Instant Backbone.js application development

CERN Document Server

Hunter, Thomas

2013-01-01

Get to grips with a new technology, understand what it is and what it can do for you, and then get to work with the most important features and tasks. This book is a practical, step-by-step tutorial that will teach you to build Backbone.js applications quickly and efficiently.This book is targeted towards developers. It is assumed that you have at least a basic understanding of JavaScript and jQuery selectors. If you are interested in building dynamic Single Page Applications that interact heavily with a backend server, then this is the book for you.

Backbone dynamics of the EIAV-Tat protein from 15N relaxation studies

International Nuclear Information System (INIS)

Ejchart, A.; Herrmann, F.; Roesch, P.; Sticht, H.; Willbold, D.

1994-01-01

The work investigates the mobility of EIAV-Tat protein backbone by measuring the relaxation parameters of the 15 N nitrogens. High degree of the flexibility, non-typical of rigid, well structured proteins was shown

Backbone assignment of the little finger domain of a Y-family DNA polymerase.

Science.gov (United States)

Ma, Dejian; Fowler, Jason D; Suo, Zucai

2011-10-01

Sulfolobus solfataricus DNA polymerase IV (Dpo4), a prototype Y-family DNA polymerase, contains a unique little finger domain besides a catalytic core. Here, we report the chemical shift assignments for the backbone nitrogens, α and β carbons, and amide protons of the little finger domain of Dpo4. This work and our published backbone assignment for the catalytic core provide the basis for investigating the conformational dynamics of Dpo4 during catalysis using solution NMR spectroscopy.

Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure

International Nuclear Information System (INIS)

Wang Lincong; Donald, Bruce Randall

2004-01-01

We have derived a quartic equation for computing the direction of an internuclear vector from residual dipolar couplings (RDCs) measured in two aligning media, and two simple trigonometric equations for computing the backbone (φ,ψ) angles from two backbone vectors in consecutive peptide planes. These equations make it possible to compute, exactly and in constant time, the backbone (φ,ψ) angles for a residue from RDCs in two media on any single backbone vector type. Building upon these exact solutions we have designed a novel algorithm for determining a protein backbone substructure consisting of α-helices and β-sheets. Our algorithm employs a systematic search technique to refine the conformation of both α-helices and β-sheets and to determine their orientations using exclusively the angular restraints from RDCs. The algorithm computes the backbone substructure employing very sparse distance restraints between pairs of α-helices and β-sheets refined by the systematic search. The algorithm has been demonstrated on the protein human ubiquitin using only backbone NH RDCs, plus twelve hydrogen bonds and four NOE distance restraints. Further, our results show that both the global orientations and the conformations of α-helices and β-strands can be determined with high accuracy using only two RDCs per residue. The algorithm requires, as its input, backbone resonance assignments, the identification of α-helices and β-sheets as well as sparse NOE distance and hydrogen bond restraints.Abbreviations: NMR - nuclear magnetic resonance; RDC - residual dipolar coupling; NOE - nuclear Overhauser effect; SVD - singular value decomposition; DFS - depth-first search; RMSD - root mean square deviation; POF - principal order frame; PDB - protein data bank; SA - simulated annealing; MD - molecular dynamics

First-line HIV treatment: evaluation of backbone choice and its budget impact

Directory of Open Access Journals (Sweden)

Orietta Zaniolo

2013-06-01

Full Text Available OBJECTIVE: The gradual increase of persons living with HIV, mainly due to the reduced mortality achieved with effective antiretroviral therapies, calls for increased rationality and awareness in health resources consumption also during the early illness phases. Aim of this work is the estimation of the budget impact related to the variation in backbone prescribing trends in naïve patients.METHODS: Target population is the number of patients starting antiretroviral therapy each year, according to the Italian HIV surveillance registry, excluding patients receiving non-authorized or non-recommended regimens. We modeled 3-year mortality and durability rates on a dynamic cohort, basing on international literature. A prevalent patients analysis has also been conducted, for which the model is fed by a closed cohort consisting of all the patients without experience of virologic failure. The aim of this collateral analysis is to estimate the difference in current annual expenditures if the past prescription trends for patients starting therapy would have led to the evaluated hypothetical scenarios. Current Italian market shares of triple regimens containing first-choice or alternative backbones (tenofovir/emtricitabine, abacavir/lamivudine, tenofovir/lamivudine and zidovudine/lamivudine are compared to three hypothetical scenarios (base-case, minimum and maximum in which increasing shares of patients eligible to abacavir/lamivudine start first line treatment with this backbone. Annual cost for each regimen comprises drugs acquisition under hospital pricing rules, monitoring exams and preventive tests, valued basing on regional reimbursement tariffs.RESULTS: According to current prescribing trends, in the next three years about 13,000 patients starting HIV therapy will receive tenofovir/emtricitabine (83% of the target population, and minor portions other regimens (9% abacavir/lamivudine, 8% zidovudine/lamivudine. Patients that would be eligible to

Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study

International Nuclear Information System (INIS)

Sahu, Sarata C.; Bhuyan, Abani K.; Udgaonkar, Jayant B.; Hosur, R.V.

2000-01-01

Backbone dynamics of uniformly 15 N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 deg. C, pH 6.6, using 15 N relaxation data obtained from proton-detected 2D { 1 H}- 15 N NMR spectroscopy. 15 N spin-lattice relaxation rate constants (R 1 ), spin-spin relaxation rate constants (R 2 ), and steady-state heteronuclear { 1 H}- 15 N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N-terminal residue) backbone amide 15 N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times (τ m ) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. The average order parameter is found to be 0.80 for free barnase and 0.86 for the complex. However, the changes are not uniform along the backbone and for about 5 residues near the binding interface there is actually a significant decrease in the order parameters on complex formation. These residues are not involved in the actual binding. For the residues where the order parameter increases, the magnitudes vary significantly. It is observed that the complex has much less internal mobility, compared to free barnase. From the changes in the order parameters, the entropic contribution of NH bond vector motion to the free energy of complex formation has been calculated. It is apparent that these motions cause significant unfavorable contributions and therefore must be compensated by many other favorable contributions to effect tight complex formation. The observed variations in the motion and their different locations with regard to the binding interface may have important implications for remote effects and regulation of the enzyme

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

Science.gov (United States)

Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

2015-05-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. © 2015 Wiley Periodicals, Inc.

Backbone upgrades and DEC equipment replacement

Science.gov (United States)

Vancamp, Warren

1991-01-01

The NASA Science Internet (NSI) dual protocol backbone is outlined. It includes DECnet link upgrades to match TCP/IP link performance. It also includes the integration of backbone resources and central management. The phase 1 transition process is outlined.

High Performance Infiltrated Backbones for Cathode-Supported SOFC's

DEFF Research Database (Denmark)

Gil, Vanesa; Kammer Hansen, Kent

2014-01-01

The concept of using highly ionic conducting backbones with subsequent infiltration of electronically conducting particles has widely been used to develop alternative anode-supported SOFC's. In this work, the idea was to develop infiltrated backbones as an alternative design based on cathode......, microstructural characterization and electrochemical testing are discussed. Data on polarization resistance, Rp, are obtained from impedance spectra recorded on quasi-symmetrical cells (YSZ backbones/YSZ/LSM-YSZ (screen printed)). The backbones are infiltrated with LSM and compared to a standard LSM-YSZ screen...

Multi-source micro-friction identification for a class of cable-driven robots with passive backbone

Science.gov (United States)

Tjahjowidodo, Tegoeh; Zhu, Ke; Dailey, Wayne; Burdet, Etienne; Campolo, Domenico

2016-12-01

This paper analyses the dynamics of cable-driven robots with a passive backbone and develops techniques for their dynamic identification, which are tested on the H-Man, a planar cabled differential transmission robot for haptic interaction. The mechanism is optimized for human-robot interaction by accounting for the cost-benefit-ratio of the system, specifically by eliminating the necessity of an external force sensor to reduce the overall cost. As a consequence, this requires an effective dynamic model for accurate force feedback applications which include friction behavior in the system. We first consider the significance of friction in both the actuator and backbone spaces. Subsequently, we study the required complexity of the stiction model for the application. Different models representing different levels of complexity are investigated, ranging from the conventional approach of Coulomb to an advanced model which includes hysteresis. The results demonstrate each model's ability to capture the dynamic behavior of the system. In general, it is concluded that there is a trade-off between model accuracy and the model cost.

Porous solid backbone impregnation for electrochemical energy conversion systems

KAUST Repository

Boulfrad, Samir; Jabbour, Ghassan

2013-01-01

An apparatus and method for impregnating a porous solid backbone. The apparatus may include a platform for holding a porous solid backbone, an ink jet nozzle configured to dispense a liquid solution onto the porous solid backbone, a positioning mechanism configured to position the ink jet nozzle proximate to a plurality of locations of the porous solid backbone, and a control unit configured to control the positioning mechanism to position the ink jet nozzle proximate to the plurality of locations and cause the ink jet nozzle to dispense the liquid solution onto the porous solid backbone.

Porous solid backbone impregnation for electrochemical energy conversion systems

KAUST Repository

Boulfrad, Samir

2013-09-19

An apparatus and method for impregnating a porous solid backbone. The apparatus may include a platform for holding a porous solid backbone, an ink jet nozzle configured to dispense a liquid solution onto the porous solid backbone, a positioning mechanism configured to position the ink jet nozzle proximate to a plurality of locations of the porous solid backbone, and a control unit configured to control the positioning mechanism to position the ink jet nozzle proximate to the plurality of locations and cause the ink jet nozzle to dispense the liquid solution onto the porous solid backbone.

Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

Czech Academy of Sciences Publication Activity Database

Kruse, H.; Mládek, Arnošt; Gkionis, Konstantinos; Hansen, A.; Grimme, S.; Šponer, Jiří

2015-01-01

Roč. 11, č. 10 (2015), s. 4972-4991 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DENSITY-FUNCTIONAL THEORY * SUGAR-PHOSPHATE BACKBONE Subject RIV: BO - Biophysics Impact factor: 5.301, year: 2015

High-resolution protein design with backbone freedom.

Science.gov (United States)

Harbury, P B; Plecs, J J; Tidor, B; Alber, T; Kim, P S

1998-11-20

Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.

Optical burst switching based satellite backbone network

Science.gov (United States)

Li, Tingting; Guo, Hongxiang; Wang, Cen; Wu, Jian

2018-02-01

We propose a novel time slot based optical burst switching (OBS) architecture for GEO/LEO based satellite backbone network. This architecture can provide high speed data transmission rate and high switching capacity . Furthermore, we design the control plane of this optical satellite backbone network. The software defined network (SDN) and network slice (NS) technologies are introduced. Under the properly designed control mechanism, this backbone network is flexible to support various services with diverse transmission requirements. Additionally, the LEO access and handoff management in this network is also discussed.

High Performance Infiltrated Backbones for Cathode-Supported SOFC's

DEFF Research Database (Denmark)

Gil, Vanesa; Kammer Hansen, Kent

2014-01-01

A four-step infiltration method has been developed to infiltrate La0.75Sr0.25MnO3+δ (LSM25) nanoparticles into porous structures (YSZ or LSM-YSZ backbones). The pore size distribution in the backbones is obtained either by using PMMA and/or graphites as pore formers or by leaching treatment of sa...... of samples with Ni remained in the YSZ structure at high temperatures. All impregnated backbones, presented Rs comparable to a standard screen printed cathode, which proves that LSM nanoparticles forms a pathway for electron conduction....

Quantitative assessments of the distinct contributions of polypeptide backbone amides versus sidechain groups to chain expansion via chemical denaturation

Science.gov (United States)

Holehouse, Alex S.; Garai, Kanchan; Lyle, Nicholas; Vitalis, Andreas; Pappu, Rohit V.

2015-01-01

In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones and therefore backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of sidechains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that sidechains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of sidechain-mediated interactions as determinants of the

Solution structure and backbone dynamics of recombinant Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.

Science.gov (United States)

Liu, J; Prakash, O; Cai, M; Gong, Y; Huang, Y; Wen, L; Wen, J J; Huang, J K; Krishnamoorthi, R

1996-02-06

The solution structure of recombinant Cucurbita maxima trypsin inhibitor-V (rCMTI-V), whose N-terminal is unacetylated and carries an extra glycine residue, was determined by means of two-dimensional (2D) homo and 3D hetero NMR experiments in combination with a distance geometry and simulated annealing algorithm. A total of 927 interproton distances and 123 torsion angle constraints were utilized to generate 18 structures. The root mean squared deviation (RMSD) of the mean structure is 0.53 A for main-chain atoms and 0.95 A for all the non-hydrogen atoms of residues 3-40 and 49-67. The average structure of rCMTI-V is found to be almost the same as that of the native protein [Cai, M., Gong, Y., Kao, J.-L., & Krishnamoorthi, R. (1995) Biochemistry 34, 5201-5211]. The backbone dynamics of uniformly 15N-labeled rCMTI-V were characterized by 2D 1H-15N NMR methods. 15N spin-lattice and spin-spin relaxation rate constants (R1 and R2, respectively) and [1H]-15N steady-state heteronuclear Overhauser effect enhancements were measured for the peptide NH units and, using the model-free formalism [Lipari, G., & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559, 4559-4570], the following parameters were determined: overall tumbling correlation time for the protein molecule (tau m), generalized order parameters for the individual N-H vectors (S2), effective correlation times for their internal motions (tau e), and terms to account for motions on a slower time scale (second) due to chemical exchange and/or conformational averaging (R(ex)). Most of the backbone NH groups of rCMTI-V are found to be highly constrained ((S2) = 0.83) with the exception of those in the binding loop (residues 41-48, (S2) = 0.71) and the N-terminal region ((S2) = 0.73). Main-chain atoms in these regions show large RMSD values in the average NMR structure. Residues involved in turns also appear to have more mobility ((S2) = 0.80). Dynamical properties of rCMTI-V were compared with those of two other

Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients

Directory of Open Access Journals (Sweden)

Restelli U

2017-06-01

Full Text Available Umberto Restelli,1,2 Giuliano Rizzardini,3,4 Andrea Antinori,5 Adriano Lazzarin,6 Marzia Bonfanti,1 Paolo Bonfanti,7 Davide Croce1,2 1Centre for Research on Health Economics, Social and Health Care Management, LIUC – Università Cattaneo, Castellanza, Varese, Italy; 2School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; 3First and Second Divisions of Infectious Diseases, “Luigi Sacco” Hospital, Milan, Italy; 4School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; 5National Institute for Infectious Diseases “L Spallanzani”, Rome, 6Department of Infectious Diseases, San Raffaele Scientific Institute, 7Department of Infectious and Tropical Diseases, A Manzoni Hospital, Lecco, Italy Background: In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG, a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER of the use of DTG+backbone compared with raltegravir (RAL+backbone, darunavir (DRV+ritonavir(r+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service’s point of view.Materials and methods: A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD] and successive lines of therapy. The model considers costs (2014 and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies.Results: In

Solution NMR Structures of Oxidized and Reduced Ehrlichia chaffeensis thioredoxin: NMR-Invisible Structure Owing to Backbone Dynamics

Energy Technology Data Exchange (ETDEWEB)

Buchko, Garry W.; Hewitt, Stephen N.; Van Voorhis, Wesley C.; Myler, Peter J.

2018-01-02

Thioredoxins (Trxs) are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site, CGPC. Here, we describe the NMR solution structures of a Trx from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, in both the oxidized and reduced states. The overall topology of the calculated structures is similar in both redox states and similar to other Trx structures, a five-strand, mixed -sheet (1:3:2:4:5) surrounded by four -helices. Unlike other Trxs studied by NMR in both redox states, the 1H-15N HSQC spectra of reduced Ec-Trx was missing eight amide cross peaks relative to the spectra of oxidized Ec-Trx. These missing amides correspond to residues C32-E39 in the active site containing helix (2) and S72-I75 in a loop near the active site and suggest a substantial change in the backbone dynamics associated with the formation of an intramolecular C32-C35 disulfide bond.

Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides.

Science.gov (United States)

Faller, Christina E; Guvench, Olgun

2015-05-21

Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide -4GlcAβ1-3GalNAcβ1-, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic "backbone" has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1-3 glycosidic linkage and (ϕ2, ψ2) about the β1-4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high-resolution, high-precision free energies of CS disaccharides as a function of all possible backbone geometries. All 10 disaccharides (β1-3 vs β1-4 linkage × five different sulfation patterns) were studied; additionally, ion effects were investigated by considering each disaccharide in the presence of either neutralizing sodium or calcium cations. GlcAβ1-3GalNAc disaccharides have a single, broad, thermodynamically important free-energy minimum, whereas GalNAcβ1-4GlcA disaccharides have two such minima. Calcium cations but not sodium cations bind to the disaccharides, and binding is primarily to the GlcA -COO(-) moiety as opposed to sulfate groups. This binding alters the glycan backbone thermodynamics in instances where a calcium cation bound to -COO(-) can act to bridge and stabilize an interaction with an adjacent sulfate group, whereas, in the absence of this cation, the proximity of a sulfate group to -COO(-) results in two like charges being both desolvated and placed adjacent to each other and is found to be destabilizing. In addition to providing information

Noncanonical alpha/gamma Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field

Czech Academy of Sciences Publication Activity Database

Zgarbová, M.; Jurečka, P.; Banáš, P.; Havrila, Marek; Šponer, Jiří; Otyepka, M.

2017-01-01

Roč. 121, č. 11 (2017), s. 2420-2433 ISSN 1520-6106 Institutional support: RVO:68081707 Keywords : molecular-dynamics simulations * sugar-phosphate backbone * free-energy landscape * ribosomal-rna Subject RIV: BO - Biophysics OBOR OECD: Physical chemistry Impact factor: 3.177, year: 2016

APPECT: An Approximate Backbone-Based Clustering Algorithm for Tags

DEFF Research Database (Denmark)

Zong, Yu; Xu, Guandong; Jin, Pin

2011-01-01

algorithm for Tags (APPECT). The main steps of APPECT are: (1) we execute the K-means algorithm on a tag similarity matrix for M times and collect a set of tag clustering results Z={C1,C2,…,Cm}; (2) we form the approximate backbone of Z by executing a greedy search; (3) we fix the approximate backbone...... as the initial tag clustering result and then assign the rest tags into the corresponding clusters based on the similarity. Experimental results on three real world datasets namely MedWorm, MovieLens and Dmoz demonstrate the effectiveness and the superiority of the proposed method against the traditional...... Agglomerative Clustering on tagging data, which possess the inherent drawbacks, such as the sensitivity of initialization. In this paper, we instead make use of the approximate backbone of tag clustering results to find out better tag clusters. In particular, we propose an APProximate backbonE-based Clustering...

Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.

Directory of Open Access Journals (Sweden)

Kevin Drew

Full Text Available Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones, oligooxopiperazines, oligo-peptoids, [Formula: see text]-peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org. This work helps address the peptidomimetic community's need for an automated and expandable

Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry.

Science.gov (United States)

Morrison, Lindsay J; Chai, Wenrui; Rosenberg, Jake A; Henkelman, Graeme; Brodbelt, Jennifer S

2017-08-02

Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.

Green Network Planning Model for Optical Backbones

DEFF Research Database (Denmark)

Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir; Jensen, Michael

2010-01-01

on the environment in general. In network planning there are existing planning models focused on QoS provisioning, investment minimization or combinations of both and other parameters. But there is a lack of a model for designing green optical backbones. This paper presents novel ideas to be able to define......Communication networks are becoming more essential for our daily lives and critically important for industry and governments. The intense growth in the backbone traffic implies an increment of the power demands of the transmission systems. This power usage might have a significant negative effect...

Internet optical infrastructure issues on monitoring and failure restoration

CERN Document Server

Tapolcai, János; Babarczi, Péter; Rónyai, Lajos

2015-01-01

This book covers the issues of monitoring, failure localization, and restoration in the Internet optical backbone, and focuses on the progress of state-of-the-art in both industry standard and academic research. The authors summarize, categorize, and analyze the developed technology in the context of Internet fault management and failure recovery under the Generalized Multi-Protocol Label Switching (GMPLS), via both aspects of network operations and theories. Examines monitoring, failure localization, and failure restoration in the Internet backbone Includes problem formulations based on combinatorial group testing and topology coding Covers state-of-the-art development for the Internet backbone fault management and failure recovery

Synthesis and Exciton Dynamics of Triplet Sensitized Conjugated Polymers

KAUST Repository

Andernach, Rolf

2015-07-22

We report the synthesis of a novel polythiophene-based host-guest copolymer incorporating a Pt-porphyrin complex (TTP-Pt) into the backbone for efficient singlet to triplet polymer exciton sensitization. We elucidated the exciton dynamics in thin films of the material by means of Transient Absorption Spectrosopcy (TAS) on multiple timescales and investigated the mechanism of triplet exciton formation. During sensitization, single exciton diffusion is followed by exciton transfer from the polymer backbone to the complex where it undergoes intersystem crossing to the triplet state of the complex. We directly monitored the triplet exciton back transfer from the Pt-porphyrin to the polymer and find that 60% of the complex triplet excitons are transferred with a time constant of 1087 ps. We propose an equilibrium between polymer and porphyrin triplet states as a result of the low triplet diffusion length in the polymer backbone and hence an increased local triplet population resulting in increased triplet-triplet annihilation. This novel system has significant implications for the design of novel materials for triplet sensitized solar cells and up-conversion layers.

Direct observation of backbone planarization via side-chain alignment in single bulky-substituted polythiophenes

Science.gov (United States)

Raithel, Dominic; Simine, Lena; Pickel, Sebastian; Schötz, Konstantin; Panzer, Fabian; Baderschneider, Sebastian; Schiefer, Daniel; Lohwasser, Ruth; Köhler, Jürgen; Thelakkat, Mukundan; Sommer, Michael; Köhler, Anna; Rossky, Peter J.; Hildner, Richard

2018-03-01

The backbone conformation of conjugated polymers affects, to a large extent, their optical and electronic properties. The usually flexible substituents provide solubility and influence the packing behavior of conjugated polymers in films or in bad solvents. However, the role of the side chains in determining and potentially controlling the backbone conformation, and thus the optical and electronic properties on the single polymer level, is currently under debate. Here, we investigate directly the impact of the side chains by studying the bulky-substituted poly(3-(2,5-dioctylphenyl)thiophene) (PDOPT) and the common poly(3-hexylthiophene) (P3HT), both with a defined molecular weight and high regioregularity, using low-temperature single-chain photoluminescence (PL) spectroscopy and quantum-classical simulations. Surprisingly, the optical transition energy of PDOPT is significantly (˜2,000 cm‑1 or 0.25 eV) red-shifted relative to P3HT despite a higher static and dynamic disorder in the former. We ascribe this red shift to a side-chain induced backbone planarization in PDOPT, supported by temperature-dependent ensemble PL spectroscopy. Our atomistic simulations reveal that the bulkier 2,5-dioctylphenyl side chains of PDOPT adopt a clear secondary helical structural motif and thus protect conjugation, i.e., enforce backbone planarity, whereas, for P3HT, this is not the case. These different degrees of planarity in both thiophenes do not result in different conjugation lengths, which we found to be similar. It is rather the stronger electronic coupling between the repeating units in the more planar PDOPT which gives rise to the observed spectral red shift as well as to a reduced calculated electron‑hole polarization.

One-year dynamic monitoring of a masonry tower

Directory of Open Access Journals (Sweden)

Guidobaldi Marco

2015-01-01

Full Text Available The paper presents some results of the continuous dynamic monitoring program carried out on the tallest historic tower in Mantua, Italy. This project follows an extensive diagnostic investigation aimed at assessing the structural condition of the tower after the Italian earthquakes of May 2012. A simple dynamic monitoring system was permanently installed in the upper part of the building and automatic modal identification was performed. The results allow to evaluate the effects of changing temperature on automatically identified natural frequencies, to verify the practical feasibility of damage detection methods based on natural frequencies shifts and provide clear evidence of the possible key role of continuous dynamic monitoring in the preventive conservation of historic towers.

Determination of backbone chain direction of PDA using FFM

Science.gov (United States)

Jo, Sadaharu; Okamoto, Kentaro; Takenaga, Mitsuru

2010-01-01

The effect of backbone chains on friction force was investigated on both Langmuir-Blodgett (LB) films of 10,12-heptacosadiynoic acid and the (0 1 0) surfaces of single crystals of 2,4-hexadiene-1,6-diol using friction force microscopy (FFM). It was observed that friction force decreased when the scanning direction was parallel to the [0 0 1] direction in both samples. Moreover, friction force decreased when the scanning direction was parallel to the crystallographic [1 0 2], [1 0 1], [1 0 0] and [1 0 1¯] directions in only the single crystals. For the LB films, the [0 0 1] direction corresponds to the backbone chain direction of 10,12-heptacosadiynoic acid. For the single crystals, both the [0 0 1] and [1 0 1] directions correspond to the backbone chain direction, and the [1 0 2], [1 0 0] and [1 0 1¯] directions correspond to the low-index crystallographic direction. In both the LB films and single crystals, the friction force was minimized when the directions of scanning and the backbone chain were parallel.

Monitoring Bridge Dynamic Responses Using Fiber Bragg Grating Tiltmeters.

Science.gov (United States)

Xiao, Feng; Chen, Gang S; Hulsey, J Leroy

2017-10-20

In bridge health monitoring, tiltmeters have been used for measuring rotation and curvature; however, their application in dynamic parameter identification has been lacking. This study installed fiber Bragg grating (FBG) tiltmeters on the bearings of a bridge and monitored the dynamic rotational angle. The dynamic features, including natural frequencies and mode shapes, have been identified successfully. The innovation presented in this paper is the first-time use of FBG tiltmeter readings to identify the natural frequencies of a long-span steel girder bridge. The identified results have been verified using a bridge finite element model. This paper introduces a new method for the dynamic monitoring of a bridge using FBG tiltmeters. Limitations and future research directions are also discussed in the conclusion.

Monitoring Bridge Dynamic Responses Using Fiber Bragg Grating Tiltmeters

Directory of Open Access Journals (Sweden)

Feng Xiao

2017-10-01

Full Text Available In bridge health monitoring, tiltmeters have been used for measuring rotation and curvature; however, their application in dynamic parameter identification has been lacking. This study installed fiber Bragg grating (FBG tiltmeters on the bearings of a bridge and monitored the dynamic rotational angle. The dynamic features, including natural frequencies and mode shapes, have been identified successfully. The innovation presented in this paper is the first-time use of FBG tiltmeter readings to identify the natural frequencies of a long-span steel girder bridge. The identified results have been verified using a bridge finite element model. This paper introduces a new method for the dynamic monitoring of a bridge using FBG tiltmeters. Limitations and future research directions are also discussed in the conclusion.

On Backbone Structure for a Future Multipurpose Network

DEFF Research Database (Denmark)

Gutierrez Lopez, Jose Manuel; Cuevas, Ruben; Riaz, M. Tahir

2008-01-01

Telecommunications are evolving towards the unification of services and infrastructures. This unification must be achieved at the highest hierarchical level for a complete synergy of services. Therefore, one of the requirements is a multipurpose backbone network capable of supporting all the curr......Telecommunications are evolving towards the unification of services and infrastructures. This unification must be achieved at the highest hierarchical level for a complete synergy of services. Therefore, one of the requirements is a multipurpose backbone network capable of supporting all...

Solution, solid phase and computational structures of apicidin and its backbone-reduced analogs.

Science.gov (United States)

Kranz, Michael; Murray, Peter John; Taylor, Stephen; Upton, Richard J; Clegg, William; Elsegood, Mark R J

2006-06-01

The recently isolated broad-spectrum antiparasitic apicidin (1) is one of the few naturally occurring cyclic tetrapeptides (CTP). Depending on the solvent, the backbone of 1 exhibits two gamma-turns (in CH(2)Cl(2)) or a beta-turn (in DMSO), differing solely in the rotation of the plane of one of the amide bonds. In the X-ray crystal structure, the peptidic C==Os and NHs are on opposite sides of the backbone plane, giving rise to infinite stacks of cyclotetrapeptides connected by three intermolecular hydrogen bonds between the backbones. Conformational searches (Amber force field) on a truncated model system of 1 confirm all three backbone conformations to be low-energy states. The previously synthesized analogs of 1 containing a reduced amide bond exhibit the same backbone conformation as 1 in DMSO, which is confirmed further by the X-ray crystal structure of a model system of the desoxy analogs of 1. This similarity helps in explaining why the desoxy analogs retain some of the antiprotozoal activities of apicidin. The backbone-reduction approach designed to facilitate the cyclization step of the acyclic precursors of the CTPs seems to retain the conformational preferences of the parent peptide backbone.

Vertical hydraulic generators experience with dynamic air gap monitoring

International Nuclear Information System (INIS)

Pollock, G.B.; Lyles, J.F.

1992-01-01

Until recently, dynamic monitoring of the rotor to stator air gap of hydraulic generators was not practical. Cost effective and reliable dyamic air gap monitoring equipment has been developed in recent years. Dynamic air gap monitoring was originally justified because of the desire of the owner to minimize the effects of catastrophic air gap failure. However, monitoring air gaps on a time basis has been shown to be beneficial by assisting in the assessment of hydraulic generator condition. The air gap monitor provides useful information on rotor and stator condition and generator vibration. The data generated by air gap monitors will assist managers in the decision process with respect to the timing and extent of required maintenance for a particular generating unit

ExScal Backbone Network Architecture

Science.gov (United States)

2005-01-01

802.11 battery powered nodes was laid over the sensor network. We adopted the Stargate platform for the backbone tier to serve as the basis for...its head. XSS Hardware and Network: XSS stands for eXtreme Scaling Stargate . A stargate is a linux-based single board computer. It has a 400 MHz

Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

Science.gov (United States)

Zhang, Qian; Xu, Zhijian; Shi, Jiye; Zhu, Weiliang

2017-07-24

Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (R F ) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too. Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 Å resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.

Cross-correlated relaxation rates between protein backbone H–X dipolar interactions

International Nuclear Information System (INIS)

Vögeli, Beat

2017-01-01

The relaxation interference between dipole–dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive H N –N and H α –C α dipole–dipole interactions. Here, we provide a detailed account of the measurement of the four types of CCR rates. All rates were obtained from at least two different pulse sequences, of which the yet unpublished ones are presented. Detailed comparisons between the different methods and corrections for unwanted pathways demonstrate that the averaged CCR rates are highly accurate and precise with errors of 1.5–3% of the entire value ranges.

Cross-correlated relaxation rates between protein backbone H–X dipolar interactions

Energy Technology Data Exchange (ETDEWEB)

Vögeli, Beat, E-mail: beat.vogeli@ucdenver.edu [University of Colorado Denver, Department of Biochemistry and Molecular Genetics (United States)

2017-03-15

The relaxation interference between dipole–dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive H{sup N}–N and H{sup α}–C{sup α} dipole–dipole interactions. Here, we provide a detailed account of the measurement of the four types of CCR rates. All rates were obtained from at least two different pulse sequences, of which the yet unpublished ones are presented. Detailed comparisons between the different methods and corrections for unwanted pathways demonstrate that the averaged CCR rates are highly accurate and precise with errors of 1.5–3% of the entire value ranges.

The dynamic state monitoring of bearings system

Directory of Open Access Journals (Sweden)

Marek Krynke

2015-03-01

Full Text Available The article discusses the methods of dynamic state monitoring of bearings system. A vibration signal contains important technical information about the machine condition and is currently the most frequently used in diagnostic bearings systems. One of the main ad-vantages of machine condition monitoring is identifying the cause of failure of the bearings and taking preventative measures, otherwise the operation of such a machine will lead to frequent replacement of the bearings. Monitoring changes in the course of the operation of machin-ery repair strategies allows keeping the conditioned state of dynamic failure conditioned preventive repairs and repairs after-failure time. In addition, the paper also presents the fundamental causes of bearing failure and identifies mechanisms related to the creation of any type of damage.

The Graphical Representation of the Digital Astronaut Physiology Backbone

Science.gov (United States)

Briers, Demarcus

2010-01-01

This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

Modern techniques for condition monitoring of railway vehicle dynamics

International Nuclear Information System (INIS)

Ngigi, R W; Pislaru, C; Ball, A; Gu, F

2012-01-01

A modern railway system relies on sophisticated monitoring systems for maintenance and renewal activities. Some of the existing conditions monitoring techniques perform fault detection using advanced filtering, system identification and signal analysis methods. These theoretical approaches do not require complex mathematical models of the system and can overcome potential difficulties associated with nonlinearities and parameter variations in the system. Practical applications of condition monitoring tools use sensors which are mounted either on the track or rolling stock. For instance, monitoring wheelset dynamics could be done through the use of track-mounted sensors, while vehicle-based sensors are preferred for monitoring the train infrastructure. This paper attempts to collate and critically appraise the modern techniques used for condition monitoring of railway vehicle dynamics by analysing the advantages and shortcomings of these methods.

Backbone Diversity Analysis in Catalyst Design

NARCIS (Netherlands)

Maldonado, A.G.; Hageman, J.A.; Mastroianni, S.; Rothenberg, G.

2009-01-01

We present a computer-based heuristic framework for designing libraries of homogeneous catalysts. In this approach, a set of given bidentate ligand-metal complexes is disassembled into key substructures (building blocks). These include metal atoms, ligating groups, backbone groups, and residue

Hydrogen exchange

DEFF Research Database (Denmark)

Jensen, Pernille Foged; Rand, Kasper Dyrberg

2016-01-01

Hydrogen exchange (HX) monitored by mass spectrometry (MS) is a powerful analytical method for investigation of protein conformation and dynamics. HX-MS monitors isotopic exchange of hydrogen in protein backbone amides and thus serves as a sensitive method for probing protein conformation...... and dynamics along the entire protein backbone. This chapter describes the exchange of backbone amide hydrogen which is highly quenchable as it is strongly dependent on the pH and temperature. The HX rates of backbone amide hydrogen are sensitive and very useful probes of protein conformation......, as they are distributed along the polypeptide backbone and form the fundamental hydrogen-bonding networks of basic secondary structure. The effect of pressure on HX in unstructured polypeptides (poly-dl-lysine and oxidatively unfolded ribonuclease A) and native folded proteins (lysozyme and ribonuclease A) was evaluated...

Thin Films Formed from Conjugated Polymers with Ionic, Water-Soluble Backbones

NARCIS (Netherlands)

Voortman, Thomas P; Chiechi, Ryan C

2015-01-01

This paper compares the morphologies of films of conjugated polymers in which the backbone (main chain) and pendant groups are varied between ionic/hydrophilic and aliphatic/hydrophobic. We observe that conjugated polymers in which the pendant groups and backbone are matched, either ionic-ionic or

Nonribosomal biosynthesis of backbone-modified peptides

Science.gov (United States)

Niquille, David L.; Hansen, Douglas A.; Mori, Takahiro; Fercher, David; Kries, Hajo; Hilvert, Donald

2018-03-01

Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-β-Phe with near-native specificity and efficiency. A co-crystal structure with a non-hydrolysable aminoacyl-AMP analogue reveals the origins of the 40,000-fold α/β-specificity switch, illuminating subtle but precise remodelling of the active site. When the engineered catalyst was paired with downstream module(s), (S)-β-Phe-containing peptides were produced at preparative scale in vitro (~1 mmol) and high titres in vivo (~100 mg l-1), highlighting the potential of biosynthetic pathway engineering for the construction of novel nonribosomal β-frameworks.

Gender features of functional condition of backbone of teenagers with scoliotic posture

Directory of Open Access Journals (Sweden)

Sergiy Afanasiev

2016-10-01

Full Text Available Purpose: to study mobility of backbone, endurance of muscles of a trunk and to define gender features of functional condition of backbone at children of the middle school age with scoliotic posture depending on the direction of the top of arch of curvature of spine. Material & Methods: 40 girls and 40 boys, including 18 girls and 18 boys with the right-side deformation of backbone in the thoracic department, the left-side – 22 girls and 22 boys are examined. Results: features of changes of indicators, depending on sex of children and frontage of the top of arch of curvature of spine column, are revealed when studying the level of flexibility of backbone and endurance of muscles of a trunk at children of the middle school age with scoliotic posture. Conclusions: it is established that the level of decrease in flexibility of backbone is higher at boys, than at girls, whereas indicators of contractile ability and tone of muscles of "muscular corset" are higher at boys.

Chemical characteristics and antithrombotic effect of chondroitin sulfates from sturgeon skull and sturgeon backbone.

Science.gov (United States)

Gui, Meng; Song, Juyi; Zhang, Lu; Wang, Shun; Wu, Ruiyun; Ma, Changwei; Li, Pinglan

2015-06-05

Chondroitin sulfates (CSs) were extracted from sturgeon skull and backbone, and their chemical composition, anticoagulant, anti-platelet and thrombolysis activities were evaluated. The average molecular weights of CS from sturgeon skull and backbone were 38.5kDa and 49.2kDa, respectively. Disaccharide analysis indicated that the sturgeon backbone CS was primarily composed of disaccharide monosulfated in position four of the GalNAc (37.8%) and disaccharide monosulfated in position six of the GalNAc (59.6%) while sturgeon skull CS was primarily composed of nonsulfated disaccharide (74.2%). Sturgeon backbone CS showed stronger antithrombotic effect than sturgeon skull CS. Sturgeon backbone CS could significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT), inhibited ADP-induced platelet aggregation and dissolved platelet plasma clots in vitro. The results suggested that sturgeon backbone CS can be explored as a functional food with antithrombotic function. Copyright © 2015 Elsevier Ltd. All rights reserved.

MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data

Energy Technology Data Exchange (ETDEWEB)

Mantsyzov, Alexey B. [M.V. Lomonosov Moscow State University, Faculty of Fundamental Medicine (Russian Federation); Shen, Yang; Lee, Jung Ho [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Hummer, Gerhard [Max Planck Institute of Biophysics (Germany); Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2015-09-15

MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts ({sup 15}N, {sup 13}C{sup α}, and {sup 13}C′), six types of J couplings ({sup 3}J{sub HNHα}, {sup 3}J{sub C′C′}, {sup 3}J{sub C′Hα}, {sup 1}J{sub HαCα}, {sup 2}J{sub CαN} and {sup 1}J{sub CαN}), as well as the {sup 15}N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3.

Monitoring Bridge Dynamic Deformation in Vibration by Digital Photography

Science.gov (United States)

Yu, Chengxin; Zhang, Guojian; Liu, Xiaodong; Fan, Li; Hai, Hua

2018-01-01

This study adopts digital photography to monitor bridge dynamic deformation in vibration. Digital photography in this study is based on PST-TBPM (photographing scale transformation-time baseline parallax method). Firstly, we monitor the bridge in static as a zero image. Then, we continuously monitor the bridge in vibration as the successive images. Based on the reference points on each image, PST-TBPM is used to calculate the images to obtain the dynamic deformation values of these deformation points. Results show that the average measurement accuracies are 0.685 pixels (0.51mm) and 0.635 pixels (0.47mm) in X and Z direction, respectively. The maximal deformations in X and Z direction of the bridge are 4.53 pixels and 5.21 pixels, respectively. PST-TBPM is valid in solving the problem that the photographing direction is not perpendicular to the bridge. Digital photography in this study can be used to assess bridge health through monitoring the dynamic deformation of a bridge in vibration. The deformation trend curves also can warn the possible dangers over time.

Characterizing the Dynamics of α-Synuclein Oligomers Using Hydrogen/Deuterium Exchange Monitored by Mass Spectrometry

DEFF Research Database (Denmark)

Mysling, Simon; Betzer, Cristine; Jensen, Poul Henning

2013-01-01

Soluble oligomers formed by α-synuclein (αSN) are suspected to play a central role in neuronal cell death during Parkinson's disease. While studies have probed the surface structure of these oligomers, little is known about the backbone dynamics of αSN when they form soluble oligomers. Using...... analyses performed on αSN fibrils and indicated a possible zipperlike maturation mechanism for αSN aggregates. We find the protected N-terminus (residues 4-17) to be of particular interest, as this region has previously been observed to be highly dynamic for both monomeric and fibrillar αSN. This region...... has mainly been described in relation to membrane binding of αSN, and structuring may be important in relation to disease....

Uganda's National Transmission Backbone Infrastructure Project: Technical Challenges and the Way Forward

Science.gov (United States)

Bulega, T.; Kyeyune, A.; Onek, P.; Sseguya, R.; Mbabazi, D.; Katwiremu, E.

2011-10-01

Several publications have identified technical challenges facing Uganda's National Transmission Backbone Infrastructure project. This research addresses the technical limitations of the National Transmission Backbone Infrastructure project, evaluates the goals of the project, and compares the results against the technical capability of the backbone. The findings of the study indicate a bandwidth deficit, which will be addressed by using dense wave division multiplexing repeaters, leasing bandwidth from private companies. Microwave links for redundancy, a Network Operation Center for operation and maintenance, and deployment of wireless interoperability for microwave access as a last-mile solution are also suggested.

Sequential backbone assignment based on dipolar amide-to-amide correlation experiments

Energy Technology Data Exchange (ETDEWEB)

Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus, E-mail: rali@nmr.mpibpc.mpg.de [Max Planck Institute for Biophysical Chemistry, Department for NMR-Based Structural Biology (Germany)

2015-07-15

Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common {sup 13}C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR.

Sequential backbone assignment based on dipolar amide-to-amide correlation experiments

International Nuclear Information System (INIS)

Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus

2015-01-01

Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common 13 C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR

Some fractal properties of the percolating backbone in two dimensions

International Nuclear Information System (INIS)

Laidlaw, D.; MacKay, G.; Jan, N.

1987-01-01

A new algorithm is presented, based on elements of artificial intelligence theory, to determine the fractal properties of the backbone of the incipient infinite cluster. It is found that fractal dimensionality of the backbone is d/sub f//sup BB/ = 1.61 +/- 0.01, the chemical dimensionality is d/sub t/ = 1.40 +/- 0.01, and the fractal dimension of the minimum path d/sub min/ = 1.15 +/- 0.02 for the two-dimensional triangular lattice

Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching

Directory of Open Access Journals (Sweden)

Bron Peter A

2012-09-01

Full Text Available Abstract Background Specific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background. Results Through genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-κB reporter cells expressing Toll like receptor (TLR-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-α after stimulation with the WTA mutants as compared to the wild-type. Conclusions The study presented here correlates structural differences in WTA to their functional characteristics, thereby

Analysis of the backbone dynamics of interleukin-1β using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy

International Nuclear Information System (INIS)

Clore, G.M.; Driscoll, P.C.; Wingfield, P.T.; Gronenborn, A.M.

1990-01-01

The backbone dynamics of uniformly 15 N-labeled interleukin-1β are investigated by using two-dimensional inverse detected heteronuclear 15 N- 1 H NMR spectroscopy. 15 N T 1 , T 2 , and NOE data at a spectrometer frequency of 600 MHz are obtained for 90% of the backbone amide groups. The data provide evidence for motions on three time scales. All the residues exhibit very fast motions on a time scale of approx-lt 20-50 ps that can be characterized by a single-order parameter with an average value of 0.82 ± 0.05. Thirty-two residues also display motions on a time scale of 0.5-4 ns, slightly less than the overall rotational correlation time of the protein (8.3 ns). While the simple formulation can account for the 15 N T 1 and T 2 data, it fails to account for the 15 N- 1 H NOE data and yields calculated values for the NOEs that are either too small or negative, whereas the observed NOEs are positive. Another 42 residues are characterized by some sort of motion on the 30-ns-10-ms time scale, which results in 15 N line broadening due to chemical exchange between different conformational substates with distinct 15 N chemical shifts. In general, the motions on both the 0.5-4-ns and 30-ns-10-ms time scales are localized in surface-accessible loops and turns connecting the β-strands, as well as at the beginning and end of strands. Finally, the kinetic and equilibrium properties of a slow conformational equilibrium between a major and a minor species, involving at least 19 residues and located on one contiguous face of the molecule, are characterized by using 1 H- 15 N correlation spectroscopy, 1 H- 15 N heteronuclear multiple quantum coherence-nuclear Overhauser enhancement spectroscopy, and 1 H- 1 H nuclear Overhauser enhancement spectroscopy

Determination of protein global folds using backbone residual dipolar coupling and long-range NOE restraints

International Nuclear Information System (INIS)

Giesen, Alexander W.; Homans, Steve W.; Brown, Jonathan Miles

2003-01-01

We report the determination of the global fold of human ubiquitin using protein backbone NMR residual dipolar coupling and long-range nuclear Overhauser effect (NOE) data as conformational restraints. Specifically, by use of a maximum of three backbone residual dipolar couplings per residue (N i -H N i , N i -C' i-1 , H N i - C' i-1 ) in two tensor frames and only backbone H N -H N NOEs, a global fold of ubiquitin can be derived with a backbone root-mean-square deviation of 1.4 A with respect to the crystal structure. This degree of accuracy is more than adequate for use in databases of structural motifs, and suggests a general approach for the determination of protein global folds using conformational restraints derived only from backbone atoms

MCBT: Multi-Hop Cluster Based Stable Backbone Trees for Data Collection and Dissemination in WSNs

Directory of Open Access Journals (Sweden)

Tae-Jin Lee

2009-07-01

Full Text Available We propose a stable backbone tree construction algorithm using multi-hop clusters for wireless sensor networks (WSNs. The hierarchical cluster structure has advantages in data fusion and aggregation. Energy consumption can be decreased by managing nodes with cluster heads. Backbone nodes, which are responsible for performing and managing multi-hop communication, can reduce the communication overhead such as control traffic and minimize the number of active nodes. Previous backbone construction algorithms, such as Hierarchical Cluster-based Data Dissemination (HCDD and Multicluster, Mobile, Multimedia radio network (MMM, consume energy quickly. They are designed without regard to appropriate factors such as residual energy and degree (the number of connections or edges to other nodes of a node for WSNs. Thus, the network is quickly disconnected or has to reconstruct a backbone. We propose a distributed algorithm to create a stable backbone by selecting the nodes with higher energy or degree as the cluster heads. This increases the overall network lifetime. Moreover, the proposed method balances energy consumption by distributing the traffic load among nodes around the cluster head. In the simulation, the proposed scheme outperforms previous clustering schemes in terms of the average and the standard deviation of residual energy or degree of backbone nodes, the average residual energy of backbone nodes after disseminating the sensed data, and the network lifetime.

Versatile phosphite ligands based on silsesquioxane backbones

NARCIS (Netherlands)

van der Vlugt, JI; Ackerstaff, J; Dijkstra, TW; Mills, AM; Kooijman, H; Spek, AL; Meetsma, A; Abbenhuis, HCL; Vogt, D

Silsesquioxanes are employed as ligand backbones for the synthesis of novel phosphite compounds with 3,3'-5,5'-tetrakis(tert-butyl)-2,2'-di-oxa-1,1'-biphenyl substituents. Both mono- and bidentate phosphites are prepared in good yields. Two types of silsesquioxanes are employed as starting

Integrative technology of massage manipulations in physical rehabilitation of students with backbone pathology

Directory of Open Access Journals (Sweden)

V.I. Kotelevskiy

2016-06-01

Full Text Available Purpose:to analyze effectiveness of massage manipulations’ integrative technology in physical rehabilitation of higher educational establishments’ students with backbone pathology. Material: in the research 195 students of 19-20 years’ age participated. All students had periodical initial neurological symptoms of functional pathology and first stage osteochondrosis in different parts of backbone. We conducted a course of 10 sessions of therapeutic massage. Results: the sense of massage integrative technology is that every specialist shall have certain optimal set of skills and knowledge in technique of manipulation sessions of massage. Integrative technology of massage manipulations consists of psycho-corrective and manipulation parts. It considers psycho-somatic, mechanical and reflex rehabilitation aspects of patho-genesis of backbone functional disorders and vertebral osteochondrosis. Conclusions: depending on pathological process or backbone functional state of every person (peculiarities of his (her psycho-somatic status or, even, his (her bents. Individual approach in choice of strategy, tactic and methodological provisioning of massage session shall be used.

NMR investigations of molecular dynamics

Science.gov (United States)

Palmer, Arthur

2011-03-01

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

Selective backbone labelling of ILV methyl labelled proteins

International Nuclear Information System (INIS)

Sibille, Nathalie; Hanoulle, Xavier; Bonachera, Fanny; Verdegem, Dries; Landrieu, Isabelle; Wieruszeski, Jean-Michel; Lippens, Guy

2009-01-01

Adding the 13 C labelled 2-keto-isovalerate and 2-oxobutanoate precursors to a minimal medium composed of 12 C labelled glucose instead of the commonly used ( 2 D, 13 C) glucose leads not only to the 13 C labelling of (I, L, V) methyls but also to the selective 13 C labelling of the backbone C α and CO carbons of the Ile and Val residues. As a result, the backbone ( 1 H, 15 N) correlations of the Ile and Val residues and their next neighbours in the (i + 1) position can be selectively identified in HN(CA) and HN(CO) planes. The availability of a selective HSQC spectrum corresponding to the sole amide resonances of the Ile and Val residues allows connecting them to their corresponding methyls by the intra-residue NOE effect, and should therefore be applicable to larger systems

Exploring of PST-TBPM in Monitoring Bridge Dynamic Deflection in Vibration

Science.gov (United States)

Zhang, Guojian; Liu, Shengzhen; Zhao, Tonglong; Yu, Chengxin

2018-01-01

This study adopts digital photography to monitor bridge dynamic deflection in vibration. Digital photography used in this study is based on PST-TBPM (photographing scale transformation-time baseline parallax method). Firstly, a digital camera is used to monitor the bridge in static as a zero image. Then, the digital camera is used to monitor the bridge in vibration every three seconds as the successive images. Based on the reference system, PST-TBPM is used to calculate the images to obtain the bridge dynamic deflection in vibration. Results show that the average measurement accuracies are 0.615 pixels and 0.79 pixels in X and Z direction. The maximal deflection of the bridge is 7.14 pixels. PST-TBPM is valid in solving the problem-the photographing direction not perpendicular to the bridge. Digital photography used in this study can assess the bridge health through monitoring the bridge dynamic deflection in vibration. The deformation trend curves depicted over time also can warn the possible dangers.

Peptoid-Peptide hybrid backbone architectures

DEFF Research Database (Denmark)

Olsen, Christian Adam

2010-01-01

Peptidomimetic oligomers and foldamers have received considerable attention for over a decade, with beta-peptides and the so-called peptoids (N-alkylglycine oligomers) representing prominent examples of such architectures. Lately, hybrid or mixed backbones consisting of both alpha- and beta......-amino acids (alpha/beta-peptides) have been investigated in some detail as well. The present Minireview is a survey of the literature concerning hybrid structures of alpha-amino acids and peptoids, including beta-peptoids (N-alkyl-beta-alanine oligomers), and is intended to give an overview of this area...

Analisa Perbandingan Quality Of Service (QoS) pada Jaringan Backbone Non-MPLS dengan Jaringan Backbone MPLS Menggunakan Routing Protocol OSPF di PT. Telekomunikasi Indonesia, Tbk. Witel Ridar Riau

OpenAIRE

Silaban, Nestor Hasudungan; Sari, Linna Oktaviana; Anhar, Anhar

2015-01-01

The development of telecommunications technology based on Internet Protocol (IP) is now growing with the competitiveness of the telecommunications company to improve the quality of service to consumers. It can be obtained by increasing the quality backbone network using Multi Protocol Label Switching (MPLS). MPLS is a new technology to forward the packet to the backbone network without changing the existing network structure. The main idea is to construct a replacement MPLS paths using label ...

Five Principles of Industrialized Transformation for Successfully Building an Operational Backbone

DEFF Research Database (Denmark)

Winkler, Till J.; Kettunen, Petteri

2018-01-01

approach that is underpinned by five principles—template-based, business-driven, matrix-organized, tight supplier steering and cascaded planning. The UPM case provides important lessons for transformation leaders seeking to build, expand or develop a value-adding operational backbone.......To move into the digital age, a globally operating company needs to have in place an operational backbone, but many struggle with achieving this and the associated transformation program. Based on the experience of UPM, a Finnish forest industry company, we describe an industrialized transformation...

AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.

Science.gov (United States)

Lapidoth, Gideon D; Baran, Dror; Pszolla, Gabriele M; Norn, Christoffer; Alon, Assaf; Tyka, Michael D; Fleishman, Sarel J

2015-08-01

Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity. © 2015 Wiley Periodicals, Inc.

Backbone-hydrazone-containing biodegradable copolymeric micelles for anticancer drug delivery

Energy Technology Data Exchange (ETDEWEB)

Xu, Jing; Luan, Shujuan; Qin, Benkai; Wang, Yingying; Wang, Kai; Qi, Peilan; Song, Shiyong, E-mail: pharmsong@henu.edu.cn [Henan University, Institute of Pharmacy (China)

2016-11-15

Well-defined biodegradable, pH-sensitive amphiphilic block polymers, poly(ethylene glycol)-Hyd-poly(lactic acid) (mPEG-Hyd-PLA) which have acid-cleavable linkages in their backbones, were synthesized via ring-opening polymerization initiated from hydrazone-containing macroinitiators. Introducing a hydrazone bond onto the backbone of an amphiphilic copolymer will find a broad-spectrum encapsulation of hydrophobic drugs. Dynamic light scattering (DLS) and transmission electron microscopy showed that the diblock copolymers self-assembled into stable micelles with average diameters of 100 nm. The mean diameters and size distribution of the hydrazone-containing micelles changed obviously in mildly acidic pH (multiple peaks from 1 to 202 nm appeared under a pH 4.0 condition) than in neutral, while there were no changes in the case of non-sensitive ones. Doxorubicin (DOX) and paclitaxel (PTX) were loaded with drug loading content ranging from 2.4 to 3.5 %, respectively. Interestingly, the anticancer drugs released from mPEG-Hyd-PLA micelles could also be promoted by the increased acidity. An in vitro cytotoxicity study showed that the DOX-loaded mPEG-Hyd-PLA micelles have significantly enhanced cytotoxicity against HepG2 cells compared with the non-sensitive poly(ethylene glycol)-block-poly(lactic acid) (mPEG-PLA) micelles. Confocal microscopy observation indicated that more DOX were delivered into the nuclei of cells following 6 or 12 h incubation with DOX-loaded mPEG-Hyd-PLA micelles. In vivo studies on H22-bearing Swiss mice demonstrated the superior anticancer activity of DOX-loaded mPEG-Hyd-PLA micelles over free DOX and DOX-loaded mPEG-PLA micelles. These hydrazone-containing pH-responsive degradable micelles provide a useful strategy for antitumor drug delivery.

Backbone-hydrazone-containing biodegradable copolymeric micelles for anticancer drug delivery

International Nuclear Information System (INIS)

Xu, Jing; Luan, Shujuan; Qin, Benkai; Wang, Yingying; Wang, Kai; Qi, Peilan; Song, Shiyong

2016-01-01

Well-defined biodegradable, pH-sensitive amphiphilic block polymers, poly(ethylene glycol)-Hyd-poly(lactic acid) (mPEG-Hyd-PLA) which have acid-cleavable linkages in their backbones, were synthesized via ring-opening polymerization initiated from hydrazone-containing macroinitiators. Introducing a hydrazone bond onto the backbone of an amphiphilic copolymer will find a broad-spectrum encapsulation of hydrophobic drugs. Dynamic light scattering (DLS) and transmission electron microscopy showed that the diblock copolymers self-assembled into stable micelles with average diameters of 100 nm. The mean diameters and size distribution of the hydrazone-containing micelles changed obviously in mildly acidic pH (multiple peaks from 1 to 202 nm appeared under a pH 4.0 condition) than in neutral, while there were no changes in the case of non-sensitive ones. Doxorubicin (DOX) and paclitaxel (PTX) were loaded with drug loading content ranging from 2.4 to 3.5 %, respectively. Interestingly, the anticancer drugs released from mPEG-Hyd-PLA micelles could also be promoted by the increased acidity. An in vitro cytotoxicity study showed that the DOX-loaded mPEG-Hyd-PLA micelles have significantly enhanced cytotoxicity against HepG2 cells compared with the non-sensitive poly(ethylene glycol)-block-poly(lactic acid) (mPEG-PLA) micelles. Confocal microscopy observation indicated that more DOX were delivered into the nuclei of cells following 6 or 12 h incubation with DOX-loaded mPEG-Hyd-PLA micelles. In vivo studies on H22-bearing Swiss mice demonstrated the superior anticancer activity of DOX-loaded mPEG-Hyd-PLA micelles over free DOX and DOX-loaded mPEG-PLA micelles. These hydrazone-containing pH-responsive degradable micelles provide a useful strategy for antitumor drug delivery.

On-line bioprocess monitoring - an academic discipline or an industrial tool?

DEFF Research Database (Denmark)

Olsson, Lisbeth; Schulze, Ulrik; Nielsen, Jens Bredal

1998-01-01

Bioprocess monitoring capabilities are gaining increasing Importance bath in physiological studies and in bioprocess development, The present article focuses on on-line analytical systems since these represent the backbone of most bioprocess monitoring systems, both in academia and in industry. W...

Structural test of the parameterized-backbone method for protein design.

