directly. The phase transition of a knotted ring chain is only one-stage collapse, which is different from the polyethylene linear and ring chains. This investigation can provide some insights into the statistical properties of knotted polymer chains.

  15. Sampling and II-Sampling Expansions

    Indian Academy of Sciences (India)

    J Sousa Pinto; R F Hoskins

    2000-11-01

    Using the hyperfinite representation of functions and generalized functions this paper develops a rigorous version of the so-called `delta method' approach to sampling theory. This yields a slightly more general version of the classical WKS sampling theorem for band-limited functions.

  16. DNA Sampling Hook

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The DNA Sampling Hook is a significant improvement on a method of obtaining a tissue sample from a live fish in situ from an aquatic environment. A tissue sample...

  17. Chorionic Villus Sampling (CVS)

    Science.gov (United States)

    ... Pregnancy > Prenatal care > Chorionic villus sampling Chorionic villus sampling E-mail to a friend Please fill in ... It's been added to your dashboard . Chorionic villus sampling (CVS) is a prenatal test . It’s used to ...

  18. Iowa Geologic Sampling Points

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — Point locations of geologic samples/files in the IGS repository. Types of samples include well cuttings, outcrop samples, cores, drillers logs, measured sections,...

  19. Network and adaptive sampling

    CERN Document Server

    Chaudhuri, Arijit

    2014-01-01

    Combining the two statistical techniques of network sampling and adaptive sampling, this book illustrates the advantages of using them in tandem to effectively capture sparsely located elements in unknown pockets. It shows how network sampling is a reliable guide in capturing inaccessible entities through linked auxiliaries. The text also explores how adaptive sampling is strengthened in information content through subsidiary sampling with devices to mitigate unmanageable expanding sample sizes. Empirical data illustrates the applicability of both methods.

  20. Exact goodness-of-fit tests for Markov chains.

    Science.gov (United States)

    Besag, J; Mondal, D

    2013-06-01

    Goodness-of-fit tests are useful in assessing whether a statistical model is consistent with available data. However, the usual χ² asymptotics often fail, either because of the paucity of the data or because a nonstandard test statistic is of interest. In this article, we describe exact goodness-of-fit tests for first- and higher order Markov chains, with particular attention given to time-reversible ones. The tests are obtained by conditioning on the sufficient statistics for the transition probabilities and are implemented by simple Monte Carlo sampling or by Markov chain Monte Carlo. They apply both to single and to multiple sequences and allow a free choice of test statistic. Three examples are given. The first concerns multiple sequences of dry and wet January days for the years 1948-1983 at Snoqualmie Falls, Washington State, and suggests that standard analysis may be misleading. The second one is for a four-state DNA sequence and lends support to the original conclusion that a second-order Markov chain provides an adequate fit to the data. The last one is six-state atomistic data arising in molecular conformational dynamics simulation of solvated alanine dipeptide and points to strong evidence against a first-order reversible Markov chain at 6 picosecond time steps.

  1. Dynamics of Chain Exchange in Block Copolymer Micelles

    Science.gov (United States)

    Lodge, Timothy

    Block copolymer micelles are rarely at equilibrium. The primary reason is the large number of repeat units in the insoluble block, Ncore, which makes the thermodynamic penalty for extracting a single chain (``unimer exchange'') substantial. As a consequence, the critical micelle concentration (CMC) is rarely accessed experimentally; however, in the proximity of a critical micelle temperature (CMT), equilibration is possible. We have been using time-resolved small angle neutron scattering (TR-SANS) to obtain a detailed picture of the mechanisms and time scales for chain exchange, at or near equilibrium. Our model system is poly(styrene)-block-poly(ethylene-alt-propylene)) (PS-PEP), in the PEP-selective solvent squalane (C30H62) . Equivalent micelles with either normal (hPS) or perdeuterated (dPS) cores are initially mixed in a blend of isotopically substituted squalane, designed to contrast-match a 50:50 hPS:dPS core. Samples are then annealed at a target temperature, and chain exchange is revealed quantitatively by the temporal decay in scattered intensity. The rate of exchange as function of concentration, temperature, Ncore, Ncorona, and chain architecture (diblock versus triblock) will be discussed.

  2. 土壤中短链氯化石蜡的气相色谱-电子捕获负化学电离-质谱分析方法%Quantification of short-chain chlorinated paraffins in soft sample using GC-ECNI-LRMS

    Institute of Scientific and Technical Information of China (English)

    韩双; 黄玉妹; 陈来国; 叶芝祥; 封永斌; 张素坤

    2012-01-01

    By evaluating the cleanup efficiency of potential interfering substances in soil samples with two cleanup methods, we developed a new method for analysis of SCCPs in soil samples. The soil samples were Soxhlet extracted, cleaned up by muhilayer silica gel column and then florisil column, and quantified using GC-ECNI- LRMS. The limit of quantification of SCCPs ranged from 100 to 600 pg·μL-1 The recoveries of SCCPs in blank spikes and matrix spikes were 130% ±8.50% and 108% ± 17.8% ( SD, n = 3), respectively. Six soil samples collected from Guangzhou suburban area were analyzed using this method, with the SCCP concentrations ranging from 12.9 to 34.5 ng.g-1, and a mean yalue of 26.1 ng.g-1%通过考察层析柱对测定短链氯化石蜡(SCCPs)干扰物去除效果的影响,结合实际土壤样品的净化需求,建立了一套适合分析土壤中SCCPs的前处理方法.土壤样品使用索氏抽提,采用硅胶复合柱和弗罗里硅土柱净化,运用气相色谱.质谱(ECNI源)检测SCCPs.SCCPs的仪器定量限为100—600Pg·μL-1.空白加标和基质加标中SCCPs的回收率分别为130%±8.50%和108%±17.8%(SD,n=3).利用该方法分析了采自广州市郊区的6个土壤样品,其SCCPs的含量范围为12.9-34.5ng·g-1,平均值为26.1ng·g-1.

  3. A possible chain of motivation

    Directory of Open Access Journals (Sweden)

    Rodica Ianole

    2007-12-01

    Full Text Available On a world-wide basis there is a growing concern about organization' s capability to retain their top talents. In the specific case of a student's organization . Team Work - we confront with the same problems: how to inspire our members to act in the spirit of the values we share: professionalism, team work and voluntariate, and how to determine them to remain part of the system. This is where motivation appears like one of those terms that can mean very different things depending on exactly where you sit. The aim of the present paper is to draw a schematic picture of how it can work a chain of motivation in Team Work and other similar organizations.

  4. The stylohyoid chain: CT imaging

    Energy Technology Data Exchange (ETDEWEB)

    Uysal Ramadan, Selma, E-mail: uysalselma@yahoo.co [Department of Radiology, Ankara Training and Research Hospital, Ankara 06590 (Turkey); Goekharman, Dilek, E-mail: gokharman@ttnet.net.t [Department of Radiology, Ankara Training and Research Hospital, Ankara 06590 (Turkey); Kosar, Pinar, E-mail: pkosar@hotmail.co [Department of Radiology, Ankara Training and Research Hospital, Ankara 06590 (Turkey); Kacar, Mahmut, E-mail: mkacar1961@gamil.co [Department of Radiology, Ankara Training and Research Hospital, Ankara 06590 (Turkey); Kosar, Ugur, E-mail: ugurkosar@hotmail.co [Department of Radiology, Ankara Training and Research Hospital, Ankara 06590 (Turkey)

    2010-09-15

    We aimed in this report to discuss the embryology, anatomy, theories of ossification and symptoms, clinical presentation, and diagnosis of the stylohyoid chain (SHC) variations, together with the role of radiographs, computed tomography (CT) and three-dimensional (3D)-CT in showing these variations. Because CT/3D-CT additionally facilitates visualization of the entire SHC with different axes, it is the most valuable method for establishing the relationship between the SHC and the surrounding tissue. SHC variation can be discovered during CT performed for indications other than ossified SHC. It is important to diagnose whether or not the SHC is ossified, since one of the treatment procedures in ossified SHC is total excision. If the clinician and radiologist are aware of these variations observed in the SHC, patients with vague symptoms may be spared unnecessary investigations and may be properly diagnosed earlier.

