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Sample records for cavity sites predictions

  1. Cavities for electron spin resonance: predicting the resonant frequency

    Science.gov (United States)

    Colton, John; Miller, Kyle; Meehan, Michael; Spencer, Ross

    Microwave cavities are used in electron spin resonance to enhance magnetic fields. Dielectric resonators (DRs), pieces of high dielectric material, can be used to tailor the resonant frequency of a cavity. However, designing cavities with DRs to obtain desired frequencies is challenging and in general can only be done numerically with expensive software packages. We present a new method for calculating the resonant frequencies and corresponding field modes for cylindrically symmetric cavities and apply it to a cavity with vertically stacked DRs. The modes of an arbitrary cavity are expressed as an expansion of empty cavity modes. The wave equation for D gives rise to an eigenvalue equation whose eigenvalues are the resonant frequencies and whose eigenvectors yield the electric and magnetic fields of the mode. A test against theory for an infinitely long dielectric cylinder inside an infinite cavity yields an accuracy better than 0.4% for nearly all modes. Calculated resonant frequencies are also compared against experiment for quasi-TE011 modes in resonant cavities with ten different configurations of DRs; experimental results agree with predicted values with an accuracy better than 1.0%. MATLAB code is provided at http://www.physics.byu.edu/research/coltonlab/cavityresonance.

  2. Axisymmetric Predictions of Fluid Flow inside a Rotating Cavity System

    Directory of Open Access Journals (Sweden)

    Mujeebuddin Memon

    2013-07-01

    Full Text Available Accurate prediction of fluid flow in the rotating cavity system is of practical interest as it is most commonly used in the gas turbine engines and compressors. This paper presents the numerical predictions of a rotating cavity flow system for Reynolds numbers of the range 1x105 < Re? < 4x105 and two different mass flow rates Cw=1092 and 2184. A finite-difference technique is employed for a Steady-state solution in the axisymmetric cylindrical polar coordinate frame of reference. The two low Reynolds number turbulence models, the low Reynolds number k-? model and the low Reynolds number second moment closure have been used to compute the basic characteristics of the flow inside the rotating cavity flow system. Different flow regions have been identified by computing flow structures and dimensions of those regions have also been studied under different flow rates. A comparison of the computed variation of moment coefficient of both the turbulence models are presented for the above mentioned parameters and the parametric effects on the moment coefficients have been discussed

  3. Prediction of turbulent cavity flow driven by buoyancy and shear

    International Nuclear Information System (INIS)

    A finite-difference numerical procedure, incorporating a buoyant of the k-turbulence model, is employed to compute turbulent, mixed convection in a square cavity for Reynolds number Re=104 to 2x105, and Archimedes number Ar=0 to 0.4. For Ar>0.04 stable advancement of the solution procedure is obtained only through the use of an 'inertial relaxation' method. The calculated flow, temperature, and turbulence fields are presented and compared with available experimental data. At high Re and low Ar the predicted heat transfer agrees with the correlation Nu=1.16 Resup(0.5). When buoyancy is pronounced the computed Nu is some 15 per cent higher than the data; this is suspected to be due to the turbulence model, and possible improvements to the model are suggested. (U.K.)

  4. Artificial Cavities and Nest Site Selection by Puerto Rican Parrots: a Multiscale Assessment

    OpenAIRE

    Thomas H. White, Jr.; G. Gordon. Brown; Collazo, Jaime A.

    2006-01-01

    We examined nest site selection by Puerto Rican Parrots, a secondary cavity nester, at several spatial scales using the nest entrance as the central focal point relative to 20 habitat and spatial variables. The Puerto Rican Parrot is unique in that, since 2001, all known nesting in the wild has occurred in artificial cavities, which also provided us with an opportunity to evaluate nest site selection without confounding effects of the actual nest cavity characteristics. Because of the data li...

  5. Probing photon correlations in the dark sites of geometrically frustrated cavity lattices

    Science.gov (United States)

    Casteels, W.; Rota, R.; Storme, F.; Ciuti, C.

    2016-04-01

    We explore theoretically the driven-dissipative physics of geometrically frustrated lattices of cavity resonators with relatively weak nonlinearities, i.e., a photon-photon interaction smaller than the loss rate. In such systems, photon modes with zero probability at dark sites are present at the single-particle level due to interference effects. In particular, we study the behavior of a cell with three coupled resonators as well as extended Lieb lattices in one and two dimensions. By considering a partial pumping scheme, with the driving field not applied to the dark sites, we predict that even in the presence of relatively weak photon-photon interactions the nominally dark sites achieve a finite photonic population with strong correlations. We show that this is a consequence of biphoton and multiphoton states that in the absence of frustration would not be visible in the observables.

  6. Differentiating nest sites characteristics of four sympatric cavity-nesting birds

    Directory of Open Access Journals (Sweden)

    Chunfa Zhou

    2012-11-01

    Full Text Available Diverse group of cavity-nesting birds inhabit secondary forests of northeastern China, accounting for about one-third of breeding avian species. We examined differences in nest-site characteristics amongfour cavity-nesting birds, including two cavity excavators (i.e., great spotted woodpecker [Dendrocopos major] and grey-headed woodpecker [Picus canus] and two secondary cavity-nesters (i.e., yellow-rumped flycatcher [Ficedula zanthopygia] and Eurasian nuthatch [Sitta europaea] in Dagang Forestry Farm, Jilin Province, China. We detected total 160 active hole nests in the breeding season of 2008, including 58 nests of cavity excavators and 102 of secondary cavity-nesters. Secondary cavity-nesters tend to prefer Salix pierotii for nestingtrees, but the excavators not. Picus canus used south-facing cavities, which may have been due to thermal advantages. Nest tree and nest-site quadrat characteristics were different between the two excavator species. Specifically, there were significant differences in the entrance diameter and cavity inner diameter between the nest sites of Dendrocopos major and Picus canus, and the entrance length and canopy height of nest tree between Ficedula zanthopygia and Sitta europaea. The characteristics at the scale of nest tree were important for distinguishing nest sites for cavity excavators as well as secondary cavity-nesters. Discriminant analyses illustrated that Ficedula zanthopygia and Sitta europaea used cavities excavated by Dendrocopos major and Picus canus, respectively. Differences in size of nesting holes excavated by different woodpeckers could affect the usage of nest sites by secondary cavity-nesters, which may have an impact on avian community structure in secondary forests.

  7. Cavities

    Science.gov (United States)

    ... the bacteria produce acids that cause decay. Tooth pain occurs after decay reaches the inside of the tooth. Dentists can detect cavities by examining the teeth and taking x-rays periodically. Good oral hygiene and regular dental care plus a healthy diet can help prevent cavities. ...

  8. Predicting the eigenmodes of a cavity containing an array of circular pipes

    DEFF Research Database (Denmark)

    Fenech, Benjamin; Jacobsen, Finn

    2005-01-01

    An array of pipes inside a cavity, as found, for example, in a shell-and-tube heat exchanger, changes the eigenfrequencies of the cavity. It can be tedious to determine the shifted eigenfrequencies with a finite-element model. Based on previous work by Meyer and Neumann, Parker proposed a simple...... eigenfrequencies for the first few modes in a cavity with pipes arranged in a rectangular configuration. The predictions are not so accurate for pipes arranged in a diamond configuration, and a modified version of the relationship is suggested for this configuration. If the number of pipes in the cavity is small...

  9. Prediction of Hydrodynamic Noise of Open Cavity Flow

    Institute of Scientific and Technical Information of China (English)

    GENG Donghan; WANG Yu

    2009-01-01

    In this paper, the hydrodynamically generated noise by the flow over an open cavity is studied. First, aeroacoustic theories and computational aeroacoustic(CAA)methodologies are reviewed in light of hydrodynamic acoustics, based on which, a hybrid method is presented. In the coupling procedure, the unsteady cavity flow field is computed using large-eddy simulation(LES), while the radiated sound is calculated by the Ffowcs Williams-Hawkings(FW-H)acoustic analogy with acoustic source terms extracted from the time-dependent solutions of the unsteady flow. The hybrid LES-FW-H acoustic analogy method is tested with an open cavity flow at Mach number of 0.006 and Reynolds number of 105. Following the reflection theorem of Powell, the contributions from different source terms are quantified, and the terms involving wall-pressure fluctuations are found to account for most of the radiated intensity. The radiation field is investigated in the frequency domain. For the longitudinal direction, the sound propagates with a dominant radiation downstream the cavity in the near-field and a flatter directivity in the far-field, while for the spanwise direction, the acoustic waves have a similar propagation along +z and-z directions, with no visible directivity.

  10. SitesIdentify: a protein functional site prediction tool

    Directory of Open Access Journals (Sweden)

    Doig Andrew J

    2009-11-01

    Full Text Available Abstract Background The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application. Results Here we present a functional site prediction tool (SitesIdentify, based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites. Conclusion SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at http://www.manchester.ac.uk/bioinformatics/sitesidentify/

  11. Exploiting protein flexibility to predict the location of allosteric sites

    Directory of Open Access Journals (Sweden)

    Panjkovich Alejandro

    2012-10-01

    Full Text Available Abstract Background Allostery is one of the most powerful and common ways of regulation of protein activity. However, for most allosteric proteins identified to date the mechanistic details of allosteric modulation are not yet well understood. Uncovering common mechanistic patterns underlying allostery would allow not only a better academic understanding of the phenomena, but it would also streamline the design of novel therapeutic solutions. This relatively unexplored therapeutic potential and the putative advantages of allosteric drugs over classical active-site inhibitors fuel the attention allosteric-drug research is receiving at present. A first step to harness the regulatory potential and versatility of allosteric sites, in the context of drug-discovery and design, would be to detect or predict their presence and location. In this article, we describe a simple computational approach, based on the effect allosteric ligands exert on protein flexibility upon binding, to predict the existence and position of allosteric sites on a given protein structure. Results By querying the literature and a recently available database of allosteric sites, we gathered 213 allosteric proteins with structural information that we further filtered into a non-redundant set of 91 proteins. We performed normal-mode analysis and observed significant changes in protein flexibility upon allosteric-ligand binding in 70% of the cases. These results agree with the current view that allosteric mechanisms are in many cases governed by changes in protein dynamics caused by ligand binding. Furthermore, we implemented an approach that achieves 65% positive predictive value in identifying allosteric sites within the set of predicted cavities of a protein (stricter parameters set, 0.22 sensitivity, by combining the current analysis on dynamics with previous results on structural conservation of allosteric sites. We also analyzed four biological examples in detail, revealing

  12. Prediction and prevention of adhesion formation of the abdominal cavity

    OpenAIRE

    Alisher, Zh; Zhandos, T.; Nurbolat, E.; Zarina, R.; Dinara, Shaki

    2015-01-01

    BACKGROUND The existence of adhesive disease was known in the middle of the XIX century, N.N. Blinov in the middle of the XX century in his monograph “Adhesive disease”, wrote that post-surgical adhesions in the abdominal cavity – is a defect of surgeon. At present time, it is known that adhesive disease is the adhesions of connective tissue between adjacent organs or the peritoneal surface resulting from damage of their walls (more often during a surgical intervention). As of today, there ar...

  13. Effect of Spatial Scale on Modeling and Predicting Mean Cavity Tree Density: A Comparison of Modeling Methods

    OpenAIRE

    Lee, Stephen S; Zhaofei Fan

    2012-01-01

    Cavity trees are integral components of healthy forest ecosystems and provide habitat and shelter for a wide variety of wildlife species. Thus, monitoring and predicting cavity tree abundance is an important part of forest management and wildlife conservation. However, cavity trees are relatively rare and their abundance can vary dramatically among forest stands, even when the stands are similar in most other respects. This makes it difficult to model and predict cavity tree density. We utili...

  14. Artificial Cavities and Nest Site Selection by Puerto Rican Parrots: a Multiscale Assessment

    Directory of Open Access Journals (Sweden)

    Thomas H. White, Jr.

    2006-12-01

    Full Text Available We examined nest site selection by Puerto Rican Parrots, a secondary cavity nester, at several spatial scales using the nest entrance as the central focal point relative to 20 habitat and spatial variables. The Puerto Rican Parrot is unique in that, since 2001, all known nesting in the wild has occurred in artificial cavities, which also provided us with an opportunity to evaluate nest site selection without confounding effects of the actual nest cavity characteristics. Because of the data limitations imposed by the small population size of this critically endangered endemic species, we employed a distribution-free statistical simulation approach to assess site selection relative to characteristics of used and unused nesting sites. Nest sites selected by Puerto Rican Parrots were characterized by greater horizontal and vertical visibility from the nest entrance, greater density of mature sierra palms, and a more westerly and leeward orientation of nest entrances than unused sites. Our results suggest that nest site selection in this species is an adaptive response to predation pressure, to which the parrots respond by selecting nest sites offering advantages in predator detection and avoidance at all stages of the nesting cycle. We conclude that identifying and replicating the “nest gestalt” of successful nesting sites may facilitate conservation efforts for this and other endangered avian species.

  15. Prediction of proprotein convertase cleavage sites

    DEFF Research Database (Denmark)

    Duckert, Peter; Brunak, Søren; Blom, Nikolaj

    2004-01-01

    has created additional focus on proprotein processing. We have developed a method for prediction of cleavage sites for PCs based on artificial neural networks. Two different types of neural networks have been constructed: a furin-specific network based on experimental results derived from the...

  16. Prediction of multipactor in the iris region of rf deflecting mode cavities

    Science.gov (United States)

    Burt, G.; Dexter, A. C.

    2011-12-01

    Multipactor is a major cause of field limitation in many superconducting rf cavities. Multipacting is a particular issue for deflecting mode cavities as the typical behavior is not well studied, understood, or parametrized. In this paper an approximate analytical model for the prediction of multipactor in the iris region of deflecting mode cavities is developed. This new but simple model yields a clear explanation on the broad range of rf field levels over which the multipactor can occur. The principle multipactors under investigation here are two-point multipactors associated with cyclotron motion in the cavity’s rf magnetic field. The predictions from the model are compared to numerical simulations and good agreement is obtained. The results are also compared to experimental results previously reported by KEK and are also found in good agreement.

  17. Dynamics of water molecules in the active-site cavity of human cytochromes P450

    DEFF Research Database (Denmark)

    Rydberg, Patrik; Rod, Thomas Holm; Olsen, Lars;

    2007-01-01

    We have studied the dynamics of water molecules in six crystal structures of four human cytochromes P450, 2A6, 2C8, 2C9, and 3A4, with molecular dynamics simulations. In the crystal structures, only a few water molecules are seen and the reported sizes of the active-site cavity vary a lot. In the...

  18. Prediction of Underground Cavity Roof Collapse using the Hoek–Brown Failure Criterion

    DEFF Research Database (Denmark)

    Suchowerska, A. M.; Merifield, R. S.; Carter, J. P.;

    2012-01-01

    described by the Hoek–Brown failure criterion. The results of the analysis allow for prediction of roof collapse and to determine whether the failure surface that develops in the rock mass remains localised or extends through the full depth of cover. This is of significance if there are overlying cavities...

  19. Predictions of buoyancy-induced flow in asymmetrical heated rotating cavity system

    International Nuclear Information System (INIS)

    This paper presents the finite difference solutions for buoyancy-induced flow in the asymmetrical heated rotating cavity system for the range of rotational Reynolds numbers Re =6.13x10/sup 5/< Re/sub theta/=4.4*10/sup 6/ and the mass flow rates C/sub w/ <28000< C/sub w/ <3000. All the simulations have been carried out through the CFD (computational Fluid Dynamics) commercial code, ANSYS Fluent 12.0, by adopting axisymmetric, steady-state and elliptic technique. Two well know models namely k-epsilon and the Reynolds stress models have been employed. The simulated results illustrate the important aspects of the heated rotating cavity flow system. The noteworthy influence of buoyancy-induced flow have been observed on the predicted stream line, static temperature contours and the local Nusselt numbers for the rotating cavity flow system. The noteworthy influence of buoyancy-induced flow have been observed on the predicted stream lines, static temperature contours and the local Nusselt numbers for the rotating cavity space. A comparison of the predicted local nusselt numbers for the hot and cold discs showed a good level of agreement with the measurement. (author)

  20. Predictions of Buoyancy-induced Flow in Asymmetrical Heated Rotating Cavity System

    Directory of Open Access Journals (Sweden)

    Abdul Fatah Abbassi

    2013-04-01

    Full Text Available This paper presents the finite difference solutions for buoyancy-induced flow in the asymmetrical heated rotating cavity system for the range of rotational Reynolds numbers Reθ =6.13x10^5 cavity flow system. The noteworthy influence of buoyancy-induced flow have been observed on the predicted stream lines, static temperature contours and the local Nusselt numbers for the rotating cavity space. A comparison of the predicted local Nusselt numbers for the hot and cold discs showed a good level of agreement with the measurements.

  1. Predicting distinct regimes of hydrogen behavior at nano-cavities in metals

    Science.gov (United States)

    Hayward, Erin; Hayward, Robert; Fu, Chu-Chun

    2016-08-01

    Hydrogen interacts strongly with structural defects and is often implicated in degradation of materials. Precise conditions and local structures favoring the formation of H2 molecules are unclear so far, and not directly accessible experimentally. We present a computational and theoretical study of properties and behavior of hydrogen at nano-cavities based on the saturation of the vacancy cluster surfaces. A predictive model is developed which characterizes two regimes of behavior: in the undersaturated regime, non-interacting atomic hydrogen decorates the surface of a nano-cavity. In the oversaturated regime, the surface is maximally covered, and stable molecular hydrogen can be formed within the bubble. We verify this model with ab initio Monte Carlo simulations to extensively explore low energy states of small vacancy clusters containing multiple hydrogen atoms. The present model is expected to be easily transferable to the study of H in other metallic systems.

  2. Text mining improves prediction of protein functional sites.

    Directory of Open Access Journals (Sweden)

    Karin M Verspoor

    Full Text Available We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites. The structure analysis was carried out using Dynamics Perturbation Analysis (DPA, which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

  3. Characterization of Microbial Communities in Subsurface Nuclear Blast Cavities of the Nevada Test Site

    International Nuclear Information System (INIS)

    This U.S. Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program's Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse and divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.

  4. Characterization of Microbial Communities in Subsurface Nuclear Blast Cavities of the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Moser, Duane P.; Bruckner, Jim; Fisher, Jen; Czerwinski, Ken; Russell, Charles E.; Zavarin, Mavrik

    2010-09-01

    This U.S. Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program’s Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse and divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.

  5. Characterization of microbial communities in subsurface nuclear blast cavities of the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Moser, Duane P; Czerwinski, Ken; Russell, Charles E; Zavarin, Mavrik

    2010-07-13

    This US Department of Energy (DOE) Environmental Remediation Sciences Project (ERSP) was designed to test fundamental hypotheses concerning the existence and nature of indigenous microbial populations of Nevada Test Site subsurface nuclear test/detonation cavities. Now called Subsurface Biogeochemical Research (SBR), this program's Exploratory Research (ER) element, which funded this research, is designed to support high risk, high potential reward projects. Here, five cavities (GASCON, CHANCELLOR, NASH, ALEMAN, and ALMENDRO) and one tunnel (U12N) were sampled using bailers or pumps. Molecular and cultivation-based techniques revealed bacterial signatures at five sites (CHANCELLOR may be lifeless). SSU rRNA gene libraries contained diverse and divergent microbial sequences affiliated with known metal- and sulfur-cycling microorganisms, organic compound degraders, microorganisms from deep mines, and bacteria involved in selenate reduction and arsenite oxidation. Close relatives of Desulforudis audaxviator, a microorganism thought to subsist in the terrestrial deep subsurface on H2 and SO42- produced by radiochemical reactions, was detected in the tunnel waters. NTS-specific media formulations were used to culture and quantify nitrate-, sulfate-, iron-reducing, fermentative, and methanogenic microorganisms. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, our results should have implications for management strategies at this and other DOE sites.

  6. Exciton dynamics in a site-controlled quantum dot coupled to a photonic crystal cavity

    Energy Technology Data Exchange (ETDEWEB)

    Jarlov, C., E-mail: clement.jarlov@epfl.ch; Lyasota, A.; Ferrier, L.; Gallo, P.; Dwir, B.; Rudra, A.; Kapon, E. [Laboratory of Physics of Nanostructures, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland)

    2015-11-09

    Exciton and cavity mode (CM) dynamics in site-controlled pyramidal quantum dots (QDs), integrated with linear photonic crystal membrane cavities, are investigated for a range of temperatures and photo-excitation power levels. The absence of spurious multi-excitonic effects, normally observed in similar structures based on self-assembled QDs, permits the observation of effects intrinsic to two-level systems embedded in a solid state matrix and interacting with optical cavity modes. The coupled exciton and CM dynamics follow the same trend, indicating that the CM is fed only by the exciton transition. The Purcell reduction of the QD and CM decay times is reproduced well by a theoretical model that includes exciton linewidth broadening and temperature dependent non-radiative processes, from which we extract a Purcell factor of 17 ± 5. For excitation powers above QD saturation, we show the influence of quantum wire barrier states at short delay time, and demonstrate the absence of multiexcitonic background emission.

  7. Exciton dynamics in a site-controlled quantum dot coupled to a photonic crystal cavity

    International Nuclear Information System (INIS)

    Exciton and cavity mode (CM) dynamics in site-controlled pyramidal quantum dots (QDs), integrated with linear photonic crystal membrane cavities, are investigated for a range of temperatures and photo-excitation power levels. The absence of spurious multi-excitonic effects, normally observed in similar structures based on self-assembled QDs, permits the observation of effects intrinsic to two-level systems embedded in a solid state matrix and interacting with optical cavity modes. The coupled exciton and CM dynamics follow the same trend, indicating that the CM is fed only by the exciton transition. The Purcell reduction of the QD and CM decay times is reproduced well by a theoretical model that includes exciton linewidth broadening and temperature dependent non-radiative processes, from which we extract a Purcell factor of 17 ± 5. For excitation powers above QD saturation, we show the influence of quantum wire barrier states at short delay time, and demonstrate the absence of multiexcitonic background emission

  8. Cavity-enhanced single photon emission from site-controlled In(Ga)As quantum dots fabricated using nanoimprint lithography

    International Nuclear Information System (INIS)

    We report on the emission dynamics of single In(Ga)As quantum dots formed in etched GaAs pits and integrated into micropillar cavities. The site-controlled quantum dots were fabricated by molecular beam epitaxy on nanoimprint lithography patterned GaAs(001) surfaces. Triggered single photon emission confirmed by photon autocorrelation measurements is demonstrated. Time-resolved photoluminescence experiments clearly show an effect of the cavity on the spontaneous emission rate of the quantum dot.

  9. Cavity-enhanced single photon emission from site-controlled In(Ga)As quantum dots fabricated using nanoimprint lithography

    Energy Technology Data Exchange (ETDEWEB)

    Tommila, J.; Hakkarainen, T. V.; Schramm, A., E-mail: andreas.schramm@tut.fi; Guina, M. [Optoelectronics Research Centre, Tampere University of Technology, P.O. Box 692, FIN-33101 Tampere (Finland); Belykh, V. V.; Sibeldin, N. N. [P.N. Lebedev Physical Institute, Russian Academy of Sciences, Moscow 119991 (Russian Federation); Heinonen, E. [Center of Microscopy and Nanotechnology, University of Oulu, P.O. Box 7150, FIN-90014 Oulu (Finland)

    2014-05-26

    We report on the emission dynamics of single In(Ga)As quantum dots formed in etched GaAs pits and integrated into micropillar cavities. The site-controlled quantum dots were fabricated by molecular beam epitaxy on nanoimprint lithography patterned GaAs(001) surfaces. Triggered single photon emission confirmed by photon autocorrelation measurements is demonstrated. Time-resolved photoluminescence experiments clearly show an effect of the cavity on the spontaneous emission rate of the quantum dot.

  10. Response to induction chemotherapy as predictive marker of tumor response to radiotherapy and survival in oral cavity cancer

    OpenAIRE

    Surendra Kumar Saini; Shelly Srivastava; Shanbhu Nath Prasad

    2015-01-01

    Background: Trials have shown some statistically nonsignificant survival advantage of taxane, platin and 5-FU (TPF) induction chemotherapy before definitive chemoradiation. We tried to find the role of induction chemotherapy in the prediction of tumor response to radiotherapy and survival in the treatment of oral cavity cancers. Patients and Methods: Patients of stage III and IV (M0) unresectable oral cavity squamous cell carcinoma were assigned to receive two cycles of TPF. On the basis of r...

  11. SVM-based prediction of caspase substrate cleavage sites

    OpenAIRE

    Wee, Lawrence JK; Tan, Tin Wee; Ranganathan, Shoba

    2006-01-01

    Background Caspases belong to a class of cysteine proteases which function as critical effectors in apoptosis and inflammation by cleaving substrates immediately after unique sites. Prediction of such cleavage sites will complement structural and functional studies on substrates cleavage as well as discovery of new substrates. Recently, different computational methods have been developed to predict the cleavage sites of caspase substrates with varying degrees of success. As the support vector...

  12. Availability of tree cavities in a sal forest of Nepal

    Directory of Open Access Journals (Sweden)

    Bhusal P

    2016-04-01

    Full Text Available Tree cavities are important structural elements of forest ecosystem that host numerous birds, mammals and other cavity-dependent organisms. Pattern of cavity distribution in temperate and boreal forests are relatively well studied, yet little is known about cavities in tropical and subtropical forests. We compared cavity availability in relation to tree condition (living tree and snag, tree species and DBH class between two different sites in a subtropical deciduous sal forest in Nepal: the Chitwan National Park Forest (the park site and the Khorsor Buffer Zone Forest (the buffer site. Surveys for tree cavities were conducted in 2013 on 50 circular sample plots of size 0.1 ha. We recorded 40 cavity trees in the park site and 31 cavity trees in the buffer site. Density of cavities was on average 22.4 ha-1 in the park site and 19.2 ha-1 in the buffer site. Cavities occurred mostly in living trees (85.9% cavity trees and were formed mostly by damage and decay (natural cavities: 74% or by woodpecker activity (excavated cavities: 26%. Most were observed on three tree species: Shorea robusta, Dillenia pentagyna and Syzygium operculatum, with a mean diameter of 43 cm (range: 12-111 cm. S. operculatum, Myrsine semiserrata and Semecarpus anacardium were overrepresented among tree species with cavities. In snags, 25.0% of all cavities were found in the park site and 8.3% in the buffer site, while snags represented 4.2% and 2.2% of all trees in the two sites, respectively. Statistical anaysis indicated that tree species, tree condition and particularly diameter (DBH were important variables for the prediction of cavity presence. We recommend cavity-bearing tree species to be better protected by forest management in order to help maintain the community of cavity dwellers.

  13. Characterization of Microbial Communities in Subsurface Nuclear Blast Cavities of the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Moser, Duane; Russell, Chuck; Marshall, Matthew; Czerwinski, Ken; Daly, Michael J; Zavarin, Mavrik

    2008-02-08

    This exploratory research project is designed to test fundamental hypotheses concerning the possible existence and nature of indigenous microbial populations in Nevada Test Site (NTS) subsurface nuclear blast cavities. Although subsurface microbiological studies have been performed at the NTS in the past, radioactive zones have yet to be addressed. Nuclear blast zone microbiology is a completely new field and our team is well-positioned to collect and analyze samples that have never before been available to microbiologists. Relevant samples are now being obtained by incorporating microbiological collections into an ongoing annual hot well sampling program being conducted by other agencies. A combination of cultivation-based and molecular microbial detection protocols is being utilized at multiple locations to survey for uncultivable microorganisms and to develop a culture collection which will be characterized for radionuclide- and metal-reduction capabilities. Given that redox manipulations mediated by microorganisms can impact the mobility of DOE contaminants, a positive outcome from this work would have significant implications for management strategies at this and other DOE sites. A primary objective of the project has been the establishment of the regulatory and technical framework necessary to enable our acquisition of samples. Thus, much of our activity in the first phase of this work has involved the development an approved Field Area Work Plan (FAWP), Radiological Work Permit (RWP), and other documentation required for radiological work at the NTS. We have also invested significant time into ensuring that all personnel possess the required training (e.g. Radworker II and 40 hr. HAZWOPER) for access to the hot well sampling sites. Laboratory facilities, required for field processing of radioactive samples as well as DNA extraction and other manipulations, have been secured both the NTS (Mercury, NV) and UNLV. Although our year-1 field work was delayed due

  14. Flood Predictions Combining Regional and Single Site Hydrometric Information

    Directory of Open Access Journals (Sweden)

    Campos–Aranda

    2010-07-01

    Full Text Available Initially, the statistic benefit of flood predictions obtained by combining reliable regional and scarce site hydrometric data is pointed out. Then the mathematical equations for combining mean and standard deviation logarithms of regional and site data are exposed, as well as the necessary expressions for desired predictions, based on Student's t distribution. Later two numerical applications are described, the first one based in Carrizal hydrometric station located in Santiago River in Nayarit and the second one which makes use of five water gauging stations in Tempoal River in Veracruz. Finally, a conclusion is formulated pointing out the simplicity of that method and the accuracy of its predictions.

  15. Pripper: prediction of caspase cleavage sites from whole proteomes

    Directory of Open Access Journals (Sweden)

    Salmi Jussi

    2010-06-01

    Full Text Available Abstract Background Caspases are a family of proteases that have central functions in programmed cell death (apoptosis and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to predict caspase cleavage sites from individual proteins, but currently none of them can be used to predict caspase cleavage sites from multiple proteins or entire proteomes, or to use several classifiers in combination. The possibility to create a database from predicted caspase cleavage products for the whole genome could significantly aid in identifying novel caspase targets from tandem mass spectrometry based proteomic experiments. Results Three different pattern recognition classifiers were developed for predicting caspase cleavage sites from protein sequences. Evaluation of the classifiers with quality measures indicated that all of the three classifiers performed well in predicting caspase cleavage sites, and when combining different classifiers the accuracy increased further. A new tool, Pripper, was developed to utilize the classifiers and predict the caspase cut sites from an arbitrary number of input sequences. A database was constructed with the developed tool, and it was used to identify caspase target proteins from tandem mass spectrometry data from two different proteomic experiments. Both known caspase cleavage products as well as novel cleavage products were identified using the database demonstrating the usefulness of the tool. Pripper is not restricted to predicting only caspase cut sites, but it gives the possibility to scan protein sequences for any given motif(s and predict cut sites once a suitable cut site prediction model for any other protease has been developed. Pripper is freely available and can be downloaded from http://users.utu.fi/mijopi/Pripper. Conclusions We have developed Pripper, a tool for

  16. A systems biology approach to transcription factor binding site prediction.

    Directory of Open Access Journals (Sweden)

    Xiang Zhou

    Full Text Available BACKGROUND: The elucidation of mammalian transcriptional regulatory networks holds great promise for both basic and translational research and remains one the greatest challenges to systems biology. Recent reverse engineering methods deduce regulatory interactions from large-scale mRNA expression profiles and cross-species conserved regulatory regions in DNA. Technical challenges faced by these methods include distinguishing between direct and indirect interactions, associating transcription regulators with predicted transcription factor binding sites (TFBSs, identifying non-linearly conserved binding sites across species, and providing realistic accuracy estimates. METHODOLOGY/PRINCIPAL FINDINGS: We address these challenges by closely integrating proven methods for regulatory network reverse engineering from mRNA expression data, linearly and non-linearly conserved regulatory region discovery, and TFBS evaluation and discovery. Using an extensive test set of high-likelihood interactions, which we collected in order to provide realistic prediction-accuracy estimates, we show that a careful integration of these methods leads to significant improvements in prediction accuracy. To verify our methods, we biochemically validated TFBS predictions made for both transcription factors (TFs and co-factors; we validated binding site predictions made using a known E2F1 DNA-binding motif on E2F1 predicted promoter targets, known E2F1 and JUND motifs on JUND predicted promoter targets, and a de novo discovered motif for BCL6 on BCL6 predicted promoter targets. Finally, to demonstrate accuracy of prediction using an external dataset, we showed that sites matching predicted motifs for ZNF263 are significantly enriched in recent ZNF263 ChIP-seq data. CONCLUSIONS/SIGNIFICANCE: Using an integrative framework, we were able to address technical challenges faced by state of the art network reverse engineering methods, leading to significant improvement in direct

  17. Glycosylation site prediction using ensembles of Support Vector Machine classifiers

    Directory of Open Access Journals (Sweden)

    Silvescu Adrian

    2007-11-01

    Full Text Available Abstract Background Glycosylation is one of the most complex post-translational modifications (PTMs of proteins in eukaryotic cells. Glycosylation plays an important role in biological processes ranging from protein folding and subcellular localization, to ligand recognition and cell-cell interactions. Experimental identification of glycosylation sites is expensive and laborious. Hence, there is significant interest in the development of computational methods for reliable prediction of glycosylation sites from amino acid sequences. Results We explore machine learning methods for training classifiers to predict the amino acid residues that are likely to be glycosylated using information derived from the target amino acid residue and its sequence neighbors. We compare the performance of Support Vector Machine classifiers and ensembles of Support Vector Machine classifiers trained on a dataset of experimentally determined N-linked, O-linked, and C-linked glycosylation sites extracted from O-GlycBase version 6.00, a database of 242 proteins from several different species. The results of our experiments show that the ensembles of Support Vector Machine classifiers outperform single Support Vector Machine classifiers on the problem of predicting glycosylation sites in terms of a range of standard measures for comparing the performance of classifiers. The resulting methods have been implemented in EnsembleGly, a web server for glycosylation site prediction. Conclusion Ensembles of Support Vector Machine classifiers offer an accurate and reliable approach to automated identification of putative glycosylation sites in glycoprotein sequences.

  18. Cavity detection and delineation research. Part 4: Microgravimetric survey: Manatee Springs Site, Florida

    Science.gov (United States)

    Butler, D. K.; Whitten, C. B.; Smith, F. L.

    1983-03-01

    Results of a microgravimetric survey at Manatee Springs, Levy County, Fla., are presented. The survey area was 100 by 400 ft, with 20-ft gravity station spacing, and with the long dimension of the area approximately perpendicular to the known trend of the main cavity. The main cavity is about 80 to 100 ft below the surface and has a cross section about 16 to 20 ft in height and 30 to 40 ft in width beneath the survey area. Using a density contrast of -1.3 g/cucm, the gravity anomaly is calculated to be -35 micro Gal with a width at half maximum of 205 ft. The microgravimetric survey results clearly indicate a broad negative anomaly coincident with the location and trend of the cavity system across the survey area. The anomaly magnitude and width are consistent with those calculated from the known depth and dimensions of the main cavity. In addition, a small, closed negative anomaly feature, superimposed on the broad negative feature due to the main cavity, satisfactorily delineated a small secondary cavity feature which was discovered and mapped by cave divers.

  19. Reliable prediction of transcription factor binding sites by phylogenetic verification

    OpenAIRE

    Li, Xiaoman; Zhong, Sheng; Wong, Wing H.

    2005-01-01

    We present a statistical methodology that largely improves the accuracy in computational predictions of transcription factor (TF) binding sites in eukaryote genomes. This method models the cross-species conservation of binding sites without relying on accurate sequence alignment. It can be coupled with any motif-finding algorithm that searches for overrepresented sequence motifs in individual species and can increase the accuracy of the coupled motif-finding algorithm. Because this method is ...

  20. Predicting web site audience demographics for web advertising targeting using multi-web site clickstream data

    OpenAIRE

    Bock, K W; D. VAN DEN POEL; S. MANIGART

    2009-01-01

    Several recent studies have explored the virtues of behavioral targeting and personalization for online advertising. In this paper, we add to this literature by proposing a cost-effective methodology for the prediction of demographic web site visitor profiles that can be used for web advertising targeting purposes. The methodology involves the transformation of web site visitors’ clickstream patterns to a set of features and the training of Random Forest classifiers that generate predictions ...

  1. Fast dynamics perturbation analysis for prediction of protein functional sites

    Directory of Open Access Journals (Sweden)

    Cohn Judith D

    2008-01-01

    Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.

  2. Polarization properties and disorder effects in H3 photonic crystal cavities incorporating site-controlled, high-symmetry quantum dot arrays

    International Nuclear Information System (INIS)

    We report on the effects of optical disorder on breaking the symmetry of the cavity modes of H3 photonic crystal cavities incorporating site-controlled pyramidal quantum dots (QDs) as the internal light source. The high in-plane symmetry of the polarization states of the pyramidal QDs simplifies the analysis of the polarization states of the H3 cavities. It is shown that the optical disorder induced by fabrication imperfections lifts the degeneracy of the two quadrupole cavity modes and tilts the elongation axes of the cavity mode patterns with respect to the ideal, hexagonal symmetry case. These results are useful for designing QD-cavity structures for polarization-entangled photon sources and few-QD lasers

  3. Reliable prediction of transcription factor binding sites by phylogenetic verification.

    Science.gov (United States)

    Li, Xiaoman; Zhong, Sheng; Wong, Wing H

    2005-11-22

    We present a statistical methodology that largely improves the accuracy in computational predictions of transcription factor (TF) binding sites in eukaryote genomes. This method models the cross-species conservation of binding sites without relying on accurate sequence alignment. It can be coupled with any motif-finding algorithm that searches for overrepresented sequence motifs in individual species and can increase the accuracy of the coupled motif-finding algorithm. Because this method is capable of accurately detecting TF binding sites, it also enhances our ability to predict the cis-regulatory modules. We applied this method on the published chromatin immunoprecipitation (ChIP)-chip data in Saccharomyces cerevisiae and found that its sensitivity and specificity are 9% and 14% higher than those of two recent methods. We also recovered almost all of the previously verified TF binding sites and made predictions on the cis-regulatory elements that govern the tight regulation of ribosomal protein genes in 13 eukaryote species (2 plants, 4 yeasts, 2 worms, 2 insects, and 3 mammals). These results give insights to the transcriptional regulation in eukaryotic organisms. PMID:16286651

  4. Computational Prediction of RNA-Binding Proteins and Binding Sites

    Directory of Open Access Journals (Sweden)

    Jingna Si

    2015-11-01

    Full Text Available Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%–8% of all proteins are RNA-binding proteins (RBPs. Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein–RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein–RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

  5. Glycosylation site prediction using ensembles of Support Vector Machine classifiers

    OpenAIRE

    Silvescu Adrian; Sinapov Jivko; Caragea Cornelia; Dobbs Drena; Honavar Vasant

    2007-01-01

    Abstract Background Glycosylation is one of the most complex post-translational modifications (PTMs) of proteins in eukaryotic cells. Glycosylation plays an important role in biological processes ranging from protein folding and subcellular localization, to ligand recognition and cell-cell interactions. Experimental identification of glycosylation sites is expensive and laborious. Hence, there is significant interest in the development of computational methods for reliable prediction of glyco...

  6. Combining specificity determining and conserved residues improves functional site prediction

    Directory of Open Access Journals (Sweden)

    Gelfand Mikhail S

    2009-06-01

    Full Text Available Abstract Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core. Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities. Results Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs, as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples. Conclusion The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.

  7. Seismic Hazard Assessment in Site Evaluation for Nuclear Installations: Ground Motion Prediction Equations and Site Response

    International Nuclear Information System (INIS)

    The objective of this publication is to provide the state-of-the-art practice and detailed technical elements related to ground motion evaluation by ground motion prediction equations (GMPEs) and site response in the context of seismic hazard assessments as recommended in IAEA Safety Standards Series No. SSG-9, Seismic Hazards in Site Evaluation for Nuclear Installations. The publication includes the basics of GMPEs, ground motion simulation, selection and adjustment of GMPEs, site characterization, and modelling of site response in order to improve seismic hazard assessment. The text aims at delineating the most important aspects of these topics (including current practices, criticalities and open problems) within a coherent framework. In particular, attention has been devoted to filling conceptual gaps. It is written as a reference text for trained users who are responsible for planning preparatory seismic hazard analyses for siting of all nuclear installations and/or providing constraints for anti-seismic design and retrofitting of existing structures

  8. A Mechanism-Based Model for the Prediction of the Metabolic Sites of Steroids Mediated by Cytochrome P450 3A4

    Directory of Open Access Journals (Sweden)

    Zi-Ru Dai

    2015-06-01

    Full Text Available Early prediction of xenobiotic metabolism is essential for drug discovery and development. As the most important human drug-metabolizing enzyme, cytochrome P450 3A4 has a large active cavity and metabolizes a broad spectrum of substrates. The poor substrate specificity of CYP3A4 makes it a huge challenge to predict the metabolic site(s on its substrates. This study aimed to develop a mechanism-based prediction model based on two key parameters, including the binding conformation and the reaction activity of ligands, which could reveal the process of real metabolic reaction(s and the site(s of modification. The newly established model was applied to predict the metabolic site(s of steroids; a class of CYP3A4-preferred substrates. 38 steroids and 12 non-steroids were randomly divided into training and test sets. Two major metabolic reactions, including aliphatic hydroxylation and N-dealkylation, were involved in this study. At least one of the top three predicted metabolic sites was validated by the experimental data. The overall accuracy for the training and test were 82.14% and 86.36%, respectively. In summary, a mechanism-based prediction model was established for the first time, which could be used to predict the metabolic site(s of CYP3A4 on steroids with high predictive accuracy.

  9. Predicting on-site environmental impacts of municipal engineering works

    Energy Technology Data Exchange (ETDEWEB)

    Gangolells, Marta, E-mail: marta.gangolells@upc.edu; Casals, Miquel, E-mail: miquel.casals@upc.edu; Forcada, Núria, E-mail: nuria.forcada@upc.edu; Macarulla, Marcel, E-mail: marcel.macarulla@upc.edu

    2014-01-15

    The research findings fill a gap in the body of knowledge by presenting an effective way to evaluate the significance of on-site environmental impacts of municipal engineering works prior to the construction stage. First, 42 on-site environmental impacts of municipal engineering works were identified by means of a process-oriented approach. Then, 46 indicators and their corresponding significance limits were determined on the basis of a statistical analysis of 25 new-build and remodelling municipal engineering projects. In order to ensure the objectivity of the assessment process, direct and indirect indicators were always based on quantitative data from the municipal engineering project documents. Finally, two case studies were analysed and found to illustrate the practical use of the proposed model. The model highlights the significant environmental impacts of a particular municipal engineering project prior to the construction stage. Consequently, preventive actions can be planned and implemented during on-site activities. The results of the model also allow a comparison of proposed municipal engineering projects and alternatives with respect to the overall on-site environmental impact and the absolute importance of a particular environmental aspect. These findings are useful within the framework of the environmental impact assessment process, as they help to improve the identification and evaluation of on-site environmental aspects of municipal engineering works. The findings may also be of use to construction companies that are willing to implement an environmental management system or simply wish to improve on-site environmental performance in municipal engineering projects. -- Highlights: • We present a model to predict the environmental impacts of municipal engineering works. • It highlights significant on-site environmental impacts prior to the construction stage. • Findings are useful within the environmental impact assessment process. • They also

  10. MetWAMer: eukaryotic translation initiation site prediction

    Directory of Open Access Journals (Sweden)

    Brendel Volker

    2008-09-01

    Full Text Available Abstract Background Translation initiation site (TIS identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations. Results MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the k-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage. Conclusion We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.

  11. High precision prediction of functional sites in protein structures.

    Directory of Open Access Journals (Sweden)

    Ljubomir Buturovic

    Full Text Available We address the problem of assigning biological function to solved protein structures. Computational tools play a critical role in identifying potential active sites and informing screening decisions for further lab analysis. A critical parameter in the practical application of computational methods is the precision, or positive predictive value. Precision measures the level of confidence the user should have in a particular computed functional assignment. Low precision annotations lead to futile laboratory investigations and waste scarce research resources. In this paper we describe an advanced version of the protein function annotation system FEATURE, which achieved 99% precision and average recall of 95% across 20 representative functional sites. The system uses a Support Vector Machine classifier operating on the microenvironment of physicochemical features around an amino acid. We also compared performance of our method with state-of-the-art sequence-level annotator Pfam in terms of precision, recall and localization. To our knowledge, no other functional site annotator has been rigorously evaluated against these key criteria. The software and predictive models are incorporated into the WebFEATURE service at http://feature.stanford.edu/wf4.0-beta.

  12. Prediction of the flooding process at the Ronneburg site - results of an integrated approach

    International Nuclear Information System (INIS)

    The flooding process of the Ronneburg uranium mine (WISMUT) was initiated at the turn of the year 1997 to 1998. In order to prepare the flooding process and to derive and optimize technological measures an integrated modelling approach was chosen which includes several coupled modules. The most important issues to be answered are: (1) prediction of the flooding time (2) prediction of the groundwater level at the post-flooding stage, assessment of amount, location and quality of flooding waters entering the receiving streams at the final stage (3) water quality prediction within the mine during the flooding process (4) definition of technological measures and assessment of their efficiency A box model which includes the three-dimensional distribution of the cavity volume in the mine represents the model core. The model considers the various types of dewatered cavity volumes for each mine level / mining field and the degree of vertical and horizontal connection between the mining fields. Different types of open mine space as well as the dewatered geological pore and joint volume are considered taking into account the contour of the depression cone prior to flooding and the characteristics of the different rock types. Based on the mine water balance and the flooding technology the model predicts the rise of the water table over time during the flooding process for each mine field separately. In order to predict the mine water quality and the efficiency of in-situ water treatment the box model was linked to a geochemical model (PHREEQC). A three-dimensional flow model is used to evaluate the post-flooding situation at the Ronneburg site. This model is coupled to the box model. The modelling results of various flooding scenarios show that a prediction of the post-flooding geohydraulic situation is possible despite of uncertainties concerning the input parameters which still exist. The post-flooding water table in the central part of the Ronneburg mine will be 270 m

  13. Site characterization and validation. Stage 2 - Preliminary predictions

    International Nuclear Information System (INIS)

    The Site Characterization and Validation (SCV) project is designed to assess how well we can characterize a volume of rock prior to using it as a repository. The programme of work focuses on the validation of the techniques used in site characterization. The SCV project contains 5 stages of work arranged in two 'cycles' of data-gathering, prediction, and validation. The first stage of work has included drilling of 6 boreholes (N2, N3, N4, W1, W2 and V3) and measurements of geology, fracture characteristics, stess, single borehole geophysical logging, radar, seismics and hydrogeology. The rock at the SCV site is granite with small lithological variations. Based essentially on radar and seismic results 5 'fracture zones' have been identified, named GA, GB, GC, GH and GI. They all extend acroos the entire SCV site. They aer basically in in two groups (GA, GB, GC and GH, GI). The first group are aligned N40 degree E with a dip of 35 degree to the south. The second group are aligned approximately N10 degree W dipping 60 degree E. From the stochastic analysis of the joint data it was possible to identify three main fracture orientation clusters. The orientation of two of these clusters agree roughly with orientation of the main features. Cluster B has roughly the same orientation as GH and GI, while features GA, GB and GC have an orientation similar to the more loosely defined cluster C. The orientation of the third cluster (A) is northwest with a dip to northeast. It is found that 94% of all measured hydraulic transmissivity is accounted for by 4% of the tested rock, not all of this 'concentrated' transmissivity is with the major features defined by geophysics. When the hydraulic connections across the site are examied they show that there are several welldefined zones which permit rapid transmission of hydraulic signals. These are essentially from the northeast to the southwest. (66 figs., 21 tabs., 33 refs.)

  14. Method of predicting Splice Sites based on signal interactions

    Directory of Open Access Journals (Sweden)

    Deogun Jitender S

    2006-04-01

    Full Text Available Abstract Background Predicting and proper ranking of canonical splice sites (SSs is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan. Results According to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE and Intronic (ISE Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments. Conclusion Designed methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site. Reviewers This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand.

  15. A resonance shift prediction based on the Boltzmann-Ehrenfest principle for cylindrical cavities with a rigid sphere.

    Science.gov (United States)

    Santillan, Arturo O; Cutanda-Henríquez, Vicente

    2008-11-01

    An investigation on the resonance frequency shift for a plane-wave mode in a cylindrical cavity produced by a rigid sphere is reported in this paper. This change of the resonance frequency has been previously considered as a cause of oscillational instabilities in single-mode acoustic levitation devices. It is shown that the use of the Boltzmann-Ehrenfest principle of adiabatic invariance allows the derivation of an expression for the resonance frequency shift in a simpler and more direct way than a method based on a Green's function reported in literature. The position of the sphere can be any point along the axis of the cavity. Obtained predictions of the resonance frequency shift with the deduced equation agree quite well with numerical simulations based on the boundary element method. The results are also confirmed by experiments. The equation derived from the Boltzmann-Ehrenfest principle appears to be more general, and for large spheres, it gives a better approximation than the equation previously reported. PMID:19045761

  16. Foraging Habitat Quality Constrains Effectiveness of Artificial Nest-Site Provisioning in Reversing Population Declines in a Colonial Cavity Nester

    Science.gov (United States)

    Catry, Inês; Franco, Aldina M. A.; Rocha, Pedro; Alcazar, Rita; Reis, Susana; Cordeiro, Ana; Ventim, Rita; Teodósio, Joaquim; Moreira, Francisco

    2013-01-01

    Among birds, breeding numbers are mainly limited by two resources of major importance: food supply and nest-site availability. Here, we investigated how differences in land-use and nest-site availability affected the foraging behaviour, breeding success and population trends of the colonial cavity-dependent lesser kestrel Falco naumanni inhabiting two protected areas. Both areas were provided with artificial nests to increase nest-site availability. The first area is a pseudo-steppe characterized by traditional extensive cereal cultivation, whereas the second area is a previous agricultural zone now abandoned or replaced by forested areas. In both areas, lesser kestrels selected extensive agricultural habitats, such as fallows and cereal fields, and avoided scrubland and forests. In the second area, tracked birds from one colony travelled significantly farther distances (6.2 km ±1.7 vs. 1.8 km ±0.4 and 1.9 km ±0.6) and had significant larger foraging-ranges (144 km2 vs. 18.8 and 14.8 km2) when compared to the birds of two colonies in the extensive agricultural area. Longer foraging trips were reflected in lower chick feeding rates, lower fledging success and reduced chick fitness. Availability and occupation of artificial nests was high in both areas but population followed opposite trends, with a positive increment recorded exclusively in the first area with a large proportion of agricultural areas. Progressive habitat loss around the studied colony in the second area (suitable habitat decreased from 32% in 1990 to only 7% in 2002) is likely the main driver of the recorded population decline and suggests that the effectiveness of bird species conservation based on nest-site provisioning is highly constrained by habitat quality in the surrounding areas. Therefore, the conservation of cavity-dependent species may be enhanced firstly by finding the best areas of remaining habitat and secondly by increasing the carrying capacity of high-quality habitat areas

  17. Primary Tumor Site as a Predictor of Treatment Outcome for Definitive Radiotherapy of Advanced-Stage Oral Cavity Cancers

    International Nuclear Information System (INIS)

    Purpose: To evaluate the outcome of definitive radiotherapy (RT) for oral cavity cancers and to assess prognostic factors. Methods and Materials: Definitive RT was performed on 115 patients with oral cavity cancers at Stages III, IVA, and IVB, with a distribution of 6%, 47%, and 47%, respectively. The median dose of RT was 72Gy (range, 62-76Gy). Cisplatin-based chemotherapy was administered to 95% of the patients. Eleven patients underwent salvage surgery after RT failure. Results: Eight-eight (76.5%) patients responded partially and 23 (20%) completely; of the patients who responded, 18% and 57%, respectively, experienced a durable effect of treatment. The 3-year overall survival, disease-specific survival, and progression-free survival were 22%, 27%, and 25%, respectively. The 3-year PFS rates based on the primary tumor sites were as follows: Group I (buccal, mouth floor, and gum) 51%, Group II (retromolar and hard palate) 18%, and Group III (tongue and lip) 6% (p < 0.0001). The 3-year progression-free survival was 41% for N0 patients and 19% for patients with N+ disease (p = 0.012). The T stage and RT technique did not affect survival. The patients who underwent salvage surgery demonstrated better 3-year overall survival and disease-specific survival (53% vs. 19%, p = 0.015 and 53% vs. 24%, p = 0.029, respectively). Subsite group, N+, and salvage surgery were the only significant prognostic factors for survival after multivariate analysis. Conclusion: The primary tumor site and neck stage are prognostic predictors in advanced-stage oral cancer patients who received radical RT. The primary tumor extension and RT technique did not influence survival.

  18. Possible salt mine and brined cavity sites for radioactive waste disposal in the northeastern southern peninsula of Michigan

    International Nuclear Information System (INIS)

    A reconnaissance report on the possibilities for disposal of radioactive waste covers Michigan only, and is more detailed than an earlier one involving the northeastern states. Revised ''ground rules'' for pinpointing both mine and dissolved salt cavern sites for waste disposal include environmental, geologic, and economic factors. The Michigan basin is a structural bowl of Paleozoic sediments resting on downwarped Precambrian rocks. The center of the bowl is in Clare and Gladwin Counties, a short distance north of the middle of the Southern Peninsula. The strata dip toward this central area, and some stratigraphic sequences, including especially the salt-containing Silurian section, increase considerably in thickness in that direction. Lesser amounts of salt are also present in the north central part of the Lower Peninsula. Michigan has been an oil and gas producing state since 1925 and widespread exploration has had two effects on the selection of waste disposal sites: (1) large areas are leased for oil and gas; and (2) the borehole concentrations, whether producing wells, dry holes, or industrial brine wells that penetrated the salt section, should be avoided. Two types of nuclear waste, low level and high level, can be stored in man-made openings in salt beds. The storage facilities are created by (1) the development of salt mines where the depths are less than 3000 ft, and (2) cavities produced by pumping water into a salt bed, and bringing brine back out. The high level waste disposal must be confined to mines of limited depth, but the low level wastes can be accommodated in brine cavities at any depth. Seven potential prospects have been investigated and are described in detail

  19. Lymph node ratio predicts the benefit of post-operative radiotherapy in oral cavity cancer

    International Nuclear Information System (INIS)

    Background: The standard treatment for non-metastatic oral cavity squamous cell carcinoma (OCSCC) is surgical resection followed by post-operative radiotherapy (PORT) with/without chemotherapy in high risk patients. Given the substantial toxicity of PORT we assessed lymph node ratio (LNR) as a predictor of PORT benefit. Design: By using the Surveillance, Epidemiology and End Results (SEER) database, we analyzed all node positive OCSCC patients diagnosed between 1988 and 2007 who underwent neck dissection. LNR was categorized into three groups: <6%, 6–12.5% and >12.5%. Results: In 3091 subjects identified, median survival was 32, 25 and 16 months for LNR Groups 1, 2 and 3, respectively. On multivariate analysis, survival was associated with age, race, grade, tumor size, nodal stage, extra-capsular extension, use of PORT and LNR. When stratified by LNR group, PORT was associated with a survival benefit only in Group 3 (LNR > 12.5%): 2 year survival 25% vs 37%. No benefit to PORT was seen when the LNR ⩽ 12.5%: 2 year survival 51% vs 54%. Conclusion: A low LNR is associated with extended survival in LN positive OCSCC. The survival benefit associated with PORT in this disease appears to be limited to those with a LNR > 12.5%. Validation is required prior to the clinical implementation of our findings

  20. Response to induction chemotherapy as predictive marker of tumor response to radiotherapy and survival in oral cavity cancer

    Directory of Open Access Journals (Sweden)

    Surendra Kumar Saini

    2015-01-01

    Full Text Available Background: Trials have shown some statistically nonsignificant survival advantage of taxane, platin and 5-FU (TPF induction chemotherapy before definitive chemoradiation. We tried to find the role of induction chemotherapy in the prediction of tumor response to radiotherapy and survival in the treatment of oral cavity cancers. Patients and Methods: Patients of stage III and IV (M0 unresectable oral cavity squamous cell carcinoma were assigned to receive two cycles of TPF. On the basis of response to chemotherapy, two groups were made. Those who had partial or more than partial response and another group who had stable disease or disease progression during chemotherapy. Concurrent chemoradiotherapy was given to all patients after induction chemotherapy. Results: A total of 128 patients who received TPF, 29 (22.6% had complete response, 57 (44.5% had partial response, 38 (29.7% had stable disease and 4 (3.1% had progressive disease. Definitive chemoradiotherapy lead to complete response in 48 (55.8% patients who had partial or more than partial response (total 86 to chemotherapy and 10 (23.8% patients among those who had stable disease or disease progression during chemotherapy (total 42. This difference in response is statistically significant (P = 0.001. Three years survival was significantly better after treatment in patients who responded more than partial (hazard ratio 0.463, 95% confidence interval 0.2789-0.7689, with an estimated 3-year survival of 35% in patients in group 1 and 14% in group 2. Conclusion: Response to induction chemotherapy can be a predictive marker for response to subsequent chemoradiotherapy and survival, with acceptable toxicities.

  1. The next generation of transcription factor binding site prediction.

    Directory of Open Access Journals (Sweden)

    Anthony Mathelier

    Full Text Available Finding where transcription factors (TFs bind to the DNA is of key importance to decipher gene regulation at a transcriptional level. Classically, computational prediction of TF binding sites (TFBSs is based on basic position weight matrices (PWMs which quantitatively score binding motifs based on the observed nucleotide patterns in a set of TFBSs for the corresponding TF. Such models make the strong assumption that each nucleotide participates independently in the corresponding DNA-protein interaction and do not account for flexible length motifs. We introduce transcription factor flexible models (TFFMs to represent TF binding properties. Based on hidden Markov models, TFFMs are flexible, and can model both position interdependence within TFBSs and variable length motifs within a single dedicated framework. The availability of thousands of experimentally validated DNA-TF interaction sequences from ChIP-seq allows for the generation of models that perform as well as PWMs for stereotypical TFs and can improve performance for TFs with flexible binding characteristics. We present a new graphical representation of the motifs that convey properties of position interdependence. TFFMs have been assessed on ChIP-seq data sets coming from the ENCODE project, revealing that they can perform better than both PWMs and the dinucleotide weight matrix extension in discriminating ChIP-seq from background sequences. Under the assumption that ChIP-seq signal values are correlated with the affinity of the TF-DNA binding, we find that TFFM scores correlate with ChIP-seq peak signals. Moreover, using available TF-DNA affinity measurements for the Max TF, we demonstrate that TFFMs constructed from ChIP-seq data correlate with published experimentally measured DNA-binding affinities. Finally, TFFMs allow for the straightforward computation of an integrated TF occupancy score across a sequence. These results demonstrate the capacity of TFFMs to accurately model DNA

  2. Prediction of flow and drawdown for the site characterization and validation site in the Stripa Mine

    International Nuclear Information System (INIS)

    Geophysical and hydrologic data from a location in the Stripa Mine in Sweden, called the Site Characterization and Validation (SCV) block, has been used to create a series of models for flow through the fracture network. The models can be characterized as ''equivalent discontinuum'' models. Equivalent discontinuum models are derived starting from a specified lattice or 6 ''template''. An inverse analysis called ''Simulated Annealing'' is used to make a random search through the elements of the lattice to find a configuration that can reproduce the measured responses. Evidence at Stripa points to hydrology which is dominated by fracture zones. These have been identified and located through extensive characterization efforts. Lattice templates were arranged to lie on the fracture zones identified by Black and Olsson. The fundamental goal of this project was to build a fracture flow model based an initial data set, and use this model to make predictions of the flow behavior during a new test. Then given data from the new test, predict a second test, etc. The first data set was an interference test called C1-2. Both a two-dimensional and a three-dimensional model were annealed to the C1-2 data and use this model to predict the behavior of the Simulated Drift Experiment (SDE). The SDE measured the flow into, and drawdown due to reducing the pressure in a group of 6 parallel boreholes. Then both the C1-2 and SDE data were used to predict the flow into and drawdown due to an excavation, the Validation Drift (VD), made through the boreholes. Finally, all the data was used to predict the hydrologic response to opening another hole, T1

  3. Prediction of flow and drawdown for the site characterization and validation site in the Stripa mine

    International Nuclear Information System (INIS)

    Geophysical and hydrologic data from a location in the Stripa mine in Sweden, called the Site Characterization and Validation (SCV) block, has been used to create a series of models for flow through the fracture network. The models can be characterized as 'equivalent discontinuum' models. Equivalent discontinuum models are derived starting from a specified lattice or 'template'. An inverse analysis called 'simulated annealing' is used to make a random search through the elements of the lattice to find a configuration that can reproduce the measured responses. Evidence at Stripa points to hydrology which is dominated by fracture zones. These have been identified and located through extensive characterization efforts. Lattice templates were arranged to lie on the fracture zones identified by Black and Olsson. The fundamental goal of this project was to build a fracture flow model based on an initial data set, and use this model to make predictions of the flow behavior during a new test. Then given data from the new test, predict a second test, etc. The first data set was an interference test called C1-2. Both a two-dimensional and a three-dimensional model were annealed to the C1-2 data and use this model to predict the behavior of the Simulated Drift Experiment (SDE). The SDE measured the flow into, and drawdown due to reducing the pressure in a group of 6 parallel boreholes. Then both the C1-2 and SDE data were used to predict the flow into a drawdown due to an excavation, the Validation Drift (VD), made through the boreholes. Finally, all the data was used to predict the hydrologic response to opening another hole, T1. Annealing to the C1-2 test gave an excellent prediction of the SDE. The VD effects were dominated by near-field physics that were not predictable. However, the calculations and measurements could be used to postulate that a dramatic decrease in hydraulic conductivity near the drift was due to degassing of nitrogen as the inflowing water was

  4. Numerical prediction of two-phase-flow pump performance by a bubbly flow model with fixed cavity; Effects of outlet blade angle and rotational speed

    Energy Technology Data Exchange (ETDEWEB)

    Minemura, Kiyoshi; Uchiyama, Tomomi (Nagoya Univ. (Japan)); Ihara, Masaru; Furukawa, Hironori

    1994-03-01

    Effects of outlet blade angle and rotational speed on the two-phase-flow pump performance are discussed based on the results calculated by a three-dimensional bubbly flow model with fixed cavity. Critical volumetric flow ratio of air to whole fluid, at which the fixed cavity on the shroud near the impeller inlet section expands rapidly to fill the section, decreases with an increases in the outlet blade angle and increases with an increase in the rotational speed. To predict the theoretical head for the higher volumetric flow ratio, the one-dimensional two-fluid model by Furuya is also applied and modified for low-specific-speed pumps. (author).

