WorldWideScience

Sample records for antibody-antigen docking compensates

  1. SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

    OpenAIRE

    Sircar, Aroop; Gray, Jeffrey J.

    2010-01-01

    High resolution structures of antibody-antigen complexes are useful for analyzing the binding interface and to make rational choices for antibody engineering. When a crystallographic structure of a complex is unavailable, the structure must be predicted using computational tools. In this work, we illustrate a novel approach, named SnugDock, to predict high-resolution antibody-antigen complex structures by simultaneously structurally optimizing the antibody-antigen rigid-body positions, the re...

  2. Multiscale sensing of antibody-antigen interactions by organic transistors and single-molecule force spectroscopy.

    Science.gov (United States)

    Casalini, Stefano; Dumitru, Andra C; Leonardi, Francesca; Bortolotti, Carlo A; Herruzo, Elena T; Campana, Alessandra; de Oliveira, Rafael F; Cramer, Tobias; Garcia, Ricardo; Biscarini, Fabio

    2015-05-26

    Antibody-antigen (Ab-Ag) recognition is the primary event at the basis of many biosensing platforms. In label-free biosensors, these events occurring at solid-liquid interfaces are complex and often difficult to control technologically across the smallest length scales down to the molecular scale. Here a molecular-scale technique, such as single-molecule force spectroscopy, is performed across areas of a real electrode functionalized for the immunodetection of an inflammatory cytokine, viz. interleukin-4 (IL4). The statistical analysis of force-distance curves allows us to quantify the probability, the characteristic length scales, the adhesion energy, and the time scales of specific recognition. These results enable us to rationalize the response of an electrolyte-gated organic field-effect transistor (EGOFET) operated as an IL4 immunosensor. Two different strategies for the immobilization of IL4 antibodies on the Au gate electrode have been compared: antibodies are bound to (i) a smooth film of His-tagged protein G (PG)/Au; (ii) a 6-aminohexanethiol (HSC6NH2) self-assembled monolayer on Au through glutaraldehyde. The most sensitive EGOFET (concentration minimum detection level down to 5 nM of IL4) is obtained with the first functionalization strategy. This result is correlated to the highest probability (30%) of specific binding events detected by force spectroscopy on Ab/PG/Au electrodes, compared to 10% probability on electrodes with the second functionalization. Specifically, this demonstrates that Ab/PG/Au yields the largest areal density of oriented antibodies available for recognition. More in general, this work shows that specific recognition events in multiscale biosensors can be assessed, quantified, and optimized by means of a nanoscale technique. PMID:25868724

  3. Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities.

    Science.gov (United States)

    Sulea, Traian; Vivcharuk, Victor; Corbeil, Christopher R; Deprez, Christophe; Purisima, Enrico O

    2016-07-25

    Affinity modulation of antibodies and antibody fragments of therapeutic value is often required in order to improve their clinical efficacies. Virtual affinity maturation has the potential to quickly focus on the critical hotspot residues without the combinatorial explosion problem of conventional display and library approaches. However, this requires a binding affinity scoring function that is capable of ranking single-point mutations of a starting antibody. We focus here on assessing the solvated interaction energy (SIE) function that was originally developed for and is widely applied to scoring of protein-ligand binding affinities. To this end, we assembled a structure-function data set called Single-Point Mutant Antibody Binding (SiPMAB) comprising several antibody-antigen systems suitable for this assessment, i.e., based on high-resolution crystal structures for the parent antibodies and coupled with high-quality binding affinity measurements for sets of single-point antibody mutants in each system. Using this data set, we tested the SIE function with several mutation protocols based on the popular methods SCWRL, Rosetta, and FoldX. We found that the SIE function coupled with a protocol limited to sampling only the mutated side chain can reasonably predict relative binding affinities with a Spearman rank-order correlation coefficient of about 0.6, outperforming more aggressive sampling protocols. Importantly, this performance is maintained for each of the seven system-specific component subsets as well as for other relevant subsets including non-alanine and charge-altering mutations. The transferability and enrichment in affinity-improving mutants can be further enhanced using consensus ranking over multiple methods, including the SIE, Talaris, and FOLDEF energy functions. The knowledge gained from this study can lead to successful prospective applications of virtual affinity maturation. PMID:27367467

  4. Characterisation of peptide microarrays for studying antibody-antigen binding using surface plasmon resonance imagery.

    Directory of Open Access Journals (Sweden)

    Claude Nogues

    Full Text Available BACKGROUND: Non-specific binding to biosensor surfaces is a major obstacle to quantitative analysis of selective retention of analytes at immobilized target molecules. Although a range of chemical antifouling monolayers has been developed to address this problem, many macromolecular interactions still remain refractory to analysis due to the prevalent high degree of non-specific binding. We describe how we use the dynamic process of the formation of self assembling monolayers and optimise physical and chemical properties thus reducing considerably non-specific binding and allowing analysis of specific binding of analytes to immobilized target molecules. METHODOLOGY/PRINCIPAL FINDINGS: We illustrate this approach by the production of specific protein arrays for the analysis of interactions between the 65kDa isoform of human glutamate decarboxylase (GAD65 and a human monoclonal antibody. Our data illustrate that we have effectively eliminated non-specific interactions with the surface containing the immobilised GAD65 molecules. The findings have several implications. First, this approach obviates the dubious process of background subtraction and gives access to more accurate kinetic and equilibrium values that are no longer contaminated by multiphase non-specific binding. Second, an enhanced signal to noise ratio increases not only the sensitivity but also confidence in the use of SPR to generate kinetic constants that may then be inserted into van't Hoff type analyses to provide comparative DeltaG, DeltaS and DeltaH values, making this an efficient, rapid and competitive alternative to ITC measurements used in drug and macromolecular-interaction mechanistic studies. Third, the accuracy of the measurements allows the application of more intricate interaction models than simple Langmuir monophasic binding. CONCLUSIONS: The detection and measurement of antibody binding by the type 1 diabetes autoantigen GAD65 represents an example of an antibody-antigen

  5. Antibody-antigen-adjuvant conjugates enable co-delivery of antigen and adjuvant to dendritic cells in cis but only have partial targeting specificity

    NARCIS (Netherlands)

    Kreutz, M.; Giquel, B.; Hu, Q.; Abuknesha, R.; Uematsu, S.; Akira, S.; Nestle, F.O.; Diebold, S.S.

    2012-01-01

    Antibody-antigen conjugates, which promote antigen-presentation by dendritic cells (DC) by means of targeted delivery of antigen to particular DC subsets, represent a powerful vaccination approach. To ensure immunity rather than tolerance induction the co-administration of a suitable adjuvant is par

  6. Antibody-antigen-adjuvant conjugates enable co-delivery of antigen and adjuvant to dendritic cells in cis but only have partial targeting specificity.

    Directory of Open Access Journals (Sweden)

    Martin Kreutz

    Full Text Available Antibody-antigen conjugates, which promote antigen-presentation by dendritic cells (DC by means of targeted delivery of antigen to particular DC subsets, represent a powerful vaccination approach. To ensure immunity rather than tolerance induction the co-administration of a suitable adjuvant is paramount. However, co-administration of unlinked adjuvant cannot ensure that all cells targeted by the antibody conjugates are appropriately activated. Furthermore, antigen-presenting cells (APC that do not present the desired antigen are equally strongly activated and could prime undesired responses against self-antigens. We, therefore, were interested in exploring targeted co-delivery of antigen and adjuvant in cis in form of antibody-antigen-adjuvant conjugates for the induction of anti-tumour immunity. In this study, we report on the assembly and characterization of conjugates consisting of DEC205-specific antibody, the model antigen ovalbumin (OVA and CpG oligodeoxynucleotides (ODN. We show that such conjugates are more potent at inducing cytotoxic T lymphocyte (CTL responses than control conjugates mixed with soluble CpG. However, our study also reveals that the nucleic acid moiety of such antibody-antigen-adjuvant conjugates alters their binding and uptake and allows delivery of the antigen and the adjuvant to cells partially independently of DEC205. Nevertheless, antibody-antigen-adjuvant conjugates are superior to antibody-free antigen-adjuvant conjugates in priming CTL responses and efficiently induce anti-tumour immunity in the murine B16 pseudo-metastasis model. A better understanding of the role of the antibody moiety is required to inform future conjugate vaccination strategies for efficient induction of anti-tumour responses.

  7. Limitation of tuning the antibody-antigen reaction by changing the value of pH and its consequence for hyperthermia.

    Science.gov (United States)

    Mleczko, J; Defort, A; Kozioł, J J; Nguyen, T T; Mirończyk, A; Zapotoczny, B; Nowak-Jary, J; Gronczewska, E; Marć, M; Dudek, M R

    2016-04-01

    Distribution of the isoelectric point (pI) was calculated for the hypervariable regions of Fab fragments of the antibody molecules, which structure is annotated in the structural antibody database SabDab. The distribution is consistent with the universal for all organisms dividing the proteome into two sets of acidic and basic proteins. It shows the additional fine structure in a form of the narrow-sized peaks of pI values. This is an explanation why a small change of the environmental pH can have a strong effect on the antibody-antigen affinity. To show this, a typical enzyme-linked immunospecific assay experiment for testing the reaction of goat anti-human IgA antibodies with human IgA immunoglobulins of saliva as antigens was modified in such a way that Fe3O4magnetic nanoparticles were added to PBS buffer. The magnetic nanoparticles were remotely heated by the radio frequency magnetic field providing the local change of temperature and pH. It was observed that short times of the heating were significantly increasing the antibody-antigen binding strength while it was not the case for a longer time. The finding discussed in the study can be useful for biopharmaceuticals using antibodies, the immunoassay techniques as well as for control over the use of hyperthermia. PMID:26634446

  8. SpaceDock: A Performance Task Platform for Spaceflight Operations

    Science.gov (United States)

    Marshburn, Thomas H.; Strangman, Gary E.; Strauss, Monica S.; Sutton, Jeffrey P.

    2003-01-01

    Preliminary evidence during both short- and long-duration spaceflight indicates that perceptual-motor coordination changes occur and persist in-flight. However, there is presently no in-flight method for evaluating astronaut performance on mission-critical tasks such as docking. We present a portable platform we have developed for attempting and evaluating docking, and describe the results of a pilot study wherein flight novices learned the docking task. Methods: A dual-joystick, six degrees of freedom platform-called SpaceDock-was developed to enable portable, adaptable performance testing in a spaceflight operations setting. Upon this platform, a simplified docking task was created, involving a constant rate of approach towards a docking target and requiring the user to correct translation in two dimensions and attitude orientation along one dimension (either pitch or roll). Ten flight naive subjects performed the task over a 45 min period and all joystick inputs and timings were collected, from which we could successfully reconstruct travel paths, input profiles and relative target displacements. Results: Subjects exhibited significant improvements in docking over the course of the experiment. Learning to compensate for roll-alterations was robust, whereas compensation for pitch-alterations was not in evidence in this population and relatively short training period. Conclusion: The SpaceDock platform can provide a novel method for training and testing subjects, on a spaceflight-relevant task, and can be used to examine behavioral learning, strategy use, and has been adapted for use in brain imaging experiments.

  9. Highly flexible protein-peptide docking using CABS-dock

    OpenAIRE

    Ciemny, Maciej Pawel; Kurcinski, Mateusz; Kozak, Konrad Jakub; Kolinski, Andrzej; Kmiecik, Sebastian

    2016-01-01

    Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and significant flexibility of a protein receptor. During CABS-dock docking, the peptide folding and bi...

  10. Fabrication of fiber-optic localized surface plasmon resonance sensor and its application to detect antibody-antigen reaction of interferon-gamma

    Science.gov (United States)

    Jeong, Hyeon-Ho; Erdene, Norov; Lee, Seung-Ki; Jeong, Dae-Hong; Park, Jae-Hyoung

    2011-12-01

    A fiber-optic localized surface plasmon (FO LSPR) sensor was fabricated by gold nanoparticles (Au NPs) immobilized on the end-face of an optical fiber. When Au NPs were formed on the end-face of an optical fiber by chemical reaction, Au NPs aggregation occurred and the Au NPs were immobilized in various forms such as monomers, dimers, trimers, etc. The component ratio of the Au NPs on the end-face of the fabricated FO LSPR sensor was slightly changed whenever the sensors were fabricated in the same condition. Including this phenomenon, the FO LSPR sensor was fabricated with high sensitivity by controlling the density of Au NPs. Also, the fabricated sensors were measured for the resonance intensity for the different optical systems and analyzed for the effect on sensitivity. Finally, for application as a biosensor, the sensor was used for detecting the antibody-antigen reaction of interferon-gamma.

  11. 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.

  12. PK/PD analysis of a novel pH-dependent antigen-binding antibody using a dynamic antibody-antigen binding model.

    Science.gov (United States)

    Haraya, Kenta; Tachibana, Tatsuhiko; Iwayanagi, Yuki; Maeda, Atsuhiko; Ozeki, Kazuhisa; Nezu, Junichi; Ishigai, Masaki; Igawa, Tomoyuki

    2016-04-01

    Previously, we have reported novel engineered antibody with pH-dependent antigen-binding (recycling antibody), and with both pH-dependent antigen-binding and increased FcRn-binding at neutral pH (sweeping antibody). The purpose of this study is to perform PK/PD predictions to better understand the potential applications of the antibodies as therapeutics. To demonstrate the applicability of recycling and sweeping antibodies over conventional antibodies, PK/PD analyses were performed. PK/PD parameters for antibody and antigen dynamics were estimated from the results of a pharmacokinetic study in human FcRn transgenic mice. A simulation study was performed using the estimated PK/PD parameters with various target antigen profiles. In comparison to conventional antibody, recycling antibody enhanced antibody-antigen complex clearance by 3 folds, while sweeping antibody accelerated antigen clearance by 10 folds in a pharmacokinetic study. Simulation results showed that recycling and sweeping antibodies can improve dosage frequency and reduce the required dose for target antigens with various clearances, plasma concentrations or binding kinetics. Moreover, importance of the association rate constant to enhance the beneficial effect of antibodies was shown. These results support the conclusion that recycling and sweeping antibodies can be applied to various target antigens with different profiles, and expand the number of antigens that antibodies can target. PMID:26944099

  13. Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex.

    Directory of Open Access Journals (Sweden)

    Masato Kiyoshi

    Full Text Available The optimization of antibodies is a desirable goal towards the development of better therapeutic strategies. The antibody 11K2 was previously developed as a therapeutic tool for inflammatory diseases, and displays very high affinity (4.6 pM for its antigen the chemokine MCP-1 (monocyte chemo-attractant protein-1. We have employed a virtual library of mutations of 11K2 to identify antibody variants of potentially higher affinity, and to establish benchmarks in the engineering of a mature therapeutic antibody. The most promising candidates identified in the virtual screening were examined by surface plasmon resonance to validate the computational predictions, and to characterize their binding affinity and key thermodynamic properties in detail. Only mutations in the light-chain of the antibody are effective at enhancing its affinity for the antigen in vitro, suggesting that the interaction surface of the heavy-chain (dominated by the hot-spot residue Phe101 is not amenable to optimization. The single-mutation with the highest affinity is L-N31R (4.6-fold higher affinity than wild-type antibody. Importantly, all the single-mutations showing increase affinity incorporate a charged residue (Arg, Asp, or Glu. The characterization of the relevant thermodynamic parameters clarifies the energetic mechanism. Essentially, the formation of new electrostatic interactions early in the binding reaction coordinate (transition state or earlier benefits the durability of the antibody-antigen complex. The combination of in silico calculations and thermodynamic analysis is an effective strategy to improve the affinity of a matured therapeutic antibody.

  14. AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

    OpenAIRE

    Morris, Garrett M.; Huey, Ruth; Lindstrom, William; Sanner, Michel F.; Belew, Richard K.; Goodsell, David S.; Olson, Arthur J.

    2009-01-01

    We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently-bound ligands, using both a grid-based docking method and a modification of the...

  15. Spacecraft rendezvous and docking

    DEFF Research Database (Denmark)

    Jørgensen, John Leif

    1999-01-01

    been based entirely on direct human supervision and control. This paper describes a vision-based system and methodology, that autonomously generates accurate guidance information that may assist a human operator in performing the tasks associated with both the rendezvous and docking navigation...... procedures. The method described generates, based on a single camera and a priory information about the target vehicle and orbit data, all necessary guidance information for closed-loop autonomous navigation, from first detection at far distance, to a close up a hold point. Furthermore, the system provide......The phenomenons and problems encountered when a rendezvous manoeuvre, and possible docking, of two spacecrafts has to be performed, have been the topic for numerous studies, and, details of a variety of scenarios has been analysed. So far, all solutions that has been brought into realization has...

  16. DockingShop: A Tool for Interactive Molecular Docking

    OpenAIRE

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-01-01

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. DockingShop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. O...

  17. AN OVERVIEW ON MOLECULAR DOCKING

    Directory of Open Access Journals (Sweden)

    Gaba Monika

    2010-06-01

    Full Text Available Molecular Docking is the computational modeling of the structure of complexes formed by two or more interacting molecules. The goal of molecular docking is the prediction of the three dimensional structures of interest. Docking itself only produces plausible candidate structures. These candidates are ranked using methods such as scoring functions to identify structures that are most likely to occur in nature. The state of the art of various computational aspects of molecular docking based virtual screening of database of small molecules is presented. This review encompasses molecular docking approaches, different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid drug targets. Limitations of current technologies as well as future prospects are also presented

  18. Spacecraft rendezvous and docking

    DEFF Research Database (Denmark)

    Jørgensen, John Leif

    1999-01-01

    procedures. The method described generates, based on a single camera and a priory information about the target vehicle and orbit data, all necessary guidance information for closed-loop autonomous navigation, from first detection at far distance, to a close up a hold point. Furthermore, the system provide...... been based entirely on direct human supervision and control. This paper describes a vision-based system and methodology, that autonomously generates accurate guidance information that may assist a human operator in performing the tasks associated with both the rendezvous and docking navigation...

  19. DockingShop: A Tool for Interactive Molecular Docking

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-04-24

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

  20. Surflex-Dock: Docking benchmarks and real-world application

    OpenAIRE

    Spitzer, R.; Jain, AN

    2012-01-01

    Benchmarks for molecular docking have historically focused on re-docking the cognate ligand of a well-determined protein-ligand complex to measure geometric pose prediction accuracy, and measurement of virtual screening performance has been focused on increasingly large and diverse sets of target protein structures, cognate ligands, and various types of decoy sets. Here, pose prediction is reported on the Astex Diverse set of 85 protein ligand complexes, and virtual screening performance is r...

  1. Customizing Scoring Functions for Docking

    OpenAIRE

    Pham, Tuan A.; Jain, Ajay N.

    2008-01-01

    Empirical scoring functions used in protein-ligand docking calculations are typically trained on a dataset of complexes with known affinities with the aim of generalizing across different docking applications. We report a novel method of scoring-function optimization that supports the use of additional information to constrain scoring function parameters, which can be used to focus a scoring function’s training towards a particular application, such as screening enrichment. The approach combi...

  2. Optical Docking Aid Containing Fresnel Lenses

    Science.gov (United States)

    Pierce, Cole J.

    1995-01-01

    Proposed device provides self-contained visual cues to aid in docking. Similar to devices used to guide pilots in landing on aircraft carriers. Positions and directions of beams of light give observer visual cues of position relative to docking target point. Optical assemblies generate directed, diverging beams of light that, together, mark approach path to docking point. Conceived for use in docking spacecraft at Space Station Freedom, device adapted to numerous industrial docking and alignment applications.

  3. Losses compensation; Compensation des pertes

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-07-01

    One mission of RTE (Electric Power Transportation), is to watch over the losses compensation resulting from the power transport on the electric power network. Since january 2001, RTE makes good the electric losses by the purchase of energy. To choose the marketers, a consultation has been realized by RTE. This document presents the rules concerning these losses compensation. (A.L.B.)

  4. Enabling Exploration Through Docking Standards

    Science.gov (United States)

    Hatfield, Caris A.

    2012-01-01

    Human exploration missions beyond low earth orbit will likely require international cooperation in order to leverage limited resources. International standards can help enable cooperative missions by providing well understood, predefined interfaces allowing compatibility between unique spacecraft and systems. The International Space Station (ISS) partnership has developed a publicly available International Docking System Standard (IDSS) that provides a solution to one of these key interfaces by defining a common docking interface. The docking interface provides a way for even dissimilar spacecraft to dock for exchange of crew and cargo, as well as enabling the assembly of large space systems. This paper provides an overview of the key attributes of the IDSS, an overview of the NASA Docking System (NDS), and the plans for updating the ISS with IDSS compatible interfaces. The NDS provides a state of the art, low impact docking system that will initially be made available to commercial crew and cargo providers. The ISS will be used to demonstrate the operational utility of the IDSS interface as a foundational technology for cooperative exploration.

  5. Flexible Ligand Docking Using Differential Evolution

    DEFF Research Database (Denmark)

    Thomsen, René

    2003-01-01

    Molecular docking of biomolecules is becoming an increasingly important part in the process of developing new drugs, as well as searching compound databases for promising drug candidates. The docking of ligands to proteins can be formulated as an optimization problem where the task is to find the...... most favorable energetic conformation among the large space of possible protein-ligand complexes. Stochastic search methods, such as evolutionary algorithms (EAs), can be used to sample large search spaces effectively and is one of the preferred methods for flexible ligand docking. The differential...... evolution algorithm (DE) is applied to the docking problem using the AutoDock program. The introduced DockDE algorithm is compared with the Lamarckian GA (LGA) provided with AutoDock, and the DockEA previously found to outperform the LGA. The comparison is performed on a suite of six commonly used docking...

  6. Elmo1 inhibits ubiquitylation of Dock180.

    Science.gov (United States)

    Makino, Yoshinori; Tsuda, Masumi; Ichihara, Shin; Watanabe, Takuya; Sakai, Mieko; Sawa, Hirofumi; Nagashima, Kazuo; Hatakeyama, Shigetsugu; Tanaka, Shinya

    2006-03-01

    Dock180, a member of the CDM family of proteins, plays roles in biological processes such as phagocytosis and motility through its association with the signalling adaptor protein Crk. Recently, the complex formation between Dock180 and Elmo1 was reported to function as a bipartite guanine nucleotide exchange factor for Rac. In this study, we demonstrated that the amount of Dock180 increased when Elmo1 was co-expressed. Dock180 was found to be ubiquitylated and Dock180 protein levels could be augmented by treatment with proteasome inhibitor. The ubiquitylation of Dock180 was enhanced by epidermal growth factor (EGF), Crk and adhesion-dependent signals. Furthermore, Elmo1 inhibited ubiquitylation of Dock180, resulting in the increase in Dock180 levels. The Elmo1 mutant Delta531, which encompasses amino acids required for Dock180 binding, preserved the inhibitory effects on ubiquitylation of Dock180. Upon EGF stimulation, both Dock180 and ubiquitin were demonstrated to translocate to the cell periphery by immunofluorescence, and we found ubiquitylation of Dock180 and its inhibition by Elmo1 to occur in cellular membrane fractions by in vivo ubiquitylation assay. These data suggest that Dock180 is ubiquitylated on the plasma membrane, and also that Elmo1 functions as an inhibitor of ubiquitylation of Dock180. Therefore, an ubiquitin-proteasome-dependent protein degradation mechanism might contribute to the local activation of Rac on the plasma membrane. PMID:16495483

  7. Experimental validation of docking and capture using space robotics testbeds

    Science.gov (United States)

    Spofford, John; Schmitz, Eric; Hoff, William

    1991-01-01

    This presentation describes the application of robotic and computer vision systems to validate docking and capture operations for space cargo transfer vehicles. Three applications are discussed: (1) air bearing systems in two dimensions that yield high quality free-flying, flexible, and contact dynamics; (2) validation of docking mechanisms with misalignment and target dynamics; and (3) computer vision technology for target location and real-time tracking. All the testbeds are supported by a network of engineering workstations for dynamic and controls analyses. Dynamic simulation of multibody rigid and elastic systems are performed with the TREETOPS code. MATRIXx/System-Build and PRO-MATLAB/Simulab are the tools for control design and analysis using classical and modern techniques such as H-infinity and LQG/LTR. SANDY is a general design tool to optimize numerically a multivariable robust compensator with a user-defined structure. Mathematica and Macsyma are used to derive symbolically dynamic and kinematic equations.

  8. CT-docking patient stretcher

    International Nuclear Information System (INIS)

    This paper assesses the use of a patient stretcher that directly docks to a CT scanner for acutely injured and/or critically ill patients. The stretcher permits performance of radiography and acts as a platform for critical care monitoring and patient support devices. During a 1-year period, the prototype CT-docking stretcher was used for 35 patients sustaining acute trauma and 25 patients from critical care units. Observations were elicited from physicians, nurses and technologists concerning the advantages or disadvantages of the docking stretcher. Advantages of the CT-docking stretcher included time saved in moving patients to the CT table from the admitting/emergency ward, transfer of critically ill patients onto the stretcher in the controlled environment of the intensive care unit rather than the CT suite, increasing CT throughput by direct docking of the patient stretcher to the CT scanner rather than manual transfer of complex support and monitoring devices with the patient, decreased risk associated with physical movement of patients with potentially unstable spinal injuries or unstable physiologic status, and decrease in potential for injury to medical personnel performing patient transfer

  9. Text Mining for Protein Docking.

    Directory of Open Access Journals (Sweden)

    Varsha D Badal

    2015-12-01

    Full Text Available The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking. Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu. The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound

  10. Docking of secretory vesicles is syntaxin dependent.

    Directory of Open Access Journals (Sweden)

    Heidi de Wit

    Full Text Available Secretory vesicles dock at the plasma membrane before they undergo fusion. Molecular docking mechanisms are poorly defined but believed to be independent of SNARE proteins. Here, we challenged this hypothesis by acute deletion of the target SNARE, syntaxin, in vertebrate neurons and neuroendocrine cells. Deletion resulted in fusion arrest in both systems. No docking defects were observed in synapses, in line with previous observations. However, a drastic reduction in morphologically docked secretory vesicles was observed in chromaffin cells. Syntaxin-deficient chromaffin cells showed a small reduction in total and plasma membrane staining for the docking factor Munc18-1, which appears insufficient to explain the drastic reduction in docking. The sub-membrane cortical actin network was unaffected by syntaxin deletion. These observations expose a docking role for syntaxin in the neuroendocrine system. Additional layers of regulation may have evolved to make syntaxin redundant for docking in highly specialized systems like synaptic active zones.