  5. Worldline as a Spin Chain

    CERN Document Server

    Fatollahi, Amir H

    2016-01-01

    The general theoretical ground for the models based on the compact angle coordinates is presented. It is observed that the proper dependence on compact coordinates has to be through the group elements and is achieved most naturally in a discrete-time formulation of the theory. By the construction, the discrete worldline inlaid by compact coordinates resembles the spin chains of magnetic systems. As examples, the models based on the groups U(1), $\\mathbb{Z}_N$ and SU(2) are explicitly constructed and their exact energy spectra are obtained. As the consequence of minima in the spectra, the models exhibit a phase transition of first-order. The dynamics by U(1) group is attempted to be fitted to the proposed role for monopoles in the dual Meissner effect of confinement mechanism.

  6. Revisiting Causality in Markov Chains

    CERN Document Server

    Shojaee, Abbas

    2016-01-01

    Identifying causal relationships is a key premise of scientific research. The growth of observational data in different disciplines along with the availability of machine learning methods offers the possibility of using an empirical approach to identifying potential causal relationships, to deepen our understandings of causal behavior and to build theories accordingly. Conventional methods of causality inference from observational data require a considerable length of time series data to capture cause-effect relationship. We find that potential causal relationships can be inferred from the composition of one step transition rates to and from an event. Also known as Markov chain, one step transition rates are a commonly available resource in different scientific disciplines. Here we introduce a simple, effective and computationally efficient method that we termed 'Causality Inference using Composition of Transitions CICT' to reveal causal structure with high accuracy. We characterize the differences in causes,...

  7. Spin chains and string theory.

    Science.gov (United States)

    Kruczenski, Martin

    2004-10-15

    Recently, an important test of the anti de Sitter/conformal field theory correspondence has been done using rotating strings with two angular momenta. We show that such a test can be described more generally as the agreement between two actions: one a low energy description of a spin chain appearing in the field theory side, and the other a limit of the string action in AdS5xS5. This gives a map between the mean value of the spin in the boundary theory and the position of the string in the bulk, and shows how a string action can emerge from a gauge theory in the large-N limit.

  8. Mathematical description of the position of mining chain links on a driving chain wheel

    Energy Technology Data Exchange (ETDEWEB)

    Dolipski, M.

    1982-01-01

    The paper analyzes effects of geometry on interaction between the chain and chain wheels of face conveyors in underground coal mines. Interaction between chain links and wheel toothing is investigated using mathematical models. Three mesh types are comparatively evaluated, so-called normal mesh, nominal mesh and special mesh. Chain position on the chain wheel is shown in 3 schemes. Mathematical formulae used for characterizing mesh types are derived. Effects of the following factors on interaction between a chain link and a chain wheel are analyzed: link quality and differences in quality and dimensions among chain links, friction wear of links and toothing, elastic and plastic chain elongation, friction between links and toothing. A geometric model of the interaction between the chain wheel and haulage chain (in the form of a double polygon) is used. The mathematical model permits the following problems to be analyzed: load distribution among chain links on a chain wheel, load distribution on toothing, load fluctuations, effects of friction wear of chain and toothing. Examples of practical use of the formulae are discussed. (14 refs.)

  9. Maximum-likelihood, self-consistent side chain free energies with applications to protein molecular dynamics

    CERN Document Server

    Jumper, John M; Sosnick, Tobin R

    2016-01-01

    To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a new methodology that computes a self-consistent approximation of the side chain free energy at every integration step. In analogy with the adiabatic Born-Oppenheimer approximation in which the nuclear dynamics are governed by the energy of the instantaneously-equilibrated electronic degrees of freedom, the protein backbone dynamics are simulated as preceding according to the dictates of the free energy of an instantaneously-equilibrated side chain potential. The side chain free energy is computed on the fly; hence, the protein backbone dynamics traverse a greatly smoothed energetic landscape, resulting in extremely rapid equilibration and sampling of the Boltzmann distribution. Because our method employs a reduced model involving single-bead side chains, we also provide a novel, maximum-likelihood type method to parameterize the side chain model using...

  10. Evaluation of urogenital Chlamydia trachomatis infections by cell culture and the polymerase chain reaction using a closed system

    DEFF Research Database (Denmark)

    Østergaard, Lars; Traulsen, J; Birkelund, Svend

    1993-01-01

    Two hundred and fifty-four specimens from males and females consulting a clinic for sexually transmitted diseases were analyzed for genital Chlamydia trachomatis infection. Each clinical sample was tested by the cell culture technique and the polymerase chain reaction using a closed system. When...... the two test systems were compared, the overall sensitivity of the polymerase chain reaction was 96% and the specificity 94% when compared to the cell culture technique. By use of a closed system for DNA extraction and sample transfer for the polymerase chain reaction, contamination of the samples...

  11. Evaluation of urogenital Chlamydia trachomatis infections by cell culture and the polymerase chain reaction using a closed system

    DEFF Research Database (Denmark)

    Østergaard, Lars; Traulsen, J; Birkelund, Svend

    1991-01-01

    Two hundred and fifty-four specimens from males and females consulting a clinic for sexually transmitted diseases were analyzed for genital Chlamydia trachomatis infection. Each clinical sample was tested by the cell culture technique and the polymerase chain reaction using a closed system. When...... the two test systems were compared, the overall sensitivity of the polymerase chain reaction was 96% and the specificity 94% when compared to the cell culture technique. By use of a closed system for DNA extraction and sample transfer for the polymerase chain reaction, contamination of the samples...

  12. Sample chambers with mother-daughter mode

    Energy Technology Data Exchange (ETDEWEB)

    Wilk, P.A.; Gregorich, K.E.; Hoffman, D.C.

    2001-07-12

    A set of eight stand-alone sample chambers with a common interface were constructed at LBNL for improved detection of alpha and fission decay chains over currently used designs. The stainless steel chambers (see Figure 1 for a schematic and Figure 2 for a photograph of a completed chamber) were constructed to allow for low background detection of a daughter event by removal of the sample following the detection of a parent event. This mother-daughter mode of operation has been utilized successfully with our Merry-go-Round (MG) detection system [Gregorich 1994].

  13. The Evolutionary Dynamics of Biofuel Value Chains

    DEFF Research Database (Denmark)

    Ponte, Stefano

    2014-01-01

    In this paper I propose to push the frontier of global value chain (GVC) governance analysis through the concept of ‘polarity’. Much of the existing GVC literature has focused on ‘unipolar’ value chains, where one group of ‘lead firms’ inhabiting a specific function in a chain plays a dominant role...... and multipolarity. Empirically, I do so by examining the evolutionary dynamics of governance in biofuel value chains, with specific focus on the key regulatory and institutional features that facilitated their emergence and expansion. First, I examine the formation, evolution, and governance of three national....../regional value chains (in Brazil, the US, and the EU); then, I provide evidence to support a trend towards the increasing but still partial formation of a global biofuel value chain and examine its governance traits....

