WorldWideScience

Sample records for cavity sites predictions

  1. DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins.

    Science.gov (United States)

    Tan, Kuan Pern; Varadarajan, Raghavan; Madhusudhan, M S

    2011-07-01

    Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

  2. ACINIC CELL CARCINOMA OF NASAL CAVITY: A RARE SITE FOR SALIVARY GLAND TUMOUR

    Directory of Open Access Journals (Sweden)

    Jayalakshmy

    2016-04-01

    Full Text Available BACKGROUND We are herewith reporting a case of acinic cell carcinoma arising in nasal cavity in a 52-year-old male patient. The diagnosis was confirmed by immunohistochemistry for DOG1, which is a novel marker for salivary acinic cell differentiation. Nasal cavity is a rare site for acinic cell carcinoma and pathologists and surgeons should include this entity also in the differential diagnosis of tumours of nasal cavity to avoid misdiagnosis

  3. Temperature characteristics of winter roost-sites for birds and mammals: tree cavities and anthropogenic alternatives.

    Science.gov (United States)

    Grüebler, Martin U; Widmer, Silv; Korner-Nievergelt, Fränzi; Naef-Daenzer, Beat

    2014-07-01

    The microclimate of potential roost-sites is likely to be a crucial determinant in the optimal roost-site selection of endotherms, in particular during the winter season of temperate zones. Available roost-sites for birds and mammals in European high trunk orchards are mainly tree cavities, wood stacks and artificial nest boxes. However, little is known about the microclimatic patterns inside cavities and thermal advantages of using these winter roost-sites. Here, we simultaneously investigate the thermal patterns of winter roost-sites in relation to winter ambient temperature and their insulation capacity. While tree cavities and wood stacks strongly buffered the daily cycle of temperature changes, nest boxes showed low buffering capacity. The buffering effect of tree cavities was stronger at extreme ambient temperatures compared to temperatures around zero. Heat sources inside roosts amplified Δ T (i.e., the difference between inside and outside temperatures), particularly in the closed roosts of nest boxes and tree cavities, and less in the open wood stacks with stronger circulation of air. Positive Δ T due to the installation of a heat source increased in cold ambient temperatures. These results suggest that orchard habitats in winter show a spatiotemporal mosaic of sites providing different thermal benefits varying over time and in relation to ambient temperatures. At cold temperatures tree cavities provide significantly higher thermal benefits than nest boxes or wood stacks. Thus, in winter ecology of hole-using endotherms, the availability of tree cavities may be an important characteristic of winter habitat quality.

  4. 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/

  5. The effect of resorption cavities on bone stiffness is site dependent.

    Science.gov (United States)

    Vanderoost, Jef; van Lenthe, G Harry

    2014-01-01

    Resorption cavities formed during the bone remodelling cycle change the structure and thus the mechanical properties of trabecular bone. We tested the hypotheses that bone stiffness loss due to resorption cavities depends on anatomical location, and that for identical eroded bone volumes, cavities would cause more stiffness loss than homogeneous erosion. For this purpose, we used beam-shell finite element models. This new approach was validated against voxel-based FE models. We found an excellent agreement for the elastic stiffness behaviour of individual trabeculae in axial compression (R(2) = 1.00) and in bending (R(2)>0.98), as well as for entire trabecular bone samples to which resorption cavities were digitally added (R(2) = 0.96, RMSE = 5.2%). After validation, this new method was used to model discrete cavities, with dimensions taken from a statistical distribution, on a dataset of 120 trabecular bone samples from three anatomical sites (4th lumbar vertebra, femoral head, iliac crest). Resorption cavities led to significant reductions in bone stiffness. The largest stiffness loss was found for samples from the 4th lumbar vertebra, the lowest for femoral head samples. For all anatomical sites, resorption cavities caused significantly more stiffness loss than homogeneous erosion did. This novel technique can be used further to evaluate the impact of resorption cavities, which are known to change in several metabolic bone diseases and due to treatment, on bone competence.

  6. 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.

  7. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

    Directory of Open Access Journals (Sweden)

    John A Capra

    2009-12-01

    Full Text Available Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone. We also demonstrate that ConCavity has state-of-the-art performance in predicting catalytic sites and drug binding pockets. Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (http://compbio.cs.princeton.edu/concavity/.

  8. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

    Science.gov (United States)

    Capra, John A; Laskowski, Roman A; Thornton, Janet M; Singh, Mona; Funkhouser, Thomas A

    2009-12-01

    Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone. We also demonstrate that ConCavity has state-of-the-art performance in predicting catalytic sites and drug binding pockets. Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (http://compbio.cs.princeton.edu/concavity/).

  9. Nest sites selection by sympatric cavity-nesting birds in miombo woodlands

    Directory of Open Access Journals (Sweden)

    Vincent R. Nyirenda

    2016-03-01

    Full Text Available Deforestation and habitat fragmentation have long been known as drivers of wildlife depletion but information on their specific impacts on cavity-nesting birds in the miombo woodlands has been lacking. A comparative study of disturbed and undisturbed sites was conducted in miombo woodlands of Zambia to assess impacts of environmental stressors on birds. Foot patrols were employed to locate, identify and count host trees and cavities for cavity-nesting birds on twenty 200 m × 200 m sample plots. Undisturbed forests had three times more cavities (the nesting sites for birds, while there were 24.6% fewer abandoned cavities in undisturbed forests than in disturbed forests. The rate of cavity abandonment was about twice as high in human-dominated forests compared to undisturbed forests (61.3% c.f. 31.9%. Cavity-nesting birds preferred larger (> 36.0 cm diameter at breast height and taller (> 5.0 m trees for nest placement, especially in human-dominated forests. A number of cavity-nesting birds preferred Brachystegia spiciformis (zebrawood, Julbernadia paniculata (munsa, Parinari curatellifolia (mobola-plum and Uapaca kirkiana (mahobohobo as host trees to 14 other miombo tree species. Arnot’s Chat (Myrmecocichla arnoti had a wider selection of host trees for cavity-nesting than the other 40 cavity-nesting birds in the study areas. Anthropogenic activities such as uncontrolled firewood collection, wild fires, logging, and land clearing for agriculture negatively influenced wood abundance and diversity, with potential implications for persistence of cavity-nesting birds. The negative impacts of anthropogenic activities could be counteracted by conservation strategies such as implementation of sound forest policies, integrative land use practices, sustainable livelihood security and stakeholders’ awareness of the need to safeguard forest-dependent avifauna.Conservation implications: This comparative study unravels specific anthropogenic impacts on

  10. 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.

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

    Science.gov (United States)

    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 relationship for predicting the shifted eigenfrequencies. In this paper, results obtained from this relationship are compared with eigenfrequencies obtained from very accurate finite element simulations. From the results it can be concluded that Parker's relationship gives fairly good predictions of the 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, the simple relationship is no longer valid. .

  12. 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

    have quite big cavities, with 41 water molecules on average in 2C8 and 54-58 in 2C9 and 3A4, giving a water volume of 1500-2100 A3. The two crystal structures of 2C9 differ quite appreciably, whereas those of 3A4 are quite similar. The active-site cavity is connected to the surroundings by three to six......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...

  13. 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

    Preventing roof collapse in underground cavities is a challenge to geotechnical engineering. In this study, three independent methods have been used to evaluate the roof collapse of underground rectangular cavities for a range of geometries and rock properties. The rock mass strength has been...... 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...

  14. Prediction of cavity growth rate during underground coal gasification using multiple regression analysis

    Institute of Scientific and Technical Information of China (English)

    Mehdi Najafi; Seyed Mohammad Esmaiel Jalali; Reza KhaloKakaie; Farrokh Forouhandeh

    2015-01-01

    During underground coal gasification (UCG), whereby coal is converted to syngas in situ, a cavity is formed in the coal seam. The cavity growth rate (CGR) or the moving rate of the gasification face is affected by controllable (operation pressure, gasification time, geometry of UCG panel) and uncontrollable (coal seam properties) factors. The CGR is usually predicted by mathematical models and laboratory experiments, which are time consuming, cumbersome and expensive. In this paper, a new simple model for CGR is developed using non-linear regression analysis, based on data from 11 UCG field trials. The empirical model compares satisfactorily with Perkins model and can reliably predict CGR.

  15. Cutoff lensing: predicting catalytic sites in enzymes

    Science.gov (United States)

    Aubailly, Simon; Piazza, Francesco

    2015-10-01

    Predicting function-related amino acids in proteins with unknown function or unknown allosteric binding sites in drug-targeted proteins is a task of paramount importance in molecular biomedicine. In this paper we introduce a simple, light and computationally inexpensive structure-based method to identify catalytic sites in enzymes. Our method, termed cutoff lensing, is a general procedure consisting in letting the cutoff used to build an elastic network model increase to large values. A validation of our method against a large database of annotated enzymes shows that optimal values of the cutoff exist such that three different structure-based indicators allow one to recover a maximum of the known catalytic sites. Interestingly, we find that the larger the structures the greater the predictive power afforded by our method. Possible ways to combine the three indicators into a single figure of merit and into a specific sequential analysis are suggested and discussed with reference to the classic case of HIV-protease. Our method could be used as a complement to other sequence- and/or structure-based methods to narrow the results of large-scale screenings.

  16. Predicted metal binding sites for phytoremediation.

    Science.gov (United States)

    Sharma, Ashok; Roy, Sudeep; Tripathi, Kumar Parijat; Roy, Pratibha; Mishra, Manoj; Khan, Feroz; Meena, Abha

    2009-09-05

    Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. The objective of the study is to design and analyze metal binding motifs against the genes involved in phytoremediation. This is being done on the basis of certain pre-requisite amino-acid residues known to bind metal ions/metal complexes in medicinal and aromatic plants (MAP's). Earlier work on MAP's have shown that heavy metals accumulated by aromatic and medicinal plants do not appear in the essential oil and that some of these species are able to grow in metal contaminated sites. A pattern search against the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases yielded true positives in each case showing the high specificity of the motifs designed for the ions of nickel, lead, molybdenum, manganese, cadmium, zinc, iron, cobalt and xenobiotic compounds. Motifs were also studied against PDB structures. Results of the study suggested the presence of binding sites on the surface of protein molecules involved. PDB structures of proteins were finally predicted for the binding sites functionality in their respective phytoremediation usage. This was further validated through CASTp server to study its physico-chemical properties. Bioinformatics implications would help in designing strategy for developing transgenic plants with increased metal binding capacity. These metal binding factors can be used to restrict metal update by plants. This helps in reducing the possibility of metal movement into the food chain.

  17. Probabilistic prediction models for aggregate quarry siting

    Science.gov (United States)

    Robinson, G.R.; Larkins, P.M.

    2007-01-01

    Weights-of-evidence (WofE) and logistic regression techniques were used in a GIS framework to predict the spatial likelihood (prospectivity) of crushed-stone aggregate quarry development. The joint conditional probability models, based on geology, transportation network, and population density variables, were defined using quarry location and time of development data for the New England States, North Carolina, and South Carolina, USA. The Quarry Operation models describe the distribution of active aggregate quarries, independent of the date of opening. The New Quarry models describe the distribution of aggregate quarries when they open. Because of the small number of new quarries developed in the study areas during the last decade, independent New Quarry models have low parameter estimate reliability. The performance of parameter estimates derived for Quarry Operation models, defined by a larger number of active quarries in the study areas, were tested and evaluated to predict the spatial likelihood of new quarry development. Population density conditions at the time of new quarry development were used to modify the population density variable in the Quarry Operation models to apply to new quarry development sites. The Quarry Operation parameters derived for the New England study area, Carolina study area, and the combined New England and Carolina study areas were all similar in magnitude and relative strength. The Quarry Operation model parameters, using the modified population density variables, were found to be a good predictor of new quarry locations. Both the aggregate industry and the land management community can use the model approach to target areas for more detailed site evaluation for quarry location. The models can be revised easily to reflect actual or anticipated changes in transportation and population features. ?? International Association for Mathematical Geology 2007.

  18. 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.

  19. 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.

  20. 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.

  1. Text mining improves prediction of protein functional sites.

    Science.gov (United States)

    Verspoor, Karin M; Cohn, Judith D; Ravikumar, Komandur E; Wall, Michael E

    2012-01-01

    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.

  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. Effective index model predicts modal frequencies of vertical-cavity lasers

    Energy Technology Data Exchange (ETDEWEB)

    SERKLAND,DARWIN K.; HADLEY,G. RONALD; CHOQUETTE,KENT D.; GEIB,KENT M.; ALLERMAN,ANDREW A.

    2000-04-18

    Previously, an effective index optical model was introduced for the analysis of lateral waveguiding effects in vertical-cavity surface-emitting lasers. The authors show that the resultant transverse equation is almost identical to the one typically obtained in the analysis of dielectric waveguide problems, such as a step-index optical fiber. The solution to the transverse equation yields the lateral dependence of the optical field and, as is recognized in this paper, the discrete frequencies of the microcavity modes. As an example, they apply this technique to the analysis of vertical-cavity lasers that contain thin-oxide apertures. The model intuitively explains the experimental data and makes quantitative predictions in good agreement with a highly accurate numerical model.

  4. Electric Field Prediction using Micro-plasma Inside a Microwave Cavity for Soot Oxidation

    Directory of Open Access Journals (Sweden)

    Al-Wakeel Haitham B.

    2014-07-01

    Full Text Available The reduction of the harmful emission soot is necessary in recent years due to the environmental protection regulation. Soot is a carbonaceous matter and a strong absorber of microwave energy. Microwave heating offers the advantage over conventional heating to oxide soot. Where plasma is high electric field that leads to instantaneous temperature rising. This paper proposes a recent concept for soot oxidation using micro-plasma in a microwave cavity. The concept was presented by simulating the electric field using microwave heating and thin metal object. Five cases were examined numerically in a mono-mode TE10 microwave cavity WR430 having closed surfaces of perfect electric conductors working under 2.45 GHz frequency and 1500 W power supply to predict the electric field and dissipated heat distribution. The methodology of prediction was implemented using ANSYS based on FEM. The present prediction results showed higher electric field (400 kV/m and high dissipated heat (3.7×1010 W/m3 can be obtained for a soot sample backed with metal rods inserted vertically with gaps not exceeding 1.5 mm between the rods tips. Also increasing the number of metal rods, from 8 to 14 increases the maximum value of electric field formed in the soot sample to 575 kV/m. The simulation results revealed the ability of achieving high electric field by using microwave heating with the assistance of metal objects.

  5. 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

  6. A Random Forest Model for Predicting Allosteric and Functional Sites on Proteins.

    Science.gov (United States)

    Chen, Ava S-Y; Westwood, Nicholas J; Brear, Paul; Rogers, Graeme W; Mavridis, Lazaros; Mitchell, John B O

    2016-04-01

    We created a computational method to identify allosteric sites using a machine learning method trained and tested on protein structures containing bound ligand molecules. The Random Forest machine learning approach was adopted to build our three-way predictive model. Based on descriptors collated for each ligand and binding site, the classification model allows us to assign protein cavities as allosteric, regular or orthosteric, and hence to identify allosteric sites. 43 structural descriptors per complex were derived and were used to characterize individual protein-ligand binding sites belonging to the three classes, allosteric, regular and orthosteric. We carried out a separate validation on a further unseen set of protein structures containing the ligand 2-(N-cyclohexylamino) ethane sulfonic acid (CHES).

  7. SVM-based prediction of caspase substrate cleavage sites

    Directory of Open Access Journals (Sweden)

    Ranganathan Shoba

    2006-12-01

    Full Text Available Abstract 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 machines (SVM algorithm has been shown to be useful in several biological classification problems, we have implemented an SVM-based method to investigate its applicability to this domain. Results A set of unique caspase substrates cleavage sites were obtained from literature and used for evaluating the SVM method. Datasets containing (i the tetrapeptide cleavage sites, (ii the tetrapeptide cleavage sites, augmented by two adjacent residues, P1' and P2' amino acids and (iii the tetrapeptide cleavage sites with ten additional upstream and downstream flanking sequences (where available were tested. The SVM method achieved an accuracy ranging from 81.25% to 97.92% on independent test sets. The SVM method successfully predicted the cleavage of a novel caspase substrate and its mutants. Conclusion This study presents an SVM approach for predicting caspase substrate cleavage sites based on the cleavage sites and the downstream and upstream flanking sequences. The method shows an improvement over existing methods and may be useful for predicting hitherto undiscovered cleavage sites.

  8. Positive-Unlabeled Learning for Pupylation Sites Prediction

    Directory of Open Access Journals (Sweden)

    Ming Jiang

    2016-01-01

    Full Text Available Pupylation plays a key role in regulating various protein functions as a crucial posttranslational modification of prokaryotes. In order to understand the molecular mechanism of pupylation, it is important to identify pupylation substrates and sites accurately. Several computational methods have been developed to identify pupylation sites because the traditional experimental methods are time-consuming and labor-sensitive. With the existing computational methods, the experimentally annotated pupylation sites are used as the positive training set and the remaining nonannotated lysine residues as the negative training set to build classifiers to predict new pupylation sites from the unknown proteins. However, the remaining nonannotated lysine residues may contain pupylation sites which have not been experimentally validated yet. Unlike previous methods, in this study, the experimentally annotated pupylation sites were used as the positive training set whereas the remaining nonannotated lysine residues were used as the unlabeled training set. A novel method named PUL-PUP was proposed to predict pupylation sites by using positive-unlabeled learning technique. Our experimental results indicated that PUL-PUP outperforms the other methods significantly for the prediction of pupylation sites. As an application, PUL-PUP was also used to predict the most likely pupylation sites in nonannotated lysine sites.

  9. A grammar inference approach for predicting kinase specific phosphorylation sites.

    Science.gov (United States)

    Datta, Sutapa; Mukhopadhyay, Subhasis

    2015-01-01

    Kinase mediated phosphorylation site detection is the key mechanism of post translational mechanism that plays an important role in regulating various cellular processes and phenotypes. Many diseases, like cancer are related with the signaling defects which are associated with protein phosphorylation. Characterizing the protein kinases and their substrates enhances our ability to understand the mechanism of protein phosphorylation and extends our knowledge of signaling network; thereby helping us to treat such diseases. Experimental methods for predicting phosphorylation sites are labour intensive and expensive. Also, manifold increase of protein sequences in the databanks over the years necessitates the improvement of high speed and accurate computational methods for predicting phosphorylation sites in protein sequences. Till date, a number of computational methods have been proposed by various researchers in predicting phosphorylation sites, but there remains much scope of improvement. In this communication, we present a simple and novel method based on Grammatical Inference (GI) approach to automate the prediction of kinase specific phosphorylation sites. In this regard, we have used a popular GI algorithm Alergia to infer Deterministic Stochastic Finite State Automata (DSFA) which equally represents the regular grammar corresponding to the phosphorylation sites. Extensive experiments on several datasets generated by us reveal that, our inferred grammar successfully predicts phosphorylation sites in a kinase specific manner. It performs significantly better when compared with the other existing phosphorylation site prediction methods. We have also compared our inferred DSFA with two other GI inference algorithms. The DSFA generated by our method performs superior which indicates that our method is robust and has a potential for predicting the phosphorylation sites in a kinase specific manner.

  10. 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.

  11. Variable context Markov chains for HIV protease cleavage site prediction.

    Science.gov (United States)

    Oğul, Hasan

    2009-06-01

    Deciphering the knowledge of HIV protease specificity and developing computational tools for detecting its cleavage sites in protein polypeptide chain are very desirable for designing efficient and specific chemical inhibitors to prevent acquired immunodeficiency syndrome. In this study, we developed a generative model based on a generalization of variable order Markov chains (VOMC) for peptide sequences and adapted the model for prediction of their cleavability by certain proteases. The new method, called variable context Markov chains (VCMC), attempts to identify the context equivalence based on the evolutionary similarities between individual amino acids. It was applied for HIV-1 protease cleavage site prediction problem and shown to outperform existing methods in terms of prediction accuracy on a common dataset. In general, the method is a promising tool for prediction of cleavage sites of all proteases and encouraged to be used for any kind of peptide classification problem as well.

  12. Nest-site competition between invasive and native cavity nesting birds and its implication for conservation.

    Science.gov (United States)

    Charter, Motti; Izhaki, Ido; Ben Mocha, Yitzchak; Kark, Salit

    2016-10-01

    Nesting cavities are often a limited resource that multiple species use. There is an ongoing discussion on whether invasive cavity nesting birds restrict the availability of this key limited resource. While the answer to this question has important conservation implications, little experimental work has been done to examine it. Here, we aimed to experimentally test whether alien cavity nesting birds affect the occupancy of cavities and the resulting breeding success of native cavity breeders in a large urban park located in Tel Aviv, Israel. Over three breeding seasons, we manipulated the entry size of nest boxes and compared the occupancy and breeding success of birds in nest boxes of two treatments. These included nest boxes with large-entrance and small-entrance holes. The large-entrance holes allowed access for both the native and invasive birds (the two main aliens in the park are the common mynas and rose-ringed parakeets). The smaller-entrance boxes, on the other hand, allowed only the smaller sized native cavity breeders (great tits and house sparrows) to enter the boxes but prevented the alien species from entering. We found that the large-entrance nest boxes were occupied by five different bird species, comprising three natives (great tit, house sparrow, Scops owl) and two invasive species (common myna, rose-ringed parakeet) while the small-entrance boxes were only occupied by the two native species. The alien common mynas and rose-ringed parakeets occupied 77.5% of the large-entrance nest boxes whereas native species, mainly great tits, occupied less than 9% of the large-entrance boxes and 36.5% of the small-entrance boxes. When examining the occupancy of those cavities that were not occupied by the aliens, natives occupied both the small and large-entrance nest boxes equally. Three quarters (78%) of the great tits breeding in the large-entrance boxes were usurped by common mynas during the breeding season and as a result breeding success was

  13. 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

  14. Selective prediction of interaction sites in protein structures with THEMATICS

    Directory of Open Access Journals (Sweden)

    Murga Leonel F

    2007-04-01

    Full Text Available Abstract Background Methods are now available for the prediction of interaction sites in protein 3D structures. While many of these methods report high success rates for site prediction, often these predictions are not very selective and have low precision. Precision in site prediction is addressed using Theoretical Microscopic Titration Curves (THEMATICS, a simple computational method for the identification of active sites in enzymes. Recall and precision are measured and compared with other methods for the prediction of catalytic sites. Results Using a test set of 169 enzymes from the original Catalytic Residue Dataset (CatRes it is shown that THEMATICS can deliver precise, localised site predictions. Furthermore, adjustment of the cut-off criteria can improve the recall rates for catalytic residues with only a small sacrifice in precision. Recall rates for CatRes/CSA annotated catalytic residues are 41.1%, 50.4%, and 54.2% for Z score cut-off values of 1.00, 0.99, and 0.98, respectively. The corresponding precision rates are 19.4%, 17.9%, and 16.4%. The success rate for catalytic sites is higher, with correct or partially correct predictions for 77.5%, 85.8%, and 88.2% of the enzymes in the test set, corresponding to the same respective Z score cut-offs, if only the CatRes annotations are used as the reference set. Incorporation of additional literature annotations into the reference set gives total success rates of 89.9%, 92.9%, and 94.1%, again for corresponding cut-off values of 1.00, 0.99, and 0.98. False positive rates for a 75-protein test set are 1.95%, 2.60%, and 3.12% for Z score cut-offs of 1.00, 0.99, and 0.98, respectively. Conclusion With a preferred cut-off value of 0.99, THEMATICS achieves a high success rate of interaction site prediction, about 86% correct or partially correct using CatRes/CSA annotations only and about 93% with an expanded reference set. Success rates for catalytic residue prediction are similar to those of

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

    OpenAIRE

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

    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 ...

  16. Prediction of break-out sound from a rectangular cavity via an elastically mounted panel.

    Science.gov (United States)

    Wang, Gang; Li, Wen L; Du, Jingtao; Li, Wanyou

    2016-02-01

    The break-out sound from a cavity via an elastically mounted panel is predicted in this paper. The vibroacoustic system model is derived based on the so-called spectro-geometric method in which the solution over each sub-domain is invariably expressed as a modified Fourier series expansion. Unlike the traditional modal superposition methods, the continuity of the normal velocities is faithfully enforced on the interfaces between the flexible panel and the (interior and exterior) acoustic media. A fully coupled vibro-acoustic system is obtained by taking into account the strong coupling between the vibration of the elastic panel and the sound fields on the both sides. The typical time-consuming calculations of quadruple integrals encountered in determining the sound power radiation from a panel has been effectively avoided by reducing them, via discrete cosine transform, into a number of single integrals which are subsequently calculated analytically in a closed form. Several numerical examples are presented to validate the system model, understand the effects on the sound transmissions of panel mounting conditions, and demonstrate the dependence on the size of source room of the "measured" transmission loss.

  17. 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...

  18. Polarization properties and disorder effects in H{sub 3} photonic crystal cavities incorporating site-controlled, high-symmetry quantum dot arrays

    Energy Technology Data Exchange (ETDEWEB)

    Surrente, Alessandro; Felici, Marco; Gallo, Pascal; Dwir, Benjamin; Rudra, Alok; Kapon, Eli, E-mail: eli.kapon@epfl.ch [Laboratory of Physics of Nanostructures, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne (Switzerland); Biasiol, Giorgio [Istituto Officina dei Materiali CNR, Laboratorio TASC, I-34149 Trieste (Italy)

    2015-07-20

    We report on the effects of optical disorder on breaking the symmetry of the cavity modes of H{sub 3} 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 H{sub 3} 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.

  19. 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.

  20. A GIS approach for predicting prehistoric site locations.

    Energy Technology Data Exchange (ETDEWEB)

    Kuiper, J. A.; Wescott, K. L.

    1999-08-04

    Use of geographic information system (GIS)-based predictive mapping to locate areas of high potential for prehistoric archaeological sites is becoming increasingly popular among archaeologists. Knowledge of the environmental variables influencing activities of original inhabitants is used to produce GIS layers representing the spatial distribution of those variables. The GIS layers are then analyzed to identify locations where combinations of environmental variables match patterns observed at known prehistoric sites. Presented are the results of a study to locate high-potential areas for prehistoric sites in a largely unsurveyed area of 39,000 acres in the Upper Chesapeake Bay region, including details of the analysis process. The project used environmental data from over 500 known sites in other parts of the region and the results corresponded well with known sites in the study area.

  1. Four-Phase Dendritic Model for the Prediction of Macrosegregation, Shrinkage Cavity, and Porosity in a 55-Ton Ingot

    Science.gov (United States)

    Ge, Honghao; Ren, Fengli; Li, Jun; Han, Xiujun; Xia, Mingxu; Li, Jianguo

    2017-03-01

    A four-phase dendritic model was developed to predict the macrosegregation, shrinkage cavity, and porosity during solidification. In this four-phase dendritic model, some important factors, including dendritic structure for equiaxed crystals, melt convection, crystals sedimentation, nucleation, growth, and shrinkage of solidified phases, were taken into consideration. Furthermore, in this four-phase dendritic model, a modified shrinkage criterion was established to predict shrinkage porosity (microporosity) of a 55-ton industrial Fe-3.3 wt pct C ingot. The predicted macrosegregation pattern and shrinkage cavity shape are in a good agreement with experimental results. The shrinkage cavity has a significant effect on the formation of positive segregation in hot top region, which generally forms during the last stage of ingot casting. The dendritic equiaxed grains also play an important role on the formation of A-segregation. A three-dimensional laminar structure of A-segregation in industrial ingot was, for the first time, predicted by using a 3D case simulation.

  2. Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes

    Directory of Open Access Journals (Sweden)

    Arakawa Kazuharu

    2011-01-01

    Full Text Available Abstract Background During the replication process of bacteria with circular chromosomes, an odd number of homologous recombination events results in concatenated dimer chromosomes that cannot be partitioned into daughter cells. However, many bacteria harbor a conserved dimer resolution machinery consisting of one or two tyrosine recombinases, XerC and XerD, and their 28-bp target site, dif. Results To study the evolution of the dif/XerCD system and its relationship with replication termination, we report the comprehensive prediction of dif sequences in silico using a phylogenetic prediction approach based on iterated hidden Markov modeling. Using this method, dif sites were identified in 641 organisms among 16 phyla, with a 97.64% identification rate for single-chromosome strains. The dif sequence positions were shown to be strongly correlated with the GC skew shift-point that is induced by replicational mutation/selection pressures, but the difference in the positions of the predicted dif sites and the GC skew shift-points did not correlate with the degree of replicational mutation/selection pressures. Conclusions The sequence of dif sites is widely conserved among many bacterial phyla, and they can be computationally identified using our method. The lack of correlation between dif position and the degree of GC skew suggests that replication termination does not occur strictly at dif sites.

  3. HMMpTM: improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction.

    Science.gov (United States)

    Tsaousis, Georgios N; Bagos, Pantelis G; Hamodrakas, Stavros J

    2014-02-01

    During the last two decades a large number of computational methods have been developed for predicting transmembrane protein topology. Current predictors rely on topogenic signals in the protein sequence, such as the distribution of positively charged residues in extra-membrane loops and the existence of N-terminal signals. However, phosphorylation and glycosylation are post-translational modifications (PTMs) that occur in a compartment-specific manner and therefore the presence of a phosphorylation or glycosylation site in a transmembrane protein provides topological information. We examine the combination of phosphorylation and glycosylation site prediction with transmembrane protein topology prediction. We report the development of a Hidden Markov Model based method, capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites along the protein sequence. Our method integrates a novel feature in transmembrane protein topology prediction, which results in improved performance for topology prediction and reliable prediction of phosphorylation and glycosylation sites. The method is freely available at http://bioinformatics.biol.uoa.gr/HMMpTM.

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

    Science.gov (United States)

    Si, Jingna; Cui, Jing; Cheng, Jin; Wu, Rongling

    2015-01-01

    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. 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.

  6. Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy

    Directory of Open Access Journals (Sweden)

    Yang Zheng

    2009-10-01

    Full Text Available Abstract Background Tyrosine sulfation is one of the most important posttranslational modifications. Due to its relevance to various disease developments, tyrosine sulfation has become the target for drug design. In order to facilitate efficient drug design, accurate prediction of sulfotyrosine sites is desirable. A predictor published seven years ago has been very successful with claimed prediction accuracy of 98%. However, it has a particularly low sensitivity when predicting sulfotyrosine sites in some newly sequenced proteins. Results A new approach has been developed for predicting sulfotyrosine sites using the random forest algorithm after a careful evaluation of seven machine learning algorithms. Peptides are formed by consecutive residues symmetrically flanking tyrosine sites. They are then encoded using an amino acid hydrophobicity scale. This new approach has increased the sensitivity by 22%, the specificity by 3%, and the total prediction accuracy by 10% compared with the previous predictor using the same blind data. Meanwhile, both negative and positive predictive powers have been increased by 9%. In addition, the random forest model has an excellent feature for ranking the residues flanking tyrosine sites, hence providing more information for further investigating the tyrosine sulfation mechanism. A web tool has been implemented at http://ecsb.ex.ac.uk/sulfotyrosine for public use. Conclusion The random forest algorithm is able to deliver a better model compared with the Hidden Markov Model, the support vector machine, artificial neural networks, and others for predicting sulfotyrosine sites. The success shows that the random forest algorithm together with an amino acid hydrophobicity scale encoding can be a good candidate for peptide classification.

  7. Gene and translation initiation site prediction in metagenomic sequences

    Energy Technology Data Exchange (ETDEWEB)

    Hyatt, Philip Douglas [ORNL; LoCascio, Philip F [ORNL; Hauser, Loren John [ORNL; Uberbacher, Edward C [ORNL

    2012-01-01

    Gene prediction in metagenomic sequences remains a difficult problem. Current sequencing technologies do not achieve sufficient coverage to assemble the individual genomes in a typical sample; consequently, sequencing runs produce a large number of short sequences whose exact origin is unknown. Since these sequences are usually smaller than the average length of a gene, algorithms must make predictions based on very little data. We present MetaProdigal, a metagenomic version of the gene prediction program Prodigal, that can identify genes in short, anonymous coding sequences with a high degree of accuracy. The novel value of the method consists of enhanced translation initiation site identification, ability to identify sequences that use alternate genetic codes and confidence values for each gene call. We compare the results of MetaProdigal with other methods and conclude with a discussion of future improvements.

  8. Assessment of Mars Exploration Rover Landing Site Predictions

    Science.gov (United States)

    Golombek, M. P.

    2005-05-01

    Comprehensive analyses of remote sensing data during the 3-year effort to select the Mars Exploration Rover landing sites at Gusev crater and Meridiani Planum correctly predicted the safe and trafficable surfaces explored by the two rovers. Gusev crater was predicted to be a relatively low relief surface that was comparably dusty, but less rocky than the Viking landing sites. Available data for Meridiani Planum indicated a very flat plain composed of basaltic sand to granules and hematite that would look completely unlike any of the existing landing sites with a dark, low albedo surface, little dust and very few rocks. Orbital thermal inertia measurements of 315 J m-2 s-0.5 K-1 at Gusev suggested surfaces dominated by duricrust to cemented soil-like materials or cohesionless sand or granules, which is consistent with observed soil characteristics and measured thermal inertias from the surface. THEMIS thermal inertias along the traverse at Gusev vary from 285 at the landing site to 330 around Bonneville rim and show systematic variations that can be related to the observed increase in rock abundance (5-30%). Meridiani has an orbital bulk inertia of ~200, similar to measured surface inertias that correspond to observed surfaces dominated by 0.2 mm sand size particles. Rock abundance derived from orbital thermal differencing techniques suggested that Meridiani Planum would have very low rock abundance, consistent with the rock free plain traversed by Opportunity. Spirit landed in an 8% orbital rock abundance pixel, consistent with the measured 7% of the surface covered by rocks >0.04 m diameter at the landing site, which is representative of the plains away from craters. The orbital albedo of the Spirit traverse varies from 0.19 to 0.30, consistent with surface measurements in and out of dust devil tracks. Opportunity is the first landing in a low albedo portion of Mars as seen from orbit, which is consistent with the dark, dust-free surface and measured albedos. The

  9. Predicting N-terminal myristoylation sites in plant proteins

    Directory of Open Access Journals (Sweden)

    Podell Sheila

    2004-06-01

    Full Text Available Abstract Background N-terminal myristoylation plays a vital role in membrane targeting and signal transduction in plant responses to environmental stress. Although N-myristoyltransferase enzymatic function is conserved across plant, animal, and fungal kingdoms, exact substrate specificities vary, making it difficult to predict protein myristoylation accurately within specific taxonomic groups. Results A new method for predicting N-terminal myristoylation sites specifically in plants has been developed and statistically tested for sensitivity, specificity, and robustness. Compared to previously available methods, the new model is both more sensitive in detecting known positives, and more selective in avoiding false positives. Scores of myristoylated and non-myristoylated proteins are more widely separated than with other methods, greatly reducing ambiguity and the number of sequences giving intermediate, uninformative results. The prediction model is available at http://plantsp.sdsc.edu/myrist.html. Conclusion Superior performance of the new model is due to the selection of a plant-specific training set, covering 266 unique sequence examples from 40 different species, the use of a probability-based hidden Markov model to obtain predictive scores, and a threshold cutoff value chosen to provide maximum positive-negative discrimination. The new model has been used to predict 589 plant proteins likely to contain N-terminal myristoylation signals, and to analyze the functional families in which these proteins occur.

  10. 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.

  11. 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.

  12. Prediction of acoustic fields radiated into a damped cavity by an N-port source through ducts

    Science.gov (United States)

    Boudoy, M.; Martin, V.

    2003-07-01

    The use of two parameters—source impedance and source strength—to model a fluid machine radiating fluid-borne sound via ducts has led to excellent predictions when the source, a ventilator, propagates in one or two plane-wave ducts. Can such previously published methods successfully be applied to the case of a multi-port source radiating via ducts into a damped cavity? The case under study here is a car ventilation/heating unit and the aim was to predict the pressure spectrum inside the passenger compartment caused by the noise propagated through the ventilation ducts. The progressive validation procedure used indicated how and why as the system increases in complexity, predictive accuracy diminishes. The final results are nevertheless convincing and the hypotheses, which can be further refined to reflect the reality better and provide higher quality results, are clearly defined.

  13. 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.

  14. Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space.

    Science.gov (United States)

    Stegemann, Björn; Klebe, Gerhard

    2012-02-01

    Small molecules are recognized in protein-binding pockets through surface-exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein-ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise to unexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein-cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein-binding pockets, and the local folding patterns next to the cofactor-binding site. State-of-the-art clustering techniques have been applied to group the different protein-cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process.

  15. Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis.

    Science.gov (United States)

    Yahashiri, Atsushi; Rubach, Jon K; Plapp, Bryce V

    2014-02-11

    A role for protein dynamics in enzymatic catalysis of hydrogen transfer has received substantial scientific support, but the connections between protein structure and catalysis remain to be established. Valine residues 203 and 207 are at the binding site for the nicotinamide ring of the coenzyme in liver alcohol dehydrogenase and have been suggested to facilitate catalysis with "protein-promoting vibrations" (PPV). We find that the V207A substitution has small effects on steady-state kinetic constants and the rate of hydrogen transfer; the introduced cavity is empty and is tolerated with minimal effects on structure (determined at 1.2 Å for the complex with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol). Thus, no evidence is found to support a role for Val-207 in the dynamics of catalysis. The protein structures and ligand geometries (including donor-acceptor distances) in the V203A enzyme complexed with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol (determined at 1.1 Å) are very similar to those for the wild-type enzyme, except that the introduced cavity accommodates a new water molecule that contacts the nicotinamide ring. The structures of the V203A enzyme complexes suggest, in contrast to previous studies, that the diminished tunneling and decreased rate of hydride transfer (16-fold, relative to that of the wild-type enzyme) are not due to differences in ground-state ligand geometries. The V203A substitution may alter the PPV and the reorganization energy for hydrogen transfer, but the protein scaffold and equilibrium thermal motions within the Michaelis complex may be more significant for enzyme catalysis.

  16. Improving prediction of surgical site infection risk with multilevel modeling.

    Directory of Open Access Journals (Sweden)

    Lauren Saunders

    Full Text Available BACKGROUND: Surgical site infection (SSI surveillance is a key factor in the elaboration of strategies to reduce SSI occurrence and in providing surgeons with appropriate data feedback (risk indicators, clinical prediction rule. AIM: To improve the predictive performance of an individual-based SSI risk model by considering a multilevel hierarchical structure. PATIENTS AND METHODS: Data were collected anonymously by the French SSI active surveillance system in 2011. An SSI diagnosis was made by the surgical teams and infection control practitioners following standardized criteria. A random 20% sample comprising 151 hospitals, 502 wards and 62280 patients was used. Three-level (patient, ward, hospital hierarchical logistic regression models were initially performed. Parameters were estimated using the simulation-based Markov Chain Monte Carlo procedure. RESULTS: A total of 623 SSI were diagnosed (1%. The hospital level was discarded from the analysis as it did not contribute to variability of SSI occurrence (p  = 0.32. Established individual risk factors (patient history, surgical procedure and hospitalization characteristics were identified. A significant heterogeneity in SSI occurrence between wards was found (median odds ratio [MOR] 3.59, 95% credibility interval [CI] 3.03 to 4.33 after adjusting for patient-level variables. The effects of the follow-up duration varied between wards (p<10-9, with an increased heterogeneity when follow-up was <15 days (MOR 6.92, 95% CI 5.31 to 9.07]. The final two-level model significantly improved the discriminative accuracy compared to the single level reference model (p<10-9, with an area under the ROC curve of 0.84. CONCLUSION: This study sheds new light on the respective contribution of patient-, ward- and hospital-levels to SSI occurrence and demonstrates the significant impact of the ward level over and above risk factors present at patient level (i.e., independently from patient case-mix.

  17. Prediction of nucleosome positioning based on transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Xianfu Yi

    Full Text Available BACKGROUND: The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is of great importance for the study of genomic control mechanisms. Transcription factors (TFs have been suggested to play a role in nucleosome positioning in vivo. PRINCIPAL FINDINGS: Here, the minimum redundancy maximum relevance (mRMR feature selection algorithm, the nearest neighbor algorithm (NNA, and the incremental feature selection (IFS method were used to identify the most important TFs that either favor or inhibit nucleosome positioning by analyzing the numbers of transcription factor binding sites (TFBSs in 53,021 nucleosomal DNA sequences and 50,299 linker DNA sequences. A total of nine important families of TFs were extracted from 35 families, and the overall prediction accuracy was 87.4% as evaluated by the jackknife cross-validation test. CONCLUSIONS: Our results are consistent with the notion that TFs are more likely to bind linker DNA sequences than the sequences in the nucleosomes. In addition, our results imply that there may be some TFs that are important for nucleosome positioning but that play an insignificant role in discriminating nucleosome-forming DNA sequences from nucleosome-inhibiting DNA sequences. The hypothesis that TFs play a role in nucleosome positioning is, thus, confirmed by the results of this study.

  18. The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase.

    OpenAIRE

    Fitzgerald, M. M.; Trester, M. L.; Jensen, G M; McRee, D. E.; Goodin, D B

    1995-01-01

    The activated state of cytochrome c peroxidase, compound ES, contains a cation radical on the Trp-191 side chain. We recently reported that replacing this tryptophan with glycine creates a buried cavity at the active site that contains ordered solvent and that will specifically bind substituted imidazoles in their protonated cationic forms (Fitzgerald MM, Churchill MJ, McRee DE, Goodin DB, 1994, Biochemistry 33:3807-3818). Proposals that a nearby carboxylate, Asp-235, and competing monovalent...

  19. Factors predicting surgical site infection after posterior lumbar surgery

    Science.gov (United States)

    Wang, Tao; Wang, Hui; Yang, Da-Long; Jiang, Li-Qiang; Zhang, Li-Jun; Ding, Wen-Yuan

    2017-01-01

    Abstract This is a retrospective study. The purpose of this study is to explore incidence and risk factors for surgical site infection (SSI) after posterior lumbar surgery. SSI is a common complication after posterior lumbar surgery, bringing mental and physical pain and prolonging hospital stay. However, predisposing factors, as reported less, remain controversial. Patients who underwent posterior lumbar surgery at 3 centers between 2006 and 2016 were included. The possible factors include 3 aspects: demographic variables-age, sex, body mass index (BMI), waist-to-hip radio (WHR), hypertension, diabetes, heart disease, smoking, drinking, steroidal injection, surgical time between June and September, preoperative shower; blood test variables-white blood cell (WBC), neutrophil, red blood cell (RBC), hemoglobin (Hb), total protein (TP), albumin, albumin/globulin (A/G), C-reactive protein (CRP), procalcitonin (PCT), erythrocyte sedimentation rate (ESR) and surgical related variables-operation time, blood loss, operative level, instrumentation, incision length. Factors related with SSI were also performed by multivariate analysis. The prevalence of SSI was 3.00% (267 cases of 8879) had a postoperative wound infection. There were significant difference in WHR (0.92 vs 0.83), WBC (4.31 vs 6.69), TP (58.7 vs 65.2), albumin (36.9 vs 43.2), CRP (2.01 vs 0.57), PCT (0.097 vs 0.067), operation time (217.9 vs 195.7), blood loss (997.1 vs 915.3) and operative level (3.05 vs 2.45) and incision length (24.1 vs 20.0) between SSI group and non-SSI group. >60 years old, female, BMI 30.0, diabetes, male smoking, preoperative steroidal injection, surgical time between June and September, no preoperative shower, instrumentation surgery were risk factors for SSI after posterior lumbar surgery. Many factors, >60 years old, female, BMI, WHR, diabetes, male smoking, preoperative steroidal injection, surgical time between June and September, preoperative shower, WBC, TP, albumin, CRP, PCT

  20. 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...