  11. Docking Design of Self-Reconfigurable Robot

    OpenAIRE

    Fei, Yanqiong

    2011-01-01

    Docking design of self‐reconfigurable robots is studied. Firstly, the self‐reconfigurable robot is presented. Its basic module is designed, which is composed of a central cube and six rotary arms. Then, the novel docking mechanism of each module is designed. It is critical for the self‐reconfigurable robot to discard any faulty modules for the self‐repairing actions. The docking process is analyzed with the geometric method. The docking forces between two modules are d...

  12. Cross-docking: State of the art

    OpenAIRE

    Van Belle, Jan; Valckenaers, Paul; Cattrysse, Dirk

    2012-01-01

    Cross-docking is a logistics strategy in which freight is unloaded from inbound vehicles and (almost) directly loaded into outbound vehicles, with little or no storage in between. This article presents an overview of the cross-docking concept. Guidelines for the successful use and implementation of cross-docking are discussed and several characteristics are described that can be used to distinguish between different cross-dock types. In addition, this article presents an extensive review of t...

  13. Questioning Compensation

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Transparent management and open information needed for the fund set up to compensate victims of the 2008 Sanlu milk scandal Almost three years after the Sanlu milk scandal that caused thousands of infants in China to develop urinary disease after drinking melamine

  14. Hydra Rendezvous and Docking Sensor

    Science.gov (United States)

    Roe, Fred; Carrington, Connie

    2007-01-01

    The U.S. technology to support a CEV AR&D activity is mature and was developed by NASA and supporting industry during an extensive research and development program conducted during the 1990's and early 2000 time frame at the Marshall Space Flight Center. Development and demonstration of a rendezvous/docking sensor was identified early in the AR&D Program as the critical enabling technology that allows automated proxinity operations and docking. A first generation rendezvous/docking sensor, the Video Guidance Sensor (VGS) was developed and successfully flown on STS 87 and again on STS 95, proving the concept of a video-based sensor. Advances in both video and signal processing technologies and the lessons learned from the two successful flight experiments provided a baseline for the development of a new generation of video based rendezvous/docking sensor. The Advanced Video Guidance Sensor (AVGS) has greatly increased performance and additional capability for longer-range operation. A Demonstration Automatic Rendezvous Technology (DART) flight experiment was flown in April 2005 using AVGS as the primary proximity operations sensor. Because of the absence of a docking mechanism on the target satellite, this mission did not demonstrate the ability of the sensor to coltrold ocking. Mission results indicate that the rendezvous sensor operated successfully in "spot mode" (2 km acquisition of the target, bearing data only) but was never commanded to "acquire and track" the docking target. Parts obsolescence issues prevent the construction of current design AVGS units to support the NASA Exploration initiative. This flight proven AR&D technology is being modularized and upgraded with additional capabilities through the Hydra project at the Marshall Space Flight Center. Hydra brings a unique engineering approach and sensor architecture to the table, to solve the continuing issues of parts obsolescence and multiple sensor integration. This paper presents an approach to

  15. Vehicle routing with cross-docking

    DEFF Research Database (Denmark)

    Wen, Min; Larsen, Jesper; Clausen, Jens; Cordeau, Jean-Francois; Laporte, Gilbert

    2009-01-01

    Over the past decade, cross-docking has emerged as an important material handling technology in transportation. A variation of the well-known Vehicle Routing Problem (VRP), the VRP with Cross-Docking (VRPCD) arises in a number of logistics planning contexts. This paper addresses the VRPCD, where a...... set of homogeneous vehicles are used to transport orders from the suppliers to the corresponding customers via a cross-dock. The orders can be consolidated at the cross-dock but cannot be stored for very long because the cross-dock does not have long-term inventory-holding capabilities. The objective...

  16. DIRECT SHIPMENT VS. CROSS DOCKING

    OpenAIRE

    TAMÁS BÁNYAI

    2012-01-01

    The globalization of production and service enterprises increased the complexity of supply chain systems and processes. The complexity of supply problems leaded to the development of new shipment strategies. The optimal design of supply chain is an important success factor of the economical operation of enterprises. Within the frame of this paper the author compare the costs of the direct shipment and the cross docking supply from the point of view of all members of supply chain. Cross dockin...

  17. Benchmarking Sets for Molecular Docking

    OpenAIRE

    Huang, Niu; Shoichet, Brian K.; Irwin, John J.

    2006-01-01

    Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 9...

  18. Open Syntaxin Docks Synaptic Vesicles

    OpenAIRE

    Marc Hammarlund; Mark T Palfreyman; Shigeki Watanabe; Shawn Olsen; Erik M. Jorgensen

    2007-01-01

    Author Summary Like Olympic swimmers crouched on their starting blocks, synaptic vesicles prepare for fusion with the neuronal plasma membrane long before the starting gun fires. This preparation enables vesicles to fuse rapidly, synchronously, and in the correct place when the signal finally arrives. A well-known but poorly understood part of vesicle preparation is docking, in which vesicles prepare for release by attaching to the plasma membrane at the eventual site of release. Here, we out...

  19. European rendezvous and docking system

    Science.gov (United States)

    Pairot, J. M.; Frezet, M.; Tailhades, J.; Fehse, W.; Tobias, A.; Getzschmann, A.

    This paper first describes the major design drivers and the key features of the European RendezVous and Docking System Concept. Stemming from technology activities led by the European Space Agency (ESA) with European Industry and National Space Agencies since the beginning of the eighties, the concept has been developed and integrated in the frame of an ESA RVD System Pre-Development Programme initiated at ESTEC in 1989, with MATRA as main contractor. The objective is to verify the overall concept and the main elements within a RVD Proof of Concept Programme in order to provide an early proof of validity to the user projects, the first of which will be the Hermes manned space shuttle. The selected mission scenarii, the RVD functions addressed and the overall system architecture are described. The results of supporting safety, performance and operations analyses are presented. The paper further presents the verification objectives and the major results obtained in the RVD System Pre-Development Programme. This verification approach involves hardware breadboards, software prototypes, development of test facilities in four main development areas: test of RV sensors on a 6 d.o.f. kinematic test facility, test of a docking mechanism front-end mock-up on the docking dynamics test facility, closed-loop test of a prototype RV control software, test of man-in-the-loop concept involving both supervisory control and manual control modes.

  20. Molecular Docking of Aromatase Inhibitors

    Directory of Open Access Journals (Sweden)

    Virapong Prachayasittikul

    2011-04-01

    Full Text Available Aromatase is an enzyme that plays a critical role in the development of estrogen receptor positive breast cancer. As aromatase catalyzes the aromatization of androstenedione to estrone, a naturally occurring estrogen, it is a promising drug target for therapeutic management. The undesirable effects found in aromatase inhibitors (AIs that are in clinical use necessitate the discovery of novel AIs with higher selectivity, less toxicity and improving potency. In this study, we elucidate the binding mode of all three generations of AI drugs to the crystal structure of aromatase by means of molecular docking. It was demonstrated that the docking protocol could reliably reproduce the interaction of aromatase with its substrate with an RMSD of 1.350 Å. The docking study revealed that polar (D309, T310, S478 and M374, aromatic (F134, F221 and W224 and non-polar (A306, A307, V370, L372 and L477 residues were important for interacting with the AIs. The insights gained from the study herein have great potential for the design of novel AIs.

  1. Why are most EU pigs tail docked?

    DEFF Research Database (Denmark)

    D'eath, R.B.; Niemi, J.K.; Vosough Ahmadi, B.;

    2016-01-01

    To limit tail biting incidence, most pig producers in Europe tail dock their piglets. This is despite EU Council Directive 2008/120/EC banning routine tail docking and allowing it only as a last resort. The paper aims to understand what it takes to fulfil the intentions of the Directive by...... pig per day) and no tail docking. A decision tree model based on data from Danish and Finnish pig production suggests that Standard Docked provides the highest economic gross margin with the least tail biting. Given our assumptions, Enhanced Undocked is the least economic, although Efficient Undocked...... is better economically and both result in a lower incidence of tail biting than Standard Undocked but higher than Standard Docked. For a pig, being bitten is worse for welfare (repeated pain, risk of infections) than being docked, but to compare welfare consequences at a farm level means considering...

  2. Scheduling Trucks in a Cross-Dock with Mixed Service Mode Dock Doors

    DEFF Research Database (Denmark)

    Bodnar, Peter; Azadeh, Kaveh; Koster, René de

    2015-01-01

    The problem considered in this paper is how to schedule inbound and outbound trucks subject to time windows at a multidoor cross-dock. Dock doors can either be dedicated to inbound or outbound trucks or be capable of handling both truck types. In addition, loads are allowed to be temporarily buff...... problems of four warehouses of a large retailer and show that substantially smaller cross-docks can be used by using dock-doors flexibly and properly scheduling the trucks....

  3. Machine learning optimization of cross docking accuracy.

    Science.gov (United States)

    Bjerrum, Esben J

    2016-06-01

    Performance of small molecule automated docking programs has conceptually been divided into docking -, scoring -, ranking - and screening power, which focuses on the crystal pose prediction, affinity prediction, ligand ranking and database screening capabilities of the docking program, respectively. Benchmarks show that different docking programs can excel in individual benchmarks which suggests that the scoring function employed by the programs can be optimized for a particular task. Here the scoring function of Smina is re-optimized towards enhancing the docking power using a supervised machine learning approach and a manually curated database of ligands and cross docking receptor pairs. The optimization method does not need associated binding data for the receptor-ligand examples used in the data set and works with small train sets. The re-optimization of the weights for the scoring function results in a similar docking performance with regard to docking power towards a cross docking test set. A ligand decoy based benchmark indicates a better discrimination between poses with high and low RMSD. The reported parameters for Smina are compatible with Autodock Vina and represent ready-to-use alternative parameters for researchers who aim at pose prediction rather than affinity prediction. PMID:27179709

  4. A Review on Quantitative Approaches for Dock Door Assignment in Cross-Docking

    Directory of Open Access Journals (Sweden)

    Adibah Shuib

    2012-01-01

    Full Text Available Cross docking is a relatively new technique in supply chain operations. It offers limited storage time to maximize the efficiency of goods transshipment. Efficient operation of a cross docking system requires an appropriate coordination of inbound and outbound flows, accurate planning and dynamic scheduling.  The planning strategies at cross docking terminals, which are receiving growing attention today, are the truck-to-door assignment and destination to door assignment problems. This paper provides a comprehensive literature review of quantitative approaches in dock door assignment problems of cross docking planning. The contributions of this paper are to identify the gap of knowledge in operational levels mainly in dock door assignment and to point out the future research direction in cross docking.

  5. Flexible Ligand Docking Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene

    2003-01-01

    search spaces effectively and is one of the commonly used methods for flexible ligand docking. During the last decade, several EAs using different variation operators have been introduced, such as the ones provided with the AutoDock program. In this paper we evaluate the performance of different EA......The docking of ligands to proteins can be formulated as a computational problem where the task is to find the most favorable energetic conformation among the large space of possible protein–ligand complexes. Stochastic search methods such as evolutionary algorithms (EAs) can be used to sample large...... settings such as choice of variation operators, population size, and usage of local search. The comparison is performed on a suite of six docking problems previously used to evaluate the performance of search algorithms provided with the AutoDock program package. The results from our investigation confirm...

  6. Computational methods for molecular docking

    Energy Technology Data Exchange (ETDEWEB)

    Klebe, G. [BASF AG, Ludwigshafen (Germany); Lengauer, T.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Recently, it has been demonstrated that the knowledge of the three-dimensional structure of the protein can be used to derive new protein ligands with improved binding properties. This tutorial focuses on the following questions: What is its binding affinity toward a particular receptor? What are putative conformations of a ligand at the binding site? What are the similarities of different ligands in terms of their recognition capabilities? Where and in which orientation will a ligand bind to the active site? How is a new putative protein ligand selected? An overview is presented of the algorithms which are presently used to handle and predict protein-ligand interactions and to dock small molecule ligands into proteins.

  7. Laser docking sensor engineering model

    Science.gov (United States)

    Dekome, Kent; Barr, Joseph M.

    1991-01-01

    NASA JSC has been involved in the development of Laser sensors for the past ten years in order to support future rendezvous and docking missions, both manned and unmanned. Although many candidate technologies have been breadboarded and evaluated, no sensor hardware designed specifically for rendezvous and docking applications has been demonstrated on-orbit. It has become apparent that representative sensors need to be flown and demonstrated as soon as possible, with minimal cost, to provide the capability of the technology in meeting NASA's future AR&C applications. Technology and commercial component reliability have progressed to where it is now feasible to fly hardware as a detailed test objective minimizing the overall cost and development time. This presentation will discuss the ongoing effort to convert an existing in-house developed breadboard to an engineering model configuration suitable for flight. The modifications include improving the ranger resolution and stability with an in-house design, replacing the rack mounted galvanometric scanner drivers with STD-bus cards, replacing the system controlling personal computer with a microcontroller, and repackaging the subsystems as appropriate. The sensor will use the performance parameters defined in previous JSC requirements working groups as design goals and be built to withstand the space environment where fiscally feasible. Testing of the in-house ranger design is expected to be completed in October. The results will be included in the presentation. Preliminary testing of the ranging circuitry indicates a range resolution of 4mm is possible. The sensor will be mounted in the payload bay on a shelf bracket and have command, control, and display capabilities using the payload general support computer via an RS422 data line.

  8. Development of a Robotics-based Satellites Docking Simulator

    NARCIS (Netherlands)

    Zebenay, M.

    2014-01-01

    The European Proximity Operation Simulator (EPOS) is a hardware-in-the-loop (HIL) system aiming, among other objectives, at emulating on-orbit docking of spacecraft for verification and validation of the docking phase. This HIL docking simulator set-up essentially consists of docking interfaces, sim

  9. Docking and scoring of metallo-beta-lactamases inhibitors

    DEFF Research Database (Denmark)

    Olsen, Lars; Pettersson, Ingrid; Hemmingsen, Lars; Adolph, Hans-Werner; Jørgensen, Flemming Steen

    2004-01-01

    The performance of the AutoDock, GOLD and FlexX docking programs was evaluated for docking of dicarboxylic acid inhibitors into metallo-beta-lactamases (MBLs). GOLD provided the best overall performance, with RMSDs between experimental and docked structures of 1.8-2.6 A and a good correlation bet...

  10. A Review on Quantitative Approaches for Dock Door Assignment in Cross-Docking

    OpenAIRE

    Adibah Shuib; Wan Nor Ashikin Wan Ahmad Fatthi

    2012-01-01

    Cross docking is a relatively new technique in supply chain operations. It offers limited storage time to maximize the efficiency of goods transshipment. Efficient operation of a cross docking system requires an appropriate coordination of inbound and outbound flows, accurate planning and dynamic scheduling.  The planning strategies at cross docking terminals, which are receiving growing attention today, are the truck-to-door assignment and destination to door assignment problems. This paper ...

  11. Which compensation for whom ?

    OpenAIRE

    Pascal Gastineau; Emmanuelle Taugourdeau

    2012-01-01

    This paper examines a situation where a decision-maker determines the appropriate compensation that should be implemented for a given ecological damage. The compensation can be either or both in monetary and environmental units to meet three goals : i) no aggregate welfare loss, ii) minimization of the cost associated with the compensation, iii) minimal environmental compensation requirement. The findings suggest that - in some cases - providing both monetary and environmental compensation ca...

  12. Use of the docking dynamics test facility for rendezvous and docking final approach verification

    Science.gov (United States)

    Noirault, P.; Pairot, J. M.

    1991-12-01

    The Docking and Dynamics Test Facility (DDTF) and its current areas of investigation are reviewed. The following topics are described: tests of an automatic scenario with a closed loop control of the approach to docking using a RV (Rendezvous) sensor breadboard; tests with a representative mockup of the future Docking/Berthing System (DBS), to derive relevant allocation between the GNC (Guidance, Navigation, and Control) system performances and the DBS capabilities; and tests on the last 5 m translation with full human control of the chaser for the Hermes/Columbus mission, where astronauts performed the docking mission. Some recommendations for a future dynamical test bench are given in conclusion.

  13. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.

    Science.gov (United States)

    Ravindranath, Pradeep Anand; Forli, Stefano; Goodsell, David S; Olson, Arthur J; Sanner, Michel F

    2015-12-01

    Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approach include the: 1) exponential growth of the search space, demanding more efficient search methods; and 2) increased number of false positives, calling for scoring functions tailored for flexible receptor docking. We present AutoDockFR-AutoDock for Flexible Receptors (ADFR), a new docking engine based on the AutoDock4 scoring function, which addresses the aforementioned challenges with a new Genetic Algorithm (GA) and customized scoring function. We validate ADFR using the Astex Diverse Set, demonstrating an increase in efficiency and reliability of its GA over the one implemented in AutoDock4. We demonstrate greatly increased success rates when cross-docking ligands into apo receptors that require side-chain conformational changes for ligand binding. These cross-docking experiments are based on two datasets: 1) SEQ17 -a receptor diversity set containing 17 pairs of apo-holo structures; and 2) CDK2 -a ligand diversity set composed of one CDK2 apo structure and 52 known bound inhibitors. We show that, when cross-docking ligands into the apo conformation of the receptors with up to 14 flexible side-chains, ADFR reports more correctly cross-docked ligands than AutoDock Vina on both datasets with solutions found for 70.6% vs. 35.3% systems on SEQ17, and 76.9% vs. 61.5% on CDK2. ADFR also outperforms AutoDock Vina in number of top ranking solutions on both datasets. Furthermore, we show that correctly docked CDK2 complexes re-create on average 79.8% of all pairwise atomic interactions between the ligand and moving receptor atoms in the holo complexes. Finally, we show that down

  14. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.

    Directory of Open Access Journals (Sweden)

    Pradeep Anand Ravindranath

    2015-12-01

    Full Text Available Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approach include the: 1 exponential growth of the search space, demanding more efficient search methods; and 2 increased number of false positives, calling for scoring functions tailored for flexible receptor docking. We present AutoDockFR-AutoDock for Flexible Receptors (ADFR, a new docking engine based on the AutoDock4 scoring function, which addresses the aforementioned challenges with a new Genetic Algorithm (GA and customized scoring function. We validate ADFR using the Astex Diverse Set, demonstrating an increase in efficiency and reliability of its GA over the one implemented in AutoDock4. We demonstrate greatly increased success rates when cross-docking ligands into apo receptors that require side-chain conformational changes for ligand binding. These cross-docking experiments are based on two datasets: 1 SEQ17 -a receptor diversity set containing 17 pairs of apo-holo structures; and 2 CDK2 -a ligand diversity set composed of one CDK2 apo structure and 52 known bound inhibitors. We show that, when cross-docking ligands into the apo conformation of the receptors with up to 14 flexible side-chains, ADFR reports more correctly cross-docked ligands than AutoDock Vina on both datasets with solutions found for 70.6% vs. 35.3% systems on SEQ17, and 76.9% vs. 61.5% on CDK2. ADFR also outperforms AutoDock Vina in number of top ranking solutions on both datasets. Furthermore, we show that correctly docked CDK2 complexes re-create on average 79.8% of all pairwise atomic interactions between the ligand and moving receptor atoms in the holo complexes. Finally, we

  15. Electrostatics in protein–protein docking

    OpenAIRE

    Heifetz, Alexander; Katchalski-Katzir, Ephraim; Eisenstein, Miriam

    2002-01-01

    A novel geometric-electrostatic docking algorithm is presented, which tests and quantifies the electrostatic complementarity of the molecular surfaces together with the shape complementarity. We represent each molecule to be docked as a grid of complex numbers, storing information regarding the shape of the molecule in the real part and information regarding the electrostatic character of the molecule in the imaginary part. The electrostatic descriptors are derived from the electrostatic pote...

  16. Rapid flexible docking using a stochastic rotamer library of ligands

    OpenAIRE

    Ding, Feng; Yin, Shuangye; Dokholyan, Nikolay V.

    2010-01-01

    Existing flexible docking approaches model the ligand and receptor flexibility either separately or in a loosely-coupled manner, which captures the conformational changes inefficiently. Here, we propose a flexible docking approach, MedusaDock, which models both ligand and receptor flexibility simultaneously with sets of discrete rotamers. We develop an algorithm to build the ligand rotamer library “on-the-fly” during docking simulations. MedusaDock benchmarks demonstrate a rapid sampling effi...

  17. Tail docking in pigs: acute physiological and behavioural responses.

    Science.gov (United States)

    Sutherland, M A; Bryer, P J; Krebs, N; McGlone, J J

    2008-02-01

    Tail docking of piglets is a routine procedure on farms to control tail-biting behaviour; however, docking can cause an acute stress response. The objectives of this research were to determine the stress responses to tail docking in piglets and to compare two methods of tail docking; cautery iron (CAUT) and the more commonly used blunt trauma cutters (BT). At approximately 6 days of age, piglets were tail docked using CAUT (n = 20), BT (n = 20) or sham tail docked with their tails remaining intact (CON; n = 40). Blood samples were taken prior to tail docking and at 30, 60 and 90 min after tail docking to evaluate the effect of tail docking on white blood cell (WBC) measures and cortisol concentrations. The above experiment was repeated to observe behaviour without the periodic blood sampling, so as not to confound the effects of blood sampling on piglet behaviour. Piglet behaviour was recorded in the farrowing crate using 1 min scan-samples via live observations for 60 min prior to and 90 min after tail docking. Total WBC counts were reduced (P > 0.05) among BT and CAUT compared with CON piglets 30 min after tail docking. Cortisol concentrations were higher (P tail docking. Cautery and BT-docked piglets spent more (P tail docking. Piglets tail docked using CAUT and BT tended to spend more (P tail docking. Elevated blood cortisol can be reduced by the use of the CAUT rather than the BT method of tail docking. Although the tail docking-induced rise in cortisol was prevented by using CAUT, the behavioural response to BT and CAUT docking methods was similar. PMID:22445023

  18. Protein-protein docking with F(2Dock 2.0 and GB-rerank.

    Directory of Open Access Journals (Sweden)

    Rezaul Chowdhury

    Full Text Available MOTIVATION: Computational simulation of protein-protein docking can expedite the process of molecular modeling and drug discovery. This paper reports on our new F(2 Dock protocol which improves the state of the art in initial stage rigid body exhaustive docking search, scoring and ranking by introducing improvements in the shape-complementarity and electrostatics affinity functions, a new knowledge-based interface propensity term with FFT formulation, a set of novel knowledge-based filters and finally a solvation energy (GBSA based reranking technique. Our algorithms are based on highly efficient data structures including the dynamic packing grids and octrees which significantly speed up the computations and also provide guaranteed bounds on approximation error. RESULTS: The improved affinity functions show superior performance compared to their traditional counterparts in finding correct docking poses at higher ranks. We found that the new filters and the GBSA based reranking individually and in combination significantly improve the accuracy of docking predictions with only minor increase in computation time. We compared F(2 Dock 2.0 with ZDock 3.0.2 and found improvements over it, specifically among 176 complexes in ZLab Benchmark 4.0, F(2 Dock 2.0 finds a near-native solution as the top prediction for 22 complexes; where ZDock 3.0.2 does so for 13 complexes. F(2 Dock 2.0 finds a near-native solution within the top 1000 predictions for 106 complexes as opposed to 104 complexes for ZDock 3.0.2. However, there are 17 and 15 complexes where F(2 Dock 2.0 finds a solution but ZDock 3.0.2 does not and vice versa; which indicates that the two docking protocols can also complement each other. AVAILABILITY: The docking protocol has been implemented as a server with a graphical client (TexMol which allows the user to manage multiple docking jobs, and visualize the docked poses and interfaces. Both the server and client are available for download. Server

  19. Compensating for environmental damages

    OpenAIRE

    GASTINEAU, Pascal; TAUGOURDEAU, Emmanuelle

    2014-01-01

    This paper examines a situation in which a decision-maker determines the appropriate compensation that should be awarded for a given amount of ecological damage. The compensation can take the form of either or both monetary and environmental units to meet three goals: i) minimisation of the cost associated with the compensation, ii) no aggregate welfare loss, and iii) minimal environmental compensation requirement. The findings suggest that – in some cases – providing both monetar...

  20. Essays in Executive Compensation

    NARCIS (Netherlands)

    D. Zhang (Dan)

    2012-01-01

    textabstractThis dissertation focuses on how executive compensation is designed and its implications for corporate finance and government regulations. Chapter 2 analyzes several proposals to restrict CEO compensation and calibrates two models of executive compensation that describe how firms would r

  1. DockQ: A Quality Measure for Protein-Protein Docking Models.

    Science.gov (United States)

    Basu, Sankar; Wallner, Björn

    2016-01-01

    The state-of-the-art to assess the structural quality of docking models is currently based on three related yet independent quality measures: Fnat, LRMS, and iRMS as proposed and standardized by CAPRI. These quality measures quantify different aspects of the quality of a particular docking model and need to be viewed together to reveal the true quality, e.g. a model with relatively poor LRMS (>10Å) might still qualify as 'acceptable' with a descent Fnat (>0.50) and iRMS (github.com/bjornwallner/DockQ/. PMID:27560519

  2. SwarmDock and the Use of Normal Modes in Protein-Protein Docking

    Directory of Open Access Journals (Sweden)

    Paul A. Bates

    2010-09-01

    Full Text Available Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.