  14. Kinetic Chain Rehabilitation: A Theoretical Framework

    Directory of Open Access Journals (Sweden)

    Aaron Sciascia

    2012-01-01

    Full Text Available Sequenced physiologic muscle activations in the upper and lower extremity result in an integrated biomechanical task. This sequencing is known as the kinetic chain, and, in upper extremity dominant tasks, the energy development and output follows a proximal to distal sequencing. Impairment of one or more kinetic chain links can create dysfunctional biomechanical output leading to pain and/or injury. When deficits exist in the preceding links, they can negatively affect the shoulder. Rehabilitation of shoulder injuries should involve evaluation for and restoration of all kinetic chain deficits that may hinder kinetic chain function. Rehabilitation programs focused on eliminating kinetic chain deficits, and soreness should follow a proximal to distal rationale where lower extremity impairments are addressed in addition to the upper extremity impairments. A logical progression focusing on flexibility, strength, proprioception, and endurance with kinetic chain influence is recommended.

  15. Kinetic chain rehabilitation: a theoretical framework.

    Science.gov (United States)

    Sciascia, Aaron; Cromwell, Robin

    2012-01-01

    Sequenced physiologic muscle activations in the upper and lower extremity result in an integrated biomechanical task. This sequencing is known as the kinetic chain, and, in upper extremity dominant tasks, the energy development and output follows a proximal to distal sequencing. Impairment of one or more kinetic chain links can create dysfunctional biomechanical output leading to pain and/or injury. When deficits exist in the preceding links, they can negatively affect the shoulder. Rehabilitation of shoulder injuries should involve evaluation for and restoration of all kinetic chain deficits that may hinder kinetic chain function. Rehabilitation programs focused on eliminating kinetic chain deficits, and soreness should follow a proximal to distal rationale where lower extremity impairments are addressed in addition to the upper extremity impairments. A logical progression focusing on flexibility, strength, proprioception, and endurance with kinetic chain influence is recommended.

  16. Position Paper on Intelligent Supply Chains

    DEFF Research Database (Denmark)

    Møller, Charles

    the concept of Intelligent Supply Chain and to establish an overall perspective based on information management. The claim made here is that the notion of the intelligent enterprise contributes with a new perspective on supply chain management that addresses the current challenges in an industrial supply...... chain. The argument is further that the existing information systems embodied in the standard enterprise information systems (EIS) have an important role in driving the development of modern supply chains though business processes. This is warranted by an analysis of the role of EIS on the development...... of intelligent supply chains. It is concluded that information management is critical to intelligent supply chains and a research agenda is outlined....

  17. Statistical mechanics approach to the sample deconvolution problem.

    Science.gov (United States)

    Riedel, N; Berg, J

    2013-04-01

    In a multicellular organism different cell types express a gene in different amounts. Samples from which gene expression levels can be measured typically contain a mixture of different cell types; the resulting measurements thus give only averages over the different cell types present. Based on fluctuations in the mixture proportions from sample to sample it is in principle possible to reconstruct the underlying expression levels of each cell type: to deconvolute the sample. We use a statistical mechanics approach to the problem of deconvoluting such partial concentrations from mixed samples, explore this approach using Markov chain Monte Carlo simulations, and give analytical results for when and how well samples can be unmixed.

  18. The effect of chain flexibility and chain mobility on radiation crosslinking of polymers

    Energy Technology Data Exchange (ETDEWEB)

    Jia Zhen, Sun

    2001-07-01

    Radiation crosslinking of polymers mainly depends on the structure of polymer chain. The flexibility and mobility of chain directly influence the possibility of the reactive radicals recombination. Flexible chain is easier to crosslink than rigid-chain polymer. The latter must be crosslinked at high temperature, as most polymers can only crosslink above their melting point. Structural effect also influences the mechanism of radiation crosslinking of polymers. We find from the results in literature and in our laboratory that, the flexibility chain polymer mainly crosslinked with H type, but the rigid chain polymer mainly crosslinked with Y type. (author)

  19. The effect of chain flexibility and chain mobility on radiation crosslinking of polymers

    Science.gov (United States)

    Jia Zhen, Sun

    2001-01-01

    Radiation crosslinking of polymers mainly depends on the structure of polymer chain. The flexibility and mobility of chain directly influence the possibility of the reactive radicals recombination. Flexible chain is easier to crosslink than rigid-chain polymer. The latter must be crosslinked at high temperature, as most polymers can only crosslink above their melting point. Structural effect also influences the mechanism of radiation crosslinking of polymers. We find from the results in literature and in our laboratory that, the flexibility chain polymer mainly crosslinked with H type, but the rigid chain polymer mainly crosslinked with Y type.

  20. The role of enterprise systems in supply chain networks: a taxonomy of supply chain strategies

    DEFF Research Database (Denmark)

    Møller, Charles

    2006-01-01

    in the supply chain and to choose the right supply chain strategy. The work is based on a comprehensive study of the Supply Chain Management (SCM) and Enterprise Resource Planning (ERP) literature and the study suggests that there is an emerging new research potential for Enterprise Systems (ES) in the supply......This paper proposes a taxonomy for supply chain integration strategies. The taxonomy is based on the contingencies of supply chain network coupling and the Extended Enterprise Systems (EES) architecture in the supply chain. The purpose of this model is to map the portfolio of relations...

  1. An Evaluation of a Markov Chain Monte Carlo Method for the Rasch Model.

    Science.gov (United States)

    Kim, Seock-Ho

    2001-01-01

    Examined the accuracy of the Gibbs sampling Markov chain Monte Carlo procedure for estimating item and person (theta) parameters in the one-parameter logistic model. Analyzed four empirical datasets using the Gibbs sampling, conditional maximum likelihood, marginal maximum likelihood, and joint maximum likelihood methods. Discusses the conditions…

  2. Strategy to Enhance International Supply Chain Security

    Science.gov (United States)

    2007-07-01

    a strategic plan to enhance the security of the international supply chain , including protocols for the expeditious resumption of the flow of trade...following a transportation disruption or transportation security incident. The Strategy to Enhance International Supply Chain Security exists within a...extensive risk analysis specific to the risk area they cover in the supply chain . Assessments are used to identify the highest risk areas and resources

  3. Evaluating Reverse Supply Chain Efficiency: Manufacturer's Perspective

    DEFF Research Database (Denmark)

    Kumar, M.; Tiwari, M. K.; Wong, K. Y.

    2014-01-01

    The paper aims to illustrate the use of fuzzy data envelopment analysis (DEA) in analyzing reverse supply chain (RSC) performance from the manufacturer's perspective. By using an alternative alpha-cut approach, the fuzzy DEA model was converted into a crisp linear programming problem, thereby...... usually ensures an environmentally friendly supply chain network, companies which have implemented RSC techniques since a longer duration do not necessarily have a more efficient supply chain in general....