  5. Establishing a predictive maintenance program at the Hanford Site

    International Nuclear Information System (INIS)

    This document contains information about a new Predictive Maintenance Program being developed and implemented at the Hanford Reservation. Details of the document include: background on persons developing the program, history of predictive maintenance, implementation of new program, engineering task analysis, network development and new software, issues to be resolved, benefits expected, and appendix gives information about the symposium from which this paper is based

  6. Crystal Structures of a Multidrug-Resistant Human Immunodeficiency Virus Type 1 Protease Reveal an Expanded Active-Site Cavity

    Energy Technology Data Exchange (ETDEWEB)

    Logsdon, Bradley C.; Vickrey, John F.; Martin, Philip; Proteasa, Gheorghe; Koepke, Jay I.; Terlecky, Stanley R.; Wawrzak, Zdzislaw; Winters, Mark A.; Merigan, Thomas C.; Kovari, Ladislau C. (Stanford); (WSU-MED); (NWU); (Stanford-MED)

    2010-03-08

    The goal of this study was to use X-ray crystallography to investigate the structural basis of resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors. We overexpressed, purified, and crystallized a multidrug-resistant (MDR) HIV-1 protease enzyme derived from a patient failing on several protease inhibitor-containing regimens. This HIV-1 variant contained codon mutations at positions 10, 36, 46, 54, 63, 71, 82, 84, and 90 that confer drug resistance to protease inhibitors. The 1.8-{angstrom} crystal structure of this MDR patient isolate reveals an expanded active-site cavity. The active-site expansion includes position 82 and 84 mutations due to the alterations in the amino acid side chains from longer to shorter (e.g., V82A and I84V). The MDR isolate 769 protease 'flaps' stay open wider, and the difference in the flap tip distances in the MDR 769 variant is 12 {angstrom}. The MDR 769 protease crystal complexes with lopinavir and DMP450 reveal completely different binding modes. The network of interactions between the ligands and the MDR 769 protease is completely different from that seen with the wild-type protease-ligand complexes. The water molecule-forming hydrogen bonds bridging between the two flaps and either the substrate or the peptide-based inhibitor are lacking in the MDR 769 clinical isolate. The S1, S1', S3, and S3' pockets show expansion and conformational change. Surface plasmon resonance measurements with the MDR 769 protease indicate higher k{sub off} rates, resulting in a change of binding affinity. Surface plasmon resonance measurements provide k{sub on} and k{sub off} data (K{sub d} = k{sub off}/k{sub on}) to measure binding of the multidrug-resistant protease to various ligands. This MDR 769 protease represents a new antiviral target, presenting the possibility of designing novel inhibitors with activity against the open and expanded protease forms.

  7. Predicting on-site environmental impacts of municipal engineering works

    OpenAIRE

    Gangolells Solanellas, Marta; Casals Casanova, Miquel; Forcada Matheu, Núria; Macarulla Martí, Marcel

    2014-01-01

    The research findings fill a gap in the body of knowledge by presenting an effective way to evaluate the significance of on-site environmental impacts of municipal engineering works prior to the construction stage. First, 42 on-site environmental impacts of municipal engineering works were identified by means of a process-oriented approach. Then, 46 indicators and their corresponding significance limits were determined on the basis of a statistical analysis of 25 new-build and remodelling mun...

  8. SSFinder: High Throughput CRISPR-Cas Target Sites Prediction Tool

    OpenAIRE

    Santosh Kumar Upadhyay; Shailesh Sharma

    2014-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets. The SSFinder is a user-friendly tool, compatible wit...

  9. Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area.

    Science.gov (United States)

    Cao, Chen; Xu, Shutan

    2016-01-01

    Protein ligand-binding site prediction is highly important for protein function determination and structure-based drug design. Over the past twenty years, dozens of computational methods have been developed to address this problem. Soga et al. identified ligand cavities based on the preferences of amino acids for the ligand-binding site (RA) and proposed the propensity for ligand binding (PLB) index to rank the cavities on the protein surface. However, we found that residues exhibit different RAs in response to changes in solvent exposure. Furthermore, previous studies have suggested that some dihedral angles of amino acids in specific regions of the Ramachandran plot are preferred at the functional sites of proteins. Based on these discoveries, the amino acid solvent-accessible surface area and dihedral angles were combined with the RA and PLB to obtain two new indexes, multi-factor RA (MF-RA) and multi-factor PLB (MF-PLB). MF-PLB, PLB and other methods were tested using two benchmark databases and two particular ligand-binding sites. The results show that MF-PLB can improve the success rate of PLB for both ligand-bound and ligand-unbound structures, particularly for top choice prediction. PMID:27619067

  10. SSFinder: High Throughput CRISPR-Cas Target Sites Prediction Tool

    Directory of Open Access Journals (Sweden)

    Santosh Kumar Upadhyay

    2014-01-01

    Full Text Available Clustered regularly interspaced short palindromic repeats (CRISPR and CRISPR-associated protein (Cas system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets. The SSFinder is a user-friendly tool, compatible with Windows, Mac OS, and Linux operating systems, and freely available online.

  11. Prediction for human transcription start site using diversity measure with quadratic discriminant

    OpenAIRE

    Lu, Jun; Luo, LiaoFu

    2008-01-01

    The accurate identification of promoter regions and transcription start sites is a challenge to the construction of human transcription regulation networks. Thus, an efficient prediction method based on theoretical formulation is necessary for this purpose. We used the method of increment diversity with quadratic discriminant analysis (IDQD) to predict transcription start sites (TSS). The method produced sensitivity and positive predictive value of more than 65% with positives to negatives ra...

  12. Prediction of PK-specific phosphorylation site based on information entropy

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Phosphorylation is a crucial way to control the activity of proteins in many eukaryotic organisms in vivo. Experimental methods to determine phosphorylation sites in substrates are usually restricted by the in vitro condition of enzymes and very intensive in time and labor. Although some in silico methods and web servers have been introduced for automatic detection of phosphorylation sites, sophisticated methods are still in urgent demand to further improve prediction performances. Protein primary se-quences can help predict phosphorylation sites catalyzed by different protein kinase and most com-putational approaches use a short local peptide to make prediction. However, the useful information may be lost if only the conservative residues that are not close to the phosphorylation site are consid-ered in prediction, which would hamper the prediction results. A novel prediction method named IEPP (Information-Entropy based Phosphorylation Prediction) is presented in this paper for automatic de-tection of potential phosphorylation sites. In prediction, the sites around the phosphorylation sites are selected or excluded by their entropy values. The algorithm was compared with other methods such as GSP and PPSP on the ABL, MAPK and PKA PK families. The superior prediction accuracies were ob-tained in various measurements such as sensitivity (Sn) and specificity (Sp). Furthermore, compared with some online prediction web servers on the new discovered phosphorylation sites, IEPP also yielded the best performance. IEPP is another useful computational resource for identification of PK-specific phosphorylation sites and it also has the advantages of simpleness, efficiency and con-venience.

  13. Cavity quantum electrodynamics studies with site-controlled InGaAs quantum dots integrated into high quality microcavities

    DEFF Research Database (Denmark)

    Reitzenstein, S.; Schneider, C.; Albert, F.;

    2011-01-01

    Semiconductor quantum dots (QDs) are fascinating nanoscopic structures for photonics and future quantum information technology. However, the random position of self-organized QDs inhibits a deterministic coupling in devices relying on cavity quantum electrodynamics (cQED) effects which complicates...

  14. Implosion of the small cavity and large cavity cannonball targets

    International Nuclear Information System (INIS)

    Recent results of cannonball target implosion research are briefly reviewed with theoretical predictions for GEKKO XII experiments. The cannonball targets are classified into two types according to the cavity size ; small cavity and large cavity. The compression mechanisms of the two types are discussed. (author)

  15. DAPPLE 2: a Tool for the Homology-Based Prediction of Post-Translational Modification Sites.

    Science.gov (United States)

    Trost, Brett; Maleki, Farhad; Kusalik, Anthony; Napper, Scott

    2016-08-01

    The post-translational modification of proteins is critical for regulating their function. Although many post-translational modification sites have been experimentally determined, particularly in certain model organisms, experimental knowledge of these sites is severely lacking for many species. Thus, it is important to be able to predict sites of post-translational modification in such species. Previously, we described DAPPLE, a tool that facilitates the homology-based prediction of one particular post-translational modification, phosphorylation, in an organism of interest using known phosphorylation sites from other organisms. Here, we describe DAPPLE 2, which expands and improves upon DAPPLE in three major ways. First, it predicts sites for many post-translational modifications (20 different types) using data from several sources (15 online databases). Second, it has the ability to make predictions approximately 2-7 times faster than DAPPLE depending on the database size and the organism of interest. Third, it simplifies and accelerates the process of selecting predicted sites of interest by categorizing them based on gene ontology terms, keywords, and signaling pathways. We show that DAPPLE 2 can successfully predict known human post-translational modification sites using, as input, known sites from species that are either closely (e.g., mouse) or distantly (e.g., yeast) related to humans. DAPPLE 2 can be accessed at http://saphire.usask.ca/saphire/dapple2 . PMID:27367363

  16. A resonance shift prediction based on the Boltzmann-Ehrenfest principle for cylindrical cavities with a rigid sphere

    DEFF Research Database (Denmark)

    Orozco Santillan, Arturo; Cutanda Henríquez, Vicente

    2008-01-01

    An investigation on the resonance frequency shift for a plane-wave mode in a cylindrical cavity produced by a rigid sphere is reported in this paper. This change of the resonance frequency has been previously considered as a cause of oscillational instabilities in singlemode acoustic levitation...

  17. A computational approach for prediction of donor splice sites with improved accuracy.

    Science.gov (United States)

    Meher, Prabina Kumar; Sahu, Tanmaya Kumar; Rao, A R; Wahi, S D

    2016-09-01

    Identification of splice sites is important due to their key role in predicting the exon-intron structure of protein coding genes. Though several approaches have been developed for the prediction of splice sites, further improvement in the prediction accuracy will help predict gene structure more accurately. This paper presents a computational approach for prediction of donor splice sites with higher accuracy. In this approach, true and false splice sites were first encoded into numeric vectors and then used as input in artificial neural network (ANN), support vector machine (SVM) and random forest (RF) for prediction. ANN and SVM were found to perform equally and better than RF, while tested on HS3D and NN269 datasets. Further, the performance of ANN, SVM and RF were analyzed by using an independent test set of 50 genes and found that the prediction accuracy of ANN was higher than that of SVM and RF. All the predictors achieved higher accuracy while compared with the existing methods like NNsplice, MEM, MDD, WMM, MM1, FSPLICE, GeneID and ASSP, using the independent test set. We have also developed an online prediction server (PreDOSS) available at http://cabgrid.res.in:8080/predoss, for prediction of donor splice sites using the proposed approach. PMID:27302911

  18. Prediction of allosteric sites and mediating interactions through bond-to-bond propensities

    CERN Document Server

    Amor, Benjamin R C; Yaliraki, Sophia N; Barahona, Mauricio

    2016-01-01

    Allosteric regulation is central to many biochemical processes. Allosteric sites provide a target to fine-tune protein activity, yet we lack computational methods to predict them. Here, we present an efficient graph-theoretical approach for identifying allosteric sites and the mediating interactions that connect them to the active site. Using an atomistic graph with edges weighted by covalent and non-covalent bond energies, we obtain a bond-to-bond propensity that quantifies the effect of instantaneous bond fluctuations propagating through the protein. We use this propensity to detect the sites and communication pathways most strongly linked to the active site, assessing their significance through quantile regression and comparison against a reference set of 100 generic proteins. We exemplify our method in detail with three well-studied allosteric proteins: caspase-1, CheY, and h-Ras, correctly predicting the location of the allosteric site and identifying key allosteric interactions. Consistent prediction of...

  19. Can one predict DNA Transcription Start Sites by studying bubbles?

    CERN Document Server

    Van Erp, T S; Hagmann, J G; Peyrard, M

    2005-01-01

    It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom which makes an accurate calculation difficult even for minimal models. In this letter, we introduce a new method that is orders of magnitude faster than MD. Using this method we are able to show that the present evidence is unsubstantiated.

  20. An Overview of the Prediction of Protein DNA-Binding Sites

    Directory of Open Access Journals (Sweden)

    Jingna Si

    2015-03-01

    Full Text Available Interactions between proteins and DNA play an important role in many essential biological processes such as DNA replication, transcription, splicing, and repair. The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. In the last decade, numerous computational approaches have been developed to predict protein DNA-binding sites based on protein sequence and/or structural information, which play an important role in complementing experimental strategies. At this time, approaches can be divided into three categories: sequence-based DNA-binding site prediction, structure-based DNA-binding site prediction, and homology modeling and threading. In this article, we review existing research on computational methods to predict protein DNA-binding sites, which includes data sets, various residue sequence/structural features, machine learning methods for comparison and selection, evaluation methods, performance comparison of different tools, and future directions in protein DNA-binding site prediction. In particular, we detail the meta-analysis of protein DNA-binding sites. We also propose specific implications that are likely to result in novel prediction methods, increased performance, or practical applications.

  1. Prediction of protein hydration sites from sequence by modular neural networks

    DEFF Research Database (Denmark)

    Ehrlich, L.; Reczko, M.; Bohr, Henrik; Wade, R.C.

    1998-01-01

    separate neural networks. These predictions are used as input together with protein sequences for networks predicting hydration of residues, backbone atoms and sidechains. These networks are teined with protein crystal structures. The prediction of hydration is improved by adding information on secondary......The hydration properties of a protein are important determinants of its structure and function. Here, modular neural networks are employed to predict ordered hydration sites using protein sequence information. First, secondary structure and solvent accessibility are predicted from sequence with two...... using the actual values. The inclusion of property information allows a smaller squence window to be used in the networks to predict hydration. It has a greater impact on the accuracy of hydration site prediction for backbone atoms than for sidechains and for non-polar than polar residues. The networks...

  2. Site investigations, design, construction, operation, shutdown and surveillance of repositories for low- and intermediate-level radioactive wastes in rock cavities

    International Nuclear Information System (INIS)

    The report provides an overview and technical guidelines for considerations and for activities to be undertaken for safety assessment, site investigations, design, construction, operation, shutdown and surveillance of repositories for the disposal of low- and intermediate-level radioactive wastes in rock cavities. A generalized sequence of investigations is introduced which proceeds through region and site selection to the stage where the site is confirmed by detailed geoscientific investigations as being suitable for a waste repository. The different procedures and somewhat specific investigative needs with respect to existing mines are dealt with separately. General design, as well as specific requirements with respect to the different stages of design and construction, are dealt with. A review of activities related to the operational and post-operational stages of repositories in rock cavities is presented. The report describes in general terms the procedures related to different stages of disposal operation; also the conditions for shutdown together with essential shutdown and sealing activities and the related safety assessment requirements. Guidance is also given on the surveillance programme which will allow for inspection, testing, maintenance and security of a disposal facility during the operational phase, as well as for the post-operational stage for periods determined as necessary by the national authorities

  3. Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites

    DEFF Research Database (Denmark)

    Julenius, Karin; Mølgaard, Anne; Gupta, Ramneek;

    2005-01-01

    experimentally investigated with regard to glycosylation status. From O-GLYCBASE a total of 86 mammalian proteins experimentally investigated for in vivo O-GalNAc sites were extracted. Mammalian protein homolog comparisons showed that a glycosylated serine or threonine is less likely to be precisely conserved...... than a nonglycosylated one. The Protein Data Bank was analyzed for structural information, and 12 glycosylated structures were obtained. All positive sites were found in coil or turn regions. A method for predicting the location for mucin-type glycosylation sites was trained using a neural network...... approach. The best overall network used as input amino acid composition, averaged surface accessibility predictions together with substitution matrix profile encoding of the sequence. To improve prediction on isolated (single) sites, networks were trained on isolated sites only. The final method combines...

  4. Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites

    DEFF Research Database (Denmark)

    Julenius, Karin; Mølgaard, Anne; Gupta, Ramneek;

    2004-01-01

    experimentally investigated with regard to glycosylation status. From O-GLYCBASE a total of 86 mammalian proteins experimentally investigated for in vivo O-GalNAc sites were extracted. Mammalian protein homolog comparisons showed that a glycosylated serine or threonine is less likely to be precisely conserved...... than a nonglycosylated one. The Protein Data Bank was analyzed for structural information, and 12 glycosylated structures were obtained. All positive sites were found in coil or turn regions. A method for predicting the location for mucin-type glycosylation sites was trained using a neural network...... approach. The best overall network used as input amino acid composition, averaged surface accessibility predictions together with substitution matrix profile encoding of the sequence. To improve prediction on isolated (single) sites, networks were trained on isolated sites only. The final method combines...

  5. Prediction and experimental verification of performance of box type solar cooker - Part I. Cooking vessel with central cylindrical cavity

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Avala Raji [Department of Mechanical Engineering, Kakatiya Institute of Technology and Science, Warangal 506 015, AP (India); Rao, A.V. Narasimha [Department of Mechanical Engineering, National Institute of Technology, Warangal 506 004, AP (India)

    2007-07-15

    The performance of conventional box type solar cookers can be improved by better designs of cooking vessels with proper understanding of the heat flow to the material to be cooked. An attempt has been made in this article to arrive at a mathematical model to understand the heat flow process to the cooking vessel and thereby to the food material. The mathematical model considers a double glazed hot box type solar cooker loaded with two different types of vessels, kept either on the floor of the cooker or on lugs. The performance of the cooking vessel with a central cylindrical cavity is compared with that of a conventional cylindrical cooking vessel. It is found from the experiments and modeling that the cooking vessel with a central cylindrical cavity on lugs results in a higher temperature of the thermic fluid than that of a conventional vessel on the floor or on lugs. The average improvement of performance of the vessel with a central cylindrical cavity kept on lugs is found to be 5.9% and 2.4% more than that of a conventional cylindrical vessel on the floor and on lugs, respectively. (author)

  6. PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites.

    Directory of Open Access Journals (Sweden)

    Jiangning Song

    Full Text Available The ability to catalytically cleave protein substrates after synthesis is fundamental for all forms of life. Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding the physiological role of a protease is to identify its natural substrate(s. Knowledge of the substrate specificity of a protease can dramatically improve our ability to predict its target protein substrates, but this information must be utilized in an effective manner in order to efficiently identify protein substrates by in silico approaches. To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. Thus, for proteases with known amino acid specificity, PROSPER provides a convenient, pre-prepared tool for use in identifying protein substrates for the enzymes. Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage site prediction, as evidenced by their contribution to performance improvement in terms of identifying known cleavage sites in substrates for these enzymes. In comparison with two state-of-the-art prediction tools, PoPS and SitePrediction, PROSPER achieves greater accuracy and coverage. To our knowledge, PROSPER is the first comprehensive server capable of predicting cleavage sites of multiple proteases within a single substrate

  7. A Data Mining Approach for the Prediction of Hepatitis C Virus protease Cleavage Sites

    Directory of Open Access Journals (Sweden)

    Ahmed mohamed samir ali gamal eldin

    2011-12-01

    Full Text Available Summary: Several papers have been published about the prediction of hepatitis C virus (HCV polyprotein cleavage sites, using symbolic and non-symbolic machine learning techniques. The published papers achieved different Levels of prediction accuracy. the achieved results depends on the used technique and the availability of adequate and accurate HCV polyprotein sequences with known cleavage sites. We tried here to achieve more accurate prediction results, and more Informative knowledge about the HCV protein cleavage sites using Decision tree algorithm. There are several factors that can affect the overall prediction accuracy. One of the most important factors is the availably of acceptable and accurate HCV polyproteins sequences with known cleavage sites. We collected latest accurate data sets to build the prediction model. Also we collected another dataset for the model testing. Motivation: Hepatitis C virus is a global health problem affecting a significant portion of the world’s population. The World Health Organization estimated that in1999; 170 million hepatitis C virus (HCV carriers were present worldwide, with 3 to 4 million new cases per year. Several approaches have been performed to analyze HCV life cycle to find out the important factors of the viral replication process. HCV polyprotein processing by the viral protease has a vital role in the virus replication. The prediction of HCV protease cleavage sites can help the biologists in the design of suitable viral inhibitors. Results: The ease to use and to understand of the decision tree enabled us to create simple prediction model. We used here the latest accurate viral datasets. Decision tree achieved here acceptable prediction accuracy results. Also it generated informative knowledge about the cleavage process itself. These results can help the researchers in the development of effective viral inhibitors. Using decision tree to predict HCV protein cleavage sites achieved high

  8. NetPhosYeast: prediction of protein phosphorylation sites in yeast

    DEFF Research Database (Denmark)

    Ingrell, C.R.; Miller, Martin Lee; Jensen, O.N.; Blom, Nikolaj

    2007-01-01

    We here present a neural network-based method for the prediction of protein phosphorylation sites in yeast-an important model organism for basic research. Existing protein phosphorylation site predictors are primarily based on mammalian data and show reduced sensitivity on yeast phosphorylation...... sites compared to those in humans, suggesting the need for an yeast-specific phosphorylation site predictor. NetPhosYeast achieves a correlation coefficient close to 0.75 with a sensitivity of 0.84 and specificity of 0.90 and outperforms existing predictors in the identification of phosphorylation sites...... in yeast....

  9. Ensemble approach combining multiple methods improves human transcription start site prediction.

    LENUS (Irish Health Repository)

    Dineen, David G

    2010-01-01

    The computational prediction of transcription start sites is an important unsolved problem. Some recent progress has been made, but many promoters, particularly those not associated with CpG islands, are still difficult to locate using current methods. These methods use different features and training sets, along with a variety of machine learning techniques and result in different prediction sets.

  10. Superconducting cavities

    International Nuclear Information System (INIS)

    The basic properties of superconducting cavities for electron accelerators are discussed with special emphasis on the following topics: technical motivation for the use of superconducting cavities; surface impedance; the critical field of superconductors; anomalous losses; materials other than niobium; technological achievements for accelerating cavities. (author)

  11. Analysis and prediction of gene splice sites in four Aspergillus genomes

    DEFF Research Database (Denmark)

    Wang, Kai; Ussery, David; Brunak, Søren

    2009-01-01

    , splice site prediction program called NetAspGene, for the genus Aspergillus. Gene sequences from Aspergillus fumigatus, the most common mould pathogen, were used to build and test our model. Compared to many animals and plants, Aspergillus contains smaller introns; thus we have applied a larger window...... better splice site prediction than other available tools. NetAspGene will be very helpful for the study in Aspergillus splice sites and especially in alternative splicing. A webpage for NetAspGene is publicly available at http://www.cbs.dtu.dk/services/NetAspGene....

  12. Using site-specific soil samples as a substitution for improved hydrological and nonpoint source predictions.

    Science.gov (United States)

    Chen, Lei; Wang, Guobo; Zhong, Yucen; Zhao, Xin; Shen, Zhenyao

    2016-08-01

    Soil databases are one of the most important inputs for watershed models, and the quality of soil properties affects how well a model performs. The objectives of this study were to (1) quantify the sensitivity of model outputs to soil properties and to (2) use site-specific soil properties as a substitution for more accurate hydrological and nonpoint source (H/NPS) predictions. Soil samples were collected from a typical mountainous watershed in China, and the impacts of soil sample parameters on H/NPS predictions were quantified using the Soil and Water Assessment Tool (SWAT). The most sensitive parameters related to predicting flow, sediment, and total phosphorus (TP) mainly were the soil hydrological, the channel erosion processes, and the initial soil chemical environment, respectively. When the site-specific soil properties were used, the uncertainties (coefficient of variation) related to predicting the hydrology, sediment and TP decreased by 75∼80 %, 75∼84 %, and 46∼61 %, respectively. Based on changes in the Nash-Sutcliff coefficient, the model performance improved by 4.9 and 19.45 % for the hydrological and sediment model, accordingly. However, site-specific soil properties did not contribute to better TP predictions because of the high spatial variability of the soil P concentrations across the large watershed. Thus, although site-specific soil samples can be used to obtain more accurate H/NPS predictions, more sampling sites are required to apply this method in large watersheds. PMID:27146539

  13. Discrete fracture modelling for the Stripa site characterization and validation drift inflow predictions

    International Nuclear Information System (INIS)

    Groundwater flow through three-dimensional networks of discrete fractures was modeled to predict the flux into a fifty meter long drift, as part of the site characterization and validation project conducted during phase 3 of the Stripa project. Predictions were made on the basis of a site scale discrete fracture conceptual model developed by synthesis of geological, geophysical, and hydrological site characterization data. Individual fractures were treated as stochastic features, described by probability distributions of geometric and hydrologic properties. Fractures were divided into three populations: Fractures within fracture zones near the drift, non-fracture zone fractures near the drift, and fractures in fracture zones over 20 meters from the drift. Fractures outside fracture zones are not modelled beyond 20 meters from the drift. Both data analysis and flow predictions were produced using the FracMan discrete fracture modelling package. Probabilistic flow predictions were produced in seven formats specified by the Stripa task force on fracture flow modelling. (au)

  14. FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions.

    Directory of Open Access Journals (Sweden)

    Daniel B Roche

    Full Text Available The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP experiment, utilizing the Matthews Correlation Coefficient (MCC and Binding-site Distance Test (BDT metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall's τ, Spearman's ρ and Pearson's r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC when Receiver Operator Characteristic (ROC analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%, and one of the top manual groups (FN293 tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site

  15. TarPmiR: a new approach for microRNA target site prediction

    Science.gov (United States)

    Ding, Jun; Li, Xiaoman; Hu, Haiyan

    2016-01-01

    Motivation: The identification of microRNA (miRNA) target sites is fundamentally important for studying gene regulation. There are dozens of computational methods available for miRNA target site prediction. Despite their existence, we still cannot reliably identify miRNA target sites, partially due to our limited understanding of the characteristics of miRNA target sites. The recently published CLASH (crosslinking ligation and sequencing of hybrids) data provide an unprecedented opportunity to study the characteristics of miRNA target sites and improve miRNA target site prediction methods. Results: Applying four different machine learning approaches to the CLASH data, we identified seven new features of miRNA target sites. Combining these new features with those commonly used by existing miRNA target prediction algorithms, we developed an approach called TarPmiR for miRNA target site prediction. Testing on two human and one mouse non-CLASH datasets, we showed that TarPmiR predicted more than 74.2% of true miRNA target sites in each dataset. Compared with three existing approaches, we demonstrated that TarPmiR is superior to these existing approaches in terms of better recall and better precision. Availability and Implementation: The TarPmiR software is freely available at http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/. Contacts: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27207945

  16. Comparison of Different Ranking Methods in Protein-Ligand Binding Site Prediction

    Science.gov (United States)

    Gao, Jun; Liu, Qi; Kang, Hong; Cao, Zhiwei; Zhu, Ruixin

    2012-01-01

    In recent years, although many ligand-binding site prediction methods have been developed, there has still been a great demand to improve the prediction accuracy and compare different prediction algorithms to evaluate their performances. In this work, in order to improve the performance of the protein-ligand binding site prediction method presented in our former study, a comparison of different binding site ranking lists was studied. Four kinds of properties, i.e., pocket size, distance from the protein centroid, sequence conservation and the number of hydrophobic residues, have been chosen as the corresponding ranking criterion respectively. Our studies show that the sequence conservation information helps to rank the real pockets with the most successful accuracy compared to others. At the same time, the pocket size and the distance of binding site from the protein centroid are also found to be helpful. In addition, a multi-view ranking aggregation method, which combines the information among those four properties, was further applied in our study. The results show that a better performance can be achieved by the aggregation of the complementary properties in the prediction of ligand-binding sites. PMID:22942732

  17. Regression applied to protein binding site prediction and comparison with classification

    Directory of Open Access Journals (Sweden)

    Gala Jean-Luc

    2009-09-01

    Full Text Available Abstract Background The structural genomics centers provide hundreds of protein structures of unknown function. Therefore, developing methods enabling the determination of a protein function automatically is imperative. The determination of a protein function can be achieved by studying the network of its physical interactions. In this context, identifying a potential binding site between proteins is of primary interest. In the literature, methods for predicting a potential binding site location generally are based on classification tools. The aim of this paper is to show that regression tools are more efficient than classification tools for patches based binding site predictors. For this purpose, we developed a patches based binding site localization method usable with either regression or classification tools. Results We compared predictive performances of regression tools with performances of machine learning classifiers. Using leave-one-out cross-validation, we showed that regression tools provide better predictions than classification ones. Among regression tools, Multilayer Perceptron ranked highest in the quality of predictions. We compared also the predictive performance of our patches based method using Multilayer Perceptron with the performance of three other methods usable through a web server. Our method performed similarly to the other methods. Conclusion Regression is more efficient than classification when applied to our binding site localization method. When it is possible, using regression instead of classification for other existing binding site predictors will probably improve results. Furthermore, the method presented in this work is flexible because the size of the predicted binding site is adjustable. This adaptability is useful when either false positive or negative rates have to be limited.

  18. Better estimation of protein-DNA interaction parameters improve prediction of functional sites

    Directory of Open Access Journals (Sweden)

    O'Flanagan Ruadhan A

    2008-12-01

    Full Text Available Abstract Background Characterizing transcription factor binding motifs is a common bioinformatics task. For transcription factors with variable binding sites, we need to get many suboptimal binding sites in our training dataset to get accurate estimates of free energy penalties for deviating from the consensus DNA sequence. One procedure to do that involves a modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment method designed to produce many such sequences. Results We analyzed low stringency SELEX data for E. coli Catabolic Activator Protein (CAP, and we show here that appropriate quantitative analysis improves our ability to predict in vitro affinity. To obtain large number of sequences required for this analysis we used a SELEX SAGE protocol developed by Roulet et al. The sequences obtained from here were subjected to bioinformatic analysis. The resulting bioinformatic model characterizes the sequence specificity of the protein more accurately than those sequence specificities predicted from previous analysis just by using a few known binding sites available in the literature. The consequences of this increase in accuracy for prediction of in vivo binding sites (and especially functional ones in the E. coli genome are also discussed. We measured the dissociation constants of several putative CAP binding sites by EMSA (Electrophoretic Mobility Shift Assay and compared the affinities to the bioinformatics scores provided by methods like the weight matrix method and QPMEME (Quadratic Programming Method of Energy Matrix Estimation trained on known binding sites as well as on the new sites from SELEX SAGE data. We also checked predicted genome sites for conservation in the related species S. typhimurium. We found that bioinformatics scores based on SELEX SAGE data does better in terms of prediction of physical binding energies as well as in detecting functional sites. Conclusion We think that training binding site detection

  19. A survey of cavity-nesting bees and wasps in loblolly pine stands of the Savannah River Site, Aiken County, South Carolina.

    Energy Technology Data Exchange (ETDEWEB)

    Horn, S.; Hanula, J., L.

    2004-03-10

    Horn, Scott, and James L. Hanula. 2004. A survey of cavity-nesting bees and wasps in loblolly pine stands of the Savannah River Site, Aiken County, South Carolina. 39(3): 464-469. Abstract: In recent years concern over widespread losses in biodiversity has grown to include a possible decline of many native pollinators, primarily bees. Factors such as habitat fragmentation, agricultural practices, use of pesticides, the introduction of invasive species, or changes in land use may negatively impact these vital organisims. Most reported studies show that human impacts on pollinators are overwhelmingly negative. Reductions in pollinator populations may profoundly impact plant population dynamics and ecosystem function. Little baseline data exists on the diversity and relative abundance of bees and wasps in southern forests. The objective of this study was to develop a simple, effective method of surveying cavity-nesting bees and wasps and to determine species diversity in mature forests of loblolly pine, the most widely planted tree species in the southern United States.

  20. Ensemble Prediction and Uncertainty Quantification of the Propagation of Weak Seismic Pulses with Minimal Site Characterization

    Science.gov (United States)

    Vecherin, S.; Ketcham, S.; Parker, M.; Picucci, J.

    2015-12-01

    To make a prediction for the propagation of seismic pulses, one needs to specify physical properties and subsurface ground structure of the site. This information is frequently unknown or estimated with significant uncertainty. We developed a methodology for the ensemble prediction of the propagation of weak seismic pulses for short ranges. The ranges of interest are 10-100 of meters, and the pulse bandwidth is up to 200 Hz. Instead of specifying specific values for viscoelastic site properties, the methodology operates with probability distribution functions of the inputs. This yields ensemble realizations of the pulse at specified locations, where mean, median, and maximum likelihood predictions can be made, and confidence intervals are estimated. Starting with the site's Vs30, the methodology creates an ensemble of plausible vertically stratified Vs profiles for the site. The number and thickness of the layers are modeled using inhomogeneous Poisson process, and the Vs values in the layers are modeled by Gaussian correlated process. The Poisson expectation rate and Vs correlation between adjacent layers take into account layers depth and thickness, and are specific for a site class, as defined by the Federal Emergency Management Agency (FEMA). High-fidelity three-dimension thin layer method (TLM) is used to yield an ensemble of frequency response functions. Comparison with experiments revealed that measured signals are not always within the predicted ensemble. Variance-based global sensitivity analysis has shown that the most significant parameter in the TLM for the prediction of the pulse energy is the shear quality factor, Qs. Some strategies how to account for significant uncertainty in this parameter and to improve accuracy of the ensemble predictions for a specific site are investigated and discussed.

  1. Predicting evolutionary site variability from structure in viral proteins: buriedness, flexibility, and design

    CERN Document Server

    Shahmoradi, Amir; Spielman, Stephanie J; Jackson, Eleisha L; Dawson, Eric T; Meyer, Austin G; Wilke, Claus O

    2014-01-01

    Several recent works have shown that protein structure can predict site-specific evolutionary sequence variation. In particular, sites that are buried and/or have many contacts with other sites in a structure have been shown to evolve more slowly, on average, than surface sites with few contacts. Here, we present a comprehensive study of the extent to which numerous structural properties can predict sequence variation. The structural properties we considered include buriedness (relative solvent accessibility and contact number), structural flexibility (B factors, root-mean-square fluctuations, and variation in dihedral angles), and variability in designed structures. We obtained structural flexibility measures both from molecular dynamics simulations performed on 9 non-homologous viral protein structures and from variation in homologous variants of those proteins, where available. We obtained measures of variability in designed structures from flexible-backbone design in the Rosetta software. We found that mo...

  2. Prediction of the key binding site of odorant-binding protein of Holotrichia oblita Faldermann (Coleoptera: Scarabaeida).

    Science.gov (United States)

    Zhuang, X; Wang, Q; Wang, B; Zhong, T; Cao, Y; Li, K; Yin, J

    2014-06-01

    The scarab beetle Holotrichia oblita Faldermann (Coleoptera: Scarabaeidae) is a predominant underground pest in the northern parts of China, and its larvae (grubs) cause great economic losses because of its wide range of host plants and covert habitats. Environmentally friendly strategies for controlling adults would have novel and broad potential applications. One potential pest management measure is the regulation of olfactory chemoreception to control target insect pests. In the process of olfactory recognition, odorant-binding proteins (OBPs) are believed to carry hydrophobic odorants from the environment to the surface of olfactory receptor neurons. To obtain a better understanding of the relationship between OBP structures and their ligands, homology modelling and molecular docking have been conducted on the interaction between HoblOBP1 and hexyl benzoate in the present study. Based on the results, site-directed mutagenesis and binding experiments were combined to describe the binding sites of HoblOBP1 and to explore its ligand-binding mechanism. After homology modelling of HoblOBP1, it was found that the three-dimensional structure of HoblOBP1 consists of six α-helices and three disulphide bridges that connect the helices, and the hydrophobic pockets are both composed of five helices. Based on the docking study, we found that van der Waals interactions and hydrophobic interactions are both important in the bonding between HoblOBP1 and hexyl benzoate. Intramolecular residues formed the hydrogen bonds in the C terminus of the protein and the bonds are crucial for the ligand-binding specificity. Finally, MET48, ILE80 and TYR111 are binding sites predicted for HoblOBP1. Using site-directed mutagenesis and fluorescence assays, it was found that ligands could not be recognized by mutant of Tyr111. A possible explanation is that the compound could not be recognized by the mutant, and remains in the binding cavity because of the loss of the intramolecular

  3. [Spatial distribution prediction of surface soil Pb in a battery contaminated site].

    Science.gov (United States)

    Liu, Geng; Niu, Jun-Jie; Zhang, Chao; Zhao, Xin; Guo, Guan-Lin

    2014-12-01

    In order to enhance the reliability of risk estimation and to improve the accuracy of pollution scope determination in a battery contaminated site with the soil characteristic pollutant Pb, four spatial interpolation models, including Combination Prediction Model (OK(LG) + TIN), kriging model (OK(BC)), Inverse Distance Weighting model (IDW), and Spline model were employed to compare their effects on the spatial distribution and pollution assessment of soil Pb. The results showed that Pb concentration varied significantly and the data was severely skewed. The variation coefficient of the site was higher in the local region. OK(LG) + TIN was found to be more accurate than the other three models in predicting the actual pollution situations of the contaminated site. The prediction accuracy of other models was lower, due to the effect of the principle of different models and datum feature. The interpolation results of OK(BC), IDW and Spline could not reflect the detailed characteristics of seriously contaminated areas, and were not suitable for mapping and spatial distribution prediction of soil Pb in this site. This study gives great contributions and provides useful references for defining the remediation boundary and making remediation decision of contaminated sites. PMID:25826945

  4. GPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm.

    Directory of Open Access Journals (Sweden)

    Yu Xue

    Full Text Available As one of the most important and ubiquitous post-translational modifications (PTMs of proteins, S-nitrosylation plays important roles in a variety of biological processes, including the regulation of cellular dynamics and plasticity. Identification of S-nitrosylated substrates with their exact sites is crucial for understanding the molecular mechanisms of S-nitrosylation. In contrast with labor-intensive and time-consuming experimental approaches, prediction of S-nitrosylation sites using computational methods could provide convenience and increased speed. In this work, we developed a novel software of GPS-SNO 1.0 for the prediction of S-nitrosylation sites. We greatly improved our previously developed algorithm and released the GPS 3.0 algorithm for GPS-SNO. By comparison, the prediction performance of GPS 3.0 algorithm was better than other methods, with an accuracy of 75.80%, a sensitivity of 53.57% and a specificity of 80.14%. As an application of GPS-SNO 1.0, we predicted putative S-nitrosylation sites for hundreds of potentially S-nitrosylated substrates for which the exact S-nitrosylation sites had not been experimentally determined. In this regard, GPS-SNO 1.0 should prove to be a useful tool for experimentalists. The online service and local packages of GPS-SNO were implemented in JAVA and are freely available at: http://sno.biocuckoo.org/.

  5. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach.

    Science.gov (United States)

    Gelfand, M S; Koonin, E V; Mironov, A A

    2000-02-01

    Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data on archaeal transcription regulation or by analogy with known bacterial regulons, and further analysis was performed using iterative profile searches. The information content of the candidate signals detected by this method is insufficient for reliable predictions to be made. Therefore, this approach has to be complemented by examination of evolutionary conservation in different archaeal genomes. This combined strategy resulted in the prediction of a conserved heat shock regulon in all euryarchaea, a nitrogen fixation regulon in the methanogens Methanococcus jannaschii and Methanobacterium thermoautotrophicum and an aromatic amino acid regulon in M.thermoautotrophicum. Unexpectedly, the heat shock regulatory site was detected not only for genes that encode known chaperone proteins but also for archaeal histone genes. This suggests a possible function for archaeal histones in stress-related changes in DNA condensation. In addition, comparative analysis of the genomes of three Pyrococcus species resulted in the prediction of their purine metabolism and transport regulon. The results demonstrate the feasibility of prediction of at least some transcription regulatory sites by comparing poorly characterized prokaryotic genomes, particularly when several closely related genome sequences are available. PMID:10637320

  6. Establishing a predictive maintenance (PdM) program at the Hanford Site

    International Nuclear Information System (INIS)

    The production reactors have been shut down for some time. But for the rest of the site, there is currently about 16,000 people engaged in a multi-billion dollar effort to safely process wastes which have been stored at the site since the 1940's. This effort also includes demolition of some older facilities and environmental restoration of much of the site. This is expected to take approximately 30 to 40 years. The concept of a site-wide predictive maintenance (PdM) program began to form in early 1993. Several informal studies showed that the stand alone predictive maintenance groups which had prevailed on site to date were less than 15% effective at trending equipment conditions and predicting failures. To improve the effectiveness of PdM within the company, an engineering analysis by Rick Winslow confirmed that utilization of software networking technology which was now available would significantly overcome many of these built in handicaps. A site-wide predictive maintenance network would make PdM technology accessible to all of the areas and facilities at the site regardless of geographical distances and company division lines. Site resident vibration experts can easily be located and provide consultations on the network. However, it was recognized that strong leadership and management skills would be required within each of the two organizations for effective implementation. To start this process, a letter of understanding and agreement between the facilities and Tank Farm divisions was drafted and endorsed by company management. The agreement assigned the primary responsibility of acquiring the network software and licensee to the Tank Farms division. The acquisition and installation of the network server would be the responsibility of the facilities division. This paper describes the rest of the network development and implementation process

  7. Predicting the Mutating Distribution at Antigenic Sites of the Influenza Virus

    OpenAIRE

    Hongyang Xu; Yiyan Yang; Shuning Wang; Ruixin Zhu; Tianyi Qiu; Jingxuan Qiu; Qingchen Zhang; Li Jin; Yungang He; Kailin Tang; Zhiwei Cao

    2016-01-01

    Mutations of the influenza virus lead to antigenic changes that cause recurrent epidemics and vaccine resistance. Preventive measures would benefit greatly from the ability to predict the potential distribution of new antigenic sites in future strains. By leveraging the extensive historical records of HA sequences for 90 years, we designed a computational model to simulate the dynamic evolution of antigenic sites in A/H1N1. With templates of antigenic sequences, the model can effectively pred...

  8. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach

    OpenAIRE

    Gelfand, M S; Koonin, E.V.; Mironov, A. A.

    2000-01-01

    Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data on archaeal transcription regulation or by analogy with known bacterial regulons, and further analysis was performed using iterative profile searches. The information content of ...

  9. PREDICTION OF ANTIGENIC AND BINDING SITES OF NEUROTOXIN 23 OF SCORPION (LYCHASMUCRONACTUS SP.)

    OpenAIRE

    Bharati K Thosare; Ingale, Arun G

    2015-01-01

    Identification of antigenic and binding site of protein is highly desirable for the design of vaccines and immunodiagnostics. The present exercise deals with a prediction of antigenic as well as binding sites of neurotoxin 23 of Lychasmucronactus. This species of scorpion having diverse molecules of toxic peptide, the peptide neurotoxin 23 is 96 amino acids long of which 23 to 96 specifically code for neurotoxin. The total of 27 such different ligand binding residue were identifie...

  10. Cavity coalescence in superplastic deformation

    Energy Technology Data Exchange (ETDEWEB)

    Stowell, M.J.; Livesey, D.W.; Ridley, N.

    1984-01-01

    An analysis of the probability distribution function of particles randomly dispersed in a solid has been applied to cavitation during superplastic deformation and a method of predicting cavity coalescence developed. Cavity size distribution data were obtained from two microduplex nickel-silver alloys deformed superplastically to various extents at elevated temperature, and compared to theoretical predictions. Excellent agreement occurred for small void sizes but the model underestimated the number of voids in the largest size groups. It is argued that the discrepancy results from a combination of effects due to non-random cavity distributions and to enhanced growth rates and incomplete spheroidization of the largest cavities.

  11. SITE-94. Discrete-feature modelling of the Aespoe Site: 3. Predictions of hydrogeological parameters for performance assessment

    Energy Technology Data Exchange (ETDEWEB)

    Geier, J.E. [Golder Associates AB, Uppsala (Sweden)

    1996-12-01

    A 3-dimensional, discrete-feature hydrological model is developed. The model integrates structural and hydrologic data for the Aespoe site, on scales ranging from semi regional fracture zones to individual fractures in the vicinity of the nuclear waste canisters. Predicted parameters for the near field include fracture spacing, fracture aperture, and Darcy velocity at each of forty canister deposition holes. Parameters for the far field include discharge location, Darcy velocity, effective longitudinal dispersion coefficient and head gradient, flow porosity, and flow wetted surface, for each canister source that discharges to the biosphere. Results are presented in the form of statistical summaries for a total of 42 calculation cases, which treat a set of 25 model variants in various combinations. The variants for the SITE-94 Reference Case model address conceptual and parametric uncertainty related to the site-scale hydrogeologic model and its properties, the fracture network within the repository, effective semi regional boundary conditions for the model, and the disturbed-rock zone around the repository tunnels and shafts. Two calculation cases simulate hydrologic conditions that are predicted to occur during future glacial episodes. 30 refs.

  12. SITE-94. Discrete-feature modelling of the Aespoe Site: 3. Predictions of hydrogeological parameters for performance assessment

    International Nuclear Information System (INIS)

    A 3-dimensional, discrete-feature hydrological model is developed. The model integrates structural and hydrologic data for the Aespoe site, on scales ranging from semi regional fracture zones to individual fractures in the vicinity of the nuclear waste canisters. Predicted parameters for the near field include fracture spacing, fracture aperture, and Darcy velocity at each of forty canister deposition holes. Parameters for the far field include discharge location, Darcy velocity, effective longitudinal dispersion coefficient and head gradient, flow porosity, and flow wetted surface, for each canister source that discharges to the biosphere. Results are presented in the form of statistical summaries for a total of 42 calculation cases, which treat a set of 25 model variants in various combinations. The variants for the SITE-94 Reference Case model address conceptual and parametric uncertainty related to the site-scale hydrogeologic model and its properties, the fracture network within the repository, effective semi regional boundary conditions for the model, and the disturbed-rock zone around the repository tunnels and shafts. Two calculation cases simulate hydrologic conditions that are predicted to occur during future glacial episodes. 30 refs

  13. Thermal performance prediction and sensitivity analysis for future deployment of molten salt cavity receiver solar power plants in Algeria

    International Nuclear Information System (INIS)

    Highlights: • Performance of power plant with molten salt cavity receiver is assessed. • A method has been used to optimize the plant solar multiple, capacity factor and LEC. • Comparison of the simulated results to those of PS20 has shown good agreement. • Higher fossil fuel fraction reduces the LEC and increases the capacity factor. • Highland and Sahara regions are suitable for CRS plants deployment. - Abstract: Of all Concentrating Solar Power (CSP) technologies available today, the molten salt solar power plant appears to be the most important option for providing a major share of the clean and renewable electricity needed in the future. In the present paper, a technical and economic analysis for the implementation of a probable molten salt cavity receiver thermal power plant in Algeria has been carried out. In order to do so, we have investigated the effect of solar field size, storage capacity factor, solar radiation intensity, hybridization and power plant capacity on the thermal efficiency and electricity cost of the selected plant. The system advisor model has been used to perform the technical performance and the economic assessment for different locations (coastal, highland and Sahara regions) in Algeria. Taking into account various factors, a method has been applied to optimize the solar multiple and the capacity factor of the plant, to get a trade-off between the incremental investment costs of the heliostat field and the thermal energy storage. The analysis has shown that the use of higher fossil fuel fraction significantly reduces the levelized electricity cost (LEC) and sensibly increases the capacity factor (CF). The present study indicates that hybrid molten salt solar tower power technology is very promising. The CF and the LEC have been found to be respectively of the order of 71% and 0.35 $/kWe. For solar-only power plants, these parameters are respectively about 27% and 0.63 $/kWe. Therefore, hybrid central receiver systems are

  14. Comparison of reactive transport model predictions for natural attenuation processes occurring at chlorinated solvent contaminated site

    Science.gov (United States)

    Chiu, H. M.; Tsai, C. H.; Lai, K. H.; Chen, J. S.

    2014-12-01

    Prediction of an analytical model and numerical model, namely BIOCLOR and HYDRODEOCHEM, for a test scenario involving the natural attenuations of dissolved solvent at chlorinated contaminated site are compared. Two models make same predictions for PCE, TCE and DCE and considerable different predictions for VC and ETH for the case of all species having identical retardation factors. Significant discrepancies between two models are observed for all species when retardation coefficients are considered to be different for all species. These differences can be attributed to the basic assumption that all the species have the same retardation factors embedded in BIOCHLOR.

  15. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes

    Science.gov (United States)

    Zhang, Shaoqiang; Xu, Minli; Su, Zhengchang

    2009-01-01

    Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the lack of efficient and accurate experimental and computational methods for their characterization, which has largely hindered our understanding of many important biological processes. In this article, we describe a novel algorithm for genome-wide de novo prediction of CRBSs with high accuracy. We designed our algorithm to circumvent three identified difficulties for CRBS prediction using comparative genomics principles based on a new method for the selection of reference genomes, a new metric for measuring the similarity of CRBSs, and a new graph clustering procedure. When operon structures are correctly predicted, our algorithm can predict 81% of known individual binding sites belonging to 94% of known cis-regulatory motifs in the Escherichia coli K12 genome, while achieving high prediction specificity. Our algorithm has also achieved similar prediction accuracy in the Bacillus subtilis genome, suggesting that it is very robust, and thus can be applied to any other sequenced prokaryotic genome. When compared with the prior state-of-the-art algorithms, our algorithm outperforms them in both prediction sensitivity and specificity. PMID:19383880

  16. Ensemble approach combining multiple methods improves human transcription start site prediction

    LENUS (Irish Health Repository)

    Dineen, David G

    2010-11-30

    Abstract Background The computational prediction of transcription start sites is an important unsolved problem. Some recent progress has been made, but many promoters, particularly those not associated with CpG islands, are still difficult to locate using current methods. These methods use different features and training sets, along with a variety of machine learning techniques and result in different prediction sets. Results We demonstrate the heterogeneity of current prediction sets, and take advantage of this heterogeneity to construct a two-level classifier (\\'Profisi Ensemble\\') using predictions from 7 programs, along with 2 other data sources. Support vector machines using \\'full\\' and \\'reduced\\' data sets are combined in an either\\/or approach. We achieve a 14% increase in performance over the current state-of-the-art, as benchmarked by a third-party tool. Conclusions Supervised learning methods are a useful way to combine predictions from diverse sources.

  17. Survey on Nucleotide Encoding Techniques and SVM Kernel Design for Human Splice Site Prediction

    Directory of Open Access Journals (Sweden)

    A.T.M. Golam Bari

    2012-12-01

    Full Text Available Splice site prediction in DNA sequence is a basic search problem for finding exon/intron and intron/exon boundaries. Removing introns and then joining the exons together forms the mRNA sequence. These sequences are the input of the translation process. It is a necessary step in the central dogma of molecular biology. The main task of splice site prediction is to find out the exact GT and AG ended sequences. Then it identifies the true and false GT and AG ended sequences among those candidate sequences. In this paper, we survey research works on splice site prediction based on support vector machine (SVM. The basic difference between these research works is nucleotide encoding technique and SVM kernel selection. Some methods encode the DNA sequence in a sparse way whereas others encode in a probabilistic manner. The encoded sequences serve as input of SVM. The task of SVM is to classify them using its learning model. The accuracy of classification largely depends on the proper kernel selection for sequence data as well as a selection of kernel parameter. We observe each encoding technique and classify them according to their similarity. Then we discuss about kernel and their parameter selection. Our survey paper provides a basic understanding of encoding approaches and proper kernel selection of SVM for splice site prediction.

  18. Long-term predictions of water table from precipitation analysis for a waste disposal site

    International Nuclear Information System (INIS)

    Long-term predictions of water table fluctuations at a waste disposal site have been made from precipitation analysis. Two methods have been applied: a statistical/empirical correlative approach, and a hydrogeologic modelling approach using the finite difference code SWIFT (Simulator for Waste Injection Flow and Transport). This paper discusses the methodology and the results of these assessments

  19. Predicting changes in protein thermostability brought about by single- or multi-site mutations

    Directory of Open Access Journals (Sweden)

    Chu Xiaoyu

    2010-07-01

    Full Text Available Abstract Background An important aspect of protein design is the ability to predict changes in protein thermostability arising from single- or multi-site mutations. Protein thermostability is reflected in the change in free energy (ΔΔG of thermal denaturation. Results We have developed predictive software, Prethermut, based on machine learning methods, to predict the effect of single- or multi-site mutations on protein thermostability. The input vector of Prethermut is based on known structural changes and empirical measurements of changes in potential energy due to protein mutations. Using a 10-fold cross validation test on the M-dataset, consisting of 3366 mutants proteins from ProTherm, the classification accuracy of random forests and the regression accuracy of random forest regression were slightly better than support vector machines and support vector regression, whereas the overall accuracy of classification and the Pearson correlation coefficient of regression were 79.2% and 0.72, respectively. Prethermut performs better on proteins containing multi-site mutations than those with single mutations. Conclusions The performance of Prethermut indicates that it is a useful tool for predicting changes in protein thermostability brought about by single- or multi-site mutations and will be valuable in the rational design of proteins.

  20. Application of GIS in prediction and assessment system of off-site accident consequence for NPP

    International Nuclear Information System (INIS)

    The assessment and prediction software system of off-site accident consequence for Guangdong Nuclear Power Plant (GNARD2.0) is a GIS-based software system. The spatial analysis of radioactive materials and doses with geographic information is available in this system. The structure and functions of the GNARD system and the method of applying ArcView GIS are presented

  1. Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams

    Directory of Open Access Journals (Sweden)

    Fernandez-Fuentes Narcis

    2011-08-01

    Full Text Available Abstract Background Protein binding site prediction by computational means can yield valuable information that complements and guides experimental approaches to determine the structure of protein complexes. Predictions become even more relevant and timely given the current resolution of protein interaction maps, where there is a very large and still expanding gap between the available information on: (i which proteins interact and (ii how proteins interact. Proteins interact through exposed residues that present differential physicochemical properties, and these can be exploited to identify protein interfaces. Results Here we present VORFFIP, a novel method for protein binding site prediction. The method makes use of broad set of heterogeneous data and defined of residue environment, by means of Voronoi Diagrams that are integrated by a two-steps Random Forest ensemble classifier. Four sets of residue features (structural, energy terms, sequence conservation, and crystallographic B-factors used in different combinations together with three definitions of residue environment (Voronoi Diagrams, sequence sliding window, and Euclidian distance have been analyzed in order to maximize the performance of the method. Conclusions The integration of different forms information such as structural features, energy term, evolutionary conservation and crystallographic B-factors, improves the performance of binding site prediction. Including the information of neighbouring residues also improves the prediction of protein interfaces. Among the different approaches that can be used to define the environment of exposed residues, Voronoi Diagrams provide the most accurate description. Finally, VORFFIP compares favourably to other methods reported in the recent literature.

  2. Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

    Directory of Open Access Journals (Sweden)

    Daniel Barry Roche

    2015-12-01

    Full Text Available Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein–ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein–ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein–ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP and the Continuous Automated Model EvaluatiOn (CAMEO projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems.

  3. PREDICTION OF ANTIGENIC AND BINDING SITES OF NEUROTOXIN 23 OF SCORPION (LYCHASMUCRONACTUS SP.

    Directory of Open Access Journals (Sweden)

    Bharati K Thosare

    2015-07-01

    Full Text Available Identification of antigenic and binding site of protein is highly desirable for the design of vaccines and immunodiagnostics. The present exercise deals with a prediction of antigenic as well as binding sites of neurotoxin 23 of Lychasmucronactus. This species of scorpion having diverse molecules of toxic peptide, the peptide neurotoxin 23 is 96 amino acids long of which 23 to 96 specifically code for neurotoxin. The total of 27 such different ligand binding residue were identified by ConSurf and Raptor X server. The web tool Ellipro which implements Modeller and Jmol viewer, predicted and visualized the linear and discontinuous antibody epitopes ofneurotoxin 23 protein sequence.Thus the information discussed here provides a clue for understanding antigenic site and molecular function of neurotoxin 23.

  4. Genetic algorithm learning as a robust approach to RNA editing site prediction

    Directory of Open Access Journals (Sweden)

    Gopal Shuba

    2006-03-01

    Full Text Available Abstract Background RNA editing is one of several post-transcriptional modifications that may contribute to organismal complexity in the face of limited gene complement in a genome. One form, known as C → U editing, appears to exist in a wide range of organisms, but most instances of this form of RNA editing have been discovered serendipitously. With the large amount of genomic and transcriptomic data now available, a computational analysis could provide a more rapid means of identifying novel sites of C → U RNA editing. Previous efforts have had some success but also some limitations. We present a computational method for identifying C → U RNA editing sites in genomic sequences that is both robust and generalizable. We evaluate its potential use on the best data set available for these purposes: C → U editing sites in plant mitochondrial genomes. Results Our method is derived from a machine learning approach known as a genetic algorithm. REGAL (RNA Editing site prediction by Genetic Algorithm Learning is 87% accurate when tested on three mitochondrial genomes, with an overall sensitivity of 82% and an overall specificity of 91%. REGAL's performance significantly improves on other ab initio approaches to predicting RNA editing sites in this data set. REGAL has a comparable sensitivity and higher specificity than approaches which rely on sequence homology, and it has the advantage that strong sequence conservation is not required for reliable prediction of edit sites. Conclusion Our results suggest that ab initio methods can generate robust classifiers of putative edit sites, and we highlight the value of combinatorial approaches as embodied by genetic algorithms. We present REGAL as one approach with the potential to be generalized to other organisms exhibiting C → U RNA editing.

  5. SPE-5 Ground-Motion Prediction at Far-Field Geophone and Accelerometer Array Sites and SPE-5 Moment and Corner-Frequency Prediction

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaoning [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Patton, Howard John [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Chen, Ting [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-03-25

    This report offers predictions for the SPE-5 ground-motion and accelerometer array sites. These predictions pertain to the waveform and spectral amplitude at certain geophone sites using Denny&Johnson source model and a source model derived from SPE data; waveform, peak velocity and peak acceleration at accelerometer sites using the SPE source model and the finite-difference simulation with LLNL 3D velocity model; and the SPE-5 moment and corner frequency.

  6. Influence Of Site Classification On Computing Empirical Ground-Motion Prediction Equations In Italy

    Science.gov (United States)

    di Alessandro, C.; Bonilla, L.; Rovelli, A.; Scotti, O.