  3. Dynamic/control interactions between flexible orbiting space-robot during grasping, docking and post-docking manoeuvres

    Science.gov (United States)

    Gasbarri, Paolo; Pisculli, Andrea

    2015-05-01

    Robotic systems are expected to play an increasingly important role in future space activities, such as repairing, upgrading, refuelling, and re-orbiting spacecraft. These technologies could potentially extend the life of satellites, enhance the capability of space systems, reduce the operation costs, and clean up the increasing space debris. Recent proposals for missions involving the use of space manipulators and/or automated transfer vehicles are presented as a solution for a lot of problems, which now affect the procedures and the performance of the in-orbit space systems. Other projects involving space manipulators have been developed by DARPA aiming to demonstrate several satellite servicing operations and technologies including rendez-vous, proximity operations and station-keeping, capture, docking, fluid transfer (specifically, "hydrazine"), and Orbit Replaceable Unit (ORU) transfer. Of course the dynamic coupling between the manipulator and its base mounting flexible solar arrays is very difficult to model. Furthermore, the motion planning of space robots is usually much more complicated than the motion planning of fixed-base manipulators. In this paper first of all the authors present a mixed NE/EL formulation suitable for synthesizing optimal control strategies during the deploying manoeuvres of robotic arms mounted on flexible orbiting platform (i.e. the chaser). Then two new control strategies able to compensate the flexibility excitations of the chaser satellite solar panels during the capturing of a flexible target spacecraft with the use of two robotic arms are presented and applied to a grasping manoeuvre. The mission is here divided into three main phases: the approaching, the docking and the post-grasping phase. Several numerical examples will complete the work.

  4. Development of a Robotics-based Satellites Docking Simulator

    OpenAIRE

    Zebenay, M.

    2014-01-01

    The European Proximity Operation Simulator (EPOS) is a hardware-in-the-loop (HIL) system aiming, among other objectives, at emulating on-orbit docking of spacecraft for verification and validation of the docking phase. This HIL docking simulator set-up essentially consists of docking interfaces, simulating the servicing satellite called chaser satellite, the serviced satellite called target satellite, a sensor of the forces and torques during contact, and two industrial robots that hold the d...

  5. Cross Coupling Between Attenuators In A Docking Mechanism

    Science.gov (United States)

    Holmberg, Arthur; Schmidt, Matthew S.; Ghofranian, Siamak

    1996-01-01

    Cross coupling between motion attenuators on opposite sides of docking mechanism proposed as means of increasing capture envelope. Prototype system for application of cross-coupling concept is one used for docking of Apollo and Soyuz spacecraft; however, given widespread use of docking mechanisms, concept may prove useful in many terrestrial applications as well.

  6. Vision-guided heterogeneous mobile robot docking

    Science.gov (United States)

    Spofford, John R.; Blitch, John; Klarquist, William N.; Murphy, Robin R.

    1999-08-01

    Teams of heterogeneous mobile robots are a key aspect of future unmanned system for operations in complex and dynamic urban environments, such as that envisioned by DARPA's Tactical Mobile Robotics program. One examples of an interaction among such team members is the docking of small robot of limited sensory and processing capability with a larger, more capable robot. Applications for such docking include the transfer of power, data, and materia, as well as physically combined maneuver or manipulation. A two-robot system is considered in this paper. The smaller 'throwable' robot contains a video camera capable of imaging the larger 'packable' robot and transmitting the imagery. The packable robot can both sense the throwable robot through an onboard camera, as well as sense itself through the throwable robot's transmitted video, and is capable of processing imagery from either source. This paper describes recent results in the development of control and sensing strategies for automatic mid-range docking of these two robots. Decisions addressed include the selection of which robot's image sensor to use and which robot to maneuver. Initial experimental results are presented for docking using sensor data from each robot.

  7. A protein–DNA docking benchmark

    NARCIS (Netherlands)

    van Dijk, M.; Bonvin, A.M.J.J.

    2008-01-01

    We present a protein–DNA docking benchmark containing 47 unbound–unbound test cases of which 13 are classified as easy, 22 as intermediate and 12 as difficult cases. The latter shows considerable structural rearrangement upon complex formation. DNA-specific modifications such as flipped out bases an

  8. Docking-mechanism attenuator with electromechanical damper

    Science.gov (United States)

    Syromyatnikov, V. S.

    1971-01-01

    Theoretical and practical problems involved in the application of electromechanical damping for spacecraft docking-mechanism attenuation are discussed. Some drawbacks of hydraulic dampers used for the purpose are pointed out. The basic scheme of the attenuator with the electromechanical damper is given.

  9. Operator learning effects in teleoperated rendezvous & docking

    Science.gov (United States)

    Wilde, M.; Harder, J.; Purschke, R.

    Teleoperation of spacecraft proximity operations and docking requires delicate timing and coordination of spacecraft maneuvers. Experience has shown that human operators show large performance fluctuations in these areas, which are a major factor to be addressed in operator training. In order to allow the quantification of the impact of these human fluctuations on control system performance and the human perception of this performance, a learning curve study was conducted with teleoperated final approach and docking scenarios. Over a period of ten experiment days, three test participants were tasked with repeatedly completing a set of three training scenarios. The scenarios were designed to contain different combinations of the major elements of any final approach and docking situation, and to feature an increasing difficulty level. The individual difficulty levels for the three operators furthermore differed in the level of operator support functions available in their human-machine interfaces. Operator performance in the test scenarios were evaluated in the fields approach success and precision, docking safety, and approach efficiency by a combination of recorded maneuver data and questionnaires. The results show that operator experience and the associated learning curves increase operator performance substantially, regardless of the support system used. The paper also shows that the fluctuations in operator performance and self-perception are substantial between as well as within experiment days, and must be reckoned with in teleoperation system design and mission planning.

  10. Understanding carbon compensation

    International Nuclear Information System (INIS)

    Today, everyone can compensate its carbon emissions on the Internet in few mouse clicks. But what is the meaning of this compensation? What are the mechanisms of voluntary compensation in the framework of the Kyoto protocol? How to participate to this system and to what organisation a company or an individual can call in to reduce his carbon footprint? Carbon compensation is one of the numerous instruments invented to fight against global warming. When it is not possible to reduce our own emissions, we can compensate them by financing projects allowing to reduce the emissions of another company or collectivity. In this book, the authors answer the questions regarding the mechanisms, implementation and efficiency of carbon compensation. (J.S.)

  11. Flexible protein-peptide docking using CABS-dock with knowledge about the binding site

    OpenAIRE

    Kurcinski, Mateusz; Ciemny, Maciej Pawel; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

    2016-01-01

    Despite considerable efforts, structural prediction of protein-peptide complexes is still a very challenging task, mainly due to two reasons: high flexibility of the peptides and transient character of their interactions with proteins. Recently we have developed an automated web server CABS-dock (http://biocomp.chem.uw.edu.pl/CABSdock), which conducts flexible protein-peptide docking without any knowledge about the binding site. Our method allows for full flexibility of the peptide, whereas t...

  12. Compensation for nature conservation

    OpenAIRE

    I D Hodge

    1989-01-01

    The approach adopted towards environmental management in the rural context is different from that in the urban context in that the first is generally based on voluntary controls accompanied by compensation, whereas the second is based on involuntary controls without compensation. The arguments relating to the payment of compensation are examined with the use of management agreements on Sites of Special Scientific Interest taken as an example. Criteria for determining whether or not compensati...

  13. VORFFIP-driven dock: V-D2OCK, a fast and accurate protein docking strategy.

    Directory of Open Access Journals (Sweden)

    Joan Segura

    Full Text Available The experimental determination of the structure of protein complexes cannot keep pace with the generation of interactomic data, hence resulting in an ever-expanding gap. As the structural details of protein complexes are central to a full understanding of the function and dynamics of the cell machinery, alternative strategies are needed to circumvent the bottleneck in structure determination. Computational protein docking is a valid and valuable approach to model the structure of protein complexes. In this work, we describe a novel computational strategy to predict the structure of protein complexes based on data-driven docking: VORFFIP-driven dock (V-D2OCK. This new approach makes use of our newly described method to predict functional sites in protein structures, VORFFIP, to define the region to be sampled during docking and structural clustering to reduce the number of models to be examined by users. V-D2OCK has been benchmarked using a validated and diverse set of protein complexes and compared to a state-of-art docking method. The speed and accuracy compared to contemporary tools justifies the potential use of VD2OCK for high-throughput, genome-wide, protein docking. Finally, we have developed a web interface that allows users to browser and visualize V-D2OCK predictions from the convenience of their web-browsers.

  14. Side docking of the da Vinci robotic system for radical prostatectomy: advantages over traditional docking.

    Science.gov (United States)

    Cestari, Andrea; Ferrari, Matteo; Zanoni, Matteo; Sangalli, Mattia; Ghezzi, Massimo; Fabbri, Fabio; Sozzi, Francesco; Rigatti, Patrizio

    2015-09-01

    The standard low lithotomic position, used during robot-assisted radical prostatectomy (RARP), with prolonged positioning in stirrups together with steep Trendelenburg may expose the patient to neurapraxia phenomena of the lower limbs and can rarely be used in patients with problems of hip abduction. To overcome these hurdles, we evaluated the clinical benefits of "side docking" (SD) of the da Vinci(®) robotic system in comparison to "traditional docking" (TD). A cohort of 120 patients submitted to RARP were prospectively randomized into two groups by docking approach: SD with the patient supine with lower limbs slightly abducted on the operating table, and TD docking time, intraoperative number of collisions between the robotic arms and postoperative neurological problems in the lower limbs were noted. Descriptive statistics was used to analyze outcomes. Docking time was shorter for the SD group [SD: median 13 min (range 10-18); TD: median 21 min (range 15-34)]. None in the SD group and six of 60 patients (10%) in the TD group suffered from temporary (<30 days) unilateral neurological deficits of the lower limbs. In both groups no collisions between the robotic arms occurred. The SD approach is technically feasible. It does not cause collisions between the robotic arms, and is a reliable method for reducing the setup time of RARP. The supine position of the patient may prevent neurological complications of the lower limbs. Based on these results, SD has become the standard docking technique used by our department. PMID:26531205

  15. Which compensation for whom?

    OpenAIRE

    GASTINEAU, Pascal; TAUGOURDEAU, Emmanuelle

    2012-01-01

    Cet article détermine la compensation optimale qu'un décideur public doit imposer de mettre en place à un pollueur responsable d'un dommage environnemental. La compensation peut être soit monétaire, soit environnementale, soit une combinaison des deux. Elle doit permettre d'atteindre trois objectifs : i) pas de perte de bien-être agrégée, ii) une minimisation du coût associé à la compensation, iii) une compensation écologique minimale. Les résultats montrent que - dans certains cas - une comp...

  16. Medical leadership compensation framework

    OpenAIRE

    Uhlíř, Tomáš

    2009-01-01

    This master thesis deals with outlining the rationale of redesigning medical leadership compensation framework within Interior Health Authority (IH). In particular, reviews IH's organizational structure, analyses job descriptions for medical leaders, recommends improvements of communication flow across the authority and designs medical leader's compensation model.

  17. Laser space rendezvous and docking tradeoff

    Science.gov (United States)

    Adelman, S.; Levinson, S.; Raber, P.; Weindling, F.

    1974-01-01

    A spaceborne laser radar (LADAR) was configured to meet the requirements for rendezvous and docking with a cooperative object in synchronous orbit. The LADAR, configurated using existing pulsed CO2 laser technology and a 1980 system technology baseline, is well suited for the envisioned space tug missions. The performance of a family of candidate LADARS was analyzed. Tradeoff studies as a function of size, weight, and power consumption were carried out for maximum ranges of 50, 100, 200, and 300 nautical miles. The investigation supports the original contention that a rendezvous and docking LADAR can be constructed to offer a cost effective and reliable solution to the envisioned space missions. In fact, the CO2 ladar system offers distinct advantages over other candidate systems.

  18. MSFC Three Point Docking Mechanism design review

    Science.gov (United States)

    Schaefer, Otto; Ambrosio, Anthony

    1992-12-01

    In the next few decades, we will be launching expensive satellites and space platforms that will require recovery for economic reasons, because of initial malfunction, servicing, repairs, or out of a concern for post lifetime debris removal. The planned availability of a Three Point Docking Mechanism (TPDM) is a positive step towards an operational satellite retrieval infrastructure. This study effort supports NASA/MSFC engineering work in developing an automated docking capability. The work was performed by the Grumman Space & Electronics Group as a concept evaluation/test for the Tumbling Satellite Retrieval Kit. Simulation of a TPDM capture was performed in Grumman's Large Amplitude Space Simulator (LASS) using mockups of both parts (the mechanism and payload). Similar TPDM simulation activities and more extensive hardware testing was performed at NASA/MSFC in the Flight Robotics Laboratory and Space Station/Space Operations Mechanism Test Bed (6-DOF Facility).

  19. MOLECULAR DOCKING, SINTESIS dan UJI AKTIVITAS SITOTOKSIK

    Directory of Open Access Journals (Sweden)

    Dian Agung Pangaribowo

    2014-06-01

    Full Text Available ABSTRAK: Senyawa 1-benzoil-1,3-dimetilurea telah dirancang, disintesis, diidentifikasi struktur, dan diuji aktivitas sitotoksik secara in vitro. Simulasi docking dilakukan dengan memposisikan senyawa ke dalam sisi aktif reseptor Checkpoint kinase 1 (Chk1 untuk menentukan model pengikatan ligan reseptor. Sintesis 1-benzoil-1,3-dimetilurea dilakukan lewat reaksi asilasi antara 1,3-dimetilurea dan benzoil klorida. Kemurnian produk hasil sintesis ditentukan dengan metode Kromatografi Lapis Tipis (KLT. Identifikasi struktur dilakukan dengan spektrofotometer UV, FT-IR dan spektrometer NMR. Hasil uji antiproliferatif menunjukkan bahwa senyawa 1-benzoil-1,3-dimetilurea memiliki aktivitas sitotoksik terhadap sel HeLa yang lebih baik dibandingkan dengan kontrol positif. Senyawa 1-benzoil-1,3-dimetilurea dengan aktivitas sitotoksik dapat menjadi agen antikanker yang potensial. Kata kunci: 1-benzoil-1,3-dimetilurea, molecular docking, aktivitas sitotoksik ABSTRACT: A novel 1-benzoyl-1,3-dimethylurea has been designed, synthesized, structurally determined, and the in vitro cytotoxic activity was evaluated. Docking simulation was performed to position this compound into the Checkpoint kinase 1 (Chk1 active site to determine the probable binding model. Synthesis of 1-benzoyl-1,3-dimethylurea was completed by acylation reaction between 1,3-dimethylurea and benzoyl chloride. The purity of synthesized product was determined by Thin Layer Chromatography. Structure identification was performed by UV spectrophotometer, FT-IR and NMR spectrometer. Antiproliferative assay result demonstrated that this compound possessed good cytotoxic activity against HeLa cells, which is comparable to the positive control. This compound with potent cytotoxic activity might be a potential anticancer agent. Keywords: 1-benzoyl-1,3-dimethylurea, molecular docking, cytotoxic activity

  20. Protein-Protein Interaction Analysis by Docking

    OpenAIRE

    Stephan Ederer; Florian Fink; Wolfram Gronwald

    2009-01-01

    Based on a protein-protein docking approach we have developed a procedure to verify or falsify protein-protein interactions that were proposed by other methods such as yeast-2-hybrid assays. Our method currently utilizes intermolecular energies but can be expanded to incorporate additional terms such as amino acid based pair-potentials. We show some early results that demonstrate the general applicability of our approach.

  1. Effects of tail docking and docking length on neuroanatomical changes in healed tail tips of pigs

    DEFF Research Database (Denmark)

    Herskin, M S; Thodberg, K; Jensen, Henrik Elvang

    2015-01-01

    In pig production, piglets are tail docked at birth in order to prevent tail biting later in life. In order to examine the effects of tail docking and docking length on the formation of neuromas, we used 65 pigs and the following four treatments: intact tails (n=18); leaving 75% (n=17); leaving 50......% (n=19); or leaving 25% (n=11) of the tail length on the pigs. The piglets were docked between day 2 and 4 after birth using a gas-heated apparatus, and were kept under conventional conditions until slaughter at 22 weeks of age, where tails were removed and examined macroscopically and histologically....... The tail lengths and diameters differed at slaughter (lengths: 30.6±0.6; 24.9±0.4; 19.8±0.6; 8.7±0.6 cm; P<0.001; tail diameter: 0.5±0.03; 0.8±0.02; 1.0±0.03; 1.4±0.04 cm; P<0.001, respectively). Docking resulted in a higher proportion of tails with neuromas (64 v. 0%; P<0.001), number of neuromas per...

  2. Effects of tail docking and docking length on neuroanatomical changes in healed tail tips of pigs.

    Science.gov (United States)

    Herskin, M S; Thodberg, K; Jensen, H E

    2015-04-01

    In pig production, piglets are tail docked at birth in order to prevent tail biting later in life. In order to examine the effects of tail docking and docking length on the formation of neuromas, we used 65 pigs and the following four treatments: intact tails (n=18); leaving 75% (n=17); leaving 50% (n=19); or leaving 25% (n=11) of the tail length on the pigs. The piglets were docked between day 2 and 4 after birth using a gas-heated apparatus, and were kept under conventional conditions until slaughter at 22 weeks of age, where tails were removed and examined macroscopically and histologically. The tail lengths and diameters differed at slaughter (lengths: 30.6±0.6; 24.9±0.4; 19.8±0.6; 8.7±0.6 cm; Ptail diameter: 0.5±0.03; 0.8±0.02; 1.0±0.03; 1.4±0.04 cm; Ptails with neuromas (64 v. 0%; Ptail (1.0±0.2 v. 0; Ptail docking piglets using hot-iron cautery causes formation of neuromas in the outermost part of the tail tip. The presence of neuromas might lead to altered nociceptive thresholds, which need to be confirmed in future studies. PMID:25482535

  3. Molecular docking using the molecular lipophilicity potential as hydrophobic descriptor: impact on GOLD docking performance.

    Science.gov (United States)

    Nurisso, Alessandra; Bravo, Juan; Carrupt, Pierre-Alain; Daina, Antoine

    2012-05-25

    GOLD is a molecular docking software widely used in drug design. In the initial steps of docking, it creates a list of hydrophobic fitting points inside protein cavities that steer the positioning of ligand hydrophobic moieties. These points are generated based on the Lennard-Jones potential between a carbon probe and each atom of the residues delimitating the binding site. To thoroughly describe hydrophobic regions in protein pockets and properly guide ligand hydrophobic moieties toward favorable areas, an in-house tool, the MLP filter, was developed and herein applied. This strategy only retains GOLD hydrophobic fitting points that match the rigorous definition of hydrophobicity given by the molecular lipophilicity potential (MLP), a molecular interaction field that relies on an atomic fragmental system based on 1-octanol/water experimental partition coefficients (log P(oct)). MLP computations in the binding sites of crystallographic protein structures revealed that a significant number of points considered hydrophobic by GOLD were actually polar according to the MLP definition of hydrophobicity. To examine the impact of this new tool, ligand-protein complexes from the Astex Diverse Set and the PDB bind core database were redocked with and without the use of the MLP filter. Reliable docking results were obtained by using the MLP filter that increased the quality of docking in nonpolar cavities and outperformed the standard GOLD docking approach. PMID:22462609

  4. Turbulence compensation: an overview

    Science.gov (United States)

    van Eekeren, Adam W. M.; Schutte, Klamer; Dijk, Judith; Schwering, Piet B. W.; van Iersel, Miranda; Doelman, Niek J.

    2012-06-01

    In general, long range visual detection, recognition and identification are hampered by turbulence caused by atmospheric conditions. Much research has been devoted to the field of turbulence compensation. One of the main advantages of turbulence compensation is that it enables visual identification over larger distances. In many (military) scenarios this is of crucial importance. In this paper we give an overview of several software and hardware approaches to compensate for the visual artifacts caused by turbulence. These approaches are very diverse and range from the use of dedicated hardware, such as adaptive optics, to the use of software methods, such as deconvolution and lucky imaging. For each approach the pros and cons are given and it is indicated for which scenario this approach is useful. In more detail we describe the turbulence compensation methods TNO has developed in the last years and place them in the context of the different turbulence compensation approaches and TNO's turbulence compensation roadmap. Furthermore we look forward and indicate the upcoming challenges in the field of turbulence compensation.

  5. Improved load-cell compensation

    Science.gov (United States)

    Egger, R. L.

    1977-01-01

    Improved bridge-compensation circuit saves considerable time in balancing bridge and wiring it for temperature compensation. Large bridge-balance compensation is made before temperature cycling and small adjustments are made with different type of wire.

  6. HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches.

    Science.gov (United States)

    Huang, Sheng-You; Li, Min; Wang, Jianxin; Pan, Yi

    2016-06-27

    Structure-based molecular docking and ligand-based similarity search are two commonly used computational methods in computer-aided drug design. Structure-based docking tries to utilize the structural information on a drug target like protein, and ligand-based screening takes advantage of the information on known ligands for a target. Given their different advantages, it would be desirable to use both protein- and ligand-based approaches in drug discovery when information for both the protein and known ligands is available. Here, we have presented a general hybrid docking protocol, referred to as HybridDock, to utilize both the protein structures and known ligands by combining the molecular docking program MDock and the ligand-based similarity search method SHAFTS, and evaluated our hybrid docking protocol on the CSAR 2013 and 2014 exercises. The results showed that overall our hybrid docking protocol significantly improved the performance in both binding affinity and binding mode predictions, compared to the sole MDock program. The efficacy of the hybrid docking protocol was further confirmed using the combination of DOCK and SHAFTS, suggesting an alternative docking approach for modern drug design/discovery. PMID:26317502

  7. Climate change and compensation

    DEFF Research Database (Denmark)

    Jensen, Karsten Klint; Flanagan, Tine Bech

    2013-01-01

    This paper presents a case for compensation of actual harm from climate change in the poorest countries. First, it is shown that climate change threatens to reverse the fight to eradicate poverty. Secondly, it is shown how the problems raised in the literature for compensation to some extent...... are based on misconceptions and do not apply to compensation of present actual harm. Finally, two arguments are presented to the effect that, in so far as developed countries accept a major commitment to mitigate climate change, they should also accept a commitment to address or compensate actual harm from...... climate change. The first argument appeals to the principle that if it is an injustice to cause risk of incurring harm in the future, then it is also an injustice to cause a similar harm now. The second argument appeals to the principle that if there is moral reason to reduce the risk of specific harms...

  8. Docking Screens for Novel Ligands Conferring New Biology.

    Science.gov (United States)

    Irwin, John J; Shoichet, Brian K

    2016-05-12

    It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years. PMID:26913380

  9. Essays in Executive Compensation

    OpenAIRE

    Zhang, Dan

    2013-01-01

    This doctoral thesis is made of three empirical research papers focused on executive compensation topics. The first chapter is a solo paper, while the second and third papers are co-authored with Antonio Parbonetti. The first chapter answers to Bushman and Smith’s (2001) call for research on compensation of executives other than CEOs. Specifically, using a sample of 586 firm-year observations over the period 2000-2009, I investigate the economic determinants and effects on shareholder va...

  10. Optimal Sales Force Compensation

    OpenAIRE

    Matthias Kräkel; Anja Schöttner

    2014-01-01

    We analyze a dynamic moral-hazard model to derive optimal sales force compensation plans without imposing any ad hoc restrictions on the class of feasible incentive contracts. We explain when the compensation plans that are most common in practice - fixed salaries, quota-based bonuses, commissions, or a combination thereof - are optimal. Fixed salaries are optimal for small revenue-cost ratios. Quota-based bonuses (commissions) should be used if the revenue-cost ratio takes intermediate (larg...

  11. Dock protein family in brain development and neurological disease

    OpenAIRE

    Shi, Lei

    2013-01-01

    The family of dedicator of cytokinesis (Dock), a protein family that belongs to the atypical Rho guanine nucleotide exchange factors (GEFs) for Rac and/or Cdc42 GTPases, plays pivotal roles in various processes of brain development. To date, 11 members of Docks have been identified in the mammalian system. Emerging evidence has suggested that members of the Dock family are associated with several neurodegenerative and neuropsychiatric diseases, including Alzheimer disease and autism spectrum ...

  12. Cembrene Diterpenoids: Conformational Studies and Molecular Docking to Tubulin

    Directory of Open Access Journals (Sweden)

    Heather E. Villanueva

    2010-04-01

    Full Text Available A conformational analysis of the cembrene diterpenoids cembrene, cembrene A, (3Z-cembrene A, isocembrene, casbene, and incensole, has been carried out using density functional theory at the B3LYP/6-31G* level of theory. A molecular docking analysis of these cembrenoids with tubulin has also been performed in order to assess the potential of tubulin binding of these cytotoxic agents. The macrocyclic cembrenoids are conformationally mobile and numerous low-energy conformations were found. Molecular docking reveals that the cembrenoids dock into the colchicine binding site of tubulin with comparable docking energies to colchicine.