Science.gov (United States)

Plecs, Joseph J; Harbury, Pehr B; Kim, Peter S; Alber, Tom

2004-09-03

Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families of structures. We report the crystal structure of RH3, a right-handed, three-helix coiled coil that was designed using a parameterized backbone and detailed modeling of core packing. This crystal structure was determined using another rationally designed feature, a metal-binding site that permitted experimental phasing of the X-ray data. RH3 adopted the intended fold, which has not been observed previously in biological proteins. Unanticipated structural asymmetry in the trimer was a principal source of variation within the RH3 structure. The sequence of RH3 differs from that of a previously characterized right-handed tetramer, RH4, at only one position in each 11 amino acid sequence repeat. This close similarity indicates that the design method is sensitive to the core packing interactions that specify the protein structure. Comparison of the structures of RH3 and RH4 indicates that both steric overlap and cavity formation provide strong driving forces for oligomer specificity.

Directional virtual backbone based data aggregation scheme for Wireless Visual Sensor Networks.

Science.gov (United States)

Zhang, Jing; Liu, Shi-Jian; Tsai, Pei-Wei; Zou, Fu-Min; Ji, Xiao-Rong

2018-01-01

Data gathering is a fundamental task in Wireless Visual Sensor Networks (WVSNs). Features of directional antennas and the visual data make WVSNs more complex than the conventional Wireless Sensor Network (WSN). The virtual backbone is a technique, which is capable of constructing clusters. The version associating with the aggregation operation is also referred to as the virtual backbone tree. In most of the existing literature, the main focus is on the efficiency brought by the construction of clusters that the existing methods neglect local-balance problems in general. To fill up this gap, Directional Virtual Backbone based Data Aggregation Scheme (DVBDAS) for the WVSNs is proposed in this paper. In addition, a measurement called the energy consumption density is proposed for evaluating the adequacy of results in the cluster-based construction problems. Moreover, the directional virtual backbone construction scheme is proposed by considering the local-balanced factor. Furthermore, the associated network coding mechanism is utilized to construct DVBDAS. Finally, both the theoretical analysis of the proposed DVBDAS and the simulations are given for evaluating the performance. The experimental results prove that the proposed DVBDAS achieves higher performance in terms of both the energy preservation and the network lifetime extension than the existing methods.

Monitoring U.S. forest dynamics with Landsat [Chapter 12

Science.gov (United States)

Jeffrey G. Masek; Sean P. Healey

2012-01-01

Forest dynamics in the United States differ substantially from those in the developing world and thus present unique monitoring requirements. While deforestation and conversion to semipermanent agriculture dominate tropical forest dynamics, the area of forest land in the United States has remained fairly constant for the last 50-60 years (Birdsey and Lewis 2003)....

Alignment of process compliance and monitoring requirements in dynamic business collaborations

Science.gov (United States)

Comuzzi, Marco

2017-07-01

Dynamic business collaborations are intrinsically characterised by change because processes can be distributed or outsourced and partners may be substituted by new ones with enhanced or different capabilities. In this context, compliance requirements management becomes particularly challenging. Partners in a collaboration may join and leave dynamically and tasks over which compliance requirements are specified may be consequently distributed or delegated to new partners. This article considers the issue of aligning compliance requirements in a dynamic business collaboration with the monitoring requirements induced on the collaborating partners when change occurs. We first provide a conceptual model of business collaborations and their compliance requirements, introducing the concept of monitoring capabilities induced by compliance requirements. Then, we present a set of mechanisms to ensure consistency between monitoring and compliance requirements in the presence of change, e.g. when tasks are delegated or backsourced in-house. We also discuss a set of metrics to evaluate the status of a collaboration in respect of compliance monitorability. Finally, we discuss a prototype implementation of our framework.

A framework to find the logic backbone of a biological network.

Science.gov (United States)

Maheshwari, Parul; Albert, Réka

2017-12-06

Cellular behaviors are governed by interaction networks among biomolecules, for example gene regulatory and signal transduction networks. An often used dynamic modeling framework for these networks, Boolean modeling, can obtain their attractors (which correspond to cell types and behaviors) and their trajectories from an initial state (e.g. a resting state) to the attractors, for example in response to an external signal. The existing methods however do not elucidate the causal relationships between distant nodes in the network. In this work, we propose a simple logic framework, based on categorizing causal relationships as sufficient or necessary, as a complement to Boolean networks. We identify and explore the properties of complex subnetworks that are distillable into a single logic relationship. We also identify cyclic subnetworks that ensure the stabilization of the state of participating nodes regardless of the rest of the network. We identify the logic backbone of biomolecular networks, consisting of external signals, self-sustaining cyclic subnetworks (stable motifs), and output nodes. Furthermore, we use the logic framework to identify crucial nodes whose override can drive the system from one steady state to another. We apply these techniques to two biological networks: the epithelial-to-mesenchymal transition network corresponding to a developmental process exploited in tumor invasion, and the network of abscisic acid induced stomatal closure in plants. We find interesting subnetworks with logical implications in these networks. Using these subgraphs and motifs, we efficiently reduce both networks to succinct backbone structures. The logic representation identifies the causal relationships between distant nodes and subnetworks. This knowledge can form the basis of network control or used in the reverse engineering of networks.

Induced helical backbone conformations of self-organizable dendronized polymers.

Science.gov (United States)

Rudick, Jonathan G; Percec, Virgil

2008-12-01

Control of function through the primary structure of a molecule presents a significant challenge with valuable rewards for nanoscience. Dendritic building blocks encoded with information that defines their three-dimensional shape (e.g., flat-tapered or conical) and how they associate with each other are referred to as self-assembling dendrons. Self-organizable dendronized polymers possess a flat-tapered or conical self-assembling dendritic side chain on each repeat unit of a linear polymer backbone. When appended to a covalent polymer, the self-assembling dendrons direct a folding process (i.e., intramolecular self-assembly). Alternatively, intermolecular self-assembly of dendrons mediated by noncovalent interactions between apex groups can generate a supramolecular polymer backbone. Self-organization, as we refer to it, is the spontaneous formation of periodic and quasiperiodic arrays from supramolecular elements. Covalent and supramolecular polymers jacketed with self-assembling dendrons self-organize. The arrays are most often comprised of cylindrical or spherical objects. The shape of the object is determined by the primary structure of the dendronized polymer: the structure of the self-assembling dendron and the length of the polymer backbone. It is therefore possible to predictably generate building blocks for single-molecule nanotechnologies or arrays of supramolecules for bottom-up self-assembly. We exploit the self-organization of polymers jacketed with self-assembling dendrons to elucidate how primary structure determines the adopted conformation and fold (i.e., secondary and tertiary structure), how the supramolecules associate (i.e., quaternary structure), and their resulting functions. A combination of experimental techniques is employed to interrogate the primary, secondary, tertiary, and quaternary structure of the self-organizable dendronized polymers. We refer to the process by which we interpolate between the various levels of structural

Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers.

Science.gov (United States)

Iadevaia, Giulia; Núñez-Villanueva, Diego; Stross, Alexander E; Hunter, Christopher A

2018-06-06

Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

Study of muscular skeletal apparatus’s functional state of junior sportsmen-power lifters, who have backbone verterbral abnormalities

Directory of Open Access Journals (Sweden)

V.R. Ilmatov

2015-10-01

Full Text Available Purpose: determination of abnormalities and disorders of muscular skeletal apparatuses’ status of power lifters, who have vertebral abnormalities of backbone. Material: 58 junior sportsmen participated in the research. 36 sportsmen were the main group of the research and had vertebral disorders in backbone. For posture testing visual examination was used. Backbone mobility was tested with goniometry method. Flat feet were registered with plantography method. Results: we determined posture abnormalities in sagittal and frontal planes; feet flat, limited maximal movements in thoracic and lumbar spines. It was determined that the most limited were rotational movements and backbone unbending. The next were side bents. These limitations were accompanied by pain syndrome. These observations indirectly confirmed theory of direct interaction of backbone structures with nervous structures. It is also a confirmation of vertebral abnormalities’ presence in junior sportsmen. Conclusions: it was found that in junior sportsmen - power lifters with backbone pathologies in 100% of cases symptoms are determined by local limitations of backbone mobility with pain syndrome. In 35% of cases they are accompanied by posture’s disorders and feet flat. Orientation and methodic of rehabilitation of such sportsmen have been determined.

Determination of Backbone Amide Hydrogen Exchange Rates of Cytochrome c Using Partially Scrambled Electron Transfer Dissociation Data

Science.gov (United States)

Hamuro, Yoshitomo; E, Sook Yen

2018-05-01

The technological goal of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is to determine backbone amide hydrogen exchange rates. The most critical challenge to achieve this goal is obtaining the deuterium incorporation in single-amide resolution, and gas-phase fragmentation may provide a universal solution. The gas-phase fragmentation may generate the daughter ions which differ by a single amino acid and the difference in deuterium incorporations in the two analogous ions can yield the deuterium incorporation at the sub-localized site. Following the pioneering works by Jørgensen and Rand, several papers utilized the electron transfer dissociation (ETD) to determine the location of deuterium in single-amide resolution. This paper demonstrates further advancement of the strategy by determining backbone amide hydrogen exchange rates, instead of just determining deuterium incorporation at a single time point, in combination with a wide time window monitoring. A method to evaluate the effects of scrambling and to determine the exchange rates from partially scrambled HDX-ETD-MS data is described. All parent ions for ETD fragmentation were regio-selectively scrambled: The deuterium in some regions of a peptide ion was scrambled while that in the other regions was not scrambled. The method determined 31 backbone amide hydrogen exchange rates of cytochrome c in the non-scrambled regions. Good fragmentation of a parent ion, a low degree of scrambling, and a low number of exchangeable hydrogens in the preceding side chain are the important factors to determine the exchange rate. The exchange rates determined by the HDX-MS are in good agreement with those determined by NMR. [Figure not available: see fulltext.

Determination of Backbone Amide Hydrogen Exchange Rates of Cytochrome c Using Partially Scrambled Electron Transfer Dissociation Data.

Science.gov (United States)

Hamuro, Yoshitomo; E, Sook Yen

2018-05-01

The technological goal of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is to determine backbone amide hydrogen exchange rates. The most critical challenge to achieve this goal is obtaining the deuterium incorporation in single-amide resolution, and gas-phase fragmentation may provide a universal solution. The gas-phase fragmentation may generate the daughter ions which differ by a single amino acid and the difference in deuterium incorporations in the two analogous ions can yield the deuterium incorporation at the sub-localized site. Following the pioneering works by Jørgensen and Rand, several papers utilized the electron transfer dissociation (ETD) to determine the location of deuterium in single-amide resolution. This paper demonstrates further advancement of the strategy by determining backbone amide hydrogen exchange rates, instead of just determining deuterium incorporation at a single time point, in combination with a wide time window monitoring. A method to evaluate the effects of scrambling and to determine the exchange rates from partially scrambled HDX-ETD-MS data is described. All parent ions for ETD fragmentation were regio-selectively scrambled: The deuterium in some regions of a peptide ion was scrambled while that in the other regions was not scrambled. The method determined 31 backbone amide hydrogen exchange rates of cytochrome c in the non-scrambled regions. Good fragmentation of a parent ion, a low degree of scrambling, and a low number of exchangeable hydrogens in the preceding side chain are the important factors to determine the exchange rate. The exchange rates determined by the HDX-MS are in good agreement with those determined by NMR. Graphical Abstract ᅟ.

Determination of Backbone Amide Hydrogen Exchange Rates of Cytochrome c Using Partially Scrambled Electron Transfer Dissociation Data

Science.gov (United States)

Hamuro, Yoshitomo; E, Sook Yen

2018-03-01

The technological goal of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is to determine backbone amide hydrogen exchange rates. The most critical challenge to achieve this goal is obtaining the deuterium incorporation in single-amide resolution, and gas-phase fragmentation may provide a universal solution. The gas-phase fragmentation may generate the daughter ions which differ by a single amino acid and the difference in deuterium incorporations in the two analogous ions can yield the deuterium incorporation at the sub-localized site. Following the pioneering works by Jørgensen and Rand, several papers utilized the electron transfer dissociation (ETD) to determine the location of deuterium in single-amide resolution. This paper demonstrates further advancement of the strategy by determining backbone amide hydrogen exchange rates, instead of just determining deuterium incorporation at a single time point, in combination with a wide time window monitoring. A method to evaluate the effects of scrambling and to determine the exchange rates from partially scrambled HDX-ETD-MS data is described. All parent ions for ETD fragmentation were regio-selectively scrambled: The deuterium in some regions of a peptide ion was scrambled while that in the other regions was not scrambled. The method determined 31 backbone amide hydrogen exchange rates of cytochrome c in the non-scrambled regions. Good fragmentation of a parent ion, a low degree of scrambling, and a low number of exchangeable hydrogens in the preceding side chain are the important factors to determine the exchange rate. The exchange rates determined by the HDX-MS are in good agreement with those determined by NMR. [Figure not available: see fulltext.

Performance of Flow-Aware Networking in LTE backbone

DEFF Research Database (Denmark)

Sniady, Aleksander; Soler, José

2012-01-01

technologies, such as Long Term Evolution (LTE). This paper proposes usage of a modified Flow Aware Networking (FAN) technique for enhancing Quality of Service (QoS) in the all-IP transport networks underlying LTE backbone. The results obtained with OPNET Modeler show that FAN, in spite of being relatively...

Dynamic Landslide Deformation Monitoring with Fiber Bragg Grating Sensors

Science.gov (United States)

Moore, J. R.; Gischig, V.; Button, E.; Loew, S.

2009-12-01

Fiber optic (FO) strain sensors are a promising new technology for in-situ landslide monitoring. General performance advantages include high resolution, fast sampling rate, and insensitivity to electrical disturbances. Here we describe a new FO monitoring system based on long-gage fiber Bragg grating sensors installed at the Randa Rockslide Laboratory in southern Switzerland. We highlight the advantages and disadvantages of the system, describe relevant first results, and compare FO data to that from traditional instruments already installed on site. The Randa rock slope has been the subject of intensive research since its failure in 1991. Around 5 million cubic meters of rock remains unstable today, moving at rates up to 20 mm / year. Traditional in-situ monitoring techniques have been employed to understand the mechanics and driving forces of the currently unstable rock mass, however these investigations are limited by the resolution and low sampling rate of the sensors. The new FO monitoring system has micro-strain resolution and offers the capability to detect sub-micrometer scale deformations in both triggered-dynamic and continuous measurements. Two types of sensors have been installed: fully-embedded borehole sensors encased in grout at depths of 38, 40, and 68 m, and surface extensometers spanning active tension cracks. Dynamic measurements are triggered by sensor deformation and recorded at 100 Hz, while continuous measurements are logged every 5 minutes. Since installation in August 2008, the FO monitoring system has been operational 90% of the time. Time series deformation data show movement rates consistent with previous borehole extensometer surveys. Accelerated displacements following installation are likely related to long-term curing and dewatering of the grout. A number of interesting transients have been recorded, which in some cases were large enough to trigger rapid sampling. The combination of short- and long-term observation offers new

Dynamic state estimation assisted power system monitoring and protection

Science.gov (United States)

Cui, Yinan

The advent of phasor measurement units (PMUs) has unlocked several novel methods to monitor, control, and protect bulk electric power systems. This thesis introduces the concept of "Dynamic State Estimation" (DSE), aided by PMUs, for wide-area monitoring and protection of power systems. Unlike traditional State Estimation where algebraic variables are estimated from system measurements, DSE refers to a process to estimate the dynamic states associated with synchronous generators. This thesis first establishes the viability of using particle filtering as a technique to perform DSE in power systems. The utility of DSE for protection and wide-area monitoring are then shown as potential novel applications. The work is presented as a collection of several journal and conference papers. In the first paper, we present a particle filtering approach to dynamically estimate the states of a synchronous generator in a multi-machine setting considering the excitation and prime mover control systems. The second paper proposes an improved out-of-step detection method for generators by means of angular difference. The generator's rotor angle is estimated with a particle filter-based dynamic state estimator and the angular separation is then calculated by combining the raw local phasor measurements with this estimate. The third paper introduces a particle filter-based dual estimation method for tracking the dynamic states of a synchronous generator. It considers the situation where the field voltage measurements are not readily available. The particle filter is modified to treat the field voltage as an unknown input which is sequentially estimated along with the other dynamic states. The fourth paper proposes a novel framework for event detection based on energy functions. The key idea is that any event in the system will leave a signature in WAMS data-sets. It is shown that signatures for four broad classes of disturbance events are buried in the components that constitute the

Wireless dynamic monitoring of the Colosseum in Rome

International Nuclear Information System (INIS)

Monti, Giorgio; Fumagalli, Fabio; Quaranta, Giuseppe; Marano, Giuseppe Carlo; Sgroi, Marco; Tommasi, Marcello; Rea Rossella; Nazzaro Barbara

2016-01-01

A key point for cultural heritage protection in many modern cities is to prevent damaging of historical monuments from urbanization disturbances, such as road and subway traffic vibrations. A typical dilemma is whether to focus on the effects of short-term vibrations due to construction activities or on the consequences of long-term traffic induced vibrations. Both case s present practical difficulties in both monitoring and data analysis procedures. Besides, specific standards do not provide indications neither on how to extract meaningful features from data, nor on how to identify proper strategic decisions for an effective maintenance of monuments. In this paper, an example of state - of - the - art monitoring system is presented with its application to the continuous trigger free dynamic monitoring of the Flavian Amphitheater , widely known as the Colosseum , in Rome . The installation of the monitoring system , composed of wireless accelerometers located on the top portion of the North façade of the Monument , has allowed to study all the features of recorded vibrations, beyond the usually considered peaks . The system architecture, the wireless protocol and the processing of the data are described in detail in this paper . A discussion on the data collected during a full year of monitoring is presented , with focus on statistical representation s of the dynamic response, such as fractiles of the peak acceleration s, which are meaningful and synthetic indicator s of the effects induced on the Monument by external actions of both natural and man-made nature.

A review on bridge dynamic displacement monitoring using global positioning system and accelerometer

Science.gov (United States)

Yunus, Mohd Zulkifli Mohd; Ibrahim, Nuremira; Ahmad, Fatimah Shafinaz

2018-02-01

This paper reviews previous research on bridge dynamic displacement monitoring using Global Positioning System (GPS) and an accelerometer for Structural Health Monitoring (SHM) of bridge. These include the review of the advantages and disadvantages of the measurement as well as the methodology of the measurements used in the recent research study. This review could provide a preliminary decision overview for students or researchers before initiating a research related to the bridge dynamic displacement monitoring.

Monitoring conformational dynamics with solid-state R1ρ experiments

International Nuclear Information System (INIS)

Quinn, Caitlin M.; McDermott, Ann E.

2009-01-01

A new application of solid-state rotating frame (R 1ρ ) relaxation experiments to observe conformational dynamics is presented. Studies on a model compound, dimethyl sulfone (DMS), show that R 1ρ relaxation due to reorientation of a chemical shift anisotropy (CSA) tensor undergoing chemical exchange can be used to monitor slow-to-intermediate timescale conformational exchange processes. Control experiments used d 6 -DMS and alanine to confirm that the technique is monitoring reorientation of the CSA tensor rather than dipolar interactions or methyl group rotation. The application of this method to proteins could represent a new site-specific probe of conformational dynamics

Aggregation of flexible polyelectrolytes: Phase diagram and dynamics.

Science.gov (United States)

Tom, Anvy Moly; Rajesh, R; Vemparala, Satyavani

2017-10-14

Similarly charged polymers in solution, known as polyelectrolytes, are known to form aggregated structures in the presence of oppositely charged counterions. Understanding the dependence of the equilibrium phases and the dynamics of the process of aggregation on parameters such as backbone flexibility and charge density of such polymers is crucial for insights into various biological processes which involve biological polyelectrolytes such as protein, DNA, etc. Here, we use large-scale coarse-grained molecular dynamics simulations to obtain the phase diagram of the aggregated structures of flexible charged polymers and characterize the morphology of the aggregates as well as the aggregation dynamics, in the presence of trivalent counterions. Three different phases are observed depending on the charge density: no aggregation, a finite bundle phase where multiple small aggregates coexist with a large aggregate and a fully phase separated phase. We show that the flexibility of the polymer backbone causes strong entanglement between charged polymers leading to additional time scales in the aggregation process. Such slowing down of the aggregation dynamics results in the exponent, characterizing the power law decay of the number of aggregates with time, to be dependent on the charge density of the polymers. These results are contrary to those obtained for rigid polyelectrolytes, emphasizing the role of backbone flexibility.

Towards a natural classification and backbone tree for Sordariomycete

Digital Repository Service at National Institute of Oceanography (India)

Maharachchikumbura, S.S.N.; Hyde, K.D.; Jones, E.B.G.; McKenzie, E.H.C.; Huang, S.-K.; Abdel-Wahab, M.A.; Daranagama, D.A.; Dayarathne, M.; D'souza, M.J.; Goonasekara, I.D.; Hongsanan, S.; Jayawardena, R.S.; Kirk, P.M.; Konta, S.; Liu, J.-K.; Liu, Z.-Y.; Norphanphoun, C.; Pang, K.-L.; Perera, R.H.; Senanayake, I.C.; Shang, Q.; Shenoy, B.D.; Xiao, Y.; Bahkali, A.H.; Kang, J.; Somrothipol, S.; Suetrong, S.; Wen, T.; Xu, J.

, lichenized or lichenicolous taxa The class includes freshwater, marine and terrestrial taxa and has a worldwide distribution This paper provides an updated outline of the Sordariomycetes and a backbone tree incorporating asexual and sexual genera in the class...

Optical alignment control of polyimide molecules containing azobenzene in the backbone structure

International Nuclear Information System (INIS)

Sakamoto, Kenji; Usami, Kiyoaki; Sasaki, Toru; Kanayama, Takashi; Ushioda, Sukekatsu

2004-01-01

Using polarized infrared absorption spectroscopy, we have determined the orientation of the polyimide backbone structure in photo-alignment films for liquid crystals (LC). The polyimide used in this study contains azobenzene in the backbone structure. Photo-alignment treatment was performed on the corresponding polyamic acid film, using a light source of wavelength 340-500 nm. The polyamic acid film (∼16 nm thick) was first irradiated at normal incidence with linearly polarized light (LP-light) of 156 J/cm 2 , and then oblique angle irradiation of unpolarized light (UP-light) was performed in the plane of incidence perpendicular to the polarization direction of the LP-light. The UP-light exposure was varied up to 882 J/cm 2 . We found that the average inclination angle of the polyimide backbone structure, measured from the surface plane, increases almost linearly with UP-light exposure. On the other hand, the in-plane anisotropy induced by the first irradiation with LP-light decreases with the increase of UP-light exposure

Analysis of stationary availability factor of two-level backbone computer networks with arbitrary topology

Science.gov (United States)

Rahman, P. A.

2018-05-01

This scientific paper deals with the two-level backbone computer networks with arbitrary topology. A specialized method, offered by the author for calculation of the stationary availability factor of the two-level backbone computer networks, based on the Markov reliability models for the set of the independent repairable elements with the given failure and repair rates and the methods of the discrete mathematics, is also discussed. A specialized algorithm, offered by the author for analysis of the network connectivity, taking into account different kinds of the network equipment failures, is also observed. Finally, this paper presents an example of calculation of the stationary availability factor for the backbone computer network with the given topology.

Dynamic generalized linear models for monitoring endemic diseases

DEFF Research Database (Denmark)

Lopes Antunes, Ana Carolina; Jensen, Dan; Hisham Beshara Halasa, Tariq

2016-01-01

The objective was to use a Dynamic Generalized Linear Model (DGLM) based on abinomial distribution with a linear trend, for monitoring the PRRS (Porcine Reproductive and Respiratory Syndrome sero-prevalence in Danish swine herds. The DGLM was described and its performance for monitoring control...... and eradication programmes based on changes in PRRS sero-prevalence was explored. Results showed a declining trend in PRRS sero-prevalence between 2007 and 2014 suggesting that Danish herds are slowly eradicating PRRS. The simulation study demonstrated the flexibility of DGLMs in adapting to changes intrends...... in sero-prevalence. Based on this, it was possible to detect variations in the growth model component. This study is a proof-of-concept, demonstrating the use of DGLMs for monitoring endemic diseases. In addition, the principles stated might be useful in general research on monitoring and surveillance...

Energy transfer dynamics in Light-Harvesting Dendrimers

Science.gov (United States)

Melinger, Joseph S.; McMorrow, Dale; Kleiman, Valeria D.

2002-03-01

We explore energy transfer dynamics in light-harvesting phenylacetylene symmetric and asymmetric dendrimers. Femtosecond pump-probe spectroscopy is used to probe the ultrafast dynamics of electronic excitations in these dendrimers. The backbone of the macromolecule consists of branches of increasing conjugation length, creating an energy gradient, which funnels energy to an accepting perylene trap. In the case of the symmetric dendrimer (nanostar), the energy transfer efficiency is known to approach nearly unity, although the nature and timescale of the energy transfer process is still unknown. For the asymmetric dendrimers, energy transfer efficiencies are very high, with the possibility of more complex transfer processes. We experimentally monitor the transport of excitons through the light-harvesting dendrimer. The transients show a number of components, with timescales ranging from <300fs to several tens of picoseconds, revealing the complex photophysics taking place in these macromolecules. We interpret our results in terms of the Förster mechanism in which energy transfer occurs through dipole-dipole interactions.

Automated backbone assignment of labeled proteins using the threshold accepting algorithm

International Nuclear Information System (INIS)

Leutner, Michael; Gschwind, Ruth M.; Liermann, Jens; Schwarz, Christian; Gemmecker, Gerd; Kessler, Horst

1998-01-01

The sequential assignment of backbone resonances is the first step in the structure determination of proteins by heteronuclear NMR. For larger proteins, an assignment strategy based on proton side-chain information is no longer suitable for the use in an automated procedure. Our program PASTA (Protein ASsignment by Threshold Accepting) is therefore designed to partially or fully automate the sequential assignment of proteins, based on the analysis of NMR backbone resonances plus C β information. In order to overcome the problems caused by peak overlap and missing signals in an automated assignment process, PASTA uses threshold accepting, a combinatorial optimization strategy, which is superior to simulated annealing due to generally faster convergence and better solutions. The reliability of this algorithm is shown by reproducing the complete sequential backbone assignment of several proteins from published NMR data. The robustness of the algorithm against misassigned signals, noise, spectral overlap and missing peaks is shown by repeating the assignment with reduced sequential information and increased chemical shift tolerances. The performance of the program on real data is finally demonstrated with automatically picked peak lists of human nonpancreatic synovial phospholipase A 2 , a protein with 124 residues

Drug-induced cellular death dynamics monitored by a highly sensitive organic electrochemical system.

Science.gov (United States)

Romeo, Agostino; Tarabella, Giuseppe; D'Angelo, Pasquale; Caffarra, Cristina; Cretella, Daniele; Alfieri, Roberta; Petronini, Pier Giorgio; Iannotta, Salvatore

2015-06-15

We propose and demonstrate a sensitive diagnostic device based on an Organic Electrochemical Transistor (OECT) for direct in-vitro monitoring cell death. The system efficiently monitors cell death dynamics, being able to detect signals related to specific death mechanisms, namely necrosis or early/late apoptosis, demonstrating a reproducible correlation between the OECT electrical response and the trends of standard cell death assays. The innovative design of the Twell-OECT system has been modeled to better correlate electrical signals with cell death dynamics. To qualify the device, we used a human lung adenocarcinoma cell line (A549) that was cultivated on the micro-porous membrane of a Transwell (Twell) support, and exposed to the anticancer drug doxorubicin. Time-dependent and dose-dependent dynamics of A549 cells exposed to doxorubicin are evaluated by monitoring cell death upon exposure to a range of doses and times that fully covers the protocols used in cancer treatment. The demonstrated ability to directly monitor cell stress and death dynamics upon drug exposure using simple electronic devices and, possibly, achieving selectivity to different cell dynamics is of great interest for several application fields, including toxicology, pharmacology, and therapeutics. Copyright © 2015 Elsevier B.V. All rights reserved.

Integrated approach to monitor water dynamics with drones

Science.gov (United States)

Raymaekers, Dries; De Keukelaere, Liesbeth; Knaeps, Els; Strackx, Gert; Decrop, Boudewijn; Bollen, Mark

2017-04-01

Remote sensing has been used for more than 20 years to estimate water quality in the open ocean and study the evolution of vegetation on land. More recently big improvements have been made to extend these practices to coastal and inland waters, opening new monitoring opportunities, eg. monitoring the impact of dredging activities on the aquatic environment. While satellite sensors can provide complete coverage and historical information of the study area, they are limited in their temporal revisit time and spatial resolution. Therefore, deployment of drones can create an added value and in combination with satellite information increase insights in the dynamics and actors of coastal and aquatic systems. Drones have the advantages of monitoring at high spatial detail (cm scale), with high frequency and are flexible. One of the important water quality parameters is the suspended sediment concentration. However, retrieving sediment concentrations from unmanned systems is a challenging task. The sediment dynamics in the port of Breskens, the Netherlands, were investigated by combining information retrieved from different data sources: satellite, drone and in-situ data were collected, analysed and inserted in sediment models. As such, historical (satellite), near-real time (drone) and predictive (sediment models) information, integrated in a spatial data infrastructure, allow to perform data analysis and can support decision makers.

Data Acquisition Backbone Core DABC release v1.0

International Nuclear Information System (INIS)

Adamczewski-Musch, J; Kurz, N; Linev, S; Essel, H G

2010-01-01

The Data Acquisition Backbone Core (DABC) is a general purpose software framework designed for the implementation of a wide-range of data acquisition systems - from various small detector test beds to high performance systems. DABC consists of a compact data-flow kernel and a number of plug-ins for various functional components like data inputs, device drivers, user functional modules and applications. DABC provides configurable components for implementing event building over fast networks like InfiniBand or Gigabit Ethernet. A generic Java GUI provides the dynamic control and visualization of control parameters and commands, provided by DIM servers. A first set of application plug-ins has been implemented to use DABC as event builder for the front-end components of the GSI standard DAQ system MBS (Multi Branch System). Another application covers the connection to DAQ readout chains from detector front-end boards (N-XYTER) linked to read-out controller boards (ROC) over UDP into DABC for event building, archiving and data serving. This was applied for data taking in the September 2008 test beamtime for the CBM experiment at GSI. DABC version 1.0 is released and available from the website.

The review of dynamic monitoring technology for crop growth

Science.gov (United States)

Zhang, Hong-wei; Chen, Huai-liang; Zou, Chun-hui; Yu, Wei-dong

2010-10-01

In this paper, crop growth monitoring methods are described elaborately. The crop growth models, Netherlands-Wageningen model system, the United States-GOSSYM model and CERES models, Australia APSIM model and CCSODS model system in China, are introduced here more focus on the theories of mechanism, applications, etc. The methods and application of remote sensing monitoring methods, which based on leaf area index (LAI) and biomass were proposed by different scholars at home and abroad, are highly stressed in the paper. The monitoring methods of remote sensing coupling with crop growth models are talked out at large, including the method of "forced law" which using remote sensing retrieval state parameters as the crop growth model parameters input, and then to enhance the dynamic simulation accuracy of crop growth model and the method of "assimilation of Law" which by reducing the gap difference between the value of remote sensing retrieval and the simulated values of crop growth model and thus to estimate the initial value or parameter values to increasing the simulation accuracy. At last, the developing trend of monitoring methods are proposed based on the advantages and shortcomings in previous studies, it is assured that the combination of remote sensing with moderate resolution data of FY-3A, MODIS, etc., crop growth model, "3S" system and observation in situ are the main methods in refinement of dynamic monitoring and quantitative assessment techniques for crop growth in future.

Flow Monitoring Experiences at the Ethernet-Layer

NARCIS (Netherlands)

Hofstede, Rick; Hofstede, R.J.; Drago, Idilio; Sperotto, Anna; Pras, Aiko; Lehnert, Ralf

2011-01-01

Flow monitoring is a scalable technology for providing summaries of network activity. Being deployed at the IP-layer, it uses fixed flow definitions, based on fields of the IP-layer and higher layers. Since several backbone network operators are considering the deployment of (Carrier) Ethernet in

Structural insights into the backbone-circularized granulocyte colony-stimulating factor containing a short connector.

Science.gov (United States)

Miyafusa, Takamitsu; Shibuya, Risa; Honda, Shinya

2018-06-02

Backbone circularization is a powerful approach for enhancing the structural stability of polypeptides. Herein, we present the crystal structure of the circularized variant of the granulocyte colony-stimulating factor (G-CSF) in which the terminal helical region was circularized using a short, two-amino acid connector. The structure revealed that the N- and C-termini were indeed connected by a peptide bond. The local structure of the C-terminal region transited from an α helix to 3 10 helix with a bend close to the N-terminal region, indicating that the structural change offset the insufficient length of the connector. This is the first-ever report of a crystal structure of the backbone of a circularized protein. It will facilitate the development of backbone circularization methodology. Copyright © 2018 Elsevier Inc. All rights reserved.

Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

Science.gov (United States)

Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

2016-02-01

Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.

Constructing Battery-Aware Virtual Backbones in Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Yang Yuanyuan

2007-01-01

Full Text Available A critical issue in battery-powered sensor networks is to construct energy efficient virtual backbones for network routing. Recent study in battery technology reveals that batteries tend to discharge more power than needed and reimburse the over-discharged power if they are recovered. In this paper we first provide a mathematical battery model suitable for implementation in sensor networks. We then introduce the concept of battery-aware connected dominating set (BACDS and show that in general the minimum BACDS (MBACDS can achieve longer lifetime than the previous backbone structures. Then we show that finding a MBACDS is NP-hard and give a distributed approximation algorithm to construct the BACDS. The resulting BACDS constructed by our algorithm is at most opt size, where is the maximum node degree and opt is the size of an optimal BACDS. Simulation results show that the BACDS can save a significant amount of energy and achieve up to longer network lifetime than previous schemes.

Polyolefin backbone substitution in binders for low temperature powder injection moulding feedstocks.

Science.gov (United States)

Hausnerova, Berenika; Kuritka, Ivo; Bleyan, Davit

2014-02-27

This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al₂O₃ feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions containing polyethylene glycol as the initial opening agent and governing the proper mechanism of the degradation process. Moreover, the replacement of synthetic polymer by the natural wax contributes to an increase of environmental sustainability of modern industrial technologies.

Synchronous monitoring of muscle dynamics and electromyogram

Science.gov (United States)

Zakir Hossain, M.; Grill, Wolfgang

2011-04-01

A non-intrusive novel detection scheme has been implemented to detect the lateral muscle extension, force of the skeletal muscle and the motor action potential (EMG) synchronously. This allows the comparison of muscle dynamics and EMG signals as a basis for modeling and further studies to determine which architectural parameters are most sensitive to changes in muscle activity. For this purpose the transmission time for ultrasonic chirp signal in the frequency range of 100 kHz to 2.5 MHz passing through the muscle under observation and respective motor action potentials are recorded synchronously to monitor and quantify biomechanical parameters related to muscle performance. Additionally an ultrasonic force sensor has been employed for monitoring. Ultrasonic traducers are placed on the skin to monitor muscle expansion. Surface electrodes are placed suitably to pick up the potential for activation of the monitored muscle. Isometric contraction of the monitored muscle is ensured by restricting the joint motion with the ultrasonic force sensor. Synchronous monitoring was initiated by a software activated audio beep starting at zero time of the subsequent data acquisition interval. Computer controlled electronics are used to generate and detect the ultrasonic signals and monitor the EMG signals. Custom developed software and data analysis is employed to analyze and quantify the monitored data. Reaction time, nerve conduction speed, latent period between the on-set of EMG signals and muscle response, degree of muscle activation and muscle fatigue development, rate of energy expenditure and motor neuron recruitment rate in isometric contraction, and other relevant parameters relating to muscle performance have been quantified with high spatial and temporal resolution.

Internet Backbone in the Democratic Republic of Congo : Feasibility ...

International Development Research Centre (IDRC) Digital Library (Canada)

Internet Backbone in the Democratic Republic of Congo : Feasibility Study and Advocacy. During 7-10 February 2005, representatives of five francophone African countries (Cameroon, Morocco, Niger, Sénégal, and the Democratic Republic of Congo - DRC) met to consider ways and means of galvanizing the appropriation ...

Monitor of dynamic parameters in real time; Monitor de parametros dinamicos en tiempo real

Energy Technology Data Exchange (ETDEWEB)

Rojas S, A.S.; Ruiz E, J.A. [ININ, 52750 La Marquesa, Estado de Mexico (Mexico)

2008-07-01

In the complex physical systems exist parameters that are necessary for monitoring in real time. In the nuclear industry, particularly in a reactor this surveillance is important, where the times of the reactions are almost instantaneous. Although many of these parameters are monitored, given the advance of the computer systems the monitoring could either be enlarged direct or indirect of other parameters. The analysis of the neutron noise in the nuclear reactors, plays an important role, the noise signal it contains information about the operation conditions of a system, when analyzing it with analysis methodologies of analogical signals to provide important information for the early detection of possible flaws and to indicate the permissible operation levels. To show the characteristics of the operation of the system of Monitoring of Dynamic Parameters in Real Time, oscillations of neutron noise of the TRIGA Mark III of the ININ were analyzed, these were caused with the control bar to a power of 10 Watts, the oscillations were carried out to a frequency of 1Hz, signal of low frequency. In this work a virtual instrument that allows by means of the spectral analysis method in frequency point by point is presented, to indicate in real time periodic variations that could be presented in the neutron noise signal, visualizing in advance the dynamic behavior of the system or nuclear plant. Another of the tests of the monitoring system presented is that of the oscillatory event happened in the reactor of Laguna Verde Nucleo electric Central, would be convenient to have an instrument of surveillance for monitoring through the neutron noise signal the behavior of some important parameter to predict and to indicate in an immediate way an abnormal condition in the reactor operation or in the plant system. These parameters can be the power, the recirculation water flow, etc. The monitor is based on a personal computer (PC), a data acquisition card (ADC) and a computer program

Dynamic monitoring of reproduction records for dairy cattle

DEFF Research Database (Denmark)

Cornou, C.; Østergaard, S.; Ancker, M. L.

2014-01-01

This application note presents a newly developed surveillance module for monitoring reproduction performances in dairy herds. It is called Critical Control Point and is part of a recently developed management tool, Dairy Management System. This management tool is commercialized as software intended...... both for farmers, extension officers, breeding advisors and veterinarians. Insemination and conception rates, for cows and heifers, are modeled at the herd level using Dynamic Generalized Linear Models for binomial data. The results are updated and monitored on a weekly basis, using control charts......, and alarms are provided when the performances are below target values. Both the number of observed inseminations and pregnancies, and the insemination and pregnancy rates are monitored. The components of the user interface are presented and some comprehensive graphs, accessible to the user, illustrate...

Oxidation Responsive Polymers with a Triggered Degradation via Arylboronate Self-Immolative Motifs on a Polyphosphazene Backbone.

Science.gov (United States)

Iturmendi, Aitziber; Monkowius, Uwe; Teasdale, Ian

2017-02-21

Oxidation responsive polymers with triggered degradation pathways have been prepared via attachment of self-immolative moieties onto a hydrolytically unstable polyphosphazene backbone. After controlled main-chain growth, postpolymerization functionalization allows the preparation of hydrolytically stable poly(organo)phosphazenes decorated with a phenylboronic ester caging group. In oxidative environments, triggered cleavage of the caging group is followed by self-immolation, exposing the unstable glycine-substituted polyphosphazene which subsequently undergoes to backbone degradation to low-molecular weight molecules. As well as giving mechanistic insights, detailed GPC and 1 H and 31 P NMR analysis reveal the polymers to be stable in aqueous solutions, but show a selective, fast degradation upon exposure to hydrogen peroxide containing solutions. Since the post-polymerization functionalization route allows simple access to polymer backbones with a broad range of molecular weights, the approach of using the inorganic backbone as a platform significantly expands the toolbox of polymers capable of stimuli-responsive degradation.

Risk-based reconfiguration of safety monitoring system using dynamic Bayesian network

International Nuclear Information System (INIS)

Kohda, Takehisa; Cui Weimin

2007-01-01

To prevent an abnormal event from leading to an accident, the role of its safety monitoring system is very important. The safety monitoring system detects symptoms of an abnormal event to mitigate its effect at its early stage. As the operation time passes by, the sensor reliability decreases, which implies that the decision criteria of the safety monitoring system should be modified depending on the sensor reliability as well as the system reliability. This paper presents a framework for the decision criteria (or diagnosis logic) of the safety monitoring system. The logic can be dynamically modified based on sensor output data monitored at regular intervals to minimize the expected loss caused by two types of safety monitoring system failure events: failed-dangerous (FD) and failed-safe (FS). The former corresponds to no response under an abnormal system condition, while the latter implies a spurious activation under a normal system condition. Dynamic Bayesian network theory can be applied to modeling the entire system behavior composed of the system and its safety monitoring system. Using the estimated state probabilities, the optimal decision criterion is given to obtain the optimal diagnosis logic. An illustrative example of a three-sensor system shows the merits and characteristics of the proposed method, where the reasonable interpretation of sensor data can be obtained

Monitoring the Como Railway Bridge based on dynamic FBG sensor system

Science.gov (United States)

Zhang, Jianzhong; Sun, Weimin; Peng, G. D.; Yuan, Libo

2007-07-01

A FBG-based dynamic strain sensor system, whose responding frequency and resolution can be high as 16Hz and ~1μɛ respectively, is described and the system is applied to monitor the dynamic strain of Como Railway Bridge in Australia. The results of one-month long measurement show that the system can figure out all dynamic strain caused by passed trains and also prove the stability of the sensor system.

[Intracranial pressure monitoring and CSF dynamics in patients with neurological disorders: indications and practical considerations].

Science.gov (United States)

Poca, M; Sahuquillo, J

2001-01-01

The study of cerebrospinal fluid (CSF) dynamics is central to the diagnosis of adult chronic hydrocephalus (ACH). At present, many neurology and neurosurgery departments use one or more tests to guide diagnosis of this syndrome and to predict patient response to shunting. In specialised centres, the study of CSF dynamics is combined with continuous intracranial pressure (ICP) monitoring. Determination of several variables of CSF dynamics and definitions of qualitative and quantitative characteristics of ICP can be used to establish whether the hydrocephalus is active, compensated or arrested. CSF dynamics and ICP monitoring can also be used to check the correct functioning of the shunt and can be of use in the clinical management of patients with pseudotumor cerebri. Moreover, ICP monitoring is used to guide the treatment of several acute neurological processes. The aim of this review is to describe the fundamentals of CSF dynamics studies and the bases of continuous ICP monitoring. The advantages and disadvantages of several hydrodynamic tests that can be performed by lumbar puncture, as well as the normal and abnormal characteristics of an ICP recording, are discussed.

Green IGP Link Weights for Energy-efficiency and Load-balancing in IP Backbone Networks

OpenAIRE

Francois, Frederic; Wang, Ning; Moessner, Klaus; Georgoulas, Stylianos; Xu, Ke

2013-01-01

The energy consumption of backbone networks has become a primary concern for network operators and regulators due to the pervasive deployment of wired backbone networks to meet the requirements of bandwidth-hungry applications. While traditional optimization of IGP link weights has been used in IP based load-balancing operations, in this paper we introduce a novel link weight setting algorithm, the Green Load-balancing Algorithm (GLA), which is able to jointly optimize both energy efficiency ...

Noninvasive Monitoring of Soil Static Characteristics and Dynamic States

DEFF Research Database (Denmark)

Cassiani, Giorgio; Ursino, Nadia; Deiana, Rita

2012-01-01

of possible climatic changes. We used long-term electromagnetic induction (EMI) time lapse monitoring and short-term irrigation experiments monitored using electrical resistivity tomography (ERT) and EMI, supported by time domain reflectometry (TDR) soil moisture measurements. Mapping of natural ?-ray...... emission, texture analysis, and laboratory calibration of an electrical constitutive relationship on soil samples complete the dataset. We observe that the growth of vegetation, with the associated below-ground allocation of biomass, has a significant impact on the soil moisture dynamics. It is well known...

Polyolefin Backbone Substitution in Binders for Low Temperature Powder Injection Moulding Feedstocks

Directory of Open Access Journals (Sweden)

Berenika Hausnerova

2014-02-01

Full Text Available This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al2O3 feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions containing polyethylene glycol as the initial opening agent and governing the proper mechanism of the degradation process. Moreover, the replacement of synthetic polymer by the natural wax contributes to an increase of environmental sustainability of modern industrial technologies.

Advances in monitoring vegetation and land use dynamics in the Sahel

DEFF Research Database (Denmark)

Mbow, Cheikh; Fensholt, Rasmus; Nielsen, Thomas Theis

2014-01-01

of CO2 in the atmosphere, grazing pressure, bush fires and agricultural expansion or contraction. The use of satellite data in combination with field data played a major role in the monitoring of vegetation dynamics and land use in the Sahel, since the mega drought of the 1970s and the 1980s. This paper...... briefly reviews the advance of satellite-based monitoring of vegetation dynamics over these 40 years. We discuss the promises of current and likely future data sources and analysis tools, as well as the need to strengthen in situ data collection to support and validate satellite-based vegetation and land...

“Pinning strategy”: a novel approach for predicting the backbone ...

Indian Academy of Sciences (India)

Prakash

To assess the quality of the strategy, we define two measures. The first one ...... modular framework of the protein backbone; Protein Eng. 12. 1063–1073 .... Richardson J S, Getzoff E D and Richardson D C 1978 The beta bulge: a common ...

Impact of Backbone Fluorination on π-Conjugated Polymers in Organic Photovoltaic Devices: A Review

Directory of Open Access Journals (Sweden)

Nicolas Leclerc

2016-01-01

Full Text Available Solution-processed bulk heterojunction solar cells have experienced a remarkable acceleration in performances in the last two decades, reaching power conversion efficiencies above 10%. This impressive progress is the outcome of a simultaneous development of more advanced device architectures and of optimized semiconducting polymers. Several chemical approaches have been developed to fine-tune the optoelectronics and structural polymer parameters required to reach high efficiencies. Fluorination of the conjugated polymer backbone has appeared recently to be an especially promising approach for the development of efficient semiconducting polymers. As a matter of fact, most currently best-performing semiconducting polymers are using fluorine atoms in their conjugated backbone. In this review, we attempt to give an up-to-date overview of the latest results achieved on fluorinated polymers for solar cells and to highlight general polymer properties’ evolution trends related to the fluorination of their conjugated backbone.

Constructing Battery-Aware Virtual Backbones in Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Chi Ma

2007-05-01

Full Text Available A critical issue in battery-powered sensor networks is to construct energy efficient virtual backbones for network routing. Recent study in battery technology reveals that batteries tend to discharge more power than needed and reimburse the over-discharged power if they are recovered. In this paper we first provide a mathematical battery model suitable for implementation in sensor networks. We then introduce the concept of battery-aware connected dominating set (BACDS and show that in general the minimum BACDS (MBACDS can achieve longer lifetime than the previous backbone structures. Then we show that finding a MBACDS is NP-hard and give a distributed approximation algorithm to construct the BACDS. The resulting BACDS constructed by our algorithm is at most (8+Δopt size, where Δ is the maximum node degree and opt is the size of an optimal BACDS. Simulation results show that the BACDS can save a significant amount of energy and achieve up to 30% longer network lifetime than previous schemes.

Monitoring land Cover Changes and Fragmentation dynamics in the ...

African Journals Online (AJOL)

Monitoring land Cover Changes and Fragmentation dynamics in the subtropical thicket of the Eastern Cape Province, South Africa. ... Baseline land use/cover maps and fragmentation analyses in a temporal framework are valuable for gaining insights into, among other things, carbon stock change trends. Keywords: Land ...

Individual Differences in Search and Monitoring for Color Targets in Dynamic Visual Displays.

Science.gov (United States)

Muhl-Richardson, Alex; Godwin, Hayward J; Garner, Matthew; Hadwin, Julie A; Liversedge, Simon P; Donnelly, Nick

2018-02-01

Many real-world tasks now involve monitoring visual representations of data that change dynamically over time. Monitoring dynamically changing displays for the onset of targets can be done in two ways: detecting targets directly, post-onset, or predicting their onset from the prior state of distractors. In the present study, participants' eye movements were measured as they monitored arrays of 108 colored squares whose colors changed systematically over time. Across three experiments, the data show that participants detected the onset of targets both directly and predictively. Experiments 1 and 2 showed that predictive detection was only possible when supported by sequential color changes that followed a scale ordered in color space. Experiment 3 included measures of individual differences in working memory capacity (WMC) and anxious affect and a manipulation of target prevalence in the search task. It found that predictive monitoring for targets, and decisions about target onsets, were influenced by interactions between individual differences in verbal and spatial WMC and intolerance of uncertainty, a characteristic that reflects worry about uncertain future events. The results have implications for the selection of individuals tasked with monitoring dynamic visual displays for target onsets. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Smectic order and backbone anisotropy of a side-chain liquid crystalline polymer by Small-Angle Neutron Scattering

Science.gov (United States)

Noirez, L.; Pépy, G.; Keller, P.; Benguigui, L.

1991-07-01

We have simultaneously measured, for the first time, the extension of the polymer backbone of a side-chain liquid crystalline polymer and the intensity of the 001 Bragg reflection, which gives the smectic order parameter Psi as a function of temperature in the smectic phase. We have qualitatively demonstrated that the more the smectic phase is ordered, the more the polymer backbone is localized between the mesogenic layers. It is shown that the Landau theory allows us to relate the radius of gyration parallel to the magnetic field of the polymer backbone to the smectic order parameter. We also show that the Renz-Warner theory is suitable at low temperatures.

Dynamic monitoring equipment for earthworks and sub grades

International Nuclear Information System (INIS)

Alvarez de Sotomayor, R.

2013-01-01

This paper take into account some dynamic auscultation equipment s that currently are available in Spain for compaction quality control on earthworks and sub grades. Closed to the equipment description, a deformation modulus calculus approximation has been developed for each of them. A standards checking has been made from national and European point of view. some important research works that have been developed in our country about dynamic monitoring equipment s for quality control in earthworks has been mentioned. In addition to this, some variables are analyzed which have an influence on deformation modulus calculi and a possibility for comparing the equipment modulus calculated with a reference laboratory test has been offered. (Author) 18 refs.

Effect of short-chain branching on interfacial polymer structure and dynamics under shear flow.

Science.gov (United States)

Jeong, Sohdam; Kim, Jun Mo; Cho, Soowon; Baig, Chunggi

2017-11-22

We present a detailed analysis on the effect of short-chain branches on the structure and dynamics of interfacial chains using atomistic nonequilibrium molecular dynamics simulations of confined polyethylene melts in a wide range of shear rates. The intrinsically fast random motions of the short branches constantly disturb the overall chain conformation, leading to a more compact and less deformed chain structure of the short-chain branched (SCB) polymer against the imposed flow field in comparison with the corresponding linear polymer. Moreover, such highly mobile short branches along the backbone of the SCB polymer lead to relatively weaker out-of-plane wagging dynamics of interfacial chains, with highly curvy backbone structures in the intermediate flow regime. In conjunction with the contribution of short branches (as opposed to that of the backbone) to the total interfacial friction between the chains and the wall, the SCB polymer shows a nearly constant behavior in the degree of slip (d s ) with respect to shear rate in the weak-to-intermediate flow regimes. On the contrary, in the strong flow regime where irregular chain rotation and tumbling dynamics occur via intensive dynamical collisions between interfacial chains and the wall, an enhancement effect on the chain detachment from the wall, caused by short branches, leads to a steeper increase in d s for the SCB polymer than for the linear polymer. Remarkably, the SCB chains at the interface exhibit two distinct types of rolling mechanisms along the backbone, with a half-dumbbell mesoscopic structure at strong flow fields, in addition to the typical hairpin-like tumbling behavior displayed by the linear chains.

Self-assembly of diphenylalanine backbone homologues and their combination with functionalized carbon nanotubes.

Science.gov (United States)

Dinesh, Bhimareddy; Squillaci, Marco A; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto

2015-10-14

The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of β and γ peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of β and γ peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.

Performance Analysis of Space Information Networks with Backbone Satellite Relaying for Vehicular Networks

Directory of Open Access Journals (Sweden)

Jian Jiao

2017-01-01

Full Text Available Space Information Network (SIN with backbone satellites relaying for vehicular network (VN communications is regarded as an effective strategy to provide diverse vehicular services in a seamless, efficient, and cost-effective manner in rural areas and highways. In this paper, we investigate the performance of SIN return channel cooperative communications via an amplify-and-forward (AF backbone satellite relaying for VN communications, where we assume that both of the source-destination and relay-destination links undergo Shadowed-Rician fading and the source-relay link follows Rician fading, respectively. In this SIN-assisted VN communication scenario, we first obtain the approximate statistical distributions of the equivalent end-to-end signal-to-noise ratio (SNR of the system. Then, we derive the closed-form expressions to efficiently evaluate the average symbol error rate (ASER of the system. Furthermore, the ASER expressions are taking into account the effect of satellite perturbation of the backbone relaying satellite, which reveal the accumulated error of the antenna pointing error. Finally, simulation results are provided to verify the accuracy of our theoretical analysis and show the impact of various parameters on the system performance.

Prediction of backbone dihedral angles and protein secondary structure using support vector machines

Directory of Open Access Journals (Sweden)

Hirst Jonathan D

2009-12-01

Full Text Available Abstract Background The prediction of the secondary structure of a protein is a critical step in the prediction of its tertiary structure and, potentially, its function. Moreover, the backbone dihedral angles, highly correlated with secondary structures, provide crucial information about the local three-dimensional structure. Results We predict independently both the secondary structure and the backbone dihedral angles and combine the results in a loop to enhance each prediction reciprocally. Support vector machines, a state-of-the-art supervised classification technique, achieve secondary structure predictive accuracy of 80% on a non-redundant set of 513 proteins, significantly higher than other methods on the same dataset. The dihedral angle space is divided into a number of regions using two unsupervised clustering techniques in order to predict the region in which a new residue belongs. The performance of our method is comparable to, and in some cases more accurate than, other multi-class dihedral prediction methods. Conclusions We have created an accurate predictor of backbone dihedral angles and secondary structure. Our method, called DISSPred, is available online at http://comp.chem.nottingham.ac.uk/disspred/.

Radiation monitoring methodologies and their applications at BARC site

International Nuclear Information System (INIS)

Divkar, J.K.; Chatterjee, M.K.; Patra, R.P; Morali, S.; Singh, Rajvir

2016-01-01

Radiation monitoring methodology can be planned for various objectives during normal as well as emergency situations. During radiological emergency, radiation monitoring data provides useful information required for management of the abnormal situation. In order to assess the possible consequences accurately and to implement adequate measure, the emergency management authorities should have a well-prepared monitoring strategy in readiness. Fixed monitoring method is useful to analyze the behavior of nuclear plant site and to develop holistic model for it mobile monitoring is useful for quick impact assessment and will be the backbone of emergency response, particularly in case of non availability of fixed monitoring system caused due to natural disaster like floods, earthquake and tsunami

Mnn10 Maintains Pathogenicity in Candida albicans by Extending α-1,6-Mannose Backbone to Evade Host Dectin-1 Mediated Antifungal Immunity.

Directory of Open Access Journals (Sweden)

Shi Qun Zhang

2016-05-01

Full Text Available The cell wall is a dynamic structure that is important for the pathogenicity of Candida albicans. Mannan, which is located in the outermost layer of the cell wall, has been shown to contribute to the pathogenesis of C. albicans, however, the molecular mechanism by which this occurs remains unclear. Here we identified a novel α-1,6-mannosyltransferase encoded by MNN10 in C. albicans. We found that Mnn10 is required for cell wall α-1,6-mannose backbone biosynthesis and polysaccharides organization. Deletion of MNN10 resulted in significant attenuation of the pathogenesis of C. albicans in a murine systemic candidiasis model. Inhibition of α-1,6-mannose backbone extension did not, however, impact the invasive ability of C. albicans in vitro. Notably, mnn10 mutant restored the invasive capacity in athymic nude mice, which further supports the notion of an enhanced host antifungal defense related to this backbone change. Mnn10 mutant induced enhanced Th1 and Th17 cell mediated antifungal immunity, and resulted in enhanced recruitment of neutrophils and monocytes for pathogen clearance in vivo. We also demonstrated that MNN10 could unmask the surface β-(1,3-glucan, a crucial pathogen-associated molecular pattern (PAMP of C. albicans recognized by host Dectin-1. Our results demonstrate that mnn10 mutant could stimulate an enhanced Dectin-1 dependent immune response of macrophages in vitro, including the activation of nuclear factor-κB, mitogen-activated protein kinase pathways, and secretion of specific cytokines such as TNF-α, IL-6, IL-1β and IL-12p40. In summary, our study indicated that α-1,6-mannose backbone is critical for the pathogenesis of C. albicans via shielding β-glucan from recognition by host Dectin-1 mediated immune recognition. Moreover, our work suggests that inhibition of α-1,6-mannose extension by Mnn10 may represent a novel modality to reduce the pathogenicity of C. albicans.

Smart-Grid Backbone Network Real-Time Delay Reduction via Integer Programming.