  4. Supply Chain Performance Evaluation: Trends and Challenges

    OpenAIRE

    Ezutah U. Olugu; Kuan Y. Wong

    2009-01-01

    Problem statement: In todays manufacturing world, globalization policies and rejuvenation have created a more intensive competition amongst manufacturers. On the other hand, manufacturers have turned to the option of adopting innovative technologies, process re-engineering and strategies such as efficient supply chain management to achieve a sustainable competitive advantage. Effective supply chain performance measurement has been identified as a key issue towards efficient supply chain manag...

  5. PRINCIPLES OF THE SUPPLY CHAIN PERFORMANCE MEASUREMENT

    OpenAIRE

    BEATA ŒLUSARCZYK; SEBASTIAN KOT

    2012-01-01

    Measurement of performance in every business management is a crucial activity allowing for effectiveness increase. The lack of suitable performance measurement is especially noticed in complex systems as supply chains. Responsible persons cannot manage effectively without suitable set of measures those are base for comparison to previous data or effects of other supply chain functioning. The analysis shows that it is very hard to find balanced set of supply chain performance measures those sh...

  6. Finding gold in the supply chain.

    Science.gov (United States)

    Caudle, Allen

    2009-12-01

    To optimize supply chain performance and achieve savings that enhance the bottom line, hospitals should: Generate purchase orders for every item purchased. Ensure the organization is protected from undue vendor influence. Keep track of where supply chain dollars are going. Review contracts regularly to ensure competitiveness. Have a contract for each product category. Buy only what the organization is sure to use. Get rid of excess inventory. Develop a strategic plan for continued supply chain savings.

  7. Toc Approach for Supply Chain Performance Enhancement

    OpenAIRE

    Brijesh Ainapur; Ritesh Singh; P.R.Vittal

    2011-01-01

    Many foundries are operating at lower levels than the installed capacities. Study of 56 foundries acrossIndia has shown that only 68% of installed capacities are being utilized. This is mainly because of lack ofco-ordination among the supply chain partners. This study is an effort in identifying these gaps using TOCapproach which will help in supply chain performance enhancement.Field of Supply Chain Management witnessed rapid growth in recent past and proved to be a successfultool for organi...

  8. Supply chain integration:challenges and solutions

    OpenAIRE

    Sweeney, Edward

    2011-01-01

    Since its introduction by management consultants in the early 1980s, supply chain management (SCM) has been primarily concerned with the integration of processes and activities both within and between organisations. The concept of supply chain integration (SCI) is based on documented evidence that suggests that much of the waste throughout businesses is a consequence of fragmented supply chain configurations. However, there is also evidence to suggest that the achievement of higher levels of ...

  9. Collaborative Planning in Modern Supply Chain

    OpenAIRE

    Nýdlová, Olga

    2009-01-01

    This master thesis describes and proves how companies can improve their operational performance and supplier relationships by using modern collaborative and planning practices, specifically the Collaborative Planning Forecasting and Replenishment (CPFR) concept. The theoretical part depicts main developments in supply chain planning over time, shows common challenges in the world of supply chain and offers possible solutions in terms of collaborative supply chain planning practices. The pract...

  10. Responsive supply chain: modeling and simulation

    Directory of Open Access Journals (Sweden)

    Amit Kumar Sinha

    2015-06-01

    Full Text Available Unexpected occurrence like natural calamity, abruptly change in customer demands, upgradation of technologies, necessity of compatible suppliers etc. is the most challenging issues even for efficient global supply chain management. Therefore, modeling of responsive supply chain is an emerging technology for sustaining any firm/industry in future competitive environment. In this paper, an attempt has been made to not only analyze the performance of efficient supply chain management but also how to improve the performance of existing supply chain with the objective of developing a modeling of responsive supply chain management. The complexity of the model is also highlighted with the help of numerical example. This paper also explores the possibility to mathematical modeling of the responsive supply chain which will be an emerging topic for researchers and practitioners. The modeling of responsive supply chain can be employed as a competitive strategy for e-commerce, green supply chain, and compatible supplier selection problem. The another salient feature of this paper is that a distinct comparative literature review of the lean, agile, efficient, and responsive supply chain management has been presented.

  11. Towards traceability in cocoa - chocolate supply chain

    OpenAIRE

    Syahruddin, Normansyah

    2011-01-01

    The multi – events of food alerts and food risks which occurred in a lengthy period and various locations, grows concern of consumers to question the safety of the food that they consumed. For food producers, occurrences of food alert forced them to review their supply chain to identify what went wrong in their supply chain. To do this, they need a good traceability system that capable in revealing the problems occurred along the chains. In general, a typical food supply chain is consists of ...

  12. Metastability of exponentially perturbed Markov chains

    Institute of Scientific and Technical Information of China (English)

    陈大岳; 冯建峰; 钱敏平

    1996-01-01

    A family of irreducible Markov chains on a finite state space is considered as an exponential perturbation of a reducible Markov chain. This is a generalization of the Freidlin-Wentzell theory, motivated by studies of stochastic Ising models, neural network and simulated annealing. It is shown that the metastability is a universal feature for this wide class of Markov chains. The metastable states are simply those recurrent states of the reducible Markov chain. Higher level attractors, related attractive basins and their pyramidal structure are analysed. The logarithmic asymptotics of the hitting time of various sets are estimated. The hitting time over its mean converges in law to the unit exponential distribution.

  13. Electronic properties of aperiodic quantum dot chains

    Science.gov (United States)

    Korotaev, P. Yu.; Vekilov, Yu. Kh.; Kaputkina, N. E.

    2012-04-01

    The electronic spectral and transport properties of aperiodic quantum dot chains are investigated. The systems with singular continuous energy spectrum are considered: Thue-Morse chain, double-periodic chain, Rudin-Shapiro chain. The influence of electronic energy in quantum dot on the spectral properties, band structure, density of states and spectral resistivity, is discussed. Low resistivity regions correspond to delocalized states and these states could be current states. Also we discuss the magnetic field application as the way to tune electronic energy in quantum dot and to obtain metallic or insulating conducting states of the systems.

  14. Tests for intact and collapsed magnetofossil chains

    Science.gov (United States)

    Egli, R.

    2012-04-01

    In recent years, new techniques for the detection of magnetofossils have been proposed, based on their unique first-order reversal curves (FORC) and ferromagnetic resonance (FMR) signatures. These signatures are related to the non-interacting (FORC) and strongly uniaxial anisotropy (FMR) of isolated chains of magnetic particles. However, little is known about the fate of these signatures in sediments where magnetosome chains collapsed during early diagenetic processes. Due to the impossibility of observing the particle arrangement in-situ, the structure of collapsed chains can only be inferred from TEM images of magnetic extracts and from first-principles consideration on the mechanical stability of magnetosome chains once the biological material around them is dissolved. The magnetic properties of double chains, produced by some strains of cocci, are also not known. According to these considerations, four main magnetofossil structures were taken into consideration: (1) isolated, linear chains, (2) double, half-staggered chains, where the gaps of one chain face the magnetosomes in the other chain, (3) double chains with side-to-side magnetosomes, which might result from a "jackknife" type of collapse of a single, long chain, and (4) zig-zag collapsed chains of elongated crystals, where the magnetosome long axes are perpendicular to the chain axis. The collapsed structures might be relevant in sediments where magnetofossils carry a significant part of the remanent magnetization, because chain collapse tends to cancel the original natural remanent magnetization. Detailed models for the hysteretic and anhysteretic properties of structures (1-4) have been calculated by taking realistic distributions of magnetosome size, elongation, and spacing into account, as inferred from a number of published TEM observations. Model calculations took a total of >2 years continuous running time on two computers in an effort to obtain realistic results, which are shown here for the