  1. Homology models of dipeptidyl peptidases 8 and 9 with a focus on loop predictions near the active site.

    Science.gov (United States)

    Rummey, Christian; Metz, Günther

    2007-01-01

    Dipeptidyl peptidase 4 (DP4) inhibitors are currently under intensive investigation in late-stage clinical trials as a treatment for type II diabetes. Lack of selectivity toward the related enzymes DP8 and DP9 has recently emerged as a possible source of drug-induced toxicity. Unlike DP4, X-ray structures of DP8 and DP9 are not yet available. As an aid to understanding the structural basis for selectivity, the authors have constructed homology models of DP8 and DP9 based on the X-ray coordinates of DP4. Accurate sequence alignment reveals common structural features indicative for a well-preserved overall fold comprising two domains, namely, a hydrolase domain and a so-called beta-propeller, which together form the active site deeply buried within the protein. The conformation of two loops inside this deep cavity is particularly relevant for the active sites. The authors used a published protocol for loop prediction based on conformational sampling and energy analysis to generate plausible solutions for these two loops. The predictive power of the approach was successfully evaluated for the template protein DP4 and two additional known structures from the same protein family, namely, FAP and DPX. The authors also show that inclusion of the covalent ligand NVP-728 greatly enhances the refinement. Based on the established evaluation protocol, the corresponding loops of DP8 and DP9 were predicted and the resulting active sites were compared with DP4. In particular, the authors conclude that differences in the P2-pocket are relevant for the design of selective DP4 inhibitors. The loss of key interactions in DP8 and DP9 as predicted from their models is consistent with the selectivity profile of the DP4 clinical candidate MK-431.

  2. 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.

  3. Reciprocity principle-based model for shielding effectiveness prediction of a rectangular cavity with a covered aperture

    Institute of Scientific and Technical Information of China (English)

    焦重庆; 李月月

    2015-01-01

    According to the reciprocity principle, we propose an efficient model to compute the shielding effectiveness of a rectangular cavity with apertures covered by conductive sheet against an external incident electromagnetic wave. This problem is converted into another problem of solving the electromagnetic field leakage from the cavity when the cavity is excited by an electric dipole placed within it. By the combination of the unperturbed cavity field and the transfer impedance of the sheet, the tangential electric field distribution on the outer surface of the sheet is obtained. Then, the field distribution is regarded as an equivalent surface magnetic current source responsible for the leakage field. The validation of this model is verified by a comparison with the circuital model and the full-wave simulations. This time-saving model can deal with arbitrary aperture shape, various wave propagation and polarization directions, and the near-field effect.

  4. MONTE CARLO ANALYSIS FOR PREDICTION OF NOISE FROM A CONSTRUCTION SITE

    Directory of Open Access Journals (Sweden)

    Zaiton Haron

    2009-06-01

    Full Text Available The large number of operations involving noisy machinery associated with construction site activities result in considerable variation in the noise levels experienced at receiver locations. This paper suggests an approach to predict noise levels generated from a site by using a Monte Carlo approach. This approach enables the determination of details regarding the statistical uncertainties associated with noise level predictions or temporal distributions. This technique could provide the basis for a generalised prediction technique and a simple noise management tool.

  5. Prognostic importance of scintigraphic left ventricular cavity dilation during intravenous dipyridamole technetium-99m sestamibi myocardial tomographic imaging in predicting coronary events.

    Science.gov (United States)

    McClellan, J R; Travin, M I; Herman, S D; Baron, J I; Golub, R J; Gallagher, J J; Waters, D; Heller, G V

    1997-03-01

    Left ventricular (LV) cavity dilation during stress myocardial perfusion imaging has been associated with multivessel disease, and may be an independent prognostic marker in addition to perfusion defects. The present study examines the predictive value for future cardiac events of transient or fixed LV dilation during dipyridamole technetium-99m (Tc-99m) sestamibi single-photon emission computed tomography (SPECT) imaging. The study included 512 consecutive patients who underwent SPECT imaging with Tc-99m sestamibi after dipyridamole infusion. Transient LV dilation was seen in 70 patients (14%) and 74 had fixed cavity dilation (14%); cavity size was normal in 368 patients (72%). Each perfusion scan was classified as normal or abnormal, and if abnormal, defects were categorized as transient or fixed, and as small, medium, or large (depending upon the number of abnormal vascular territories). Events during a mean follow-up of 12.8 +/- 6.8 months were tabulated by direct review of hospital charts and death certificates. The cardiac event rate (cardiac death or nonfatal infarction) was 1.9% in patients with normal cavity size, 11.4% with transient LV dilation, and 13.5% with fixed LV dilation (p < 0.01). Compared with patients with normal cavity size, those with transient LV dilation were more likely to sustain a myocardial infarction (p < 0.01) and those with fixed dilation more frequently suffered cardiac death (p < 0.01) and hospitalization for heart failure (p < 0.01). The group with the highest risk had both a large perfusion defect and cavity dilation. By Cox proportional hazard regression analysis, both transient and fixed LV dilation were strong independent predictors of cardiac events. Transient or fixed LV dilation are commonly seen during dipyridamole Tc-99m sestamibi SPECT imaging (14% incidence for each) and are useful predictors of cardiac events.

  6. Cavity spin optodynamics

    CERN Document Server

    Brahms, N

    2010-01-01

    The dynamics of a large quantum spin coupled parametrically to an optical resonator is treated in analogy with the motion of a cantilever in cavity optomechanics. New spin optodynamic phenonmena are predicted, such as cavity-spin bistability, optodynamic spin-precession frequency shifts, coherent amplification and damping of spin, and the spin optodynamic squeezing of light.

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

    DEFF Research Database (Denmark)

    Ehrlich, L.; Reczko, M.; Bohr, Henrik;

    1998-01-01

    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 t...... provide insight into the mutual interdependencies between the location of ordered water sites and the structural and chemical characteristics of the protein residues.......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...... structure and solvent accessibility and, using actual values of these properties, redidue hydration can be predicted to 77% accuracy with a Metthews coefficient of 0.43. However, predicted property data with an accuracy of 60-70% result in less than half the improvement in predictive performance observed...

  8. 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.

  9. Prediction of calcium-binding sites by combining loop-modeling with machine learning

    Directory of Open Access Journals (Sweden)

    Altman Russ B

    2009-12-01

    Full Text Available Abstract Background Protein ligand-binding sites in the apo state exhibit structural flexibility. This flexibility often frustrates methods for structure-based recognition of these sites because it leads to the absence of electron density for these critical regions, particularly when they are in surface loops. Methods for recognizing functional sites in these missing loops would be useful for recovering additional functional information. Results We report a hybrid approach for recognizing calcium-binding sites in disordered regions. Our approach combines loop modeling with a machine learning method (FEATURE for structure-based site recognition. For validation, we compared the performance of our method on known calcium-binding sites for which there are both holo and apo structures. When loops in the apo structures are rebuilt using modeling methods, FEATURE identifies 14 out of 20 crystallographically proven calcium-binding sites. It only recognizes 7 out of 20 calcium-binding sites in the initial apo crystal structures. We applied our method to unstructured loops in proteins from SCOP families known to bind calcium in order to discover potential cryptic calcium binding sites. We built 2745 missing loops and evaluated them for potential calcium binding. We made 102 predictions of calcium-binding sites. Ten predictions are consistent with independent experimental verifications. We found indirect experimental evidence for 14 other predictions. The remaining 78 predictions are novel predictions, some with intriguing potential biological significance. In particular, we see an enrichment of beta-sheet folds with predicted calcium binding sites in the connecting loops on the surface that may be important for calcium-mediated function switches. Conclusion Protein crystal structures are a potentially rich source of functional information. When loops are missing in these structures, we may be losing important information about binding sites and active

  10. 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.

  11. 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...

  12. A predictive model of intein insertion site for use in the engineering of molecular switches.

    Directory of Open Access Journals (Sweden)

    James Apgar

    Full Text Available Inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. Successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. By analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant correlation with the location of the intein insertion sites, and therefore may be useful in predicting insertion sites in other proteins that provide native-like intein function. Three of these properties, the distance to the active site and dimer interface site, the SVM score of the splice site cassette, and the sequence conservation of the site showed statistically significant correlation and strong predictive power, with area under the curve (AUC values of 0.79, 0.76, and 0.73 respectively, while the distance to secondary structure/loop junction showed significance but with less predictive power (AUC of 0.54. In a case study of 20 insertion sites in the XynB xylanase, two features of native insertion sites showed correlation with the splice sites and demonstrated predictive value in selecting non-native splice sites. Structural modeling of intein insertions at two sites highlighted the role that the insertion site location could play on the ability of the intein to modulate activity of the host protein. These findings can be used to enrich the selection of insertion sites capable of supporting intein splicing and hosting an intein switch.

  13. 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

    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...... could be predicted from averaged properties together with the fact that glycosylation sites are not precisely conserved indicates that mucin-type glycosylation in most cases is a bulk property and not a very site-specific one. NetOGlyc 3.1 is made available at www.cbs.dtu.dk/services/netoglyc....

  14. 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

    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...... could be predicted from averaged properties together with the fact that glycosylation sites are not precisely conserved indicates that mucin-type glycosylation in most cases is a bulk property and not a very site-specific one. NetOGlyc 3.1 is made available at www.cbs.dtu.dk/services/netoglyc....

  15. Recent Progress in Predicting Posttranslational Modification Sites in Proteins.

    Science.gov (United States)

    Xu, Yan; Chou, Kuo-Chen

    2016-01-01

    The posttranslational modification or PTM is a later but subtle step in protein biosynthesis via which to change the properties of a protein by adding a modified group to its one or more amino acid residues. PTMs are responsible for many significant biological processes, and meanwhile for many major diseases as well, such as cancer. Facing the avalanche of biological sequences generated in the post-genomic age, it is important for both basic research and drug development to timely identify the PTM sites in proteins. This Review is devoted to summarize the recent progresses in this area, with a focus on those predictors, which were developed based on the pseudo amino acid composition or PseAAC approach, and for which a publicly accessible web-server has been established. Meanwhile, the future challenge in this area has also been briefly addressed.

  16. Predicting DNA-binding sites of proteins based on sequential and 3D structural information.

    Science.gov (United States)

    Li, Bi-Qing; Feng, Kai-Yan; Ding, Juan; Cai, Yu-Dong

    2014-06-01

    Protein-DNA interactions play important roles in many biological processes. To understand the molecular mechanisms of protein-DNA interaction, it is necessary to identify the DNA-binding sites in DNA-binding proteins. In the last decade, computational approaches have been developed to predict protein-DNA-binding sites based solely on protein sequences. In this study, we developed a novel predictor based on support vector machine algorithm coupled with the maximum relevance minimum redundancy method followed by incremental feature selection. We incorporated not only features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure, solvent accessibility, but also five three-dimensional (3D) structural features calculated from PDB data to predict the protein-DNA interaction sites. Feature analysis showed that 3D structural features indeed contributed to the prediction of DNA-binding site and it was demonstrated that the prediction performance was better with 3D structural features than without them. It was also shown via analysis of features from each site that the features of DNA-binding site itself contribute the most to the prediction. Our prediction method may become a useful tool for identifying the DNA-binding sites and the feature analysis described in this paper may provide useful insights for in-depth investigations into the mechanisms of protein-DNA interaction.

  17. 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.

  18. Structural descriptor database: a new tool for sequence-based functional site prediction

    Directory of Open Access Journals (Sweden)

    Vasconcelos Ana

    2008-11-01

    Full Text Available Abstract Background The Structural Descriptor Database (SDDB is a web-based tool that predicts the function of proteins and functional site positions based on the structural properties of related protein families. Structural alignments and functional residues of a known protein set (defined as the training set are used to build special Hidden Markov Models (HMM called HMM descriptors. SDDB uses previously calculated and stored HMM descriptors for predicting active sites, binding residues, and protein function. The database integrates biologically relevant data filtered from several databases such as PDB, PDBSUM, CSA and SCOP. It accepts queries in fasta format and predicts functional residue positions, protein-ligand interactions, and protein function, based on the SCOP database. Results To assess the SDDB performance, we used different data sets. The Trypsion-like Serine protease data set assessed how well SDDB predicts functional sites when curated data is available. The SCOP family data set was used to analyze SDDB performance by using training data extracted from PDBSUM (binding sites and from CSA (active sites. The ATP-binding experiment was used to compare our approach with the most current method. For all evaluations, significant improvements were obtained with SDDB. Conclusion SDDB performed better when trusty training data was available. SDDB worked better in predicting active sites rather than binding sites because the former are more conserved than the latter. Nevertheless, by using our prediction method we obtained results with precision above 70%.

  19. Human Papillomavirus Infections are Common and Predict Mortality in a Retrospective Cohort Study of Taiwanese Patients With Oral Cavity Cancer.

    Science.gov (United States)

    Lee, Li-Ang; Huang, Chung-Guei; Tsao, Kuo-Chien; Liao, Chun-Ta; Kang, Chung-Jan; Chang, Kai-Ping; Huang, Shiang-Fu; Chen, I-How; Fang, Tuan-Jen; Li, Hsueh-Yu; Yang, Shu-Li; Lee, Li-Yu; Hsueh, Chuen; Lin, Chien-Yu; Fan, Kang-Hsing; Chang, Tung-Chieh; Wang, Hung-Ming; Ng, Shu-Hang; Yen, Tzu-Chen

    2015-11-01

    Human papillomavirus (HPV) infections are deemed to play a role in the pathogenesis of oral cavity cancer (OCC). However, their exact prevalence and clinical significance remain unclear. Herein, we investigated the prevalence and prognostic value of HPV infections in a large sample of Taiwanese OCC patients.This study was designed as a retrospective cohort study. Between 2004 and 2011, we identified 1002 consecutive patients with newly diagnosed OCC who were scheduled for standard treatment. HPV genotyping was performed in tumor specimens using polymerase chain reaction-based HPV blots. To investigate the temporal trends of HPV infections and their impact on 5-year overall survival (OS), patients were divided into 2 cohorts according to calendar periods: "2004 cohort" (2004-2007; n = 466) and "2008 cohort" (2008-2011; n = 536). Univariate and multivariate Cox regression models were also used to identify the independent predictors of OS in the 2 cohorts. A weighted risk score was assigned to each factor based on the range of their corresponding hazard ratios and validated in both cohorts using the c-statistic.The overall prevalence of HPV infections was 19%, with a trend toward decreasing rates from 2004 to 2011. In patients without risky oral habits, the 5-year OS rate of HPV-positive patients was significantly lower than that of HPV-negative cases (49% vs 80%; P = 0.021). In the 2004 cohort, multivariate analysis identified HPV16, pathological T3/T4, pathological N1/N2, and extracapsular spread as independent adverse prognostic factors for OS. In the 2008 cohort, pathological N1/N2, pathological stage III/IV, and histological tumor depth >8 mm were identified as independent adverse prognostic factors. Using a weighted grading system incorporating HPV16 infection, we devised a prognostic index that identified 4 distinct risk categories with 5-year OS rates ranging from 25% to 89% (c-statistic = 0.76) in the 2004 cohort. The validity of the index was internally

  20. 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

  1. 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...

  2. Aeroacoustic power generated by a compact axisymmetric cavity: Prediction of self-sustained osciallation and influence of depth

    NARCIS (Netherlands)

    Nakiboglu, G.; Manders, H.B.M.; Hirschberg, A.

    2012-01-01

    Aeroacoustic power generation due to a self-sustained oscillation by an axisymmetric compact cavity exposed to a low-Mach-number grazing flow is studied both experimentally and numerically. The feedback effect is produced by the velocity fluctuations resulting from a coupling with acoustic standing

  3. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

    Science.gov (United States)

    Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

    2011-07-01

    The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

  4. Using TESS to predict transcription factor binding sites in DNA sequence.

    Science.gov (United States)

    Schug, Jonathan

    2008-03-01

    This unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites (TFBS) in DNA sequence using two different kinds of models of sites, strings and positional weight matrices. The binding of transcription factors to DNA is a major part of the control of gene expression. Transcription factors exhibit sequence-specific binding; they form stronger bonds to some DNA sequences than to others. Identification of a good binding site in the promoter for a gene suggests the possibility that the corresponding factor may play a role in the regulation of that gene. However, the sequences transcription factors recognize are typically short and allow for some amount of mismatch. Because of this, binding sites for a factor can typically be found at random every few hundred to a thousand base pairs. TESS has features to help sort through and evaluate the significance of predicted sites.

  5. 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.

  6. Genome-wide prediction, display and refinement of binding sites with information theory-based models

    Directory of Open Access Journals (Sweden)

    Leeder J Steven

    2003-09-01

    Full Text Available Abstract Background We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices. Results Parameters for genome scans are entered using a Java-based GUI interface and backend scripts in Perl. Multi-processor CPU load-sharing minimized the average response time for scans of different chromosomes. Scans of human genome assemblies required 4–6 hours for transcription factor binding sites and 10–19 hours for splice sites, respectively, on 24- and 3-node Mosix and Beowulf clusters. Individual binding sites are displayed either as high-resolution sequence walkers or in low-resolution custom tracks in the UCSC genome browser. For large datasets, we applied a data reduction strategy that limited displays of binding sites exceeding a threshold information content to specific chromosomal regions within or adjacent to genes. An HTML document is produced listing binding sites ranked by binding site strength or chromosomal location hyperlinked to the UCSC custom track, other annotation databases and binding site sequences. Post-genome scan tools parse binding site annotations of selected chromosome intervals and compare the results of genome scans using different weight matrices. Comparisons of multiple genome scans can display binding sites that are unique to each scan and identify sites with significantly altered binding strengths

  7. The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase.

    Science.gov (United States)

    Fitzgerald, M M; Trester, M L; Jensen, G M; McRee, D E; Goodin, D B

    1995-09-01

    The activated state of cytochrome c peroxidase, compound ES, contains a cation radical on the Trp-191 side chain. We recently reported that replacing this tryptophan with glycine creates a buried cavity at the active site that contains ordered solvent and that will specifically bind substituted imidazoles in their protonated cationic forms (Fitzgerald MM, Churchill MJ, McRee DE, Goodin DB, 1994, Biochemistry 33:3807-3818). Proposals that a nearby carboxylate, Asp-235, and competing monovalent cations should modulate the affinity of the W191G cavity for ligand binding are addressed in this study. Competitive binding titrations of the imidazolium ion to W191G as a function of [K+] show that potassium competes weakly with the binding of imidazoles. The dissociation constant observed for potassium binding (18 mM) is more than 3,000-fold higher than that for 1,2-dimethylimidazole (5.5 microM) in the absence of competing cations. Significantly, the W191G-D235N double mutant shows no evidence for binding imidazoles in their cationic or neutral forms, even though the structure of the cavity remains largely unperturbed by replacement of the carboxylate. Refined crystallographic B-values of solvent positions indicate that the weakly bound potassium in W191G is significantly depopulated in the double mutant. These results demonstrate that the buried negative charge of Asp-235 is an essential feature of the cation binding determinant and indicate that this carboxylate plays a critical role in stabilizing the formation of the Trp-191 radical cation.

  8. 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.

  9. 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.

  10. Cross-prediction of the groundwater chemistry at the SKB sites in Sweden. Pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Skaarman, C.; Laaksoharju, M. [Intera KB (Sweden)

    1997-08-01

    The possibility to perform a large scale prediction throughout Sweden was tested. The aim of the work was: to collect data and create a groundwater database for current and future use; to see if there is any correlation between data at different sites; to perform a modelling where the groundwater composition at different regions in Sweden is predicted. The outcome of the predictions were compared with the measured data at different sites. The results show that it is possible but more work needs to be done to improve the prediction models. More measurements at depth are needed to enable the use of 3D models. It is also important to include hydrogeological parameters in the groundwater chemical prediction models that are used. 8 refs, 115 figs.

  11. Predicting Polymerase Ⅱ Core Promoters by Cooperating Transcription Factor Binding Sites in Eukaryotic Genes

    Institute of Scientific and Technical Information of China (English)

    Xiao-Tu MA; Min-Ping QIAN; Hai-Xu TANG

    2004-01-01

    Several discriminate functions for predicting core promoters that based on the potential cooperation between transcription factor binding sites (TFBSs) are discussed. It is demonstrated that the promoter predicting accuracy is improved when the cooperation among TFBSs is taken into consideration.The core promoter region of a newly discovered gene CKLFSF1 is predicted to locate more than 1.5 kb far away from the 5′ end of the transcript and in the last intron of its upstream gene, which is experimentally confirmed later. The core promoters of 3402 human RefSeq sequences, obtained by extending the mRNAs in human genome sequences, are predicted by our algorithm, and there are about 60% of the predicted core promoters locating within the ± 500 bp region relative to the annotated transcription start site.

  12. MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets

    Science.gov (United States)

    Bandyopadhyay, Sanghamitra; Ghosh, Dip; Mitra, Ramkrishna; Zhao, Zhongming

    2015-01-01

    MicroRNA (miRNA) regulates gene expression by binding to specific sites in the 3'untranslated regions of its target genes. Machine learning based miRNA target prediction algorithms first extract a set of features from potential binding sites (PBSs) in the mRNA and then train a classifier to distinguish targets from non-targets. However, they do not consider whether the PBSs are functional or not, and consequently result in high false positive rates. This substantially affects the follow up functional validation by experiments. We present a novel machine learning based approach, MBSTAR (Multiple instance learning of Binding Sites of miRNA TARgets), for accurate prediction of true or functional miRNA binding sites. Multiple instance learning framework is adopted to handle the lack of information about the actual binding sites in the target mRNAs. Biologically validated 9531 interacting and 973 non-interacting miRNA-mRNA pairs are identified from Tarbase 6.0 and confirmed with PAR-CLIP dataset. It is found that MBSTAR achieves the highest number of binding sites overlapping with PAR-CLIP with maximum F-Score of 0.337. Compared to the other methods, MBSTAR also predicts target mRNAs with highest accuracy. The tool and genome wide predictions are available at http://www.isical.ac.in/~bioinfo_miu/MBStar30.htm.

  13. Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks.

    Science.gov (United States)

    Pettie, Kade P; Dresch, Jacqueline M; Drewell, Robert A

    2016-08-01

    In the development of the Drosophila embryo, gene expression is directed by the sequence-specific interactions of a large network of protein transcription factors (TFs) and DNA cis-regulatory binding sites. Once the identity of the typically 8-10bp binding sites for any given TF has been determined by one of several experimental procedures, the sequences can be represented in a position weight matrix (PWM) and used to predict the location of additional TF binding sites elsewhere in the genome. Often, alignments of large (>200bp) genomic fragments that have been experimentally determined to bind the TF of interest in Chromatin Immunoprecipitation (ChIP) studies are trimmed under the assumption that the majority of the binding sites are located near the center of all the aligned fragments. In this study, ChIP/chip datasets are analyzed using the corresponding PWMs for the well-studied TFs; CAUDAL, HUNCHBACK, KNIRPS and KRUPPEL, to determine the distribution of predicted binding sites. All four TFs are critical regulators of gene expression along the anterio-posterior axis in early Drosophila development. For all four TFs, the ChIP peaks contain multiple binding sites that are broadly distributed across the genomic region represented by the peak, regardless of the prediction stringency criteria used. This result suggests that ChIP peak trimming may exclude functional binding sites from subsequent analyses.

  14. 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

  15. Numerical Study for the Prediction of the Thermal Comfort in a Rectangular Enclosure Simulated as an Ondol Cavity with the Ondol Heating System

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Yong Il [Department of Building Equipment Engineering, Shin Heung Junior College, Eui-Jungbu (Korea, Republic of); Kwon, Sun Sok [Department of Mechanical Engineering, College of Engineering, Dong-A University, Pusan (Korea, Republic of)

    1996-09-15

    The Ondol heating system used for winter is changed from a hypocaust with floor indirectly heated by hot flue gas to that with floor heated by hot water. Residents using the Ondol heating system usually do not use a bedstead and has a sedentary life. Therefore, a perimeter zone near window is not equipped with a convector or a radiator. The activity space of residential occupants is usually over 1.5m from the floor so that the prediction of the thermal comfort in this space is required. In this study, the bottom floor surface is heated by hot water and the window is cooled by the cold outdoor air, both being assumed at uniform temperatures. The values of PMV and PPD proposed by Fanger are calculated for predicting the thermal comfort in the Ondol cavity. It is investigated that the radiant heat transfer affects to convection heat transfer in the Ondol cavity with transparent air for radiation. (author). 11 refs., 10 figs.

  16. 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....... size on single local networks for training, to cover both donor and acceptor site information. We have applied NetAspGene to other Aspergilli, including Aspergillus nidulans, Aspergillus oryzae, and Aspergillus niger. Evaluation with independent data sets reveal that NetAspGene performs substantially...

  17. 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...

  18. Computational predictions provide insights into the biology of TAL effector target sites.

    Science.gov (United States)

    Grau, Jan; Wolf, Annett; Reschke, Maik; Bonas, Ulla; Posch, Stefan; Boch, Jens

    2013-01-01

    Transcription activator-like (TAL) effectors are injected into host plant cells by Xanthomonas bacteria to function as transcriptional activators for the benefit of the pathogen. The DNA binding domain of TAL effectors is composed of conserved amino acid repeat structures containing repeat-variable diresidues (RVDs) that determine DNA binding specificity. In this paper, we present TALgetter, a new approach for predicting TAL effector target sites based on a statistical model. In contrast to previous approaches, the parameters of TALgetter are estimated from training data computationally. We demonstrate that TALgetter successfully predicts known TAL effector target sites and often yields a greater number of predictions that are consistent with up-regulation in gene expression microarrays than an existing approach, Target Finder of the TALE-NT suite. We study the binding specificities estimated by TALgetter and approve that different RVDs are differently important for transcriptional activation. In subsequent studies, the predictions of TALgetter indicate a previously unreported positional preference of TAL effector target sites relative to the transcription start site. In addition, several TAL effectors are predicted to bind to the TATA-box, which might constitute one general mode of transcriptional activation by TAL effectors. Scrutinizing the predicted target sites of TALgetter, we propose several novel TAL effector virulence targets in rice and sweet orange. TAL-mediated induction of the candidates is supported by gene expression microarrays. Validity of these targets is also supported by functional analogy to known TAL effector targets, by an over-representation of TAL effector targets with similar function, or by a biological function related to pathogen infection. Hence, these predicted TAL effector virulence targets are promising candidates for studying the virulence function of TAL effectors. TALgetter is implemented as part of the open-source Java library

  19. Computational predictions provide insights into the biology of TAL effector target sites.

    Directory of Open Access Journals (Sweden)

    Jan Grau

    Full Text Available Transcription activator-like (TAL effectors are injected into host plant cells by Xanthomonas bacteria to function as transcriptional activators for the benefit of the pathogen. The DNA binding domain of TAL effectors is composed of conserved amino acid repeat structures containing repeat-variable diresidues (RVDs that determine DNA binding specificity. In this paper, we present TALgetter, a new approach for predicting TAL effector target sites based on a statistical model. In contrast to previous approaches, the parameters of TALgetter are estimated from training data computationally. We demonstrate that TALgetter successfully predicts known TAL effector target sites and often yields a greater number of predictions that are consistent with up-regulation in gene expression microarrays than an existing approach, Target Finder of the TALE-NT suite. We study the binding specificities estimated by TALgetter and approve that different RVDs are differently important for transcriptional activation. In subsequent studies, the predictions of TALgetter indicate a previously unreported positional preference of TAL effector target sites relative to the transcription start site. In addition, several TAL effectors are predicted to bind to the TATA-box, which might constitute one general mode of transcriptional activation by TAL effectors. Scrutinizing the predicted target sites of TALgetter, we propose several novel TAL effector virulence targets in rice and sweet orange. TAL-mediated induction of the candidates is supported by gene expression microarrays. Validity of these targets is also supported by functional analogy to known TAL effector targets, by an over-representation of TAL effector targets with similar function, or by a biological function related to pathogen infection. Hence, these predicted TAL effector virulence targets are promising candidates for studying the virulence function of TAL effectors. TALgetter is implemented as part of the open

  20. [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.

  1. 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/.

  2. Prediction of Signal Peptide Cleavage Sites with Subsite-Coupled and Template Matching Fusion Algorithm.

    Science.gov (United States)

    Zhang, Shao-Wu; Zhang, Ting-He; Zhang, Jun-Nan; Huang, Yufei

    2014-03-01

    Fast and effective prediction of signal peptides (SP) and their cleavage sites is of great importance in computational biology. The approaches developed to predict signal peptide can be roughly divided into machine learning based, and sliding windows based. In order to further increase the prediction accuracy and coverage of organism for SP cleavage sites, we propose a novel method for predicting SP cleavage sites called Signal-CTF that utilizes machine learning and sliding windows, and is designed for N-termial secretory proteins in a large variety of organisms including human, animal, plant, virus, bacteria, fungi and archaea. Signal-CTF consists of three distinct elements: (1) a subsite-coupled and regularization function with a scaled window of fixed width that selects a set of candidates of possible secretion-cleavable segment for a query secretory protein; (2) a sum fusion system that integrates the outcomes from aligning the cleavage site template sequence with each of the aforementioned candidates in a scaled window of fixed width to determine the best candidate cleavage sites for the query secretory protein; (3) a voting system that identifies the ultimate signal peptide cleavage site among all possible results derived from using scaled windows of different width. When compared with Signal-3L and SignalP 4.0 predictors, the prediction accuracy of Signal-CTF is 4-12 %, 10-25 % higher than that of Signal-3L for human, animal and eukaryote, and SignalP 4.0 for eukaryota, Gram-positive bacteria and Gram-negative bacteria, respectively. Comparing with PRED-SIGNAL and SignalP 4.0 predictors on the 32 archaea secretory proteins of used in Bagos's paper, the prediction accuracy of Signal-CTF is 12.5 %, 25 % higher than that of PRED-SIGNAL and SignalP 4.0, respectively. The predicting results of several long signal peptides show that the Signal-CTF can better predict cleavage sites for long signal peptides than SignalP, Phobius, Philius, SPOCTOPUS, Signal

  3. 利用天然树洞繁殖的五种鸟的巢位特征及繁殖成功率%Nest-site characteristics and reproductive success of five species of birds breeding in natural cavities

    Institute of Scientific and Technical Information of China (English)

    王海涛; 高玮; 万冬梅; 刘多; 邓文洪

    2003-01-01

    对吉林省左家自然保护区次生阔叶林中的大山雀(Parus major)、沼泽山雀(Parus palustris)、普通(币鸟)(Sitta europacea)、白眉姬鹟(Ficedula zanthopygia)和灰椋鸟(Sturnus cineraceus) 5种利用天然树洞繁殖的次级洞巢鸟进行了巢位选择和繁殖成功率研究.本研究中共发现141巢.五种鸟对树洞类型的选择存在种间差异,普通(币鸟)不利用裂洞,沼泽山雀不利用啄洞,其它3种鸟对3种洞均有利用,但有一定的倾向性.对5种鸟9个巢位变量的比较中,只有洞口方向差异不显著(p>0.05),其它8个变量均差异显著(p0.05). But all the remaining eight variables are significant (p<0.05). The results indicate that the 5 species of SCNBs select nest-sites with their own nesting requirements. The horizontal diameter and vertical diameter of nest entrance, diameter of tree at cavity height, inner breadth of the cavity and the nest height above ground are important variables in nest-site selection and are predictive of species occupancy. Most of the nests that failed occur before the laying and hatching stage, as 35 out of 44 failed nests loss during these two stages. The nest success of Great Tit is the lowest and Ashy Starling is the highest. Hatching success among the five species of SCNBs' are at high level, all exceeding 90%. Depredation (included by man and animals) is the main cause for nest failure, accounting for 61.4% of total failure nests. SCNBs' reproductive success is influenced by important variables in nest-site selection. Reproductive success of Nutchatch is influenced by HDE and NH, Marsh Tit by VDE, DBH and BC, Great Tit by HDE, NH and BC, Ashy Staring by BC and DC, and Tricolor Flycatcher by VDE, NH and CA. The horizontal and vertical diameter of nest entrance of failed nests are bigger than those of successful nests, and the depth of the cavity and breadth of the cavity of failure nests are smaller than those of successful nests. Distances from ground level

  4. 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.

  5. 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

    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 refin...

  6. 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.

  7. PREDICTIONS OF ION PRODUCTION RATES AND ION NUMBER DENSITIES WITHIN THE DIAMAGNETIC CAVITY OF COMET 67P/CHURYUMOV-GERASIMENKO AT PERIHELION

    Energy Technology Data Exchange (ETDEWEB)

    Vigren, E.; Galand, M., E-mail: e.vigren@imperial.ac.uk [Department of Physics, Imperial College London, London SW7 2AZ (United Kingdom)

    2013-07-20

    We present a one-dimensional ion chemistry model of the diamagnetic cavity of comet 67P/Churyumov-Gerasimenko, the target comet for the ESA Rosetta mission. We solve the continuity equations for ionospheric species and predict number densities of electrons and selected ions considering only gas-phase reactions. We apply the model to the subsolar direction and consider conditions expected to be encountered by Rosetta at perihelion (1.29 AU) in 2015 August. Our default simulation predicts a maximum electron number density of {approx}8 Multiplication-Sign 10{sup 4} cm{sup -3} near the surface of the comet, while the electron number densities for cometocentric distances r > 10 km are approximately proportional to 1/r {sup 1.23} assuming that the electron temperature is equal to the neutral temperature. We show that even a small mixing ratio ({approx}0.3%-1%) of molecules having higher proton affinity than water is sufficient for the proton transfer from H{sub 3}O{sup +} to occur so readily that other ions than H{sub 3}O{sup +}, such as NH{sub 4} {sup +} or CH{sub 3}OH{sub 2} {sup +}, become dominant in terms of volume mixing ratio in part of, if not throughout, the diamagnetic cavity. Finally, we test how the predicted electron and ion densities are influenced by changes of model input parameters, including the neutral background, the impinging EUV solar spectrum, the solar zenith angle, the cross sections for photo- and electron-impact processes, the electron temperature profile, and the temperature dependence of ion-neutral reactions.

  8. A machine-learning approach for predicting palmitoylation sites from integrated sequence-based features.

    Science.gov (United States)

    Li, Liqi; Luo, Qifa; Xiao, Weidong; Li, Jinhui; Zhou, Shiwen; Li, Yongsheng; Zheng, Xiaoqi; Yang, Hua

    2017-02-01

    Palmitoylation is the covalent attachment of lipids to amino acid residues in proteins. As an important form of protein posttranslational modification, it increases the hydrophobicity of proteins, which contributes to the protein transportation, organelle localization, and functions, therefore plays an important role in a variety of cell biological processes. Identification of palmitoylation sites is necessary for understanding protein-protein interaction, protein stability, and activity. Since conventional experimental techniques to determine palmitoylation sites in proteins are both labor intensive and costly, a fast and accurate computational approach to predict palmitoylation sites from protein sequences is in urgent need. In this study, a support vector machine (SVM)-based method was proposed through integrating PSI-BLAST profile, physicochemical properties, [Formula: see text]-mer amino acid compositions (AACs), and [Formula: see text]-mer pseudo AACs into the principal feature vector. A recursive feature selection scheme was subsequently implemented to single out the most discriminative features. Finally, an SVM method was implemented to predict palmitoylation sites in proteins based on the optimal features. The proposed method achieved an accuracy of 99.41% and Matthews Correlation Coefficient of 0.9773 for a benchmark dataset. The result indicates the efficiency and accuracy of our method in prediction of palmitoylation sites based on protein sequences.

  9. 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.

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

    Science.gov (United States)

    Roche, Daniel Barry; Brackenridge, Danielle Allison; McGuffin, Liam James

    2015-12-15

    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.

  11. Probabilistic Assessment of Above Zone Pressure Predictions at a Geologic Carbon Storage Site

    Science.gov (United States)

    Namhata, Argha; Oladyshkin, Sergey; Dilmore, Robert M.; Zhang, Liwei; Nakles, David V.

    2016-12-01

    Carbon dioxide (CO2) storage into geological formations is regarded as an important mitigation strategy for anthropogenic CO2 emissions to the atmosphere. This study first simulates the leakage of CO2 and brine from a storage reservoir through the caprock. Then, we estimate the resulting pressure changes at the zone overlying the caprock also known as Above Zone Monitoring Interval (AZMI). A data-driven approach of arbitrary Polynomial Chaos (aPC) Expansion is then used to quantify the uncertainty in the above zone pressure prediction based on the uncertainties in different geologic parameters. Finally, a global sensitivity analysis is performed with Sobol indices based on the aPC technique to determine the relative importance of different parameters on pressure prediction. The results indicate that there can be uncertainty in pressure prediction locally around the leakage zones. The degree of such uncertainty in prediction depends on the quality of site specific information available for analysis. The scientific results from this study provide substantial insight that there is a need for site-specific data for efficient predictions of risks associated with storage activities. The presented approach can provide a basis of optimized pressure based monitoring network design at carbon storage sites.

  12. Site of metabolism prediction based on ab initio derived atom representations.

    Science.gov (United States)

    Finkelmann, Arndt R; Göller, Andreas H; Schneider, Gisbert

    2017-03-21

    Machine learning models for site of metabolism (SoM) prediction offer the ability to identify metabolic soft spots in low molecular weight drug molecules at low computational cost and enable data-based reactivity prediction. SoM prediction is an atom classification problem. Successful construction of machine learning models requires atom representations that capture the reactivity-determining features of a potential reaction site. We have developed a descriptor scheme that characterizes an atom's steric and electronic environment and its relative location in the molecular structure. The partial charge distributions were obtained from fast quantum mechanical calculations. We successfully trained machine learning classifiers on curated cytochrome p450 metabolism data. The models based on the new atom descriptors showed sustained accuracy for retrospective analyses of metabolism optimization campaigns and lead optimization projects from Bayer Pharmaceuticals. The results obtained demonstrate the practicality of quantum-chemistry-supported machine learning models for hit-to-lead optimization.

  13. STarMir Tools for Prediction of microRNA binding sites

    Science.gov (United States)

    Kanoria, Shaveta; Rennie, William; Liu, Chaochun; Carmack, C. Steven; Lu, Jun; Ding, Ye

    2017-01-01

    MicroRNAs (miRNAs) are a class of endogenous short non-coding RNAs that regulate gene expression by targeting messenger RNAs (mRNAs), which results in translational repression and/or mRNA degradation. As regulatory molecules, miRNAs are involved in many mammalian biological processes and also in the manifestation of certain human diseases. As miRNAs play central role in the regulation of gene expression, understanding miRNA-binding patterns is essential to gain an insight of miRNA mediated gene regulation and also holds promise for therapeutic applications. Computational prediction of miRNA binding sites on target mRNAs facilitates experimental investigation of miRNA functions. This chapter provides protocols for using the STarMir web server for improved predictions of miRNA binding sites on a target mRNA. As an application module of the Sfold RNA package, the current version of STarMir is an implementation of logistic prediction models developed with high throughput miRNA binding data from crosslinking immuno-precipitation (CLIP) studies. The models incorporated comprehensive thermodynamic, structural and sequence features, and were found to make improved predictions of both seed and seedless sites, in comparison to the established algorithms [1]. Their broad applicability was indicated by their good performance in cross-species validation. STarMir is freely available at http://sfold.wadsworth.org/starmir.html PMID:27665594

  14. Spatial characterization and prediction of Neanderthal sites based on environmental information and stochastic modelling

    Science.gov (United States)

    Maerker, Michael; Bolus, Michael

    2014-05-01

    We present a unique spatial dataset of Neanderthal sites in Europe that was used to train a set of stochastic models to reveal the correlations between the site locations and environmental indices. In order to assess the relations between the Neanderthal sites and environmental variables as described above we applied a boosted regression tree approach (TREENET) a statistical mechanics approach (MAXENT) and support vector machines. The stochastic models employ a learning algorithm to identify a model that best fits the relationship between the attribute set (predictor variables (environmental variables) and the classified response variable which is in this case the types of Neanderthal sites. A quantitative evaluation of model performance was done by determining the suitability of the model for the geo-archaeological applications and by helping to identify those aspects of the methodology that need improvements. The models' predictive performances were assessed by constructing the Receiver Operating Characteristics (ROC) curves for each Neanderthal class, both for training and test data. In a ROC curve the Sensitivity is plotted over the False Positive Rate (1-Specificity) for all possible cut-off points. The quality of a ROC curve is quantified by the measure of the parameter area under the ROC curve. The dependent variable or target variable in this study are the locations of Neanderthal sites described by latitude and longitude. The information on the site location was collected from literature and own research. All sites were checked for site accuracy using high resolution maps and google earth. The study illustrates that the models show a distinct ranking in model performance with TREENET outperforming the other approaches. Moreover Pre-Neanderthals, Early Neanderthals and Classic Neanderthals show a specific spatial distribution. However, all models show a wide correspondence in the selection of the most important predictor variables generally showing less

  15. 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.

  16. 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.

  17. Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation.

    Science.gov (United States)

    Tsujikawa, Hiroto; Sato, Kenta; Wei, Cao; Saad, Gul; Sumikoshi, Kazuya; Nakamura, Shugo; Terada, Tohru; Shimizu, Kentaro

    2016-09-01

    We present a new method for predicting protein-ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Ligand-binding sites were predicted by combining the interaction energy and the amino acid conservation score. The performance of our prediction method was evaluated using a non-redundant dataset of 348 ligand-bound and ligand-unbound protein structure pairs, constructed by filtering entries in a ligand-binding site structure database, LigASite. Ligand-bound structure prediction (bound prediction) indicated that 74.0 % of predicted ligand-binding sites overlapped with real ligand-binding sites by over 25 % of their volume. Ligand-unbound structure prediction (unbound prediction) indicated that 73.9 % of predicted ligand-binding residues overlapped with real ligand-binding residues. The amino acid conservation score improved the average prediction accuracy by 17.0 and 17.6 points for the bound and unbound predictions, respectively. These results demonstrate the effectiveness of the combined use of the interaction energy and amino acid conservation in the ligand-binding site prediction.

  18. 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.

  19. A python analytical pipeline to identify prohormone precursors and predict prohormone cleavage sites.

    Science.gov (United States)

    Southey, Bruce R; Sweedler, Jonathan V; Rodriguez-Zas, Sandra L

    2008-01-01

    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.

  20. 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.

  1. Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping.

    Science.gov (United States)

    Scarabelli, Guido; Morra, Giulia; Colombo, Giorgio

    2010-05-19

    An increasing number of functional studies of proteins have shown that sequence and structural similarities alone may not be sufficient for reliable prediction of their interaction properties. This is particularly true for proteins recognizing specific antibodies, where the prediction of antibody-binding sites, called epitopes, has proven challenging. The antibody-binding properties of an antigen depend on its structure and related dynamics. Aiming to predict the antibody-binding regions of a protein, we investigate a new approach based on the integrated analysis of the dynamical and energetic properties of antigens, to identify nonoptimized, low-intensity energetic interaction networks in the protein structure isolated in solution. The method is based on the idea that recognition sites may correspond to localized regions with low-intensity energetic couplings with the rest of the protein, which allows them to undergo conformational changes, to be recognized by a binding partner, and to tolerate mutations with minimal energetic expense. Upon analyzing the results on isolated proteins and benchmarking against antibody complexes, it is found that the method successfully identifies binding sites located on the protein surface that are accessible to putative binding partners. The combination of dynamics and energetics can thus discriminate between epitopes and other substructures based only on physical properties. We discuss implications for vaccine design.

  2. Predicting carbon dioxide and energy fluxes across global FLUXNET sites with regression algorithms

    Science.gov (United States)

    Tramontana, Gianluca; Jung, Martin; Schwalm, Christopher R.; Ichii, Kazuhito; Camps-Valls, Gustau; Ráduly, Botond; Reichstein, Markus; Altaf Arain, M.; Cescatti, Alessandro; Kiely, Gerard; Merbold, Lutz; Serrano-Ortiz, Penelope; Sickert, Sven; Wolf, Sebastian; Papale, Dario

    2016-07-01

    Spatio-temporal fields of land-atmosphere fluxes derived from data-driven models can complement simulations by process-based land surface models. While a number of strategies for empirical models with eddy-covariance flux data have been applied, a systematic intercomparison of these methods has been missing so far. In this study, we performed a cross-validation experiment for predicting carbon dioxide, latent heat, sensible heat and net radiation fluxes across different ecosystem types with 11 machine learning (ML) methods from four different classes (kernel methods, neural networks, tree methods, and regression splines). We applied two complementary setups: (1) 8-day average fluxes based on remotely sensed data and (2) daily mean fluxes based on meteorological data and a mean seasonal cycle of remotely sensed variables. The patterns of predictions from different ML and experimental setups were highly consistent. There were systematic differences in performance among the fluxes, with the following ascending order: net ecosystem exchange (R2 0.6), gross primary production (R2> 0.7), latent heat (R2 > 0.7), sensible heat (R2 > 0.7), and net radiation (R2 > 0.8). The ML methods predicted the across-site variability and the mean seasonal cycle of the observed fluxes very well (R2 > 0.7), while the 8-day deviations from the mean seasonal cycle were not well predicted (R2 Fluxes were better predicted at forested and temperate climate sites than at sites in extreme climates or less represented by training data (e.g., the tropics). The evaluated large ensemble of ML-based models will be the basis of new global flux products.