Science.gov (United States)

Pagadrai, Sasikanth; Yilmaz, Muhittin; Valluri, Pratyush

2016-08-01

This research investigates an optimal delay-based virtual topology design using integer linear programming (ILP), which is applied to the current backbone networks such as smart-grid real-time communication systems. A network traffic matrix is applied and the corresponding virtual topology problem is solved using the ILP formulations that include a network delay-dependent objective function and lightpath routing, wavelength assignment, wavelength continuity, flow routing, and traffic loss constraints. The proposed optimization approach provides an efficient deterministic integration of intelligent sensing and decision making, and network learning features for superior smart grid operations by adaptively responding the time-varying network traffic data as well as operational constraints to maintain optimal virtual topologies. A representative optical backbone network has been utilized to demonstrate the proposed optimization framework whose simulation results indicate that superior smart-grid network performance can be achieved using commercial networks and integer programming.

Continuous dynamic monitoring of a lively footbridge for serviceability assessment and damage detection

Science.gov (United States)

Hu, Wei-Hua; Moutinho, Carlos; Caetano, Elsa; Magalhães, Filipe; Cunha, Álvaro

2012-11-01

This paper aims at analyzing the feasibility of applying a vibration based damage detection approach, based on Principal Components Analysis (PCA), to eliminate environmental effects using the large amount of high quality data continuously collected by the dynamic monitoring system of Pedro e Inês footbridge since 2007. Few works describe real data, regularly collected along several years by reliable continuous dynamic monitoring systems in bridge structures. One main contribution is to show a large difference between making academic research based on numerical simulations or limited experimental samples, and making validity tests of innovative procedures using large high quality databases collected in real structures. The monitoring system, installed with the only initial objective of checking the efficiency of vibration control devices used to mitigate lateral and vertical vibrations, was therefore further developed for research purposes by implementing LabVIEW based automated signal processing and output-only modal identification routines, that enabled the analysis of the correlation of modal estimates with the temperature and the vibration level, as well as the automatic tracking of modal parameters along several years. With the final purpose of detecting potential structural damage at an early stage, the Principal Components Analysis (PCA) was employed to effectively eliminate temperature effects, whereas Novelty Analysis on the residual errors of the PCA model was used to provide a statistical indication of damage. The efficiency of this vibration based damage detection approach was verified using 3 years of measurements at Pedro e Inês footbridge under operational conditions and simulating several realistic damage scenarios affecting the boundary conditions. It is demonstrated that such a dynamic monitoring system, apart from providing relevant instantaneous dynamic information, working as an alert system associated to the verification of vibration

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks.

Science.gov (United States)

Schmidtgall, Boris; Höbartner, Claudia; Ducho, Christian

2015-01-01

Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T-T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X-T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A-T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues.

A distributed scheme to manage the dynamic coexistence of IEEE 802.15.4-based health-monitoring WBANs.

Science.gov (United States)

Deylami, Mohammad N; Jovanov, Emil

2014-01-01

The overlap of transmission ranges between wireless networks as a result of mobility is referred to as dynamic coexistence. The interference caused by coexistence may significantly affect the performance of wireless body area networks (WBANs) where reliability is particularly critical for health monitoring applications. In this paper, we analytically study the effects of dynamic coexistence on the operation of IEEE 802.15.4-based health monitoring WBANs. The current IEEE 802.15.4 standard lacks mechanisms for effectively managing the coexistence of mobile WBANs. Considering the specific characteristics and requirements of health monitoring WBANs, we propose the dynamic coexistence management (DCM) mechanism to make IEEE 802.15.4-based WBANs able to detect and mitigate the harmful effects of coexistence. We assess the effectiveness of this scheme using extensive OPNET simulations. Our results indicate that DCM improves the successful transmission rates of dynamically coexisting WBANs by 20%-25% for typical medical monitoring applications.

CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

International Nuclear Information System (INIS)

Swain, Monalisa; Atreya, Hanudatta S.

2009-01-01

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1 H α and 13 C' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment

Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

DEFF Research Database (Denmark)

Eildal, Jonas N N; Hultqvist, Greta; Balle, Thomas

2013-01-01

-protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains...... of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding...... to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1...

Effect of oligonucleic acid (ONA) backbone features on assembly of ONA-star polymer conjugates: a coarse-grained molecular simulation study.

Science.gov (United States)

Condon, Joshua E; Jayaraman, Arthi

2017-10-04

Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (T m ) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (T a ) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA T m in these systems, as the number of ONA-star polymer arms increase, the assembly temperature T a increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.

Effect of backbone structure on charge transport along isolated conjugated polymer chains

International Nuclear Information System (INIS)

Siebbeles, Laurens D.A.; Grozema, Ferdinand C.; Haas, Matthijs P. de; Warman, John M.

2005-01-01

Fast charge transport in conjugated polymers is essential for their application in opto-electronic devices. In the present paper, measurements and theoretical modeling of the mobility of excess charges along isolated chains of conjugated polymers in dilute solution are presented. Charge carriers were produced by irradiation of the polymer solution with 3-MeV electrons from a Van de Graaff accelerator. The mobilities of the charges along the polymer chains were obtained from time-resolved microwave conductivity measurements. The mobilities are strongly dependent on the chemical nature of the polymer backbone. Comparison of the experimental data with results from ab initio quantum mechanical calculations shows that the measured mobilities are strongly limited by torsional disorder, chemical defects and chain ends. Improvement of the structure of polymer backbones is therefore expected to significantly enhance the performance of these materials in 'plastic electronics'

Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

Science.gov (United States)

Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

2010-03-17

Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

Characterization of Charge-Carrier Transport in Semicrystalline Polymers: Electronic Couplings, Site Energies, and Charge-Carrier Dynamics in Poly(bithiophene- alt -thienothiophene) [PBTTT

KAUST Repository

Poelking, Carl; Cho, Eunkyung; Malafeev, Alexander; Ivanov, Viktor; Kremer, Kurt; Risko, Chad; Bré das, Jean-Luc; Andrienko, Denis

2013-01-01

We establish a link between the microscopic ordering and the charge-transport parameters for a highly crystalline polymeric organic semiconductor, poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT). We find that the nematic and dynamic order parameters of the conjugated backbones, as well as their separation, evolve linearly with temperature, while the side-chain dynamic order parameter and backbone paracrystallinity change abruptly upon the (also experimentally observed) melting of the side chains around 400 K. The distribution of site energies follows the behavior of the backbone paracrystallinity and can be treated as static on the time scale of a single-charge transfer reaction. On the contrary, the electronic couplings between adjacent backbones are insensitive to side-chain melting and vary on a much faster time scale. The hole mobility, calculated after time-averaging of the electronic couplings, reproduces well the value measured in a short-channel thin-film transistor. The results underline that to secure efficient charge transport in lamellar arrangements of conjugated polymers: (i) the electronic couplings should present high average values and fast dynamics, and (ii) the energetic disorder (paracrystallinity) should be small. © 2013 American Chemical Society.

Characterization of Charge-Carrier Transport in Semicrystalline Polymers: Electronic Couplings, Site Energies, and Charge-Carrier Dynamics in Poly(bithiophene- alt -thienothiophene) [PBTTT

KAUST Repository

Poelking, Carl

2013-01-31

We establish a link between the microscopic ordering and the charge-transport parameters for a highly crystalline polymeric organic semiconductor, poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT). We find that the nematic and dynamic order parameters of the conjugated backbones, as well as their separation, evolve linearly with temperature, while the side-chain dynamic order parameter and backbone paracrystallinity change abruptly upon the (also experimentally observed) melting of the side chains around 400 K. The distribution of site energies follows the behavior of the backbone paracrystallinity and can be treated as static on the time scale of a single-charge transfer reaction. On the contrary, the electronic couplings between adjacent backbones are insensitive to side-chain melting and vary on a much faster time scale. The hole mobility, calculated after time-averaging of the electronic couplings, reproduces well the value measured in a short-channel thin-film transistor. The results underline that to secure efficient charge transport in lamellar arrangements of conjugated polymers: (i) the electronic couplings should present high average values and fast dynamics, and (ii) the energetic disorder (paracrystallinity) should be small. © 2013 American Chemical Society.

Synthesis and Exciton Dynamics of Triplet Sensitized Conjugated Polymers

KAUST Repository

Andernach, Rolf; Utzat, Hendrik; Dimitrov, Stoichko; McCulloch, Iain; Heeney, Martin; Durrant, James; Bronstein, Hugo

2015-01-01

We report the synthesis of a novel polythiophene-based host-guest copolymer incorporating a Pt-porphyrin complex (TTP-Pt) into the backbone for efficient singlet to triplet polymer exciton sensitization. We elucidated the exciton dynamics in thin

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

DEFF Research Database (Denmark)

Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

2008-01-01

. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...

Marburg virus VP35 can both fully coat the backbone and cap the ends of dsRNA for interferon antagonism.

Directory of Open Access Journals (Sweden)

Shridhar Bale

2012-09-01

Full Text Available Filoviruses, including Marburg virus (MARV and Ebola virus (EBOV, cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (dsRNA-binding domain (RBD of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules.

Generation of marker- and/or backbone-free transgenic wheat plants via Agrobacterium-mediated transformation

Directory of Open Access Journals (Sweden)

Wang Genping

2016-09-01

Full Text Available Horizontal transfer of antibiotic resistance genes to animals and vertical transfer of herbicide resistance genes to the weedy relatives are perceived as major biosafety concerns in genetically modified (GM crops. In this study, five novel vectors which used gusA and bar as a reporter gene and a selection marker gene, respectively, were constructed based on the pCLEAN dual binary vector system. Among these vectors, 1G7B and 5G7B carried two T-DNAs located on two respective plasmids with 5G7B possessing an additional virGwt gene. 5LBTG154 and 5TGTB154 carried two T-DNAs in the target plasmid with either one or double right borders, and 5BTG154 carried the selectable marker gene on the backbone outside of the T-DNA left border in the target plasmid. In addition, 5BTG154, 5LBTG154 and 5TGTB154 used pAL154 as a helper plasmid which contains Komari fragment to facilitate transformation. These five dual binary vector combinations were transformed into Agrobacterium strain AGL1 and used to transform durum wheat cv Stewart 63. Evaluation of the co-transformation efficiencies, the frequencies of marker-free transgenic plants and integration of backbone sequences in the obtained transgenic lines indicated that two vectors (5G7B and 5TGTB154 were more efficient in generating marker-free transgenic wheat plants with no or minimal integration of backbone sequences in the wheat genome. The vector series developed in this study for generation of marker- and/or backbone-free transgenic wheat plants via Agrobacterium-mediated transformation will be useful to facilitate the creation of ‘clean’ GM wheat containing only the foreign genes of agronomic importance.

Generation of Marker- and/or Backbone-Free Transgenic Wheat Plants via Agrobacterium-Mediated Transformation.

Science.gov (United States)

Wang, Gen-Ping; Yu, Xiu-Dao; Sun, Yong-Wei; Jones, Huw D; Xia, Lan-Qin

2016-01-01

Horizontal transfer of antibiotic resistance genes to animals and vertical transfer of herbicide resistance genes to the weedy relatives are perceived as major biosafety concerns in genetically modified (GM) crops. In this study, five novel vectors which used gusA and bar as a reporter gene and a selection marker gene, respectively, were constructed based on the pCLEAN dual binary vector system. Among these vectors, 1G7B and 5G7B carried two T-DNAs located on two respective plasmids with 5G7B possessing an additional virGwt gene. 5LBTG154 and 5TGTB154 carried two T-DNAs in the target plasmid with either one or double right borders, and 5BTG154 carried the selectable marker gene on the backbone outside of the T-DNA left border in the target plasmid. In addition, 5BTG154, 5LBTG154, and 5TGTB154 used pAL154 as a helper plasmid which contains Komari fragment to facilitate transformation. These five dual binary vector combinations were transformed into Agrobacterium strain AGL1 and used to transform durum wheat cv Stewart 63. Evaluation of the co-transformation efficiencies, the frequencies of marker-free transgenic plants, and integration of backbone sequences in the obtained transgenic lines indicated that two vectors (5G7B and 5TGTB154) were more efficient in generating marker-free transgenic wheat plants with no or minimal integration of backbone sequences in the wheat genome. The vector series developed in this study for generation of marker- and/or backbone-free transgenic wheat plants via Agrobacterium -mediated transformation will be useful to facilitate the creation of "clean" GM wheat containing only the foreign genes of agronomic importance.

Aromatic Copolyamides with Anthrazoline Units in the Backbone: Synthesis, Characterization, Pervaporation Application

Directory of Open Access Journals (Sweden)

Galina A. Polotskaya

2016-10-01

Full Text Available Copolyamides with anthrazoline units in the backbone (coPA were synthesized and dense nonporous films were prepared by solvent evaporation. Glass transition temperature, density, and fractional free volume were determined for the dense nonporous films composed of polyamide and two of its copolymers containing 20 and 30 mol % anthrazoline units in the backbone. Transport properties of the polymer films were estimated by sorption and pervaporation tests toward methanol, toluene, and their mixtures. An increase in anthrazoline fragments content leads to an increasing degree of methanol sorption but to a decreasing degree of toluene sorption. Pervaporation of a methanol–toluene mixture was studied over a wide range of feed concentration (10–90 wt % methanol. Maximal separation factor was observed for coPA-20 containing 20 mol % fragments with anthrazoline units; maximal total flux was observed for coPA-30 with the highest fractional free volume.

CORBA and MPI-based 'backbone' for coupling advanced simulation tools

International Nuclear Information System (INIS)

Seydaliev, M.; Caswell, D.

2014-01-01

There is a growing international interest in using coupled, multidisciplinary computer simulations for a variety of purposes, including nuclear reactor safety analysis. Reactor behaviour can be modeled using a suite of computer programs simulating phenomena or predicting parameters that can be categorized into disciplines such as Thermalhydraulics, Neutronics, Fuel, Fuel Channels, Fission Product Release and Transport, Containment and Atmospheric Dispersion, and Severe Accident Analysis. Traditionally, simulations used for safety analysis individually addressed only the behaviour within a single discipline, based upon static input data from other simulation programs. The limitation of using a suite of stand-alone simulations is that phenomenological interdependencies or temporal feedback between the parameters calculated within individual simulations cannot be adequately captured. To remove this shortcoming, multiple computer simulations for different disciplines must exchange data during runtime to address these interdependencies. This article describes the concept of a new framework, which we refer to as the 'Backbone', to provide the necessary runtime exchange of data. The Backbone, currently under development at AECL for a preliminary feasibility study, is a hybrid design using features taken from the Common Object Request Broker Architecture (CORBA), a standard defined by the Object Management Group, and the Message Passing Interface (MPI), a standard developed by a group of researchers from academia and industry. Both have well-tested and efficient implementations, including some that are freely available under the GNU public licenses. The CORBA component enables individual programs written in different languages and running on different platforms within a network to exchange data with each other, thus behaving like a single application. MPI provides the process-to-process intercommunication between these programs. This paper outlines the different CORBA and

Ca-C backbone fragmentation dominates in electron detachment dissociation of gas-phase polypeptide polyanions

DEFF Research Database (Denmark)

Kjeldsen, Frank; Silivra, Oleg A; Ivonin, Igor A

2005-01-01

the dissociation of oxidized radical anions [M-nH]((n-1)-*. We demonstrate that C(alpha)-C cleavages, which are otherwise rarely observed in tandem mass spectrometry, can account for most of the backbone fragmentation, with even-electron x fragments dominating over radical a* ions. Ab initio calculations at the B3...... LYP level of theory with the 6-311+G(2 p,2 d)//6-31+G(d,p) basis set suggested a unidirectional mechanism for EDD (cleavage always N-terminal to the radical site), with a*, x formation being favored over a, x* fragmentation by 74.2 kJ mol(-1). Thus, backbone C(alpha)-C bonds N-terminal to proline...

Dynamic contrast enhanced ultrasound for therapy monitoring

Energy Technology Data Exchange (ETDEWEB)

Hudson, John M. [Department of Medical Biophysics, University of Toronto, Toronto, ON (Canada); Williams, Ross [Imaging Research, Sunnybrook Research Institute, Toronto, ON (Canada); Tremblay-Darveau, Charles; Sheeran, Paul S. [Department of Medical Biophysics, University of Toronto, Toronto, ON (Canada); Milot, Laurent [Department of Medical Imaging, University of Toronto, Toronto, ON (Canada); Bjarnason, Georg A. [Department of Medical Oncology, University of Toronto, and Sunnybrook Odette Cancer Centre, Toronto, ON (Canada); Burns, Peter N., E-mail: burns@sri.utoronto.ca [Department of Medical Biophysics, University of Toronto, Toronto, ON (Canada); Imaging Research, Sunnybrook Research Institute, Toronto, ON (Canada); Department of Medical Imaging, University of Toronto, Toronto, ON (Canada)

2015-09-15

Quantitative imaging is a crucial component of the assessment of therapies that target the vasculature of angiogenic or inflamed tissue. Dynamic contrast-enhanced ultrasound (DCE-US) using microbubble contrast offers the advantages of being sensitive to perfusion, non-invasive, cost effective and well suited to repeated use at the bedside. Uniquely, it employs an agent that is truly intravascular. This papers reviews the principles and methodology of DCE-US, especially as applied to anti-angiogenic cancer therapies. Reproducibility is an important attribute of such a monitoring method: results are discussed. More recent technical advances in parametric and 3D DCE-US imaging are also summarised and illustrated.

Effects of backbone conformation and surface texture of polyimide alignment film on the pretilt angle of liquid crystals

International Nuclear Information System (INIS)

Chang, Chi-Jung; Chou, Ray-Lin; Lin, Yu-Chi; Liang, Bau-Jy; Chen, Jyun-Ji

2011-01-01

Polyimides (PIs) with different inclination angle of polymer backbones, together with polar hydroxyl group and/or nonpolar trifluoromethyl group at various sites of the backbone were synthesized and used as liquid crystal alignment layers. The molecular conformation, surface chemistry, surface energy, surface morphology, and pretilt angle of the PI film were investigated. The distributions of fluorinated group and hydroxyl group at different depths of the PI surfaces were analyzed by X-ray photoelectron spectroscopy. Effects of the conformation of the PI molecular backbone on the surface morphology of the rubbed PI layer, the pretilt angle and surface energy of the alignment film were studied. The PI which contains both nonpolar fluorinated groups sticking out of the surface and the polar hydroxyl groups on the surface exhibits high pretilt angle.

Electric field induced localization phenomena in a ladder network with superlattice configuration: Effect of backbone environment

Energy Technology Data Exchange (ETDEWEB)

Dutta, Paramita; Karmakar, S. N. [Condensed Matter Physics Division, Saha Institute of Nuclear Physics, Sector-I, Block-AF, Bidhannagar, Kolkata-700 064 (India); Maiti, Santanu K., E-mail: santanu.maiti@isical.ac.in [Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata-700 108 (India)

2014-09-15

Electric field induced localization properties of a tight-binding ladder network in presence of backbone sites are investigated. Based on Green's function formalism we numerically calculate two-terminal transport together with density of states for different arrangements of atomic sites in the ladder and its backbone. Our results lead to a possibility of getting multiple mobility edges which essentially plays a switching action between a completely opaque to fully or partly conducting region upon the variation of system Fermi energy, and thus, support in fabricating mesoscopic or DNA-based switching devices.

Network Traffic Monitoring Using Poisson Dynamic Linear Models

Energy Technology Data Exchange (ETDEWEB)

Merl, D. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2011-05-09

In this article, we discuss an approach for network forensics using a class of nonstationary Poisson processes with embedded dynamic linear models. As a modeling strategy, the Poisson DLM (PoDLM) provides a very flexible framework for specifying structured effects that may influence the evolution of the underlying Poisson rate parameter, including diurnal and weekly usage patterns. We develop a novel particle learning algorithm for online smoothing and prediction for the PoDLM, and demonstrate the suitability of the approach to real-time deployment settings via a new application to computer network traffic monitoring.

Influence of Backbone Fluorination in Regioregular Poly(3-alkyl-4-fluoro)thiophenes

KAUST Repository

Fei, Zhuping

2015-06-03

© 2015 American Chemical Society. We report two strategies toward the synthesis of 3-alkyl-4-fluorothiophenes containing straight (hexyl and octyl) and branched (2-ethylhexyl) alkyl groups. We demonstrate that treatment of the dibrominated monomer with 1 equiv of alkyl Grignard reagent leads to the formation of a single regioisomer as a result of the pronounced directing effect of the fluorine group. Polymerization of the resulting species affords highly regioregular poly(3-alkyl-4-fluoro)thiophenes. Comparison of their properties to those of the analogous non-fluorinated polymers shows that backbone fluorination leads to an increase in the polymer ionization potential without a significant change in optical band gap. Fluorination also results in an enhanced tendency to aggregate in solution, which is ascribed to a more co-planar backbone on the basis of Raman and DFT calculations. Average charge carrier mobilities in field-effect transistors are found to increase by up to a factor of 5 for the fluorinated polymers.

Designing a Softwarized Network Deployed on a Fleet of Drones for Rural Zone Monitoring

Directory of Open Access Journals (Sweden)

Corrado Rametta

2017-03-01

Full Text Available In the last decade, the differences in the information communication technology (ICT infrastructures between urban and rural areas have registered a tremendous increase. ICT infrastructures could strongly help rural communities where many operations are time consuming, labor-intensive and expensive due to limited access and large distances to cover. One of the most attractive solutions, which is widely recognized as promising for filling this gap, is the use of drone fleets. In this context, this paper proposes a video monitoring platform as a service (VMPaaS for wide rural areas not covered by Internet access. The platform is realized with a Software-Defined Network (SDN/Network Functions Virtualization (NFV-based flying ad-hoc network (FANET, whose target is providing a flexible and dynamic connectivity backbone, and a set of drones equipped with high-resolution cameras, each transmitting a video stream of a portion of the considered area. After describing the architecture of the proposed platform, service chains to realize the video delivery service are described, and an analytical model is defined to evaluate the computational load of the platform nodes in such a way so as to allow the network orchestrator to decide the backbone drones where running the virtual functions, and the relative resources to be allocated. Numerical analysis is carried out in a case study.

Data Acquisition Backbone Core DABC

International Nuclear Information System (INIS)

Adamczewski, J; Essel, H G; Kurz, N; Linev, S

2008-01-01

For the new experiments at FAIR new concepts of data acquisition systems have to be developed like the distribution of self-triggered, time stamped data streams over high performance networks for event building. The Data Acquisition Backbone Core (DABC) is a software package currently under development for FAIR detector tests, readout components test, and data flow investigations. All kinds of data channels (front-end systems) are connected by program plug-ins into functional components of DABC like data input, combiner, scheduler, event builder, analysis and storage components. After detailed simulations real tests of event building over a switched network (InfiniBand clusters with up to 110 nodes) have been performed. With the DABC software more than 900 MByte/s input and output per node can be achieved meeting the most demanding requirements. The software is ready for the implementation of various test beds needed for the final design of data acquisition systems at FAIR. The development of key components is supported by the FutureDAQ project of the European Union (FP6 I3HP JRA1)

A classification-based approach to monitoring the safety of dynamic systems

DEFF Research Database (Denmark)

Zhong, Shengtong; Langseth, Helge; Nielsen, Thomas Dyhre

2014-01-01

Monitoring a complex process often involves keeping an eye on hundreds or thousands of sensors to determine whether or not the process is stable. We have been working with dynamic data from an oil production facility in the North sea, where unstable situations should be identified as soon...

Monitoring 'monitoring' and evaluating 'evaluation': an ethical framework for monitoring and evaluation in public health.

Science.gov (United States)

Gopichandran, Vijayaprasad; Indira Krishna, Anil Kumar

2013-01-01

Monitoring and evaluation (M&E) is an essential part of public health programmes. Since M&E is the backbone of public health programmes, ethical considerations are important in their conduct. Some of the key ethical considerations are avoiding conflicts of interest, maintaining independence of judgement, maintaining fairness, transparency, full disclosure, privacy and confidentiality, respect, responsibility, accountability, empowerment and sustainability. There are several ethical frameworks in public health, but none focusing on the monitoring and evaluation process. There is a need to institutionalise the ethical review of M&E proposals. A theoretical framework for ethical considerations is proposed in this paper. This proposed theoretical framework can act as the blueprint for building the capacity of ethics committees to review M&E proposals. A case study is discussed in this context. After thorough field testing, this practical and field-based ethical framework can be widely used by donor agencies, M&E teams, institutional review boards and ethics committees.

A Dynamic and Interactive Monitoring System of Data Center Resources

Directory of Open Access Journals (Sweden)

Yu Ling-Fei

2016-01-01

Full Text Available To maximize the utilization and effectiveness of resources, it is very necessary to have a well suited management system for modern data centers. Traditional approaches to resource provisioning and service requests have proven to be ill suited for virtualization and cloud computing. The manual handoffs between technology teams were also highly inefficient and poorly documented. In this paper, a dynamic and interactive monitoring system for data center resources, ResourceView, is presented. By consolidating all data center management functionality into a single interface, ResourceView shares a common view of the timeline metric status, while providing comprehensive, centralized monitoring of data center physical and virtual IT assets including power, cooling, physical space and VMs, so that to improve availability and efficiency. In addition, servers and VMs can be monitored from several viewpoints such as clusters, racks and projects, which is very convenient for users.

A Data Transmission Algorithm Based on Dynamic Grid Division for Coal Goaf Temperature Monitoring

Directory of Open Access Journals (Sweden)

Qingsong Hu

2014-01-01

Full Text Available WSN (wireless sensor network is a perfect tool of temperature monitoring in coal goaf. Based on the three-zone theory of goaf, the GtmWSN model is proposed, and its dynamic features are analyzed. Accordingly, a data transmission scheme, named DTDGD, is worked out. Firstly, sink nodes conduct dynamic grid division on the GtmWSN according to virtual semicircle. Secondly, each node will confirm to which grid it belongs based on grid number. Finally, data will be delivered to sink nodes with greedy forward and hole avoidance. Simulation results and field data showed that the GtmWSN and DTDGD satisfied the lifetime need of goaf temperature monitoring.

Inferential backbone assignment for sparse data

International Nuclear Information System (INIS)

Vitek, Olga; Bailey-Kellogg, Chris; Craig, Bruce; Vitek, Jan

2006-01-01

This paper develops an approach to protein backbone NMR assignment that effectively assigns large proteins while using limited sets of triple-resonance experiments. Our approach handles proteins with large fractions of missing data and many ambiguous pairs of pseudoresidues, and provides a statistical assessment of confidence in global and position-specific assignments. The approach is tested on an extensive set of experimental and synthetic data of up to 723 residues, with match tolerances of up to 0.5 ppm for C α and C β resonance types. The tests show that the approach is particularly helpful when data contain experimental noise and require large match tolerances. The keys to the approach are an empirical Bayesian probability model that rigorously accounts for uncertainty in the data at all stages in the analysis, and a hybrid stochastic tree-based search algorithm that effectively explores the large space of possible assignments

Systemic Case Formulation, Individualized Process Monitoring, and State Dynamics in a Case of Dissociative Identity Disorder.

Science.gov (United States)

Schiepek, Günter K; Stöger-Schmidinger, Barbara; Aichhorn, Wolfgang; Schöller, Helmut; Aas, Benjamin

2016-01-01

Objective: The aim of this case report is to demonstrate the feasibility of a systemic procedure (synergetic process management) including modeling of the idiographic psychological system and continuous high-frequency monitoring of change dynamics in a case of dissociative identity disorder. The psychotherapy was realized in a day treatment center with a female client diagnosed with borderline personality disorder (BPD) and dissociative identity disorder. Methods: A three hour long co-creative session at the beginning of the treatment period allowed for modeling the systemic network of the client's dynamics of cognitions, emotions, and behavior. The components (variables) of this idiographic system model (ISM) were used to create items for an individualized process questionnaire for the client. The questionnaire was administered daily through an internet-based monitoring tool (Synergetic Navigation System, SNS), to capture the client's individual change process continuously throughout the therapy and after-care period. The resulting time series were reflected by therapist and client in therapeutic feedback sessions. Results: For the client it was important to see how the personality states dominating her daily life were represented by her idiographic system model and how the transitions between each state could be explained and understood by the activating and inhibiting relations between the cognitive-emotional components of that system. Continuous monitoring of her cognitions, emotions, and behavior via SNS allowed for identification of important triggers, dynamic patterns, and psychological mechanisms behind seemingly erratic state fluctuations. These insights enabled a change in management of the dynamics and an intensified trauma-focused therapy. Conclusion: By making use of the systemic case formulation technique and subsequent daily online monitoring, client and therapist continuously refer to detailed visualizations of the mental and behavioral network and

Systemic Case Formulation, Individualized Process Monitoring, and State Dynamics in a Case of Dissociative Identity Disorder.

Directory of Open Access Journals (Sweden)

Guenter Karl Schiepek

2016-10-01

Full Text Available Objective. The aim of this case report is to demonstrate the feasibility of a systemic procedure (synergetic process management including modeling of the idiographic psychological system and continuous high-frequency monitoring of change dynamics in a case of dissociative identity disorder. The psychotherapy was realized in a day treatment center with a female client diagnosed with borderline personality disorder (BPD and dissociative identity disorder. Methods. A three hour long co-creative session at the beginning of the treatment period allowed for modeling the systemic network of the client’s dynamics of cognitions, emotions, and behavior. The components (variables of this idiographic system model (ISM were used to create items for an individualized process questionnaire for the client. The questionnaire was administered daily through an internet-based monitoring tool (Synergetic Navigation System, SNS, to capture the client’s individual change process continuously throughout the therapy and after-care period. The resulting time series were reflected by therapist and client in therapeutic feedback sessions. Results. For the client it was important to see how the personality states dominating her daily life were represented by her idiographic system model and how the transitions between each state could be explained and understood by the activating and inhibiting relations between the cognitive-emotional components of that system. Continuous monitoring of her cognitions, emotions, and behavior via SNS allowed for identification of important triggers, dynamic patterns, and psychological mechanisms behind seemingly erratic state fluctuations. These insights enabled a change in management of the dynamics and an intensified trauma-focused therapy. Conclusion. By making use of the systemic case formulation technique and subsequent daily online monitoring, client and therapist continuously refer to detailed visualizations of the mental and

SEVA Linkers: A Versatile and Automatable DNA Backbone Exchange Standard for Synthetic Biology

DEFF Research Database (Denmark)

Kim, Se Hyeuk; Cavaleiro, Mafalda; Rennig, Maja

2016-01-01

flexibility, and different researchers prefer and master different molecular technologies. Here, we describe a new, highly versatile and automatable standard “SEVA linkers” for vector exchange. SEVA linkers enable backbone swapping with 20 combinations of classical enzymatic restriction/ligation, Gibson...

Dynamically Coupled Residues within the SH2 Domain of FYN Are Key to Unlocking Its Activity

NARCIS (Netherlands)

Huculeci, Radu; Cilia, Elisa; Lyczek, Agatha; Buts, Lieven; Houben, Klaartje; Seeliger, Markus A; van Nuland, Nico; Lenaerts, Tom

2016-01-01

Src kinase activity is controlled by various mechanisms involving a coordinated movement of kinase and regulatory domains. Notwithstanding the extensive knowledge related to the backbone dynamics, little is known about the more subtle side-chain dynamics within the regulatory domains and their role

Cognitive conflict without explicit conflict monitoring in a dynamical agent.

Science.gov (United States)

Ward, Robert; Ward, Ronnie

2006-11-01

We examine mechanisms for resolving cognitive conflict in an embodied, situated, and dynamic agent, developed through an evolutionary learning process. The agent was required to solve problems of response conflict in a dual-target "catching" task, focusing response on one of the targets while ignoring the other. Conflict in the agent was revealed at the behavioral level in terms of increased latencies to the second target. This behavioral interference was correlated to peak violations of the network's stable state equation. At the level of the agent's neural network, peak violations were also correlated to periods of disagreement in source inputs to the agent's motor effectors. Despite observing conflict at these numerous levels, we did not find any explicit conflict monitoring mechanisms within the agent. We instead found evidence of a distributed conflict management system, characterized by competitive sources within the network. In contrast to the conflict monitoring hypothesis [Botvinick, M. M., Braver, T. S., Barch, D. M., Carter, C. S., & Cohen, J. D. (2001). Conflict monitoring and cognitive control. Psychological Review, 108(3), 624-652], this agent demonstrates that resolution of cognitive conflict does not require explicit conflict monitoring. We consider the implications of our results for the conflict monitoring hypothesis.

Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

Directory of Open Access Journals (Sweden)

Gendrault-Jacquemard A

2005-07-01

Full Text Available Abstract Background Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. Results Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. Conclusion The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

Treatment Results of Injuries of Thoracic and Lumbar Backbone Departments at Osteoporosis Patients

Directory of Open Access Journals (Sweden)

D.Y. Sumin

2009-06-01

Full Text Available Information relates to radiologic (computer tomography manifestations providing the visualization of thoracic and lumbar backbone department injuries at osteoporotic patients. Contemporary methods of transcutaneous and trans-pedicle vertebroplasty with bone cement allows to obtain a stable positive healing effect against such pathologies.

Coupling between myosin head conformation and the thick filament backbone structure.

Science.gov (United States)

Hu, Zhongjun; Taylor, Dianne W; Edwards, Robert J; Taylor, Kenneth A

2017-12-01

The recent high-resolution structure of the thick filament from Lethocerus asynchronous flight muscle shows aspects of thick filament structure never before revealed that may shed some light on how striated muscles function. The phenomenon of stretch activation underlies the function of asynchronous flight muscle. It is most highly developed in flight muscle, but is also observed in other striated muscles such as cardiac muscle. Although stretch activation is likely to be complex, involving more than a single structural aspect of striated muscle, the thick filament itself, would be a prime site for regulatory function because it must bear all of the tension produced by both its associated myosin motors and any externally applied force. Here we show the first structural evidence that the arrangement of myosin heads within the interacting heads motif is coupled to the structure of the thick filament backbone. We find that a change in helical angle of 0.16° disorders the blocked head preferentially within the Lethocerus interacting heads motif. This observation suggests a mechanism for how tension affects the dynamics of the myosin heads leading to a detailed hypothesis for stretch activation and shortening deactivation, in which the blocked head preferentially binds the thin filament followed by the free head when force production occurs. Copyright © 2017 Elsevier Inc. All rights reserved.

TACN-based cationic lipids with amino acid backbone and double tails: materials for non-viral gene delivery.

Science.gov (United States)

Wang, Bing; Yi, Wen-Jing; Zhang, Ji; Zhang, Qin-Fang; Xun, Miao-Miao; Yu, Xiao-Qi

2014-04-01

Cationic lipids have become an efficient type of non-viral vectors for gene delivery. In this Letter, four cationic lipids containing 1,4,7-triazacyclononane (TACN) headgroup, glutamic/aspartic acid backbone and dioleyl tails were designed and synthesized. The TACN headgroup gives these lipids excellent pH buffering capacities, which were higher than branched 25 kDa PEI. Cationic liposomes prepared from these lipids and DOPE showed good DNA affinity, and full DNA condensation was found at N/P ratio of 3 via agarose gel electrophoresis. The lipoplexes were characterized by dynamic light scattering (DLS) assay, which gave proper particle sizes and zeta-potentials for transfection. In vitro gene transfection results in two cell lines reveal that TAN (with aspartic acid and amide bond in the structure) shows the best transfection efficiency, which is close to commercially available transfection agent Lipofectamine 2000. Copyright © 2014 Elsevier Ltd. All rights reserved.

Lactobacillus rhamnosus accelerates zebrafish backbone calcification and gonadal differentiation through effects on the GnRH and IGF systems.

Directory of Open Access Journals (Sweden)

Matteo A Avella

Full Text Available Endogenous microbiota play essential roles in the host's immune system, physiology, reproduction and nutrient metabolism. We hypothesized that a continuous administration of an exogenous probiotic might also influence the host's development. Thus, we treated zebrafish from birth to sexual maturation (2-months treatment with Lactobacillus rhamnosus, a probiotic species intended for human use. We monitored for the presence of L. rhamnosus during the entire treatment. Zebrafish at 6 days post fertilization (dpf exhibited elevated gene expression levels for Insulin-like growth factors -I and -II, Peroxisome proliferator activated receptors -α and -β, VDR-α and RAR-γ when compared to untreated-10 days old zebrafish. Using a gonadotropin-releasing hormone 3 GFP transgenic zebrafish (GnRH3-GFP, higher GnRH3 expression was found at 6, 8 and 10 dpf upon L. rhamnosus treatment. The same larvae exhibited earlier backbone calcification and gonad maturation. Noteworthy in the gonad development was the presence of first testes differentiation at 3 weeks post fertilization in the treated zebrafish population -which normally occurs at 8 weeks- and a dramatic sex ratio modulation (93% females, 7% males in control vs. 55% females, 45% males in the treated group. We infer that administration of L. rhamnosus stimulated the IGF system, leading to a faster backbone calcification. Moreover we hypothesize a role for administration of L. rhamnosus on GnRH3 modulation during early larval development, which in turn affects gonadal development and sex differentiation. These findings suggest a significant role of the microbiota composition on the host organism development profile and open new perspectives in the study of probiotics usage and application.

Life estimation and analysis of dielectric strength, hydrocarbon backbone and oxidation of high voltage multi stressed EPDM composites

Science.gov (United States)

Khattak, Abraiz; Amin, Muhammad; Iqbal, Muhammad; Abbas, Naveed

2018-02-01

Micro and nanocomposites of ethylene propylene diene monomer (EPDM) are recently studied for different characteristics. Study on life estimation and effects of multiple stresses on its dielectric strength and backbone scission and oxidation is also vital for endorsement of these composites for high voltage insulation and other outdoor applications. In order to achieve these goals, unfilled EPDM and its micro and nanocomposites are prepared at 23 phr micro silica and 6 phr nanosilica loadings respectively. Prepared samples are energized at 2.5 kV AC voltage and subjected for a long time to heat, ultraviolet radiation, acid rain, humidity and salt fog in accelerated manner in laboratory. Dielectric strength, leakage current and intensity of saturated backbone and carbonyl group are periodically measured. Loss in dielectric strength, increase in leakage current and backbone degradation and oxidation were observed in all samples. These effects were least in the case of EPDM nanocomposite. The nanocomposite sample also demonstrated longest shelf life.

Protein backbone angle restraints from searching a database for chemical shift and sequence homology

Energy Technology Data Exchange (ETDEWEB)

Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

1999-03-15

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C{alpha}, 13C{beta}, 13C', 1H{alpha} and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar {phi} and {psi} backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 deg. Approximately 3% of the predictions made by TALOS are found to be in error.

Controlled Conjugated Backbone Twisting for an Increased Open-Circuit Voltage while Having a High Short-Circuit Current in Poly(hexylthiophene) Derivatives

KAUST Repository

Ko, Sangwon

2012-03-21

Conjugated polymers with nearly planar backbones have been the most commonly investigated materials for organic-based electronic devices. More twisted polymer backbones have been shown to achieve larger open-circuit voltages in solar cells, though with decreased short-circuit current densities. We systematically impose twists within a family of poly(hexylthiophene)s and examine their influence on the performance of polymer:fullerene bulk heterojunction (BHJ) solar cells. A simple chemical modification concerning the number and placement of alkyl side chains along the conjugated backbone is used to control the degree of backbone twisting. Density functional theory calculations were carried out on a series of oligothiophene structures to provide insights on how the sterically induced twisting influences the geometric, electronic, and optical properties. Grazing incidence X-ray scattering measurements were performed to investigate how the thin-film packing structure was affected. The open-circuit voltage and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone-due to an increase in the polymer ionization potential-while the short-circuit current decreased as a result of a larger optical gap and lower hole mobility. A controlled, moderate degree of twist along the poly(3,4-dihexyl-2,2′:5′,2′′- terthiophene) (PDHTT) conjugated backbone led to a 19% enhancement in the open-circuit voltage (0.735 V) vs poly(3-hexylthiophene)-based devices, while similar short-circuit current densities, fill factors, and hole-carrier mobilities were maintained. These factors resulted in a power conversion efficiency of 4.2% for a PDHTT:[6,6]-phenyl-C 71-butyric acid methyl ester (PC 71BM) blend solar cell without thermal annealing. This simple approach reveals a molecular design avenue to increase open-circuit voltage while retaining the short-circuit current. © 2012 American

Controlled conjugated backbone twisting for an increased open-circuit voltage while having a high short-circuit current in poly(hexylthiophene) derivatives.

Science.gov (United States)

Ko, Sangwon; Hoke, Eric T; Pandey, Laxman; Hong, Sanghyun; Mondal, Rajib; Risko, Chad; Yi, Yuanping; Noriega, Rodrigo; McGehee, Michael D; Brédas, Jean-Luc; Salleo, Alberto; Bao, Zhenan

2012-03-21

Conjugated polymers with nearly planar backbones have been the most commonly investigated materials for organic-based electronic devices. More twisted polymer backbones have been shown to achieve larger open-circuit voltages in solar cells, though with decreased short-circuit current densities. We systematically impose twists within a family of poly(hexylthiophene)s and examine their influence on the performance of polymer:fullerene bulk heterojunction (BHJ) solar cells. A simple chemical modification concerning the number and placement of alkyl side chains along the conjugated backbone is used to control the degree of backbone twisting. Density functional theory calculations were carried out on a series of oligothiophene structures to provide insights on how the sterically induced twisting influences the geometric, electronic, and optical properties. Grazing incidence X-ray scattering measurements were performed to investigate how the thin-film packing structure was affected. The open-circuit voltage and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone--due to an increase in the polymer ionization potential--while the short-circuit current decreased as a result of a larger optical gap and lower hole mobility. A controlled, moderate degree of twist along the poly(3,4-dihexyl-2,2':5',2''-terthiophene) (PDHTT) conjugated backbone led to a 19% enhancement in the open-circuit voltage (0.735 V) vs poly(3-hexylthiophene)-based devices, while similar short-circuit current densities, fill factors, and hole-carrier mobilities were maintained. These factors resulted in a power conversion efficiency of 4.2% for a PDHTT:[6,6]-phenyl-C(71)-butyric acid methyl ester (PC(71)BM) blend solar cell without thermal annealing. This simple approach reveals a molecular design avenue to increase open-circuit voltage while retaining the short-circuit current.

Dynamic monitoring of weight data at the pen vs at the individual level

DEFF Research Database (Denmark)

Jensen, Dan; Toft, Nils; Kristensen, A. R. K.

recorded weight data from finisher pigs. Data are collected at insertion and at the exit of the first pigs in the pen, and in few pens, the weight is recorded weekly. Dynamic linear models are fitted on the weight data, at the pig level (univariate), at the double pen level using averaged weight...... (univariate) and using individual pig values as parameters in a hierarchical (multivariate) model including section, double pen, and individual level. Variance components of the different models are estimated using the Expectation Maximization algorithm. The difference of information obtained...... at the individual vs pen level is thereafter assessed. Whereas weight data is usually monitored after a batch is being sent to the slaughter house, this method provides weekly updating of the data. Perspectives of application include dynamic monitoring of weight data in relation to events such as diarrhoea, tail...

Dynamic monitoring of weight data at the pen vs at the individual level

DEFF Research Database (Denmark)

Jensen, Dan Børge; Toft, Nils; Kristensen, Anders Ringgaard

recorded weight data from finisher pigs. Data are collected at insertion and at the exit of the first pigs in the pen, and in few pens, the weight is recorded weekly. Dynamic linear models are fitted on the weight data, at the pig level (univariate), at the double pen level using averaged weight...... (univariate) and using individual pig values as parameters in a hierarchical (multivariate) model including section, double pen, and individual level. Variance components of the different models are estimated using the Expectation Maximization algorithm. The difference of information obtained...... at the individual vs. pen level is thereafter assessed. Whereas weight data is usually monitored after a batch is being sent to the slaughter house, this method provides with weekly updating of the data. Perspectives of application include dynamic monitoring of weight data in relation to events such as diarrhoea...

Beta-scission of alkoxyl radicals on peptides and proteins can give rise to backbone cleavage and loss of side-chains

International Nuclear Information System (INIS)

Headlam, H.A.; Davies, M.J.; Mortimer, A.; Easton, C.J.

2000-01-01

Full text: Exposure of proteins to radicals in the presence of O 2 brings about multiple changes including side-chain oxidation, backbone fragmentation, cross-linking, unfolding, changes in hydrophobicity and conformation, altered susceptibility to proteolytic enzymes and formation of new reactive groups (e.g. hydroperoxides and 3,4-dihydroxyphenylalanine). All of these processes can result in loss of structural or enzymatic activity. The mechanisms that give rise to backbone cleavage are only partly understood. Whilst it is known that direct hydrogen atom abstraction at a-carbon sites gives backbone cleavages it has also been proposed that initial attack at side-chain sites might also give rise to backbone cleavage. In this study we have examined whether initial attack at the β- (C-3) position can give rise to α-carbon radicals (and hence backbone cleavage) via the formation, and subsequent β- scission, of C-3 alkoxyl radicals. This process has been observed previously with protected amino acids in organic solvents (J. Chem. Soc. Perkin Trans. 2, 1997, 503-507) but the occurrence of such reactions with proteins in aqueous solution has not been explored. Alkoxyl radicals were generated at the C-3 position of a variety of protected amino acids and small peptides by two methods: metal-ion catalysed decomposition of hydroperoxides formed as a result of γ-radiolysis in the presence of O 2 , and UV photolysis of nitrate esters. In most cases radicals have been detected by EPR spectroscopy using nitroso and nitrone spin traps, which can be assigned by comparison with literature data to α-carbon radicals; in some case assignments were confirmed by the generation of the putative species by other routes. With Ala peptide hydroperoxides and nitrate esters, and MNP as the spin trap, the major radical detected in each case has been assigned to the adduct of an α-carbon radical with partial structure - NH- . CH-C(O) - consistent with the rapid occurrence of the above

Mars - robust automatic backbone assignment of proteins

International Nuclear Information System (INIS)

Jung, Young-Sang; Zweckstetter, Markus

2004-01-01

MARS a program for robust automatic backbone assignment of 13 C/ 15 N labeled proteins is presented. MARS does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds and it can work with a wide variety of NMR experiments. Using only 13 C α / 13 C β connectivity information, MARS allows automatic, error-free assignment of 96% of the 370-residue maltose-binding protein. MARS can successfully be used when data are missing for a substantial portion of residues or for proteins with very high chemical shift degeneracy such as partially or fully unfolded proteins. Other sources of information, such as residue specific information or known assignments from a homologues protein, can be included into the assignment process. MARS exports its result in SPARKY format. This allows visual validation and integration of automated and manual assignment

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

Science.gov (United States)

Haupt, V. Joachim; Schroeder, Michael; Labudde, Dirk

2018-01-01

The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes. PMID:29659563

Improving VANETs Connectivity with a Totally Ad Hoc Living Mobile Backbone

Directory of Open Access Journals (Sweden)

Joilson Alves Junior

2015-01-01

Full Text Available The vehicular ad hoc network (VANET for intelligent transportation systems is an emerging concept to improve transportation security, reliability, and management. The network behavior can be totally different in topological aspects because of the mobility of vehicular nodes. The topology can be fully connected when the flow of vehicles is high and may have low connectivity or be invalid when the flow of vehicles is low or unbalanced. In big cities, the metropolitan buses that travel on exclusive lanes may be used to set up a metropolitan vehicular data network (backbone, raising the connectivity among the vehicles. Therefore, this paper proposes the implementation of a living mobile backbone, totally ad hoc (MOB-NET, which will provide infrastructure and raise the network connectivity. In order to show the viability of MOB-NET, statistical analyses were made with real data of express buses that travel through exclusive lanes, besides evaluations through simulations and analytic models. The statistic, analytic, and simulation results prove that the buses that travel through exclusive lanes can be used to build a communication network totally ad hoc and provide connectivity in more than 99% of the time, besides raising the delivery rate up to 95%.

Yellow River Icicle Hazard Dynamic Monitoring Using UAV Aerial Remote Sensing Technology

International Nuclear Information System (INIS)

Wang, H B; Wang, G H; Tang, X M; Li, C H

2014-01-01

Monitoring the response of Yellow River icicle hazard change requires accurate and repeatable topographic surveys. A new method based on unmanned aerial vehicle (UAV) aerial remote sensing technology is proposed for real-time data processing in Yellow River icicle hazard dynamic monitoring. The monitoring area is located in the Yellow River ice intensive care area in southern BaoTou of Inner Mongolia autonomous region. Monitoring time is from the 20th February to 30th March in 2013. Using the proposed video data processing method, automatic extraction covering area of 7.8 km 2 of video key frame image 1832 frames took 34.786 seconds. The stitching and correcting time was 122.34 seconds and the accuracy was better than 0.5 m. Through the comparison of precise processing of sequence video stitching image, the method determines the change of the Yellow River ice and locates accurate positioning of ice bar, improving the traditional visual method by more than 100 times. The results provide accurate aid decision information for the Yellow River ice prevention headquarters. Finally, the effect of dam break is repeatedly monitored and ice break five meter accuracy is calculated through accurate monitoring and evaluation analysis

Dynamic goal states: adjusting cognitive control without conflict monitoring.

Science.gov (United States)

Scherbaum, Stefan; Dshemuchadse, Maja; Ruge, Hannes; Goschke, Thomas

2012-10-15

A central topic in the cognitive sciences is how cognitive control is adjusted flexibly to changing environmental demands at different time scales to produce goal-oriented behavior. According to an influential account, the context-sensitive recruitment of cognitive control is mediated by a specialized conflict monitoring process that registers current conflict and signals the demand for enhanced control in subsequent trials. This view has been immensely successful not least due to supporting evidence from neuroimaging studies suggesting that the conflict monitoring function is localized within the anterior cingulate cortex (ACC) which, in turn, signals the demand for enhanced control to the prefrontal cortex (PFC). In this article, we propose an alternative model of the adaptive regulation of cognitive control based on multistable goal attractor network dynamics and adjustments of cognitive control within a conflict trial. Without incorporation of an explicit conflict monitoring module, the model mirrors behavior in conflict tasks accounting for effects of response congruency, sequential conflict adaptation, and proportion of incongruent trials. Importantly, the model also mirrors frequency tagged EEG data indicating continuous conflict adaptation and suggests a reinterpretation of the correlation between ACC and the PFC BOLD data reported in previous imaging studies. Together, our simulation data propose an alternative interpretation of both behavioral data as well as imaging data that have previously been interpreted in favor of a specialized conflict monitoring process in the ACC. Copyright © 2012 Elsevier Inc. All rights reserved.

Comparing the Reliability of Regular Topologies on a Backbone Network. A Case Study

DEFF Research Database (Denmark)

Cecilio, Sergio Labeage; Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir

2009-01-01

The aim of this paper is to compare the reliability of regular topologies on a backbone network. The study is focused on a large-scale fiberoptic network. Different regular topological solutions as single ring, double ring or 4-Regular grid are applied to the case study, and compared in terms...

The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone

DEFF Research Database (Denmark)

Kumar, P.; Sharma, P. K.; Madsen, Charlotte S.

2013-01-01

Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand.......Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand....

Enhanced dynamic wedge and independent monitor unit verification

International Nuclear Information System (INIS)

Howlett, SJ.

2005-01-01

Some serious radiation accidents have occurred around the world during the delivery of radiotherapy treatment. The regrettable incident in Panama clearly indicated the need for independent monitor unit (MU) verification. Indeed the International Atomic Energy Agency (IAEA), after investigating the incident, made specific recommendations for radiotherapy centres which included an independent monitor unit check for all treatments. Independent monitor unit verification is practiced in many radiotherapy centres in developed countries around the world. It is mandatory in USA but not yet in Australia. This paper describes development of an independent MU program, concentrating on the implementation of the Enhanced Dynamic Wedge (EDW) component. The difficult case of non centre of field (COF) calculation points under the EDW was studied in some detail. Results of a survey of Australasian centres regarding the use of independent MU check systems is also presented. The system was developed with reference to MU calculations made by Pinnacle 3 D Radiotherapy Treatment Planning (RTP) system (ADAC - Philips) for 4MV, 6MV and 18MV X-ray beams used at the Newcastle Mater Misericordiae Hospital (NMMH) in the clinical environment. A small systematic error was detected in the equation used for the EDW calculations. Results indicate that COF equations may be used in the non COF situation with similar accuracy to that achieved with profile corrected methods. Further collaborative work with other centres is planned to extend these findings

Development of structural health monitoring techniques using dynamics testing

Energy Technology Data Exchange (ETDEWEB)

James, G.H. III [Sandia National Labs., Albuquerque, NM (United States). Experimental Structural Dynamics Dept.

1996-03-01

Today`s society depends upon many structures (such as aircraft, bridges, wind turbines, offshore platforms, buildings, and nuclear weapons) which are nearing the end of their design lifetime. Since these structures cannot be economically replaced, techniques for structural health monitoring must be developed and implemented. Modal and structural dynamics measurements hold promise for the global non-destructive inspection of a variety of structures since surface measurements of a vibrating structure can provide information about the health of the internal members without costly (or impossible) dismantling of the structure. In order to develop structural health monitoring for application to operational structures, developments in four areas have been undertaken within this project: operational evaluation, diagnostic measurements, information condensation, and damage identification. The developments in each of these four aspects of structural health monitoring have been exercised on a broad range of experimental data. This experimental data has been extracted from structures from several application areas which include aging aircraft, wind energy, aging bridges, offshore structures, structural supports, and mechanical parts. As a result of these advances, Sandia National Laboratories is in a position to perform further advanced development, operational implementation, and technical consulting for a broad class of the nation`s aging infrastructure problems.

Design of an IPTV Multicast System for Internet Backbone Networks

Directory of Open Access Journals (Sweden)

T. H. Szymanski

2010-01-01

Full Text Available The design of an IPTV multicast system for the Internet backbone network is presented and explored through extensive simulations. In the proposed system, a resource reservation algorithm such as RSVP, IntServ, or DiffServ is used to reserve resources (i.e., bandwidth and buffer space in each router in an IP multicast tree. Each router uses an Input-Queued, Output-Queued, or Crosspoint-Queued switch architecture with unity speedup. A recently proposed Recursive Fair Stochastic Matrix Decomposition algorithm used to compute near-perfect transmission schedules for each IP router. The IPTV traffic is shaped at the sources using Application-Specific Token Bucker Traffic Shapers, to limit the burstiness of incoming network traffic. The IPTV traffic is shaped at the destinations using Application-Specific Playback Queues, to remove residual network jitter and reconstruct the original bursty IPTV video streams at each destination. All IPTV traffic flows are regenerated at the destinations with essentially zero delay jitter and essentially-perfect QoS. The destination nodes deliver the IPTV streams to the ultimate end users using the same IPTV multicast system over a regional Metropolitan Area Network. It is shown that all IPTV traffic is delivered with essentially-perfect end-to-end QoS, with deterministic bounds on the maximum delay and jitter on each video frame. Detailed simulations of an IPTV distribution system, multicasting several hundred high-definition IPTV video streams over several essentially saturated IP backbone networks are presented.

The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain.

Directory of Open Access Journals (Sweden)

Søren W. Pedersen

Full Text Available Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.

Shape selection in Landsat time series: A tool for monitoring forest dynamics

Science.gov (United States)

Gretchen G. Moisen; Mary C. Meyer; Todd A. Schroeder; Xiyue Liao; Karen G. Schleeweis; Elizabeth A. Freeman; Chris Toney

2016-01-01

We present a new methodology for fitting nonparametric shape-restricted regression splines to time series of Landsat imagery for the purpose of modeling, mapping, and monitoring annual forest disturbance dynamics over nearly three decades. For each pixel and spectral band or index of choice in temporal Landsat data, our method delivers a smoothed rendition of...

Static and Dynamic Strain Monitoring of Reinforced Concrete Components through Embedded Carbon Nanotube Cement-Based Sensors

Directory of Open Access Journals (Sweden)

Antonella D’Alessandro

2017-01-01

Full Text Available The paper presents a study on the use of cement-based sensors doped with carbon nanotubes as embedded smart sensors for static and dynamic strain monitoring of reinforced concrete (RC elements. Such novel sensors can be used for the monitoring of civil infrastructures. Because they are fabricated from a structural material and are easy to utilize, these sensors can be integrated into structural elements for monitoring of different types of constructions during their service life. Despite the scientific attention that such sensors have received in recent years, further research is needed to understand (i the repeatability and accuracy of sensors’ behavior over a meaningful number of sensors, (ii testing configurations and calibration methods, and (iii the sensors’ ability to provide static and dynamic strain measurements when actually embedded in RC elements. To address these research needs, this paper presents a preliminary characterization of the self-sensing capabilities and the dynamic properties of a meaningful number of cement-based sensors and studies their application as embedded sensors in a full-scale RC beam. Results from electrical and electromechanical tests conducted on small and full-scale specimens using different electrical measurement methods confirm that smart cement-based sensors show promise for both static and vibration-based structural health monitoring applications of concrete elements but that calibration of each sensor seems to be necessary.