  13. A Review: Mathematical Modles for Cross Docking Planning

    Directory of Open Access Journals (Sweden)

    Dwi Agustina

    2010-09-01

    Full Text Available This paper provides a comprehensive literature review of mathematical models in cross docking planning. From the reviews, the models are classified in three different levels regarding its decisions level which are operational, tactical, and strategic level. The researches in operational level are mainly related to develop model in scheduling, dock door assignment, transhipment problem, vehicle routing, and product allocation. For tactical and strategic level, the researches are mainly proposing model to design the layout and the network of cross docking respectively. The contribution of this paper is to realize the gaps of knowledge in strategic, tactical and operational levels and point out the future research directions in cross docking.

  14. Compensation committee composition and CEO compensation – Finnish evidence

    OpenAIRE

    Uusitalo, Mikael

    2012-01-01

    PURPOSE OF THE STUDY The purpose of this study is to examine the effect of compensation committee composition on the level of CEO compensation. The composition of the compensation committee is analyzed by using five variables which are: 1) the proportion of non-independent directors, 2) the proportion of long-serving directors, 3) the proportion of CEO-directors, 4) the proportion of busy directors and 5) the presence of a blockholder on the compensation committee. CEO compensation is measure...

  15. Design und Betrieb von Cross Docks

    OpenAIRE

    Sinja-Katharina Tiedemann; Nils Boysen

    2009-01-01

    Die hohen Anforderungen an heutige Wertschöpfungsnetzwerke in Bezug auf Flexibilität und Lieferbereitschaft stellen die Distribution vor die Aufgabe, Güter immer häufiger und in immer kleineren Mengen ausliefern zu müssen. Ein Ansatz, diesen Forderungen auf möglichst wirtschaftliche Art und Weise gerecht zu werden, besteht darin, bestehende Distributionsnetze um sogenannte Cross Docks zu erweitern. In solchen lagerlosen Umschlagzentren können dann kleine Warensendungen mit ähnlicher Destinati...

  16. Multilevel Parallelization of AutoDock 4.2

    Directory of Open Access Journals (Sweden)

    Norgan Andrew P

    2011-04-01

    Full Text Available Abstract Background Virtual (computational screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing molecular docking, the prediction of ligand-receptor interactions. AutoDock is a serial application, though several previous efforts have parallelized various aspects of the program. In this paper, we report on a multi-level parallelization of AutoDock 4.2 (mpAD4. Results Using MPI and OpenMP, AutoDock 4.2 was parallelized for use on MPI-enabled systems and to multithread the execution of individual docking jobs. In addition, code was implemented to reduce input/output (I/O traffic by reusing grid maps at each node from docking to docking. Performance of mpAD4 was examined on two multiprocessor computers. Conclusions Using MPI with OpenMP multithreading, mpAD4 scales with near linearity on the multiprocessor systems tested. In situations where I/O is limiting, reuse of grid maps reduces both system I/O and overall screening time. Multithreading of AutoDock's Lamarkian Genetic Algorithm with OpenMP increases the speed of execution of individual docking jobs, and when combined with MPI parallelization can significantly reduce the execution time of virtual screens. This work is significant in that mpAD4 speeds the execution of certain molecular docking workloads and allows the user to optimize the degree of system-level (MPI and node-level (OpenMP parallelization to best fit both workloads and computational resources.

  17. Stealth Compensation Via Retirement Benefits

    OpenAIRE

    Lucian Arye Bebchuk; Fried, Jesse M.

    2004-01-01

    This paper analyzes an important form of "stealth compensation" provided to managers of public companies. We show how boards have been able to camouflage large amount of executive compensation through the use of retirement benefits and payments. Our study highlights the significant role that camouflage and stealth compensation play in the design of compensation arrangements. Our study also highlights the significance of whether information about compensation arrangements is not merely publicl...

  18. Endeavor Approaches Docking Port of ISS

    Science.gov (United States)

    2002-01-01

    Pictured here is the forward docking port on the International Space Station's (ISS) Destiny Laboratory as seen by one of the STS-111 crewmembers from the Space Shuttle Orbiter Endeavour just prior to docking. In June 2002, STS-111 provided the Space Station with a new crew, Expedition Five, replacing Expedition Four after remaining a record-setting 196 days in space. Three spacewalks enabled the STS-111 crew to accomplish additional mission objectives: the delivery and installation of a new platform for the ISS robotic arm, the Mobile Base System (MBS) which is an important part of the Station's Mobile Servicing System allowing the robotic arm to travel the length of the Station; the replacement of a wrist roll joint on the Station's robotic arm; and unloading supplies and science experiments form the Leonardo Multi-Purpose Logistics Module, which made its third trip to the orbital outpost. The STS-111 mission, the 14th Shuttle mission to visit the ISS, was launched on June 5, 2002 and landed June 19, 2002.

  19. Compensation for nuclear damage

    International Nuclear Information System (INIS)

    To secure fair and efficient compensation for damage likely to be caused by the utilisation of nuclear energy, a special civil liability regime was set up by several international conventions. Three of these conventions are in force and Spain is a Contracting Party to all three. The principles established in the first instance at European level by the Paris Convention (absolute and exclusive liability of the nuclear operator, limitation of such liability, compulsory insurance...) are intended to guarantee that possible victims of a nuclear incident will obtain compensation for damage suffered. The Brussels Convention Supplementary to the Paris Convention provides for official funds to compensate victims through intervention by the Contracting Parties. Each Contracting Party should implement these Conventions at national level by appropriate legislation, which is what Spain did with its Act on Nuclear Energy of 29th April 1964, as supplemented in 1967 by the Regulations on Cover for Nuclear Hazards. (N.E.A.)

  20. Modeling, Stability Analysis, and Testing of a Hybrid Docking Simulator

    OpenAIRE

    Zebenaya, M.; Boge, T.; Choukroun, D.

    2014-01-01

    A hybrid docking simulator is a hardware-in-the-loop (HIL) simulator that includes a hardware element within a numerical simulation loop. One of the goals of performing a HIL simulation at the European Proximity Operation Simulator (EPOS) is the verification and validation of the docking phase in an on-orbit servicing mission.....

  1. 18 CFR 1304.204 - Docks, piers, and boathouses.

    Science.gov (United States)

    2010-04-01

    ... structures due to extreme water level fluctuations. Roofs over docks or piers to provide shade are allowed on... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Docks, piers, and boathouses. 1304.204 Section 1304.204 Conservation of Power and Water Resources TENNESSEE VALLEY...

  2. PERANCANGAN FLOATING DOCK UNTUK DAERAH PERAIRAN PELABUHAN KOTA TEGAL

    Directory of Open Access Journals (Sweden)

    Kiryanto Kiryanto

    2013-06-01

    Full Text Available Floating dock merupakan bangunan air sebagai tempat reparasi kapal yang dinilai cukup efisien dalam pembangunannya karena tidak membutuhkan dana yang terlalu mahal. Di sektor indusrti perkapalan kota tegal sudah memiliki galangan dan dock reparasi kapal yang cukup berkembang.  Ide perancangan floating dock ini dirancang sebagai alternatif baru pelayanan reparasi kapal. Perancangan floating dock ini juga memperhatikan dengan detail kapasitas kapal – kapal yang pernah melakukan repararasi di sekitar galangan di Kota Tegal agar ditemukan ukuran utama floating dock yang tepat. Dari Kapasitas kapal yang ada dan berdasarkan metode perbandingan ukuran beberapa floating dock, maka ditemukan ukuran utama yang tepat untuk menampung kebutuhan pelayanan reparasi kapal yaitu LOA = 136,37 m, Lpt = 114.80 m, Bmax = 36,40 m, Bmd: 30,80 m, Tmin = 0,86 m, Tmax = 1,58 m, Hpt = 2,10 m, HOA = 9,60 m. Berdasarkan perhitungan ditemukan juga Ton Lifting Capacity (TLC sebesar 3000 ton. Perancangan menggunakan software perkapalan yaitu dengan menggunakan AutoCad, Delftship, Maxsurf dan Hidromax. Dengan analisa stabilitas menggunakan software Hidromax diketahui bahwa floating dock ini mampu memiliki stabilitas yang baik dengan 4 kondisi yang semua memenuhi criteria  International Maritime Organisation (IMO. Perancangan floating dock ini juga menghitung analisa ekonomis dan investasi. Dari rekapitulasi dana investasi pembangunan floating dock yaitu sebesar Rp.136.622.888.000,00 dengan nilai kembali atau break even point selama 10 tahun dengan modal sendiri, 14 tahun dengan 50% modal sendiri dan 50 % pinjaman bank, dan break event point 18 tahun untuk dana pembangunan floating dock yang berasal dari 100 % pinjaman bank

  3. Coase Competition and Compensation

    OpenAIRE

    Hal Varian

    1994-01-01

    I show that the Pigovian solution to a simple externalities problem and a particular Coasian solution can be viewed as competitive equilibria from different initial endowments. I also describe the ``compensation mechanism,'' a mechanism that implements either the Coasian or Pigovian solution as the outcome of an economically natural bargaining game.

  4. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

    OpenAIRE

    Ravindranath, Pradeep Anand; Forli, Stefano; Goodsell, David S.; Olson, Arthur J.; Sanner, Michel F.

    2015-01-01

    Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approach include the: 1) exponential growth of the search space, demanding more efficient search methods; ...

  5. Initial Investigation of Reaction Control System Design on Spacecraft Handling Qualities for Earth Orbit Docking

    Science.gov (United States)

    Bailey, Randall E.; Jackson, E. Bruce; Goodrich, Kenneth H.; Ragsdale, W. Al; Neuhaus, Jason; Barnes, Jim

    2008-01-01

    A program of research, development, test, and evaluation is planned for the development of Spacecraft Handling Qualities guidelines. In this first experiment, the effects of Reaction Control System design characteristics and rotational control laws were evaluated during simulated proximity operations and docking. Also, the influence of piloting demands resulting from varying closure rates was assessed. The pilot-in-the-loop simulation results showed that significantly different spacecraft handling qualities result from the design of the Reaction Control System. In particular, cross-coupling between translational and rotational motions significantly affected handling qualities as reflected by Cooper-Harper pilot ratings and pilot workload, as reflected by Task-Load Index ratings. This influence is masked but only slightly by the rotational control system mode. While rotational control augmentation using Rate Command Attitude Hold can reduce the workload (principally, physical workload) created by cross-coupling, the handling qualities are not significantly improved. The attitude and rate deadbands of the RCAH introduced significant mental workload and control compensation to evaluate when deadband firings would occur, assess their impact on docking performance, and apply control inputs to mitigate that impact.

  6. Dock treatment process : M/T King Darwin spill

    Energy Technology Data Exchange (ETDEWEB)

    Starkes, R. [Eastern Canada Response Corp. Ltd., Dartmouth, NS (Canada)

    2009-07-01

    This paper discussed the challenges that oil spill responder face when dealing with an incident on docks, piers and other marine structures. In September 2008, Bunker C fuel oil was spilled from the M/T King Darwin during the offloading operation when a pipe flange broke on the deck of the tanker. An estimated 64 tonnes of fuel was spilled in the West Wharf in Dalhousie, New Brunswick. The incident provided an opportunity to develop a response process designed for under-dock structures. The response process involved the following 3 phases: (1) survey and documentation, (2) assessment and characterization, and (3) under-dock treatment plan, development and implementation. Containment booms were deployed around the vessel and dock to control the movement of oil. Oil was also contained on the surface decking of the dock. Most of the oil was contained to the immediate area of the dock. Only a small amount of oil escaped outside the containment boom. The methodology used in this incident proved to be effective and has broader application for future spills. The development of a Dock Oiling Cleanup Assessment Technique (DOCAT) that is complimentary to the established Shoreline Cleanup Assessment Technique (SCAT) process was recommended. 2 refs., 2 tabs., 6 figs.

  7. RELIABILITY OF LENTICULAR EXPANSION COMPENSATORS

    Directory of Open Access Journals (Sweden)

    Gabriel BURLACU,

    2011-11-01

    Full Text Available Axial lenticular compensators are made to take over the longitudinal heat expansion, shock , vibration and noise, made elastic connections for piping systems. In order to have a long life for installations it is necessary that all elements, including lenticular compensators, have a good reliability. This desire can be did by technology of manufactoring and assembly of compensators, the material for lenses and by maintenance.of compensator

  8. Investigation of MM-PBSA rescoring of docking poses.

    Science.gov (United States)

    Thompson, David C; Humblet, Christine; Joseph-McCarthy, Diane

    2008-05-01

    Target-based virtual screening is increasingly used to generate leads for targets for which high quality three-dimensional (3D) structures are available. To allow large molecular databases to be screened rapidly, a tiered scoring scheme is often employed whereby a simple scoring function is used as a fast filter of the entire database and a more rigorous and time-consuming scoring function is used to rescore the top hits to produce the final list of ranked compounds. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approaches are currently thought to be quite effective at incorporating implicit solvation into the estimation of ligand binding free energies. In this paper, the ability of a high-throughput MM-PBSA rescoring function to discriminate between correct and incorrect docking poses is investigated in detail. Various initial scoring functions are used to generate docked poses for a subset of the CCDC/Astex test set and to dock one set of actives/inactives from the DUD data set. The effectiveness of each of these initial scoring functions is discussed. Overall, the ability of the MM-PBSA rescoring function to (i) regenerate the set of X-ray complexes when docking the bound conformation of the ligand, (ii) regenerate the X-ray complexes when docking conformationally expanded databases for each ligand which include "conformation decoys" of the ligand, and (iii) enrich known actives in a virtual screen for the mineralocorticoid receptor in the presence of "ligand decoys" is assessed. While a pharmacophore-based molecular docking approach, PhDock, is used to carry out the docking, the results are expected to be general to use with any docking method. PMID:18465849

  9. Firm performance and CEO compensation : Determinants of CEO compensation

    OpenAIRE

    Singh, Minu; Yavuz, Cigdem

    2015-01-01

    CEO compensation is a much discussed concept in the media and in the society in general. The center of the discussion is mostly around the high CEO compensations and the gaps between the compensation to the CEOs and to rest of the employees. As this is an interesting and topical concept, we hence wanted to examine how CEO compensation is determined in firms listed on the Oslo Stock Exchange. We wanted to examine if CEOs actually get their compensation for obtained firm performance, or if ther...

  10. Compensation Consultants and CEO Pay

    NARCIS (Netherlands)

    Kabir, Rezaul; Minhat, Marizah

    2014-01-01

    The study examines the practice of employing multiple compensation consultants. Examining data of a sample of UK companies over the period 2003–2006 we find that CEOs receive higher equity-based pay when firms employ more than one compensation consultant. An increase in the number of compensation co

  11. Astronaut Brand and Cosmonaut Ivanchenko in Docking Module trainer

    Science.gov (United States)

    1974-01-01

    Astronaut Vance D. Brand (foreground) and Cosmonaut Aleksandr S. Ivanchenko are seated in the Docking Module trainer in bldg 35 during Apollo Soyuz Test Project (ASTP) simulation training at JSC. Brand is the command module pilot of the American ASTP prime crew. Ivanchenko is the engineer on the Soviet ASTP fourth crew (back-up). During the exercise the American ASTP crew and the Soviet ASTP crew simulated docking the Apollo and Soyuz in Earth orbit and transferring to each other's spacecraft. This view is looking from inside the Command Module into the Docking Module. The hatchway leading into the Soyuz spacecraft orbital module mock-up is in the background.

  12. Short term storage of goods in cross-docking operations

    OpenAIRE

    I F A Vis; Roodbergen, K.J.

    2004-01-01

    Cross docking is one of the options to reduce lead times and inventories and to improve customer response time in supply chains. Cross-docking centres are dynamic environments where products arrive, are regrouped, and leave the same day. In this paper we focus on the process of short-term storage of unit-Ioads in a cross-docking environment. The goal is to determine temporary storage locations for incoming unit loads such that the travel distances of the forklift trucks with these unit loads ...

  13. Design of a Docking Wall-Climbing Robot

    OpenAIRE

    Rong Liu; Ran Liang

    2013-01-01

    This paper introduces an innovative wall‐climbing robot. The robot consists of two single‐body negative pressure adsorption robots which could dock together as a mother‐robot or separate into two independent child‐robots. The child‐robots connect with each other through a docking mechanism which can not only lock solidly and unlock smoothly but which can also adjust the relative position of the two child‐robots. This design guarantees that while in dock mode the mother robot will be able to c...

  14. Protein–ligand docking with multiple flexible side chains

    OpenAIRE

    Zhao, Yong; Sanner, Michel F.

    2007-01-01

    In this work, we validate and analyze the results of previously published cross docking experiments and classify failed dockings based on the conformational changes observed in the receptors. We show that a majority of failed experiments (i.e. 25 out of 33, involving four different receptors: cAPK, CDK2, Ricin and HIVp) are due to conformational changes in side chains near the active site. For these cases, we identify the side chains to be made flexible during docking calculation by superimpo...

  15. Strategic Promotion and Compensation.

    OpenAIRE

    Bernhardt, Dan

    1995-01-01

    Within a hierarchical firm structure, this paper details how the composition of a worker's skills and the nonobservability of a worker's ability affect wage and promotion paths. Promotion-based compensation schemes derive naturally from the worker's asymmetrically observed ability. Promotion takes place over time and is inefficient since employers strategically exploit their knowledge of an able worker's ability. Conversely, employers may be unable to efficiently demote and retain bad manager...

  16. Compensability index for compensation radiotherapy after treatment interruptions

    Directory of Open Access Journals (Sweden)

    Putora Paul

    2012-12-01

    Full Text Available Abstract Background The goal of our work was to develop a simple method to evaluate a compensation treatment after unplanned treatment interruptions with respect to their tumour- and normal tissue effect. Methods We developed a software tool in java programming language based on existing recommendations to compensate for treatment interruptions. In order to express and visualize the deviations from the originally planned tumour and normal tissue effects we defined the compensability index. Results The compensability index represents an evaluation of the suitability of compensatory radiotherapy in a single number based on the number of days used for compensation and the preference of preserving the originally planned tumour effect or not exceeding the originally planned normal tissue effect. An automated tool provides a method for quick evaluation of compensation treatments. Conclusions The compensability index calculation may serve as a decision support system based on existing and established recommendations.

  17. Compensability index for compensation radiotherapy after treatment interruptions

    International Nuclear Information System (INIS)

    The goal of our work was to develop a simple method to evaluate a compensation treatment after unplanned treatment interruptions with respect to their tumour- and normal tissue effect. We developed a software tool in java programming language based on existing recommendations to compensate for treatment interruptions. In order to express and visualize the deviations from the originally planned tumour and normal tissue effects we defined the compensability index. The compensability index represents an evaluation of the suitability of compensatory radiotherapy in a single number based on the number of days used for compensation and the preference of preserving the originally planned tumour effect or not exceeding the originally planned normal tissue effect. An automated tool provides a method for quick evaluation of compensation treatments. The compensability index calculation may serve as a decision support system based on existing and established recommendations

  18. Dictyostelium Dock180-related RacGEFs Regulate the Actin Cytoskeleton during Cell Motility

    OpenAIRE

    Para, Alessia; Krischke, Miriam; Merlot, Sylvain; Shen, Zhouxin; Oberholzer, Michael; Lee, Susan; Briggs, Steven; Firtel, Richard A.

    2009-01-01

    Cell motility of amoeboid cells is mediated by localized F-actin polymerization that drives the extension of membrane protrusions to promote forward movements. We show that deletion of either of two members of the Dictyostelium Dock180 family of RacGEFs, DockA and DockD, causes decreased speed of chemotaxing cells. The phenotype is enhanced in the double mutant and expression of DockA or DockD complements the reduced speed of randomly moving DockD null cells' phenotype, suggesting that DockA ...

  19. 300,000-tonnage Crude Oil Dock Put into Operation

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Aproject of Jointly establishing 300,000-tonnage crude oil dock of Tianjin Port has been put into operations, thanks to its outut grid successfully connected with oil pipeline of Sinopec Tanggu reservior.

  20. AggieSat: Autonomous Rendezvous and Docking Technology Demonstrator Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Current autonomous rendezvous and docking (AR&D) capability in low Earth orbit (LEO) is constrained by sensor and effector mass, power, and accuracy limits. To...

  1. Optimal Rendezvous and Docking Simulator for Elliptical Orbits Project

    Data.gov (United States)

    National Aeronautics and Space Administration — It is proposed to develop and implement a simulation of spacecraft rendezvous and docking guidance, navigation, and control in elliptical orbit. The foundation of...

  2. Focused grid-based resampling for protein docking and mapping.

    Science.gov (United States)

    Mamonov, Artem B; Moghadasi, Mohammad; Mirzaei, Hanieh; Zarbafian, Shahrooz; Grove, Laurie E; Bohnuud, Tanggis; Vakili, Pirooz; Ch Paschalidis, Ioannis; Vajda, Sandor; Kozakov, Dima

    2016-04-30

    The fast Fourier transform (FFT) sampling algorithm has been used with success in application to protein-protein docking and for protein mapping, the latter docking a variety of small organic molecules for the identification of binding hot spots on the target protein. Here we explore the local rather than global usage of the FFT sampling approach in docking applications. If the global FFT based search yields a near-native cluster of docked structures for a protein complex, then focused resampling of the cluster generally leads to a substantial increase in the number of conformations close to the native structure. In protein mapping, focused resampling of the selected hot spot regions generally reveals further hot spots that, while not as strong as the primary hot spots, also contribute to ligand binding. The detection of additional ligand binding regions is shown by the improved overlap between hot spots and bound ligands. © 2016 Wiley Periodicals, Inc. PMID:26837000

  3. Collision Analysis of the Spar Upper Module Docking

    Institute of Scientific and Technical Information of China (English)

    Yan Liu; Liping Sun; Chunlin Wu; Guo Wei

    2014-01-01

    In order to assess the possible collision effect, a numerical simulation for the upper module and spar platform docking at the speed of 0.2 m/s was conducted by using the software ANSYS/LS-DYNA, and the time history of the collision force, energy absorption and structural deformation during the collision was described. The purpose was to ensure that the platform was safely put into operation. Furthermore, this paper analyzes different initial velocities and angles on the Von Mises stress and collision resultant force during the docking collision. The results of this paper showed that the docking could be conducted with higher security. The data in this paper can provide useful references for the determination of the upper module’s offshore hoisting scheme and practical construction by contrasting the numerical simulation results of the parameters on the docking collision.

  4. Molecular docking studies in factor XIa binding site

    Science.gov (United States)

    Balaji, Govardhan A.; Balaji, Vitukudi N.; Rao, Shashidhar N.

    2016-03-01

    Factor XIa inhibitors have been identified to have potential as anticoagulants with robust efficacy and low bleeding risks. In light of their significance and the availability of their 3-D X-ray data in the PDB, we present molecular docking studies carried out with a view to obtain docking protocols that will successfully reproduce the experimentally observed protein-ligand interactions in the case of various X-ray ligands. In this context, we have specifically investigated the efficacy of various cross-docking protocols in reproducing experimental data. Our studies demonstrate that an ensemble of the three apo proteins is capable of accurately docking a majority of the X-ray ligands accurately without invoking any additional conformational flexibility than that present in their experimental structures. Further, we demonstrate that such an ensemble is successfully able to enrich a collection of known active factor XIa inhibitors embedded in a decoy database of drug-like molecules.

  5. Fault-Tolerant Relative Navigation System (RNS) for Docking Project

    Data.gov (United States)

    National Aeronautics and Space Administration — A method is propsed to develop a sensor fusion process for blending GPS/IMU/EO data for fault tolerant rendezvous and docking of spacecraft. The methodology takes...

  6. Feasibility of the SIMAC for the NASA Docking System

    Science.gov (United States)

    Motaghedi, Pejmun; Ghofranian, Siamak

    2014-01-01

    In April 2012, NASA directed Boeing to conduct a study to assess the feasibility of implementing a simplified soft capture system, as a possible replacement for the soft capture system portion of the baseline NASA Docking System (NDS). This paper describes the study conducted and conclusions drawn that supported the selection of the Soft Impact Mating and Attenuation Concept (SIMAC) as the replacement of the International Low Impact Docking System's (iLIDS) soft capture system.

  7. JUST IN SEQUENCE SUPPLY WITH MULTILEVEL CROSS DOCKING

    OpenAIRE

    ÁGOTA BÁNYAI

    2013-01-01

    The globalisation of the economy, which can be described by the reduction of transportation, communication and management costs, has changed the structure of logistics processes including purchasing, production, distribution and recycling. Production companies try to optimise their supply chain to reduce the logistics costs. One of the most powerful methods to simplify the supply chain is the cross docking. The aim of cross docking is to sort products intended for different production destina...

  8. Horizontale en verticale samenwerking in distributieketens met cross-docks

    OpenAIRE

    Buijs, Paul

    2014-01-01

    Logistiek dienstverleners staan voor grote uitdagingen op het gebied van duurzaamheid, in het bijzonder vanwege de steeds kleiner wordende zendingen die just-in-time bij de klant moeten worden afgeleverd. Samenwerking tussen partners in de distributieketen en met concurrenten daarbuiten biedt kansen om deze uitdagingen het hoofd te bieden. Dit proefschrift richt zich op samenwerkingsvormen in distributieketens met cross-docks. Cross-docks zijn logistieke centra die bedrijven in staat stellen ...

  9. Arbitrary protein−protein docking targets biologically relevant interfaces

    OpenAIRE

    Martin Juliette; Lavery Richard

    2012-01-01

    Abstract Background Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible ...