  3. 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.

  4. Snoring Sounds Predict Obstruction Sites and Surgical Response in Patients with Obstructive Sleep Apnea Hypopnea Syndrome

    Science.gov (United States)

    Lee, Li-Ang; Lo, Yu-Lun; Yu, Jen-Fang; Lee, Gui-She; Ni, Yung-Lun; Chen, Ning-Hung; Fang, Tuan-Jen; Huang, Chung-Guei; Cheng, Wen-Nuan; Li, Hsueh-Yu

    2016-01-01

    Snoring sounds generated by different vibrators of the upper airway may be useful indicators of obstruction sites in patients with obstructive sleep apnea hypopnea syndrome (OSAHS). This study aimed to investigate associations between snoring sounds, obstruction sites, and surgical responses (≥50% reduction in the apnea-hypopnea index [AHI] and DISE), and relocation pharyngoplasty. All patients received follow-up polysomnography after 6 months. Fifteen (42%) patients with at least two complete obstruction sites defined by DISE were significantly, positively associated with maximal snoring sound intensity (40–300 Hz; odds ratio [OR], 1.25, 95% confidence interval [CI] 1.05–1.49) and body mass index (OR, 1.48, 95% CI 1.02–2.15) after logistic regression analysis. Tonsil obstruction was significantly, inversely correlated with mean snoring sound intensity (301–850 Hz; OR, 0.84, 95% CI 0.74–0.96). Moreover, baseline tonsil obstruction detected by either DISE or mean snoring sound intensity (301–850 Hz), and AHI could significantly predict the surgical response. Our findings suggest that snoring sound detection may be helpful in determining obstruction sites and predict surgical responses. PMID:27471038

  5. 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.

    2016-08-01

    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.

  6. 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

    2014-03-07

    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.

  7. Position-specific prediction of methylation sites from sequence conservation based on information theory.

    Science.gov (United States)

    Shi, Yinan; Guo, Yanzhi; Hu, Yayun; Li, Menglong

    2015-07-23

    Protein methylation plays vital roles in many biological processes and has been implicated in various human diseases. To fully understand the mechanisms underlying methylation for use in drug design and work in methylation-related diseases, an initial but crucial step is to identify methylation sites. The use of high-throughput bioinformatics methods has become imperative to predict methylation sites. In this study, we developed a novel method that is based only on sequence conservation to predict protein methylation sites. Conservation difference profiles between methylated and non-methylated peptides were constructed by the information entropy (IE) in a wider neighbor interval around the methylation sites that fully incorporated all of the environmental information. Then, the distinctive neighbor residues were identified by the importance scores of information gain (IG). The most representative model was constructed by support vector machine (SVM) for Arginine and Lysine methylation, respectively. This model yielded a promising result on both the benchmark dataset and independent test set. The model was used to screen the entire human proteome, and many unknown substrates were identified. These results indicate that our method can serve as a useful supplement to elucidate the mechanism of protein methylation and facilitate hypothesis-driven experimental design and validation.

  8. SPEER-SERVER: a web server for prediction of protein specificity determining sites

    Science.gov (United States)

    Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J.; Panchenko, Anna R.; Chakrabarti, Saikat

    2012-01-01

    Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids’ Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/. PMID:22689646

  9. 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

  10. 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.

  11. 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.

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

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Nielsen, Henrik

    1997-01-01

    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 global sequence information. Furthermore, analysis of false predictions shows that AUGs in frame with the actual start codon are more frequently selected than out-of-frame AUGs, suggesting that our nteworks use reading frame detection. A number of conflicts between neural network predictions and database...... annotations are analysed in detail, leading to identification of possible database errors....

  13. Selection and Assessment of Predictions of the Mars Pathfinder Landing Site

    Science.gov (United States)

    Golombek, M. P.; Moore, H. J.; Haldemann, A. F. C.; Cook, R. A.; Parker, T. J.; Schofield, J. T.

    1998-01-01

    The successful landing of the Mars Pathfinder spacecraft on Mars allows the review of the process of selecting the landing site and assessing predictions made for the site based on Viking and Earth-based data. Selection of the landing site for Mars Pathfinder was a two-phase process. The first phase took place from October 1993 to June 1994 and involved: initial identification of engineering constraints, definition of environmental conditions at the site for spacecraft design, and evaluation of the scientific potential of different landing sites. This phase culminated with the first "Mars Pathfinder Landing Site Workshop", held at the Lunar and Planetary Institute in Houston, Texas on April 18-19, 1994, in which suggested approaches and landing sites were solicited from the entire scientific community. A preliminary site was selected by the project for design purposes in June 1994. The second phase took place from July 1994 to March 1996 and involved: developing criteria for evaluating site safety using images and remote sensing data, testing of the spacecraft and landing subsystems (with design improvements) to establish quantitative engineering constraints on landing site characteristics, evaluating all potential landing sites on Mars, and certification of the site by the project. This phase included a second open workshop, "Mars Pathfinder Landing Site Workshop II: Characteristics of the Ares Vallis Region and Field Trips in the Channeled Scabland, Washington" held in Spokane and Moses Lake September 24-30, 1995 and formal acceptance of the site by NASA Headquarters. Engineering constraints on Pathfinder landing sites were developed from the initial design of the spacecraft and the entry, descent and landing scenario. The site must be within 5 degrees of the subsolar latitude at the time of landing (15N for maximum solar power and flexible communications with Earth. It also must be below 0 km elevation to enable enough time for the parachute to bring the lander

  14. Combining features in a graphical model to predict protein binding sites.

    Science.gov (United States)

    Wierschin, Torsten; Wang, Keyu; Welter, Marlon; Waack, Stephan; Stanke, Mario

    2015-05-01

    Large efforts have been made in classifying residues as binding sites in proteins using machine learning methods. The prediction task can be translated into the computational challenge of assigning each residue the label binding site or non-binding site. Observational data comes from various possibly highly correlated sources. It includes the structure of the protein but not the structure of the complex. The model class of conditional random fields (CRFs) has previously successfully been used for protein binding site prediction. Here, a new CRF-approach is presented that models the dependencies of residues using a general graphical structure defined as a neighborhood graph and thus our model makes fewer independence assumptions on the labels than sequential labeling approaches. A novel node feature "change in free energy" is introduced into the model, which is then denoted by ΔF-CRF. Parameters are trained with an online large-margin algorithm. Using the standard feature class relative accessible surface area alone, the general graph-structure CRF already achieves higher prediction accuracy than the linear chain CRF of Li et al. ΔF-CRF performs significantly better on a large range of false positive rates than the support-vector-machine-based program PresCont of Zellner et al. on a homodimer set containing 128 chains. ΔF-CRF has a broader scope than PresCont since it is not constrained to protein subgroups and requires no multiple sequence alignment. The improvement is attributed to the advantageous combination of the novel node feature with the standard feature and to the adopted parameter training method.

  15. E1DS: catalytic site prediction based on 1D signatures of concurrent conservation.

    Science.gov (United States)

    Chien, Ting-Ying; Chang, Darby Tien-Hao; Chen, Chien-Yu; Weng, Yi-Zhong; Hsu, Chen-Ming

    2008-07-01

    Large-scale automatic annotation of protein sequences remains challenging in postgenomics era. E1DS is designed for annotating enzyme sequences based on a repository of 1D signatures. The employed sequence signatures are derived using a novel pattern mining approach that discovers long motifs consisted of several sequential blocks (conserved segments). Each of the sequential blocks is considerably conserved among the protein members of an EC group. Moreover, a signature includes at least three sequential blocks that are concurrently conserved, i.e. frequently observed together in sequences. In other words, a sequence signature is consisted of residues from multiple regions of the protein sequence, which echoes the observation that an enzyme catalytic site is usually constituted of residues that are largely separated in the sequence. E1DS currently contains 5421 sequence signatures that in total cover 932 4-digital EC numbers. E1DS is evaluated based on a collection of enzymes with catalytic sites annotated in Catalytic Site Atlas. When compared to the famous pattern database PROSITE, predictions based on E1DS signatures are considered more sensitive in identifying catalytic sites and the involved residues. E1DS is available at http://e1ds.ee.ncku.edu.tw/ and a mirror site can be found at http://e1ds.csbb.ntu.edu.tw/.

  16. Short communication: genetic variability in the predicted microRNA target sites of caprine casein genes.

    Science.gov (United States)

    Zidi, A; Amills, M; Tomás, A; Vidal, O; Ramírez, O; Carrizosa, J; Urrutia, B; Serradilla, J M; Clop, A

    2010-04-01

    The main goal of the current work was to identify single nucleotide polymorphisms (SNP) that might create or disrupt microRNA (miRNA) target sites in the caprine casein genes. The 3' untranslated regions of the goat alpha(S1)-, alpha(S2)-, beta-, and kappa-casein genes (CSN1S1, CSN1S2, CSN2, and CSN3, respectively) were resequenced in 25 individuals of the Murciano-Granadina, Cashmere, Canarian, Saanen, and Sahelian breeds. Five SNP were identified through this strategy: c.175C>T at CSN1S1; c.109T>C, c.139G>C, and c.160T>C at CSN1S2; and c.216C>T at CSN2. Analysis with the Patrocles Finder tool predicted that all of these SNP are located within regions complementary to the seed of diverse miRNA sequences. These in silico results suggest that polymorphism at miRNA target sites might have some effect on casein expression. We explored this issue by genotyping the c.175C>T SNP (CSN1S1) in 85 Murciano-Granadina goats with records for milk CSN1S1 concentrations. This substitution destroys a putative target site for miR-101, a miRNA known to be expressed in the bovine mammary gland. Although TT goats had higher levels (6.25 g/L) of CSN1S1 than their CT (6.05 g/L) and CC (6.04 g/L) counterparts, these differences were not significant. Experimental confirmation of the miRNA target sites predicted in the current work and performance of additional association analyses in other goat populations will be an essential step to find out if polymorphic miRNA target sites constitute an important source of variation in casein expression.

  17. Predicting sites of new hemorrhage with amyloid imaging in cerebral amyloid angiopathy

    Science.gov (United States)

    Dierksen, Gregory; Betensky, Rebecca; Gidicsin, Christopher; Halpin, Amy; Becker, Alex; Carmasin, Jeremy; Ayres, Alison; Schwab, Kristin; Viswanathan, Anand; Salat, David; Rosand, Jonathan; Johnson, Keith A.; Greenberg, Steven M.

    2012-01-01

    Objective: We aimed to determine whether amyloid imaging can help predict the location and number of future hemorrhages in cerebral amyloid angiopathy (CAA). Methods: We performed a longitudinal cohort study of 11 patients with CAA without dementia who underwent serial brain MRIs after baseline amyloid imaging with Pittsburgh compound B (PiB). Mean distribution volume ratio (DVR) of PiB was determined at the sites of new micro/macrobleeds identified on follow-up MRI and compared with PiB retention at “simulated” hemorrhages, randomly placed in the same subjects using a probability distribution map of CAA-hemorrhage location. Mean PiB retention at the sites of observed new bleeds was also compared to that in shells concentrically surrounding the bleeds. Finally the association between number of incident bleeds and 3 regional amyloid measures were obtained. Results: Nine of 11 subjects had at least one new microbleed on follow-up MRI (median 4, interquartile range [IQR] 1–9) and 2 had 5 new intracerebral hemorrhages. Mean DVR was greater at the sites of incident bleeds (1.34, 95% confidence interval [CI] 1.23–1.46) than simulated lesions (1.14, 95% CI 1.07–1.22, p < 0.0001) in multivariable models. PiB retention decreased with increasing distance from sites of observed bleeds (p < 0.0001). Mean DVR in a superior frontal/parasagittal region of interest correlated independently with number of future hemorrhages after adjustment for relevant covariates (p = 0.003). Conclusions: Our results provide direct evidence that new CAA-related hemorrhages occur preferentially at sites of increased amyloid deposition and suggest that PiB-PET imaging may be a useful tool in prediction of incident hemorrhages in patients with CAA. PMID:22786597

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Impediments to predicting site response: Seismic property estimation and modeling simplifications

    Science.gov (United States)

    Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Guzina, B.B.

    2009-01-01

    We compare estimates of the empirical transfer function (ETF) to the plane SH-wave theoretical transfer function (TTF) within a laterally constant medium for invasive and noninvasive estimates of the seismic shear-wave slownesses at 13 Kiban-Kyoshin network stations throughout Japan. The difference between the ETF and either of the TTFs is substantially larger than the difference between the two TTFs computed from different estimates of the seismic properties. We show that the plane SH-wave TTF through a laterally homogeneous medium at vertical incidence inadequately models observed amplifications at most sites for both slowness estimates, obtained via downhole measurements and the spectral analysis of surface waves. Strategies to improve the predictions can be separated into two broad categories: improving the measurement of soil properties and improving the theory that maps the 1D soil profile onto spectral amplification. Using an example site where the 1D plane SH-wave formulation poorly predicts the ETF, we find a more satisfactory fit to the ETF by modeling the full wavefield and incorporating spatially correlated variability of the seismic properties. We conclude that our ability to model the observed site response transfer function is limited largely by the assumptions of the theoretical formulation rather than the uncertainty of the soil property estimates.

  3. 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

    2016-01-01

    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.

  4. 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.

  5. A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs.

    Directory of Open Access Journals (Sweden)

    Zhichao Miao

    2015-12-01

    Full Text Available Computational prediction of nucleic acid binding sites in proteins are necessary to disentangle functional mechanisms in most biological processes and to explore the binding mechanisms. Several strategies have been proposed, but the state-of-the-art approaches display a great diversity in i the definition of nucleic acid binding sites; ii the training and test datasets; iii the algorithmic methods for the prediction strategies; iv the performance measures and v the distribution and availability of the prediction programs. Here we report a large-scale assessment of 19 web servers and 3 stand-alone programs on 41 datasets including more than 5000 proteins derived from 3D structures of protein-nucleic acid complexes. Well-defined binary assessment criteria (specificity, sensitivity, precision, accuracy… are applied. We found that i the tools have been greatly improved over the years; ii some of the approaches suffer from theoretical defects and there is still room for sorting out the essential mechanisms of binding; iii RNA binding and DNA binding appear to follow similar driving forces and iv dataset bias may exist in some methods.

  6. 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.

  7. Selection and Assessment of Predictions of the Mars Pathfinder Landing Site

    Science.gov (United States)

    Golombek, M. P.; Moore, H. J.; Haldemann, A. F. C.; Cook, R. A.; Parker, T. J.; Schofield, J. T.

    1998-01-01

    The successful landing of the Mars Pathfinder spacecraft on Mars allows the review of the process of selecting the landing site and assessing predictions made for the site based on Viking and Earth-based data. Selection of the landing site for Mars Pathfinder was a two-phase process. The first phase took place from October 1993 to June 1994 and involved: initial identification of engineering constraints, definition of environmental conditions at the site for spacecraft design, and evaluation of the scientific potential of different landing sites. This phase culminated with the first "Mars Pathfinder Landing Site Workshop", held at the Lunar and Planetary Institute in Houston, Texas on April 18-19, 1994, in which suggested approaches and landing sites were solicited from the entire scientific community. A preliminary site was selected by the project for design purposes in June 1994. The second phase took place from July 1994 to March 1996 and involved: developing criteria for evaluating site safety using images and remote sensing data, testing of the spacecraft and landing subsystems (with design improvements) to establish quantitative engineering constraints on landing site characteristics, evaluating all potential landing sites on Mars, and certification of the site by the project. This phase included a second open workshop, "Mars Pathfinder Landing Site Workshop II: Characteristics of the Ares Vallis Region and Field Trips in the Channeled Scabland, Washington" held in Spokane and Moses Lake September 24-30, 1995 and formal acceptance of the site by NASA Headquarters. Engineering constraints on Pathfinder landing sites were developed from the initial design of the spacecraft and the entry, descent and landing scenario. The site must be within 5 degrees of the subsolar latitude at the time of landing (15N for maximum solar power and flexible communications with Earth. It also must be below 0 km elevation to enable enough time for the parachute to bring the lander

  8. RADIOLYTIC HYDROGEN GENERATION INSAVANNAH RIVER SITE (SRS) HIGH LEVEL WASTETANKS COMPARISON OF SRS AND HANFORDMODELING PREDICTIONS

    Energy Technology Data Exchange (ETDEWEB)

    Crawford, C; Ned Bibler, N

    2009-04-15

    In the high level waste tanks at the Savannah River Site (SRS), hydrogen is produced continuously by interaction of the radiation in the tank with water in the waste. Consequently, the vapor spaces of the tanks are purged to prevent the accumulation of H{sub 2} and possible formation of a flammable mixture in a tank. Personnel at SRS have developed an empirical model to predict the rate of H{sub 2} formation in a tank. The basis of this model is the prediction of the G value for H{sub 2} production. This G value is the number of H{sub 2} molecules produced per 100 eV of radiolytic energy absorbed by the waste. Based on experimental studies it was found that the G value for H{sub 2} production from beta radiation and from gamma radiation were essentially equal. The G value for H{sub 2} production from alpha radiation was somewhat higher. Thus, the model has two equations, one for beta/gamma radiation and one for alpha radiation. Experimental studies have also indicated that both G values are decreased by the presence of nitrate and nitrite ions in the waste. These are the main scavengers for the precursors of H{sub 2} in the waste; thus the equations that were developed predict G values for hydrogen production as a function of the concentrations of these two ions in waste. Knowing the beta/gamma and alpha heat loads in the waste allows one to predict the total generation rate for hydrogen in a tank. With this prediction a ventilation rate can be established for each tank to ensure that a flammable mixture is not formed in the vapor space in a tank. Recently personnel at Hanford have developed a slightly different model for predicting hydrogen G values. Their model includes the same precursor for H{sub 2} as the SRS model but also includes an additional precursor not in the SRS model. Including the second precursor for H{sub 2} leads to different empirical equations for predicting the G values for H{sub 2} as a function of the nitrate and nitrite concentrations in

  9. Archaeology Through Computational Linguistics: Inscription Statistics Predict Excavation Sites of Indus Valley Artifacts.

    Science.gov (United States)

    Recchia, Gabriel L; Louwerse, Max M

    2016-11-01

    Computational techniques comparing co-occurrences of city names in texts allow the relative longitudes and latitudes of cities to be estimated algorithmically. However, these techniques have not been applied to estimate the provenance of artifacts with unknown origins. Here, we estimate the geographic origin of artifacts from the Indus Valley Civilization, applying methods commonly used in cognitive science to the Indus script. We show that these methods can accurately predict the relative locations of archeological sites on the basis of artifacts of known provenance, and we further apply these techniques to determine the most probable excavation sites of four sealings of unknown provenance. These findings suggest that inscription statistics reflect historical interactions among locations in the Indus Valley region, and they illustrate how computational methods can help localize inscribed archeological artifacts of unknown origin. The success of this method offers opportunities for the cognitive sciences in general and for computational anthropology specifically.

  10. 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...

  11. The effects of reading comprehension and launch site on frequency-predictability interactions during paragraph reading.

    Science.gov (United States)

    Whitford, Veronica; Titone, Debra

    2014-01-01

    We used eye movement measures of paragraph reading to examine whether word frequency and predictability interact during the earliest stages of lexical processing, with a specific focus on whether these effects are modulated by individual differences in reading comprehension or launch site (i.e., saccade length between the prior and currently fixated word--a proxy for the amount of parafoveal word processing). The joint impact of frequency and predictability on reading will elucidate whether these variables additively or multiplicatively affect the earliest stages of lexical access, which, in turn, has implications for computational models of eye movements during reading. Linear mixed effects models revealed additive effects during both early- and late-stage reading, where predictability effects were comparable for low- and high-frequency words. Moreover, less cautious readers (e.g., readers who engaged in skimming, scanning, mindless reading) demonstrated smaller frequency effects than more cautious readers. Taken together, our findings suggest that during extended reading, frequency and predictability exert additive influences on lexical and postlexical processing, and that individual differences in reading comprehension modulate sensitivity to the effects of word frequency.

  12. 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.

  13. Predicting Protein-Protein Interaction Sites with a Novel Membership Based Fuzzy SVM Classifier.

    Science.gov (United States)

    Sriwastava, Brijesh K; Basu, Subhadip; Maulik, Ujjwal

    2015-01-01

    Predicting residues that participate in protein-protein interactions (PPI) helps to identify, which amino acids are located at the interface. In this paper, we show that the performance of the classical support vector machine (SVM) algorithm can further be improved with the use of a custom-designed fuzzy membership function, for the partner-specific PPI interface prediction problem. We evaluated the performances of both classical SVM and fuzzy SVM (F-SVM) on the PPI databases of three different model proteomes of Homo sapiens, Escherichia coli and Saccharomyces Cerevisiae and calculated the statistical significance of the developed F-SVM over classical SVM algorithm. We also compared our performance with the available state-of-the-art fuzzy methods in this domain and observed significant performance improvements. To predict interaction sites in protein complexes, local composition of amino acids together with their physico-chemical characteristics are used, where the F-SVM based prediction method exploits the membership function for each pair of sequence fragments. The average F-SVM performance (area under ROC curve) on the test samples in 10-fold cross validation experiment are measured as 77.07, 78.39, and 74.91 percent for the aforementioned organisms respectively. Performances on independent test sets are obtained as 72.09, 73.24 and 82.74 percent respectively. The software is available for free download from http://code.google.com/p/cmater-bioinfo.

  14. Prediction of extreme wind velocity at the site of the Runyang Suspension Bridge

    Institute of Scientific and Technical Information of China (English)

    Yang DENG; You-liang DING; Ai-qun LI; Guang-dong ZHOU

    2011-01-01

    This paper presents a distribution free method for predicting the extreme wind velocity from wind monitoring data at the site of the Runyang Suspension Bridge (RSB),China using the maximum entropy theory.The maximum entropy theory is a rational approach for choosing the most unbiased probability distribution from a small sample,which is consistent with available data and contains a minimum of spurious information.In this paper,the theory is used for estimating a joint probability density function considering the combined action of wind speed and direction based on statistical analysis of wind monitoring data at the site of the RSB.The joint probability distribution model is further used to estimate the extreme wind velocity at the deck level of the RSB.The results of the analysis reveal that the probability density function of the maximum entropy method achieves a result that fits well with the monitoring data.Hypothesis testing shows that the distributions of the wind velocity data collected during the past three years do not obey the Gumbel distribution.Finally,our comparison shows that the wind predictions of the maximum entropy method are higher than that of the Gumbel distribution,but much lower than the design wind speed.

  15. Computational Prediction of O-linked Glycosylation Sites that Preferentially Map on Intrinsically Disordered Regions of Extracellular Proteins

    Directory of Open Access Journals (Sweden)

    Satoshi Fukuchi

    2010-12-01

    Full Text Available O-glycosylation of mammalian proteins is one of the important posttranslational modifications. We applied a support vector machine (SVM to predict whether Ser or Thr is glycosylated, in order to elucidate the O-glycosylation mechanism. O-glycosylated sites were often found clustered along the sequence, whereas other sites were located sporadically. Therefore, we developed two types of SVMs for predicting clustered and isolated sites separately. We found that the amino acid composition was effective for predicting the clustered type, whereas the site-specific algorithm was effective for the isolated type. The highest prediction accuracy for the clustered type was 74%, while that for the isolated type was 79%. The existence frequency of amino acids around the O-glycosylation sites was different in the two types: namely, Pro, Val and Ala had high existence probabilities at each specific position relative to a glycosylation site, especially for the isolated type. Independent component analyses for the amino acid sequences around O-glycosylation sites showed the position-specific existences of the identified amino acids as independent components. The O-glycosylation sites were preferentially located within intrinsically disordered regions of extracellular proteins: particularly, more than 90% of the clustered O-GalNAc glycosylation sites were observed in intrinsically disordered regions. This feature could be the key for understanding the non-conservation property of O-glycosylation, and its role in functional diversity and structural stability.

  16. Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites.

    Science.gov (United States)

    Qin, Zhaohui S; McCue, Lee Ann; Thompson, William; Mayerhofer, Linda; Lawrence, Charles E; Liu, Jun S

    2003-04-01

    The identification of co-regulated genes and their transcription-factor binding sites (TFBS) are key steps toward understanding transcription regulation. In addition to effective laboratory assays, various computational approaches for the detection of TFBS in promoter regions of coexpressed genes have been developed. The availability of complete genome sequences combined with the likelihood that transcription factors and their cognate sites are often conserved during evolution has led to the development of phylogenetic footprinting. The modus operandi of this technique is to search for conserved motifs upstream of orthologous genes from closely related species. The method can identify hundreds of TFBS without prior knowledge of co-regulation or coexpression. Because many of these predicted sites are likely to be bound by the same transcription factor, motifs with similar patterns can be put into clusters so as to infer the sets of co-regulated genes, that is, the regulons. This strategy utilizes only genome sequence information and is complementary to and confirmative of gene expression data generated by microarray experiments. However, the limited data available to characterize individual binding patterns, the variation in motif alignment, motif width, and base conservation, and the lack of knowledge of the number and sizes of regulons make this inference problem difficult. We have developed a Gibbs sampling-based Bayesian motif clustering (BMC) algorithm to address these challenges. Tests on simulated data sets show that BMC produces many fewer errors than hierarchical and K-means clustering methods. The application of BMC to hundreds of predicted gamma-proteobacterial motifs correctly identified many experimentally reported regulons, inferred the existence of previously unreported members of these regulons, and suggested novel regulons.

  17. Prediction of O-glycosylation Sites Using Random Forest and GA-Tuned PSO Technique.

    Science.gov (United States)

    Hassan, Hebatallah; Badr, Amr; Abdelhalim, M B

    2015-01-01

    O-glycosylation is one of the main types of the mammalian protein glycosylation; it occurs on the particular site of serine (S) or threonine (T). Several O-glycosylation site predictors have been developed. However, a need to get even better prediction tools remains. One challenge in training the classifiers is that the available datasets are highly imbalanced, which makes the classification accuracy for the minority class to become unsatisfactory. In our previous work, we have proposed a new classification approach, which is based on particle swarm optimization (PSO) and random forest (RF); this approach has considered the imbalanced dataset problem. The PSO parameters setting in the training process impacts the classification accuracy. Thus, in this paper, we perform parameters optimization for the PSO algorithm, based on genetic algorithm, in order to increase the classification accuracy. Our proposed genetic algorithm-based approach has shown better performance in terms of area under the receiver operating characteristic curve against existing predictors. In addition, we implemented a glycosylation predictor tool based on that approach, and we demonstrated that this tool could successfully identify candidate glycosylation sites in case study protein.

  18. Predicting and mapping potential Whooping Crane stopover habitat to guide site selection for wind energy projects.

    Science.gov (United States)

    Belaire, J Amy; Kreakie, Betty J; Keitt, Timothy; Minor, Emily

    2014-04-01

    Migratory stopover habitats are often not part of planning for conservation or new development projects. We identified potential stopover habitats within an avian migratory flyway and demonstrated how this information can guide the site-selection process for new development. We used the random forests modeling approach to map the distribution of predicted stopover habitat for the Whooping Crane (Grus americana), an endangered species whose migratory flyway overlaps with an area where wind energy development is expected to become increasingly important. We then used this information to identify areas for potential wind power development in a U.S. state within the flyway (Nebraska) that minimize conflicts between Whooping Crane stopover habitat and the development of clean, renewable energy sources. Up to 54% of our study area was predicted to be unsuitable as Whooping Crane stopover habitat and could be considered relatively low risk for conflicts between Whooping Cranes and wind energy development. We suggest that this type of analysis be incorporated into the habitat conservation planning process in areas where incidental take permits are being considered for Whooping Cranes or other species of concern. Field surveys should always be conducted prior to construction to verify model predictions and understand baseline conditions.

  19. 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.

  20. 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.

  1. Feature Selection Combined with Neural Network Structure Optimization for HIV-1 Protease Cleavage Site Prediction

    Directory of Open Access Journals (Sweden)

    Hui Liu

    2015-01-01

    Full Text Available It is crucial to understand the specificity of HIV-1 protease for designing HIV-1 protease inhibitors. In this paper, a new feature selection method combined with neural network structure optimization is proposed to analyze the specificity of HIV-1 protease and find the important positions in an octapeptide that determined its cleavability. Two kinds of newly proposed features based on Amino Acid Index database plus traditional orthogonal encoding features are used in this paper, taking both physiochemical and sequence information into consideration. Results of feature selection prove that p2, p1, p1′, and p2′ are the most important positions. Two feature fusion methods are used in this paper: combination fusion and decision fusion aiming to get comprehensive feature representation and improve prediction performance. Decision fusion of subsets that getting after feature selection obtains excellent prediction performance, which proves feature selection combined with decision fusion is an effective and useful method for the task of HIV-1 protease cleavage site prediction. The results and analysis in this paper can provide useful instruction and help designing HIV-1 protease inhibitor in the future.

  2. 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.

  3. 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.

  4. Evaluation of different approaches for identifying optimal sites to predict mean hillslope soil moisture content

    Science.gov (United States)

    Liao, Kaihua; Zhou, Zhiwen; Lai, Xiaoming; Zhu, Qing; Feng, Huihui

    2017-04-01

    The identification of representative soil moisture sampling sites is important for the validation of remotely sensed mean soil moisture in a certain area and ground-based soil moisture measurements in catchment or hillslope hydrological studies. Numerous approaches have been developed to identify optimal sites for predicting mean soil moisture. Each method has certain advantages and disadvantages, but they have rarely been evaluated and compared. In our study, surface (0-20 cm) soil moisture data from January 2013 to March 2016 (a total of 43 sampling days) were collected at 77 sampling sites on a mixed land-use (tea and bamboo) hillslope in the hilly area of Taihu Lake Basin, China. A total of 10 methods (temporal stability (TS) analyses based on 2 indices, K-means clustering based on 6 kinds of inputs and 2 random sampling strategies) were evaluated for determining optimal sampling sites for mean soil moisture estimation. They were TS analyses based on the smallest index of temporal stability (ITS, a combination of the mean relative difference and standard deviation of relative difference (SDRD)) and based on the smallest SDRD, K-means clustering based on soil properties and terrain indices (EFs), repeated soil moisture measurements (Theta), EFs plus one-time soil moisture data (EFsTheta), and the principal components derived from EFs (EFs-PCA), Theta (Theta-PCA), and EFsTheta (EFsTheta-PCA), and global and stratified random sampling strategies. Results showed that the TS based on the smallest ITS was better (RMSE = 0.023 m3 m-3) than that based on the smallest SDRD (RMSE = 0.034 m3 m-3). The K-means clustering based on EFsTheta (-PCA) was better (RMSE sampling design stratified by the land use was more efficient than the global random method. Forty and 60 sampling sites are needed for stratified sampling and global sampling respectively to make their performances comparable to the best K-means method (EFsTheta-PCA). Overall, TS required only one site, but its

  5. Finemet cavity impedance studies

    CERN Document Server

    Persichelli, S; Migliorati, M; Salvant, B

    2013-01-01

    The aim of the study is to evaluate the impedance of the Finemet kicker cavity to be installed in the PS straight section 02 during LS1, under realistic assumptions of bunch length. Time domain simulations with CST Particle Studio have been performed in order to get the impedance of the cavity and make a comparison with the longitudinal impedance measured for a single cell prototype. The study has been performed on simplified 3D geometries imported from a mechanical CATIA drawing, assuming that the simplications have small impact on the nal results. Simulations confirmed that the longitudinal impedance observed with measurements can be excited by bunches circulating in the PS. In the six-cells Finemet cavity, PS bunches circulating in the center can excite a longitudinal impedance, the real part of which has a maximum of 2 kOhm at 4 MHz. This mode does not seem to have any transverse component. All the eigenmodes of the cavity are strongly damped by the Finemet rings: we predict to have no issues regarding tr...

  6. Prediction of primate splice site using inhomogeneous Markov chain and neural network.

    Science.gov (United States)

    Liu, Libin; Ho, Yee-Kin; Yau, Stephen

    2007-07-01

    The inhomogeneous Markov chain model is used to discriminate acceptor and donor sites in genomic DNA sequences. It outperforms statistical methods such as homogeneous Markov chain model, higher order Markov chain and interpolated Markov chain models, and machine-learning methods such as k-nearest neighbor and support vector machine as well. Besides its high accuracy, another advantage of inhomogeneous Markov chain model is its simplicity in computation. In the three states system (acceptor, donor, and neither), the inhomogeneous Markov chain model is combined with a three-layer feed forward neural network. Using this combined system 3175 primate splice-junction gene sequences have been tested, with a prediction accuracy of greater than 98%.

  7. 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 well above that of the publicly available chloroplast localization predictor PSORT. Cleavage sites are predicted using a scoring matrix derived by an automatic motif-finding algorithm. Approximately 60% of the known cleavage sites in our sequence collection were predicted to within +/-2 residues from...

  8. Cell-type specificity of ChIP-predicted transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Håndstad Tony

    2012-08-01

    Full Text Available Abstract Background Context-dependent transcription factor (TF binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq identifies genome-wide TF binding sites for one particular context—the cells used in the experiment. But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding? Results We compared ChIP-seq data on TF binding for multiple TFs in two different cell types and found that on average only a third of ChIP-seq peak regions are common to both cell types. Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whereas chromatin differences characterize cell-type specific TF binding. We also find, however, that genotype differences between the cell types can explain differences in binding. Moreover, ChIP-seq signal intensity and peak clustering are the strongest predictors of common peaks. Compared with strong peaks located in regions containing peaks for multiple transcription factors, weak and isolated peaks are less common between the cell types and are less associated with data that indicate regulatory activity. Conclusions Together, the results suggest that experimental noise is prevalent among weak peaks, whereas strong and clustered peaks represent high-confidence binding events that often occur in other cellular contexts. Nevertheless, 30-40% of the strongest and most clustered peaks show context-dependent regulation. We show that by combining signal intensity with additional data—ranging from context independent information such as binding site conservation and position weight matrix scores to context dependent chromatin structure—we can predict whether a ChIP-seq peak is likely to be present in other cellular contexts.

  9. Prediction of evacuation time for emergency planning zone of Uljin nuclear site

    Energy Technology Data Exchange (ETDEWEB)

    Jeon, In Young; Lee, Jai Ki [Hanyang Univ., Seoul (Korea, Republic of)

    2002-09-15

    The time for evacuation of residents in Emergency Planning Zone (EPZ) of Uljin nuclear site in case of a radiological emergency was estimated with traffic analysis. Evacuees were classified into 4 groups by considering population density, local jurisdictions, and whether they are residents or transients. The survey to investigate the behavioral characteristics of the residents was made for 200 households and included a hypothetical scenario explaining the accident situation and questions such as dwelling place, time demand for evacuation preparation, transportation means for evacuation, sheltering place, and evacuation direction. The microscopic traffic simulation model, CORSIM, was used to simulate the behavior of evacuating vehicles on networks. The results showed that the evacuation time required for total vehicles to move out from EPZ took longer in the daytime than at night in spite that the delay times at intersections were longer at night than in the daytime. This was analyzed due to the differences of the trip generation time distribution. To validate whether the CORSIM model can appropriately simulate the congested traffic phenomena assumable in case of emergency, a benchmark study was conducted at an intersection without an actuated traffic signal near Uljin site during the traffic peak-time in the morning. This study indicated that the predicted output by the CORSIM model was in good agreement with the observed data, satisfying the purpose of this study.

  10. SNP2TFBS – a database of regulatory SNPs affecting predicted transcription factor binding site affinity

    Science.gov (United States)

    Kumar, Sunil; Ambrosini, Giovanna; Bucher, Philipp

    2017-01-01

    SNP2TFBS is a computational resource intended to support researchers investigating the molecular mechanisms underlying regulatory variation in the human genome. The database essentially consists of a collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. A SNP's effect on TF binding is estimated based on a position weight matrix (PWM) model for the binding specificity of the corresponding factor. These data files are regenerated at regular intervals by an automatic procedure that takes as input a reference genome, a comprehensive SNP catalogue and a collection of PWMs. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs. Homepage: http://ccg.vital-it.ch/snp2tfbs/. PMID:27899579

  11. GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs.

    Science.gov (United States)

    Zhao, Qi; Xie, Yubin; Zheng, Yueyuan; Jiang, Shuai; Liu, Wenzhong; Mu, Weiping; Liu, Zexian; Zhao, Yong; Xue, Yu; Ren, Jian

    2014-07-01

    Small ubiquitin-like modifiers (SUMOs) regulate a variety of cellular processes through two distinct mechanisms, including covalent sumoylation and non-covalent SUMO interaction. The complexity of SUMO regulations has greatly hampered the large-scale identification of SUMO substrates or interaction partners on a proteome-wide level. In this work, we developed a new tool called GPS-SUMO for the prediction of both sumoylation sites and SUMO-interaction motifs (SIMs) in proteins. To obtain an accurate performance, a new generation group-based prediction system (GPS) algorithm integrated with Particle Swarm Optimization approach was applied. By critical evaluation and comparison, GPS-SUMO was demonstrated to be substantially superior against other existing tools and methods. With the help of GPS-SUMO, it is now possible to further investigate the relationship between sumoylation and SUMO interaction processes. A web service of GPS-SUMO was implemented in PHP+JavaScript and freely available at http://sumosp.biocuckoo.org.

  12. A Text Analysis Based Seamless Framework for Predicting Human Personality Traits from Social Networking Sites

    Directory of Open Access Journals (Sweden)

    Harish Kumar

    2012-09-01

    Full Text Available Predicting human behavior based on the usage of text on social networking sites can be a challenging area of interest to a particular community. Text mining being a major interest in Data Mining has vast applications in various fields. Clients can assess an individual’s behavior using the proposed framework that is based on person’s textual interaction with other people. In this paper, a framework is proposed for predicting human behavior in three phases- Text Extraction, Text cleaning and Text Analysis. For cleaning text, all the stop words have been removed and then the text is utilized for further processing. Then, the terms from the text are clustered based on semantic similarity and then gets associated with respective physiological parameters that identify a human behavior. This application is best suited for the fields of Criminal Sciences, Medical Sciences, Human Resource Department and Political Science and even for Matrimonial purposes. The proposed framework is applied on some famous world known celebrities and the results are quite encouraging.

  13. PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse

    Science.gov (United States)

    Reuter, Kerstin; Helms, Volkhard

    2016-01-01

    Translation of mRNA sequences into proteins typically starts at an AUG triplet. In rare cases, translation may also start at alternative non–AUG codons located in the annotated 5’ UTR which leads to an increased regulatory complexity. Since ribosome profiling detects translational start sites at the nucleotide level, the properties of these start sites can then be used for the statistical evaluation of functional open reading frames. We developed a linear regression approach to predict in–frame and out–of–frame translational start sites within the 5’ UTR from mRNA sequence information together with their translation initiation confidence. Predicted start codons comprise AUG as well as near–cognate codons. The underlying datasets are based on published translational start sites for human HEK293 and mouse embryonic stem cells that were derived by the original authors from ribosome profiling data. The average prediction accuracy of true vs. false start sites for HEK293 cells was 80%. When applied to mouse mRNA sequences, the same model predicted translation initiation sites observed in mouse ES cells with an accuracy of 76%. Moreover, we illustrate the effect of in silico mutations in the flanking sequence context of a start site on the predicted initiation confidence. Our new webservice PreTIS visualizes alternative start sites and their respective ORFs and predicts their ability to initiate translation. Solely, the mRNA sequence is required as input. PreTIS is accessible at http://service.bioinformatik.uni-saarland.de/pretis. PMID:27768687

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Interactome-wide prediction of protein-protein binding sites reveals effects of protein sequence variation in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Felipe Leal Valentim

    Full Text Available The specificity of protein-protein interactions is encoded in those parts of the sequence that compose the binding interface. Therefore, understanding how changes in protein sequence influence interaction specificity, and possibly the phenotype, requires knowing the location of binding sites in those sequences. However, large-scale detection of protein interfaces remains a challenge. Here, we present a sequence- and interactome-based approach to mine interaction motifs from the recently published Arabidopsis thaliana interactome. The resultant proteome-wide predictions are available via www.ab.wur.nl/sliderbio and set the stage for further investigations of protein-protein binding sites. To assess our method, we first show that, by using a priori information calculated from protein sequences, such as evolutionary conservation and residue surface accessibility, we improve the performance of interface prediction compared to using only interactome data. Next, we present evidence for the functional importance of the predicted sites, which are under stronger selective pressure than the rest of protein sequence. We also observe a tendency for compensatory mutations in the binding sites of interacting proteins. Subsequently, we interrogated the interactome data to formulate testable hypotheses for the molecular mechanisms underlying effects of protein sequence mutations. Examples include proteins relevant for various developmental processes. Finally, we observed, by analysing pairs of paralogs, a correlation between functional divergence and sequence divergence in interaction sites. This analysis suggests that large-scale prediction of binding sites can cast light on evolutionary processes that shape protein-protein interaction networks.

  19. New Method to Improve the Accelerating Gradient of Superconducting Cavity

    CERN Document Server

    Liu, Zhenchao

    2013-01-01

    Quench is a common phenomenon in a superconducting cavity and often limits the accelerating gradient of the cavity. Accurate location of the quench site can be located by second sound detection. For multi-cell superconducting cavity, one defect may cause the cell with defect quenches and then the whole cavity quenches. Now we proposed a new method to eliminate the bad influence of the quench cell to the whole cavity.

  20. Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics

    Science.gov (United States)

    Bhakat, Soumendranath; Söderhjelm, Pär

    2017-01-01

    The funnel metadynamics method enables rigorous calculation of the potential of mean force along an arbitrary binding path and thereby evaluation of the absolute binding free energy. A problem of such physical paths is that the mechanism characterizing the binding process is not always obvious. In particular, it might involve reorganization of the solvent in the binding site, which is not easily captured with a few geometrically defined collective variables that can be used for biasing. In this paper, we propose and test a simple method to resolve this trapped-water problem by dividing the process into an artificial host-desolvation step and an actual binding step. We show that, under certain circumstances, the contribution from the desolvation step can be calculated without introducing further statistical errors. We apply the method to the problem of predicting host-guest binding free energies in the SAMPL5 blind challenge, using two octa-acid hosts and six guest molecules. For one of the hosts, well-converged results are obtained and the prediction of relative binding free energies is the best among all the SAMPL5 submissions. For the other host, which has a narrower binding pocket, the statistical uncertainties are slightly higher; longer simulations would therefore be needed to obtain conclusive results.

  1. A Model for Predicting Late Prehistoric Architectural Sites at the Pinon Canyon Maneuver Site in Southeastern Colorado

    Science.gov (United States)

    2007-01-01

    Stage Canyon ..................... 44 1.43 Photograph of Rio Grande rock art along the Puragatoire River ...................................... 45... Sangre de Cristo Mountains and south of the Arkansas River. It is likely Apishapa peoples also lived along the northwestern edge of the Oklahoma...that Athabaskans replaced the Apishapa at the end of the phase. Some rock art sites along the Purgatoire River display Rio Grande rock art tradition

  2. Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome.

    Science.gov (United States)

    Zuo, Yongchun; Zhang, Pengfei; Liu, Li; Li, Tao; Peng, Yong; Li, Guangpeng; Li, Qianzhong

    2014-09-01

    More and more reported results of nucleosome positioning and histone modifications showed that DNA structure play a well-established role in splicing. In this study, a set of DNA geometric flexibility parameters originated from molecular dynamics (MD) simulations were introduced to discuss the structure organization around splice sites at the DNA level. The obtained profiles of specific flexibility/stiffness around splice sites indicated that the DNA physical-geometry deformation could be used as an alternative way to describe the splicing junction region. In combination with structural flexibility as discriminatory parameter, we developed a hybrid computational model for predicting potential splicing sites. And the better prediction performance was achieved when the benchmark dataset evaluated. Our results showed that the mechanical deformability character of a splice junction is closely correlated with both the splice site strength and structural information in its flanking sequences.

  3. 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.

  4. Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context.