Flexible Graphene Electrodes for Prolonged Dynamic ECG Monitoring

Directory of Open Access Journals (Sweden)

Cunguang Lou

2016-11-01

Full Text Available This paper describes the development of a graphene-based dry flexible electrocardiography (ECG electrode and a portable wireless ECG measurement system. First, graphene films on polyethylene terephthalate (PET substrates and graphene paper were used to construct the ECG electrode. Then, a graphene textile was synthesized for the fabrication of a wearable ECG monitoring system. The structure and the electrical properties of the graphene electrodes were evaluated using Raman spectroscopy, scanning electron microscopy (SEM, and alternating current impedance spectroscopy. ECG signals were then collected from healthy subjects using the developed graphene electrode and portable measurement system. The results show that the graphene electrode was able to acquire the typical characteristics and features of human ECG signals with a high signal-to-noise (SNR ratio in different states of motion. A week-long continuous wearability test showed no degradation in the ECG signal quality over time. The graphene-based flexible electrode demonstrates comfortability, good biocompatibility, and high electrophysiological detection sensitivity. The graphene electrode also combines the potential for use in long-term wearable dynamic cardiac activity monitoring systems with convenience and comfort for use in home health care of elderly and high-risk adults.

Tritium containing polymers having a polymer backbone substantially void of tritium

Science.gov (United States)

Jensen, G.A.; Nelson, D.A.; Molton, P.M.

1992-03-31

A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium. 2 figs.

Nonlinear dynamics of zigzag molecular chains (in Russian)

DEFF Research Database (Denmark)

Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth

1999-01-01

models (two-dimensional alpha-spiral, polyethylene transzigzag backbone, and the zigzag chain of hydrogen bonds) shows that the zigzag structure essentially limits the soliton dynamics to finite, relatively narrow, supersonic soliton velocity intervals and may also result in that several acoustic soliton......Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...

Dynamic optical tweezers based assay for monitoring early drug resistance

International Nuclear Information System (INIS)

Wu, Xiaojing; Zhu, Siwei; Feng, Jie; Zhang, Yuquan; Min, Changjun; Yuan, X-C

2013-01-01

In this letter, a dynamic optical tweezers based assay is proposed and investigated for monitoring early drug resistance with Pemetrexed-resistant non-small cell lung cancer (NSCLC) cell lines. The validity and stability of the method are verified experimentally in terms of the physical parameters of the optical tweezers system. The results demonstrate that the proposed technique is more convenient and faster than traditional techniques when the capability of detecting small variations of the response of cells to a drug is maintained. (letter)

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2013-07-15

A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

Science.gov (United States)

Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

2015-11-01

The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. © 2015 Wiley Periodicals, Inc.

Continuous monitoring the vehicle dynamics and driver behavior using navigation systems

Science.gov (United States)

Ene, George

2017-10-01

In all fields cost is very important and the increasing amount of data that are needed for active safety systems, like ADAS, lead to implementation of some complex and powerful unit for processing raw data. In this manner is necessary a cost-effective method to estimate the maximum available tire road friction during acceleration and braking by continuous monitoring the vehicle dynamics and driver behavior. The method is based on the hypothesis that short acceleration and braking periods can indicate vehicle dynamics, and thus the available tire road friction coefficient, and also human behavior and his limits. Support for this hypothesis is found in the literature and is supported by the result of experiments conducted under different conditions and seasons.

Training in remote monitoring technology. Digital camera module-14(DCM-14)

International Nuclear Information System (INIS)

Caskey, Susan

2006-01-01

The DCM-14 (Digital Camera Module) is the backbone of current IAEA remote monitoring surveillance systems. The control module is programmable with features for encryption, authentication, image compression and scene change detection. It can take periodic or triggered images under a variety of time sequences. This training session covered the DCM-14 features and related programming in DCMSET. It also described the processes for receiving, archiving and backing up the camera images using DCMPOLL and GEMINI software. Setting up a DCM-14 camera controller in the configuration of the remote monitoring system at Joyo formed an exercise. (author)

Identification of process dynamics. Stability monitoring in BWR type reactors

International Nuclear Information System (INIS)

Abrahamsson, P.; Hallgren, P.

1991-06-01

Identification of process dynamics is used for stability monitoring in nuclear reactors (Boiling Water Reactor). This report treats the problem of estimating a damping factor and a resonance frequency from the neutron flux as measured in the reactor. A new parametric online method for identification is derived and presented, and is shown to meet the requirements of stability monitoring. The technique for estimating the process parameters is based on a recursive lattice filter algorithm. The problem of time varying parameters and offset, as well as offline experiments and signal processing are treated. All parts are implemented in a realtime program, using the language C. In comparison with earlier identifications, the new way of estimating the damping factor is shown to work well. Estimates of both the damping factor and the resonance frequency show a stable and reliable behavior. Future development and improvements are also indicated. (au)

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

Science.gov (United States)

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

Extracting the information backbone in online system.

Directory of Open Access Journals (Sweden)

Qian-Ming Zhang

Full Text Available Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such "less can be more" feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency.

Extracting the information backbone in online system.

Science.gov (United States)

Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

2013-01-01

Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such "less can be more" feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency.

Extracting the Information Backbone in Online System

Science.gov (United States)

Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

2013-01-01

Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such “less can be more” feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency. PMID:23690946

Progress and monitoring system on compression and transmission technologies of dynamic image

International Nuclear Information System (INIS)

Kobayashi, Hiroyuki; Saijo, Nobuyuki; Nakajo, Ken

2001-01-01

The Toshiba Corporation developed a real-time dynamic image transmission matched with quality of transmission circuit by using MPEG-4 which was recent international standard system for the dynamic image coding system. Concretely, this system made possible on real-time dynamic image transmission even at transmission on wireless circuit such as portable telephone, PHS, wireless LAN, and so on, at viewpoint of the mobile communication. And, by using the wireless circuit, it could be built without any limit of transmission cable, to realize its layout-free establishment. In addition, this system uses only image for communication without using voice, and some devices were carried out to upgrade image and frame speed as possible. Here were described on outlines of transmission system and principle of detection MPEG-4, and function and application of monitoring system using this system. (G.K.)

Backbone resonance assignments of the outer membrane lipoprotein FrpD from Neisseria meningitidis

Czech Academy of Sciences Publication Activity Database

Bumba, Ladislav; Sviridova, E.; Kutá-Smatanová, Ivana; Řezáčová, Pavlína; Veverka, Václav

2014-01-01

Roč. 8, č. 1 (2014), s. 53-55 ISSN 1874-2718 R&D Projects: GA ČR(CZ) GAP207/11/0717; GA MŠk(CZ) LK11205 Institutional support: RVO:61388963 ; RVO:61388971 ; RVO:67179843 Keywords : Neisseria meningitidis * FrpC * FrpD * backbone assignments * NMR * iron-regulated protein Subject RIV: CE - Biochemistry Impact factor: 0.760, year: 2014

Long-Term Dynamic Monitoring of the Historical Masonry FAÇADE: the Case of Palazzo Ducale in Venice, Italy

Science.gov (United States)

Noh, J.; Russo, S.

2017-08-01

Long-term dynamic monitoring of the masonry façade of Palazzo Ducale known as Doge's palace in Venice, Italy was performed from September 2010 to October 2012. This article demonstrates the results of preliminary analysis on the data set of the first 12-month long monitoring campaign for out-of-plumb dynamic responses of the medieval façade of the monument. The aim of the analysis of the dynamic signals is to validate the data set and investigate dynamic characteristics of the vibration signature of the historical masonry wall in the long-term. Palazzo Ducale is a heavily visited heritage due to its high cultural importance and architectural value. Nevertheless, little is known about the dynamic behaviour of the double-leaf masonry façade. In this study, the dynamic properties of the structure are presented by dynamic identification carried out with the effect of the ambient vibration measured at four different locations on the façade and portico level. The trend and intensity of the vibration at each measurement locations are identified over the year. In addition, the issue on eliminating the noise blended in the signals for reliable analysis are also discussed.

Using white noise to gate organic transistors for dynamic monitoring of cultured cell layers.

Science.gov (United States)

Rivnay, Jonathan; Leleux, Pierre; Hama, Adel; Ramuz, Marc; Huerta, Miriam; Malliaras, George G; Owens, Roisin M

2015-06-26

Impedance sensing of biological systems allows for monitoring of cell and tissue properties, including cell-substrate attachment, layer confluence, and the "tightness" of an epithelial tissue. These properties are critical for electrical detection of tissue health and viability in applications such as toxicological screening. Organic transistors based on conducting polymers offer a promising route to efficiently transduce ionic currents to attain high quality impedance spectra, but collection of complete impedance spectra can be time consuming (minutes). By applying uniform white noise at the gate of an organic electrochemical transistor (OECT), and measuring the resulting current noise, we are able to dynamically monitor the impedance and thus integrity of cultured epithelial monolayers. We show that noise sourcing can be used to track rapid monolayer disruption due to compounds which interfere with dynamic polymerization events crucial for maintaining cytoskeletal integrity, and to resolve sub-second alterations to the monolayer integrity.

Mother-adolescent monitoring dynamics and the legitimacy of parental authority.

Science.gov (United States)

Keijsers, Loes; Laird, Robert D

2014-07-01

This multi-informant longitudinal study aimed to understand whether the family dynamics that underlie adolescent voluntary disclosure regarding their leisure time behavior differs when adolescents strongly or weakly endorse the legitimacy of parental authority. Longitudinal linkages between parental monitoring behaviors and adolescents' secrecy and disclosure were tested among youths with strong and weak legitimacy beliefs. The sample included 197 adolescents (51% female, M age 12 years) and their mothers. Mothers reported on several of their own monitoring efforts (i.e., solicitation, active involvement, observing and listening, and obtaining information from spouses, siblings, and others). Adolescents reported their disclosure, secrecy, and legitimacy beliefs. Only among youths reporting strong legitimacy beliefs, more mother engagement and supervision (indexed by mother-reported active involvement and observing and listening) predicted more adolescent disclosure and less secrecy over time, and more mother solicitation predicted less secrecy. Copyright © 2014 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Routing protocol for wireless quantum multi-hop mesh backbone network based on partially entangled GHZ state

Science.gov (United States)

Xiong, Pei-Ying; Yu, Xu-Tao; Zhang, Zai-Chen; Zhan, Hai-Tao; Hua, Jing-Yu

2017-08-01

Quantum multi-hop teleportation is important in the field of quantum communication. In this study, we propose a quantum multi-hop communication model and a quantum routing protocol with multihop teleportation for wireless mesh backbone networks. Based on an analysis of quantum multi-hop protocols, a partially entangled Greenberger-Horne-Zeilinger (GHZ) state is selected as the quantum channel for the proposed protocol. Both quantum and classical wireless channels exist between two neighboring nodes along the route. With the proposed routing protocol, quantum information can be transmitted hop by hop from the source node to the destination node. Based on multi-hop teleportation based on the partially entangled GHZ state, a quantum route established with the minimum number of hops. The difference between our routing protocol and the classical one is that in the former, the processes used to find a quantum route and establish quantum channel entanglement occur simultaneously. The Bell state measurement results of each hop are piggybacked to quantum route finding information. This method reduces the total number of packets and the magnitude of air interface delay. The deduction of the establishment of a quantum channel between source and destination is also presented here. The final success probability of quantum multi-hop teleportation in wireless mesh backbone networks was simulated and analyzed. Our research shows that quantum multi-hop teleportation in wireless mesh backbone networks through a partially entangled GHZ state is feasible.

Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.

Science.gov (United States)

Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C

2013-11-07

Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

On The Ubiquity of Nonstationary Fluvial Suspended Sediment Dynamics: A Call for Long Term Monitoring and Dynamical Sediment Management Strategies

Science.gov (United States)

Gray, A. B.

2017-12-01

Watersheds with sufficient monitoring data have been predominantly found to display nonstationary suspended sediment dynamics, whereby the relationship between suspended sediment concentration and discharge changes over time. Despite the importance of suspended sediment as a keystone of geophysical and biochemical processes, and as a primary mediator of water quality, stationary behavior remains largely assumed in the context of these applications. This study presents an investigation into the time dependent behavior of small mountainous rivers draining the coastal ranges of the western continental US over interannual to interdecadal time scales. Of the 250+ small coastal (drainage area systems. Temporal patterns of non-stationary behavior provided some evidence for spatial coherence, which may be related to synoptic hydro-metrological patterns and regional scale changes in land use patterns. However, the results also highlight the complex, integrative nature of watershed scale fluvial suspended sediment dynamics. This underscores the need for in-depth, forensic approaches for initial processes identification, which require long term, high resolution monitoring efforts in order to adequately inform management. The societal implications of nonstationary sediment dynamics and their controls were further explored through the case of California, USA, where over 150 impairment listings have resulted in more than 50 sediment TMDLs, only 3 of which are flux based - none of which account for non-stationary behavior.

Influence of structures of polymer backbones on cooperative photoreorientation behavior of p-cyanoazobenzene side chains

DEFF Research Database (Denmark)

Han, Mina; Kidowaki, Masatoshi; Ichimura, Kunihiro

2001-01-01

Photoinduced orientational behavior of a polymethacrylate (CN6) and a polyester (p6a12) with p-cyanoazobenzene side chains was studied to reveal the structural effect of the liquid crystalline polymer backbones. Irradiation with linearly polarized W light resulted in the reorientation of the azob...

Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme

OpenAIRE

Buck, Matthias; Bouguet-Bonnet, Sabine; Pastor, Richard W.; MacKerell, Alexander D.

2005-01-01

The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.

[Study for portable dynamic ECG monitor and recorder].

Science.gov (United States)

Yang, Pengcheng; Li, Yongqin; Chen, Bihua

2012-09-01

This Paper presents a portable dynamic ECG monitor system based on MSP430F149 microcontroller. The electrocardiogram detecting system consists of ECG detecting circuit, man-machine interaction module, MSP430F149 and upper computer software. The ECG detecting circuit including a preamplifier, second-order Butterworth low-pass filter, high-pass filter, and 50Hz trap circuit to detects electrocardiogram and depresses various kinds of interference effectively. A microcontroller is used to collect three channel analog signals which can be displayed on TFT LCD. A SD card is used to record real-time data continuously and implement the FTA16 file system. In the end, a host computer system interface is also designed to analyze the ECG signal and the analysis results can provide diagnosis references to clinical doctors.

Dynamic performance of the beam position monitor support at the SSRF.

Science.gov (United States)

Wang, Xiao; Cao, Yun; Du, Hanwen; Yin, Lixin

2009-01-01

Electron beam stability is very important for third-generation light sources, especially for the Shanghai Synchrotron Radiation Facility whose ground vibrations are much larger than those for other light sources. Beam position monitors (BPMs), used to monitor the position of the electron beam, require a greater stability than other mechanical structures. This paper concentrates on an investigation of the dynamic performance of the BPM support prototype. Modal and response analyses have been carried out by finite-element (FE) calculations and vibration measurements. Inconsistent results between calculation and measurement have motivated a change in the soft connections between the support and the ground from a ground bolt in the initial design to full grout. As a result the mechanical stability of the BPM support is greatly improved, showing an increase in the first eigenfrequency from 20.2 Hz to 50.2 Hz and a decrease in the ratio of the root-mean-square displacement (4-50 Hz) between the ground and the top of the support from 4.36 to 1.23 in the lateral direction. An example is given to show how FE analysis can guide the mechanical design and dynamic measurements (i.e. it is not just used as a verification method). Similar ideas can be applied to improve the stability of other mechanical structures.

Integrated monitoring of multi-domain backbone connections Operational experience in the LHC optical private network

CERN Document Server

Marcu, Patricia; Fritz, Wolfgang; Yampolskiy, Mark; Hommel, Wolfgang

2011-01-01

Novel large scale research projects often require cooperation between various different project partners that are spread among the entire world. They do not only need huge computing resources, but also a reliable network to operate on. The Large Hadron Collider (LHC) at CERN is a representative example for such a project. Its experiments result in a vast amount of data, which is interesting for researchers around the world. For transporting the data from CERN to 11 data processing and storage sites, an optical private network (OPN) has been constructed. As the experiment data is highly valuable, LHC defines very high requirements to the underlying network infrastructure. In order to fulfil those requirements, the connections have to be managed and monitored permanently. In this paper, we present the integrated monitoring solution developed for the LHCOPN. We first outline the requirements and show how they are met on the single network layers. After that, we describe, how those single measurements can be comb...

A multi-dimensional dynamic linear model for monitoring slaughter pig production

DEFF Research Database (Denmark)

Jensen, Dan Børge; Cornou, Cecile; Toft, Nils

Scientists and farmers still lack an efficient way to unify the large number of different types of data series, which are increasingly being generated in relation to automatic herd monitoring. Such a unifying model should be able to account for the correlations between the various types of data......, feed-and water consumption), measured at different levels of detail (individual pig and double-pen level) and with different observational frequencies (weekly and daily), using series collected for the Danish PigIT project. The presented three-dimensional model serves as a proof of concept......, resulting in a model which could potentially yield more information than can be gained from the individual components separately. Here we present such a model for monitoring slaughter pig production, in the form of a multivariate dynamic linear model. This model unifies three types of data (live weight...

Research progress of laser welding process dynamic monitoring technology based on plasma characteristics signal

Directory of Open Access Journals (Sweden)

Teng WANG

2017-02-01

Full Text Available During the high-power laser welding process, plasmas are induced by the evaporation of metal under laser radiation, which can affect the coupling of laser energy and the workpiece, and ultimately impact on the reliability of laser welding quality and process directly. The research of laser-induced plasma is a focus in high-power deep penetration welding field, which provides a promising research area for realizing the automation of welding process quality inspection. In recent years, the research of laser welding process dynamic monitoring technology based on plasma characteristics is mainly in two aspects, namely the research of plasma signal detection and the research of laser welding process modeling. The laser-induced plasma in the laser welding is introduced, and the related research of laser welding process dynamic monitoring technology based on plasma characteristics at home and abroad is analyzed. The current problems in the field are summarized, and the future development trend is put forward.

(1)H, (13)C, and (15)N backbone resonance assignments of the full-length 40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog.

Science.gov (United States)

Moro, Sean L; Cocco, Melanie J

2015-10-01

The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity. Short extension past the lesion allows the high-fidelity polymerase to switch back onto the site of replication. Dbh and the other Y-family polymerases have been used as structural models to investigate the mechanisms of DNA polymerization and lesion bypass. Many high-resolution crystal structures of Y-family polymerases have been reported. NMR dynamics studies can complement these structures by providing a measure of protein motions. Here we report the (15)N, (1)H, and (13)C backbone resonance assignments at two temperatures (35 and 50 °C) for Sulfolobus acidocaldarius Dbh polymerase. Backbone resonance assignments have been obtained for 86 % of the residues. The polymerase active site is assigned as well as the majority of residues in each of the four domains.

The study of remote sensing dynamic monitoring for coalfield fire area in Shuixigou, Xinjiang

International Nuclear Information System (INIS)

Xia, Jun; Tashpolat-Tiyip

2014-01-01

The dynamic monitoring of fire area is particularly important in the controlling of underground coalfield fire. This paper took the Xinjiang Shuixigou coalfield fire area as an example, through the normalized processing of the multi-temporal thermal infrared images a generalized single-channel algorithm was used to retrieval the surface temperature. Combined with the method of single band optimal density split Sec-segmentation followed by dividing the fire area into the background region, serious combust region and more serious combust region. Thermal anomaly information in the coalfield fire area and analyse the spatial and temporal dynamics change of underground coalfield were calculated as follows:(1)fire area increased 2.03 times between 1990 and 2011, the annual average degree of dynamic changes was 1.28 in the first ten years and increased to 4.57 in the last ten years;(2)the gravity of the little serious area of the coalfield fire integrally moved north to northwest from 1990 to 2001, then northeast from 2001 to 2011;(3)there were three original independent child fire area A, B and C, but A and B merged between 1990 to 2001, C also trended close A and B until 2011. Remote sensing technology provides a feasible method for the dynamic monitoring of coalfield fire area and provides theory basis and scientific guidance for the prevention of coalfield fire disaster and implementation of coalfield fires fighting engineering

Static and Dynamic Behaviour Assessment of the Trajan Arch by Means of New Monitoring Technologies

Science.gov (United States)

Petti, L.; Barone, F.; Mammone, A.; Giordano, G.

2017-08-01

An effective assessment of the static and dynamic structural behavior of historical monuments requires the development and validation of suitable adaptive structural models using high-quality experimental data acquired with an effectively continuous and distributed monitoring. Furthermore, the adaptive strategy allows an efficient evaluation of the health status and of the evolution along the time of a historical monument, providing relevant information to plan appropriate actions for its long-term preservation. The Trajan Arch in Benevento chosen as a case of study to develop and apply this new adaptive strategy in cultural heritage conservation. The paper, after a description of the innovative monitoring system, based on state-of-the-art mechanical sensors, presents and discusses the results of two tests, comparing the measurements with the predictions of an adaptive structural FEM model developed for the dynamical simulation of the Trajan Arch.

Wavepacket dynamics of a Rydberg atom monitored by a pair of time-delayed laser pulses

Science.gov (United States)

Xin, PeiPei; Cheng, Hong; Zhang, ShanShan; Wang, HanMu; Liu, HongPing

2018-02-01

We have investigated the Rydberg state population of an argon atom by an intense laser pulse and its wavepacket dynamics monitored by another successive laser pulse in the tunneling regime. A wavepacket comprising a superposition of close high-lying Rydberg states is irradiated by a multicycle laser pulse, where the sub-wave components in the wavepacket have fixed relative phases. A time-delayed second laser pulse is employed to apply on the excited Rydberg atom. If the time is properly chosen, one of the sub-wave components will be guided towards the ionization area while the rest remains intact. By means of this pump-probe technique, we could control and monitor the Rydberg wavepacket dynamics and reveal some interesting phenomenon such as the survival rate of individual Rydberg states related to the classical orbital period of electron.

LONG-TERM DYNAMIC MONITORING OF THE HISTORICAL MASONRY FAÇADE: THE CASE OF PALAZZO DUCALE IN VENICE, ITALY

Directory of Open Access Journals (Sweden)

J. Noh

2017-08-01

Full Text Available Long-term dynamic monitoring of the masonry façade of Palazzo Ducale known as Doge’s palace in Venice, Italy was performed from September 2010 to October 2012. This article demonstrates the results of preliminary analysis on the data set of the first 12-month long monitoring campaign for out-of-plumb dynamic responses of the medieval façade of the monument. The aim of the analysis of the dynamic signals is to validate the data set and investigate dynamic characteristics of the vibration signature of the historical masonry wall in the long-term. Palazzo Ducale is a heavily visited heritage due to its high cultural importance and architectural value. Nevertheless, little is known about the dynamic behaviour of the double-leaf masonry façade. In this study, the dynamic properties of the structure are presented by dynamic identification carried out with the effect of the ambient vibration measured at four different locations on the façade and portico level. The trend and intensity of the vibration at each measurement locations are identified over the year. In addition, the issue on eliminating the noise blended in the signals for reliable analysis are also discussed.

Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

Directory of Open Access Journals (Sweden)

Colin A Smith

Full Text Available Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface, interactions between and within parts of the structure (e.g. domains can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

Langevin dynamics for ramified structures

Science.gov (United States)

Méndez, Vicenç; Iomin, Alexander; Horsthemke, Werner; Campos, Daniel

2017-06-01

We propose a generalized Langevin formalism to describe transport in combs and similar ramified structures. Our approach consists of a Langevin equation without drift for the motion along the backbone. The motion along the secondary branches may be described either by a Langevin equation or by other types of random processes. The mean square displacement (MSD) along the backbone characterizes the transport through the ramified structure. We derive a general analytical expression for this observable in terms of the probability distribution function of the motion along the secondary branches. We apply our result to various types of motion along the secondary branches of finite or infinite length, such as subdiffusion, superdiffusion, and Langevin dynamics with colored Gaussian noise and with non-Gaussian white noise. Monte Carlo simulations show excellent agreement with the analytical results. The MSD for the case of Gaussian noise is shown to be independent of the noise color. We conclude by generalizing our analytical expression for the MSD to the case where each secondary branch is n dimensional.

Remote Sensing Dynamic Monitoring of Biological Invasive Species Based on Adaptive PCNN and Improved C-V Model

Directory of Open Access Journals (Sweden)

PENG Gang

2014-12-01

Full Text Available Biological species invasion problem bring serious damage to the ecosystem, and have become one of the six major enviromental problems that affect the future economic development, also have become one of the hot topic in domestic and foreign scholars. Remote sensing technology has been successfully used in the investigation of coastal zone resources, dynamic monitoring of the resources and environment, and other fields. It will cite a new remote sensing image change detection algorithm based on adaptive pulse coupled neural network (PCNN and improved C-V model, for remote sensing dynamic monitoring of biological species invasion. The experimental results show that the algorithm is effective in the test results of biological species invasions.

MICROBIOLOGICAL MONITORING AND AUTOMATED EVENT SAMPLING AT KARST SPRINGS USING LEO-SATELLITES

Science.gov (United States)

Stadler, Hermann; Skritek, Paul; Sommer, Regina; Mach, Robert L.; Zerobin, Wolfgang; Farnleitner, Andreas H.

2010-01-01

Data communication via Low-Earth-Orbit Satellites between portable hydro-meteorological measuring stations is the backbone of our system. This networking allows automated event sampling with short time increments also for E.coli field analysis. All activities of the course of the event-sampling can be observed on an internet platform based on a Linux-Server. Conventionally taken samples by hand compared with the auto-sampling procedure revealed corresponding results and were in agreement to the ISO 9308-1 reference method. E.coli concentrations were individually corrected by event specific die-off rates (0.10–0.14 day−1) compensating losses due to sample storage at spring temperature in the auto sampler. Two large summer events 2005/2006 at a large alpine karst spring (LKAS2) were monitored including detailed analysis of E.coli dynamics (n = 271) together with comprehensive hydrological characterisations. High resolution time series demonstrated a sudden increase of E.coli concentrations in spring water (approx. 2 log10 units) with a specific time delay after the beginning of the event. Statistical analysis suggested the spectral absorbent coefficient measured at 254nm (SAC254) as an early warning surrogate for real time monitoring of faecal input. Together with the LEO-Satellite based system it is a helpful tool for Early-Warning-Systems in the field of drinking water protection. PMID:18776628

PESI - a taxonomic backbone for Europe

Science.gov (United States)

Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D.; Boegh, Phillip S.; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M.; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M.J.C.; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M. de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A.; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

2015-01-01

Abstract Background Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. PMID:26491393

Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions

Energy Technology Data Exchange (ETDEWEB)

Ngaojampa, C.; Nimmanpipug, P. [Computer Simulation and Modeling Laboratory (CSML), Department of Chemistry and Center for Innovation Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Yu, L.D., E-mail: yuld@fnrf.science.cmu.ac.t [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok 10400 (Thailand); Anuntalabhochai, S. [Molecular Biology Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Lee, V.S., E-mail: vannajan@gmail.co [Computer Simulation and Modeling Laboratory (CSML), Department of Chemistry and Center for Innovation Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok 10400 (Thailand)

2011-02-15

In order to promote understanding of the fundamentals of ultra-low-energy ion interaction with DNA, molecular dynamics simulations using combined quantum-mechanics/molecular-mechanics of poly-AT and poly-GC A-DNA double strands irradiated by <200 eV carbon ions were performed to investigate the molecular implications of mutation bias. The simulations were focused on the responses of the DNA backbones and nitrogenous bases to irradiation. Analyses of the root mean square displacements of the backbones and non-hydrogen atoms of base rings of the simulated DNA structure after irradiation revealed a potential preference of DNA double strand separation, dependent on the irradiating energy. The results show that for the backbones, the large difference in the displacement between poly-GC and poly-AT in the initial time period could be the reason for the backbone breakage; for the nitrogenous base pairs, A-T is 30% more sensitive or vulnerable to ion irradiation than G-C, demonstrating a preferential, instead of random, effect of irradiation-induced mutation.

Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions

International Nuclear Information System (INIS)

Ngaojampa, C.; Nimmanpipug, P.; Yu, L.D.; Anuntalabhochai, S.; Lee, V.S.

2011-01-01

In order to promote understanding of the fundamentals of ultra-low-energy ion interaction with DNA, molecular dynamics simulations using combined quantum-mechanics/molecular-mechanics of poly-AT and poly-GC A-DNA double strands irradiated by <200 eV carbon ions were performed to investigate the molecular implications of mutation bias. The simulations were focused on the responses of the DNA backbones and nitrogenous bases to irradiation. Analyses of the root mean square displacements of the backbones and non-hydrogen atoms of base rings of the simulated DNA structure after irradiation revealed a potential preference of DNA double strand separation, dependent on the irradiating energy. The results show that for the backbones, the large difference in the displacement between poly-GC and poly-AT in the initial time period could be the reason for the backbone breakage; for the nitrogenous base pairs, A-T is 30% more sensitive or vulnerable to ion irradiation than G-C, demonstrating a preferential, instead of random, effect of irradiation-induced mutation.

Dual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics.

Science.gov (United States)

Davis, Caitlin M; Reddish, Michael J; Dyer, R Brian

2017-05-05

Time-resolved temperature-jump (T-jump) coupled with fluorescence and infrared (IR) spectroscopy is a powerful technique for monitoring protein dynamics. Although IR spectroscopy of the polypeptide amide I mode is more technically challenging, it offers complementary information because it directly probes changes in the protein backbone, whereas, fluorescence spectroscopy is sensitive to the environment of specific side chains. With the advent of widely tunable quantum cascade lasers (QCL) it is possible to efficiently probe multiple IR frequencies with high sensitivity and reproducibility. Here we describe a dual time-resolved T-jump fluorescence and IR spectrometer and its application to study protein folding dynamics. A Q-switched Ho:YAG laser provides the T-jump source for both time-resolved IR and fluorescence spectroscopy, which are probed by a QCL and Ti:Sapphire laser, respectively. The Ho:YAG laser simultaneously pumps the time-resolved IR and fluorescence spectrometers. The instrument has high sensitivity, with an IR absorbance detection limit of jump induced difference spectrum from 50ns to 0.5ms. This study demonstrates the power of the dual time-resolved T-jump fluorescence and IR spectroscopy to resolve complex folding mechanisms by complementary IR absorbance and fluorescence measurements of protein dynamics. Copyright © 2017 Elsevier B.V. All rights reserved.

Electrochemical synthesis of polyaniline in the presence of poly(amidosulfonic acid)s with different rigidity of polymer backbone and characterization of the films obtained

International Nuclear Information System (INIS)

Nekrasov, A.A.; Gribkova, O.L.; Eremina, T.V.; Isakova, A.A.; Ivanov, V.F.; Tverskoj, V.A.; Vannikov, A.V.

2008-01-01

We have studied electrochemical matrix polymerization of aniline in the presence of poly(amidosulfonic acid)s of different nature: poly(2-acrylamido-2-methyl-1-propanosulfonic acid) (PAMPSA, flexible backbone); poly(p,p'-(2,2'-disulfoacid)-diphenylene-iso-phthalamid) (i-PASA, semi-rigid backbone); poly(p,p'-(2,2'-disulfoacid)-diphelylene-tere-phthalamid) (t-PASA, rigid backbone). Also, we have investigated spectral and electrochemical properties of the films obtained, as well as their surface morphology. The matrix polymerization results in the formation of interpolymer complexes of polyaniline (PANI) and the above-cited polyacids. The acceleration of aniline electropolymerization in the presence of poly(amidosulfonic acid)s was observed due to association of aniline molecules to sulfonic groups of the polyacid and higher local concentration of protons near the polyacid backbone. The rigid-chain polyacids interfere with the normal course of the electropolymerization, which manifests itself in the changes of the shape of time dependences of absorbance and charge. Cyclic voltammetry and spectroelectrochemical experiments showed that the formation of interpolymer complex with rigid-chain polyacids distorts spectroelectrochemical characteristics of PANI. This evidently results from steric hindrances in the formation of quinoid units

Charge transport properties of poly(dA)-poly(dT) DNA in variation of backbone disorder and amplitude of base-pair twisting motion

Energy Technology Data Exchange (ETDEWEB)

Rahmi, Kinanti Aldilla, E-mail: kinanti.aldilla@ui.ac.id; Yudiarsah, Efta [Physics Department, FMIPA, Universitas Indonesia, Kampus UI Depok (Indonesia)

2016-04-19

By using tight binding Hamiltonian model, charge transport properties of poly(dA)-poly(dT) DNA in variation of backbone disorder and amplitude of base-pair twisting motion is studied. The DNA chain used is 32 base pairs long poly(dA)-poly(dT) molecule. The molecule is contacted to electrode at both ends. The influence of environment on charge transport in DNA is modeled as variation of backbone disorder. The twisting motion amplitude is taking into account by assuming that the twisting angle distributes following Gaussian distribution function with zero average and standard deviation proportional to square root of temperature and inversely proportional to the twisting motion frequency. The base-pair twisting motion influences both the onsite energy of the bases and electron hopping constant between bases. The charge transport properties are studied by calculating current using Landauer-Buttiker formula from transmission probabilities which is calculated by transfer matrix methods. The result shows that as the backbone disorder increases, the maximum current decreases. By decreasing the twisting motion frequency, the current increases rapidly at low voltage, but the current increases slower at higher voltage. The threshold voltage can increase or decrease with increasing backbone disorder and increasing twisting frequency.

Remotely Sensed Monitoring of Small Reservoir Dynamics: A Bayesian Approach

Directory of Open Access Journals (Sweden)

Dirk Eilander

2014-01-01

Full Text Available Multipurpose small reservoirs are important for livelihoods in rural semi-arid regions. To manage and plan these reservoirs and to assess their hydrological impact at a river basin scale, it is important to monitor their water storage dynamics. This paper introduces a Bayesian approach for monitoring small reservoirs with radar satellite images. The newly developed growing Bayesian classifier has a high degree of automation, can readily be extended with auxiliary information and reduces the confusion error to the land-water boundary pixels. A case study has been performed in the Upper East Region of Ghana, based on Radarsat-2 data from November 2012 until April 2013. Results show that the growing Bayesian classifier can deal with the spatial and temporal variability in synthetic aperture radar (SAR backscatter intensities from small reservoirs. Due to its ability to incorporate auxiliary information, the algorithm is able to delineate open water from SAR imagery with a low land-water contrast in the case of wind-induced Bragg scattering or limited vegetation on the land surrounding a small reservoir.

Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations

Directory of Open Access Journals (Sweden)

Yingliang Liu

2017-07-01

Full Text Available Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm–1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.

Protonation–deprotonation of the glycine backbone as followed by Raman scattering and multiconformational analysis

Energy Technology Data Exchange (ETDEWEB)

Hernández, Belén; Pflüger, Fernando [Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex (France); Kruglik, Sergei G. [Laboratoire Jean Perrin, FRE 3231, Université Pierre et Marie Curie (Paris 6), Case courrier 138, 75252 Paris Cedex 05 (France); Ghomi, Mahmoud, E-mail: mahmoud.ghomi@univ-paris13.fr [Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex (France)

2013-11-08

Highlights: • New pH-dependent Raman spectra in the middle wavenumber region (1800-300 cm{sup −1}). • New quantum mechanical calculations for exploring the Gly conformational landscape. • Construction of muticonformation based theoretical Raman spectra. - Abstract: Because of the absence of the side chain in its chemical structure and its well defined Raman spectra, glycine was selected here to follow its backbone protonation–deprotonation. The scan of the recorded spectra in the 1800–300 cm{sup −1} region led us to assign those obtained at pH 1, 6 and 12 to the cationic, zwitterionic and anionic species, respectively. These data complete well those previously published by Bykov et al. (2008) [16] devoted to the high wavenumber Raman spectra (>2500 cm{sup −1}). To reinforce our discussion, DFT calculations were carried out on the clusters of glycine + 5H{sub 2}O, mimicking reasonably the first hydration shell of the amino acid. Geometry optimization of 141 initial clusters, reflecting plausible combinations of the backbone torsion angles, allowed exploration of the conformational features, as well as construction of the theoretical Raman spectra by considering the most stable clusters containing each glycine species.

Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

Energy Technology Data Exchange (ETDEWEB)

Lee, Andrew Loyd [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

1996-05-01

Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the δ-Al-ε activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a βαβ-βαβ pattern of secondary structure, with the two helices packed against a 4-stranded anti-parallel β-sheet. In addition ¹⁵N T₁, T₂, and ¹⁵N/¹H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone ¹H, ¹³C, and ¹⁵N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and ¹⁵N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.

Preface: Current perspectives in modelling, monitoring, and predicting geophysical fluid dynamics

Science.gov (United States)

Mancho, Ana M.; Hernández-García, Emilio; López, Cristóbal; Turiel, Antonio; Wiggins, Stephen; Pérez-Muñuzuri, Vicente

2018-02-01

The third edition of the international workshop Nonlinear Processes in Oceanic and Atmospheric Flows was held at the Institute of Mathematical Sciences (ICMAT) in Madrid from 6 to 8 July 2016. The event gathered oceanographers, atmospheric scientists, physicists, and applied mathematicians sharing a common interest in the nonlinear dynamics of geophysical fluid flows. The philosophy of this meeting was to bring together researchers from a variety of backgrounds into an environment that favoured a vigorous discussion of concepts across different disciplines. The present Special Issue on Current perspectives in modelling, monitoring, and predicting geophysical fluid dynamics contains selected contributions, mainly from attendants of the workshop, providing an updated perspective on modelling aspects of geophysical flows as well as issues on prediction and assimilation of observational data and novel tools for describing transport and mixing processes in these contexts. More details on these aspects are discussed in this preface.

Adsorption of molecular brushes with polyelectrolyte backbones onto oppositely charged surfaces: A self-consistent field theory

NARCIS (Netherlands)

Feuz, L.; Leermakers, F.A.M.; Textor, M.; Borisov, O.V.

2008-01-01

The two-gradient version of the Scheutjens¿Fleer self-consistent field (SF-SCF) theory is employed to model the interaction between a molecular bottle brush with a polyelectrolyte backbone and neutral hydrophilic side chains and an oppositely charged surface. Our system mimics graft-copolymers with

A fusion networking model for smart grid power distribution backbone communication network based on PTN

Directory of Open Access Journals (Sweden)

Wang Hao

2016-01-01

Full Text Available In current communication network for distribution in Chinese power grid systems, the fiber communication backbone network for distribution and TD-LTE power private wireless backhaul network of power grid are both bearing by the SDH optical transmission network, which also carries the communication network of transformer substation and main electric. As the data traffic of the distribution communication and TD-LTE power private wireless network grow rapidly in recent years, it will have a big impact with the SDH network’s bearing capacity which is mainly used for main electric communication in high security level. This paper presents a fusion networking model which use a multiple-layer PTN network as the unified bearing of the TD-LTE power private wireless backhaul network and fiber communication backbone network for distribution. Network dataflow analysis shows that this model can greatly reduce the capacity pressure of the traditional SDH network as well as ensure the reliability of the transmission of the communication network for distribution and TD-LTE power private wireless network.

Interim monitoring of cost dynamics for publicly supported energy technologies

Energy Technology Data Exchange (ETDEWEB)

Nemet, Gregory F. [La Follette School of Public Affairs, University of Wisconsin, 1225 Observatory Drive, Madison, WI 53706 (United States)]|[Nelson Institute for Environmental Studies, University of Wisconsin, Madison, WI 53726 (United States)

2009-03-15

The combination of substantial public funding of nascent energy technologies and recent increases in the costs of those that have been most heavily supported has raised questions about whether policy makers should sustain, alter, enhance, or terminate such programs. This paper uses experience curves for photovoltaics (PV) and wind to (1) estimate ranges of costs for these public programs and (2) introduce new ways of evaluating recent cost dynamics. For both technology cases, the estimated costs of the subsidies required to reach targets are sensitive to the choice of time period on which cost projections are based. The variation in the discounted social cost of subsidies exceeds an order of magnitude. Vigilance is required to avoid the very expensive outcomes contained within these distributions of social costs. Two measures of the significance of recent deviations are introduced. Both indicate that wind costs are within the expected range of prior forecasts but that PV costs are not. The magnitude of the public funds involved in these programs heightens the need for better analytical tools with which to monitor and evaluate cost dynamics. (author)

Monitoring water phase dynamics in winter clouds

Science.gov (United States)

Campos, Edwin F.; Ware, Randolph; Joe, Paul; Hudak, David

2014-10-01

This work presents observations of water phase dynamics that demonstrate the theoretical Wegener-Bergeron-Findeisen concepts in mixed-phase winter storms. The work analyzes vertical profiles of air vapor pressure, and equilibrium vapor pressure over liquid water and ice. Based only on the magnitude ranking of these vapor pressures, we identified conditions where liquid droplets and ice particles grow or deplete simultaneously, as well as the conditions where droplets evaporate and ice particles grow by vapor diffusion. The method is applied to ground-based remote-sensing observations during two snowstorms, using two distinct microwave profiling radiometers operating in different climatic regions (North American Central High Plains and Great Lakes). The results are compared with independent microwave radiometer retrievals of vertically integrated liquid water, cloud-base estimates from a co-located ceilometer, reflectivity factor and Doppler velocity observations by nearby vertically pointing radars, and radiometer estimates of liquid water layers aloft. This work thus makes a positive contribution toward monitoring and nowcasting the evolution of supercooled droplets in winter clouds.

Nonlinear dynamics of interacting populations

CERN Document Server

Bazykin, Alexander D

1998-01-01

This book contains a systematic study of ecological communities of two or three interacting populations. Starting from the Lotka-Volterra system, various regulating factors are considered, such as rates of birth and death, predation and competition. The different factors can have a stabilizing or a destabilizing effect on the community, and their interplay leads to increasingly complicated behavior. Studying and understanding this path to greater dynamical complexity of ecological systems constitutes the backbone of this book. On the mathematical side, the tool of choice is the qualitative the

Telemetered sensors for dynamic activity and structural performance monitoring

Science.gov (United States)

Townsend, Christopher P.; Hamel, Michael J.; Arms, Steven W.

2001-08-01

The development of improved structures requires knowledge of their dynamic behavior. Minimally intrusive wireless systems, capable of monitoring vibration and impact, are needed in order to provide this knowledge. Our objective was to design, build, and test a high speed data collection and wireless data communications system, including microsensors, and capable of being embedded or externally worn. Our previous transmitter designs were small and could be used to transmit multichannel digital data, but they were not capable of fast data transmission rates. The addition of a remotely triggered datalogger allowed us to overcome the limitations of our earlier designs. A bi-directional RF communications link was used to trigger a sample to be logged (from 30 meters), as well as to request data to be transmitted to the host PC for data acquisition/analysis. Sweep rates of 2000 Hz were successfully demonstrated from a triad of MEMs accelerometers. The remote datalogger and transceiver and accelerometer package measured 12 mm by 24 mm by 6 mm thick; these were mounted to the feet of thoroughbred horses to study their impact levels. These small, fast, wireless data recording systems can be used to monitor rotating/ vibrating machinery and civil/automotive/aerospace structures.

Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences.

Science.gov (United States)

Walsh, Patrick S; Dean, Jacob C; McBurney, Carl; Kang, Hyuk; Gellman, Samuel H; Zwier, Timothy S

2016-04-28

The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase. This work seeks a bottom-up understanding of the role played by glutamine residues in directing peptide structures that lead to neurodegenerative diseases. Resonant ion-dip infrared (RIDIR) spectroscopy is used to record single-conformation infrared spectra in the NH stretch, amide I and amide II regions. Comparison of the experimental spectra with the predictions of calculations carried out at the DFT M05-2X/6-31+G(d) level of theory lead to firm assignments for the H-bonding architectures of a total of eight conformers of four molecules, including three in Z-Gln-OH, one in Z-Gln-NHMe, three in Ac-Gln-NHBn, and one in Ac-Ala-Gln-NHBn. The Gln side chain engages actively in forming H-bonds with nearest-neighbor amide groups, forming C8 H-bonds to the C-terminal side, C9 H-bonds to the N-terminal side, and an amide-stacked geometry, all with an extended (C5) peptide backbone about the Gln residue. The Gln side chain also stabilizes an inverse γ-turn in the peptide backbone by forming a pair of H-bonds that bridge the γ-turn and stabilize it. Finally, the entire conformer population of Ac-Ala-Gln-NHBn is funneled into a single structure that incorporates the peptide backbone in a type I β-turn, stabilized by the Gln side chain forming a C7 H-bond to the central amide group in the β-turn not otherwise involved in a hydrogen bond. This β-turn backbone structure is nearly identical to that observed in a series of X-(AQ)-Y β-turns in the protein data bank, demonstrating that the gas-phase structure is robust to perturbations imposed by the crystalline protein environment.

Polystyrene Backbone Polymers Consisting of Alkyl-Substituted Triazine Side Groups for Phosphorescent OLEDs

OpenAIRE

Salert, Beatrice Ch. D.; Wedel, Armin; Grubert, Lutz; Eberle, Thomas; Anémian, Rémi; Krueger, Hartmut

2012-01-01

This paper describes the synthesis of new electron-transporting styrene monomers and their corresponding polystyrenes all with a 2,4,6-triphenyl-1,3,5-triazine basic structure in the side group. The monomers differ in the alkyl substitution and in the meta-/paralinkage of the triazine to the polymer backbone. The thermal and spectroscopic properties of the new electron-transporting polymers are discussed in regard to their chemical structures. Phosphorescent OLEDs were prepared using the obta...

Required sample size for monitoring stand dynamics in strict forest reserves: a case study

Science.gov (United States)

Diego Van Den Meersschaut; Bart De Cuyper; Kris Vandekerkhove; Noel Lust

2000-01-01

Stand dynamics in European strict forest reserves are commonly monitored using inventory densities of 5 to 15 percent of the total surface. The assumption that these densities guarantee a representative image of certain parameters is critically analyzed in a case study for the parameters basal area and stem number. The required sample sizes for different accuracy and...

Ultra-sensitive EUV resists based on acid-catalyzed polymer backbone breaking

Science.gov (United States)

Manouras, Theodoros; Kazazis, Dimitrios; Koufakis, Eleftherios; Ekinci, Yasin; Vamvakaki, Maria; Argitis, Panagiotis

2018-03-01

The main target of the current work was to develop new sensitive polymeric materials for lithographic applications, focusing in particular to EUV lithography, the main chain of which is cleaved under the influence of photogenerated acid. Resist materials based on the cleavage of polymer main chain are in principle capable to create very small structures, to the dimensions of the monomers that they consist of. Nevertheless, in the case of the commonly used nonchemically amplified materials of this type issues like sensitivity and poor etch resistance limit their areas of application, whereas inadequate etch resistance and non- satisfactory process reliability are the usual problems encountered in acid catalysed materials based on main chain scission. In our material design the acid catalyzed chain cleavable polymers contain very sensitive moieties in their backbone while they remain intact in alkaline ambient. These newly synthesized polymers bear in addition suitable functional groups for the achievement of desirable lithographic characteristics (thermal stability, acceptable glass transition temperature, etch resistance, proper dissolution behavior, adhesion to the substrate). Our approach for achieving acceptable etch resistance, a main drawback in other main chain cleavable resists, is based on the introduction of polyaromatic hydrocarbons in the polymeric backbone, whereas the incorporation of an inorganic component further enhances the etch resistance. Single component systems can also be designed following the proposed approach by the incorporation of suitable PAGs and base quencher molecules in the main chain. Resist formulations based on a random copolymer designed according to the described rules evaluated in EUV exhibit ultrahigh sensitivity, capability for high resolution patterning and overall processing characteristics that make them strong candidates for industrial use upon further optimization.

Excited-State Dynamics of Carotenoids Studied by Femtosecond Transient Absorption Spectroscopy

International Nuclear Information System (INIS)

Lee, Ingu; Pang, Yoonsoo; Lee, Sebok

2014-01-01

Carotenoids, natural antenna pigments in photosynthesis share a symmetric backbone of conjugated polyenes. Contrary to the symmetric and almost planar geometries of carotenoids, excited state structure and dynamics of carotenoids are exceedingly complex. In this paper, recent infrared and visible transient absorption measurements and excitation dependent dynamics of 8'-apo-β-caroten-8'-al and 7',7'-dicyano-7'-apo-β-carotene will be reviewed. The recent visible transient absorption measurements of 8'-apo-β-caroten-8'-al in polar and nonpolar solvents will also be introduced to emphasize the complex excited-state dynamics and unsolved problems in the S 2 and S 1 excited states

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

Directory of Open Access Journals (Sweden)

Lyngsø Rune

2010-04-01

Full Text Available Abstract Background The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. Results Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family. Conclusions As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.

Stability mechanisms of a thermophilic laccase probed by molecular dynamics.

Directory of Open Access Journals (Sweden)

Niels J Christensen

Full Text Available Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K, probing structural changes associated with enthalpy-entropy compensation. Approaching T opt (∼350 K from 300 K, this change correlated with a beginning "unzipping" of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive at 400 K, suggesting a general salt stabilization effect. In contrast, F(- (but not Cl(- specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F(- intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes.

A method for the automated long-term monitoring of three-spined stickleback Gasterosteus aculeatus shoal dynamics.

Science.gov (United States)

Kleinhappel, T K; Al-Zoubi, A; Al-Diri, B; Burman, O; Dickinson, P; John, L; Wilkinson, A; Pike, T W

2014-04-01

This paper describes and evaluates a flexible, non-invasive tagging system for the automated identification and long-term monitoring of individual three-spined sticklebacks Gasterosteus aculeatus. The system is based on barcoded tags, which can be reliably and robustly detected and decoded to provide information on an individual's identity and location. Because large numbers of fish can be individually tagged, it can be used to monitor individual- and group-level dynamics within fish shoals. © 2014 The Fisheries Society of the British Isles.

Monitoring and modeling infiltration–recharge dynamics of managed aquifer recharge with desalinated seawater

OpenAIRE

Ganot, Y.; Ganot, Y.; Holtzman, R.; Weisbrod, N.; Nitzan, I.; Katz, Y.; Kurtzman, D.

2017-01-01

We study the relation between surface infiltration and groundwater recharge during managed aquifer recharge (MAR) with desalinated seawater in an infiltration pond, at the Menashe site that overlies the northern part of the Israeli Coastal Aquifer. We monitor infiltration dynamics at multiple scales (up to the scale of the entire pond) by measuring the ponding depth, sediment water content and groundwater levels, using pressure sensors, single-ring infiltrometers, soil senso...

Dynamic Sleep Scheduling on Air Pollution Levels Monitoring with Wireless Sensor Network

OpenAIRE

Gezaq Abror; Rusminto Tjatur Widodo; M. Udin Harun Al Rasyid

2018-01-01

Wireless Sensor Network (WSN) can be applied for Air Pollution Level Monitoring System that have been determined by the Environmental Impact Management Agency which is  PM10, SO2, O3, NO2 and CO. In WSN, node system is constrained to a limited power supply, so that the node system has a lifetime. To doing lifetime maximization, power management scheme is required and sensor nodes should use energy efficiently. This paper proposes dynamic sleep scheduling using Time Category-Fuzzy Logic (Time-...

Prediction of methyl-side Chain Dynamics in Proteins

International Nuclear Information System (INIS)

Ming Dengming; Brueschweiler, Rafael

2004-01-01

A simple analytical model is presented for the prediction of methyl-side chain dynamics in comparison with S 2 order parameters obtained by NMR relaxation spectroscopy. The model, which is an extension of the local contact model for backbone order parameter prediction, uses a static 3D protein structure as input. It expresses the methyl-group S 2 order parameters as a function of local contacts of the methyl carbon with respect to the neighboring atoms in combination with the number of consecutive mobile dihedral angles between the methyl group and the protein backbone. For six out of seven proteins the prediction results are good when compared with experimentally determined methyl-group S 2 values with an average correlation coefficient r-bar=0.65±0.14. For the unusually rigid cytochrome c 2 no significant correlation between prediction and experiment is found. The presented model provides independent support for the reliability of current side-chain relaxation methods along with their interpretation by the model-free formalism

Transforming plastic surfaces with electrophilic backbones from hydrophobic to hydrophilic.

Science.gov (United States)

Kim, Samuel; Bowen, Raffick A R; Zare, Richard N

2015-01-28

We demonstrate a simple nonaqueous reaction scheme for transforming the surface of plastics from hydrophobic to hydrophilic. The chemical modification is achieved by base-catalyzed trans-esterification with polyols. It is permanent, does not release contaminants, and causes no optical or mechanical distortion of the plastic. We present contact angle measurements to show successful modification of several types of plastics including poly(ethylene terephthalate) (PET) and polycarbonate (PC). Its applicability to blood analysis is explored using chemically modified PET blood collection tubes and found to be quite satisfactory. We expect this approach will reduce the cost of manufacturing plastic devices with optimized wettability and can be generalized to other types of plastic materials having an electrophilic linkage as its backbone.

Regional passive seismic monitoring reveals dynamic glacier activity on Spitsbergen, Svalbard

Directory of Open Access Journals (Sweden)

Andreas Köhler

2015-12-01

Full Text Available Dynamic glacier activity is increasingly observed through passive seismic monitoring. We analysed near-regional-scale seismicity on the Arctic archipelago of Svalbard to identify seismic icequake signals and to study their spatial–temporal distribution within the 14-year period from 2000 until 2013. This is the first study that uses seismic data recorded on permanent broadband stations to detect and locate icequakes in different regions of Spitsbergen, the main island of the archipelago. A temporary local seismic network and direct observations of glacier calving and surging were used to identify icequake sources. We observed a high number of icequakes with clear spectral peaks between 1 and 8 Hz in different parts of Spitsbergen. Spatial clusters of icequakes could be associated with individual grounded tidewater glaciers and exhibited clear seasonal variability each year with more signals observed during the melt season. Locations at the termini of glaciers, and correlation with visual calving observations in situ at Kronebreen, a glacier in the Kongsfjorden region, show that these icequakes were caused dominantly by calving. Indirect evidence for glacier surging through increased calving seismicity was found in 2003 at Tunabreen, a glacier in central Spitsbergen. Another type of icequake was observed in the area of the Nathorstbreen glacier system. Seismic events occurred upstream of the glacier within a short time period between January and May 2009 during the initial phase of a major glacier surge. This study is the first step towards the generation and implementation of an operational seismic monitoring strategy for glacier dynamics in Svalbard.

Low-Cost Monitoring System of Sensors for Evaluating Dynamic Solicitations of Semitrailer Structure

Directory of Open Access Journals (Sweden)

Pablo Luque

2016-01-01

Full Text Available Analysis of the fatigue life of a semitrailer structure necessitates identification of the loads and dynamic solicitations in the structure. These forces can be introduced in computer simulation software (multibody + finite element for analysing the response of different design solutions to them. These numerical models must be validated and some parameters need to be measured directly in a field test with real vehicles under various driving conditions. In this study, a low-cost monitoring system is developed for application to a real fleet of semitrailers. According to the definition of the numerical model, the guidance of a virtual vehicle is defined by the three-dimensional kinematics of the kingpin. For characterisation of these movements, a monitoring system having a low-cost inertial measurement unit (IMU and global positioning system (GPS antennas is developed with different configurations to enable analysis of the best cost-benefit (result accuracy solution, and an extended Kalman filter (EKF that characterises the kinematic guidance of the kingpin is proposed. A semitrailer was equipped with the experimental low-cost monitoring system and high-precision sensors (IMU, GPS in order to validate the results obtained by the experimental low-cost monitoring system and the inertial-extended Kalman filter developed. The validated system has applicability in the low-cost monitoring of a fleet of real vehicles.

Dynamics of Interocular Suppression in Amblyopic Children during Electronically Monitored Occlusion Therapy: First Insight.

Science.gov (United States)

Kehrein, Stephan; Kohnen, Thomas; Fronius, Maria

2016-06-01

Interocular suppression is assumed to be the mechanism leading to impaired visual acuity, especially in strabismic amblyopia. Little is known about the dynamics of suppression during treatment. The aim of our study was to assess the development of the depth of suppression and its relation to changes in visual acuity during electronically monitored occlusion treatment. In a prospective pilot study, 15 amblyopes (8 with and 7 without strabismus) aged 5 to 16 years (mean 10.24 years) were examined before initiation of patching and then every 3 to 6 weeks for 4 months. To quantify suppression, a red filter ladder (Sbisa bar) was used, attenuating the image of the dominant eye until the patients reported a binocular perception (diplopia, rivalry, color mixture) or a change in eye dominance. Acuity was assessed with crowded Landolt rings. Daily occlusion was recorded using occlusion dose monitors. The depth of interocular suppression showed a biphasic change: it increased significantly during the first month (P=0.02), while visual acuity improved (mean 0.14 log units ±0.13; Pocclusion and suppression changes was not statistically significant. This first insight into the functional changes during electronically monitored patching suggests a complex relationship between visual acuity and interocular suppression that seems to be influenced by the presence of strabismus. Knowledge of the dynamics of interocular suppression is crucial for enhancing the outcome of occlusion treatment and also for the evaluation of its future role compared to emerging dichoptic treatments.

Solution structure and dynamics of melanoma inhibitory activity protein

International Nuclear Information System (INIS)

Lougheed, Julie C.; Domaille, Peter J.; Handel, Tracy M.

2002-01-01

Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 A over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 A over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures

Monitoring and modeling infiltration-recharge dynamics of managed aquifer recharge with desalinated seawater

OpenAIRE

Ganot, Yonatan; Holtzman, Ran; Weisbrod, Noam; Nitzan, Ido; Katz, Yoram; Kurtzman, Daniel

2016-01-01

We study the relation between surface infiltration and groundwater recharge during managed aquifer recharge (MAR) with desalinated seawater in an infiltration pond, at the Menashe site that overlies the northern part of the Israeli Coastal Aquifer. We monitor infiltration dynamics at multiple scales (up to the scale of the entire pond) by measuring the ponding depth, sediment water content and groundwater levels, using pressure sensors, single-ring infiltrometers, soil sensors and observation...