    2008-12-01

    In this study, we investigate a site classification method for stations of the Italian Accelerometric Network based on the predominant period of ground motion at the site. The site predominant period is identified from the average horizontal-to-vertical (H/V) spectral ratios of the 5%-damped response spectra of Italian earthquake records. We selected a data-set of 610 three-component analogue and digital recordings from 120 earthquakes recorded at 214 seismic stations within an hypocentral distance of 200 km. Selected events are in the moment-magnitude Mw range of 4.0 to 6.8 and the focal depth ranges from 5 to 40 km. Whenever possible, we classified each site by assigning them to one of six predominant period classes (in the range 0.05 to 2 seconds) that we propose as a modification of the Zhao et al. (2006) procedure. We then investigated the impact of this classification scheme on empirical ground-motion prediction equations. We adopted the same functional form of Fukushima et al. (2007) and we computed a nonlinear period- dependent regression that allowed us to derive site coefficients using the proposed six predominant period classes. We also derived site coefficients for a simplified classification based on the general soil conditions at each site. This classification uses two classes (which we call A-B and C-D, with Vs ≥ 360 m/s and Vs < 360 m/s, respectively) based on the four basic ground categories in the current European (CEN 2004) and Italian seismic codes. Our empirical site classification scheme based on strong-motion data provides the opportunity to explore whether we can decrease the misfit by improving the site characterization of the Italian data set. Comparison of our results with other empirical ground-motion prediction equations (GMPEs) based on conventional site classifications do not display a significant reduction of overall standard deviation. However, our site classification schemes shows promise in reducing the uncertainty in ground

  7. Improved Species-Specific Lysine Acetylation Site Prediction Based on a Large Variety of Features Set.

    Science.gov (United States)

    Wuyun, Qiqige; Zheng, Wei; Zhang, Yanping; Ruan, Jishou; Hu, Gang

    2016-01-01

    Lysine acetylation is a major post-translational modification. It plays a vital role in numerous essential biological processes, such as gene expression and metabolism, and is related to some human diseases. To fully understand the regulatory mechanism of acetylation, identification of acetylation sites is first and most important. However, experimental identification of protein acetylation sites is often time consuming and expensive. Therefore, the alternative computational methods are necessary. Here, we developed a novel tool, KA-predictor, to predict species-specific lysine acetylation sites based on support vector machine (SVM) classifier. We incorporated different types of features and employed an efficient feature selection on each type to form the final optimal feature set for model learning. And our predictor was highly competitive for the majority of species when compared with other methods. Feature contribution analysis indicated that HSE features, which were firstly introduced for lysine acetylation prediction, significantly improved the predictive performance. Particularly, we constructed a high-accurate structure dataset of H.sapiens from PDB to analyze the structural properties around lysine acetylation sites. Our datasets and a user-friendly local tool of KA-predictor can be freely available at http://sourceforge.net/p/ka-predictor. PMID:27183223

  8. Improving N(6)-methyladenosine site prediction with heuristic selection of nucleotide physical-chemical properties.

    Science.gov (United States)

    Zhang, Ming; Sun, Jia-Wei; Liu, Zi; Ren, Ming-Wu; Shen, Hong-Bin; Yu, Dong-Jun

    2016-09-01

    N(6)-methyladenosine (m(6)A) is one of the most common and abundant post-transcriptional RNA modifications found in viruses and most eukaryotes. m(6)A plays an essential role in many vital biological processes to regulate gene expression. Because of its widespread distribution across the genomes, the identification of m(6)A sites from RNA sequences is of significant importance for better understanding the regulatory mechanism of m(6)A. Although progress has been achieved in m(6)A site prediction, challenges remain. This article aims to further improve the performance of m(6)A site prediction by introducing a new heuristic nucleotide physical-chemical property selection (HPCS) algorithm. The proposed HPCS algorithm can effectively extract an optimized subset of nucleotide physical-chemical properties under the prescribed feature representation for encoding an RNA sequence into a feature vector. We demonstrate the efficacy of the proposed HPCS algorithm under different feature representations, including pseudo dinucleotide composition (PseDNC), auto-covariance (AC), and cross-covariance (CC). Based on the proposed HPCS algorithm, we implemented an m(6)A site predictor, called M6A-HPCS, which is freely available at http://csbio.njust.edu.cn/bioinf/M6A-HPCS. Experimental results over rigorous jackknife tests on benchmark datasets demonstrated that the proposed M6A-HPCS achieves higher success rates and outperforms existing state-of-the-art sequence-based m(6)A site predictors. PMID:27293216

  9. Dental cavities

    Science.gov (United States)

    ... leading to cavities. Treatment may involve: Fillings Crowns Root canals Dentists fill teeth by removing the decayed tooth ... gold, porcelain, or porcelain attached to metal. A root canal is recommended if the nerve in a tooth ...

  10. A Python analytical pipeline to identify prohormone precursors and predict prohormone cleavage sites

    Directory of Open Access Journals (Sweden)

    Bruce Southey

    2008-12-01

    Full Text Available Neuropeptides and hormones are signaling molecules that support cell-cell communication in the central nervous system. Experimentally characterizing neuropeptides requires significant efforts because of the complex and variable processing of prohormone precursor proteins into neuropeptides and hormones. We demonstrate the power and flexibility of the Python language to develop components of an bioinformatic analytical pipeline to identify precursors from genomic data and to predict cleavage as these precursors are en route to the final bioactive peptides. We identified 75 precursors in the rhesus genome, predicted cleavage sites using support vector machines and compared the rhesus predictions to putative assignments based on homology to human sequences. The correct classification rate of cleavage using the support vector machines was over 97% for both human and rhesus data sets. The functionality of Python has been important to develop and maintain NeuroPred (http://neuroproteomics.scs.uiuc.edu/neuropred.html, a user-centered web application for the neuroscience community that provides cleavage site prediction from a wide range of models, precision and accuracy statistics, post-translational modifications, and the molecular mass of potential peptides. The combined results illustrate the suitability of the Python language to implement an all-inclusive bioinformatics approach to predict neuropeptides that encompasses a large number of interdependent steps, from scanning genomes for precursor genes to identification of potential bioactive neuropeptides.

  11. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information

    DEFF Research Database (Denmark)

    Hebsgaard, Stefan M.; Korning, Peter G.; Tolstrup, Niels;

    1996-01-01

    experimentally observed in A.thaliana transformants. Predictions for alternatively spliced genes are also presented, together with examples of genes from other dicots, monocots and algae. The method has been made available through electronic mail (NetPlantGene@cbs.dtu.dk), or the WWW at http://www.cbs.dtu.dk/NetPlantGene.html......Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction of the coding potential regulates a cutoff level for a local predicition of splice sites, is refined...... by rules based on splice site confidence values, prediction scores, coding context and distances between potential splice sites. In this approach, the prediction of splice sites mutually affect each other in a non-local manner. The combined approach drastically reduces the large amount of false...

  12. radiofrequency cavity

    CERN Multimedia

    1988-01-01

    The pulse of a particle accelerator. 128 of these radio frequency cavities were positioned around CERN's 27-kilometre LEP ring to accelerate electrons and positrons. The acceleration was produced by microwave electric oscillations at 352 MHz. The electrons and positrons were grouped into bunches, like beads on a string, and the copper sphere at the top stored the microwave energy between the passage of individual bunches. This made for valuable energy savings as it reduced the heat generated in the cavity.

  13. Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome analysis

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Nielsen, Henrik

    Translation in eukaryotes does not always start at the first AUG in an mRNA, implying that context information also plays a role.This makes prediction of translation initiation sites a non-trivial task, especially when analysing EST and genome data where the entire mature mRNA sequence is not known...... and database annotations are analysed in detail, leading to identification of possible database errors....

  14. Teenagers and social network sites: Do off-line inequalities predict their online social networks?

    OpenAIRE

    Ahn, June

    2011-01-01

    This study analyzes a data set of 701 U.S. teenagers (ages 12-18) that merges an online survey of social network site (SNS) preferences with administrative records from their public school districts. Using a multinomial logistic model, I examine whether offline divides across gender, ethnicity, socioeconomic status, self-esteem, and social capital predict teenagers’ membership into the popular SNSs, Facebook and Myspace. The results show that the characteristics of teens that use Facebook, ...

  15. LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains

    OpenAIRE

    Helft, Laura; Reddy, Vignyan; Chen, Xiyang; Koller, Teresa; Federici, Luca; Fernández-Recio, Juan; Gupta, Rishabh; Bent, Andrew

    2011-01-01

    Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs) are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM...

  16. Suction Drain Tip Culture after Spine Surgery: Can It Predict a Surgical Site Infection?

    OpenAIRE

    Ahn, Jae-Sung; Lee, Ho-Jin; Park, Eugene; Park, Il-Young; Lee, Jae Won

    2015-01-01

    Study Design Retrospective clinical study. Purpose To assess the diagnostic value of suction drain tip culture in patients undergoing primary posterior spine surgery. Overview of Literature To date, the diagnostic value of suction drain tip culture for predicting surgical site infection (SSI) has not been firmly established in orthopedic or spinal surgery. Methods In total, 133 patients who underwent primary posterior spine surgery from January 2013 to April 2015 were included in this retrosp...

  17. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes

    OpenAIRE

    Zhang, Shaoqiang; Xu, Minli; Li, Shan; Su, Zhengchang

    2009-01-01

    Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the lack of efficient and accurate experimental and computational methods for their characterization, which has largely hindered our understanding of many important biological processes. In this article, we describe a novel algorithm for genome-wide de novo prediction of CRBSs with high accuracy. We desi...

  18. On splice site prediction using weight array models: a comparison of smoothing techniques

    International Nuclear Information System (INIS)

    In most eukaryotic genes, protein-coding exons are separated by non-coding introns which are removed from the primary transcript by a process called 'splicing'. The positions where introns are cut and exons are spliced together are called 'splice sites'. Thus, computational prediction of splice sites is crucial for gene finding in eukaryotes. Weight array models are a powerful probabilistic approach to splice site detection. Parameters for these models are usually derived from m-tuple frequencies in trusted training data and subsequently smoothed to avoid zero probabilities. In this study we compare three different ways of parameter estimation for m-tuple frequencies, namely (a) non-smoothed probability estimation, (b) standard pseudo counts and (c) a Gaussian smoothing procedure that we recently developed

  19. On splice site prediction using weight array models: a comparison of smoothing techniques

    Science.gov (United States)

    Taher, Leila; Meinicke, Peter; Morgenstern, Burkhard

    2007-11-01

    In most eukaryotic genes, protein-coding exons are separated by non-coding introns which are removed from the primary transcript by a process called "splicing". The positions where introns are cut and exons are spliced together are called "splice sites". Thus, computational prediction of splice sites is crucial for gene finding in eukaryotes. Weight array models are a powerful probabilistic approach to splice site detection. Parameters for these models are usually derived from m-tuple frequencies in trusted training data and subsequently smoothed to avoid zero probabilities. In this study we compare three different ways of parameter estimation for m-tuple frequencies, namely (a) non-smoothed probability estimation, (b) standard pseudo counts and (c) a Gaussian smoothing procedure that we recently developed.

  20. Prediction of posttranslational modification sites from amino acid sequences with kernel methods.

    Science.gov (United States)

    Xu, Yan; Wang, Xiaobo; Wang, Yongcui; Tian, Yingjie; Shao, Xiaojian; Wu, Ling-Yun; Deng, Naiyang

    2014-03-01

    Post-translational modification (PTM) is the chemical modification of a protein after its translation and one of the later steps in protein biosynthesis for many proteins. It plays an important role which modifies the end product of gene expression and contributes to biological processes and diseased conditions. However, the experimental methods for identifying PTM sites are both costly and time-consuming. Hence computational methods are highly desired. In this work, a novel encoding method PSPM (position-specific propensity matrices) is developed. Then a support vector machine (SVM) with the kernel matrix computed by PSPM is applied to predict the PTM sites. The experimental results indicate that the performance of new method is better or comparable with the existing methods. Therefore, the new method is a useful computational resource for the identification of PTM sites. A unified standalone software PTMPred is developed. It can be used to predict all types of PTM sites if the user provides the training datasets. The software can be freely downloaded from http://www.aporc.org/doc/wiki/PTMPred. PMID:24291233

  1. Prediction and assignment of site occupation and energy levels for Pb2+ ions in crystal hosts

    International Nuclear Information System (INIS)

    The environmental factor he of the host was calculated quantitatively in Pb2+-doped 23 compounds based on the dielectric theory of chemical bond for complex crystals. The relationship between the A band energy EA of Pb2+ and the environmental factor he was intensively studied. The results indicate that EA of Pb2+ decreases linearly with increasing of he. A linear model was proposed which allows us to correctly predict and assign the site occupations and the position of A band for Pb2+-doped compounds if the crystal structure and the refraction index were known. Applied to SrGa2O4:Pb2+, CaAl2B2O7:Pb2+ and SrAl2B2O7:Pb2+, the theoretical predictions are in very good agreement with the experimental data. In SrGa2O4:Pb2+, the excitation spectrum of Pb2+ from two different cation sites was identified: the higher energy band of A (265 nm) from the site of Sr2, and the lower ones (280 nm) from the site of Sr1. - Graphical abstract: The A band energy EA of Pb2+ has linear relationship with environmental factor he.

  2. Prediction of allosteric sites and mediating interactions through bond-to-bond propensities

    Science.gov (United States)

    Amor, B. R. C.; Schaub, M. T.; Yaliraki, S. N.; Barahona, M.

    2016-01-01

    Allostery is a fundamental mechanism of biological regulation, in which binding of a molecule at a distant location affects the active site of a protein. Allosteric sites provide targets to fine-tune protein activity, yet we lack computational methodologies to predict them. Here we present an efficient graph-theoretical framework to reveal allosteric interactions (atoms and communication pathways strongly coupled to the active site) without a priori information of their location. Using an atomistic graph with energy-weighted covalent and weak bonds, we define a bond-to-bond propensity quantifying the non-local effect of instantaneous bond fluctuations propagating through the protein. Significant interactions are then identified using quantile regression. We exemplify our method with three biologically important proteins: caspase-1, CheY, and h-Ras, correctly predicting key allosteric interactions, whose significance is additionally confirmed against a reference set of 100 proteins. The almost-linear scaling of our method renders it suitable for high-throughput searches for candidate allosteric sites. PMID:27561351

  3. NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm

    Directory of Open Access Journals (Sweden)

    Jin Changjiang

    2006-10-01

    Full Text Available Abstract Background Protein palmitoylation, an essential and reversible post-translational modification (PTM, has been implicated in cellular dynamics and plasticity. Although numerous experimental studies have been performed to explore the molecular mechanisms underlying palmitoylation processes, the intrinsic feature of substrate specificity has remained elusive. Thus, computational approaches for palmitoylation prediction are much desirable for further experimental design. Results In this work, we present NBA-Palm, a novel computational method based on Naïve Bayes algorithm for prediction of palmitoylation site. The training data is curated from scientific literature (PubMed and includes 245 palmitoylated sites from 105 distinct proteins after redundancy elimination. The proper window length for a potential palmitoylated peptide is optimized as six. To evaluate the prediction performance of NBA-Palm, 3-fold cross-validation, 8-fold cross-validation and Jack-Knife validation have been carried out. Prediction accuracies reach 85.79% for 3-fold cross-validation, 86.72% for 8-fold cross-validation and 86.74% for Jack-Knife validation. Two more algorithms, RBF network and support vector machine (SVM, also have been employed and compared with NBA-Palm. Conclusion Taken together, our analyses demonstrate that NBA-Palm is a useful computational program that provides insights for further experimentation. The accuracy of NBA-Palm is comparable with our previously described tool CSS-Palm. The NBA-Palm is freely accessible from: http://www.bioinfo.tsinghua.edu.cn/NBA-Palm.

  4. High DNA melting temperature predicts transcription start site location in human and mouse.

    LENUS (Irish Health Repository)

    Dineen, David G

    2009-12-01

    The accurate computational prediction of transcription start sites (TSS) in vertebrate genomes is a difficult problem. The physicochemical properties of DNA can be computed in various ways and a many combinations of DNA features have been tested in the past for use as predictors of transcription. We looked in detail at melting temperature, which measures the temperature, at which two strands of DNA separate, considering the cooperative nature of this process. We find that peaks in melting temperature correspond closely to experimentally determined transcription start sites in human and mouse chromosomes. Using melting temperature alone, and with simple thresholding, we can predict TSS with accuracy that is competitive with the most accurate state-of-the-art TSS prediction methods. Accuracy is measured using both experimentally and manually determined TSS. The method works especially well with CpG island containing promoters, but also works when CpG islands are absent. This result is clear evidence of the important role of the physical properties of DNA in the process of transcription. It also points to the importance for TSS prediction methods to include melting temperature as prior information.

  5. The 340-cavity in neuraminidase provides new opportunities for influenza drug development: A molecular dynamics simulation study.

    Science.gov (United States)

    Han, Nanyu; Mu, Yuguang; Miao, Huabiao; Yang, Yunjuan; Wu, Qian; Li, Junjun; Ding, Junmei; Xu, Bo; Huang, Zunxi

    2016-01-29

    Influenza neuraminidase (NA) is a pivotal target for viral infection control. However, the accumulating of mutations compromise the efficacy of NA inhibitors. Thus, it is critical to design new drugs targeted to different motifs of NA. Recently, a new motif called 340-cavity was discovered in NA subtypes close to the calcium binding site. The presence of calcium is known to influence NA activity and thermostability. Therefore, the 340-cavity is a putative ligand-binding site for affecting the normal function of NA. In this study, we performed molecular dynamics simulations of different NA subtypes to explore the mechanism of 340-loop formation. Ligand-binding site prediction and fragment library screening were also carried out to provide evidence for the 340-cavity as a druggable pocket. We found that residues G342 and P/R344 in the 340-loop determine the size of the 340-cavity, and the calcium ion plays an important role in maintaining the conformation of the 340-loop through contacts with G345 and Q347. In addition, the 340-cavity is predicted to be a ligand-binding site by metaPocket, and a sequence analysis method is proposed to predict the existence of the 340-cavity. Our study shows that the 340-cavity is not an occasional or atypical domain in NA subtypes, and it has potential to function as a new hotspot for influenza drug binding. PMID:26768362

  6. Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes

    Science.gov (United States)

    Xu, Minli; Su, Zhengchang

    2009-01-01

    Background Cyclic AMP receptor protein (CRP), also known as catabolite gene activator protein (CAP), is an important transcriptional regulator widely distributed in many bacteria. The biological processes under the regulation of CRP are highly diverse among different groups of bacterial species. Elucidation of CRP regulons in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. Previously, CRP has been experimentally studied in only two cyanobacterial strains: Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120; therefore, a systematic genome-scale study of the potential CRP target genes and binding sites in cyanobacterial genomes is urgently needed. Results We have predicted and analyzed the CRP binding sites and regulons in 12 sequenced cyanobacterial genomes using a highly effective cis-regulatory binding site scanning algorithm. Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli. Furthermore, CRP regulons in different cyanobacterial species/ecotypes are also highly diversified, ranging from photosynthesis, carbon fixation and nitrogen assimilation, to chemotaxis and signal transduction. In addition, our prediction indicates that crp genes in modern cyanobacteria are likely inherited from a common ancestral gene in their last common ancestor, and have adapted various cellular functions in different environments, while some cyanobacteria lost their crp genes as well as CRP binding sites during the course of evolution. Conclusion The CRP regulons in cyanobacteria are highly diversified, probably as a result of divergent evolution to adapt to various ecological niches. Cyanobacterial CRPs may function as lineage-specific regulators participating in various cellular processes, and are important in some lineages. However, they are dispensable in some other lineages. The loss of CRPs in these species

  7. Computational prediction of cAMP receptor protein (CRP binding sites in cyanobacterial genomes

    Directory of Open Access Journals (Sweden)

    Su Zhengchang

    2009-01-01

    Full Text Available Abstract Background Cyclic AMP receptor protein (CRP, also known as catabolite gene activator protein (CAP, is an important transcriptional regulator widely distributed in many bacteria. The biological processes under the regulation of CRP are highly diverse among different groups of bacterial species. Elucidation of CRP regulons in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. Previously, CRP has been experimentally studied in only two cyanobacterial strains: Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120; therefore, a systematic genome-scale study of the potential CRP target genes and binding sites in cyanobacterial genomes is urgently needed. Results We have predicted and analyzed the CRP binding sites and regulons in 12 sequenced cyanobacterial genomes using a highly effective cis-regulatory binding site scanning algorithm. Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli. Furthermore, CRP regulons in different cyanobacterial species/ecotypes are also highly diversified, ranging from photosynthesis, carbon fixation and nitrogen assimilation, to chemotaxis and signal transduction. In addition, our prediction indicates that crp genes in modern cyanobacteria are likely inherited from a common ancestral gene in their last common ancestor, and have adapted various cellular functions in different environments, while some cyanobacteria lost their crp genes as well as CRP binding sites during the course of evolution. Conclusion The CRP regulons in cyanobacteria are highly diversified, probably as a result of divergent evolution to adapt to various ecological niches. Cyanobacterial CRPs may function as lineage-specific regulators participating in various cellular processes, and are important in some lineages. However, they are dispensable in some other lineages. The

  8. Diffusion stabilizes cavity solitons in bidirectional lasers

    OpenAIRE

    Perez-Arjona, Isabel; Sanchez-Morcillo, Victor; Redondo, Javier; Staliunas, Kestutis; Roldan, Eugenio

    2009-01-01

    We study the influence of field diffusion on the spatial localized structures (cavity solitons) recently predicted in bidirectional lasers. We find twofold positive role of the diffusion: 1) it increases the stability range of the individual (isolated) solitons; 2) it reduces the long-range interaction between the cavity solitons. Latter allows the independent manipulation (writing and erasing) of individual cavity solitons.

  9. A gravimetric 3D global inversion for cavity detection

    Energy Technology Data Exchange (ETDEWEB)

    Camacho, A.G.; Vieira, R.; Montesinos, F.G. (Inst. de Astronomia y Geodesia, Madrid (Spain). Faculty de CC. Matematicas); Cuellar, V. (Lab. de Geotecnia del Centro de Estudios y Experimentacion de Obras Publicas, Madrid (Spain))

    1994-02-01

    A gravimetric survey, covering a site 200 m square, was carried out in order to locate karstic cavities. After eliminating the regional trend using a polynomial fit, the residual is modeled by least-squares prediction. Correlated signals for several wavelengths are detected. The inversion of these anomalies is performed by a global 3D adjustment using spherical bodies as models. The adjustment is repeated in order to obtain a stable configuration. The results show the probable presence of a system of cavities and galleries. Data collected from boreholes and the subsequent appearance of sink-holes are consistent with the results.

  10. MicroRNAs MiR-218, MiR-125b, and Let-7g predict prognosis in patients with oral cavity squamous cell carcinoma.

    Directory of Open Access Journals (Sweden)

    Shih-Chi Peng

    Full Text Available MicroRNAs (miRNAs have a major impact on regulatory networks in human carcinogenesis. In this study, we sought to investigate the prognostic significance of miRNAs in patients with oral cavity squamous cell carcinoma (OSCC. In a discovery phase, RNA was extracted from 58 OSCC tumor samples and paired normal tissues. MiRNAs expression was evaluated with TaqMan Array Card and TaqMan MicroRNA assays. The prognostic significance of the miRNA signature identified in the discovery phase was validated by qRT-PCR in a replication set consisting of 141 formalin-fixed, paraffin-embedded (FFPE samples. We identified a miRNA regulatory network centered on the three hub genes (SP1, MYC, and TP53 that predicted distinct clinical endpoints. Three miRNAs (miR-218, miR-125b, and let-7g and their downstream response genes had a concordant prognostic significance on disease-free survival and disease-specific survival rates. In addition, patients with a reduced expression of miR-218, miR-125b, and let-7g have a higher risk of poor outcomes in presence of specific risk factors (p-stage III-IV, pT3-4, or pN+. Our findings indicate that specific miRNAs have prognostic significance in OSCC patients and may improve prognostic stratification over traditional risk factors.

  11. Predicting functional sites with an automated algorithm suitable for heterogeneous datasets

    Directory of Open Access Journals (Sweden)

    Livesay Dennis R

    2005-05-01

    Full Text Available Abstract Background In a previous report (La et al., Proteins, 2005, we have demonstrated that the identification of phylogenetic motifs, protein sequence fragments conserving the overall familial phylogeny, represent a promising approach for sequence/function annotation. Across a structurally and functionally heterogeneous dataset, phylogenetic motifs have been demonstrated to correspond to a wide variety of functional site archetypes, including those defined by surface loops, active site clefts, and less exposed regions. However, in our original demonstration of the technique, phylogenetic motif identification is dependent upon a manually determined similarity threshold, prohibiting large-scale application of the technique. Results In this report, we present an algorithmic approach that determines thresholds without human subjectivity. The approach relies on significant raw data preprocessing to improve signal detection. Subsequently, Partition Around Medoids Clustering (PAMC of the similarity scores assesses sequence fragments where functional annotation remains in question. The accuracy of the approach is confirmed through comparisons to our previous (manual results and structural analyses. Triosephosphate isomerase and arginyl-tRNA synthetase are discussed as exemplar cases. A quantitative functional site prediction assessment algorithm indicates that the phylogenetic motif predictions, which require sequence information only, are nearly as good as those from evolutionary trace methods that do incorporate structure. Conclusion The automated threshold detection algorithm has been incorporated into MINER, our web-based phylogenetic motif identification server. MINER is freely available on the web at http://www.pmap.csupomona.edu/MINER/. Pre-calculated functional site predictions of the COG database and an implementation of the threshold detection algorithm, in the R statistical language, can also be accessed at the website.

  12. Rapid and accurate prediction and scoring of water molecules in protein binding sites.

    Directory of Open Access Journals (Sweden)

    Gregory A Ross

    Full Text Available Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

  13. accelerating cavity

    CERN Multimedia

    On the inside of the cavitytThere is a layer of niobium. Operating at 4.2 degrees above absolute zero, the niobium is superconducting and carries an accelerating field of 6 million volts per metre with negligible losses. Each cavity has a surface of 6 m2. The niobium layer is only 1.2 microns thick, ten times thinner than a hair. Such a large area had never been coated to such a high accuracy. A speck of dust could ruin the performance of the whole cavity so the work had to be done in an extremely clean environment.

  14. The Prediction of Calpain Cleavage Sites with the mRMR and IFS Approaches

    Directory of Open Access Journals (Sweden)

    Wenyi Zhang

    2013-01-01

    Full Text Available Calpains are an important family of the Ca2+-dependent cysteine proteases which catalyze the limited proteolysis of many specific substrates. Calpains play crucial roles in basic physiological and pathological processes, and identification of the calpain cleavage sites may facilitate the understanding of the molecular mechanisms and biological function. But traditional experiment approaches to predict the sites are accurate, and are always labor-intensive and time-consuming. Thus, it is common to see that computational methods receive increasing attention due to their convenience and fast speed in recent years. In this study, we develop a new predictor based on the support vector machine (SVM with the maximum relevance minimum redundancy (mRMR method followed by incremental feature selection (IFS. And we concern the feature of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure, and solvent accessibility to represent the calpain cleavage sites. Experimental results show that the performance of our predictor is better than several other state-of- the-art predictors, whose average prediction accuracy is 79.49%, sensitivity is 62.31%, and specificity is 88.12%. Since user-friendly and publicly accessible web servers represent the future direction for developing practically more useful predictors, here we have provided a web-server for the method presented in this paper.

  15. A homology-based pipeline for global prediction of post-translational modification sites

    Science.gov (United States)

    Chen, Xiang; Shi, Shao-Ping; Xu, Hao-Dong; Suo, Sheng-Bao; Qiu, Jian-Ding

    2016-05-01

    The pathways of protein post-translational modifications (PTMs) have been shown to play particularly important roles for almost any biological process. Identification of PTM substrates along with information on the exact sites is fundamental for fully understanding or controlling biological processes. Alternative computational strategies would help to annotate PTMs in a high-throughput manner. Traditional algorithms are suited for identifying the common organisms and tissues that have a complete PTM atlas or extensive experimental data. While annotation of rare PTMs in most organisms is a clear challenge. In this work, to this end we have developed a novel homology-based pipeline named PTMProber that allows identification of potential modification sites for most of the proteomes lacking PTMs data. Cross-promotion E-value (CPE) as stringent benchmark has been used in our pipeline to evaluate homology to known modification sites. Independent-validation tests show that PTMProber achieves over 58.8% recall with high precision by CPE benchmark. Comparisons with other machine-learning tools show that PTMProber pipeline performs better on general predictions. In addition, we developed a web-based tool to integrate this pipeline at http://bioinfo.ncu.edu.cn/PTMProber/index.aspx. In addition to pre-constructed prediction models of PTM, the website provides an extensional functionality to allow users to customize models.

  16. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

    Directory of Open Access Journals (Sweden)

    Schroeder Michael

    2006-09-01

    Full Text Available Abstract Background Identifying pockets on protein surfaces is of great importance for many structure-based drug design applications and protein-ligand docking algorithms. Over the last ten years, many geometric methods for the prediction of ligand-binding sites have been developed. Results We present LIGSITEcsc, an extension and implementation of the LIGSITE algorithm. LIGSITEcsc is based on the notion of surface-solvent-surface events and the degree of conservation of the involved surface residues. We compare our algorithm to four other approaches, LIGSITE, CAST, PASS, and SURFNET, and evaluate all on a dataset of 48 unbound/bound structures and 210 bound-structures. LIGSITEcsc performs slightly better than the other tools and achieves a success rate of 71% and 75%, respectively. Conclusion The use of the Connolly surface leads to slight improvements, the prediction re-ranking by conservation to significant improvements of the binding site predictions. A web server for LIGSITEcsc and its source code is available at scoppi.biotec.tu-dresden.de/pocket.

  17. Prediction of TF target sites based on atomistic models of protein-DNA complexes

    Directory of Open Access Journals (Sweden)

    Collado-Vides Julio

    2008-10-01

    Full Text Available Abstract Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition.

  18. Sequence-based prediction of protein-peptide binding sites using support vector machine.

    Science.gov (United States)

    Taherzadeh, Ghazaleh; Yang, Yuedong; Zhang, Tuo; Liew, Alan Wee-Chung; Zhou, Yaoqi

    2016-05-15

    Protein-peptide interactions are essential for all cellular processes including DNA repair, replication, gene-expression, and metabolism. As most protein-peptide interactions are uncharacterized, it is cost effective to investigate them computationally as the first step. All existing approaches for predicting protein-peptide binding sites, however, are based on protein structures despite the fact that the structures for most proteins are not yet solved. This article proposes the first machine-learning method called SPRINT to make Sequence-based prediction of Protein-peptide Residue-level Interactions. SPRINT yields a robust and consistent performance for 10-fold cross validations and independent test. The most important feature is evolution-generated sequence profiles. For the test set (1056 binding and non-binding residues), it yields a Matthews' Correlation Coefficient of 0.326 with a sensitivity of 64% and a specificity of 68%. This sequence-based technique shows comparable or more accurate than structure-based methods for peptide-binding site prediction. SPRINT is available as an online server at: http://sparks-lab.org/. © 2016 Wiley Periodicals, Inc. PMID:26833816

  19. Magnetosheath cavities: case studies using Cluster observations

    OpenAIRE

    Katırcıoğlu, F. T.; Z. Kaymaz; D. G. Sibeck; Dandouras, I.

    2009-01-01

    This paper presents examples of magnetosheath cavities in Cluster spacecraft observations. The cavities are accompanied by high energy particles in the magnetosheath and characterized by depressed magnetic fields and densities. Flow speeds decrease and temperatures increase within the cavities. All magnetosheath parameters show increased variability within the cavities when the energetic particle flux is high. We predict outward motion of the magnetopause boundary in respons...

  20. Big-Five Personality Prediction Based on User Behaviors at Social Network Sites

    CERN Document Server

    Bai, Shuotian; Cheng, Li

    2012-01-01

    Many customer services are already available at Social Network Sites (SNSs), including user recommendation and media interaction, to name a few. There are strong desires to provide online users more dedicated and personalized services that fit into individual's need, usually strongly depending on the inner personalities of the user. However, little has been done to conduct proper psychological analysis, crucial for explaining the user's outer behaviors from their inner personality. In this paper, we propose an approach that intends to facilitate this line of research by directly predicting the so called Big-Five Personality from user's SNS behaviors. Comparing to the conventional inventory-based psychological analysis, we demonstrate via experimental studies that users' personalities can be predicted with reasonable precision based on their online behaviors. Except for proving some former behavior-personality correlation results, our experiments show that extraversion is positively related to one's status rep...

  1. Sequence-based prediction of protein-protein interaction sites with L1-logreg classifier.

    Science.gov (United States)

    Dhole, Kaustubh; Singh, Gurdeep; Pai, Priyadarshini P; Mondal, Sukanta

    2014-05-01

    Protein-protein interactions are of central importance for virtually every process in a living cell. Information about the interaction sites in proteins improves our understanding of disease mechanisms and can provide the basis for new therapeutic approaches. Since a multitude of unique residue-residue contacts facilitate the interactions, protein-protein interaction sites prediction has become one of the most important and challenging problems of computational biology. Although much progress in this field has been reported, this problem is yet to be satisfactorily solved. Here, a novel method (LORIS: L1-regularized LOgistic Regression based protein-protein Interaction Sites predictor) is proposed, that identifies interaction residues, using sequence features and is implemented via the L1-logreg classifier. Results show that LORIS is not only quite effective, but also, performs better than existing state-of-the art methods. LORIS, available as standalone package, can be useful for facilitating drug-design and targeted mutation related studies, which require a deeper knowledge of protein interactions sites. PMID:24486250

  2. Prediction of pollution into ore bearing aquifer from ISL-site

    International Nuclear Information System (INIS)

    Outcomes of present mineralogical investigations explain some phenomena observed in previous sorption experiences. First of all they elucidate cutback of filtration coefficients of sediments exposed under pollution process as granulometric fractions of these permeable sediments decreased in its weight ratio in according to impermeable ones. Then sorption graphics are explained by chemical and mineralogical changes in experienced substance. Explores made diagnoses and estimation about 45 authigenous and technogenous minerals playing the essential role in the process of mass transfer of uranium and polluted components in ISL-sites. They are considered in all basic fractions of studied sediments. Bright peculiarities are noticed for gravel and coarse sands, which went to pieces as a result of dilution or decomposition of its cement. Mineral composition of clayey fraction also significantly changed after pollution process. Steep lost of weight of fraction 0.005-0.001mm consisted with partial decomposition of clayey minerals basically of montmorillonite. These investigations show also that ones of the main minerals playing such the essential role are sorptive such as silica, silica gel, common opal, opal-CT, noble opal, allophane, montmorillonite and zeolite minerals. In conclusion the given work shows some filtration properties of aquifer in an ISL-site and predicts the spread of a possible pollution for ISL-site to environment. The extension of pollution could be more one-two dimension of affected by ISL-process. The prediction would be exact if the previous investigation included the desorptive characteristics and sorptive data depending on temperature and pressure. Current investigations continued pervious ones after which some inexplicable matters of migration of contaminated halo from an ISL-polygon are as follows: Identification and specification of all minerals outside ISL-polygon; Calculation of mineral balance for contaminated sites; Specification of flow

  3. IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES).

    Science.gov (United States)

    Kolekar, Pandurang; Pataskar, Abhijeet; Kulkarni-Kale, Urmila; Pal, Jayanta; Kulkarni, Abhijeet

    2016-01-01

    Cellular mRNAs are predominantly translated in a cap-dependent manner. However, some viral and a subset of cellular mRNAs initiate their translation in a cap-independent manner. This requires presence of a structured RNA element, known as, Internal Ribosome Entry Site (IRES) in their 5' untranslated regions (UTRs). Experimental demonstration of IRES in UTR remains a challenging task. Computational prediction of IRES merely based on sequence and structure conservation is also difficult, particularly for cellular IRES. A web server, IRESPred is developed for prediction of both viral and cellular IRES using Support Vector Machine (SVM). The predictive model was built using 35 features that are based on sequence and structural properties of UTRs and the probabilities of interactions between UTR and small subunit ribosomal proteins (SSRPs). The model was found to have 75.51% accuracy, 75.75% sensitivity, 75.25% specificity, 75.75% precision and Matthews Correlation Coefficient (MCC) of 0.51 in blind testing. IRESPred was found to perform better than the only available viral IRES prediction server, VIPS. The IRESPred server is freely available at http://bioinfo.net.in/IRESPred/. PMID:27264539

  4. Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates.

    Directory of Open Access Journals (Sweden)

    Sonu Kumar

    Full Text Available Caspases are enzymes belonging to a conserved family of cysteine-dependent aspartic-specific proteases that are involved in vital cellular processes and play a prominent role in apoptosis and inflammation. Determining all relevant protein substrates of caspases remains a challenging task. Over 1500 caspase substrates have been discovered in the human proteome according to published data and new substrates are discovered on a daily basis. To aid the discovery process we developed a caspase cleavage prediction method using the recently published curated MerCASBA database of experimentally determined caspase substrates and a Random Forest classification method. On both internal and external test sets, the ranking of predicted cleavage positions is superior to all previously developed prediction methods. The in silico predicted caspase cleavage positions in human proteins are available from a relational database: CaspDB. Our database provides information about potential cleavage sites in a verified set of all human proteins collected in Uniprot and their orthologs, allowing for tracing of cleavage motif conservation. It also provides information about the positions of disease-annotated single nucleotide polymorphisms, and posttranslational modifications that may modulate the caspase cleaving efficiency.

  5. Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates.

    Science.gov (United States)

    Kumar, Sonu; van Raam, Bram J; Salvesen, Guy S; Cieplak, Piotr

    2014-01-01

    Caspases are enzymes belonging to a conserved family of cysteine-dependent aspartic-specific proteases that are involved in vital cellular processes and play a prominent role in apoptosis and inflammation. Determining all relevant protein substrates of caspases remains a challenging task. Over 1500 caspase substrates have been discovered in the human proteome according to published data and new substrates are discovered on a daily basis. To aid the discovery process we developed a caspase cleavage prediction method using the recently published curated MerCASBA database of experimentally determined caspase substrates and a Random Forest classification method. On both internal and external test sets, the ranking of predicted cleavage positions is superior to all previously developed prediction methods. The in silico predicted caspase cleavage positions in human proteins are available from a relational database: CaspDB. Our database provides information about potential cleavage sites in a verified set of all human proteins collected in Uniprot and their orthologs, allowing for tracing of cleavage motif conservation. It also provides information about the positions of disease-annotated single nucleotide polymorphisms, and posttranslational modifications that may modulate the caspase cleaving efficiency. PMID:25330111

  6. Predictive Models for Halogen-bond Basicity of Binding Sites of Polyfunctional Molecules.

    Science.gov (United States)

    Glavatskikh, Marta; Madzhidov, Timur; Solov'ev, Vitaly; Marcou, Gilles; Horvath, Dragos; Graton, Jérôme; Le Questel, Jean-Yves; Varnek, Alexandre

    2016-02-01

    Halogen bonding (XB) strength assesses the ability of an electron-enriched group to be involved in complexes with polarizable electrophilic halogenated or diatomic halogen molecules. Here, we report QSPR models of XB of particular relevance for an efficient screening of large sets of compounds. The basicity is described by pKBI2 , the decimal logarithm of the experimental 1 : 1 (B : I2 ) complexation constant K of organic compounds (B) with diiodine (I2 ) as a reference halogen-bond donor in alkanes at 298 K. Modeling involved ISIDA fragment descriptors, using SVM and MLR methods on a set of 598 organic compounds. Developed models were then challenged to make predictions for an external test set of 11 polyfunctional compounds for which unambiguous assignment of the measured effective complexation constant to specific groups out of the putative acceptor sites is not granted. At this stage, developed models were used to predict pKBI2 of all putative acceptor sites, followed by an estimation of the predicted effective complexation constant using the ChemEqui program. The best consensus models perform well both in cross-validation (root mean squared error RMSE=0.39-0.47 logKBI2 units) and external predictions (RMSE=0.49). The SVM models are implemented on our website (http://infochim.u-strasbg.fr/webserv/VSEngine.html) together with the estimation of their applicability domain and an automatic detection of potential halogen-bond acceptor atoms. PMID:27491792

  7. A Cascade Random Forests Algorithm for Predicting Protein-Protein Interaction Sites.

    Science.gov (United States)

    Wei, Zhi-Sen; Yang, Jing-Yu; Shen, Hong-Bin; Yu, Dong-Jun

    2015-10-01

    Protein-protein interactions exist ubiquitously and play important roles in the life cycles of living cells. The interaction sites (residues) are essential to understanding the underlying mechanisms of protein-protein interactions. Previous research has demonstrated that the accurate identification of protein-protein interaction sites (PPIs) is helpful for developing new therapeutic drugs because many drugs will interact directly with those residues. Because of its significant potential in biological research and drug development, the prediction of PPIs has become an important topic in computational biology. However, a severe data imbalance exists in the PPIs prediction problem, where the number of the majority class samples (non-interacting residues) is far larger than that of the minority class samples (interacting residues). Thus, we developed a novel cascade random forests algorithm (CRF) to address the serious data imbalance that exists in the PPIs prediction problem. The proposed CRF resolves the negative effect of data imbalance by connecting multiple random forests in a cascade-like manner, each of which is trained with a balanced training subset that includes all minority samples and a subset of majority samples using an effective ensemble protocol. Based on the proposed CRF, we implemented a new sequence-based PPIs predictor, called CRF-PPI, which takes the combined features of position-specific scoring matrices, averaged cumulative hydropathy, and predicted relative solvent accessibility as model inputs. Benchmark experiments on both the cross validation and independent validation datasets demonstrated that the proposed CRF-PPI outperformed the state-of-the-art sequence-based PPIs predictors. The source code for CRF-PPI and the benchmark datasets are available online at http://csbio.njust.edu.cn/bioinf/CRF-PPI for free academic use. PMID:26441427

  8. SuccinSite: a computational tool for the prediction of protein succinylation sites by exploiting the amino acid patterns and properties.

    Science.gov (United States)

    Hasan, Md Mehedi; Yang, Shiping; Zhou, Yuan; Mollah, Md Nurul Haque

    2016-03-23

    Lysine succinylation is an emerging protein post-translational modification, which plays an important role in regulating the cellular processes in both eukaryotic and prokaryotic cells. However, the succinylation modification site is particularly difficult to detect because the experimental technologies used are often time-consuming and costly. Thus, an accurate computational method for predicting succinylation sites may help researchers towards designing their experiments and to understand the molecular mechanism of succinylation. In this study, a novel computational tool termed SuccinSite has been developed to predict protein succinylation sites by incorporating three sequence encodings, i.e., k-spaced amino acid pairs, binary and amino acid index properties. Then, the random forest classifier was trained with these encodings to build the predictor. The SuccinSite predictor achieves an AUC score of 0.802 in the 5-fold cross-validation set and performs significantly better than existing predictors on a comprehensive independent test set. Furthermore, informative features and predominant rules (i.e. feature combinations) were extracted from the trained random forest model for an improved interpretation of the predictor. Finally, we also compiled a database covering 4411 experimentally verified succinylation proteins with 12 456 lysine succinylation sites. Taken together, these results suggest that SuccinSite would be a helpful computational resource for succinylation sites prediction. The web-server, datasets, source code and database are freely available at . PMID:26739209

  9. Feature selection for splice site prediction: A new method using EDA-based feature ranking

    Directory of Open Access Journals (Sweden)

    Rouzé Pierre

    2004-05-01

    Full Text Available Abstract Background The identification of relevant biological features in large and complex datasets is an important step towards gaining insight in the processes underlying the data. Other advantages of feature selection include the ability of the classification system to attain good or even better solutions using a restricted subset of features, and a faster classification. Thus, robust methods for fast feature selection are of key importance in extracting knowledge from complex biological data. Results In this paper we present a novel method for feature subset selection applied to splice site prediction, based on estimation of distribution algorithms, a more general framework of genetic algorithms. From the estimated distribution of the algorithm, a feature ranking is derived. Afterwards this ranking is used to iteratively discard features. We apply this technique to the problem of splice site prediction, and show how it can be used to gain insight into the underlying biological process of splicing. Conclusion We show that this technique proves to be more robust than the traditional use of estimation of distribution algorithms for feature selection: instead of returning a single best subset of features (as they normally do this method provides a dynamical view of the feature selection process, like the traditional sequential wrapper methods. However, the method is faster than the traditional techniques, and scales better to datasets described by a large number of features.

  10. Two-cavity gyroklystron with self-excited input cavity

    Energy Technology Data Exchange (ETDEWEB)

    Sokolov, E.V.; Zasypkin, E.V. [Inst. of Applied Physics, Novgorod (Russian Federation)

    1995-12-31

    A new type of gyro-oscillator-two cavity gyroklystron with self-excited input cavity (or, for simplicity, two-cavity gyrokylstron oscillator) is proposed. In this device, the autooscillations excited in the first cavity modulate electrons by energy, electrons are bunched in the drift space, and then the bunches excite powerful oscillations in the second (output) cavity. Since, as in gyroklystron, the optimal second cavity length L{sub 2} does not exceed 2-2.5 {lambda} ({lambda} is the operating wavelength), its Q-factor Q{sub 2} {approximately} (L{sub 2}/{lambda}){sup 2} should be essentially lower than cavity Q-factor of a traditional gyrotron. It allows to diminish the RF ohmic losses in the second cavity and to enhance the output power without the efficiency reduction. A simplest theory of such oscillator has been developed. Predicted by theory, the output power enhancement (in comparison with that for an ordinary gyrotron) has been demonstrated experimentally.

  11. Conserved functional motifs and homology modelling to predict hidden moonlighting functional sites

    Directory of Open Access Journals (Sweden)

    Helen R Irving

    2015-06-01

    Full Text Available Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here we review how hidden moonlighting functional centers which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico which in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  12. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites

    KAUST Repository

    Wong, Aloysius Tze

    2015-06-09

    Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  13. Prediction of P53 mutants (multiple sites transcriptional activity based on structural (2D&3D properties.

    Directory of Open Access Journals (Sweden)

    R Geetha Ramani

    Full Text Available Prediction of secondary site mutations that reinstate mutated p53 to normalcy has been the focus of intense research in the recent past owing to the fact that p53 mutants have been implicated in more than half of all human cancers and restoration of p53 causes tumor regression. However laboratory investigations are more often laborious and resource intensive but computational techniques could well surmount these drawbacks. In view of this, we formulated a novel approach utilizing computational techniques to predict the transcriptional activity of multiple site (one-site to five-site p53 mutants. The optimal MCC obtained by the proposed approach on prediction of one-site, two-site, three-site, four-site and five-site mutants were 0.775,0.341,0.784,0.916 and 0.655 respectively, the highest reported thus far in literature. We have also demonstrated that 2D and 3D features generate higher prediction accuracy of p53 activity and our findings revealed the optimal results for prediction of p53 status, reported till date. We believe detection of the secondary site mutations that suppress tumor growth may facilitate better understanding of the relationship between p53 structure and function and further knowledge on the molecular mechanisms and biological activity of p53, a targeted source for cancer therapy. We expect that our prediction methods and reported results may provide useful insights on p53 functional mechanisms and generate more avenues for utilizing computational techniques in biological data analysis.

  14. Integrated Model of DNA Sequence Numerical Representation and Artificial Neural Network for Human Donor and Acceptor Sites Prediction

    Directory of Open Access Journals (Sweden)

    Mohammed Abo-Zahhad

    2014-07-01

    Full Text Available Human Genome Project has led to a huge inflow of genomic data. After the completion of human genome sequencing, more and more effort is being put into identification of splicing sites of exons and introns (donor and acceptor sites. These invite bioinformatics to analysis the genome sequences and identify the location of exon and intron boundaries or in other words prediction of splicing sites. Prediction of splice sites in genic regions of DNA sequence is one of the most challenging aspects of gene structure recognition. Over the last two decades, artificial neural networks gradually became one of the essential tools in bioinformatics. In this paper artificial neural networks with different numerical mapping techniques have been employed for building integrated model for splice site prediction in genes. An artificial neural network is trained and then used to find splice sites in human genes. A comparison between different mapping methods using trained neural network in terms of their precision in prediction of donor and acceptor sites will be presented in this paper. Training and measuring performance of neural network are carried out using sequences of the human genome (GRch37/hg19- chr21. Simulation results indicate that using Electron-Ion Interaction Potential numerical mapping method with neural network yields to the best performance in prediction.

  15. Meteorological predictions for Mars 2020 Exploration Rover high-priority landing sites throug MRAMS Mesoscale Modeling

    Science.gov (United States)

    Pla-García, Jorge; Rafkin, Scot C. R.

    2015-04-01

    The Mars Regional Atmospheric Modeling System (MRAMS) is used to predict meteorological conditions that are likely to be encountered by the Mars 2020 Exploration Rover at several proposed landing sites during entry, descent, and landing (EDL). The meteorology during the EDL window at most of the sites is dynamic. The intense heating of the lower atmosphere drives intense thermals and mesoscale thermal circulations. Moderate mean winds, wind shear, turbulence, and vertical air currents associated with convection are present and potentially hazardous to EDL [1]. Nine areas with specific high-priority landing ellipses of the 2020 Rover, are investigated: NE Syrtis, Nili Fossae, Nili Fossae Carbonates, Jezero Crater Delta, Holden Crater, McLaughlin Crater, Southwest Melas Basin, Mawrth Vallis and East Margaritifer Chloride. MRAMS was applied to the landing site regions using nested grids with a spacing of 330 meters on the innermost grid that is centered over each landing site. MRAMS is ideally suited for this investigation; the model is explicitly designed to simulate Mars' atmospheric thermal circulations at the mesoscale and smaller with realistic, high-resolution surface properties [2, 3]. Horizontal wind speeds, both vertical profiles and vertical cross-sections wind speeds, are studied. For some landing sites simulations, two example configurations -including and not including Hellas basin in the mother domain- were generated, in order to study how the basin affects the innermost grids circulations. Afternoon circulations at all sites pose some risk entry, descent, and landing. Most of the atmospheric hazards are not evident in current observational data and general circulation model simulations and can only be ascertained through mesoscale modeling of the region. Decide where to go first and then design a system that can tolerate the environment would greatly minimize risk. References: [1] Rafkin, S. C. R., and T. I. Michaels (2003), J. Geophys. Res., 108(E12

  16. Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins.

    Directory of Open Access Journals (Sweden)

    Yang Jiang

    Full Text Available Most of pyruvoyl-dependent proteins observed in prokaryotes and eukaryotes are critical regulatory enzymes, which are primary targets of inhibitors for anti-cancer and anti-parasitic therapy. These proteins undergo an autocatalytic, intramolecular self-cleavage reaction in which a covalently bound pyruvoyl group is generated on a conserved serine residue. Traditional detections of the modified serine sites are performed by experimental approaches, which are often labor-intensive and time-consuming. In this study, we initiated in an attempt for the computational predictions of such serine sites with Feature Selection based on a Random Forest. Since only a small number of experimentally verified pyruvoyl-modified proteins are collected in the protein database at its current version, we only used a small dataset in this study. After removing proteins with sequence identities >60%, a non-redundant dataset was generated and was used, which contained only 46 proteins, with one pyruvoyl serine site for each protein. Several types of features were considered in our method including PSSM conservation scores, disorders, secondary structures, solvent accessibilities, amino acid factors and amino acid occurrence frequencies. As a result, a pretty good performance was achieved in our dataset. The best 100.00% accuracy and 1.0000 MCC value were obtained from the training dataset, and 93.75% accuracy and 0.8441 MCC value from the testing dataset. The optimal feature set contained 9 features. Analysis of the optimal feature set indicated the important roles of some specific features in determining the pyruvoyl-group-serine sites, which were consistent with several results of earlier experimental studies. These selected features may shed some light on the in-depth understanding of the mechanism of the post-translational self-maturation process, providing guidelines for experimental validation. Future work should be made as more pyruvoyl-modified proteins are

  17. PhosphoScan: A Probability-Based Method for Phosphorylation Site Prediction Using MS2/MS3 Pair Information

    OpenAIRE

    Wan, Yunhu; Cripps, Diane; Thomas, Stefani; Campbell, Patricia; Ambulos, Nicholas; CHEN Ting; Yang, Austin

    2008-01-01

    Phosphopeptide identification and phosphorylation site localization are crucial aspects of many biological studies. Furthermore, multiple phosphorylations of peptides make site localization even more difficult. We developed a probability-based method to unambiguously determine phosphorylation sites within phosphopeptides using MS2/3 pair information. A comparison test was performed with SEQUEST and MASCOT predictions using a spectral data set from a synthetic doubly phosphorylated peptide, an...

  18. Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands

    DEFF Research Database (Denmark)

    Vasanthanathan, P.; Hritz, Jozef; Taboureau, Olivier; Olsen, Lars; Jørgensen, F.S.; Vermeulen, N.P.E.; Oostenbrink, C.

    2009-01-01

    questions have been addressed: 1. Binding orientations and conformations were successfully predicted for various substrates. 2. A virtual screen was performed with satisfying enrichment rates. 3. A classification of individual compounds into active and inactive was performed. It was found that while docking...... can be used successfully to address the first two questions, it seems to be more difficult to perform the classification. Different scoring functions were included, and the well-characterized water molecule in the active site was included in various ways. Results are compared to experimental data and...... earlier classification data using machine learning methods. The possibilities and limitations of using structure-based drug design tools for cytochrome P450 1A2 come to light and are discussed....

  19. High density of tree-cavities and snags in tropical dry forest of western Mexico raises questions for a latitudinal gradient.

    Directory of Open Access Journals (Sweden)

    Leopoldo Vázquez

    Full Text Available It has been suggested that a latitudinal gradient exists of a low density of snags and high density of naturally-formed tree-cavities in tropical vs. temperate forests, though few cavities may have characteristics suitable for nesting by birds. We determined snag and cavity density, characteristics, and suitability for birds in a tropical dry forest biome of western Mexico, and evaluated whether our data fits the trend of snag and cavity density typically found in tropical moist and wet forests. We established five 0.25-ha transects to survey and measure tree-cavities and snags in each of three vegetation types of deciduous, semi-deciduous, and mono-dominant Piranhea mexicana forest, comprising a total of 3.75 ha. We found a high density of 77 cavities/ha, with 37 cavities suitable for birds/ha, where density, and characteristics of cavities varied significantly among vegetation types. Lowest abundance of cavities occurred in deciduous forest, and these were in smaller trees, at a lower height, and with a narrower entrance diameter. Only 8.6% of cavities were excavated by woodpeckers, and only 11% of cavities were occupied, mainly by arthropods, though 52% of all cavities were unsuitable for birds. We also found a high density of 56 snags/ha, with greatest density in deciduous forest (70 snags/ha, though these were of significantly smaller diameter, and snags of larger diameter were more likely to contain cavities. The Chamela-Cuixmala tropical dry forest had the highest density of snags recorded for any tropical or temperate forest, and while snag density was significantly correlated with mean snag dbh, neither latitude nor mean dbh predicted snag density in ten forest sites. The high spatial aggregation of snag and cavity resources in tropical dry forest may limit their availability, particularly for large-bodied cavity adopters, and highlights the importance of habitat heterogeneity in providing resources for primary and secondary cavity-nesters.

  20. High density of tree-cavities and snags in tropical dry forest of western Mexico raises questions for a latitudinal gradient.

    Science.gov (United States)

    Vázquez, Leopoldo; Renton, Katherine

    2015-01-01

    It has been suggested that a latitudinal gradient exists of a low density of snags and high density of naturally-formed tree-cavities in tropical vs. temperate forests, though few cavities may have characteristics suitable for nesting by birds. We determined snag and cavity density, characteristics, and suitability for birds in a tropical dry forest biome of western Mexico, and evaluated whether our data fits the trend of snag and cavity density typically found in tropical moist and wet forests. We established five 0.25-ha transects to survey and measure tree-cavities and snags in each of three vegetation types of deciduous, semi-deciduous, and mono-dominant Piranhea mexicana forest, comprising a total of 3.75 ha. We found a high density of 77 cavities/ha, with 37 cavities suitable for birds/ha, where density, and characteristics of cavities varied significantly among vegetation types. Lowest abundance of cavities occurred in deciduous forest, and these were in smaller trees, at a lower height, and with a narrower entrance diameter. Only 8.6% of cavities were excavated by woodpeckers, and only 11% of cavities were occupied, mainly by arthropods, though 52% of all cavities were unsuitable for birds. We also found a high density of 56 snags/ha, with greatest density in deciduous forest (70 snags/ha), though these were of significantly smaller diameter, and snags of larger diameter were more likely to contain cavities. The Chamela-Cuixmala tropical dry forest had the highest density of snags recorded for any tropical or temperate forest, and while snag density was significantly correlated with mean snag dbh, neither latitude nor mean dbh predicted snag density in ten forest sites. The high spatial aggregation of snag and cavity resources in tropical dry forest may limit their availability, particularly for large-bodied cavity adopters, and highlights the importance of habitat heterogeneity in providing resources for primary and secondary cavity-nesters. PMID:25615612

  1. Real-time prediction of earthquake ground motion: time evolutional prediction using data assimilation and real-time correction of site amplification factors

    Science.gov (United States)

    Hoshiba, M.

    2012-12-01

    In this presentation, I propose a new approach for real-time prediction of seismic ground motion which is applicable to Earthquake Early Waning (EEW). Many methods of EEW are based on a network method in which hypocenter and magnitude (source parameters) are quickly determined (that is, interpretation of current wavefield), and then the ground motions are predicted, and warnings are issued depending on the strength of the predicted ground motion. In this method, though we can predict ground motions using a few parameters (location of hypocenter, magnitude, site factors) at any points, it is necessary to determine the hypocenter and magnitude at first, and error of the source parameters leads directly to the error of the prediction. It is not easy to take the effects of rupture directivity and source extent into account, and it is impossible to fully reproduce the current wavefield from the interpreted source parameters. In general, wave motion is predictable when boundary condition and initial condition are given. Time evolutional prediction is a method based on this approach using the current wavefield as an initial condition, that is u(x, t+Δt)=H(u(x, t)), where u is the wave motion at location x at lapse time t, and H is the prediction operator. Future wave motion, u(x, t+Δt), is predicted from the distribution of the current wave motion u(x, t) using H. For H, finite difference technique or boundary integral equation method, such as Kirchhoff integral, is used. In the time evolutional prediction, determination of detailed distribution of current wave motion is a key, so that dense seismic observation network is required. Data assimilation is a technique to produce artificially denser network, which is widely used for numerical weather prediction and oceanography. Distribution of current wave motion is estimated from not only the current real observation of u(x, t), but also the prediction of one step before, H(u(x, t-Δt)). Combination of them produces denser

  2. MicroRNA transcription start site prediction with multi-objective feature selection.

    Science.gov (United States)

    Bhattacharyya, Malay; Feuerbach, Lars; Bhadra, Tapas; Lengauer, Thomas; Bandyopadhyay, Sanghamitra

    2012-01-01

    MicroRNAs (miRNAs) are non-coding, short (21-23nt) regulators of protein-coding genes that are generally transcribed first into primary miRNA (pri-miR), followed by the generation of precursor miRNA (pre-miR). This finally leads to the production of the mature miRNA. A large amount of information is available on the pre- and mature miRNAs. However, very little is known about the pri-miRs, due to a lack of knowledge about their transcription start sites (TSSs). Based on the genomic loci, miRNAs can be categorized into two types --intragenic (intra-miR) and intergenic (inter-miR). While it is already an established fact that intra-miRs are commonly transcribed in conjunction with their host genes, the transcription machinery of inter-miRs is poorly understood. Although it is assumed that miRNA promoters are similar in structure to gene promoters, since both are transcribed by RNA polymerase II (Pol II), computational validations exhibit poor performance of gene promoter prediction methods on miRNAs. In this paper, we concentrate on the problem of TSS prediction for miRNAs. The present study begins with the identification of positive and negative promoter samples from recently published data stemming from RNA-sequencing studies. From these samples of experimentally validated miRNA TSSs, a number of standard sequence features are extracted. Furthermore, to account for potential footprints related to promoter regulation by CpG dinucleotide targeted DNA methylation, a number of novel features are defined. We develop a support vector machine (SVM) with RBF kernel for the prediction of miRNA TSSs trained on human miRNA promoters. A novel feature reduction technique based on archived multi-objective simulated annealing (AMOSA) identifies the final set of features. The resulting model trained on miRNA promoters shows improved performance over the one trained on protein-coding gene promoters in terms of classification accuracy, sensitivity and specificity. Results are also

  3. Prediction of Water Binding to Protein Hydration Sites with a Discrete, Semiexplicit Solvent Model.

    Science.gov (United States)

    Setny, Piotr

    2015-12-01

    Buried water molecules are ubiquitous in protein structures and are found at the interface of most protein-ligand complexes. Determining their distribution and thermodynamic effect is a challenging yet important task, of great of practical value for the modeling of biomolecular structures and their interactions. In this study, we present a novel method aimed at the prediction of buried water molecules in protein structures and estimation of their binding free energies. It is based on a semiexplicit, discrete solvation model, which we previously introduced in the context of small molecule hydration. The method is applicable to all macromolecular structures described by a standard all-atom force field, and predicts complete solvent distribution within a single run with modest computational cost. We demonstrate that it indicates positions of buried hydration sites, including those filled by more than one water molecule, and accurately differentiates them from sterically accessible to water but void regions. The obtained estimates of water binding free energies are in fair agreement with reference results determined with the double decoupling method. PMID:26642995

  4. Cavity magnomechanics

    Science.gov (United States)

    Zou, Chang-Ling; Zhang, Xufeng; Jiang, Liang; Tang, Hong

    2016-05-01

    Recently, cavity magnonics has attracted much attention for potential applications of coherent information transduction and hybrid quantum devices. The magnon is a collective spin wave excitation in ferromagnetic material. It is magnetically tunability, with long coherence time and non-reciprocical interaction with electro-magnetic fields. We report the coherent coupling between magnon, microwave photon and phonon. First, we demonstrate strong coupling and ultrastrong coupling between the magnon in YIG sphere and microwave photon in three-dimensional cavity. Then, based on the hybridized magnon-photon modes, we observe the triply resonant magnon-mcirowave photon-phonon coupling, where the ultrahigh-Q mechanical vibration of YIG sphere is dispersively coupled with the magnon via magnetostrictive interaction. We observe interesting phenomena, including electromagnetically induced transparency/absorption and parametric amplification. In particular, benefit from the large tunability of the magnon, we demonstrate a tunable microwave amplifier with gain as high as 30 dB. The single crystal YIG also has excellent optical properties, and thus provide a unique platform bridging MHz, GHz and THz information carriers. Finally, we present the latest progress towards coherent magnon to optical photon conversion.