    Science.gov (United States)

    Kel, Alexander E; Niehof, Monika; Matys, Volker; Zemlin, Rüdiger; Borlak, Jürgen

    2008-01-01

    We report an application of machine learning algorithms that enables prediction of the functional context of transcription factor binding sites in the human genome. We demonstrate that our method allowed de novo identification of hepatic nuclear factor (HNF)4alpha binding sites and significantly improved an overall recognition of faithful HNF4alpha targets. When applied to published findings, an unprecedented high number of false positives were identified. The technique can be applied to any transcription factor.

  5. 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.

  6. Cavity Optomechanical Magnetometer

    CERN Document Server

    Forstner, S; Knittel, J; van Ooijen, E D; Swaim, J D; Harris, G I; Szorkovszky, A; Bowen, W P; Rubinsztein-Dunlop, H

    2011-01-01

    A cavity optomechanical magnetometer is demonstrated where the magnetic field induced expansion of a magnetostrictive material is transduced onto the physical structure of a highly compliant optical microresonator. The resulting motion is read out optically with ultra-high sensitivity. Detecting the magnetostrictive deformation of Terfenol-D with a toroidal whispering gallery mode (TWGM) resonator a peak sensitivity of 400 nT/Hz^.5 was achieved with theoretical modelling predicting that sensitivities of up to 500 fT/Hz^.5 may be possible. This chip-based magnetometer combines high-sensitivity and large dynamic range with small size and room temperature operation.

  7. Cavity optomechanical magnetometer.

    Science.gov (United States)

    Forstner, S; Prams, S; Knittel, J; van Ooijen, E D; Swaim, J D; Harris, G I; Szorkovszky, A; Bowen, W P; Rubinsztein-Dunlop, H

    2012-03-23

    A cavity optomechanical magnetometer is demonstrated. The magnetic-field-induced expansion of a magnetostrictive material is resonantly transduced onto the physical structure of a highly compliant optical microresonator and read out optically with ultrahigh sensitivity. A peak magnetic field sensitivity of 400  nT  Hz(-1/2) is achieved, with theoretical modeling predicting the possibility of sensitivities below 1  pT  Hz(-1/2). This chip-based magnetometer combines high sensitivity and large dynamic range with small size and room temperature operation.

  8. 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.

  9. Sterility of the uterine cavity

    DEFF Research Database (Denmark)

    Møller, Birger R.; Kristiansen, Frank V.; Thorsen, Poul;

    1995-01-01

    from the same sites. Nearly a quarter of all the patients harbored one or more microorganisms in the uterus, mostly Gardnerella vaginalis, Enterobacter and Streptococcus agalactiae. We found that in a significant number of cases, the uterine cavity is colonized with potentially pathogenic organisms...

  10. NetPhosYeast: prediction of protein phosphorylation sites in yeast

    DEFF Research Database (Denmark)

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

    2007-01-01

    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...

  11. Neural network model for the prediction of PM10 daily concentrations in two sites in the Western Mediterranean.

    Science.gov (United States)

    de Gennaro, Gianluigi; Trizio, Livia; Di Gilio, Alessia; Pey, Jorge; Pérez, Noemi; Cusack, Michael; Alastuey, Andrés; Querol, Xavier

    2013-10-01

    An artificial neural network (ANN) was developed and tested to forecast PM10 daily concentration in two contrasted environments in NE Spain, a regional background site (Montseny), and an urban background site (Barcelona-CSIC), which was highly influenced by vehicular emissions. In order to predict 24-h average PM10 concentrations, the artificial neural network previously developed by Caselli et al. (2009) was improved by using hourly PM concentrations and deterministic factors such as a Saharan dust alert. In particular, the model input data for prediction were the hourly PM10 concentrations 1-day in advance, local meteorological data and information about air masses origin. The forecasted performance indexes for both sites were calculated and they showed better results for the regional background site in Montseny (R(2)=0.86, SI=0.75) than for urban site in Barcelona (R(2)=0.73, SI=0.58), influenced by local and sometimes unexpected sources. Moreover, a sensitivity analysis conducted to understand the importance of the different variables included among the input data, showed that local meteorology and air masses origin are key factors in the model forecasts. This result explains the reason for the improvement of ANN's forecasting performance at the Montseny site with respect to the Barcelona site. Moreover, the artificial neural network developed in this work could prove useful to predict PM10 concentrations, especially, at regional background sites such as those on the Mediterranean Basin which are primarily affected by long-range transports. Hence, the artificial neural network presented here could be a powerful tool for obtaining real time information on air quality status and could aid stakeholders in their development of cost-effective control strategies.

  12. 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/.

  13. Dynamic neural networks for real-time water level predictions of sewerage systems-covering gauged and ungauged sites

    Directory of Open Access Journals (Sweden)

    Yen-Ming Chiang

    2010-07-01

    Full Text Available In this research, we propose recurrent neural networks (RNNs to build a relationship between rainfalls and water level patterns of an urban sewerage system based on historical torrential rain/storm events. The RNN allows signals to propagate in both forward and backward directions, which offers the network dynamic memories. Besides, the information at the current time-step with a feedback operation can yield a time-delay unit that provides internal input information at the next time-step to effectively deal with time-varying systems. The RNN is implemented at both gauged and ungauged sites for 5-, 10-, 15-, and 20-min-ahead water level predictions. The results show that the RNN is capable of learning the nonlinear sewerage system and producing satisfactory predictions at the gauged sites. Concerning the ungauged sites, there are no historical data of water level to support prediction. In order to overcome such problem, a set of synthetic data, generated from a storm water management model (SWMM under cautious verification process of applicability based on the data from nearby gauging stations, are introduced as the learning target to the training procedure of the RNN and moreover evaluating the performance of the RNN at the ungauged sites. The results demonstrate that the potential role of the SWMM coupled with nearby rainfall and water level information can be of great use in enhancing the capability of the RNN at the ungauged sites. Hence we can conclude that the RNN is an effective and suitable model for successfully predicting the water levels at both gauged and ungauged sites in urban sewerage systems.

  14. 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

    Directory of Open Access Journals (Sweden)

    Dörte Wolf

    2015-01-01

    Full Text Available 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–<4 years, average age 1.8 years, treated only with 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.

  15. Prediction of suspended-sediment concentrations at selected sites in the Fountain Creek watershed, Colorado, 2008-09

    Science.gov (United States)

    Stogner, Robert W.; Nelson, Jonathan M.; McDonald, Richard R.; Kinzel, Paul J.; Mau, David P.

    2013-01-01

    In 2008, the U.S. Geological Survey (USGS), in cooperation with Pikes Peak Area Council of Governments, Colorado Water Conservation Board, Colorado Springs City Engineering, and the Lower Arkansas Valley Water Conservancy District, began a small-scale pilot study to evaluate the effectiveness of the use of a computational model of streamflow and suspended-sediment transport for predicting suspended-sediment concentrations and loads in the Fountain Creek watershed in Colorado. Increased erosion and sedimentation damage have been identified by the Fountain Creek Watershed Plan as key problems within the watershed. A recommendation in the Fountain Creek Watershed plan for management of the basin is to establish measurable criteria to determine if progress in reducing erosion and sedimentation damage is being made. The major objective of this study was to test a computational method to predict local suspended-sediment loads at two sites with different geomorphic characteristics in order to evaluate the feasibility of using such an approach to predict local suspended-sediment loads throughout the entire watershed. Detailed topographic surveys, particle-size data, and suspended-sediment samples were collected at two gaged sites: Monument Creek above Woodmen Road at Colorado Springs, Colorado (USGS gage 07103970), and Sand Creek above mouth at Colorado Springs, Colorado (USGS gage 07105600). These data were used to construct three-dimensional computational models of relatively short channel reaches at each site. The streamflow component of these models predicted a spatially distributed field of water-surface elevation, water velocity, and bed shear stress for a range of stream discharges. Using the model predictions, along with measured particle sizes, the sediment-transport component of the model predicted the suspended-sediment concentration throughout the reach of interest. These computed concentrations were used with predicted flow patterns and channel morphology to

  16. 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.

  17. Using Geoarchaeology to Predict the Presence of Offshore Sites in Southern California (Invited)

    Science.gov (United States)

    Hildebrand, J.; York, A.

    2013-12-01

    During the late Pleistocene and early Holocene, the continental shelves off southern California were exposed and available for occupation by prehistoric peoples. Subsequent sealevel rise and marine transgression of the continental shelf resulted in both submergence and potentially reworking of site materials. A model has been developed and tested for continental shelf site locations, using geoarchaeological methods including seismic reflection imaging, coring, and invertebrate fossil identification. In this model, such factors as topography, rate of sea level rise, sediment thickness and context of deposition are all applied to the assessment of potential for site presence and preservation. The most desirable locations for site preservation are found in offshore valley floors and flanks, whereas adjacent uplands are prone to site erosion. Cultural materials from the La Jollan Complex were recovered from two separate offshore sites by large-scale dredging operations. Transgression at these sites occurred prior to about 8000 B.P.. The relation of these cultural materials to the offshore site location model will be discussed.

  18. Unusual adsorption site behavior in PCN-14 metal-organic framework predicted from Monte Carlo simulation.

    Science.gov (United States)

    Lucena, Sebastião M P; Mileo, Paulo G M; Silvino, Pedro F G; Cavalcante, Célio L

    2011-12-01

    The adsorption equilibrium of methane in PCN-14 was simulated by the Monte Carlo technique in the grand canonical ensemble. A new force field was proposed for the methane/PCN-14 system, and the temperature dependence of the molecular siting was investigated. A detailed study of the statistics of the center of mass and potential energy showed a surprising site behavior with no energy barriers between weak and strong sites, allowing open metal sites to guide methane molecules to other neighboring sites. Moreover, this study showed that a model assuming weakly adsorbing open metal clusters in PCN-14, densely populated only at low temperatures (below 150 K), can explain published experimental data. These results also explain previously observed discrepancies between neutron diffraction experiments and Monte Carlo simulations.

  19. 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.

  20. ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.

    Science.gov (United States)

    Konc, Janez; Miller, Benjamin T; Štular, Tanja; Lešnik, Samo; Woodcock, H Lee; Brooks, Bernard R; Janežič, Dušanka

    2015-11-23

    Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( http://probis.cmm.ki.si ) and CHARMMing ( http://www.charmming.org ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at http://probis.nih.gov.

  1. 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

  2. WAsP prediction errors due to site orography[Wind Atlas Analysis and Application Program

    Energy Technology Data Exchange (ETDEWEB)

    Bowen, A.J.; Mortensen, N.G.

    2004-12-01

    The influence of rugged terrain on the prediction accuracy of the Wind Atlas Analysis and Application Program (WAsP) is investigated using a case study of field measurements taken in rugged terrain. The parameters that could cause substantial errors in a prediction are identified and discussed. In particular, the effects from extreme orography are investigated. A suitable performance indicator is developed which predicts the sign and approximate magnitude of such errors due to orography. This procedure allows the user to assess the consequences of using WAsP outside its operating envelope and could provide a means of correction for rugged terrain effects. (au)

  3. Tumor characteristics and metastatic sites may predict bevacizumab efficacy in the first-line treatment of metastatic colorectal cancer

    OpenAIRE

    Varol, Umut; Oktay, Esin; YILDIRIM, Mustafa; SURMELI, ZEKI GOKHAN; Dirican, Ahmet; Meydan, Nezih; KARACA, BURCAK; Karabulut, Bulent; Uslu, Ruchan

    2013-01-01

    Colorectal cancer (CRC) is among the most frequently diagnosed cancers and a major cause of cancer-related mortality worldwide. The aim of the present study was to determine whether there was an improvement in the time to disease progression (TTP) in patients with metastatic colorectal cancer (mCRC) treated with first-line bevacizumab plus chemotherapy, according to tumor characteristics and metastatic sites. Tumor characteristics and tumor burden were considered to be predictive markers of t...

  4. 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-w......-wide data sets. Discrimination between cleaved signal peptides and uncleaved N-terminal signal-anchor sequences is also possible, though with lower precision....

  5. pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model

    Directory of Open Access Journals (Sweden)

    Schneider Georg

    2007-01-01

    Full Text Available Abstract Background Protein kinase A (cAMP-dependent kinase, PKA is a serine/threonine kinase, for which ca. 150 substrate proteins are known. Based on a refinement of the recognition motif using the available experimental data, we wished to apply the simplified substrate protein binding model for accurate prediction of PKA phosphorylation sites, an approach that was previously successful for the prediction of lipid posttranslational modifications and of the PTS1 peroxisomal translocation signal. Results Approximately 20 sequence positions flanking the phosphorylated residue on both sides have been found to be restricted in their sequence variability (region -18...+23 with the site at position 0. The conserved physical pattern can be rationalized in terms of a qualitative binding model with the catalytic cleft of the protein kinase A. Positions -6...+4 surrounding the phosphorylation site are influenced by direct interaction with the kinase in a varying degree. This sequence stretch is embedded in an intrinsically disordered region composed preferentially of hydrophilic residues with flexible backbone and small side chain. This knowledge has been incorporated into a simplified analytical model of productive binding of substrate proteins with PKA. Conclusion The scoring function of the pkaPS predictor can confidently discriminate PKA phosphorylation sites from serines/threonines with non-permissive sequence environments (sensitivity of ~96% at a specificity of ~94%. The tool "pkaPS" has been applied on the whole human proteome. Among new predicted PKA targets, there are entirely uncharacterized protein groups as well as apparently well-known families such as those of the ribosomal proteins L21e, L22 and L6. Availability The supplementary data as well as the prediction tool as WWW server are available at http://mendel.imp.univie.ac.at/sat/pkaPS. Reviewers Erik van Nimwegen (Biozentrum, University of Basel, Switzerland, Sandor Pongor (International

  6. 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.

  7. JET2 Viewer: a database of predicted multiple, possibly overlapping, protein–protein interaction sites for PDB structures

    Science.gov (United States)

    Ripoche, Hugues; Laine, Elodie; Ceres, Nicoletta; Carbone, Alessandra

    2017-01-01

    The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET2 at large-scale on more than 20 000 chains. JET2 strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET2 analyses. Predictions were evaluated on more than 15 000 experimentally characterized protein interfaces. This is, to our knowledge, the largest evaluation of a protein binding site prediction method. The overall performance of JET2 on all interfaces are: Sen = 52.52, PPV = 51.24, Spe = 80.05, Acc = 75.89. The data can be used to foster new strategies for protein–protein interactions modulation and interaction surface redesign. PMID:27899675

  8. 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.

  9. Verification of geomechanical integrity and prediction of long-term mineral trapping for the Ketzin CO2 storage pilot site

    Science.gov (United States)

    Kempka, Thomas; De Lucia, Marco; Kühn, Michael

    2014-05-01

    Static and dynamic numerical modelling generally accompany the entire CO2 storage site life cycle. Thereto, it is required to match the employed models with field observations on a regular basis in order to predict future site behaviour. We investigated the coupled processes at the Ketzin CO2 storage pilot site [1] using a model coupling concept focusing on the temporal relevance of processes involved (hydraulic, chemical and mechanical) at given time-scales (site operation, abandonment and long-term stabilization). For that purpose, long-term dynamic multi-phase flow simulations [2], [3] established the basis for all simulations discussed in the following. Hereby, pressure changes resulting in geomechanical effects are largest during site operation, whereas geochemical reactions are governed by slow kinetics resulting in a long-term stabilization. To account for mechanical integrity, which may be mainly affected during site operation, we incorporated a regional-scale coupled hydro-mechanical model. Our simulation results show maximum ground surface displacements of about 4 mm, whereas shear and tensile failure are not observed. Consequently, the CO2 storage operation at the Ketzin pilot site does not compromise reservoir, caprock and fault integrity. Chemical processes responsible for mineral trapping are expected to mainly occur during long-term stabilization at the Ketzin pilot site [4]. Hence, our previous assessment [3] was extended by integrating two long-term mineral trapping scenarios. Thereby, mineral trapping contributes to the trapping mechanisms with 11.7 % after 16,000 years of simulation in our conservative and with 30.9 % in our maximum reactivity scenarios. Dynamic flow simulations indicate that only 0.2 % of the CO2 injected (about 67,270 t CO2 in total) is in gaseous state, but structurally trapped after 16,000 years. Depending on the studied long-term scenario, CO2 dissolution is the dominating trapping mechanism with 68.9 % and 88

  10. 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

  11. 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

  12. Using Tree-Ring Width Data From 1000 Sites to Predict how American Forests Will Respond to Climate Change

    Science.gov (United States)

    Williams, P.; Still, C. J.; Leavitt, S. W.; Fischer, D. T.

    2007-12-01

    Beginning in the early 1900s, tree-ring scientists began analyzing the relative widths of annual growth rings preserved in the cross-sections of trees. Over the years, many ring-width index chronologies, each representing a specific site and species, have been developed and analyzed to infer details regarding past climate, growth response to environmental fluctuation, fire activity, logging practices by past societies, and more. Of the many ring-width chronologies constructed, 1035 represent sites within the continental United States and have been published online within The International Tree-Ring Data Bank as of September 2007 (ITRDB, http://www.ncdc.noaa.gov/paleo/treering.html). Approximately 85% of these sites are located west of the Mississippi River. Here we present results from a three-step study, using this large reserve of tree-growth data to determine how various tree species in various regions have responded to climate fluctuations in the past and how they can be expected to respond to future change. In the first step, we used linear regression to compare each time series of ring-width index values to a suite of local monthly climate variables that may influence tree growth, such as rainfall, temperature, and drought severity (PDSI). We identified the range of months (of a 24- month period) during which each climate parameter most strongly affects growth by comparing Pearson correlation coefficients. In the second step, we identified all sites where at least one climate parameter, during some rage of months, correlates significantly (95% confidence) with ring-width index values. For each of these sites, we constructed a growth model that uses each significantly correlating climate parameter as a growth predictor. In the third step, we applied the growth model to predict the next 100 years of growth response to a monthly climate forecast created by the Hadley Centre for Climate Prediction and Research. This forecast (HadCM3 IS92a) assumes a business as

  13. 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

  14. Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models.

    Science.gov (United States)

    Park, Byungkyu; Im, Jinyong; Tuvshinjargal, Narankhuu; Lee, Wook; Han, Kyungsook

    2014-11-01

    As many structures of protein-DNA complexes have been known in the past years, several computational methods have been developed to predict DNA-binding sites in proteins. However, its inverse problem (i.e., predicting protein-binding sites in DNA) has received much less attention. One of the reasons is that the differences between the interaction propensities of nucleotides are much smaller than those between amino acids. Another reason is that DNA exhibits less diverse sequence patterns than protein. Therefore, predicting protein-binding DNA nucleotides is much harder than predicting DNA-binding amino acids. We computed the interaction propensity (IP) of nucleotide triplets with amino acids using an extensive dataset of protein-DNA complexes, and developed two support vector machine (SVM) models that predict protein-binding nucleotides from sequence data alone. One SVM model predicts protein-binding nucleotides using DNA sequence data alone, and the other SVM model predicts protein-binding nucleotides using both DNA and protein sequences. In a 10-fold cross-validation with 1519 DNA sequences, the SVM model that uses DNA sequence data only predicted protein-binding nucleotides with an accuracy of 67.0%, an F-measure of 67.1%, and a Matthews correlation coefficient (MCC) of 0.340. With an independent dataset of 181 DNAs that were not used in training, it achieved an accuracy of 66.2%, an F-measure 66.3% and a MCC of 0.324. Another SVM model that uses both DNA and protein sequences achieved an accuracy of 69.6%, an F-measure of 69.6%, and a MCC of 0.383 in a 10-fold cross-validation with 1519 DNA sequences and 859 protein sequences. With an independent dataset of 181 DNAs and 143 proteins, it showed an accuracy of 67.3%, an F-measure of 66.5% and a MCC of 0.329. Both in cross-validation and independent testing, the second SVM model that used both DNA and protein sequence data showed better performance than the first model that used DNA sequence data. To the best of

  15. Dawn of Cavity Spintronics

    OpenAIRE

    Hu, Can-Ming

    2015-01-01

    Merging the progress of spintronics with the advancement in cavity quantum electrodynamics and cavity polaritons, a new field of Cavity Spintronics is forming, which connects some of the most exciting modern physics, such as quantum information and quantum optics, with one of the oldest science on the earth, the magnetism.

  16. Evaluation of WEPP for runoff and sediment yield prediction on natural gas well sites

    Science.gov (United States)

    Natural gas exploration and production, with nearly 30,000 new wells drilled each year in the US, requires land disturbing activities that can accelerate soil loss. Erosion modeling has been successfully used for decades to predict soil loss and conservation effects on agricultural fields, rangelan...

  17. 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.

  18. 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

  19. 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.

  20. Polymorphisms in MicroRNA Binding Sites Predict Colorectal Cancer Survival

    Science.gov (United States)

    Yang, Ying-Pi; Ting, Wen-Chien; Chen, Lu-Min; Lu, Te-Ling; Bao, Bo-Ying

    2017-01-01

    Background: MicroRNAs (miRNAs) mediate negative regulation of target genes through base pairing, and aberrant miRNA expression has been described in cancers. We hypothesized that single nucleotide polymorphisms (SNPs) within miRNA target sites might influence clinical outcomes in patients with colorectal cancer. Methods: Sixteen common SNPs within miRNA target sites were identified, and the association between these SNPs and overall survival was assessed in colorectal cancer patients using Kaplan-Meier analysis, Cox regression model, and survival tree analysis. Results: Survival tree analysis identified a higher-order genetic interaction profile consisting of the RPS6KB1 rs1051424 and ZNF839 rs11704 that was significantly associated with overall survival. The 5-year survival rates were 74.6%, 62.7%, and 57.1% for the low-, medium-, and high-risk genetic profiles, respectively (P = 0.006). The genetic interaction profile remained significant even after adjusting for potential risk factors. Additional in silico analysis provided evidence that rs1051424 and rs11704 affect RPS6KB1 and ZNF839 expressions, which in turn is significantly correlated with prognosis in colorectal cancer. Conclusion: Our results suggest that the genetic interaction profiles among SNPs within miRNA target sites might be prognostic markers for colorectal cancer survival. PMID:28138309

  1. 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...

  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. 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.

  4. 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

  5. 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.

  6. Supersonic flows over cavities

    Institute of Scientific and Technical Information of China (English)

    Tianwen FANG; Meng DING; Jin ZHOU

    2008-01-01

    The characteristics of supersonic cold flows over cavities were investigated experimentally and numer-ically, and the effects of cavities of different sizes on super-sonic flow field were analyzed. The results indicate that the ratio of length to depth L/D within the range of 5-9 has little relevance to integral structures of cavity flow. The bevel angle of the rear wall does not alter the overall structure of the cavity flow within the range of 30°-60°, but it can exert obvious effect on the evolvement of shear layer and vortexes in cavities.

  7. Missense mutations in the TP53 DNA-binding domain predict outcomes in patients with advanced oral cavity squamous cell carcinoma.

    Science.gov (United States)

    Lapke, Nina; Lu, Yen-Jung; Liao, Chun-Ta; Lee, Li-Yu; Lin, Chien-Yu; Wang, Hung-Ming; Ng, Shu-Hang; Chen, Shu-Jen; Yen, Tzu-Chen

    2016-07-12

    TP53 mutations have been linked to reduced survival in patients with oral cavity squamous cell carcinoma (OSCC). However, the impact of different types of TP53 mutations remains unclear. Here, we demonstrate that the carriage of missense mutations in the TP53 DNA binding domain (DBD missense mutations) is associated with decreased disease-specific survival (DSS) compared with wild-type TP53 (P=0.002) in a cohort of 345 OSCC patients. In contrast, DSS of patients bearing all of the remaining TP53 mutations did not differ from that observed in wild-type TP53 patients (P=0.955). Our classification method for TP53 mutations was superior to previously reported approaches (disruptive, truncating, Evolutionary Action score, mutations in L2/L3/LSH) for distinguishing between low- and high-risk patients. When analyzed in combination with traditional clinicopathological factors, TP53 DBD missense mutations were an independent prognostic factor for shorter DSS (P=0.014) alongside with advanced AJCC T- and N-classifications and the presence of extracapsular spread. A scoring system that included the four independent prognostic factors allowed a reliable patient stratification into distinct risk groups (high-risk patients, 16.2%). Our results demonstrate the usefulness of TP53 DBD missense mutations combined with clinicopathological factors for improving the prognostic stratification of OSCC patients.

  8. RESONANT CAVITY EXCITATION SYSTEM

    Science.gov (United States)

    Baker, W.R.; Kerns, Q.A.; Riedel, J.

    1959-01-13

    An apparatus is presented for exciting a cavity resonator with a minimum of difficulty and, more specifically describes a sub-exciter and an amplifier type pre-exciter for the high-frequency cxcitation of large cavities. Instead of applying full voltage to the main oscillator, a sub-excitation voltage is initially used to establish a base level of oscillation in the cavity. A portion of the cavity encrgy is coupled to the input of the pre-exciter where it is amplified and fed back into the cavity when the pre-exciter is energized. After the voltage in the cavity resonator has reached maximum value under excitation by the pre-exciter, full voltage is applied to the oscillator and the pre-exciter is tunned off. The cavity is then excited to the maximum high voltage value of radio frequency by the oscillator.

  9. 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....... A 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......-glycosylation signals in these evolutionary-related glycoproteins were found in their first hypervariable loop, V1. However, the strain variation for HIV-1 gp120 was significant. A computer server, available through WWW or E-mail, has been developed for prediction of mucin type O-glycosylation sites in proteins based...

  10. 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.

  11. Cloning and characterization of a novel nuclease from shrimp hepatopancreas, and prediction of its active site.

    Science.gov (United States)

    Wang, W Y; Liaw, S H; Liao, T H

    2000-03-15

    Approximately 95% of the amino acid sequence of a shrimp (Penaeus japonicus) nuclease was derived from protease-digested peptides. A 1461-base cDNA for the nuclease was amplified and sequenced with degenerate primers based on the amino acid sequence and then specific primers by 3' and 5' RACE (rapid amplification of cDNA ends). It contains an open reading frame encoding a putative 21-residue signal peptide and a 381-residue mature protein. The N-terminus of the enzyme is pyroglutamate, deduced from composition and matrix-assisted laser desorption ionization-time-of-flight MS analyses, and confirmed by a glutamine residue in the cDNA sequence. The enzyme has 11 Cys residues, forming five intramolecular disulphides. The eleventh Cys residue was linked to a thiol compound with an estimated molecular mass of between 500 and 700 Da. A sequence similarity search revealed no homologous proteins but residues 205-255 shared a conserved active-site motif within a distinct group of nucleases. His(211) in this conserved motif was shown to be very important in catalysis by site-specific modification with (14)C-labelled iodoacetate. The shrimp nuclease, previously designated DNase I, does indeed possess a low level of hydrolytic activity towards RNA in the presence of Mg(2+) and Ca(2+). The conservation of functionally important residues during distant evolution might imply that the catalytic mechanisms are similar in these nucleases, which should be classified in one subfamily. Finally, an active-site structure for shrimp nuclease was proposed on the basis of published structural data and the results of mutational and biochemical analyses of Serratia nuclease.

  12. 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.

  13. 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

  14. On the nature of Parr functions to predict the most reactive sites along organic polar reactions

    Science.gov (United States)

    Chamorro, Eduardo; Pérez, Patricia; Domingo, Luis R.

    2013-09-01

    Very recently, local electrophilic and nucleophilic “Parr functions” were empirically introduced (L.R. Domingo, P. Pérez, J.A. Saez RSC Adv. 3 (2013) 1486) in order to properly characterize the most reactive sites along polar chemical reactions. This Letter reports a theoretical advance to the new methodology by identifying these quantities with key Fukui descriptors of the spin-polarized density functional theory. Given such framework properly incorporates the treatment of both charge-transfer and spin-polarization, this finding provides a significant insight and substantial step forward within the field of a chemical reactivity theory based on the conceptual framework of density functional theory.

  15. Identification of off-target cleavage sites of zinc finger nucleases and TAL effector nucleases using predictive models.

    Science.gov (United States)

    Fine, Eli J; Cradick, Thomas J; Bao, Gang

    2014-01-01

    Using engineered nucleases, such as Zinc Finger Nucleases (ZFNs) or Transcription Activator-Like Effector Nucleases (TALENs), to make targeted genomic modifications has become a common technique to create new model organisms and custom cell lines, and has shown great promise for disease treatment. However, these nucleases have the potential for off-target cleavage that could confound interpretation of experimental results and be detrimental for therapeutic use. Here, we describe a method to test for nuclease cleavage at potential off-target sites predicted by bioinformatics models.

  16. Prominence Mass Supply and the Cavity

    CERN Document Server

    Schmit, Donald; Luna, Manuel; Karpen, Judy; Innes, Davina

    2013-01-01

    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 emission (EUV) 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 SDO/AIA 171\\AA\\ 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 ...

  17. 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.

  18. 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....

  19. No site unseen: predicting the failure to control problematic Internet use among young adults.

    Science.gov (United States)

    Yamada, Tetsuhiro; Moshier, Samantha J; Otto, Michael W

    2016-11-01

    Problematic Internet use has been associated with the neglect of valued activities such as work, exercise, social activities, and relationships. In the present study, we expanded the understanding of problematic Internet use by identifying an important predictor of the inability to curb Internet use despite the desire to do so. Specifically, in a college student sample reporting a mean of 27.8 h of recreational Internet use in the past week, we investigated the role of distress intolerance (DI)-an individual difference variable that refers to the inability of an individual to tolerate emotional discomfort and to engage in goal-directed behavior when distressed-to predict the failure to meet personal restrictions on Internet use. Consistent with hypotheses, DI emerged as a significant predictor of the failure to meet self-control goals in both bivariate and multivariate models, indicating that DI offers unique prediction of self-control failure with problematic Internet use. Given that DI is a modifiable trait, these results encourage consideration of DI-focused early intervention strategies.

  20. 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;

    2015-01-01

    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 pat...

  1. Understanding Land-Atmosphere Coupling and its Predictability at the ARM Southern Great Plains Site

    Science.gov (United States)

    Ferguson, C. R.; Song, H. J.; Roundy, J. K.

    2015-12-01

    Ten years ago, the Global Energy and Water EXchanges Global Land Atmosphere Coupling Experiment (GLACE) spotlighted the Southern Great Plains (SGP) for being one of three hotspots globally for land-derived precipitation predictability. Since then, the GLACE results have served as the underlying motivation for numerous subsequent land-atmosphere (L-A) coupling studies over the SGP domain. The range of these studies includes: local point scale studies leveraging surface meteorological and flux measurements at the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement SGP (ARM-SGP) Central Facility, regional pentad to monthly scale atmospheric moisture budget analyses based on atmospheric reanalysis, and regional limited duration (2-7 day) coupled model sensitivity experiments. This study has the following three objectives: (1) to provide the common historical context necessary for bridging past and future interdisciplinary characterizations of L-A coupling, (2) to isolate the mechanism(s) for the region's L-A coupling signal, and (3) to evaluate the short range (12-18hr) predictability of soil moisture-precipitation feedbacks. We produce a convective triggering potential—low-level humidity index (CTP-HI)—based climatology of L-A coupling at ARM-SGP for the period 1979-2014 using North American Regional Reanalysis and North American Land Data Assimilation System Phase 2 data. We link the underlying coupling regime classification timeseries to corresponding synoptic-mesoscale weather patterns and bulk atmospheric moisture budget analyses. On the whole, the region's precipitation variability is largely dependent on large-scale moisture transport and the role of the land is nominal. However, we show that surface sensible heat flux can play an important role in modulating diurnal precipitation cycle phase and amplitude—either directly (enhancing CTP) in water-limited conditions or indirectly (increasing HI) in energy-limited conditions. In fact, both 0700

  2. The application analyze of laser cavity treatment varicose vein of lower limb by predictive nursing%预见性护理在腔内激光治疗下肢静脉曲张的应用分析

    Institute of Scientific and Technical Information of China (English)

    方巧红; 罗敏

    2014-01-01

    Objective To approach application result of laser cavity treatment varicose vein of lower limb by predictive nursing. Method To analyze 60 cases clinical data of varicose vein of lower limb patients,which was to be divided into two groups,predictive nursing group of 30 cases and primary care group of 30 cases. Results The body function、mental function、social function、substance function and total points of predictive nursing group were better than primary care group,t=5. 40、4. 90、3. 33、3. 59、7. 60,there was statistical significance( P<0. 05 ). Conclusion The living quality is improved of laser cavity treatment varicose vein of lower limb by predictive nursing,which is to be used.%目的:探讨预见性护理在腔内激光治疗下肢静脉曲张的应用效果。方法:分析收治的下肢静脉曲张患者60例临床资料,依据护理措施不同进行分组,预见性护理措施组30例和常规护理组30例。结果:预见性护理措施组腔内激光治疗下肢静脉曲张患者躯体功能、心理功能、社会功能、物质功能及总分均优于常规护理组,t=5.40、4.90、3.33、3.59、7.60,差异均有统计学意义( P<0.05)。结论:预见性护理在腔内激光治疗下肢静脉曲张患者应用后可以明显提高生活质量,值得临床推广应用。

  3. AthMethPre: a web server for the prediction and query of mRNA m(6)A sites in Arabidopsis thaliana.

    Science.gov (United States)

    Xiang, Shunian; Yan, Zhangming; Liu, Ke; Zhang, Yaou; Sun, Zhirong

    2016-10-18

    N(6)-Methyladenosine (m(6)A) is the most prevalent and abundant modification in mRNA that has been linked to many key biological processes. High-throughput experiments have generated m(6)A-peaks across the transcriptome of A. thaliana, but the specific methylated sites were not assigned, which impedes the understanding of m(6)A functions in plants. Therefore, computational prediction of mRNA m(6)A sites becomes emergently important. Here, we present a method to predict the m(6)A sites for A. thaliana mRNA sequence(s). To predict the m(6)A sites of an mRNA sequence, we employed the support vector machine to build a classifier using the features of the positional flanking nucleotide sequence and position-independent k-mer nucleotide spectrum. Our method achieved good performance and was applied to a web server to provide service for the prediction of A. thaliana m(6)A sites. The server also provides a comprehensive database of predicted transcriptome-wide m(6)A sites and curated m(6)A-seq peaks from the literature for query and visualization. The AthMethPre web server is the first web server that provides a user-friendly tool for the prediction and query of A. thaliana mRNA m(6)A sites, which is freely accessible for public use at .

  4. Prediction of S-Nitrosylation Modification Sites Based on Kernel Sparse Representation Classification and mRMR Algorithm

    Directory of Open Access Journals (Sweden)

    Guohua Huang

    2014-01-01

    Full Text Available Protein S-nitrosylation plays a very important role in a wide variety of cellular biological activities. Hitherto, accurate prediction of S-nitrosylation sites is still of great challenge. In this paper, we presented a framework to computationally predict S-nitrosylation sites based on kernel sparse representation classification and minimum Redundancy Maximum Relevance algorithm. As much as 666 features derived from five categories of amino acid properties and one protein structure feature are used for numerical representation of proteins. A total of 529 protein sequences collected from the open-access databases and published literatures are used to train and test our predictor. Computational results show that our predictor achieves Matthews’ correlation coefficients of 0.1634 and 0.2919 for the training set and the testing set, respectively, which are better than those of k-nearest neighbor algorithm, random forest algorithm, and sparse representation classification algorithm. The experimental results also indicate that 134 optimal features can better represent the peptides of protein S-nitrosylation than the original 666 redundant features. Furthermore, we constructed an independent testing set of 113 protein sequences to evaluate the robustness of our predictor. Experimental result showed that our predictor also yielded good performance on the independent testing set with Matthews’ correlation coefficients of 0.2239.

  5. Parameter estimation method and updating of regional prediction equations for ungaged sites in the desert region of California

    Science.gov (United States)

    Barth, Nancy A.; Veilleux, Andrea G.

    2012-01-01

    The U.S. Geological Survey (USGS) is currently updating at-site flood frequency estimates for USGS streamflow-gaging stations in the desert region of California. The at-site flood-frequency analysis is complicated by short record lengths (less than 20 years is common) and numerous zero flows/low outliers at many sites. Estimates of the three parameters (mean, standard deviation, and skew) required for fitting the log Pearson Type 3 (LP3) distribution are likely to be highly unreliable based on the limited and heavily censored at-site data. In a generalization of the recommendations in Bulletin 17B, a regional analysis was used to develop regional estimates of all three parameters (mean, standard deviation, and skew) of the LP3 distribution. A regional skew value of zero from a previously published report was used with a new estimated mean squared error (MSE) of 0.20. A weighted least squares (WLS) regression method was used to develop both a regional standard deviation and a mean model based on annual peak-discharge data for 33 USGS stations throughout California’s desert region. At-site standard deviation and mean values were determined by using an expected moments algorithm (EMA) method for fitting the LP3 distribution to the logarithms of annual peak-discharge data. Additionally, a multiple Grubbs-Beck (MGB) test, a generalization of the test recommended in Bulletin 17B, was used for detecting multiple potentially influential low outliers in a flood series. The WLS regression found that no basin characteristics could explain the variability of standard deviation. Consequently, a constant regional standard deviation model was selected, resulting in a log-space value of 0.91 with a MSE of 0.03 log units. Yet drainage area was found to be statistically significant at explaining the site-to-site variability in mean. The linear WLS regional mean model based on drainage area had a Pseudo- 2 R of 51 percent and a MSE of 0.32 log units. The regional parameter

  6. 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.

  7. Prediction of the flooding process at the Ronneburg site - results of an integrated approach; Flutungsprognose am Standort Ronneburg - Ergebnisse eines integrierten Modellansatzes

    Energy Technology Data Exchange (ETDEWEB)

    Paul, M.; Saenger, H.-J.; Snagowski, S. [Wismut GmbH, Chemnitz (Germany); Maerten, H. [UIT Dresden (Germany); Eckart, M. [Geocontrol Gera (Germany)

    1998-12-31

    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

  8. 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

  9. Dopamine transporter comparative molecular modeling and binding site prediction using the LeuT(Aa) leucine transporter as a template.

    Science.gov (United States)

    Indarte, Martín; Madura, Jeffry D; Surratt, Christopher K

    2008-02-15

    Pharmacological and behavioral studies indicate that binding of cocaine and the amphetamines by the dopamine transporter (DAT) protein is principally responsible for initiating the euphoria and addiction associated with these drugs. The lack of an X-ray crystal structure for the DAT or any other member of the neurotransmitter:sodium symporter (NSS) family has hindered understanding of psychostimulant recognition at the atomic level; structural information has been obtained largely from mutagenesis and biophysical studies. The recent publication of a crystal structure for the bacterial leucine transporter LeuT(Aa), a distantly related NSS family homolog, provides for the first time a template for three-dimensional comparative modeling of NSS proteins. A novel computational modeling approach using the capabilities of the Molecular Operating Environment program MOE 2005.06 in conjunction with other comparative modeling servers generated the LeuT(Aa)-directed DAT model. Probable dopamine and amphetamine binding sites were identified within the DAT model using multiple docking approaches. Binding sites for the substrate ligands (dopamine and amphetamine) overlapped substantially with the analogous region of the LeuT(Aa) crystal structure for the substrate leucine. The docking predictions implicated DAT side chains known to be critical for high affinity ligand binding and suggest novel mutagenesis targets in elucidating discrete substrate and inhibitor binding sites. The DAT model may guide DAT ligand QSAR studies, and rational design of novel DAT-binding therapeutics.

  10. Timing of initial arrival at the breeding site predicts age at first reproduction in a long-lived migratory bird.

    Science.gov (United States)

    Becker, Peter H; Dittmann, Tobias; Ludwigs, Jan-Dieter; Limmer, Bente; Ludwig, Sonja C; Bauch, Christina; Braasch, Alexander; Wendeln, Helmut

    2008-08-26

    In long-lived vertebrates, individuals generally visit potential breeding areas or populations during one or more seasons before reproducing for the first time. During these years of prospecting, they select a future breeding site, colony, or mate and improve various skills and their physical condition to meet the requirements of reproduction. One precondition of successful reproduction is arrival in time on the breeding grounds. Here, we study the intricate links among the date of initial spring arrival, body mass, sex, and the age of first breeding in the common tern Sterna hirundo, a long-lived migratory colonial seabird. The study is based on a unique, individual-based, long-term dataset of sexed birds, marked with transponders, which allow recording their individual arrival, overall attendance, and clutch initiation remotely and automatically year by year over the entire lifetime at the natal colony site. We show that the seasonal date of initial arrival at the breeding grounds predicts the individual age at first reproduction, which mostly occurs years later. Late first-time arrivals remain delayed birds throughout subsequent years. Our findings reveal that timing of arrival at the site of reproduction and timing of reproduction itself are coherent parameters of individual quality, which are linked with the prospects of the breeding career and may have consequences for fitness.

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

    Energy Technology Data Exchange (ETDEWEB)

    Alam, Aftab [Ames Laboratory; Johnson, Duane D. [Ames Laboratory

    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.

  12. 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.

  13. Structure prediction and binding sites analysis of curcin protein of Jatropha curcas using computational approaches.

    Science.gov (United States)

    Srivastava, Mugdha; Gupta, Shishir K; Abhilash, P C; Singh, Nandita

    2012-07-01

    Ribosome inactivating proteins (RIPs) are defense proteins in a number of higher-plant species that are directly targeted toward herbivores. Jatropha curcas is one of the biodiesel plants having RIPs. The Jatropha seed meal, after extraction of oil, is rich in curcin, a highly toxic RIP similar to ricin, which makes it unsuitable for animal feed. Although the toxicity of curcin is well documented in the literature, the detailed toxic properties and the 3D structure of curcin has not been determined by X-ray crystallography, NMR spectroscopy or any in silico techniques to date. In this pursuit, the structure of curcin was modeled by a composite approach of 3D structure prediction using threading and ab initio modeling. Assessment of model quality was assessed by methods which include Ramachandran plot analysis and Qmean score estimation. Further, we applied the protein-ligand docking approach to identify the r-RNA binding residue of curcin. The present work provides the first structural insight into the binding mode of r-RNA adenine to the curcin protein and forms the basis for designing future inhibitors of curcin. Cloning of a future peptide inhibitor within J. curcas can produce non-toxic varieties of J. curcas, which would make the seed-cake suitable as animal feed without curcin detoxification.

  14. 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.

  15. 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.

  16. A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs.

    Science.gov (United States)

    Li, Haifeng; Jiang, Tao

    2005-01-01

    The prediction of translation initiation sites (TISs) in eukaryotic mRNAs has been a challenging problem in computational molecular biology. In this paper, we present a new algorithm to recognize TISs with a very high accuracy. Our algorithm includes two novel ideas. First, we introduce a class of new sequence-similarity kernels based on string editing, called edit kernels, for use with support vector machines (SVMs) in a discriminative approach to predict TISs. The edit kernels are simple and have significant biological and probabilistic interpretations. Although the edit kernels are not positive definite, it is easy to make the kernel matrix positive definite by adjusting the parameters. Second, we convert the region of an input mRNA sequence downstream to a putative TIS into an amino acid sequence before applying SVMs to avoid the high redundancy in the genetic code. The algorithm has been implemented and tested on previously published data. Our experimental results on real mRNA data show that both ideas improve the prediction accuracy greatly and that our method performs significantly better than those based on neural networks and SVMs with polynomial kernels or Salzberg kernels.

  17. Accurate microRNA target prediction using detailed binding site accessibility and machine learning on proteomics data

    Directory of Open Access Journals (Sweden)

    Martin eReczko

    2012-01-01

    Full Text Available MicroRNAs (miRNAs are a class of small regulatory genes regulating gene expression by targetingmessenger RNA. Though computational methods for miRNA target prediction are the prevailingmeans to analyze their function, they still miss a large fraction of the targeted genes and additionallypredict a large number of false positives. Here we introduce a novel algorithm called DIANAmicroT-ANN which combines multiple novel target site features through an artificial neural network(ANN and is trained using recently published high-throughput data measuring the change of proteinlevels after miRNA overexpression, providing positive and negative targeting examples. The featurescharacterizing each miRNA recognition element include binding structure, conservation level and aspecific profile of structural accessibility. The ANN is trained to integrate the features of eachrecognition element along the 3’ untranslated region into a targeting score, reproducing the relativerepression fold change of the protein. Tested on two different sets the algorithm outperforms otherwidely used algorithms and also predicts a significant number of unique and reliable targets notpredicted by the other methods. For 542 human miRNAs DIANA-microT-ANN predicts 120,000targets not provided by TargetScan 5.0. The algorithm is freely available athttp://microrna.gr/microT-ANN.