Local dynamics of proteins and DNA evaluated from crystallographic B factors

International Nuclear Information System (INIS)

Schneider, Bohdan; Gelly, Jean-Christophe; Brevern, Alexandre G. de; Černý, Jiří

2014-01-01

Distributions of scaled B factors from 704 protein–DNA complexes reflect primarily the neighbourhood of amino-acid and nucleotide residues: their flexibility grows from the protein core to protein–protein and protein–DNA interfaces, to solvent-exposed residues. Some of the findings clearly observed at higher resolution structures can no longer be observed for structures at low resolution indicating problems in refinement protocols. The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are

Local dynamics of proteins and DNA evaluated from crystallographic B factors

Energy Technology Data Exchange (ETDEWEB)

Schneider, Bohdan, E-mail: bohdan.schneider@gmail.com [Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic); Gelly, Jean-Christophe; Brevern, Alexandre G. de [INSERM, U1134, DSIMB, 75739 Paris (France); Université Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, 75739 Paris (France); Institut National de la Transfusion Sanguine (INTS), 75739 Paris (France); Laboratoire d’Excellence GR-Ex, 75739 Paris (France); Černý, Jiří [Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic)

2014-09-01

Distributions of scaled B factors from 704 protein–DNA complexes reflect primarily the neighbourhood of amino-acid and nucleotide residues: their flexibility grows from the protein core to protein–protein and protein–DNA interfaces, to solvent-exposed residues. Some of the findings clearly observed at higher resolution structures can no longer be observed for structures at low resolution indicating problems in refinement protocols. The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are

Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein

International Nuclear Information System (INIS)

Żerko, Szymon; Byrski, Piotr; Włodarczyk-Pruszyński, Paweł; Górka, Michał; Ledolter, Karin; Masliah, Eliezer; Konrat, Robert; Koźmiński, Wiktor

2016-01-01

New experiments dedicated for large IDPs backbone resonance assignment are presented. The most distinctive feature of all described techniques is the employment of MOCCA-XY16 mixing sequences to obtain effective magnetization transfers between carbonyl carbon backbone nuclei. The proposed 4 and 5 dimensional experiments provide a high dispersion of obtained signals making them suitable for use in the case of large IDPs (application to 354 a. a. residues of Tau protein 3x isoform is presented) as well as provide both forward and backward connectivities. What is more, connecting short chains interrupted with proline residues is also possible. All the experiments employ non-uniform sampling.

Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein

Energy Technology Data Exchange (ETDEWEB)

Żerko, Szymon; Byrski, Piotr; Włodarczyk-Pruszyński, Paweł; Górka, Michał [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland); Ledolter, Karin [University of Vienna, Department of Computational and Structural Biology, Max F. Perutz Laboratories (Austria); Masliah, Eliezer [University of California, San Diego, Departments of Neuroscience and Pathology (United States); Konrat, Robert [University of Vienna, Department of Computational and Structural Biology, Max F. Perutz Laboratories (Austria); Koźmiński, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland)

2016-08-15

New experiments dedicated for large IDPs backbone resonance assignment are presented. The most distinctive feature of all described techniques is the employment of MOCCA-XY16 mixing sequences to obtain effective magnetization transfers between carbonyl carbon backbone nuclei. The proposed 4 and 5 dimensional experiments provide a high dispersion of obtained signals making them suitable for use in the case of large IDPs (application to 354 a. a. residues of Tau protein 3x isoform is presented) as well as provide both forward and backward connectivities. What is more, connecting short chains interrupted with proline residues is also possible. All the experiments employ non-uniform sampling.

Pemetrexed With Platinum Combination as a Backbone for Targeted Therapy in Non-Small-Cell Lung Cancer.

Science.gov (United States)

Stinchcombe, Thomas E; Borghaei, Hossein; Barker, Scott S; Treat, Joseph Anthony; Obasaju, Coleman

2016-01-01

Standard platinum-based chemotherapy combinations for advanced non-small-cell lung cancer (NSCLC) have reached a plateau in terms of the survival benefit they offer for patients. In addition, the emerging clinical trend of tailored treatment based on patient characteristics has led to the development of therapeutic strategies that target specific cancer-related molecular pathways, including epidermal growth factor receptor (EGFR), angiogenesis, and anaplastic lymphoma kinase inhibitors. Current research is focused on combining targeted therapy with platinum-based chemotherapy in an endeavor to achieve an additional benefit in specific patient populations. Currently, pemetrexed is indicated for use in the first-line, maintenance, and second-line settings for the treatment of nonsquamous NSCLC. The combination of pemetrexed and cisplatin is well tolerated and is the approved standard first-line therapy. Thus, the pemetrexed-platinum backbone provides an attractive option for combination with targeted therapies. This review aims to summarize the current knowledge and future prospects of the use of pemetrexed-platinum as a backbone for combination with targeted therapies for NSCLC. Copyright © 2016 Elsevier Inc. All rights reserved.

Contribution of peptide backbone to Anti-citrulline-dependent antibody reactivity

DEFF Research Database (Denmark)

Trier, Nicole Hartwig; Dam, Catharina; Olsen, Dorthe

2015-01-01

for ACPA reactivity and to be cross-reactive between the selected citrullinated peptides. The remaining amino acids within the citrullinated peptides were found to be of less importance for antibody reactivity. Moreover, these findings indicated that the Cit-Gly motif in combination with peptide backbone...... found in up to 70% of RA patients’ sera, have received much attention. Several citrullinated proteins are associated with RA, suggesting that ACPAs may react with different sequence patterns, separating them from traditional antibodies, whose reactivity usually is specific towards a single target...... homology rather than sequence homology are favored between citrullinated epitopes. These findings are important in relation to clarifying the etiology of RA and to determine the nature of ACPAs, e.g. why some Cit-Gly-containing sequences are not targeted by ACPAs....

On the purported "backbone fluorescence" in protein three-dimensional fluorescence spectra

DEFF Research Database (Denmark)

Bortolotti, Annalisa; Wong, Yin How; Korsholm, Stine S.

2016-01-01

In this study, several proteins (albumin, lysozyme, insulin) and model compounds (Trp, Tyr, homopolypeptides) were used to demonstrate the origin of the fluorescence observed upon their excitation at 220-230 nm. In the last 10 years we have observed a worrying increase in the number of articles...... as any traditional protein emission spectrum. The many papers in reputable journals erroneously reporting this peak assignment, contradicting 5 decades of prior knowledge, have led to the creation of a new dogma, where many authors and reviewers now take the purported backbone fluorescence...... as an established fact. We hope the current paper helps counter this new situation and leads to a reassessment of those papers that make this erroneous claim....

Excited-State Dynamics of Carotenoids Studied by Femtosecond Transient Absorption Spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Lee, Ingu; Pang, Yoonsoo [Department of Physics and Photon Science, Gwangju (Korea, Republic of); Lee, Sebok [Gwangju Institute of Science and Technology, Gwangju (Korea, Republic of)

2014-03-15

Carotenoids, natural antenna pigments in photosynthesis share a symmetric backbone of conjugated polyenes. Contrary to the symmetric and almost planar geometries of carotenoids, excited state structure and dynamics of carotenoids are exceedingly complex. In this paper, recent infrared and visible transient absorption measurements and excitation dependent dynamics of 8'-apo-β-caroten-8'-al and 7',7'-dicyano-7'-apo-β-carotene will be reviewed. The recent visible transient absorption measurements of 8'-apo-β-caroten-8'-al in polar and nonpolar solvents will also be introduced to emphasize the complex excited-state dynamics and unsolved problems in the S{sub 2} and S{sub 1} excited states.

Developing a capillary electrophoresis based method for dynamically monitoring enzyme cleavage activity using quantum dots-peptide assembly.

Science.gov (United States)

Wang, Jianhao; Fan, Jie; Liu, Li; Ding, Shumin; Liu, Xiaoqian; Wang, Jianpeng; Gao, Liqian; Chattopadhaya, Souvik; Miao, Peng; Xia, Jiang; Qiu, Lin; Jiang, Pengju

2017-10-01

Herein, a novel assay has been developed for monitoring PreScission protease (His-PSP) mediated enzyme cleavage of ATTO 590 labeled peptide substrate (ATTO-LEV). This novel method is based on combining the use of capillary electrophoresis and fluorescence detection (CE-FL) to dynamically monitor the enzyme cleavage activity. A multivalent peptide substrate was first constructed by immobilizing His-tagged ATTO 590 labeled peptide substrate (ATTO-LEVH6) onto the surface of CdSe/ZnS quantum dots (QDs). Once successfully immobilized, the novel multivalent peptide substrate resulted in the Förster resonance energy transfer (FRET) from QDs to ATTO 590. The ATTO-LEVH6-QD assembly was then incubated with His-PSP to study the proteolytic cleavage of surface bound ATTO-LEVH6 by CE-FL. Our data suggests that PreScission-mediated proteolytic cleavage is enzyme concentration- and incubation time-dependent. By combining capillary electrophoresis, QDs and FRET, our study herein not only provides a new method for the detection and dynamically monitoring of PSP enzyme cleavage activity, but also can be extended to the detection of many other enzymes and proteases. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Online monitoring of dynamic tip clearance of turbine blades in high temperature environments

Science.gov (United States)

Han, Yu; Zhong, Chong; Zhu, Xiaoliang; Zhe, Jiang

2018-04-01

Minimized tip clearance reduces the gas leakage over turbine blade tips and improves the thrust and efficiency of turbomachinery. An accurate tip clearance sensor, measuring the dynamic clearances between blade tips and the turbine case, is a critical component for tip clearance control. This paper presents a robust inductive tip clearance sensor capable of monitoring dynamic tip clearances of turbine machines in high-temperature environments and at high rotational speeds. The sensor can also self-sense the temperature at a blade tip in situ such that temperature effect on tip clearance measurement can be estimated and compensated. To evaluate the sensor’s performance, the sensor was tested for measuring the tip clearances of turbine blades under various working temperatures ranging from 700 K to 1300 K and at turbine rotational speeds ranging from 3000 to 10 000 rpm. The blade tip clearance was varied from 50 to 2000 µm. The experiment results proved that the sensor can accurately measure the blade tip clearances with a temporal resolution of 10 µm. The capability of accurately measuring the tip clearances at high temperatures (~1300 K) and high turbine rotation speeds (~30 000 rpm), along with its compact size, makes it promising for online monitoring and active control of blade tip clearances of high-temperature turbomachinery.

Dynamic UAV-based traffic monitoring under uncertainty as a stochastic arc-inventory routing policy

Directory of Open Access Journals (Sweden)

Joseph Y.J. Chow

2016-10-01

Full Text Available Given the rapid advances in unmanned aerial vehicles, or drones, and increasing need to monitor at a city level, one of the current research gaps is how to systematically deploy drones over multiple periods. We propose a real-time data-driven approach: we formulate the first deterministic arc-inventory routing problem and derive its stochastic dynamic policy. The policy is expected to be of greatest value in scenarios where uncertainty is highest and costliest, such as city monitoring during major events. The Bellman equation for an approximation of the proposed inventory routing policy is formulated as a selective vehicle routing problem. We propose an approximate dynamic programming algorithm based on Least Squares Monte Carlo simulation to find that policy. The algorithm has been modified so that the least squares dependent variable is defined to be the “expected stock out cost upon the next replenishment”. The new algorithm is tested on 30 simulated instances of real time trajectories over 5 time periods of the selective vehicle routing problem to evaluate the proposed policy and algorithm. Computational results on the selected instances show that the algorithm on average outperforms the myopic policy by 23–28%, depending on the parametric design. Further tests are conducted on classic benchmark arc routing problem instances. The 11-link instance gdb19 (Golden et al., 1983 is expanded into a sequential 15-period stochastic dynamic example and used to demonstrate why a naïve static multi-period deployment plan would not be effective in real networks.

Dynamic Monitoring of Cellular Remodeling Induced by the Transforming Growth Factor-β1

Directory of Open Access Journals (Sweden)

Kubala Lukáš

2009-01-01

Full Text Available Abstract The plasticity of differentiated adult cells could have a great therapeutic potential, but at the same time, it is characteristic of progression of serious pathological states such as cancer and fibrosis. In this study, we report on the application of a real-time noninvasive system for dynamic monitoring of cellular plasticity. Analysis of the cell impedance profile recorded as cell index using a real-time cell analyzer revealed its significant increase after the treatment of prostate epithelial cells with the transforming growth factor-β1. Changes in the cell index profile were paralleled with cytoskeleton rebuilding and induction of epithelial–mesenchymal transition and negatively correlated with cell proliferation. This novel application of such approach demonstrated a great potential of the impedance-based system for noninvasive and real-time monitoring of cellular fate.

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Delaglio, Frank [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Cornilescu, Gabriel [National Magnetic Resonance Facility (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

2009-08-15

NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between {sup 13}C, {sup 15}N and {sup 1}H chemical shifts and backbone torsion angles {phi} and {psi} (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted {phi} and {psi} angles, equals {+-}13{sup o}. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.

Direct current (DC) resistivity and induced polarization (IP) monitoring of active layer dynamics at high temporal resolution

DEFF Research Database (Denmark)

Doetsch, Joseph; Ingeman-Nielsen, Thomas; Christiansen, Anders V.

2015-01-01

With permafrost thawing and changes in active layer dynamics induced by climate change, interactions between biogeochemical and thermal processes in the ground are of great importance. Here, active layer dynamics have been monitored using direct current (DC) resistivity and induced polarization (IP...... in resistivity. While the freezing horizon generally moves deeper with time, some variations in the freezing depth are observed along the profile. Comparison with depth-specific soil temperature indicates an exponential relationship between resistivity and below-freezing temperature. Time-lapse inversions...

Enhanced dynamic wedge and independent monitor unit verification

International Nuclear Information System (INIS)

Howlett, S.J.; University of Newcastle, NSW

2004-01-01

Full text: Some serious radiation accidents have occurred around the world during the delivery of radiotherapy treatment. The regrettable incident in Panama clearly indicated the need for independent monitor unit (MU) verification. Indeed the International Atomic Energy Agency (IAEA), after investigating the incident, made specific recommendations for radiotherapy centres which included an independent monitor unit check for all treatments. Independent monitor unit verification is practiced in many radiotherapy centres in developed countries around the world. It is mandatory in USA but not yet in Australia. The enhanced dynamic wedge factor (EDWF) presents some significant problems in accurate MU calculation, particularly in the case of non centre of field position (COF). This paper describes development of an independent MU program, concentrating on the implementation of the EDW component. The difficult case of non COF points under the EDW was studied in detail. A survey of Australasian centres regarding the use of independent MU check systems was conducted. The MUCalculator was developed with reference to MU calculations made by Pinnacle 3D RTP system (Philips) for 4MV, 6MV and 18MV X-ray beams from Varian machines used at the Newcastle Mater Misericordiae Hospital (NMMH) in the clinical environment. Ionisation chamber measurements in solid water TM and liquid water were performed based on a published test data set. Published algorithms combined with a depth dependent profile correction were applied in an attempt to match measured data with maximum accuracy. The survey results are presented. Substantial data is presented in tabular form and extensive comparison with published data. Several different methods for calculating EDWF are examined. A small systematic error was detected in the Gibbon equation used for the EDW calculations. Generally, calculations were within +2% of measured values, although some setups exceeded this variation. Results indicate that COF

Piezoelectric dynamic strain monitoring for detecting local seismic damage in steel buildings

International Nuclear Information System (INIS)

Kurata, Masahiro; Li, Xiaohua; Fujita, Kohei; Yamaguchi, Mayako

2013-01-01

This research presents a methodology for damage detection along with a sensing system for monitoring seismic damage in steel buildings. The system extracts the location and extent of local damage, such as fracture at a beam–column connection, from changes in the bending moment distribution in a steel moment-resisting frame. We developed a dynamic strain-based sensing system utilizing piezoelectric film sensors and wireless sensing techniques to estimate the bending moments resisted by individual structural members under small amplitude loadings such as ambient vibrations and minor earthquakes. We introduce a new damage index that extracts local damage information from the comparative study of the dynamic strain responses of the structural members before and after a large earthquake event. The damage detection scheme was examined both analytically and numerically using a simple frame example. Then, the entire local damage detection scheme was verified through a series of vibration tests using a one-quarter-scale steel testbed that simulated seismic damage at member ends. (paper)

Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15N or 13C′ chemical shifts of multiple contiguous residues in highly resolved 3D spectra

International Nuclear Information System (INIS)

Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A.

2015-01-01

Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone 1 H N , 15 N H , and 13 C′ resonance assignments to be completed from a single pair of 3D experiments

Postharvest Monitoring of Tomato Ripening Using the Dynamic Laser Speckle

Science.gov (United States)

Pieczywek, Piotr Mariusz; Nowacka, Małgorzata; Dadan, Magdalena; Wiktor, Artur; Rybak, Katarzyna; Witrowa-Rajchert, Dorota; Zdunek, Artur

2018-01-01

The dynamic laser speckle (biospeckle) method was tested as a potential tool for the assessment and monitoring of the maturity stage of tomatoes. Two tomato cultivars—Admiro and Starbuck—were tested. The process of climacteric maturation of tomatoes was monitored during a shelf life storage experiment. The biospeckle phenomena were captured using 640 nm and 830 nm laser light wavelength, and analysed using two activity descriptors based on biospeckle pattern decorrelation—C4 and ε. The well-established optical parameters of tomatoes skin were used as a reference method (luminosity, a*/b*, chroma). Both methods were tested with respect to their prediction capabilities of the maturity and destructive indicators of tomatoes—firmness, chlorophyll and carotenoids content. The statistical significance of the tested relationships were investigated by means of linear regression models. The climacteric maturation of tomato fruit was associated with an increase in biospckle activity. Compared to the 830 nm laser wavelength the biospeckle activity measured at 640 nm enabled more accurate predictions of firmness, chlorophyll and carotenoids content. At 640 nm laser wavelength both activity descriptors (C4 and ε) provided similar results, while at 830 nm the ε showed slightly better performance. The linear regression models showed that biospeckle activity descriptors had a higher correlation with chlorophyll and carotenoids content than the a*/b* ratio and luminosity. The results for chroma were comparable with the results for both biospeckle activity indicators. The biospeckle method showed very good results in terms of maturation monitoring and the prediction of the maturity indices of tomatoes, proving the possibility of practical implementation of this method for the determination of the maturity stage of tomatoes. PMID:29617343

Postharvest Monitoring of Tomato Ripening Using the Dynamic Laser Speckle

Directory of Open Access Journals (Sweden)

Piotr Mariusz Pieczywek

2018-04-01

Full Text Available The dynamic laser speckle (biospeckle method was tested as a potential tool for the assessment and monitoring of the maturity stage of tomatoes. Two tomato cultivars—Admiro and Starbuck—were tested. The process of climacteric maturation of tomatoes was monitored during a shelf life storage experiment. The biospeckle phenomena were captured using 640 nm and 830 nm laser light wavelength, and analysed using two activity descriptors based on biospeckle pattern decorrelation—C4 and ε. The well-established optical parameters of tomatoes skin were used as a reference method (luminosity, a*/b*, chroma. Both methods were tested with respect to their prediction capabilities of the maturity and destructive indicators of tomatoes—firmness, chlorophyll and carotenoids content. The statistical significance of the tested relationships were investigated by means of linear regression models. The climacteric maturation of tomato fruit was associated with an increase in biospckle activity. Compared to the 830 nm laser wavelength the biospeckle activity measured at 640 nm enabled more accurate predictions of firmness, chlorophyll and carotenoids content. At 640 nm laser wavelength both activity descriptors (C4 and ε provided similar results, while at 830 nm the ε showed slightly better performance. The linear regression models showed that biospeckle activity descriptors had a higher correlation with chlorophyll and carotenoids content than the a*/b* ratio and luminosity. The results for chroma were comparable with the results for both biospeckle activity indicators. The biospeckle method showed very good results in terms of maturation monitoring and the prediction of the maturity indices of tomatoes, proving the possibility of practical implementation of this method for the determination of the maturity stage of tomatoes.

Fabrication of nanochannels on polyimide films using dynamic plowing lithography

Science.gov (United States)

Stoica, Iuliana; Barzic, Andreea Irina; Hulubei, Camelia

2017-12-01

Three distinct polyimide films were analyzed from the point of view of their morphology in order to determine if their surface features can be adapted for applications where surface anisotropy is mandatory. Channels of nanometric dimensions were created on surface of the specimens by using a less common atomic force microscopy (AFM) method, namely Dynamic Plowing Lithography (DPL). The changes generated by DPL procedure were monitored through the surface texture and other functional parameters, denoting the surface orientation degree and also bearing and fluid retention properties. The results revealed that in the same nanolithography conditions, the diamine and dianhydride moieties have affected the characteristics of the nanochannels. This was explained based on the aliphatic/aromatic nature of the monomers and the backbone flexibility. The reported data are of great importance in designing custom nanostructures with enhanced anisotropy on surface of polyimide films for liquid crystal orientation or guided cell growth purposes. At the end, to track the effect of the nanolithography process on the tip sharpness, degradation and contamination, the blind tip reconstruction was performed on AFM probe, before and after lithography experiments, using TGT1 test grating AFM image.

Assessment of dynamic and long-term performance of an innovative multi-story timber building via structural monitoring and dynamic testing

Science.gov (United States)

Omenzetter, Piotr; Morris, Hugh; Worth, Margaret; Gaul, Andrew; Jager, Simon; Desgeorges, Yohann

2012-04-01

An innovative three-story timber building, using self-centering, post-tensioned timber shear walls as the main horizontal load resisting system and lightweight non-composite timber-concrete floors, has recently been completed in Nelson, New Zealand. It is expected to be the trailblazer for similar but taller structures to be more widely adopted. Performance based standards require an advanced understanding of building responses and in order to meet the need for in-situ performance data the building has been subjected to forced vibration testing and instrumented for continuous monitoring using a total of approximately 90 data channels to capture its dynamic and long-term responses. The first part of the paper presents a brief discussion of the existing research on the seismic performance of timber frame buildings and footfall induced floor vibrations. An outline of the building structural system, focusing on the novel design solutions, is then discussed. This is followed by the description of the monitoring system. The analysis of monitoring results starts with a discussion of the monitoring of long-term deformations. Next, the assessment of the floor vibration serviceability performance is outlined. Then, the forced vibration tests conducted on the whole building at different construction stages are reviewed. The system identification results from seismic shaking records are also discussed. Finally, updating of a finite element model of the building is conducted.

A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

Energy Technology Data Exchange (ETDEWEB)

Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

2007-01-15

Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the {alpha} and {beta} regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

A Dynamic Programming Model for Optimizing Frequency of Time-Lapse Seismic Monitoring in Geological CO2 Storage

Science.gov (United States)

Bhattacharjya, D.; Mukerji, T.; Mascarenhas, O.; Weyant, J.

2005-12-01

Designing a cost-effective and reliable monitoring program is crucial to the success of any geological CO2 storage project. Effective design entails determining both, the optimal measurement modality, as well as the frequency of monitoring the site. Time-lapse seismic provides the best spatial coverage and resolution for reservoir monitoring. Initial results from Sleipner (Norway) have demonstrated effective monitoring of CO2 plume movement. However, time-lapse seismic is an expensive monitoring technique especially over the long term life of a storage project and should be used judiciously. We present a mathematical model based on dynamic programming that can be used to estimate site-specific optimal frequency of time-lapse surveys. The dynamics of the CO2 sequestration process are simplified and modeled as a four state Markov process with transition probabilities. The states are M: injected CO2 safely migrating within the target zone; L: leakage from the target zone to the adjacent geosphere; R: safe migration after recovery from leakage state; and S: seepage from geosphere to the biosphere. The states are observed only when a monitoring survey is performed. We assume that the system may go to state S only from state L. We also assume that once observed to be in state L, remedial measures are always taken to bring it back to state R. Remediation benefits are captured by calculating the expected penalty if CO2 seeped into the biosphere. There is a trade-off between the conflicting objectives of minimum discounted costs of performing the next time-lapse survey and minimum risk of seepage and its associated costly consequences. A survey performed earlier would spot the leakage earlier. Remediation methods would have been utilized earlier, resulting in savings in costs attributed to excessive seepage. On the other hand, there are also costs for the survey and remedial measures. The problem is solved numerically using Bellman's optimality principal of dynamic

UAV-Assisted Dynamic Clustering of Wireless Sensor Networks for Crop Health Monitoring.

Science.gov (United States)

Uddin, Mohammad Ammad; Mansour, Ali; Jeune, Denis Le; Ayaz, Mohammad; Aggoune, El-Hadi M

2018-02-11

In this study, a crop health monitoring system is developed by using state of the art technologies including wireless sensors and Unmanned Aerial Vehicles (UAVs). Conventionally data is collected from sensor nodes either by fixed base stations or mobile sinks. Mobile sinks are considered a better choice nowadays due to their improved network coverage and energy utilization. Usually, the mobile sink is used in two ways: either it goes for random walk to find the scattered nodes and collect data, or follows a pre-defined path established by the ground network/clusters. Neither of these options is suitable in our scenario due to the factors like dynamic data collection, the strict targeted area required to be scanned, unavailability of a large number of nodes, dynamic path of the UAV, and most importantly, none of these are known in advance. The contribution of this paper is the formation of dynamic runtime clusters of field sensors by considering the above mentioned factors. Furthermore a mechanism (Bayesian classifier) is defined to select best node as cluster head. The proposed system is validated through simulation results, lab and infield experiments using concept devices. The obtained results are encouraging, especially in terms of deployment time, energy, efficiency, throughput and ease of use.

Direct current (DC) resistivity and Induced Polarization (IP) monitoring of active layer dynamics at high temporal resolution

DEFF Research Database (Denmark)

Doetsch, J.; Fiandaca, G.; Ingeman-Nielsen, Thomas

2015-01-01

With permafrost thawing and changes in active layer dynamics induced by climate change, interactions between biogeochemical and thermal processes in the ground are of great importance. Here, active layer dynamics have been monitored using direct current (DC) resistivity and induced polarization (IP...... the soil freezing as a strong increase in resistivity. While the freezing horizon generally moves deeper with time, some variations in the freezing depth are observed along the profile. Comparison with depth-specific soil temperature indicates an exponential relationship between resistivity and below...

Leaky feeder: the communication backbone

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-01-01

The need to communicate with all areas of the underground operation in monitoring the movement of men, materials and vehicles, as well as the optimum performance of conveyor systems, has been effectively met with the installation of a Flexcom leaky feeder cable network at a coliery in Mpumalanga. Installed by the South African subsidiary of Mine Radio Systems (MRS), based in Canada, Flexcom is an RF communications highway for underground mines. The system can provide up to 32 voice/data control channels and up to 16 video channels, all operating simultaneously. The system uses a series of bi-directional amplifiers (or signal boosters) spaced at 350 m intervals along the leaky feeder cable, with branching units and termination units added as required. Communication is possible within 50 m of the leaky feeder cable. MRS has 11 conveyors monitored via the SCADA program at the mine and the system produces reports as required which are accessible via cellphone from anywhere in the world. The wireless monitoring of miners and equipment contributes to mine safety. 3 figs.

Live Zika virus chimeric vaccine candidate based on a yellow fever 17-D attenuated backbone

OpenAIRE

Nougairede, Antoine; Klitting, Raphaelle; Aubry, Fabien; Gilles, Magali; Touret, Franck; De Lamballerie, Xavier

2018-01-01

Zika virus (ZIKV) recently dispersed throughout the tropics and sub-tropics causing epidemics associated with congenital disease and neurological complications. There is currently no commercial vaccine for ZIKV. Here we describe the initial development of a chimeric virus containing the prM/E proteins of a ZIKV epidemic strain incorporated into a yellow fever 17-D attenuated backbone. Using the versatile and rapid ISA (Infectious Subgenomic Amplicons) reverse genetics method, we compared diff...

The role of social capital on trust development and dynamics: Implications for cooperation, monitoring and team performance

NARCIS (Netherlands)

Costa, A.C.; Bijlsma-Frankema, K.M.; de Jong, B.A.

2009-01-01

This study examined the development and dynamics of trust in project teams and explored the relation with cooperation, monitoring and team performance. Two types of teams were distinguished at the start of the projects: low prior social-capital teams (teams composed of members that have no previous

Gas dynamics considerations in a non-invasive profile monitor for charged particle beams

CERN Document Server

Tzoganis, Vasilis; Welsch, Carsten P

2014-01-01

A non-invasive, gas jet-based, beam profile monitor has been developed in the QUASAR Group at the Cockcroft Institute, UK. This allows on-line measurement of the 2-dimensional transverse profile of particle beams with negligible disturbance to either primary beam or accelerator vacuum. The monitor is suitable for use with beams across a wide range of energies and intensities. In this setup a nozzle-skimmer system shapes a thin supersonic gas jet into a curtain. However, the small dimensions of the gas inlet nozzle and subsequent skimmers were shown to be the cause of many operational problems. In this paper, the dynamics of gas jet formation transport and shaping is discussed before an image-processing based alignment technique is introduced. Furthermore, experimental results obtained with a 5 keV electron beam are discussed and the effects of gas stagnation pressure on the acquired beam are presented.

Effects of a vanadium post-metallocene catalyst-induced polymer backbone inhomogeneity on UV oxidative degradation of the resulting polyethylene film

KAUST Repository

Atiqullah, M.; Winston, M. S.; Bercaw, J. E.; Hussain, I.; Fazal, A.; Al-Harthi, M. A.; Emwas, A. H M; Khan, M. J.; Hossaen, A.

2012-01-01

(nm-CopolyPE) with 1-hexene having very low backbone unsaturation. The nm-CopolyPE inhomogeneity was reflected in the distributions of short chain branches, 1-hexene composition, and methylene sequence length. The 1-hexene incorporation

Optimized set of two-dimensional experiments for fast sequential assignment, secondary structure determination, and backbone fold validation of 13C/15N-labelled proteins

International Nuclear Information System (INIS)

Bersch, Beate; Rossy, Emmanuel; Coves, Jacques; Brutscher, Bernhard

2003-01-01

NMR experiments are presented which allow backbone resonance assignment, secondary structure identification, and in favorable cases also molecular fold topology determination from a series of two-dimensional 1 H- 15 N HSQC-like spectra. The 1 H- 15 N correlation peaks are frequency shifted by an amount ± ω X along the 15 N dimension, where ω X is the C α , C β , or H α frequency of the same or the preceding residue. Because of the low dimensionality (2D) of the experiments, high-resolution spectra are obtained in a short overall experimental time. The whole series of seven experiments can be performed in typically less than one day. This approach significantly reduces experimental time when compared to the standard 3D-based methods. The here presented methodology is thus especially appealing in the context of high-throughput NMR studies of protein structure, dynamics or molecular interfaces

Geophysical monitoring of active hydrologic processes as part of the Dynamic Underground Stripping Project

International Nuclear Information System (INIS)

Newmark, R.L.

1992-05-01

Lawrence Livermore National Laboratory, in collaboration with University of California at Berkeley and Lawrence Berkeley Laboratory, is conducting the Dynamic Underground Stripping Project (DUSP), an integrated project demonstrating the use of active thermal techniques to remove subsurface organic contamination. Complementary techniques address a number of environmental restoration problems: (1) steam flood strips organic contaminants from permeable zones, (2) electrical heating drives contaminants from less permeable zones into the more permeable zones from which they can be extracted, and (3) geophysical monitoring tracks and images the progress of the thermal fronts, providing feedback and control of the active processes. The first DUSP phase involved combined steam injection and vapor extraction in a ''clean'' site in the Livermore Valley consisting of unconsolidated alluvial interbeds of clays, sands and gravels. Steam passed rapidly through a high-permeability gravel unit, where in situ temperatures reached 117 degree C. An integrated program of geophysical monitoring was carried out at the Clean Site. We performed electrical resistance tomography (ERT), seismic tomography (crossborehole), induction tomography, passive seismic monitoring, a variety of different temperature measurement techniques and conventional geophysical well logging

Synthesis of branched–backbone oligosaccharides of the pectic RG-I plant cell wall polysaccharide

DEFF Research Database (Denmark)

Awan, Shahid Iqbal; Clausen, Mads Hartvig

with numerous branches of galactan, arabinan, or arabinogalactan positioned at C-4 of the rhamnose residues. The use of defined oligosaccharides rather than isolated polysaccharides can aid in obtaining detailedinformation about biosynthetic pathways, plant evolution, and agronomical properties. Furthermore......,biological testing can provide new insight into plant biology; important for plant preservation, engineering,and utilization of plants as a source of bioenergy. Present work towards defined RG-I substructures involvesa [4+3]-coupling to furnish a heptasaccharide backbone unit (see Figure 1). Moreover, installation...

Investigation of novel solid oxide fuel cell cathodes based on impregnation of SrTixFe1-xO3-δ into ceria-based backbones

DEFF Research Database (Denmark)

Brinch-Larsen, Mathias; Søgaard, Martin; Hjelm, Johan

2013-01-01

Solid oxide fuel cell (SOFC) cathodes were prepared by impregnating the nitrates corresponding to SrTixFe1-xO3-δ (STF), x= 0; 0.1; 0.2; 0.3; 0.4 and 0.5, into a porous backbone of Ce 0.9Gd0.1O2-δ (CGO). STF was chosen as very high oxygen surface exchange rate, high ionic conductivity and electroc......Solid oxide fuel cell (SOFC) cathodes were prepared by impregnating the nitrates corresponding to SrTixFe1-xO3-δ (STF), x= 0; 0.1; 0.2; 0.3; 0.4 and 0.5, into a porous backbone of Ce 0.9Gd0.1O2-δ (CGO). STF was chosen as very high oxygen surface exchange rate, high ionic conductivity...... backbone. All prepared electrodes were characterized as symmetric cells using impedance spectroscopy. Within the investigated series the infiltrate with x = 0.1 (STF10) showed the best performance with an area specific resistance (ASR) of ASR ≈ 6.4 Ω cm2 (STF10) at 600°C in air. The relatively poor...

Near infrared spectroscopy based monitoring of extraction processes of raw material with the help of dynamic predictive modeling

Science.gov (United States)

Wang, Haixia; Suo, Tongchuan; Wu, Xiaolin; Zhang, Yue; Wang, Chunhua; Yu, Heshui; Li, Zheng

2018-03-01

The control of batch-to-batch quality variations remains a challenging task for pharmaceutical industries, e.g., traditional Chinese medicine (TCM) manufacturing. One difficult problem is to produce pharmaceutical products with consistent quality from raw material of large quality variations. In this paper, an integrated methodology combining the near infrared spectroscopy (NIRS) and dynamic predictive modeling is developed for the monitoring and control of the batch extraction process of licorice. With the spectra data in hand, the initial state of the process is firstly estimated with a state-space model to construct a process monitoring strategy for the early detection of variations induced by the initial process inputs such as raw materials. Secondly, the quality property of the end product is predicted at the mid-course during the extraction process with a partial least squares (PLS) model. The batch-end-time (BET) is then adjusted accordingly to minimize the quality variations. In conclusion, our study shows that with the help of the dynamic predictive modeling, NIRS can offer the past and future information of the process, which enables more accurate monitoring and control of process performance and product quality.

Thermoresponsive Poly(2-oxazoline) Molecular Brushes by Living Ionic Polymerization: Kinetic Investigations of Pendant Chain Grafting and Cloud Point Modulation by Backbone and Side Chain Length Variation

KAUST Repository

Zhang, Ning

2012-04-17

Molecular brushes of poly(2-oxazoline)s were prepared by living anionic polymerization of 2-iso-propenyl-2-oxazoline to form the backbone and subsequent living cationic ring-opening polymerization of 2-n- or 2-iso-propyl-2-oxazoline for pendant chain grafting. In situ kinetic studies indicate that the initiation efficiency and polymerization rates are independent from the number of initiator functions per initiator molecule. This was attributed to the high efficiency of oxazolinium salt and the stretched conformation of the backbone, which is caused by the electrostatic repulsion of the oxazolinium moieties along the macroinitiator. The resulting molecular brushes showed thermoresponsive properties, that is, having a defined cloud point (CP). The dependence of the CP as a function of backbone and side chain length as well as concentration was studied. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Trappist: european project dedicated to an open backbone structure for NDT expertise

International Nuclear Information System (INIS)

Nouailhas, B.; Vailhen, O.

1993-01-01

Non Destructive Testing (NDT) on critical components such as the reactor vessel, primary coolant pipes and steam generators have already been, and are still the subject of many development concerning the improvement of measuring techniques, data processing and on site operation. The tools developed for these tests are generally closed, difficult to extend and of proprietary type. Productivity could be increased if an open backbone structure common to several types of test were available. Moreover, these components are generally submitted to a test involving a single method. In certain cases, the produced information is an insufficient basis for drawing up a satisfactory diagnosis: the test operator or expert often faces problems in extracting more information from signals that are generally noisy. It may prove necessary to complete the inspection with another NDT method based on different principles in order to obtain better performances. It is then by combining the information obtained by two complementary methods that it will be possible to draw up a more reliable diagnosis. These components have also a complex shape. In the case of ultrasonic testing, the accurate following of probe paths requires 3D representation of the geometry, as it is built, to position and display the data obtained from the inspection. To take these geometric constraints into account, it is imperative to use computer tools allowing the three-dimensional representation of the reconstructed information on the components' actual geometry. This specific difficulty, which has long been appreciated, is the subject of developments resulting to industrial products that are more or less satisfactory. The aim of the European Project TRAPPIST (Race Program) is to study an open backbone structure. A mock-up of an analysis station dedicated to NDT expertise will be built and evaluated with specific examples. (authors). 6 figs., 1 ref

Hydration dynamics near a model protein surface

International Nuclear Information System (INIS)

Russo, Daniela; Hura, Greg; Head-Gordon, Teresa

2003-01-01

The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering and molecular dynamics simulation for both the completely deuterated and completely hydrogenated leucine monomer. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational water dynamics are analyzed in a first approximation with a jump diffusion model. At the highest solute concentrations, the hydration water dynamics is significantly suppressed and characterized by a long residential time and a slow diffusion coefficient. The analysis of the more dilute concentration solutions takes into account the results of the 2.0M solution as a model of the first hydration shell. Subtracting the first hydration layer based on the 2.0M spectra, the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis shows spatially heterogeneous dynamics at high concentration that becomes homogeneous at more dilute concentrations. We discuss the hydration dynamics results of this model protein system in the context of glassy systems, protein function, and protein-protein interfaces

40-Gbps optical backbone network deep packet inspection based on FPGA

Science.gov (United States)

Zuo, Yuan; Huang, Zhiping; Su, Shaojing

2014-11-01

In the era of information, the big data, which contains huge information, brings about some problems, such as high speed transmission, storage and real-time analysis and process. As the important media for data transmission, the Internet is the significant part for big data processing research. With the large-scale usage of the Internet, the data streaming of network is increasing rapidly. The speed level in the main fiber optic communication of the present has reached 40Gbps, even 100Gbps, therefore data on the optical backbone network shows some features of massive data. Generally, data services are provided via IP packets on the optical backbone network, which is constituted with SDH (Synchronous Digital Hierarchy). Hence this method that IP packets are directly mapped into SDH payload is named POS (Packet over SDH) technology. Aiming at the problems of real time process of high speed massive data, this paper designs a process system platform based on ATCA for 40Gbps POS signal data stream recognition and packet content capture, which employs the FPGA as the CPU. This platform offers pre-processing of clustering algorithms, service traffic identification and data mining for the following big data storage and analysis with high efficiency. Also, the operational procedure is proposed in this paper. Four channels of 10Gbps POS signal decomposed by the analysis module, which chooses FPGA as the kernel, are inputted to the flow classification module and the pattern matching component based on TCAM. Based on the properties of the length of payload and net flows, buffer management is added to the platform to keep the key flow information. According to data stream analysis, DPI (deep packet inspection) and flow balance distribute, the signal is transmitted to the backend machine through the giga Ethernet ports on back board. Practice shows that the proposed platform is superior to the traditional applications based on ASIC and NP.

Numerical methods in multibody dynamics

CERN Document Server

Eich-Soellner, Edda

1998-01-01

Today computers play an important role in the development of complex mechanical systems, such as cars, railway vehicles or machines. Efficient simulation of these systems is only possible when based on methods that explore the strong link between numerics and computational mechanics. This book gives insight into modern techniques of numerical mathematics in the light of an interesting field of applications: multibody dynamics. The important interaction between modeling and solution techniques is demonstrated by using a simplified multibody model of a truck. Different versions of this mechanical model illustrate all key concepts in static and dynamic analysis as well as in parameter identification. The book focuses in particular on constrained mechanical systems. Their formulation in terms of differential-algebraic equations is the backbone of nearly all chapters. The book is written for students and teachers in numerical analysis and mechanical engineering as well as for engineers in industrial research labor...

Control of polymer-packing orientation in thin films through synthetic tailoring of backbone coplanarity

KAUST Repository

Chen, Mark S.

2013-10-22

Controlling solid-state order of π-conjugated polymers through macromolecular design is essential for achieving high electronic device performance; yet, it remains a challenge, especially with respect to polymer-packing orientation. Our work investigates the influence of backbone coplanarity on a polymer\\'s preference to pack face-on or edge-on relative to the substrate. Isoindigo-based polymers were synthesized with increasing planarity by systematically substituting thiophenes for phenyl rings in the acceptor comonomer. This increasing backbone coplanarity, supported by density functional theory (DFT) calculations of representative trimers, leads to the narrowing of polymer band gaps as characterized by ultraviolet-visible-near infrared (UV-vis-NIR) spectroscopy and cyclic voltammetry. Among the polymers studied, regiosymmetric II and TII polymers exhibited the highest hole mobilities in organic field-effect transistors (OFETs), while in organic photovoltaics (OPVs), TBII polymers that display intermediate levels of planarity provided the highest power conversion efficiencies. Upon thin-film analysis by atomic force microscropy (AFM) and grazing-incidence X-ray diffraction (GIXD), we discovered that polymer-packing orientation could be controlled by tuning polymer planarity and solubility. Highly soluble, planar polymers favor face-on orientation in thin films while the less soluble, nonplanar polymers favor an edge-on orientation. This study advances our fundamental understanding of how polymer structure influences nanostructural order and reveals a new synthetic strategy for the design of semiconducting materials with rationally engineered solid-state properties. © 2013 American Chemical Society.

Towards Quantification of Glacier Dynamic Ice Loss through Passive Seismic Monitoring

Science.gov (United States)

Köhler, A.; Nuth, C.; Weidle, C.; Schweitzer, J.; Kohler, J.; Buscaino, G.

2015-12-01

Global glaciers and ice caps loose mass through calving, while existing models are currently not equipped to realistically predict dynamic ice loss. This is mainly because long-term continuous calving records, that would help to better understand fine scale processes and key climatic-dynamic feedbacks between calving, climate, terminus evolution and marine conditions, do not exist. Combined passive seismic/acoustic strategies are the only technique able to capture rapid calving events continuously, independent of daylight or meteorological conditions. We have produced such a continuous calving record for Kronebreen, a tidewater glacier in Svalbard, using data from permanent seismic stations between 2001 and 2014. However, currently no method has been established in cryo-seismology to quantify the calving ice loss directly from seismic data. Independent calibration data is required to derive 1) a realistic estimation of the dynamic ice loss unobserved due to seismic noise and 2) a robust scaling of seismic calving signals to ice volumes. Here, we analyze the seismic calving record at Kronebreen and independent calving data in a first attempt to quantify ice loss directly from seismic records. We make use of a) calving flux data with weekly to monthly resolution obtained from satellite remote sensing and GPS data between 2007 and 2013, and b) direct, visual calving observations in two weeks in 2009 and 2010. Furthermore, the magnitude-scaling property of seismic calving events is analyzed. We derive and discuss an empirical relation between seismic calving events and calving flux which for the first time allows to estimate a time series of calving volumes more than one decade back in time. Improving our model requires to incorporate more precise, high-resolution calibration data. A new field campaign will combine innovative, multi-disciplinary monitoring techniques to measure calving ice volumes and dynamic ice-ocean interactions simultaneously with terrestrial laser

An integrated, multisensor system for the continuous monitoring of water dynamics in rice fields under different irrigation regimes.

Science.gov (United States)

Chiaradia, Enrico Antonio; Facchi, Arianna; Masseroni, Daniele; Ferrari, Daniele; Bischetti, Gian Battista; Gharsallah, Olfa; Cesari de Maria, Sandra; Rienzner, Michele; Naldi, Ezio; Romani, Marco; Gandolfi, Claudio

2015-09-01

The cultivation of rice, one of the most important staple crops worldwide, has very high water requirements. A variety of irrigation practices are applied, whose pros and cons, both in terms of water productivity and of their effects on the environment, are not completely understood yet. The continuous monitoring of irrigation and rainfall inputs, as well as of soil water dynamics, is a very important factor in the analysis of these practices. At the same time, however, it represents a challenging and costly task because of the complexity of the processes involved, of the difference in nature and magnitude of the driving variables and of the high variety of field conditions. In this paper, we present the prototype of an integrated, multisensor system for the continuous monitoring of water dynamics in rice fields under different irrigation regimes. The system consists of the following: (1) flow measurement devices for the monitoring of irrigation supply and tailwater drainage; (2) piezometers for groundwater level monitoring; (3) level gauges for monitoring the flooding depth; (4) multilevel tensiometers and moisture sensor clusters to monitor soil water status; (5) eddy covariance station for the estimation of evapotranspiration fluxes and (6) wireless transmission devices and software interface for data transfer, storage and control from remote computer. The system is modular and it is replicable in different field conditions. It was successfully applied over a 2-year period in three experimental plots in Northern Italy, each one with a different water management strategy. In the paper, we present information concerning the different instruments selected, their interconnections and their integration in a common remote control scheme. We also provide considerations and figures on the material and labour costs of the installation and management of the system.

Oral dosing of chemical indicators for in vivo monitoring of Ca2+ dynamics in insect muscle.

Directory of Open Access Journals (Sweden)

Ferdinandus

Full Text Available This paper proposes a remarkably facile staining protocol to visually investigate dynamic physiological events in insect tissues. We attempted to monitor Ca2+ dynamics during contraction of electrically stimulated living muscle. Advances in circuit miniaturization and insect neuromuscular physiology have enabled the hybridization of living insects and man-made electronic components, such as microcomputers, the result of which has been often referred as a Living Machine, Biohybrid, or Cyborg Insect. In order for Cyborg Insects to be of practical use, electrical stimulation parameters need to be optimized to induce desired muscle response (motor action and minimize the damage in the muscle due to the electrical stimuli. Staining tissues and organs as well as measuring the dynamics of chemicals of interest in muscle should be conducted to quantitatively and systematically evaluate the effect of various stimulation parameters on the muscle response. However, existing staining processes require invasive surgery and/or arduous procedures using genetically encoded sensors. In this study, we developed a non-invasive and remarkably facile method for staining, in which chemical indicators can be orally administered (oral dosing. A chemical Ca2+ indicator was orally introduced into an insect of interest via food containing the chemical indicator and the indicator diffused from the insect digestion system to the target muscle tissue. We found that there was a positive relationship between the fluorescence intensity of the indicator and the frequency of electrical stimulation which indicates the orally dosed indicator successfully monitored Ca2+ dynamics in the muscle tissue. This oral dosing method has a potential to globally stain tissues including neurons, and investigating various physiological events in insects.

Oral dosing of chemical indicators for in vivo monitoring of Ca2+ dynamics in insect muscle.

Science.gov (United States)

Ferdinandus; Arai, Satoshi; Ishiwata, Shin'ichi; Suzuki, Madoka; Sato, Hirotaka

2015-01-01

This paper proposes a remarkably facile staining protocol to visually investigate dynamic physiological events in insect tissues. We attempted to monitor Ca2+ dynamics during contraction of electrically stimulated living muscle. Advances in circuit miniaturization and insect neuromuscular physiology have enabled the hybridization of living insects and man-made electronic components, such as microcomputers, the result of which has been often referred as a Living Machine, Biohybrid, or Cyborg Insect. In order for Cyborg Insects to be of practical use, electrical stimulation parameters need to be optimized to induce desired muscle response (motor action) and minimize the damage in the muscle due to the electrical stimuli. Staining tissues and organs as well as measuring the dynamics of chemicals of interest in muscle should be conducted to quantitatively and systematically evaluate the effect of various stimulation parameters on the muscle response. However, existing staining processes require invasive surgery and/or arduous procedures using genetically encoded sensors. In this study, we developed a non-invasive and remarkably facile method for staining, in which chemical indicators can be orally administered (oral dosing). A chemical Ca2+ indicator was orally introduced into an insect of interest via food containing the chemical indicator and the indicator diffused from the insect digestion system to the target muscle tissue. We found that there was a positive relationship between the fluorescence intensity of the indicator and the frequency of electrical stimulation which indicates the orally dosed indicator successfully monitored Ca2+ dynamics in the muscle tissue. This oral dosing method has a potential to globally stain tissues including neurons, and investigating various physiological events in insects.

Remote sensing techniques to monitor nitrogen-driven carbon dynamics in field corn

Science.gov (United States)

Corp, Lawrence A.; Middleton, Elizabeth M.; Campbell, Petya K. E.; Huemmrich, K. Fred; Cheng, Yen-Ben; Daughtry, Craig S. T.

2009-08-01

Patterns of change in vegetation growth and condition are one of the primary indicators of the present and future ecological status of the globe. Nitrogen (N) is involved in photochemical processes and is one of the primary resources regulating plant growth. As a result, biological carbon (C) sequestration is driven by N availability. Large scale monitoring of photosynthetic processes are currently possible only with remote sensing systems that rely heavily on passive reflectance (R) information. Unlike R, fluorescence (F) emitted from chlorophyll is directly related to photochemical reactions and has been extensively used for the elucidation of the photosynthetic pathways. Recent advances in passive fluorescence instrumentation have made the remote acquisition of solar-induced fluorescence possible. The goal of this effort is to evaluate existing reflectance and emerging fluorescence methodologies for determining vegetation parameters related to photosynthetic function and carbon sequestration dynamics in plants. Field corn N treatment levels of 280, 140, 70, and 0 kg N / ha were sampled from an intensive test site for a multi-disciplinary project, Optimizing Production Inputs for Economic and Environmental Enhancement (OPE). Aircraft, near-ground, and leaf-level measurements were used to compare and contrast treatment effects within this experiment site assessed with both reflectance and fluorescence approaches. A number of spectral indices including the R derivative index D730/D705, the normalized difference of R750 vs. R705, and simple ratio R800/R750 differentiated three of the four N fertilization rates and yielded high correlations to three important carbon parameters: C:N, light use efficiency, and grain yield. These results advocate the application of hyperspectral sensors for remotely monitoring carbon cycle dynamics in terrestrial ecosystems.

The impact of kosmotropes and chaotropes on bulk and hydration shell water dynamics in a model peptide solution

International Nuclear Information System (INIS)

Russo, Daniela

2008-01-01

Kosmotropic (order-making) and chaotropic (order-breaking) co-solvents influence stability and biochemical equilibrium in aqueous solutions of proteins, acting indirectly through the structure and dynamics of the hydration water that surrounds the protein molecules. We have investigated the influence of kosmotropic and chaotropic co-solvents on the hydrogen bonding network dynamics of both bulk water and hydration water. To this end the evolution of bulk water and hydration water dynamics of a prototypical hydrophobic amino acid with polar backbone, N-acetyl-leucine-methylamide (NALMA), has been studied by quasielastic neutron scattering as a function of solvent composition. The results show that bulk water and hydration water dynamics, apart from a dynamical suppression that depends on the NALMA solute, exhibit the same dependence on addition of co-solvent for all of the co-solvents studied (urea, glycerol, MgSO 4 , and dimethyl sulfoxide). The hydrophobic solute and the high concentration water-structuring additive have the same effect on the water hydrogen bonding network. Water remains the preferential hydration of the hydrophobic side chain and backbone. We also find that the reorganization of the bulk water hydrogen bond network, upon addition of kosmotrope and chaotrope additives, is not dynamically perturbed, and that the hydrogen bond lifetime is maintained at 1 ps as in pure bulk water. On the other hand the addition of NALMA to the water/co-solvent binary system causes reorganization of the hydrogen bonds, resulting in an increased hydrogen bond lifetime. Furthermore, the solute's side chain dynamics is not affected by high concentrations of co-solvent. We shall discuss the hydration dynamics results in the context of protein folding and protein-solvent interactions

Contamination Event Detection with Multivariate Time-Series Data in Agricultural Water Monitoring

Directory of Open Access Journals (Sweden)

Yingchi Mao

2017-12-01

Full Text Available Time series data of multiple water quality parameters are obtained from the water sensor networks deployed in the agricultural water supply network. The accurate and efficient detection and warning of contamination events to prevent pollution from spreading is one of the most important issues when pollution occurs. In order to comprehensively reduce the event detection deviation, a spatial–temporal-based event detection approach with multivariate time-series data for water quality monitoring (M-STED was proposed. The M-STED approach includes three parts. The first part is that M-STED adopts a Rule K algorithm to select backbone nodes as the nodes in the CDS, and forward the sensed data of multiple water parameters. The second part is to determine the state of each backbone node with back propagation neural network models and the sequential Bayesian analysis in the current timestamp. The third part is to establish a spatial model with Bayesian networks to estimate the state of the backbones in the next timestamp and trace the “outlier” node to its neighborhoods to detect a contamination event. The experimental results indicate that the average detection rate is more than 80% with M-STED and the false detection rate is lower than 9%, respectively. The M-STED approach can improve the rate of detection by about 40% and reduce the false alarm rate by about 45%, compared with the event detection with a single water parameter algorithm, S-STED. Moreover, the proposed M-STED can exhibit better performance in terms of detection delay and scalability.

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2007-01-01

Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ 1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ 1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C', respectively, including outliers

Free vibration analysis of a robotic fish based on a continuous and non-uniform flexible backbone with distributed masses

Science.gov (United States)

Coral, W.; Rossi, C.; Curet, O. M.

2015-12-01

This paper presents a Differential Quadrature Element Method for free transverse vibration of a robotic fish based on a continuous and non-uniform flexible backbone with distributed masses (fish ribs). The proposed method is based on the theory of a Timoshenko cantilever beam. The effects of the masses (number, magnitude and position) on the value of natural frequencies are investigated. Governing equations, compatibility and boundary conditions are formulated according to the Differential Quadrature rules. The convergence, efficiency and accuracy are compared to other analytical solution proposed in the literature. Moreover, the proposed method has been validate against the physical prototype of a flexible fish backbone. The main advantages of this method, compared to the exact solutions available in the literature are twofold: first, smaller computational cost and second, it allows analysing the free vibration in beams whose section is an arbitrary function, which is normally difficult or even impossible with other analytical methods.

Imaging groundwater infiltration dynamics in the karst vadose zone with long-term ERT monitoring

Science.gov (United States)

Watlet, Arnaud; Kaufmann, Olivier; Triantafyllou, Antoine; Poulain, Amaël; Chambers, Jonathan E.; Meldrum, Philip I.; Wilkinson, Paul B.; Hallet, Vincent; Quinif, Yves; Van Ruymbeke, Michel; Van Camp, Michel

2018-03-01

Water infiltration and recharge processes in karst systems are complex and difficult to measure with conventional hydrological methods. In particular, temporarily saturated groundwater reservoirs hosted in the vadose zone can play a buffering role in water infiltration. This results from the pronounced porosity and permeability contrasts created by local karstification processes of carbonate rocks. Analyses of time-lapse 2-D geoelectrical imaging over a period of 3 years at the Rochefort Cave Laboratory (RCL) site in south Belgium highlight variable hydrodynamics in a karst vadose zone. This represents the first long-term and permanently installed electrical resistivity tomography (ERT) monitoring in a karst landscape. The collected data were compared to conventional hydrological measurements (drip discharge monitoring, soil moisture and water conductivity data sets) and a detailed structural analysis of the local geological structures providing a thorough understanding of the groundwater infiltration. Seasonal changes affect all the imaged areas leading to increases in resistivity in spring and summer attributed to enhanced evapotranspiration, whereas winter is characterised by a general decrease in resistivity associated with a groundwater recharge of the vadose zone. Three types of hydrological dynamics, corresponding to areas with distinct lithological and structural features, could be identified via changes in resistivity: (D1) upper conductive layers, associated with clay-rich soil and epikarst, showing the highest variability related to weather conditions; (D2) deeper and more resistive limestone areas, characterised by variable degrees of porosity and clay contents, hence showing more diffuse seasonal variations; and (D3) a conductive fractured zone associated with damped seasonal dynamics, while showing a great variability similar to that of the upper layers in response to rainfall events. This study provides detailed images of the sources of drip

Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3

International Nuclear Information System (INIS)

Diehl, Carl; Genheden, Samuel; Modig, Kristofer; Ryde, Ulf; Akke, Mikael

2009-01-01

The conformational entropy of proteins can make significant contributions to the free energy of ligand binding. NMR spin relaxation enables site-specific investigation of conformational entropy, via order parameters that parameterize local reorientational fluctuations of rank-2 tensors. Here we have probed the conformational entropy of lactose binding to the carbohydrate recognition domain of galectin-3 (Gal3), a protein that plays an important role in cell growth, cell differentiation, cell cycle regulation, and apoptosis, making it a potential target for therapeutic intervention in inflammation and cancer. We used 15 N spin relaxation experiments and molecular dynamics simulations to monitor the backbone amides and secondary amines of the tryptophan and arginine side chains in the ligand-free and lactose-bound states of Gal3. Overall, we observe good agreement between the experimental and computed order parameters of the ligand-free and lactose-bound states. Thus, the 15 N spin relaxation data indicate that the molecular dynamics simulations provide reliable information on the conformational entropy of the binding process. The molecular dynamics simulations reveal a correlation between the simulated order parameters and residue-specific backbone entropy, re-emphasizing that order parameters provide useful estimates of local conformational entropy. The present results show that the protein backbone exhibits an increase in conformational entropy upon binding lactose, without any accompanying structural changes

Dynamic covalent chemistry of bisimines at the solid/liquid interface monitored by scanning tunnelling microscopy.