  15. Lymphoplasmacytic lymphoma causing light chain cast nephropathy.

    Science.gov (United States)

    Pérez, Nuria S; Garcia-Herrera, Adriana; Rosiñol, Laura; Palos, Lily; Santiago, Evelyn; Espinosa, Gerard; Solé, Manel; Campistol, Josep M; Quintana, Luis F

    2012-01-01

    Plasma cell dyscrasias are frequently associated with kidney disease through the production of monoclonal immunoglobulin but with a diverse set of pathologic renal patterns. While almost all patients with a renal biopsy showing a cast nephropathy have myeloma, kidney involvement associated with pathological immunoglobulin light chains and lymphoma is rare. To our knowledge, this is the first report of a cast nephropathy associated with lymphoplasmacytic lymphoma. We emphasize the relation between light chain deposition and renal dysfunction in this disease with production of light chains. A therapeutic approach that decreases light chain production appears to be warranted in these patients.

  16. Molecular Wring Resonances in Chain Molecules

    DEFF Research Database (Denmark)

    Bohr, Henrik; Brunak, Søren; Bohr, Jakob

    1997-01-01

    It is shown that the eigenfrequency of collective twist excitations in chain molecules can be in the megahertz and gigahertz range. Accordingly, resonance states can be obtained at specific frequencies, and phenomena that involve structural properties can take place. Chain molecules can alter...... their conformation and their ability to function, and a breaking of the chain can result. It is suggested that this phenomenon forms the basis for effects caused by the interaction of microwaves and biomolecules, e.g. microwave assisted hydrolysis of chain molecules....

  17. Improved Signal Chains for Readout of CMOS Imagers

    Science.gov (United States)

    Pain, Bedabrata; Hancock, Bruce; Cunningham, Thomas

    2009-01-01

    An improved generic design has been devised for implementing signal chains involved in readout from complementary metal oxide/semiconductor (CMOS) image sensors and for other readout integrated circuits (ICs) that perform equivalent functions. The design applies to any such IC in which output signal charges from the pixels in a given row are transferred simultaneously into sampling capacitors at the bottoms of the columns, then voltages representing individual pixel charges are read out in sequence by sequentially turning on column-selecting field-effect transistors (FETs) in synchronism with source-follower- or operational-amplifier-based amplifier circuits. The improved design affords the best features of prior source-follower-and operational- amplifier-based designs while overcoming the major limitations of those designs. The limitations can be summarized as follows: a) For a source-follower-based signal chain, the ohmic voltage drop associated with DC bias current flowing through the column-selection FET causes unacceptable voltage offset, nonlinearity, and reduced small-signal gain. b) For an operational-amplifier-based signal chain, the required bias current and the output noise increase superlinearly with size of the pixel array because of a corresponding increase in the effective capacitance of the row bus used to couple the sampled column charges to the operational amplifier. The effect of the bus capacitance is to simultaneously slow down the readout circuit and increase noise through the Miller effect.

  18. Supply chain performance: the role of regional markets

    Directory of Open Access Journals (Sweden)

    Ali Ghasemi

    2015-05-01

    Full Text Available This paper investigates the role of exports in the regional markets on the performance of supply chain. The study first determines critical variables affecting exports for entering into the regional markets and then measures the effects of these variables on the effectiveness of supply chain performance. The study uses two questionnaires, one for measuring the effects of various factors on export development and the other for measuring supply chain performance in Likert scale. Cronbach alpha for the mentioned questionnaires were calculated as 0.84 and 0.78, respectively. The population of the survey includes all small and medium enterprises active in city of Tehran, Iran and the study selects a sample of 250 people as a sample size. Using factor analysis, the study has determined seven factors including product development, government support, strategic orientation, customer satisfaction, competitive pressures, organizational capability and distribution strategies for entry into regional markets. In addition, the implementation of structural equation modeling has disclosed that product development and distribution strategies maintained the highest impact on export activities.

  19. 9 CFR 147.30 - Laboratory procedure recommended for the polymerase chain reaction (PCR) test for Mycoplasma...

    Science.gov (United States)

    2010-01-01

    ... the polymerase chain reaction (PCR) test for Mycoplasma gallisepticum and M. synoviae. 147.30 Section... Examination Procedures § 147.30 Laboratory procedure recommended for the polymerase chain reaction (PCR) test... sample (100 to 2000 ng/5 μl) with one of the following 45 μl PCR cocktails: (i) 5 μl 10x PCR buffer, 1...

  20. Self-assembly of long chain fatty acids: Effect of a methyl branch

    DEFF Research Database (Denmark)

    Liljeblad, Jonathan F. D.; Tyrode, Eric; Thormann, Esben

    2014-01-01

    chains of the straight chain fatty acids appear to be oriented perpendicular to the sample surface, based on an orientational analysis of VSFS data and the odd/even effect. In addition, the selection of the subphase (neat water or CdCl2 containing water buffered to pH 6.0) used for the LB-deposition has...... a profound influence on the monolayer morphology, packing density, compressibility, and conformational order. Finally, the orientation of the 19-MEA dimethyl moiety is estimated, and a strategy for performing an orientational analysis to determine the complete molecular orientation of the aliphatic chains...

  1. Discrete Equilibrium Sampling with Arbitrary Nonequilibrium Processes

    CERN Document Server

    Hamze, Firas

    2015-01-01

    We present a novel framework for performing statistical sampling, expectation estimation, and partition function approximation using \\emph{arbitrary} heuristic stochastic processes defined over discrete state spaces. Using a highly parallel construction we call the \\emph{sequential constraining process}, we are able to simultaneously generate states with the heuristic process and accurately estimate their probabilities, even when they are far too small to be realistically inferred by direct counting. After showing that both theoretically correct importance sampling and Markov chain Monte Carlo are possible using the sequential constraining process, we integrate it into a methodology called \\emph{state space sampling}, extending the ideas of state space search from computer science to the sampling context. The methodology comprises a dynamic data structure that constructs a robust Bayesian model of the statistics generated by the heuristic process subject to an accuracy constraint, the posterior Kullback-Leibl...

  2. ARTIFACT FORMATION DURING NEUTRALIZATION OF TANK 50 SAMPLES

    Energy Technology Data Exchange (ETDEWEB)

    Crump, S.; Young, J.

    2014-08-01

    Degradation products have been identified in the extracts of Tank 50 samples analyzed by semivolatile organic compound analysis (SVOA) using gas chromatography/mass spectrometry (GC/MS). These materials, identified as short chain alkyl alcohols, were formed by acidification during sample preparation. A number of questions were raised about the formation of these and other materials reported in Tank 50 surface samples, and this report serves to address these questions.

  3. Effects of enterprise technology on supply chain collaboration: analysis of China-linked supply chain

    Science.gov (United States)

    Li, Ling

    2012-02-01

    Supply chain collaboration has received increasing attention from scholars and practitioners in recent years. However, our understanding of how enterprise information technology facilitates supply chain collaboration is still very limited, especially with regard to Chinese enterprise ownerships such as state-owned firms, joint-venture firms and local village-owned firms. This paper extends the theory established in enterprise information technology (IT) and supply chain collaboration literature and relates it with coordination in China-linked supply chain. Drawing upon an empirical study from 177 Chinese companies, we provide three major findings: (i) uncovered the importance of leveraging enterprise IT through supply chain collaboration; (ii) identified the relationship between enterprise ownership and enterprise technology use and supply chain collaboration in China-linked supply chain and (iii) illustrated effects of supply chain collaborative activities on operational and market performance.