  5. Predicting DNA-binding sites of proteins from amino acid sequence

    Directory of Open Access Journals (Sweden)

    Wu Feihong

    2006-05-01

    Full Text Available Abstract Background Understanding the molecular details of protein-DNA interactions is critical for deciphering the mechanisms of gene regulation. We present a machine learning approach for the identification of amino acid residues involved in protein-DNA interactions. Results We start with a Naïve Bayes classifier trained to predict whether a given amino acid residue is a DNA-binding residue based on its identity and the identities of its sequence neighbors. The input to the classifier consists of the identities of the target residue and 4 sequence neighbors on each side of the target residue. The classifier is trained and evaluated (using leave-one-out cross-validation on a non-redundant set of 171 proteins. Our results indicate the feasibility of identifying interface residues based on local sequence information. The classifier achieves 71% overall accuracy with a correlation coefficient of 0.24, 35% specificity and 53% sensitivity in identifying interface residues as evaluated by leave-one-out cross-validation. We show that the performance of the classifier is improved by using sequence entropy of the target residue (the entropy of the corresponding column in multiple alignment obtained by aligning the target sequence with its sequence homologs as additional input. The classifier achieves 78% overall accuracy with a correlation coefficient of 0.28, 44% specificity and 41% sensitivity in identifying interface residues. Examination of the predictions in the context of 3-dimensional structures of proteins demonstrates the effectiveness of this method in identifying DNA-binding sites from sequence information. In 33% (56 out of 171 of the proteins, the classifier identifies the interaction sites by correctly recognizing at least half of the interface residues. In 87% (149 out of 171 of the proteins, the classifier correctly identifies at least 20% of the interface residues. This suggests the possibility of using such classifiers to identify

  6. Availability of tree cavities in a sal forest of Nepal

    OpenAIRE

    Bhusal P; Czeszczewik D; Walankiewicz W; Churski M; Baral R; Lamichhane BR; Mikusinski G

    2016-01-01

    Tree cavities are important structural elements of forest ecosystem that host numerous birds, mammals and other cavity-dependent organisms. Pattern of cavity distribution in temperate and boreal forests are relatively well studied, yet little is known about cavities in tropical and subtropical forests. We compared cavity availability in relation to tree condition (living tree and snag), tree species and DBH class between two different sites in a subtropical deciduous sal forest in Nepal: the ...

  7. Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis.

    Directory of Open Access Journals (Sweden)

    Lu-Lu Zheng

    Full Text Available Pyrrolidone carboxylic acid (PCA is formed during a common post-translational modification (PTM of extracellular and multi-pass membrane proteins. In this study, we developed a new predictor to predict the modification sites of PCA based on maximum relevance minimum redundancy (mRMR and incremental feature selection (IFS. We incorporated 727 features that belonged to 7 kinds of protein properties to predict the modification sites, including sequence conservation, residual disorder, amino acid factor, secondary structure and solvent accessibility, gain/loss of amino acid during evolution, propensity of amino acid to be conserved at protein-protein interface and protein surface, and deviation of side chain carbon atom number. Among these 727 features, 244 features were selected by mRMR and IFS as the optimized features for the prediction, with which the prediction model achieved a maximum of MCC of 0.7812. Feature analysis showed that all feature types contributed to the modification process. Further site-specific feature analysis showed that the features derived from PCA's surrounding sites contributed more to the determination of PCA sites than other sites. The detailed feature analysis in this paper might provide important clues for understanding the mechanism of the PCA formation and guide relevant experimental validations.

  8. Predicted impacts of future water level decline on monitoring wells using a ground-water model of the Hanford Site

    International Nuclear Information System (INIS)

    A ground-water flow model was used to predict water level decline in selected wells in the operating areas (100, 200, 300, and 400 Areas) and the 600 Area. To predict future water levels, the unconfined aquifer system was stimulated with the two-dimensional version of a ground-water model of the Hanford Site, which is based on the Coupled Fluid, Energy, and Solute Transport (CFEST) Code in conjunction with the Geographic Information Systems (GIS) software package. The model was developed using the assumption that artificial recharge to the unconfined aquifer system from Site operations was much greater than any natural recharge from precipitation or from the basalt aquifers below. However, artificial recharge is presently decreasing and projected to decrease even more in the future. Wells currently used for monitoring at the Hanford Site are beginning to go dry or are difficult to sample, and as the water table declines over the next 5 to 10 years, a larger number of wells is expected to be impacted. The water levels predicted by the ground-water model were compared with monitoring well completion intervals to determine which wells will become dry in the future. Predictions of wells that will go dry within the next 5 years have less uncertainty than predictions for wells that will become dry within 5 to 10 years. Each prediction is an estimate based on assumed future Hanford Site operating conditions and model assumptions

  9. Predictive modelling of a long-term diffusion experiment at the Grimsel test site, Switzerland

    International Nuclear Information System (INIS)

    Full text of publication follows: Matrix diffusion has been well documented and studied on small-scale in the laboratory, and metre-scale field tracer tests have also been successfully interpreted using transport models incorporating matrix diffusion. However, direct measurements of the diffusion properties of relevant fractured rocks at scales larger than the typical laboratory scale (cm) are rare. Also, laboratory-based studies of matrix diffusion have several significant problems and only a few cases have produced relevant information. These potential problems include: - Sample collection and preparation will lead to de-stressing of the rock inducing non-reversible changes to the geometry of matrix porosity. In general, the changes tend to cause overestimation of the rock diffusivity and rock porosity. - A complete and integrated approach to study matrix pore heterogeneity has not yet been undertaken. Recent studies have shown that matrix pore space is highly heterogeneous and small-scale laboratory experiments may not give a true reflection of rock retardation properties. The pore structure heterogeneities at cm scales from ongoing studies are taken into account in this predictive modelling attempt. The new Long Term Diffusion (LTD) experiment at the Grimsel Test Site (GTS) in Switzerland plans a series of in situ and laboratory experiments to verify the well established theoretical basis for matrix diffusion (see www.grimsel.com for more information). One of the planned experiments aims to verify current models of matrix diffusion via a full-scale in situ monopole experiment in the IAEA Radiation Controlled Zone. It is currently planned to circulate a radionuclide cocktail (containing 14C, 90Sr, 99Tc, 129I, 137Cs, 152Eu and 239Pu, plus chemical homologues) deep in undisturbed rock matrix. The duration of the experiment will be at least one year in the first phase of the project. After circulating the solution during the required experimental time, the

  10. Measured and predicted aerosol light scattering enhancement factors at the high alpine site Jungfraujoch

    Directory of Open Access Journals (Sweden)

    R. Fierz-Schmidhauser

    2009-09-01

    Full Text Available Ambient relative humidity (RH determines the water content of atmospheric aerosol particles and thus has an important influence on the amount of visible light scattered by particles. The RH dependence of the particle light scattering coefficient (σsp is therefore an important variable for climate forcing calculations. We used a humidification system for a nephelometer which allows for the measurement of σsp at a defined RH in the range of 20–95%. In this paper we present measurements of light scattering enhancement factors f(RH=σsp(RH/σsp(dry from a 1-month campaign (May 2008 at the high alpine site Jungfraujoch (3580 m a.s.l., Switzerland. At this site, f(RH=85% varied between 1.2 and 3.3. Measured f(RH agreed well with f(RH calculated with Mie theory using measurements of the size distribution, chemical composition and hygroscopic diameter growth factors as input. Good f(RH predictions at RH<85% were also obtained with a simplified model, which uses the Ångström exponent of σsp(dry as input. RH influences further intensive optical aerosol properties. The backscatter fraction decreased by about 30% from 0.128 to 0.089, and the single scattering albedo increased on average by 0.05 at 85% RH compared to dry conditions. These changes in σsp, backscatter fraction and single scattering albedo have a distinct impact on the radiative forcing of the Jungfraujoch aerosol.

  11. Measured and predicted aerosol light scattering enhancement factors at the high alpine site Jungfraujoch

    Directory of Open Access Journals (Sweden)

    R. Fierz-Schmidhauser

    2010-03-01

    Full Text Available Ambient relative humidity (RH determines the water content of atmospheric aerosol particles and thus has an important influence on the amount of visible light scattered by particles. The RH dependence of the particle light scattering coefficient (σsp is therefore an important variable for climate forcing calculations. We used a humidification system for a nephelometer which allows for the measurement of σsp at a defined RH in the range of 20–95%. In this paper we present measurements of light scattering enhancement factors f(RH=σsp(RH/σsp(dry from a 1-month campaign (May 2008 at the high alpine site Jungfraujoch (3580 m a.s.l., Switzerland. Measurements at the Jungfraujoch are representative for the lower free troposphere above Central Europe. For this aerosol type hardly any information about the f(RH is available so far. At this site, f(RH=85% varied between 1.2 and 3.3. Measured f(RH agreed well with f(RH calculated with Mie theory using measurements of the size distribution, chemical composition and hygroscopic diameter growth factors as input. Good f(RH predictions at RH<85% were also obtained with a simplified model, which uses the Ångström exponent of σsp(dry as input. RH influences further intensive optical aerosol properties. The backscatter fraction decreased by about 30% from 0.128 to 0.089, and the single scattering albedo increased on average by 0.05 at 85% RH compared to dry conditions. These changes in σsp, backscatter fraction and single scattering albedo have a distinct impact on the radiative forcing of the Jungfraujoch aerosol.

  12. Malignant melanoma of the oral cavity

    OpenAIRE

    M.S. Hashemi Pour

    2006-01-01

    Oral malignant melanoma is a rare disease. The common sites of its occurrence are the palate and gingiva with the maxillary arch being affected 80% of the time. Because of their presence at relatively obscure areas in the oral cavity, most of the malignant melanomas of the oral cavity are diagnosed at a late stage. These lesions are associated with poor prognosis. The dental clinician must therefore carefully examine the head, neck, and oral cavity, and any pigmented lesion that may ex...

  13. Analysis of the resonance frequency shift in cylindrical cavities containing a sphere and its prediction based on the Boltzmann-Ehrenfest principle

    DEFF Research Database (Denmark)

    Orozco Santillán, Arturo; Cutanda Henriquez, Vicente

    2008-01-01

    It is known that forces generated by high-level acoustic waves can compensate for the weight of small samples, which can be suspended in a fluid. To achieve this, a standing wave is created in a resonant enclosure, which can be open or closed to the external medium. This phenomenon, called Acoustic...... levitation, has numerous applications in containerless study and processing of materials. Although it is possible to levitate a sample for long periods of time, instabilities can appear under certain conditions. One of the causes of oscillational instabilities is the change of the resonance frequency...... of the cavity due to the presence of the levitated object. The Boltzmann-Ehrenfest principle has been used to obtain an analytical expression for the resonance frequency shift in a cylindrical cavity produced by a small sphere, with kR

  14. A new method for splice site prediction based on the sequence patterns of splicing signals and regulatory elements

    Institute of Scientific and Technical Information of China (English)

    SUN ZongXiao; SANG LingJie; JU LiNing; ZHU HuaiQiu

    2008-01-01

    It is of significance for splice site prediction to develop novel algorithms that combine the sequence patterns of regulatory elements such as enhancers and silencers with the patterns of splicing signals. In this paper, a statistical model of splicing signals was built based on the entropy density profile (EDP) method, weight array method (WAM) and κ test; moreover, the model of splicing regulatory elements was developed by an unsupervised self-learning method to detect motifs associated with regulatory elements. With two models incorporated, a multi-level support vector machine (SVM) system was de-vised to perform ab initio prediction for splice sites originating from DNA sequence in eukaryotic ge-home. Results of large scale tests on human genomic splice sites show that the new method achieves a comparative high performance in splice site prediction. The method is demonstrated to be with at least the same level of performance and usually better performance than the existing SpliceScan method based on modeling regulatory elements, and shown to have higher accuracies than the traditional methods with modeling splicing signals such as the GeneSplicer. In particular, the method has evident advantage over splice site prediction for the genes with lower GC content.

  15. Predicting transcription factor binding sites using local over-representation and comparative genomics

    Directory of Open Access Journals (Sweden)

    Touzet Hélène

    2006-08-01

    Full Text Available Abstract Background Identifying cis-regulatory elements is crucial to understanding gene expression, which highlights the importance of the computational detection of overrepresented transcription factor binding sites (TFBSs in coexpressed or coregulated genes. However, this is a challenging problem, especially when considering higher eukaryotic organisms. Results We have developed a method, named TFM-Explorer, that searches for locally overrepresented TFBSs in a set of coregulated genes, which are modeled by profiles provided by a database of position weight matrices. The novelty of the method is that it takes advantage of spatial conservation in the sequence and supports multiple species. The efficiency of the underlying algorithm and its robustness to noise allow weak regulatory signals to be detected in large heterogeneous data sets. Conclusion TFM-Explorer provides an efficient way to predict TFBS overrepresentation in related sequences. Promising results were obtained in a variety of examples in human, mouse, and rat genomes. The software is publicly available at http://bioinfo.lifl.fr/TFM-Explorer.

  16. Does radiation dose to the salivary glands and oral cavity predict patient-rated xerostomia and sticky saliva in head and neck cancer patients treated with curative radiotherapy?

    International Nuclear Information System (INIS)

    Background and Purpose: To investigate the association between the mean salivary gland and oral cavity dose, with patient-rated moderate and severe xerostomia and sticky saliva. Patients and methods: One hundred and fifty-seven patients treated with bilateral irradiation for head and neck cancer were included. The parotid and submandibular glands and the oral cavity were delineated on plannings-CT scans. At baseline and 6 and 12 months self-reported xerostomia and sticky saliva were assessed using the EORTC QLQ-H and N35 questionnaire. Results: At 6 months a significant association between the mean parotid (MDpar) and mean submandibular dose (MDsubm) and xerostomia was observed (OR-MDpar: 1.17; P=0.002 and OR-MDsubm: 1.08; P=0.02). Between MDpar and MDsubm, a significant interaction term was present. No significant association was found with the oral cavity dose. Xerostomia was reversible depending on MDpar and MDsubm. Considering Sticky saliva, a significant association was found at 6 and 12 months with MDsubm (OR: 1.03; Ppar and MDsubm influence the risk of xerostomia in irradiated patients at 6 months. This probability as a function of the mean parotid dose significantly depended on the mean dose in the submandibular glands. Sticky saliva mainly depends on MDsubm

  17. Cavity magnomechanics

    Science.gov (United States)

    Zhang, Xufeng; Zou, Changling; Jiang, Liang; Tang, Hong X.

    Mechanical oscillators have been recently widely utilized to couple with optical and microwave photons in a variety of hybrid quantum systems, but they all lack the tunability. The magnetostrictive force provides an alternative mechanism to allow phonon to couple with a different type of information carrier-magnon, the collective excitation of magnetization whose frequency can be tuned by a bias magnetic field. Here, we demonstrate an intriguing hybrid system that consists of a magnonic, a mechanical, and a microwave resonator. The magnon-phonon interaction results in hallmark coherent phenomena such as magnomechanically induced transparency/absorption and magnomechanical parametric amplification. The magnetic field dependence of magnon provides our system with unprecedented tunability. Moreover, the great flexibility of our system allows us to achieve triple resonance among magnon, phonon and photon, which drastically enhances the magnomechanical interaction. Our work demonstrates the fundamental principle of cavity magnetomechanics, opening up great opportunities in various applications, such as tunable microwave filter and amplifier, long-lifetime quantum memories, microwave-to-optics conversion.

  18. Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites

    Science.gov (United States)

    Vukovic, Sinisa; Brennan, Paul E.; Huggins, David J.

    2016-09-01

    The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.

  19. Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites.

    Science.gov (United States)

    Vukovic, Sinisa; Brennan, Paul E; Huggins, David J

    2016-09-01

    The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process. PMID:27367338

  20. A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engelbrecht, Jacob; Brunak, Søren;

    1997-01-01

    We have developed a new method for the identication of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequences. The method performs signicantly better than previous prediction schemes, and can easily be applied to genome...

  1. MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence

    OpenAIRE

    Passerini, A.; Lippi, M.; P. Frasconi

    2011-01-01

    MetalDetector identifies CYS and HIS involved in transition metal protein binding sites, starting from sequence alone. A major new feature of release 2.0 is the ability to predict which residues are jointly involved in the coordination of the same metal ion. The server is available at http://metaldetector.dsi.unifi.it/v2.0/.

  2. A novel method for protein-protein interaction site prediction using phylogenetic substitution models

    OpenAIRE

    La, David; Kihara, Daisuke

    2011-01-01

    Protein-protein binding events mediate many critical biological functions in the cell. Typically, functionally important sites in proteins can be well identified by considering sequence conservation. However, protein-protein interaction sites exhibit higher sequence variation than other functional regions, such as catalytic sites of enzymes. Consequently, the mutational behavior leading to weak sequence conservation poses significant challenges to the protein-protein interaction site predicti...

  3. Predicting pupylation sites in prokaryotic proteins using semi-supervised self-training support vector machine algorithm.

    Science.gov (United States)

    Ju, Zhe; Gu, Hong

    2016-08-15

    As one important post-translational modification of prokaryotic proteins, pupylation plays a key role in regulating various biological processes. The accurate identification of pupylation sites is crucial for understanding the underlying mechanisms of pupylation. Although several computational methods have been developed for the identification of pupylation sites, the prediction accuracy of them is still unsatisfactory. Here, a novel bioinformatics tool named IMP-PUP is proposed to improve the prediction of pupylation sites. IMP-PUP is constructed on the composition of k-spaced amino acid pairs and trained with a modified semi-supervised self-training support vector machine (SVM) algorithm. The proposed algorithm iteratively trains a series of support vector machine classifiers on both annotated and non-annotated pupylated proteins. Computational results show that IMP-PUP achieves the area under receiver operating characteristic curves of 0.91, 0.73, and 0.75 on our training set, Tung's testing set, and our testing set, respectively, which are better than those of the different error costs SVM algorithm and the original self-training SVM algorithm. Independent tests also show that IMP-PUP significantly outperforms three other existing pupylation site predictors: GPS-PUP, iPUP, and pbPUP. Therefore, IMP-PUP can be a useful tool for accurate prediction of pupylation sites. A MATLAB software package for IMP-PUP is available at https://juzhe1120.github.io/. PMID:27197054

  4. The Number of Pathologically Positive Lymph Nodes and Pathological Tumor Depth Predicts Prognosis in Patients With Poorly Differentiated Squamous Cell Carcinoma of the Oral Cavity

    International Nuclear Information System (INIS)

    Purpose: The objective of this retrospective study was twofold: (1) to investigate prognostic factors for clinical outcomes in patients with poorly differentiated oral cavity squamous cell carcinoma and (2) to identify specific prognostic subgroups that may help to guide treatment decisions. Methods and Materials: We examined 102 patients with poorly differentiated oral cavity squamous cell carcinoma. All patients were followed for at least 24 months after surgery or until death. The 5-year rates of local control, neck control, distant metastasis, disease-free, disease-specific, and overall survival served as main outcome measures. Results: The 5-year rates were as follows: local control (79%), neck control (64%), distant metastases (27%), disease-free survival (48%), disease-specific survival (52%), and overall survival (42%). Multivariable analysis showed that the number of pathologically positive nodes (≥4 vs. ≤3) was a significant predictor of neck control, distant metastasis, and disease-free, disease-specific, and overall survival rates. In addition, the presence of tumor depth of ≥11 mm (vs. <11 mm) was a significant predictor of distant metastasis, disease-specific survival, and overall survival rates. The combination of the two predictors (26.5%, 27/102) was independently associated with poorer neck control (p = 0.0319), distant metastasis (p < 0.0001), and disease-free (p < 0.0001), disease-specific (p < 0.0001), and overall survival (p < 0.0001) rates. Conclusions: In patients with poorly differentiated oral cavity squamous cell carcinoma, the presence of at least 4 pathologically positive lymph nodes and of a pathological tumor depth ≥11 mm identifies a subset of subjects with poor clinical outcomes. Patients carrying both risk factors are suitable candidates for the development of novel therapeutic approaches.

  5. Prediction of protein binding sites using physical and chemical descriptors and the support vector machine regression method

    Institute of Scientific and Technical Information of China (English)

    Sun Zhong-Hua; Jiang Fan

    2010-01-01

    In this paper a new continuous variable called core-ratio is defined to describe the probability for a residue to be in a binding site, thereby replacing the previous binary description of the interface residue using 0 and 1. So we can use the support vector machine regression method to fit the core-ratio value and predict the protein binding sites. We also design a new group of physical and chemical descriptors to characterize the binding sites. The new descriptors are more effective, with an averaging procedure used. Our test shows that much better prediction results can be obtained by the support vector regression (SVR) method than by the support vector classification method.

  6. Prediction of Protein-Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures.

    Science.gov (United States)

    Liu, Guang-Hui; Shen, Hong-Bin; Yu, Dong-Jun

    2016-04-01

    Accurately predicting protein-protein interaction sites (PPIs) is currently a hot topic because it has been demonstrated to be very useful for understanding disease mechanisms and designing drugs. Machine-learning-based computational approaches have been broadly utilized and demonstrated to be useful for PPI prediction. However, directly applying traditional machine learning algorithms, which often assume that samples in different classes are balanced, often leads to poor performance because of the severe class imbalance that exists in the PPI prediction problem. In this study, we propose a novel method for improving PPI prediction performance by relieving the severity of class imbalance using a data-cleaning procedure and reducing predicted false positives with a post-filtering procedure: First, a machine-learning-based data-cleaning procedure is applied to remove those marginal targets, which may potentially have a negative effect on training a model with a clear classification boundary, from the majority samples to relieve the severity of class imbalance in the original training dataset; then, a prediction model is trained on the cleaned dataset; finally, an effective post-filtering procedure is further used to reduce potential false positive predictions. Stringent cross-validation and independent validation tests on benchmark datasets demonstrated the efficacy of the proposed method, which exhibits highly competitive performance compared with existing state-of-the-art sequence-based PPIs predictors and should supplement existing PPI prediction methods. PMID:26563228

  7. Synchronization in an optomechanical cavity.

    Science.gov (United States)

    Shlomi, Keren; Yuvaraj, D; Baskin, Ilya; Suchoi, Oren; Winik, Roni; Buks, Eyal

    2015-03-01

    We study self-excited oscillations (SEO) in an on-fiber optomechanical cavity. Synchronization is observed when the optical power that is injected into the cavity is periodically modulated. A theoretical analysis based on the Fokker-Planck equation evaluates the expected phase space distribution (PSD) of the self-oscillating mechanical resonator. A tomography technique is employed for extracting PSD from the measured reflected optical power. Time-resolved state tomography measurements are performed to study phase diffusion and phase locking of the SEO. The detuning region inside which synchronization occurs is experimentally determined and the results are compared with the theoretical prediction. PMID:25871175

  8. Crab Cavity Development

    CERN Document Server

    Calaga, R; Burt, G; Ratti, A

    2015-01-01

    The HL-LHC upgrade will use deflecting (or crab) cavities to compensate for geometric luminosity loss at low β* and non-zero crossing angle. A local scheme with crab cavity pairs across the IPs is used employing compact crab cavities at 400 MHz. Design of the cavities, the cryomodules and the RF system is well advanced. The LHC crab cavities will be validated initially with proton beam in the SPS.

  9. Statistics of magnetoconductance in ballistic cavities

    International Nuclear Information System (INIS)

    The statistical properties of magnetoconductance in ballistic microcavities are investigated numerically. The distribution of conductance for chaotic cavities is found to follow the renormalized Porter-Thomas distribution suggested by random-matrix theory for the Gaussian ensemble while the conductance distribution of regular cavities in magnetic fields is nonuniversal and shifted towards the maximum value for a given number of open channels. The renormalized Porter-Thomas distribution implies a universal dependence of fluctuation amplitude on the mean conductance for chaotic cavities in the absence of time-reversal symmetry. The fluctuation amplitude for regular cavities is found to be larger than the saturation value of the fluctuation amplitude of chaotic cavities predicted by random-matrix theory. The change of the mean conductance as a function of the external magnetic field is consistent with semiclassical predictions

  10. Prediction of hydraulic conductivity and conductive fracture frequency by multivariate analysis of data from the Klipperaas study site

    International Nuclear Information System (INIS)

    The present study is a pilot study on the possibility to predict the hydraulic conductivity and conductive fracture frequency in boreholes in crystalline rock using multivariate data analysis. The data set used was very extensive and included data from core mapping, fracture fillings, geophysical logs, tubewave measurements and hydraulic tests from five deep boreholes at the Klipperaas study site. In the study, multivariate data analysis proved to be a powerful technique to systematically analyze an extensive data material and to study different correlation structures within the data set. With the models derived, about 80-90% of the variation of hydraulic conductivity of an input data set (consisting of 233 conductivity values in 1 m-sections) could be explained by utilizing 35-45% of the total information contained in the data set. The hydraulic conductivity of about 4500 one meter sections was predicted. The predicted transmissivity was generally in good agreement with measured transmissivity values in 20 m-sections. The predicted values in 1 m-sections provided a more detailed picture of the hydraulic conductivity distribution along the boreholes. The predicted conductivities were found to be very unevenly distributed. The highest values generally occur in borehole intervals with altered and deformed rock with increased fracture density. The predicted conductive fracture frequency (CFF) was also unevenly distributed. Fissure fillings, in particular iron minerals, are regarded as useful information in predicting the CFF. The predicted average CFF of the rock mass varied between 0.17 0.25 (conductive) fractures per meter. This corresponds to an average fracture spacing of about 4-6 m. The frequency of subhorizontal fractures in granite generally correlates best to the hydraulic conductivity. The study also showed that both the geological and hydrogeological properties of different rock types may vary considerably within a site. (25 figs., 30 tabs., 35 refs.)

  11. Predicting ambient aerosol thermal-optical reflectance (TOR) measurements from infrared spectra: extending the predictions to different years and different sites

    Science.gov (United States)

    Reggente, Matteo; Dillner, Ann M.; Takahama, Satoshi

    2016-02-01

    Organic carbon (OC) and elemental carbon (EC) are major components of atmospheric particulate matter (PM), which has been associated with increased morbidity and mortality, climate change, and reduced visibility. Typically OC and EC concentrations are measured using thermal-optical methods such as thermal-optical reflectance (TOR) from samples collected on quartz filters. In this work, we estimate TOR OC and EC using Fourier transform infrared (FT-IR) absorbance spectra from polytetrafluoroethylene (PTFE Teflon) filters using partial least square regression (PLSR) calibrated to TOR OC and EC measurements for a wide range of samples. The proposed method can be integrated with analysis of routinely collected PTFE filter samples that, in addition to OC and EC concentrations, can concurrently provide information regarding the functional group composition of the organic aerosol. We have used the FT-IR absorbance spectra and TOR OC and EC concentrations collected in the Interagency Monitoring of PROtected Visual Environments (IMPROVE) network (USA). We used 526 samples collected in 2011 at seven sites to calibrate the models, and more than 2000 samples collected in 2013 at 17 sites to test the models. Samples from six sites are present both in the calibration and test sets. The calibrations produce accurate predictions both for samples collected at the same six sites present in the calibration set (R2 = 0.97 and R2 = 0.95 for OC and EC respectively), and for samples from 9 of the 11 sites not included in the calibration set (R2 = 0.96 and R2 = 0.91 for OC and EC respectively). Samples collected at the other two sites require a different calibration model to achieve accurate predictions. We also propose a method to anticipate the prediction error; we calculate the squared Mahalanobis distance in the feature space (scores determined by PLSR) between new spectra and spectra in the calibration set. The squared Mahalanobis distance provides a crude method for assessing the

  12. Computational Characterization and Prediction of Estrogen Receptor Coactivator Binding Site Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Bennion, B J; Kulp, K S; Cosman, M; Lightstone, F C

    2005-08-26

    Many carcinogens have been shown to cause tissue specific tumors in animal models. The mechanism for this specificity has not been fully elucidated and is usually attributed to differences in organ metabolism. For heterocyclic amines, potent carcinogens that are formed in well-done meat, the ability to either bind to the estrogen receptor and activate or inhibit an estrogenic response will have a major impact on carcinogenicity. Here we describe our work with the human estrogen receptor alpha (hERa) and the mutagenic/carcinogenic heterocyclic amines PhIP, MeIQx, IFP, and the hydroxylated metabolite of PhIP, N2-hydroxy-PhIP. We found that PhIP, in contrast to the other heterocyclic amines, increased cell-proliferation in MCF-7 human breast cancer cells and activated the hERa receptor. We show mechanistic data supporting this activation both computationally by homology modeling and docking, and by NMR confirmation that PhIP binds with the ligand binding domain (LBD). This binding competes with estradiol (E2) in the native E2 binding cavity of the receptor. We also find that other heterocyclic amines and N2-hydroxy-PhIP inhibit ER activation presumably by binding into another cavity on the LBD. Moreover, molecular dynamics simulations of inhibitory heterocyclic amines reveal a disruption of the surface of the receptor protein involved with protein-protein signaling. We therefore propose that the mechanism for the tissue specific carcinogenicity seen in the rat breast tumors and the presumptive human breast cancer associated with the consumption of well-done meat maybe mediated by this receptor activation.

  13. Efficacy and Safety of a Lidocaine Gel in Patients from 6 Months up to 8 Years with Acute Painful Sites in the Oral Cavity: A Randomized, Placebo-Controlled, Double-Blind, Comparative Study.

    Science.gov (United States)

    Wolf, Dörte; Otto, Joachim

    2015-01-01

    Lidocaine is a well-accepted topical anaesthetic, also used in minors to treat painful conditions on mucosal membranes. This randomized, double-blind, placebo-controlled study (registered prospectively as EudraCT number 2011-005336-25) was designed to generate efficacy and safety data for a lidocaine gel (2%) in younger children with painful conditions in the oral cavity. One hundred sixty-one children were included in two subgroups: 4-8 years, average age 6.4 years, treated with verum or placebo and 6 months-verum. Pain reduction was measured from the time prior to administration to 10 or 30 minutes after. In addition, adverse events and local tolerability were evaluated. In group I, pain was reduced significantly after treatment with verum compared to placebo at both time points. In group II, the individual pain rating shift showed statistically significant lower pain after treatment. Only seven out of 161 patients reported an adverse event but none were classified as being related to the study medication. The local tolerability was assessed as very good in over 97% of cases. For painful sites in the oral cavity, a 2% lidocaine gel is a meaningful tool for short-term treatment in the paediatric population. PMID:26693229

  14. Predicting Nonlinear Site Response Using Spectral Acceleration Vs PGV/Vs30: A Case History Using the Volvi-Test Site

    Science.gov (United States)

    Guéguen, Philippe

    2015-12-01

    In this study, we analyze the efficiency of the ratio between particle velocity and shear wave velocity as a strain proxy for evaluating the nonlinear seismic response of sediments. The in situ stress-strain relationships are derived from accelerometric vertical array recordings at the TST site in Volvi (Thessaloniki, Greece). First, the shear wave velocity between two successive sensors was computed by seismic interferometry and strain was computed as the velocity ratio or the relative displacement between sensors. The shear-wave velocity profile and in situ shear modulus degradation curve with strain were compared with previous studies performed at the TST site. Finally, the stress-strain relationships were derived from data recorded at the surface by extending the strain proxy and stress values to the ratio between peak ground velocity and the Vs30 parameter used for site classification, i.e. without requiring the accelerometric vertical array. Our model captures the in situ nonlinear response of the site, without consideration of azimuth or distance of the earthquakes. In conclusion, the acceleration (stress) values, based on the accelerometric response spectra instead of peak ground acceleration compared with the deformation (strain) proxy, provide an effective model of the in situ nonlinear response, providing information that can be integrated into ground motion prediction equations.

  15. Exploration of normative and predictive expectations of bank web site features: a tale of two task scenarios

    OpenAIRE

    Waite, Kathryn Mary

    2009-01-01

    The aim of this thesis is to explore differences between consumer expectations of web site functionality in the context of online banking in terms of whether the task under consideration is information seeking or account access and whether the expectation is predictive or normative. The Internet has emerged as a new and distinct information source. Statistics show that the Internet is used extensively by companies for information provision and in general by consumers for inform...

  16. Predicting functional divergence in protein evolution by site-specific rate shifts

    Science.gov (United States)

    Gaucher, Eric A.; Gu, Xun; Miyamoto, Michael M.; Benner, Steven A.

    2002-01-01

    Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.

  17. Performance predictions for mechanical excavators in Yucca Mountain tuffs; Yucca Mountain Site Characterization Project

    Energy Technology Data Exchange (ETDEWEB)

    Ozdemir, L.; Gertsch, L.; Neil, D.; Friant, J. [Colorado School of Mines, Golden, CO (United States). Earth Mechanics Inst.

    1992-09-01

    The performances of several mechanical excavators are predicted for use in the tuffs at Yucca Mountain: Tunnel boring machines, the Mobile Miner, a roadheader, a blind shaft borer, a vertical wheel shaft boring machine, raise drills, and V-Moles. Work summarized is comprised of three parts: Initial prediction using existing rock physical property information; Measurement of additional rock physical properties; and Revision of the initial predictions using the enhanced database. The performance predictions are based on theoretical and empirical relationships between rock properties and the forces-experienced by rock cutters and bits during excavation. Machine backup systems and excavation design aspects, such as curves and grades, are considered in determining excavator utilization factors. Instanteous penetration rate, advance rate, and cutter costs are the fundamental performance indicators.

  18. High-current SRF cavity design

    Science.gov (United States)

    Meidlinger, D.; Grimm, T. L.; Hartung, W.

    2006-07-01

    For high current applications, it is desirable for the cavity shape to have a low longitudinal loss factor and to have a high beam-breakup threshold current. This paper briefly describes three different cavities designed for this purpose: a six-cell elliptical cavity for particles traveling at the speed of light, a two-cell elliptical cavity for subluminal particle speeds, and a single cell cavity which uses the TM012 mode for acceleration. SUPERFISH simulations predict the peak fields in both of the elliptical cavities will not exceed the TeSLA values by more than 10% but both will have 28.7% larger apertures. The elliptical designs assume the bunch frequency equals the accelerating mode frequency. The beam pipe radius is chosen so that the cutoff frequency is less than twice that of the accelerating mode. Hence all of the monopole and dipole higher-order modes (HOMs) that can be driven by the beam have low loaded Q values. This simplifies the problem of HOM damping. The TM012 cavity is predicted to have much higher peak fields than a π-mode elliptical cavity, but offers potential advantages from its simplified shape; it is essentially a circular waveguide with curved end plates. This basic shape results in easier fabrication and simplified tuning.

  19. High-current SRF cavity design

    International Nuclear Information System (INIS)

    For high current applications, it is desirable for the cavity shape to have a low longitudinal loss factor and to have a high beam-breakup threshold current. This paper briefly describes three different cavities designed for this purpose: a six-cell elliptical cavity for particles traveling at the speed of light, a two-cell elliptical cavity for subluminal particle speeds, and a single cell cavity which uses the TM012 mode for acceleration. SUPERFISH simulations predict the peak fields in both of the elliptical cavities will not exceed the TeSLA values by more than 10% but both will have 28.7% larger apertures. The elliptical designs assume the bunch frequency equals the accelerating mode frequency. The beam pipe radius is chosen so that the cutoff frequency is less than twice that of the accelerating mode. Hence all of the monopole and dipole higher-order modes (HOMs) that can be driven by the beam have low loaded Q values. This simplifies the problem of HOM damping. The TM012 cavity is predicted to have much higher peak fields than a π-mode elliptical cavity, but offers potential advantages from its simplified shape; it is essentially a circular waveguide with curved end plates. This basic shape results in easier fabrication and simplified tuning

  20. Exploiting structural and topological information to improve prediction of RNA-protein binding sites

    Directory of Open Access Journals (Sweden)

    Yuan Zheng

    2009-10-01

    Full Text Available Abstract Background RNA-protein interactions are important for a wide range of biological processes. Current computational methods to predict interacting residues in RNA-protein interfaces predominately rely on sequence data. It is, however, known that interface residue propensity is closely correlated with structural properties. In this paper we systematically study information obtained from sequences and structures and compare their contributions in this prediction problem. Particularly, different geometrical and network topological properties of protein structures are evaluated to improve interface residue prediction accuracy. Results We have quantified the impact of structural information on the prediction accuracy in comparison to the purely sequence based approach using two machine learning techniques: Naïve Bayes classifiers and Support Vector Machines. The highest AUC of 0.83 was achieved by a Support Vector Machine, exploiting PSI-BLAST profile, accessible surface area, betweenness-centrality and retention coefficient as input features. Taking into account that our results are based on a larger non-redundant data set, the prediction accuracy is considerably higher than reported in previous, comparable studies. A protein-RNA interface predictor (PRIP and the data set have been made available at http://www.qfab.org/PRIP. Conclusion Graph-theoretic properties of residue contact maps derived from protein structures such as betweenness-centrality can supplement sequence or structure features to improve the prediction accuracy for binding residues in RNA-protein interactions. While Support Vector Machines perform better on this task, Naïve Bayes classifiers also have been found to achieve good prediction accuracies but require much less training time and are an attractive choice for large scale predictions.

  1. Key role of water in proton transfer at the Q(o)-site of the cytochrome bc(1) complex predicted by atomistic molecular dynamics simulations

    DEFF Research Database (Denmark)

    Postila, P. A.; Kaszuba, K.; Sarewicz, M.;

    2013-01-01

    Cytochrome (cyt) bc(1) complex, which is an integral part of the respiratory chain and related energy-conserving systems, has two quinone-binding cavities (Q(o)- and Q(i)-sites), where the substrate participates in electron and proton transfer. Due to its complexity, many of the mechanistic details...... of the cyt bc(1) function have remained unclear especially regarding the substrate binding at the Q(o)-site. In this work we address this issue by performing extensive atomistic molecular dynamics simulations with the cyt bc(1) complex of Rhodobacter capsulatus embedded in a lipid bilayer. Based on...

  2. Evolution of neural networks for the prediction of hydraulic conductivity as a function of borehole geophysical logs: Shobasama site, Japan.

    Energy Technology Data Exchange (ETDEWEB)

    Reeves, Paul C.; McKenna, Sean Andrew

    2004-06-01

    This report describes the methodology and results of a project to develop a neural network for the prediction of the measured hydraulic conductivity or transmissivity in a series of boreholes at the Tono, Japan study site. Geophysical measurements were used as the input to EL feed-forward neural network. A simple genetic algorithm was used to evolve the architecture and parameters of the neural network in conjunction with an optimal subset of geophysical measurements for the prediction of hydraulic conductivity. The first attempt was focused on the estimation of the class of the hydraulic conductivity, high, medium or low, from the geophysical logs. This estimation was done while using the genetic algorithm to simultaneously determine which geophysical logs were the most important and optimizing the architecture of the neural network. Initial results showed that certain geophysical logs provided more information than others- most notably the 'short-normal', micro-resistivity, porosity and sonic logs provided the most information on hydraulic conductivity. The neural network produced excellent training results with accuracy of 90 percent or greater, but was unable to produce accurate predictions of the hydraulic conductivity class. The second attempt at prediction was done using a new methodology and a modified data set. The new methodology builds on the results of the first attempts at prediction by limiting the choices of geophysical logs to only those that provide significant information. Additionally, this second attempt uses a modified data set and predicts transmissivity instead of hydraulic conductivity. Results of these simulations indicate that the most informative geophysical measurements for the prediction of transmissivity are depth and sonic log. The long normal resistivity and self potential borehole logs are moderately informative. In addition, it was found that porosity and crack counts (clear, open, or hairline) do not inform predictions

  3. Prediction of functional sites based on the fuzzy oil drop model.

    Directory of Open Access Journals (Sweden)

    Michał Bryliński

    2007-05-01

    Full Text Available A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localization of active sites in proteins. This paper describes a computational model that can be used to identify potential areas that are able to interact with other molecules (ligands, substrates, inhibitors, etc.. The model for active site recognition is based on the analysis of hydrophobicity distribution in protein molecules. It is shown, based on the analyses of proteins with known biological activity and of proteins of unknown function, that the region of significantly irregular hydrophobicity distribution in proteins appears to be function related.

  4. Predictive and prognostic values of transient ischemic dilatation of left ventricular cavity for coronary artery disease and impact of various managements on clinical outcome using technetium-99m sestamibi gated myocardial perfusion imaging

    International Nuclear Information System (INIS)

    Transient ischemic dilatation (TID) of left ventricular (LV) cavity during stress gated myocardial perfusion imaging (GMPI) is known as a predictor of severe coronary artery disease (CAD) and signifies worse prognosis. To assess predictive and prognostic value of TID of LV cavity using GMPI and clinical outcome in patients treated conservatively or with revascularization. 189 patients out of 2689 were recruited (M:F 127/62, mean age 56±9 years) whose same-day stress GMPI revealed TID ratio (>1.22) with no (sum stress score, SSS 2). Coronary angiography (CA) was performed within 3 months in 125/189 cases who were followed for mean period of 18±4 months for fatal or non-fatal myocardial infraction (MI). CA was positive in 121/125 patients with TID for significant CAD (left anterior descending (LAD) =11, multi vessel disease =110 patients, positive predictive value 95%) and negative for obstructive disease in 4/125 (false-positive cases). 41/121 underwent revascularization within 2 months of CA (Intervention group), and remaining 80/121 were managed conservatively (Non-Intervention group). Overall event rate was 20% (4/16%: fatal/non-fatal MIs). Kaplan-Meier survival curves revealed event-free survival in Intervention and Non-Intervention groups for fatal MI 98/96% (P=0.758), and for non-fatal MI, it was 97/58%, respectively (P=0.042). We conclude that TID is a reliable predictor of multi vessel CAD and is associated with high incidence of non-fatal MIs than fatal MIs. Revascularization (percutaneous coronary intervention (PCI)/coronary artery bypass graft (CABG)) rather than medical treatment should be considered in patients with TID for better clinical outcome. (author)

  5. Superconducting crab cavity

    International Nuclear Information System (INIS)

    Complete overlapping of the electron and positron bunches at colliding point can be attained by using the strong time-depending electromagnetic RF field in the superconducting crab cavity. Commissioning of the crab cavities started in February 2007 at KEKB. Effective head-on collision of electron and positron has been achieved successfully. After introduction of crab crossing and crab cavity, the structure and the fabrication of the KEKB superconducting crab cavity are discussed. (author)

  6. RF Cavity Design

    CERN Document Server

    Jensen, E

    2014-01-01

    After a short overview of a general approach to cavity design, we sketch the derivation of waveguide modes from plane waves and of cavity fields from waveguide modes. The characteristic parameters describing cavities and their performance are defined and explained. An equivalent circuit is introduced and extended to explain beam loading and higher order modes. Finally travelling- and standing-wave multi-gap cavities are introduced using the Brillouin diagram.

  7. Predicting success of oligomerized pool engineering (OPEN for zinc finger target site sequences

    Directory of Open Access Journals (Sweden)

    Goodwin Mathew J

    2010-11-01

    Full Text Available Abstract Background Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligomerized Pool ENgineering (OPEN is a recently developed method for engineering C2H2 zinc finger proteins (ZFPs designed to bind specific DNA sequences with high affinity and specificity in vivo. Because generation of ZFPs using OPEN requires considerable effort, a computational method for identifying the sites in any given gene that are most likely to be successfully targeted by this method is desirable. Results Analysis of the base composition of experimentally validated ZFP target sites identified important constraints on the DNA sequence space that can be effectively targeted using OPEN. Using alternate encodings to represent ZFP target sites, we implemented Naïve Bayes and Support Vector Machine classifiers capable of distinguishing "active" targets, i.e., ZFP binding sites that can be targeted with a high rate of success, from those that are "inactive" or poor targets for ZFPs generated using current OPEN technologies. When evaluated using leave-one-out cross-validation on a dataset of 135 experimentally validated ZFP target sites, the best Naïve Bayes classifier, designated ZiFOpT, achieved overall accuracy of 87% and specificity+ of 90%, with an ROC AUC of 0.89. When challenged with a completely independent test set of 140 newly validated ZFP target sites, ZiFOpT performance was comparable in terms of overall accuracy (88% and specificity+ (92%, but with reduced ROC AUC (0.77. Users can rank potentially active ZFP target sites using a confidence score derived from the posterior probability returned by ZiFOpT. Conclusion ZiFOpT, a machine learning classifier trained to identify DNA sequences amenable for targeting by OPEN-generated zinc finger arrays, can guide users to target sites that are most likely to function

  8. A sequence-based dynamic ensemble learning system for protein ligand-binding site prediction

    KAUST Repository

    Chen, Peng

    2015-12-03

    Background: Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands is important for drug design and protein docking studies. Most of the successful protein-ligand binding predictions were based on known structures. However, structural information is not largely available in practice due to the huge gap between the number of known protein sequences and that of experimentally solved structures

  9. Constructing query-driven dynamic machine learning model with application to protein-ligand binding sites prediction.

    Science.gov (United States)

    Yu, Dong-Jun; Hu, Jun; Li, Qian-Mu; Tang, Zhen-Min; Yang, Jing-Yu; Shen, Hong-Bin

    2015-01-01

    We are facing an era with annotated biological data rapidly and continuously generated. How to effectively incorporate new annotated data into the learning step is crucial for enhancing the performance of a bioinformatics prediction model. Although machine-learning-based methods have been extensively used for dealing with various biological problems, existing approaches usually train static prediction models based on fixed training datasets. The static approaches are found having several disadvantages such as low scalability and impractical when training dataset is huge. In view of this, we propose a dynamic learning framework for constructing query-driven prediction models. The key difference between the proposed framework and the existing approaches is that the training set for the machine learning algorithm of the proposed framework is dynamically generated according to the query input, as opposed to training a general model regardless of queries in traditional static methods. Accordingly, a query-driven predictor based on the smaller set of data specifically selected from the entire annotated base dataset will be applied on the query. The new way for constructing the dynamic model enables us capable of updating the annotated base dataset flexibly and using the most relevant core subset as the training set makes the constructed model having better generalization ability on the query, showing "part could be better than all" phenomenon. According to the new framework, we have implemented a dynamic protein-ligand binding sites predictor called OSML (On-site model for ligand binding sites prediction). Computer experiments on 10 different ligand types of three hierarchically organized levels show that OSML outperforms most existing predictors. The results indicate that the current dynamic framework is a promising future direction for bridging the gap between the rapidly accumulated annotated biological data and the effective machine-learning-based predictors. OSML

  10. Social Networking Site Use Predicts Changes in Young Adults' Psychological Adjustment

    Science.gov (United States)

    Szwedo, David E.; Mikami, Amori Yee; Allen, Joseph P.

    2012-01-01

    This study examined youths' friendships and posted pictures on social networking sites as predictors of changes in their adjustment over time. Observational, self-report, and peer-report data were obtained from a community sample of 89 young adults interviewed at age 21 and again at age 22. Findings were consistent with a leveling effect for…

  11. Does ecosystem sensitivity to precipitation at the site-level conform to regional-scale predictions?.

    Science.gov (United States)

    Wilcox, Kevin R; Blair, John M; Smith, Melinda D; Knapp, Alan K

    2016-03-01

    Central to understanding global C cycle dynamics is the functional relationship between precipitation and net primary production (NPP). At large spatial (regional) scales, the responsiveness of aboveground NPP (ANPP) to interannual variation in annual precipitation (AP; ANPPsens) is inversely related to site-level ANPP, coinciding with turnover of plant communities along precipitation gradients. Within ecosystems experiencing chronic alterations in water availability, plant community change will also occur with unknown consequences for ANPPsens. To examine the role plant community shifts may play in determining alterations in site-level ANPPPsens, we experimentally increased precipitation by approximately 35% for two decades in a native Central U.S. grassland. Consistent with regional models, ANPPsens decreased initially as water availability and ANPP increased. However, ANPPsens shifted back to ambient levels when mesic species increased in abundance in the plant community. Similarly, in grassland sites with distinct mesic and xeric plant communities and corresponding 50% differences in ANPP, ANPPsens did not differ over almost three decades. We conclude that responses in ANPPsens to chronic alterations in water availability within an ecosystem may not conform to regional AP-ANPP patterns, despite expected changes in ANPP and plant communities. The result is unanticipated functional resistance to climate change at the site scale. PMID:27197383

  12. Casimir forces of metallic microstructures into cavities

    Science.gov (United States)

    Kenanakis, George; Soukoulis, Costas M.; Economou, Eleftherios N.

    2015-08-01

    A theoretical estimate of the Casimir force of a metallic structure embedded into a cubic cavity is proposed. We demonstrate that by calculating the eigenmodes of the system we can determine the Casimir force, which can be either attractive or repulsive, by simply changing the geometry of the structures relative to the walls of the cavity. In this analysis, several cases of structures are taken into account, from rectangular slabs to chiral "omega" particles, and the predicted data are consistent with recent literature. We demonstrate that the sidewalls of the studied cavity contribute decisively to the repulsive Casimir force between the system and the nearby top surface of the cavity. Finally, we provide evidence that the medium embedded into the studied cavity (and especially its permittivity) can change the intensity of the Casimir force, while its repulsive nature, once established (owing to favorable geometrical features), remains quite robust.

  13. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engelbrecht, Jacob; Brunak, Søren;

    1997-01-01

    We have developed a new method for the identification of signal peptides and their cleavage based on neural networks trained on separate sets of prokaryotic and eukaryotic sequence. The method performs significantly better than previous prediction schemes and can easily be applied on genome...

  14. Paper Highlight: Biomarker Identified for Predicting Early Prostate Cancer Aggressiveness — Site

    Science.gov (United States)

    A team led by Cory Abate-Shen, Michael Shen, and Andrea Califano at Columbia University found that measuring the expression levels of three genes associated with aging can be used to predict the aggressiveness of seemingly low-risk prostate cancer.

  15. Cavity pressure history of contained nuclear explosions

    International Nuclear Information System (INIS)

    Knowledge of pressure in cavities created by contained nuclear explosions is useful for estimating the possibility of venting radioactive debris to the atmosphere. Measurements of cavity pressure, or temperature, would be helpful in evaluating the correctness of present code predictions of underground explosions. In instrumenting and interpreting such measurements it is necessary to have good theoretical estimates of cavity pressures. In this paper cavity pressure is estimated at the time when cavity growth is complete. Its subsequent decrease due to heat loss from the cavity to the surrounding media is also predicted. The starting pressure (the pressure at the end of cavity growth) is obtained by adiabatic expansion to the final cavity size of the vaporized rock gas sphere created by the explosion. Estimates of cavity size can be obtained by stress propagation computer codes, such as SOC and TENSOR. However, such estimates require considerable time and effort. In this paper, cavity size is estimated using a scheme involving simple hand calculations. The prediction is complicated by uncertainties in the knowledge of silica water system chemistry and a lack of information concerning possible blowoff of wall material during cavity growth. If wall material blows off, it can significantly change the water content in the cavity, compared to the water content in the ambient media. After cavity growth is complete, the pressure will change because of heat loss to the surrounding media. Heat transfer by convection, radiation and conduction is considered, and its effect on the pressure is calculated. Analysis of cavity heat transfer is made difficult by the complex nature of processes which occur at the wall where melting, vaporization and condensation of the gaseous rock can all occur. Furthermore, the melted wall material could be removed by flowing or dripping to the cavity floor. It could also be removed by expansion of the steam contained in the melt (blowoff) and by

  16. Tuberculosis involving the oral cavity

    OpenAIRE

    Ferguson, Kathleen A.; McCormack, David G

    1993-01-01

    The oral cavity is a rare site for extrapulmonary tuberculosis. A case is reported of a young woman with dysphagia and oral ulceration. The original mucosal biopsy was negative on smear for acid-fast bacilli, and the patient subsequently developed pulmonary symptoms. A diagnosis of Mycobacterium tuberculosis was ultimately made on open lung biopsy. Complete resolution of both mouth lesion and chest involvement occurred with standard antituberculous therapy.

  17. SVM-based prediction of propeptide cleavage sites in spider toxins identifies toxin innovation in an Australian tarantula.

    Directory of Open Access Journals (Sweden)

    Emily S W Wong

    Full Text Available Spider neurotoxins are commonly used as pharmacological tools and are a popular source of novel compounds with therapeutic and agrochemical potential. Since venom peptides are inherently toxic, the host spider must employ strategies to avoid adverse effects prior to venom use. It is partly for this reason that most spider toxins encode a protective proregion that upon enzymatic cleavage is excised from the mature peptide. In order to identify the mature toxin sequence directly from toxin transcripts, without resorting to protein sequencing, the propeptide cleavage site in the toxin precursor must be predicted bioinformatically. We evaluated different machine learning strategies (support vector machines, hidden Markov model and decision tree and developed an algorithm (SpiderP for prediction of propeptide cleavage sites in spider toxins. Our strategy uses a support vector machine (SVM framework that combines both local and global sequence information. Our method is superior or comparable to current tools for prediction of propeptide sequences in spider toxins. Evaluation of the SVM method on an independent test set of known toxin sequences yielded 96% sensitivity and 100% specificity. Furthermore, we sequenced five novel peptides (not used to train the final predictor from the venom of the Australian tarantula Selenotypus plumipes to test the accuracy of the predictor and found 80% sensitivity and 99.6% 8-mer specificity. Finally, we used the predictor together with homology information to predict and characterize seven groups of novel toxins from the deeply sequenced venom gland transcriptome of S. plumipes, which revealed structural complexity and innovations in the evolution of the toxins. The precursor prediction tool (SpiderP is freely available on ArachnoServer (http://www.arachnoserver.org/spiderP.html, a web portal to a comprehensive relational database of spider toxins. All training data, test data, and scripts used are available from

  18. SVM-based prediction of propeptide cleavage sites in spider toxins identifies toxin innovation in an Australian tarantula.

    Science.gov (United States)

    Wong, Emily S W; Hardy, Margaret C; Wood, David; Bailey, Timothy; King, Glenn F

    2013-01-01

    Spider neurotoxins are commonly used as pharmacological tools and are a popular source of novel compounds with therapeutic and agrochemical potential. Since venom peptides are inherently toxic, the host spider must employ strategies to avoid adverse effects prior to venom use. It is partly for this reason that most spider toxins encode a protective proregion that upon enzymatic cleavage is excised from the mature peptide. In order to identify the mature toxin sequence directly from toxin transcripts, without resorting to protein sequencing, the propeptide cleavage site in the toxin precursor must be predicted bioinformatically. We evaluated different machine learning strategies (support vector machines, hidden Markov model and decision tree) and developed an algorithm (SpiderP) for prediction of propeptide cleavage sites in spider toxins. Our strategy uses a support vector machine (SVM) framework that combines both local and global sequence information. Our method is superior or comparable to current tools for prediction of propeptide sequences in spider toxins. Evaluation of the SVM method on an independent test set of known toxin sequences yielded 96% sensitivity and 100% specificity. Furthermore, we sequenced five novel peptides (not used to train the final predictor) from the venom of the Australian tarantula Selenotypus plumipes to test the accuracy of the predictor and found 80% sensitivity and 99.6% 8-mer specificity. Finally, we used the predictor together with homology information to predict and characterize seven groups of novel toxins from the deeply sequenced venom gland transcriptome of S. plumipes, which revealed structural complexity and innovations in the evolution of the toxins. The precursor prediction tool (SpiderP) is freely available on ArachnoServer (http://www.arachnoserver.org/spiderP.html), a web portal to a comprehensive relational database of spider toxins. All training data, test data, and scripts used are available from the Spider

  19. Does the site of platelet sequestration predict the response to splenectomy in adult patients with immune thrombocytopenic purpura?

    Science.gov (United States)

    Navez, Julie; Hubert, Catherine; Gigot, Jean-François; Navez, Benoit; Lambert, Catherine; Jamar, François; Danse, Etienne; Lannoy, Valérie; Jabbour, Nicolas

    2015-01-01

    Splenectomy is the only potentially curative treatment for chronic immune thrombocytopenic purpura (ITP) in adults. However, one-third of the patients relapse without predictive factors identified. We evaluate the predictive value of the site of platelet sequestration on the response to splenectomy in patients with ITP. Eighty-two consecutive patients with ITP treated by splenectomy between 1992 and 2013 were retrospectively reviewed. Platelet sequestration site was studied by (111)Indium-oxinate-labeled platelets in 93% of patients. Response to splenectomy was defined at last follow-up as: complete response (CR) for platelet count (PC) ≥100 × 10(9)/L, response (R) for PC≥30 × 10(9)/L and 100 versus <=100, 95% CI [0.025-0.493], p = 0.004) were significant predictors of recurrence-free survival in multivariate analysis. Response to splenectomy was independent of the site of platelet sequestration in patients with ITP. Pre-operative platelet sequestration study in these patients cannot be recommended. PMID:25275667

  20. Predictability of PV power grid performance on insular sites without weather stations: use of artificial neural networks

    CERN Document Server

    Voyant, Cyril; Paoli, Christophe; Nivet, Marie Laure; Poggi, Philippe; Haurant, P; 10.4229/24thEUPVSEC2009-5BV.2.35

    2010-01-01

    The official meteorological network is poor on the island of Corsica: only three sites being about 50 km apart are equipped with pyranometers which enable measurements by hourly and daily step. These sites are Ajaccio (41\\degree 55'N and 8\\degree 48'E, seaside), Bastia (42\\degree 33'N, 9\\degree 29'E, seaside) and Corte (42\\degree 30'N, 9\\degree 15'E average altitude of 486 meters). This lack of weather station makes difficult the predictability of PV power grid performance. This work intends to study a methodology which can predict global solar irradiation using data available from another location for daily and hourly horizon. In order to achieve this prediction, we have used Artificial Neural Network which is a popular artificial intelligence technique in the forecasting domain. A simulator has been obtained using data available for the station of Ajaccio that is the only station for which we have a lot of data: 16 years from 1972 to 1987. Then we have tested the efficiency of this simulator in two places w...

  1. Skin sites to predict deep-body temperature while wearing firefighters' personal protective equipment during periodical changes in air temperature.

    Science.gov (United States)

    Kim, Siyeon; Lee, Joo-Young

    2016-04-01

    The aim of this study was to investigate stable and valid measurement sites of skin temperatures as a non-invasive variable to predict deep-body temperature while wearing firefighters' personal protective equipment (PPE) during air temperature changes. Eight male firefighters participated in an experiment which consisted of 60-min exercise and 10-min recovery while wearing PPE without self-contained breathing apparatus (7.75 kg in total PPE mass). Air temperature was periodically fluctuated from 29.5 to 35.5 °C with an amplitude of 6 °C. Rectal temperature was chosen as a deep-body temperature, and 12 skin temperatures were recorded. The results showed that the forehead and chest were identified as the most valid sites to predict rectal temperature (R(2) = 0.826 and 0.824, respectively) in an environment with periodically fluctuated air temperatures. This study suggests that particular skin temperatures are valid as a non-invasive variable when predicting rectal temperature of an individual wearing PPE in changing ambient temperatures. Practitioner Summary: This study should offer assistance for developing a more reliable indirect indicating system of individual heat strain for firefighters in real time, which can be used practically as a precaution of firefighters' heat-related illness and utilised along with physiological monitoring. PMID:26214379

  2. Predicting the macroseismic intensity from early radiated P wave energy for on-site earthquake early warning in Italy

    Science.gov (United States)

    Brondi, P.; Picozzi, M.; Emolo, A.; Zollo, A.; Mucciarelli, M.

    2015-10-01

    Earthquake Early Warning Systems (EEWS) are potentially effective tools for risk mitigation in active seismic regions. The present study explores the possibility of predicting the macroseismic intensity within EEW timeframes using the squared velocity integral (IV2) measured on the early P wave signals, a proxy for the P wave radiated energy of earthquakes. This study shows that IV2 correlates better than the peak displacement measured on P waves with both the peak ground velocity and the Housner Intensity, with the latter being recognized by engineers as a reliable proxy for damage assessment. Therefore, using the strong motion recordings of the Italian Accelerometric Archive, a novel relationship between the parameter IV2 and the macroseismic intensity (IM) has been derived. The validity of this relationship has been assessed using the strong motion recordings of the Istituto Nazionale di Geofisica e Vulcanologia Strong Motion Data and Osservatorio Sismico delle Strutture databases, as well as, in the case of the MW 6, 29 May 2012 Emilia earthquake (Italy), comparing the predicted intensities with the ones observed after a macroseismic survey. Our results indicate that P wave IV2 can become a key parameter for the design of on-site EEWS, capable of proving real-time predictions of the IM at target sites.