Science.gov (United States)

Ciesielski, Artur; El Garah, Mohamed; Haar, Sébastien; Kovaříček, Petr; Lehn, Jean-Marie; Samorì, Paolo

2014-11-01

Dynamic covalent chemistry relies on the formation of reversible covalent bonds under thermodynamic control to generate dynamic combinatorial libraries. It provides access to numerous types of complex functional architectures, and thereby targets several technologically relevant applications, such as in drug discovery, (bio)sensing and dynamic materials. In liquid media it was proved that by taking advantage of the reversible nature of the bond formation it is possible to combine the error-correction capacity of supramolecular chemistry with the robustness of covalent bonding to generate adaptive systems. Here we show that double imine formation between 4-(hexadecyloxy)benzaldehyde and different α,ω-diamines as well as reversible bistransimination reactions can be achieved at the solid/liquid interface, as monitored on the submolecular scale by in situ scanning tunnelling microscopy imaging. Our modular approach enables the structurally controlled reversible incorporation of various molecular components to form sophisticated covalent architectures, which opens up perspectives towards responsive multicomponent two-dimensional materials and devices.

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

Science.gov (United States)

Kamisetty, Hetunandan; Bailey-Kellogg, Chris; Pandurangan, Gopal

2006-01-15

Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were 'close enough'. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for alpha-helices and beta-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise. This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental beta-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to

(nBuCp)2ZrCl2-catalyzed Ethylene-4M1P Copolymerization: Copolymer Backbone Structure, Melt Behavior, and Crystallization

KAUST Repository

Atiqullah, Muhammad; Adamu, Sagir; Malaibari, Zuhair O.; Al-Harthi, Mamdouh A.; Emwas, Abdul-Hamid M.

2016-01-01

The judicious design of methylaluminoxane (MAO) anions expands the scope for developing industrial metallocene catalysts. Therefore, the effects of MAO anion design on the backbone structure, melt behavior, and crystallization of ethylene−4-methyl-1

Remote consultation and diagnosis in medical imaging using a global PACS backbone network

Science.gov (United States)

Martinez, Ralph; Sutaria, Bijal N.; Kim, Jinman; Nam, Jiseung

1993-10-01

A Global PACS is a national network which interconnects several PACS networks at medical and hospital complexes using a national backbone network. A Global PACS environment enables new and beneficial operations between radiologists and physicians, when they are located in different geographical locations. One operation allows the radiologist to view the same image folder at both Local and Remote sites so that a diagnosis can be performed. The paper describes the user interface, database management, and network communication software which has been developed in the Computer Engineering Research Laboratory and Radiology Research Laboratory. Specifically, a design for a file management system in a distributed environment is presented. In the remote consultation and diagnosis operation, a set of images is requested from the database archive system and sent to the Local and Remote workstation sites on the Global PACS network. Viewing the same images, the radiologists use pointing overlay commands, or frames to point out features on the images. Each workstation transfers these frames, to the other workstation, so that an interactive session for diagnosis takes place. In this phase, we use fixed frames and variable size frames, used to outline an object. The data pockets for these frames traverses the national backbone in real-time. We accomplish this feature by using TCP/IP protocol sockets for communications. The remote consultation and diagnosis operation has been tested in real-time between the University Medical Center and the Bowman Gray School of Medicine at Wake Forest University, over the Internet. In this paper, we show the feasibility of the operation in a Global PACS environment. Future improvements to the system will include real-time voice and interactive compressed video scenarios.

Use of Landsat thermal imagery for dynamically monitoring spontaneous combustion of Datong Jurassic coalfields in China

Science.gov (United States)

Xue, Yongan; Liu, Jin; Li, Jun; Shang, Changsheng; Zhao, Jinling; Zhang, Mingmei

2018-06-01

It is highly helpful and necessary to investigate and monitor the status of coal seam. Fortunately, remote sensing has facilitated the identification and dynamical monitoring of spontaneous combustion for a large area coal mining area, especially using the time series remotely-sensed datasets. In this paper, Datong Jurassic coal mining area is used as the study area, China, and an exclusion method and a multiple-factor analysis method are jointly used to identify the spontaneous combustion, including land surface temperature (LST), burnt rocks, and land use and land cover change (LUCC). The LST is firstly retrieved using a single-window algorithm due to a thermal infrared band of Landsat-5 TM (Thematic Mapper). Burnt rocks is then extracted using a decision-tree classification method based on a high-resolution SPOT-5 image. The thermal anomaly areas are identified and refined by the spatial overlay analysis of the above affecting factors. Three-period maps of coal fire areas are obtained and dynamically analyzed in 2007, 2009 and 2010. The results show that a total of 12 coal fire areas have been identified, which account for more than 1% of the total area of the study area. In general, there is an increasing trend yearly and a total of 771,970 m2 is increased. The average annual increase is 257,320 m2, the average annual growth rate is 3.78%, and the dynamic degree is 11.29%.

Effects of a vanadium post-metallocene catalyst-induced polymer backbone inhomogeneity on UV oxidative degradation of the resulting polyethylene film

KAUST Repository

Atiqullah, M.

2012-07-01

A Group 5 post-metallocene precatalyst, (ONO)VCl(THF) 2 (ONO = a bis(phenolate)pyridine LX 2 pincer ligand), activated with modified methylaluminoxane (MMAO-3A) produced a linear ethylene homopolymer (nm-HomoPE)and an unusual inhomogeneous copolymer (nm-CopolyPE) with 1-hexene having very low backbone unsaturation. The nm-CopolyPE inhomogeneity was reflected in the distributions of short chain branches, 1-hexene composition, and methylene sequence length. The 1-hexene incorporation into the polyethylene backbone strongly depended on the molecular weight of the growing polymer chain. (ONO)VCl(THF) 2, because of site diversity and easier removal of a tertiary (vs. a secondary) hydrogen, produced a skewed short chain branching (SCB) profile, incorporating 1-hexene more efficiently in the low molecular weight region than in the high molecular weight region. The significant decrease in molecular weight by 1-hexene showed that the (ONO)VCl(THF) 2 catalytic sites were also highly responsive to chain-transfer directly to 1-hexene itself, producing vinyl and trans-vinylene termini. Subsequently, the effect of backbone inhomogeneity on the UV oxidative degradation of films made from both polyethylenes was investigated. The major functional group accumulated in the branched nm-CopolyPE film was carbonyl followed by carboxyl, then vinyl/ester, whereas that in the linear nm-HomoPE film was carboxyl. However, (carbonyl, carboxyl, vinyl, and ester) nm-CopolyPE film >> (carboxyl) nm-HomoPE film). The distributions of the tertiary C-H sites and methylene sequence length in the branched nm-CopolyPE film enhanced abstraction of H, decomposition of hydroperoxide group ROOH, and generation of carbonyl compounds as compared with those in the linear nm-HomoPE film. This clearly establishes the role played by the backbone inhomogeneity. The effect of short chain branches and sequence length distributions on peak melting temperature T pm, and most probably lamellar thickness L o, was

Cardiorespiratory dynamics measured from continuous ECG monitoring improves detection of deterioration in acute care patients: A retrospective cohort study

Science.gov (United States)

Clark, Matthew T.; Calland, James Forrest; Enfield, Kyle B.; Voss, John D.; Lake, Douglas E.; Moorman, J. Randall

2017-01-01

Background Charted vital signs and laboratory results represent intermittent samples of a patient’s dynamic physiologic state and have been used to calculate early warning scores to identify patients at risk of clinical deterioration. We hypothesized that the addition of cardiorespiratory dynamics measured from continuous electrocardiography (ECG) monitoring to intermittently sampled data improves the predictive validity of models trained to detect clinical deterioration prior to intensive care unit (ICU) transfer or unanticipated death. Methods and findings We analyzed 63 patient-years of ECG data from 8,105 acute care patient admissions at a tertiary care academic medical center. We developed models to predict deterioration resulting in ICU transfer or unanticipated death within the next 24 hours using either vital signs, laboratory results, or cardiorespiratory dynamics from continuous ECG monitoring and also evaluated models using all available data sources. We calculated the predictive validity (C-statistic), the net reclassification improvement, and the probability of achieving the difference in likelihood ratio χ2 for the additional degrees of freedom. The primary outcome occurred 755 times in 586 admissions (7%). We analyzed 395 clinical deteriorations with continuous ECG data in the 24 hours prior to an event. Using only continuous ECG measures resulted in a C-statistic of 0.65, similar to models using only laboratory results and vital signs (0.63 and 0.69 respectively). Addition of continuous ECG measures to models using conventional measurements improved the C-statistic by 0.01 and 0.07; a model integrating all data sources had a C-statistic of 0.73 with categorical net reclassification improvement of 0.09 for a change of 1 decile in risk. The difference in likelihood ratio χ2 between integrated models with and without cardiorespiratory dynamics was 2158 (p value: <0.001). Conclusions Cardiorespiratory dynamics from continuous ECG monitoring detect

The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone.

Science.gov (United States)

Kumar, Pawan; Sharma, Pawan K; Madsen, Charlotte S; Petersen, Michael; Nielsen, Poul

2013-06-17

Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A review on sustainable construction management strategies for monitoring, diagnosing, and retrofitting the building’s dynamic energy performance: Focused on the operation and maintenance phase

International Nuclear Information System (INIS)

Hong, Taehoon; Koo, Choongwan; Kim, Jimin; Lee, Minhyun; Jeong, Kwangbok

2015-01-01

Highlights: • This study reviews the state-of-the-art in “energy” as well as “building”. • Building’s dynamic energy performance should be managed in the built environments. • This study summarizes recent progress in the building’s dynamic energy performance. • The major phases can be categorized into monitoring, diagnosing, and retrofitting. • This study proposes the specific future development directions and challenges by phase. - Abstract: According to a press release, the building sector accounts for about 40% of the global primary energy consumption. Energy savings can be achieved in the building sector by improving the building’s dynamic energy performance in terms of sustainable construction management in the urban-based built environments (referred to as an “Urban Organism”). This study implements the concept of “dynamic approach” to reflect the unexpected changes in the climate and energy environments as well as in the energy policies and technologies. Research in this area is very significant for the future of the building, energy, and environmental industries around the world. However, there is a lack of studies from the perspective of the dynamic approach and the system integration, and thus, this study is designed to fill the research gap. This study highlights the state-of-the-art in the major phases for a building’s dynamic energy performance (i.e., monitoring, diagnosing, and retrofitting phases), focusing on the operation and maintenance phase. This study covers a wide range of research works and provides various illustrative examples of the monitoring, diagnosing, and retrofitting of a building’s dynamic energy performance. Finally, this study proposes the specific future developments and challenges by phase and suggests the future direction of system integration for the development of a carbon-integrated management system as a large complex system. It is expected that researchers and practitioners can

Spectral dynamics in the B800 band of LH2 from Rhodospirillum molischianum: a single-molecule study

International Nuclear Information System (INIS)

Hofmann, Clemens; Aartsma, Thijs J; Michel, Hartmut; Koehler, Juergen

2004-01-01

The BChl a absorptions in the B800 spectrum of individual LH2 complexes from Rhodospirillum molischianum show sudden, reversible spectral jumps between a finite number of spectral positions. From our data, we conclude that these fluctuations result from conformational changes of the protein backbone in close vicinity of the chromophores which provides a sensitive tool to monitor local modulations of the pigment-protein interaction

Probing charge transfer dynamics in self-assembled monolayers by core hole clock approach

International Nuclear Information System (INIS)

Zharnikov, Michael

2015-01-01

This article reviews recent progress in the application of core hole clock approach in the framework of resonant Auger electron spectroscopy to the monomolecular assembles of alkyl, oligophenyl, and oligo(phenylene–ethynylene) based molecules on Au(1 1 1) substrates, referring mostly to the work by the author et al. The major goal was to study electron transfer (ET) dynamics in these systems serving as prototypes of molecular electronics (ME) devices. The ET pathway to the conductive substrate was unambiguously defined by resonant excitation of the nitrile tailgroup attached to the molecular backbone. Characteristic ET times within the femtosecond domain were determined, along with the attenuation factors for the ET dynamics, analogous to the case of the static transport. The above parameters were found to exhibit strong dependence on the character of the molecular orbital which mediates the ET process. In addition, certain spectral features, which can be associated with an inverse ET from the molecular backbone to the excitation site, were observed upon exchange of the nitrile group by strongly electronegative nitro moiety. The reported results represent a valuable input for theory and a certain potential for applications such as ME devices where optimization of ET can have significant technological impact.

Monitoring of brown stink bug (Hemiptera: Pentatomidae) population dynamics in corn to predict its abundance using weather data

Science.gov (United States)

The brown stink bug (BSB), Euschistus servus (Say) (Hemiptera: Pentatomidae), is a serious economic pest of corn production in the Southeastern U. S. The BSB population dynamics was monitored for 17 wks from tasseling to pre-harvest of corn plants (i.e., late May to mid-September) using pheromone ...

Dynamic monitoring equipment for earthworks and sub grades; Euipos de auscultacion dinamica para obras de tierra

Energy Technology Data Exchange (ETDEWEB)

Alvarez de Sotomayor, R.

2013-06-01

This paper take into account some dynamic auscultation equipment s that currently are available in Spain for compaction quality control on earthworks and sub grades. Closed to the equipment description, a deformation modulus calculus approximation has been developed for each of them. A standards checking has been made from national and European point of view. some important research works that have been developed in our country about dynamic monitoring equipment s for quality control in earthworks has been mentioned. In addition to this, some variables are analyzed which have an influence on deformation modulus calculi and a possibility for comparing the equipment modulus calculated with a reference laboratory test has been offered. (Author) 18 refs.

Controlled Conjugated Backbone Twisting for an Increased Open-Circuit Voltage while Having a High Short-Circuit Current in Poly(hexylthiophene) Derivatives

KAUST Repository

Ko, Sangwon; Hoke, Eric T.; Pandey, Laxman; Hong, Sanghyun; Mondal, Rajib; Risko, Chad; Yi, Yuanping; Noriega, Rodrigo; McGehee, Michael D.; Bré das, Jean-Luc; Salleo, Alberto; Bao, Zhenan

2012-01-01

and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone-due to an increase in the polymer ionization potential-while the short-circuit current decreased

Enhancing the performance of mine communication, warning and condition monitoring systems

Energy Technology Data Exchange (ETDEWEB)

Myszkowski, M.; Rellecke, R.; Widera, K. (and others) [DMT GmbH, Essen (Germany)

2008-07-01

This project investigated improvements in power line communications (PLC), condition monitoring techniques and diagnostic aids, together with improving audible communication systems underground. The work on PLC investigated narrow-band, low data rate technologies and high data bandwidth broadband PLC technologies. It is concluded that broadband PLC technologies cannot currently meet the requirements of providing backbone communications in mining and that fibre-optic methods offer better performance. However, short range broadband applications are feasible and an innovative voice and data transmission system, including remote control features, has been developed for coalface communications, using radiofrequency and digital voice technologies not previously used for this application. This system accommodates all the new digital interfaces: Bluetooth, PLC, twisted pair cables, etc. The condition monitoring research has led to a suite of new specialised ATEX-certified sensors together with the development of new vibration signature tracking and classification devices and methods, which provide an early indication of incipient failure. Particular value of these methods is anticipated with coalface equipment. A further component of the work examined the practicability of implementing noise reduction techniques in mining communications systems and noisy workplaces by means of active noise cancellation (ANC). Whilst ANC-based techniques would not be currently cost-effective, several other practical communication improvements are worth considering further. These include new hearing protector technologies and a simple but effective 'waveshape compressor' to improve speech dynamic range in communication systems. A final component of the project examined the issue of mining alerts and alarms, where significant advances in signal design tools have been made. 60 refs., 138 figs., 8 tabs., 1 app.

The ortho backbone amide linker (o-BAL) is an easily prepared and highly acid-labile handle for solid-phase synthesis

DEFF Research Database (Denmark)

Boas, Ulrik; Brask, Jesper; Christensen, J.B.

2002-01-01

The tris(alkoxy)benzyl backbone amide linker (BAL) has found widespread application in solid-phase synthesis. The key intermediate for preparation of para BAL (p-BAL) is 2,6-dimethoxy-4-hydroxybenzaldehyde; several reports on its synthesis have appeared. However, the ortho analogue of the handle (o...

Stability mechanisms of a thermophilic laccase probed by molecular dynamics

DEFF Research Database (Denmark)

Christensen, Niels Johan; Kepp, Kasper Planeta

2013-01-01

Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response...... integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F(-) intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes....

Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A

Science.gov (United States)

Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K.

2017-01-01

Abstract In the canonical DNA double helix, Watson–Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02–0.4%) and short-lived (lifetimes ∼0.2–2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. PMID:28369571

Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design.

Science.gov (United States)

Ludwiczak, Jan; Jarmula, Adam; Dunin-Horkawicz, Stanislaw

2018-07-01

Computational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensembles and showed that such a combined approach generates 20-30% more diverse sequences than currently available methods with only a slight increase in computation time. Importantly, the increase in diversity is achieved without a loss in the quality of the designed sequences assessed by their resemblance to natural sequences. We demonstrate that the MD-based procedure is also applicable to de novo design tasks started from backbone structures without any sequence information. In addition, we implemented a protocol that can be used to assess the stability of designed models and to select the best candidates for experimental validation. In sum our results demonstrate that the MD ensemble-based flexible backbone design can be a viable method for protein design, especially for tasks that require a large pool of diverse sequences. Copyright © 2018 Elsevier Inc. All rights reserved.

Exploring of PST-TBPM in Monitoring Dynamic Deformation of Steel Structure in Vibration

Science.gov (United States)

Chen, Mingzhi; Zhao, Yongqian; Hai, Hua; Yu, Chengxin; Zhang, Guojian

2018-01-01

In order to monitor the dynamic deformation of steel structure in the real-time, digital photography is used in this paper. Firstly, the grid method is used correct the distortion of digital camera. Then the digital cameras are used to capture the initial and experimental images of steel structure to obtain its relative deformation. PST-TBPM (photographing scale transformation-time baseline parallax method) is used to eliminate the parallax error and convert the pixel change value of deformation points into the actual displacement value. In order to visualize the deformation trend of steel structure, the deformation curves are drawn based on the deformation value of deformation points. Results show that the average absolute accuracy and relative accuracy of PST-TBPM are 0.28mm and 1.1‰, respectively. Digital photography used in this study can meet accuracy requirements of steel structure deformation monitoring. It also can warn the safety of steel structure and provide data support for managers’ safety decisions based on the deformation curves on site.

Monitoring the thinning dynamics of soap films by phase shift interferometry. The case of perfluoropolyether surfactants.

Science.gov (United States)

Gambi, Cecilia M C; Vannoni, Maurizio; Sordini, Andrea; Molesini, Giuseppe

2014-02-01

An interferometric method to monitor the thinning process of vertical soap films from a water solution of surfactant materials is reported. Raw data maps of optical path difference introduced by the film are obtained by conventional phase shift interferometry. Off-line re-processing of such raw data taking into account the layered structure of soap films leads to an accurate measurement of the geometrical thickness. As an example of data acquisition and processing, the measuring chain is demonstrated on perfluoropolyether surfactants; the section profile of vertical films is monitored from drawing to black film state, and quantitative data on the dynamics of the thinning process are presented. The interferometric method proves effective to the task, and lends itself to further investigate the physical properties of soap films.

Remote Monitoring of Near-Surface Soil Moisture Dynamics In Unstable Slopes Using a Low-Power Autonomous Resistivity Imaging System

Science.gov (United States)

Chambers, J. E.; Meldrum, P.; Gunn, D.; Wilkinson, P. B.; Uhlemann, S.; Swift, R. T.; Kuras, O.; Inauen, C.; Hutchinson, D.; Butler, S.

2016-12-01

ERT monitoring has been demonstrated in numerous studies as an effective means of imaging near surface processes for applications as diverse as permafrost studies and contaminated land assessment. A limiting factor in applying time-lapse ERT for long-term studies in remote locations has been the availability of cost-effective ERT measurement systems designed specifically for monitoring applications. Typically, monitoring is undertaken using repeated manual data collection, or by building conventional survey instruments into a monitoring setup. The latter often requires high power and is therefore difficult to operate remotely without access to mains electricity. We describe the development of a low-power resistivity imaging system designed specifically for remote monitoring, taking advantage of, e.g., solar power and data telemetry. Here, we present the results of two field deployments. The system has been installed on an active railway cutting to provide insights into the effect of vegetation on the moisture dynamics in unstable infrastructure slopes and to gather subsurface information for pro-active remediation measures. The system, comprising 255 electrodes, acquires 4596 reciprocal measurement pairs twice daily during standard operation. In case of severe weather events, the measurement schedule is reactively changed, to gather high temporal resolution data to image rainfall infiltration processes. The system has also been installed along a leaking and marginally stable canal embankment; a less favourable location for remote monitoring, with limited solar power and poor mobile reception. Nevertheless, the acquired data indicated the effectiveness of remedial actions on the canal. The ERT results showed that one leak was caused by the canal and fixed during remediation, while two other "leaks" were shown to be effects of groundwater dynamics. The availability of cost-effective, low-power ERT monitoring instrumentation, combined with an automated workflow of

Distributed Dynamic State Estimator, Generator Parameter Estimation and Stability Monitoring Demonstration

Energy Technology Data Exchange (ETDEWEB)

Meliopoulos, Sakis [Georgia Inst. of Technology, Atlanta, GA (United States); Cokkinides, George [Georgia Inst. of Technology, Atlanta, GA (United States); Fardanesh, Bruce [New York Power Authority, NY (United States); Hedrington, Clinton [U.S. Virgin Islands Water and Power Authority (WAPA), St. Croix (U.S. Virgin Islands)

2013-12-31

This is the final report for this project that was performed in the period: October1, 2009 to June 30, 2013. In this project, a fully distributed high-fidelity dynamic state estimator (DSE) that continuously tracks the real time dynamic model of a wide area system with update rates better than 60 times per second is achieved. The proposed technology is based on GPS-synchronized measurements but also utilizes data from all available Intelligent Electronic Devices in the system (numerical relays, digital fault recorders, digital meters, etc.). The distributed state estimator provides the real time model of the system not only the voltage phasors. The proposed system provides the infrastructure for a variety of applications and two very important applications (a) a high fidelity generating unit parameters estimation and (b) an energy function based transient stability monitoring of a wide area electric power system with predictive capability. Also the dynamic distributed state estimation results are stored (the storage scheme includes data and coincidental model) enabling an automatic reconstruction and “play back” of a system wide disturbance. This approach enables complete play back capability with fidelity equal to that of real time with the advantage of “playing back” at a user selected speed. The proposed technologies were developed and tested in the lab during the first 18 months of the project and then demonstrated on two actual systems, the USVI Water and Power Administration system and the New York Power Authority’s Blenheim-Gilboa pumped hydro plant in the last 18 months of the project. The four main thrusts of this project, mentioned above, are extremely important to the industry. The DSE with the achieved update rates (more than 60 times per second) provides a superior solution to the “grid visibility” question. The generator parameter identification method fills an important and practical need of the industry. The “energy function” based

Side chain and backbone contributions of Phe508 to CFTR folding

Energy Technology Data Exchange (ETDEWEB)

Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

2010-12-07

Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

External Monitoring and Dynamic Behavior in Mutual Funds

Directory of Open Access Journals (Sweden)

Jian Wang

2016-01-01

Full Text Available This paper studies the impact of external monitoring on the behavior in mutual funds. Specifically, we investigate how and why external monitoring can alleviate contracting inefficiency caused by information asymmetry between investors and the manager. It is shown that efficiency loss emerges when investors contract with the manager just relying on her investment return history. The establishment of external monitoring that provides investors more information about the manager’s ability can improve contracting efficiency, which converges to first-best as external monitoring strengthens. These results provide strong support for tightening supervision in mutual fund industry.

Real-time isotope monitoring network at the Biosphere 2 Landscape Evolution Observatory resolves meter-to-catchment scale flow dynamics

Science.gov (United States)

Volkmann, T. H. M.; Van Haren, J. L. M.; Kim, M.; Harman, C. J.; Pangle, L.; Meredith, L. K.; Troch, P. A.

2017-12-01

Stable isotope analysis is a powerful tool for tracking flow pathways, residence times, and the partitioning of water resources through catchments. However, the capacity of stable isotopes to characterize catchment hydrological dynamics has not been fully exploited as commonly used methodologies constrain the frequency and extent at which isotopic data is available across hydrologically-relevant compartments (e.g. soil, plants, atmosphere, streams). Here, building upon significant recent developments in laser spectroscopy and sampling techniques, we present a fully automated monitoring network for tracing water isotopes through the three model catchments of the Landscape Evolution Observatory (LEO) at the Biosphere 2, University of Arizona. The network implements state-of-the-art techniques for monitoring in great spatiotemporal detail the stable isotope composition of water in the subsurface soil, the discharge outflow, and the atmosphere above the bare soil surface of each of the 330-m2 catchments. The extensive valving and probing systems facilitate repeated isotope measurements from a total of more than five-hundred locations across the LEO domain, complementing an already dense array of hydrometric and other sensors installed on, within, and above each catchment. The isotope monitoring network is operational and was leveraged during several months of experimentation with deuterium-labelled rain pulse applications. Data obtained during the experiments demonstrate the capacity of the monitoring network to resolve sub-meter to whole-catchment scale flow and transport dynamics in continuous time. Over the years to come, the isotope monitoring network is expected to serve as an essential tool for collaborative interdisciplinary Earth science at LEO, allowing us to disentangle changes in hydrological behavior as the model catchments evolve in time through weathering and colonization by plant communities.

Monitoring of vegetation dynamics and assessing vegetation response to drought in the Iberian Peninsula

Energy Technology Data Exchange (ETDEWEB)

Garcia-Haro, F. J.; Moreno, A.; Perez-Hoyos, A.; Gilabert, M. A.; Melia, J.; Belda, F.; Poquet, D.; Martinez, B.; Verger, A.

2009-07-01

Monitoring the vegetation activity over long time-scales is necessary to discern ecosystem response to climate variability. Spatial and temporally consistent estimates of the biophysical variables such as fractional vegetation cover (FVC) and leaf area index (LAI) have been obtained in the context of DULCINEA Project. We used long-term monthly climate statistics to build simple climatic indices (SPI, moisture index) at different time scales. From these indices, we estimated that the climatic disturbances affected both the growing season and the total amount of vegetation. This implies that the anomaly of vegetation cover is a good indicator of moisture condition and can be an important data source when used for detecting an monitoring drought in the Iberian Peninsula. The impact of climate variability on the vegetation dynamics has shown not to be the same for every region. We concluded that the relationships between vegetation anomaly and moisture availability are significant for the arid and semiarid areas. (Author) 6 refs.

Monitoring of vegetation dynamics and assessing vegetation response to drought in the Iberian Peninsula

International Nuclear Information System (INIS)

Garcia-Haro, F. J.; Moreno, A.; Perez-Hoyos, A.; Gilabert, M. A.; Melia, J.; Belda, F.; Poquet, D.; Martinez, B.; Verger, A.

2009-01-01

Monitoring the vegetation activity over long time-scales is necessary to discern ecosystem response to climate variability. Spatial and temporally consistent estimates of the biophysical variables such as fractional vegetation cover (FVC) and leaf area index (LAI) have been obtained in the context of DULCINEA Project. We used long-term monthly climate statistics to build simple climatic indices (SPI, moisture index) at different time scales. From these indices, we estimated that the climatic disturbances affected both the growing season and the total amount of vegetation. This implies that the anomaly of vegetation cover is a good indicator of moisture condition and can be an important data source when used for detecting an monitoring drought in the Iberian Peninsula. The impact of climate variability on the vegetation dynamics has shown not to be the same for every region. We concluded that the relationships between vegetation anomaly and moisture availability are significant for the arid and semiarid areas. (Author) 6 refs.

Effects of solvent concentration and composition on protein dynamics: 13C MAS NMR studies of elastin in glycerol-water mixtures.

Science.gov (United States)

Demuth, Dominik; Haase, Nils; Malzacher, Daniel; Vogel, Michael

2015-08-01

We use (13)C CP MAS NMR to investigate the dependence of elastin dynamics on the concentration and composition of the solvent at various temperatures. For elastin in pure glycerol, line-shape analysis shows that larger-scale fluctuations of the protein backbone require a minimum glycerol concentration of ~0.6 g/g at ambient temperature, while smaller-scale fluctuations are activated at lower solvation levels of ~0.2 g/g. Immersing elastin in various glycerol-water mixtures, we observe at room temperature that the protein mobility is higher for lower glycerol fractions in the solvent and, thus, lower solvent viscosity. When decreasing the temperature, the elastin spectra approach the line shape for the rigid protein at 245 K for all studied samples, indicating that the protein ceases to be mobile on the experimental time scale of ~10(-5) s. Our findings yield evidence for a strong coupling between elastin fluctuations and solvent dynamics and, hence, such interaction is not restricted to the case of protein-water mixtures. Spectral resolution of different carbon species reveals that the protein-solvent couplings can, however, be different for side chain and backbone units. We discuss these results against the background of the slaving model for protein dynamics. Copyright © 2015 Elsevier B.V. All rights reserved.

Accessing ns-μs side chain dynamics in ubiquitin with methyl RDCs

International Nuclear Information System (INIS)

Fares, Christophe; Lakomek, Nils-Alexander; Walter, Korvin F. A.; Frank, Benedikt T. C.; Meiler, Jens; Becker, Stefan; Griesinger, Christian

2009-01-01

This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-τ c dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time τ c . In fact, the average amplitude of motion expressed in terms of order parameters S 2 associated with the supra-τ c window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959-8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471-1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains

Imaging groundwater infiltration dynamics in the karst vadose zone with long-term ERT monitoring

Directory of Open Access Journals (Sweden)

A. Watlet

2018-03-01

Full Text Available Water infiltration and recharge processes in karst systems are complex and difficult to measure with conventional hydrological methods. In particular, temporarily saturated groundwater reservoirs hosted in the vadose zone can play a buffering role in water infiltration. This results from the pronounced porosity and permeability contrasts created by local karstification processes of carbonate rocks. Analyses of time-lapse 2-D geoelectrical imaging over a period of 3 years at the Rochefort Cave Laboratory (RCL site in south Belgium highlight variable hydrodynamics in a karst vadose zone. This represents the first long-term and permanently installed electrical resistivity tomography (ERT monitoring in a karst landscape. The collected data were compared to conventional hydrological measurements (drip discharge monitoring, soil moisture and water conductivity data sets and a detailed structural analysis of the local geological structures providing a thorough understanding of the groundwater infiltration. Seasonal changes affect all the imaged areas leading to increases in resistivity in spring and summer attributed to enhanced evapotranspiration, whereas winter is characterised by a general decrease in resistivity associated with a groundwater recharge of the vadose zone. Three types of hydrological dynamics, corresponding to areas with distinct lithological and structural features, could be identified via changes in resistivity: (D1 upper conductive layers, associated with clay-rich soil and epikarst, showing the highest variability related to weather conditions; (D2 deeper and more resistive limestone areas, characterised by variable degrees of porosity and clay contents, hence showing more diffuse seasonal variations; and (D3 a conductive fractured zone associated with damped seasonal dynamics, while showing a great variability similar to that of the upper layers in response to rainfall events. This study provides detailed images of

Monitoring Evolution at CERN

CERN Document Server

Andrade, P; Murphy, S; Pigueiras, L; Santos, M

2015-01-01

Over the past two years, the operation of the CERN Data Centres went through significant changes with the introduction of new mechanisms for hardware procurement, new services for cloud provisioning and configuration management, among other improvements. These changes resulted in an increase of resources being operated in a more dynamic environment. Today, the CERN Data Centres provide over 11000 multi-core processor servers, 130 PB disk servers, 100 PB tape robots, and 150 high performance tape drives. To cope with these developments, an evolution of the data centre monitoring tools was also required. This modernisation was based on a number of guiding rules: sustain the increase of resources, adapt to the new dynamic nature of the data centres, make monitoring data easier to share, give more flexibility to Service Managers on how they publish and consume monitoring metrics and logs, establish a common repository of monitoring data, optimise the handling of monitoring notifications, and replace the previous ...

Radioactive aerosol detection station for near real-time atmospheric monitoring

International Nuclear Information System (INIS)

Mason, L.R.; Bohner, John D.

1997-01-01

A radionuclide aerosol detection station has been developed to measure radioactivity in the environment. The objective is to monitor the atmosphere for anthropogenic radioactivity that could be indicative of nuclear weapons tests to verify the Comprehensive Nuclear Test Ban Treaty. Eighty stations will form the backbone of the International Monitoring System in which stations are linked to a central analysis facility called the International Data Centre. Data are transmitted to this centre in near real-time to facilitate rapid detection. Principal process of the field measurement are collection, separation, and assay. Collection of airborne radioactivity is achieved through high-volume air sampling. Aerosols separation is accomplished by high-efficiency particulate filtration. Radionuclides assay is achieved by in-situ high resolution gamma spectrometry. These modules are integrated into a unit that provides power, control, and communication support subsystems. Station operation is semi-automatic requiring only minimal human interaction. (author). 6 refs., 3 figs., 3 tabs

Monitoring the Orientational Changes of Alamethicin during Incorporation into Bilayer Lipid Membranes.

Science.gov (United States)

Forbrig, Enrico; Staffa, Jana K; Salewski, Johannes; Mroginski, Maria Andrea; Hildebrandt, Peter; Kozuch, Jacek

2018-02-13

Antimicrobial peptides (AMPs) are the first line of defense after contact of an infectious invader, for example, bacterium or virus, with a host and an integral part of the innate immune system of humans. Their broad spectrum of biological functions ranges from cell membrane disruption over facilitation of chemotaxis to interaction with membrane-bound or intracellular receptors, thus providing novel strategies to overcome bacterial resistances. Especially, the clarification of the mechanisms and dynamics of AMP incorporation into bacterial membranes is of high interest, and different mechanistic models are still under discussion. In this work, we studied the incorporation of the peptaibol alamethicin (ALM) into tethered bilayer lipid membranes on electrodes in combination with surface-enhanced infrared absorption (SEIRA) spectroscopy. This approach allows monitoring the spontaneous and potential-induced ion channel formation of ALM in situ. The complex incorporation kinetics revealed a multistep mechanism that points to peptide-peptide interactions prior to penetrating the membrane and adopting the transmembrane configuration. On the basis of the anisotropy of the backbone amide I and II infrared absorptions determined by density functional theory calculations, we employed a mathematical model to evaluate ALM reorientations monitored by SEIRA spectroscopy. Accordingly, ALM was found to adopt inclination angles of ca. 69°-78° and 21° in its interfacially adsorbed and transmembrane incorporated states, respectively. These orientations can be stabilized efficiently by the dipolar interaction with lipid head groups or by the application of a potential gradient. The presented potential-controlled mechanistic study suggests an N-terminal integration of ALM into membranes as monomers or parallel oligomers to form ion channels composed of parallel-oriented helices, whereas antiparallel oligomers are barred from intrusion.

Real time monitoring of slope condition for transmission tower safety in Kenyir, Malaysia

Science.gov (United States)

Omar, R. C.; Ismail, A.; Khalid, N. H. N.; Din, N. M.; Hussain, H.; Jamaludin, M. Z.; Abdullah, F.; Arazad, A. Z.; Yusop, H.

2013-06-01

The Malaysia national electricity grid traverses throughout the nation over urban and rural areas including mountainous terrain. A major number of the transmission towers have been in existence for over 40 years and some traversed through very remote and high altitude areas like the Titiwangsa range that forms the backbone of the Malay Peninsula. This paper describes the instrumentation and real time monitoring in a transmission tower site in Kenyir, a hilly terrain in the East Coast of Malaysia. The site itself which is between 300-500m above sea level is deep in the rainforest area of Kenyir. The site and surrounding areas has been identified with signs of slope failure. A design concern is the real time slope monitoring sensors reliability and data integrity from the remote area with potential interference to the electronics equipment from the power line. The monitoring system comprised of an automated system for collecting and reporting field monitoring data. The instruments collect readings and transmit real time through GSM to the monitoring office over designated intervals. This initiative is a part of a project on developing an early warning system for monitoring landslide hazards at selected transmission towers. This paper reviews the various instrumentation used and challenges faced and the output received for slope movement warnings.

Real time monitoring of slope condition for transmission tower safety in Kenyir, Malaysia

International Nuclear Information System (INIS)

Omar, R C; Ismail, A; Khalid, N H N; Din, N M; Hussain, H; Jamaludin, M Z; Abdullah, F; Arazad, A Z; Yusop, H

2013-01-01

The Malaysia national electricity grid traverses throughout the nation over urban and rural areas including mountainous terrain. A major number of the transmission towers have been in existence for over 40 years and some traversed through very remote and high altitude areas like the Titiwangsa range that forms the backbone of the Malay Peninsula. This paper describes the instrumentation and real time monitoring in a transmission tower site in Kenyir, a hilly terrain in the East Coast of Malaysia. The site itself which is between 300–500m above sea level is deep in the rainforest area of Kenyir. The site and surrounding areas has been identified with signs of slope failure. A design concern is the real time slope monitoring sensors reliability and data integrity from the remote area with potential interference to the electronics equipment from the power line. The monitoring system comprised of an automated system for collecting and reporting field monitoring data. The instruments collect readings and transmit real time through GSM to the monitoring office over designated intervals. This initiative is a part of a project on developing an early warning system for monitoring landslide hazards at selected transmission towers. This paper reviews the various instrumentation used and challenges faced and the output received for slope movement warnings.

Introduction to monitoring dynamic environmental phenomena of the world using satellite data collection systems, 1978

Science.gov (United States)

Carter, William Douglas; Paulson, Richard W.

1979-01-01

The rapid development of satellite technology, especially in the area of radio transmission and imaging systems, makes it possible to monitor dynamic surface phenomena of the Earth in considerable detail. The monitoring systems that have been developed are compatible with standard monitoring systems such as snow, stream, and rain gages; wind, temperature and humidity measuring instruments; tiltmeters and seismic event counters. Supported by appropriate power, radios and antennae, remote stations can be left unattended for at least 1 year and consistently relay local information via polar orbiting or geostationary satellites. These data, in conjunction with timely Landsat images, can provide a basis for more accurate estimates on snowfall, water runoff, reservoir level changes, flooding, drought effects, and vegetation trends and may be of help in forecasting volcanic eruptions. These types of information are critical for resource inventory and development, especially in developing countries where remote regions are commonly difficult to access. This paper introduces the reader to the systems available, describes their features and limitations, and provides suggestions on how to employ them. An extensive bibliography is provided for those who wish more information.

Configuration of Risk Monitor System by PLant Defense-In.Depth Monitor and Relability Monitor

DEFF Research Database (Denmark)

Yoshikawa, Hidekazu; Lind, Morten; Yang, Ming

2012-01-01

A new method of risk monitor system of a nuclear power plant has been proposed from the aspect by what degree of safety functions incorporated in the plant system is maintained by multiple barriers of defense-in-depth (DiD). Wherein, the central idea is plant DiD risk monitor and reliability...... monitor derived from the four aspects of (i) design principle of nuclear safety to realize DiD concept, (ii) definition of risk and risk to be monitored, (iii) severe accident phenomena as major risk, (iv) scheme of risk ranking, and (v) dynamic risk display. In this paper, the overall frame...... of the proposed frame on risk monitor system is summarized and the detailed discussion is made on the definitions of major terminologies of risk, risk ranking, anatomy of fault occurrence, two-layer configuration of risk monitor, how to configure individual elements of plant DiD risk monitor and its example...

Effects of Tryptophan Content and Backbone Spacing on the Uptake Efficiency of Cell-Penetrating Peptides

KAUST Repository

Rydberg, Hanna A.; Matson, Maria; Å mand, Helene L.; Esbjö rner, Elin K.; Nordé n, Bengt

2012-01-01

Cell-penetrating peptides (CPPs) are able to traverse cellular membranes and deliver macromolecular cargo. Uptake occurs through both endocytotic and nonendocytotic pathways, but the molecular requirements for efficient internalization are not fully understood. Here we investigate how the presence of tryptophans and their position within an oligoarginine influence uptake mechanism and efficiency. Flow cytometry and confocal fluorescence imaging are used to estimate uptake efficiency, intracellular distribution and toxicity in Chinese hamster ovarian cells. Further, membrane leakage and lipid membrane affinity are investigated. The peptides contain eight arginine residues and one to four tryptophans, the tryptophans positioned either at the N-terminus, in the middle, or evenly distributed along the amino acid sequence. Our data show that the intracellular distribution varies among peptides with different tryptophan content and backbone spacing. Uptake efficiency is higher for the peptides with four tryptophans in the middle, or evenly distributed along the peptide sequence, than for the peptide with four tryptophans at the N-terminus. All peptides display low cytotoxicity except for the one with four tryptophans at the N-terminus, which was moderately toxic. This finding is consistent with their inability to induce efficient leakage of dye from lipid vesicles. All peptides have comparable affinities for lipid vesicles, showing that lipid binding is not a decisive parameter for uptake. Our results indicate that tryptophan content and backbone spacing can affect both the CPP uptake efficiency and the CPP uptake mechanism. The low cytotoxicity of these peptides and the possibilities of tuning their uptake mechanism are interesting from a therapeutic point of view. © 2012 American Chemical Society.

Effects of Tryptophan Content and Backbone Spacing on the Uptake Efficiency of Cell-Penetrating Peptides

KAUST Repository

Rydberg, Hanna A.

2012-07-10

Cell-penetrating peptides (CPPs) are able to traverse cellular membranes and deliver macromolecular cargo. Uptake occurs through both endocytotic and nonendocytotic pathways, but the molecular requirements for efficient internalization are not fully understood. Here we investigate how the presence of tryptophans and their position within an oligoarginine influence uptake mechanism and efficiency. Flow cytometry and confocal fluorescence imaging are used to estimate uptake efficiency, intracellular distribution and toxicity in Chinese hamster ovarian cells. Further, membrane leakage and lipid membrane affinity are investigated. The peptides contain eight arginine residues and one to four tryptophans, the tryptophans positioned either at the N-terminus, in the middle, or evenly distributed along the amino acid sequence. Our data show that the intracellular distribution varies among peptides with different tryptophan content and backbone spacing. Uptake efficiency is higher for the peptides with four tryptophans in the middle, or evenly distributed along the peptide sequence, than for the peptide with four tryptophans at the N-terminus. All peptides display low cytotoxicity except for the one with four tryptophans at the N-terminus, which was moderately toxic. This finding is consistent with their inability to induce efficient leakage of dye from lipid vesicles. All peptides have comparable affinities for lipid vesicles, showing that lipid binding is not a decisive parameter for uptake. Our results indicate that tryptophan content and backbone spacing can affect both the CPP uptake efficiency and the CPP uptake mechanism. The low cytotoxicity of these peptides and the possibilities of tuning their uptake mechanism are interesting from a therapeutic point of view. © 2012 American Chemical Society.

Metabolic 19F MRI an dynamic 18F PET for chemotherapy monitoring in experimental tumors

International Nuclear Information System (INIS)

Brix, G.; Haberkorn, U.; Bellemann, M.E.

1999-01-01

The efficient clinical use of chemotherapeutic agents requires the assessment of the uptake and metabolism of the drugs in the tumor as well as in the various organs of the body by using noninvasive imaging techniques such as magnetic resonance imaging (MRI) and positron emission tomography (PET). In this overview, we present different metabolic 19 F MRI and dynamic 18 F PET techniques for noninvasive monitoring of fluorine-containing anticancer drugs and evaluate their potentials and limitations within the framework of experimental animal studies. (orig.) [de

Revealing the Linkage Network Dynamic Structures of Chinese Maritime Ports through Automatic Information System Data

Directory of Open Access Journals (Sweden)

Hongchu Yu

2017-10-01

Full Text Available Marine economic cooperation has emerged as a major theme in this era of globalization; hence, maritime network connectivity and dynamics have attracted more and more attention. Port construction and maritime route improvements increase maritime trade and thus facilitate economic viability and resource sustainability. This paper reveals the regional dimension of inter-port linkage dynamic structure of Chinese maritime ports from a complex multilayer perspective that is meaningful for strategic forecasting and regional long-term economic development planning. In this research, Automatic Information System (AIS-derived traffic flows were used to construct a maritime network and subnetworks based on the geographical locations of ports. The linkage intensity between subnetworks, the linkage tightness within subnetworks, the spatial isolation between high-intensity backbones and tight skeleton networks, and a linkage concentration index for each port were calculated. The ports, in turn, were analyzed based on these network attributes. This study analyzed the external competitiveness and internal cohesion of each subnetwork. The results revealed problems in port management and planning, such as unclear divisions in port operations. More critically, weak complementary relationships between the backbone and skeleton networks among the ports reduce connectivity and must be strengthened. This research contributes to the body of work supporting strategic decision-making for future development.

Safety of Russian-backbone seasonal trivalent, live-attenuated influenza vaccine in a phase II randomized placebo-controlled clinical trial among children in urban Bangladesh.

Science.gov (United States)

Ortiz, Justin R; Goswami, Doli; Lewis, Kristen D C; Sharmeen, Amina Tahia; Ahmed, Moshtaq; Rahman, Mustafizur; Rahman, Mohammed Z; Feser, Jodi; Neuzil, Kathleen M; Brooks, W Abdullah

2015-06-26

Live-attenuated influenza vaccines (LAIVs) have the potential to be affordable, effective, and logistically feasible for immunization of children in low-resource settings. We conducted a phase II, randomized, double-blind, parallel group, placebo-controlled trial on the safety of the Russian-backbone, seasonal trivalent LAIV among children aged 24 through 59 months in Dhaka, Bangladesh in 2012. After vaccination, we monitored participants for six months with weekly home visits and study clinic surveillance for solicited and unsolicited adverse events, protocol-defined wheezing illness (PDWI), and serious adverse events (SAEs), including all cause hospitalizations. Three hundred children were randomized and administered LAIV (n=150) or placebo (n=150). No immediate post-vaccination reactions occurred in either group. Solicited reactions were similar between vaccine and placebo groups during the first 7 days post-vaccination and throughout the entire trial. There were no statistically significant differences in participants experiencing PDWI between LAIV and placebo groups throughout the trial (n=13 vs. n=16, p=0.697). Of 131 children with a history of medical treatment or hospitalization for asthma or wheezing at study entry, 65 received LAIV and 66 received placebo. Among this subset, there was no statistical difference in PDWI occurring throughout the trial between the LAIV or placebo groups (7.7% vs. 19.7%, p=0.074). While there were no related SAEs, LAIV recipients had six unrelated SAEs and placebo recipients had none. These SAEs included three due to traumatic injury and bone fracture, and one each due to accidental overdose of paracetamol, abdominal pain, and acute gastroenteritis. None of the participants with SAEs had laboratory-confirmed influenza, wheezing illness, or other signs of acute respiratory illness at the time of their events. In this randomized, controlled trial among 300 children aged 24 through 59 months in urban Bangladesh, Russian-backbone

New theories for smectic and nematic liquid-crystal polymers: Backbone LCPs [liquid crystalline polymers] and their mixtures and side-chain LCPs

International Nuclear Information System (INIS)

Dowell, F.

1987-01-01

A summary of predictions and explanations from statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with backbone LCPs are presented. Trends in the thermodynamic and molecular ordering properties have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. The theoretical results are found to be in good agreement with existing experimental data. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories can be used to design new LCPs and new solvents as well as to predict and explain properties. 27 refs., 4 tabs

Oligomerized backbone pilin helps piliated Lactococcus lactis to withstand shear flow.

Science.gov (United States)

Castelain, Mickaël; Duviau, Marie-Pierre; Oxaran, Virginie; Schmitz, Philippe; Cocaign-Bousquet, Muriel; Loubière, Pascal; Piard, Jean-Christophe; Mercier-Bonin, Muriel

2016-09-01

The present work focuses on the role of pili present at the cell surface of Lactococcus lactis in bacterial adhesion to abiotic (hydrophobic polystyrene) and biotic (mucin-coated polystyrene) surfaces. Native pili-displaying strains and isogenic derivatives in which pilins or sortase C structural genes had been modified were used. Surface physico-chemistry, morphology and shear-flow-induced detachment of lactococcal cells were evaluated. The involvement of pili in L. lactis adhesion was clearly demonstrated, irrespective of the surface characteristics (hydrophobic/hydrophilic, presence or not of specific binding sites). The accessory pilin, PilC, and the backbone pilin, PilB, were revealed to play a major role in adhesion, provided that the PilB was present in its polymerized form. Within the population fraction that remained attached to the surface under increasing shear flow, different association behaviors were observed, showing that pili could serve as anchoring sites thus hampering the effect of shear flow on cell orientation and detachment.

Correlation between protein secondary structure, backbone bond angles, and side-chain orientations

Science.gov (United States)

Lundgren, Martin; Niemi, Antti J.

2012-08-01

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central Cα carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the Cβ carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the Cα-Cβ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

Data acquisition backbone core DABC release v1.0

Energy Technology Data Exchange (ETDEWEB)

Adamczewski-Musch, Joern; Essel, Hans G.; Kurz, Nikolaus; Linev, S. [GSI Helmholtzzentrum fuer Schwerionenforschung, Darmstadt (Germany)

2010-07-01

The new experiments at FAIR require new concepts of data acquisition systems for the distribution of self-triggered, time stamped data streams over high performance networks for event building. The Data Acquisition Backbone Core (DABC) is a general purpose software framework developed for the implementation of such data acquisition systems. A DABC application consists of functional components like data input, combiner, scheduler, event builder, filter, analysis and storage which can be configured at runtime. Application specific code including the support of all kinds of data channels (front-end systems) is implemented by C++ program plug-ins. DABC is also well suited as environment for various detector and readout components test beds. A set of DABC plug-ins has been developed for the FAIR experiment CBM (Compressed Baryonic Matter) at GSI. This DABC application is used as DAQ system for test beamtimes. Front-end boards equipped with n-XYTER ASICs and ADCs are connected to read-out controller boards (ROC). From there the data is sent over Ethernet (UDP), or over optics and PCIe interface cards into Linux PCs. DABC does the controlling, event building, archiving and data serving. The first release of DABC was published in 2009 and is available under GPL license.

Monitoring vegetation dynamics with medium resolution MODIS-EVI time series at sub-regional scale in southern Africa

Science.gov (United States)

Dubovyk, Olena; Landmann, Tobias; Erasmus, Barend F. N.; Tewes, Andreas; Schellberg, Jürgen

2015-06-01

Currently there is a lack of knowledge on spatio-temporal patterns of land surface dynamics at medium spatial scale in southern Africa, even though this information is essential for better understanding of ecosystem response to climatic variability and human-induced land transformations. In this study, we analysed vegetation dynamics across a large area in southern Africa using the 14-years (2000-2013) of medium spatial resolution (250 m) MODIS-EVI time-series data. Specifically, we investigated temporal changes in the time series of key phenometrics including overall greenness, peak and timing of annual greenness over the monitoring period and study region. In order to specifically capture spatial and per pixel vegetation changes over time, we calculated trends in these phenometrics using a robust trend analysis method. The results showed that interannual vegetation dynamics followed precipitation patterns with clearly differentiated seasonality. The earliest peak greenness during 2000-2013 occurred at the end of January in the year 2000 and the latest peak greenness was observed at the mid of March in 2012. Specifically spatial patterns of long-term vegetation trends allowed mapping areas of (i) decrease or increase in overall greenness, (ii) decrease or increase of peak greenness, and (iii) shifts in timing of occurrence of peak greenness over the 14-year monitoring period. The observed vegetation decline in the study area was mainly attributed to human-induced factors. The obtained information is useful to guide selection of field sites for detailed vegetation studies and land rehabilitation interventions and serve as an input for a range of land surface models.

Systematic coarse-graining of the dynamics of entangled polymer melts: the road from chemistry to rheology

International Nuclear Information System (INIS)

Padding, J T; Briels, W J

2011-01-01

For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review current and past computer simulation techniques and critically assess their ability to provide such a link between chemistry and rheology. We distinguish between two classes of coarse-graining levels, which we term coarse-grained molecular dynamics (CGMD) and coarse-grained stochastic dynamics (CGSD). In CGMD the coarse-grained beads are still relatively hard, thus automatically preventing bond crossing. This also implies an upper limit on the number of atoms that can be lumped together (up to five backbone carbon atoms) and therefore on the longest chain lengths that can be studied. To reach a higher degree of coarse-graining, in CGSD many more atoms are lumped together (more than ten backbone carbon atoms), leading to relatively soft beads. In that case friction and stochastic forces dominate the interactions, and action must be undertaken to prevent bond crossing. We also review alternative methods that make use of the tube model of polymer dynamics, by obtaining the entanglement characteristics through a primitive path analysis and by simulation of a primitive chain network. We finally review super-coarse-grained methods in which an entire polymer is represented by a single particle, and comment on ways to include memory effects and transient forces. (topical review)

Backbone resonance assignments for G protein α(i3) subunit in the GDP-bound state.

Science.gov (United States)

Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2014-10-01

Guanine-nucleotide binding proteins (G proteins) serve as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of the G protein α subunit with GDP (Gα·GDP) and the G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP-GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα·GTP) and Gβγ. Then, Gα·GTP and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. The G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Here, we established the backbone resonance assignments of human Gαi3, a member of the i/o family with a molecular weight of 41 K, in complex with GDP. The chemical shifts were compared with those of Gα(i3) in complex with a GTP-analogue, GTPγS, which we recently reported, indicating that the residues with significant chemical shift differences are mostly consistent with the regions with the structural differences between the GDP- and GTPγS-bound states, as indicated in the crystal structures. The assignments of Gα(i3)·GDP would be useful for the analyses of the dynamics of Gα(i3) and its interactions with various target molecules.

Protein backbone motions viewed by intraresidue and sequential H{sup N}-H{sup {alpha}} residual dipolar couplings

Energy Technology Data Exchange (ETDEWEB)

Voegeli, Beat; Yao Lishan; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

2008-05-15

Triple resonance E.COSY-based techniques were used to measure intra-residue and sequential H{sup N}-H{sup {alpha}} residual dipolar couplings (RDCs) for the third IgG-binding domain of protein G (GB3), aligned in Pf1 medium. Measurements closely correlate with values predicted on the basis of an NMR structure, previously determined on the basis of a large number of one-bond backbone RDCs measured in five alignment media. However, in particular the sequential H{sup N}-H{sup {alpha}} RDCs are smaller than predicted for a static structure, suggesting a degree of motion for these internuclear vectors that exceeds that of the backbone amide N-H vectors. Of all experimentally determined GB3 structures available, the best correlation between experimental {sup 1}H-{sup 1}H couplings is observed for a GB3 ensemble, previously derived to generate a realistic picture of the conformational space sampled by GB3 (Clore and Schwieters, J Mol Biol 355:879-886, 2006). However, for both NMR and X-ray-derived structures the {sup 1}H-{sup 1}H couplings are found to be systematically smaller than expected on the basis of alignment tensors derived from {sup 15}N-{sup 1}H amide RDCs, assuming librationally corrected N-H bond lengths of 1.041 A.

Solid state radiation chemistry of the DNA backbone

International Nuclear Information System (INIS)

Bernhard, W.A.

1989-09-01

The long term goal of this program is to determine the fundamental rules needed to predict the type and yield of damage produced in DNA due to direct effects of ionizing radiation. The focus is on damage to the sugar-phosphate backbone, damage that would lead to strand breaks. Model systems have been chosen that permit various aspects of this problem to be investigated. The emphasis will be on single crystals of monosaccharides, nucleosides, and nucleotides but will also include some powder work on polynucleotides. In these model systems, free radical products and reactions are observed by electron spin resonance (ESR) and electron nuclear double resonance (ENDOR) techniques. The information thus gained is used in constructing rules that predict what primary free radicals are formed in single crystals of model compounds and the reactions stemming from the primary radicals. The formulation of a set of rules that work in model systems will represent a major advance toward formulating a set of rules that predict the direct damage in DNA itself. In a broader context this program is part of the effort to understand and predict the effects of exposure to ionizing radiation received at low dose rates over long periods of time. Assessment of low dose effects requires a basic understanding of the action of radiation at the molecular level. By contributing to that basic understanding, this program will help solve the problems of risk assessment under low dose conditions. 5 refs., 3 figs

Velocity dependent passive sampling for monitoring of micropollutants in dynamic stormwater discharges

DEFF Research Database (Denmark)

Birch, Heidi; Sharma, Anitha Kumari; Vezzaro, Luca

2013-01-01

Micropollutant monitoring in stormwater discharges is challenging because of the diversity of sources and thus large number of pollutants found in stormwater. This is further complicated by the dynamics in runoff flows and the large number of discharge points. Most passive samplers are non......-ideal for sampling such systems because they sample in a time-integrative manner. This paper reports test of a flow-through passive sampler, deployed in stormwater runoff at the outlet of a residential-industrial catchment. Momentum from the water velocity during runoff events created flow through the sampler...... resulting in velocity dependent sampling. This approach enables the integrative sampling of stormwater runoff during periods of weeks to months while weighting actual runoff events higher than no flow periods. Results were comparable to results from volume-proportional samples and results obtained from...