  4. An online algorithm for generating fractal hash chains applied to digital chains of custody

    CERN Document Server

    Bradford, Phillip G

    2007-01-01

    This paper gives an online algorithm for generating Jakobsson's fractal hash chains. Our new algorithm compliments Jakobsson's fractal hash chain algorithm for preimage traversal since his algorithm assumes the entire hash chain is precomputed and a particular list of Ceiling(log n) hash elements or pebbles are saved. Our online algorithm for hash chain traversal incrementally generates a hash chain of n hash elements without knowledge of n before it starts. For any n, our algorithm stores only the Ceiling(log n) pebbles which are precisely the inputs for Jakobsson's amortized hash chain preimage traversal algorithm. This compact representation is useful to generate, traverse, and store a number of large digital hash chains on a small and constrained device. We also give an application using both Jakobsson's and our new algorithm applied to digital chains of custody for validating dynamically changing forensics data.

  5. Markov chain Monte Carlo simulation for Bayesian Hidden Markov Models

    Science.gov (United States)

    Chan, Lay Guat; Ibrahim, Adriana Irawati Nur Binti

    2016-10-01

    A hidden Markov model (HMM) is a mixture model which has a Markov chain with finite states as its mixing distribution. HMMs have been applied to a variety of fields, such as speech and face recognitions. The main purpose of this study is to investigate the Bayesian approach to HMMs. Using this approach, we can simulate from the parameters' posterior distribution using some Markov chain Monte Carlo (MCMC) sampling methods. HMMs seem to be useful, but there are some limitations. Therefore, by using the Mixture of Dirichlet processes Hidden Markov Model (MDPHMM) based on Yau et. al (2011), we hope to overcome these limitations. We shall conduct a simulation study using MCMC methods to investigate the performance of this model.

  6. Consumer-perceived quality in 'traditional' food chains

    DEFF Research Database (Denmark)

    Krystallis, Athanasios; Chryssochoidis, George; Scholderer, Joachim

    2007-01-01

    pressing yet? The present paper seeks to answer this question based on a survey conducted in the Athens area, involving a sample of 268 participants responsible for food purchasing decisions. The survey mainly aims to develop an integrated model of factors that affect consumer-perceived meat quality...... and to develop the profile of different consumer segments in relation to these perceptions. The substantial findings of the survey include the fact that, despite their enormous per capita consumption, the majority of consumers are not particularly involved in the meat-purchasing process. Rather they attach......Recent food scares have increased consumer concern about meat safety. However, the Greek 'traditional' meat supply chain from producers to local butchers does not seem to realise the pressing consumer demand for certified meat quality. Or is it that, in such food chains, this demand is not so...

  7. Sampling in Practice

    DEFF Research Database (Denmark)

    Petersen, Lars; Esbensen, Kim Harry

    2005-01-01

    A basic knowledge of the Theory of Sampling (TOS) and a set of only eight sampling unit operations is all the practical sampler needs to ensure representativeness of samples extracted from all kinds of lots: production batches, - truckloads, - barrels, sub-division in the laboratory, sampling...... in nature and in the field (environmental sampling, forestry, geology, biology), from raw materials or manufactory processes etc. We here can only give a brief introduction to the Fundamental Sampling Principle (FSP) and these eight Sampling Unit Operations (SUO’s). Always respecting FSP and invoking only...... the necessary SUO’s (dependent on the practical situation) is the only prerequisite needed for eliminating all sampling bias and simultaneously minimizing sampling variance, and this is in addition a sure guarantee for making the final analytical results trustworthy. No reliable conclusions can be made unless...

  8. Supply Chain Systems Architecture and Engineering Design: Green-field Supply Chain Integration

    OpenAIRE

    Radanliev, Petar

    2015-01-01

    This paper developed a new theory for supply chain architecture, and engineering design that enables integration of the business and supply chain strategies. The architecture starts with individual supply chain participants and derives insights into the complex and abstract concept of green-field integration design. The paper presented a conceptual system for depicting the interactions between business and supply chain strategy engineering. The system examines the decisions made when engineer...

  9. Geometry behind chordal Loewner chains

    CERN Document Server

    Contreras, Manuel D; Gumenyuk, Pavel

    2010-01-01

    Loewner Theory is a deep technique in Complex Analysis affording a basis for many further important developments such as the proof of famous Bieberbach's conjecture and well-celebrated Schramm's Stochastic Loewner Evolution (SLE). It provides analytic description of expanding domains dynamics in the plane. Two cases have been developed in the classical theory, namely the {\\it radial} and the {\\it chordal} Loewner evolutions, referring to the associated families of holomorphic self-mappings being normalized at an internal or boundary point of the reference domain, respectively. Recently there has been introduced a new approach [arXiv:0807.1594v1, arXiv:0807.1715v1, arXiv:0902.3116v1] bringing together, and containing as quite special cases, radial and chordal variants of Loewner Theory. In the framework of this approach we address the question what kind of systems of simply connected domains can be described by means of Loewner chains of chordal type. As an answer to this question we establish a necessary and ...

  10. Jetfighter: An Experiential Value Chain Exercise

    Science.gov (United States)

    Sheehan, Norman T.; Gamble, Edward N.

    2010-01-01

    Value chain analysis is widely taught in business schools and applied by practitioners to improve business performance. Despite its ubiquity, many students struggle to understand and apply value chain concepts in practice. JetFighter uses a complex manufacturing process (making intricate paper planes) to provide students an opportunity to enhance…

  11. The Future of Resilient Supply Chains

    DEFF Research Database (Denmark)

    Donadoni, Mattia; Roden, Sinéad; Scholten, Kirstin

    This research aims to advance theoretical understanding around the management of supply chain disruptions through a multi-stage Delphi study on supply chain resilience. Stage one focused on polling academic experts followed by a second stage with practitioners from automotive, electronics and food...

  12. Achieving Supply Chain Integration within Construction Industry

    Directory of Open Access Journals (Sweden)

    Peter McDermotti

    2012-11-01

    Full Text Available The main driver behind the adoption of supply chain management (SCM philosophy into the construction industry was the successes within other industry sectors. SCM can be defined as network of different organisations, linked upstream and downstream in a chain, aiming to produce quality and value in the services and products for the end consumers through integrated processes and activities. In order to achieve the optimised level of integration of the whole supply chain, the industry has responded in various forms. This paper will discuss different initiatives by the researchers,construction industry,and the UK government in order to achieve optimal level of supply chain integration. This paper will discuss the concept of aggregation,and also look at other supply chain integration related concepts including client-led supply chain, knowledge about the whole supply chain, effects of procurement on integration of supply chain, etc. The paper will give a brief overview and initial findings of a project undertaken by the authors, and also include examples from the UK construction industry on bundling of the supply and demand.