  3. Beam cavity interaction

    CERN Document Server

    Gamp, A

    2011-01-01

    We begin by giving a description of the rf generator-cavity-beam coupled system in terms of basic quantities. Taking beam loading and cavity detuning into account, expressions for the cavity impedance as seen by the generator and as seen by the beam are derived. Subsequently methods of beam-loading compensation by cavity detuning, rf feedback, and feed-forward are described. Examples of digital rf phase and amplitude control for the special case of superconducting cavities are also given. Finally, a dedicated phase loop for damping synchrotron oscillations is discussed.

  4. The Predicting Model of E-commerce Site Based on the Ideas of Curve Fitting

    Science.gov (United States)

    Tao, Zhang; Li, Zhang; Dingjun, Chen

    On the basis of the idea of the second multiplication curve fitting, the number and scale of Chinese E-commerce site is analyzed. A preventing increase model is introduced in this paper, and the model parameters are solved by the software of Matlab. The validity of the preventing increase model is confirmed though the numerical experiment. The experimental results show that the precision of preventing increase model is ideal.

  5. Prediction of functional sites based on the fuzzy oil drop model.

    OpenAIRE

    Michał Bryliński; Katarzyna Prymula; Wiktor Jurkowski; Marek Kochańczyk; Ewa Stawowczyk; Leszek Konieczny; Irena Roterman

    2007-01-01

    A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localiza...

  6. Prediction of Functional Sites Based on the Fuzzy Oil Drop Model

    OpenAIRE

    Bryliński, Michał; Prymula, Katarzyna; Jurkowski, Wiktor; Kochańczyk, Marek; Stawowczyk, Ewa; Konieczny, Leszek; Roterman, Irena

    2007-01-01

    A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localiza...

  7. Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA

    OpenAIRE

    Veprintsev, Dmitry B.; Fersht, Alan R.

    2008-01-01

    The tumour suppressor p53 is a transcription factor that binds DNA in the vicinity of the genes it controls. The affinity of p53 for specific binding sites relative to other DNA sequences is an inherent driving force for specificity, all other things being equal. We measured the binding affinities of systematically mutated consensus p53 DNA-binding sequences using automated fluorescence anisotropy titrations. Based on measurements of the effects of every possible single base-pair substitution...

  8. Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins

    OpenAIRE

    Jiang, Yang; Li, Bi-Qing; Zhang, Yuchao; Feng, Yuan-Ming; Gao, Yu-Fei; Zhang, Ning; Cai, Yu-Dong

    2013-01-01

    Most of pyruvoyl-dependent proteins observed in prokaryotes and eukaryotes are critical regulatory enzymes, which are primary targets of inhibitors for anti-cancer and anti-parasitic therapy. These proteins undergo an autocatalytic, intramolecular self-cleavage reaction in which a covalently bound pyruvoyl group is generated on a conserved serine residue. Traditional detections of the modified serine sites are performed by experimental approaches, which are often labor-intensive and time-cons...

  9. Prediction

    OpenAIRE

    Woollard, W.J.

    2006-01-01

    In this chapter we will look at the ways in which you can use ICT in the classroom to support hypothesis and prediction and how modern technology is enabling: pattern seeking, extrapolation and interpolation to meet the challenges of the information explosion of the 21st century.

  10. Predicting long-term moisture contents of earthen covers at uranium mill tailings sites

    International Nuclear Information System (INIS)

    The three methods for long-term moisture prediction covered in this report are: estimates from water retention (permanent wilting point) data, correlation with climate and soil type, and detailed model simulation. The test results have shown: soils vary greatly in residual moisture. Expected long-term moisture saturation ratios (based on generalized soil characteristics) range from 0.2 to 0.8 for soils ranging in texture from sand to clay, respectively. These values hold for noncompacted field soils. Measured radon diffusion coefficients for soils at 15-bar water contents ranged from 5.0E-2 cm2/s to 5.0E-3 cm2/s for sands and clays, respectively, at typical field densities. In contrast, fine-textured pit-run earthen materials, subjected to optimum compaction (>85% Proctor density) and dried to the 15-bar water content, ranged from 0.7 to 0.9 moisture saturation. Compacted pit-run soils at these moisture contents exhibited radon diffusion coefficients as low as 3.0E-4 cm2/s. The residual moisture saturation for cover soils is not known since no engineered barrier has been in place for more than a few years. A comparison of methods for predicting moisture saturation indicates that model simulations are useful for predicting effects of climatic changes on residual soil moisture, but that long-term moisture also can be predicted with some degree of confidence using generalized soil properties or empirical correlations based both on soils and climatic information. The optimal soil cover design will likely include more than one layer of soil. A two-layer system using a thick (1-m minimum) plant root zone of uncompacted soil placed over a moistened, tightly compacted fine-textured soil is recommended. This design concept has been tested successfully at the Grand Junction, Colorado, tailings piles

  11. Predicting species distributions from checklist data using site-occupancy models

    Science.gov (United States)

    Kery, M.; Gardner, B.; Monnerat, C.

    2010-01-01

    Aim: (1) To increase awareness of the challenges induced by imperfect detection, which is a fundamental issue in species distribution modelling; (2) to emphasize the value of replicate observations for species distribution modelling; and (3) to show how 'cheap' checklist data in faunal/floral databases may be used for the rigorous modelling of distributions by site-occupancy models. Location: Switzerland. Methods: We used checklist data collected by volunteers during 1999 and 2000 to analyse the distribution of the blue hawker, Aeshna cyanea (Odonata, Aeshnidae), a common dragonfly in Switzerland. We used data from repeated visits to 1-ha pixels to derive 'detection histories' and apply site-occupancy models to estimate the 'true' species distribution, i.e. corrected for imperfect detection. We modelled blue hawker distribution as a function of elevation and year and its detection probability of elevation, year and season. Results: The best model contained cubic polynomial elevation effects for distribution and quadratic effects of elevation and season for detectability. We compared the site-occupancy model with a conventional distribution model based on a generalized linear model, which assumes perfect detectability (p = 1). The conventional distribution map looked very different from the distribution map obtained using site-occupancy models that accounted for the imperfect detection. The conventional model underestimated the species distribution by 60%, and the slope parameters of the occurrence-elevation relationship were also underestimated when assuming p = 1. Elevation was not only an important predictor of blue hawker occurrence, but also of the detection probability, with a bell-shaped relationship. Furthermore, detectability increased over the season. The average detection probability was estimated at only 0.19 per survey. Main conclusions: Conventional species distribution models do not model species distributions per se but rather the apparent

  12. Staging of early lymph node metastases with the sentinel lymph node technique and predictive factors in T1/T2 oral cavity cancer

    DEFF Research Database (Denmark)

    Pedersen, Nicklas Juel; Jensen, David Hebbelstrup; Hedbäck, Nora; Frendø, Martin; Kiss, Katalin; Lelkaitis, Giedrius; Mortensen, Jann; Christensen, Anders; Specht, Lena; von Buchwald, Christian

    BACKGROUND: The purpose of this study was to examine the diagnostic accuracy of detecting lymph node metastases and to identify predictive and prognostic clinicopathological factors in patients with oral squamous cell carcinoma (OSCC) undergoing sentinel lymph node biopsy (SLNB). METHODS: All...... factors for the presence of metastases. CONCLUSION: These data support the use of the SLNB technique as an accurate and safe staging tool in patients with OSCC with a cN0 neck. © 2015 Wiley Periodicals, Inc. Head Neck, 2015....

  13. Cavity turnover and equilibrium cavity densities in a cottonwood bottomland

    Science.gov (United States)

    Sedgwick, James A.; Knopf, Fritz L.

    1992-01-01

    A fundamental factor regulating the numbers of secondary cavity nesting (SCN) birds is the number of extant cavities available for nesting. The number of available cavities may be thought of as being in an approximate equilibrium maintained by a very rough balance between recruitment and loss of cavities. Based on estimates of cavity recruitment and loss, we ascertained equilibrium cavity densities in a mature plains cottonwood (Populus sargentii) bottomland along the South Platte River in northeastern Colorado. Annual cavity recruitment, derived from density estimates of primary cavity nesting (PCN) birds and cavity excavation rates, was estimated to be 71-86 new cavities excavated/100 ha. Of 180 active cavities of 11 species of cavity-nesting birds found in 1985 and 1986, 83 were no longer usable by 1990, giving an average instantaneous rate of cavity loss of r = -0.230. From these values of cavity recruitment and cavity loss, equilibrium cavity density along the South Platte is 238-289 cavities/100 ha. This range of equilibrium cavity density is only slightly above the minimum of 205 cavities/100 ha required by SCN's and suggests that cavity availability may be limiting SCN densities along the South Platte River. We submit that snag management alone does not adequately address SCN habitat needs, and that cavity management, expressed in terms of cavity turnover and cavity densities, may be more useful.

  14. Comparing U.S. and Russian experience with cavity decoupling in salt

    Science.gov (United States)

    Glenn, L. A.

    1993-05-01

    Recently released Russian data on two underground nuclear explosions in an Azgir salt dome allow comparison for the first time with similar U.S. explosions. In both cases, highly tamped explosions were employed to form cavities and, after a period of several years, much smaller explosions were then carried out in these same cavities. The seismic decoupling factor obtained from the Russian tests appears to be a factor of 4 less than is predicted, based on the U.S. experience. However, the Russian data are found to be entirely consistent with smaller scale U.S. experiments with chemical explosives. These results can be explained by the extent of damage in the immediate vicinity of the cavity walls, but it remains unclear why the damage should exist at the Russian site, and not at the U.S.

  15. Micro-Cavity Fluidic Dye Laser

    DEFF Research Database (Denmark)

    Helbo, Bjarne; Kristensen, Anders; Menon, Aric Kumaran

    2003-01-01

    We have successfully designed, fabricated and characterized a micro-cavity fluidic dye laser with metallic mirrors, which can be integrated with polymer based lab-on-a-chip microsystems without further processing steps. A simple rate-equation model is used to predict the average pumping power...... threshold for lasing as function of cavity-mirror reflectance, laser dye concentration and cavity length. The laser device is characterized using the laser dye Rhodamine 6G dissolved in ethanol. Lasing is observed, and the influence of dye concentration is investigated....

  16. Repeatable source, site, and path effects on the standard deviation for empirical ground-motion prediction models

    Science.gov (United States)

    Lin, P.-S.; Chiou, B.; Abrahamson, N.; Walling, M.; Lee, C.-T.; Cheng, C.-T.

    2011-01-01

    In this study, we quantify the reduction in the standard deviation for empirical ground-motion prediction models by removing ergodic assumption.We partition the modeling error (residual) into five components, three of which represent the repeatable source-location-specific, site-specific, and path-specific deviations from the population mean. A variance estimation procedure of these error components is developed for use with a set of recordings from earthquakes not heavily clustered in space.With most source locations and propagation paths sampled only once, we opt to exploit the spatial correlation of residuals to estimate the variances associated with the path-specific and the source-location-specific deviations. The estimation procedure is applied to ground-motion amplitudes from 64 shallow earthquakes in Taiwan recorded at 285 sites with at least 10 recordings per site. The estimated variance components are used to quantify the reduction in aleatory variability that can be used in hazard analysis for a single site and for a single path. For peak ground acceleration and spectral accelerations at periods of 0.1, 0.3, 0.5, 1.0, and 3.0 s, we find that the singlesite standard deviations are 9%-14% smaller than the total standard deviation, whereas the single-path standard deviations are 39%-47% smaller.

  17. Surface properties of the Mars Science Laboratory candidate landing sites: characterization from orbit and predictions

    Science.gov (United States)

    Fergason, R.L.; Christensen, P.R.; Golombek, M.P.; Parker, T.J.

    2012-01-01

    This work describes the interpretation of THEMIS-derived thermal inertia data at the Eberswalde, Gale, Holden, and Mawrth Vallis Mars Science Laboratory (MSL) candidate landing sites and determines how thermophysical variations correspond to morphology and, when apparent, mineralogical diversity. At Eberswalde, the proportion of likely unconsolidated material relative to exposed bedrock or highly indurated surfaces controls the thermal inertia of a given region. At Gale, the majority of the landing site region has a moderate thermal inertia (250 to 410 J m-2 K-1 s-1/2), which is likely an indurated surface mixed with unconsolidated materials. The primary difference between higher and moderate thermal inertia surfaces may be due to the amount of mantling material present. Within the mound of stratified material in Gale, layers are distinguished in the thermal inertia data; the MSL rover could be traversing through materials that are both thermophysically and compositionally diverse. The majority of the Holden ellipse has a thermal inertia of 340 to 475 J m-2 K-1 s-1/2 and consists of bed forms with some consolidated material intermixed. Mawrth Vallis has a mean thermal inertia of 310 J m-2 K-1 s-1/2 and a wide variety of materials is present contributing to the moderate thermal inertia surfaces, including a mixture of bedrock, indurated surfaces, bed forms, and unconsolidated fines. Phyllosilicates have been identified at all four candidate landing sites, and these clay-bearing units typically have a similar thermal inertia value (400 to 500 J m-2 K-1 s-1/2), suggesting physical properties that are also similar.

  18. Type 2 diabetes mellitus: phylogenetic motifs for predicting protein functional sites

    Indian Academy of Sciences (India)

    Ashok Sharma; Tanuja Rastogi; Meenakshi Bhartiya; A K Shasany; S P S Khanuja

    2007-08-01

    Diabetes mellitus, commonly referred to as diabetes, is a medical condition associated with abnormally high levels of glucose (or sugar) in the blood. Keeping this view, we demonstrate the phylogenetic motifs (PMs) identification in type 2 diabetes mellitus very likely corresponding to protein functional sites. In this article, we have identified PMs for all the candidate genes for type 2 diabetes mellitus. Glycine 310 remains conserved for glucokinase and potassium channel KCNJ11. Isoleucine 137 was conserved for insulin receptor and regulatory subunit of a phosphorylating enzyme. Whereas residues valine, leucine, methionine were highly conserved for insulin receptor. Occurrence of proline was very high for calpain 10 gene and glucose transporter

  19. Improved Computational Target Site Prediction for Pentatricopeptide Repeat RNA Editing Factors

    OpenAIRE

    TAKENAKA, MIZUKI; Zehrmann, Anja; Brennicke, Axel; Graichen, Knut

    2013-01-01

    Pentatricopeptide repeat (PPR) proteins with an E domain have been identified as specific factors for C to U RNA editing in plant organelles. These PPR proteins bind to a unique sequence motif 5′ of their target editing sites. Recently, involvement of a combinatorial amino acid code in the P (normal length) and S type (short) PPR domains in sequence specific RNA binding was reported. PPR proteins involved in RNA editing, however, contain not only P and S motifs but also their long variants L ...

  20. In Silico Structure Prediction of Human Fatty Acid Synthase-Dehydratase: A Plausible Model for Understanding Active Site Interactions.

    Science.gov (United States)

    John, Arun; Umashankar, Vetrivel; Samdani, A; Sangeetha, Manoharan; Krishnakumar, Subramanian; Deepa, Perinkulam Ravi

    2016-01-01

    Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. X-ray crystallographic structures of some of its domains, such as β-ketoacyl synthase, acetyl transacylase, malonyl transacylase, enoyl reductase, β-ketoacyl reductase, and thioesterase, (TE) are already reported. Here, we have attempted an in silico elucidation of the uncrystallized dehydratase (DH) catalytic domain of human FASN. This theoretical model for DH domain was predicted using comparative modeling methods. Different stand-alone tools and servers were used to validate and check the reliability of the predicted models, which suggested it to be a highly plausible model. The stereochemical analysis showed 92.0% residues in favorable region of Ramachandran plot. The initial physiological substrate β-hydroxybutyryl group was docked into active site of DH domain using Glide. The molecular dynamics simulations carried out for 20 ns in apo and holo states indicated the stability and accuracy of the predicted structure in solvated condition. The predicted model provided useful biochemical insights into the substrate-active site binding mechanisms. This model was then used for identifying potential FASN inhibitors using high-throughput virtual screening of the National Cancer Institute database of chemical ligands. The inhibitory efficacy of the top hit ligands was validated by performing molecular dynamics simulation for 20 ns, where in the ligand NSC71039 exhibited good enzyme inhibition characteristics and exhibited dose-dependent anticancer cytotoxicity in retinoblastoma cancer cells in vitro. PMID:27559295

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

    Science.gov (United States)

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

    2011-03-01

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

  2. Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments

    Directory of Open Access Journals (Sweden)

    Sekinger Edward

    2006-10-01

    Full Text Available Abstract Background High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. Tiling arrays are increasingly used in chromatin immunoprecipitation (IP experiments (ChIP on chip. ChIP on chip facilitates the generation of genome-wide maps of in-vivo interactions between DNA-associated proteins including transcription factors and DNA. Analysis of the hybridization of an immunoprecipitated sample to a tiling array facilitates the identification of ChIP-enriched segments of the genome. These enriched segments are putative targets of antibody assayable regulatory elements. The enrichment response is not ubiquitous across the genome. Typically 5 to 10% of tiled probes manifest some significant enrichment. Depending upon the factor being studied, this response can drop to less than 1%. The detection and assessment of significance for interactions that emanate from non-canonical and/or un-annotated regions of the genome is especially challenging. This is the motivation behind the proposed algorithm. Results We have proposed a novel rank and replicate statistics-based methodology for identifying and ascribing statistical confidence to regions of ChIP-enrichment. The algorithm is optimized for identification of sites that manifest low levels of enrichment but are true positives, as validated by alternative biochemical experiments. Although the method is described here in the context of ChIP on chip experiments, it can be generalized to any treatment-control experimental design. The results of the algorithm show a high degree of concordance with independent biochemical validation methods. The sensitivity and specificity of the algorithm have been characterized via quantitative PCR and independent computational approaches

  3. Predictive value of intracutaneous xenon clearance for healing of amputation and cutaneous ulcer sites

    International Nuclear Information System (INIS)

    A previously reported technique for the assessment of skin blood flow in the lower extremities of patients with ischemic lesions was evaluated using intracutaneous xenon clearance. The radioisotope was injected above and below both the ankle and the knee and flow was measured using a gamma camera with a low-energy collimator, 88-keV photopeak, and a 20% window. Healing was more frequent when skin blood flow was equal to or greater than 2.4 ml/min/100 g (38/39 patients) than when flow was less than 2.4 ml/min/100 g (4/7 patients). The authors conclude that this technique can be used to help determine the appropriate site for amputation in lower limb ischemic lesions

  4. Predictive factors of post-discharge surgical site infections among patients from a teaching hospital

    Directory of Open Access Journals (Sweden)

    Adriana Estela Biasotti Gomes

    2014-05-01

    Full Text Available Introduction Surgical site infections (SSIs often manifest after patients are discharged and are missed by hospital-based surveillance. Methods We conducted a case-reference study nested in a prospective cohort of patients from six surgical specialties in a teaching hospital. The factors related to SSI were compared for cases identified during the hospital stay and after discharge. Results Among 3,427 patients, 222 (6.4% acquired an SSI. In 138 of these patients, the onset of the SSI occurred after discharge. Neurological surgery and the use of steroids were independently associated with a greater likelihood of SSI diagnosis during the hospital stay. Conclusions Our results support the idea of a specialty-based strategy for post-discharge SSI surveillance.

  5. Condition monitoring and service life prediction of near surface disposal module located at three different sites in India

    International Nuclear Information System (INIS)

    In India, reinforced concrete trenches (RCT) are used extensively for disposal of low and intermediate level solid radioactive waste in near surface disposal facilities (NSDF), co-located with nuclear power plants at seven different sites in the country. In order to study the performance of RCTs, an extensive programme was undertaken for three representative sites located at Rajasthan (inland) and Trombay and Tarapur (coastal), which are under operation for last three to four decades. Central Building Research Institute (CBRI) a national research organization was engaged in this study in view of their in-depth expertise in design of civil structures, condition monitoring and remediation. The condition monitoring of RCTs was done using various non-destructive techniques to estimate strength of concrete and probability of corrosion of reinforcement bars. Concrete was also characterized for chemical properties to test the depth of carbonation and chloride penetration in the RCT. Besides this, effect of soil and groundwater on RCT was taken into consideration. Mathematical model and computer code based on reliability theory was developed and validated to predict the service life of trenches. Probability of failure for different target life has been calculated for different values of safety indices. In this paper, details of condition monitoring and residual service life prediction are presented. (author)

  6. Tritium monitoring in groundwater and evaluation of model predictions for the Hanford Site 200 Area Effluent Treatment Facility

    International Nuclear Information System (INIS)

    The Effluent Treatment Facility (ETF) disposal site, also known as the State-Approved Land Disposal Site (SALDS), receives treated effluent containing tritium, which is allowed to infiltrate through the soil column to the water table. Tritium was first detected in groundwater monitoring wells around the facility in July 1996. The SALDS groundwater monitoring plan requires revision of a predictive groundwater model and reevaluation of the monitoring well network one year from the first detection of tritium in groundwater. This document is written primarily to satisfy these requirements and to report on analytical results for tritium in the SALDS groundwater monitoring network through April 1997. The document also recommends an approach to continued groundwater monitoring for tritium at the SALDS. Comparison of numerical groundwater models applied over the last several years indicate that earlier predictions, which show tritium from the SALDS approaching the Columbia River, were too simplified or overly robust in source assumptions. The most recent modeling indicates that concentrations of tritium above 500 pCi/L will extend, at most, no further than ∼1.5 km from the facility, using the most reasonable projections of ETF operation. This extent encompasses only the wells in the current SALDS tritium-tracking network

  7. Electromagnetic SCRF Cavity Tuner

    Energy Technology Data Exchange (ETDEWEB)

    Kashikhin, V.; Borissov, E.; Foster, G.W.; Makulski, A.; Pischalnikov, Y.; Khabiboulline, T.; /Fermilab

    2009-05-01

    A novel prototype of SCRF cavity tuner is being designed and tested at Fermilab. This is a superconducting C-type iron dominated magnet having a 10 mm gap, axial symmetry, and a 1 Tesla field. Inside the gap is mounted a superconducting coil capable of moving {+-} 1 mm and producing a longitudinal force up to {+-} 1.5 kN. The static force applied to the RF cavity flanges provides a long-term cavity geometry tuning to a nominal frequency. The same coil powered by fast AC current pulse delivers mechanical perturbation for fast cavity tuning. This fast mechanical perturbation could be used to compensate a dynamic RF cavity detuning caused by cavity Lorentz forces and microphonics. A special configuration of magnet system was designed and tested.

  8. Superconducting cavity development

    International Nuclear Information System (INIS)

    Design and development work of the superconducting cavities for the Neutron Science Project is being continued since 1995. In the cavity design work, RF and structural analyses were carried out in order to determine the cavity shape and to obtain the RF and structural parameters. In the cavity development work, preparation of the test facility, fabrication and tests of the two single-cell prototype cavities of β=0.5 were performed. Good performance of the cavity was demonstrated in the test; obtained surface peak electric field of 44 MV/m is much higher than the design value of 16 MV/m. Resonant frequency shifts due to the vacuum load and the Lorentz force were also measured in the test. (author)

  9. LEP copper accelerating cavities

    CERN Multimedia

    Laurent Guiraud

    1999-01-01

    These copper cavities were used to generate the radio frequency electric field that was used to accelerate electrons and positrons around the 27-km Large Electron-Positron (LEP) collider at CERN, which ran from 1989 to 2000. The copper cavities were gradually replaced from 1996 with new superconducting cavities allowing the collision energy to rise from 90 GeV to 200 GeV by mid-1999.

  10. Model 96 of the Aespoe site. Results of prediction and outcome based on surface and underground bore hole investigations

    International Nuclear Information System (INIS)

    The site characterisation work of the bedrock around Aespoe has been carried out as an interdisciplinary work in the fields of geology, hydrogeology and hydrochemistry. It has been carried out in different steps focusing on different scales simultaneously. The descriptions have been focused on regional, site and block scales representing areas/volumes of 10x20 km, 500x500x500 m and 50x50x50 m respectively during the pre-construction phase. During the tunnel construction phase the models have been focusing scales of 0-10, 10-100 and 100-1000 metres. The models after the pre-investigation stage were the base for predictions of geological, rock mechanical, hydrogeological and hydrochemical conditions along the planned tunnel for the Aespoe HRL. During construction of the tunnel geological and hydrogeological mapping were made and comprehensive investigation were performed to get geological, rock mechanical, hydrogeological and hydrochemical conditions which could be compared to the predicted. One objective was to test the ability to obtain a thorough understanding of the rock conditions based on investigations of the surface and investigations in and between bore holes from the surface. By 'understanding' we here mean to obtain sufficient knowledge to show how things are, but also to show how things cannot be. An important part of the comparison of the predictions with the outcome was to evaluate the usefulness and feasibility of pre-investigation methods. (Discussed in an other contribution to this conference). Another purpose was to evaluate the models made. This is discussed in the present contribution

  11. Prediction of DtxR regulon: Identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae

    Directory of Open Access Journals (Sweden)

    Hasnain Seyed

    2004-09-01

    Full Text Available Abstract Background The diphtheria toxin repressor, DtxR, of Corynebacterium diphtheriae has been shown to be an iron-activated transcription regulator that controls not only the expression of diphtheria toxin but also of iron uptake genes. This study aims to identify putative binding sites and operons controlled by DtxR to understand the role of DtxR in patho-physiology of Corynebacterium diphtheriae. Result Positional Shannon relative entropy method was used to build the DtxR-binding site recognition profile and the later was used to identify putative regulatory sites of DtxR within C. diphtheriae genome. In addition, DtxR-regulated operons were also identified taking into account the predicted DtxR regulatory sites and genome annotation. Few of the predicted motifs were experimentally validated by electrophoretic mobility shift assay. The analysis identifies motifs upstream to the novel iron-regulated genes that code for Formamidopyrimidine-DNA glycosylase (FpG, an enzyme involved in DNA-repair and starvation inducible DNA-binding protein (Dps which is involved in iron storage and oxidative stress defense. In addition, we have found the DtxR motifs upstream to the genes that code for sortase which catalyzes anchoring of host-interacting proteins to the cell wall of pathogenic bacteria and the proteins of secretory system which could be involved in translocation of various iron-regulated virulence factors including diphtheria toxin. Conclusions We have used an in silico approach to identify the putative binding sites and genes controlled by DtxR in Corynebacterium diphtheriae. Our analysis shows that DtxR could provide a molecular link between Fe+2-induced Fenton's reaction and protection of DNA from oxidative damage. DtxR-regulated Dps prevents lethal combination of Fe+2 and H2O2 and also protects DNA by nonspecific DNA-binding. In addition DtxR could play an important role in host interaction and virulence by regulating the levels of sortase

  12. Directed Hierarchical Patterning of Polycarbonate Bisphenol A Glass Surface along Predictable Sites

    Directory of Open Access Journals (Sweden)

    Mazen Khaled

    2015-01-01

    Full Text Available This paper reports a new approach in designing textured and hierarchical surfaces on polycarbonate bisphenol A type glass to improve hydrophobicity and dust repellent application for solar panels. Solvent- and vapor-induced crystallization of thermoplastic glass polycarbonate bisphenol A (PC is carried out to create hierarchically structured surfaces. In this approach dichloromethane (DCM and acetone are used in sequence. Samples are initially immersed in DCM liquid to generate nanopores, followed by exposing to acetone vapor resulting in the generation of hierarchical structure along the interporous sites. The effects of exposure time on the size, density, and distance of the generated spherules and gaps are studied and correlated with the optical transmittance and contact angle measurements at the surface. At optimized exposure time a contact angle of 98° was achieved with 80% optical transmittance. To further increase the hydrophobicity while maintaining optical properties, the hierarchical surfaces were coated with a transparent composite of tetraethyl orthosilicate as precursor and hexamethyldisilazane as silylation agent resulting in an average contact angle of 135.8° and transmittance of around 70%. FTIR and AFM characterization techniques are employed to study the composition and morphology of the generated surfaces.

  13. Predicting the preferential sites to liquid droplet erosion of the bellows assemblies by CFD

    International Nuclear Information System (INIS)

    Highlights: → The first convolution of the bellows encounters the severest erosion damage. → The bigger droplet causes severer liquid droplet erosion on the bellows assemblies. → The LDE distribution is not dependent on the liquid droplet size. → The weld seam can mitigate the LDE of the bellows downstream. → The optimal dimensions of the protecting cover are calculated by CFD. - Abstract: Bellows assemblies are placed within extraction steam lines to absorb the differential displacement (driven primarily by thermal growth) between the turbine lower casing and the condenser shell in nuclear power plants. The thin wall thickness and service environmental conditions of the bellows predetermine their vulnerable endurance to the liquid droplet erosion (LDE). A three-dimensional computational fluid dynamics (CFD) bellows model proposed in this paper consists of a hydraulic model and a LDE model aiming to investigate the LDE on the external surface of the bellows assemblies. The result shows that the most prone site to LDE locates at the upwind side of the first bellows convolution (USFBC). The droplet diameter has significant effect on the LDE extent, rather than the LDE distribution. Moreover, the addition of the weld seam before the bellows can mitigate the LDE of the bellows downstream. In addition, the protecting cover (PC) effectively prevents the bellows from the LDE, but causes the droplet accumulation on the convolution, which possible leads to corrosive damage. The PC structure was designed optimization according to the requirements of the displacement compensation, the manufacture cost and the LDE resistance.

  14. Agenda Trending: Reciprocity and the Predictive Capacity of Social Networking Sites in Intermedia Agenda Setting across Topics over Time

    Directory of Open Access Journals (Sweden)

    Jacob Groshek

    2013-08-01

    Full Text Available In the contemporary converged media environment, agenda setting is being transformed by the dramatic growth of audiences that are simultaneously media users and producers. The study reported here addresses related gaps in the literature by first comparing the topical agendas of two leading traditional media outlets (New York Times and CNN with the most frequently shared stories and trending topics on two widely popular Social Networking Sites (Facebook and Twitter. Time-series analyses of the most prominent topics identify the extent to which traditional media sets the agenda for social media as well as reciprocal agenda-setting effects of social media topics entering traditional media agendas. In addition, this study examines social intermedia agenda setting topically and across time within social networking sites, and in so doing, adds a vital understanding of where traditional media, online uses, and social media content intersect around instances of focusing events, particularly elections. Findings identify core differences between certain traditional and social media agendas, but also within social media agendas that extend from uses examined here. Additional results further suggest important topical and event-oriented limitations upon the predictive capacit of social networking sites to shape traditional media agendas over time.

  15. Mixed valency and site-preference chemistry for cerium and its compounds: A predictive density-functional theory study

    Science.gov (United States)

    Alam, Aftab; Johnson, D. D.

    2014-06-01

    Cerium and its technologically relevant compounds are examples of anomalous mixed valency, originating from two competing oxidation states—itinerant Ce4+ and localized Ce3+. Under applied stress, anomalous transitions are observed but not well understood. Here we treat mixed valency as an "alloy" problem involving two valences with competing and numerous site-occupancy configurations. We use density-functional theory with Hubbard U (i.e., DFT+U) to evaluate the effective valence and predict properties, including controlling the valence by pseudoternary alloying. For Ce and its compounds, such as (Ce,La)2(Fe,Co)14B permanent magnets, we find a stable mixed-valent α state near the spectroscopic value of νs=3.53. Ce valency in compounds depends on its steric volume and local chemistry. For La doping, Ce valency shifts towards γ-like Ce3+, as expected from steric volume; for Co doping, valency depends on local Ce-site chemistry and steric volume. Our approach captures the key origins of anomalous valency and site-preference chemistry in complex compounds.

  16. SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features.

    Science.gov (United States)

    Zhou, Yuan; Zeng, Pan; Li, Yan-Hui; Zhang, Ziding; Cui, Qinghua

    2016-06-01

    N(6)-methyladenosine (m(6)A) is a prevalent RNA methylation modification involved in the regulation of degradation, subcellular localization, splicing and local conformation changes of RNA transcripts. High-throughput experiments have demonstrated that only a small fraction of the m(6)A consensus motifs in mammalian transcriptomes are modified. Therefore, accurate identification of RNA m(6)A sites becomes emergently important. For the above purpose, here a computational predictor of mammalian m(6)A site named SRAMP is established. To depict the sequence context around m(6)A sites, SRAMP combines three random forest classifiers that exploit the positional nucleotide sequence pattern, the K-nearest neighbor information and the position-independent nucleotide pair spectrum features, respectively. SRAMP uses either genomic sequences or cDNA sequences as its input. With either kind of input sequence, SRAMP achieves competitive performance in both cross-validation tests and rigorous independent benchmarking tests. Analyses of the informative features and overrepresented rules extracted from the random forest classifiers demonstrate that nucleotide usage preferences at the distal positions, in addition to those at the proximal positions, contribute to the classification. As a public prediction server, SRAMP is freely available at http://www.cuilab.cn/sramp/. PMID:26896799

  17. Summary of ground motion prediction results for Nevada Test Site underground nuclear explosions related to the Yucca Mountain project

    International Nuclear Information System (INIS)

    This report summarizes available data on ground motions from underground nuclear explosions recorded on and near the Nevada Test Site, with emphasis on the ground motions recorded at stations on Yucca Mountain, the site of a potential high-level radioactive waste repository. Sandia National Laboratories, through the Weapons Test Seismic Investigations project, collected and analyzed ground motion data from NTS explosions over a 14-year period, from 1977 through 1990. By combining these data with available data from earlier, larger explosions, prediction equations for several ground motion parameters have been developed for the Test Site area for underground nuclear explosion sources. Also presented are available analyses of the relationship between surface and downhole motions and spectra and relevant crustal velocity structure information for Yucca Mountain derived from the explosion data. The data and associated analyses demonstrate that ground motions at Yucca Mountain from nuclear tests have been at levels lower than would be expected from moderate to large earthquakes in the region; thus nuclear explosions, while located relatively close, would not control seismic design criteria for the potential repository

  18. Prediction

    CERN Document Server

    Sornette, Didier

    2010-01-01

    This chapter first presents a rather personal view of some different aspects of predictability, going in crescendo from simple linear systems to high-dimensional nonlinear systems with stochastic forcing, which exhibit emergent properties such as phase transitions and regime shifts. Then, a detailed correspondence between the phenomenology of earthquakes, financial crashes and epileptic seizures is offered. The presented statistical evidence provides the substance of a general phase diagram for understanding the many facets of the spatio-temporal organization of these systems. A key insight is to organize the evidence and mechanisms in terms of two summarizing measures: (i) amplitude of disorder or heterogeneity in the system and (ii) level of coupling or interaction strength among the system's components. On the basis of the recently identified remarkable correspondence between earthquakes and seizures, we present detailed information on a class of stochastic point processes that has been found to be particu...

  19. Optically measuring interior cavities

    Science.gov (United States)

    Stone, Gary Franklin

    2009-11-03

    A method of measuring the three-dimensional volume or perimeter shape of an interior cavity includes the steps of collecting a first optical slice of data that represents a partial volume or perimeter shape of the interior cavity, collecting additional optical slices of data that represents a partial volume or perimeter shape of the interior cavity, and combining the first optical slice of data and the additional optical slices of data to calculate of the three-dimensional volume or perimeter shape of the interior cavity.

  20. GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites

    Science.gov (United States)

    Xie, Yubin; Zheng, Yueyuan; Li, Hongyu; Luo, Xiaotong; He, Zhihao; Cao, Shuo; Shi, Yi; Zhao, Qi; Xue, Yu; Zuo, Zhixiang; Ren, Jian

    2016-01-01

    As one of the most common post-translational modifications in eukaryotic cells, lipid modification is an important mechanism for the regulation of variety aspects of protein function. Over the last decades, three classes of lipid modifications have been increasingly studied. The co-regulation of these different lipid modifications is beginning to be noticed. However, due to the lack of integrated bioinformatics resources, the studies of co-regulatory mechanisms are still very limited. In this work, we developed a tool called GPS-Lipid for the prediction of four classes of lipid modifications by integrating the Particle Swarm Optimization with an aging leader and challengers (ALC-PSO) algorithm. GPS-Lipid was proven to be evidently superior to other similar tools. To facilitate the research of lipid modification, we hosted a publicly available web server at http://lipid.biocuckoo.org with not only the implementation of GPS-Lipid, but also an integrative database and visualization tool. We performed a systematic analysis of the co-regulatory mechanism between different lipid modifications with GPS-Lipid. The results demonstrated that the proximal dual-lipid modifications among palmitoylation, myristoylation and prenylation are key mechanism for regulating various protein functions. In conclusion, GPS-lipid is expected to serve as useful resource for the research on lipid modifications, especially on their co-regulation.

  1. GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites.

    Science.gov (United States)

    Xie, Yubin; Zheng, Yueyuan; Li, Hongyu; Luo, Xiaotong; He, Zhihao; Cao, Shuo; Shi, Yi; Zhao, Qi; Xue, Yu; Zuo, Zhixiang; Ren, Jian

    2016-01-01

    As one of the most common post-translational modifications in eukaryotic cells, lipid modification is an important mechanism for the regulation of variety aspects of protein function. Over the last decades, three classes of lipid modifications have been increasingly studied. The co-regulation of these different lipid modifications is beginning to be noticed. However, due to the lack of integrated bioinformatics resources, the studies of co-regulatory mechanisms are still very limited. In this work, we developed a tool called GPS-Lipid for the prediction of four classes of lipid modifications by integrating the Particle Swarm Optimization with an aging leader and challengers (ALC-PSO) algorithm. GPS-Lipid was proven to be evidently superior to other similar tools. To facilitate the research of lipid modification, we hosted a publicly available web server at http://lipid.biocuckoo.org with not only the implementation of GPS-Lipid, but also an integrative database and visualization tool. We performed a systematic analysis of the co-regulatory mechanism between different lipid modifications with GPS-Lipid. The results demonstrated that the proximal dual-lipid modifications among palmitoylation, myristoylation and prenylation are key mechanism for regulating various protein functions. In conclusion, GPS-lipid is expected to serve as useful resource for the research on lipid modifications, especially on their co-regulation. PMID:27306108

  2. Sensitivity and predictive uncertainty of the ACASA model at a spruce forest site

    Directory of Open Access Journals (Sweden)

    K. Staudt

    2010-06-01

    Full Text Available The sensitivity and predictive uncertainty of the Advanced Canopy-Atmosphere-Soil Algorithm (ACASA was assessed by employing the Generalized Likelihood Uncertainty Estimation (GLUE method. ACASA is a stand-scale, multi-layer soil-vegetation-atmosphere transfer model that incorporates a third order closure method to simulate the turbulent exchange of energy and matter within and above the canopy. Fluxes simulated by the model were compared to sensible and latent heat fluxes as well as the net ecosystem exchange measured by an eddy-covariance system above the spruce canopy at the FLUXNET-station Waldstein-Weidenbrunnen in the Fichtelgebirge Mountains in Germany. From each of the intensive observation periods carried out within the EGER project (ExchanGE processes in mountainous Regions in autumn 2007 and summer 2008, five days of flux measurements were selected. A large number (20 000 of model runs using randomly generated parameter sets were performed and goodness of fit measures for all fluxes for each of these runs calculated. The 10% best model runs for each flux were used for further investigation of the sensitivity of the fluxes to parameter values and to calculate uncertainty bounds.

    A strong sensitivity of the individual fluxes to a few parameters was observed, such as the leaf area index. However, the sensitivity analysis also revealed the equifinality of many parameters in the ACASA model for the investigated periods. The analysis of two time periods, each representing different meteorological conditions, provided an insight into the seasonal variation of parameter sensitivity. The calculated uncertainty bounds demonstrated that all fluxes were well reproduced by the ACASA model. In general, uncertainty bounds encompass measured values better when these are conditioned on the respective individual flux only and not on all three fluxes concurrently. Structural weaknesses of the ACASA model concerning the soil respiration

  3. Sensitivity and predictive uncertainty of the ACASA model at a spruce forest site

    Directory of Open Access Journals (Sweden)

    K. Staudt

    2010-11-01

    Full Text Available The sensitivity and predictive uncertainty of the Advanced Canopy-Atmosphere-Soil Algorithm (ACASA was assessed by employing the Generalized Likelihood Uncertainty Estimation (GLUE method. ACASA is a stand-scale, multi-layer soil-vegetation-atmosphere transfer model that incorporates a third order closure method to simulate the turbulent exchange of energy and matter within and above the canopy. Fluxes simulated by the model were compared to sensible and latent heat fluxes as well as the net ecosystem exchange measured by an eddy-covariance system above the spruce canopy at the FLUXNET-station Waldstein-Weidenbrunnen in the Fichtelgebirge Mountains in Germany. From each of the intensive observation periods carried out within the EGER project (ExchanGE processes in mountainous Regions in autumn 2007 and summer 2008, five days of flux measurements were selected. A large number (20000 of model runs using randomly generated parameter sets were performed and goodness of fit measures for all fluxes for each of these runs were calculated. The 10% best model runs for each flux were used for further investigation of the sensitivity of the fluxes to parameter values and to calculate uncertainty bounds.

    A strong sensitivity of the individual fluxes to a few parameters was observed, such as the leaf area index. However, the sensitivity analysis also revealed the equifinality of many parameters in the ACASA model for the investigated periods. The analysis of two time periods, each representing different meteorological conditions, provided an insight into the seasonal variation of parameter sensitivity. The calculated uncertainty bounds demonstrated that all fluxes were well reproduced by the ACASA model. In general, uncertainty bounds encompass measured values better when these are conditioned on the respective individual flux only and not on all three fluxes concurrently. Structural weaknesses of the ACASA model concerning the soil respiration

  4. Malignant melanoma of the oral cavity

    Directory of Open Access Journals (Sweden)

    Ebenezer Jagadish

    2006-01-01

    Full Text Available Oral malignant melanoma is a rare disease. The common sites of its occurrence are the palate and gingiva with the maxillary arch being affected 80% of the time. Because of their presence at relatively obscure areas in the oral cavity, most of the malignant melanomas of the oral cavity are diagnosed at a late stage. These lesions are associated with poor prognosis. The dental clinician must therefore carefully examine the head, neck, and oral cavity, and any pigmented lesion that may exhibit growth potential must be biopsied. This article describes a case of malignant melanoma that was present in the oral cavity and briefly reviews the relevant literature that explains the nature of this lesion.

  5. Formation of cavities in Si and their chemisorption of metals

    International Nuclear Information System (INIS)

    Nanometer-size cavities formed in Si by He+ implantation and annealing are examined with cross-section TEM. During annealing at 700 C or above, He degasses from the specimens, leaving uhv cavities with reactive Si bonds on their walls. Cavity microstructures have been characterized in detail for an implanted fluence of 1 x 1017 He/cm2: cavity volume remains approximately constant (0.75 lattice sites/He) for anneals from 700 to ∼1000 C, while surface area (3 to 7 times the wafer area) decreases with temperature as the cavities coarsen. The cavities are found to getter up to ∼1 monolayer of Cu or Au from solution in Si without second-phase formation, thus identifying the trapping mechanism as chemisorption on the cavity walls

  6. SPS accelerating cavity

    CERN Multimedia

    CERN PhotoLab

    1981-01-01

    One of the SPS accelerating cavities (200 MHz, travelling wave structure). The power that is fed into the upstream end of the cavity is extracted at the downstream end and sent into a dump load. See 7603195 for more details, 7411032 for the travelling wave structure, and also 8011289, 8302397.

  7. SPS accelerating cavity

    CERN Multimedia

    1980-01-01

    One of the SPS acceleration cavities (200 MHz, travelling wave structure). On the ceiling one sees the coaxial transmission line which feeds the power from the amplifier, located in a surface building above, to the upstream end of the cavity. See 7603195 for more details, 7411032 for the travelling wave structure, and also 8104138, 8302397.

  8. Superconducting RF cavities

    CERN Document Server

    Bernard, Philippe

    1999-01-01

    It was 20 years ago when the research and development programme for LEP superconducting cavities was initiated. It lasted about 10 years. Today, my aim is not to tell you in great detail about the many innovations made thanks to our research, but I would like to point out some milestones in the development of superconducting cavities where Emilio's influence was particularly important.

  9. Ferrite loaded rf cavity

    International Nuclear Information System (INIS)

    The mechanism of a ferrite-loaded rf cavity is explained from the point of view of its operation. Then, an analysis of the automatic cavity-tuning system is presented using the transfer function; and a systematic analysis of a beam-feedback system using transfer functions is also presented. (author)

  10. Superconducting cavities for LEP

    CERN Multimedia

    1983-01-01

    Above: a 350 MHz superconducting accelerating cavity in niobium of the type envisaged for accelerating electrons and positrons in later phases of LEP. Below: a small 1 GHz cavity used for investigating the surface problems of superconducting niobium. Albert Insomby stays on the right. See Annual Report 1983 p. 51.

  11. Radionuclide migration in ground water at a low-level waste disposal site: a comparison of predicted radionuclide transport modeling versus field observations

    International Nuclear Information System (INIS)

    At the Chalk River Nuclear Laboratories (CRNL), in Ontario, Canada, a number of LLW shallow-land burial facilities have existed for 25-30 years. These facilities are useful for testing the concept of site modelability. In 1984, CRNL and the Pacific Northwest Laboratory (PNL) established a cooperative research program to examine two disposal sites having plumes of slightly contaminated ground water for study. This report addresses the LLW Nitrate Disposal Pit site, which received liquid wastes containing approximately 1000-1500 curies of mixed fission products during 1953-54. The objective of this study is to test the regulatory requirement that a site be modeled and to use the Nitrate Disposal Pit site as a field site for testing the reliability of models in predicting radionuclide movement in ground water. The study plan was to approach this site as though it were to be licensed under the requirements of 10 CFR 61. Under the assumption that little was known about this site, a characterization plan was prepared describing the geologic, hydrologic, and geochemical information needed to assess site performance. After completion of the plan, site data generated by CRNL were selected to fill the plan data requirements. This paper describes the site hydrogeology, modeling of ground water flow, the comparison of observed and predicted radionuclide movement, and summarizes the conclusions and recommendations. 3 references, 10 figures

  12. Predicting Social Networking Site Use and Online Communication Practices among Adolescents: The Role of Access and Device Ownership

    Directory of Open Access Journals (Sweden)

    Drew P. Cingel

    2014-06-01

    Full Text Available Given adolescents' heavy social media use, this study examined a number of predictors of adolescent social media use, as well as predictors of online communication practices. Using data collected from a national sample of 467 adolescents between the ages of 13 and 17, results indicate that demographics, technology access, and technology ownership are related to social media use and communication practices. Specifically, females log onto and use more constructive com-munication practices on Facebook compared to males. Additionally, adolescents who own smartphones engage in more constructive online communication practices than those who share regular cell phones or those who do not have access to a cell phone. Overall, results imply that ownership of mobile technologies, such as smartphones and iPads, may be more predictive of social networking site use and online communication practices than general ownership of technology.

  13. Predicting Social Networking Site Use and Online Communication Practices among Adolescents: The Role of Access and Device Ownership

    Directory of Open Access Journals (Sweden)

    Drew P. Cingel

    2014-01-01

    Full Text Available Given adolescents' heavy social media use, this study examined a number of predictors of adolescent social media use, as well as predictors of online communication practices. Using data collected from a national sample of 467 adolescents between the ages of 13 and 17, results indicate that demographics, technology access, and technology ownership are related to social media use and communication practices. Specifically, females log onto and use more constructive communication practices on Facebook compared to males. Additionally, adolescents who own smartphones engage in more constructive online communication practices than those who share regular cell phones or those who do not have access to a cell phone. Overall, results imply that ownership of mobile technologies, such as smartphones and iPads, may be more predictive of social networking site use and online communication practices than general ownership of technology.

  14. Passivated niobium cavities

    Science.gov (United States)

    Myneni, Ganapati Rao; Hjorvarsson, Bjorgvin; Ciovati, Gianluigi

    2006-12-19

    A niobium cavity exhibiting high quality factors at high gradients is provided by treating a niobium cavity through a process comprising: 1) removing surface oxides by plasma etching or a similar process; 2) removing hydrogen or other gases absorbed in the bulk niobium by high temperature treatment of the cavity under ultra high vacuum to achieve hydrogen outgassing; and 3) assuring the long term chemical stability of the niobium cavity by applying a passivating layer of a superconducting material having a superconducting transition temperature higher than niobium thereby reducing losses from electron (cooper pair) scattering in the near surface region of the interior of the niobium cavity. According to a preferred embodiment, the passivating layer comprises niobium nitride (NbN) applied by reactive sputtering.

  15. Improvement of AEP Predictions Using Diurnal CFD Modelling with Site-Specific Stability Weightings Provided from Mesoscale Simulation

    Science.gov (United States)

    Hristov, Y.; Oxley, G.; Žagar, M.

    2014-06-01

    The Bolund measurement campaign, performed by Danish Technical University (DTU) Wind Energy Department (also known as RISØ), provided significant insight into wind flow modeling over complex terrain. In the blind comparison study several modelling solutions were submitted with the vast majority being steady-state Computational Fluid Dynamics (CFD) approaches with two equation k-epsilon turbulence closure. This approach yielded the most accurate results, and was identified as the state-of-the-art tool for wind turbine generator (WTG) micro-siting. Based on the findings from Bolund, further comparison between CFD and field measurement data has been deemed essential in order to improve simulation accuracy for turbine load and long-term Annual Energy Production (AEP) estimations. Vestas Wind Systems A/S is a major WTG original equipment manufacturer (OEM) with an installed base of over 60GW in over 70 countries accounting for 19% of the global installed base. The Vestas Performance and Diagnostic Centre (VPDC) provides online live data to more than 47GW of these turbines allowing a comprehensive comparison between modelled and real-world energy production data. In previous studies, multiple sites have been simulated with a steady neutral CFD formulation for the atmospheric surface layer (ASL), and wind resource (RSF) files have been generated as a base for long-term AEP predictions showing significant improvement over predictions performed with the industry standard linear WAsP tool. In this study, further improvements to the wind resource file generation with CFD are examined using an unsteady diurnal cycle approach with a full atmospheric boundary layer (ABL) formulation, with the unique stratifications throughout the cycle weighted according to mesoscale simulated sectorwise stability frequencies.

  16. Improvement of AEP Predictions Using Diurnal CFD Modelling with Site-Specific Stability Weightings Provided from Mesoscale Simulation

    International Nuclear Information System (INIS)

    The Bolund measurement campaign, performed by Danish Technical University (DTU) Wind Energy Department (also known as RISØ), provided significant insight into wind flow modeling over complex terrain. In the blind comparison study several modelling solutions were submitted with the vast majority being steady-state Computational Fluid Dynamics (CFD) approaches with two equation k-ε turbulence closure. This approach yielded the most accurate results, and was identified as the state-of-the-art tool for wind turbine generator (WTG) micro-siting. Based on the findings from Bolund, further comparison between CFD and field measurement data has been deemed essential in order to improve simulation accuracy for turbine load and long-term Annual Energy Production (AEP) estimations. Vestas Wind Systems A/S is a major WTG original equipment manufacturer (OEM) with an installed base of over 60GW in over 70 countries accounting for 19% of the global installed base. The Vestas Performance and Diagnostic Centre (VPDC) provides online live data to more than 47GW of these turbines allowing a comprehensive comparison between modelled and real-world energy production data. In previous studies, multiple sites have been simulated with a steady neutral CFD formulation for the atmospheric surface layer (ASL), and wind resource (RSF) files have been generated as a base for long-term AEP predictions showing significant improvement over predictions performed with the industry standard linear WAsP tool. In this study, further improvements to the wind resource file generation with CFD are examined using an unsteady diurnal cycle approach with a full atmospheric boundary layer (ABL) formulation, with the unique stratifications throughout the cycle weighted according to mesoscale simulated sectorwise stability frequencies

  17. Metastatic Tumours to the Oral Cavity: Report of Three Cases

    OpenAIRE

    Kalaitsidou, Ioanna G.; Ioannis T. Astreidis; Kontos, Konstantinos I.; Lazaridou, Maria N.; Eleni T. Bourlidou; Gerasimidou, Domniki K; Vladika, Natalia P.; Mangoudi, Doxa L.

    2015-01-01

    ABSTRACT Background Metastatic tumours to the oral cavity from distant organs are uncommon and represent approximately 1 - 3% of all oral malignancies. Such metastases can occur to the bone or to the oral soft tissues. Almost any malignancy from any site is capable of metastasis to the oral cavity and a wide variety of tumours have been reported to spread to the mouth. Methods Careful examination of the oral cavity and a high degree of clinical suspicion as well as a multidisciplinary approac...

  18. The subperitoneal space and peritoneal cavity: basic concepts

    OpenAIRE

    Harpreet K. Pannu; Oliphant, Michael

    2015-01-01

    The subperitoneal space and peritoneal cavity are two mutually exclusive spaces that are separated by the peritoneum. Each is a single continuous space with interconnected regions. Disease can spread either within the subperitoneal space or within the peritoneal cavity to distant sites in the abdomen and pelvis via these interconnecting pathways. Disease can also cross the peritoneum to spread from the subperitoneal space to the peritoneal cavity or vice versa.

  19. Oral cavity metastasis: An unusual presentation of carcinoma prostate

    OpenAIRE

    Damodaran, Dileep; Kathiresan, N.; Satheesan, B.

    2008-01-01

    Oral cavity cancers form the third most common cancers among men in south India. The oral cavity is a very rare site for metastases and has been described in various cancers, particularly lung, breast, kidney and colon carcinoma. Here a very rare case of a buccal metastasis from prostate carcinoma that was originally evaluated as a primary oral cavity malignancy is presented. Histopathological examination of a biopsy of the lesion revealed papillary adenocarcinoma Grade II, nuclear Grade II, ...

  20. Compensation of the Crossing Angle with Crab Cavities at KEKB

    CERN Document Server

    Abe, T; Akemoto, M; Akiyama, A; Arinaga, M; Ebihara, K; Egawa, K; Enomoto, A; Flanagan, J; Fukuda, S; Fukuma, H; Funakoshi, Y; Furukawa, K; Furuya, T; Hara, K; Higo, T; Hiramatsu, S; Hisamatsu, H; Honma, H; Honma, T; Hosoyama, K; Ieiri, T; Iida, N; Ikeda, H; Ikeda, M; Inagaki, S; Isagawa, S; Ishii, H; Kabe, A; Kadokura, E; Kageyama, T; Kakihara, K; Kako, E; Kamada, S; Kamitani, T; Kanazawa, K; Katagiri, H; Kato, S; Kawamoto, T; Kazakov, S; Kikuchi, M; Kikutani, E; Kitagawa, K; Koiso, H; Kojima, Y; Komada, I; Kubo, T; Kudo, K; Kudo, N; Marutsuka, K; Masuzawa, M; Matsumoto, S; Matsumoto, T; Michizono, S; Mikawa, K; Mimashi, T; Mitsunobu, S; Mori, K; Morita, A; Morita, Y; Nakai, H; Nakajima, H; Nakamura, T T; Nakanishi, H; Nakanishi, K; Nakao, K; Ninomiya, S; Ogawa, Y; Ohmi, K; Ohsawa, S; Ohsawa, Y; Ohnishi, Y; Ohuchi, N; Oide, K; Ono, M; Ozaki, T; Saitô, K; Sakai, H; Sakamoto, Y; Sato, M; Satoh, M; Shibata, K; Shidara, T; Shirai, M; Shirakawa, A; Sueno, T; Suetake, M; Suetsugu, Y; Sugahara, R; Sugimura, T; Suwada, T; Tajima, O; Takano, S; Takasaki, S; Takenaka, T; Takeuchi, Y; Tawada, M; Tejima, M; Tobiyama, M; Tokuda, N; Uehara, S; Uno, S; Yamamoto, Y; Yano, Y; Yokoyama, K; Yoshida, Ma; Yoshida, Mi; Yoshimoto, S; Yoshino, K; Perevedentsev, E; Shatilov, D N

    2007-01-01

    Crab cavities have been installed in the KEKB B--Factory rings to compensate the crossing angle at the collision point and thus increase luminosity. The beam operation with crab crossing has been done since February 2007. This is the first experience with such cavities in colliders or storage rings. The crab cavities have been working without serious issues. While higher specific luminosity than the geometrical gain has been achieved, further study is necessary and under way to reach the prediction of simulation.

  1. SPS RF Accelerating Cavity

    CERN Multimedia

    1979-01-01

    This picture shows one of the 2 new cavities installed in 1978-1979. The main RF-system of the SPS comprises four cavities: two of 20 m length and two of 16.5 m length. They are all installed in one long straight section (LSS 3). These cavities are of the travelling-wave type operating at a centre frequency of 200.2 MHz. They are wideband, filling time about 700 ns and untuned. The power amplifiers, using tetrodes are installed in a surface building 200 m from the cavities. Initially only two cavities were installed, a third cavity was installed in 1978 and a forth one in 1979. The number of power amplifiers was also increased: to the first 2 MW plant a second 2 MW plant was added and by end 1979 there were 8 500 kW units combined in pairs to feed each of the 4 cavities with up to about 1 MW RF power, resulting in a total accelerating voltage of about 8 MV. See also 7412016X, 7412017X, 7411048X

  2. SPS RF Cavity

    CERN Multimedia

    1975-01-01

    The picture shows one of the two initially installed cavities. The main RF-system of the SPS comprises four cavities: two of 20 m length and two of 16.5 m length. They are all installed in one long straight section (LSS 3). These cavities are of the travelling-wave type operating at a centre frequency of 200.2 MHz. They are wideband, filling time about 700 ns and untuned. The power amplifiers, using tetrodes are installed in a surface building 200 m from the cavities. Initially only two cavities were installed, a third cavity was installed in 1978 and a forth one in 1979. The number of power amplifiers was also gradually increased: by end 1980 there were 8 500 kW units combined in pairs to feed each of the 4 cavities with up to about 1 MW RF power, resulting in a total accelerating voltage of about 8 MV. See also 7412017X, 7411048X, 7505074.

  3. Thermal Protection System Cavity Heating for Simplified and Actual Geometries Using Computational Fluid Dynamics Simulations with Unstructured Grids

    Science.gov (United States)

    McCloud, Peter L.

    2010-01-01

    Thermal Protection System (TPS) Cavity Heating is predicted using Computational Fluid Dynamics (CFD) on unstructured grids for both simplified cavities and actual cavity geometries. Validation was performed using comparisons to wind tunnel experimental results and CFD predictions using structured grids. Full-scale predictions were made for simplified and actual geometry configurations on the Space Shuttle Orbiter in a mission support timeframe.

  4. Hydroforming of elliptical cavities

    Science.gov (United States)

    Singer, W.; Singer, X.; Jelezov, I.; Kneisel, P.

    2015-02-01

    Activities of the past several years in developing the technique of forming seamless (weldless) cavity cells by hydroforming are summarized. An overview of the technique developed at DESY for the fabrication of single cells and multicells of the TESLA cavity shape is given and the major rf results are presented. The forming is performed by expanding a seamless tube with internal water pressure while simultaneously swaging it axially. Prior to the expansion the tube is necked at the iris area and at the ends. Tube radii and axial displacements are computer controlled during the forming process in accordance with results of finite element method simulations for necking and expansion using the experimentally obtained strain-stress relationship of tube material. In cooperation with industry different methods of niobium seamless tube production have been explored. The most appropriate and successful method is a combination of spinning or deep drawing with flow forming. Several single-cell niobium cavities of the 1.3 GHz TESLA shape were produced by hydroforming. They reached accelerating gradients Eacc up to 35 MV /m after buffered chemical polishing (BCP) and up to 42 MV /m after electropolishing (EP). More recent work concentrated on fabrication and testing of multicell and nine-cell cavities. Several seamless two- and three-cell units were explored. Accelerating gradients Eacc of 30 - 35 MV /m were measured after BCP and Eacc up to 40 MV /m were reached after EP. Nine-cell niobium cavities combining three three-cell units were completed at the company E. Zanon. These cavities reached accelerating gradients of Eacc=30 - 35 MV /m . One cavity is successfully integrated in an XFEL cryomodule and is used in the operation of the FLASH linear accelerator at DESY. Additionally the fabrication of bimetallic single-cell and multicell NbCu cavities by hydroforming was successfully developed. Several NbCu clad single-cell and double-cell cavities of the TESLA shape have been

  5. Cavity-enhanced spectroscopies

    CERN Document Server

    van Zee, Roger

    2003-01-01

    ""Cavity-Enhanced Spectroscopy"" discusses the use of optical resonators and lasers to make sensitive spectroscopic measurements. This volume is written by the researcchers who pioneered these methods. The book reviews both the theory and practice behind these spectroscopic tools and discusses the scientific discoveries uncovered by these techniques. It begins with a chapter on the use of optical resonators for frequency stabilization of lasers, which is followed by in-depth chapters discussing cavity ring-down spectroscopy, frequency-modulated, cavity-enhanced spectroscopy, intracavity spectr

  6. SPS RF cavity

    CERN Multimedia

    1974-01-01

    The main RF-system of the SPS comprises four cavities: two of 20 m length and two of 16.5 m length. They are all installed in one long straight section (LSS 3). These cavities are of the travelling-wave type operating at a centre frequency of 200.2 MHz. They are wideband, filling time about 700 ns and untuned. A power of up to 790 kW can be supplied to each giving a total accelerating voltage of about 8 MV. The power amplifiers, using tetrodes are installed in a surface building 200 m from the cavities.