Configuration of risk monitor system by plant defense-in-depth risk monitor and reliability monitor

International Nuclear Information System (INIS)

Yoshikawa, Hidekazu; Lind Morten; Yang Ming; Hashim Muhammad; Zhang Zhijian

2012-01-01

A new method of risk monitor system of a nuclear power plant has been proposed from the aspect by what degree of safety functions incorporated in the plant system is maintained by multiple barriers of defense-in-depth (DiD). Wherein, the central idea is plant DiD risk monitor and reliability monitor derived from the five aspects of (1) design principle of nuclear safety based on DiD concept, (2) definition of risk and risk to be monitored, (3) severe accident phenomena as major risk, (4) scheme of risk ranking, and (5) dynamic risk display. In this paper, the overall frame of the proposed risk monitor system is summarized and the detailed discussion is made on major items such as definition of risk and risk ranking, anatomy of fault occurrence, two-layer configuration of risk monitor, how to configure individual elements of plant DiD risk monitor, and lastly how to apply for a PWR safety system. (author)

A novel thermoplastic elastomer based on dynamically vulcanized polypropylene/acrylic rubber blends

Directory of Open Access Journals (Sweden)

2008-08-01

Full Text Available Thermoplastic elastomer based on polypropylene (PP and acrylic rubber (ACM was investigated, with special attention on the compatibilization and dynamic vulcanization. ACM component contains chlorine and carboxyl groups along the backbone, which act as center for the curing and reactive compatibilization. The last event was carried out by adding a combination of maleic anhydride-modified PP (PP-g-MA and triethylene tetramine (TETA, which act as interfacial agents between PP and ACM phases. The effectiveness of the compatibilization was suggested from mixing torque and viscosity, determined from rheological measurements. Outstanding mechanical performance, especially elongation at break, and better tensile set (lower values were obtained with the compatibilization. The dynamic vulcanization also resulted in good mechanical properties for compatibilized blends, but the performance was inferior to that observed for non vulcanized blends. The effect of the compatibilization and/or dynamic vulcanization on the dynamic mechanical, thermal, morphological and stress relaxation properties was investigated.

A High-Resolution Sensor Network for Monitoring Glacier Dynamics

Science.gov (United States)

Edwards, S.; Murray, T.; O'Farrell, T.; Rutt, I. C.; Loskot, P.; Martin, I.; Selmes, N.; Aspey, R.; James, T.; Bevan, S. L.; Baugé, T.

2013-12-01

Changes in Greenland and Antarctic ice sheets due to ice flow/ice-berg calving are a major uncertainty affecting sea-level rise forecasts. Latterly GNSS (Global Navigation Satellite Systems) have been employed extensively to monitor such glacier dynamics. Until recently however, the favoured methodology has been to deploy sensors onto the glacier surface, collect data for a period of time, then retrieve and download the sensors. This approach works well in less dynamic environments where the risk of sensor loss is low. In more extreme environments e.g. approaching the glacial calving front, the risk of sensor loss and hence data loss increases dramatically. In order to provide glaciologists with new insights into flow dynamics and calving processes we have developed a novel sensor network to increase the robustness of data capture. We present details of the technological requirements for an in-situ Zigbee wireless streaming network infrastructure supporting instantaneous data acquisition from high resolution GNSS sensors thereby increasing data capture robustness. The data obtained offers new opportunities to investigate the interdependence of mass flow, uplift, velocity and geometry and the network architecture has been specifically designed for deployment by helicopter close to the calving front to yield unprecedented detailed information. Following successful field trials of a pilot three node network during 2012, a larger 20 node network was deployed on the fast-flowing Helheim glacier, south-east Greenland over the summer months of 2013. The utilisation of dual wireless transceivers in each glacier node, multiple frequencies and four ';collector' stations located on the valley sides creates overlapping networks providing enhanced capacity, diversity and redundancy of data 'back-haul', even close to ';floor' RSSI (Received Signal Strength Indication) levels around -100 dBm. Data loss through radio packet collisions within sub-networks are avoided through the

Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.

Science.gov (United States)

Sathyamoorthy, Bharathwaj; Shi, Honglue; Zhou, Huiqing; Xue, Yi; Rangadurai, Atul; Merriman, Dawn K; Al-Hashimi, Hashim M

2017-05-19

In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Molecular dynamics studies of the conformation of sorbitol

Science.gov (United States)

Lerbret, A.; Mason, P.E.; Venable, R.M.; Cesàro, A.; Saboungi, M.-L.; Pastor, R.W.; Brady, J.W.

2009-01-01

Molecular dynamics simulations of a 3 m aqueous solution of D-sorbitol (also called D-glucitol) have been performed at 300 K, as well as at two elevated temperatures to promote conformational transitions. In principle, sorbitol is more flexible than glucose since it does not contain a constraining ring. However, a conformational analysis revealed that the sorbitol chain remains extended in solution, in contrast to the bent conformation found experimentally in the crystalline form. While there are 243 staggered conformations of the backbone possible for this open-chain polyol, only a very limited number were found to be stable in the simulations. Although many conformers were briefly sampled, only eight were significantly populated in the simulation. The carbon backbones of all but two of these eight conformers were completely extended, unlike the bent crystal conformation. These extended conformers were stabilized by a quite persistent intramolecular hydrogen bond between the hydroxyl groups of carbon C-2 and C-4. The conformational populations were found to be in good agreement with the limited available NMR data except for the C-2–C-3 torsion (spanned by the O-2–O-4 hydrogen bond), where the NMR data supports a more bent structure. PMID:19744646

Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics

International Nuclear Information System (INIS)

Lakomek, Nils-Alexander; Walter, Korvin F. A.; Fares, Christophe; Lange, Oliver F.; Groot, Bert L. de; Grubmueller, Helmut; Brueschweiler, Rafael; Munk, Axel; Becker, Stefan; Meiler, Jens; Griesinger, Christian

2008-01-01

Residual dipolar couplings (RDCs) provide information about the dynamic average orientation of inter-nuclear vectors and amplitudes of motion up to milliseconds. They complement relaxation methods, especially on a time-scale window that we have called supra-τ c (τ c c rdc > = 0.72 ± 0.02 compared to LS 2 > = 0.778 ± 0.003 for the Lipari-Szabo order parameters, indicating that the inclusion of the supra-τ c window increases the averaged amplitude of mobility observed in the sub-τ c window by about 34%. For the β-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S rdc 2 (NH) = (0.59, 0.72, 0.59) was extracted. The backbone of Lys48, whose side chain is known to be involved in the poly-ubiquitylation process that leads to protein degradation, is very mobile on the supra-τ c time scale (S rdc 2 (NH) = 0.59 ± 0.03), while it is inconspicuous (S LS 2 (NH) = 0.82) on the sub-τ c as well as on μs-ms relaxation dispersion time scales. The results of this work differ from previous RDC dynamics studies of ubiquitin in the sense that the results are essentially independent of structural noise providing a much more robust assessment of dynamic effects that underlie the RDC data

Characterizing Motif Dynamics of Electric Brain Activity Using Symbolic Analysis

Directory of Open Access Journals (Sweden)

Massimiliano Zanin

2014-10-01

Full Text Available Motifs are small recurring circuits of interactions which constitute the backbone of networked systems. Characterizing motif dynamics is therefore key to understanding the functioning of such systems. Here we propose a method to define and quantify the temporal variability and time scales of electroencephalogram (EEG motifs of resting brain activity. Given a triplet of EEG sensors, links between them are calculated by means of linear correlation; each pattern of links (i.e., each motif is then associated to a symbol, and its appearance frequency is analyzed by means of Shannon entropy. Our results show that each motif becomes observable with different coupling thresholds and evolves at its own time scale, with fronto-temporal sensors emerging at high thresholds and changing at fast time scales, and parietal ones at low thresholds and changing at slower rates. Finally, while motif dynamics differed across individuals, for each subject, it showed robustness across experimental conditions, indicating that it could represent an individual dynamical signature.

Insight into a conformation of the PNA-PNA duplex with (2‧R,4‧R)- and (2‧R,4‧S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbones

Science.gov (United States)

Maitarad, Amphawan; Poomsuk, Nattawee; Vilaivan, Chotima; Vilaivan, Tirayut; Siriwong, Khatcharin

2018-04-01

Suitable conformations for peptide nucleic acid (PNA) self-hybrids with (2‧R,4‧R)- and (2‧R,4‧S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbones (namely, acpcPNA and epi-acpcPNA, respectively) were investigated based on molecular dynamics simulations. The results revealed that hybridization of the acpcPNA was observed only in the parallel direction, with a conformation close to the P-type structure. In contrast, self-hybrids of the epi-acpcPNA were formed in the antiparallel and parallel directions; the antiparallel duplex adopted the B-form conformation, and the parallel duplex was between B- and P-forms. The calculated binding energies and the experimental data indicate that the antiparallel epi-acpcPNA self-hybrid was more stable than the parallel duplex.

A wide dynamic range BF3 neutron monitor with front-end electronics based on a logarithmic amplifier

International Nuclear Information System (INIS)

Ferrarini, M.; Varoli, V.; Favalli, A.; Caresana, M.; Pedersen, B.

2010-01-01

This paper describes a wide dynamic range neutron monitor based on a BF 3 neutron detector. The detector is used in current mode, and front-end electronics based on a logarithmic amplifier are used in order to have a measurement capability ranging over many orders of magnitude. The system has been calibrated at the Polytechnic of Milan, CESNEF, with an AmBe neutron source, and has been tested in a pulsed field at the PUNITA facility at JRC, Ispra. The detector has achieved a dynamic range of over 6 orders of magnitude, being able to measure single neutron pulses and showing saturation-free response for a reaction rate up to 10 6 s -1 . It has also proved effective in measuring the PUNITA facility pulse integral fluence.

New software tool for dynamic radiological characterisation and monitoring in nuclear sites

International Nuclear Information System (INIS)

Szoeke, Istvan; Louka, Michael N.; Mark, Niels K.; Bryntesen, Tom R.; Bratteli, Joachim; Edvardsen, Svein T.; Gustavsen, Morten A.; Toppe, Aleksander L.; Johnsen, Terje; Rindahl, Grete

2012-01-01

The Halden Reactor Project (HRP) is a jointly sponsored international cooperation, under the aegis of the Organisation for Economic Co-operation and Development - Nuclear Energy Agency. Extensive and valuable guidance and tools, connected to safe and reliable operation of nuclear facilities, has been elaborated throughout the years within the frame of this programme. The HRP has particularly high level results in virtual-reality based tools for real-time areal and personal monitoring. The techniques, developed earlier, are now being supplemented to enhance the planning and monitoring capabilities, and support general radiological characterisation connected to nuclear sites and facilities. Due to the complexity and abundance of the input information required, software tools, dedicated to the radiological characterization of contaminated materials, buildings, land and groundwater, are applied to review, evaluate and visualize the data. Characterisation of the radiation situation in a realistic environment can be very complex, and efficient visualisation of the data to the user is not straight forward. The monitoring and planning tools elaborated in the frame of the HRP feature very sophisticated three-dimensional (3D) high definition visualisation and user interfaces to promote easy interpretation of the input data. The visualisation tools permit dynamic visualisation of radiation fields in virtual or augmented reality by various techniques and real-time personal monitoring of humanoid models. In addition new techniques are being elaborated to visualise the 3D distribution of activities in structures and materials. The dosimetric algorithms, feeding information to the visualisation and user interface of these planning tools, include deterministic radiation transport techniques suitable for fast photon dose estimates, in case physical and radio- and spectrometric characteristics of the gamma sources are known. The basic deterministic model, implemented in earlier

Polystyrene Backbone Polymers Consisting of Alkyl-Substituted Triazine Side Groups for Phosphorescent OLEDs

Directory of Open Access Journals (Sweden)

Beatrice Ch. D. Salert

2012-01-01

Full Text Available This paper describes the synthesis of new electron-transporting styrene monomers and their corresponding polystyrenes all with a 2,4,6-triphenyl-1,3,5-triazine basic structure in the side group. The monomers differ in the alkyl substitution and in the meta-/paralinkage of the triazine to the polymer backbone. The thermal and spectroscopic properties of the new electron-transporting polymers are discussed in regard to their chemical structures. Phosphorescent OLEDs were prepared using the obtained electron-transporting polymers as the emissive layer material in blend systems together with a green iridium-based emitter 13 and a small molecule as an additional cohost with wideband gap characteristics (CoH-001. The performance of the OLEDs was characterized and discussed in regard to the chemical structure of the new electron-transporting polymers.

Extensive Air Showers: from the muonic smoking guns to the hadronic backbone

Directory of Open Access Journals (Sweden)

Cazon L.

2013-06-01

Full Text Available Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many kilometers almost unaffected. Muons are smoking guns of the hadronic cascade: the energy, transverse momentum, spatial distribution and depth of production are key to reconstruct the history of the air shower. In this work, we overview the phenomenology of muons on the air shower and its relation to the hadronic cascade. We briefly review the experimental efforts to analyze muons within air showers and discuss possible paths to use this information.

Backbone of complex networks of corporations: The flow of control

Science.gov (United States)

Glattfelder, J. B.; Battiston, S.

2009-09-01

We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

Red fluorescent probes for real-time imaging of the cell cycle by dynamic monitoring of the nucleolus and chromosome.

Science.gov (United States)

Wang, Kang-Nan; Chao, Xi-Juan; Liu, Bing; Zhou, Dan-Jie; He, Liang; Zheng, Xiao-Hui; Cao, Qian; Tan, Cai-Ping; Zhang, Chen; Mao, Zong-Wan

2018-03-08

Two cationic molecular rotors, 1 and 2, capable of real-time cell-cycle imaging by specifically dynamic monitoring of nucleolus and chromosome changes were developed. A further study shows that fluorescence enhancements in the nucleolus and chromosome are attributed to a combination effect of interaction with nucleic acid and high condensation of the nucleolus and chromosome.

Dynamic wall demonstration project

Energy Technology Data Exchange (ETDEWEB)

Nakatsui, L.; Mayhew, W.

1990-12-01

The dynamic wall concept is a ventilation strategy that can be applied to a single family dwelling. With suitable construction, outside air can be admitted through the exterior walls of the house to the interior space to function as ventilation air. The construction and performance monitoring of a demonstration house built to test the dynamic wall concept in Sherwood Park, Alberta, is described. The project had the objectives of demonstrating and assessing the construction methods; determining the cost-effectiveness of the concept in Alberta; analyzing the operation of the dynamic wall system; and determining how other components and systems in the house interact with the dynamic wall. The exterior wall construction consisted of vinyl siding, spun-bonded polyolefin-backed (SBPO) rigid fiberglass sheathing, 38 mm by 89 mm framing, fiberglass batt insulation and 12.7 mm drywall. The mechanical system was designed to operate in the dynamic (negative pressure) mode, however flexibility was provided to allow operation in the static (balanced pressure) mode to permit monitoring of the walls as if they were in a conventional house. The house was monitored by an extensive computerized monitoring system. Dynamic wall operation was dependent on pressure and temperature differentials between indoor and outdoor as well as wind speed and direction. The degree of heat gain was found to be ca 74% of the indoor-outdoor temperature differential. Temperature of incoming dynamic air was significantly affected by solar radiation and measurement of indoor air pollutants found no significant levels. 4 refs., 34 figs., 11 tabs.

PROSPECTIVE PRIMARY SCHOOL TEACHERS’ FOREIGN LANGUAGE SOCIOCULTURAL COMPETENCE: MONITORING PRINCIPLES

Directory of Open Access Journals (Sweden)

Olena Ishutina

2016-04-01

Full Text Available The paper substantiates the necessity and importance of the organization of prospective primary school teachers’ foreign language sociocultural competence monitoring in the educational process of high school. The author notes that prospective primary school teachers’ foreign language sociocultural competence is inseparably linked with linguomethodological competence. It is proved that the measurement of foreign language sociocultural competence of primary school foreign language teachers should be performed in the process of lingvomethodological training of the students as lingvomethodological competence occupies a dominant place and is a unifying and a backbone for other competencies of the future teacher’s professiogram. In this regard, the concept of “foreign language sociocultural competence of prospective primary school teacher” is clarified, the essence of lingvomethodological monitoring of foreign language sociocultural competence is revealed. It is emphasized that linguistic disciplines (“The practice of oral and written language”, “Practical grammar of a foreign language”, “Practical phonetics of a foreign language”, etc. and linguomethodological courses (“Methods of teaching English at primary school”, “ICT in learning foreign languages”, “Innovative technologies of learning foreign languages”, etc. play very important role in forming “foreign language sociocultural competence of prospective primary school teacher”. Specific principles of lingvomethodological monitoring of foreign language sociocultural competence are identified and characterized. They are complexity, lingvomethodological orientation, validity, multi-vector monitoring procedures.

Computational Model and Numerical Simulation for Submerged Mooring Monitoring Platform’s Dynamical Response

Directory of Open Access Journals (Sweden)

He Kongde

2015-01-01

Full Text Available Computational model and numerical simulation for submerged mooring monitoring platform were formulated aimed at the dynamical response by the action of flow force, which based on Hopkinson impact load theory, taken into account the catenoid effect of mooring cable and revised the difference of tension and tangential direction action force by equivalent modulus of elasticity. Solved the equation by hydraulics theory and structural mechanics theory of oceaneering, studied the response of buoy on flow force. The validity of model were checked and the results were in good agreement; the result show the buoy will engender biggish heave and swaying displacement, but the swaying displacement got stable quickly and the heaven displacement cause vibration for the vortex-induced action by the flow.

Track-monitoring from the dynamic response of an operational train

Science.gov (United States)

Lederman, George; Chen, Siheng; Garrett, James; Kovačević, Jelena; Noh, Hae Young; Bielak, Jacobo

2017-03-01

We explore a data-driven approach for monitoring rail infrastructure from the dynamic response of a train in revenue-service. Presently, track inspection is performed either visually or with dedicated track geometry cars. In this study, we examine a more economical approach where track inspection is performed by analyzing vibration data collected from an operational passenger train. The high frequency with which passenger trains travel each section of track means that faults can be detected sooner than with dedicated inspection vehicles, and the large number of passes over each section of track makes a data-driven approach statistically feasible. We have deployed a test-system on a light-rail vehicle and have been collecting data for the past two years. The collected data underscores two of the main challenges that arise in train-based track monitoring: the speed of the train at a given location varies from pass to pass and the position of the train is not known precisely. In this study, we explore which feature representations of the data best characterize the state of the tracks despite these sources of uncertainty (i.e., in the spatial domain or frequency domain), and we examine how consistently change detection approaches can identify track changes from the data. We show the accuracy of these different representations, or features, and different change detection approaches on two types of track changes, track replacement and tamping (a maintenance procedure to improve track geometry), and two types of data, simulated data and operational data from our test-system. The sensing, signal processing, and data analysis we propose in the study could facilitate safer trains and more cost-efficient maintenance in the future. Moreover, the proposed approach is quite general and could be extended to other parts of the infrastructure, including bridges.

Effects of chemical modifications on photophysics and exciton dynamics on {pi}-conjugation attenuated and metal-chelated photoconducting polymers

Energy Technology Data Exchange (ETDEWEB)

Chen, L. X.; Jager, W. J. H.; Gosztola, D. J.; Niemczyk, M. P.; Wasielewski, M. R.

2000-03-11

Effects of two types of chemical modifications on photoconducting polymers consisting of polyphenylenevinylene (PPV) derivatives are studied by static and ultrafast transient optical spectroscopy as well as semi-empirical ZINDO calculations. The first type of modification inserts 2,2{prime}-bipyridyl-5-vinylene units (bpy V) in the PPV backbone, and the second type involves metal-chelation with the bpy sites. Photoluminescence and exciton dynamics of polymers 1 and 2 with PV:bpyV ratios of 1 and 3 were examined in solution, and compared to those of the homopolymer, poly(2,5-bis(2{prime}-ethylhexyloxy)-1,4-phenylenevinylene) (BEH-PPV). Similar studies were carried out for several metal-chelated polymers. These results can be explained by changes in {pi}-conjugation throughout the polymer backbone. The attenuation in {pi}-conjugation by the chemical modifications transforms a conducting polymer from one-dimensional semiconductor to molecular aggregates.

APSY-NMR for protein backbone assignment in high-throughput structural biology

Energy Technology Data Exchange (ETDEWEB)

Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

2015-01-15

A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network.

Science.gov (United States)

Lyons, James; Dehzangi, Abdollah; Heffernan, Rhys; Sharma, Alok; Paliwal, Kuldip; Sattar, Abdul; Zhou, Yaoqi; Yang, Yuedong

2014-10-30

Because a nearly constant distance between two neighbouring Cα atoms, local backbone structure of proteins can be represented accurately by the angle between C(αi-1)-C(αi)-C(αi+1) (θ) and a dihedral angle rotated about the C(αi)-C(αi+1) bond (τ). θ and τ angles, as the representative of structural properties of three to four amino-acid residues, offer a description of backbone conformations that is complementary to φ and ψ angles (single residue) and secondary structures (>3 residues). Here, we report the first machine-learning technique for sequence-based prediction of θ and τ angles. Predicted angles based on an independent test have a mean absolute error of 9° for θ and 34° for τ with a distribution on the θ-τ plane close to that of native values. The average root-mean-square distance of 10-residue fragment structures constructed from predicted θ and τ angles is only 1.9Å from their corresponding native structures. Predicted θ and τ angles are expected to be complementary to predicted ϕ and ψ angles and secondary structures for using in model validation and template-based as well as template-free structure prediction. The deep neural network learning technique is available as an on-line server called Structural Property prediction with Integrated DEep neuRal network (SPIDER) at http://sparks-lab.org. Copyright © 2014 Wiley Periodicals, Inc.

Assignment by Negative-Ion Electrospray Tandem Mass Spectrometry of the Tetrasaccharide Backbones of Monosialylated Glycans Released from Bovine Brain Gangliosides

Science.gov (United States)

Chai, Wengang; Zhang, Yibing; Mauri, Laura; Ciampa, Maria G.; Mulloy, Barbara; Sonnino, Sandro; Feizi, Ten

2018-05-01

Gangliosides, as plasma membrane-associated sialylated glycolipids, are antigenic structures and they serve as ligands for adhesion proteins of pathogens, for toxins of bacteria, and for endogenous proteins of the host. The detectability by carbohydrate-binding proteins of glycan antigens and ligands on glycolipids can be influenced by the differing lipid moieties. To investigate glycan sequences of gangliosides as recognition structures, we have underway a program of work to develop a "gangliome" microarray consisting of isolated natural gangliosides and neoglycolipids (NGLs) derived from glycans released from them, and each linked to the same lipid molecule for arraying and comparative microarray binding analyses. Here, in the first phase of our studies, we describe a strategy for high-sensitivity assignment of the tetrasaccharide backbones and application to identification of eight of monosialylated glycans released from bovine brain gangliosides. This approach is based on negative-ion electrospray mass spectrometry with collision-induced dissociation (ESI-CID-MS/MS) of the desialylated glycans. Using this strategy, we have the data on backbone regions of four minor components among the monosialo-ganglioside-derived glycans; these are of the ganglio-, lacto-, and neolacto-series.

Dynamic system for the evaluation of CIM monitoring and control techniques; Sistema dinamico para avaliacao de tecnicas de monitoracao e controle da CIM

Energy Technology Data Exchange (ETDEWEB)

Penna, Monica de Oliveira [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES). Biotecnologia e Ecossistemas]. E-mail: mpena@cenpes.petrobras.com.br; Baptista, Walmar; Brito, Rosane Fernandes de [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES). Tecnologia de Materiais, Equipamentos e Corrosao]. E-mails: walmar@cenpes.petrobras.com.br; rosanef@cenpes.petrobras.com.br; Silva, Edilson Domingos da; Nascimento, Juliana Rangel do [Fundacao Gorceix, Ouro Preto, MG (Brazil)]. E-mails: edilson@cenpes.petrobras.com.br; julianarn@cenpes.petrobras.com.br; Coutinho, Claudia M.L.M. [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Inst. de Biologia. Dept. de Biologia Celular e Molecular

2002-03-01

In general, the two main problems associated to the water injection system for secondary petroleum recovery are the corrosion control and the decrease in solid injection in the reservoir. Corrosion problems in injection water systems may have abiotic as well as biotic causes, and the occurrence of reservoir plugs can result from the injection of particles (suspended solids as well as corrosion products), bacteria and fouling formation. Due to the need to implement a methodology for the evaluation of abiotic and biotic corrosive processes, monitoring techniques and MIC control in a dynamic system, an apparatus was built that simulates the characteristics of a water injection system. The apparatus allows monitoring and control of the parameters that, when varied, may influence the performance of the quality of the injected water. The dynamic system was designed to simulate as precisely as possible the conditions that allow the SRB and heterotrophic bacteria to create fouling in a water injection system. This article discusses the dynamic system, analytical methods and some preliminary results. (author)

Complete resonance assignment for the polypeptide backbone of interleukin 1β using three-dimensional heteronuclear NMR spectroscopy

International Nuclear Information System (INIS)

Driscoll, P.C.; Clore, G.M.; Marion, D.; Gronenborn, A.M.; Wingfield, P.T.

1990-01-01

The complete sequence-specific assignment of the 15 N and 1 H backbone resonances of the NMR spectrum of recombinant human interleukin 1β has been obtained by using primarily 15 N- 1 H heteronuclear three-dimensional (3D) NMR techniques in combination with 15 N- 1 H heteronuclear and 1 H homonuclear two-dimensional NMR. The fingerprint region of the spectrum was analyzed by using a combination of 3D heteronuclear 1 H Hartmann-Hahn 15 N- 1 H multiple quantum coherence (3D HOHAHA-HMQC) and 3D heteronuclear 1 H nuclear Overhauser 15 N- 1 H multiple quantum coherence (3D NOESY-HMQC) spectroscopies. The authors show that the problems of amide NH and C α H chemical shift degeneracy that are prevalent for proteins of the size are readily overcome by using the 3D heteronuclear NMR technique. A doubling of some peaks in the spectrum was found to be due to N-terminal heterogeneity of the 15 N-labeled protein, corresponding to a mixture of wild-type and des-Ala-1-interleukin 1β. The complete list of 15 N and 1 H assignments is given for all the amide NH and C α H resonances of all non-proline residues, as well as the 1 H assignments for some of the amino acid side chains. This first example of the sequence-specific assignment of a protein using heteronuclear 3D NMR provides a basis for further conformational and dynamic studies of interleukin 1β

Monitoring of Bridges by a Laser Pointer: Dynamic Measurement of Support Rotations and Elastic Line Displacements: Methodology and First Test.

Science.gov (United States)

Artese, Serena; Achilli, Vladimiro; Zinno, Raffaele

2018-01-25

Deck inclination and vertical displacements are among the most important technical parameters to evaluate the health status of a bridge and to verify its bearing capacity. Several methods, both conventional and innovative, are used for structural rotations and displacement monitoring; however, none of these allow, at the same time, precision, automation, static and dynamic monitoring without using high cost instrumentation. The proposed system uses a common laser pointer and image processing. The elastic line inclination is measured by analyzing the single frames of an HD video of the laser beam imprint projected on a flat target. For the image processing, a code was developed in Matlab ® that provides instantaneous rotation and displacement of a bridge, charged by a mobile load. An important feature is the synchronization of the load positioning, obtained by a GNSS receiver or by a video. After the calibration procedures, a test was carried out during the movements of a heavy truck maneuvering on a bridge. Data acquisition synchronization allowed us to relate the position of the truck on the deck to inclination and displacements. The inclination of the elastic line at the support was obtained with a precision of 0.01 mrad. The results demonstrate the suitability of the method for dynamic load tests, and the control and monitoring of bridges.

Monitoring of Bridges by a Laser Pointer: Dynamic Measurement of Support Rotations and Elastic Line Displacements: Methodology and First Test

Directory of Open Access Journals (Sweden)

Serena Artese

2018-01-01

Full Text Available Deck inclination and vertical displacements are among the most important technical parameters to evaluate the health status of a bridge and to verify its bearing capacity. Several methods, both conventional and innovative, are used for structural rotations and displacement monitoring; however, none of these allow, at the same time, precision, automation, static and dynamic monitoring without using high cost instrumentation. The proposed system uses a common laser pointer and image processing. The elastic line inclination is measured by analyzing the single frames of an HD video of the laser beam imprint projected on a flat target. For the image processing, a code was developed in Matlab® that provides instantaneous rotation and displacement of a bridge, charged by a mobile load. An important feature is the synchronization of the load positioning, obtained by a GNSS receiver or by a video. After the calibration procedures, a test was carried out during the movements of a heavy truck maneuvering on a bridge. Data acquisition synchronization allowed us to relate the position of the truck on the deck to inclination and displacements. The inclination of the elastic line at the support was obtained with a precision of 0.01 mrad. The results demonstrate the suitability of the method for dynamic load tests, and the control and monitoring of bridges.

On non-linear dynamics of a coupled electro-mechanical system

DEFF Research Database (Denmark)

Darula, Radoslav; Sorokin, Sergey

2012-01-01

Electro-mechanical devices are an example of coupled multi-disciplinary weakly non-linear systems. Dynamics of such systems is described in this paper by means of two mutually coupled differential equations. The first one, describing an electrical system, is of the first order and the second one...... excitation. The results are verified using a numerical model created in MATLAB Simulink environment. Effect of non-linear terms on dynamical response of the coupled system is investigated; the backbone and envelope curves are analyzed. The two phenomena, which exist in the electro-mechanical system: (a......, for mechanical system, is of the second order. The governing equations are coupled via linear and weakly non-linear terms. A classical perturbation method, a method of multiple scales, is used to find a steadystate response of the electro-mechanical system exposed to a harmonic close-resonance mechanical...

AUTOBA: automation of backbone assignment from HN(C)N suite of experiments.

Science.gov (United States)

Borkar, Aditi; Kumar, Dinesh; Hosur, Ramakrishna V

2011-07-01

Development of efficient strategies and automation represent important milestones of progress in rapid structure determination efforts in proteomics research. In this context, we present here an efficient algorithm named as AUTOBA (Automatic Backbone Assignment) designed to automate the assignment protocol based on HN(C)N suite of experiments. Depending upon the spectral dispersion, the user can record 2D or 3D versions of the experiments for assignment. The algorithm uses as inputs: (i) protein primary sequence and (ii) peak-lists from user defined HN(C)N suite of experiments. In the end, one gets H(N), (15)N, C(α) and C' assignments (in common BMRB format) for the individual residues along the polypeptide chain. The success of the algorithm has been demonstrated, not only with experimental spectra recorded on two small globular proteins: ubiquitin (76 aa) and M-crystallin (85 aa), but also with simulated spectra of 27 other proteins using assignment data from the BMRB.

Monitoring groundwater storage changes in the highly dynamic Bengal Basin: validation of GRACE measurements

Science.gov (United States)

Shamsudduha, M.; Taylor, R. G.; Longuevergne, L.

2011-12-01

Monitoring of spatio-temporal changes in terrestrial water storage (ΔTWS) provides valuable information regarding the basin-scale dynamics of hydrological systems. Recent satellite measurements of the ΔTWS under the Gravity Recovery and Climate Experiment (GRACE) enable the derivation of groundwater storage changes (ΔGWS) where in situ data are limited. In the well monitored and highly-dynamic Bengal Basin of Bangladesh, we test the ability of GRACE measurements to trace the seasonality and trend in groundwater storage associated with intensive groundwater abstraction for dry-season irrigation and wet-season (monsoonal) recharge. Two different GRACE products (CSR and GRGS) and data processing methods (gridded and spherical harmonics) are also compared. Results show that GRACE derived estimates of recent (2003 to 2007) ΔGWS correlate well (r=0.77 to 0.93, p-value CSR for these estimates. ΔGWS accounts for 44% of the total variation in ΔTWS in the Bengal Basin. Changes in surface water storage (ΔSWS) estimated from a network of 298 river gauging stations and soil moisture storage (ΔSMS) derived from Land Surface Models explain 22% and 33% of ΔTWS respectively. Groundwater depletion estimated from borehole hydrographs (-0.52±0.30 km3/yr) is within the range of satellite-derived estimates (-0.44 to -2.04 km3/yr) that result from uncertainty associated with ΔSMS (CLM, NOAH, VIC) and GRACE data processing techniques. Recent (2003 to 2007) estimates of groundwater depletion are substantially greater than the long-term (1985 to 2007) mean (-0.21±0.03 km3/yr) and are explained primarily by substantial increases in groundwater abstraction for the dry-season irrigation and drinking water supplies over the last two decades.

A density functional study of backbone structures of polydiacetylene: destabilization of butatriene structure

International Nuclear Information System (INIS)

Katagiri, Hideki; Shimoi, Yukihiro; Abe, Shuji

2004-01-01

Backbone structures of polydiacetylene are studied with first-principles electronic structure method using plane-waves within generalized gradient approximation (GGA) of density functional theory. In spin-restricted calculations a coarse k-point sampling gives a potential energy curve with two local minima corresponding to acetylene and butatriene structures. However, the potential barrier between the two structures rapidly decreases with increasing number of k-points, which results in destabilization of the butatriene structure. Spin polarization effects also destabilize the butatriene structure, inducing atom-centered spin-density-wave state. These potential energies were compared with those obtained by Hartree-Fock, density functional within local density approximation (LDA) and GGA, and hybrid density functional methods using a gaussian basis set. The comparison shows that the density functional methods within LDA and GGA favor the destabilization of the butatriene structure in contrast to the Hartree-Fock method

Experimental Tracking of Limit-Point Bifurcations and Backbone Curves Using Control-Based Continuation

Science.gov (United States)

Renson, Ludovic; Barton, David A. W.; Neild, Simon A.

Control-based continuation (CBC) is a means of applying numerical continuation directly to a physical experiment for bifurcation analysis without the use of a mathematical model. CBC enables the detection and tracking of bifurcations directly, without the need for a post-processing stage as is often the case for more traditional experimental approaches. In this paper, we use CBC to directly locate limit-point bifurcations of a periodically forced oscillator and track them as forcing parameters are varied. Backbone curves, which capture the overall frequency-amplitude dependence of the system’s forced response, are also traced out directly. The proposed method is demonstrated on a single-degree-of-freedom mechanical system with a nonlinear stiffness characteristic. Results are presented for two configurations of the nonlinearity — one where it exhibits a hardening stiffness characteristic and one where it exhibits softening-hardening.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

Directory of Open Access Journals (Sweden)

Mingyuan Xu

2018-05-01

Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Combined approach with therapeutic drug monitoring and pharmacogenomics in renal transplant recipients

Directory of Open Access Journals (Sweden)

S Manvizhi

2013-01-01

Full Text Available In patients undergoing renal transplantation, dose individualization for tacrolimus is routinely achieved with therapeutic drug monitoring (TDM. The patient started on 5.5 mg/day of tacrolimus had a significantly elevated tacrolimus trough concentration. The tacrolimus dose was regularly reduced following TDM at many time periods in the post transplant period but the tacrolimus concentration was consistently elevated. Genomic analysis done after four years revealed mutations in the genes encoding for CYP3A5 and MDR1 (2677G > T. Pharmacogenomics alongside TDM, will soon emerge as the backbone of dose individualization. But for genomics to be beneficial, it should be advocated in the pre-transplant or early post transplant period.

Power system observability and dynamic state estimation for stability monitoring using synchrophasor measurements

Energy Technology Data Exchange (ETDEWEB)

Sun, Kai; Qi, Junjian; Kang, Wei

2016-08-01

Growing penetration of intermittent resources such as renewable generations increases the risk of instability in a power grid. This paper introduces the concept of observability and its computational algorithms for a power grid monitored by the wide-area measurement system (WAMS) based on synchrophasors, e.g. phasor measurement units (PMUs). The goal is to estimate real-time states of generators, especially for potentially unstable trajectories, the information that is critical for the detection of rotor angle instability of the grid. The paper studies the number and siting of synchrophasors in a power grid so that the state of the system can be accurately estimated in the presence of instability. An unscented Kalman filter (UKF) is adopted as a tool to estimate the dynamic states that are not directly measured by synchrophasors. The theory and its computational algorithms are illustrated in detail by using a 9-bus 3-generator power system model and then tested on a 140-bus 48-generator Northeast Power Coordinating Council power grid model. Case studies on those two systems demonstrate the performance of the proposed approach using a limited number of synchrophasors for dynamic state estimation for stability assessment and its robustness against moderate inaccuracies in model parameters.

Characterization of Bifunctional Spin Labels for Investigating the Structural and Dynamic Properties of Membrane Proteins Using EPR Spectroscopy.

Science.gov (United States)

Sahu, Indra D; Craig, Andrew F; Dunagum, Megan M; McCarrick, Robert M; Lorigan, Gary A

2017-10-05

Site-directed spin labeling (SDSL) coupled with electron paramagnetic resonance (EPR) spectroscopy is a very powerful technique to study structural and dynamic properties of membrane proteins. The most widely used spin label is methanthiosulfonate (MTSL). However, the flexibility of this spin label introduces greater uncertainties in EPR measurements obtained for determining structures, side-chain dynamics, and backbone motion of membrane protein systems. Recently, a newer bifunctional spin label (BSL), 3,4-bis(methanethiosulfonylmethyl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-1-yloxy, has been introduced to overcome the dynamic limitations associated with the MTSL spin label and has been invaluable in determining protein backbone dynamics and inter-residue distances due to its restricted internal motion and fewer size restrictions. While BSL has been successful in providing more accurate information about the structure and dynamics of several proteins, a detailed characterization of the spin label is still lacking. In this study, we characterized BSLs by performing CW-EPR spectral line shape analysis as a function of temperature on spin-labeled sites inside and outside of the membrane for the integral membrane protein KCNE1 in POPC/POPG lipid bilayers and POPC/POPG lipodisq nanoparticles. The experimental data revealed a powder pattern spectral line shape for all of the KCNE1-BSL samples at 296 K, suggesting the motion of BSLs approaches the rigid limit regime for these series of samples. BSLs were further utilized to report for the first time the distance measurement between two BSLs attached on an integral membrane protein KCNE1 in POPC/POPG lipid bilayers at room temperature using dipolar line broadening CW-EPR spectroscopy. The CW dipolar line broadening EPR data revealed a 15 ± 2 Å distance between doubly attached BSLs on KCNE1 (53/57-63/67) which is consistent with molecular dynamics modeling and the solution NMR structure of KCNE1 which yielded a

Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA.

Science.gov (United States)

Hithell, Gordon; Shaw, Daniel J; Donaldson, Paul M; Greetham, Gregory M; Towrie, Michael; Burley, Glenn A; Parker, Anthony W; Hunt, Neil T

2016-05-05

Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA.

CODAS object monitoring service

International Nuclear Information System (INIS)

Wheatley, M.R.; Rainford, M.

2001-01-01

The primary Control and Data Acquisition System (CODAS) of JET is based on a TCP/IP network of more than 150 computers. The CODAS computers provide the JET machine control and data acquisition for over 70,000 digital and analog signals. The Object Monitoring Service (OMS) is used by applications for monitoring objects for presentation to the JET machine operators and for the operation of individual software components (such as valve state, access control, mimic definition changes and internal data distribution). Each server typically handles connections from around 60 clients monitoring upwards of 2000 objects. Some servers have over 150 clients and 5000 objects. Acquisition libraries are dynamically linked into a running server as required either to acquire data values for objects or to forward requests to other OMS servers. A mechanism involving dynamic linking allows new libraries to be integrated without stopping or changing running software. OMS provides a very reliable and highly successful 'data-type independent' means of monitoring many different objects. It allows applications to take advantage of new data sources, without the need to change existing code

Corrosion Resistant FBG-Based Quasi-Distributed Sensor for Crude Oil Tank Dynamic Temperature Profile Monitoring

Science.gov (United States)

da Silva Marques, Rogério; Prado, Adilson Ribeiro; da Costa Antunes, Paulo Fernando; de Brito André, Paulo Sérgio; Ribeiro, Moisés R. N.; Frizera-Neto, Anselmo; Pontes, Maria José

2015-01-01

This article presents a corrosion resistant, maneuverable, and intrinsically safe fiber Bragg grating (FBG)-based temperature optical sensor. Temperature monitoring is a critical activity for the oil and gas industry. It typically involves acquiring the desired parameters in a hazardous and corrosive environment. The use of polytetrafluoroethylene (PTFE) was proposed as a means of simultaneously isolating the optical fiber from the corrosive environment and avoiding undesirable mechanical tensions on the FBGs. The presented sensor head is based on multiple FBGs inscribed in a lengthy single mode fiber. The sensor presents an average thermal sensitivity of 8.82 ± 0.09 pm/°C, resulting in a typical temperature resolution of ~0.1 °C and an average time constant value of 6.25 ± 0.08 s. Corrosion and degradation resistance were verified by infrared spectroscopy and scanning electron microscopy during 90 days exposure to high salinity crude oil samples. The developed sensor was tested in a field pilot test, mimicking the operation of an inland crude tank, demonstrating its abilities to dynamically monitor temperature profile. PMID:26690166

Methodology of Dynamic Monitoring of Structures in the Vicinity of Hydrotechnical Works - Selected Case Studies

Science.gov (United States)

Wyjadłowski, Marek

2017-12-01

The constant development of geotechnical technologies imposes the necessity of monitoring techniques to provide a proper quality and the safe execution of geotechnical works. Several monitoring methods enable the preliminary design of work process and current control of hydrotechnical works (pile driving, sheet piling, ground improvement methods). Wave parameter measurements and/or continuous histogram recording of shocks and vibrations and its dynamic impact on engineering structures in the close vicinity of the building site enable the modification of the technology parameters, such as vibrator frequency or hammer drop height. Many examples of practical applications have already been published and provide a basis for the formulation of guidelines, for work on the following sites. In the current work the author's experience gained during sheet piling works for the reconstruction of City Channel in Wrocław (Poland) was presented. The examples chosen describe ways of proceedings in the case of new and old residential buildings where the concrete or masonry walls were exposed to vibrations and in the case of the hydrotechnical structures (sluices, bridges).

Automated modal tracking and fatigue assessment of a wind turbine based on continuous dynamic monitoring

Directory of Open Access Journals (Sweden)

Oliveira Gustavo

2015-01-01

Full Text Available The paper describes the implementation of a dynamic monitoring system at a 2.0 MW onshore wind turbine. The system is composed by two components aiming at the structural integrity and fatigue assessment. The first component enables the continuous tracking of modal characteristics of the wind turbine (natural frequency values, modal damping ratios and mode shapes in order to detect abnormal deviations of these properties, which may be caused by the occurrence of structural damage. On the other hand, the second component allows the estimation of the remaining fatigue lifetime of the structure based on the analysis of the measured cycles of structural vibration.

A wearable wireless ECG monitoring system with dynamic transmission power control for long-term homecare.

Science.gov (United States)

Wang, Yishan; Doleschel, Sammy; Wunderlich, Ralf; Heinen, Stefan

2015-03-01

This paper presents a wearable wireless ECG monitoring system based on novel 3-Lead electrode placements for long-term homecare. The experiment for novel 3-Lead electrode placements is carried out, and the results show that the distance between limb electrodes can be significantly reduced. Based on the new electrode position, a small size sensor node, which is powered by a rechargeable battery, is designed to detect, amplify, filter and transmit the ECG signals. The coordinator receives the data and sends it to PC. Finally the signals are displayed on the GUI. In order to control the power consumption of sensor node, a dynamic power adjustment method is applied to automatically adjust the transmission power of the sensor node according to the received signal strength indicator (RSSI), which is related to the distance and obstacle between sensor node and coordinator. The system is evaluated when the user, who wears the sensor, is walking and running. A promising performance is achieved even under body motion. The power consumption can be significantly reduced with this dynamic power adjustment method.

Assignment of protein backbone resonances using connectivity, torsion angles and 13Cα chemical shifts

International Nuclear Information System (INIS)

Morris, Laura C.; Valafar, Homayoun; Prestegard, James H.

2004-01-01

A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just 13 C α chemical shifts (δ( 13 C α )) and data restricting the φ and ψ backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in δ( 13 C α ), φ, and ψ space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and 13 C α chemical shift data are available

Comparison of dynamic monitoring strategies based on CD4 cell counts in virally suppressed, HIV-positive individuals on combination antiretroviral therapy in high-income countries: a prospective, observational study

NARCIS (Netherlands)

Caniglia, Ellen C.; Cain, Lauren E.; Sabin, Caroline A.; Robins, James M.; Logan, Roger; Abgrall, Sophie; Mugavero, Michael J.; Hernández-Díaz, Sonia; Meyer, Laurence; Seng, Remonie; Drozd, Daniel R.; Seage, George R.; Bonnet, Fabrice; Dabis, Francois; Moore, Richard D.; Reiss, Peter; van Sighem, Ard; Mathews, William C.; del Amo, Julia; Moreno, Santiago; Deeks, Steven G.; Muga, Roberto; Boswell, Stephen L.; Ferrer, Elena; Eron, Joseph J.; Napravnik, Sonia; Jose, Sophie; Phillips, Andrew; Justice, Amy C.; Tate, Janet P.; Gill, John; Pacheco, Antonio; Veloso, Valdilea G.; Bucher, Heiner C.; Egger, Matthias; Furrer, Hansjakob; Porter, Kholoud; Touloumi, Giota; Crane, Heidi; Miro, Jose M.; Sterne, Jonathan A.; Costagliola, Dominique; Saag, Michael; Hernán, Miguel A.

2017-01-01

Clinical guidelines vary with respect to the optimal monitoring frequency of HIV-positive individuals. We compared dynamic monitoring strategies based on time-varying CD4 cell counts in virologically suppressed HIV-positive individuals. In this observational study, we used data from prospective

On-line dynamic monitoring automotive exhausts: using BP-ANN for distinguishing multi-components

Science.gov (United States)

Zhao, Yudi; Wei, Ruyi; Liu, Xuebin

2017-10-01

Remote sensing-Fourier Transform infrared spectroscopy (RS-FTIR) is one of the most important technologies in atmospheric pollutant monitoring. It is very appropriate for on-line dynamic remote sensing monitoring of air pollutants, especially for the automotive exhausts. However, their absorption spectra are often seriously overlapped in the atmospheric infrared window bands, i.e. MWIR (3 5μm). Artificial Neural Network (ANN) is an algorithm based on the theory of the biological neural network, which simplifies the partial differential equation with complex construction. For its preferable performance in nonlinear mapping and fitting, in this paper we utilize Back Propagation-Artificial Neural Network (BP-ANN) to quantitatively analyze the concentrations of four typical industrial automotive exhausts, including CO, NO, NO2 and SO2. We extracted the original data of these automotive exhausts from the HITRAN database, most of which virtually overlapped, and established a mixed multi-component simulation environment. Based on Beer-Lambert Law, concentrations can be retrieved from the absorbance of spectra. Parameters including learning rate, momentum factor, the number of hidden nodes and iterations were obtained when the BP network was trained with 80 groups of input data. By improving these parameters, the network can be optimized to produce necessarily higher precision for the retrieved concentrations. This BP-ANN method proves to be an effective and promising algorithm on dealing with multi-components analysis of automotive exhausts.

On the Computational Complexity of the Languages of General Symbolic Dynamical Systems and Beta-Shifts

DEFF Research Database (Denmark)

Simonsen, Jakob Grue

2009-01-01

We consider the computational complexity of languages of symbolic dynamical systems. In particular, we study complexity hierarchies and membership of the non-uniform class P/poly. We prove: 1.For every time-constructible, non-decreasing function t(n)=@w(n), there is a symbolic dynamical system...... with language decidable in deterministic time O(n^2t(n)), but not in deterministic time o(t(n)). 2.For every space-constructible, non-decreasing function s(n)=@w(n), there is a symbolic dynamical system with language decidable in deterministic space O(s(n)), but not in deterministic space o(s(n)). 3.There...... are symbolic dynamical systems having hard and complete languages under @?"m^l^o^g^s- and @?"m^p-reduction for every complexity class above LOGSPACE in the backbone hierarchy (hence, P-complete, NP-complete, coNP-complete, PSPACE-complete, and EXPTIME-complete sets). 4.There are decidable languages of symbolic...

Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

International Nuclear Information System (INIS)

Mugnai, Mauro L.; Elber, Ron

2015-01-01

We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide

Application of online chemistry monitoring programs and technology

International Nuclear Information System (INIS)

Perkins, D.; Choi, S.; Haas, C.

2010-01-01

To fully understand the impact of chemistry changes, several plant parameters must be considered and reviewed with actual chemistry analyses and compared to plant operating parameters. In some cases, this requires the ability to rapidly correlate plant operational data with laboratory and chemistry data. An effective online monitoring system should be able to: Integrate and extract online data from the plant laboratory and operating information from various plant data sources continuously; Interrogate and extract laboratory data from manually entered data on predefined frequencies; Interact with multiple laboratories in multiple locations; Evaluate data against plant limits (calculated or static) and provide personnel with action level or notification of plant exceeding limits; and, Provide the ability to evaluate against a standard and site specific set of calculations. The nuclear power industry continues to refine and apply new technologies in an effort to notify operators of changes in chemical conditions, calculate complex high temperature results, and monitor system performance. EPRI developed software specifically focused on plant chemistry program optimization using power operation and shutdown data applied with plant equipment. This software evolved into the family of software referred to as EPRI ChemWorks™ applications. As technology changed and improved, the application of online monitoring was essential for plant personnel working offsite. These changes in technology prompted EPRI to the development of SMART ChemWorks™ using the EPRI ChemWorks™ plant chemistry simulator and MULTEQ applications as the backbone for these simulations and calculations. SMART ChemWorks™ is an online monitoring system that queries plant databases and continuously monitors plant and chemistry parameters. The system uses a real-time intelligence engine to perform virtual sensing, identify normal and off-normal conditions and compare in-line instrument output to grab

Instrument failure monitoring in nuclear power systems

International Nuclear Information System (INIS)

Tylee, J.L.

1982-01-01

Methods of monitoring dynamic systems for instrument failures were developed and evaluated. In particular, application of these methods to nuclear power plant components is addressed. For a linear system, statistical tests on the innovations sequence of a Kalman filter driven by all system measurements provides a failure detection decision and identifies any failed sensor. This sequence (in an unfailed system) is zero-mean with calculable covariance; hence, any major deviation from these properties is assumed to be due to an instrument failure. Once a failure is identified, the failed instrument is replaced with an optimal estimate of the measured parameter. This failure accommodation is accomplished using optimally combined data from a bank of accommodation Kalman filters (one for each sensor), each driven by a single measurement. Using such a sensor replacement allows continued system operation under failed conditions and provides a system operator with information otherwise unavailable. To demonstrate monitor performance, a liner failure monitor was developed for the pressurizer in the Loss-of-Fluid Test (LOFT) reactor plant. LOFT is a small-scale pressurized water reactor (PWR) research facility located at the Idaho National Engineering Laboratory. A linear, third-order model of the pressurizer dynamics was developed from first principles and validated. Using data from the LOFT L6 test series, numerous actual and simulated water level, pressure, and temperature sensor failures were employed to illustrate monitor capabilities. Failure monitor design was applied to nonlinear dynamic systems by replacing all monitor linear Kalman filters with extended Kalman filters. A nonlinear failure monitor was derived for LOFT reactor instrumentation. A sixth-order reactor model, including descriptions of reactor kinetics, fuel rod heat transfer, and core coolant dynamics, was obtained and verified with test data

A wide dynamic range BF{sub 3} neutron monitor with front-end electronics based on a logarithmic amplifier

Energy Technology Data Exchange (ETDEWEB)

Ferrarini, M., E-mail: michele.ferrarini@polimi.i [Politecnico di Milano, Dipartimento Energia, via G. Ponzio 34/3, I-20133 Milano (Italy); Fondazione CNAO, via Caminadella 16, 20123 Milano (Italy); Varoli, V. [Politecnico di Milano, Dipartimento Energia, via G. Ponzio 34/3, I-20133 Milano (Italy); Favalli, A. [European Commission, Joint Research Centre, Institute for the Protection and Security of Citizen, TP 800, Via E. Fermi, 21027 Ispra (Vatican City State, Holy See) (Italy); Caresana, M. [Politecnico di Milano, Dipartimento Energia, via G. Ponzio 34/3, I-20133 Milano (Italy); Pedersen, B. [European Commission, Joint Research Centre, Institute for the Protection and Security of Citizen, TP 800, Via E. Fermi, 21027 Ispra (Italy)

2010-02-01

This paper describes a wide dynamic range neutron monitor based on a BF{sub 3} neutron detector. The detector is used in current mode, and front-end electronics based on a logarithmic amplifier are used in order to have a measurement capability ranging over many orders of magnitude. The system has been calibrated at the Polytechnic of Milan, CESNEF, with an AmBe neutron source, and has been tested in a pulsed field at the PUNITA facility at JRC, Ispra. The detector has achieved a dynamic range of over 6 orders of magnitude, being able to measure single neutron pulses and showing saturation-free response for a reaction rate up to 10{sup 6} s{sup -1}. It has also proved effective in measuring the PUNITA facility pulse integral fluence.

An Unusual Conformational Isomer of Verrucosidin Backbone from a Hydrothermal Vent Fungus, Penicillium sp. Y-50-10.

Science.gov (United States)

Pan, Chengqian; Shi, Yutong; Auckloo, Bibi Nazia; Chen, Xuegang; Chen, Chen-Tung Arthur; Tao, Xinyi; Wu, Bin

2016-08-18

A new verrucosidin derivative, methyl isoverrucosidinol (1), was isolated from the marine fungus Penicillium sp. Y-50-10, dwelling in sulfur rich sediment in the Kueishantao hydrothermal vents off Taiwan. The structure was established by spectroscopic means including HRMS and 2D-NMR spectroscopic analysis. The absolute configuration was defined mainly by comparison of quantum chemical TDDFT calculated and experimental ECD spectra. Among hitherto known compounds with a verrucosidine backbone isolated from natural resource, compound 1 represents the first example of a new conformational isomer of its skeleton, exhibiting antibiotic activity against Bacillus subtilis with MIC value 32 μg/mL.

Rigidity of the polypeptide backbone in the triple-stranded collagen molecule.

Science.gov (United States)

Nemethy, G

1981-02-01

Conformational energy computations were carried out on collagen-like triple-stranded conformations of several polytripeptides with the structure CH3CO(GXY)3NHCH3, where X and Y can be Pro, Ala, or Gly. The computed minimum-energy conformations for various sequences are compared with that computed earlier for poly(Gly-Pro-Pro). Usually, substitution of Ala or Gly residues for Pro does not cause any strain or distortion of the conformation of the triple-stranded complex. Thus, the structure is a very stable and essentially rigid one. Unfavorable interactions were found only in the case of CH3CO(Gly-Ala-Pro)NHCH3. These interactions are a consequence of differences between the residue geometry of Ala and Pro. They result in small changes of some backbone dihedral angles and in an increase of intra- and interchain energies. The presence of a single Gly-Ala-Pro tripeptide within a sequence of Gly-Pro-Pro tripeptides is not sufficient, however, to cause even a small distoration of the triple strand. No deviation of the peptide groups from planarity is required to stabilize the triple-stranded structure.

The surface elevation table and marker horizon technique: A protocol for monitoring wetland elevation dynamics

Science.gov (United States)

James C. Lynch,; Phillippe Hensel,; Cahoon, Donald R.

2015-01-01

The National Park Service, in response to the growing evidence and awareness of the effects of climate change on federal lands, determined that monitoring wetland elevation change is a top priority in North Atlantic Coastal parks (Stevens et al, 2010). As a result, the NPS Northeast Coastal and Barrier Network (NCBN) in collaboration with colleagues from the U.S. Geological Survey (USGS) and The National Oceanic and Atmospheric Administration (NOAA) have developed a protocol for monitoring wetland elevation change and other processes important for determining the viability of wetland communities. Although focused on North Atlantic Coastal parks, this document is applicable to all coastal and inland wetland regions. Wetlands exist within a narrow range of elevation which is influenced by local hydrologic conditions. For coastal wetlands in particular, local hydrologic conditions may be changing as sea levels continue to rise. As sea level rises, coastal wetland systems may respond by building elevation to maintain favorable hydrologic conditions for their survival. This protocol provides the reader with instructions and guidelines on designing a monitoring plan or study to: A) Quantify elevation change in wetlands with the Surface Elevation Table (SET). B) Understand the processes that influence elevation change, including vertical accretion (SET and Marker Horizon methods). C) Survey the wetland surface and SET mark to a common reference datum to allow for comparing sample stations to each other and to local tidal datums. D) Survey the SET mark to monitor its relative stability. This document is divided into two parts; the main body that presents an overview of all aspects of monitoring wetland elevation dynamics, and a collection of Standard Operating Procedures (SOP) that describes in detail how to perform or execute each step of the methodology. Detailed instruction on the installation, data collection, data management and analysis are provided in this report

On the structure of dynamic principal component analysis used in statistical process monitoring

DEFF Research Database (Denmark)

Vanhatalo, Erik; Kulahci, Murat; Bergquist, Bjarne

2017-01-01

When principal component analysis (PCA) is used for statistical process monitoring it relies on the assumption that data are time independent. However, industrial data will often exhibit serial correlation. Dynamic PCA (DPCA) has been suggested as a remedy for high-dimensional and time...... for determining the number of principal components to retain. The number of retained principal components is determined by visual inspection of the serial correlation in the squared prediction error statistic, Q (SPE), together with the cumulative explained variance of the model. The methods are illustrated using...... driven method to determine the maximum number of lags in DPCA with a foundation in multivariate time series analysis. The method is based on the behavior of the eigenvalues of the lagged autocorrelation and partial autocorrelation matrices. Given a specific lag structure we also propose a method...