  10. Towards predictive docking at aminergic G-protein coupled receptors.

    Science.gov (United States)

    Jakubík, Jan; El-Fakahany, Esam E; Doležal, Vladimír

    2015-11-01

    G protein-coupled receptors (GPCRs) are hard to crystallize. However, attempts to predict their structure have boomed as a result of advancements in crystallographic techniques. This trend has allowed computer-aided molecular modeling of GPCRs. We analyzed the performance of four molecular modeling programs in pose evaluation of re-docked antagonists / inverse agonists to 11 original crystal structures of aminergic GPCRs using an induced fit-docking procedure. AutoDock and Glide were used for docking. AutoDock binding energy function, GlideXP, Prime MM-GB/SA, and YASARA binding function were used for pose scoring. Root mean square deviation (RMSD) of the best pose ranged from 0.09 to 1.58 Å, and median RMSD of the top 60 poses ranged from 1.47 to 3.83 Å. However, RMSD of the top pose ranged from 0.13 to 7.33 Å and ranking of the best pose ranged from the 1st to 60th out of 60 poses. Moreover, analysis of ligand-receptor interactions of top poses revealed substantial differences from interactions found in crystallographic structures. Bad ranking of top poses and discrepancies between top docked poses and crystal structures render current simple docking methods unsuitable for predictive modeling of receptor-ligand interactions. Prime MM-GB/SA optimized for 3NY9 by multiple linear regression did not work well at 3NY8 and 3NYA, structures of the same receptor with different ligands. However, 9 of 11 trajectories of molecular dynamics simulations by Desmond of top poses converged with trajectories of crystal structures. Key interactions were properly detected for all structures. This procedure also worked well for cross-docking of tested β2-adrenergic antagonists. Thus, this procedure represents a possible way to predict interactions of antagonists with aminergic GPCRs. PMID:26453085

  11. Scheduling inbound and outbound trucks at cross docking terminals

    OpenAIRE

    Nils Boysen; Malte Fliedner; Armin Scholl

    2007-01-01

    At cross docking terminals, shipments from inbound trucks are unloaded, sorted and moved to dispatch points where they are directly loaded onto outbound trucks for an immediate delivery elsewhere in the distribution system. This warehouse management concept aims at realizing economies in transportation cost by consolidating divergent shipments to full truckloads without requiring excessive inventory at the cross dock. The efficient operation of such a system requires an appropriate coordinati...

  12. A Review: Mathematical Modles for Cross Docking Planning

    OpenAIRE

    Dwi Agustina; Lee, C.K.M.; Rajesh Piplani

    2010-01-01

    This paper provides a comprehensive literature review of mathematical models in cross docking planning. From the reviews, the models are classified in three different levels regarding its decisions level which are operational, tactical, and strategic level. The researches in operational level are mainly related to develop model in scheduling, dock door assignment, transhipment problem, vehicle routing, and product allocation. For tactical and strategic level, the researches are mainly proposi...

  13. Effects of administration of a local anaesthetic and/or an NSAID and of docking length on the behaviour of piglets during 5 h after tail docking

    DEFF Research Database (Denmark)

    Herskin, Mette S.; Di Giminiani, Pierpaolo; Thodberg, Karen

    2016-01-01

    In many countries, piglets are tail docked to prevent tail biting. The aim of this study was 1) to evaluate the efficacy of a local anaesthetic and/or NSAID to reduce pain caused by tail docking; and 2) to examine interactions with docking length. This was examined in 295 piglets docked by hot iron...... cautery 2–4 days after birth and based on behaviour during docking as well as the following 5 h. The study involved three main factors: local anaesthetic (Lidocain), NSAID (Meloxicam) and docking length. Either 100%, 75%, 50% or 25% of the tails were left on the body of the piglets. Irrespective of the...... tail length, tail docking led to signs of procedural pain, which could be reduced by administration of Lidocain. Preemptive use of Meloxicam did not affect the signs of procedural pain. The results show that tail docking led to behavioural changes throughout the 5 h observation period indicating that...

  14. Combination of scoring schemes for protein docking

    Directory of Open Access Journals (Sweden)

    Schomburg Dietmar

    2007-08-01

    Full Text Available Abstract Background Docking algorithms are developed to predict in which orientation two proteins are likely to bind under natural conditions. The currently used methods usually consist of a sampling step followed by a scoring step. We developed a weighted geometric correlation based on optimised atom specific weighting factors and combined them with our previously published amino acid specific scoring and with a comprehensive SVM-based scoring function. Results The scoring with the atom specific weighting factors yields better results than the amino acid specific scoring. In combination with SVM-based scoring functions the percentage of complexes for which a near native structure can be predicted within the top 100 ranks increased from 14% with the geometric scoring to 54% with the combination of all scoring functions. Especially for the enzyme-inhibitor complexes the results of the ranking are excellent. For half of these complexes a near-native structure can be predicted within the first 10 proposed structures and for more than 86% of all enzyme-inhibitor complexes within the first 50 predicted structures. Conclusion We were able to develop a combination of different scoring schemes which considers a series of previously described and some new scoring criteria yielding a remarkable improvement of prediction quality.

  15. Fukushima: liability and compensation

    International Nuclear Information System (INIS)

    On 11 March 2011, Japan endured one of the worst natural disasters in its history when a massive earthquake struck the Pacific coast of the country and was followed by a tsunami which led to considerable loss of lives. It also led to a major accident at the Fukushima Daiichi nuclear power plant. Soon afterwards, the operator of the plant, Tokyo Electric Power Company (TEPCO), assumed responsibility and liability for the nuclear accident. On 28 April 2011, TEPCO established a dedicated contact line to provide consulting services for financial compensation related to the damage caused

  16. A Holonic Logistics Execution System for Cross-docking (Een holonisch logistiek uitvoeringssysteem voor cross-docking)

    OpenAIRE

    Van Belle, Jan

    2013-01-01

    The coordination and control of cross-docking operations is a complex task and a challenging problem. A severe competition in the logistics sector and ever-increasing traffic (congestion) make that cross-docks should be able to operate efficiently in uncertain and dynamic environments. Moreover, the operational coordination and control is a going concern, so 'one-shot optimization' is not sufficient.As the logistics and manufacturing domain are characterized by similar properties (e.g. large ...

  17. The Interplay between Director Compensation and CEO Compensation

    OpenAIRE

    Dan Lin; Lu Lin

    2014-01-01

    This paper empirically examines the determinants of director compensation and CEO compensation and investigates whether director compensation has an effect on CEO compensation. Based on 713 firms (or 2,852 firm-years) between 2007 and 2010, we find that CEO tenure is related to the ability of the CEO in influencing the board’s pay determination process. However, sitting on the board does not strengthen the CEO’s power over the board during the pay negotiation process. More importantly, we...

  18. Executive Compensation, Incentives, and Risk

    OpenAIRE

    Jenter, Dirk

    2004-01-01

    This paper analyzes the link between equity-based compensation and created incentives by (1) deriving a measure of incentives suitable for both linear and non-linear compensation contracts, (2) analyzing the effect of risk on incentives, and (3) clarifying the role of the agent's private trading decisions in incentive creation. With option-based compensation contracts, the average pay-forperformance sensitivity is not an adequate measure of ex-ante incentives. Pay-for-performance covaries neg...

  19. Compensations during Unsteady Locomotion.

    Science.gov (United States)

    Qiao, Mu; Jindrich, Devin L

    2014-12-01

    Locomotion in a complex environment is often not steady, but the mechanisms used by animals to power and control unsteady locomotion (stability and maneuverability) are not well understood. We use behavioral, morphological, and impulsive perturbations to determine the compensations used during unsteady locomotion. At the level both of the whole-body and of joints, quasi-stiffness models are useful for describing adjustments to the functioning of legs and joints during maneuvers. However, alterations to the mechanics of legs and joints often are distinct for different phases of the step cycle or for specific joints. For example, negotiating steps involves independent changes of leg stiffness during compression and thrust phases of stance. Unsteady locomotion also involves parameters that are not part of the simplest reduced-parameter models of locomotion (e.g., the spring-loaded inverted pendulum) such as moments of the hip joint. Extensive coupling among translational and rotational parameters must be taken into account to stabilize locomotion or maneuver. For example, maneuvers with morphological perturbations (increased rotational inertial turns) involve changes to several aspects of movement, including the initial conditions of rotation and ground-reaction forces. Coupled changes to several parameters may be employed to control maneuvers on a trial-by-trial basis. Compensating for increased rotational inertia of the body during turns is facilitated by the opposing effects of several mechanical and behavioral parameters. However, the specific rules used by animals to control translation and rotation of the body to maintain stability or maneuver have not been fully characterized. We initiated direct-perturbation experiments to investigate the strategies used by humans to maintain stability following center-of-mass (COM) perturbations. When walking, humans showed more resistance to medio-lateral perturbations (lower COM displacement). However, when running, humans

  20. Machine Vision for Relative Spacecraft Navigation During Approach to Docking

    Science.gov (United States)

    Chien, Chiun-Hong; Baker, Kenneth

    2011-01-01

    This paper describes a machine vision system for relative spacecraft navigation during the terminal phase of approach to docking that: 1) matches high contrast image features of the target vehicle, as seen by a camera that is bore-sighted to the docking adapter on the chase vehicle, to the corresponding features in a 3d model of the docking adapter on the target vehicle and 2) is robust to on-orbit lighting. An implementation is provided for the case of the Space Shuttle Orbiter docking to the International Space Station (ISS) with quantitative test results using a full scale, medium fidelity mock-up of the ISS docking adapter mounted on a 6-DOF motion platform at the NASA Marshall Spaceflight Center Flight Robotics Laboratory and qualitative test results using recorded video from the Orbiter Docking System Camera (ODSC) during multiple orbiter to ISS docking missions. The Natural Feature Image Registration (NFIR) system consists of two modules: 1) Tracking which tracks the target object from image to image and estimates the position and orientation (pose) of the docking camera relative to the target object and 2) Acquisition which recognizes the target object if it is in the docking camera Field-of-View and provides an approximate pose that is used to initialize tracking. Detected image edges are matched to the 3d model edges whose predicted location, based on the pose estimate and its first time derivative from the previous frame, is closest to the detected edge1 . Mismatches are eliminated using a rigid motion constraint. The remaining 2d image to 3d model matches are used to make a least squares estimate of the change in relative pose from the previous image to the current image. The changes in position and in attitude are used as data for two Kalman filters whose outputs are smoothed estimate of position and velocity plus attitude and attitude rate that are then used to predict the location of the 3d model features in the next image.

  1. Arbitrary protein−protein docking targets biologically relevant interfaces

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2012-05-01

    Full Text Available Abstract Background Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations. Results In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking

  2. Arbitrary protein−protein docking targets biologically relevant interfaces

    International Nuclear Information System (INIS)

    Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations. In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking using PEBP (Phosphatidylethanolamine binding

  3. GOMoDo: A GPCRs online modeling and docking webserver.

    Directory of Open Access Journals (Sweden)

    Massimo Sandal

    Full Text Available G-protein coupled receptors (GPCRs are a superfamily of cell signaling membrane proteins that include >750 members in the human genome alone. They are the largest family of drug targets. The vast diversity and relevance of GPCRs contrasts with the paucity of structures available: only 21 unique GPCR structures have been experimentally determined as of the beginning of 2013. User-friendly modeling and small molecule docking tools are thus in great demand. While both GPCR structural predictions and docking servers exist separately, with GOMoDo (GPCR Online Modeling and Docking, we provide a web server to seamlessly model GPCR structures and dock ligands to the models in a single consistent pipeline. GOMoDo can automatically perform template choice, homology modeling and either blind or information-driven docking by combining together proven, state of the art bioinformatic tools. The web server gives the user the possibility of guiding the whole procedure. The GOMoDo server is freely accessible at http://molsim.sci.univr.it/gomodo.

  4. Inspection by docking of nuclear-powered ship 'Mutsu'

    International Nuclear Information System (INIS)

    Japan Atomic Energy Research Institute carried out the docking and inspection of the nuclear-powered ship 'Mutsu' at Sekinehama Port, Mutsu City, Aomori Prefecture, from the middle of June to late in July, 1989. In this inspection, the Mutsu was mounted on a floating dock off the coast, the dock was towed by tugboats into the port and moored at the pier, and after completing the works in the dock, the dock was towed to the outside of the port, and the Mutsu was launched. The Mutsu was built as a nuclear power experiment ship, and length 130 m, breadth 19 m, depth 13.2 m, design draft at full load 6.9 m, 8242 GT. One PWR of 36 MWt and one steam turbine of 10000 ps are installed, and velocity is 16.5 knots. In September, 1974, after the first criticality, the leak of radioactivity occurred. The repair of shield and general inspection on safety were carried out in Sasebo Shipyard from August, 1980 to August, 1982. Thereafter, the Mutsu stayed in Ominato, but in January, 1988, after the completion of Sekinehama Port, the Mutsu was brought there. The Sekinehama Port, the test and inspection of the Mutsu carried out so far and the plan of hereafter are reported. (K.I.)

  5. Molecular docking assessment of pyridone derivatives as glucokinase activators

    Directory of Open Access Journals (Sweden)

    Y. Nanda Kumar

    2012-10-01

    Full Text Available Background: Mutations in glucokinase (GK gene results in maturity onset diabetes of the young 2 (MODY2. It has been observed that GK activators (GKAs can activate GK structure and promote glucose phosphorylation and bring blood glucose levels to normal condition. The present study is aimed to identify the binding mode of pyridone derivatives (PDs as GKAs through molecular docking study. Methods: GK structure was retrieved from the Protein Data Bank (PDB, protonated and energy minimized. A database was constructed with 29 PDs and docked into the allosteric site specified with Y61, R63, S69 and Y215 residues using Molecular Operating Environment (MOE software. Docking conformations were generated using triangle match algorithm and ranked by London dG scoring function. The binding orientations and strength of interactions were evaluated by ligand interaction module of MOE. Results: Molecular docking of 29 PDs in allosteric site of GK gave reliable docking scores, interestingly arene cationic interactions were observed with the compounds PD1, PD12, PD20 and PD21. R63 residue of allosteric site played a predominant role in binding with PDs. Conclusions: PDs can be potentially useful agents in future management strategies of type 2 diabetes mellitus.

  6. Granuphilin exclusively mediates functional granule docking to the plasma membrane

    Science.gov (United States)

    Mizuno, Kouichi; Fujita, Takuji; Gomi, Hiroshi; Izumi, Tetsuro

    2016-01-01

    In regulated exocytosis, it is generally assumed that vesicles must stably “dock” at the plasma membrane before they are primed to become fusion-competent. However, recent biophysical analyses in living cells that visualize fluorescent secretory granules have revealed that exocytic behaviors are not necessarily uniform: some granules beneath the plasma membrane are resistant to Ca2+ -triggered release, while others are accelerated to fuse without a pause for stable docking. These findings suggest that stable docking is unnecessary, and can even be inhibitory or nonfunctional, for fusion. Consistently, pancreatic β cells deficient in the Rab27 effector, granuphilin, lack insulin granules directly attached to the plasma membrane in electron micrographs but nevertheless exhibit augmented exocytosis. Here we directly compare the exocytic behaviors between granuphilin-positive and -negative insulin granules. Although granuphilin makes granules immobile and fusion-reluctant beneath the plasma membrane, those granuphilin-positive, docked granules release a portion of granuphilin upon fusion, and fuse at a frequency and time course similar to those of granuphilin-negative undocked granules. Furthermore, granuphilin forms a 180-nm cluster at the site of each docked granule, along with granuphilin-interacting Rab27a and Munc18-1 clusters. These findings indicate that granuphilin is an exclusive component of the functional and fusion-inhibitory docking machinery of secretory granules. PMID:27032672

  7. Sales Force Motivation and Compensation

    OpenAIRE

    Anca-Mihaela TEAU

    2013-01-01

    This article illustrate how sales managers can use sales incentives and compensations to motivate their sales team. To motivate sales people effectively, sales managers must have a thorough understanding of human needs and the concepts of motivation. They must also learn how to use the various forms of sales incentives and compensation to meet their salespeople’s needs.

  8. An overview of turbulence compensation

    NARCIS (Netherlands)

    Schutte, K.; Eekeren, A.W.M. van; Dijk, J.; Schwering, P.B.W.; Iersel, M. van; Doelman, N.J.

    2012-01-01

    In general, long range visual detection, recognition and identification are hampered by turbulence caused by atmospheric conditions. Much research has been devoted to the field of turbulence compensation. One of the main advantages of turbulence compensation is that it enables visual identification

  9. Primary-care physician compensation.

    Science.gov (United States)

    Olson, Arik

    2012-01-01

    This article reviews existing models of physician compensation and presents information about current compensation patterns for primary-care physicians in the United States. Theories of work motivation are reviewed where they have relevance to the desired outcome of satisfied, productive physicians whose skills and expertise are retained in the workforce. Healthcare reforms that purport to bring accountability for healthcare quality and value-rather than simply volume-bring opportunities to redesign primary-care physician compensation and may allow for new compensation methodologies that increase job satisfaction. Physicians are increasingly shunning the responsibility of private practice and choosing to work as employees of a larger organization, often a hospital. Employers of physicians are seeking compensation models that reward both productivity and value. PMID:22786738

  10. 38 CFR 3.459 - Death compensation.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Death compensation. 3.459..., Compensation, and Dependency and Indemnity Compensation Apportionments § 3.459 Death compensation. (a) Death compensation will be apportioned if the child or children of the deceased veteran are not in the custody of...

  11. [Vestibular compensation studies]. [Vestibular Compensation and Morphological Studies

    Science.gov (United States)

    Perachio, Adrian A. (Principal Investigator)

    1996-01-01

    The following topics are reported: neurophysiological studies on MVN neurons during vestibular compensation; effects of spinal cord lesions on VNC neurons during compensation; a closed-loop vestibular compensation model for horizontally canal-related MVN neurons; spatiotemporal convergence in VNC neurons; contributions of irregularly firing vestibular afferents to linear and angular VOR's; application to flight studies; metabolic measures in vestibular neurons; immediate early gene expression following vestibular stimulation; morphological studies on primary afferents, central vestibular pathways, vestibular efferent projection to the vestibular end organs, and three-dimensional morphometry and imaging.

  12. Laser space rendezvous and docking system study continuation

    Science.gov (United States)

    Adelman, S.; Heynau, H.; Levinson, S.; Weindling, F.

    1977-01-01

    Investigations were made of a configuration for a spaceborne laser radar (ladar) to meet the requirements for rendezvous and docking with a cooperative object in synchronous orbit. An analysis was completed of laser phase locking techniques, while experimental verification was made of pulse repetition frequency and resonant scanning control loops. Data measurements on a satellite mock-up were also made. The investigation supports the original contention that a rendezvous and docking ladar can be configured to offer a cost effective and reliable solution to envisioned space missions.

  13. The pickup and delivery problem with cross-docking opportunity

    DEFF Research Database (Denmark)

    Petersen, Hanne Løhmann; Røpke, Stefan

    2011-01-01

    In this paper, we consider the pickup and delivery problem with cross-docking opportunity (PDPCD). The problem arises from an industry application, and includes pickup requests, delivery requests, and pickup-and-delivery requests. Each pickup-and-delivery request can be served either as direct...... delivery by one truck, or by being picked up and transported to the cross-dock by one vehicle, and subsequently delivered at its final destination by another vehicle. Handling times at customers sites and terminal are given. A typical daily instance includes 500-1,000 requests. We solve the problem using a...

  14. Optical processing for semiautonomous terminal navigation and docking

    Science.gov (United States)

    Scholl, M. S.

    1993-01-01

    An optical cross correlator that recognizes a single object is suitable for performing a single-vision function, such as pattern recognition for semiautonomous navigation, landing, and docking of vehicles to a predesignated landing mark. The optical cross correlator, with a video input from a simple imaging system and the output of the optical correlation plane processed with standard star tracker software, produces sufficient information for a spacecraft's terminal homing navigation system to complete a docking maneuver. We describe the application of the optical cross correlator to a landing on a simulated space station.

  15. Compensated pulsed alternator

    International Nuclear Information System (INIS)

    This invention relates to an electromechanical energy converter with inertial energy storage. The device, a single phase, two or multi-pole alternator with stationary field coils, and a rotating armature is provided. The rotor itself may be of laminated steel for slower pulses or for faster pulses should be nonmagnetic and electrically nonconductive in order to allow rapid penetration of the field as the armature coil rotates. The armature coil comprises a plurality of power generating conductors mounted on the rotor. The alternator may also include a stationary or counterrotating compensating coil to increase the output voltage thereof and to reduce the internal impedance of the alternator at the moment of peak output. As the machine voltage rises sinusoidally, an external trigger switch is adapted to be closed at the appropriate time to create the desired output current from said alternator to an external load circuit, and as the output current passes through zero a self-commutating effect is provided to allow the switch to disconnect the generator from the external circuit

  16. Synaptotagmin-1 docks secretory vesicles to syntaxin-1/SNAP-25 acceptor complexes

    DEFF Research Database (Denmark)

    de Wit, Heidi; Walter, Alexander M; Milosevic, Ira; Gulyás-Kovács, Attila; Riedel, Dietmar; Sørensen, Jakob B; Verhage, Matthijs

    2009-01-01

    the minimal docking machinery. Moreover, we show that the requirement for Munc18-1 in docking, but not fusion, can be overcome by stabilizing syntaxin/SNAP-25 acceptor complexes. These findings, together with cross-rescue, double-knockout, and electrophysiological data, lead us to propose that......Docking, the initial association of secretory vesicles with the plasma membrane, precedes formation of the SNARE complex, which drives membrane fusion. For many years, the molecular identity of the docked state, and especially the vesicular docking protein, has been unknown, as has the link to...... SNARE complex assembly. Here, using adrenal chromaffin cells, we identify the vesicular docking partner as synaptotagmin-1, the calcium sensor for exocytosis, and SNAP-25 as an essential plasma membrane docking factor, which, together with the previously known docking factors Munc18-1 and syntaxin, form...

  17. Scheduling trucks in cross docking systems with temporary storage and dock repeat truck holding pattern using genetic algorithm

    Directory of Open Access Journals (Sweden)

    Ehsan Ghobadian

    2013-02-01

    Full Text Available Cross docking is one of the most important issues in management of supply chains. In cross docking, different items delivered to a warehouse by inbound trucks are directly arranged and reorganized based on customer demands, routed and loaded into outbound trucks for delivery purposes to customers without virtually keeping them at the warehouse. If any item is kept in storage, it is normally for a short amount of time, say less than 24 hours. In this paper, we consider a special case of cross docking where there is temporary storage and implements genetic algorithm to solve the resulted problem for some realistic test problems. In our method, we first use some heuristics as initial solutions and then improve the final solution using genetic algorithm. The performance of the proposed model is compared with alternative solution strategy, the GRASP method.

  18. An overview of turbulence compensation

    Science.gov (United States)

    Schutte, Klamer; van Eekeren, Adam W. M.; Dijk, Judith; Schwering, Piet B. W.; van Iersel, Miranda; Doelman, Niek J.

    2012-09-01

    In general, long range visual detection, recognition and identification are hampered by turbulence caused by atmospheric conditions. Much research has been devoted to the field of turbulence compensation. One of the main advantages of turbulence compensation is that it enables visual identification over larger distances. In many (military) scenarios this is of crucial importance. In this paper we give an overview of several software and hardware approaches to compensate for the visual artifacts caused by turbulence. These approaches are very diverse and range from the use of dedicated hardware, such as adaptive optics, to the use of software methods, such as deconvolution and lucky imaging. For each approach the pros and cons are given and it is indicated for which type of scenario this approach is useful. In more detail we describe the turbulence compensation methods TNO has developed in the last years and place them in the context of the different turbulence compensation approaches and TNO's turbulence compensation roadmap. Furthermore we look forward and indicate the upcoming challenges in the field of turbulence compensation.

  19. Technology Development of Automated Rendezvous and Docking/Capture Sensors and Docking Mechanism for the Asteroid Redirect Crewed Mission

    Science.gov (United States)

    Hinkel, Heather; Strube, Matthew; Zipay, John J.; Cryan, Scott

    2016-01-01

    This paper will describe the technology development efforts NASA has underway for Automated Rendezvous and Docking/Capture (AR&D/C) sensors and a docking mechanism and the challenges involved. The paper will additionally address how these technologies will be extended to other missions requiring AR&D/C whether robotic or manned. NASA needs AR&D/C sensors for both the robotic and crewed segments of the Asteroid Redirect Mission (ARM). NASA recently conducted a commonality assessment of the concept of operations for the robotic Asteroid Redirect Vehicle (ARV) and the crewed mission segment using the Orion spacecraft. The commonality assessment also considered several future exploration and science missions requiring an AR&D/C capability. Missions considered were asteroid sample return, satellite servicing, and planetary entry, descent, and landing. This assessment determined that a common sensor suite consisting of one or more visible wavelength cameras, a three-dimensional LIDAR along with long-wavelength infrared cameras for robustness and situational awareness could be used on each mission to eliminate the cost of multiple sensor developments and qualifications. By choosing sensor parameters at build-time instead of at design-time and, without having to requalify flight hardware, a specific mission can design overlapping bearing, range, relative attitude, and position measurement availability to suit their mission requirements with minimal non-recurring engineering costs. The resulting common sensor specification provides the union of all performance requirements for each mission and represents an improvement over the current systems used for AR&D/C today. These sensor specifications are tightly coupled to the docking system capabilities and requirements for final docking conditions. The paper will describe NASA's efforts to develop a standard docking system for use across NASA human spaceflight missions to multiple destinations. It will describe the current

  20. Efficient docking of peptides to proteins without prior knowledge of the binding site

    OpenAIRE

    Hetényi, Csaba; van der Spoel, David

    2002-01-01

    Reliability in docking of ligand molecules to proteins or other targets is an important challenge for molecular modeling. Applications of the docking technique include not only prediction of the binding mode of novel drugs, but also other problems like the study of protein-protein interactions. Here we present a study on the reliability of the results obtained with the popular AutoDock program. We have performed systematical studies to test the ability of AutoDock to reproduce eight different...