  7. Multifocal Carcinoma of Oral Cavity: A Case Report

    OpenAIRE

    Anilkumar L Bhoweer; Sudarshan Ranpise

    2016-01-01

    Oral Carcinoma is most common among several other cancers in our country (over 40%). The most causative factor is tobacco in various forms. It is very rare to have multiple foci or centres for cancer in oral cavity. The case presents a rarity, having multiple (about 4) cancer sites in the oral cavity.

  8. SPS accelerating cavity

    CERN Multimedia

    1983-01-01

    See photo 8202397: View towards the downstream end of one of the SPS accelerating cavities (200 MHz, travelling wave structure). See 7603195 and 8011289 for more details, 7411032 for the travelling wave structure, and also 8104138.

  9. SPS accelerating cavity

    CERN Multimedia

    1983-01-01

    View towards the downstream end of one of the SPS accelerating cavities (200 MHz, travelling wave structure). See 7603195 and 8011289 for more details, 7411032 for the travelling wave structure, and also 8104138.

  10. accelerating cavity from LEP

    CERN Multimedia

    This is an accelerating cavity from LEP, with a layer of niobium on the inside. Operating at 4.2 degrees above absolute zero, the niobium is superconducting and carries an accelerating field of 6 million volts per metre with negligible losses. Each cavity has a surface of 6 m2. The niobium layer is only 1.2 microns thick, ten times thinner than a hair. Such a large area had never been coated to such a high accuracy. A speck of dust could ruin the performance of the whole cavity so the work had to be done in an extremely clean environment. These challenging requirements pushed European industry to new achievements. 256 of these cavities are now used in LEP to double the energy of the particle beams.

  11. Moving Detectors in Cavities

    CERN Document Server

    Obadia, N

    2007-01-01

    We consider two-level detectors, coupled to a quantum scalar field, moving inside cavities. We highlight some pathological resonant effects due to abrupt boundaries, and decide to describe the cavity by switching smoothly the interaction by a time-dependent gate-like function. Considering uniformly accelerated trajectories, we show that some specific choices of non-adiabatic switching have led to hazardous interpretations about the enhancement of the Unruh effect in cavities. More specifically, we show that the emission/absorption ratio takes arbitrary high values according to the emitted quanta properties and to the transients undergone at the entrance and the exit of the cavity, {\\it independently of the acceleration}. An explicit example is provided where we show that inertial and uniformly accelerated world-lines can even lead to the same ``pseudo-temperature''.

  12. SPS accelerating cavity

    CERN Multimedia

    1976-01-01

    The SPS started up with 2 accelerating cavities (each consisting of 5 tank sections) in LSS3. They have a 200 MHz travelling wave structure (see 7411032 and 7802190) and 750 kW of power is fed to each of the cavities from a 1 MW tetrode power amplifier, located in a surface building above, via a coaxial transmission line. Clemens Zettler, builder of the SPS RF system, is standing at the side of one of the cavities. In 1978 and 1979 another 2 cavities were added and entered service in 1980. These were part of the intensity improvement programme and served well for the new role of the SPS as proton-antiproton collider. See also 7411032, 8011289, 8104138, 8302397.

  13. Melatonin and Oral Cavity

    OpenAIRE

    Murat İnanç Cengiz; Seda Cengiz; Hom-Lay Wang

    2012-01-01

    While initially the oral cavity was considered to be mainly a source of various bacteria, their toxins and antigens, recent studies showed that it may also be a location of oxidative stress and periodontal inflammation. Accordingly, this paper focuses on the involvement of melatonin in oxidative stress diseases of oral cavity as well as on potential therapeutic implications of melatonin in dental disorders. Melatonin has immunomodulatory and antioxidant activities, stimulates the proliferatio...

  14. Oral cavity and leprosy

    OpenAIRE

    Shambulingappa Pallagatti; Soheyl Sheikh; Anupreet Kaur; Amit Aggarwal; Ravinder Singh2

    2012-01-01

    Although leprosy involves the oral cavity in up to 60% of the patients, examination of the oral cavity in leprosy clinics or oral health science clinics is often neglected. Oral involvement in leprosy can broadly be divided into non-specific and specific lesions. In this review, we discuss various oral manifestations in leprosy patients so as to increase the awareness about this aspect among dermatologists and dental surgeons.

  15. Hydroforming of Elliptical Cavities

    OpenAIRE

    W. Singer; Singer, X.; Jelezov, I.; Kneisel, P.

    2015-01-01

    Activities of the past several years in developing the technique of forming seamless (weldless) cavity cells by hydroforming are summarized. An overview of the technique developed at DESY for the fabrication of single cells and multicells of the TESLA cavity shape is given and the major rf results are presented. The forming is performed by expanding a seamless tube with internal water pressure while simultaneously swaging it axially. Prior to the expansion the tube is necked at the iris area ...

  16. Hybrid vertical cavity laser

    DEFF Research Database (Denmark)

    Chung, Il-Sug; Mørk, Jesper

    2010-01-01

    A new hybrid vertical cavity laser structure for silicon photonics is suggested and numerically investigated. It incorporates a silicon subwavelength grating as a mirror and a lateral output coupler to a silicon ridge waveguide.......A new hybrid vertical cavity laser structure for silicon photonics is suggested and numerically investigated. It incorporates a silicon subwavelength grating as a mirror and a lateral output coupler to a silicon ridge waveguide....

  17. Preoperative [18F]Fluorodeoxyglucose Positron Emission Tomography Standardized Uptake Value of Neck Lymph Nodes Predicts Neck Cancer Control and Survival Rates in Patients With Oral Cavity Squamous Cell Carcinoma and Pathologically Positive Lymph Nodes

    International Nuclear Information System (INIS)

    Purpose: Survival in oral cavity squamous cell carcinoma (OSCC) depends heavily on locoregional control. In this prospective study, we sought to investigate whether preoperative maximum standardized uptake value of the neck lymph nodes (SUVnodal-max) may predict prognosis in OSCC patients. Methods and Materials: A total of 120 OSCC patients with pathologically positive lymph nodes were investigated. All subjects underwent a [18F]fluorodeoxyglucose (FDG) positron emission tomography (PET) scan within 2 weeks before radical surgery and neck dissection. All patients were followed up for at least 24 months after surgery or until death. Postoperative adjuvant therapy was performed in the presence of pathologic risk factors. Optimal cutoff values of SUVnodal-max were chosen based on 5-year disease-free survival (DFS), disease-specific survival (DSS), and overall survival (OS). Independent prognosticators were identified by Cox regression analysis. Results: The median follow-up for surviving patients was 41 months. The optimal cutoff value for SUVnodal-max was 5.7. Multivariate analyses identified the following independent predictors of poor outcome: SUVnodal-max ≥5.7 for the 5-year neck cancer control rate, distant metastatic rate, DFS, DSS, and extracapsular spread (ECS) for the 5-year DSS and OS. Among ECS patients, the presence of a SUVnodal-max ≥5.7 identified patients with the worst prognosis. Conclusion: A SUVnodal-max of 5.7, either alone or in combination with ECS, is an independent prognosticator for 5-year neck cancer control and survival rates in OSCC patients with pathologically positive lymph nodes.

  18. Pretreatment Primary Tumor SUVmax Measured by FDG-PET and Pathologic Tumor Depth Predict for Poor Outcomes in Patients With Oral Cavity Squamous Cell Carcinoma and Pathologically Positive Lymph Nodes

    International Nuclear Information System (INIS)

    Purpose: The pathologic tumor depth is an independent prognosticator for local control (LC) and survival in patients with oral cavity squamous cell carcinoma (OSCC). We sought to investigate the prognostic value of the preoperative maximal standardized uptake value (SUVmax) at the primary tumor in OSCC patients with pathologically positive lymph nodes. Methods and Materials: A total of 109 OSCC patients with pathologically positive lymph nodes were investigated. All patients underwent 2-deoxy-2[(18)F]fluoro-D-glucose-positron emission tomography within 2 weeks before surgery and neck dissection. All patients were followed for ≥24 months after surgery or until death. The optimal cutoff value for the primary tumor SUVmax was selected according to the 5-year LC rate. Independent prognosticators were identified by Cox regression analysis. Results: The median follow-up for all patients was 26 months (39 months for surviving patients). A cutoff SUVmax of 19.3 provided the greatest prognostic information for the 5-year LC rate (55% vs. 88%, p = 0.0135). A tumor depth ≥12 mm appeared to be the most appropriate cutoff for predicting the 5-year LC rate (76% vs. 95%, p = 0.0075). A scoring system using the primary tumor SUVmax and tumor depth was formulated to define distinct prognostic groups. Patients with both a SUVmax of ≥19.3 and tumor depth of ≥12 mm (n = 8) had significantly poorer 5-year LC, 5-year disease-free, 5-year disease-specific, and 5-year overall survival rates compared with the other patient groups. Conclusion: The combination of the primary tumor SUVmax (≥19.3) and pathologic tumor depth (≥12 mm) identified a subgroup of OSCC patients at greatest risk of poor LC and death

  19. Multiple repeats of Helicobacter pylori CagA EPIYA-C phosphorylation sites predict risk of gastric ulcer in Iran.

    Science.gov (United States)

    Honarmand-Jahromy, Sahar; Siavoshi, Farideh; Malekzadeh, Reza; Sattari, Taher Nejad; Latifi-Navid, Saeid

    2015-12-01

    Biological activity of Helicobacter pylori oncoprotein CagA is determined by a diversity in the tyrosine phosphorylation motif sites. In the present study, the diversity and the type of the H. pylori CagA EPIYA motifs and their association with gastric ulcer (GU) and duodenal ulcer (DU) in Iranian dyspeptic patients were assessed. PCR amplification, sequencing, and bioinformatic analysis were performed to determine the pattern of CagA EPIYA motifs. Of 168 H. pylori cagA(+) strains, the frequency of ABC was 93.50%, ABCCC 5.40%, ABC + ABCCC 0.6% and ABCC 0.6%. There was no EPIYA-D segment. The ABCCC pattern of EPIYA motif was more frequent in the H. pylori isolates from GU (8/50, 16%) than in those from chronic gastritis (CG) (0/81, 0%) (P = 0). In contrast, The ABC pattern of EPIYA motif was less frequent in the H. pylori isolates from GU (41/50, 82%) than in those from CG (80/81, 98.80%) (Age-sex-adjusted odds ratio (OR) = 0.020, 95% CI = 0.002-0.259; P = 0.003). The distribution of the ABC motif was almost the same in H. pylori isolates from CG (98.80%) and DU diseases (97.30%). There was no significant association between the number of CagA EPIYA-C segment and DU (P > 0.05). We have proposed that CagA from Iranian H. pylori strains were Western type and all strains had active phosphorylation sites. The three EPIYA-C motifs of CagA were more frequently observed in the H. pylori strains from GU; thus it might be an important biomarker for predicting the GU risk in Iran. PMID:26408373

  20. Predicting summer site occupancy for an invasive species, the common brushtail possum (Trichosurus vulpecula, in an urban environment.

    Directory of Open Access Journals (Sweden)

    Amy L Adams

    Full Text Available Invasive species are often favoured in fragmented, highly-modified, human-dominated landscapes such as urban areas. Because successful invasive urban adapters can occupy habitat that is quite different from that in their original range, effective management programmes for invasive species in urban areas require an understanding of distribution, habitat and resource requirements at a local scale that is tailored to the fine-scale heterogeneity typical of urban landscapes. The common brushtail possum (Trichosurus vulpecula is one of New Zealand's most destructive invasive pest species. As brushtail possums traditionally occupy forest habitat, control in New Zealand has focussed on rural and forest habitats, and forest fragments in cities. However, as successful urban adapters, possums may be occupying a wider range of habitats. Here we use site occupancy methods to determine the distribution of brushtail possums across five distinguishable urban habitat types during summer, which is when possums have the greatest impacts on breeding birds. We collected data on possum presence/absence and habitat characteristics, including possible sources of supplementary food (fruit trees, vegetable gardens, compost heaps, and the availability of forest fragments from 150 survey locations. Predictive distribution models constructed using the programme PRESENCE revealed that while occupancy rates were highest in forest fragments, possums were still present across a large proportion of residential habitat with occupancy decreasing as housing density increased and green cover decreased. The presence of supplementary food sources was important in predicting possum occupancy, which may reflect the high nutritional value of these food types. Additionally, occupancy decreased as the proportion of forest fragment decreased, indicating the importance of forest fragments in determining possum distribution. Control operations to protect native birds from possum predation in

  1. A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease

    Directory of Open Access Journals (Sweden)

    Wang Tianyuan

    2009-04-01

    Full Text Available Abstract Transcription factors are key mediators of human complex disease processes. Identifying the target genes of transcription factors will increase our understanding of the biological network leading to disease risk. The prediction of transcription factor binding sites (TFBSs is one method to identify these target genes; however, current prediction methods need improvement. We chose the transcription factor upstream stimulatory factor l (USF1 to evaluate the performance of our novel TFBS prediction method because of its known genetic association with coronary artery disease (CAD and the recent availability of USF1 chromatin immunoprecipitation microarray (ChIP-chip results. The specific goals of our study were to develop a novel and accurate genome-scale method for predicting USF1 binding sites and associated target genes to aid in the study of CAD. Previously published USF1 ChIP-chip data for 1 per cent of the genome were used to develop and evaluate several kernel logistic regression prediction models. A combination of genomic features (phylogenetic conservation, regulatory potential, presence of a CpG island and DNaseI hypersensitivity, as well as position weight matrix (PWM scores, were used as variables for these models. Our most accurate predictor achieved an area under the receiver operator characteristic curve of 0.827 during cross-validation experiments, significantly outperforming standard PWM-based prediction methods. When applied to the whole human genome, we predicted 24,010 USF1 binding sites within 5 kilobases upstream of the transcription start site of 9,721 genes. These predictions included 16 of 20 genes with strong evidence of USF1 regulation. Finally, in the spirit of genomic convergence, we integrated independent experimental CAD data with these USF1 binding site prediction results to develop a prioritised set of candidate genes for future CAD studies. We have shown that our novel prediction method, which employs

  2. On the development of a model predicting the recrystallization texture of aluminum using the Taylor model for rolling textures and the coincidence lattice site theory

    Science.gov (United States)

    T, Morimoto; F, Yoshida; A, Yanagida; J, Yanagimoto

    2015-04-01

    First, hardening model in f.c.c. metals was formulated with collinear interactions slips, Hirth slips and Lomer-Cottrell slips. Using the Taylor and the Sachs rolling texture prediction model, the residual dislocation densities of cold-rolled commercial pure aluminum were estimated. Then, coincidence site lattice grains were investigated from observed cold rolling texture. Finally, on the basis of oriented nucleation theory and coincidence site lattice theory, the recrystallization texture of commercial pure aluminum after low-temperature annealing was predicted.

  3. Thermal and dynamic effects in electron beam welding cavities

    International Nuclear Information System (INIS)

    An experimental and analytical study of the temperature distributions along the molten metal surface in an electron beam welding cavity is described. Surface temperature distributions in cavities were measured with a narrow band infrared radiation pyrometer. The availability of the cavity temperature measurements allowed estimates to be made for the vapor pressure and surface energy forces as a function of cavity position. The results indicated a force imbalance occurred in the cavity. It is postulated that at the location of the force imbalance a liquid material projection forms periodically and moves into the path of the electron beam. The liquid in this projection is driven towards the bottom, partially filling the cavity. This action is followed by the electron beam pushing the liquid aside to form a maximum depth cavity. This process is then repeated. An analysis for predicting cavity oscillation frequency shows reasonable agreement with frequencies measured at the weld root determined from weld sections. A study of the measured temperature distributions in cavities of varying depth combined with the force imbalance observations led to an interpretation of when spiking might occur. A procedure is proposed for determining the spiking tendency for a given set of weld parameters. The results of this study permit a designer to select apriori the best set of weld parameters to achieve a weld of predictable quality

  4. UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

    Science.gov (United States)

    Lua, Rhonald C; Wilson, Stephen J; Konecki, Daniel M; Wilkins, Angela D; Venner, Eric; Morgan, Daniel H; Lichtarge, Olivier

    2016-01-01

    The structure and function of proteins underlie most aspects of biology and their mutational perturbations often cause disease. To identify the molecular determinants of function as well as targets for drugs, it is central to characterize the important residues and how they cluster to form functional sites. The Evolutionary Trace (ET) achieves this by ranking the functional and structural importance of the protein sequence positions. ET uses evolutionary distances to estimate functional distances and correlates genotype variations with those in the fitness phenotype. Thus, ET ranks are worse for sequence positions that vary among evolutionarily closer homologs but better for positions that vary mostly among distant homologs. This approach identifies functional determinants, predicts function, guides the mutational redesign of functional and allosteric specificity, and interprets the action of coding sequence variations in proteins, people and populations. Now, the UET database offers pre-computed ET analyses for the protein structure databank, and on-the-fly analysis of any protein sequence. A web interface retrieves ET rankings of sequence positions and maps results to a structure to identify functionally important regions. This UET database integrates several ways of viewing the results on the protein sequence or structure and can be found at http://mammoth.bcm.tmc.edu/uet/. PMID:26590254

  5. Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites

    OpenAIRE

    Kemp Bruce E; Huber Thomas; Brinkworth Ross I; Saunders Neil FW; Kobe Bostjan

    2008-01-01

    Abstract Background We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so determine the sequence surrounding the phosphorylation site. Predikin was implemented originally as a web application written in Javascript. Results Here, we describe a...

  6. Prominence mass supply and the cavity

    International Nuclear Information System (INIS)

    A prevalent but untested paradigm is often used to describe the prominence-cavity system: the cavity is under-dense because it is evacuated by supplying mass to the condensed prominence. The thermal non-equilibrium (TNE) model of prominence formation offers a theoretical framework to predict the thermodynamic evolution of the prominence and the surrounding corona. We examine the evidence for a prominence-cavity connection by comparing the TNE model with diagnostics of dynamic extreme ultraviolet (EUV) emission surrounding the prominence, specifically prominence horns. Horns are correlated extensions of prominence plasma and coronal plasma which appear to connect the prominence and cavity. The TNE model predicts that large-scale brightenings will occur in the Solar Dynamics Observatory Atmospheric Imaging Assembly 171 Å bandpass near the prominence that are associated with the cooling phase of condensation formation. In our simulations, variations in the magnitude of footpoint heating lead to variations in the duration, spatial scale, and temporal offset between emission enhancements in the other EUV bandpasses. While these predictions match well a subset of the horn observations, the range of variations in the observed structures is not captured by the model. We discuss the implications of our one-dimensional loop simulations for the three-dimensional time-averaged equilibrium in the prominence and the cavity. Evidence suggests that horns are likely caused by condensing prominence plasma, but the larger question of whether this process produces a density-depleted cavity requires a more tightly constrained model of heating and better knowledge of the associated magnetic structure.

  7. Cavity parameters identification for TESLA control system development

    International Nuclear Information System (INIS)

    The control system modeling for the TESLA - TeV-Energy Superconducting Linear Accelerator project has been developed for the efficient stabilization of the pulsed, accelerating EM field of the resonator. The cavity parameters identification is an essential task for the comprehensive control algorithm. The TESLA cavity simulator has been successfully implemented by applying very high speed FPGA - Field Programmable Gate Array technology. The electromechanical model of the cavity resonator includes the basic features - Lorentz force detuning and beam loading. The parameters identification bases on the electrical model of the cavity. The model is represented by the state space equation for the envelope of the cavity voltage driven by the current generator and the beam loading. For a given model structure, the over-determined matrix equation is created covering the long enough measurement range with the solution according to the least squares method. A low degree polynomial approximation is applied to estimate the time-varying cavity detuning during the pulse. The measurement channel distortion is considered, leading to the external cavity model seen by the controller. The comprehensive algorithm of the cavity parameters identification has been implemented in the Matlab system with different modes of the operation. Some experimental results have been presented for different cavity operational conditions. The following considerations have lead to the synthesis of the efficient algorithm for the cavity control system predicted for the potential FPGA technology implementation. (orig.)

  8. Short-cavity squeezing in barium

    Science.gov (United States)

    Hope, D. M.; Bachor, H-A.; Manson, P. J.; Mcclelland, D. E.

    1992-01-01

    Broadband phase sensitive noise and squeezing were experimentally observed in a system of barium atoms interacting with a single mode of a short optical cavity. Squeezing of 13 +/- 3 percent was observed. A maximum possible squeezing of 45 +/- 8 percent could be inferred for out experimental conditions, after correction for measured loss factors. Noise reductions below the quantum limit were found over a range of detection frequencies 60-170 MHz and were best for high cavity transmission and large optical depths. The amount of squeezing observed is consistent with theoretical predictions from a full quantum statistical model of the system.

  9. Fundamental Research in Superconducting RF Cavity Design

    Energy Technology Data Exchange (ETDEWEB)

    Georg Hoffstaetter

    2012-11-13

    This is a 3-year SRF R&D proposal with two main goals: 1) to benefit near term high gradient SRF applications by understanding the causes of quench at high fields in present-day niobium cavities 2) to open the long-range prospects for SRF applications by experimentally verifying the recent exciting theoretical predication for new cavity materials such as Nb3Sn and MgB2. These predictions shwo that ultimately gradients of 100Mv/m to 200MV/m may become possible as material imperfections are overcome.

  10. Development and Validation of a Preprocedural Risk Score to Predict Access Site Complications After Peripheral Vascular Interventions Based on the Vascular Quality Initiative Database

    Directory of Open Access Journals (Sweden)

    Daniel Ortiz

    2016-01-01

    Full Text Available Purpose: Access site complications following peripheral vascular intervention (PVI are associated with prolonged hospitalization and increased mortality. Prediction of access site complication risk may optimize PVI care; however, there is no tool designed for this. We aimed to create a clinical scoring tool to stratify patients according to their risk of developing access site complications after PVI. Methods: The Society for Vascular Surgery’s Vascular Quality Initiative database yielded 27,997 patients who had undergone PVI at 131 North American centers. Clinically and statistically significant preprocedural risk factors associated with in-hospital, post-PVI access site complications were included in a multivariate logistic regression model, with access site complications as the outcome variable. A predictive model was developed with a random sample of 19,683 (70% PVI procedures and validated in 8,314 (30%. Results: Access site complications occurred in 939 (3.4% patients. The risk tool predictors are female gender, age > 70 years, white race, bedridden ambulatory status, insulin-treated diabetes mellitus, prior minor amputation, procedural indication of claudication, and nonfemoral arterial access site (model c-statistic = 0.638. Of these predictors, insulin-treated diabetes mellitus and prior minor amputation were protective of access site complications. The discriminatory power of the risk model was confirmed by the validation dataset (c-statistic = 0.6139. Higher risk scores correlated with increased frequency of access site complications: 1.9% for low risk, 3.4% for moderate risk and 5.1% for high risk. Conclusions: The proposed clinical risk score based on eight preprocedural characteristics is a tool to stratify patients at risk for post-PVI access site complications. The risk score may assist physicians in identifying patients at risk for access site complications and selection of patients who may benefit from bleeding avoidance

  11. Cavity solitons in broad-area vertical-cavity surface-emitting lasers below threshold

    International Nuclear Information System (INIS)

    Cavity solitons are stationary self-organized bright intensity peaks which form over a homogeneous background in the section of broad area radiation beams. They are generated by shining a writing/erasing laser pulse into a nonlinear optical cavity, driven by a holding beam. The ability to control their location and their motion by introducing phase or amplitude gradients in the holding beam makes them interesting as mobile pixels for all-optical processing units. We show the generation of a number of cavity solitons in broad-area vertical cavity semiconductor microresonators electrically pumped above transparency but slightly below threshold. We analyze the switching process in details. The observed spots can be written, erased, and manipulated as independent objects, as predicted by the theoretical model. An especially tailored one is used to simulate the studied phenomena and to compare our simulations to the experimental findings with good agreement

  12. The use of microperforated plates to attenuate cavity resonances

    DEFF Research Database (Denmark)

    Fenech, Benjamin; Keith, Graeme; Jacobsen, Finn

    2006-01-01

    The use of microperforated plates to introduce damping in a closed cavity is examined. By placing a microperforated plate well inside the cavity instead of near a wall as traditionally done in room acoustics, high attenuation can be obtained for specific acoustic modes, compared with the lower...... attenuation that can be obtained in a broad frequency range with the conventional position of the plate. An analytical method for predicting the attenuation is presented. The method involves finding complex eigenvalues and eigenfunctions for the modified cavity and makes it possible to predict Green......'s functions. The results, which are validated experimentally, show that a microperforated plate can provide substantial attenuation of modes in a cavity. One possible application of these findings is the treatment of boiler tones in heat-exchanger cavities....

  13. Real-time prediction of earthquake ground motion: application of data assimilation and real-time correction of site amplification factors

    Science.gov (United States)

    Hoshiba, M.

    2013-12-01

    In this presentation, I explain the data assimilation technique and real-time correction of frequency-dependent site amplification factor for time evolutional prediction of seismic ground motion (waveforms) which is applicable to Earthquake Early Warning (EEW). At present, many methods of EEW determine hypocenter and magnitude (source parameters) rapidly at first, and then ground motion is predicted using the hypocenter and magnitude. The warnings are issued depending on the strength of the predicted ground motion. In this method, however, it is not easy to take source extent and the effects of rupture directivity into account. Although S-wave arrival does not necessary means the start of the strong motion for large earthquakes as experienced during the 2011 Tohoku earthquake (Mw9.0), it is hard to predict the time evolution of ground motion strength. In general, wave motion is predictable when boundary condition and initial condition are given. Time evolutional prediction is a method based on this approach using the current wavefield as an initial condition, that is u(x, t+Δt)=P(u(x, t)), where u is the wave motion at location x at lapse time t, and P is the prediction operator. Future wave motion, u(x, t+Δt), is predicted using P from the distribution of the current wavefield, u(x, t). For P, finite difference technique or boundary integral equation method, such as Kirchhoff integral, is used. The time evolutional prediction enables us to predict the time evolution of ground motion strength. In the time evolutional prediction, determination of detailed distribution of current wave motion is a key, so that dense seismic observation network is required. Data assimilation is a technique to produce artificially denser network, which is widely used for numerical weather forecast and oceanography. Distribution of current wave motion is estimated from not only the current actual observation of u(x, t), but also the prediction of one step before, P(u(x, t

  14. Metasurface external cavity laser

    Science.gov (United States)

    Xu, Luyao; Curwen, Christopher A.; Hon, Philip W. C.; Chen, Qi-Sheng; Itoh, Tatsuo; Williams, Benjamin S.

    2015-11-01

    A vertical-external-cavity surface-emitting-laser is demonstrated in the terahertz range, which is based upon an amplifying metasurface reflector composed of a sub-wavelength array of antenna-coupled quantum-cascade sub-cavities. Lasing is possible when the metasurface reflector is placed into a low-loss external cavity such that the external cavity—not the sub-cavities—determines the beam properties. A near-Gaussian beam of 4.3° × 5.1° divergence is observed and an output power level >5 mW is achieved. The polarized response of the metasurface allows the use of a wire-grid polarizer as an output coupler that is continuously tunable.

  15. Metasurface external cavity laser

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Luyao, E-mail: luyaoxu.ee@ucla.edu; Curwen, Christopher A.; Williams, Benjamin S. [Department of Electrical Engineering, University of California, Los Angeles, California 90095 (United States); California NanoSystems Institute, University of California, Los Angeles, California 90095 (United States); Hon, Philip W. C.; Itoh, Tatsuo [Department of Electrical Engineering, University of California, Los Angeles, California 90095 (United States); Chen, Qi-Sheng [Northrop Grumman Aerospace Systems, Redondo Beach, California 90278 (United States)

    2015-11-30

    A vertical-external-cavity surface-emitting-laser is demonstrated in the terahertz range, which is based upon an amplifying metasurface reflector composed of a sub-wavelength array of antenna-coupled quantum-cascade sub-cavities. Lasing is possible when the metasurface reflector is placed into a low-loss external cavity such that the external cavity—not the sub-cavities—determines the beam properties. A near-Gaussian beam of 4.3° × 5.1° divergence is observed and an output power level >5 mW is achieved. The polarized response of the metasurface allows the use of a wire-grid polarizer as an output coupler that is continuously tunable.

  16. Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Kemp Bruce E

    2008-05-01

    Full Text Available Abstract Background We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so determine the sequence surrounding the phosphorylation site. Predikin was implemented originally as a web application written in Javascript. Results Here, we describe a new version of Predikin, completely revised and rewritten as a modular framework that provides multiple enhancements compared with the original. Predikin now consists of two components: (i PredikinDB, a database of phosphorylation sites that links substrates to kinase sequences and (ii a Perl module, which provides methods to classify protein kinases, reliably identify substrate-determining residues, generate scoring matrices and score putative phosphorylation sites in query sequences. The performance of Predikin as measured using receiver operator characteristic (ROC graph analysis equals or surpasses that of existing comparable methods. The Predikin website has been redesigned to incorporate the new features. Conclusion New features in Predikin include the use of SQL queries to PredikinDB to generate predictions, scoring of predictions, more reliable identification of substrate-determining residues and putative phosphorylation sites, extended options to handle protein kinase and substrate data and an improved web interface. The new features significantly enhance the ability of Predikin to analyse protein kinases and their substrates. Predikin is available at http://predikin.biosci.uq.edu.au.

  17. Experimental investigation of cavity flows

    Energy Technology Data Exchange (ETDEWEB)

    Loeland, Tore

    1998-12-31

    This thesis uses LDV (Laser Doppler Velocimetry), PIV (Particle Image Velocimetry) and Laser Sheet flow Visualisation to study flow inside three different cavity configurations. For sloping cavities, the vortex structure inside the cavities is found to depend upon the flow direction past the cavity. The shape of the downstream corner is a key factor in destroying the boundary layer flow entering the cavity. The experimental results agree well with numerical simulations of the same geometrical configurations. The results of the investigations are used to find the influence of the cavity flow on the accuracy of the ultrasonic flowmeter. A method to compensate for the cavity velocities is suggested. It is found that the relative deviation caused by the cavity velocities depend linearly on the pipe flow. It appears that the flow inside the cavities should not be neglected as done in the draft for the ISO technical report on ultrasonic flowmeters. 58 refs., 147 figs., 2 tabs.

  18. Effect of Pure Dephasing and Phonon Scattering on the Coupling of Semiconductor Quantum Dots to Optical Cavities

    Science.gov (United States)

    Jarlov, C.; Wodey, É.; Lyasota, A.; Calic, M.; Gallo, P.; Dwir, B.; Rudra, A.; Kapon, E.

    2016-08-01

    Using site-controlled semiconductor quantum dots (QDs) free of multiexcitonic continuum states, integrated with photonic crystal membrane cavities, we clarify the effects of pure dephasing and phonon scattering on exciton-cavity coupling in the weak-coupling regime. In particular, the observed QD-cavity copolarization and cavity mode feeding versus QD-cavity detuning are explained quantitatively by a model of a two-level system embedded in a solid-state environment.

  19. Radionuclide Partitioning in an Underground Nuclear Test Cavity

    Energy Technology Data Exchange (ETDEWEB)

    Rose, T P; Hu, Q; Zhao, P; Conrado, C L; Dickerson, R; Eaton, G F; Kersting, A B; Moran, J E; Nimz, G; Powell, B A; Ramon, E C; Ryerson, F J; Williams, R W; Wooddy, P T; Zavarin, M

    2009-01-09

    In 2004, a borehole was drilled into the 1983 Chancellor underground nuclear test cavity to investigate the distribution of radionuclides within the cavity. Sidewall core samples were collected from a range of depths within the re-entry hole and two sidetrack holes. Upon completion of drilling, casing was installed and a submersible pump was used to collect groundwater samples. Test debris and groundwater samples were analyzed for a variety of radionuclides including the fission products {sup 99}Tc, {sup 125}Sb, {sup 129}I, {sup 137}Cs, and {sup 155}Eu, the activation products {sup 60}Co, {sup 152}Eu, and {sup 154}Eu, and the actinides U, Pu, and Am. In addition, the physical and bulk chemical properties of the test debris were characterized using Scanning Electron Microscopy (SEM) and Electron Microprobe measurements. Analytical results were used to evaluate the partitioning of radionuclides between the melt glass, rubble, and groundwater phases in the Chancellor test cavity. Three comparative approaches were used to calculate partitioning values, though each method could not be applied to every nuclide. These approaches are based on: (1) the average Area 19 inventory from Bowen et al. (2001); (2) melt glass, rubble, and groundwater mass estimates from Zhao et al. (2008); and (3) fission product mass yield data from England and Rider (1994). The U and Pu analyses of the test debris are classified and partitioning estimates for these elements were calculated directly from the classified Miller et al. (2002) inventory for the Chancellor test. The partitioning results from this study were compared to partitioning data that were previously published by the IAEA (1998). Predictions of radionuclide distributions from the two studies are in agreement for a majority of the nuclides under consideration. Substantial differences were noted in the partitioning values for {sup 99}Tc, {sup 125}Sb, {sup 129}I, and uranium. These differences are attributable to two factors

  20. Molecular dynamics study of naturally existing cavity couplings in proteins.

    Directory of Open Access Journals (Sweden)

    Montserrat Barbany

    Full Text Available Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100 ns from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.

  1. SPS accelerating cavity

    CERN Multimedia

    1983-01-01

    See photo 8302397: View from the downstream end of one of the SPS accelerating cavities (200 MHz, travelling wave structure). See 7603195 and 8011289 for more details, 7411032 for the travelling wave structure, and also 8104138. Giacomo Primadei stands on the left.

  2. Laser cavity modelling

    OpenAIRE

    Damakoa, I.; Audounet, J.; Bouyssou, G.; Vassilieff, G.

    1993-01-01

    Two approachs of modelling nonhomogeneous cavity laser are presented. They are based on the beam propagation method which allows the use of fast Fourier transform (FFT). The resulting procedures provide selfconsistent solutions to the Maxwell and diffusion equations. Results are given to illustrate the two methods.


  3. LEP superconducting cavity

    CERN Multimedia

    1995-01-01

    Engineers work in a clean room on one of the superconducting cavities for the upgrade to the LEP accelerator, known as LEP-2. The use of superconductors allow higher electric fields to be produced so that higher beam energies can be reached.

  4. Cavity launchers for ICRF

    International Nuclear Information System (INIS)

    A type of resonant coil cavity is analyzed as a launcher for ICRF. This approach offers the advantages of: (1) convenient and flexible sizing, (2) ease of operation and maintenance, and (3) high power handling capability. We present results for resonance conditions, mode structures, power handling capabilities, and sensitivity to variation in plasma parameters

  5. Statistical electromagnetics: Complex cavities

    NARCIS (Netherlands)

    Naus, H.W.L.

    2008-01-01

    A selection of the literature on the statistical description of electromagnetic fields and complex cavities is concisely reviewed. Some essential concepts, for example, the application of the central limit theorem and the maximum entropy principle, are scrutinized. Implicit assumptions, biased choic

  6. What's a Cavity?

    Science.gov (United States)

    ... and deeper over time. Cavities are also called dental caries (say: KARE-eez), and if you have a ... made up mostly of the germs that cause tooth decay. The bacteria in your mouth make acids and when plaque clings to your teeth, the acids can eat away at the outermost ...

  7. Niobium superconducting cavity

    CERN Multimedia

    1980-01-01

    This 5-cell superconducting cavity, made from bulk-Nb, stems from the period of general studies, not all directed towards direct use at LEP. This one is dimensioned for 1.5 GHz, the frequency used at CEBAF and also studied at Saclay (LEP RF was 352.2 MHz). See also 7908227, 8007354, 8209255, 8210054, 8312339.

  8. Predicting ambient aerosol thermal-optical reflectance (TOR measurements from infrared spectra: extending the predictions to different years and different sites

    Directory of Open Access Journals (Sweden)

    M. Reggente

    2015-11-01

    We also propose a method to anticipate the prediction error: we calculate the squared Mahalanobis distance in the feature space (scores determined by PLSR between new spectra and spectra in the calibration set. The squared Mahalanobis distance provides a crude method for assessing the magnitude of mean error when applying a calibration model to a new set of samples.

  9. Seismic wave interaction with underground cavities

    Science.gov (United States)

    Schneider, Felix M.; Esterhazy, Sofi; Perugia, Ilaria; Bokelmann, Götz

    2016-04-01

    Realization of the future Comprehensive Nuclear Test Ban Treaty (CTBT) will require ensuring its compliance, making the CTBT a prime example of forensic seismology. Following indications of a nuclear explosion obtained on the basis of the (IMS) monitoring network further evidence needs to be sought at the location of the suspicious event. For such an On-Site Inspection (OSI) at a possible nuclear test site the treaty lists several techniques that can be carried out by the inspection team, including aftershock monitoring and the conduction of active seismic surveys. While those techniques are already well established, a third group of methods labeled as "resonance seismometry" is less well defined and needs further elaboration. A prime structural target that is expected to be present as a remnant of an underground nuclear explosion is a cavity at the location and depth the bomb was fired. Originally "resonance seismometry" referred to resonant seismic emission of the cavity within the medium that could be stimulated by an incident seismic wave of the right frequency and observed as peaks in the spectrum of seismic stations in the vicinity of the cavity. However, it is not yet clear which are the conditions for which resonant emissions of the cavity could be observed. In order to define distance-, frequency- and amplitude ranges at which resonant emissions could be observed we study the interaction of seismic waves with underground cavities. As a generic model for possible resonances we use a spherical acoustic cavity in an elastic full-space. To solve the forward problem for the full elastic wave field around acoustic spherical inclusions, we implemented an analytical solution (Korneev, 1993). This yields the possibility of generating scattering cross-sections, amplitude spectrums and synthetic seismograms for plane incident waves. Here, we focus on the questions whether or not we can expect resonant responses in the wave field scattered from the cavity. We show

  10. Prediction of Pseudo relative velocity response spectra at Yucca Mountain for underground nuclear explosions conducted in the Pahute Mesa testing area at the Nevada testing site

    International Nuclear Information System (INIS)

    The Yucca Mountain Site Characterization Project (YMP), managed by the Office of Geologic Disposal of the Office of Civilian Radioactive Waste Management of the US Department of Energy, is examining the feasibility of siting a repository for commercial, high-level nuclear wastes at Yucca Mountain on and adjacent to the Nevada Test Site (NTS). This work, intended to extend our understanding of the ground motion at Yucca Mountain resulting from testing of nuclear weapons on the NTS, was funded by the Yucca Mountain project and the Military Applications Weapons Test Program. This report summarizes one aspect of the weapons test seismic investigations conducted in FY88. Pseudo relative velocity response spectra (PSRV) have been calculated for a large body of surface ground motions generated by underground nuclear explosions. These spectra have been analyzed and fit using multiple linear regression techniques to develop a credible prediction technique for surface PSRVs. In addition, a technique for estimating downhole PSRVs at specific stations is included. A data summary, data analysis, prediction development, prediction evaluation, software summary and FORTRAN listing of the prediction technique are included in this report

  11. Coupled Geomechanical Simulations of UCG Cavity Evolution

    Energy Technology Data Exchange (ETDEWEB)

    Morris, J P; Buscheck, T A; Hao, Y

    2009-07-13

    This paper presents recent work from an ongoing project to develop predictive tools for cavity/combustion-zone growth and to gain quantitative understanding of the processes and conditions (both natural and engineered) affecting underground coal gasification (UCG). In this paper we will focus upon the development of coupled geomechanical capabilities for simulating the evolution of the UCG cavity using discrete element methodologies. The Discrete Element Method (DEM) has unique advantages for facilitating the prediction of the mechanical response of fractured rock masses, such as cleated coal seams. In contrast with continuum approaches, the interfaces within the coal can be explicitly included and combinations of both elastic and plastic anisotropic response are simulated directly. Additionally, the DEM facilitates estimation of changes in hydraulic properties by providing estimates of changes in cleat aperture. Simulation of cavity evolution involves a range of coupled processes and the mechanical response of the host coal and adjoining rockmass plays a role in every stage of UCG operations. For example, cavity collapse during the burn has significant effect upon the rate of the burn itself. In the vicinity of the cavity, collapse and fracturing may result in enhanced hydraulic conductivity of the rock matrix in the coal and caprock above the burn chamber. Even far from the cavity, stresses due to subsidence may be sufficient to induce new fractures linking previously isolated aquifers. These mechanical processes are key in understanding the risk of unacceptable subsidence and the potential for groundwater contamination. These mechanical processes are inherently non-linear, involving significant inelastic response, especially in the region closest to the cavity. In addition, the response of the rock mass involves both continuum and discrete mechanical behavior. We have recently coupled the LDEC (Livermore Distinct Element Code) and NUFT (Non

  12. Seamless/bonded niobium cavities

    Science.gov (United States)

    Singer, W.

    2006-07-01

    Technological aspects and performance of seamless cavities produced by hydroforming are presented. Problems related to the fabrication of seamless cavities from bulk niobium are mainly solved thanks to the progress of the last years. The highest achieved accelerating gradients are comparable for both seamless and welded versions (ca. 40 MV/m) Nevertheless further development of seamless cavities is desirable in order to avoid the careful preparation of parts for welding and get reliable statistic. Fabrication of NbCu clad cavities from bimetallic tubes is an interesting option that gives new opportunity to the seamless technique. On the one hand it allows reducing the niobium costs contribution; on the other hand it increases the thermal stability of the cavity. The highest accelerating gradient achieved on seamless NbCu clad single cell cavities (ca. 40 MV/m) is comparable to the one reached on bulk Nb cavities. Fabrication of multi-cell NbCu cavities by hydroforming was recently proven.

  13. Development of a regression model to predict copper toxicity to Daphnia magna and site-specific copper criteria across multiple surface-water drainages in an arid landscape.

    Science.gov (United States)

    Fulton, Barry A; Meyer, Joseph S

    2014-08-01

    The water effect ratio (WER) procedure developed by the US Environmental Protection Agency is commonly used to derive site-specific criteria for point-source metal discharges into perennial waters. However, experience is limited with this method in the ephemeral and intermittent systems typical of arid climates. The present study presents a regression model to develop WER-based site-specific criteria for a network of ephemeral and intermittent streams influenced by nonpoint sources of Cu in the southwestern United States. Acute (48-h) Cu toxicity tests were performed concurrently with Daphnia magna in site water samples and hardness-matched laboratory waters. Median effect concentrations (EC50s) for Cu in site water samples (n=17) varied by more than 12-fold, and the range of calculated WER values was similar. Statistically significant (α=0.05) univariate predictors of site-specific Cu toxicity included (in sequence of decreasing significance) dissolved organic carbon (DOC), hardness/alkalinity ratio, alkalinity, K, and total dissolved solids. A multiple-regression model developed from a combination of DOC and alkalinity explained 85% of the toxicity variability in site water samples, providing a strong predictive tool that can be used in the WER framework when site-specific criteria values are derived. The biotic ligand model (BLM) underpredicted toxicity in site waters by more than 2-fold. Adjustments to the default BLM parameters improved the model's performance but did not provide a better predictive tool compared with the regression model developed from DOC and alkalinity. PMID:24796294

  14. Changeability of Oral Cavity Environment

    OpenAIRE

    Surdacka, Anna; Strzyka³a, Krystyna; Rydzewska, Anna

    2007-01-01

    Objectives In dentistry, the results of in vivo studies on drugs, dental fillings or prostheses are routinely evaluated based on selected oral cavity environment parameters at specific time points. Such evaluation may be confounded by ongoing changes in the oral cavity environment induced by diet, drug use, stress and other factors. The study aimed to confirm oral cavity environment changeability. Methods 24 healthy individuals aged 20–30 had their oral cavity environment prepared by having p...

  15. Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions

    Directory of Open Access Journals (Sweden)

    Merkulova Tatyana I

    2007-12-01

    Full Text Available Abstract Background Reliable transcription factor binding site (TFBS prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the high false-positive rates that occur when only sequence conservation at the core binding-sites is considered. Results To improve this situation, we have quantified the performance of several Position Weight Matrix (PWM algorithms, using exhaustive approaches to find their optimal length and position. We applied these approaches to bio-medically important TFBSs involved in the regulation of cell growth and proliferation as well as in inflammatory, immune, and antiviral responses (NF-κB, ISGF3, IRF1, STAT1, obesity and lipid metabolism (PPAR, SREBP, HNF4, regulation of the steroidogenic (SF-1 and cell cycle (E2F genes expression. We have also gained extra specificity using a method, entitled SiteGA, which takes into account structural interactions within TFBS core and flanking regions, using a genetic algorithm (GA with a discriminant function of locally positioned dinucleotide (LPD frequencies. To ensure a higher confidence in our approach, we applied resampling-jackknife and bootstrap tests for the comparison, it appears that, optimized PWM and SiteGA have shown similar recognition performances. Then we applied SiteGA and optimized PWMs (both separately and together to sequences in the Eukaryotic Promoter Database (EPD. The resulting SiteGA recognition models can now be used to search sequences for BSs using the web tool, SiteGA. Analysis of dependencies between close and distant LPDs revealed by SiteGA models has shown that the most significant correlations are between close LPDs, and are generally located in the core (footprint region. A greater number of less significant correlations are mainly between distant LPDs, which spanned both core and flanking regions. When SiteGA and optimized PWM models were applied

  16. A Cultural Heritage Management Methodology for Assessing the Vulnerabilities of Archaeological Sites to Predicted Climate Change Focuing on Ireland's Two World Heritage Sites

    OpenAIRE

    Daly, Caithleen, [Thesis

    2014-01-01

    The affect climate change will have on cultural heritage preservation poses a global challenge and is being addressed by international organisations such as UNESCO and ICOMOS. The aim of this doctoral research is to assist heritage managers in understanding the implications of climate change for the sites in their care. It addresses the question of how to approach the assessment and measurement of climate change impacts on cultural heritage. The potential future effects of climate change on c...

  17. Predictions of Cleavability of Calpain Proteolysis by Quantitative Structure-Activity Relationship Analysis Using Newly Determined Cleavage Sites and Catalytic Efficiencies of an Oligopeptide Array.

    Science.gov (United States)

    Shinkai-Ouchi, Fumiko; Koyama, Suguru; Ono, Yasuko; Hata, Shoji; Ojima, Koichi; Shindo, Mayumi; duVerle, David; Ueno, Mika; Kitamura, Fujiko; Doi, Naoko; Takigawa, Ichigaku; Mamitsuka, Hiroshi; Sorimachi, Hiroyuki

    2016-04-01

    Calpains are intracellular Ca(2+)-regulated cysteine proteases that are essential for various cellular functions. Mammalian conventional calpains (calpain-1 and calpain-2) modulate the structure and function of their substrates by limited proteolysis. Thus, it is critically important to determine the site(s) in proteins at which calpains cleave. However, the calpains' substrate specificity remains unclear, because the amino acid (aa) sequences around their cleavage sites are very diverse. To clarify calpains' substrate specificities, 84 20-mer oligopeptides, corresponding to P10-P10' of reported cleavage site sequences, were proteolyzed by calpains, and the catalytic efficiencies (kcat/Km) were globally determined by LC/MS. This analysis revealed 483 cleavage site sequences, including 360 novel ones. Thekcat/Kms for 119 sites ranged from 12.5-1,710 M(-1)s(-1) Although most sites were cleaved by both calpain-1 and -2 with a similarkcat/Km, sequence comparisons revealed distinct aa preferences at P9-P7/P2/P5'. The aa compositions of the novel sites were not statistically different from those of previously reported sites as a whole, suggesting calpains have a strict implicit rule for sequence specificity, and that the limited proteolysis of intact substrates is because of substrates' higher-order structures. Cleavage position frequencies indicated that longer sequences N-terminal to the cleavage site (P-sites) were preferred for proteolysis over C-terminal (P'-sites). Quantitative structure-activity relationship (QSAR) analyses using partial least-squares regression and >1,300 aa descriptors achievedkcat/Kmprediction withr= 0.834, and binary-QSAR modeling attained an 87.5% positive prediction value for 132 reported calpain cleavage sites independent of our model construction. These results outperformed previous calpain cleavage predictors, and revealed the importance of the P2, P3', and P4' sites, and P1-P2 cooperativity. Furthermore, using our binary-QSAR model

  18. Predictive mutagenesis of ligation-independent cloning (LIC) vectors for protein expression and site-specific chemical conjugation

    DEFF Research Database (Denmark)

    Vernet, Erik; Sauer, Jørgen; Andersen, Peter Andreas;

    2011-01-01

    Ligation-independent cloning (LIC) allows for cloning of DNA constructs independent of insert restriction sites and ligases. However, any required mutations are typically introduced by additional, time-consuming steps. We present a rapid, inexpensive method for mutagenesis in the 5' LIC site...

  19. Prediction of antigenic sites on ALS1 and HWP1 protein sequences in vaginal isolated C. albicans of using bioinformatics analysis

    Directory of Open Access Journals (Sweden)

    Mona Pakdel

    2015-04-01

    Full Text Available Background and Aim: The ability to predict antigenic sites on proteins is of major importance for medication. The aim of this study was to predict the antigenic sites on Agglutin in Like Sequence (ALS1 and Hyphal Wall Protein Sequences (HWP1 in Candida albicans isolated of vaginal infections using Physico-Chemical Profiles server. Materials and Methods: 7 isolates were obtained from women with vaginal infection which were collected from various medical centers of Tehran in 2011 and 2012. At the first,DNA was extracted  by Phenol-Chloroform method. Multiplex PCR was performed by using specific primers. In order to do bioinformatic studies, the genes were sequenced and then translated. Antigenic sites of protein sequences were identified by Physico-Chemical Profiles program. Results: The results showed that the presence of two genes als1 and hwp1 in isolates. In ALS1 and HWP1, respectively 2 and 1 antigenic site with the most antigenicity were identified. Conclusions: According to previous studies, Serine and Threonine phosphorylation is an important mechanism in pathogenesis of ALS1 and HWP1 proteins. Results in this study showed that serine and threonine are the most amino acids in the antigenic sites with high antigenicity property.

  20. Hollow waveguide cavity ringdown spectroscopy

    Science.gov (United States)

    Dreyer, Chris (Inventor); Mungas, Greg S. (Inventor)

    2012-01-01

    Laser light is confined in a hollow waveguide between two highly reflective mirrors. This waveguide cavity is used to conduct Cavity Ringdown Absorption Spectroscopy of loss mechanisms in the cavity including absorption or scattering by gases, liquid, solids, and/or optical elements.

  1. Colloquium: cavity optomechanics

    CERN Multimedia

    2011-01-01

    Monday 14 November 2011, 17:00 Ecole de Physique, Auditoire Stueckelberg Université de Genève Cavity optomechanics: controlling micro mechanical oscillators with laser light Prof. Tobias Kippenberg EPFL, Lausanne Laser light can be used to cool and to control trapped ions, atoms and molecules at the quantum level. This has lead to spectacular advances such as the most precise atomic clocks. An outstanding frontier is the control with lasers of nano- and micro-mechancial systems. Recent advances in cavity optomechanics have allowed such elementary control for the first time, enabling mechanical systems to be ground state cooled leading to readout with quantum limited sensitivity and permitting to explore new device concepts resulting from radiation pressure.  

  2. RF superconducting cavities

    CERN Document Server

    Kojima, Y

    1980-01-01

    The history and present activity in research on RF superconducting cavities in various countries are reviewed. The program of the July 1980 Karlsruhe workshop is reproduced and research activity in this field at Stanford HEPL and SLAC, Cornell, Oregon, Brookhaven, KEK (Japan), Weismann (Israel), Genoa, CERN and Karlsruhe (KfK) listed. The theoretical basis of surface resistance and intracavity magnetic field, multipacing and non-resonant electron loading are outlined. (20 refs).

  3. Entangling atoms in bad cavities

    OpenAIRE

    Sorensen, Anders S.; Molmer, Klaus

    2002-01-01

    We propose a method to produce entangled spin squeezed states of a large number of atoms inside an optical cavity. By illuminating the atoms with bichromatic light, the coupling to the cavity induces pairwise exchange of excitations which entangles the atoms. Unlike most proposals for entangling atoms by cavity QED, our proposal does not require the strong coupling regime g^2/\\kappa\\Gamma>> 1, where g is the atom cavity coupling strength, \\kappa is the cavity decay rate, and \\Gamma is the dec...

  4. Cavity Backed Slot Antenna

    Directory of Open Access Journals (Sweden)

    Sarang Masani, Ila Parmar, Hitendra Jadeja

    2013-05-01

    Full Text Available Among the current driving forces in wireless communications, there is a need for compact, efficient, inexpensive and reproducible antennas. In some instances, particularly long-distance applications, radiators with directive, high-gain characteristics are necessary. This paper proposes a cavity-backed slot antenna to that end. This antenna will enhance the gain, directivity and can also be easily flush mounted to the flying object. The shape and size of the slot can be effectively utilized to get the desired result. The proposed antenna is feed by waveguide which facilitate it to be applicable at high power operation where coaxial cable fails due to skin effect. Present antenna is verified using Numerical Technique called Finite Element Method FEM. The conception of this antenna is realized by the software HFSS “Ansoft-High Frequency Structure Simulator”. By properly selecting shapes, dimensions of the slots and number of slot affects the parameters like return loss, gain along Θ, Ø directions, Cartesian plot and radiation pattern .The Backing of cavity to the slot antenna provide the basics of the gain enhancement and the slot loading effect and the cavity volume plays an important role in achieving the desired return loss at the specific frequency.The simulated antenna shows the 7.0944 db of gain and return loss of -28.60. The proposed antenna works at 6 GHz.

  5. Prediction of outcome of tubal ectopic pregnancy on the basis of site of implantation of embryo in the fallopian tube

    Directory of Open Access Journals (Sweden)

    Rajshree D. Katke

    2015-10-01

    Conclusions: Early detection of tubal ectopic and its site of implantation can help in deciding further management especially to go for conservative or surgical management. [Int J Reprod Contracept Obstet Gynecol 2015; 4(5.000: 1431-1435

  6. Predicting Bird and Bat Fatality Risk at Wind Farms and Proposed Wind Farm Sites Using Acoustic-Ultrasonic Recorders

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This project has three objectives: (1) evaluate the ability of dual acoustic-ultrasonic recorders to capture nocturnal calls of birds and bats at wind power sites;...

  7. Incorporating root hydraulic redistribution in CLM4.5: Effects on predicted site and global evapotranspiration, soil moisture, and water storage

    Science.gov (United States)

    Tang, Jinyun; Riley, William J.; Niu, Jie

    2015-12-01

    We implemented the Amenu-Kumar model in the Community Land Model (CLM4.5) to simulate plant Root Hydraulic Redistribution (RHR) and analyzed its influence on CLM hydrology from site to global scales. We evaluated two numerical implementations: the first solved the coupled equations of root and soil water transport concurrently, while the second solved the two equations sequentially. Through sensitivity analysis, we demonstrate that the sequentially coupled implementation (SCI) is numerically incorrect, whereas the tightly coupled implementation (TCI) is numerically robust with numerical time steps varying from 1 to 30 min. At the site-level, we found the SCI approach resulted in better agreement with measured evapotranspiration (ET) at the AmeriFlux Blodgett Forest site, California, whereas the two approaches resulted in equally poor agreement between predicted and measured ET at the LBA Tapajos KM67 Mature Forest site in Amazon, Brazil. Globally, the SCI approach overestimated annual land ET by as much as 3.5 mm d-1 in some grid cells when compared to the TCI estimates. These comparisons demonstrate that TCI is a more robust numerical implementation of RHR. However, we found, even with TCI, that incorporating RHR resulted in worse agreement with measured soil moisture at both the Blodgett Forest and Tapajos sites and degraded the agreement between simulated terrestrial water storage anomaly and Gravity Recovery and Climate Experiment (GRACE) observations. We find including RHR in CLM4.5 improved ET predictions compared with the FLUXNET-MTE estimates north of 20° N but led to poorer predictions in the tropics. The biases in ET were robust and significant regardless of the four different pedotransfer functions or of the two meteorological forcing data sets we applied. We also found that the simulated water table was unrealistically sensitive to RHR. Therefore, we contend that further structural and data improvements are warranted to improve the hydrological

  8. MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence

    OpenAIRE

    Lippi, Marco; Passerini, Andrea; Punta, Marco; Rost, Burkhard; Frasconi, Paolo

    2008-01-01

    Summary: The web server MetalDetector classifies histidine residues in proteins into one of two states (free or metal bound) and cysteines into one of three states (free, metal bound or disulfide bridged). A decision tree integrates predictions from two previously developed methods (DISULFIND and Metal Ligand Predictor). Cross-validated performance assessment indicates that our server predicts disulfide bonding state at 88.6% precision and 85.1% recall, while it identifies cysteines and histi...

  9. Imbalanced multi-modal multi-label learning for subcellular localization prediction of human proteins with both single and multiple sites.

    Directory of Open Access Journals (Sweden)

    Jianjun He

    Full Text Available It is well known that an important step toward understanding the functions of a protein is to determine its subcellular location. Although numerous prediction algorithms have been developed, most of them typically focused on the proteins with only one location. In recent years, researchers have begun to pay attention to the subcellular localization prediction of the proteins with multiple sites. However, almost all the existing approaches have failed to take into account the correlations among the locations caused by the proteins with multiple sites, which may be the important information for improving the prediction accuracy of the proteins with multiple sites. In this paper, a new algorithm which can effectively exploit the correlations among the locations is proposed by using gaussian process model. Besides, the algorithm also can realize optimal linear combination of various feature extraction technologies and could be robust to the imbalanced data set. Experimental results on a human protein data set show that the proposed algorithm is valid and can achieve better performance than the existing approaches.

  10. Final predictions of ambient conditions along the east-west cross drift using the 3-D UZ site-scale model. Level 4 milestone SP33ABM4

    International Nuclear Information System (INIS)

    In 1998, the Yucca Mountain Site Characterization Project (YMP) is expected to continue construction of an East-West Cross Drift. The 5-meter diameter drift will extend from the North Ramp of the Exploratory Studies Facility (ESF), near Station 19+92, southwest through the repository block, and over to and through the Solitario Canyon Fault. This drift is part of a program designed to enhance characterization of Yucca Mountain and to complement existing surface-based and ESF testing studies. The objective of this milestone is to use the three-dimensional (3-D) unsaturated zone (UZ) site-scale model to predict ambient conditions along the East-West Cross Drift. These predictions provide scientists and engineers with a priori information that can support design and construction of the East-West Cross Drift and associated testing program. The predictions also provide, when compared with data collected after drift construction, an opportunity to test and verify the calibration of the 3-D UZ site-scale model

  11. Crab Cavities for Linear Colliders

    International Nuclear Information System (INIS)

    Crab cavities have been proposed for a wide number of accelerators and interest in crab cavities has recently increased after the successful operation of a pair of crab cavities in KEK-B. In particular crab cavities are required for both the ILC and CLIC linear colliders for bunch alignment. Consideration of bunch structure and size constraints favour a 3.9 GHz superconducting, multi-cell cavity as the solution for ILC, whilst bunch structure and beam-loading considerations suggest an X-band copper travelling wave structure for CLIC. These two cavity solutions are very different in design but share complex design issues. Phase stabilisation, beam loading, wakefields and mode damping are fundamental issues for these crab cavities. Requirements and potential design solutions will be discussed for both colliders.

  12. Crab Cavities for Linear Colliders

    Energy Technology Data Exchange (ETDEWEB)

    Burt, G.; Ambattu, P.; Carter, R.; Dexter, A.; Tahir, I.; /Cockcroft Inst. Accel. Sci. Tech. /Lancaster U.; Beard, C.; Dykes, M.; Goudket, P.; Kalinin, A.; Ma, L.; McIntosh, P.; /Daresbury; Shulte, D.; /CERN; Jones, Roger M.; /Cockcroft Inst. Accel. Sci. Tech. /Manchester U.; Bellantoni, L.; Chase, B.; Church, M.; Khabouline, T.; Latina, A.; /Fermilab; Adolphsen, C.; Li, Z.; Seryi, Andrei; /SLAC

    2011-11-08

    Crab cavities have been proposed for a wide number of accelerators and interest in crab cavities has recently increased after the successful operation of a pair of crab cavities in KEK-B. In particular crab cavities are required for both the ILC and CLIC linear colliders for bunch alignment. Consideration of bunch structure and size constraints favour a 3.9 GHz superconducting, multi-cell cavity as the solution for ILC, whilst bunch structure and beam-loading considerations suggest an X-band copper travelling wave structure for CLIC. These two cavity solutions are very different in design but share complex design issues. Phase stabilisation, beam loading, wakefields and mode damping are fundamental issues for these crab cavities. Requirements and potential design solutions will be discussed for both colliders.