The Borexino Thermal Monitoring & Management System and simulations of the fluid-dynamics of the Borexino detector under asymmetrical, changing boundary conditions

Science.gov (United States)

Bravo-Berguño, D.; Mereu, R.; Cavalcante, P.; Carlini, M.; Ianni, A.; Goretti, A.; Gabriele, F.; Wright, T.; Yokley, Z.; Vogelaar, R. B.; Calaprice, F.; Inzoli, F.

2018-03-01

A comprehensive monitoring system for the thermal environment inside the Borexino neutrino detector was developed and installed in order to reduce uncertainties in determining temperatures throughout the detector. A complementary thermal management system limits undesirable thermal couplings between the environment and Borexino's active sections. This strategy is bringing improved radioactive background conditions to the region of interest for the physics signal thanks to reduced fluid mixing induced in the liquid scintillator. Although fluid-dynamical equilibrium has not yet been fully reached, and thermal fine-tuning is possible, the system has proven extremely effective at stabilizing the detector's thermal conditions while offering precise insights into its mechanisms of internal thermal transport. Furthermore, a Computational Fluid-Dynamics analysis has been performed, based on the empirical measurements provided by the thermal monitoring system, and providing information into present and future thermal trends. A two-dimensional modeling approach was implemented in order to achieve a proper understanding of the thermal and fluid-dynamics in Borexino. It was optimized for different regions and periods of interest, focusing on the most critical effects that were identified as influencing background concentrations. Literature experimental case studies were reproduced to benchmark the method and settings, and a Borexino-specific benchmark was implemented in order to validate the modeling approach for thermal transport. Finally, fully-convective models were applied to understand general and specific fluid motions impacting the detector's Active Volume.

Monitoring coastal wetlands in a highly dynamic tropical environment

International Nuclear Information System (INIS)

Saynor, M.J.; Finlayson, C.M.; Spiers, A.; Eliot, I.

2001-01-01

The Alligator Rivers Region in the wet-dry tropics of northern Australia has been selected by government and collaborating agencies as a key study area for the monitoring of natural and human-induced coastal change. The Region contains the floodplain wetlands of Kakadu National Park which have been recognised internationally for their natural and cultural heritage value. A coastal monitoring program for assessing and monitoring environmental change in the Alligator Rivers Region has been established at the Environmental Research Institute of the Supervising Scientist. This program has developed a regional capacity to measure and assess change on the wetlands, floodplains and coastline within the region. Field assessment and monitoring procedures have been developed for the program. The assessment procedures require use of georeferencing and data handling techniques to facilitate comparison and relational overlay of a wide variety of information. Monitoring includes regular survey of biophysical and cultural processes on the floodplains; such as the extension of tidal creeks and mangroves, shoreline movement, dieback in Melaleuca wetlands, and weed invasion of freshwater wetlands. A differential Global Positioning System is used to accurately georeference spatial data and a Geographic Information System is then used to store and assess information. The assessment and monitoring procedures can be applied to the wet-dry tropics in general. These studies are all particularly pertinent with the possibility of greenhouse gases causing global warming and potential sea-level rise, a major possible threat to the valued wetlands of Kakadu National Park, and across the wet-dry tropics in general

CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data

DEFF Research Database (Denmark)

Hallin, Peter Fischer; Ussery, David

2004-01-01

, these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web...... and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently...... content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues....

Dynamics of a Novel Class of Polymers: Polymerized Sulfur

Science.gov (United States)

Masser, Kevin; Kim, Jenny; Oleshko, Vladimir; Griebel, Jared; Chung, Woo; Simmons, Adam; Pyun, Jeff; Soles, Christopher

2013-03-01

In this study we investigate the dynamics of a new type of polymer, consisting mainly of sulfur. Room-temperature stable polymerized sulfur samples were prepared by crosslinking the well-known living sulfur polymers formed at elevated temperatures by the addition of a crosslinking agent. This reverse vulcanization process was used to create a series of samples with different amounts of crosslinking agent. These polymers show great promise for use in advanced batteries as cathode materials. Each system exhibits a glassy-state beta relaxation, with the intensity of this relaxation proportional to the crosslinking content. A dynamic glass transition is also observed for each system, and the glass transition temperature/segmental relaxation moves to higher temperatures with increased crosslink content as is typically observed in crosslinked systems. As is typical of polymers, ion motion in these systems is closely coupled to the backbone motion of the host polymer. National Research Council Postdoctoral Fellowship

Effects of ambient vibrations on heritage buildings: overview and wireless dynamic monitoring application

International Nuclear Information System (INIS)

Monti, G.; Quaranta, G.; Fumagalli, F.; Marano, G.C.; Rea, R.; Nazzaro, B.

2015-01-01

Growing awareness of the negative effects due to ambient vibrations caused by transportations infrastructures in Historical centres is attributable to the high vulnerability of heritage buildings as a consequence of deterioration phenomena and damages that reduced the structural capacity of such valuable constructions over the past centuries. As the mobility demand increases, several cities hosting heritage buildings are subjected to raising traffic loadings, so that constructions of new infrastructures is often required. Hence, assessing the effects of short-term vibrations due to construction activities or the consequences of the long-term vibrations caused by traffic is very important for the preservation of cultural heritage. An operative approach for evaluating the effects of ambient vibrations based on experimental measurements is a useful tool when a new infrastructure is being built, and can support strategic decisions for the elaboration of transportation plans at the urban level. Therefore, an overview is here presented of existing studies, guidelines and codes that provide pertinent information on this topic. Of special importance is the analysis of existing proposed thresholds, i.e. limit values that, if compiled with, damage due to ambient vibrations is not likely to occur. On the basis of such overview, the selection of threshold values for the Flavian Amphitheater is discussed, along with current efforts towards a wireless dynamic monitoring of its dynamic response.

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

International Nuclear Information System (INIS)

Lehtivarjo, Juuso; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino; Peräkylä, Mikael

2012-01-01

While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1 H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6–17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for 1 Hα, 1 HN, 13 Cα, 13 Cβ, 13 CO and backbone 15 N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

Energy Technology Data Exchange (ETDEWEB)

Lehtivarjo, Juuso, E-mail: juuso.lehtivarjo@uef.fi; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino [University of Eastern Finland, School of Pharmacy (Finland); Peraekylae, Mikael [University of Eastern Finland, Institute of Biomedicine (Finland)

2012-03-15

While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein {sup 1}H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6-17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for {sup 1}H{alpha}, {sup 1}HN, {sup 13}C{alpha}, {sup 13}C{beta}, {sup 13}CO and backbone {sup 15}N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

Monitoring hillslope moisture dynamics with surface ERT for enhancing spatial significance of hydrometric point measurements

Science.gov (United States)

Hübner, R.; Heller, K.; Günther, T.; Kleber, A.

2015-01-01

Besides floodplains, hillslopes are basic units that mainly control water movement and flow pathways within catchments of subdued mountain ranges. The structure of their shallow subsurface affects water balance, e.g. infiltration, retention, and runoff. Nevertheless, there is still a gap in the knowledge of the hydrological dynamics on hillslopes, notably due to the lack of generalization and transferability. This study presents a robust multi-method framework of electrical resistivity tomography (ERT) in addition to hydrometric point measurements, transferring hydrometric data into higher spatial scales to obtain additional patterns of distribution and dynamics of soil moisture on a hillslope. A geoelectrical monitoring in a small catchment in the eastern Ore Mountains was carried out at weekly intervals from May to December 2008 to image seasonal moisture dynamics on the hillslope scale. To link water content and electrical resistivity, the parameters of Archie's law were determined using different core samples. To optimize inversion parameters and methods, the derived spatial and temporal water content distribution was compared to tensiometer data. The results from ERT measurements show a strong correlation with the hydrometric data. The response is congruent to the soil tension data. Water content calculated from the ERT profile shows similar variations as that of water content from soil moisture sensors. Consequently, soil moisture dynamics on the hillslope scale may be determined not only by expensive invasive punctual hydrometric measurements, but also by minimally invasive time-lapse ERT, provided that pedo-/petrophysical relationships are known. Since ERT integrates larger spatial scales, a combination with hydrometric point measurements improves the understanding of the ongoing hydrological processes and better suits identification of heterogeneities.

Tracking Dynamic Changes and Monitoring Socioeconomic Parameters in Algeria Between 1993 and 2012, Using Nighttime Light Remote Sensing

Science.gov (United States)

Faouzi, B.; Washaya, P.

2017-09-01

This paper is based on using DMSP-OLS data from satellites nighttime light observations to detect both sources of light emissions in Algeria from human settlement areas and gas flaring from oil-extraction and natural gas production. We used the time series of data from DMSP-OLS images to examine the spatial and temporal characteristics of urban development in 48 Algerian provinces from 1993 to 2012. A systematic nighttime light calibration method was used to improve the consistency and comparability of the DSMPOSL images and then a separation is made between light detected from human settlements and light detected from gas flaring in order to allow us to study human settlements without other light emissions and then assess the suitability of using DMSP data in southern Algeria and its ability to monitor gas flaring. Linear regression methods were developed to identify the dynamic change of nighttime light and estimated its growth directions at pixel level. This work is the first to use nighttime light observations to detect and monitor the growth of human settlements in North Africa. In this study, we made use of DMSP-OLS data as a return ticket to the years of crises and we found the most affected provinces during that period. The DMSP-OLS data proved to be an index of growth in the economy during the period of stability in Algeria expressed by positive dynamic changes in the lighted area in all Algerian provinces. We used NTL data as an alternative to annual growth indexes for each province, which are unavailable, and its help as a monitoring system for socioeconomic parameters to fill the gap of data availability. We also proposed nighttime light remote sensing data as a useful tool to control and reduce CO2 emissions in Algeria's petroleum sector.

Development of biocompatible glycodynameric hydrogels joining two natural motifs by dynamic constitutional chemistry.

Science.gov (United States)

Marin, Luminita; Ailincai, Daniela; Morariu, Simona; Tartau-Mititelu, Liliana

2017-08-15

The paper focusses on the synthesis of novel hydrogels by joining natural biodegradable compounds with the aim to achieve biocompatible materials for bio related applications. The hydrogels were prepared from chitosan and citral by constitutional dynamic chemistry, incorporating both molecular and supramolecular dynamic features. The hydrophobic flexible citral has been reversible immobilized onto the hydrophilic chitosan backbone via imine bonds to form amphiphilic glycodynamers, which further self-ordered through supramolecular interactions into a 3D-network of biodynameric hydrogel. The synthetic pathway has been demonstrated by NMR and FTIR spectroscopy, X-ray diffraction and polarized light microscopy. Studies of the hydrogel morphology revealed a 3D porous microstructure, whose pores size correlated with the crosslinking degree. Rheological investigations evidenced high elasticity, thermo-responsiveness and thixotropic behavior. As a proof of the concept, the hydrogels proved in vivo biocompatibility on laboratory mice. The paper successfully implements the constitutional dynamic chemistry in generation of chitosan high performance hydrogels. Copyright © 2017 Elsevier Ltd. All rights reserved.

The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

Directory of Open Access Journals (Sweden)

Manuel Michaël

2010-02-01

Full Text Available Abstract Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving

Dynamics of a Tularemia Outbreak in a Closely Monitored Free-Roaming Population of Wild House Mice.

Science.gov (United States)

Dobay, Akos; Pilo, Paola; Lindholm, Anna K; Origgi, Francesco; Bagheri, Homayoun C; König, Barbara

2015-01-01

Infectious disease outbreaks can be devastating because of their sudden occurrence, as well as the complexity of monitoring and controlling them. Outbreaks in wildlife are even more challenging to observe and describe, especially when small animals or secretive species are involved. Modeling such infectious disease events is relevant to investigating their dynamics and is critical for decision makers to accomplish outbreak management. Tularemia, caused by the bacterium Francisella tularensis, is a potentially lethal zoonosis. Of the few animal outbreaks that have been reported in the literature, only those affecting zoo animals have been closely monitored. Here, we report the first estimation of the basic reproduction number R0 of an outbreak in wildlife caused by F. tularensis using quantitative modeling based on a susceptible-infected-recovered framework. We applied that model to data collected during an extensive investigation of an outbreak of tularemia caused by F. tularensis subsp. holarctica (also designated as type B) in a closely monitored, free-roaming house mouse (Mus musculus domesticus) population in Switzerland. Based on our model and assumptions, the best estimated basic reproduction number R0 of the current outbreak is 1.33. Our results suggest that tularemia can cause severe outbreaks in small rodents. We also concluded that the outbreak self-exhausted in approximately three months without administrating antibiotics.

Dynamics of a Tularemia Outbreak in a Closely Monitored Free-Roaming Population of Wild House Mice.

Directory of Open Access Journals (Sweden)

Akos Dobay

Full Text Available Infectious disease outbreaks can be devastating because of their sudden occurrence, as well as the complexity of monitoring and controlling them. Outbreaks in wildlife are even more challenging to observe and describe, especially when small animals or secretive species are involved. Modeling such infectious disease events is relevant to investigating their dynamics and is critical for decision makers to accomplish outbreak management. Tularemia, caused by the bacterium Francisella tularensis, is a potentially lethal zoonosis. Of the few animal outbreaks that have been reported in the literature, only those affecting zoo animals have been closely monitored. Here, we report the first estimation of the basic reproduction number R0 of an outbreak in wildlife caused by F. tularensis using quantitative modeling based on a susceptible-infected-recovered framework. We applied that model to data collected during an extensive investigation of an outbreak of tularemia caused by F. tularensis subsp. holarctica (also designated as type B in a closely monitored, free-roaming house mouse (Mus musculus domesticus population in Switzerland. Based on our model and assumptions, the best estimated basic reproduction number R0 of the current outbreak is 1.33. Our results suggest that tularemia can cause severe outbreaks in small rodents. We also concluded that the outbreak self-exhausted in approximately three months without administrating antibiotics.

Condition Monitoring Of Operating Pipelines With Operational Modal Analysis Application

Directory of Open Access Journals (Sweden)

Mironov Aleksey

2015-12-01

Full Text Available In the petroleum, natural gas and petrochemical industries, great attention is being paid to safety, reliability and maintainability of equipment. There are a number of technologies to monitor, control, and maintain gas, oil, water, and sewer pipelines. The paper focuses on operational modal analysis (OMA application for condition monitoring of operating pipelines. Special focus is on the topicality of OMA for definition of the dynamic features of the pipeline (frequencies and mode shapes in operation. The research was conducted using two operating laboratory models imitated a part of the operating pipeline. The results of finite-element modeling, identification of pipe natural modes and its modification under the influence of virtual failure are discussed. The work considers the results of experimental research of dynamic behavior of the operating pipe models using one of OMA techniques and comparing dynamic properties with the modeled data. The study results demonstrate sensitivity of modal shape parameters to modification of operating pipeline technical state. Two strategies of pipeline repair – with continuously condition-based monitoring with proposed technology and without such monitoring, was discussed. Markov chain reliability models for each strategy were analyzed and reliability improvement factor for proposed technology of monitoring in compare with traditional one was evaluated. It is resumed about ability of operating pipeline condition monitoring by measuring dynamic deformations of the operating pipe and OMA techniques application for dynamic properties extraction.

Multiple-Optimizing Dynamic Sensor Networks with MIMO Technology (PREPRINT)

Science.gov (United States)

2010-06-01

cluster edge is always d and never changes. A backbone is a rooted tree formed by cluster heads. The transmission distance for a backbone-edge...optimization considerations and algorithms,” IEEE Transactions on Mobile Computing, 2004. 15. T. Tang, M. Park, R. W. Heath, Jr. and Scott M. Nettles , “A

Dynamics of transportan in bicelles is surface charge dependent

Energy Technology Data Exchange (ETDEWEB)

Barany-Wallje, Elsa; Andersson, August; Graeslund, Astrid; Maeler, Lena [Stockholm University, Department of Biochemistry and Biophysics, Arrhenius Laboratories (Sweden)], E-mail: lena.maler@dbb.su.se

2006-06-15

In this study we investigated the dynamic behavior of the chimeric cell-penetrating peptide transportan in membrane-like environments using NMR. Backbone amide {sup 15}N spin relaxation was used to investigate the dynamics in two bicelles: neutral DMPC bicelles and partly negatively charged DMPG-containing bicelles. The structure of the peptide as judged from CD and chemical shifts is similar in the two cases. Both the overall motion as well as the local dynamics is, however, different in the two types of bicelles. The overall dynamics of the peptide is significantly slower in the partly negatively charged bicelle environment, as evidenced by longer global correlation times for all measured sites. The local motion, as judged from generalized order parameters, is for all sites in the peptide more restricted when bound to negatively charged bicelles than when bound to neutral bicelles (increase in S{sup 2} is on average 0.11 {+-} 0.07). The slower dynamics of transportan in charged membrane model systems cause significant line broadening in the proton NMR spectrum, which in certain cases limits the observation of {sup 1}H signals for transportan when bound to the membrane. The effect of transportan on DMPC and DHPC motion in zwitterionic bicelles was also investigated, and the motion of both components in the bicelle was found to be affected.

Dynamics of transportan in bicelles is surface charge dependent

International Nuclear Information System (INIS)

Barany-Wallje, Elsa; Andersson, August; Graeslund, Astrid; Maeler, Lena

2006-01-01

In this study we investigated the dynamic behavior of the chimeric cell-penetrating peptide transportan in membrane-like environments using NMR. Backbone amide 15 N spin relaxation was used to investigate the dynamics in two bicelles: neutral DMPC bicelles and partly negatively charged DMPG-containing bicelles. The structure of the peptide as judged from CD and chemical shifts is similar in the two cases. Both the overall motion as well as the local dynamics is, however, different in the two types of bicelles. The overall dynamics of the peptide is significantly slower in the partly negatively charged bicelle environment, as evidenced by longer global correlation times for all measured sites. The local motion, as judged from generalized order parameters, is for all sites in the peptide more restricted when bound to negatively charged bicelles than when bound to neutral bicelles (increase in S 2 is on average 0.11 ± 0.07). The slower dynamics of transportan in charged membrane model systems cause significant line broadening in the proton NMR spectrum, which in certain cases limits the observation of 1 H signals for transportan when bound to the membrane. The effect of transportan on DMPC and DHPC motion in zwitterionic bicelles was also investigated, and the motion of both components in the bicelle was found to be affected

An Enhanced Backbone-Assisted Reliable Framework for Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Amna Ali

2010-03-01

Full Text Available An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability.

Wearable sensors for human health monitoring

Science.gov (United States)

Asada, H. Harry; Reisner, Andrew

2006-03-01

Wearable sensors for continuous monitoring of vital signs for extended periods of weeks or months are expected to revolutionize healthcare services in the home and workplace as well as in hospitals and nursing homes. This invited paper describes recent research progress in wearable health monitoring technology and its clinical applications, with emphasis on blood pressure and circulatory monitoring. First, a finger ring-type wearable blood pressure sensor based on photo plethysmogram is presented. Technical issues, including motion artifact reduction, power saving, and wearability enhancement, will be addressed. Second, sensor fusion and sensor networking for integrating multiple sensors with diverse modalities will be discussed for comprehensive monitoring and diagnosis of health status. Unlike traditional snap-shot measurements, continuous monitoring with wearable sensors opens up the possibility to treat the physiological system as a dynamical process. This allows us to apply powerful system dynamics and control methodologies, such as adaptive filtering, single- and multi-channel system identification, active noise cancellation, and adaptive control, to the monitoring and treatment of highly complex physiological systems. A few clinical trials illustrate the potentials of the wearable sensor technology for future heath care services.

Monitoring Dynamic Interactions between Breast Cancer Cells and Human Bone Tissue in a Co-Culture Model

Science.gov (United States)

Contag, Christopher H.; Lie, Wen-Rong; Bammer, Marie C.; Hardy, Jonathan W.; Schmidt, Tobi L.; Maloney, William J.; King, Bonnie L.

2015-01-01

Purpose Bone is a preferential site of breast cancer metastasis and models are needed to study this process at the level of the microenvironment. We have used bioluminescence imaging (BLI) and multiplex biomarker immunoassays to monitor dynamic breast cancer cell behaviors in co-culture with human bone tissue. Procedures Femur tissue fragments harvested from hip replacement surgeries were co-cultured with luciferase-positive MDA-MB-231-fLuc cells. BLI was performed to quantify breast cell division and track migration relative to bone tissue. Breast cell colonization of bone tissues was assessed with immunohistochemistry. Biomarkers in co-culture supernatants were profiled with MILLIPLEX® immunoassays. Results BLI demonstrated increased MDA-MB-231-fLuc proliferation (pbones, and revealed breast cell migration toward bone. Immunohistochemistry illustrated MDA-MB-231-fLuc colonization of bone, and MILLIPLEX® profiles of culture supernatants suggested breast/bone crosstalk. Conclusions Breast cell behaviors that facilitate metastasis occur reproducibly in human bone tissue co-cultures and can be monitored and quantified using BLI and multiplex immunoassays. PMID:24008275

Distributed intelligent monitoring and reporting facilities

Science.gov (United States)

Pavlou, George; Mykoniatis, George; Sanchez-P, Jorge-A.

1996-06-01

Distributed intelligent monitoring and reporting facilities are of paramount importance in both service and network management as they provide the capability to monitor quality of service and utilization parameters and notify degradation so that corrective action can be taken. By intelligent, we refer to the capability of performing the monitoring tasks in a way that has the smallest possible impact on the managed network, facilitates the observation and summarization of information according to a number of criteria and in its most advanced form and permits the specification of these criteria dynamically to suit the particular policy in hand. In addition, intelligent monitoring facilities should minimize the design and implementation effort involved in such activities. The ISO/ITU Metric, Summarization and Performance management functions provide models that only partially satisfy the above requirements. This paper describes our extensions to the proposed models to support further capabilities, with the intention to eventually lead to fully dynamically defined monitoring policies. The concept of distributing intelligence is also discussed, including the consideration of security issues and the applicability of the model in ODP-based distributed processing environments.

Molecular dynamics of bacteriorhodopsin.

Science.gov (United States)

Lupo, J A; Pachter, R

1997-02-01

A model of bacteriorhodopsin (bR), with a retinal chromophore attached, has been derived for a molecular dynamics simulation. A method for determining atomic coordinates of several ill-defined strands was developed using a structure prediction algorithm based on a sequential Kalman filter technique. The completed structure was minimized using the GROMOS force field. The structure was then heated to 293 K and run for 500 ps at constant temperature. A comparison with the energy-minimized structure showed a slow increase in the all-atom RMS deviation over the first 200 ps, leveling off to approximately 2.4 A relative to the starting structure. The final structure yielded a backbone-atom RMS deviation from the crystallographic structure of 2.8 A. The residue neighbors of the chromophore atoms were followed as a function of time. The set of persistent near-residue neighbors supports the theory that differences in pKa values control access to the Schiff base proton, rather than formation of a counterion complex.

Thermoresponsive Poly(2-oxazoline) Molecular Brushes by Living Ionic Polymerization: Kinetic Investigations of Pendant Chain Grafting and Cloud Point Modulation by Backbone and Side Chain Length Variation

KAUST Repository

Zhang, Ning; Luxenhofer, Robert; Jordan, Rainer

2012-01-01

and the stretched conformation of the backbone, which is caused by the electrostatic repulsion of the oxazolinium moieties along the macroinitiator. The resulting molecular brushes showed thermoresponsive properties, that is, having a defined cloud point (CP

Generalized monitor unit calculation for the Varian enhanced dynamic wedge field

International Nuclear Information System (INIS)

Liu Chihray; Kim, Siyong; Kahler, Darren L.; Palta, Jatinder R.

2003-01-01

The generalized monitor unit (MU) calculation equation for the Varian enhanced dynamic wedge (EDW) is derived. The assumption of this MU calculation method is that the wedge factor of the EDW at the center of the field is a function of field size, the position of the center of the field in the wedge direction, and the final position of the moving jaw. The wedge factors at the center of the field in both symmetric and asymmetric fields are examined. The difference between calculated and measured wedge factors is within 1.0%. The method developed here is easy to implement. The only datum required in addition to the standard set of conventional physical wedge implementation data is the off-axis output factor for the open field in the reference condition. The off-center point calculation is also examined. For the off-center point calculation, the dose profile in the wedge direction for the largest EDW field is used to obtain the relative off-center ratio in any smaller wedge field. The accuracy of the off-center point calculation decreases when the point of calculation is too close to the field edge

Integrating real-time and manual monitored data to predict hillslope soil moisture dynamics with high spatio-temporal resolution using linear and non-linear models

Science.gov (United States)

Spatio-temporal variability of soil moisture (') is a challenge that remains to be better understood. A trade-off exists between spatial coverage and temporal resolution when using the manual and real-time ' monitoring methods. This restricted the comprehensive and intensive examination of ' dynamic...

An Unusual Conformational Isomer of Verrucosidin Backbone from a Hydrothermal Vent Fungus, Penicillium sp. Y-50-10

Directory of Open Access Journals (Sweden)

Chengqian Pan

2016-08-01

Full Text Available A new verrucosidin derivative, methyl isoverrucosidinol (1, was isolated from the marine fungus Penicillium sp. Y-50-10, dwelling in sulfur rich sediment in the Kueishantao hydrothermal vents off Taiwan. The structure was established by spectroscopic means including HRMS and 2D-NMR spectroscopic analysis. The absolute configuration was defined mainly by comparison of quantum chemical TDDFT calculated and experimental ECD spectra. Among hitherto known compounds with a verrucosidine backbone isolated from natural resource, compound 1 represents the first example of a new conformational isomer of its skeleton, exhibiting antibiotic activity against Bacillus subtilis with MIC value 32 μg/mL.

Dynamically Coupled Residues within the SH2 Domain of FYN Are Key to Unlocking Its Activity.

Science.gov (United States)

Huculeci, Radu; Cilia, Elisa; Lyczek, Agatha; Buts, Lieven; Houben, Klaartje; Seeliger, Markus A; van Nuland, Nico; Lenaerts, Tom

2016-11-01

Src kinase activity is controlled by various mechanisms involving a coordinated movement of kinase and regulatory domains. Notwithstanding the extensive knowledge related to the backbone dynamics, little is known about the more subtle side-chain dynamics within the regulatory domains and their role in the activation process. Here, we show through experimental methyl dynamic results and predicted changes in side-chain conformational couplings that the SH2 structure of Fyn contains a dynamic network capable of propagating binding information. We reveal that binding the phosphorylated tail of Fyn perturbs a residue cluster near the linker connecting the SH2 and SH3 domains of Fyn, which is known to be relevant in the regulation of the activity of Fyn. Biochemical perturbation experiments validate that those residues are essential for inhibition of Fyn, leading to a gain of function upon mutation. These findings reveal how side-chain dynamics may facilitate the allosteric regulation of the different members of the Src kinase family. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ground Monitoring Neotropical Dry Forests: A Sensor Network for Forest and Microclimate Dynamics in Semi-Arid Environments (Enviro-Net°)

Science.gov (United States)

Rankine, C. J.; Sánchez-Azofeifa, G.

2011-12-01

In the face of unprecedented global change driven by anthropogenic pressure on natural systems it has become imperative to monitor and better understand potential shifts in ecosystem functioning and services from local to global scales. The utilization of automated sensors technologies offers numerous advantages over traditional on-site ecosystem surveying techniques and, as a result, sensor networks are becoming a powerful tool in environmental monitoring programs. Tropical forests, renowned for their biodiversity, are important regulators of land-atmosphere fluxes yet the seasonally dry tropical forests, which account for 40% of forested ecosystems in the American tropics, have been severely degraded over the past several decades and not much is known of their capacity to recover. With less than 1% of these forests protected, our ability to monitor the dynamics and quantify changes in the remaining primary and recovering secondary tropical dry forests is vital to understanding mechanisms of ecosystem stress responses and climate feedback with respect to annual productivity and desertification processes in the tropics. The remote sensing component of the Tropi-Dry: Human and Biophysical Dimensions of Tropical Dry Forests in the Americas research network supports a network of long-term tropical ecosystem monitoring platforms which focus on the dynamics of seasonally dry tropical forests in the Americas. With over 25 sensor station deployments operating across a latitudinal gradient in Mexico, Costa Rica, Brazil, and Argentina continuously collecting hyper-temporal sensory input based on standardized deployment parameters, this monitoring system is unique among tropical environments. Technologies used in the network include optical canopy phenology towers, understory wireless sensing networks, above and below ground microclimate stations, and digital cameras. Sensory data streams are uploaded to a cyber-infrastructure initiative, denominated Enviro-Net°, for data

Chemical synthesis of membrane proteins by the removable backbone modification method.

Science.gov (United States)

Tang, Shan; Zuo, Chao; Huang, Dong-Liang; Cai, Xiao-Ying; Zhang, Long-Hua; Tian, Chang-Lin; Zheng, Ji-Shen; Liu, Lei

2017-12-01

Chemical synthesis can produce membrane proteins bearing specifically designed modifications (e.g., phosphorylation, isotope labeling) that are difficult to obtain through recombinant protein expression approaches. The resulting homogeneously modified synthetic membrane proteins are valuable tools for many advanced biochemical and biophysical studies. This protocol describes the chemical synthesis of membrane proteins by condensation of transmembrane peptide segments through native chemical ligation. To avoid common problems encountered due to the poor solubility of transmembrane peptides in almost any solvent, we describe an effective procedure for the chemical synthesis of membrane proteins through the removable-backbone modification (RBM) strategy. Two key steps of this protocol are: (i) installation of solubilizing Arg4-tagged RBM groups into the transmembrane peptides at any primary amino acid through Fmoc (9-fluorenylmethyloxycarbonyl) solid-phase peptide synthesis and (ii) native ligation of the full-length sequence, followed by removal of the RBM tags by TFA (trifluoroacetic acid) cocktails to afford the native protein. The installation of RBM groups is achieved by using 4-methoxy-5-nitrosalicyladehyde by reduction amination to incorporate an activated O-to-N acyl transfer auxiliary. The Arg4-tag-modified membrane-spanning peptide segments behave like water-soluble peptides to facilitate their purification, ligation and mass characterization.

Application of monitoring to dynamic characterization and damage detection in bridges

OpenAIRE

Gonzalez, Ignacio

2014-01-01

The field of bridge monitoring is one of rapid development. Advances in sensor technologies, in data communication and processing algorithms all affect the possibilities of Structural Monitoring in Bridges. Bridges are a very critical part of a country’s infrastructure, they are expensive to build and maintain, and many uncertainties surround important factors determining their serviceability and deterioration state. As such, bridges are good candidates for monitoring. Monitoring can extend t...

Geo mathematic tools for the design of a radioisotopes monitoring network in order to modelling the groundwater dynamics processes and hydrodynamic management

International Nuclear Information System (INIS)

Peralta, J.L.; Gil, R.; Leyva, D.; Molerio, L.F.; Pin, M.

2004-01-01

The present paper, shows the application of geo mathematic tools [Mangin,1981; Molerio,1997] for the design of a radioisotopes monitoring network in order to modelling the groundwater dynamics processes and hydrodynamic management of a Karstic Basin (Almendares-Vento watershed), which is very difficult to evaluate due to the physical-geographical, geologic and hydrogeological characteristics. The Almendares Vento watershed (AVW) is close to the Jaruco-Aguacate watershed, with a similar hydrogeologic and geologic structure, therefore similar result must be expected. In the AVW case is necessary to identify, with more precision, the water propagation limits of the stratified layers according to the waters transit times, recharges and dynamics aquifers, residence time, groundwater contamination and the groundwater-surface water interaction due to the dam placed on the basin. The paper allowed the identification of a monitoring points network, taking into account, between other statistical approaches, the good correlation, the high memory effect, etc. According to the analysis of the variances spectral, have been obtained and optimized the sampling frequency of the network points in the Basin. Besides, it have been identified the necessities to include the detailed evaluation of a specific point of the network in the hydrodynamic study (Vento watershed). In order to evaluate the optimization of the designed monitoring network, the geo mathematic study developed was compared with the results of the mathematical model AQUIMPE, the final result showed the validation of the obtained design. The results of the work allow the best monitoring of the parameters in order to determine the aquifer recharge, residence times, the vulnerability to the waters contamination and the groundwater-surface water interaction

Monitoring and Modeling Carbon Dynamics at a Network of Intensive Sites in the USA and Mexico

Science.gov (United States)

Birdsey, R.; Wayson, C.; Johnson, K. D.; Pan, Y.; Angeles, G.; De Jong, B. H.; Andrade, J. L.; Dai, Z.

2013-05-01

The Forest Services of the USA and Mexico, supported by NASA and USAID, have begun to establish a network of intensive forest carbon monitoring sites. These sites are used for research and teaching, developing forest management practices, and forging links to the needs of communities. Several of the sites have installed eddy flux towers to basic meteorology data and daily estimates of forest carbon uptake and release, the processes that determine forest growth. Field sampling locations at each site provide estimates of forest biomass and carbon stocks, and monitor forest dynamic processes such as growth and mortality rates. Remote sensing facilitates scaling up to the surrounding landscapes. The sites support information requirements for implementing programs such as Reducing Emissions from Deforestation and Forest Degradation (REDD+), enabling communities to receive payments for ecosystem services such as reduced carbon emissions or improved forest management. In addition to providing benchmark data for REDD+ projects, the sites are valuable for validating state and national estimates from satellite remote sensing and the national forest inventory. Data from the sites provide parameters for forest models that support strategic management analysis, and support student training and graduate projects. The intensive monitoring sites may be a model for other countries in Latin America. Coordination among sites in the USA, Mexico and other Latin American countries can ensure harmonization of approaches and data, and share experiences and knowledge among countries with emerging opportunities for implementing REDD+ and other conservation programs.

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns

Science.gov (United States)

Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

2018-01-01

Abstract Background Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Conclusions Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. PMID:29186447

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.

Science.gov (United States)

Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

2018-02-01

Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. © The Authors 2017. Published by Oxford University Press.

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny.

Science.gov (United States)

Chen, Meng-Yun; Liang, Dan; Zhang, Peng

2015-11-01

Incongruence between different phylogenomic analyses is the main challenge faced by phylogeneticists in the genomic era. To reduce incongruence, phylogenomic studies normally adopt some data filtering approaches, such as reducing missing data or using slowly evolving genes, to improve the signal quality of data. Here, we assembled a phylogenomic data set of 58 jawed vertebrate taxa and 4682 genes to investigate the backbone phylogeny of jawed vertebrates under both concatenation and coalescent-based frameworks. To evaluate the efficiency of extracting phylogenetic signals among different data filtering methods, we chose six highly intractable internodes within the backbone phylogeny of jawed vertebrates as our test questions. We found that our phylogenomic data set exhibits substantial conflicting signal among genes for these questions. Our analyses showed that non-specific data sets that are generated without bias toward specific questions are not sufficient to produce consistent results when there are several difficult nodes within a phylogeny. Moreover, phylogenetic accuracy based on non-specific data is considerably influenced by the size of data and the choice of tree inference methods. To address such incongruences, we selected genes that resolve a given internode but not the entire phylogeny. Notably, not only can this strategy yield correct relationships for the question, but it also reduces inconsistency associated with data sizes and inference methods. Our study highlights the importance of gene selection in phylogenomic analyses, suggesting that simply using a large amount of data cannot guarantee correct results. Constructing question-specific data sets may be more powerful for resolving problematic nodes. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Quality assurance of radiation protection monitoring instruments in India

International Nuclear Information System (INIS)

Tripathi, S.M.; Daniel, Liji; Rao, Suresh; Sharma, D.N.

2008-01-01

Bhabha Atomic Research Centre (BARC) is the National Metrology Institute (NMI) for developing, maintaining and disseminating standards for ionizing radiation in India. Radiation Safety Systems Division (RSSD) of BARC has the requisite infrastructure in the form of experts, trained manpower, laboratories, equipment and facilities for providing calibration services to users and ascertaining traceability to international standards. It periodically participates in various international inter-comparisons. RSSD maintains reference radiation fields that are required for calibrating Radiation Protection Monitoring Instruments that form the backbone of the radiation monitoring programme for harnessing the benefits of nuclear energy and ionizing radiations. These instruments are type-tested and periodically calibrated at standard reference radiation fields to ensure their healthy working condition and fitness for their intended use. This paper describes the details of the standardization procedures adopted for reference radiation fields and infrastructure established and maintained at RSSD, BARC in accordance with the recommendations of ISO-4037. The paper describes the various tests that are carried out for radiation protection monitoring instrument to study the variation of the calibration factor with influencing quantities like linearity of response, energy response, angular dependence and overload characteristics. The results of these tests for typical instruments are also discussed. The present work also describes various types of indigenously developed radiation protection monitoring instruments and their performance characteristics. Adaptability of these instruments for the implementation of operational quantities are discussed briefly. It also dwells on the IAEA Quality Audit for radiation protection level calibrations, which RSSD has been participating since 2001. Our results of the quality audit are well within the acceptance limit (±7%) set by IAEA for the

Local structural mechanism for frozen-in dynamics in metallic glasses

Science.gov (United States)

Liu, X. J.; Wang, S. D.; Wang, H.; Wu, Y.; Liu, C. T.; Li, M.; Lu, Z. P.

2018-04-01

The nature of the glass transition is a fundamental and long-standing intriguing issue in the condensed-matter physics and materials science community. In particular, the structural response by which a liquid is arrested dynamically to form a glass or amorphous solid upon approaching its freezing temperature [the glass transition temperature (Tg)] remains unclear. Various structural scenarios in terms of the percolation theory have been proposed recently to understand such a phenomenon; however, there is still no consensus on what the general percolation entity is and how the entity responds to the sudden slowdown dynamics during the glass transition. In this paper, we demonstrate that one-dimensional local linear ordering (LLO) is a universal structural motif associated with the glass transition for various metallic glasses. The quantitative evolution of LLO with temperature indicates that a percolating LLO network forms to serve as the backbone of the rigid glass solid when the temperature approaches the freezing point, resulting in the frozen-in dynamics accompanying the glass transition. The percolation transition occurs by pinning different LLO networks together, which only needs the introduction of a small number of "joint" atoms between them, and therefore the energy expenditure is very low.

Veno-occlusive disease nurse management: development of a dynamic monitoring tool by the GITMO nursing group.

Science.gov (United States)

Botti, Stefano; Orlando, Laura; Gargiulo, Gianpaolo; Cecco, Valentina De; Banfi, Marina; Duranti, Lorenzo; Samarani, Emanuela; Netti, Maria Giovanna; Deiana, Marco; Galuppini, Vera; Pignatelli, Adriana Concetta; Ceresoli, Rosanna; Vedovetto, Alessio; Rostagno, Elena; Bambaci, Marilena; Dellaversana, Cristina; Luminari, Stefano; Bonifazi, Francesca

2016-01-01

Veno-occlusive disease (VOD) is a complication arising from the toxicity of conditioning regimens that have a significant impact on the survival of patients who undergo stem cell transplantation. There are several known risk factors for developing VOD and their assessment before the start of conditioning regimens could improve the quality of care. Equally important are early identification of signs and symptoms ascribable to VOD, rapid diagnosis, and timely adjustment of support therapy and treatment. Nurses have a fundamental role at the stages of assessment and monitoring for signs and symptoms; therefore, they should have documented skills and training. The literature defines nurses' areas of competence in managing VOD, but in the actual clinical practice, this is not so clear. Moreover, there is an intrinsic difficulty in managing VOD due to its rapid and often dramatic evolution, together with a lack of care tools to guide nurses. Through a complex evidence-based process, the Gruppo Italiano per il Trapianto di Midollo Osseo (GITMO), cellule staminali emopoietiche e terapia cellulare nursing board has developed an operational flowchart and a dynamic monitoring tool applicable to haematopoietic stem cell transplantation patients, whether they develop this complication or not.

Monitoring activities of satellite data processing services in real-time with SDDS Live Monitor

Science.gov (United States)

Duc Nguyen, Minh

2017-10-01

This work describes Live Monitor, the monitoring subsystem of SDDS - an automated system for space experiment data processing, storage, and distribution created at SINP MSU. Live Monitor allows operators and developers of satellite data centers to identify errors occurred in data processing quickly and to prevent further consequences caused by the errors. All activities of the whole data processing cycle are illustrated via a web interface in real-time. Notification messages are delivered to responsible people via emails and Telegram messenger service. The flexible monitoring mechanism implemented in Live Monitor allows us to dynamically change and control events being shown on the web interface on our demands. Physicists, whose space weather analysis models are functioning upon satellite data provided by SDDS, can use the developed RESTful API to monitor their own events and deliver customized notification messages by their needs.

Influence of the strength of the smectic order on the backbone anisotropy of side-chain liquid crystal polymers as revealed by SANS

Science.gov (United States)

Noirez, L.; Keller, P.; Cotton, J. P.

1992-06-01

It is proposed that the strength of the smectic order determines the backbone anisotropy of side-chain liquid crystal polymers. Here this strength increases with the length of the alkyl terminal group of the mesogens. Two liquid crystal polymethacrylates differing only by the mesogenic tails —OCH3 and —OC4H9 are considered. The backbone anisotropy of these polymers is measured by small angle neutron scattering (SANS) whereas the smectic order is evaluated from the intensity of the 001 Bragg peak. Il est proposé que la qualité de l'ordre smectique détermine l'anisotropie du squelette de polymères mésomorphes en peigne confinés dans les lamelles. Ici l'ordre smectique est augmenté en allongeant le groupe alkyl terminal des mésogènes. Nous étudions deux polyméthacrylates cristal liquide qui ne différent que par leurs groupes terminaux : —OCH3 et —OC4H9. L'anisotropie du squellete est mesurée par diffusion de neutrons aux petits angles tandis que l'ordre smectique est évalué à l'aide de l'intensité du pic de Bragg 001.

A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

Directory of Open Access Journals (Sweden)

Maurer Till

2005-04-01

Full Text Available Abstract Background We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral angles and their standard deviations are used which are calculated with an algorithm described earlier by Döker et al. (1999, BBRC, 257, 348–350. The overall long-range contacts are established via a small number of distance restraints between atoms involved in hydrogen bonds and backbone atoms of conserved residues. Employing the restraints generated by PERMOL three-dimensional structures are obtained using standard molecular dynamics programs such as DYANA or CNS. Results To test this modeling approach it has been used for predicting the structure of the histidine-containing phosphocarrier protein HPr from E. coli and the structure of the human peroxisome proliferator activated receptor γ (Ppar γ. The divergence between the modeled HPr and the previously determined X-ray structure was comparable to the divergence between the X-ray structure and the published NMR structure. The modeled structure of Ppar γ was also very close to the previously solved X-ray structure with an RMSD of 0.262 nm for the backbone atoms. Conclusion In summary, we present a new method for homology modeling capable of producing high-quality structure models. An advantage of the method is that it can be used in combination with incomplete NMR data to obtain reasonable structure models in accordance with the experimental data.

Recognition of RNA by amide modified backbone nucleic acids: molecular dynamics simulations of DNA-RNA hybrids in aqueous solution.

Science.gov (United States)

Nina, Mafalda; Fonné-Pfister, Raymonde; Beaudegnies, Renaud; Chekatt, Habiba; Jung, Pierre M J; Murphy-Kessabi, Fiona; De Mesmaeker, Alain; Wendeborn, Sebastian

2005-04-27

Thermodynamic and structural properties of a chemically modified DNA-RNA hybrid in which a phosphodiester linkage is replaced by a neutral amide-3 linkage (3'-CH(2)-CONH-5') were investigated using UV melting experiments, molecular dynamics simulations in explicit water, and continuum solvent models. van't Hoff analysis of the experimental UV melting curves suggests that the significant increase of the thermodynamic stability of a 15-mer DNA-RNA with seven alternated amide-3 modifications (+11 degrees C) is mainly due to an increased binding enthalpy. To further evaluate the origin in the observed affinities differences, the electrostatic contribution to the binding free energy was calculated by solving the Poisson-Boltzmann equation numerically. The nonelectrostatic contribution was estimated as the product of a hydrophobic surface tension coefficient and the surface area that is buried upon double strand formation. Structures were taken from 10 ns molecular dynamics simulations computed in a consistent fashion using explicit solvent, counterions, and the particle-mesh Ewald procedure. The present preliminary thermodynamic study suggests that the favorable binding free energy of the amide-3 DNA single strand to the complementary RNA is equally driven by electrostatic and nonpolar contributions to the binding compared to their natural analogues. In addition, molecular dynamics simulations in explicit water were performed on an amide-3 DNA single strand and the corresponding natural DNA. Results from the conformations cluster analysis of the simulated amide-3 DNA single strand ensembles suggest that the 25% of the population sampled within 10 ns has a pre-organized conformation where the sugar C3' endo pucker is favored at the 3'-flanking nucleotides. These structural and thermodynamic features contribute to the understanding of the observed increased affinities of the amide-3 DNA-RNA hybrids at the microscopic level.

Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking

Science.gov (United States)

Tsvetkov, Vladimir B.; Serbin, Alexander V.

2014-06-01

In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 ( HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [ HR1]3 of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics ( MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]3 in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands-target interactions. Some newly MD-discovered aspects of the ligand's backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.

Monitoring cognitive and emotional processes through pupil and cardiac response during dynamic versus logical task.

Science.gov (United States)

Causse, Mickaël; Sénard, Jean-Michel; Démonet, Jean François; Pastor, Josette

2010-06-01

The paper deals with the links between physiological measurements and cognitive and emotional functioning. As long as the operator is a key agent in charge of complex systems, the definition of metrics able to predict his performance is a great challenge. The measurement of the physiological state is a very promising way but a very acute comprehension is required; in particular few studies compare autonomous nervous system reactivity according to specific cognitive processes during task performance and task related psychological stress is often ignored. We compared physiological parameters recorded on 24 healthy subjects facing two neuropsychological tasks: a dynamic task that require problem solving in a world that continually evolves over time and a logical task representative of cognitive processes performed by operators facing everyday problem solving. Results showed that the mean pupil diameter change was higher during the dynamic task; conversely, the heart rate was more elevated during the logical task. Finally, the systolic blood pressure seemed to be strongly sensitive to psychological stress. A better taking into account of the precise influence of a given cognitive activity and both workload and related task-induced psychological stress during task performance is a promising way to better monitor operators in complex working situations to detect mental overload or pejorative stress factor of error.

The feasibility of automated online flow cytometry for in-situ monitoring of microbial dynamics in aquatic ecosystems

Science.gov (United States)

Besmer, Michael D.; Weissbrodt, David G.; Kratochvil, Bradley E.; Sigrist, Jürg A.; Weyland, Mathias S.; Hammes, Frederik

2014-01-01

Fluorescent staining coupled with flow cytometry (FCM) is often used for the monitoring, quantification and characterization of bacteria in engineered and environmental aquatic ecosystems including seawater, freshwater, drinking water, wastewater, and industrial bioreactors. However, infrequent grab sampling hampers accurate characterization and subsequent understanding of microbial dynamics in all of these ecosystems. A logic technological progression is high throughput and full automation of the sampling, staining, measurement, and data analysis steps. Here we assess the feasibility and applicability of automated FCM by means of actual data sets produced with prototype instrumentation. As proof-of-concept we demonstrate examples of microbial dynamics in (i) flowing tap water from a municipal drinking water supply network and (ii) river water from a small creek subject to two rainfall events. In both cases, automated measurements were done at 15-min intervals during 12–14 consecutive days, yielding more than 1000 individual data points for each ecosystem. The extensive data sets derived from the automated measurements allowed for the establishment of baseline data for each ecosystem, as well as for the recognition of daily variations and specific events that would most likely be missed (or miss-characterized) by infrequent sampling. In addition, the online FCM data from the river water was combined and correlated with online measurements of abiotic parameters, showing considerable potential for a better understanding of cause-and-effect relationships in aquatic ecosystems. Although several challenges remain, the successful operation of an automated online FCM system and the basic interpretation of the resulting data sets represent a breakthrough toward the eventual establishment of fully automated online microbiological monitoring technologies. PMID:24917858

Dynamic Strain and Crack Monitoring Sensor, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — Los Gatos Research proposes to develop a new automated vehicle health monitoring sensor system capable of measuring loads and detecting crack, corrosion, and...

Fractal dimensions of silica gels generated using reactive molecular dynamics simulations

International Nuclear Information System (INIS)

Bhattacharya, Sudin; Kieffer, John

2005-01-01

We have used molecular dynamics simulations based on a three-body potential with charge transfer to generate nanoporous silica aerogels. Care was taken to reproduce the sol-gel condensation reaction that forms the gel backbone as realistically as possible and to thereby produce credible gel structures. The self-similarity of aerogel structures was investigated by evaluating their fractal dimension from geometric correlations. For comparison, we have also generated porous silica glasses by rupturing dense silica and computed their fractal dimension. The fractal dimension of the porous silica structures was found to be process dependent. Finally, we have determined that the effect of supercritical drying on the fractal nature of condensed silica gels is not appreciable

Comparison of non-invasive electrohysterographic recording techniques for monitoring uterine dynamics.

Science.gov (United States)

Alberola-Rubio, J; Prats-Boluda, G; Ye-Lin, Y; Valero, J; Perales, A; Garcia-Casado, J

2013-12-01

Non-invasive recording of uterine myoelectric activity (electrohysterogram, EHG) could provide an alternative to monitoring uterine dynamics by systems based on tocodynamometers (TOCO). Laplacian recording of bioelectric signals has been shown to give better spatial resolution and less interference than mono- and bipolar surface recordings. The aim of this work was to study the signal quality obtained from monopolar, bipolar and Laplacian techniques in EHG recordings, as well as to assess their ability to detect uterine contractions. Twenty-two recording sessions were carried out on singleton pregnant women during the active phase of labour. In each session the following simultaneous recordings were obtained: internal uterine pressure (IUP), external tension of abdominal wall (TOCO) and EHG signals (5 monopolar and 4 bipolar recordings, 1 discrete approximation to the Laplacian of the potential and 2 estimates of the Laplacian from two active annular electrodes). The results obtained show that EHG is able to detect a higher number of uterine contractions than TOCO. Laplacian recordings give improved signal quality over monopolar and bipolar techniques, reduce maternal cardiac interference and improve the signal-to-noise ratio. The optimal position for recording EHG was found to be the uterine median axis and the lower centre-right umbilical zone. Copyright © 2013 IPEM. Published by Elsevier Ltd. All rights reserved.

Measurement of Vehicle-Bridge-Interaction force using dynamic tire pressure monitoring

Science.gov (United States)

Chen, Zhao; Xie, Zhipeng; Zhang, Jian

2018-05-01

The Vehicle-Bridge-Interaction (VBI) force, i.e., the normal contact force of a tire, is a key component in the VBI mechanism. The VBI force measurement can facilitate experimental studies of the VBI as well as input-output bridge structural identification. This paper introduces an innovative method for calculating the interaction force by using dynamic tire pressure monitoring. The core idea of the proposed method combines the ideal gas law and a basic force model to build a relationship between the tire pressure and the VBI force. Then, unknown model parameters are identified by the Extended Kalman Filter using calibration data. A signal filter based on the wavelet analysis is applied to preprocess the effect that the tire rotation has on the pressure data. Two laboratory tests were conducted to check the proposed method's validity. The effects of different road irregularities, loads and forward velocities were studied. Under the current experiment setting, the proposed method was robust to different road irregularities, and the increase in load and velocity benefited the performance of the proposed method. A high-speed test further supported the use of this method in rapid bridge tests. Limitations of the derived theories and experiment were also discussed.

Ionomer Dynamics: Insights from Broadband Dielectric Spectroscopy

Science.gov (United States)

Runt, James

2015-03-01

Ionomers (polymers containing ionic functionality) have been traditionally used as packaging materials and in molding applications, and are now of increasing interest as candidate single ion conductors for energy storage devices, in energy conversion, and for other electroactive materials applications. The focus of this presentation is on the insight that broadband dielectric (impedance) spectroscopy brings to our understanding of ion and polymer dynamics of this family of materials. As an example of our recent work on relatively conductive ionomers, the first portion of the presentation will focus on anion conducting polyphosphazene ionomers, in which polymer bound cations are quaternized with either short alkyl or short ether oxygen chains. The low Tg, amorphous nature, and cation-solvating backbone distinguish polyphosphazenes as promising materials for ion conduction, the iodide variants being of particular interest in solar cells. In the second part of this overview, the first findings on the molecular dynamics of linear precise polyethylene-based ionomers containing 1-methylimidazolium bromide pendants on exactly every 9th, 15th, or 21st carbon atom will be summarized. In order to develop a robust interpretation of the dynamics of these materials, it is imperative to develop a thorough understanding of microphase separation (e.g. ion aggregation), and each of the above studies is complimented by multiangle X-ray scattering experiments. Supported by the NSF Polymers Program and DOE Basic Energy Sciences.

Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae.

Science.gov (United States)

Panero, Jose L; Freire, Susana E; Ariza Espinar, Luis; Crozier, Bonnie S; Barboza, Gloria E; Cantero, Juan J

2014-11-01

A backbone phylogeny that fully resolves all subfamily and deeper nodes of Asteraceae was constructed using 14 chloroplast DNA loci. The recently named genus Famatinanthus was found to be sister to the Mutisioideae-Asteroideae clade that represents more than 99% of Asteraceae and was found to have the two chloroplast inversions present in all Asteraceae except the nine genera of Barnadesioideae. A monotypic subfamily Famatinanthoideae and tribe Famatinantheae are named herein as new. Relationships among the basal lineages of the family were resolved with strong support in the Bayesian analysis as (Barnadesioideae (Famatinanthoideae (Mutisioideae (Stifftioideae (Wunderlichioideae-Asteroideae))))). Ancestral state reconstruction of ten morphological characters at the root node of the Asteraceae showed that the ancestral sunflower would have had a woody habit, alternate leaves, solitary capitulescences, epaleate receptacles, smooth styles, smooth to microechinate pollen surface sculpturing, white to yellow corollas, and insect-mediated pollination. Herbaceous habit, echinate pollen surface, pubescent styles, and cymose capitulescences were reconstructed for backbone nodes of the phylogeny corresponding to clades that evolved shortly after Asteraceae dispersed out of South America. No support was found for discoid capitula, multiseriate involucres or bird pollination as the ancestral character condition for any node. Using this more resolved phylogenetic tree, the recently described Raiguenrayun cura+Mutisiapollis telleriae fossil should be associated to a more derived node than previously suggested when time calibrating phylogenies of Asteraceae. Copyright © 2014 Elsevier Inc. All rights reserved.

The internal model: A study of the relative contribution of proprioception and visual information to failure detection in dynamic systems. [sensitivity of operators versus monitors to failures

Science.gov (United States)

Kessel, C.; Wickens, C. D.

1978-01-01

The development of the internal model as it pertains to the detection of step changes in the order of control dynamics is investigated for two modes of participation: whether the subjects are actively controlling those dynamics or are monitoring an autopilot controlling them. A transfer of training design was used to evaluate the relative contribution of proprioception and visual information to the overall accuracy of the internal model. Sixteen subjects either tracked or monitored the system dynamics as a 2-dimensional pursuit display under single task conditions and concurrently with a sub-critical tracking task at two difficulty levels. Detection performance was faster and more accurate in the manual as opposed to the autopilot mode. The concurrent tracking task produced a decrement in detection performance for all conditions though this was more marked for the manual mode. The development of an internal model in the manual mode transferred positively to the automatic mode producing enhanced detection performance. There was no transfer from the internal model developed in the automatic mode to the manual mode.

Millisecond dynamics in glutaredoxin during catalytic turnover is dependent on substrate binding and absent in the resting states

DEFF Research Database (Denmark)

Jensen, Kristine Steen; Winther, Jakob R; Teilum, Kaare

2011-01-01

to the glutathione exchange rate was observed for 23 residues. Binding of reduced glutathione resulted in competitive inhibition of the reduced enzyme having kinetics similar to that of the reaction. This observation couples the motions observed during catalysis directly to substrate binding. Backbone motions......Conformational dynamics is important for enzyme function. Which motions of enzymes determine catalytic efficiency and whether the same motions are important for all enzymes, however, are not well understood. Here we address conformational dynamics in glutaredoxin during catalytic turnover...... with a combination of NMR magnetization transfer, R(2) relaxation dispersion, and ligand titration experiments. Glutaredoxins catalyze a glutathione exchange reaction, forming a stable glutathinoylated enzyme intermediate. The equilibrium between the reduced state and the glutathionylated state was biochemically...