  18. A comprehensive software suite for protein family construction and functional site prediction

    Science.gov (United States)

    Haft, David Renfrew; Haft, Daniel H.

    2017-01-01

    In functionally diverse protein families, conservation in short signature regions may outperform full-length sequence comparisons for identifying proteins that belong to a subgroup within which one specific aspect of their function is conserved. The SIMBAL workflow (Sites Inferred by Metabolic Background Assertion Labeling) is a data-mining procedure for finding such signature regions. It begins by using clues from genomic context, such as co-occurrence or conserved gene neighborhoods, to build a useful training set from a large number of uncharacterized but mutually homologous proteins. When training set construction is successful, the YES partition is enriched in proteins that share function with the user’s query sequence, while the NO partition is depleted. A selected query sequence is then mined for short signature regions whose closest matches overwhelmingly favor proteins from the YES partition. High-scoring signature regions typically contain key residues critical to functional specificity, so proteins with the highest sequence similarity across these regions tend to share the same function. The SIMBAL algorithm was described previously, but significant manual effort, expertise, and a supporting software infrastructure were required to prepare the requisite training sets. Here, we describe a new, distributable software suite that speeds up and simplifies the process for using SIMBAL, most notably by providing tools that automate training set construction. These tools have broad utility for comparative genomics, allowing for flexible collection of proteins or protein domains based on genomic context as well as homology, a capability that can greatly assist in protein family construction. Armed with this new software suite, SIMBAL can serve as a fast and powerful in silico alternative to direct experimentation for characterizing proteins and their functional interactions. PMID:28182651

  19. 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

  20. Theoretical prediction of single-site enthalpies of surface protonation for oxides and silicates in water

    Energy Technology Data Exchange (ETDEWEB)

    Sverjensky, D.A.; Sahai, N. [Johns Hopkins Univ., Baltimore, MD (United States). Morton K. Blaustein Dept. of Earth and Planetary Sciences

    1998-12-01

    Surface protonation is the most fundamental adsorption process of geochemical interest. Yet remarkably little is known about protonation of mineral surfaces at temperatures greater than 25 C. Experimentally derived standard enthalpies of surface protonation, {Delta}H{degree}{sub r,1}, {Delta}H{degree}{sub r,2}, and {Delta}H{degree}{sub r,ZPC}, correspond to the reactions >SOH + H{sup +} = >SOH{sub 2}{sup +}; >SO{sup {minus}} + H{sup +} = >SOH; and >SO{sup {minus}} + 2H{sup +} = >SOH{sub 2}{sup +}, respectively, and provide a starting point for evaluating the role of surface protonation in geochemical processes at elevated temperatures. However, the experimental data for oxides do not have a theoretical explanation, and data are completely lacking for silicates other than SiO{sub 2}. In the present study, the combination of crystal chemical and Born solvation theory provides a theoretical basis for explaining the variation of the enthalpies of protonation of oxides. Experimental values of {Delta}H{degree}{sub r,1}, {Delta}H{degree}{sub r,2}, and {Delta}H{degree}{sub r,ZPC} consistent with the triple layer model can be expressed in terms of the inverse of the dielectric constant (1/{epsilon}) and the Pauling bond strength per angstrom (s/r{sub M-OH}) of each mineral. Predicted standard enthalpies of surface protonation for oxides and silicates extend over the ranges (in kcal/mole):{Delta}H{degree}{sub r,1} {approx} {minus}3 to {minus}15; {Delta}H{degree}{sub r,2} {approx} {minus}5 to {minus}18; {Delta}H{degree}{sub r,ZPC} {approx} {minus}4 to {minus}33.

  1. Dissipative structures in optomechanical cavities

    Science.gov (United States)

    Ruiz-Rivas, Joaquín; Navarrete-Benlloch, Carlos; Patera, Giuseppe; Roldán, Eugenio; de Valcárcel, Germán J.

    2016-03-01

    Motivated by the increasing interest in the properties of multimode optomechanical devices, here we study a system in which a driven longitudinal mode of a large-area optical cavity is dispersively coupled to a deformable mechanical element. Two different models naturally appear in such scenario, for which we predict the formation of periodic patterns, localized structures (cavity solitons), and domain walls, among other complex nonlinear phenomena. Further, we propose a realistic design based on intracavity membranes where our models can be studied experimentally. Apart from its relevance to the field of nonlinear optics, the results put forward here are a necessary step towards understanding the quantum properties of optomechanical systems in the multimode regime of both the optical and the mechanical degrees of freedom.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Ultra-high-Q toroidal microresonators for cavity quantum electrodynamics

    CERN Document Server

    Spillane, S M; Vahala, K J; Goh, K W; Wilcut, E; Kimble, H J

    2004-01-01

    We investigate the suitability of toroidal microcavities for strong-coupling cavity quantum electrodynamics (QED). Numerical modeling of the optical modes demonstrate a significant reduction of modal volume with respect to the whispering gallery modes of dielectric spheres, while retaining the high quality factors representative of spherical cavities. The extra degree of freedom of toroid microcavities can be used to achieve improved cavity QED characteristics. Numerical results for atom-cavity coupling strength, critical atom number N_0 and critical photon number n_0 for cesium are calculated and shown to exceed values currently possible using Fabry-Perot cavities. Modeling predicts coupling rates g/(2*pi) exceeding 700 MHz and critical atom numbers approaching 10^{-7} in optimized structures. Furthermore, preliminary experimental measurements of toroidal cavities at a wavelength of 852 nm indicate that quality factors in excess of 100 million can be obtained in a 50 micron principal diameter cavity, which w...

  9. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists

    Science.gov (United States)

    Kalani, M. Yashar S.; Vaidehi, Nagarajan; Hall, Spencer E.; Trabanino, Rene J.; Freddolino, Peter L.; Kalani, Maziyar A.; Floriano, Wely B.; Tak Kam, Victor Wai; Goddard, William A., III

    2004-03-01

    Dopamine neurotransmitter and its receptors play a critical role in the cell signaling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for such disorders as Parkinson's disease and schizophrenia would be significantly enhanced with the availability of the 3D structure for the dopamine receptors and of the binding site for dopamine and other agonists and antagonists. We report here the 3D structure of the long isoform of the human D2 dopamine receptor, predicted from primary sequence using first-principles theoretical and computational techniques (i.e., we did not use bioinformatic or experimental 3D structural information in predicting structures). The predicted 3D structure is validated by comparison of the predicted binding site and the relative binding affinities of dopamine, three known dopamine agonists (antiparkinsonian), and seven known antagonists (antipsychotic) in the D2 receptor to experimentally determined values. These structures correctly predict the critical residues for binding dopamine and several antagonists, identified by mutation studies, and give relative binding affinities that correlate well with experiments. The predicted binding site for dopamine and agonists is located between transmembrane (TM) helices 3, 4, 5, and 6, whereas the best antagonists bind to a site involving TM helices 2, 3, 4, 6, and 7 with minimal contacts to TM helix 5. We identify characteristic differences between the binding sites of agonists and antagonists.

  10. Backaction-driven transport of Bloch oscillating atoms in ring cavities.

    Science.gov (United States)

    Goldwin, J; Venkatesh, B Prasanna; O'Dell, D H J

    2014-08-15

    We predict that an atomic Bose-Einstein condensate strongly coupled to an intracavity optical lattice can undergo resonant tunneling and directed transport when a constant and uniform bias force is applied. The bias force induces Bloch oscillations, causing amplitude and phase modulation of the lattice which resonantly modifies the site-to-site tunneling. For the right choice of parameters a net atomic current is generated. The transport velocity can be oriented oppositely to the bias force, with its amplitude and direction controlled by the detuning between the pump laser and the cavity. The transport can also be enhanced through imbalanced pumping of the two counterpropagating running wave cavity modes. Our results add to the cold atoms quantum simulation toolbox, with implications for quantum sensing and metrology.

  11. 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

  12. 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.

  13. 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

  14. Tuned optical cavity magnetometer

    Science.gov (United States)

    Okandan, Murat; Schwindt, Peter

    2010-11-02

    An atomic magnetometer is disclosed which utilizes an optical cavity formed from a grating and a mirror, with a vapor cell containing an alkali metal vapor located inside the optical cavity. Lasers are used to magnetically polarize the alkali metal vapor and to probe the vapor and generate a diffracted laser beam which can be used to sense a magnetic field. Electrostatic actuators can be used in the magnetometer for positioning of the mirror, or for modulation thereof. Another optical cavity can also be formed from the mirror and a second grating for sensing, adjusting, or stabilizing the position of the mirror.

  15. Prediction of translation initiation sites in human mRNA sequences with AUG start codon in weak Kozak context: A neural network approach.

    Science.gov (United States)

    Tikole, Suhas; Sankararamakrishnan, Ramasubbu

    2008-05-16

    Translation of eukaryotic mRNAs is often regulated by nucleotides around the start codon. A purine at position -3 and a guanine at position +4 contribute significantly to enhance the translation efficiency. Algorithms to predict the translation initiation site often fail to predict the start site if the sequence context is not present. We have developed a neural network method to predict the initiation site of mRNA sequences that lack the preferred nucleotides at the positions -3 and +4 surrounding the translation initiation site. Neural networks of various architectures comprising different number of hidden layers were designed and tested for various sizes of windows of nucleotides surrounding translation initiation sites. We found that the neural network with two hidden layers showed a sensitivity of 83% and specificity of 73% indicating a vastly improved performance in successfully predicting the translation initiation site of mRNA sequences with weak Kozak context. WeakAUG server is freely available at http://bioinfo.iitk.ac.in/AUGPred/.

  16. 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.

  17. 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.

  18. 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.

  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.

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

    Science.gov (United States)

    Adams, Amy L; Dickinson, Katharine J M; Robertson, Bruce C; van Heezik, Yolanda

    2013-01-01

    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 cities should

  2. Ambulatory teaching: Do approaches to learning predict the site and preceptor characteristics valued by clerks and residents in the ambulatory setting?

    Directory of Open Access Journals (Sweden)

    Kirby John R

    2005-10-01

    Full Text Available Abstract Background In a study to determine the site and preceptor characteristics most valued by clerks and residents in the ambulatory setting we wished to confirm whether these would support effective learning. The deep approach to learning is thought to be more effective for learning than surface approaches. In this study we determined how the approaches to learning of clerks and residents predicted the valued site and preceptor characteristics in the ambulatory setting. Methods Postal survey of all medical residents and clerks in training in Ontario determining the site and preceptor characteristics most valued in the ambulatory setting. Participants also completed the Workplace Learning questionnaire that includes 3 approaches to learning scales and 3 workplace climate scales. Multiple regression analysis was used to predict the preferred site and preceptor characteristics as the dependent variables by the average scores of the approaches to learning and perception of workplace climate scales as the independent variables. Results There were 1642 respondents, yielding a 47.3% response rate. Factor analysis revealed 7 preceptor characteristics and 6 site characteristics valued in the ambulatory setting. The Deep approach to learning scale predicted all of the learners' preferred preceptor characteristics (β = 0.076 to β = 0.234, p Direction was more strongly associated with the Surface Rational approach (β = .252, p Surface Disorganized approach to learning (β = .154, p Deep approach. The Deep approach to learning scale predicted valued site characteristics of Office Management, Patient Logistics, Objectives and Preceptor Interaction (p Surface Rational approach to learning predicted valuing Learning Resources and Clinic Set-up (β = .09, p = .001; β = .197, p Surface Disorganized approach to learning weakly negatively predicted Patient Logistics (β = -.082, p = .003 and positively the Learning Resources (β = .088, p = .003. Climate

  3. 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....

  4. eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape

    Science.gov (United States)

    Kinoshita, Kengo; Murakami, Yoichi; Nakamura, Haruki

    2007-01-01

    We have developed a method to predict ligand-binding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek). PMID:17567616

  5. The Superconducting TESLA Cavities

    CERN Document Server

    Aune, B.; Bloess, D.; Bonin, B.; Bosotti, A.; Champion, M.; Crawford, C.; Deppe, G.; Dwersteg, B.; Edwards, D.A.; Edwards, H.T.; Ferrario, M.; Fouaidy, M.; Gall, P-D.; Gamp, A.; Gössel, A.; Graber, J.; Hubert, D.; Hüning, M.; Juillard, M.; Junquera, T.; Kaiser, H.; Kreps, G.; Kuchnir, M.; Lange, R.; Leenen, M.; Liepe, M.; Lilje, L.; Matheisen, A.; Möller, W-D.; Mosnier, A.; Padamsee, H.; Pagani, C.; Pekeler, M.; Peters, H-B.; Peters, O.; Proch, D.; Rehlich, K.; Reschke, D.; Safa, H.; Schilcher, T.; Schmüser, P.; Sekutowicz, J.; Simrock, S.; Singer, W.; Tigner, M.; Trines, D.; Twarowski, K.; Weichert, G.; Weisend, J.; Wojtkiewicz, J.; Wolff, S.; Zapfe, K.

    2000-01-01

    The conceptional design of the proposed linear electron-positron colliderTESLA is based on 9-cell 1.3 GHz superconducting niobium cavities with anaccelerating gradient of Eacc >= 25 MV/m at a quality factor Q0 > 5E+9. Thedesign goal for the cavities of the TESLA Test Facility (TTF) linac was set tothe more moderate value of Eacc >= 15 MV/m. In a first series of 27industrially produced TTF cavities the average gradient at Q0 = 5E+9 wasmeasured to be 20.1 +- 6.2 MV/m, excluding a few cavities suffering fromserious fabrication or material defects. In the second production of 24 TTFcavities additional quality control measures were introduced, in particular aneddy-current scan to eliminate niobium sheets with foreign material inclusionsand stringent prescriptions for carrying out the electron-beam welds. Theaverage gradient of these cavities at Q0 = 5E+9 amounts to 25.0 +- 3.2 MV/mwith the exception of one cavity suffering from a weld defect. Hence only amoderate improvement in production and preparation technique...

  6. Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology

    Directory of Open Access Journals (Sweden)

    Hammesfahr Björn

    2011-06-01

    Full Text Available Abstract Background Alternative splicing of pre-mature RNA is an important process eukaryotes utilize to increase their repertoire of different protein products. Several types of different alternative splice forms exist including exon skipping, differential splicing of exons at their 3'- or 5'-end, intron retention, and mutually exclusive splicing. The latter term is used for clusters of internal exons that are spliced in a mutually exclusive manner. Results We have implemented an extension to the WebScipio software to search for mutually exclusive exons. Here, the search is based on the precondition that mutually exclusive exons encode regions of the same structural part of the protein product. This precondition provides restrictions to the search for candidate exons concerning their length, splice site conservation and reading frame preservation, and overall homology. Mutually exclusive exons that are not homologous and not of about the same length will not be found. Using the new algorithm, mutually exclusive exons in several example genes, a dynein heavy chain, a muscle myosin heavy chain, and Dscam were correctly identified. In addition, the algorithm was applied to the whole Drosophila melanogaster X chromosome and the results were compared to the Flybase annotation and an ab initio prediction. Clusters of mutually exclusive exons might be subsequent to each other and might encode dozens of exons. Conclusions This is the first implementation of an automatic search for mutually exclusive exons in eukaryotes. Exons are predicted and reconstructed in the same run providing the complete gene structure for the protein query of interest. WebScipio offers high quality gene structure figures with the clusters of mutually exclusive exons colour-coded, and several analysis tools for further manual inspection. The genome scale analysis of all genes of the Drosophila melanogaster X chromosome showed that WebScipio is able to find all but two of the 28

  7. 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.

  8. 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.

  9. 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...

  10. Physical simulations of cavity closure in a creeping material

    Energy Technology Data Exchange (ETDEWEB)

    Sutherland, H.J.; Preece, D.S.

    1985-09-01

    The finite element method has been used extensively to predict the creep closure of underground petroleum storage cavities in rock salt. Even though the numerical modeling requires many simplifying assumptions, the predictions have generally correlated with field data from instrumented wellheads, however, the field data are rather limited. To gain an insight into the behavior of three-dimensional arrays of cavities and to obtain a larger data base for the verification of analytical simulations of creep closure, a series of six centrifuge simulation experiments were performed using a cylindrical block of modeling clay, a creeping material. Three of the simulations were conducted with single, centerline cavities, and three were conducted with a symmetric array of three cavities surrounding a central cavity. The models were subjected to body force loading using a centrifuge. For the single cavity experiments, the models were tested at accelerations of 100, 125 and 150 g's for 2 hours. For the multi-cavity experiments, the simulations were conducted at 100 g's for 3.25 hours. The results are analyzed using dimensional analyses. The analyses illustrate that the centrifuge simulations yield self-consistent simulations of the creep closure of fluid-filled cavities and that the interaction of three-dimensional cavity layouts can be investigated using this technique.

  11. Research on Field Emission and Dark Current in ILC Cavities

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Kexin; Li, Yongming; Palczewski, Ari; Geng, Rongli

    2013-09-01

    Field emission and dark current are issues of concern for SRF cavity performance and SRF linac operation. Complete understanding and reliable control of the issue are still needed, especially in full-scale multi-cell cavities. Our work aims at developing a generic procedure for finding an active field emitter in a multi-cell cavity and benchmarking the procedure through cavity vertical test. Our ultimate goal is to provide feedback to cavity preparation and cavity string assembly in order to reduce or eliminate filed emission in SRF cavities. Systematic analysis of behaviors of field emitted electrons is obtained by ACE3P developed by SLAC. Experimental benchmark of the procedure was carried out in a 9-cell cavity vertical test at JLab. The energy spectrum of Bremsstrahlung X-rays is measured using a NaI(Tl) detector. The end-point energy in the X-ray energy spectrum is taken as the highest kinetic electron energy to predict longitudinal position of the active field emitter. Angular location of the field emitter is determined by an array of silicon diodes around irises of the cavity. High-resolution optical inspection was conducted at the predicted field emitter location.

  12. Prominence Mass Supply and the Cavity

    Science.gov (United States)

    Schmit, Donald J.; Gibson, S.; Luna, M.; Karpen, J.; Innes, D.

    2013-01-01

    A prevalent but untested paradigm is often used to describe the prominence-cavity system; the cavity is under-dense because it it 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 evolutin of the prominence and the surrounding corona. We examine the evidence for a prominence-cavity connection by comparing the TNE model and diagnostics of dynamic extreme ultraviolet (EUV) emission surrounding the prominence, specifically prominence horns. Horns are correlated extensions of prminence 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 A badpass near he 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 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.

  13. 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.

  14. Nonlinear Analysis of Cavities in Rock Salt

    DEFF Research Database (Denmark)

    Ottosen, N. S.; Krenk, Steen

    1979-01-01

    The paper covers some material and computational aspects of the rock mechanics of leached cavities in salt. A material model is presented in which the instantaneous stiffness of the salt is obtained by interpolation between the unloaded state and a relevant failure state. The model enables predic...... prediction of short term triaxial behaviour from uniaxial stress-strain curves. Key results from a nonlinear finite element calculation of a gas-filled cavity are given, and the general features are related to a simple nonlinear method of stress evaluation....

  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. Development of a Regression Kriging Model Conditioned with Sequential Gaussian Simulation to Predict the Spatial Distribution of Site Index for The Savannah River Site.

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, Lloyd [USDA Forest Service, Southern Research Station; Parresol, Bernie [USDA Forest Service, Southern Research Station

    2012-09-17

    The primary research objective of the project is to determine an optimum model to spatially interpolate point derived tree site index (SI). This optimum model will use relevant data from 635 measured sample points to create continuous 40 meter SI raster layer of entire study extent.

  18. 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.

  19. 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; Yucca Mountain Site Characterization Project

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, J.S.

    1991-12-01

    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.

  20. 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

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

    Science.gov (United States)

    Barbany, Montserrat; Meyer, Tim; Hospital, Adam; Faustino, Ignacio; D'Abramo, Marco; Morata, Jordi; Orozco, Modesto; de la Cruz, Xavier

    2015-01-01

    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.

  2. Report on the use of stability parameters and mesoscale modelling in short-term prediction[Wind speed at wind farm sites

    Energy Technology Data Exchange (ETDEWEB)

    Badger, J.; Giebel, G.; Guo Larsen, X.; Skov Nielsen, T.; Aalborg Nielsen, H.; Madsen, Henrik; Toefting, J.

    2007-06-15

    In this report investigations using atmospheric stability measures to improve wind speed predictions at wind farm sites are described. Various stability measures have been calculated based on numerical weather prediction model output. Their ability to improve the wind speed predictions is assessed at three locations. One of the locations is in complex terrain. Mesoscale modelling has been carried out using KAMM at this location. The characteristics of the measured winds are captured well by the mesoscale modelling. It can be seen that the atmospheric stability plays an important role in determining how the flow is influence by the terrain. A prediction system employing a look-up table approach based on wind class simulations is presented. The mesoscale modelling results produced by KAMM were validated using an alternative mesoscale model called WRF. A good agreement in the results of KAMM and WRF was found. It is shown that including a stability parameter in physical and/or statistical modelling can improve the wind speed predictions at a wind farm site. A concept for the inclusion of a stability measure in the WPPT prediction system is presented, and the testing of the concept is outlined. (au)

  3. 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.

  4. Vertical cavity laser

    DEFF Research Database (Denmark)

    2016-01-01

    The present invention provides a vertical cavity laser comprising a grating layer comprising an in-plane grating, the grating layer having a first side and having a second side opposite the first side and comprising a contiguous core grating region having a grating structure, wherein an index...

  5. 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.

  6. Melatonin and oral cavity.

    Science.gov (United States)

    Cengiz, Murat İnanç; Cengiz, Seda; Wang, Hom-Lay

    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 proliferation of collagen and osseous tissue, and acts as a protector against cellular degeneration associated with aging and toxin exposure. Arising out of its antioxidant actions, melatonin protects against inflammatory processes and cellular damage caused by the toxic derivates of oxygen. As a result of these actions, melatonin may be useful as a coadjuvant in the treatment of certain conditions of the oral cavity. However, the most important effect of melatonin seems to result from its potent antioxidant, immunomodulatory, protective, and anticancer properties. Thus, melatonin could be used therapeutically for instance, locally, in the oral cavity damage of mechanical, bacterial, fungal, or viral origin, in postsurgical wounds caused by tooth extractions and other oral surgeries. Additionally, it can help bone formation in various autoimmunological disorders such as Sjorgen syndrome, in periodontal diseases, in toxic effects of dental materials, in dental implants, and in oral cancers.

  7. Melatonin and Oral Cavity

    Directory of Open Access Journals (Sweden)

    Murat İnanç Cengiz

    2012-01-01

    Full Text Available 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 proliferation of collagen and osseous tissue, and acts as a protector against cellular degeneration associated with aging and toxin exposure. Arising out of its antioxidant actions, melatonin protects against inflammatory processes and cellular damage caused by the toxic derivates of oxygen. As a result of these actions, melatonin may be useful as a coadjuvant in the treatment of certain conditions of the oral cavity. However, the most important effect of melatonin seems to result from its potent antioxidant, immunomodulatory, protective, and anticancer properties. Thus, melatonin could be used therapeutically for instance, locally, in the oral cavity damage of mechanical, bacterial, fungal, or viral origin, in postsurgical wounds caused by tooth extractions and other oral surgeries. Additionally, it can help bone formation in various autoimmunological disorders such as Sjorgen syndrome, in periodontal diseases, in toxic effects of dental materials, in dental implants, and in oral cancers.

  8. 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

  9. Filling a Conical Cavity

    Science.gov (United States)

    Nye, Kyle; Eslam-Panah, Azar

    2016-11-01

    Root canal treatment involves the removal of infected tissue inside the tooth's canal system and filling the space with a dense sealing agent to prevent further infection. A good root canal treatment happens when the canals are filled homogeneously and tightly down to the root apex. Such a tooth is able to provide valuable service for an entire lifetime. However, there are some examples of poorly performed root canals where the anterior and posterior routes are not filled completely. Small packets of air can be trapped in narrow access cavities when restoring with resin composites. Such teeth can cause trouble even after many years and lead the conditions like acute bone infection or abscesses. In this study, the filling of dead-end conical cavities with various liquids is reported. The first case studies included conical cavity models with different angles and lengths to visualize the filling process. In this investigation, the rate and completeness at which a variety of liquids fill the cavity were observed to find ideal conditions for the process. Then, a 3D printed model of the scaled representation of a molar with prepared post spaces was used to simulate the root canal treatment. The results of this study can be used to gain a better understanding of the restoration for endodontically treated teeth.

  10. Primary leiomyosarcoma of peritoneal cavity

    Directory of Open Access Journals (Sweden)

    Jyotsna Naresh Bharti

    2014-03-01

    Full Text Available Leiomyosarcomas of soft tissue are the rare tumors and the retroperitoneum is the most common site involved. We report a case of primary leiomyosarcoma of the peritoneal cavity which clinically presented with suprapubic, freely mobile, nontender mass which measured 10×10 cm in size. Contrast enhanced computed tomography revealed well defined heterogenous hypodense solid cystic mass. The mass was surgically excised out in its entirety. The histopathological examination revealed spindle cells arranged in alternating fascicles having pleomorphic nuclei, indistinct margin and eosinophilic cytoplasm with foci of haemorrhage, necrosis and 5-6 mitosis/HPF. The spindle cells were immunoreactive for smooth muscle actin, desmin and negative for S-100, CD-34 and c-kit. Histopathology and immunohistochemistry were helpful in making the final confirmatory diagnosis. Leiomyosarcomas are aggressive tumors, with poor prognosis and often difficult to treat. The survival rates are lowest among all soft tissue sarcomas.

  11. Teleportation of Cavity Field States via Cavity QED

    CERN Document Server

    Guerra, E S

    2004-01-01

    In this article we discuss two schemes of teleportation of cavity field states. In the first scheme we consider cavities prepared in a coherent state and in the second scheme we consider cavities prepared in a superposition of zero and one Fock states.

  12. Scores of amino acid 0D-3D information as applied in cleavage site prediction and better specificity elucidation for human immunodeficiency virus type 1 protease

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A new set of descriptors,namely score vectors of the zero dimension,one dimension,two dimensions and three dimensions(SZOTT),was derived from principle component analysis of a matrix of 1369 structural variables including 0D,1D,2D and 3D information for the 20 coded amino acids. SZOTT scales were then used in cleavage site prediction of human immunodeficiency virus type 1 protease. Linear discriminant analysis(LDA) and support vector machines(SVM) were applied to developing models to predict the cleavage sites. The results obtained by linear discriminant analysis(LDA) and support vector machines(SVM) are as follows. The Matthews correlation coefficients(MCC) by the resubstitution test,leave-one-out cross validation(LOOCV) and external validation are 0.879 and 0.911,0.849 and 0.901,0.822 and 0.846,respectively. The receiver operating characteristic(ROC) analysis showed that the SVM model possesses better simulative and predictive ability in comparison with the LDA model. Satisfactory results show that SZOTT descriptors can be further used to predict cleavage sites of human immunodeficiency virus type 1 protease.

  13. Scores of amino acid 0D-3D information as applied in cleavage site prediction and better specificity elucidation for human immunodeficiency virus type 1 protease

    Institute of Scientific and Technical Information of China (English)

    KANG LiFang; LIANG GuiZhao; SHU Mao; YANG ShanBin; LI ZhiLiang

    2008-01-01

    A new set of descriptors, namely score vectors of the zero dimension, one dimension, two dimensions and three dimensions (SZOTT), was derived from principle component analysis of a matrix of 1369 structural variables including 0D, 1D, 2D and 3D information for the 20 coded amino acids. SZOTT scales were then used in cleavage site prediction of human immunodeficiency virus type 1 protease. Linear discriminant analysis (LDA) and support vector machines (SVM) were applied to developing models to predict the cleavage sites. The results obtained by linear discriminant analysis (LDA) and support vector machines (SVM) are as follows. The Matthews correlation coefficients (MCC) by the resubstitution test, leave-one-out cross validation (LOOCV) and external validation are 0.879 and 0.911, 0.649 and 0.901, 0.822 and 0.846, respectively. The receiver operating characteristic (ROC) analysis showed that the SVM model possesses better simulative and predictive ability in comparison with the LDA model. Satisfactory results show that SZOTT descriptors can be further used to predict cleavage sites of human immunodeficiency virus type 1 protease.

  14. 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

  15. Apply Woods Model in the Predictions of Ambient Air Particles and Metallic Elements (Mn, Fe, Zn, Cr, and Cu at Industrial, Suburban/Coastal, and Residential Sampling Sites

    Directory of Open Access Journals (Sweden)

    Guor-Cheng Fang

    2012-01-01

    Full Text Available The main purpose for this study was to monitor ambient air particles and metallic elements (Mn, Fe, Zn, Cr, and Cu in total suspended particulates (TSPs concentration, dry deposition at three characteristic sampling sites of central Taiwan. Additionally, the calculated/measured dry deposition flux ratios of ambient air particles and metallic elements were calculated with Woods models at these three characteristic sampling sites during years of 2009-2010. As for ambient air particles, the results indicated that the Woods model generated the most accurate dry deposition prediction results when particle size was 18 μm in this study. The results also indicated that the Woods model exhibited better dry deposition prediction performance when the particle size was greater than 10 μm for the ambient air metallic elements in this study. Finally, as for Quan-xing sampling site, the main sources were many industrial factories under process around these regions and were severely polluted areas. In addition, the highest average dry deposition for Mn, Fe, Zn, and Cu species occurred at Bei-shi sampling site, and the main sources were the nearby science park, fossil fuel combustion, and Taichung thermal power plant (TTPP. Additionally, as for He-mei sampling site, the main sources were subjected to traffic mobile emissions.

  16. 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.

  17. Random forest algorithm yields accurate quantitative prediction models of benthic light at intertidal sites affected by toxic Lyngbya majuscula blooms

    NARCIS (Netherlands)

    Kehoe, M.J.; O’ Brien, K.; Grinham, A.; Rissik, D.; Ahern, K.S.; Maxwell, P.

    2012-01-01

    It is shown that targeted high frequency monitoring and modern machine learning methods lead to highly predictive models of benthic light flux. A state-of-the-art machine learning technique was used in conjunction with a high frequency data set to calibrate and test predictive benthic lights models

  18. 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.

  19. 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

  20. 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;...

  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. Access cavity preparation.

    Science.gov (United States)

    Adams, N; Tomson, P L

    2014-03-01

    Each stage of root canal treatment should be carried out to the highest possible standard. The access cavity is arguably the most important technical stage, as subsequent preparation of the root canal(s) can be severely comprised if this is not well executed. Inadequate access can lead to canals being left untreated, poorly disinfected, difficult to shape and obturate, and may ultimately lead to the failure of the treatment. This paper highlights common features in root canal anatomy and outlines basic principles for locating root canals and producing a good access cavity. It also explores each phase of the preparation in detail and offers suggestions of instruments that have been specifically designed to overcome potential difficulties in the process. Good access design and preparation will result in an operative environment which will facilitate cleaning, shaping and obturation of the root canal system in order to maximise success.

  3. Cavity enhanced atomic magnetometry

    CERN Document Server

    Crepaz, Herbert; Dumke, Rainer

    2015-01-01

    Atom sensing based on Faraday rotation is an indispensable method for precision measurements, universally suitable for both hot and cold atomic systems. Here we demonstrate an all-optical magnetometer where the optical cell for Faraday rotation spectroscopy is augmented with a low finesse cavity. Unlike in previous experiments, where specifically designed multipass cells had been employed, our scheme allows to use conventional, spherical vapour cells. Spherical shaped cells have the advantage that they can be effectively coated inside with a spin relaxation suppressing layer providing long spin coherence times without addition of a buffer gas. Cavity enhancement shows in an increase in optical polarization rotation and sensitivity compared to single-pass configurations.

  4. Cavity enhanced atomic magnetometry.

    Science.gov (United States)

    Crepaz, Herbert; Ley, Li Yuan; Dumke, Rainer

    2015-10-20

    Atom sensing based on Faraday rotation is an indispensable method for precision measurements, universally suitable for both hot and cold atomic systems. Here we demonstrate an all-optical magnetometer where the optical cell for Faraday rotation spectroscopy is augmented with a low finesse cavity. Unlike in previous experiments, where specifically designed multipass cells had been employed, our scheme allows to use conventional, spherical vapour cells. Spherical shaped cells have the advantage that they can be effectively coated inside with a spin relaxation suppressing layer providing long spin coherence times without addition of a buffer gas. Cavity enhancement shows in an increase in optical polarization rotation and sensitivity compared to single-pass configurations.

  5. An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins.

    Directory of Open Access Journals (Sweden)

    Cheng Zheng

    Full Text Available Zinc-binding proteins are the most abundant metalloproteins in the Protein Data Bank where the zinc ions usually have catalytic, regulatory or structural roles critical for the function of the protein. Accurate prediction of zinc-binding sites is not only useful for the inference of protein function but also important for the prediction of 3D structure. Here, we present a new integrative framework that combines multiple sequence and structural properties and graph-theoretic network features, followed by an efficient feature selection to improve prediction of zinc-binding sites. We investigate what information can be retrieved from the sequence, structure and network levels that is relevant to zinc-binding site prediction. We perform a two-step feature selection using random forest to remove redundant features and quantify the relative importance of the retrieved features. Benchmarking on a high-quality structural dataset containing 1,103 protein chains and 484 zinc-binding residues, our method achieved >80% recall at a precision of 75% for the zinc-binding residues Cys, His, Glu and Asp on 5-fold cross-validation tests, which is a 10%-28% higher recall at the 75% equal precision compared to SitePredict and zincfinder at residue level using the same dataset. The independent test also indicates that our method has achieved recall of 0.790 and 0.759 at residue and protein levels, respectively, which is a performance better than the other two methods. Moreover, AUC (the Area Under the Curve and AURPC (the Area Under the Recall-Precision Curve by our method are also respectively better than those of the other two methods. Our method can not only be applied to large-scale identification of zinc-binding sites when structural information of the target is available, but also give valuable insights into important features arising from different levels that collectively characterize the zinc-binding sites. The scripts and datasets are available at http://protein.cau.edu.cn/zincidentifier/.

  6. Cavity enhanced atomic magnetometry

    OpenAIRE

    Herbert Crepaz; Li Yuan Ley; Rainer Dumke

    2015-01-01

    Atom sensing based on Faraday rotation is an indispensable method for precision measurements, universally suitable for both hot and cold atomic systems. Here we demonstrate an all-optical magnetometer where the optical cell for Faraday rotation spectroscopy is augmented with a low finesse cavity. Unlike in previous experiments, where specifically designed multipass cells had been employed, our scheme allows to use conventional, spherical vapour cells. Spherical shaped cells have the advantage...

  7. Prediction of Post-Closure Water Balance for Monolithic Soil Covers at Waste Disposal Sites in the Greater Accra Metropolitan Area of Ghana

    OpenAIRE

    Kodwo Beedu Keelson

    2014-01-01

    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 i...

  8. Cavity QED by the Numbers

    Science.gov (United States)

    Kimble, H. J.; Boca, A.; Boozer, A. D.; Bowen, W. P.; Buck, J. R.; Chou, C. W.; Duan, L.-M.; Kuzmich, A.; McKeever, J.

    2004-12-01

    Observations of cooling and trapping of N = 1,2,3,... atoms inside a small optical cavity are described. The atom-cavity system operates in a regime of strong coupling for which single photons are sufficient to saturate the atomic response. New theoretical protocols for the efficient engineering of multi-atom entanglement within the setting of cavity QED are described. By trapping a single atom within the cavity mode, a one-atom laser is experimentally realized in a regime of strong coupling. Beyond the setting of cavity QED, quantum correlations have been observed for photon pairs emitted from an atomic ensemble and with a programmable time offset.

  9. Capillary condensation for fluids in spherical cavities

    OpenAIRE

    Urrutia, Ignacio; Szybisz, Leszek

    2005-01-01

    The capillary condensation for fluids into spherical nano-cavities is analyzed within the frame of two theoretical approaches. One description is based on a widely used simplified version of the droplet model formulated for studying atomic nuclei. The other, is a more elaborated calculation performed by applying a density functional theory. The agreement between both models is examined and it is shown that a small correction to the simple fluid model improves the predictions. A connection to ...

  10. Multi-Site Validation of the SWAT Model on the Bani Catchment: Model Performance and Predictive Uncertainty

    Directory of Open Access Journals (Sweden)

    Jamilatou Chaibou Begou

    2016-04-01

    Full Text Available The objective of this study was to assess the performance and predictive uncertainty of the Soil and Water Assessment Tool (SWAT model on the Bani River Basin, at catchment and subcatchment levels. The SWAT model was calibrated using the Generalized Likelihood Uncertainty Estimation (GLUE approach. Potential Evapotranspiration (PET and biomass were considered in the verification of model outputs accuracy. Global Sensitivity Analysis (GSA was used for identifying important model parameters. Results indicated a good performance of the global model at daily as well as monthly time steps with adequate predictive uncertainty. PET was found to be overestimated but biomass was better predicted in agricultural land and forest. Surface runoff represents the dominant process on streamflow generation in that region. Individual calibration at subcatchment scale yielded better performance than when the global parameter sets were applied. These results are very useful and provide a support to further studies on regionalization to make prediction in ungauged basins.

  11. 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.

  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. Macrophage inflammatory protein-1α shows predictive value as a risk marker for subjects and sites vulnerable to bone loss in a longitudinal model of aggressive periodontitis.

    Directory of Open Access Journals (Sweden)

    Daniel H Fine

    Full Text Available Improved diagnostics remains a fundamental goal of biomedical research. This study was designed to assess cytokine biomarkers that could predict bone loss (BL in localized aggressive periodontitis. 2,058 adolescents were screened. Two groups of 50 periodontally healthy adolescents were enrolled in the longitudinal study. One group had Aggregatibacter actinomycetemcomitans (Aa, the putative pathogen, while the matched cohort did not. Cytokine levels were assessed in saliva and gingival crevicular fluid (GCF. Participants were sampled, examined, and radiographed every 6 months for 2-3 years. Disease was defined as radiographic evidence of BL. Saliva and GCF was collected at each visit, frozen, and then tested retrospectively after detection of BL. Sixteen subjects with Aa developed BL. Saliva from Aa-positive and Aa-negative healthy subjects was compared to subjects who developed BL. GCF was collected from 16 subjects with BL and from another 38 subjects who remained healthy. GCF from BL sites in the 16 subjects was compared to healthy sites in these same subjects and to healthy sites in subjects who remained healthy. Results showed that cytokines in saliva associated with acute inflammation were elevated in subjects who developed BL (i.e., MIP-1α MIP-1β IL-α, IL-1β and IL-8; p<0.01. MIP-1α was elevated 13-fold, 6 months prior to BL. When MIP-1α levels were set at 40 pg/ml, 98% of healthy sites were below that level (Specificity; whereas, 93% of sites with BL were higher (Sensitivity, with comparable Predictive Values of 98%; p<0.0001; 95% C.I. = 42.5-52.7. MIP-1α consistently showed elevated levels as a biomarker for BL in both saliva and GCF, 6 months prior to BL. MIP-1α continues to demonstrate its strong candidacy as a diagnostic biomarker for both subject and site vulnerability to BL.

  15. Monte carlo simulation of base and nucleotide excision repair of clustered DNA damage sites. II. Comparisons of model predictions to measured data.

    Science.gov (United States)

    Semenenko, V A; Stewart, R D

    2005-08-01

    Clustered damage sites other than double-strand breaks (DSBs) have the potential to contribute to deleterious effects of ionizing radiation, such as cell killing and mutagenesis. In the companion article (Semenenko et al., Radiat. Res. 164, 180-193, 2005), a general Monte Carlo framework to simulate key steps in the base and nucleotide excision repair of DNA damage other than DSBs is proposed. In this article, model predictions are compared to measured data for selected low-and high-LET radiations. The Monte Carlo model reproduces experimental observations for the formation of enzymatic DSBs in Escherichia coli and cells of two Chinese hamster cell lines (V79 and xrs5). Comparisons of model predictions with experimental values for low-LET radiation suggest that an inhibition of DNA backbone incision at the sites of base damage by opposing strand breaks is active over longer distances between the damaged base and the strand break in hamster cells (8 bp) compared to E. coli (3 bp). Model estimates for the induction of point mutations in the human hypoxanthine guanine phosphoribosyl transferase (HPRT) gene by ionizing radiation are of the same order of magnitude as the measured mutation frequencies. Trends in the mutation frequency for low- and high-LET radiation are predicted correctly by the model. The agreement between selected experimental data sets and simulation results provides some confidence in postulated mechanisms for excision repair of DNA damage other than DSBs and suggests that the proposed Monte Carlo scheme is useful for predicting repair outcomes.

  16. DR-predictor: incorporating flexible docking with specialized electronic reactivity and machine learning techniques to predict CYP-mediated sites of metabolism.

    Science.gov (United States)

    Huang, Tao-wei; Zaretzki, Jed; Bergeron, Charles; Bennett, Kristin P; Breneman, Curt M

    2013-12-23

    Computational methods that can identify CYP-mediated sites of metabolism (SOMs) of drug-like compounds have become required tools for early stage lead optimization. In recent years, methods that combine CYP binding site features with CYP/ligand binding information have been sought in order to increase the prediction accuracy of such hybrid models over those that use only one representation. Two challenges that any hybrid ligand/structure-based method must overcome are (1) identification of the best binding pose for a specific ligand with a given CYP and (2) appropriately incorporating the results of docking with ligand reactivity. To address these challenges we have created Docking-Regioselectivity-Predictor (DR-Predictor)--a method that incorporates flexible docking-derived information with specialized electronic reactivity and multiple-instance-learning methods to predict CYP-mediated SOMs. In this study, the hybrid ligand-structure-based DR-Predictor method was tested on substrate sets for CYP 1A2 and CYP 2A6. For these data, the DR-Predictor model was found to identify the experimentally observed SOM within the top two predicted rank-positions for 86% of the 261 1A2 substrates and 83% of the 100 2A6 substrates. Given the accuracy and extendibility of the DR-Predictor method, we anticipate that it will further facilitate the prediction of CYP metabolism liabilities and aid in in-silico ADMET assessment of novel structures.

  17. 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.

  18. Analytical modeling of printed metasurface cavities for computational imaging

    Science.gov (United States)

    F. Imani, Mohammadreza; Sleasman, Timothy; Gollub, Jonah N.; Smith, David R.

    2016-10-01

    We derive simple analytical expressions to model the electromagnetic response of an electrically large printed cavity. The analytical model is then used to develop printed cavities for microwave imaging purposes. The proposed cavity is excited by a cylindrical source and has boundaries formed by subwavelength metallic cylinders (vias) placed at subwavelength distances apart. Given their small size, the electric currents induced on the vias are assumed to have no angular dependence. Applying this approximation simplifies the electromagnetic problem to a matrix equation which can be solved to directly compute the electric current induced on each via. Once the induced currents are known, the electromagnetic field inside the cavity can be computed for every location. We verify the analytical model by comparing its prediction to full-wave simulations. To utilize this cavity in imaging settings, we perforate one side of the printed cavity with radiative slots such that they act as the physical layer of a computational imaging system. An analytical approximation for the slots is also developed, enabling us to obtain estimates of the cavity performance in imaging scenarios. This ability allows us to make informed decisions on the design of the printed metasurface cavity. The utility of the proposed model is further highlighted by demonstrating high-quality experimental imaging; performance metrics, which are consistent between theory and experiment, are also estimated.

  19. Observation of Three Mode Parametric Interactions in Long Optical Cavities

    CERN Document Server

    Zhao, C; Fan, Y; Slagmolen, S Gras B J J; Miao, H; Blair, P Barriga D G; Hosken, D J; Brooks, A F; Veitch, P J; Mudge, D; Munch, J

    2008-01-01

    We report the first observation of three-mode opto-acoustic parametric interactions of the type predicted to cause parametric instabilities in an 80 m long, high optical power cavity that uses suspended sapphire mirrors. Resonant interaction occurs between two distinct optical modes and an acoustic mode of one mirror when the difference in frequency between the two optical cavity modes is close to the frequency of the acoustic mode. Experimental results validate the theory of parametric instability in high power optical cavities.