  13. Crab cavities for linear colliders

    CERN Document Server

    Burt, G; Carter, R; Dexter, A; Tahir, I; Beard, C; Dykes, M; Goudket, P; Kalinin, A; Ma, L; McIntosh, P; Shulte, D; Jones, Roger M; Bellantoni, L; Chase, B; Church, M; Khabouline, T; Latina, A; Adolphsen, C; Li, Z; Seryi, Andrei; Xiao, L

    2008-01-01

    Crab cavities have been proposed for a wide number of accelerators and interest in crab cavities has recently increased after the successful operation of a pair of crab cavities in KEK-B. In particular crab cavities are required for both the ILC and CLIC linear colliders for bunch alignment. Consideration of bunch structure and size constraints favour a 3.9 GHz superconducting, multi-cell cavity as the solution for ILC, whilst bunch structure and beam-loading considerations suggest an X-band copper travelling wave structure for CLIC. These two cavity solutions are very different in design but share complex design issues. Phase stabilisation, beam loading, wakefields and mode damping are fundamental issues for these crab cavities. Requirements and potential design solutions will be discussed for both colliders.

  14. Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities.

    Directory of Open Access Journals (Sweden)

    Sarah Barelier

    Full Text Available A key challenge in structure-based discovery is accounting for modulation of protein-ligand interactions by ordered and bulk solvent. To investigate this, we compared ligand binding to a buried cavity in Cytochrome c Peroxidase (CcP, where affinity is dominated by a single ionic interaction, versus a cavity variant partly opened to solvent by loop deletion. This opening had unexpected effects on ligand orientation, affinity, and ordered water structure. Some ligands lost over ten-fold in affinity and reoriented in the cavity, while others retained their geometries, formed new interactions with water networks, and improved affinity. To test our ability to discover new ligands against this opened site prospectively, a 534,000 fragment library was docked against the open cavity using two models of ligand solvation. Using an older solvation model that prioritized many neutral molecules, three such uncharged docking hits were tested, none of which was observed to bind; these molecules were not highly ranked by the new, context-dependent solvation score. Using this new method, another 15 highly-ranked molecules were tested for binding. In contrast to the previous result, 14 of these bound detectably, with affinities ranging from 8 µM to 2 mM. In crystal structures, four of these new ligands superposed well with the docking predictions but two did not, reflecting unanticipated interactions with newly ordered waters molecules. Comparing recognition between this open cavity and its buried analog begins to isolate the roles of ordered solvent in a system that lends itself readily to prospective testing and that may be broadly useful to the community.

  15. The discrete Planck spectrum of a spherical cavity

    International Nuclear Information System (INIS)

    The energy spectrum of black body radiation at the absolute temperature, T, in an ideal spherical cavity of radius, R, is studied. The departures from the classical predictions of Planck's theory, due to the discrete energies of the radiation quanta confined inside the cavity, depend on the adiabatic invariant RT and are significant for RT ≤ 40 cm · K. Special attention was paid to evidence strong changes in the spectrum intensities, forbidden bands of frequency, as well as major modifications of the total energy for RT ≤ 2 cm · K. Similar effects were present in the case of a cubic cavity. (author)

  16. Cavity-Induced Spin-Orbit Coupling in Cold Atoms

    Science.gov (United States)

    Zhu, Chuanzhou; Dong, Lin; Pu, Han

    2016-05-01

    We consider a single ultracold atom trapped inside a single-mode optical cavity, where a two-photon Raman process induces an effective coupling between atom's pseudo-spin and external center-of-mass (COM) motion. Without the COM motion, this system is described by the Jaynes-Cummings (JC) model. We show how the atomic COM motion dramatically modifies the predictions based on the JC model, and how the cavity photon field affects the properties of spin-orbit coupled system. We take a quantum Master equation approach to investigate the situation when the cavity pumping and decay are taken into account.

  17. A model for flow-induced noise of Helmholtz resonator-like cavities

    NARCIS (Netherlands)

    Golliard, J.

    2003-01-01

    This paper presents a single prediction model for the noise generated by a turbulent boundry layer flow grazing on the opening of a Helmholtz-resonator like cavity. The prediction model is validated by comparison with an experimental study. The measured spectra inside the cavity are correctly predic

  18. Characterization of a gyrotron cavity at 10 GHz

    International Nuclear Information System (INIS)

    Experiments have been conducted to characterize a gyrotron cavity designed to operate in the Te 021 mode at 10 GHz. Small holes were introduced into the cavity to couple in and detect the probing power. Evaluation of the loaded Q factor is based on bandwidth measurements whereas standing-wave electric field profile is determined by using perturbation techniques. Good agreement between measured and predicted values of resonant frequencies and Q factors for several fundamental TE modes is found. (author)

  19. Shielding Studies for Superconducting RF Cavities at Fermilab

    Energy Technology Data Exchange (ETDEWEB)

    Ginsburg, Camille; Rakhno, Igor; /Fermilab

    2010-07-20

    A semi-empirical method that allows us to predict intensity of generated field emission in superconducting RF cavities is described. Spatial, angular and energy distributions of the generated radiation are calculated with the FISHPACT code. The Monte Carlo code MARS15 is used for modeling the radiation transport in matter. A comparison with dose rate measurements performed in the Fermilab Vertical Test Facility for ILC-type cavities with accelerating gradients up to 35 MV/m is presented as well.

  20. Cavity cooling and normal-mode spectroscopy of a bound atom-cavity system

    International Nuclear Information System (INIS)

    Full text: Single atoms strongly coupled to the field of an optical cavity form an attractive system for the realization of an atom-light interface useful for quantum information protocols. An experimental implementation of these schemes requires atoms which are trapped, cooled and localized in the cavity mode at a region of strong coupling. In the experiment presented here, single atoms are trapped and stored in a far-detuned intracavity dipole trap. We demonstrate cavity cooling by illuminating the system with a weak, slightly blue-detuned light beam. This extends the storage time of an atom, which is limited by parametric heating from fluctuations of the intracavity dipole trap, by more than a factor of two. The observed cooling force is of Sisyphus-type and was predicted. A special feature of this force is that it does not rely on the spontaneous emission of a photon by the atom, and therefore the cooling force is at least five times larger than the force achievable for free-space cooling methods with comparable excitation of a two-level atom. Preparing single atoms strongly-coupled to the mode of a high-finesse cavity in this way, we observe two well-resolved normal-mode peaks both in transmission of the cavity as well as in the trap lifetime. The experimental data agree well with a Monte Carlo simulation, demonstrating the localization of the atom to within a tenth of a wavelength at a cavity antinode. The ability to individually excite the normal modes of a bound atom-cavity system shows that we have reached good control over this fundamental quantum system. (author)

  1. ChloroP, a neural network-based method for predicting chloroplast transitpeptides and their cleavage sites

    DEFF Research Database (Denmark)

    Emanuelsson, O.; Nielsen, Henrik; von Heijne, Gunnar

    1999-01-01

    We present a neural network based method (ChloroP) for identifying chloroplast transit peptides and their cleavage sites. Using cross-validation, 88% of the sequences in our homology reduced training set were correctly classified as transit peptides or nontransit peptides. This performance level is...... the cleavage sites given in SWISS-PROT. An analysis of 715 Arabidopsis thaliana sequences from SWISS-PROT suggests that the ChloroP method should be useful for the identification of putative transit peptides in genome-wide sequence data. The ChloroP predictor is available as a web-server at http......://www.cbs.dtu.dk/services/ ChloroP/. 0...

  2. Recent ORNL experience in site performance prediction: the Gas Centrifuge Enrichment Plant and the Oak Ridge Central Waste Disposal Facility

    International Nuclear Information System (INIS)

    The suitability of the Portsmouth Gas Centrifuge Enrichment Plant Landfill and the Oak Ridge, Tennessee, Central Waste Disposal Facility for disposal of low-level radioactive waste was evaluated using pathways analyses. For these evaluations, a conservative approach was selected; that is, conservatism was built into the analyses when assumptions concerning future events had to be made or when uncertainties concerning site or waste characteristics existed. Data from comprehensive laboratory and field investigations were used in developing the conceptual and numerical models that served as the basis for the numerical simulations of the long-term transport of contamination to man. However, the analyses relied on conservative scenarios to describe the generation and migration of contamination and the potential human exposure to the waste. Maximum potential doses to man were calculated and compared to the appropriate standards. Even under this conservative framework, the sites were found to provide adequate buffer to persons outside the DOE reservations and conclusions concerning site capacity and site acceptability were drawn. Our experience through these studies has shown that in reaching conclusions in such studies, some consideration must be given to the uncertainties and conservatisms involved in the analyses. Analytical methods to quantitatively assess the probability of future events to occur and to quantitatively determine the sensitivity of the results to data uncertainty may prove useful in relaxing some of the conservatism built into the analyses. The applicability of such methods to pathways analyses is briefly discussed

  3. Tree Growth Prediction in Relation to Simple Set of Site Quality Indicators for Six Native Tree Species in the Philippines

    Directory of Open Access Journals (Sweden)

    F. Santos Martin

    2010-01-01

    Full Text Available The gain in precision to explain the variation on tree growth performance as a function of a set of site indicators was analysed in a stepwise form, increasing its complexity and costs. Six native timber tree species were commonly found on farmer's fields and planted under different types of agroforestry systems. Localization of trees to be used for measurement was achieved through individual interviews to assess timing of introduction of trees. Results proved that native tree species planted on farmers' fields have similar growth rate other exotic timber species as Swietenia macrophylla that are widely spread in the Philippines. Nevertheless, the large fraction of the variation in tree performance that could not be explained by the biophysical site indicators measured implies that farmers take considerable risk in planting trees on the basis of current “scientific” knowledge. The complement of “site characteristics” is probably “management”, and the low determination of tree growth by site properties may in fact be good news for the farmers.

  4. ISR RF cavities

    CERN Multimedia

    1983-01-01

    In each ISR ring the radiofrequency cavities were installed in one 9 m long straight section. The RF system of the ISR had the main purpose to stack buckets of particles (most of the time protons)coming from the CPS and also to accelerate the stacked beam. The installed RF power per ring was 18 kW giving a peak accelerating voltage of 20 kV. The system had a very fine regulation feature allowing to lower the voltage down to 75 V in a smooth and well controlled fashion.

  5. LRRK2 Kinase Activity and Biology are Not Uniformly Predicted by its Autophosphorylation and Cellular Phosphorylation Site Status

    Directory of Open Access Journals (Sweden)

    April Reynolds

    2014-06-01

    Full Text Available Missense mutations in the Leucine Rich Repeat protein Kinase 2 (LRRK2 gene are the most common genetic predisposition to develop Parkinson’s disease (PD LRRK2 is a large multi-domain phosphoprotein with a GTPase domain and a serine/threonine protein kinase domain whose activity is implicated in neuronal toxicity; however the precise mechanism is unknown. LRRK2 autophosphorylates on several serine/threonine residues across the enzyme and is found constitutively phosphorylated on Ser910, Ser935, Ser955 and Ser973, which are proposed to be regulated by upstream kinases. Here we investigate the phosphoregulation at these sites by analyzing the effects of disease-associated mutations Arg1441Cys, Arg1441Gly, Ala1442Pro, Tyr1699Cys, Ile2012Thr, Gly2019Ser, and Ile2020Thr. We also studied alanine substitutions of phosphosite serines 910, 935, 955 and 973 and specific LRRK2 inhibition on autophosphorylation of LRRK2 Ser1292, Thr1491, Thr2483 and phosphorylation at the cellular sites. We found that mutants in the Roc-COR domains, including Arg1441Cys, Arg1441His, Ala1442Pro and Tyr1699Cys, can positively enhance LRRK2 kinase activity while concomitantly inducing the dephosphorylation of the cellular sites. Mutation of the cellular sites individually did not affect LRRK2 intrinsic kinase activity; however, Ser910/935/955/973Ala mutations trended toward increased kinase activity of LRRK2. Increased cAMP levels did not lead to increased LRRK2 cellular site phosphorylation, 14-3-3 binding or kinase activity. In cells, inhibition of LRRK2 kinase activity leads to dephosphorylation of Ser1292 by Calyculin A and okadaic acid sensitive phosphatases, while the cellular sites are dephosphorylated by Calyculin A sensitive phosphatases. These findings indicate that comparative analysis of both Ser1292 and Ser910/935/955/973 phosphorylation sites will provide important and distinct measures of LRRK2 kinase and biological activity in vitro and in vivo.

  6. The Development of Statistical Models for Predicting Surgical Site Infections in Japan: Toward a Statistical Model-Based Standardized Infection Ratio.

    Science.gov (United States)

    Fukuda, Haruhisa; Kuroki, Manabu

    2016-03-01

    OBJECTIVE To develop and internally validate a surgical site infection (SSI) prediction model for Japan. DESIGN Retrospective observational cohort study. METHODS We analyzed surveillance data submitted to the Japan Nosocomial Infections Surveillance system for patients who had undergone target surgical procedures from January 1, 2010, through December 31, 2012. Logistic regression analyses were used to develop statistical models for predicting SSIs. An SSI prediction model was constructed for each of the procedure categories by statistically selecting the appropriate risk factors from among the collected surveillance data and determining their optimal categorization. Standard bootstrapping techniques were applied to assess potential overfitting. The C-index was used to compare the predictive performances of the new statistical models with those of models based on conventional risk index variables. RESULTS The study sample comprised 349,987 cases from 428 participant hospitals throughout Japan, and the overall SSI incidence was 7.0%. The C-indices of the new statistical models were significantly higher than those of the conventional risk index models in 21 (67.7%) of the 31 procedure categories (PSSI prediction models were shown to generally have higher accuracy than conventional risk index models. These new models may have applications in assessing hospital performance and identifying high-risk patients in specific procedure categories. Infect. Control Hosp. Epidemiol. 2016;37(3):260-271. PMID:26694760

  7. Study of the sorption of actinide analogues on calcite and smectite as a model to predict the evolution of radioactive waste disposal in geological sites

    International Nuclear Information System (INIS)

    In the framework of the problem of the radioactive waste disposal in deep geological sites, the purpose of this study is to predict the sorption of radionuclides on minerals within the geological barrier, after the rupture of the containers and the release of the radionuclides into underground water. Neodymium labelled by 147Nd was used as an analogue of trivalent actinides. Calcite and smectite were used as examples of altered minerals of granitic sites. In simple media, neodymium is retained with a high affinity on both minerals. Fast kinetics of fixation, high distribution coefficients and sorption capacities are favorable factors for the slowing down of radionuclide migration in underground water. Fixation on calcite is quasi irreversible. A second kinetic step was observed, leading to an increase of the retention capacity. In the first step, this is probably a superficial sorption, but with a non-homogeneous affinity for sorption sites. An exchange mechanism of Nd3+ with Na+ et Ca2+ ions of smectite occurs. The Freundlich isotherm observed for both minerals can be used for predicting the retention of radioelements as a function of their concentration and introducing these data in a migration model after comparison with the results of dynamic and field experiments. (author)

  8. Predictions of tracer transport in interwell tracer tests at the C-Hole complex. Yucca Mountain site characterization project report milestone 4077

    International Nuclear Information System (INIS)

    This report presents predictions of tracer transport in interwell tracer tests that are to be conducted at the C-Hole complex at the Nevada Test Site on behalf of the Yucca Mountain Site Characterization Project. The predictions are used to make specific recommendations about the manner in which the tracer test should be conducted to best satisfy the needs of the Project. The objective of he tracer tests is to study flow and species transport under saturated conditions in the fractured tuffs near Yucca Mountain, Nevada, the site of a potential high-level nuclear waste repository. The potential repository will be located in the unsaturated zone within Yucca Mountain. The saturated zone beneath and around the mountain represents the final barrier to transport to the accessible environment that radionuclides will encounter if they breach the engineered barriers within the repository and the barriers to flow and transport provided by the unsaturated zone. Background information on the C-Holes is provided in Section 1.1, and the planned tracer testing program is discussed in Section 1.2

  9. Frequency control of radiofrequency cavity

    OpenAIRE

    Menart, Jure

    2014-01-01

    This work describes the design, development and application of the system for frequency control of EMMA accelerator radiofrequency cavity. The problem with the radiofrequency cavities is, that because of various factors (change in the environmental temperature, mechanical stress, ...), they are continuously frequency detuning. The consequence of the frequency detuning is that electromagnetic field in the cavity is not optimal for the acceleration of the particles. For this reason the resonant...

  10. Agenda Trending: Reciprocity and the Predictive Capacity of Social Networking Sites in Intermedia Agenda Setting across Topics over Time

    OpenAIRE

    Jacob Groshek; Megan Clough Groshek

    2013-01-01

    In the contemporary converged media environment, agenda setting is being transformed by the dramatic growth of audiences that are simultaneously media users and producers. The study reported here addresses related gaps in the literature by first comparing the topical agendas of two leading traditional media outlets (New York Times and CNN) with the most frequently shared stories and trending topics on two widely popular Social Networking Sites (Facebook and Twitter). Time-series analyses of t...

  11. Prediction of residual stress due to early age behaviour of massive concrete structures: on site experiments and macroscopic modelling

    OpenAIRE

    Zreiki, Jihad; Lamour, Vincent; Chaouche, Mohend; Moranville, Micheline

    2008-01-01

    Early age behaviour of concrete is based on complex multi-physical and multiscale phenomena. The predication of both cracking risk and residual stresses in hardened concrete structures is still a challenging task. We propose in this paper a practical method to characterize in the construction site the material parameters and to identify a macroscopic model from simple tests. We propose for instance to use a restrained shrinkage ring test to identify a basic early age creep model based on a si...

  12. Single ion cavity QED experiments

    International Nuclear Information System (INIS)

    Full text: We have set up a spherical Paul trap for a storing a single Ca+ ion placed in the center of a high finesse near confocal resonator. We report on experiments demonstrating the coupling of the narrow S1/2-D5/2 transition to the cavity internal light field. Due to the coupling, the ion acts as sensitive probe for the cavity internal field. We are able to map the field distribution by measuring the excitation probability. Scanning the cavity over the resonance imprints a Doppler frequency shift on the cavity field which leads to a spectral shift and a asymmetric broadening of the S-D transition. (author)

  13. Surface state photonic bandgap cavities

    OpenAIRE

    Rahachou, A. I.; Zozoulenko, I. V.

    2005-01-01

    We propose and analyze a new type of a resonant high-Q cavity for lasing, sensing or filtering applications, which is based on a surface states of a finite photonic crystal. We demonstrate that such the cavity can have a Q factor comparable with that one of conventional photonic band-gap defect mode cavities. At the same time, the distinguished feature of the surface mode cavity is that it is situated directly at the surface of the photonic crystal. This might open up new possibilities for de...

  14. Nanofriction in Cavity Quantum Electrodynamics.

    Science.gov (United States)

    Fogarty, T; Cormick, C; Landa, H; Stojanović, Vladimir M; Demler, E; Morigi, Giovanna

    2015-12-01

    The dynamics of cold trapped ions in a high-finesse resonator results from the interplay between the long-range Coulomb repulsion and the cavity-induced interactions. The latter are due to multiple scatterings of laser photons inside the cavity and become relevant when the laser pump is sufficiently strong to overcome photon decay. We study the stationary states of ions coupled with a mode of a standing-wave cavity as a function of the cavity and laser parameters, when the typical length scales of the two self-organizing processes, Coulomb crystallization and photon-mediated interactions, are incommensurate. The dynamics are frustrated and in specific limiting cases can be cast in terms of the Frenkel-Kontorova model, which reproduces features of friction in one dimension. We numerically recover the sliding and pinned phases. For strong cavity nonlinearities, they are in general separated by bistable regions where superlubric and stick-slip dynamics coexist. The cavity, moreover, acts as a thermal reservoir and can cool the chain vibrations to temperatures controlled by the cavity parameters and by the ions' phase. These features are imprinted in the radiation emitted by the cavity, which is readily measurable in state-of-the-art setups of cavity quantum electrodynamics. PMID:26684118

  15. Atomic spatial coherence with spontaneous emission in a strong coupling cavity

    CERN Document Server

    Fang, Zhen; Zhou, Xiaoji; Chen, Xuzong

    2010-01-01

    The role of spontaneous emission in the interaction between a two-level atom and a pumped micro-cavity in the strong coupling regime is discussed in this paper. Especially, using a quantum Monte-Carlo simulation, we investigate atomic spatial coherence. It is found that atomic spontaneous emission destroys the coherence between neighboring lattice sites, while the cavity decay does not. Furthermore, our computation of the spatial coherence function shows that the in-site locality is little affected by the cavity decay, but greatly depends on the cavity pump amplitude.

  16. In-vivo autofluorescence diagnosis of the cancer of oral cavity

    International Nuclear Information System (INIS)

    The results of an in-vivo study carried out on 25 patients with histologically confirmed squamous cell carcinoma (SCC) of the oral cavity are reported. Spectra from different sites of the oral cavity were recorded using a N2 laser based portable fluorimeter developed in-house. The spectral data acquisition was computer controlled. On an average, 5 spectra from the SCC tissue sites and 4 spectra from the visually normal tissue sites were recorded.The autofluorescence spectra was recorded from different cancerous and normal sites of the oral cavity of a patient

  17. High Gradient Accelerator Cavities Using Atomic Layer Deposition

    Energy Technology Data Exchange (ETDEWEB)

    Ives, Robert Lawrence [Calabazas Creek Research, Inc., San Mateo, CA (United States); Parsons, Gregory [North Carolina State Univ., Raleigh, NC (United States); Williams, Philip [North Carolina State Univ., Raleigh, NC (United States); Oldham, Christopher [North Carolina State Univ., Raleigh, NC (United States); Mundy, Zach [North Carolina State Univ., Raleigh, NC (United States); Dolgashev, Valery [SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2014-12-09

    In the Phase I program, Calabazas Creek Research, Inc. (CCR), in collaboration with North Carolina State University (NCSU), fabricated copper accelerator cavities and used Atomic Layer Deposition (ALD) to apply thin metal coatings of tungsten and platinum. It was hypothesized that a tungsten coating would provide a robust surface more resistant to arcing and arc damage. The platinum coating was predicted to reduce processing time by inhibiting oxides that form on copper surfaces soon after machining. Two sets of cavity parts were fabricated. One was coated with 35 nm of tungsten, and the other with approximately 10 nm of platinum. Only the platinum cavity parts could be high power tested during the Phase I program due to schedule and funding constraints. The platinum coated cavity exhibit poor performance when compared with pure copper cavities. Not only did arcing occur at lower power levels, but the processing time was actually longer. There were several issues that contributed to the poor performance. First, machining of the base copper cavity parts failed to achieve the quality and cleanliness standards specified to SLAC National Accelerator Center. Secondly, the ALD facilities were not configured to provide the high levels of cleanliness required. Finally, the nanometer coating applied was likely far too thin to provide the performance required. The coating was ablated or peeled from the surface in regions of high fields. It was concluded that the current ALD process could not provide improved performance over cavities produced at national laboratories using dedicated facilities.

  18. Predict Location(s of Apis dorsata Nesting Sites Using Remote Sensing and Geographic Information System in Melaleuca Foresti

    Directory of Open Access Journals (Sweden)

    M. M. Saberioon

    2010-01-01

    Full Text Available Problem statement: The Asiatic Giant honeybees (Apis dorsata are seasonally abounded throughout the upland and lowland rainforests in South East Asia. The colonies of A. dorsata are found to nest in aggregates on tall bee trees (tree emergent in the open, as well as, nesting singly in concealed locations when nesting low, especially in the submerged forest of Melaleuca cajuputi as in the vast hectare of Melaleuca forest along the coastal areas of Terengganu. The trunk and branches of the Melaleuca trees are almost upright and the bark are papery and loose that it is unsuitable to serve as nesting support for A. dorsata. Therefore, other trees with sloping branches in the vicinity of the Melaleuca forest are chosen as nesting supports for the A. dorsata colonies. Melaleuca cajuputi and Acacia auriculiformis trees are major sources of nectar and pollen for A. dorsata. Approach: A pilot study were conducted to determine the vegetation distribution area of Melaleuca cajuputi and Acacia auriculiformis, colony distribution and density Apis dorsata colonies using the remote-sensing and field survey by GPS hand held in the submerged Melaleuca forest around the village of Gong Beris, Marang district, Terengganu (Upper left 5°219.223N, 103°104.092E and lower down 4°5342.31N, 103°2237.90E. Result: Based on the map and field survey, it is clear that almost all Apis dorsata nesting sites were located in the Acacia auriculiformis areas Melaleuca cajuputi is mostly using by Apis dorsata as source of nectar and pollen in Marang district, Malaysia Conclusion: The outcome on the distribution area and feral colonies nesting sites will be used to propose the locating of possible A. dorsata nesting sites and understand better nesting behavior of Apis dorsata to improvement searching ability for honey hunters in Marang district.

  19. NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility

    DEFF Research Database (Denmark)

    Hansen, Jan Erik; Lund, Ole; Tolstrup, Niels;

    1998-01-01

    The specificities of the UDP-GalNAc; polypeptide N-acetylgalactosaminyltransferases which link the carbohydrate GalNAc to the side-chain of certain serine and threonine residues in mucin type glycoproteins, are presently unknown. The specificity seems to be modulated by sequence context, secondary...... jury of artifical neural networks was trained to recognize the sequence context and surface accessibility of 299 known and verified mucin type O-glycosylation sites extracted from O-GLYCBASE. The cross-validated NetOglyc network system correctly found 83% of the glycosylated and 90% of the non...

  20. Pressure Gradient Effects on Hypersonic Cavity Flow Heating

    Science.gov (United States)

    Everhart, Joel L.; Alter, Stephen J.; Merski, N. Ronald; Wood, William A.; Prabhu, Ramdas K.

    2007-01-01

    The effect of a pressure gradient on the local heating disturbance of rectangular cavities tested at hypersonic freestream conditions has been globally assessed using the two-color phosphor thermography method. These experiments were conducted in the Langley 31-Inch Mach 10 Tunnel and were initiated in support of the Space Shuttle Return-To-Flight Program. Two blunted-nose test surface geometries were developed, including an expansion plate test surface with nearly constant negative pressure gradient and a flat plate surface with nearly zero pressure gradient. The test surface designs and flow characterizations were performed using two-dimensional laminar computational methods, while the experimental boundary layer state conditions were inferred using the measured heating distributions. Three-dimensional computational predictions of the entire model geometry were used as a check on the design process. Both open-flow and closed-flow cavities were tested on each test surface. The cavity design parameters and the test condition matrix were established using the computational predictions. Preliminary conclusions based on an analysis of only the cavity centerline data indicate that the presence of the pressure gradient did not alter the open cavity heating for laminar-entry/laminar-exit flows, but did raise the average floor heating for closed cavities. The results of these risk-reduction studies will be used to formulate a heating assessment of potential damage scenarios occurring during future Space Shuttle flights.

  1. Frequency Tuning for a DQW Crab Cavity

    CERN Document Server

    Verdú-Andrés, Silvia; Ben-Zvi, Ilan; Calaga, Rama; Capatina, Ofelia; Leuxe, Raphael; Skaritka, John; Wu, Qiong; Xiao, Binping; Zanoni, Carlo

    2016-01-01

    The nominal operating frequency for the HL-LHC crab cavities is 400.79 MHz within a bandwidth of ±60kHz. Attaining the required cavity tune implies a good understanding of all the processes that influence the cavity frequency from the moment when the cavity parts are being fabricated until the cavity is installed and under operation. Different tuning options will be available for the DQW crab cavity of LHC. This paper details the different steps in the cavity fabrication and preparation that may introduce a shift in the cavity frequency and introduces the different tuning methods foreseen to bring the cavity frequency to meet the specifications.

  2. Evaluation of Cavity Collapse and Surface Crater Formation at the Norbo Underground Nuclear Test in U8c, Nevada Nuclear Security Site, and the Impact on Stability of the Ground Surface

    Energy Technology Data Exchange (ETDEWEB)

    Pawloski, G A

    2012-06-18

    Lawrence Livermore National Laboratory (LLNL) Containment Program performed a review of nuclear test-related data for the Norbo underground nuclear test in U8c to assist in evaluating this legacy site as a test bed for application technologies for use in On-Site Inspections (OSI) under the Comprehensive Nuclear Test Ban Treaty. This request is similar to one made for the Salut site in U8c (Pawloski, 2012b). Review of the Norbo site is complicated because the test first exhibited subsurface collapse, which was not unusual, but it then collapsed to the surface over one year later, which was unusual. Of particular interest is the stability of the ground surface above the Norbo detonation point. Proposed methods for on-site verification include radiological signatures, artifacts from nuclear testing activities, and imaging to identify alteration to the subsurface hydrogeology due to the nuclear detonation. Aviva Sussman from the Los Alamos National Laboratory (LANL) has also proposed work at this site. Both proposals require physical access at or near the ground surface of specific underground nuclear test locations at the Nevada Nuclear Security Site (NNSS), formerly the Nevada Test Site (NTS), and focus on possible activities such as visual observation, multispectral measurements, and shallow and deep geophysical surveys.

  3. Cancer of the oral cavity

    International Nuclear Information System (INIS)

    Squamous cell carcinomas of the oral cavity are curable. When early tumor (T1 and T2) is diagnosed and treated, cure rates by surgery or irradiation are high. The choice of therapeutic modalities for these lesions is complex and depends on the site of origin and size of the tumor, the presence or absence of nodal metastases, and the age, physical, medical, and socioeconomic status of the patient. Other factors include the willingness of the patient to return for a protracted course of radiation therapy, the skill of the physician, and the relative morbidity and cosmesis of the two forms of treatment. In general, surgery may be considered for early (T1) lesions if the deformity resulting from surgery is minimal. If resection involves major morbidity, such as a deformity that alters cosmesis or the function of the speech and swallowing mechanisms, then radiation therapy is preferred. For medium-sized (T2) tumors, superficial radiation therapy is the treatment of choice, for it controls the disease and preserves normal function and anatomy. Surgery is reserved for radiation failures. Extensive disease (T3 and T4) often associated with bone and muscle involvement and cervical lymph node metastases is rarely curable by radiation therapy or surgery alone; a combined approach using radiation therapy and surgery is therefore the procedure of choice

  4. A Scanning Cavity Microscope

    CERN Document Server

    Mader, Matthias; Hänsch, Theodor W; Hunger, David

    2014-01-01

    Imaging of the optical properties of individual nanosystems beyond fluorescence can provide a wealth of information. However, the minute signals for absorption and dispersion are challenging to observe, and only specialized techniques requiring sophisticated noise rejection are available. Here we use signal enhancement in a scanning optical microcavity to demonstrate ultra-sensitive imaging. Harnessing multiple interactions of probe light with a sample within an optical resonator, we achieve a 1700-fold signal enhancement compared to diffraction-limited microscopy. We demonstrate quantitative imaging of the extinction cross section of gold nanoparticles with a sensitivity below 1 nm2, we show a method to improve spatial resolution potentially below the diffraction limit by using higher order cavity modes, and we present measurements of the birefringence and extinction contrast of gold nanorods. The demonstrated simultaneous enhancement of absorptive and dispersive signals promises intriguing potential for opt...

  5. Genetic effects of radiation and prediction of hereditary pathology of population of areas around the former Semipalatinsk test site

    International Nuclear Information System (INIS)

    Epidemiological analysis of diseases and mortality of the population living in areas around Semipalatinsk test site is not only theoretically interesting in terms of the human being genetics, but is important for the health-care in practice, since it allows correct planning the score of medical social aid to the sick people and their families, including measures. Assessment of posterior consequences of low dose radiation effect on health of the population of the areas around the former Semipalatinsk nuclear test site is of special interest. Many underground, atmospheric and above-ground tests of nuclear weapon resulted in a significant increase of the oncologic and blood diseases rate among several generations of the effected people. Moreover, consequences of the above-ground and atmospheric tests of nuclear and hydrogen weapon will show up in the next century, taking into account the fact that the 'open' tests were ceased only at the middle of 60-th. The birth rate of children with the inherent intelligence defects was determined according to the accounting records of the new-born children within 1986-1992 years. Analysis of perinatal mortality was carried out based on the records on autopsy within 1985-1992 years. The two-fold increase of the onco diseases rate was revealed among children. The rate of spontaneous aborts in the Eginbulak district was 9.99% and exceeded the average rate in the region and indexes of other regions

  6. Natural convection and in-cavity oxidation of combustible gases

    International Nuclear Information System (INIS)

    The question of complete in-cavity oxidation of combustible gases produced by core-concrete interactions following vessel breach has been investigated. Because a variety of phenomena, such as steam inerting and oxygen transport by natural convection, may influence the degree of in-cavity oxidation that takes place, assuming a complete oxidation may be overly optimistic. The Hydrogen Event: Containment Transient Response (HECTR) analyses of an ice-condenser containment during an S2HF drain-closed accident show that the in-cavity oxidation process is limited by the rate at which oxygen is transported into the reactor cavity region. Accumulation and subsequent combustion of hydrogen and carbon monoxide in the upper and lower compartments generate a peak pressu8re at 384 kPa (56 psig) at 7.4 hours that an earlier Industry Degraded Core Rulemaking (IDCOR) analysis did not predict

  7. Natural convection and in-cavity oxidation of combustible gases

    International Nuclear Information System (INIS)

    The question of complete in-cavity oxidation of combustible gases produced by core-concrete interactions following vessel breach has been investigated. It is overly optimistic to assume a complete oxidation because a variety of phenomena, such as steam inerting and oxygen transport by natural convection, may influence the degree of in-cavity oxidation that takes place. HECTR analyses of an ice-condenser containment during an S2HF drain-closed accident show that the in-cavity oxidation process is limited by the rate at which oxygen is transported into the reactor cavity region. Accumulation and subsequent combustion of hydrogen and carbon monoxide in the upper and lower compartments generate a peak pressure of 384 kPa (56 psig) at 7.4 hours, that an earlier IDCOR analysis did not predict

  8. Superconducting cavity model for LEP

    CERN Multimedia

    1979-01-01

    A superconducting cavity model is being prepared for testing in a vertical cryostat.At the top of the assembly jig is H.Preis while A.Scharding adjusts some diagnostic equipment to the cavity. See also photo 7912501X.

  9. Fiber cavities for atom chips

    OpenAIRE

    Klappauf, B.G.; Horak, P.; Kazansky, P. G.

    2003-01-01

    We present experimental realizations of several micro-cavities, constructed from standard fiber optic components, which meet the theoretical criteria for single atom detection from laser-cooled samples. We discuss integration of these cavities into state-of-the-art 'atom chips'.

  10. Design of a cavity filter

    International Nuclear Information System (INIS)

    A cavity filter was developed for the SSRF 0-mode beam feedback. The filter is used to pick up the 500 MHz signal from the storage ring beam. The Superfish was used to simulate the model of the cavity bandpass filter. The design method, parameters of the filter and results of beam measurements are described in this paper. (authors)

  11. Study on superconducting accelerating cavities

    International Nuclear Information System (INIS)

    A test cavity of cylindrical shape has been designed and constructed to study superconducting accelerating cavities for TRISTAN e+e- Ring. Higher order modes have been calculated by using SUPERFISH program and an analytical method, and measured. The measured resonant frequencies well agree with the calculated results. (author)

  12. Technical tasks in superconducting cavities

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Kenji [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan)

    1997-11-01

    The feature of superconducting rf cavities is an extremely small surface resistance on the wall. It brings a large energy saving in the operation, even those are cooled with liquid helium. That also makes possible to operate themselves in a higher field gradient comparing to normal conducting cavities, and brings to make accelerators compact. These merits are very important for the future accelerator engineering which is planed at JAERI for the neutron material science and nuclear waste transmutation. This machine is a high intensity proton linac and uses sc cavities in the medium and high {beta} sections. In this paper, starting R and D of proton superconducting cavities, several important technical points which come from the small surface resistance of sc cavities, are present to succeed it and also differences between the medium and high - {beta} structures are discussed. (author)

  13. Mechanical Properties of Niobium Cavities

    Energy Technology Data Exchange (ETDEWEB)

    Ciovati, Gianluigi [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Dhakal, Pashupati [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Matalevich, Joseph R. [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Myneni, Ganapati Rao [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States)

    2015-09-01

    The mechanical stability of bulk Nb cavity is an important aspect to be considered in relation to cavity material, geometry and treatments. Mechanical properties of Nb are typically obtained from uniaxial tensile tests of small samples. In this contribution we report the results of measurements of the resonant frequency and local strain along the contour of single-cell cavities made of ingot and fine-grain Nb of different purity subjected to increasing uniform differential pressure, up to 6 atm. Measurements have been done on cavities subjected to different heat treatments. Good agreement between finite element analysis simulations and experimental data in the elastic regime was obtained with a single set of values of Young’s modulus and Poisson’s ratio. The experimental results indicate that the yield strength of medium-purity ingot Nb cavities is higher than that of fine-grain, high-purity Nb.

  14. Prediction of residual stress due to early age behaviour of massive concrete structures: on site experiments and macroscopic modelling

    CERN Document Server

    Zreiki, Jihad; Chaouche, Mohend; Moranville, Micheline

    2008-01-01

    Early age behaviour of concrete is based on complex multi-physical and multiscale phenomena. The predication of both cracking risk and residual stresses in hardened concrete structures is still a challenging task. We propose in this paper a practical method to characterize in the construction site the material parameters and to identify a macroscopic model from simple tests. We propose for instance to use a restrained shrinkage ring test to identify a basic early age creep model based on a simple ageing visco-elastic Kelvin model. The strain data obtained from this test can be treated through an early age finite element incremental procedure such that the fitting parameters of the creep law can be quickly identified. The others properties of concrete have been measured at different ages (elastic properties, hydration kinetics, and coefficient of thermal expansion). From the identified early age model, we computed the temperature rise and the stress development in a non reinforced concrete stress for nuclear w...

  15. pRNAm-PC: Predicting N(6)-methyladenosine sites in RNA sequences via physical-chemical properties.

    Science.gov (United States)

    Liu, Zi; Xiao, Xuan; Yu, Dong-Jun; Jia, Jianhua; Qiu, Wang-Ren; Chou, Kuo-Chen

    2016-03-15

    Just like PTM or PTLM (post-translational modification) in proteins, PTCM (post-transcriptional modification) in RNA plays very important roles in biological processes. Occurring at adenine (A) with the genetic code motif (GAC), N(6)-methyldenosine (m(6)A) is one of the most common and abundant PTCMs in RNA found in viruses and most eukaryotes. Given an uncharacterized RNA sequence containing many GAC motifs, which of them can be methylated, and which cannot? It is important for both basic research and drug development to address this problem. Particularly with the avalanche of RNA sequences generated in the postgenomic age, it is highly demanded to develop computational methods for timely identifying the N(6)-methyldenosine sites in RNA. Here we propose a new predictor called pRNAm-PC, in which RNA sequence samples are expressed by a novel mode of pseudo dinucleotide composition (PseDNC) whose components were derived from a physical-chemical matrix via a series of auto-covariance and cross covariance transformations. It was observed via a rigorous jackknife test that, in comparison with the existing predictor for the same purpose, pRNAm-PC achieved remarkably higher success rates in both overall accuracy and stability, indicating that the new predictor will become a useful high-throughput tool for identifying methylation sites in RNA, and that the novel approach can also be used to study many other RNA-related problems and conduct genome analysis. A user-friendly Web server for pRNAm-PC has been established at http://www.jci-bioinfo.cn/pRNAm-PC, by which users can easily get their desired results without needing to go through the mathematical details. PMID:26748145

  16. Quantitative relationship between naphthalene catabolic gene frequency and expression in predicting PAH degradation in soils at town gas manufacturing sites

    International Nuclear Information System (INIS)

    The inability to monitor in situ expression of biodegradative genes to predict rates of pollutant degradation or to evaluate the efficacy of engineering applications of bioremediation in complex environments such as contaminated soils has limited the routine acceptance of this technology in hazardous waste management. To overcome this limitation, an approach has been developed to measure catabolic gene expression in PAH-contaminated soils. In soils populated with as few as 106 naphthalene degradative bacteria g-1, in situ isolation and quantitation of mRNA levels was achieved for the NAH7 naphthalene dioxygenase (nahA) gene. NahA transcript levels correlated positively with [14C]naphthalene mineralization rates, soil naphthalene concentration, and nahA gene frequency. 30 refs., 4 figs., 2 tabs

  17. Plasmonic mediated nucleation of resonant nano-cavities in metallic layers

    OpenAIRE

    Karpov, V. G.; Nardone, M.; Subashiev, A. V.

    2012-01-01

    We predict plasmonic mediated nucleation of pancake shaped resonant nano-cavities in metallic layers that are penetrable to laser fields. The underlying physics is that the cavity provides a narrow plasmonic resonance that maximizes its polarizability in an external field. The resonance yields a significant energy gain making the formation of such cavities highly favorable. Possible implications include nano-optics and generation of the dielectric bits in conductive films that underlie the ex...

  18. Measurements of the tonal component of cavity noise and comparison with theory. [aircraft noise

    Science.gov (United States)

    Block, P. J. W.

    1977-01-01

    The frequency of the tonal noise generated by a flow-excited rectangular cavity was measured using Mach numbers ranging from 0.05 to 0.40, and cavity length-to-depth ratios varying from 0.1 to 8. The data are used to evaluate a current prediction method, and good agreement is shown. Measurements of the minimum streamwise cavity length required for oscillation were also made.

  19. Evaluation of Cavity Collapse and Surface Crater Formation at the Salut Underground Nuclear Test in U20ak, Nevada National Security Site, and the Impact of Stability of the Ground Surface

    Energy Technology Data Exchange (ETDEWEB)

    Pawloski, G A

    2012-04-25

    At the request of Jerry Sweeney, the LLNL Containment Program performed a review of nuclear test-related data for the Salut underground nuclear test in U20ak to assist in evaluating this legacy site as a test bed for application technologies for use in On-Site Inspections (OSI) under the Comprehensive Nuclear Test Ban Treaty. Review of the Salut site is complicated because the test experienced a subsurface, rather than surface, collapse. Of particular interest is the stability of the ground surface above the Salut detonation point. Proposed methods for on-site verification include radiological signatures, artifacts from nuclear testing activities, and imaging to identify alteration to the subsurface hydrogeologogy due to the nuclear detonation. Sweeney's proposal requires physical access at or near the ground surface of specific underground nuclear test locations at the Nevada Nuclear Test Site (NNSS, formerly the Nevada Test Site), and focuses on possible activities such as visual observation, multispectral measurements, and shallow, and deep geophysical surveys.

  20. 35 GHz, 4-Cavity Gyroklystron Amplifier Experiment

    Science.gov (United States)

    Garven, M.; Calame, J. P.; Danly, B. G.; Levush, B.; Wood, F.

    1998-11-01

    Gyroklystron amplifiers operating in the Ka-band are attractive sources for the next generation of millimeter wave radars and are currently under investigation at the Naval Research Laboratory (NRL). A four-cavity, 35 GHz gyroklystron experiment has been designed to demonstrate higher saturated gain (50dB) than previous experiments at NRL( J. J. Choi et al, IEEE Trans. Plasma Sci. 26(3), 416, 1998.). Non-linear, time-dependent simulations of the 4-cavity gyroklystron amplifier design using MAGYKL(P. E. Latham et al IEEE Trans. Plasma Sci. 22, 804, 1994.) predict 35% efficiency, 225 kW peak power, 50 dB saturated gain and a -3 dB bandwidth of 0.6%. For this four-cavity gyroklystron, the interaction between the TE_01 mode and a 70 kV, 9 A electron beam was studied with α=1.3 and an rms perpendicular velocity spread of 9%. Initial studies have shown that variations in magnetic field and voltage affect the trade-offs between power, bandwidth and efficiency. Theoretical design studies and experimental progress will be presented.

  1. Multiple metastatic tumors in the oral cavity

    OpenAIRE

    V.T. Beena; Swagatika Panda; Heera, R.; Rajeev, R.

    2011-01-01

    Metastatic lesions to the oral region are uncommon and account for approximately 1% of all malignant oral tumors. In 25% of the cases, oral metastases are found to be the first sign of the metastatic spread; and in 23% of the cases, it is the first indication of an undiscovered malignancy at a distant site. Metastases to oral soft tissues are even less frequent than jaw bones. Because of its rarity, the clinical presentation of a metastatic lesion in the oral cavity can be deceiving, leading ...

  2. Predicting phosphorylation sites of Poplar protein%杨树蛋白质磷酸化位点预测

    Institute of Scientific and Technical Information of China (English)

    高光芹; 黄家荣; 周俊朝; 谢鹏芳

    2015-01-01

    以小黑杨磷酸化蛋白质组为研究对象,用人工神经网络表达丝氨酸、苏氨酸等残基位点的磷酸化与氨基酸序列的结构特征之间的非线性关系,建立了BP 人工神经网络模型,并用磷酸化数据对所建模型进行训练和分析,得适宜的结构为21×16 : 8 : 4,拟合准确度为90%,Acc、Sn、Sp、MCC分别为78%、89%、67%、0.57,对比分析结果表明,所建模型具有较强的预测能力.%In this paper, the phosphoproteome of Populus simonii × P nigra was used as the research object. The nonlinear relationship between the structure characteristics of amino acid sequence and phosphorylation of serine and threonine was expressed by artificial neural network. A BP artificial neural network model was established and trained by using the real data on phosphorylation. The appropriate structure is 21 x 16 : 8 : 4, the fitting accuracy is 90%, and the Acc, Sn, Sp, MCC are 78%, 89%, 67%, and 0. 57, respectively. The comparative results show that the model has strong prediction ability.

  3. Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.

    KAUST Repository

    Olimpieri, Pier Paolo

    2013-06-26

    MOTIVATION: Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular structure makes it easy to re-engineer them for specific purposes. Short of undergoing a trial and error process, these experiments, as well as others, need to rely on an understanding of the specific determinants of the antibody binding mode. RESULTS: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen. The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts. We believe that it can be of great help in re-design experiments as well as a guide for molecular docking experiments. The results that we obtained also allowed us to dissect which features of the antibody sequence contribute most to the involvement of specific residues in binding to the antigen. AVAILABILITY: http://www.biocomputing.it/proABC. CONTACT: anna.tramontano@uniroma1.it or paolo.marcatili@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

  4. Analysis of K-net and Kik-net data: implications for ground motion prediction - acceleration time histories, response spectra and nonlinear site response

    International Nuclear Information System (INIS)

    This thesis intends to characterize ground motion during earthquake. This work is based on two Japanese networks. It deals with databases of shallow events, depth less than 25 km, with magnitude between 4.0 and 7.3. The analysis of K-net allows to compute a spectral ground motion prediction equation and to review the shape of the Eurocode 8 design spectra. We show the larger amplification at short period for Japanese data and bring in light the soil amplification that takes place at large period. In addition, we develop a new empirical model for simulating synthetic stochastic nonstationary acceleration time histories. By specifying magnitude, distance and site effect, this model allows to produce many time histories, that a seismic event is liable to produce at the place of interest. Furthermore, the study of near-field borehole records of the Kik-net allows to explore the validity domain of predictive equations and to explain what occurs by extrapolating ground motion predictions. Finally, we show that nonlinearity reduces the dispersion of ground motion at the surface. (author)

  5. A PBPK Model to Predict Disposition of CYP3A-Metabolized Drugs in Pregnant Women: Verification and Discerning the Site of CYP3A Induction.

    Science.gov (United States)

    Ke, A B; Nallani, S C; Zhao, P; Rostami-Hodjegan, A; Unadkat, J D

    2012-01-01

    Besides logistical and ethical concerns, evaluation of safety and efficacy of medications in pregnant women is complicated by marked changes in pharmacokinetics (PK) of drugs. For example, CYP3A activity is induced during the third trimester (T3). We explored whether a previously published physiologically based pharmacokinetic (PBPK) model could quantitatively predict PK profiles of CYP3A-metabolized drugs during T3, and discern the site of CYP3A induction (i.e., liver, intestine, or both). The model accounted for gestational age-dependent changes in maternal physiological function and hepatic CYP3A activity. For model verification, mean plasma area under the curve (AUC), peak plasma concentration (Cmax), and trough plasma concentration (Cmin) of midazolam (MDZ), nifedipine (NIF), and indinavir (IDV) were predicted and compared with published studies. The PBPK model successfully predicted MDZ, NIF, and IDV disposition during T3. A sensitivity analysis suggested that CYP3A induction in T3 is most likely hepatic and not intestinal. Our PBPK model is a useful tool to evaluate different dosing regimens during T3 for drugs cleared primarily via CYP3A metabolism.CPT: Pharmacometrics & Systems Pharmacology (2012) 1, e3; doi:10.1038/psp.2012.2; advance online publication 26 September 2012. PMID:23835883

  6. PSNO: Predicting Cysteine S-Nitrosylation Sites by Incorporating Various Sequence-Derived Features into the General Form of Chou’s PseAAC

    Directory of Open Access Journals (Sweden)

    Jian Zhang

    2014-06-01

    Full Text Available S-nitrosylation (SNO is one of the most universal reversible post-translational modifications involved in many biological processes. Malfunction or dysregulation of SNO leads to a series of severe diseases, such as developmental abnormalities and various diseases. Therefore, the identification of SNO sites (SNOs provides insights into disease progression and drug development. In this paper, a new bioinformatics tool, named PSNO, is proposed to identify SNOs from protein sequences. Firstly, we explore various promising sequence-derived discriminative features, including the evolutionary profile, the predicted secondary structure and the physicochemical properties. Secondly, rather than simply combining the features, which may bring about information redundancy and unwanted noise, we use the relative entropy selection and incremental feature selection approach to select the optimal feature subsets. Thirdly, we train our model by the technique of the k-nearest neighbor algorithm. Using both informative features and an elaborate feature selection scheme, our method, PSNO, achieves good prediction performance with a mean Mathews correlation coefficient (MCC value of about 0.5119 on the training dataset using 10-fold cross-validation. These results indicate that PSNO can be used as a competitive predictor among the state-of-the-art SNOs prediction tools. A web-server, named PSNO, which implements the proposed method, is freely available at http://59.73.198.144:8088/PSNO/.

  7. Frequency-feedback cavity enhanced spectrometer

    Science.gov (United States)

    Hovde, David Christian; Gomez, Anthony

    2015-08-18

    A spectrometer comprising an optical cavity, a light source capable of producing light at one or more wavelengths transmitted by the cavity and with the light directed at the cavity, a detector and optics positioned to collect light transmitted by the cavity, feedback electronics causing oscillation of amplitude of the optical signal on the detector at a frequency that depends on cavity losses, and a sensor measuring the oscillation frequency to determine the cavity losses.

  8. Impairment of an atrophic mandible by preparation of the implant cavity: a biomechanical study.

    Science.gov (United States)

    Steiner, Timm; Torsiglieri, Tobias; Rau, Andrea; Möhlhenrich, Stephan C; Eichhorn, Stefan; Grohmann, Isabella; Deppe, Herbert; Hölzle, Frank; Raith, Stefan

    2016-07-01

    An important complication during insertion of implants in atrophic mandibles is the fracture that can be induced by preparation of the cavity. We designed this study to identify which configuration of cavities in the interforaminal region was the least likely to fracture. An electromechanical testing machine was used to measure breaking loads of specifically-designed synthetic models of atrophic mandibles. The implant cavities correlated with the common clinical patterns. Intact atrophied synthetic mandibles broke at a mean (SD) load of 729.48 (59.94) N (control group). Models with four different configurations of cavities fractured as follows: two short, wide cavities (8 x 4.2mm) at a mean (SD) load of 569.17 (67.7) N; two long, thin cavities (15 x2.8mm) at a load of 563.40 (62.0) N; four short, wide cavities (8 x 4.2mm) at a load of 667.01 (71.89) N; and four long, thin cavities (15 x 2.8mm) at a load of 409.50 (43.61) N. Biomechanical findings showed that there was a greater risk of fracture of atrophic mandibular models in long, thin implant cavities with more preparation sites. Each cavity prepared for an implant increased the risk of fracture in an atrophic mandible. The risk of fracture is greatest with long, thin cavities. PMID:27068851

  9. Habitat composition and connectivity predicts bat presence and activity at foraging sites in a large UK conurbation.

    Directory of Open Access Journals (Sweden)

    James D Hale

    Full Text Available BACKGROUND: Urbanization is characterized by high levels of sealed land-cover, and small, geometrically complex, fragmented land-use patches. The extent and density of urbanized land-use is increasing, with implications for habitat quality, connectivity and city ecology. Little is known about densification thresholds for urban ecosystem function, and the response of mammals, nocturnal and cryptic taxa are poorly studied in this respect. Bats (Chiroptera are sensitive to changing urban form at a species, guild and community level, so are ideal model organisms for analyses of this nature. METHODOLOGY/PRINCIPAL FINDINGS: We surveyed bats around urban ponds in the West Midlands conurbation, United Kingdom (UK. Sites were stratified between five urban land classes, representing a gradient of built land-cover at the 1 km(2 scale. Models for bat presence and activity were developed using land-cover and land-use data from multiple radii around each pond. Structural connectivity of tree networks was used as an indicator of the functional connectivity between habitats. All species were sensitive to measures of urban density. Some were also sensitive to landscape composition and structural connectivity at different spatial scales. These results represent new findings for an urban area. The activity of Pipistrellus pipistrellus (Schreber 1774 exhibited a non-linear relationship with the area of built land-cover, being much reduced beyond the threshold of ∼60% built surface. The presence of tree networks appears to mitigate the negative effects of urbanization for this species. CONCLUSIONS/SIGNIFICANCE: Our results suggest that increasing urban density negatively impacts the study species. This has implications for infill development policy, built density targets and the compact city debate. Bats were also sensitive to the composition and structure of the urban form at a range of spatial scales, with implications for land-use planning and management

  10. Cavity beam position monitors

    International Nuclear Information System (INIS)

    Beam-based alignment and feedback systems are essential for the operation of future linear colliders and free electron lasers. A certain number of beam position monitors with a resolution in the submicron range are needed at selected locations. Most beam position monitors detect the electric or the magnetic field excited by a beam of charged particles at different locations around the beam pipe. In resonant monitors, however, the excitation of special field configurations by an off-center beam is detected. These structures offer a large signal per micron displacement. This paper is an attempt to summarize the fundamental characteristics of resonant monitors, their advantages and shortcomings. Emphasis will be on the design of cylindrical cavities, in particular on the estimation of expected signals, of resolution limits and the resulting beam distortion. This includes also a short introduction into numerical methods. Fabrication, tuning, and other practical problems will be reviewed briefly. Finally, some resonant devices used for beam position diagnostics will be discussed and listed

  11. Three-dimensional cavity calculations

    International Nuclear Information System (INIS)

    The existence of a code that solves for the resonant electromagnetic modes of oscillation in arbitrarily-shaped three-dimensional cavities opens new possibilities in rf-structure analysis and research. The URMEL-3D code, the product of a multi-year collaboration between DESY, KFA-Juelich, and Los Alamos, has been used in some exploratory studies to determine the feasibility of using a 3-D code to calculate the properties of several practical rf structures. The results are reported here for three cases: the jungle gym, two coupled cavities, and a waveguide-cavity coupling problem

  12. Beam - cavity interaction beam loading

    International Nuclear Information System (INIS)

    The interaction of a beam with a cavity and a generator in cyclic accelerators or storage rings is investigated. Application of Maxwell's equations together with the nonuniform boundary condition allows one to get an equivalent circuit for a beam-loaded cavity. The general equation for beam loading is obtained on the basis of the equivalent circuit, and the beam admittance is calculated. Formulas for power consumption by a beam-loaded cavity are derived, and the optimal tuning and coupling factor are analyzed. (author)

  13. Transferring a cavity field entangled state in cavity QED

    Energy Technology Data Exchange (ETDEWEB)

    Ye Liu [Anhui Key Laboratory of Information Material and Devices, School of Physics and Material Science, Anhui University, Hefei 230039 (China); Guo Guangcan [Key Laboratory of Quantum Information, University of Science and Technology of China, Chinese Academy of Sciences, Hefei 230026 (China)

    2005-08-01

    We propose a scheme for transferring an entanglement of zero- and one-photon states from one cavity to another. The scheme, which has 100% success probability, is mainly based on a two-mode cavity dispersively interacting with a three-level atom in the {lambda} configuration and does not involve Bell-state measurement. This scheme can also be used to teleport an unknown atomic state.

  14. E-beam accelerator cavity development for the ground-based free electron laser

    Science.gov (United States)

    Bultman, N. K.; Spalek, G.

    Los Alamos National Laboratory is designing and developing four prototype accelerator cavities for high power testing on the Modular Component Technology Development (MCTD) test stand at Boeing. These cavities provide the basis for the e-beam accelerator hardware that will be used in the Ground Based Free Electron Laser (GBFEL) to be sited at the White Sands Missile Range (WSMR) in New Mexico.

  15. Glucocorticoid-Induced Changes in the Geometry of Osteoclast Resorption Cavities Affect Trabecular Bone Stiffness

    DEFF Research Database (Denmark)

    Vanderoost, Jef; Søe, Kent; Merrild, Ditte Marie Horslev;

    2012-01-01

    /BV, which is closely related to the shape of the cavities, highly determines the stiffness effect. The lumbar spine was the anatomic site most affected by the GC-induced changes on the shape of the cavities. These findings might explain the clinical observation that the prevalence of vertebral fractures...

  16. Analysis of Cavity Volumes in Proteins Using Percolation Theory

    Science.gov (United States)

    Green, Sheridan; Jacobs, Donald; Farmer, Jenny

    Molecular packing is studied in a diverse set of globular proteins in their native state ranging in size from 34 to 839 residues An new algorithm has been developed that builds upon the classic Hoshen-Kopelman algorithm for site percolation combined with a local connection criterion that classifies empty space within a protein as a cavity when large enough to hold a spherical shaped probe of radius, R, otherwise a microvoid. Although microvoid cannot fit an object (e.g. molecule or ion) that is the size of the probe or larger, total microvoid volume is a major contribution to protein volume. Importantly, the cavity and microvoid classification depends on probe radius. As probe size decreases, less microvoid forms in favor of more cavities. As probe size is varied from large to small, many disconnected cavities merge to form a percolating path. For fixed probe size, microvoid, cavity and solvent accessible boundary volume properties reflect conformational fluctuations. These results are visualized on three-dimensional structures. Analysis of the cluster statistics within the framework of percolation theory suggests interconversion between microvoid and cavity pathways regulate the dynamics of solvent penetration during partial unfolding events important to protein function.

  17. Summary on the Fundamental Mode Damper Experiments of the 56 MHz SRF Cavity

    Energy Technology Data Exchange (ETDEWEB)

    Choi,E.; Hahn, H.

    2008-07-01

    This report summarizes the experimental results done with the fundamental damper for the 56 MHz prototype Cu cavity. Various measurements were done on the cavity including determination of the position of the fundamental damper and measurement of the frequency and Q factor changes while the damper is withdrawn. Prediction on the dissipated power while the damper is withdrawn was made by experiments.

  18. Weak Langmuir optical turbulence in a fiber cavity

    Science.gov (United States)

    Xu, G.; Garnier, J.; Mussot, A.; Trillo, S.; Churkin, D.; Tarasov, N.; Turitsyn, S.; Picozzi, A.

    2016-07-01

    We study theoretically and numerically the dynamics of a passive optical fiber ring cavity pumped by a highly incoherent wave: an incoherently injected fiber laser. The theoretical analysis reveals that the turbulent dynamics of the cavity is dominated by the Raman effect. The forced-dissipative nature of the fiber cavity is responsible for a large diversity of turbulent behaviors: Aside from nonequilibrium statistical stationary states, we report the formation of a periodic pattern of spectral incoherent solitons, or the formation of different types of spectral singularities, e.g., dispersive shock waves and incoherent spectral collapse behaviors. We derive a mean-field kinetic equation that describes in detail the different turbulent regimes of the cavity and whose structure is formally analogous to the weak Langmuir turbulence kinetic equation in the presence of forcing and damping. A quantitative agreement is obtained between the simulations of the nonlinear Schrödinger equation with cavity boundary conditions and those of the mean-field kinetic equation and the corresponding singular integrodifferential reduction, without using adjustable parameters. We discuss the possible realization of a fiber cavity experimental setup in which the theoretical predictions can be observed and studied.