  1. Essential role of Elmo1 in Dock2-dependent lymphocyte migration.

    Science.gov (United States)

    Stevenson, Catherine; de la Rosa, Gonzalo; Anderson, Christopher S; Murphy, Patrick S; Capece, Tara; Kim, Minsoo; Elliott, Michael R

    2014-06-15

    Elmo1 and Elmo2 are highly homologous cytoplasmic adaptor proteins that interact with Dock family guanine nucleotide exchange factors to promote activation of the small GTPase Rac. In T lymphocytes, Dock2 is essential for CCR7- and CXCR4-dependent Rac activation and chemotaxis, but the role of Elmo proteins in regulating Dock2 function in primary T cells is not known. In this article, we show that endogenous Elmo1, but not Elmo2, interacts constitutively with Dock2 in mouse and human primary T cells. CD4(+) T cells from Elmo1(-/-) mice were profoundly impaired in polarization, Rac activation, and chemotaxis in response to CCR7 and CXCR4 stimulation. Transfection of full-length Elmo1, but not Elmo2 or a Dock2-binding mutant of Elmo1, rescued defective migration of Elmo1(-/-) T cells. Interestingly, Dock2 protein levels were reduced by 4-fold in Elmo1(-/-) lymphocytes despite normal levels of Dock2 mRNA. Dock2 polyubiquitination was increased in Elmo1(-/-) T cells, and treatment with proteasome inhibitors partially restored Dock2 levels in Elmo1(-/-) T cells. Finally, we show that Dock2 is directly ubiquitinated in CD4(+) T cells and that Elmo1 expression in heterologous cells inhibits ubiquitination of Dock2. Taken together, these findings reveal a previously unknown, nonredundant role for Elmo1 in controlling Dock2 levels and Dock2-dependent T cell migration in primary lymphocytes. Inhibition of Dock2 has therapeutic potential as a means to control recruitment of pathogenic lymphocytes in diseased tissues. This work provides valuable insights into the molecular regulation of Dock2 by Elmo1 that can be used to design improved inhibitors that target the Elmo-Dock-Rac signaling complex. PMID:24821968

  2. A Mathematical Model for Two Dimensional Loading Problem in Cross-Docking Network Design

    OpenAIRE

    Küükoğlu, İlker; Aksoy, Aslı; Ene, Seval; ÖZTÜRK, Nursel

    2013-01-01

    In this paper, the transportation problem of cross-docking network is taken into account. Cross-docking centers differ from distribution centers or warehouses in that the loads are transported from origins to destinations through cross-docking centers without storing them for a long time. Goods are unloaded from incoming trucks and reloaded immediately onto outgoing trucks in these cross-docking centers. This problem is formulated using a mixed integer programming with two-dimensional loading...

  3. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

    OpenAIRE

    Jain, Ajay N.

    2009-01-01

    Computational methods for docking ligands have been shown to be remarkably dependent on precise protein conformation, where acceptable results in pose prediction have been generally possible only in the artificial case of re-docking a ligand into a protein binding site whose conformation was determined in the presence of the same ligand (the “cognate” docking problem). In such cases, on well curated protein/ligand complexes, accurate dockings can be returned as top-scoring over 75% of the tim...

  4. Scheduling trucks in cross docking systems with temporary storage and dock repeat truck holding pattern using GRASP method

    OpenAIRE

    Hassan Javanshir; Reza Tavakkoli-Moghaddam; Ehsan Ghobadian; Mahdi Naderi-Beni

    2012-01-01

    Cross docking play an important role in management of supply chains where items delivered to a warehouse by inbound trucks are directly sorted out, reorganized based on customer demands, routed and loaded into outbound trucks for delivery to customers without virtually keeping them at the warehouse. If any item is held in storage, it is usually for a short time, which is normally less than 24 hours. The proposed model of this paper considers a special case of cross docking where there is temp...

  5. Scheduling trucks in cross docking systems with temporary storage and dock repeat truck holding pattern using genetic algorithm

    OpenAIRE

    Ehsan Ghobadian; Reza Tavakkoli-Moghaddam; Mahdi Naderi-Beni; Hassan Javanshir

    2013-01-01

    Cross docking is one of the most important issues in management of supply chains. In cross docking, different items delivered to a warehouse by inbound trucks are directly arranged and reorganized based on customer demands, routed and loaded into outbound trucks for delivery purposes to customers without virtually keeping them at the warehouse. If any item is kept in storage, it is normally for a short amount of time, say less than 24 hours. In this paper, we consider a special case of cross ...

  6. Knowledge-guided docking: Accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock

    OpenAIRE

    Cleves, AE; Jain, AN

    2015-01-01

    © 2015 The Author(s). Prediction of the bound configuration of small-molecule ligands that differ substantially from the cognate ligand of a protein co-crystal structure is much more challenging than re-docking the cognate ligand. Success rates for cross-docking in the range of 20-30 % are common. We present an approach that uses structural information known prior to a particular cutoff-date to make predictions on ligands whose bounds structures were determined later. The knowledge-guided doc...

  7. 33 CFR 136.113 - Other compensation.

    Science.gov (United States)

    2010-07-01

    ...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS... claimant must include an accounting, including the source and value, of all other compensation...

  8. China Accomplished Its First Space Rendezvous and Docking

    Institute of Scientific and Technical Information of China (English)

    Chen Xiaoli

    2011-01-01

    At 1:36 am on November 3,China's Shenzhou 8 unmanned spaceship and Tiangong 1 space lab spacecraft accomplished the country's first space docking procedure and coupling in space at more than 343km above Earth's surface,marking a great leap in China's space program.

  9. Design of a Docking Wall-Climbing Robot

    Directory of Open Access Journals (Sweden)

    Rong Liu

    2013-02-01

    Full Text Available This paper introduces an innovative wall‐climbing robot. The robot consists of two single‐body negative pressure adsorption robots which could dock together as a mother‐robot or separate into two independent child‐robots. The child‐robots connect with each other through a docking mechanism which can not only lock solidly and unlock smoothly but which can also adjust the relative position of the two child‐robots. This design guarantees that while in dock mode the mother robot will be able to cross some barriers which are impossible to surmount for a single‐body wall‐climbing robot, while in separate mode the child‐robots maintain agility and mobility compared to other two‐body robots. In this paper, an overview of the mechanical structure of the robot is first presented and then three possible mechanisms for barrier‐crossing are discussed and a reasonable one is selected. An analysis of the initial docking condition of the selected design is also given which provides the basis for the experiments and research for the future.

  10. The truck scheduling problem at cross-docking terminals

    OpenAIRE

    Berghman, Lotte; Briand, Cyril; Leus, Roel; Lopez, Pierre

    2012-01-01

    We study the general case of crossdocking, in which each dock can be used both for loading and unloading (so-called mixed mode). We propose a time-indexed linear programming formulation and a branch-and- bound algorithm to solve the problem.

  11. CEO Compensation and Bank Performance

    OpenAIRE

    Athar, Iqbal; Khan, Muhammad Irfan; Ali, Saffar

    2012-01-01

    This study sets out to discover the determinants of compensation of the chief executive officers in the banking industry of Pakistan. Accounting based performance measures and size of the firm have been used as predictors. Results of the study are consistent with arguments, suggesting significant and positive impact of size (assets) of the firm on CEO compensation while no association is found with either of the performance measure of the firm except income before tax (IBT). Return on Assets ...

  12. BOARD STRUCTURE AND CEO COMPENSATION

    OpenAIRE

    Anjam, Zeshan

    2010-01-01

    This study examines the relationship between board structure (non executive directors, executive directors and independent non executive directors) and CEO compensation, in the context of an emerging and developing economy of Pakistan in year 2009. Most of the previous studies about board structure and CEO compensation are based in developed economies but this study is about a developing and emerging economy Pakistan and possibly this attempt will contributes to literature. Data for 86 listed...

  13. Recent trends in compensation practices

    OpenAIRE

    David E. Lebow; Louise Sheiner; Lawrence Slifman; Martha Starr-McCluer

    1999-01-01

    According to some accounts, compensation practices have recently been undergoing marked changes, with an increasing number of firms said to be substituting lump-sum payments for regular pay increases, allowing for greater variability of remuneration across individuals or groups, and making greater use of profit sharing or stock options. Many of these practices are outside the scope of the typical measures of economy-wide compensation growth. Moreover, intensified use of these schemes ought to...

  14. Option compensation and industry competition

    OpenAIRE

    Wong, KP; Stoughton, NM

    2009-01-01

    Compensation policy has become one of the most important ingredients of corporate governance. In this paper we take a new look at the issue, by contrasting the use of options with that of stock. We do this by integrating the repricing or resetting aspect of options with that of industrial structure. We show that industry competition may play an important role in dictating which form of compensation is optimal. When aggressive competition for key professional staff is an issue, the flexibility...

  15. Tail Docking and Ear Cropping Dogs: Public Awareness and Perceptions.

    Science.gov (United States)

    Mills, Katelyn E; Robbins, Jesse; von Keyserlingk, Marina A G

    2016-01-01

    Tail docking and ear cropping are two surgical procedures commonly performed on many dog breeds. These procedures are classified as medically unnecessary surgeries whose purpose is primarily cosmetic. Available attitude research surrounding these controversial practices has been limited to surveys of veterinarians and dog breeders familiar with both practices. The aim of this project was to: 1) assess public awareness of tail docking and ear cropping, 2) determine whether physical alteration of a dog affects how the dog, and 3) owner are perceived. In Experiment 1 awareness was measured using a combination of both explicit and implicit measures. We found that 42% of participants (n = 810) were unable to correctly explain the reason why tail docked and ear cropped dogs had short ears and tails. Similarly, an implicit measure of awareness ('nature vs nurture task'), found that the majority of participants believed short tails and erect ears were a consequence of genetics rather than something the owner or breeder had done. The results obtained in Experiment 2 (n = 392) provide evidence that ear cropped and tail docked dogs are perceived differently than an identical dog in its 'natural' state. Modified dogs were perceived as being more aggressive, more dominant, less playful and less attractive than natural dogs. Experiment 3 (n = 410) is the first evidence that owners of modified dogs are perceived as being more aggressive, more narcissistic, less playful, less talkative and less warm compared to owners of natural dogs. Taken together, these results suggest that although a significant proportion of subjects appear unaware of the practices of tail docking and ear cropping in dogs, these procedures have significant impacts on how modified dogs and their owners are perceived by others. PMID:27348817

  16. Autonomous Vision-Based Tethered-Assisted Rover Docking

    Science.gov (United States)

    Tsai, Dorian; Nesnas, Issa A.D.; Zarzhitsky, Dimitri

    2013-01-01

    Many intriguing science discoveries on planetary surfaces, such as the seasonal flows on crater walls and skylight entrances to lava tubes, are at sites that are currently inaccessible to state-of-the-art rovers. The in situ exploration of such sites is likely to require a tethered platform both for mechanical support and for providing power and communication. Mother/daughter architectures have been investigated where a mother deploys a tethered daughter into extreme terrains. Deploying and retracting a tethered daughter requires undocking and re-docking of the daughter to the mother, with the latter being the challenging part. In this paper, we describe a vision-based tether-assisted algorithm for the autonomous re-docking of a daughter to its mother following an extreme terrain excursion. The algorithm uses fiducials mounted on the mother to improve the reliability and accuracy of estimating the pose of the mother relative to the daughter. The tether that is anchored by the mother helps the docking process and increases the system's tolerance to pose uncertainties by mechanically aligning the mating parts in the final docking phase. A preliminary version of the algorithm was developed and field-tested on the Axel rover in the JPL Mars Yard. The algorithm achieved an 80% success rate in 40 experiments in both firm and loose soils and starting from up to 6 m away at up to 40 deg radial angle and 20 deg relative heading. The algorithm does not rely on an initial estimate of the relative pose. The preliminary results are promising and help retire the risk associated with the autonomous docking process enabling consideration in future martian and lunar missions.

  17. Tail Docking and Ear Cropping Dogs: Public Awareness and Perceptions

    Science.gov (United States)

    Mills, Katelyn E.; Robbins, Jesse; von Keyserlingk, Marina A. G.

    2016-01-01

    Tail docking and ear cropping are two surgical procedures commonly performed on many dog breeds. These procedures are classified as medically unnecessary surgeries whose purpose is primarily cosmetic. Available attitude research surrounding these controversial practices has been limited to surveys of veterinarians and dog breeders familiar with both practices. The aim of this project was to: 1) assess public awareness of tail docking and ear cropping, 2) determine whether physical alteration of a dog affects how the dog, and 3) owner are perceived. In Experiment 1 awareness was measured using a combination of both explicit and implicit measures. We found that 42% of participants (n = 810) were unable to correctly explain the reason why tail docked and ear cropped dogs had short ears and tails. Similarly, an implicit measure of awareness (‘nature vs nurture task’), found that the majority of participants believed short tails and erect ears were a consequence of genetics rather than something the owner or breeder had done. The results obtained in Experiment 2 (n = 392) provide evidence that ear cropped and tail docked dogs are perceived differently than an identical dog in its ‘natural’ state. Modified dogs were perceived as being more aggressive, more dominant, less playful and less attractive than natural dogs. Experiment 3 (n = 410) is the first evidence that owners of modified dogs are perceived as being more aggressive, more narcissistic, less playful, less talkative and less warm compared to owners of natural dogs. Taken together, these results suggest that although a significant proportion of subjects appear unaware of the practices of tail docking and ear cropping in dogs, these procedures have significant impacts on how modified dogs and their owners are perceived by others. PMID:27348817

  18. Compensation: current thinking in France

    International Nuclear Information System (INIS)

    Nuclear third party Liability law constitutes an exception to the general law of tort liability in several respects, notably the channelling of all liability to the nuclear operator even where the operator has not been at fault, and the obligation imposed upon the operator to provide financial security covering its liability. In addition, French law gives priority to compensating personal injuries, fixes the list of radioactively-induced diseases and establishes compensation based on a lump sum payment. The Group examined how these principles could be concretely implemented. It recommended two actions be taken before all else and as soon as possible: the creation of a medical group responsible for ongoing health surveillance apart from any possibility of an accident; and the establishment of a standard compensation agreement which would be prepared in advance and in consultation with interested stakeholders, to allow for compensation to be distributed quickly. Concerning organisational matters, the Group proposed setting up a 'Monitoring Committee' which would bring together all interested parties. The Group also investigated the possibility of setting up a 'One-Stop Shop' which would enable victims to contact one single agency in their quest for compensation for damage suffered, regardless of the source of the compensation funds. (author)

  19. The effect of local or general anesthesia on the physiology and behavior of tail docked pigs.

    Science.gov (United States)

    Sutherland, M A; Davis, B L; McGlone, J J

    2011-06-01

    Tail docking of pigs is a routine procedure on farms to help control tail-biting behavior; however, docking can cause pain. The objective of this research was to evaluate the effect of local or general anesthesia on the physiology (experiment 1) and behavior (experiment 2) of tail docked pigs. Pigs were allocated to one of six treatment groups: (i) sham docking (CON); (ii) docking using conventional cutting (CUT) with side-cutting pliers; (iii) CUT docking plus local anesthesia injected immediately before docking (LA); (iv) CUT docking plus short-acting local anesthesia applied topically to the tail wound (SHORT); (v) CUT docking plus long-acting anesthesia applied topically to the tail wound (LONG) and (vi) CUT docking while the pig was anesthetized with carbon dioxide gas (CO(2)). In experiment 1, blood samples were collected from pigs (10 pigs per treatment) before and 30, 60 and 120 min after docking to measure leukocyte counts and percentages and cortisol concentrations. In experiment 2, the above treatments were repeated (10 pigs per treatment); the percentage of stress vocalizations were recorded during the administration of the treatments and behavior was recorded for up to 120 min after docking or handling. All pigs were weighed before and 24 h after docking and wound healing was recorded until weaning. The neutrophil/lymphocyte ratio was greater (P pigs. At 30 min, cortisol concentrations were greater (P pigs. Cortisol concentrations did not differ (P > 0.05) between SHORT and CON pigs 30 min after docking. Cortisol concentrations did not differ (P > 0.05) among pigs given pain relief at the time of docking compared with pigs' docked without pain relief. Body weight change and wound scores did not differ (P > 0.05) among treatments. The percentage of stress vocalizations increased (P pigs in response to docking or handling. The percentage of time pigs spent lying without contact after docking tended to be greater (P = 0.06) in CUT pigs compared with all

  20. No dry dock: safely strategy for avoiding unplanned dry dock and reducing safety, health and environment risks

    Energy Technology Data Exchange (ETDEWEB)

    Constantinis, Danny A.; Brett, David E. [EM and I Alliance, Cheshire (United Kingdom)

    2012-07-01

    There are currently over 150 operational FPUs with an expected increase of a further 100 units in the next 5 years. This results from several factors: increasing demand for hydrocarbons; new reserves in deep water; pipeline infrastructure is not required and FPU design fits many field requirements. FPUs are increasingly chosen for large, deep water, longer life developments. Units are bigger and more complex. Regulators and oil majors are imposing more stringent integrity requirements to protect against safety, environmental and operational risks related to loss of containment and loss of hull structure integrity which could lead to HSE risks, increased costs and production losses which would become particularly onerous should the unit have to dry dock. There are a number of other important components the context of asset integrity, e.g. mooring and sub sea systems, but these are outside the scope of this paper. The 'No Dry dock....Safely' approach is based on the principle of Criticality Based Integrity which identifies components whose integrity is critical to avoiding incidents and the risk of dry docking. Once critical components are identified the challenge is to establish integrity status and maintain fitness-for-service. Various JIPs e.g. the Hull Inspection Techniques and Strategies are looking at best practice inspection methodologies. The industry is progressing ways of maintaining and repairing critical items without going to dry dock. The challenges include coating maintenance, structural and pressure system repairs. Advances in cathodic protection and coating maintenance strategies are proving successful as are techniques for carrying out major structural repairs. The 'No Dry dock...Safely' methodology is a proven solution and case histories have been included. Technological advances will further improve integrity in the industry. There is no reason why FPUs cannot be kept on station and in production for 25 years or more whilst

  1. Self-adaptive differential evolution algorithm incorporating local search for protein-ligand docking

    International Nuclear Information System (INIS)

    Differential Evolution (DE) algorithm is powerful in optimization problems over several real parameters. DE depends on strategies to generate new trial solutions and the associated parameter values for searching performance. In self-adaptive DE, the automatic learning about previous evolution was used to determine the best mutation strategy and its parameter settings. By combining the self-adaptive DE and Hooke Jeeves local search, we developed a new docking method named SADock (Strategy Adaptation Dock) with the help of AutoDock4 scoring function. As the accuracy and performance of SADock was evaluated in self-docking using the Astex diverse set, the introduced SADock showed better success ratio (89%) than the success ratio (60%) of the Lamarckian genetic algorithm (LGA) of AutoDock4. The self-adapting scheme enabled our new docking method to converge fast and to be robust through the various docking problems.

  2. How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases

    DEFF Research Database (Denmark)

    Udatha, D. B. R. K. Gupta; Sugaya, Nobuyoshi; Olsson, Lisbeth; Panagiotou, Gianni

    2012-01-01

    Molecular docking is the most commonly used technique in the modern drug discovery process where computational approaches involving docking algorithms are used to dock small molecules into macromolecular target structures. Over the recent years several evaluation studies have been reported by...... independent scientists comparing the performance of the docking programs by using default 'black box' protocols supplied by the software companies. Such studies have to be considered carefully as the docking programs can be tweaked towards optimum performance by selecting the parameters suitable for the...... target of interest. In this study we address the problem of selecting an appropriate docking and scoring function combination (88 docking algorithm-scoring functions) for substrate specificity predictions for feruloyl esterases, an industrially relevant enzyme family. We also propose the 'Key Interaction...

  3. EDGA: A Population Evolution Direction-Guided Genetic Algorithm for Protein-Ligand Docking.

    Science.gov (United States)

    Guan, Boxin; Zhang, Changsheng; Ning, Jiaxu

    2016-07-01

    Protein-ligand docking can be formulated as a search algorithm associated with an accurate scoring function. However, most current search algorithms cannot show good performance in docking problems, especially for highly flexible docking. To overcome this drawback, this article presents a novel and robust optimization algorithm (EDGA) based on the Lamarckian genetic algorithm (LGA) for solving flexible protein-ligand docking problems. This method applies a population evolution direction-guided model of genetics, in which search direction evolves to the optimum solution. The method is more efficient to find the lowest energy of protein-ligand docking. We consider four search methods-a tradition genetic algorithm, LGA, SODOCK, and EDGA-and compare their performance in docking of six protein-ligand docking problems. The results show that EDGA is the most stable, reliable, and successful. PMID:26895461

  4. X-Chromosome dosage compensation.

    Science.gov (United States)

    Meyer, Barbara J

    2005-01-01

    In mammals, flies, and worms, sex is determined by distinctive regulatory mechanisms that cause males (XO or XY) and females (XX) to differ in their dose of X chromosomes. In each species, an essential X chromosome-wide process called dosage compensation ensures that somatic cells of either sex express equal levels of X-linked gene products. The strategies used to achieve dosage compensation are diverse, but in all cases, specialized complexes are targeted specifically to the X chromosome(s) of only one sex to regulate transcript levels. In C. elegans, this sex-specific targeting of the dosage compensation complex (DCC) is controlled by the same developmental signal that establishes sex, the ratio of X chromosomes to sets of autosomes (X:A signal). Molecular components of this chromosome counting process have been defined. Following a common step of regulation, sex determination and dosage compensation are controlled by distinct genetic pathways. C. elegans dosage compensation is implemented by a protein complex that binds both X chromosomes of hermaphrodites to reduce transcript levels by one-half. The dosage compensation complex resembles the conserved 13S condensin complex required for both mitotic and meiotic chromosome resolution and condensation, implying the recruitment of ancient proteins to the new task of regulating gene expression. Within each C. elegans somatic cell, one of the DCC components also participates in the separate mitotic/meiotic condensin complex. Other DCC components play pivotal roles in regulating the number and distribution of crossovers during meiosis. The strategy by which C. elegans X chromosomes attract the condensin-like DCC is known. Small, well-dispersed X-recognition elements act as entry sites to recruit the dosage compensation complex and to nucleate spreading of the complex to X regions that lack recruitment sites. In this manner, a repressed chromatin state is spread in cis over short or long distances, thus establishing the

  5. 48 CFR 970.2270 - Unemployment compensation.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Unemployment compensation... Unemployment compensation. (a) Each state has its own unemployment compensation system to provide payments to... unemployment compensation benefits through a payroll tax on employers. Most DOE contractors are subject to...

  6. The Mechanical Performance of Subscale Candidate Elastomer Docking Seals

    Science.gov (United States)

    Bastrzyk, Marta B.; Daniels, Christopher C.

    2010-01-01

    The National Aeronautics and Space Administration is developing a Low Impact Docking System (LIDS) for future exploration missions. The mechanism is a new state-of-the-art device for in-space assembly of structures and rendezvous of vehicles. At the interface between two pressurized modules, each with a version of the LIDS attached, a composite elastomer-metal seal assembly prevents the breathable air from escaping into the vacuum of space. Attached to the active LIDS, this seal mates against the passive LIDS during docking operation. The main interface seal assembly must exhibit low leak and outgas values, must be able to withstand various harsh space environments, must remain operational over a range of temperatures from -50 C to 75 C, and perform after numerous docking cycles. This paper presents results from a comprehensive study of the mechanical performance of four candidate subscale seal assembly designs at -50, 23, 50, and 75 C test temperatures. In particular, the force required to fully compress the seal during docking, and that which is required for separation during the undocking operation were measured. The height of subscale main interface seal bulbs, as well as the test temperature, were shown to have a significant effect on the forces the main interface seal of the LIDS may experience during docking and undocking operations. The average force values required to fully compress each of the seal assemblies were shown to increase with test temperature by approximately 50% from -50 to 75 C. Also, the required compression forces were shown to increase as the height of the seal bulb was increased. The seal design with the tallest elastomer seal bulb, which was 31% taller than that with the shortest bulb, required force values approximately 45% higher than those for the shortest bulb, independent of the test temperature. The force required to separate the seal was shown to increase with decreasing temperature after 15 hours of simulated docking. No adhesion

  7. Design of an Automatic Autonomous Mini Prone-cone Microsatellite Docking Mechanism

    Institute of Scientific and Technical Information of China (English)

    LAI Yinan; DAI Ye; TIAN Hao; ZHANG Dawei

    2010-01-01

    The capability of docking, refueling, repairing, and updating microsatellites using automatic autonomous vehicles will be of significance critical value for design and operation of several space systems in the near feature. Automatic docking capability was successfully tested by many institutions such as National Space Development Agency in Japan, European Space Agency, National Aeronautics and Space Administration in USA, etc. However, there is still much more space for improvement of degree of automation during the process of docking with large deviations of the initial attitude. A novel automatic autonomous probe-cone docking mechanism used for microsatellite docking is proposed. This docking mechanism is designed according to the design indices such as miniaturization, degree of automation and automatic capture capability within large deviation of the initial attitude. On the basis of the virtual work principle, the dynamics modeling of the docking process is presented. The position of the contact point is then analyzed. Comprehensive system level simulation is conducted in the 13 kinds of typical operating conditions with the initial deviations. Capture performance is analyzed. The simulation results show that the docking mechanism can be smoothly captured within 2 s in all cases of large attitude deviation between the active and passive spacecrafts. A virtual prototype model of the docking mechanism is established through ADAMS for further verifying the correctness of the buffer parameter model and the autonomous docking capability. A laboratory platform is designed for on-the-ground experimental validation of the property of mini probe-cone docking mechanism. Repeated docking tests prove the proposed design of the mini probe-cone docking mechanism system for its high reliability, and automatic capture capability within large attitude range. The kinetic model of the docking capture process and the mechanism structure could provide some References for similar

  8. On international compensations for environmental stocks

    OpenAIRE

    Stähler, Frank

    1993-01-01

    This paper sheds some light on the possible implications of compensations which are paid for the maintenance of an environmental stock. It shows that serious complications can arise if the resource-owner can vary the compensation price. In that case, extraction-driven stock preservation policies can conflict with compensation-driven ones and imply instability. Whether compensation policies can neglect this aspect depends crucially on the credibility of sticky compensation prices.