  20. Two Domain Flow Method for Leachate PredictionThrough Municipal Solid Waste Layers in Al–Amari Landfill Site

    Directory of Open Access Journals (Sweden)

    Hayder Mohammed Abdul–Hameed

    2008-01-01

    Full Text Available Existing leachate models over–or underestimates leachate generation by up to three orders of magnitude. Practical experiments show that channeled flow in waste leads to rapid discharge of large leachate volumes and heterogeneous moisture distribution. In order to more accurately predict leachate generation, leachate models must be improved. To predict moisture movement through waste, the two–domain PREFLO, are tested. Experimental waste and leachate flow values are compared with model predictions. When calibrated with experimental parameters, the PREFLO provides estimates of breakthrough time. In the short term, field capacity has to be reduced to 0.12 and effective storage and hydraulic conductivity of the waste must be increased to 0.12 and effective storage and hydraulic conductivity of the wasted must be increased to 0.2 and 2.2 cm/s respectively. In the long term, a new modeling approach must be developed to adequately describe the moisture movement mechanisms.

  1. Design of photonic crystal microcavities for cavity QED.

    Science.gov (United States)

    Vucković, Jelena; Loncar, Marko; Mabuchi, Hideo; Scherer, Axel

    2002-01-01

    We discuss the optimization of optical microcavity designs based on two-dimensional photonic crystals for the purpose of strong coupling between the cavity field and a single neutral atom trapped within a hole. We present numerical predictions for the quality factors and mode volumes of localized defect modes as a function of geometric parameters, and discuss some experimental challenges related to the coupling of a defect cavity to gas-phase atoms.

  2. Interactome-Wide Prediction of Protein-Protein Binding Sites Reveals Effects of Protein Sequence Variation in Arabidopsis thaliana

    NARCIS (Netherlands)

    Valentim, F.L.; Neven, F.; Boyen, P.; Dijk, van A.D.J.

    2012-01-01

    The specificity of protein-protein interactions is encoded in those parts of the sequence that compose the binding interface. Therefore, understanding how changes in protein sequence influence interaction specificity, and possibly the phenotype, requires knowing the location of binding sites in thos

  3. LRRK2 Kinase Activity and Biology are Not Uniformly Predicted by its Autophosphorylation and Cellular Phosphorylation Site Status

    Directory of Open Access Journals (Sweden)

    April eReynolds

    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.

  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. 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.

  6. Predicting the Metabolic Sites by Flavin-Containing Monooxygenase on Drug Molecules Using SVM Classification on Computed Quantum Mechanics and Circular Fingerprints Molecular Descriptors

    Science.gov (United States)

    Fu, Chien-wei; Lin, Thy-Hou

    2017-01-01

    As an important enzyme in Phase I drug metabolism, the flavin-containing monooxygenase (FMO) also metabolizes some xenobiotics with soft nucleophiles. The site of metabolism (SOM) on a molecule is the site where the metabolic reaction is exerted by an enzyme. Accurate prediction of SOMs on drug molecules will assist the search for drug leads during the optimization process. Here, some quantum mechanics features such as the condensed Fukui function and attributes from circular fingerprints (called Molprint2D) are computed and classified using the support vector machine (SVM) for predicting some potential SOMs on a series of drugs that can be metabolized by FMO enzymes. The condensed Fukui function fA− representing the nucleophilicity of central atom A and the attributes from circular fingerprints accounting the influence of neighbors on the central atom. The total number of FMO substrates and non-substrates collected in the study is 85 and they are equally divided into the training and test sets with each carrying roughly the same number of potential SOMs. However, only N-oxidation and S-oxidation features were considered in the prediction since the available C-oxidation data was scarce. In the training process, the LibSVM package of WEKA package and the option of 10-fold cross validation are employed. The prediction performance on the test set evaluated by accuracy, Matthews correlation coefficient and area under ROC curve computed are 0.829, 0.659, and 0.877 respectively. This work reveals that the SVM model built can accurately predict the potential SOMs for drug molecules that are metabolizable by the FMO enzymes. PMID:28072829

  7. Effects of soil depth and subsurface flow along the subsurface topography on shallow landslide predictions at the site of a small granitic hillslope

    Science.gov (United States)

    Kim, Min Seok; Onda, Yuichi; Uchida, Taro; Kim, Jin Kwan

    2016-10-01

    Shallow landslides are affected by various conditions, including soil depth and subsurface flow via an increase in the pore water pressure. In this study, we evaluate the effect of soil depth and subsurface flow on shallow landslide prediction using the shallow landslide stability (SHALSTAB) model. Three detailed soil depth data-the average soil depth, weathered soil depth, and bedrock soil depth-were collected using a knocking pole test at a small hillslope site composed of granite in the Republic of Korea. The SHALSTAB model was applied to a ground surface topographic digital elevation model (DEM) using the three soil depths and upslope contributing area (SCA) assuming subsurface flow calculated from four DEMs: a ground surface topography (GSTO) DEM, weathered soil topography (WSTO) DEM, bedrock topography (BSTO) DEM, and low-level bedrock topography (EBSTO) DEM. The model performance was measured using a receiver operating characteristic (ROC) analysis. While evaluating the effect of the soil depth with SCA using GSTO DEM, it was found that the bedrock soil depth had higher prediction accuracy compared to that of the average soil depth or weathered soil depth. To evaluate the saturated subsurface flow between the soil and bedrock, SCAs calculated using WSTO and BSTO DEMs were applied. From these simulations, we found that SCA from BSTO DEM and the bedrock soil depth affect the shallow landslide prediction; however, these prediction effects are not significantly increased by large differences in the elevation (between the lowest and highest elevation values). Therefore, we considered the influence of the bedrock depression and SCA from EBSTO DEM. In applying SCA from EBSTO, the prediction accuracy was significantly increased compared to the other predictions. Our results demonstrate that the influence of the bedrock topography on the prediction of shallow landslides may be particularly significant at the scale of a hillslope.

  8. Practical Cost-Optimization of Characterization and Remediation Decisions at DNAPL Sites with Consideration of Prediction Uncertainty

    Science.gov (United States)

    2011-05-01

    many refinements through the project to simulate electron donor-limited biodecay, thermal remediation, and other processes . Mike Cardiff, under the...were undertaken to reduce source zone uncertainty. The method was also used to optimize source and plume bioremediation at the EGDY site, using whey ...with a 93% probability of success when using relatively low whey injection rates. The methodology was applied to Dover AFB Area 5 to optimize

  9. Applications of cavity optomechanics

    Energy Technology Data Exchange (ETDEWEB)

    Metcalfe, Michael [Booz Allen Hamilton, 3811 Fairfax Drive, Arlington, Virginia 22203 (United States)

    2014-09-15

    Cavity-optomechanics” aims to study the quantum properties of mechanical systems. A common strategy implemented in order to achieve this goal couples a high finesse photonic cavity to a high quality factor mechanical resonator. Then, using feedback forces such as radiation pressure, one can cool the mechanical mode of interest into the quantum ground state and create non-classical states of mechanical motion. On the path towards achieving these goals, many near-term applications of this field have emerged. After briefly introducing optomechanical systems and describing the current state-of-the-art experimental results, this article summarizes some of the more exciting practical applications such as ultra-sensitive, high bandwidth accelerometers and force sensors, low phase noise x-band integrated microwave oscillators and optical signal processing such as optical delay-lines, wavelength converters, and tunable optical filters. In this rapidly evolving field, new applications are emerging at a fast pace, but this article concentrates on the aforementioned lab-based applications as these are the most promising avenues for near-term real-world applications. New basic science applications are also becoming apparent such as the generation of squeezed light, testing gravitational theories and for providing a link between disparate quantum systems.

  10. Applications of cavity optomechanics

    Science.gov (United States)

    Metcalfe, Michael

    2014-09-01

    "Cavity-optomechanics" aims to study the quantum properties of mechanical systems. A common strategy implemented in order to achieve this goal couples a high finesse photonic cavity to a high quality factor mechanical resonator. Then, using feedback forces such as radiation pressure, one can cool the mechanical mode of interest into the quantum ground state and create non-classical states of mechanical motion. On the path towards achieving these goals, many near-term applications of this field have emerged. After briefly introducing optomechanical systems and describing the current state-of-the-art experimental results, this article summarizes some of the more exciting practical applications such as ultra-sensitive, high bandwidth accelerometers and force sensors, low phase noise x-band integrated microwave oscillators and optical signal processing such as optical delay-lines, wavelength converters, and tunable optical filters. In this rapidly evolving field, new applications are emerging at a fast pace, but this article concentrates on the aforementioned lab-based applications as these are the most promising avenues for near-term real-world applications. New basic science applications are also becoming apparent such as the generation of squeezed light, testing gravitational theories and for providing a link between disparate quantum systems.

  11. JLEIC SRF cavity RF Design

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Shaoheng [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Guo, Jiquan [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Wang, Haipeng [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Rimmer, Robert A. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    2016-05-01

    The initial design of a low higher order modes (HOM) impedance superconducting RF (SRF) cavity is presented in this paper. The design of this SRF cavity is for the proposed Jefferson Lab Electron Ion Collider (JLEIC). The electron ring of JLEIC will operate with electrons of 3 to 10 GeV energy. The ion ring of JLEIC will operate with protons of up to 100 GeV energy. The bunch lengths in both rings are ~12 mm (RMS). In order to maintain the short bunch length in the ion ring, SRF cavities are adopted to provide large enough gradient. In the first phase of JLEIC, the PEP II RF cavities will be reused in the electron ring to lower the initial cost. The frequency of the SRF cavities is chosen to be the second harmonic of PEP II cavities, 952.6 MHz. In the second phase of JLEIC, the same frequency SRF cavities may replace the normal conducting PEP II cavities to achieve higher luminosity at high energy. At low energies, the synchro-tron radiation damping effect is quite weak, to avoid the coupled bunch instability caused by the intense closely-spaced electron bunches, low HOM impedance of the SRF cavities combined with longitudinal feedback sys-tem will be necessary.

  12. 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.

  13. In silico prediction of the site of oxidation by cytochrome P450 3A4 that leads to the formation of the toxic metabolites of pyrrolizidine alkaloids.

    Science.gov (United States)

    Fashe, Muluneh M; Juvonen, Risto O; Petsalo, Aleksanteri; Vepsäläinen, Jouko; Pasanen, Markku; Rahnasto-Rilla, Minna

    2015-04-20

    In humans, the metabolic bioactivation of pyrrolizidine alkaloids (PAs) is mediated mainly by cytochrome P450 3A4 (CYP3A4) via the hydroxylation of their necine bases at C3 or C8 of heliotridine- and retronecine-type PAs or at the N atom of the methyl substituent of otonecine-type PAs. However, no attempts have been made to identify which C atom is the most favorable site for hydroxylation in silico. Here, in order to determine the site of hydroxylation that eventually leads to the formation of the toxic metabolites produced from lasiocarpine, retrorsine, and senkirkin, we utilized the ligand-based electrophilic Fukui function f(-)(r) and hydrogen-bond dissociation energies (BDEs) as well as structure-based molecular docking. The ligand-based computations revealed that the C3 and C8 atoms of lasiocarpine and retrorsine and the C26 atom of senkirkin were chemically the most susceptible locations for electrophilic oxidizing reactions. Similarly, according to the predicted binding orientation in the active site of the crystal structure of human CYP3A4 (PDB code: 4I4G ), the alkaloids were positioned in such a way that the C3 atom of lasiocarpine and retrorsine and the C26 of senkirkin were closest to the catalytic heme Fe. Thus, it is concluded that the C3 atom of lasiocarpine and retrorsine and C26 of senkirkin are the most favored sites of hydroxylation that lead to the production of their toxic metabolites.

  14. 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.

  15. Receptor site topographies for phencyclidine-like and sigma drugs: predictions from quantitative conformational, electrostatic potential, and radioreceptor analyses.

    Science.gov (United States)

    Manallack, D T; Wong, M G; Costa, M; Andrews, P R; Beart, P M

    1988-12-01

    Computer-assisted molecular modelling techniques and electrostatic analyses of a wide range of phenycyclidine (PCP) and sigma ligands, in conjunction with radioreceptor studies, were used to determine the topographies of the PCP and sigma receptors. The PCP receptor model was defined using key molecules from the arylcyclohexylamine, benzomorphan, bridged benz[f]isoquinoline, and dibenzocycloalkenimine drug classes. Hypothetical receptor points (R1, R2) were constructed onto the aromatic ring of each compound to represent hydrophobic interactions with the receptor, along with an additional receptor point (R3) representing a hydrogen bond between the nitrogen atom and the receptor. The superimposition of these key molecules gave the coordinates of the receptor points and nitrogen defining the primary PCP pharmacophore as follows: R1 (0.00, 3.50, 0.00), R2 (0.00, -3.50, 0.00), R3 (6.66, -1.13, 0.00), and N (3.90, -1.46, -0.32). Additional analyses were used to describe secondary binding sites for an additional hydrogen bonding site and two lipophilic clefts. Similarly, the sigma receptor model was constructed from ligands of the benzomorphan, octahydrobenzo[f]quinoline, phenylpiperidine, and diphenylguanidine drug classes. Coordinates for the primary sigma pharmacophore are as follows: R1 (0.00, 3.50, 0.00), R2 (0.00, -3.50, 0.00), R3 (6.09, 2.09, 0.00), and N (4.9, -0.12, -1.25). Secondary binding sites for sigma ligands were proposed for the interaction of aromatic ring substituents and large N-substituted lipophilic groups with the receptor. The sigma receptor model differs from the PCP model in the position of nitrogen atom, direction of the nitrogen lone pair vector, and secondary sigma binding sites. This study has thus demonstrated that the differing quantitative structure-activity relationships of PCP and sigma ligands allow the definition of discrete receptors. These models may be used in conjunction with rational drug design techniques to design novel PCP

  16. Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA as a model region.

    Directory of Open Access Journals (Sweden)

    Marie-Laure Endale Ahanda

    Full Text Available THE SLA (swine leukocyte antigen, MHC: SLA genes are the most important determinants of immune, infectious disease and vaccine response in pigs; several genetic associations with immunity and swine production traits have been reported. However, most of the current knowledge on SLA is limited to gene coding regions. MicroRNAs (miRNAs are small molecules that post-transcriptionally regulate the expression of a large number of protein-coding genes in metazoans, and are suggested to play important roles in fine-tuning immune mechanisms and disease responses. Polymorphisms in either miRNAs or their gene targets may have a significant impact on gene expression by abolishing, weakening or creating miRNA target sites, possibly leading to phenotypic variation. We explored the impact of variants in the 3'-UTR miRNA target sites of genes within the whole SLA region. The combined predictions by TargetScan, PACMIT and TargetSpy, based on different biological parameters, empowered the identification of miRNA target sites and the discovery of polymorphic miRNA target sites (poly-miRTSs. Predictions for three SLA genes characterized by a different range of sequence variation provided proof of principle for the analysis of poly-miRTSs from a total of 144 M RNA-Seq reads collected from different porcine tissues. Twenty-four novel SNPs were predicted to affect miRNA-binding sites in 19 genes of the SLA region. Seven of these genes (SLA-1, SLA-6, SLA-DQA, SLA-DQB1, SLA-DOA, SLA-DOB and TAP1 are linked to antigen processing and presentation functions, which is reminiscent of associations with disease traits reported for altered miRNA binding to MHC genes in humans. An inverse correlation in expression levels was demonstrated between miRNAs and co-expressed SLA targets by exploiting a published dataset (RNA-Seq and small RNA-Seq of three porcine tissues. Our results support the resource value of RNA-Seq collections to identify SNPs that may lead to altered mi

  17. Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA) as a model region.

    Science.gov (United States)

    Endale Ahanda, Marie-Laure; Fritz, Eric R; Estellé, Jordi; Hu, Zhi-Liang; Madsen, Ole; Groenen, Martien A M; Beraldi, Dario; Kapetanovic, Ronan; Hume, David A; Rowland, Robert R R; Lunney, Joan K; Rogel-Gaillard, Claire; Reecy, James M; Giuffra, Elisabetta

    2012-01-01

    THE SLA (swine leukocyte antigen, MHC: SLA) genes are the most important determinants of immune, infectious disease and vaccine response in pigs; several genetic associations with immunity and swine production traits have been reported. However, most of the current knowledge on SLA is limited to gene coding regions. MicroRNAs (miRNAs) are small molecules that post-transcriptionally regulate the expression of a large number of protein-coding genes in metazoans, and are suggested to play important roles in fine-tuning immune mechanisms and disease responses. Polymorphisms in either miRNAs or their gene targets may have a significant impact on gene expression by abolishing, weakening or creating miRNA target sites, possibly leading to phenotypic variation. We explored the impact of variants in the 3'-UTR miRNA target sites of genes within the whole SLA region. The combined predictions by TargetScan, PACMIT and TargetSpy, based on different biological parameters, empowered the identification of miRNA target sites and the discovery of polymorphic miRNA target sites (poly-miRTSs). Predictions for three SLA genes characterized by a different range of sequence variation provided proof of principle for the analysis of poly-miRTSs from a total of 144 M RNA-Seq reads collected from different porcine tissues. Twenty-four novel SNPs were predicted to affect miRNA-binding sites in 19 genes of the SLA region. Seven of these genes (SLA-1, SLA-6, SLA-DQA, SLA-DQB1, SLA-DOA, SLA-DOB and TAP1) are linked to antigen processing and presentation functions, which is reminiscent of associations with disease traits reported for altered miRNA binding to MHC genes in humans. An inverse correlation in expression levels was demonstrated between miRNAs and co-expressed SLA targets by exploiting a published dataset (RNA-Seq and small RNA-Seq) of three porcine tissues. Our results support the resource value of RNA-Seq collections to identify SNPs that may lead to altered miRNA regulation patterns.

  18. The cavity approach to parallel dynamics of Ising spins on a graph

    Science.gov (United States)

    Neri, I.; Bollé, D.

    2009-08-01

    We use the cavity method to study the parallel dynamics of disordered Ising models on a graph. In particular, we derive a set of recursive equations in single-site probabilities of paths propagating along the edges of the graph. These equations are analogous to the cavity equations for equilibrium models and are exact on a tree. On graphs with exclusively directed edges we find an exact expression for the stationary distribution. We present the phase diagrams for an Ising model on an asymmetric Bethe lattice and for a neural network with Hebbian interactions on an asymmetric scale-free graph. For graphs with a nonzero fraction of symmetric edges the equations can be solved for a finite number of time steps. Theoretical predictions are confirmed by simulations. Using a heuristic method the cavity equations are extended to a set of equations that determine the marginals of the stationary distribution of Ising models on graphs with a nonzero fraction of symmetric edges. The results from this method are discussed and compared with simulations.

  19. Predicting the right spacing between protein immobilization sites on self-assembled monolayers to optimize ligand binding.

    Science.gov (United States)

    Perez, Javier Batista; Tyagi, Deependra; Yang, Mo; Calvo, Loany; Perez, Rolando; Moreno, Ernesto; Zhu, Jinsong

    2015-09-01

    Self-assembled monolayers designed to immobilize capture antibodies are usually prepared using a mixture of functional and inactive linkers. Here, using low molar ratios (1:1 to 1:100) of the two linkers resulted in loss of binding capability of the anti-EGFR (epidermal growth factor receptor) antibody nimotuzumab, as assessed by surface plasmon resonance imaging. We then developed a simple theoretical model to predict the optimal surface density of the functional linker, taking into account the antibody size and linker diameter. A high (1:1000) dilution of the functional linker yielded the best results. As an advantage, this approach does not require chemical modification of the protein.

  20. 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.

  1. 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...

  2. Shock induced cavity collapse

    Science.gov (United States)

    Skidmore, Jonathan; Doyle, Hugo; Tully, Brett; Betney, Matthew; Foster, Peta; Ringrose, Tim; Ramasamy, Rohan; Parkin, James; Edwards, Tom; Hawker, Nicholas

    2016-10-01

    Results from the experimental investigation of cavity collapse driven by a strong planar shock (>6km/s) are presented. Data from high speed framing cameras, laser backlit diagnostics and time-resolved pyromety are used to validate the results of hydrodynamic front-tracking simulations. As a code validation exercise, a 2-stage light gas gun was used to accelerate a 1g Polycarbonate projectile to velocities exceeding 6km/s; impact with a PMMA target containing a gas filled void results in the formation of a strong shockwave with pressures exceeding 1Mbar. The subsequent phenomena associated with the collapse of the void and excitation of the inert gas fill are recorded and compared to simulated data. Variation of the mass density and atomic number of the gas fill is used to alter the plasma parameters furthering the extent of the code validation.

  3. 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.

  4. 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...

  5. A GIS-based prediction and assessment system of off-site accident consequence for Guangdong nuclear power plant.

    Science.gov (United States)

    Wang, X Y; Qu, J Y; Shi, Z Q; Ling, Y S

    2003-01-01

    GNARD (Guangdong Nuclear Accident Real-time Decision support system) is a decision support system for off-site emergency management in the event of an accidental release from the nuclear power plants located in Guangdong province, China. The system is capable of calculating wind field, concentrations of radionuclide in environmental media and radiation doses. It can also estimate the size of the area where protective actions should be taken and provide other information about population distribution and emergency facilities available in the area. Furthermore, the system can simulate and evaluate the effectiveness of countermeasures assumed and calculate averted doses by protective actions. All of the results can be shown and analysed on the platform of a geographical information system (GIS).

  6. LEP radio-frequency cavity

    CERN Multimedia

    1991-01-01

    One of the copper radio-frequency accelerating cavities installed for the first phase of LEP (1989-1995). Bunches of electrons and positrons circulated in LEP in opposite directions and were accelerated in eight different sets of 16 cavities (situated on either side of the four experiments), gaining 400 million volts of accelerating power per turn.

  7. Single and Coupled Nanobeam Cavities

    DEFF Research Database (Denmark)

    Ivinskaya, Aliaksandra; Lavrinenko, Andrei; Shyroki, Dzmitry M.

    2013-01-01

    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 characteristics...

  8. Quantum entanglement purification in cavities

    CERN Document Server

    Romero, J L; Saavedra, C; Retamal, J C

    2002-01-01

    A physical implementation of an entanglement purification protocol is studied using a cavity quantum electrodynamic based proposal, where, the quantum information is stored in quantum field sates inside cavities. Also a procedure is given for quantifying the degree of entanglement between quantum fields. (Author)

  9. 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.

  10. Theoretical prediction of single-site surface-protonation equilibrium constants for oxides and silicates in water

    Energy Technology Data Exchange (ETDEWEB)

    Sverjensky, D.A.; Sahai, N. [Johns Hopkins Univ., Baltimore, MD (United States)

    1996-10-01

    The equilibrium constants for surface protonation of solid oxides and silicates can be estimated from theoretical considerations and known properties of the solids for use in the constant capacitance, diffuse double layer or triple layer models of surface complexation. The theoretical considerations take into account Born solvation theory for the adsorbing proton, electrostatic interactions of the adsorbing proton with a surface oxygen and an underlying metal, and an intrinsic binding of the proton to the surface. As a consequence, the equilibrium constants for the {nu}th ({nu} = 1 or 2) surface protonation reaction on the kth solid can be expressed in terms of the inverse of the dielectric constant of the solid (1/{epsilon}{sub k}) and an average Pauling bond strength per angstrom (s/r{sub M-OH}) for the solid according to log K{sub {nu}} = M{sub {nu}}(1/{epsilon}{sub k}) - B{sub {nu}}(s/r{sub M-OH}) + log K{sub ii,{nu}}{sup {double_prime}}, where the coefficients M{sub {nu}} B{sub {nu}} and K{sub ii{nu}}{sup {double_prime}} are constants characteristic of all oxides and silicates for each surface complexation model. Evaluation of these constants using experimental data for TiO{sub 2}, {gamma}-alumina, Al{sub 2}O{sub 3} FeOOH, Fe(OH){sub 3}, silica, quartz. and kaolinite permits widespread prediction of surface protonation equilibrium constants from the known bulk structure properties 1/{epsilon}{sub k} and s/r{sub M-OH}. Such predictions should replace attempts to estimate surface protonation equilibrium constants for solids from empirical correlations with aqueous equilibrium constants. Surface protonation constants should also not be estimated from correlations with only the Pauling bond strength because these neglect specific treatment of salvation. 92 refs., 14 figs., 4 tabs.

  11. SDS-Page and numerical analysis of Candida albicans from human oral cavity and other anatomical sites Eletroforese de proteínas totais e análise numérica de Candida albicans isolada da cavidade oral e outros sítios anatômicos de humanos

    Directory of Open Access Journals (Sweden)

    Cristina Crespo Rodrigues

    2004-06-01

    Full Text Available The aim of the present research was to evaluate the protein polymorphism degrees among forty-eight C. albicans isolates from fourteen anatomical sites of clinical patients by polyacrylamide gel electrophoresis (SDS-PAGE and numerical analyzes, in order to identify subspecies and their similarities in some infectious niches. Cell cultures were grown in YEPD medium, collected by centrifugation, and washed in cold saline solution. The whole-cell proteins were extracted by cell disruption using glass beads and submitted to SDS-PAGE technique. After electrophoresis, the protein bands were stained with coomassie-blue and analyzed by statistics package NTSYS-pc version 1.70 software. Similarity matrixes and dendrograms were generated by application of similarity coefficient of simple matching and UPGMA algorithm, respectively. The results obtained showed several C. albicans subtypes and their similarity degrees (80% to 100%. Such data showed that same patients may be infected by two or more C. albicans subtypes in certain anatomical sites (i.e. only in oral cavity of immunocompromised patients, blood, or tracheal secretion, or yet, two or more patients can be infected in identical anatomical sites (i.e. bronchial washing, urine, oral cavity, tracheal secretion, vaginal secretion, and healthy saliva with a same C. albicans subtype. However, two or more patients also can show infections in corresponding sites (i.e. oral cavity of immunocompromised patients, blood, oropharyngeal secretion, oral cavity, tracheal secretion, vaginal secretion, and healthy saliva by different C. albicans subtypes. Besides, two or more patients also can be infected with identical or different C. albicans subtypes in different anatomical sites (i.e.1. identical subtypes in vaginal secretion, tracheal secretion, and urine; abdominal secretion and spittle; drainage and oral cavity; catheter and healthy saliva - i.e.2. subtypes different in bronchial washing, oropharyngeal

  12. Data-Model Assimilation at the FACE and AmeriFlux Sites Toward Predictive Understanding of Carbon Sequestration at Ecosystem and Regional Scales

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Yiqi [Univ. of Oklahoma, Norman, OK (United States)

    2013-01-09

    The project was conducted during the period from 9/1/2007 to 8/31/2011 with three major tasks: (1) development of data assimilation (DA) techniques for terrestrial carbon research; (2) applications of DA techniques to analysis of carbon cycle at Duke and other FACE sites; and (3) inverse analysis at AmeriFlux sites. During this period, we have developed a variety of techniques, including (1) ensemble Kalman filter to estimate model parameters or state variables (Gao et al. 2011), (2) Conditional inversion to estimate parameters of a carbon cycle model (Wu et al. 2009), and (3) various methods to quantify uncertainty of estimated parameters and predicted C sinks (e.g., Weng et al. 2011), and (4) information theory to evaluate information content of different model structures and data sets (Weng and Luo 2011). We applied the DA techniques to and did modeling at the Duke FACE and other global change experimental sites. We addressed the following issues: (1) interactive effects of CO2, warming and precipitation on ecosystem processes (e.g., Luo et al. 2008, Weng and Luo 2008, Zhou et al. 2008), (2) effects of warming on estimated parameters related to photosynthesis and residence times (Zhou et al. 2010); and (3) uncertainty in estimated parameters and predicted C sequestration (Gao et al. 2011, Weng and Luo 2011). In addition, we have done data assimilation to estimate carbon residence and carbon sequestration in US continent (Zhou and Luo 2008) and temperature sensitivity at the global scale (Zhou et al. 2009).

  13. Use of Mutual Information Arrays to Predict Coevolving Sites in the Full Length HIV gp120 Protein for Subtypes B and C

    Institute of Scientific and Technical Information of China (English)

    Bo Wei; Na Han; Hai-zhou Liu; Anthony Rayner; Simon Rayner

    2011-01-01

    It is well established that different sites within a protein evolve at different rates according to their role within the protein; identification of these correlated mutations can aid in tasks such as ab initio protein structure,structure function analysis or sequence alignment.Mutual Information is a standard measure for coevolution between two sites but its application is limited by signal to noise ratio.In this work we report a preliminary study to investigate whether larger sequence sets could circumvent this problem by calculating mutual information arrays for two sets of drug naive sequences from the HIV gp120 protein for the B and C subtypes.Our results suggest that while the larger sequences sets can improve the signal to noise ratio,the gain is offset by the high mutation rate of the HIV virus which makes it more difficult to achieve consistent alignments.Nevertheless,we were able to predict a number of coevolving sites that were supported by previous experimental studies as well as a region close to the C terminal of the protein that was highly variable in the C subtype but highly conserved in the B subtype.

  14. Palatal Augmentation Technique: A Predictable Method to Increase the Palatal Connective Tissue at Donor Sites- A Consecutive Case Series.

    Science.gov (United States)

    Carnio, João; Koutouzis, Theofilos

    2015-01-01

    The palatal masticatory mucosa between the canine and first molar is the main source of connective tissue graft (CTG) for use in periodontal plastic surgery. The purpose of this study was to evaluate the palatal augmentation technique (PAT) to increase the palatal connective tissue donor area using a collagen sponge inserted between the palatal flap and bone. The 26 patients enrolled in this study were referred for root coverage and ridge augmentation procedures. All patients lacked adequate donor palatal tissue thickness. The PAT uses a full-thickness flap and insertion of a sterile lyophilized bovine collagen sponge between the flap and bone. The palatal thickness was clinically assessed before and after collagen sponge insertion. A manual probe was inserted in the mucosal surface perpendicular to the long axis of each tooth approximately 6 mm from the gingival margin. Probing depth (PD) and recession (REC) were also recorded. Treatment with PAT resulted in a statistically significant increase in the palatal thickness. The overall mean increase was from 2.03 mm before surgery to 3.57 mm after surgery, with no major alterations in PD and REC. Healing proceeded uneventfully and occurred by primary intention. PAT appeared to be a predictable procedure to create connective tissue donor graft in deficient areas and had uneventful postoperative healing.

  15. 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.

  16. Predicting ESR Peaks in Copper (II Chelates Having Quadrupolar Coordinating Sites by NMR, ESR and NQR Techniques: A DFT Study

    Directory of Open Access Journals (Sweden)

    Harminder Singh

    2015-06-01

    Full Text Available Computational chemistry was helpful in predicting the number of ESR peaks in Cu (II complexes having a large number of spatially different NMR and ESR active nuclei. The presence of the large Jahn-Teller effect and the high value of spin-orbit coupling constant of the metal ion made the experimental determination of the exact number of ESR peaks quite difficult in such complexes. Fourteen distorted poly-dentate chelating Cu(II complexes included in this study were of two types such as [Cu(gly2] , [Cu(edta]4-,[Cu(tpyX2] (X= Cl, Br, I, NCS and [Cu(en2]2+, [Cu(teta]2+, Cu(tepa]2+ ,[Cu(peha]2+, [Cu(detaX2] (X= Cl, Br, I, NCS.The latter eight complexes belonged to an important class of ligands called polyethylene polyamines. Density functional theory implemented in ADF: 2010.02 was applied. Three parameters of both the ESR (A ten and NQR (NQCC, for the Cu(II and the coordinating atoms of the ligands were obtained from “ESR/EPR program” and two NMR parameters namely the shielding constants (σ and chemical shifts (δ were obtained from “NMR/EPR program” after optimization of the complexes. The species having the same values of these 5 parameters were expected to be spatially equivalent to undergo the same hyperfine interaction with Cu (II.

  17. 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/.

  18. 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

  19. Monte Carlo simulation of base and nucleotide excision repair of clustered DNA damage sites. I. Model properties and predicted trends

    Energy Technology Data Exchange (ETDEWEB)

    Semenenko, Vladimir; Stewart, Robert D.; Ackerman, Eric J.

    2005-12-31

    Single-cell irradiators and new experimental assays are rapidly expanding our ability to quantify the molecular mechanisms responsible for phenomena such as toxicant-induced adaptations in DNA repair and signal-mediated changes to the genome stability of cells not directly damaged by radiation (i.e., bystander cells). To advance our understanding of, and ability to predict and mitigate, the potentially harmful effects of radiological agents, effective strategies must be devised to incorporate information from molecular and cellular studies into mechanism-based, hierarchical models. A key advantage of the hierarchical modeling approach is that information from DNA repair and other in vitro assays can be systematically integrated into higher-level cell transformation and, eventually, carcinogenesis models. This presentation will outline the hierarchical modeling strategy used to integrate information from in vitro studies into the Virtual Cell (VC) radiobiology software (see Endnote). A new multi-path genomic instability model will be introduced and used to link biochemical processing of double strand breaks (DSBs) to neoplastic cell transformation. Bystander and directly damaged cells are treated explicitly in the model using a microdosimetric approach, although many of the details of the bystander response model are of a necessarily preliminary nature. The new model will be tested against several published radiobiological datasets. Results illustrating how hypothesized bystander mechanisms affect the shape of dose-response curves for neoplastic transformation as a function of Linear Energy Transfer (LET) will be presented. EndNote: R.D. Stewart, Virtual Cell (VC) Radiobiology Software. PNNL-13579, July 2001. Available at http://www.pnl.gov/berc/kbem/vc/ The DNA repair model used in the VC computer program is based on the Two-Lesion Kinetic (TLK) model [Radiat. Res. 156(4), 365-378 October 2001].

  20. Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins.

    Science.gov (United States)

    Desdouits, Nathan; Nilges, Michael; Blondel, Arnaud

    2015-02-01

    Protein conformation has been recognized as the key feature determining biological function, as it determines the position of the essential groups specifically interacting with substrates. Hence, the shape of the cavities or grooves at the protein surface appears to drive those functions. However, only a few studies describe the geometrical evolution of protein cavities during molecular dynamics simulations (MD), usually with a crude representation. To unveil the dynamics of cavity geometry evolution, we developed an approach combining cavity detection and Principal Component Analysis (PCA). This approach was applied to four systems subjected to MD (lysozyme, sperm whale myoglobin, Dengue envelope protein and EF-CaM complex). PCA on cavities allows us to perform efficient analysis and classification of the geometry diversity explored by a cavity. Additionally, it reveals correlations between the evolutions of the cavities and structures, and can even suggest how to modify the protein conformation to induce a given cavity geometry. It also helps to perform fast and consensual clustering of conformations according to cavity geometry. Finally, using this approach, we show that both carbon monoxide (CO) location and transfer among the different xenon sites of myoglobin are correlated with few cavity evolution modes of high amplitude. This correlation illustrates the link between ligand diffusion and the dynamic network of internal cavities.

  1. Wave Dynamical Chaos in Superconducting Microwave Cavities

    CERN Document Server

    Rehfeld, H; Dembowski, C; Gräf, H D; Hofferbert, R; Richter, A; Lengeler, Herbert

    1997-01-01

    During the last few years we have studied the chaotic behavior of special Euclidian geometries, so-called billiards, from the quantum or in more general sense "wave dynamical" point of view. Due to the equivalence between the stationary Schroedinger equation and the classical Helmholtz equation in the two-dimensional case (plain billiards), it is possible to simulate "quantum chaos" with the help of macroscopic, superconducting microwave cavities. Using this technique we investigated spectra of three billiards from the family of Pascal's Snails (Robnik-Billiards) with a different chaoticity in each case in order to test predictions of standard stochastical models for classical chaotic systems.

  2. User comment behavior prediction in social networking sites%社交网站中用户评论行为预测

    Institute of Scientific and Technical Information of China (English)

    孔庆超; 毛文吉; 张育浩

    2015-01-01

    Social networking sites provide a convenient way for users to communicate with others and to present opin⁃ions. Related researches on modeling and predicting user behaviors in social networking sites are of vital importance for many applications in the domains of security and business. The aim of this paper is to predict user comment behav⁃ior based on postings in social networking sites. A feature⁃based machine learning approach is employed, which in⁃cludes features from the postings, content, user behaviors and social relations, and introduces a parameter to control the imbalanceness of the dataset. Real⁃world datasets from Douban Group were used in the experiments. The experi⁃mental results showed that the user behavior and social relation features and the imbalance processing technique effec⁃tively improved the prediction performance of user comment behaviors. This further demonstrates that the user com⁃ment behavior is largely affected by their behavior history and social network.%社交网站为用户相互交流、发表意见和观点提供了非常便利的平台。对社交网站的用户行为进行建模和预测对于安全、商业等多个领域具有十分重要的社会意义和应用价值,近年来逐渐得到研究者的重视。面向社交网站中用户评论行为,预测用户是否会参与讨论。采用基于特征的机器学习方法,其中特征包括讨论帖子及其内容、用户行为特征和社交关系,并引入参数控制数据集的不平衡性。实验采用来自豆瓣小组的真实数据。实验结果表明,新提出的用户行为和社交关系特征以及对不平衡数据集的处理方法能够有效提高用户评论行为的预测效果,进一步说明用户的历史行为和所在的社交关系网络对当前的评论行为有较大影响。

  3. Cavity cooling beyond the Lamb-Dicke approximation

    CERN Document Server

    Blake, Tony; Beige, Almut

    2011-01-01

    Calculations based on the Lamb-Dicke approximation suggest that cavity cooling and ordinary laser cooling are essentially the same [see e.g. T. Blake et al., J. Mod. Opt., in press (2011)]. However, going beyond this approximation we obtain very different results. Here we show that cavity cooling can transfer particles to much lower temperatures than currently assumed, when the phonon frequency nu is comparable to or larger than the spontaneous cavity decay rate kappa. For nu << kappa, we predict much higher final phonon numbers than previous calculations. Moreover, we show that the optimal laser detuning is in both cases close to kappa. Our results should be more accurate than earlier predictions, since our calculations involve fewer approximations.

  4. Optical cavity integrated surface ion trap for enhanced light collection

    Science.gov (United States)

    Benito, Francisco M.

    Ion trap systems allow the faithful storage and manipulation of qubits encoded in the energy levels of the ions, and can be interfaced with photonic qubits that can be transmitted to connect remote quantum systems. Single photons transmitted from two remote sites, each entangled with one quantum memory, can be used to entangle distant quantum memories by interfering on a beam splitter. Efficient remote entanglement generation relies upon efficient light collection from single ions into a single mode fiber. This can be realized by integrating an ion trap with an optical cavity and employing the Purcell effect for enhancing the light collection. Remote entanglement can be used as a resource for a quantum repeater for provably secure long-distance communication or as a method for communicating within a distributed quantum information processor. We present the integration of a 1 mm optical cavity with a micro-fabricated surface ion trap. The plano-concave cavity is oriented normal to the chip surface where the planar mirror is attached underneath the trap chip. The cavity is locked using a 780 nm laser which is stabilized to Rubidium and shifted to match the 369 nm Doppler transition in Ytterbium. The linear ion trap allows ions to be shuttled in and out of the cavity mode. The Purcell enhancement of spontaneous emission into the cavity mode would then allow efficient collection of the emitted photons, enabling faster remote entanglement generation.

  5. Prediction and conformation by synthesis of two antigenic sites in human haemoglobin by extrapolation from the known antigenic structure of sperm-whale myoglobin.

    Science.gov (United States)

    Kazim, A L; Atassi, M Z

    1977-10-01

    The complete antigenic structure of sperm-whale myoglobin was previously determined in our laboratory. By structural analogy with myoglobin, two regions in human haemoglobin were predicted to comprise antigenic sites. One region was on the alpha-chain [alpha-(15-23)] and the other on the beta-chain [beta-(16-23)]. These two regions were synthesized, purified and characterized, and their immunochemistry was studied. Each peptide was able specifically to bind considerable amounts of haemoglobin antibodies. In a set of homologous proteins, barring any drastic conformational or electrostatic inductive effects exerted by the substitutions, and allowing for obstruction due to subunit interaction, the determination of the antigenic structure of one protein may serve as a useful starting model for the others.

  6. 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...

  7. 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.

  8. Vibration insensitive optical ring cavity

    Institute of Scientific and Technical Information of China (English)

    Miao Jin; Jiang Yan-Yi; Fang Su; Bi Zhi-Yi; Ma Long-Sheng

    2009-01-01

    The mounting configuration of an optical ring cavity is optimized for vibration insensitivity by finite element analysis. A minimum response to vertical accelerations is found by simulations made for different supporting positions.

  9. 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.

  10. Imaging of the oral cavity.

    Science.gov (United States)

    Meesa, Indu Rekha; Srinivasan, Ashok

    2015-01-01

    The oral cavity is a challenging area in head and neck imaging because of its complex anatomy and the numerous pathophysiologies that involve its contents. This challenge is further compounded by the ubiquitous artifacts that arise from the dental amalgam, which compromise image quality. In this article, the anatomy of the oral cavity is discussed in brief, followed by a description of the imaging technique and some common pathologic abnormalities.

  11. LEP Radio Frequency Copper Cavity

    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.

  12. 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

    Bone fracture risk can increase through bone microstructural changes observed in bone pathologies, such as glucocorticoid-induced osteoporosis. Resorption cavities present one of these microstructural aspects. We recently found that glucocorticoids (GCs) affect the shape of the resorption cavities...... 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 during GC...

  13. TESLA superconducting RF cavity development

    Energy Technology Data Exchange (ETDEWEB)

    Koepke, K. [Fermi National Accelerator Lab., Batavia, IL (United States); TESLA Collaboration

    1995-05-01

    The TESLA collaboration has made steady progress since its first official meeting at Cornell in 1990. The infrastructure necessary to assemble and test superconducting rf cavities has been installed at the TESLA Test Facility (TTF) at DESY. 5-cell, 1.3 GHz cavities have been fabricated and have reached accelerating fields of 25 MV/m. Full sized 9-cell copper cavities of TESLA geometry have been measured to verify the higher order modes present and to evaluate HOM coupling designs. The design of the TESLA 9-cell cavity has been finalized and industry has started delivery. Two prototype 9-cell niobium cavities in their first tests have reached accelerating fields of 10 MV/m and 15 MV/m in a vertical dewar after high peak power (HPP) conditioning. The first 12 m TESLA cryomodule that will house 8 9-cell cavities is scheduled to be delivered in Spring 1995. A design report for the TTF is in progress. The TTF test linac is scheduled to be commissioned in 1996/1997. (orig.).

  14. 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.

  15. Genetic variants in microRNAs and microRNA target sites predict biochemical recurrence after radical prostatectomy in localized prostate cancer.

    Science.gov (United States)

    Huang, Shu-Pin; Lévesque, Eric; Guillemette, Chantal; Yu, Chia-Cheng; Huang, Chao-Yuan; Lin, Victor C; Chung, I-Che; Chen, Lih-Chyang; Laverdière, Isabelle; Lacombe, Louis; Fradet, Yves; Chang, Ta-Yuan; Lee, Hong-Zin; Juang, Shin-Hun; Bao, Bo-Ying

    2014-12-01

    Recent evidence indicates that microRNAs might participate in prostate cancer initiation, progression and treatment response. Germline variations in microRNAs might alter target gene expression and modify the efficacy of prostate cancer therapy. To determine whether genetic variants in microRNAs and microRNA target sites are associated with the risk of biochemical recurrence (BCR) after radical prostatectomy (RP). We retrospectively studied two independent cohorts composed of 320 Asian and 526 Caucasian men with pathologically organ-confined prostate cancer who had a median follow-up of 54.7 and 88.8 months after RP, respectively. Patients were systematically genotyped for 64 single-nucleotide polymorphisms (SNPs) in microRNAs and microRNA target sites, and their prognostic significance on BCR was assessed by Kaplan-Meier analysis and Cox regression model. After adjusting for known clinicopathologic risk factors, two SNPs (MIR605 rs2043556 and CDON rs3737336) remained associated with BCR. The numbers of risk alleles showed a cumulative effect on BCR [perallele hazard ratio (HR) 1.60, 95% confidence interval (CI) 1.16-2.21, p for trend = 0.005] in Asian cohort, and the risk was replicated in Caucasian cohort (HR 1.55, 95% CI 1.15-2.08, p for trend = 0.004) and in combined analysis (HR 1.57, 95% CI 1.26-1.96, p for trend microRNAs and microRNA target sites can be predictive biomarkers for BCR after RP.