  19. Orion EFT-1 Cavity Heating Tile Experiments and Environment Reconstruction

    Science.gov (United States)

    Salazar, Giovanni; Amar, Adam; Oliver, Brandon; Hyatt, Andrew; Rezin, Marc

    2016-01-01

    Developing aerothermodynamic environments for deep cavities, such as those produced by micrometeoroids and orbital debris impacts, poses a great challenge for engineers. In order to assess existing cavity heating models, two one-inch diameter cavities were flown on the Orion Multi-Purpose Crew Vehicle during Exploration Flight Test 1 (EFT1). These cavities were manufactured with depths of 1.0 in and 1.4 in, and they were both instrumented. Instrumentation included surface thermocouples upstream, downstream and within the cavities, and additional thermocouples at the TPS-structure interface. This paper will present the data obtained, and comparisons with computational predictions will be shown. Additionally, the development of a 3D material thermal model will be described, which will be used to account for the three-dimensionality of the problem when interpreting the data. Furthermore, using a multi-dimensional inverse heat conduction approach, a reconstruction of a time- and space-dependent flight heating distribution during EFT1 will be presented. Additional discussions will focus on instrumentation challenges and calibration techniques specific to these experiments. The analysis shown will highlight the accuracies and/or deficiencies of current computational techniques to model cavity flows during hypersonic re-entry.

  20. Harmonically resonant cavity as a bunch-length monitor

    Science.gov (United States)

    Roberts, B.; Hannon, F.; Ali, M. M.; Forman, E.; Grames, J.; Kazimi, R.; Moore, W.; Pablo, M.; Poelker, M.; Sanchez, A.; Speirs, D.

    2016-05-01

    A compact, harmonically resonant cavity with fundamental resonant frequency 1497 MHz was used to evaluate the temporal characteristics of electron bunches produced by a 130 kV dc high voltage spin-polarized photoelectron source at the Continuous Electron Beam Accelerator Facility (CEBAF) photoinjector, delivered at 249.5 and 499 MHz repetition rates and ranging in width from 45 to 150 picoseconds (FWHM). A cavity antenna attached directly to a sampling oscilloscope detected the electron bunches as they passed through the cavity bore with a sensitivity of ˜1 mV /μ A . The oscilloscope waveforms are a superposition of the harmonic modes excited by the beam, with each cavity mode representing a term of the Fourier series of the electron bunch train. Relatively straightforward post-processing of the waveforms provided a near-real time representation of the electron bunches revealing bunch-length and the relative phasing of interleaved beams. The noninvasive measurements from the harmonically resonant cavity were compared to measurements obtained using an invasive RF-deflector-cavity technique and to predictions from particle tracking simulations.

  1. Cavity Heating Experiments Supporting Shuttle Columbia Accident Investigation

    Science.gov (United States)

    Everhart, Joel L.; Berger, Karen T.; Bey, Kim S.; Merski, N. Ronald; Wood, William A.

    2011-01-01

    The two-color thermographic phosphor method has been used to map the local heating augmentation of scaled idealized cavities at conditions simulating the windward surface of the Shuttle Orbiter Columbia during flight STS-107. Two experiments initiated in support of the Columbia Accident Investigation were conducted in the Langley 20-Inch Mach 6 Tunnel. Generally, the first test series evaluated open (length-to-depth less than 10) rectangular cavity geometries proposed as possible damage scenarios resulting from foam and ice impact during launch at several discrete locations on the vehicle windward surface, though some closed (length-to-depth greater than 13) geometries were briefly examined. The second test series was designed to parametrically evaluate heating augmentation in closed rectangular cavities. The tests were conducted under laminar cavity entry conditions over a range of local boundary layer edge-flow parameters typical of re-entry. Cavity design parameters were developed using laminar computational predictions, while the experimental boundary layer state conditions were inferred from the heating measurements. An analysis of the aeroheating caused by cavities allowed exclusion of non-breeching damage from the possible loss scenarios being considered during the investigation.

  2. Radiotherapy for Oral Cavity Cancer

    International Nuclear Information System (INIS)

    Eighty five patients of oral cavity cancer, treated with radiation at the Department of Therapeutic Radiology, Korea Cancer Center Hospital, during the period from March 1985 to September 1990 were analyzed retrospectively. Among 85 patients, 37 patients were treated with radiation only and 48 patients were treated with radiation following surgery And 70 patients received external irradiation only by 60Co with or without electron, the others were 7 patients for external irradiation plus interstitial implantation and 8 patients for external irradiation plus oral cone electron therapy. Primary sites were mobile tongue for 40 patients, mouth floor for 17 patients, palate for 12 patients, gingiva including retromolar trigone for 10 patients, buccal mucosa for 5 patients, and lip for 1 patient. According to pathologic classification, squamous cell carcinoma was the most common (77 patients). According to AJC TNM stage, stage I + II were 28 patients and stage III + IV were 57 patients. Acturial overall survival rate at 3 years was 43.9%, 3 year survival rates were 60.9% for stage I + II, and 23.1% for stage III + IV, respectively. As a prognostic factor, primary T stage was a significant factor (p<0.01). The others, age, location, lymph node metastasis, surgery, radiation dose, and cell differentiation were not statistically significant. Among those factors, radiation plus surgery was more effective than radiation only in T3 + T4 or in any N stage although it was not statistically sufficient(p<0.1). From those results, it was conclusive that definitive radiotherapy was more effective than surgery especially in the view of pertaining of anatomical integrity and function in early stage, and radiation plus surgery was considered to be better therapeutic tool in advanced stage

  3. SRF Cavity Fabrication and Materials

    CERN Document Server

    Singer, W

    2014-01-01

    The technological and metallurgical requirements of material for highgradient superconducting cavities are described. High-purity niobium, as the preferred metal for the fabrication of superconducting accelerating cavities, should meet exact specifications. The content of interstitial impurities such as oxygen, nitrogen, and carbon must be below 10μg/g. The hydrogen content should be kept below 2μg/g to prevent degradation of the Q-value under certain cool-down conditions. The material should be free of flaws (foreign material inclusions or cracks and laminations) that can initiate a thermal breakdown. Defects may be detected by quality control methods such as eddy current scanning and identified by a number of special methods. Conventional and alternative cavity fabrication methods are reviewed. Conventionally, niobium cavities are fabricated from sheet niobium by the formation of half-cells by deep drawing, followed by trim machining and Electron-Beam Welding (EBW). The welding of half-cells is a delicate...

  4. Niobium LEP 2 accelerating cavities

    CERN Multimedia

    An accelerating cavity from LEP. This could be cut open to show the layer of niobium on the inside. Operating at 4.2 degrees above absolute zero, the niobium is superconducting and carries an accelerating field of 6 million volts per metre with negligible losses. Each cavity has a surface of 6 m2. The niobium layer is only 1.2 microns thick, ten times thinner than a hair. Such a large area had never been coated to such a high accuracy. A speck of dust could ruin the performance of the whole cavity so the work had to be done in an extremely clean environment. These challenging requirements pushed European industry to new achievements. 256 of these cavities were used in an upgrade of the LEP accelerator to double the energy of the particle beams.

  5. Geometry-Invariant Resonant Cavities

    CERN Document Server

    Liberal, Iñigo; Engheta, Nader

    2015-01-01

    Resonant cavities are one of the basic building blocks in various disciplines of science and technology, with numerous applications ranging from abstract theoretical modeling to everyday life devices. The eigenfrequencies of conventional cavities are a function of its geometry, and, thus, the size and shape of a resonant cavity is selected in order to operate at a specific frequency. Here, we demonstrate theoretically the existence of geometry-invariant resonant cavities, i.e., resonators whose eigenfrequency is invariant with respect to geometrical deformations. This effect is obtained by exploiting the unusual properties of zero-index metamaterials, which enable decoupling of the time and spatial field variations. This new class of resonators may inspire alternative design concepts, and it might lead to the first generation of deformable resonant devices.

  6. CRAB Cavity in CERN SPS

    International Nuclear Information System (INIS)

    Beam collisions with a crossing angle at the interaction point are often necessary in colliders to reduce the effects of parasitic collisions which induce emittance growth and decrease beam lifetime. The crossing angle reduces the geometrical overlap of the beams and hence the luminosity. Crab cavity offer a promising way to compensate the crossing angle and to realize effective head-on collisions. Moreover, the crab crossing mitigates the synchro-betatron resonances due to the crossing angle. A crab cavity experiment in SPS is proposed as a proof of principle before deciding on a full crab-cavity implementation in the LHC. In this paper, we investigate the effects of a single crab cavity on beam dynamics in the SPS and life time.

  7. Analysis of reactor cavity radiation streaming: some practical considerations

    International Nuclear Information System (INIS)

    A description is presented of a cost effective analysis procedure for use in the prediction of radiation environments in the cavity and containment building of a nuclear power reactor. Comments are offered on potential problems in certification of analysis procedures and the availability of benchmarkable data sets, both measurements and calculations

  8. LEP Radio Frequency Copper Cavities

    CERN Multimedia

    The pulse of a particle accelerator. 128 of these radio frequency cavities were positioned around CERN's 27-kilometre LEP ring to accelerate electrons and positrons. The acceleration was produced by microwave electric oscillations at 352 MHz. The electrons and positrons were grouped into bunches, like beads on a string, and the copper sphere at the top stored the microwave energy between the passage of individual bunches. This made for valuable energy savings as it reduced the heat generated in the cavity.

  9. Single and Coupled Nanobeam Cavities

    DEFF Research Database (Denmark)

    Ivinskaya, Aliaksandra; Lavrinenko, Andrei; Shyroki, Dzmitry M.; A. Sukhorukov, Andrey

    This book collects chapters on different theoretical and experimental aspects of photonics crystals for Nanophotonics applications. It is divided in two parts - a theoretical section and an experimental and applicative section. The first part includes chapters developing several numerical methods...... for analysis and design of photonic crystal devices, such as 2D ring resonators for filters, single and coupled nanobeam cavities, birefringence in photonic crystal cavities, threshold analysis in photonic crystal lasers, gap solitons in photonic crystals, novel photonic atolls, dynamic...

  10. RRR Characteristics for SRF Cavities

    OpenAIRE

    Jung, Yoochul; Hyun, Myungook; Joung, Mijoung

    2015-01-01

    The first heavy ion accelerator is being constructed by the rare isotope science project (RISP) launched by the Institute of Basic Science (IBS) in South Korea. Four different types of superconducting cavities were designed, and prototypes were fabricated such as a quarter wave resonator (QWR), a half wave resonator (HWR) and a single spoke resonator (SSR). One of the critical factors determining performances of the superconducting cavities is a residual resistance ratio (RRR). The RRR values...

  11. Deterministic Loading of Individual Atoms to a High-Finesse Optical Cavity

    International Nuclear Information System (INIS)

    Individual laser-cooled atoms are delivered on demand from a single atom magneto-optic trap to a high-finesse optical cavity using an atom conveyor. Strong coupling of the atom with the cavity field allows simultaneous cooling and detection of individual atoms for time scales exceeding 15 s. The single atom scatter rate is studied as a function of probe-cavity detuning and probe Rabi frequency, and the experimental results are in qualitative agreement with theoretical predictions. We demonstrate the ability to manipulate the position of a single atom relative to the cavity mode with excellent control and reproducibility

  12. A microwave cavity resonator based sensor for the detection of carbon monoxide in hydrogen

    International Nuclear Information System (INIS)

    A resonant-cavity based microwave differential technique is proposed for the detection of carbon monoxide (CO) in hydrogen in the low-ppm range. The determination of the contaminant content is related to the shift in the resonant frequency of a measuring cavity compared to a reference cavity. We expect a CO-detection threshold of about 60 ppm in hydrogen at atmospheric pressure. Accordingly, preliminary measurements carried out when both cavities are filled with helium as a test gas show an equivalent detection threshold around 100 ppm of CO, which compares well with theoretical predictions. (author)

  13. Coupling of cavities - the way to impose control over their modes

    DEFF Research Database (Denmark)

    Ivinskaya, Aliaksandra; Lavrinenko, Andrei; Sukhorukov, Andrey A.; Shyroki, Dmitry; Ha, Sangwoo; Kivshar, Yuri S.

    2010-01-01

    In this work, we demonstrate that the compound mode properties of coupled photonic-crystal cavities can depend critically on the interplay of distance between cavities and their longitudinal shifts. Thus the robust control over the cavity modes can be imposed. The simple coupled-mode theory...... employed for such systems predicts a peculiar behavior of band dispersion in the slow light regime at the photonic band-edge. In particular, it reveals an interesting effect that the frequency detuning of the fundamental supermodes in the coupled cavities can be reduced down to zero. We anticipate that...

  14. Mechanical optimization of superconducting cavities in continuous wave operation

    Science.gov (United States)

    Posen, Sam; Liepe, Matthias

    2012-02-01

    Several planned accelerator facilities call for hundreds of elliptical cavities operating cw with low effective beam loading, and therefore require cavities that have been mechanically optimized to operate at high QL by minimizing df/dp, the sensitivity to microphonics detuning from fluctuations in helium pressure. Without such an optimization, the facilities would suffer either power costs driven up by millions of dollars or an extremely high per-cavity trip rate. ANSYS simulations used to predict df/dp are presented as well as a model that illustrates factors that contribute to this parameter in elliptical cavities. For the Cornell Energy Recovery Linac (ERL) main linac cavity, df/dp is found to range from 2.5 to 17.4Hz/mbar, depending on the radius of the stiffening rings, with minimal df/dp for very small or very large radii. For the Cornell ERL injector cavity, simulations predict a df/dp of 124Hz/mbar, which fits well within the range of measurements performed with the injector cryomodule. Several methods for reducing df/dp are proposed, including decreasing the diameter of the tuner bellows and increasing the stiffness of the enddishes and the tuner. Using measurements from a Tesla Test Facility cavity as the baseline, if both of these measures were implemented and the stiffening rings were optimized, simulations indicate that df/dp would be reduced from ˜30Hz/mbar to just 2.9Hz/mbar, and the power required to maintain the accelerating field would be reduced by an order of magnitude. Finally, other consequences of optimizing the stiffening ring radius are investigated. It is found that stiffening rings larger than 70% of the iris-equator distance make the cavity impossible to tune. Small rings, on the other hand, leave the cavity susceptible to plastic deformation during handling and have lower frequency mechanical resonances, which is undesirable for active compensation of microphonics. Additional simulations of Lorentz force detuning are discussed, and

  15. Quantitative prediction of physical properties of imidazolium based room temperature ionic liquids through determination of condensed phase site charges: a refined force field.

    Science.gov (United States)

    Mondal, Anirban; Balasubramanian, Sundaram

    2014-03-27

    Quantitative prediction of physical properties of room temperature ionic liquids through nonpolarizable force field based molecular dynamics simulations is a challenging task. The challenge lies in the fact that mean ion charges in the condensed phase can be less than unity due to polarization and charge transfer effects whose magnitude cannot be fully captured through quantum chemical calculations conducted in the gas phase. The present work employed the density-derived electrostatic and chemical (DDEC/c3) charge partitioning method to calculate site charges of ions using electronic charge densities obtained from periodic density functional theory (DFT) calculations of their crystalline phases. The total ion charges obtained thus range between -0.6e for chloride and -0.8e for the PF6 ion. The mean value of the ion charges obtained from DFT calculations of an ionic liquid closely matches that obtained from the corresponding crystal thus confirming the suitability of using crystal site charges in simulations of liquids. These partial charges were deployed within the well-established force field developed by Lopes et al., and consequently, parameters of its nonbonded and torsional interactions were refined to ensure that they reproduced quantum potential energy scans for ion pairs in the gas phase. The refined force field was employed in simulations of seven ionic liquids with six different anions. Nearly quantitative agreement with experimental measurements was obtained for the density, surface tension, enthalpy of vaporization, and ion diffusion coefficients. PMID:24605817

  16. Prediction of Post-Closure Water Balance for Monolithic Soil Covers at Waste Disposal Sites in the Greater Accra Metropolitan Area of Ghana

    Directory of Open Access Journals (Sweden)

    Kodwo Beedu Keelson

    2014-04-01

    Full Text Available The Ghana Landfill Guidelines require the provision of a final cover system during landfill closure as a means of minimizing the harmful environmental effects of uncontrolled leachate discharges. However, this technical manual does not provide explicit guidance on the material types or configurations that would be suitable for the different climatic zones in Ghana. The aim of this study was to simulate and predict post-closure landfill cover water balance for waste disposal sites located in the Greater Accra Metropolitan Area using the USGS Thornthwaite monthly water balance computer program. Five different cover soil types were analyzed under using historical climatic data for the metropolis from 1980 to 2001. The maximum annual percolation and evapotranspiration rates for the native soil type were 337 mm and 974 mm respectively. Monthly percolation rates exhibited a seasonal pattern similar to the bimodal precipitation regime whereas monthly evapotranspiration did not. It was also observed that even though soils with a high clay content would be the most suitable option as landfill cover material in the Accra metropolis the maximum thickness of 600 mm recommended in the Ghana Landfill Guidelines do not seem to provide significant reduction in percolation rates into the buried waste mass when the annual rainfall exceeds 700 mm. The findings from this research should provide additional guidance to landfill managers on the specification of cover designs for waste disposal sites with similar climatic conditions.

  17. A new flooding correlation development and its critical heat flux predictions under low air-water flow conditions in Savannah River Site assembly channels

    International Nuclear Information System (INIS)

    The upper limit to countercurrent flow, namely, flooding, is important to analyze the reactor coolability during an emergency cooling system (ECS) phase as a result of a large-break loss-of-coolant accident (LOCA) such as a double-ended guillotine break in the Savannah River Site (SRS) reactor system. During normal operation, the reactor coolant system utilizes downward flow through concentric heated tubes with ribs, which subdivided each annular channel into four subchannels. In this paper, a new flooding correlation has been developed based on the analytical models and literature data for adiabatic, steady-state, one-dimensional, air-water flow to predict flooding phenomenon in the SRS reactor assembly channel, which may have a counter-current air-water flow pattern during the ECS phase. In addition, the correlation was benchmarked against the experimental data conducted under the Oak Ridge National Laboratory multislit channel, which is close to the SRS assembly geometry. Furthermore, the correlation has also been used as a constitutive relationship in a new two-component two-phase thermal-hydraulics code FLOWTRAN-TF, which has been developed for a detailed analysis of SRS reactor assembly behavior during LOCA scenarios. Finally, the flooding correlation was applied to the predictions of critical heat flux, and the results were compared with the data taken by the SRS heat transfer laboratory under a single annular channel with ribs and a multiannular prototypic test rig

  18. Operational strategy for soil concentration predictions of strontium/yttrium-90 and cesium-137 in surface soil at the West Valley Demonstration Project site

    International Nuclear Information System (INIS)

    There are difficulties associated with the assessment of the interpretation of field measurements, determination of guideline protocols and control and disposal of low level radioactive contaminated soil in the environmental health physics field. Questions are raised among scientists and in public forums concerning the necessity and high costs of large area soil remediation versus the risks of low-dose radiation health effects. As a result, accurate soil activity assessments become imperative in decontamination situations. The West Valley Demonstration Project (WVDP), a US Department of Energy facility located in West Valley, New York is managed and operated by West Valley Nuclear Services Co., Inc. (WVNS). WVNS has identified contaminated on-site soil areas with a mixed variety of radionuclides (primarily fission product). Through the use of data obtained from a previous project performed during the summer of 1994 entitled ''Field Survey Correlation and Instrumentation Response for an In Situ Soil Measurement Program'' (Myers), the WVDP offers a unique research opportunity to investigate the possibility of soil concentration predictions based on exposure or count rate responses returned from a survey detector probe. In this study, correlations are developed between laboratory measured soil beta activity and survey probe response for the purposes of determining the optimal detector for field use and using these correlations to establish predictability of soil activity levels

  19. Exploring the predicted effect of social networking site use on perceived social capital and psychological well-being of Chinese international students in Japan.

    Science.gov (United States)

    Guo, Yu; Li, Yiwei; Ito, Naoya

    2014-01-01

    This study investigated how social networking sites (SNSs) use by Chinese international students in Japan influenced their perceived social capital and psychological well-being. In addition, it examined how, as sojourners, Chinese international students' perceived acculturative stress varied. Data were collected from 142 Chinese international students. The results indicated that the intensity of SNS use was unable to predict individuals' perceived social capital and psychological well-being. The effect of SNS use varied according to the functions it serves. Specifically, SNS use for social and informational functions (SIF) increased individuals' levels of perceived bridging social capital and perceived life satisfaction, while SNS use for entertaining recreational functions (ERF) was unable to predict perceived social capital but increased individuals' levels of loneliness. It was also found that, in the intercultural environment, Chinese international students' levels of perceived acculturative stress were decreased by their perceived bonding social capital and increased by their perceived loneliness but had no relationship with their SNS use. Findings of the study suggest that individuals using SNSs to stay informed and connected will benefit with regard to their social network building and psychological well-being. PMID:23971431

  20. Right and left ventricular ejection fraction after an acute inferior wall myocardial infarction and the value of V4R to predict the site of obstruction

    Energy Technology Data Exchange (ETDEWEB)

    Braat, S.H.; Brugada, P.; Den Dulk, K.; Wellens, H.J.J.

    1984-01-01

    This study was undertaken to compare the right (RVEF) and left ventricular ejection fraction (LVEF) after an acute inferior wall myocardial infarction (MI) caused by an obstruction in the right coronary artery (RCA) or circumflex coronary artery (CX) and to evaluate the value of lead V4R to predict the site of stenosis which caused the MI. In 42 consecutive patients (pts) admitted with an acute inferior wall MI a standard ECG and V4R were recorded. A nuclear angiogram was made one week after the acute MI and the RVEF and LVEF were calculated. Ten to 14 days (mean 12.7) after the acute MI a coronary angiogram was performed to determine the site of occlusion, which had caused the acute MI. According to the site of occlusion the pts were divided in three groups: Group A: the stenosis which had caused the MI was located in the RCA above the first branch to the right ventricle (RV); Group B: the stenosis was below the first branch to the RV in the RCA and Group C: the stenosis was located in the CX. The RVEF and LVEF in these groups are given. Nineteen pts had ST-segment elevation greater than or equal to 1 mm in V/sub 4/R and 17 of these pts had an obstruction above the first branch to the RV in the RCA. There is statistically no significant difference between the LVEF in the three different groups while the RVEF is significantly lower in group A. These pts can be identified by recording V4R.

  1. Design, fabrication, and testing of superconducting RF cavities for high average beam currents

    Science.gov (United States)

    Meidlinger, David Joseph

    For high current applications, it is desirable for the cavity shape to have a low longitudinal loss factor and to have a high beam-breakup threshold current. This dissertation describes three different cavities designed for this purpose: a six-cell elliptical cavity for particles traveling at the speed of light, a two-cell elliptical cavity for subluminal particle speeds, and a single cell cavity which uses the TM012 mode for acceleration. SUPERFISH simulations predict the peak fields in both of the elliptical cavities will not exceed the TeSLA values by more than 10% but both will have 28.7% larger apertures. The elliptical designs assume the bunch frequency equals the accelerating mode frequency. The beam pipe radius is chosen so that the cutoff frequency is less than twice that of the accelerating mode. Hence all of the monopole and dipole higher-order modes (HOMs) that can be driven by a Fourier component of the beam have low loaded Q values. This simplifies the problem of HOM damping. The TM012 cavity is predicted to have much higher peak fields than a pi-mode elliptical cavity, but offers potential advantages from its simplified shape; it is essentially a circular waveguide with curved end plates. This basic shape results in easier fabrication and simplified tuning. Two prototype two-cell cavities were fabricated and tested at cryogenic temperatures without beam.

  2. A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0.

    Directory of Open Access Journals (Sweden)

    Kuo-Chen Chou

    Full Text Available Information of subcellular locations of proteins is important for in-depth studies of cell biology. It is very useful for proteomics, system biology and drug development as well. However, most existing methods for predicting protein subcellular location can only cover 5 to 12 location sites. Also, they are limited to deal with single-location proteins and hence failed to work for multiplex proteins, which can simultaneously exist at, or move between, two or more location sites. Actually, multiplex proteins of this kind usually posses some important biological functions worthy of our special notice. A new predictor called "Euk-mPLoc 2.0" is developed by hybridizing the gene ontology information, functional domain information, and sequential evolutionary information through three different modes of pseudo amino acid composition. It can be used to identify eukaryotic proteins among the following 22 locations: (1 acrosome, (2 cell wall, (3 centriole, (4 chloroplast, (5 cyanelle, (6 cytoplasm, (7 cytoskeleton, (8 endoplasmic reticulum, (9 endosome, (10 extracell, (11 Golgi apparatus, (12 hydrogenosome, (13 lysosome, (14 melanosome, (15 microsome (16 mitochondria, (17 nucleus, (18 peroxisome, (19 plasma membrane, (20 plastid, (21 spindle pole body, and (22 vacuole. Compared with the existing methods for predicting eukaryotic protein subcellular localization, the new predictor is much more powerful and flexible, particularly in dealing with proteins with multiple locations and proteins without available accession numbers. For a newly-constructed stringent benchmark dataset which contains both single- and multiple-location proteins and in which none of proteins has pairwise sequence identity to any other in a same location, the overall jackknife success rate achieved by Euk-mPLoc 2.0 is more than 24% higher than those by any of the existing predictors. As a user-friendly web-server, Euk-mPLoc 2.0 is freely accessible at http

  3. TEM observations of crack tip: cavity interactions

    International Nuclear Information System (INIS)

    Crack tip-cavity interactions have been studied by performing room temperature deformation experiments in a transmission electron microscope on ion-irradiated type 316 stainless steel with small helium containing cavities. Slip dislocations emitted from a crack tip cut, sheared, and thereby elongated cavities without a volume enlargement. As the crack tip approached, a cavity volume enlargement occurred. Instead of the cavities continuing to enlarge until they touch, the walls between the cavities fractured. Fracture surface dimples do not correlate in size or density with these enlarged cavities

  4. Investigation Of Breakdown Induced Surface Damage On 805 Mhz Pillbox Cavity Interior Surfaces

    CERN Document Server

    Jana, M R; Leonova, M; Moretti, A; Tollestrup, A; Yonehara, K; Freemire, B; Torun, Y; Bowring, D; Flanagan, G

    2014-01-01

    The MuCool Test Area (MTA) at Fermilab is a facility to develop the technology required for ionization cooling for a future Muon Collider and/or Neutrino Factory. As part of this research program, we have tested two 805 MHz vacuum RF cavities in a multi-Tesla magnetic field to study the effects of the static magnetic field on the cavity operation. This study gives useful information on field emitters in the cavity, dark current, surface conditioning, breakdown mechanisms and material properties of the cavity. All these factors determine the maximum accelerating gradient in the cavity. This paper discusses the image processing technique for quantitative estimation of spark damage spot distribution on cavity interior surfaces. The distribution is compared with the electric field distribution predicted by a computer code calculation. The local spark density is proportional to probability of surface breakdown and shows a power law dependence on the maximum electric field (E). This E dependence is consistent with ...

  5. The cavity-nest ant Temnothorax crassispinus prefers larger nests

    OpenAIRE

    Mitrus, S.

    2014-01-01

    Colonies of the ant Temnothorax crassispinus inhabit mostly cavities in wood and hollow acorns. Typically in the field, nest sites that can be used by the ant are a limited resource. In a field experiment, it was investigated whether the ants prefer a specific size of nest, when different ones are available. In July 2011, a total of 160 artificial nests were placed in a beech-pine forest. Four artificial nests (pieces of wood with volume cavities, ca 415, 605, 730, and 980 mm3, respectively) ...

  6. Radionuclide distribution in a nuclear test cavity: the baseball event

    International Nuclear Information System (INIS)

    In 1994 two holes were drilled into the cavity formed in 1981 by the underground nuclear test named Baseball. An extensive set of side wall samples were collected in these holes. We have analyzed the samples for tritium and for gamma-emitting radionuclides (both fission products and neutron activation products). It appears that the distribution pattern of these radioactive materials, established at the time of the detonation, have persisted even though the cavity has been under water for 13 years. These findings are discussed in the context of radionuclide migration and groundwater contamination at the Nevada Test Site. (orig.)

  7. Active Wavelength Control of an External Cavity Quantum Cascade Laser

    Science.gov (United States)

    Tsai, Tracy; Wysocki, Gerard

    2012-01-01

    We present an active wavelength control system for grating-based external cavity lasers that increases the accuracy of predicting the lasing wavelength based on the grating equation and significantly improves scan-to-scan wavelength/frequency repeatability. The ultimate 3σ precision of a frequency scan is determined by the scan-to-scan repeatability of 0.042 cm−1. Since this control method can be applied to any external cavity laser with little to no modification, such a precision provides an excellent opportunity for spectroscopic applications that target molecular absorption lines at standard atmospheric conditions. PMID:23483850

  8. Active Wavelength Control of an External Cavity Quantum Cascade Laser

    OpenAIRE

    Tsai, Tracy; Wysocki, Gerard

    2012-01-01

    We present an active wavelength control system for grating-based external cavity lasers that increases the accuracy of predicting the lasing wavelength based on the grating equation and significantly improves scan-to-scan wavelength/frequency repeatability. The ultimate 3σ precision of a frequency scan is determined by the scan-to-scan repeatability of 0.042 cm−1. Since this control method can be applied to any external cavity laser with little to no modification, such a precision provides an...

  9. Normal Conducting RF Cavity for MICE

    Energy Technology Data Exchange (ETDEWEB)

    Li, D.; DeMello, A.; Virostek, S.; Zisman, M.; Summers, D.

    2010-05-23

    Normal conducting RF cavities must be used for the cooling section of the international Muon Ionization Cooling Experiment (MICE), currently under construction at Rutherford Appleton Laboratory (RAL) in the UK. Eight 201-MHz cavities are needed for the MICE cooling section; fabrication of the first five cavities is complete. We report the cavity fabrication status including cavity design, fabrication techniques and preliminary low power RF measurements.

  10. Normal Conducting RF Cavity for MICE

    International Nuclear Information System (INIS)

    Normal conducting RF cavities must be used for the cooling section of the international Muon Ionization Cooling Experiment (MICE), currently under construction at Rutherford Appleton Laboratory (RAL) in the UK. Eight 201-MHz cavities are needed for the MICE cooling section; fabrication of the first five cavities is complete. We report the cavity fabrication status including cavity design, fabrication techniques and preliminary low power RF measurements.

  11. Study on pool-nucleate boiling heat transfer characteristics by using artificial cavities

    International Nuclear Information System (INIS)

    Pool boiling heat transfer experiments were performed by using the well-controlled/defined heat transfer surface for water. Uni-size and -shape artificial cavities were created on the mirror-finished silicon plate by utilizing the MEMS technology. Experimental results agreed well with what were predicted by the traditional boiling theory. The mirror finished surface showed only the tendency of natural circulation heat transfer. The artificial-cavity heat transfer surface followed the pool-nucleate boiling trend. The onset of the pool-nucleate boiling was well predicted by the traditional pool-nucleate boiling theory. These results indicated that the artificial cavities behave just like natural cavities. The results indicated the artificial cavities are quite useful and promising to examine the true features of complicated boiling that have been overshadowed by complicatedness. (authors)

  12. Cavity optomechanics and its applications

    Science.gov (United States)

    Bhattacharya, Mishkatul

    2009-05-01

    Cavity optomechanics is an emerging field at the intersection of quantum optics, atomic physics, nanoscience and gravitational wave interferometry. It involves cavities (with one or more mechanical degrees of freedom) driven by laser radiation. The ensuing optical control of macroscopic mechanical motion may have implications for precision sensing, coherent control of atoms and molecules, and quantum information processing. Due to recent innovations optomechanical physics has been realized in a variety of experimental systems spanning many orders of magnitude in mass and time-scales. In this talk, I will first introduce the basic paradigm of a laser-driven two mirror cavity used for cooling a vibrational mode. A three-mirror configuration recently implemented using a partially transmissive dielectric membrane in a high finesse cavity will then be discussed, and shown to be superior to the two-mirror design in a number of ways. One implication of the three-mirror configuration is the possibility of scaling optomechanical techniques to multiple oscillators. This topic will be explored by analysing the case of two membranes in a cavity where it will be shown that the collective(center-of-mass and breathing) modes of vibration can be cooled independently, analogous to a chain of trapped ions. Finally, future directions for possible applications to the control of atoms and molecules will be indicated briefly.

  13. Development of Side Coupled Cavities

    International Nuclear Information System (INIS)

    Side coupled Cavities are good candidates for proton accelerations in the 90-180 MeV range, as it has been first proposed for the CERN LINAC4 project. A side coupled Linac is made of a lump chain of resonant cavities, alternatively accelerating and coupling. A side coupled cavity has been designed in a CERN-LPSC collaboration to achieve LINAC4 requirements. After RF studies, a complete thermal study has been done, showing that 10-15% is the absolute maximum duty-cycle achievable by such a cavity. Error studies have been developed. They have shown that a tuning ring is mandatory and that a K equals 3% coupling factor is a good choice. A prototype has been built and each cell has been measured and tuned. A simple and accurate method has been used to get both the resonant frequency and the coupling factor, with a movable tuner and a linear fit. A similar method has been used to get the second order coupling factor. A large dispersion is observed on K. This is mainly due to the shape of the coupling apertures, which are very sensitive to mechanical errors. A future and realistic design must be very careful to guarantee a constant aperture (the important parameter is more the dispersion of k than its exact value). Finally, we analyse how to tune the cavity. This has to checked carefully and probably improved or corrected. Results are expected for mid-2008

  14. The ESS spoke cavity cryomodules

    Science.gov (United States)

    Bousson, Sebastien; Darve, Christine; Duthil, Patxi; Elias, Nuno; Molloy, Steve; Reynet, Denis; Thermeau, Jean-Pierre

    2014-01-01

    The European Spallation Source (ESS) is a multi-disciplinary research centre under design and construction in Lund, Sweden. This new facility is funded by a collaboration of 17 European countries and is expected to be up to 30 times brighter than today's leading facilities and neutron sources. The ESS will enable new opportunities for researchers in the fields of life sciences, energy, environmental technology, cultural heritage and fundamental physics. A 5 MW long pulse proton accelerator is used to reach this goal. The pulsed length is 2.86 ms, the repetition frequency is 14 Hz (4 % duty cycle), and the beam current is 62.5 mA. It is composed of one string of spoke cavity cryomodule and two strings of elliptical cavity cryomodules. This paper introduces the thermo-mechanical design and expected operation of the ESS spoke cavity cryomodules. These cryomodules contain two double spoke bulk Niobium cavities operating at 2 K and at a frequency of 352.21 MHz. The superconducting section of the Spoke Linac accelerates the beam from 90 MeV to 220 MeV. A Spoke Cavity Cryomodule Technology Demonstrator will be built and tested in order to validate the ESS series production.

  15. The ESS elliptical cavity cryomodules

    Science.gov (United States)

    Darve, Christine; Bosland, Pierre; Devanz, Guillaume; Olivier, Gilles; Renard, Bertrand; Thermeau, Jean-Pierre

    2014-01-01

    The European Spallation Source (ESS) is a multi-disciplinary research centre under design and construction in Lund, Sweden. This new facility is funded by a collaboration of 17 European countries and is expected to be up to 30 times brighter than today's leading facilities and neutron sources. The ESS will enable new opportunities for researchers in the fields of life sciences, energy, environmental technology, cultural heritage and fundamental physics. A 5 MW long pulse proton accelerator is used to reach this goal. The pulsed length is 2.86 ms, the repetition frequency is 14 Hz (4 % duty cycle), and the beam current is 62.5 mA. The superconducting section of the Linac accelerates the beam from 80 MeV to 2.0 GeV. It is composed of one string of spoke cavity cryomodule and two strings of elliptical cavity cryomodules. These cryomodules contain four elliptical Niobium cavities operating at 2 K and at a frequency of 704.42 MHz. This paper introduces the thermo-mechanical design, the prototyping and the expected operation of the ESS elliptical cavity cryomodules. An Elliptical Cavity Cryomodule Technology Demonstrator (ECCTD) will be built and tested in order to validate the ESS series production.

  16. Polymer indentation: Numerical analysis and comparison with a spherical cavity model

    DEFF Research Database (Denmark)

    Tvergaard, Viggo; Needleman, A.

    2011-01-01

    found to be smaller for sharper indenters. The calculated values of both the nominal and true hardness do not differ significantly for the two indenter shapes. An expanding spherical cavity model is also considered and the predictions of this model are compared with the finite element results for...... various indenter shapes and indentation rates. The spherical cavity model is found to give fairly good agreement with the predictions of the finite element analyses for the nominal polymer hardness for both indenter shapes....

  17. Sub-gigahertz beam switching of vertical-cavity surface-emitting laser with transverse coupled cavity

    Energy Technology Data Exchange (ETDEWEB)

    Nakahama, M.; Gu, X.; Sakaguchi, T. [Photonics Integration System Research Center, Tokyo Institute of Technology, 4259-R2-22, Nagatsuta, Midori-ku, Yokohama 226-8503 (Japan); Matsutani, A. [Semiconductor and MEMS Processing Center, Tokyo Institute of Technology, 4259-R2-22, Nagatsuta, Midori-ku, Yokohama 226-8503 (Japan); Ahmed, M.; Bakry, A. [Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589 (Saudi Arabia); Koyama, F. [Photonics Integration System Research Center, Tokyo Institute of Technology, 4259-R2-22, Nagatsuta, Midori-ku, Yokohama 226-8503 (Japan); Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589 (Saudi Arabia)

    2015-08-17

    We report a high-speed electrical beam switching of vertical cavity surface emitting laser with a transverse coupled cavity. A high speed (sub-gigahertz) and large deflection angle (>30°) beam switching is demonstrated by employing the transverse mode switching. The angular switching speed of 900 MHz is achieved with narrow beam divergence of below 4° and extinction ratio of 8 dB. We also measured the near- and far-field patterns to clarify the origin of the beam switching. We present a simple one-dimensional Bragg reflector waveguide model, which well predicts the beam switching characteristic.

  18. Impact of Lorentz forces on a Spoke cavity with β 0.15 and on a Spiral-2 cavity with β 0.12

    International Nuclear Information System (INIS)

    Mono-spoke superconducting cavities have been proposed for the acceleration of radioactive ion beams. The interaction of the electromagnetic field with the surface electrical current generates Lorentz forces that operate on the intern wall of the cavity, the distribution of these forces is highly non-linear and varying. The stability of a superconducting cavity is directly linked to the frequency variation due to Lorentz forces and as a consequence the optimized design of a cavity must take into account these forces. In order to optimize the design of a cavity, 3 complementary software have been developed: Catia, a computer-aided-design software, Soprano for electromagnetic modeling and Cast3m for mechanical modeling. Preliminary results show a good agreement between predicted values and experimental data. (A.C.)

  19. A SURVEY OF CORONAL CAVITY DENSITY PROFILES

    International Nuclear Information System (INIS)

    Coronal cavities are common features of the solar corona that appear as darkened regions at the base of coronal helmet streamers in coronagraph images. Their darkened appearance indicates that they are regions of lowered density embedded within the comparatively higher density helmet streamer. Despite interfering projection effects of the surrounding helmet streamer (which we refer to as the cavity rim), Fuller et al. have shown that under certain conditions it is possible to use a Van de Hulst inversion of white-light polarized brightness (pB) data to calculate the electron density of both the cavity and cavity rim plasma. In this article, we apply minor modifications to the methods of Fuller et al. in order to improve the accuracy and versatility of the inversion process, and use the new methods to calculate density profiles for both the cavity and cavity rim in 24 cavity systems. We also examine trends in cavity morphology and how departures from the model geometry affect our density calculations. The density calculations reveal that in all 24 cases the cavity plasma has a flatter density profile than the plasma of the cavity rim, meaning that the cavity has a larger density depletion at low altitudes than it does at high altitudes. We find that the mean cavity density is over four times greater than that of a coronal hole at an altitude of 1.2 Rsun and that every cavity in the sample is over twice as dense as a coronal hole at this altitude. Furthermore, we find that different cavity systems near solar maximum span a greater range in density at 1.2 Rsun than do cavity systems near solar minimum, with a slight trend toward higher densities for systems nearer to solar maximum. Finally, we found no significant correlation of cavity density properties with cavity height-indeed, cavities show remarkably similar density depletions-except for the two smallest cavities that show significantly greater depletion.

  20. Beating quantum limits in an optomechanical sensor by cavity detuning

    International Nuclear Information System (INIS)

    We study the quantum limits in an optomechanical sensor based on a detuned high-finesse cavity with a movable mirror. We show that the radiation pressure exerted on the mirror by the light in the detuned cavity induces a modification of the mirror dynamics and makes the mirror motion sensitive to the signal. This leads to an amplification of the signal by the mirror dynamics, and to an improvement of the sensor sensitivity beyond the standard quantum limit, up to an ultimate quantum limit only related to the mechanical dissipation of the mirror. This improvement is somewhat similar to the one predicted in detuned signal-recycled gravitational-wave interferometers, and makes a high-finesse cavity a model system to test these quantum effects

  1. Autonomous quantum thermal machines in atom-cavity systems

    CERN Document Server

    Mitchison, Mark T; Prior, Javier; Woods, Mischa P; Plenio, Martin B

    2016-01-01

    An autonomous quantum thermal machine comprising a trapped atom or ion placed inside an optical cavity is proposed and analysed. Such a machine can operate as a heat engine whose working medium is the quantised atomic motion, or as an absorption refrigerator which cools without any work input. Focusing on the refrigerator mode, we predict that it is possible with state-of-the-art technology to cool a trapped ion almost to its motional ground state using a thermal light source such as sunlight. We nonetheless find that a laser or similar reference system is necessary to stabilise the cavity frequencies. Furthermore, we establish a direct and heretofore unacknowledged connection between the abstract theory of quantum absorption refrigerators and practical sideband cooling techniques. We also highlight and clarify some assumptions underlying several recent theoretical studies on self-contained quantum engines and refrigerators. Our work indicates that cavity quantum electrodynamics is a promising and versatile e...

  2. Phoxonic crystals and cavity optomechanics

    Science.gov (United States)

    Djafari-Rouhani, Bahram; El-Jallal, Said; Pennec, Yan

    2016-05-01

    Phoxonic crystals are dual phononic/photonic crystals exhibiting simultaneously band gaps for both types of excitations. Therefore, they have the ability to confine phonons and photons in the same cavity and in turn allow the enhancement of their interaction. In this paper, we review some of our theoretical works on cavity optomechanical interactions in different types of phoxonic crystals, including two-dimensional, slab, and nanobeam structures. Two mechanisms are behind the phonon-photon interaction, namely the photoelastic and the moving interface effects. Coupling rates of a few MHz are obtained with high-frequency phonons of a few GHz. Finally, we give some preliminary results about the optomechanical interaction when a metallic nanoparticle is introduced into the cavity, giving rise to coupled photon-plasmon modes or, in the case of very small particles, to an enhancement of the electric field at the position of the particle. xml:lang="fr"

  3. Crab cavities for the LHC

    International Nuclear Information System (INIS)

    For the high-luminosity LHC upgrade program (HL-LHC), the installation of crab cavities (CC) is essential to compensate the geometric luminosity loss due to the crossing angle and for luminosity leveling. One of the major challenges is the compatibility with machine protection in the regime of >500 MJ stored beam energy. Especially in a failure case (e.g. a CC quench or sparking in the coupler), the voltage and/or phase of a CC can change significantly with a fast time-constant of the order of a LHC-turn. This can lead to large, global betatron oscillations of the beam. The status of the LHC crab cavity upgrade program is presented and the influence of crab cavities on the beam dynamics is discussed. Necessary countermeasures to limit the impact of CC failures to an acceptable level are specified and operational scenarios that are compatible with machine protection considerations are proposed.

  4. RRR Characteristics for SRF cavities

    Science.gov (United States)

    Jung, Yoochul; Hyun, Myungook; Joung, Mijoung

    2015-10-01

    The first heavy ion accelerator is being constructed by the rare isotope science project (RISP) launched by the Institute of Basic Science (IBS) in South Korea. Four different types of superconducting cavities were designed, and prototypes such as a quarter-wave resonator (QWR), a half-wave resonator (HWR) and a single-spoke resonator (SSR) were fabricated. One of the critical factors determining the performances of superconducting cavities is the residual resistance ratio (RRR). The RRR values essentially represent how pure niobium is and how fast niobium can transmit heat. In general, the RRR degrades during electron beam welding due to impurity incorporation. Thus, it is important to maintain the RRR above a certain value at which a niobium cavity shows target performance. In this study, RRR degradation related with electron beam welding conditions, for example, the welding power, welding speed, and vacuum level, will be discussed.

  5. RRR Characteristics for SRF Cavities

    CERN Document Server

    Jung, Yoochul; Joung, Mijoung

    2015-01-01

    The first heavy ion accelerator is being constructed by the rare isotope science project (RISP) launched by the Institute of Basic Science (IBS) in South Korea. Four different types of superconducting cavities were designed, and prototypes were fabricated such as a quarter wave resonator (QWR), a half wave resonator (HWR) and a single spoke resonator (SSR). One of the critical factors determining performances of the superconducting cavities is a residual resistance ratio (RRR). The RRR values essentially represent how much niobium is pure and how fast niobium can transmit heat as well. In general, the RRR degrades during electron beam welding due to the impurity incorporation. Thus it is important to maintain RRR above a certain value at which a niobium cavity shows target performance. In this study, RRR degradation related with electron beam welding conditions, for example, welding power, welding speed, and vacuum level will be discussed.

  6. IMRT in oral cavity cancer

    International Nuclear Information System (INIS)

    Except for early T1,2 N0 stages, the prognosis for patients with oral cavity cancer (OCC) is reported to be worse than for carcinoma in other sites of the head and neck (HNC). The aim of this work was to assess disease outcome in OCC following IMRT. Between January 2002 and January 2007, 346 HNC patients have been treated with curative intensity modulated radiation therapy (IMRT) at the Department of Radiation Oncology, University Hospital Zurich. Fifty eight of these (16%) were referred for postoperative (28) or definitive (30) radiation therapy of OCC. 40 of the 58 OCC patients (69%) presented with locally advanced T3/4 or recurred lesions. Doses between 60 and 70 Gy were applied, combined with simultaneous cisplatin based chemotherapy in 78%. Outcome analyses were performed using Kaplan Meier curves. In addition, comparisons were performed between this IMRT OCC cohort and historic in-house cohorts of 33 conventionally irradiated (3DCRT) and 30 surgery only patients treated over the last 10 years. OCC patients treated with postoperative IMRT showed the highest local control (LC) rate of all assessed treatment sequence subgroups (92% LC at 2 years). Historic postoperative 3DCRT patients and patients treated with surgery alone reached LC rates of ~70–80%. Definitively irradiated patients revealed poorest LC rates with ~30 and 40% following 3DCRT and IMRT, respectively. T1 stage resulted in an expectedly significantly higher LC rate (95%, n = 19, p < 0.05) than T2-4 and recurred stages (LC ~50–60%, n = 102). Analyses according to the diagnosis revealed significantly lower LC in OCC following definitive IMRT than that in pharyngeal tumors treated with definitive IMRT in the same time period (43% vs 82% at 2 years, p < 0.0001), while the LC rate of OCC following postoperative IMRT was as high as in pharyngeal tumors treated with postoperative IMRT (>90% at 2 years). Postoperative IMRT of OCC resulted in the highest local control rate of the assessed treatment

  7. Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape.

    Science.gov (United States)

    Zoete, Vincent; Schuepbach, Thierry; Bovigny, Christophe; Chaskar, Prasad; Daina, Antoine; Röhrig, Ute F; Michielin, Olivier

    2016-02-01

    Molecular docking is a computational approach for predicting the most probable position of ligands in the binding sites of macromolecules and constitutes the cornerstone of structure-based computer-aided drug design. Here, we present a new algorithm called Attracting Cavities that allows molecular docking to be performed by simple energy minimizations only. The approach consists in transiently replacing the rough potential energy hypersurface of the protein by a smooth attracting potential driving the ligands into protein cavities. The actual protein energy landscape is reintroduced in a second step to refine the ligand position. The scoring function of Attracting Cavities is based on the CHARMM force field and the FACTS solvation model. The approach was tested on the 85 experimental ligand-protein structures included in the Astex diverse set and achieved a success rate of 80% in reproducing the experimental binding mode starting from a completely randomized ligand conformer. The algorithm thus compares favorably with current state-of-the-art docking programs. PMID:26558715

  8. Cavity Solitons in VCSEL Devices

    Directory of Open Access Journals (Sweden)

    S. Barbay

    2011-01-01

    Full Text Available We review advances on the experimental study of cavity solitons in VCSELs in the past decade. We emphasize on the design and fabrication of electrically or optically pumped broad-area VCSELs used for CSs formation and review different experimental configurations. Potential applications of CSs in the field of photonics are discussed, in particular the use of CSs for all-optical processing of information and for VCSELs characterization. Prospects on self-localization studies based on vertical cavity devices involving new physical mechanisms are also given.

  9. Radiography of the abdominal cavity

    International Nuclear Information System (INIS)

    Radiography is a very important part of the diagnostic procedure in many small animal diseases. Technically perfect X-rays are essential for the exact diagnosis. The general appearance of the abdominal cavity should be evaluated at first, e.g. the overall contrast and the definition of the visualized organs. Then particular attention should be paid, if there is any peritoneal effusion or free air in the peritoneal cavity. Subsequently each radiographically visible organ has to be evaluated for its position, size, shape and radiographic density

  10. Protein dynamics: hydration and cavities

    Directory of Open Access Journals (Sweden)

    K. Heremans

    2005-08-01

    Full Text Available The temperature-pressure behavior of proteins seems to be unique among the biological macromolecules. Thermodynamic as well as kinetic data show the typical elliptical stability diagram. This may be extended by assuming that the unfolded state gives rise to volume and enthalpy-driven liquid-liquid transitions. A molecular interpretation follows from the temperature and the pressure dependence of the hydration and cavities. We suggest that positron annihilation spectroscopy can provide additional quantitative evidence for the contributions of cavities to the dynamics of proteins. Only mature amyloid fibrils that form from unfolded proteins are very resistant to pressure treatment.

  11. Nanobeam Cavities for Reconfigurable Photonics

    OpenAIRE

    Deotare, Parag

    2012-01-01

    We investigate the design, fabrication, and experimental characterization of high quality factor photonic crystal nanobeam cavities, with theoretical quality factors of \\(1.4 × 10^7\\) in silicon, operating at ~1550 nm. By detecting the cross-polarized resonantly scattered light from a normally incident laser beam, we measure a quality factor of nearly \\(7.5 × 10^5\\). We show on-chip integration of the cavities using waveguides and an inverse taper geometry based mode size converters, and also...

  12. Sterility of the uterine cavity

    DEFF Research Database (Denmark)

    Møller, Birger R.; Kristiansen, Frank V.; Thorsen, Poul;

    1995-01-01

    In a prospective open study the sterility of the uterine cavity was evaluated in 99 women admitted for hysterectomy. The indications for hysterectomy were in most cases persistent irregular vaginal bleeding and fibromyomas of the uterus. Samples for both aerobic and anaerobic bacteria, Chlamydia...... trachomatis, yeasts and viruses were taken preoperatively from the apex of the vagina and cervical os. Immediately after hysterectomy the uterus was opened under sterile conditions and samples obtained from the isthmus and fundus of the uterine cavity for microbiological examination. Wet smears were taken...

  13. DCH dispersal and entrainment experiment in a scaled annular cavity

    International Nuclear Information System (INIS)

    The objective of this experiment was to measure the amount of corium dispersal and the droplet size distribution during high pressure melt ejection from a CE reactor. The melt and the steam flowed to the containment through a narrow annular cavity. The experiment was carried out on a 1/20th scaled model of the cavity and the containment. The scaling was based on dimensionless numbers obtained from a two-phase flow model of the dispersal and entrainment mechanisms in the cavity. Furthermore, the model shows that the flow in the cavity was choked, so high levels of dispersal and entrainment were possible. The experiment consisted of air-water, air-helium, air-woods metal and helium-woods metal tests; the main result being that the level of dispersal was very high in all cases. The woods metal data supported a separated flow model in the cavity, implying that the gas choked velocity was very high and the droplets very small. In contrast, the measured drop sizes for the water tests were much larger than the separated flow model predictions. This discrepancy could not be resolved because the entrainment mechanism is not properly understood at the present time. (orig.)

  14. A Tracer Experiment to Understand Dispersion Characteristics at a Nuclear Power Plant Site-Focusing on the Comparison with Predictive Results using Reg. Guide 1.145 model

    International Nuclear Information System (INIS)

    There remains disagreement regarding the application of a Gaussian plume model in PAVAN, as it relates to the complicated geographical features of a coastal area. Therefore, this study was performed in order to figure out the characteristics of the PAVAN program that was developed based on the equations of Gaussian Plume Model, which reflected the actual measured concentration of radioactive materials released to the air. It also evaluated the appropriateness of using a Gaussian plume model for assessing the environmental impact of radiation from a nuclear power plant. In order to analyze the dispersion characteristics of radioactive materials released into the air from the Wolsong nuclear power plant, SF6 gas was released from the site at night for one hour under stable atmospheric conditions disadvantageous to dilute a tracer gas in this study. The measured concentrations were compared with theoretical estimates derived from meteorological data observed during the experiment period to evaluate the prediction capabilities of the Gaussian plume model. This study conducted a tracer dispersion experiment at the site of Wolsong Nuclear Power Plant site in Korea to analyze the atmospheric dispersion characteristics of radioactive materials. It compared the experimental value with the calculated value using the Gaussian Plume Model as suggested in Reg. 1.145, based on the meteorological data observed in the experiment time period, and evaluated the conservative estimate of the calculated value. In the area where the calculated value is relatively high, the calculated value tends to show higher than the experimental value, which confirmed the conservative manner of the estimating of the calculated value using the Gaussian Plume Model. The short-term exposure of radiation to a human body caused by a nuclear accident would be higher in the area where the atmospheric concentration of radiation is high. Therefore, it is a sufficiently conservative manner to use the Gaussian

  15. Imaging of the peritoneal cavity in CAPD.

    Science.gov (United States)

    Wankowicz, Z; Pietrzak, B; Skrobowska, E

    1996-01-01

    The aim of our study was the use of the optimal imaging of the peritoneal cavity (PC) for continuous ambulatory peritoneal dialysis (CAPD)-related problems. Ultrasonography (USG), direct abdominal radiography (DAR), peritoneoscintigraphy (PSG), and standard peritoneo-computed tomography (PCT) with reconstruction (R-PCT) were performed in 25 patients on CAPD from three to 44 months. Studies were done at the beginning of CAPD (1-3 months) as well as in the noncomplicated and complicated course of CAPD. Group 1 comprised 17 patients in whom 77 PC images were taken in the non-complicated course of CAPD. Group II comprised 15 patients in whom 65 images were taken during or after complications. For USG and DAR we used standard equipment, PSG was done with sulfur colloid labeled with technetium 99m (Tc 99m), PCT, and R-PCT were done with Omnipaque and Somatom HiQ Siemens unit. In PCT, two- and three dimensional reconstruction were done by our own computer program. USG was recommended for imaging of tunnel infections, exit-site infection (ESI), and adhesion. PSG was useful in almost all observed complications of CAPD except thickening of the peritoneal membrane (PM). Standard PCT with R-PCT was more useful than PCT because of a more legible image of the peritoneal cavity, which gives the possibility of monitoring fluid distribution and measuring of intraperitoneal fluid volume. PMID:8728239

  16. Devil's Staircase in an Optomechanical Cavity

    CERN Document Server

    Wang, Hui; Buks, Eyal

    2016-01-01

    We study self-excited oscillation (SEO) in an on-fiber optomechanical cavity. While the phase of SEO randomly diffuses in time when the laser power that is injected into the cavity is kept constant, phase locking may occur when the laser power is periodically modulated in time. We investigate the dependence of phase locking on the amplitude and frequency of the laser power modulation. We find that phase locking can be induced with a relatively low modulation amplitude provided that the ratio between the modulation frequency and the frequency of SEO is tuned close to a rational number of relatively low hierarchy in the Farey tree. To account for the experimental results a one dimensional map, which allows evaluating the time evolution of the phase of SEO, is theoretically derived. By calculating the winding number of the one dimensional map the regions of phase locking can be mapped in the plane of modulation amplitude and modulation frequency. Comparison between the theoretical predictions and the experimenta...

  17. Further studies of the seismic characteristics of Russian explosions in cavities: Implications for cavity decoupling of underground nuclear explosions. Final report, August 1993-November 1995

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, J.R.; Kitov, I.O.; Rimer, N.; Sultanov, D.D.; Barker, B.W.

    1996-01-01

    This report provides a summary of the results of a joint research program under which an attempt is made to develop a better understanding of the effects of cavity decoupling on the seismic signals produced by underground nuclear explosions. Investigations conducted under this program have focused on analyses of seismic data recorded from a series of HE cavity decoupling experiments conducted by the Russians in Kirghizia in 1960, and from a sequence of nuclear tests conducted in a water-filled cavity at the Soviet Azgir test site during the period 1975-1979. The Kirghizia series included tests designed to assess the influence of cavity geometry on decoupling effectiveness, and comparisons of near-field seismic data recorded from these tests indicate that the low frequency decoupling factor is independent of cavity shape for elongated cavities with length to width ratios of 6 or more, in agreement with previous theoretical simulation results. Broadband seismic data recorded from the Azgir water-filled cavity tests are analyzed to estimate cavity/tamped source spectral ratios, and the results are compared with theoretical finite difference simulations of these tests.

  18. Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site.

    Science.gov (United States)

    Bjelic, Sinisa; Aqvist, Johan

    2004-11-23

    The histo-aspartic protease (HAP) from the malaria parasite P. falciparum is one of several new promising targets for drug intervention. The enzyme possesses a novel type of active site, but its 3D structure and mechanism of action are still unknown. Here we use a combination of homology modeling, automated docking searches, and molecular dynamics/reaction free energy profile simulations to predict the enzyme structure, conformation of bound substrate, catalytic mechanism, and rate of the peptide cleavage reaction. We find that the computational tools are sufficiently reliable both for identifying substrate binding modes and for distinguishing between different possible reaction mechanisms. It is found that the favored pathway only involves direct participation by the catalytic aspartate, with the neighboring histidine providing critical stabilization (by a factor of approximately 10000) along the reaction. The calculated catalytic rate constant of about 0.1 s(-1) for a hexapeptide substrate derived from the alpha chain of human hemoglobin is in excellent agreement with experimental kinetic data for a similar peptide fragment. PMID:15544322

  19. Theoretical study on setup of expanded-base pile considering cavity contraction

    Institute of Scientific and Technical Information of China (English)

    齐昌广; 刘干斌; 王艳; 邓岳保

    2015-01-01

    When an expanded-base pile is installed into ground, the cavity expansion associated with penetration of the enlarged pile base is followed by cavity contraction along the smaller-diameter pile shaft. In order to account for the influence of cavity contraction on the change of bearing capacity of expanded-base pile, a theoretical calculation methodology, predicting the setup of expanded-base pile, was established by employing the cavity contraction theory to estimate the shaft resistance of expanded-base pile, and horizontal consolidation theory to predict the dissipation of excess pore pressure. Finally, the numerical solutions for the setup of expanded-base pile were obtained. The parametric study about the influence of cavity contraction on setup of expanded-base pile was carried out, while a field test was introduced. The parametric study shows that the decrements in radial pressure and the maximum pore water pressure after considering cavity contraction are increased as the expanded ratio (base diameter/shaft diameter) and rigidity index of soil are raised. The comparison between calculated and measured values shows that the calculated results of ultimate bearing capacity for expanded-base pile considering cavity contraction agree well with the measured values; however, the computations ignoring cavity contraction are 2.5−3.0 times the measured values.

  20. Theoretical study on setup of expanded-base pile considering cavity contraction

    Institute of Scientific and Technical Information of China (English)

    齐昌广; 刘干斌; 王艳; 邓岳保

    2015-01-01

    When an expanded-base pile is installed into ground, the cavity expansion associated with penetration of the enlarged pile base is followed by cavity contraction along the smaller-diameter pile shaft. In order to account for the influence of cavity contraction on the change of bearing capacity of expanded-base pile, a theoretical calculation methodology, predicting the setup of expanded-base pile, was established by employing the cavity contraction theory to estimate the shaft resistance of expanded-base pile, and horizontal consolidation theory to predict the dissipation of excess pore pressure. Finally, the numerical solutions for the setup of expanded-base pile were obtained. The parametric study about the influence of cavity contraction on setup of expanded-base pile was carried out, while a field test was introduced. The parametric study shows that the decrements in radial pressure and the maximum pore water pressure after considering cavity contraction are increased as the expanded ratio(base diameter/shaft diameter) and rigidity index of soil are raised. The comparison between calculated and measured values shows that the calculated results of ultimate bearing capacity for expanded-base pile considering cavity contraction agree well with the measured values; however, the computations ignoring cavity contraction are 2.5-3.0 times the measured values.