  13. Design Principles for Closed Loop Supply Chains

    NARCIS (Netherlands)

    H.R. Krikke (Harold); C.P. Pappis (Costas); G.T. Tsoulfas; J.M. Bloemhof-Ruwaard (Jacqueline)

    2001-01-01

    textabstractIn this paper we study design principles for closed loop supply chains. Closed loop supply chains aim at closing material flows thereby limiting emission and residual waste, but also providing customer service at low cost. We study 'traditional' and 'new' design principles known in the l

  14. A modeling framework for supply chain simulation

    NARCIS (Netherlands)

    van der Zee, D.J.; van der Vorst, J.G.A.J.

    2002-01-01

    In many industries logistic optimization on a company scale is no longer sufficient to meet the competition. Nowadays, competition takes place between supply chains. Intrinsic to the concept and success of a supply chain is the tuning of the activities of the companies involved. Given the complexity

  15. Using Games to Teach Markov Chains

    Science.gov (United States)

    Johnson, Roger W.

    2003-01-01

    Games are promoted as examples for classroom discussion of stationary Markov chains. In a game context Markov chain terminology and results are made concrete, interesting, and entertaining. Game length for several-player games such as "Hi Ho! Cherry-O" and "Chutes and Ladders" is investigated and new, simple formulas are given. Slight…

  16. Towards effective food chains : models and applications

    NARCIS (Netherlands)

    Trienekens, J.H.; Top, J.L.; Vorst, van der J.G.A.J.; Beulens, A.J.M.

    2010-01-01

    Food chain management research can help in the analysis and redesign of value creation and the product flow throughout the chain from primary producer down to the consumer. The aim is to meet consumer and societal requirements effectively at minimal cost. In the Wageningen UR strategic research prog

  17. Operational excellence in logistics and supply chains

    OpenAIRE

    2015-01-01

    This volume contains research contributions by an international group of authors focusing on innovative models to optimize logistics and supply chains at an operational level. They address process efficiency and data-related aspects. Supply chain security insights are also given.

  18. Current Control Strategy of Chain Circuit STATCOM

    Institute of Scientific and Technical Information of China (English)

    WANG Xuan; FU Jian; TENG Letian; SUN Lijing; ZHAO Ruibin; WU Shouyuan; DENG Zhanfeng

    2012-01-01

    In order to study the current control strategy based on the chain circuit static synchronous compensator (STATCOM) dynamic model and the design control system with good stability and tracking accuracy, this paper applies the chain circuit STATCOM small signal AC model, and proposes the following assumptions:

  19. On robustness in food supply chain networks

    NARCIS (Netherlands)

    Vlajic, J.V.; Vorst, van der J.G.A.J.; Hendrix, E.M.T.

    2010-01-01

    Purpose: Today's business environment is characterized by challenges of strong global competition where companies tend to achieve leanness and maximum responsiveness to customer demand. Lean supply chain networks are vulnerable to all kind of disruptions. For food supply chain networks (FSCNs), due

  20. Using management information in broiler supply chains

    NARCIS (Netherlands)

    Yassin, H.

    2012-01-01

    The Dutch broiler supply chain involves several interdependent firms such as breeding and feed companies, rearing farms, breeder farms, broiler hatcheries and broiler farms. To stay competitive and sustain continuity, evaluation of production at each level of the chain is crucial. Good quality data

  1. Localized Lymph Node Light Chain Amyloidosis

    Directory of Open Access Journals (Sweden)

    Binod Dhakal

    2015-01-01

    Full Text Available Immunoglobulin-derived light chain amyloidosis can occasionally be associated with localized disease. We present a patient with localized lymph node light chain amyloidosis without an underlying monoclonal protein or lymphoproliferative disorder and review the literature of lymph node amyloidosis discussing work-up and risk factors for systemic progression.

  2. Waste Reduction in Fresh Food Supply Chains

    DEFF Research Database (Denmark)

    Kaipia, Riikka; Loikkanen, Lauri; Dukovska-Popovska, Iskra

    2011-01-01

    The paper studies a well-known phenomenon, information sharing in supply chains, in a new context, fresh foods, with a specific goal, supporting sustainable performance in the supply chain. Fresh foods are important for retail stores, representing around half of retail sales, but form a challenging...

  3. Molecular dynamics studies of entangled polymer chains

    NARCIS (Netherlands)

    Bulacu, Monica Iulia

    2008-01-01

    The thesis presents three molecular dynamics studies of polymeric ensembles in which the chain entanglement plays the major role in the internal dynamics of the system. A coarse-grained model is used for representing the polymer chains as strings of beads connected by finite-extensible springs. In a

  4. Bethe vectors for XXX-spin chain

    Science.gov (United States)

    Burdík, Čestmír; Fuksa, Jan; Isaev, Alexei

    2014-11-01

    The paper deals with algebraic Bethe ansatz for XXX-spin chain. Generators of Yang-Baxter algebra are expressed in basis of free fermions and used to calculate explicit form of Bethe vectors. Their relation to N-component models is used to prove conjecture about their form in general. Some remarks on inhomogeneous XXX-spin chain are included.

  5. Qualitative methodology for efficient food chain design

    NARCIS (Netherlands)

    Apaiah, R.K.; Hendrix, E.M.T.; Meerdink, G.; Linnemann, A.R.

    2005-01-01

    This paper presents a methodology to efficiently design food supply chains. The goals of quality, cost and environmental load are looked at independently of each other. Food chains are made up of links and are designed to deliver a particular product with consumer-specified attributes. These attribu

  6. Synchronize Your Supply Chain with RFID

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    1 Executive Summary Driving efficiencies throughout your supply chain and increasing the velocity of items through the supply chain from creation to consumer is more than a business mandate today; it’s a matter of business survival. If your company doesn’t do it, your competition will. Radio Frequency Identification (RFID) is a true next-generation

  7. Cooperation and profit allocation in distribution chains

    NARCIS (Netherlands)

    Guardiola, L.A.; Meca, A.; Timmer, J.B.

    2005-01-01

    We study the coordination of actions and the allocation of profit in distribution chains under decentralized control. We consider distribution chains in which a single supplier supplies goods for replenishment of stocks of several retailers who, in turn, sell these goods to their own separate market

  8. Extremal hexagonal chains concerning largest eigenvalue

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this paper, we define a roll-attaching operation of a hexagonal chain, and prove Gutman's conjecture affirmatively by using the operation. The idea of the proof is also applicable to the results concerning extremal hexagonal chains for the Hosoya index and Merrifield-Simmons index.

  9. Effective food supply chains; generating, modelling and evaluating supply chain scenarios

    NARCIS (Netherlands)

    Vorst, van der J.G.A.J.

    2000-01-01

    Logistical co-ordination in FMCG supply chains

    The overall objectives of the research described in this thesis were to obtain insight into the applicability of the concept Supply Chain Management (SCM) in food supply chains (SCs) from a logistical point of view, and to find an efficient and

  10. A conceptual framework for supply chain governance: An application to agri-food chains in China

    NARCIS (Netherlands)

    Zhang, X.Y.; Aramyan, L.H.