  9. Host state incentives and compensation:

    International Nuclear Information System (INIS)

    After reviewing several options for selecting a host state, the Commission elected to proceed with anoption that builds upon developing grass-roots acceptance and support. To foster such support the Commission has adopted an incentives and compensation package. The purpose of the package is that the incentives and compensations offered are designed to encourage an objective and unbiased review of accepting the responsibilities of a host state or community, and the package helps to guarantee that a facility will become a state/community asset and not impose economic, environmenta, or social hardships for the host community. This report, which describes the Commission's host state incentive and compensation package, the monetary benefit to the host community and state will be substantial. Community benefits will exceed $40 million over 20 years and benefits to the state will be approximately $24 million over the 20-year expected life of the facility. 10 refs., 4 tabs

  10. An electromechanical attenuator/actuator for Space Station docking

    Science.gov (United States)

    Stokes, Lebarian; Glenn, Dean; Carroll, Monty B.

    1987-01-01

    The development of a docking system for aerospace vehicles has identified the need for reusable and variably controlled attenuators/actuators for energy absorption and compliance. One approach to providing both the attenuator and the actuator functions is by way of an electromechanical attenuator/actuator (EMAA) as opposed to a hydraulic system. The use of the electromechanical devices is considered to be more suitable for a space environment because of the absence of contamination from hydraulic fluid leaks and because of the cost effectiveness of maintenance. A smart EMAA that uses range/rate/attitude sensor information to preadjust a docking interface to eliminate misalignments and to minimize contact and stroking forces is described. A prototype EMAA was fabricated and is being tested and evaluated. Results of preliminary testing and analysis already performed have established confidence that this concept is feasible and will provide the desired reliability and low maintenance for repetitive long term operation typical of Space Station requirements.

  11. Flexible Docking of Proteins and "Drug-like" Ligands.

    Science.gov (United States)

    Tang, Hai-Xu; Ye, Yu-Zhen; Ding, Da-Fu

    1998-01-01

    By using "tabu search" algorithm and Gehlhaar potential function, a new approach is presented for flexible docking of protein and its "drug-like" ligand has been developed. Computational test for this method with a set of 100 complexes has been performed, which indicated that the deviation of 89% of the predicted complex conformation was less than 0.25 nm. Compared with GOLD, a program of genetic algorithm, our method has high accuracy, low limit and short computation time. PMID:12168000

  12. Homology Modeling and Molecular Docking for the Science Curriculum

    OpenAIRE

    Owen M. McDougal; Comia, Nic; Sambasivarao, S.V.; Remm, Andrew; Mallory, Chris; Oxford, Julia Thom; Maupin, C. Mark; Andersen, Tim

    2013-01-01

    DockoMatic 2.0 is a powerful open source software program (downloadable from sourceforge.net) that simplifies the exploration of computational biochemistry. This manuscript describes a practical tutorial for use in the undergraduate curriculum that introduces students to macromolecular structure creation, ligand binding calculations, and visualization of docking results. A student procedure is provided that illustrates use of DockoMatic to create a homology model for the amino propeptide regi...

  13. Griffin Technology RoadDock PSP固定带

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    长途旅行的车程中,用PSP看部电影打发时光已经成为很多人必做的事。只是PSP在车上找不到合适的固定点,从而让你的手累得慌。Griffin Technology推出的RoadDock PSP固定带就专为此设计。

  14. Freight Distribution Systems with Cross Docking: A Multidisciplinary Analysis

    OpenAIRE

    Gonzalez-Feliu, Jesus

    2012-01-01

    Freight transport assures a vital link between suppliers and customers and it represents a major source of employment. Multi-echelon distribution is one of the most common strategies in this field. This paper presents the main concepts of multi-echelon distribution with cross-docking through a multidisciplinary analysis that includes an optimization study and an interview-based analysis. The optimization analysis uses both a geographic approach based on the concept of accessibility and a scen...

  15. Freight distribution systems with cross-docking: a multidisciplinary analysis

    OpenAIRE

    Gonzalez-Feliu, Jesus

    2012-01-01

    Freight transport constitutes one of the main activities that influences economy and society, as it assures a vital link between suppliers and customers and it represents a major source of employment. Multi-echelon distribution is one of the most common strategies adopted by the transport companies in an aim of cost reduction. This paper presents the main concepts of multi-echelon distribution with cross-docks through a multidisciplinary analysis that includes an optimisation study (using bot...

  16. Towards predictive docking at aminergic G-protein coupled receptors

    Czech Academy of Sciences Publication Activity Database

    Jakubík, Jan; El-Fakahany, E. E.; Doležal, Vladimír

    2015-01-01

    Roč. 21, č. 11 (2015), s. 284. ISSN 1610-2940 R&D Projects: GA ČR(CZ) GBP304/12/G069; GA ČR(CZ) GA14-05696S; GA ČR(CZ) GA305/09/0681 Institutional support: RVO:67985823 Keywords : induced-fit docking * pose scoring * molecular dynamics * ligand-receptor interaction Subject RIV: FH - Neurology Impact factor: 1.736, year: 2014

  17. Electronic amplifiers for automatic compensators

    CERN Document Server

    Polonnikov, D Ye

    1965-01-01

    Electronic Amplifiers for Automatic Compensators presents the design and operation of electronic amplifiers for use in automatic control and measuring systems. This book is composed of eight chapters that consider the problems of constructing input and output circuits of amplifiers, suppression of interference and ensuring high sensitivity.This work begins with a survey of the operating principles of electronic amplifiers in automatic compensator systems. The succeeding chapters deal with circuit selection and the calculation and determination of the principal characteristics of amplifiers, as

  18. Adaptive Motion Compensation in Radiotherapy

    CERN Document Server

    Murphy, Martin J

    2011-01-01

    External-beam radiotherapy has long been challenged by the simple fact that patients can (and do) move during the delivery of radiation. Recent advances in imaging and beam delivery technologies have made the solution--adapting delivery to natural movement--a practical reality. Adaptive Motion Compensation in Radiotherapy provides the first detailed treatment of online interventional techniques for motion compensation radiotherapy. This authoritative book discusses: Each of the contributing elements of a motion-adaptive system, including target detection and tracking, beam adaptation, and pati

  19. Depth Compensated Spectral Domain Optical Coherence Tomography via Digital Compensation

    CERN Document Server

    Boroomand, Ameneh; Shafiee, Mohammad Javad; Bizheva, Kostadinka; Wong, Alexander

    2015-01-01

    Spectral Domain Optical Coherence Tomography (SD-OCT) is a well-known imaging modality which allows for \\textit{in-vivo} visualization of the morphology of different biological tissues at cellular level resolutions. The overall SD-OCT imaging quality in terms of axial resolution and Signal-to-Noise Ratio (SNR) degrades with imaging depth, while the lateral resolution degrades with distance from the focal plane. This image quality degradation is due both to the design of the SD-OCT imaging system and the optical properties of the imaged object. Here, we present a novel Depth Compensated SD-OCT (DC-OCT) system that integrates a Depth Compensating Digital Signal Processing (DC-DSP) module to improve the overall imaging quality via digital compensation. The designed DC-DSP module can be integrated to any SD-OCT system and is able to simultaneously compensate for the depth-dependent loss of axial and lateral resolutions, depth-varying SNR, as well as sidelobe artifact for improved imaging quality. The integrated D...

  20. Global Positioning System Synchronized Active Light Autonomous Docking System

    Science.gov (United States)

    Howard, Richard T. (Inventor); Book, Michael L. (Inventor); Bryan, Thomas C. (Inventor); Bell, Joseph L. (Inventor)

    1996-01-01

    A Global Positioning System Synchronized Active Light Autonomous Docking System (GPSSALADS) for automatically docking a chase vehicle with a target vehicle comprising at least one active light emitting target which is operatively attached to the target vehicle. The target includes a three-dimensional array of concomitantly flashing lights which flash at a controlled common frequency. The GPSSALADS further comprises a visual tracking sensor operatively attached to the chase vehicle for detecting and tracking the target vehicle. Its performance is synchronized with the flash frequency of the lights by a synchronization means which is comprised of first and second internal clocks operatively connected to the active light target and visual tracking sensor, respectively, for providing timing control signals thereto, respectively. The synchronization means further includes first and second Global Positioning System receivers operatively connected to the first and second internal clocks, respectively, for repeatedly providing simultaneous synchronization pulses to the internal clocks, respectively. In addition, the GPSSALADS includes a docking process controller means which is operatively attached to the chase vehicle and is responsive to the visual tracking sensor for producing commands for the guidance and propulsion system of the chase vehicle.

  1. Modeling of metal interaction geometries for protein-ligand docking.

    Science.gov (United States)

    Seebeck, Birte; Reulecke, Ingo; Kämper, Andreas; Rarey, Matthias

    2008-05-15

    The accurate modeling of metal coordination geometries plays an important role for structure-based drug design applied to metalloenzymes. For the development of a new metal interaction model, we perform a statistical analysis of metal interaction geometries that are relevant to protein-ligand complexes. A total of 43,061 metal sites of the Protein Data Bank (PDB), containing amongst others magnesium, calcium, zinc, iron, manganese, copper, cadmium, cobalt, and nickel, were evaluated according to their metal coordination geometry. Based on statistical analysis, we derived a model for the automatic calculation and definition of metal interaction geometries for the purpose of molecular docking analyses. It includes the identification of the metal-coordinating ligands, the calculation of the coordination geometry and the superposition of ideal polyhedra to identify the optimal positions for free coordination sites. The new interaction model was integrated in the docking software FlexX and evaluated on a data set of 103 metalloprotein-ligand complexes, which were extracted from the PDB. In a first step, the quality of the automatic calculation of the metal coordination geometry was analyzed. In 74% of the cases, the correct prediction of the coordination geometry could be determined on the basis of the protein structure alone. Secondly, the new metal interaction model was tested in terms of predicting protein-ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements. PMID:18041759

  2. Performance of Subscale Docking Seals Under Simulated Temperature Conditions

    Science.gov (United States)

    Smith, Ian M.; Daniels, Christopher C.

    2008-01-01

    A universal docking system is being developed by the National Aeronautics and Space Administration (NASA) to support future space exploration missions to low Earth orbit (LEO), to the moon, and to Mars. The candidate docking seals for the system are a composite design consisting of elastomer seal bulbs molded into the front and rear sides of a metal ring. The test specimens were subscale seals with two different elastomer cross-sections and a 12-in. outside diameter. The seal assemblies were mated in elastomer seal-on-metal plate and elastomer seal-on-elastomer seal configurations. The seals were manufactured from S0383-70 silicone elastomer compound. Nominal and off-nominal joint configurations were examined. Both the compression load required to mate the seals and the leak rate observed were recorded while the assemblies were subjected to representative docking system operating temperatures of -58, 73, and 122 F (-50, 23, and 50 C). Both the loads required to fully compress the seals and their leak rates were directly proportional to the test temperature.

  3. Scheduling trucks in cross docking systems with temporary storage and dock repeat truck holding pattern using GRASP method

    Directory of Open Access Journals (Sweden)

    Hassan Javanshir

    2012-10-01

    Full Text Available Cross docking play an important role in management of supply chains where items delivered to a warehouse by inbound trucks are directly sorted out, reorganized based on customer demands, routed and loaded into outbound trucks for delivery to customers without virtually keeping them at the warehouse. If any item is held in storage, it is usually for a short time, which is normally less than 24 hours. The proposed model of this paper considers a special case of cross docking where there is temporary storage and uses GRASP technique to solve the resulted problem for some realistic test problems. In our method, we first use some heuristics as initial solutions and then improve the final solution using GRASP method. The preliminary test results indicate that the GRASP method performs better than alternative solution strategies.

  4. Annual Pay and Compensation Report.

    Science.gov (United States)

    Vocino, Joe

    2003-01-01

    Presents results of the 2002 Human Resource Management Compensation Survey (n=1,084) indicating that salaries for training and development professionals increased only 1.8 percent over 2001. Tables depict salaries at various levels, by geographic area, and by industry. (JOW)

  5. Can Education Compensate for Society?

    Science.gov (United States)

    Pring, Richard

    2011-01-01

    The extent to which education can compensate for social disadvantage is a matter of political controversy, especially in the context of policies for social mobility. On the one hand, to blame poor achievement on social class or poverty was seen to dodge the professional responsibility of teachers. On the other, the strong correlation between…

  6. Psychology of Pay and Compensation

    NARCIS (Netherlands)

    Thierry, Hk.; Smelser, N.J.; Baltes, P.B.

    2002-01-01

    In most industrialized countries the compensation, of managers and employees is structured along quite comparable patterns. One part consists of base pay, a second part of results-oriented pay, and a third part of secondary labor conditions. In many instances part four is composed of perquisites: be

  7. Compensation for oil pollution damage

    Science.gov (United States)

    Matugina, E. G.; Glyzina, T. S.; Kolbysheva, Yu V.; Klyuchnikov, A. S.; Vusovich, O. V.

    2015-11-01

    The commitment of national industries to traditional energy sources, as well as constantly growing energy demand combined with adverse environmental impact of petroleum production and transportation urge to establish and maintain an appropriate legal and administrative framework for oil pollution damage compensation. The article considers management strategies for petroleum companies that embrace not only production benefits but also environmental issues.

  8. NASA Docking System (NDS) Interface Definitions Document (IDD). Revision F, Dec. 15, 2011

    Science.gov (United States)

    Lewis, James

    2011-01-01

    The NASA Docking System (NDS) mating system supports low approach velocity docking and provides a modular and reconfigurable standard interface, supporting crewed and autonomous vehicles during mating and assembly operations. The NDS is NASA s implementation for the International Docking System Standard (IDSS) using low impact docking technology. All NDS configurations can mate with the configuration specified in the IDSS Interface Definition Document (IDD), Revision A, released May 13, 2011. The NDS evolved from the Low Impact Docking System (LIDS). The term (and its associated acronym), international Low Impact Docking System (iLIDS) is also used to describe this system. NDS and iLIDS may be used interchangeability. Some of the heritage documentation and implementations (e.g., software command names) used on the NDS will continue to use the LIDS acronym.

  9. A High Performance Cloud-Based Protein-Ligand Docking Prediction Algorithm

    OpenAIRE

    Jui-Le Chen; Chun-Wei Tsai; Ming-Chao Chiang; Chu-Sing Yang

    2013-01-01

    The potential of predicting druggability for a particular disease by integrating biological and computer science technologies has witnessed success in recent years. Although the computer science technologies can be used to reduce the costs of the pharmaceutical research, the computation time of the structure-based protein-ligand docking prediction is still unsatisfied until now. Hence, in this paper, a novel docking prediction algorithm, named fast cloud-based protein-ligand docking predictio...

  10. Design and synthesis of new nonsteroidal glucocorticoid modulators through application of an "agreement docking" method.

    Science.gov (United States)

    Barker, Mike; Clackers, Margaret; Demaine, Derek A; Humphreys, Davina; Johnston, Michael J; Jones, Haydn T; Pacquet, Francois; Pritchard, John M; Salter, Mark; Shanahan, Stephen E; Skone, Philip A; Vinader, Victoria M; Uings, Iain; McLay, Iain M; Macdonald, Simon J F

    2005-07-14

    Structurally related glucocorticoid receptor (GR) binders were docked into the GR active site to select the binding mode closest to the true docking mode. This process, termed an "agreement docking method", led to the design of tetrahydronaphthalene 9. The method was validated by the syntheses of 9 and related analogues, which are potent binders of GR. 15a is a partial agonist while 9e and 15a are micromolar antagonists in a mouse mammary tumor virus transactivation assay. PMID:15999989

  11. A study of autonomous docking with an AUV using intelligent controls

    OpenAIRE

    Jantapremjit, Pakpong; Wilson, P.A.; Murphy, Alan J.

    2006-01-01

    Autonomous docking using underwater vehicles will play an important role in long-term underwater explorations and surveys. The autonomous docking mission for an autonomous underwater vehicle at a stationary platform involves a vehicle and a platform matching both position, orientation and velocity. The docking missions therefore require intelligent control systems for precise and soft operations. A study of the sliding mode control and the fuzzy logic controller is pro...

  12. 75 FR 76079 - Sound Incentive Compensation Guidance

    Science.gov (United States)

    2010-12-07

    ... incentive compensation practices in the banking industry by providing a common prudential foundation for incentive compensation arrangements across banking organizations and promoting the overall movement of the industry towards better practices. Supervisory action could play a critical role in addressing...

  13. 75 FR 53023 - Sound Incentive Compensation Guidance

    Science.gov (United States)

    2010-08-30

    ... incentive compensation practices in the banking industry by providing a common prudential foundation for incentive compensation arrangements across banking organizations and promoting the overall movement of the industry towards better practices. Supervisory action could play a critical role in addressing...

  14. 75 FR 22679 - Sound Incentive Compensation Guidance

    Science.gov (United States)

    2010-04-29

    ... incentive compensation practices in the banking industry by providing a common prudential foundation for incentive compensation arrangements across banking organizations and promoting the overall movement of the industry towards better practices. Supervisory action could play a critical role in addressing...

  15. SPACECRAFT DOCKING SIMULATION USING HARDWARE-IN-THE-LOOP SIMULATOR WITH STEWART PLATFORM

    Institute of Scientific and Technical Information of China (English)

    Huang Qitao; Jiang Hongzhou; Zhang Shangying; Han Junwei

    2005-01-01

    A ground-based hardware-in-the-loop (HIL) simulation system with hydraulically driven Stewart platform for spacecraft docking simulation is presented. The system is used for simulating docking process of the on-orbit spacecraft. Principle and structure of the six-degree-of-freedom simulation system are introduced. The docking process dynamic of the vehicles is modeled. Experiment results and mathematical simulation data are compared to validating the simulation system. The comparisons of the results prove that the simulation system proposed can effectively simulate the on-orbit docking process of the spacecraft.

  16. Essential role of Elmo1 in Dock2-dependent lymphocyte migration

    OpenAIRE

    Stevenson, Catherine; de la Rosa, Gonzalo; Anderson, Christopher S.; Murphy, Patrick S.; Capece, Tara; Elliott, Minsoo Kim and Michael R.

    2014-01-01

    Elmo1 and Elmo2 are highly homologous cytoplasmic adapter proteins that interact with Dock family guanine nucleotide exchange factors to promote activation of the small GTPase Rac. In T lymphocytes, Dock2 is essential for CCR7- and CXCR4-dependent Rac activation and chemotaxis, but the role of Elmo proteins in regulating Dock2 function in primary T cells is not known. Here we show that endogenous Elmo1 but not Elmo2 interacts constitutively with Dock2 in mouse and human primary T cells. CD4+ ...

  17. CEO Compensation in Canada, 1971-2008

    OpenAIRE

    Patrice Gelinas; Lisa Baillargeon

    2013-01-01

    This paper draws from a unique database spanning over 35 years of Canadian CEOs’ compensation to explorethe interplay among: the information available to boards of directors of Canadian companies for makingexecutive pay decisions, the Canadian business environment, and the compensation that Canadian CEOsreceived. We find a very strong correlation between Canadian CEOs’ compensation and the amount ofinformation on CEO compensation available to boards of directors. We further note that the evol...

  18. Dynamic Phase Compensation of wind turbines

    DEFF Research Database (Denmark)

    Soerensen, P.; Skaarup, J.; Iov, Florin

    2004-01-01

    This paper describes a dynamic phase compensation unit for a wind turbine with directly connected induction generators. The compensation unit is based on thyristor switched capacitors, where conventional wind turbine compensations use mechanical contactors to switch the capacitors. The unit modules...... are tested and simulated, and preliminary studies on the impact on power quality are performed....

  19. A model capturing ethics and executive compensation

    OpenAIRE

    Gago Rodríguez, Susana; Rodgers, Waymond

    2003-01-01

    This article develops and applies a knowledge-based framework for understanding and interpreting executive compensation under the rubric of ethical consideration. This framework classifies six major ethical considerations that reflect issues in compensation design. We emphasize that these six ethical considerations are influenced by liberty and equality concepts. This framework helps to highlight areas where executive compensation has not been well spelled out

  20. Executive Compensation Concentration and Institutional Ownership Power

    OpenAIRE

    Wei Li; Tingting Guo

    2015-01-01

    In this paper, we examine whether institutional shareholders prefer concentrated or dispersed executive compensation structure. To address this question, we study the relationship between executive compensation concentration and institutional ownership power because institutional investors can influence executive compensation more when they have more power. We measure institutional ownership power using institutional ownership level and institutional ownership concentration. We find a signifi...

  1. Incentives, School Organization and Teacher Compensation.

    Science.gov (United States)

    Odden, Allan

    In order for teacher compensation to serve as an incentive that reinforces broader organizational goals, the norms of the compensation structure must be aligned with the norms of the school organization. The first section of this paper presents a brief overview of changes in teacher compensation from 1820 to 1950. It describes how such changes…

  2. Solving molecular docking problems with multi-objective metaheuristics.

    Science.gov (United States)

    García-Godoy, María Jesús; López-Camacho, Esteban; García-Nieto, José; Aldana-Montes, Antonio J Nebroand José F

    2015-01-01

    Molecular docking is a hard optimization problem that has been tackled in the past with metaheuristics, demonstrating new and challenging results when looking for one objective: the minimum binding energy. However, only a few papers can be found in the literature that deal with this problem by means of a multi-objective approach, and no experimental comparisons have been made in order to clarify which of them has the best overall performance. In this paper, we use and compare, for the first time, a set of representative multi-objective optimization algorithms applied to solve complex molecular docking problems. The approach followed is focused on optimizing the intermolecular and intramolecular energies as two main objectives to minimize. Specifically, these algorithms are: two variants of the non-dominated sorting genetic algorithm II (NSGA-II), speed modulation multi-objective particle swarm optimization (SMPSO), third evolution step of generalized differential evolution (GDE3), multi-objective evolutionary algorithm based on decomposition (MOEA/D) and S-metric evolutionary multi-objective optimization (SMS-EMOA). We assess the performance of the algorithms by applying quality indicators intended to measure convergence and the diversity of the generated Pareto front approximations. We carry out a comparison with another reference mono-objective algorithm in the problem domain (Lamarckian genetic algorithm (LGA) provided by the AutoDock tool). Furthermore, the ligand binding site and molecular interactions of computed solutions are analyzed, showing promising results for the multi-objective approaches. In addition, a case study of application for aeroplysinin-1 is performed, showing the effectiveness of our multi-objective approach in drug discovery. PMID:26042856

  3. Solving Molecular Docking Problems with Multi-Objective Metaheuristics

    Directory of Open Access Journals (Sweden)

    María Jesús García-Godoy

    2015-06-01

    Full Text Available Molecular docking is a hard optimization problem that has been tackled in the past with metaheuristics, demonstrating new and challenging results when looking for one objective: the minimum binding energy. However, only a few papers can be found in the literature that deal with this problem by means of a multi-objective approach, and no experimental comparisons have been made in order to clarify which of them has the best overall performance. In this paper, we use and compare, for the first time, a set of representative multi-objective optimization algorithms applied to solve complex molecular docking problems. The approach followed is focused on optimizing the intermolecular and intramolecular energies as two main objectives to minimize. Specifically, these algorithms are: two variants of the non-dominated sorting genetic algorithm II (NSGA-II, speed modulation multi-objective particle swarm optimization (SMPSO, third evolution step of generalized differential evolution (GDE3, multi-objective evolutionary algorithm based on decomposition (MOEA/D and S-metric evolutionary multi-objective optimization (SMS-EMOA. We assess the performance of the algorithms by applying quality indicators intended to measure convergence and the diversity of the generated Pareto front approximations. We carry out a comparison with another reference mono-objective algorithm in the problem domain (Lamarckian genetic algorithm (LGA provided by the AutoDock tool. Furthermore, the ligand binding site and molecular interactions of computed solutions are analyzed, showing promising results for the multi-objective approaches. In addition, a case study of application for aeroplysinin-1 is performed, showing the effectiveness of our multi-objective approach in drug discovery.

  4. Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking.