  16. 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.

  17. Mapping of ligand-binding cavities in proteins.

    Science.gov (United States)

    Andersson, C David; Chen, Brian Y; Linusson, Anna

    2010-05-01

    The complex interactions between proteins and small organic molecules (ligands) are intensively studied because they play key roles in biological processes and drug activities. Here, we present a novel approach to characterize and map the ligand-binding cavities of proteins without direct geometric comparison of structures, based on Principal Component Analysis of cavity properties (related mainly to size, polarity, and charge). This approach can provide valuable information on the similarities and dissimilarities, of binding cavities due to mutations, between-species differences and flexibility upon ligand-binding. The presented results show that information on ligand-binding cavity variations can complement information on protein similarity obtained from sequence comparisons. The predictive aspect of the method is exemplified by successful predictions of serine proteases that were not included in the model construction. The presented strategy to compare ligand-binding cavities of related and unrelated proteins has many potential applications within protein and medicinal chemistry, for example in the characterization and mapping of "orphan structures", selection of protein structures for docking studies in structure-based design, and identification of proteins for selectivity screens in drug design programs.

  18. The noise generated by a landing gear wheel with hub and rim cavities

    Science.gov (United States)

    Wang, Meng; Angland, David; Zhang, Xin

    2017-03-01

    Wheels are one of the major noise sources of landing gears. Accurate numerical predictions of wheel noise can provide an insight into the physical mechanism of landing gear noise generation and can aid in the design of noise control devices. The major noise sources of a 33% scaled isolated landing gear wheel are investigated by simulating three different wheel configurations using high-order numerical simulations to compute the flow field and the FW-H equation to obtain the far-field acoustic pressures. The baseline configuration is a wheel with a hub cavity and two rim cavities. Two additional simulations are performed; one with the hub cavity covered (NHC) and the other with both the hub cavity and rim cavities covered (NHCRC). These simulations isolate the effects of the hub cavity and rim cavities on the overall wheel noise. The surface flow patterns are visualised by shear stress lines and show that the flow separations and attachments on the side of the wheel, in both the baseline and the configuration with only the hub cavity covered, are significantly reduced by covering both the hub and rim cavities. A frequency-domain FW-H equation is used to identify the noise source regions on the surface of the wheel. The tyre is the main low frequency noise source and shows a lift dipole and side force dipole pattern depending on the frequency. The hub cavity is identified as the dominant middle frequency noise source and radiates in a frequency range centered around the first and second depth modes of the cylindrical hub cavity. The rim cavities are the main high-frequency noise sources. With the hub cavity and rim cavities covered, the largest reduction in Overall Sound Pressure Level (OASPL) is achieved in the hub side direction. In the other directivities, there is also a reduction in the radiated sound.

  19. 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

  20. Polishing Difficult-To-Reach Cavities

    Science.gov (United States)

    Malinzak, R. Michael; Booth, Gary N.

    1990-01-01

    Springy abrasive tool used to finish surfaces of narrow cavities made by electrical-discharge machining. Robot arm moves vibrator around perimeters of cavities, polishing walls of cavities as it does so. Tool needed because such cavities inaccessible or at least difficult to reach with most surface-finishing tools.

  1. Inter-assemblage facilitation: the functional diversity of cavity-producing beetles drives the size diversity of cavity-nesting bees.

    Science.gov (United States)

    Sydenham, Markus A K; Häusler, Lise D; Moe, Stein R; Eldegard, Katrine

    2016-01-01

    Inter-specific interactions are important drivers and maintainers of biodiversity. Compared to trophic and competitive interactions, the role of non-trophic facilitation among species has received less attention. Cavity-nesting bees nest in old beetle borings in dead wood, with restricted diameters corresponding to the body size of the bee species. The aim of this study was to test the hypothesis that the functional diversity of cavity-producing wood boring beetles - in terms of cavity diameters - drives the size diversity of cavity-nesting bees. The invertebrate communities were sampled in 30 sites, located in forested landscapes along an elevational gradient. We regressed the species richness and abundance of cavity nesting bees against the species richness and abundance of wood boring beetles, non-wood boring beetles and elevation. The proportion of cavity nesting bees in bee species assemblage was regressed against the species richness and abundance of wood boring beetles. We also tested the relationships between the size diversity of cavity nesting bees and wood boring beetles. The species richness and abundance of cavity nesting bees increased with the species richness and abundance of wood boring beetles. No such relationship was found for non-wood boring beetles. The abundance of wood boring beetles was also related to an increased proportion of cavity nesting bee individuals. Moreover, the size diversity of cavity-nesting bees increased with the functional diversity of wood boring beetles. Specifically, the mean and dispersion of bee body sizes increased with the functional dispersion of large wood boring beetles. The positive relationships between cavity producing bees and cavity nesting bees suggest that non-trophic facilitative interactions between species assemblages play important roles in organizing bee species assemblages. Considering a community-wide approach may therefore be required if we are to successfully understand and conserve wild bee

  2. Xenon and halogenated alkanes track putative substrate binding cavities in the soluble methane monooxygenase hydroxylase.

    Science.gov (United States)

    Whittington, D A; Rosenzweig, A C; Frederick, C A; Lippard, S J

    2001-03-27

    To investigate the role of protein cavities in facilitating movement of the substrates, methane and dioxygen, in the soluble methane monooxygenase hydroxylase (MMOH), we determined the X-ray structures of MMOH from Methylococcus capsulatus (Bath) cocrystallized with dibromomethane or iodoethane, or by using crystals pressurized with xenon gas. The halogenated alkanes bind in two cavities within the alpha-subunit that extend from one surface of the protein to the buried dinuclear iron active site. Two additional binding sites were located in the beta-subunit. Pressurization of two crystal forms of MMOH with xenon resulted in the identification of six binding sites located exclusively in the alpha-subunit. These results indicate that hydrophobic species bind preferentially in preexisting cavities in MMOH and support the hypothesis that such cavities may play a functional role in sequestering and enhancing the availability of the physiological substrates for reaction at the active site.

  3. 3D cavity detection technique and its application based on cavity auto scanning laser system

    Institute of Scientific and Technical Information of China (English)

    LIU Xi-ling; LI Xi-bing; LI Fa-ben; ZHAO Guo-yan; QIN Yu-hui

    2008-01-01

    Ground constructions and mines are severely threatened by underground cavities especially those unsafe or inaccessible ones. Safe and precise cavity detection is vital for reasonable cavity evaluation and disposal. The conventional cavity detection methods and their limitation were analyzed. Those methods cannot form 3D model of underground cavity which is used for instructing the cavity disposal; and their precisions in detection are always greatly affected by the geological circumstance. The importance of 3D cavity detection in metal mine for safe exploitation was pointed out; and the 3D cavity laser detection method and its principle were introduced. A cavity auto scanning laser system was recommended to actualize the cavity 3D detection after comparing with the other laser detection systems. Four boreholes were chosen to verify the validity of the cavity auto scanning laser system. The results show that the cavity auto scanning laser system is very suitable for underground 3D cavity detection, especially for those inaccessible ones.

  4. Estimating the risk of glacier cavity collapse during artificial drainage: The case of Tête Rousse Glacier

    Science.gov (United States)

    Gagliardini, O.; Gillet-Chaulet, F.; Durand, G.; Vincent, C.; Duval, P.

    2011-05-01

    During the summer of 2010, the presence of a pressurized water-filled subglacial-cavity of at least 50,000 m3 was detected within the Tête Rousse Glacier (French Alps). Artificial drainage was started to avoid an uncontrolled rupture of the ice dam, but was interrupted soon after to evaluate the capacity of the cavity-roof to bear itself. The risk was that the release of pressure within the cavity during the artificial drainage would precipitate the collapse of the cavity roof and potentially flush out the remaining water flooding the valley below. An unprecedented modeling effort was deployed to answer the question of the cavity roof stability. We set up a model of the glacier with its water cavity, solved the three-dimensional full-Stokes problem, predicted the upper surface and cavity surface displacements for various drainage scenarios, and quantified the risk of the cavity failure during artificial drainage. We found that the maximum tensile stress in the cavity roof was below the rupture value, indicating a low risk of collapse. A post drainage survey of the glacier surface displacements has confirmed the accuracy of the model prediction. This practical application demonstrates that ice flow models have reached sufficient maturity to become operational and assist policy-makers when faced with glaciological hazards, thus opening new perspectives in risk management of glacier hazards in high mountain regions.

  5. Fabrication of elliptical SRF cavities

    Science.gov (United States)

    Singer, W.

    2017-03-01

    The technological and metallurgical requirements of material for high-gradient 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 10 μg g-1. The hydrogen content should be kept below 2 μg g-1 to prevent degradation of the quality factor (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. Traditional and alternative cavity mechanical 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. The welding of half-cells is a delicate procedure, requiring intermediate cleaning steps and a careful choice of weld parameters to achieve full penetration of the joints. A challenge for a welded construction is the tight mechanical and electrical tolerances. These can be maintained by a combination of mechanical and radio-frequency measurements on half-cells and by careful tracking of weld shrinkage. The main aspects of quality assurance and quality management are mentioned. The experiences of 800 cavities produced for the European XFEL are presented. Another cavity fabrication approach is slicing discs from the ingot and producing cavities by deep drawing and electron beam welding. Accelerating gradients at the level of 35-45 MV m-1 can be achieved by applying electrochemical polishing treatment. The single-crystal option (grain boundary free) is discussed. It seems that in this case, high performance can be achieved by a simplified treatment procedure. Fabrication of the elliptical resonators from a seamless pipe as an alternative is briefly described. This technology has yielded good

  6. 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 ...

  7. Universal statistics of the scattering coefficient of chaotic microwave cavities.

    Science.gov (United States)

    Hemmady, Sameer; Zheng, Xing; Antonsen, Thomas M; Ott, Edward; Anlage, Steven M

    2005-05-01

    We consider the statistics of the scattering coefficient S of a chaotic microwave cavity coupled to a single port. We remove the nonuniversal effects of the coupling from the experimental S data using the radiation impedance obtained directly from the experiments. We thus obtain the normalized scattering coefficient whose probability density function (PDF) is predicted to be universal in that it depends only on the loss (quality factor) of the cavity. We compare experimental PDFs of the normalized scattering coefficients with those obtained from random matrix theory (RMT), and find excellent agreement. The results apply to scattering measurements on any wave chaotic system.

  8. 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.

  9. 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.

  10. Improved cavity detection from coupled seismic and hydrologic models

    Science.gov (United States)

    Desilets, S.; Bonal, N. D.; Desilets, D.

    2012-12-01

    Seismic methods hold much promise for cavity detection, but the results from field measurements have been frustratingly inconsistent between field sites. The reasons for the inconsistencies are not fully understood, though water saturation in the near-surface may be responsible to some extent. The conventional approach has been to focus on reflections and refractions generated from the impedance contrast of the cavity wall itself, where the dimensions and geometry of the cavity should play key roles. Here, we instead focus on the influence of impedance contrasts that are generated by hydrologic processes in the adjacent porous medium. These contrasts can potentially increase or decrease the reflection/refraction footprint of the cavity itself. Detectable hydrologic anomalies can be created by the simple drainage of groundwater into the cavity (initially saturated conditions) or by the creation of a capillary barrier around the cavity (initially unsaturated conditions). Because both processes ultimately involve unsaturated conditions we use HYDRUS 2D to numerically solve the Richard's equation and simulate flow through the vadose zone. Using the generated soil moisture information and Brutsaert's (1964) saturation-velocity relation, we constructed velocity models. Our simulations suggest several scenarios where changes in saturation due to the cavity may be utilized to enhance cavity detection with seismic waves. One simulation is for unsaturated conditions in the top 10 meters of soil, where capillary forces exert a major influence on velocity. In this case, the impedance contrast is greatest for near-saturated soils. Deeper cavities (100s of meters) in permeable saturated materials are also favorable due to the sharp impedance contrast between saturated and unsaturated material. Our hydrology-determined velocity models are then used in finite-difference wave propagation simulations to determine the effects on seismic waves at various depths and saturations

  11. Ground motions recorded in Rome during the April 2009 L’Aquila seismic sequence: site response and comparison with ground‐motion predictions based on a global dataset

    Science.gov (United States)

    Caserta, Arrigo; Boore, David; Rovelli, Antonio; Govoni, Aladino; Marra, Fabrizio; Monica, Gieseppe Della; Boschi, Enzo

    2013-01-01

    The mainshock and moderate‐magnitude aftershocks of the 6 April 2009 M 6.3 L’Aquila seismic sequence, about 90 km northeast of Rome, provided the first earthquake ground‐motion recordings in the urban area of Rome. Before those recordings were obtained, the assessments of the seismic hazard in Rome were based on intensity observations and theoretical considerations. The L’Aquila recordings offer an unprecedented opportunity to calibrate the city response to central Apennine earthquakes—earthquakes that have been responsible for the largest damage to Rome in historical times. Using the data recorded in Rome in April 2009, we show that (1) published theoretical predictions of a 1 s resonance in the Tiber valley are confirmed by observations showing a significant amplitude increase in response spectra at that period, (2) the empirical soil‐transfer functions inferred from spectral ratios are satisfactorily fit through 1D models using the available geological, geophysical, and laboratory data, but local variability can be large for individual events, (3) response spectra for the motions recorded in Rome from the L’Aquila earthquakes are significantly amplified in the radial component at periods near 1 s, even at a firm site on volcanic rocks, and (4) short‐period response spectra are smaller than expected when compared to ground‐motion predictions from equations based on a global dataset, whereas the observed response spectra are higher than expected for periods near 1 s.

  12. Cavity Control and Cooling of Nanoparticles in High Vacuum

    Science.gov (United States)

    Millen, James

    2016-05-01

    Levitated systems are a fascinating addition to the world of optically-controlled mechanical resonators. It is predicted that nanoparticles can be cooled to their c.o.m. ground state via the interaction with an optical cavity. By freeing the oscillator from clamping forces dissipation and decoherence is greatly reduced, leading to the potential to produce long-lived, macroscopically spread, mechanical quantum states, allowing tests of collapse models and any mass limit of quantum physics. Reaching the low pressures required to cavity-cool to the ground state has proved challenging. Our approach is to cavity cool a beam of nanoparticles in high vacuum. We can cool the c.o.m. motion of nanospheres, and control the rotation of nanorods, with the potential to produce cold, aligned nanostructures. Looking forward, we will utilize novel microcavities to enhance optomechanical cooling, preparing particles in a coherent beam ideally suited to ultra-high mass interferometry at 107 a.m.u.

  13. Cavity Cooling of Nanoparticles: Towards Matter-Wave experiments

    Science.gov (United States)

    Millen, James; Kuhn, Stefan; Arndt, Markus

    2016-05-01

    Levitated systems are a fascinating addition to the world of optically-controlled mechanical resonators. It is predicted that nanoparticles can be cooled to their c.o.m. ground state via the interaction with an optical cavity. By freeing the oscillator from clamping forces dissipation and decoherence is greatly reduced, leading to the potential to produce long-lived, macroscopically spread, mechanical quantum states, allowing tests of collapse models and any mass limit of quantum physics. Reaching the low pressures required to cavity-cool to the ground state has proved challenging. Our approach is to cavity cool a beam of nanoparticles in high vacuum. We can cool the c.o.m. motion of nanospheres a few hundred nanometers in size. Looking forward, we will utilize novel microcavities to enhance optomechanical cooling, preparing particles in a coherent beam ideally suited to ultra-high mass interferometry at 107 a.m.u.

  14. All-Optical Switching in Photonic Crystal Cavities

    DEFF Research Database (Denmark)

    Heuck, Mikkel

    All-Optical switching in photonic crystal waveguide-cavity structures is studied predominantly theoretically and numerically, but also from an experimental point of view. We have calculated the first order perturbations to the resonance frequency and decay rate of cavity modes, using a mathematical...... separated. This device was fabricated and characterized by colleagues within the group, and it was shown to perform very well in terms of cross-talk between the signal and pump. Theoretical investigations as well as practical design proposals have resulted from a study of waveguide-cavity structures...... exhibiting Fano resonances. These devices were predicted to be superior to structures with the more well-known Lorentzian line shape in terms of energy consumption and switching contrast. Finally, the mathematical framework of optimal control theory was employed as a general setting, in which the optical...

  15. Ultra-high-Q nanobeam cavity design in Diamond

    CERN Document Server

    Bayn, Igal; Kalish, Rafi

    2010-01-01

    A novel nanobeam design with a triangular cross-section is proposed. This design makes possible implementing nanocavities with improved optical properties. The dependence of a diamond-based cavity quality factor Q and mode volume Vm on geometry parameter space are studied via 3D FDTD computations. An ultra-high-Q cavity with Q\\aprox 2.51 \\times 10^6 and Vm=1.06 \\times ({\\lambda}/n)^3 is predicted. The mode preferential radiation is upward. The implications on the potential applications are discussed. The proposed nanobeam enables fabrication of the cavity without relying on a pre-existing free-standing diamond membrane as required in most previous approaches.

  16. 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...

  17. 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.

  18. A micropillar for cavity optomechanics

    CERN Document Server

    Kuhn, A G; Ducloux, O; Chartier, C; Traon, O Le; Briant, T; Cohadon, P -F; Heidmann, A; Michel, C; Pinard, L; Flaminio, R

    2011-01-01

    We present a new micromechanical resonator designed for cavity optomechanics. We have used a micropillar geometry to obtain a high-frequency mechanical resonance with a low effective mass and a very high quality factor. We have coated a 60-$\\mu$m diameter low-loss dielectric mirror on top of the pillar and are planning to use this micromirror as part of a high-finesse Fabry-Perot cavity, to laser cool the resonator down to its quantum ground state and to monitor its quantum position fluctuations by quantum-limited optical interferometry.

  19. Quantum dynamic behaviour in a coupled cavities system

    Institute of Scientific and Technical Information of China (English)

    Peng Jun; Wu Yun-Wen; Li Xiao-Juan

    2012-01-01

    The dynamic behaviour of the two-site coupled cavities model which is doped with ta wo-level system is investigated.The exact dynamic solutions in the general condition are obtained via Laplace transform.The simple analytical solutions are obtained in several particular cases,which demonstrate the clear and simple physical picture for the quantum state transition of the system.In the large detuning or hoppling case,the quantum states transferring between qubits follow a slow periodic oscillation induced by the very weak excitation of the cavity mode.In the large coupling case,the system can be interpreted as two Jaynes-Cummings model subsystems which interact through photon hop between the two cavities.In the case of λ≈△(》) g,the quantum states transition of qubits is accompanied by the excitation of the cavity,and the cavity modes have the same dynamic behaviours and the amplitude of probability is equal to 0.25 which does not change with the variation of parameter.

  20. Influence of the Vapor Cavity Depth on Liquid Flow through a Microchannel Exhibiting Superhydrophobic Walls

    Science.gov (United States)

    Maynes, Daniel; Jeffs, Kevin; Woolford, Brady; Webb, Brent

    2007-11-01

    We report results of an analytical and experimental investigation of laminar flow in a parallel-plate microchannel with superhydrophobic walls. The walls are fabricated with hydrophobically coated micro-ribs and cavities that are oriented parallel to the flow direction and are modeled in an idealized fashion, with the shape of the liquid-vapor meniscus approximated as flat. An analytical model of the flow in the vapor cavity is employed and coupled with a numerical model of the liquid flow. The numerical predictions show that the effective slip length and the reduction in the classical friction factor-Reynolds number product increase with increasing relative cavity width and depth, and decreasing relative micro-rib/cavity module length. Comparisons are also made between the zero shear interface model and the liquid-vapor cavity coupled model. The results illustrate that the zero shear interface model under-predicts the overall flow resistance. Further, the deviation between the two models was found to be significantly larger for increasing values of both the relative rib/cavity module width and the cavity fraction. The trends in the frictional pressure drop predictions are in good agreement with experimental measurements made at similar conditions and a generalized expression for predicting the friction factor is proposed.

  1. Entanglement swapping between atom and cavity and generation of entangled state of cavity fields

    Institute of Scientific and Technical Information of China (English)

    Chen Ai-Xi; Deng Li

    2007-01-01

    This paper proposes a scheme where entanglement swapping between atom and cavity can be realized. A-type three-level atoms interacting resonantly with cavity field are considered. By detecting atom and cavity field, it realizes entanglement swapping between atom and cavity. It uses the technique of entanglement swapping to generate an entangled state of two cavity fields by measuring on atoms. It discusses the experimental feasibility of the proposed scheme and application of entangled state of cavity fields.

  2. New Solutions of Translation Initiation Site Prediction for Prokaryotic Genomes%原核基因翻译起始位点预测的新方法

    Institute of Scientific and Technical Information of China (English)

    胡钢清; 刘永初; 郑晓斌; 杨一帆; 余振苏; 朱怀球

    2008-01-01

    翻译起始位点(TIS,即基因5′端)的精确定位是原核生物基因预测的一个关键问题,而基因组GC含量和翻译起始机制的多样性是影响当前TIS预测水平的重要因素.结合基因组结构的复杂信息(包括GC含量、TIS邻近序列及上游调控信号、序列编码潜能、操纵子结构等),发展刻画翻译起始机制的数学统计模型,据此设计TIS预测的新算法MED-StartPlus.并将MED-StartPlus与同类方法RBSfinder、GS-Finder、MED-Start、TiCo和Hon-yaku等进行系统地比较和评价.测试针对两种数据集进行:当前14个已知的TIS被确认的基因数据集,以及300个物种中功能已知的基因数据集.测试结果表明,MED-StartPlus的预测精度在总体上超过同类方法.尤其是对高GC含量基因组以及具有复杂翻译起始机制的基因组,MED-StartPlus具有明显的优势.%Accurate prediction of the translation initiation site (TIS) is an important issue for prokaryotic genome annotation. However, it is still a challenge for the existing methods to predict the TIS in the genomes over a wide variety of GC content. Besides, the existing methods have not yet undergone a comprehensive evaluation, leaving prediction reliability as a largely open problem. A new algorithm MED-StartPlus, a tool that predicts TIS in prokaryotic genomes with a wide variety of GC content was presented. It makes several efforts to model the nucleotide composition bias, the regulatory motifs upstream of the TIS, the sequence patterns around the TIS, and the operon structure. Tests on hundreds of reliable data sets, with TISs confirmed by experiments or having annotated functions, show that the new method achieves a totally high accuracy of TIS prediction. Compared with existing TIS predictors, the method reports a totally higher performance, especially for genomes that are GC-rich or have complex initiation mechanisms. The potential application of the method to improve the TIS annotation

  3. Protein–Protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM

    Indian Academy of Sciences (India)

    Brijesh Kumar Sriwastava; Subhadip Basu; Ujjwal Maulik

    2015-10-01

    Protein–protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown that the performance of the classical SVM can be enhanced with the help of an interaction-affinity based fuzzy membership function. The performances of both SVM and F-SVM on the PPI databases of the Homo sapiens and E. coli organisms are evaluated and estimated the statistical significance of the developed method over classical SVM and other fuzzy membership-based SVM methods available in the literature. Our membership function uses the residue-level interaction affinity scores for each pair of positive and negative sequence fragments. The average AUC scores in the 10-fold cross-validation experiments are measured as 79.94% and 80.48% for the Homo sapiens and E. coli organisms respectively. On the independent test datasets, AUC scores are obtained as 76.59% and 80.17% respectively for the two organisms. In almost all cases, the developed F-SVM method improves the performances obtained by the corresponding classical SVM and the other classifiers, available in the literature.

  4. Protein-protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM.

    Science.gov (United States)

    Sriwastava, Brijesh Kumar; Basu, Subhadip; Maulik, Ujjwal

    2015-10-01

    Protein-protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown that the performance of the classical SVM can be enhanced with the help of an interaction-affinity based fuzzy membership function. The performances of both SVM and F-SVM on the PPI databases of the Homo sapiens and E. coli organisms are evaluated and estimated the statistical significance of the developed method over classical SVM and other fuzzy membership-based SVM methods available in the literature. Our membership function uses the residue-level interaction affinity scores for each pair of positive and negative sequence fragments. The average AUC scores in the 10-fold cross-validation experiments are measured as 79.94% and 80.48% for the Homo sapiens and E. coli organisms respectively. On the independent test datasets, AUC scores are obtained as 76.59% and 80.17% respectively for the two organisms. In almost all cases, the developed F-SVM method improves the performances obtained by the corresponding classical SVM and the other classifiers, available in the literature.

  5. Localization transition in the presence of cavity backaction

    Science.gov (United States)

    Rojan, Katharina; Kraus, Rebecca; Fogarty, Thomás; Habibian, Hessam; Minguzzi, Anna; Morigi, Giovanna

    2016-07-01

    We study the localization transition of an atom confined by an external optical lattice in a high-finesse cavity. The atom-cavity coupling yields an effective secondary lattice potential, whose wavelength is incommensurate with the periodicity of the optical lattice. The cavity lattice can induce localization of the atomic wave function analogously to the Aubry-André localization transition. Starting from the master equation for the cavity and the atom we perform a mapping of the system dynamics to a Hubbard Hamiltonian, which can be reduced to the Harper's Hamiltonian in appropriate limits. We evaluate the phase diagram for the atom's ground state and show that the transition between extended and localized wave function is controlled by the strength of the cavity nonlinearity, which determines the size of the localized region and the behavior of the Lyapunov exponent. The Lyapunov exponent, in particular, exhibits resonancelike behavior in correspondence with the optomechanical resonances. Finally we discuss the experimental feasibility of these predictions.

  6. On cavity modification of stimulated Raman scattering

    CERN Document Server

    Matsko, A B; Letargat, R J; Ilchenko, V S; Maleki, L

    2003-01-01

    We study theoretically stimulated Raman scattering (SRS) in a nonlinear dielectric microcavity and compare SRS thresholds for the cavity and the bulk material it is made of. We show that cavity SRS enhancement results solely from the intensity build up in the cavity and from the differences of the SRS dynamics in free and confined space. There is no significant modification of the Raman gain due to cavity QED effects. We show that the SRS threshold depends significantly on the nature of the dominating cavity decay as well as on the coupling technique with the cavity used for SRS measurements.

  7. 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...

  8. Analysis of K-net and Kik-net data: implications for ground motion prediction - acceleration time histories, response spectra and nonlinear site response; Analyse des donnees accelerometriques de K-net et Kik-net: implications pour la prediction du mouvement sismique - accelerogrammes et spectres de reponse - et la prise en compte des effets de site non-lineaire

    Energy Technology Data Exchange (ETDEWEB)

    Pousse, G

    2005-10-15

    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)

  9. Hybrid Vertical-Cavity Laser

    DEFF Research Database (Denmark)

    2010-01-01

    The present invention provides a light source (2) for light circuits on a silicon platform (3). A vertical laser cavity is formed by a gain region (101) arranged between a top mirror (4) and a bottom grating-mirror (12) in a grating region (11) in a silicon layer (10) on a substrate. A waveguide...

  10. Droplet based cavities and lasers

    DEFF Research Database (Denmark)

    Mølhave, Kristian; Kristensen, Anders; Mortensen, Asger

    2009-01-01

    The self-organized and molecularly smooth surface on liquid microdroplets makes them attractive as optical cavities with very high quality factors. This chapter describes the basic theory of optical modes in spherical droplets. The mechanical properties including vibrational excitation are also d...

  11. "Grinding" cavities in polyurethane foam

    Science.gov (United States)

    Brower, J. R.; Davey, R. E.; Dixon, W. F.; Robb, P. H.; Zebus, P. P.

    1980-01-01

    Grinding tool installed on conventional milling machine cuts precise cavities in foam blocks. Method is well suited for prototype or midsize production runs and can be adapted to computer control for mass production. Method saves time and materials compared to bonding or hot wire techniques.

  12. A STUDY OF FERRITE CAVITY.

    Energy Technology Data Exchange (ETDEWEB)

    ZHAO, Y.

    2002-04-19

    This note addresses the general concerns for the design of a ferrite cavity. The parameters are specified for the RCMS, for which the frequency ramp is in the range of 1.27 MHz to 6.44 MHz, or a ratio of 1:5.

  13. A 200 MHz prebunching cavity

    CERN Multimedia

    1977-01-01

    This cavity was installed in the PS ring and proved very efficient in providing a modulation on the PS beam before it is injected into the SPS machine. Moreover it allowed longitudinal instabilities studies at high intensities. Roberto Cappi stands on the left.

  14. Cavity length below chute aerators

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    It is proved that air entrainment is one of the efficient measures dealing with cavi-tation control for the release works of hydropower projects. There are many factors to be considered in designing a chute aerator. One of the most important factors concerns the cavity length below the aerator,which has outstanding effects on air entrainment against cavitation damage. It is crucial to determine reasonable emergence angle for the calculation of the cavity length. In the present paper the overall effects of structural and hydraulic parameters on the emergence angle of the flow from the aerator were analyzed. Four improved expressions of the emer-gence angle with weight coefficient were investigated through experimental data of 68 points observed from 12 aerators of 6 hydropower projects,of both model and prototype,on the basis of error theory. A method to calculate the cavity length be-low aerators was suggested,which considers overall effects of the above men-tioned parameters. Comparison between the method in this paper and the other five methods of calculating the cavity length showed that the present method is much more reliable than the existing methods while the mean error of the method is less than others.

  15. Cavity length below chute aerators

    Institute of Scientific and Technical Information of China (English)

    WU JianHua; RUAN ShiPing

    2008-01-01

    It is proved that air entrainment is one of the efficient measures dealing with cavitation control for the release works of hydropower projects. There are many factors to be considered in designing a chute aerator. One of the most important factors concerns the cavity length below the aerator, which has outstanding effects on air entrainment against cavitation damage. It is crucial to determine reasonable emergence angle for the calculation of the cavity length. In the present paper the overall effects of structural and hydraulic parameters on the emergence angle of the flow from the aerator were analyzed. Four improved expressions of the emergence angle with weight coefficient were investigated through experimental data of 68 points observed from 12 aerators of 6 hydropower projects, of both model and prototype, on the basis of error theory. A method to calculate the cavity length below aerators was suggested, which considers overall effects of the above mentioned parameters. Comparison between the method in this paper and the other five methods of calculating the cavity length showed that the present method is much more reliable than the existing methods while the mean error of the method is less than others.

  16. 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.

  17. 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.

  18. Climate Modeling: Ocean Cavities below Ice Shelves

    Energy Technology Data Exchange (ETDEWEB)

    Petersen, Mark Roger [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Computer, Computational, and Statistical Sciences Division

    2016-09-12

    The Accelerated Climate Model for Energy (ACME), a new initiative by the U.S. Department of Energy, includes unstructured-mesh ocean, land-ice, and sea-ice components using the Model for Prediction Across Scales (MPAS) framework. The ability to run coupled high-resolution global simulations efficiently on large, high-performance computers is a priority for ACME. Sub-ice shelf ocean cavities are a significant new capability in ACME, and will be used to better understand how changing ocean temperature and currents influence glacial melting and retreat. These simulations take advantage of the horizontal variable-resolution mesh and adaptive vertical coordinate in MPAS-Ocean, in order to place high resolution below ice shelves and near grounding lines.

  19. Water Quality, Cyanobacteria, and Environmental Factors and Their Relations to Microcystin Concentrations for Use in Predictive Models at Ohio Lake Erie and Inland Lake Recreational Sites, 2013-14

    Science.gov (United States)

    Francy, Donna S.; Graham, Jennifer L.; Stelzer, Erin A.; Ecker, Christopher D.; Brady, Amie M G.; Pam Struffolino,; Loftin, Keith A.

    2015-11-06

    Harmful cyanobacterial “algal” blooms (cyanoHABs) and associated toxins, such as microcystin, are a major water-quality issue for Lake Erie and inland lakes in Ohio. Predicting when and where a bloom may occur is important to protect the public that uses and consumes a water resource; however, predictions are complicated and likely site specific because of the many factors affecting toxin production. Monitoring for a variety of environmental and water-quality factors, for concentrations of cyanobacteria by molecular methods, and for algal pigments such as chlorophyll and phycocyanin by using optical sensors may provide data that can be used to predict the occurrence of cyanoHABs.

  20. Cavity QED experiments with ion Coulomb crystals

    DEFF Research Database (Denmark)

    Herskind, Peter Fønss; Dantan, Aurélien; Marler, Joan

    2009-01-01

    Cavity QED experimental results demonstrating collective strong coupling between ensembles of atomic ions cooled into Coulomb crystals and optical cavity fields have been achieved. Collective Zeeman coherence times of milliseconds have furthermore been obtained....

  1. 21 CFR 872.3260 - Cavity varnish.

    Science.gov (United States)

    2010-04-01

    ... DENTAL DEVICES Prosthetic Devices § 872.3260 Cavity varnish. (a) Identification. Cavity varnish is a... restorative materials. The device is intended to prevent penetration of restorative materials, such as...

  2. Prototype storage cavity for LEP accelerating RF

    CERN Multimedia

    1980-01-01

    The principle of an RF storage cavity was demonstrated with this prototype, working at 500 MHz. Ian Wilso seems to hold it in his hands. The storage cavities had 4 portholes, 1 each for: RF feed; tuning; connection to the accelerating cavity; vacuum pump. The final storage cavities were larger, to suit the lower LEP accelerating frequency of 352.2 MHz. See also 8002294, 8006510X, 8109346, 8407619X, and Annual Report 1980, p.115.

  3. Theory and technology for superconducting cavities

    CERN Document Server

    Lengeler, Herbert

    1993-01-01

    The course will address Physicist and Engineers who are newcomers in the field of accelerators and accelerating cavities. The elements of RF-Superconductivity will be presented with special relevance to accelerating cavities. The present ststus of achievable accelerating fields and RF losses will be given and their link to the special technologies for cavity fabrication and surface treatments will be stressed. Cavity auxiliaries like main couplers, higher order mode couplers and frequency tuners will be described.

  4. Exploring the ubiquinone binding cavity of respiratory complex I.

    Science.gov (United States)

    Tocilescu, Maja A; Fendel, Uta; Zwicker, Klaus; Kerscher, Stefan; Brandt, Ulrich

    2007-10-05

    Proton pumping respiratory complex I is a major player in mitochondrial energy conversion. Yet little is known about the molecular mechanism of this large membrane protein complex. Understanding the details of ubiquinone reduction will be prerequisite for elucidating this mechanism. Based on a recently published partial structure of the bacterial enzyme, we scanned the proposed ubiquinone binding cavity of complex I by site-directed mutagenesis in the strictly aerobic yeast Yarrowia lipolytica. The observed changes in catalytic activity and inhibitor sensitivity followed a consistent pattern and allowed us to define three functionally important regions near the ubiquinone-reducing iron-sulfur cluster N2. We identified a likely entry path for the substrate ubiquinone and defined a region involved in inhibitor binding within the cavity. Finally, we were able to highlight a functionally critical structural motif in the active site that consisted of Tyr-144 in the 49-kDa subunit, surrounded by three conserved hydrophobic residues.

  5. White Lesions in the Oral Cavity: A Clinicopathological Study from a Tertiary Care Dermatology Centre in Kerala, India

    OpenAIRE

    S M Simi; G Nandakumar; T S Anish

    2013-01-01

    Context: White lesions in the oral cavity may be benign, pre-malignant or malignant. There are no signs and symptoms which can reliably predict whether a leukoplakia will undergo malignant change or not. Many systemic conditions appear initially in the oral cavity and prompt diagnosis and management can help in minimizing disease progression and organ destruction. Aim : The aim of the paper was to study the clinical and histopathological patterns of white lesions in the oral cavity presented ...

  6. Diagram of a LEP superconducting cavity

    CERN Multimedia

    1991-01-01

    This diagram gives a schematic representation of the superconducting radio-frequency cavities at LEP. Liquid helium is used to cool the cavity to 4.5 degrees above absolute zero so that very high electric fields can be produced, increasing the operating energy of the accelerator. Superconducting cavities were used only in the LEP-2 phase of the accelerator, from 1996 to 2000.

  7. Power coupler for the ILC crab cavity

    Energy Technology Data Exchange (ETDEWEB)

    Burt, G.; Dexter, A.; Jenkins, R.; /Lancaster U.; Beard, C.; Goudket, P.; McIntosh, P.A.; /Daresbury; Bellantoni, Leo; /Fermilab

    2007-06-01

    The ILC crab cavity will require the design of an appropriate power coupler. The beam-loading in dipole mode cavities is considerably more variable than accelerating cavities, hence simulations have been performed to establish the required external Q. Simulations of a suitable coupler were then performed and were verified using a normal conducting prototype with variable coupler tips.

  8. Digital Cavities and Their Potential Applications

    CERN Document Server

    Karki, Khadga; Widom, Julia R; Marcus, Andrew H; Pullerits, Tonu

    2013-01-01

    The concept of a digital cavity is presented. The functionality of a tunable radio-frequency/microwave cavity with unrestricted Q-factor is implemented. The theoretical aspects of the cavity and its potential applications in high resolution spectroscopy and synchronization of clocks together with examples in signal processing and data acquisition are discussed.

  9. White lesions in the oral cavity: A clinicopathological study from a tertiary care dermatology centre in Kerala, India

    Directory of Open Access Journals (Sweden)

    S M Simi

    2013-01-01

    Full Text Available Context: White lesions in the oral cavity may be benign, pre-malignant or malignant. There are no signs and symptoms which can reliably predict whether a leukoplakia will undergo malignant change or not. Many systemic conditions appear initially in the oral cavity and prompt diagnosis and management can help in minimizing disease progression and organ destruction. Aim : The aim of the paper was to study the clinical and histopathological patterns of white lesions in the oral cavity presented at the study setting and to study the factors associated with the histopathological patterns of the lesions. Settings and Design: A hospital based cross-sectional study of patients with white lesions in the oral cavity attending the Department of Dermatology and Venereology, Medical College, Thiruvananthapuram was done. Materials and Methods: After taking a detailed history, microscopic examination of Potassium hydroxide smear and an oral biopsy with histopathologial examination was done. Results : Out of the 50 patients in the study, clinically the diagnoses made were Lichen planus (32 patients; 64%, Frictional Keratosis (4;8%, Dysplasia (2;4%, Oral Hairy Leukoplakia (1;2%, Pemphigus Vulgaris (2;4%, Cutaneous Lupus Erythematosus (1;2%, Oral Submucous fibrosis (3;6% and Oral Candidiasis alone (5;10%. Out of the 45 patients who had undergone biopsy, 25 (55.6% had Lichen planus, 9 (20% had Frictional Keratosis and mild Dysplasia was found in 4 (8.9% patients. Conclusion : The measure of agreement between the clinical and pathological diagnosis was only 32%. Older age, difficulty in opening the mouth, consumption of non-smoked tobacco, site of the lesion (gingival, floor of mouth or lingual vestibule and presence of tenderness on the lesion were significantly associated with Dysplasia.

  10. Structural and energetic consequences of mutations in a solvated hydrophobic cavity

    Science.gov (United States)

    Adamek, D. H.; Guerrero, L.; Blaber, M.; Caspar, D. L. D.

    2005-01-01

    The structural and energetic consequences of modifications to the hydrophobic cavity of interleukin 1-beta (IL-1beta) are described. Previous reports demonstrated that the entirely hydrophobic cavity of IL-1beta contains positionally disordered water. To gain a better understanding of the nature of this cavity and the water therein, a number of mutant proteins were constructed by site-directed mutagenesis, designed to result in altered hydrophobicity of the cavity. These mutations involve the replacement of specific phenylalanine residues, which circumscribe the cavity, with tyrosine, tryptophan, leucine and isoleucine. Using differential scanning calorimetry to determine the relative stabilities of the wild-type and mutant proteins, we found all of the mutants to be destabilizing. X-ray crystallography was used to identify the structural consequences of the mutations. No clear correlation between the hydrophobicities of the specific side-chains introduced and the resulting stabilities was found.

  11. III-nitride tunable cup-cavities supporting quasi whispering gallery modes from ultraviolet to infrared

    Science.gov (United States)

    Shubina, T. V.; Pozina, G.; Jmerik, V. N.; Davydov, V. Yu.; Hemmingsson, C.; Andrianov, A. V.; Kazanov, D. R.; Ivanov, S. V.

    2015-12-01

    Rapidly developing nanophotonics needs microresonators for different spectral ranges, formed by chip-compatible technologies. In addition, the tunable ones are much in demand. Here, we present site-controlled III-nitride monocrystal cup-cavities grown by molecular beam epitaxy. The cup-cavities can operate from ultraviolet to near-infrared, supporting quasi whispering gallery modes up to room temperature. Besides, their energies are identical in large ’ripened’ crystals. In these cavities, the refractive index variation near an absorption edge causes the remarkable effect of mode switching, which is accompanied by the spatial redistribution of electric field intensity with concentration of light into a subwavelength volume. Our results shed light on the mode behavior in semiconductor cavities and open the way for single-growth-run manufacturing the devices comprising an active region and a cavity with tunable mode frequencies.

  12. A study of resonant-cavity and fiberglass-filled parallel baffles as duct silencers. [for wind tunnels

    Science.gov (United States)

    Soderman, P. T.

    1982-01-01

    Acoustical performance and pressure drop were measured for two types of splitters designed to attenuate sound propagating in ducts - resonant-cavity baffles and fiberglass-filled baffles. Arrays of four baffles were evaluated in the 7- by 10-foot wind tunnel number 1 at Ames Research Center at flow speeds from 0 to 41 m/sec. The baffles were 2.1 m high, 305 to 406 mm thick, and 3.1 to 4.4 m long. Emphasis was on measurements of silencer insertion loss as affected by variations of such parameters as baffle length, baffle thickness, perforated skin geometry, cavity size and shape, cavity damping, wind speed, and acoustic field directivity. An analytical method for predicting silencer performance is described and compared with measurements. With the addition of cavity damping in the form of 25-mm foam linings, the insertion loss above 250 Hz of the resonant-cavity baffles was improved 2 to 7 db compared with the undamped baffles; the loss became equal to or greater than the insertion loss of comparable size fiberglass baffles at frequencies above 250 Hz. Variations of cavity size and shape showed that a series of cavities with triangular cross-sections (i.e., variable depth) were superior to cavities with rectangular cross sections (i.e., constant depth). In wind, the undamped, resonant-cavity baffles generated loud cavity-resonance tones; the tones could be eliminated by cavity damping.

  13. Drum silencer with shallow cavity filled with helium.

    Science.gov (United States)

    Choy, Y S; Huang, Lixi

    2003-09-01

    The motivation of this study is twofold: (a) to produce a flow-through silencer with zero pressure loss for pressure-critical applications, and (b) to tackle low frequency noise with limited sideway space using cavities filled with helium. The work represents a further development of our recently conceived device of a drum-like silencer with conventional air cavity [Huang, J. Acoust. Soc. Am. 112, 2014-2025 (2002); Choy and Huang, ibid. 112, 2026-2035 (2002)]. Theoretical predictions are validated by experimental data. The new silencer consists of two highly tensioned membranes lining part of a duct, and each membrane is backed by a cavity filled with helium. For a typical configuration of a duct with height h, membrane length L = 7h, cavity depth h = 0.2h, and tension T = 0.52rho0c0(2)h2, where rho0 and c0 are the ambient density and speed of sound in air, respectively, the transmission loss has a continuous stop band of TL > 6.35 dB for frequency 0.03c0/h to 0.064c0/h, which is much better than traditional duct lining. In addition to the mechanisms at work for drum silencers with air cavity, the low density of helium reduces the masslike reactance of the cavity on the second in vacuo mode of membrane vibration. The reduction greatly enhances the membrane response at this mode, which is found to be critical for achieving a broadband performance in the low-frequency regime.