    2009-01-01

    Purpose - Chinese agri-food chains consist of the millions of small scale farmers, who are not well structured and organized in the supply chain. Owing to market liberalization and globalization, one of the most challenging issues along agri-food chains in China is becoming the issue of how to link

  11. Teaching Lean Six Sigma within a Supply Chain Context: The Airplane Supply Chain Simulation

    Science.gov (United States)

    Ellis, Scott C.; Goldsby, Thomas J.; Bailey, Ana M.; Oh, Jae-Young

    2014-01-01

    Lean six sigma is a management methodology that firms can employ to achieve substantial improvement in supply chain performance. However, few pedagogical exercises facilitate students' use of a comprehensive set of lean six sigma principles within a supply chain context. We describe the Airplane Supply Chain Simulation that helps students…

  12. Integrating product design into the supply chain

    DEFF Research Database (Denmark)

    Khan, Omera; Stolte, Terje; Creazza, Alessandro

    2016-01-01

    of opportunities and challenges when integrating product design and the supply chain and subsequently a step-by-step guide is developed to address these. Practical Implications: The research provides key recommendations to companies on how to create competitive capabilities by integrating product design...... into the supply chain. Originality/Value: This paper provides novel insights to both practitioners and researchers. For practitioners detailed recommendations are given on how they can maximise benefits through integrating product design into the supply chain. The RBV has been harnessed to highlight how......Purpose: The aim of the research is to illustrate how companies can create competitive capabilities through integration of product design into the supply chain. In doing so the paper reveals the challenges and the opportunities that companies face when integrating product design and supply chain...

  13. Direct current hopping conductance along DNA chain

    Institute of Scientific and Technical Information of China (English)

    Ma Song-Shan; Xu Hui; Liu Xiao-Liang; Li Ming-Jun

    2007-01-01

    This paper proposes a model of direct current(DC) electron hopping transport in DNA,in which DNA is considered as a binary one-dimensional disordered system.To quantitatively study the DC conductivity in DNA,it numerically calculates the DC conductivity of DNA chains with difierent parameter values.The result shows that the DC conductivity of DNA chain increases with the increase of temperature.And the conductivity of DNA chain is depended on the probability P.which represents the degree of compositional disorder in a DNA sequence to some extent.For P<0.5,the conductivity of DNA chain decreases with the increase of P,while for P≥0.5,the conductivity increases with the increase of p.The DC conductivity in DNA chain also varies with the change of the electric field,it presents non-Ohm's law conductivity characteristics.

  14. Chain graph models and their causal interpretations

    DEFF Research Database (Denmark)

    Lauritzen, Steffen Lilholt; Richardson, Thomas S.

    2002-01-01

    the equilibrium distributions of dynamic models with feed-back. These dynamic interpretations lead to a simple theory of intervention, extending the theory developed for directed acyclic graphs. Finally, we contrast chain graph models under this interpretation with simultaneous equation models which have......Chain graphs are a natural generalization of directed acyclic graphs and undirected graphs. However, the apparent simplicity of chain graphs belies the subtlety of the conditional independence hypotheses that they represent. There are many simple and apparently plausible, but ultimately fallacious......, interpretations of chain graphs that are often invoked, implicitly or explicitly. These interpretations also lead to flawed methods for applying background knowledge to model selection. We present a valid interpretation by showing how the distribution corresponding to a chain graph may be generated from...

  15. Structural repertoire of immunoglobulin λ light chains

    KAUST Repository

    Chailyan, Anna

    2011-03-01

    The immunoglobulin λ isotype is present in nearly all vertebrates and plays an important role in the human immune system. Despite its importance, few systematic studies have been performed to analyze the structural conformation of its variable regions, contrary to what is the case for κ and heavy chains. We show here that an analysis of the structures of λ chains allows the definition of a discrete set of recurring conformations (canonical structures) of their hypervariable loops and, most importantly, the identification of sequence constraints that can be used to predict their structure. We also show that the structural repertoire of λ chains is different and more varied than that of the κ chains, consistently with the current view of the involvement of the two major light-chain families in complementary strategies of the immune system to ensure a fine tuning between diversity and stability in antigen recognition. © 2011 Wiley-Liss, Inc.

  16. Quantum Markov Chain Mixing and Dissipative Engineering

    DEFF Research Database (Denmark)

    Kastoryano, Michael James

    2012-01-01

    This thesis is the fruit of investigations on the extension of ideas of Markov chain mixing to the quantum setting, and its application to problems of dissipative engineering. A Markov chain describes a statistical process where the probability of future events depends only on the state...... of the system at the present point in time, but not on the history of events. Very many important processes in nature are of this type, therefore a good understanding of their behaviour has turned out to be very fruitful for science. Markov chains always have a non-empty set of limiting distributions...... (stationary states). The aim of Markov chain mixing is to obtain (upper and/or lower) bounds on the number of steps it takes for the Markov chain to reach a stationary state. The natural quantum extensions of these notions are density matrices and quantum channels. We set out to develop a general mathematical...

  17. IMPLEMENTING SUSTAINABILITY INTO SUPPLY CHAIN OPERATIONS

    DEFF Research Database (Denmark)

    Jørsfeldt, Lilyana Makarowa

    2016-01-01

    Sustainability is acknowledged as a top strategic agenda by many global companies. As increasing globalization and outsourcing trends shift competition from single company affairs to competition among supply chains, the implementation of sustainability within companies’ supply chain operations...... of sustainable supply chain management SSCM in practice. This study aims to explore in detail the implementation of sustainability in ongoing supply chain operations. Specifically, it investigates how a company approaches the implementation of sustainability in different areas of its supply chain operations...... functions and across the organizations involved in the supply chain—to achieve sustainability deployment. The outcomes of the study are as follows: (1) Conceptual frameworks are developed based on empirical data from the case study. These frameworks cover three different levels of the business system...

  18. The Tax-Efficient Supply Chain

    DEFF Research Database (Denmark)

    Webber, Stuart

    2011-01-01

    Many multinational enterprises are restructuring supply chains to reduce their cost structures. As trade barriers fall and communications technologies improve, it has become easier and more cost-effective to manage business operations across international borders. This has motivated businesses...... their supply chains, and they should endeavor to maximize net income when doing so. This recommendation differs from the great majority of supply chain literature, which has generally recommended that businesses seek to minimize pretax costs. One of the most important activities for both supply chain and tax...... -- specifically a variety of legal organizations within the MNE -- to determine the best opportunities for integrated supply chain and income tax planning. This article also identifies a number of tax issues firms need to consider when making these important decisions....

  19. Research Methodologies in Supply Chain Management

    DEFF Research Database (Denmark)

    Kotzab, Herbert

    While supply chain management has risen to great prominence in recent year, there are hardly related developments in research methodologies. Yet, as supply chains cover more than one company, one central issue is how to collect and analyse data along the whole or relevant part of the supply chain....... Within the 36 chapters 70 authors bring together a rich selection of theoretical and practical examples of how research methodologies are applied in supply chain management. The book contains papers on theoretical implications as well as papers on a range of key methods, such as modelling, surveys, case...... studies or action research. It will be of great interest to researchers in the area of supply chain management and logistics, but also to neighbouring fields, such as network management or global operations....

  20. Environmental management the supply chain perspective

    CERN Document Server

    Wong, Christina W Y; Lun, Y H Venus; Cheng, T C E

    2015-01-01

    In view of the increasing quest for environmental management in businesses, this book provides a good reference to firms to understand how they may manage their supply chains to improve business and environmental performance. The book consists of six chapters covering such topics as environmental management, environmental management practices with supply chain efforts, collaborative environmental management, organizational capabilities in environmental management, environmental disclosure, and closed-loop supply chains. The book presents theory-driven discussions on the link between environmental management and business performance in the context of supply chain management. The book will be useful for firms to learn from the research findings and real-life cases to develop plans to implement environmental management practices jointly with supply chain partners.