  14. Cavities in molecular liquids and the theory of hydrophobic solubilities

    Science.gov (United States)

    Pohorille, A.; Pratt, L. R.; MacElroy, R. (Principal Investigator)

    1990-01-01

    Thermal configurational data on neat liquids are used to obtain the work of formation of hard spherical cavities of atomic size in six molecular solvents: n-hexane, n-dodecane, n-undecyl alcohol, chloroform, carbon tetrachloride, and water. These results are used to test a recent suggestion that the differences between nonaqueous solvents and liquid water in solvation of inert gases are not principally due to the hydrogen-bonded structure of liquid water but rather to the comparatively small size of the water molecule. The frequencies of occurrence of cavities in liquid water can be meaningfully distinguished from those in the organic solvents. Liquid water has a larger fractional free volume, but that free volume is distributed in smaller packets. With respect to cavity work, water is compared to a solvent of the same molecular density and composed of hard spheres of the same size as the water molecule. That comparison indicates that the hard-sphere liquid finds more ways to configure its free volume in order to accommodate an atomic solute of substantial size and thus, would be more favorable solvent for inert gases. The scaled particle model of inert gas solubility in liquid water predicts cavity works 20% below the numerical data for TIP4P water at 300 K and 1.0 g/cm3 for cavity radii near 2.0 angstroms. It is argued that the sign of this difference is just the sign that ought to be expected and that the magnitude of this difference measures structural differences between water and the directly comparable hard-sphere liquid. In conjunction with previous data, these results indicate that atomic sized cavities should be considered submacroscopic.

  15. Cavity Voltage Phase Modulation MD

    CERN Document Server

    Mastoridis, Themistoklis; Molendijk, John; Timko, Helga; CERN. Geneva. ATS Department

    2016-01-01

    The LHC RF/LLRF system is currently configured for extremely stable RF voltage to minimize transient beam loading effects. The present scheme cannot be extended beyond nominal beam current since the demanded power would exceed the peak klystron power and lead to saturation. A new scheme has therefore been proposed: for beam currents above nominal (and possibly earlier), the cavity phase modulation by the beam will not be corrected (transient beam loading), but the strong RF feedback and One-Turn Delay feedback will still be active for loop and beam stability in physics. To achieve this, the voltage set point will be adapted for each bunch. The goal of this MD was to test a new algorithm that would adjust the voltage set point to achieve the cavity phase modulation that would minimize klystron forward power.

  16. A micropillar for cavity optomechanics

    Energy Technology Data Exchange (ETDEWEB)

    Kuhn, Aurélien; Neuhaus, Leonhard; Deléglise, Samuel; Briant, Tristan; Cohadon, Pierre-François; Heidmann, Antoine [Laboratoire Kastler Brossel, UPMC-ENS-CNRS, Paris (France); Van Brackel, Emmanuel [Département de Physique, ENS, Paris (France); Chartier, Claude; Ducloux, Olivier; Le Traon, Olivier [Département Mesures Physiques, ONERA, Châtillon (France); Michel, Christophe; Pinard, Laurent; Flaminio, Raffaele [Laboratoire des Matériaux Avancés, IN2P3-CNRS, Lyon (France)

    2014-12-04

    Demonstrating the quantum ground state of a macroscopic mechanical object is a major experimental challenge in physics, at the origin of the rapid emergence of cavity optomechanics. We have developed a new generation of optomechanical devices, based on a microgram quartz micropillar with a very high mechanical quality factor. The structure is used as end mirror in a Fabry-Perot cavity with a high optical finesse, leading to ultra-sensitive interferometric measurement of the resonator displacement. We expect to reach the ground state of this optomechanical resonator by combining cryogenic cooling in a dilution fridge at 30 mK and radiation-pressure cooling. We have already carried out a quantum-limited measurement of the micropillar thermal noise at low temperature.

  17. Retention proposal in complex cavities.

    Directory of Open Access Journals (Sweden)

    Pedro Alvarez Rodríguez

    2003-12-01

    Full Text Available Background: Dental Operatory is the main structure in which Odontology lies. It is not an easy discipline that gives enjoyable results with little effort due to the difficulties that a correct reconstruction of a destroyed dental element offers.The frequency with which pulpar injury occurs while anchoring additional retainers in complex cavities, the technical difficulties the lack of these devices cause and the need to simplify dental procedures lead this study to show the advantages to substitute additional retainers for a retainer surcus. Method: An observational descriptive study was applied to 53 patients(42% of the universe , sample which was selected by means of a simple randomized sample . From a proximal-occlusal cavity, the preparations were extended in a box-like shape towards the bucal or lingual region and the additional retainers were substituted for a surcus which was performed in the gingival wall of the preparation. Calcium Hydroxide of rapid dryness was used as a cavity cover and Policarboxilate cement as a base; then the amalgam restoration was performed. The number of restorations were studied taking into account the patient´s age and the failures due to fractures of amalgam, loss of vitality and periapical changes were assessed taking into consideration the patient´s age and a one- year follow up. Results: Most of the amalgam restorations were performed in patients aged from 35 to 59 years and the relative frequencies due to fractures of amalgam, loss of vitality and periapical changes were very low. Conclusion: The substitution of additional retainers for a retainer surcus in complex cavities of vital molars showed to be advantageous because it guarantees a less degree of pulpar damage and less pulpar damage.

  18. Angioleiomyoma of the Nasal Cavity

    Directory of Open Access Journals (Sweden)

    Arruda, Milena Moreira

    2014-01-01

    Full Text Available Introduction Vascular leiomyoma of the nasal cavity is an extremely rare tumor that represents less than 1% of all vascular leiomyomas. It is more prevalent in women between the fourth and sixth decades, reaching primarily the inferior nasal turbinates. Objectives Reporting and assisting the systematization of more accurate diagnostic methods in clinical and complementary investigation of vascular leiomyoma in the nasal cavity. Resumed Report We present the case of a 49-year-old woman diagnosed with vascular leiomyoma in the nasal cavity, which manifested mainly with nasal obstruction. During investigation, computer tomography was not diagnostic, the cytologic study was not conclusive, and according to the biopsy, it was a squamous papilloma. Conclusion We suggest that the technical difficulty in obtaining an adequate amount of material for preoperative biopsy, associated with the topography of the lesion in the vestibular nasal region, may have contributed to changing the postoperative diagnosis. Thus, pathologic study of the surgical fragment is the more accurate method for diagnosis.

  19. Angioleiomyoma of the Nasal Cavity

    Science.gov (United States)

    Arruda, Milena Moreira; Monteiro, Daniela Yasbek; Fernandes, Atilio Maximino; Menegatti, Vanessa; Thomazzi, Emerson; Hubner, Ricardo Arthur; Lima, Luiz Guilherme Cernaglia Aureliano de

    2014-01-01

    Introduction Vascular leiomyoma of the nasal cavity is an extremely rare tumor that represents less than 1% of all vascular leiomyomas. It is more prevalent in women between the fourth and sixth decades, reaching primarily the inferior nasal turbinates. Objectives Reporting and assisting the systematization of more accurate diagnostic methods in clinical and complementary investigation of vascular leiomyoma in the nasal cavity. Resumed Report We present the case of a 49-year-old woman diagnosed with vascular leiomyoma in the nasal cavity, which manifested mainly with nasal obstruction. During investigation, computer tomography was not diagnostic, the cytologic study was not conclusive, and according to the biopsy, it was a squamous papilloma. Conclusion We suggest that the technical difficulty in obtaining an adequate amount of material for preoperative biopsy, associated with the topography of the lesion in the vestibular nasal region, may have contributed to changing the postoperative diagnosis. Thus, pathologic study of the surgical fragment is the more accurate method for diagnosis. PMID:25992133

  20. Optomechanic interactions in phoxonic cavities

    Energy Technology Data Exchange (ETDEWEB)

    Djafari-Rouhani, Bahram; Oudich, Mourad; Pennec, Yan [Institut d’Electronique, de Microélectronique et de Nanotechnologie (IEMN), UMR CNRS 8520, UFR de physique, Université Lille1, Cité Scientifique, 59652, Villeneuve d’Ascq (France); El-Jallal, Said [Institut d’Electronique, de Microélectronique et de Nanotechnologie (IEMN), UMR CNRS 8520, UFR de physique, Université Lille1, Cité Scientifique, 59652, Villeneuve d’Ascq (France); Physique du Rayonnement et de l’Interaction Laser Matière, Faculté des sciences, Université de Moulay Ismail, Meknès (Morocco)

    2014-12-15

    Phoxonic crystals are periodic structures exhibiting simultaneous phononic and photonic band gaps, thus allowing the confinement of both excitations in the same cavity. The phonon-photon interaction can be enhanced due to the overlap of both waves in the cavity. In this paper, we discuss some of our recent theoretical works on the strength of the optomechanic coupling, based on both photoelastic and moving interfaces mechanisms, in different (2D, slabs, strips) phoxonic crystals cavities. The cases of two-dimensional infinite and slab structures will enable us to mention the important role of the symmetry and degeneracy of the modes, as well as the role of the materials whose photoelastic constants can be wavelength dependent. Depending on the phonon-photon pair, the photoelastic and moving interface mechanisms can contribute in phase or out-of-phase. Then, the main part of the paper will be devoted to the optomechanic interaction in a corrugated nanobeam waveguide exhibiting dual phononic/photonic band gaps. Such structures can provide photonic modes with very high quality factor, high frequency phononic modes of a few GHz inside a gap and optomechanical coupling rate reaching a few MHz.

  1. Optomechanic interactions in phoxonic cavities

    Directory of Open Access Journals (Sweden)

    Bahram Djafari-Rouhani

    2014-12-01

    Full Text Available Phoxonic crystals are periodic structures exhibiting simultaneous phononic and photonic band gaps, thus allowing the confinement of both excitations in the same cavity. The phonon-photon interaction can be enhanced due to the overlap of both waves in the cavity. In this paper, we discuss some of our recent theoretical works on the strength of the optomechanic coupling, based on both photoelastic and moving interfaces mechanisms, in different (2D, slabs, strips phoxonic crystals cavities. The cases of two-dimensional infinite and slab structures will enable us to mention the important role of the symmetry and degeneracy of the modes, as well as the role of the materials whose photoelastic constants can be wavelength dependent. Depending on the phonon-photon pair, the photoelastic and moving interface mechanisms can contribute in phase or out-of-phase. Then, the main part of the paper will be devoted to the optomechanic interaction in a corrugated nanobeam waveguide exhibiting dual phononic/photonic band gaps. Such structures can provide photonic modes with very high quality factor, high frequency phononic modes of a few GHz inside a gap and optomechanical coupling rate reaching a few MHz.

  2. Differential cavity mode spectroscopy: A new cavity enhanced technique for the detection of weak transitions

    Energy Technology Data Exchange (ETDEWEB)

    Vine, Glenn de [Centre for Gravitational Physics, Faculty of Science, The Australian National University, Canberra ACT 0200 (Australia)], E-mail: glenn.devine@jpl.nasa.gov; McClelland, David E.; Gray, Malcolm B. [Centre for Gravitational Physics, Faculty of Science, The Australian National University, Canberra ACT 0200 (Australia)

    2008-06-16

    We present a new cavity enhanced, continuous wave spectroscopic technique for the detection of weak atomic and molecular transitions. Differential Cavity Mode Spectroscopy (DCMS) measures the difference in absorption between two adjacent cavity longitudinal modes to yield a highly sensitive, yet relatively simple, cavity enhanced spectroscopic technique. In addition this relative absorption measurement is, to first order, independent of both laser frequency noise and cavity acoustic noise. Here we present both a theoretical description of this new technique and an initial experimental demonstration.

  3. LHC crab-cavity aspects and strategy

    Energy Technology Data Exchange (ETDEWEB)

    Calaga, R.; Tomas, R.; Zimmermann, F.

    2010-05-23

    The 3rd LHC Crab Cavity workshop (LHC-CC09) took place at CERN in October 2009. It reviewed the current status and identified a clear strategy towards a future crab-cavity implementation. Following the success of crab cavities in KEK-B and the strong potential for luminosity gain and leveling, CERN will pursue crab crossing for the LHC upgrade. We present a summary and outcome of the variousworkshop sessions which have led to the LHC crab-cavity strategy, covering topics like layout, cavity design, integration, machine protection, and a potential validation test in the SPS.

  4. Coupled-bunch instabilities due to fundamental cavity impedance

    CERN Document Server

    Mastoridis, Themistoklis; Chapochnikova, Elena; Esteban Muller, Juan; Molendijk, John; Timko, Helga; CERN. Geneva. ATS Department

    2017-01-01

    The purpose of this MD was to estimate the stability threshold due to longitudinal coupled-bunch instabilities (CBIs) driven by the RF cavities' fundamental impedance. These instabilities are not a concern for the LHC. A model was developed to study the stability threshold for the High-Luminosity LHC (HL-LHC). The goal of this MD was to validate this model and thus its predictions for the HL-LHC stability margins.

  5. Interacting factors driving a major loss of large trees with cavities in a forest ecosystem.

    Science.gov (United States)

    Lindenmayer, David B; Blanchard, Wade; McBurney, Lachlan; Blair, David; Banks, Sam; Likens, Gene E; Franklin, Jerry F; Laurance, William F; Stein, John A R; Gibbons, Philip

    2012-01-01

    Large trees with cavities provide critical ecological functions in forests worldwide, including vital nesting and denning resources for many species. However, many ecosystems are experiencing increasingly rapid loss of large trees or a failure to recruit new large trees or both. We quantify this problem in a globally iconic ecosystem in southeastern Australia--forests dominated by the world's tallest angiosperms, Mountain Ash (Eucalyptus regnans). Tree, stand and landscape-level factors influencing the death and collapse of large living cavity trees and the decay and collapse of dead trees with cavities are documented using a suite of long-term datasets gathered between 1983 and 2011. The historical rate of tree mortality on unburned sites between 1997 and 2011 was >14% with a mortality spike in the driest period (2006-2009). Following a major wildfire in 2009, 79% of large living trees with cavities died and 57-100% of large dead trees were destroyed on burned sites. Repeated measurements between 1997 and 2011 revealed no recruitment of any new large trees with cavities on any of our unburned or burned sites. Transition probability matrices of large trees with cavities through increasingly decayed condition states projects a severe shortage of large trees with cavities by 2039 that will continue until at least 2067. This large cavity tree crisis in Mountain Ash forests is a product of: (1) the prolonged time required (>120 years) for initiation of cavities; and (2) repeated past wildfires and widespread logging operations. These latter factors have resulted in all landscapes being dominated by stands ≤72 years and just 1.16% of forest being unburned and unlogged. We discuss how the features that make Mountain Ash forests vulnerable to a decline in large tree abundance are shared with many forest types worldwide.

  6. Novel Geometries for the LHC Crab Cavity

    Energy Technology Data Exchange (ETDEWEB)

    Hall, B. [Lancaster Univ. (United Kingdom); Burt, G. [Lancaster Univ. (United Kingdom); Smith, J. D.A. [Lancaster Univ. (United Kingdom); Rimmer, R. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Wang, H. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Delayen, J. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Calaga, R. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2009-05-01

    In 2017 the LHC is envisioned to increase its luminosity via an upgrade. This upgrade is likely to require a large crossing angle hence a crab cavity is required to align the bunches prior to collision. There are two possible schemes for crab cavity implementation, global and local. In a global crab cavity the crab cavity is far from the IP and the bunch rotates back and forward as it traverses around the accelerator in a closed orbit. For this scheme a two-cell elliptical squashed cavity at 800 MHz is preferred. To avoid any potential beam instabilities all the parasitic modes of the cavities must be damped strongly, however crab cavities have lower order and same order modes in addition to the usual higher order modes and hence a novel damping scheme must be used to provide sufficient damping of these modes. In the local scheme two crab cavities are placed at each side of the IP two start and stop rotation of the bunches. This would require crab cavities much smaller transversely than in the global scheme but the frequency cannot be increased any higher due to the long bunch length of the LHC beam. This will require a novel compact crab cavity design. A superconducting version of a two rod coaxial deflecting cavity as a suitable design is proposed in this paper.

  7. Plasmonic Coupled Cavities on Moire Surfaces

    Science.gov (United States)

    Balci, Sinan; Kocabas, Askin; Karabiyik, Mustafa; Kocabas, Coskun; Aydinli, Atilla

    2010-03-01

    We investigate surface plasmon polariton (SPP) coupled cavity modes on Moire surfaces. An experimental study has been made of the propagation of SPPs on a thin silver surface that is textured with Moire surface pattern using interference lithography. The Moire surface contains periodic array of one dimensional cavities. The distance between the cavities can be controlled by changing the periodicities of Moire surface. When the SPP cavity separation is sufficiently small, we show splitting of strongly coupled plasmonic cavity modes through numerical simulations. Conversely, when the SPP cavity separation is sufficiently large, SPP cavity modes are found to be localized and do not show splitting of SPP cavity modes . This splitting of SPP cavity modes are well explained with a tight binding model that has been succesfully applied in photonic coupled cavities. Reflection measurements and numerical simulation of a large number of adjacent SPP cavities have shown a coupled resonator optical waveguide (CROW) type plasmonic waveguide band formation within the band gap region of unperturbed uniform grating.

  8. CHECHIA cavity driving with FPGA controller

    Energy Technology Data Exchange (ETDEWEB)

    Czarski, T.; Koprek, W.; Pozniak, K.T.; Romaniuk, R.S. [Technical Univ. Warsaw (Poland). ELHEP Laboratory, ISE; Simrock, S. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). TESLA

    2005-07-01

    The initial control of the superconductive cavity has recently been performed by applying the FPGA (Field Programmable Gate Array) technology system in DESY Hamburg. This first experiment turned attention to the general recognition of the cavity features and projected control methods. The electrical model of the cavity is taken as a consideration origin. The calibration of the signal channel is considered as a key preparation for an efficient cavity driving. The cavity parameters identification is confirmed as a proper approach for the required performance: driving on resonance during filling and field stabilization during flattop time with reasonable power consumption. The feed-forward and feedback modes were applied successfully for the CHECHIA cavity driving. Representative results of experiments are presented for different levels of the cavity field gradient. (orig.)

  9. Novel Geometries for the LHC Crab Cavity

    Energy Technology Data Exchange (ETDEWEB)

    B. Hall, G. Burt, C. Lingwood, R. Rimmer, H. Wang

    2010-05-23

    The planned luminosity upgrade to LHC is likely to necessitate a large crossing angle and a local crab crossing scheme. For this scheme crab cavities align bunches prior to collision. The scheme requires at least four such cavities, a pair on each beam line either side of the interaction point (IP). Upstream cavities initiate rotation and downstream cavities cancel rotation. Cancellation is usually done at a location where the optics has re-aligned the bunch. The beam line separation near the IP necessitates a more compact design than is possible with elliptical cavities such as those used at KEK. The reduction in size must be achieved without an increase in the operational frequency to maintain compatibility with the long bunch length of the LHC. This paper proposes a suitable superconducting variant of a four rod coaxial deflecting cavity (to be phased as a crab cavity), and presents analytical models and simulations of suitable designs.

  10. SPS RF System an Accelerating 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.

  11. Highly stable piezoelectrically tunable optical cavities

    CERN Document Server

    Möhle, Katharina; Döringshoff, Klaus; Nagel, Moritz; Peters, Achim

    2013-01-01

    We have implemented highly stable and tunable frequency references using optical high finesse cavities which incorporate a piezo actuator. As piezo material we used ceramic PZT, crystalline quartz, or PZN-PT single crystals. Lasers locked to these cavities show a relative frequency stability better than 1 x 10^{-14}, which is most likely not limited by the piezo actuators. The piezo cavities can be electrically tuned over more than one free spectral range (> 1.5 GHz) with only a minor decrease in frequency stability. Furthermore, we present a novel cavity design, where the piezo actuator is prestressed between the cavity spacer components. This design features a hermetically sealable intra cavity volume suitable for, e.g., cavity enhanced spectroscopy.

  12. Optical Material Characterization Using Microdisk Cavities

    Science.gov (United States)

    Michael, Christopher P.

    + density and the control offered by the precise epitaxy. The growth and fabrication methods are discussed. Spectral measurements at cryogenic and room temperatures show negligible background losses and resonant Er3+ absorption strong enough to produce cavity-polaritons that persist to above 361 K. Cooperative relaxation and upconversion limit the optical performance in the telecommunications bands by transferring the excitations to quenching sites or by further exciting the ions up to visible transitions. Future prospects and alternative applications for Er2O3 and other epitaxial rare-earth oxides are also considered.

  13. Neurilemmoma of Retromolar Region in the Oral Cavity

    Directory of Open Access Journals (Sweden)

    Ajit Singh Rathore

    2015-01-01

    Full Text Available Neurilemmoma also known as schwannoma is benign nerve sheath tumor rarely occurring in the oral cavity. Only 1% of all extracranial schwannomas show that intraoral occurrence with tongue is the commonest site and retromolar region is the least common site. It presents as encapsulated, slow growing, solitary, smooth-surfaced, usually asymptomatic tumor. We report a case of 70-year-old male with well-defined mass on left retromolar region which was painless and slow growing. Diagnosis is made by histological examination and immunohistochemistry analysis to confirm the neural tissue origin of the lesion. The treatment is complete surgical excision of the lesion without recurrence.

  14. Neurilemmoma of Retromolar Region in the Oral Cavity.

    Science.gov (United States)

    Rathore, Ajit Singh; Srivastava, Deepti; Narwal, Nidhi; Shetty, Devi Charan

    2015-01-01

    Neurilemmoma also known as schwannoma is benign nerve sheath tumor rarely occurring in the oral cavity. Only 1% of all extracranial schwannomas show that intraoral occurrence with tongue is the commonest site and retromolar region is the least common site. It presents as encapsulated, slow growing, solitary, smooth-surfaced, usually asymptomatic tumor. We report a case of 70-year-old male with well-defined mass on left retromolar region which was painless and slow growing. Diagnosis is made by histological examination and immunohistochemistry analysis to confirm the neural tissue origin of the lesion. The treatment is complete surgical excision of the lesion without recurrence.

  15. A case of ruptured descending thoracic aortic aneurysm into the right pleural cavity: importance of preoperative drainage of the right pleural cavity.

    Science.gov (United States)

    Akiyama, K; Takazawa, A; Hirota, J; Yamagishi, H; Akazawa, T

    1998-12-01

    We present an unusual case of a ruptured descending thoracic aortic aneurysm into the right pleural cavity of a patient with pectus carinatum. The presence of pectus carinatum played an important role in the development of the aneurysm at the atypical site and the rupture into the right pleural cavity. A small amount of right pleural bleeding on admission can increase and develop to massive hemothorax until emergency operation. Massive bleeding in the right pleural cavity where the dependent lung is located causes atelectasis and increased shunt fraction under one lung ventilation. Therefore, continuous drainage of the right pleural cavity is essential to prevent serious hypoxia during graft replacement in a case of ruptured descending thoracic aneurysm into the right hemithorax.

  16. Cavities

    Science.gov (United States)

    ... Information Drug Information, Search Drug Names, Generic and Brand Natural Products, Search Pill Identifier News & Commentary ALL NEWS > Resources First Aid Videos Figures Images Audio Pronunciations The One-Page Manual of Health ...

  17. Hinode and IRIS Observations of a Prominence-Cavity System

    Science.gov (United States)

    Jibben, Patricia R.; Reeves, Kathy; Su, Yingna

    2016-05-01

    Long-lived solar prominences often have a coronal cavity enclosing the prominence. Within the cavity, hot X-ray emission can persist above the prominence and in the central regions of the cavity. We present the results of an Interface Region Imaging Spectrograph (IRIS) and Hinode coordinated Observation Program (IHOP 264) study of a prominence-cavity system. The X-ray Telescope (XRT) observes an inflow of bright X-ray emission that strikes and envelops the prominence-cavity system causing an eruption of chromospheric plasma near the base of the prominence. During and after the eruption, an increase in X-ray emission forms within the cavity and above the prominence. IRIS and the EUV Imaging Spectrometer (EIS) observe strong blue shifts in both chromosphere and coronal lines during the eruption. The Solar Optical Telescope (SOT) Ca II H-line data show bright emission along the eruption path with complex turbulent plasma motions. The IRIS Si IV 1394 Angstrom spectra along the on-disk portion of the prominence show a region of decreased emission near the base of the prominence, suggesting a magnetic field bald-patch topology along the Polarity Inversion Line (PIL). Combined, these observations imply a cylindrical flux rope best represents the prominence-cavity system. A model of the magnetic structure of the prominence-cavity system comprised of a weakly twisted flux rope can explain the observed loops in the X-ray and EUV data. Observations from the Coronal Multichannel Polarimeter (CoMP) are compared to predicted models and are inconclusive. We find that more sensitive measurements of the magnetic field strength along the line-of-sight are needed to verify this configuration.Patricia Jibben and Kathy Reeves are supported by under contract 80111112705 from Lockheed-Martin to SAO, contract NNM07AB07C from NASA to SAO, grant number NNX12AI30G from NASA to SAO, and contract Z15-12504 from HAO to SAO under a grant from AFOSR. Yingna Su is supported by the Youth Fund of

  18. Middle ear cavity morphology is consistent with an aquatic origin for testudines.

    Directory of Open Access Journals (Sweden)

    Katie L Willis

    Full Text Available The position of testudines in vertebrate phylogeny is being re-evaluated. At present, testudine morphological and molecular data conflict when reconstructing phylogenetic relationships. Complicating matters, the ecological niche of stem testudines is ambiguous. To understand how turtles have evolved to hear in different environments, we examined middle ear morphology and scaling in most extant families, as well as some extinct species, using 3-dimensional reconstructions from micro magnetic resonance (MR and submillimeter computed tomography (CT scans. All families of testudines exhibited a similar shape of the bony structure of the middle ear cavity, with the tympanic disk located on the rostrolateral edge of the cavity. Sea Turtles have additional soft tissue that fills the middle ear cavity to varying degrees. When the middle ear cavity is modeled as an air-filled sphere of the same volume resonating in an underwater sound field, the calculated resonances for the volumes of the middle ear cavities largely fell within testudine hearing ranges. Although there were some differences in morphology, there were no statistically significant differences in the scaling of the volume of the bony middle ear cavity with head size among groups when categorized by phylogeny and ecology. Because the cavity is predicted to resonate underwater within the testudine hearing range, the data support the hypothesis of an aquatic origin for testudines, and function of the middle ear cavity in underwater sound detection.

  19. Output field-quadrature measurements and squeezing in ultrastrong cavity-QED

    Science.gov (United States)

    Stassi, Roberto; Savasta, Salvatore; Garziano, Luigi; Spagnolo, Bernardo; Nori, Franco

    2016-12-01

    We study the squeezing of output quadratures of an electro-magnetic field escaping from a resonator coupled to a general quantum system with arbitrary interaction strengths. The generalized theoretical analysis of output squeezing proposed here is valid for all the interaction regimes of cavity-quantum electrodynamics: from the weak to the strong, ultrastrong, and deep coupling regimes. For coupling rates comparable or larger then the cavity resonance frequency, the standard input-output theory for optical cavities fails to calculate the variance of output field-quadratures and predicts a non-negligible amount of output squeezing, even if the system is in its ground state. Here we show that, for arbitrary interaction strength and for general cavity-embedded quantum systems, no squeezing can be found in the output-field quadratures if the system is in its ground state. We also apply the proposed theoretical approach to study the output squeezing produced by: (i) an artificial two-level atom embedded in a coherently-excited cavity; and (ii) a cascade-type three-level system interacting with a cavity field mode. In the latter case the output squeezing arises from the virtual photons of the atom-cavity dressed states. This work extends the possibility of predicting and analyzing the results of continuous-variable optical quantum-state tomography when optical resonators interact very strongly with other quantum systems.

  20. CAVITY LIKE COMPLETIONS IN WEAK SANDS PREFERRED UPSTREAM MANAGEMENT PRACTICES

    Energy Technology Data Exchange (ETDEWEB)

    Ian Palmer; John McLennan

    2004-04-30

    The technology referred to as Cavity Like Completions (CLC) offers a new technique to complete wells in friable and unconsolidated sands. A successfully designed CLC provides significant increases in well PI (performance index) at lower costs than alternative completion techniques. CLC technology is being developed and documented by a partnership of major oil and gas companies through a GPRI (Global Petroleum Research Institute) joint venture. Through the DOE-funded PUMP program, the experiences of the members of the joint venture will be described for other oil and gas producing companies. To date six examples of CLC completions have been investigated by the JV. The project was performed to introduce a new type of completion (or recompletion) technique to the industry that, in many cases, offers a more cost effective method to produce oil and gas from friable reservoirs. The project's scope of work included: (1) Further develop theory, laboratory and field data into a unified model to predict performance of cavity completion; (2) Perform at least one well test for cavity completion (well provided by one of the sponsor companies); (3) Provide summary of geo-mechanical models for PI increase; and (4) Develop guidelines to evaluate success of potential cavity completion. The project tracks the experiences of a joint industry consortium (GPRI No. 17) over a three year period and compiles results of the activities of this group.

  1. Cavity Optical Pulse Extraction: ultra-short pulse generation as seeded Hawking radiation.

    Science.gov (United States)

    Eilenberger, Falk; Kabakova, Irina V; de Sterke, C Martijn; Eggleton, Benjamin J; Pertsch, Thomas

    2013-01-01

    We show that light trapped in an optical cavity can be extracted from that cavity in an ultrashort burst by means of a trigger pulse. We find a simple analytic description of this process and show that while the extracted pulse inherits its pulse length from that of the trigger pulse, its wavelength can be completely different. Cavity Optical Pulse Extraction is thus well suited for the development of ultrashort laser sources in new wavelength ranges. We discuss similarities between this process and the generation of Hawking radiation at the optical analogue of an event horizon with extremely high Hawking temperature. Our analytic predictions are confirmed by thorough numerical simulations.

  2. Phonon-dressed Mollow triplet in the regime of cavity quantum electrodynamics: excitation-induced dephasing and nonperturbative cavity feeding effects.

    Science.gov (United States)

    Roy, C; Hughes, S

    2011-06-17

    We study the resonance fluorescence spectra of a driven quantum dot placed inside a high-Q semiconductor cavity and interacting with an acoustic phonon bath. The dynamics is calculated using a time-convolutionless master equation in the polaron frame. We predict pronounced spectral broadening of the Mollow sidebands through off-resonant cavity emission which, for small cavity-coupling rates, increases quadratically with the Rabi frequency in direct agreement with recent experiments using semiconductor micropillars [S. M. Ulrich et al., preceding Letter, Phys. Rev. Lett. 106, 247402 (2011)]. We also demonstrate that, surprisingly, phonon coupling actually helps resolve signatures of the elusive second rungs of the Jaynes-Cummings ladder states via off-resonant cavity feeding. Both multiphonon and multiphoton effects are shown to play a qualitatively important role on the fluorescence spectra.

  3. Aespoe HRL - Geoscientific evaluation 1997/3. Results from pre-investigation and detailed site characterization. Comparison of predictions and observations. Geology and mechanical stability

    Energy Technology Data Exchange (ETDEWEB)

    Stanfors, R. [RS Consulting, Lund (Sweden); Olsson, Paer [Skanska AB Stockholm (Sweden); Stille, H. [Royal Inst. of Tech., Stockholm (Sweden)

    1997-05-01

    Prior to excavation of the laboratory in 1990 predictions were made for the excavation phase. The predictions concern five key issues: Geology, groundwater flow, groundwater chemistry, transport of solutes, and mechanical stability. Comparisons between predictions and observations were made during excavation in order to verify the reliability of the pre-investigations. This report presents a comparison between the geological and mechanical stability predictions and observations and an evaluation of data and investigation methods used for the 700-2874 m section of the tunnel. The report is specially highlighting the following conclusions: It is possible to localize major fracture zones during the pre-investigation at shallow (<200 m) depths; A number of minor fracture zones striking NNW-NNE were predicted to be hydraulically important and penetrate the southern area. A number of narrow fracture zone indications - 0.1-1 m wide - striking WNW-NE were mapped in the tunnel and pre-grouted sections confirm hydraulic conductors; It has not been possible to confirm the gently dipping zone EW-5, which was predicted as `possible`, with data from the tunnel; Predictions of the amount of different rock types were generally reliable as regards the major rocks, but the prediction of the distribution in space were poor as regards the minor rock types; The prediction of rock stress orientation corresponds well to the outcome; The prediction of rock quality for the tunnel, while applying the RMR-system, shows good correspondence to the observations made in the tunnel. 59 refs, 51 figs, 21 tabs.

  4. Dynamical tunneling in optical cavities

    CERN Document Server

    Hackenbroich, G; Hackenbroich, Gregor; Noeckel, Jens U.

    1998-01-01

    The lifetime of whispering gallery modes in a dielectric cavity with a metallic inclusion is shown to fluctuate by orders of magnitude when size and location of the inclusion are varied. We ascribe these fluctuations to tunneling transitions between resonances quantized in different regions of phase space. This interpretation is confirmed by a comparison of the classical phase space structure with the Husimi distribution of the resonant modes. A model Hamiltonian is introduced that describes the phenomenon and shows that it can be expected in a more general class of systems.

  5. Basketballs as spherical acoustic cavities

    Science.gov (United States)

    Russell, Daniel A.

    2010-06-01

    The sound field resulting from striking a basketball is found to be rich in frequency content, with over 50 partials in the frequency range of 0-12 kHz. The frequencies are found to closely match theoretical expectations for standing wave patterns inside a spherical cavity. Because of the degenerate nature of the mode shapes, explicit identification of the modes is not possible without internal investigation with a microphone probe. A basketball proves to be an interesting application of a boundary value problem involving spherical coordinates.

  6. Clinical and mycological analysis of dog's oral cavity

    Directory of Open Access Journals (Sweden)

    Rosema Santin

    2013-01-01

    Full Text Available The oral microbiota of humans and animals is made up of a wide variety of yeasts and bacteria, but microbiota of dogs is not totally described. Although such identification is an important step to establish the etiopathogenesis and adequate therapy for the periodontal disease The aim of this study was to evaluate and correlate oral alterations with the presence of yeasts in oral cavity of female dogs. After clinical evaluation samples from healthy and from dogs with oral diseases were obtained from three different oral sites by swabs, curettes, millimeter periodontal probes and HA membrane tip in cellulose ester. Yeast identification was performed through macroscopic and microscopic colony features and biochemical tests. Dental calculus was the most prevalent occurrence in the oral cavity of 59 females. However, the isolation of yeasts was significantly higher (p < 0.05 in animals suffering from halitosis. Eleven yeast species were identified, namely: Malassezia pachydermatis, Rhodotorula spp., Candida albicans, C. catenulata, C. famata, C. guilliermondii, C. parapsilosis, C. intermedia, Trichosporon asahii, T. mucoides and Cryptococcus albidus. It could be concluded that the yeasts are part of the microbiota from the different sites of the oral cavity of the female canines studied without causing any significant alterations except halitosis.

  7. Nanobeam photonic crystal cavity quantum dot laser

    CERN Document Server

    Gong, Yiyang; Shambat, Gary; Sarmiento, Tomas; Harris, James S; Vuckovic, Jelena

    2010-01-01

    The lasing behavior of one dimensional GaAs nanobeam cavities with embedded InAs quantum dots is studied at room temperature. Lasing is observed throughout the quantum dot PL spectrum, and the wavelength dependence of the threshold is calculated. We study the cavity lasers under both 780 nm and 980 nm pump, finding thresholds as low as 0.3 uW and 19 uW for the two pump wavelengths, respectively. Finally, the nanobeam cavity laser wavelengths are tuned by up to 7 nm by employing a fiber taper in near proximity to the cavities. The fiber taper is used both to efficiently pump the cavity and collect the cavity emission.

  8. Rationale for designing cavity preparations.

    Science.gov (United States)

    Laswell, H R; Welk, D A

    1985-04-01

    Increased resistance to caries, increased dental awareness, superior diagnostic capabilities, better illumination, optical aids that significantly enhance vision, improved and standardized materials for restoration, and a deeper understanding of the caries process enable a far more conservative approach to tooth preparation. The dentist can concentrate on preserving as much sound tooth structure as possible with less attention being devoted to resistance and retention form that previously demanded in bulk restorations and massive channels and locks that are no longer appropriate. Although caries inhibitory effects have been shown with materials such as silicate cement, glass ionomers, and resins that leach fluoride, in general, dentists should not rely on restorative materials to inhibit the development of future decay. Characteristics of the carious lesion are unique for each tooth according to many factors centering around the plaque pattern for that tooth and not according to zones of natural susceptibility or immunity strictly dictated by morphology. Therefore, no single cavity preparation duplicated from a textbook is likely to be satisfactory for an individual tooth. Furthermore, novices learning the subject of cavity preparation often leave decalcified enamel when they attempt to replicate under clinical conditions that which they have learned in technique courses. This is the major invitation to future caries reappearing adjacent to restorations. Also, failure to duplicate the exact morphology of the tooth surface that has been replaced is likely to alter the pattern of plaque accumulation and create other caries prone areas.(ABSTRACT TRUNCATED AT 250 WORDS)

  9. Cavity QED-based quantum walk

    Science.gov (United States)

    di, Tiegang; Hillery, Mark; Zubairy, M. Suhail

    2004-09-01

    We discuss a possible experimental scheme for the implementation of a quantum walk. The scheme is based on the passage of an atom inside a high- Q cavity. The chirality is characterized by the atomic states and the displacement is characterized by the photon number inside the cavity. The quantum steps are described by appropriate interactions with a sequence of classical and quantized cavity fields.

  10. Ray splitting in paraxial optical cavities

    CERN Document Server

    Puentes, G; Woerdman, J P

    2003-01-01

    We present a numerical investigation of the ray dynamics in a paraxial optical cavity when a ray splitting mechanism is present. The cavity is a conventional two-mirror stable resonator and the ray splitting is achieved by inserting an optical beam splitter perpendicular to the cavity axis. We show that depending on the position of the beam splitter the optical resonator can become unstable and the ray dynamics displays a positive Lyapunov exponent.

  11. Tunable Cavity Optomechanics with Ultracold Atoms

    CERN Document Server

    Purdy, T P; Botter, T; Brahms, N; Ma, Z -Y; Stamper-Kurn, D M

    2010-01-01

    We present an atom-chip-based realization of quantum cavity optomechanics with cold atoms localized within a Fabry-Perot cavity. Effective sub-wavelength positioning of the atomic ensemble allows for tuning the linear and quadratic optomechanical coupling parameters, varying the sensitivity to the displacement and strain of a compressible gaseous cantilever. We observe effects of such tuning on cavity optical nonlinearity and optomechanical frequency shifts, providing their first characterization in the quadratic-coupling regime.

  12. Continuously tunable, split-cavity gyrotrons

    Science.gov (United States)

    Brand, G. F.; Gross, M.

    1985-12-01

    Attention is given to a gyrotron cavity configuration which is split in halves longitudinally, to allow any frequency lying between the fixed cavity resonance to be assessed by mechanically changing the separation of the two halves. Experimental results are presented which demonstrate that the rate-of-change in resonant frequency with separation is greatest if the minor axis of the cavity cross section is the one undergoing change. Excellent agreement with theory is noted for these results.

  13. Dither Cavity Length Controller with Iodine Locking

    Directory of Open Access Journals (Sweden)

    Lawson Marty

    2016-01-01

    Full Text Available A cavity length controller for a seeded Q-switched frequency doubled Nd:YAG laser is constructed. The cavity length controller uses a piezo-mirror dither voltage to find the optimum length for the seeded cavity. The piezo-mirror dither also dithers the optical frequency of the output pulse. [1]. This dither in optical frequency is then used to lock to an Iodine absorption line.

  14. Mechanical Properties of Ingot Nb Cavities

    Energy Technology Data Exchange (ETDEWEB)

    Ciovati, Gianluigi; Dhakal, Pashupati; Kneisel, Peter; Mammosser, John; Matalevich, Joseph; Rao Myneni, Ganapati

    2014-07-01

    This contribution presents the results of measurements of the resonant frequency and of strain along the contour of a single-cell cavity made of ingot Nb subjected to increasing uniform differential pressure, up to 6 atm. The data were used to infer mechanical properties of this material after cavity fabrication, by comparison with the results from simulation calculations done with ANSYS. The objective is to provide useful information about the mechanical properties of ingot Nb cavities which can be used in the design phase of SRF cavities intended to be built with this material.

  15. Novel Geometries for the LHC CRAB Cavity

    CERN Document Server

    Hall, Ben

    2010-01-01

    In 2017 the LHC is envisioned to increase its luminosity via an upgrade. This upgrade is likely to require a large crossing angle hence a crab cavity is required to align the bunches prior to collision. There are two possible schemes for crab cavity implementation, global and local. In a global crab cavity the crab cavity is far from the IP and the bunch rotates back and forward as it traverses around the accelerator in a closed orbit. For this scheme a two-cell elliptical squashed cavity at 800 MHz is preferred. To avoid any potential beam instabilities all the parasitic modes of the cavities must be damped strongly, however crab cavities have lower order and same order modes in addition to the usual higher order modes and hence a novel damping scheme must be used to provide sufficient damping of these modes. In the local scheme two crab cavities are placed at each side of the IP two start and stop rotation of the bunches. This would require crab cavities much smaller transversely than in the global scheme b...

  16. Cavity quantum electrodynamics: coherence in context.

    Science.gov (United States)

    Mabuchi, H; Doherty, A C

    2002-11-15

    Modern cavity quantum electrodynamics (cavity QED) illuminates the most fundamental aspects of coherence and decoherence in quantum mechanics. Experiments on atoms in cavities can be described by elementary models but reveal intriguing subtleties of the interplay of coherent dynamics with external couplings. Recent activity in this area has pioneered powerful new approaches to the study of quantum coherence and has fueled the growth of quantum information science. In years to come, the purview of cavity QED will continue to grow as researchers build on a rich infrastructure to attack some of the most pressing open questions in micro- and mesoscopic physics.

  17. Design of the ILC Crab Cavity System

    Energy Technology Data Exchange (ETDEWEB)

    Adolphsen, C.; Beard, C.; Bellantoni, L.; Burt, G.; Carter, R.; Chase, B.; Church, M.; Dexter, A.; Dykes, M.; Edwards, H.; Goudket, P; Jenkins, R.; Jones, R.M.; Kalinin,; Khabiboulline, T.; Ko, K.; Latina, A.; Li, Z.; Ma, L.; McIntosh, P.; Ng, C.; /SLAC /Daresbury /Fermilab /Cockcroft Inst. Accel. Sci. Tech. /CERN

    2007-08-15

    The International Linear Collider (ILC) has a 14 mrad crossing angle in order to aid extraction of spent bunches. As a result of the bunch shape at the interaction point, this crossing angle at the collision causes a large luminosity loss which can be recovered by rotating the bunches prior to collision using a crab cavity. The ILC baseline crab cavity is a 9-cell superconducting dipole cavity operating at a frequency of 3.9 GHz. In this paper the design of the ILC crab cavity and its phase control system, as selected for the RDR in February 2007 is described in fuller detail.

  18. Engineering topological materials in microwave cavity arrays

    CERN Document Server

    Anderson, Brandon M; Owens, Clai; Schuster, David I; Simon, Jonathan

    2016-01-01

    We present a scalable architecture for the exploration of interacting topological phases of photons in arrays of microwave cavities, using established techniques from cavity and circuit quantum electrodynamics. A time-reversal symmetry breaking (non-reciprocal) flux is induced by coupling the microwave cavities to ferrites, allowing for the production of a variety of topological band structures including the $\\alpha=1/4$ Hofstadter model. Effective photon-photon interactions are included by coupling the cavities to superconducting qubits, and are sufficient to produce a $\

  19. State of the Art SRF Cavity Performance

    CERN Document Server

    Lilje, L

    2004-01-01

    The paper will review superconducting RF cavity performance for β=1 cavities used in both linear and circular accelerators. These superconducting cavities are used in two kinds of applications: High current storage rings and efficient high duty cycle linacs. In recent years the performance of those cavities has been improving steadily. High accelerating gradients have been achieved using advanced surface preparation techniques like electropolishing and surface cleaning methods like high pressure water rinsing. High intensity beams can be handled with advanced higher-order-mode damping schemes.

  20. Comparison of coherently coupled multi-cavity and quantum dot embedded single cavity systems.

    Science.gov (United States)

    Kocaman, Serdar; Sayan, Gönül Turhan

    2016-12-12

    Temporal group delays originating from the optical analogue to electromagnetically induced transparency (EIT) are compared in two systems. Similar transmission characteristics are observed between a coherently coupled high-Q multi-cavity array and a single quantum dot (QD) embedded cavity in the weak coupling regime. However, theoretically generated group delay values for the multi-cavity case are around two times higher. Both configurations allow direct scalability for chip-scale optical pulse trapping and coupled-cavity quantum electrodynamics (QED).