    Science.gov (United States)

    Nivedha, Anita K; Thieker, David F; Makeneni, Spandana; Hu, Huimin; Woods, Robert J

    2016-02-01

    Molecular docking programs are primarily designed to align rigid, drug-like fragments into the binding sites of macromolecules and frequently display poor performance when applied to flexible carbohydrate molecules. A critical source of flexibility within an oligosaccharide is the glycosidic linkages. Recently, Carbohydrate Intrinsic (CHI) energy functions were reported that attempt to quantify the glycosidic torsion angle preferences. In the present work, the CHI-energy functions have been incorporated into the AutoDock Vina (ADV) scoring function, subsequently termed Vina-Carb (VC). Two user-adjustable parameters have been introduced, namely, a CHI- energy weight term (chi_coeff) that affects the magnitude of the CHI-energy penalty and a CHI-cutoff term (chi_cutoff) that negates CHI-energy penalties below a specified value. A data set consisting of 101 protein-carbohydrate complexes and 29 apoprotein structures was used in the development and testing of VC, including antibodies, lectins, and carbohydrate binding modules. Accounting for the intramolecular energies of the glycosidic linkages in the oligosaccharides during docking led VC to produce acceptable structures within the top five ranked poses in 74% of the systems tested, compared to a success rate of 55% for ADV. An enzyme system was employed in order to illustrate the potential application of VC to proteins that may distort glycosidic linkages of carbohydrate ligands upon binding. VC represents a significant step toward accurately predicting the structures of protein-carbohydrate complexes. Furthermore, the described approach is conceptually applicable to any class of ligands that populate well-defined conformational states. PMID:26744922

  5. IDENTIFICATION OF PHARMACOLOGICAL TARGETS COMBINING DOCKING AND MOLECULAR DYNAMICS SIMULATIONS

    Directory of Open Access Journals (Sweden)

    Ilizaliturri-Flores Ian

    2013-01-01

    Full Text Available Studies that include both experimental data and computational simulations (in silico have increased in number because the techniques are complementary. In silico methodologies are currently an essential component of drug design; moreover, identification and optimization of the best ligand based on the structures of biomolecules are common scientific challenges. Geometric structural properties of biomolecules explain their behavior and interactions and when this information is used by a combination of algorithms, a dynamic model based on atomic details can be produced. Docking studies enable researchers to determine the best position for a ligand to bind on a macromolecule, whereas Molecular Dynamics (MD simulations describe the relevant interactions that maintain this binding. MD simulations have the advantage of illustrating the macromolecule movements in more detail. In the case of a protein, the side chain, backbone and domain movements can explain how ligands are trapped during different conformational states. Additionally, MD simulations can depict several binding sites of ligands that can be explored by docking studies, sampling many protein conformations. Following the previously mentioned strategy, it is possible to identify each binding site that might be able to accommodate different ligands through atomic motion. Another important advantage of MD is to explore the movement of side chains of key catalytic residues, which could provide information about the formation of transition states of a protein. All this information can be used to propose ligands and their most probable site of interaction, which are daily tasks of drug design. In this review, the most frequent criteria that are considered when determining pharmacological targets are gathered, particularly when docking and MD are combined.

  6. Ligand pose and orientational sampling in molecular docking.

    Directory of Open Access Journals (Sweden)

    Ryan G Coleman

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

  7. Development of watershed compensation programs

    International Nuclear Information System (INIS)

    British Columbia Hydro is developing fish and wildlife watershed compensation programs to address water license requirements of recent hydroelectric developments and outstanding issues associated with older projects. Historically, no funding was provided for environmental impacts. In more recent times, a one-time payment was made to the appropriate government agencies. With no long-term commitment by B.C. Hydro, fish and wildlife resource needs were often not addressed, leading to the degradation or loss of the resource and the perception that B.C. Hydro was not addressing its responsibilities with respect to other water users. B.C. Hydro's activities are reviewed with respect to developing ongoing fisheries compensation or mitigation programs through trust funds that ensure a long term commitment towards replacing or improving, and maintaining fish resources associated with B.C. Hydro's hydroelectric developments. 2 figs

  8. Compensating Differentials for Sexual Harassment

    OpenAIRE

    Joni Hersch

    2011-01-01

    Workplace sexual harassment is illegal, but many workers report that they have been sexually harassed. Exposure to the risk of sexual harassment may decrease productivity, which would reduce wages. Alternatively, workers may receive a compensating differential for exposure to sexual harassment, which would increase wages. Data on claims of sexual harassment filed with the Equal Employment Opportunity Commission are used to calculate the first measures of sexual harassment risks by industry, a...

  9. Bank Efficiency and Executive Compensation

    OpenAIRE

    Timothy King; Jonathan Williams

    2013-01-01

    We investigate whether handsomely rewarding bank executives’ realizes superior efficiency by determining if executive remuneration contracts produce incentives that offset potential agency problems and lead to improvements in bank efficiency. We calculate executive Delta and Vega to proxy executives’ risk-taking following changes in their compensation contracts and estimate their relationship with alternative profit efficiency. Our study uses novel instruments to account for the potentially e...

  10. Circadian Pacemaker – Temperature Compensation

    OpenAIRE

    Gerkema, Menno P.; Binder, Marc D.; Hirokawa, Nobutaka; Windhorst, Uwe

    2009-01-01

    One of the defining characteristics of circadian pacemakers and indicates the independence of the speed of circadian clock processes of environmental temperature. Mechanisms involved, so far not elucidated in full detail, entail at least two processes that are similarly affected by temperature changes, but with an opposing and counterbalancing effect on the periodicity of the clock system. As a result of temperature compensation, the increase in reaction velocity for every 10° rise in tempera...

  11. Has compensation become more flexible?

    OpenAIRE

    Sandra A. Cannon; Bruce C. Fallick; Michael Lettau; Raven E. Saks

    2000-01-01

    In recent years, numerous observers have argued that global competition, increased reliance on contingent workers, and the breakdown of implicit contracts have made compensation practices in the United States more flexible; in particular, employers have become more concerned with how an employee's pay compares to that in other firms and less concerned with considerations of equity or relative pay within the firm. This paper uses establishment-level data from the Bureau of Labor Statistics' Em...

  12. Spacecraft Rendevouz and Docking. An Autonomy assisted Human Operator Approach

    DEFF Research Database (Denmark)

    Jørgensen, John Leif; Thuesen, Gøsta

    1999-01-01

    .The method described generates, based on a single camera and a priory information about the target vehicle and orbit data, all necessary guidance information for closed loop autonomous navigation, from first detection at far distance to a close up hold point. Furthermore, the system provides relative pose...... based entirely on direct human supervision and control.This paper describes a vision based system and methodology, that autonomously generates accurate guidance information that may assist a human operator in performing the tasks associated with both the rendezvous and docking navigation procedures...

  13. Laser space rendevous and docking trade-off

    Science.gov (United States)

    1974-01-01

    A spaceborne LADAR sensor, which will meet the requirements for rendezvous and docking with a cooperative object in synchronous orbit is presented. The sensor is being configured around a pulsed CO2 laser which can be constructed and deployed using technology which presently exists or is being developed, and which appears to lend itself very well to the envisioned family of space missions. In order to determine the applicability of the type of sensor being considered, the performance of a family of candidate sensors is being traded off as a function of size, weight, and power consumption. The maximum ranges being considered are 50, 100, 200, and 300 nautical miles.

  14. 38 CFR 21.3023 - Nonduplication; pension, compensation, and dependency and indemnity compensation.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Nonduplication; pension, compensation, and dependency and indemnity compensation. 21.3023 Section 21.3023 Pensions, Bonuses, and... Nonduplication; pension, compensation, and dependency and indemnity compensation. (a) Child; age 18. A child...

  15. Compensation Techniques in Accelerator Physics

    Energy Technology Data Exchange (ETDEWEB)

    Sayed, Hisham Kamal [Old Dominion Univ., Norfolk, VA (United States)

    2011-05-01

    Accelerator physics is one of the most diverse multidisciplinary fields of physics, wherein the dynamics of particle beams is studied. It takes more than the understanding of basic electromagnetic interactions to be able to predict the beam dynamics, and to be able to develop new techniques to produce, maintain, and deliver high quality beams for different applications. In this work, some basic theory regarding particle beam dynamics in accelerators will be presented. This basic theory, along with applying state of the art techniques in beam dynamics will be used in this dissertation to study and solve accelerator physics problems. Two problems involving compensation are studied in the context of the MEIC (Medium Energy Electron Ion Collider) project at Jefferson Laboratory. Several chromaticity (the energy dependence of the particle tune) compensation methods are evaluated numerically and deployed in a figure eight ring designed for the electrons in the collider. Furthermore, transverse coupling optics have been developed to compensate the coupling introduced by the spin rotators in the MEIC electron ring design.

  16. Accurate refinement of docked protein complexes using evolutionary information and deep learning.

    Science.gov (United States)

    Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit

    2016-06-01

    One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein-protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work, we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 Å error margin on average, by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures. PMID:26846813

  17. Waste Isolation Pilot Plant TruDock crane system analysis

    International Nuclear Information System (INIS)

    The WIPP TruDock crane system located in the Waste Handling Building was identified in the WIPP Safety Analysis Report (SAR), November 1995, as a potential accident concern due to failures which could result in a dropped load. The objective of this analysis is to evaluate the frequency of failure of the TruDock crane system resulting in a dropped load and subsequent loss of primary containment, i.e. drum failure. The frequency of dropped loads was estimated to be 9.81E-03/year or approximately one every 102 years (or, for the 25% contingency, 7.36E-03/year or approximately one every 136 years). The dominant accident contributor was the failure of the cable/hook assemblies, based on failure data obtained from NUREG-0612, as analyzed by PLG, Inc. The WIPP crane system undergoes a rigorous test and maintenance program, crane operation is discontinued following any abnormality, and the crane operator and load spotter are required to be trained in safe crane operation, therefore it is felt that the WIPP crane performance will exceed the data presented in NUREG-0612 and the estimated failure frequency is felt to be conservative

  18. Attitudes of Dutch Pig Farmers Towards Tail Biting and Tail Docking

    NARCIS (Netherlands)

    Bracke, M.B.M.; Lauwere, de C.C.; Wind, S.M.M.; Zonderland, J.J.

    2013-01-01

    The Dutch policy objective of a fully sustainable livestock sector without mutilations by 2023 is not compatible with the routine practice of tail docking to minimize the risk of tail biting. To examine farmer attitudes towards docking, a telephone survey was conducted among 487 conventional and 33

  19. 48 CFR 52.247-40 - Ex Dock, Pier, or Warehouse, Port of Importation.

    Science.gov (United States)

    2010-10-01

    ... Warehouse, Port of Importation. 52.247-40 Section 52.247-40 Federal Acquisition Regulations System FEDERAL... Provisions and Clauses 52.247-40 Ex Dock, Pier, or Warehouse, Port of Importation. As prescribed in 47.303-12..., pier, or warehouse, port of importation: Ex Dock, Pier, or Warehouse, Port of Importation (APR 1984)...

  20. Satellite-rocket docking ring recognition method based on mathematical morphology

    Science.gov (United States)

    Xu, Zhiqiang; Shang, Yang; Ma, Xuan

    2015-10-01

    Satellite-rocket docking ring recognition method based on mathematical morphology is presented in this paper, according to the geometric and grayscale characteristics of the docking ring typical structure. The docking ring used in this paper is a circle with a cross in the middle. Most of spacecrafts are transported into orbit by rocket, and they retain the connection component with the rocket. The tracing spacecraft should capture the target spacecraft first before operating the target spacecraft. The docking ring is one of the typical parts of a spacecraft, and it can be recognized automatically. Thereby we can capture the spacecraft through the information of the docking ring. Firstly a multi-step mathematical morphology processing is applied to the image of the target spacecraft with different structure element, followed by edge detection and line detection, and finally docking ring typical structure is located in the image by relative geometry analysis. The images used in this paper are taken of real satellite in lab. The docking ring can be recognized when the distance between the two spacecraft is different. The results of physical simulation experiment show that the method in this paper can recognize docking ring typical structure accurately when the tracing spacecraft is approaching the target spacecraft.

  1. CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.

    Directory of Open Access Journals (Sweden)

    Sjoerd J de Vries

    Full Text Available BACKGROUND: Macromolecular complexes are the molecular machines of the cell. Knowledge at the atomic level is essential to understand and influence their function. However, their number is huge and a significant fraction is extremely difficult to study using classical structural methods such as NMR and X-ray crystallography. Therefore, the importance of large-scale computational approaches in structural biology is evident. This study combines two of these computational approaches, interface prediction and docking, to obtain atomic-level structures of protein-protein complexes, starting from their unbound components. METHODOLOGY/PRINCIPAL FINDINGS: Here we combine six interface prediction web servers into a consensus method called CPORT (Consensus Prediction Of interface Residues in Transient complexes. We show that CPORT gives more stable and reliable predictions than each of the individual predictors on its own. A protocol was developed to integrate CPORT predictions into our data-driven docking program HADDOCK. For cases where experimental information is limited, this prediction-driven docking protocol presents an alternative to ab initio docking, the docking of complexes without the use of any information. Prediction-driven docking was performed on a large and diverse set of protein-protein complexes in a blind manner. Our results indicate that the performance of the HADDOCK-CPORT combination is competitive with ZDOCK-ZRANK, a state-of-the-art ab initio docking/scoring combination. Finally, the original interface predictions could be further improved by interface post-prediction (contact analysis of the docking solutions. CONCLUSIONS/SIGNIFICANCE: The current study shows that blind, prediction-driven docking using CPORT and HADDOCK is competitive with ab initio docking methods. This is encouraging since prediction-driven docking represents the absolute bottom line for data-driven docking: any additional biological knowledge will greatly

  2. DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations

    Directory of Open Access Journals (Sweden)

    Alberto Cuzzolin

    2015-05-01

    Full Text Available Virtual screening (VS is a computational methodology that streamlines the drug discovery process by reducing costs and required resources through the in silico identification of potential drug candidates. Structure-based VS (SBVS exploits knowledge about the three-dimensional (3D structure of protein targets and uses the docking methodology as search engine for novel hits. The success of a SBVS campaign strongly depends upon the accuracy of the docking protocol used to select the candidates from large chemical libraries. The identification of suitable protocols is therefore a crucial step in the setup of SBVS experiments. Carrying out extensive benchmark studies, however, is usually a tangled task that requires users’ proficiency in handling different file formats and philosophies at the basis of the plethora of existing software packages. We present here DockBench 1.0, a platform available free of charge that eases the pipeline by automating the entire procedure, from docking benchmark to VS setups. In its current implementation, DockBench 1.0 handles seven docking software packages and offers the possibility to test up to seventeen different protocols. The main features of our platform are presented here and the results of the benchmark study of human Checkpoint kinase 1 (hChk1 are discussed as validation test.

  3. PaFlexPepDock: parallel ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta.

    Directory of Open Access Journals (Sweden)

    Haiou Li

    Full Text Available Structural information related to protein-peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein-peptide interactions explored by experimental ways. Protein-peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide folding, peptide docking with its receptor, and refinement of some flexible areas of the receptor as the peptide is approaching. Several existing methods have been used to sample the degrees of freedom in the three processes, which are usually triggered in an organized sequential scheme. In this paper, we proposed a parallel approach that combines all the three processes during the docking of a folding peptide with a flexible receptor. This approach mimics the actual protein-peptide docking process in parallel way, and is expected to deliver better performance than sequential approaches. We used 22 unbound protein-peptide docking examples to evaluate our method. Our analysis of the results showed that the explicit refinement of the flexible areas of the receptor facilitated more accurate modeling of the interfaces of the complexes, while combining all of the moves in parallel helped the constructing of energy funnels for predictions.

  4. Developing a cross-docking network design model under uncertain environment

    Science.gov (United States)

    Seyedhoseini, S. M.; Rashid, Reza; Teimoury, E.

    2014-09-01

    Cross-docking is a logistic concept, which plays an important role in supply chain management by decreasing inventory holding, order packing, transportation costs and delivery time. Paying attention to these concerns, and importance of the congestion in cross docks, we present a mixed-integer model to optimize the location and design of cross docks at the same time to minimize the total transportation and operating costs. The model combines queuing theory for design aspects, for that matter, we consider a network of cross docks and customers where two M/M/c queues have been represented to describe operations of indoor trucks and outdoor trucks in each cross dock. To prepare a perfect illustration for performance of the model, a real case also has been examined that indicated effectiveness of the proposed model.

  5. Docking of B-cell epitope antigen to specific hepatitis B antibody

    Indian Academy of Sciences (India)

    R Rajkannan; E J Padma Malar

    2007-09-01

    The interaction of pres1 region of hepatitis B virus B-cell epitope antigen with specific hepatitis B neutralizing monoclonal antibody was examined by docking study. We modelled the 3D complex structure of B-cell epitope antigen residues CTTPAQGNSMFPSCCCTKPTDGNCY by homology modelling and docked it with the crystal structure of monoclonal antibody specific for the pres1 region of the hepatitis B virus. At the optimized docked conformation, the interactions between the amino acids of antigen and antibody were examined. It is found that the docked complex is stabilized by 59.3 kcal/mol. The stability of the docked antigen-antibody complex is due to hydrogen bonding and van der Waals interactions. The amino acids of the antigen and antibody responsible for the interaction were identified.

  6. Two-dimensional PSD based automatic docking of self-reconfiguration modular exploration robot system

    Institute of Scientific and Technical Information of China (English)

    Zhang Liping; Ma Shugen; Li Bin; Zhang Zheng; Cao Binggang

    2007-01-01

    Based on the design of a docking mechanism, this paper thoroughly investigates the space automatic docking of self-reconfiguration modular exploration robot system (RMERS). The method that leads robot to achieve space docking by using two-dimensional PSD is put forward innovatively for the median size robot system. At the same time, in order to enlarge the detecting extension and the precision of PSD and reduce its dependence on lighting signal, the PSD was remade by increasing the optical device over its light-sensitive surface. The emission board and LED light scheduling were designed according to docking arithmetic, and the operating principle of docking process was analyzed based on these. The simulation experiments were carried out and their results are presented.

  7. Theoretical Studies on Docking Dynamics and Electronic Structure in Metalloprotein Complexes

    Science.gov (United States)

    Sugiyama, Ayumu; Nishikawa, Keigo; Yamamoto, Tetsunori; Purqon, Acep; Nishikawa, Kiyoshi; Nagao, Hidemi

    2007-12-01

    An investigating of docking structure and dynamics between metalloprotein is interested from the viewpoint of searching the function of protein. We investigate the cytochrome c551 and azurin complexes by three computational methods, quantum mechanical calculation, docking searching algorism and molecular dynamics simulation. At first we present the docking structure of the cytochrome c551-azurin complexes expected by ZDOCK searching algorism. Quantum chemical calculation is tools to estimate the charge distrubution around the active site for each protein and force field parameters. From these parameters, we reproduce the protein docking dynamics by molecular dynamics simulation. We analyze some physical properties of complex system such as binding free energy, dynamical cross correlation map, and so on. We discuss the docking stability and dynamical effect of the cytochrome c551-azurin complexes.

  8. Accessible high-throughput virtual screening molecular docking software for students and educators.

    Directory of Open Access Journals (Sweden)

    Reed B Jacob

    2012-05-01

    Full Text Available We survey low cost high-throughput virtual screening (HTVS computer programs for instructors who wish to demonstrate molecular docking in their courses. Since HTVS programs are a useful adjunct to the time consuming and expensive wet bench experiments necessary to discover new drug therapies, the topic of molecular docking is core to the instruction of biochemistry and molecular biology. The availability of HTVS programs coupled with decreasing costs and advances in computer hardware have made computational approaches to drug discovery possible at institutional and non-profit budgets. This paper focuses on HTVS programs with graphical user interfaces (GUIs that use either DOCK or AutoDock for the prediction of DockoMatic, PyRx, DockingServer, and MOLA since their utility has been proven by the research community, they are free or affordable, and the programs operate on a range of computer platforms.

  9. Respiratory load compensation in uremia.

    Science.gov (United States)

    Heinzmann, H G; Kassabian, J; Naqui, M N; Lavietes, M H

    1981-01-01

    The clinical significance of respiratory-system load-compensation is unknown. We have measured the responses to random presentation of single, elastic inspiratory loads in 36 subjects: 8 normal personnel (N), 9 with obesity (O), 10 with chronic renal failure under hemodialysis (H), 5 with pneumonia (P), and 4 with interstitial lung disease (CILD). We have expressed these responses as: (1) the ratio of elastance (or rigidity) of the system during loaded breathing to the elastance without loading (E'RS/ERS); (2) the ratio of tidal volume (VT) achieved when breathing from an inspiratory load to the VT predicted in the absence of load compensation (VTL/VTP); (3) the ratio of inspiratory flow rates during loaded and unloaded breaths; (4) the ratio of inspiratory time of loaded and unloaded breaths. We found E'RS/ERS in the O, H and P groups less than that of either CILD patients or N controls (F = 6.79; p less than 0.001). Passive elastance (ERS) although greater in groups O and H than in N (F = 3.88; p less than 0.025) did not account for the difference i E'RS in all groups. When expressed as VTL/VTP, the response to a 37-cm H2O/l load for groups H, O and P was less than that for N (F = 5.51; p less than 0.05). Diminished inspiratory time was observed in H, O and P patients when inspiring from this load. In contrast, inspiratory flow did not differ from that of normal subjects. Nerve conduction velocity was slightly reduced or normal in the H patients. Respiratory load compensation is deficient in H, O and P patients. The mechanism, which does not involve peripheral neuropathy, is unclear. PMID:7244394

  10. Driver Compensation: Impairment or Improvement?

    Science.gov (United States)

    Young, Richard A

    2015-12-01

    Strayer et al.'s conclusion that their "cognitive distraction scale" for auditory-vocal tasks indicates "significant impairments to driving" is not supported by their data. Additional analysis demonstrates that slower brake reaction times during auditory-vocal tasks were fully compensated for by longer following distances to the lead car. Naturalistic driving data demonstrate that cellular conversation decreases crash risk, the opposite of the article's assumption. Hence, the scale's internal and external validities for indicating driving impairment are highly questionable. PMID:26534851

  11. DC-Compensated Current Transformer.

    Science.gov (United States)

    Ripka, Pavel; Draxler, Karel; Styblíková, Renata

    2016-01-01

    Instrument current transformers (CTs) measure AC currents. The DC component in the measured current can saturate the transformer and cause gross error. We use fluxgate detection and digital feedback compensation of the DC flux to suppress the overall error to 0.15%. This concept can be used not only for high-end CTs with a nanocrystalline core, but it also works for low-cost CTs with FeSi cores. The method described here allows simultaneous measurements of the DC current component. PMID:26805830

  12. Scheduling Trucks in Multi-Door Cross Docking Systems: An Adaptive Genetic Algorithm with a Dispatching Rule

    OpenAIRE

    Byung Soo Kim; Cheol Min Joo

    2015-01-01

    One of the most important operational management problems of a cross docking system is the truck scheduling problem. Cross docking is a logistics management concept in which products delivered to a distribution center by inbound trucks are immediately sorted out, routed and loaded into outbound trucks for delivery to customers. The truck scheduling problem in a multi-door cross docking system considered in this paper comprises the assignment of trucks to dock doors and the determination of do...

  13. ANALISA TEKNIS DAN EKONOMIS SISTEM PERBAIKAN DAUN PROPELLER YANG PATAH PADA KM. MANDIRI DUA TANPA DOCKING

    Directory of Open Access Journals (Sweden)

    Parlindungan Manik

    2012-03-01

    Full Text Available At a sailing in a territorial to sea or river, ship propeller frequently collide object or foreign object which float, causing damage at propeller, throw in the form of curving, crack or broken at propeller blade. When this damage do not improve immediately; repaired will generate harm effect to ship construction or parts of machinery. Therefore ship should be immediately to repair (emergency docking to improve the propeller. But is not easy to get docking space to repair because docking space schedule is very strike, existing graving dock in country. So that ship have to kick one's heels to be able to docking space, which meaning of big loss of time and also expense. The air of this research technical analysis possibility implementation to propeller repairf by floating repair system in territorial water closest with damage location of propeller and compare efficiency economic value and time if repair of propeller done in graving dock or executed by floating repair in graving dock. In this research, repair propeller without docking can be executed by arranging ship trim by arranging ballast tank to be reached space which last for working. Hereinafter worked repair of blade propeller thickly , pitch, aerofoil, wide of blade, obtained mains material type from source which have been collected by either from Owner Surveyor, picture - technique picture and also blade propeller which still goodness. Result of analysis indicate that technically repair of propeller which broken can be executed without docking and economically will be more be efficient up to 700%,in comparison with executed in Graving Dock, and will be more be efficient up to 300% when compared with executed in floating repair system

  14. Finding correct protein–protein docking models using ProQDock

    Science.gov (United States)

    Basu, Sankar; Wallner, Björn

    2016-01-01

    Motivation: Protein–protein interactions are a key in virtually all biological processes. For a detailed understanding of the biological processes, the structure of the protein complex is essential. Given the current experimental techniques for structure determination, the vast majority of all protein complexes will never be solved by experimental techniques. In lack of experimental data, computational docking methods can be used to predict the structure of the protein complex. A common strategy is to generate many alternative docking solutions (atomic models) and then use a scoring function to select the best. The success of the computational docking technique is, to a large degree, dependent on the ability of the scoring function to accurately rank and score the many alternative docking models. Results: Here, we present ProQDock, a scoring function that predicts the absolute quality of docking model measured by a novel protein docking quality score (DockQ). ProQDock uses support vector machines trained to predict the quality of protein docking models using features that can be calculated from the docking model itself. By combining different types of features describing both the protein–protein interface and the overall physical chemistry, it was possible to improve the correlation with DockQ from 0.25 for the best individual feature (electrostatic complementarity) to 0.49 for the final version of ProQDock. ProQDock performed better than the state-of-the-art methods ZRANK and ZRANK2 in terms of correlations, ranking and finding correct models on an independent test set. Finally, we also demonstrate that it is possible to combine ProQDock with ZRANK and ZRANK2 to improve performance even further. Availability and implementation: http://bioinfo.ifm.liu.se/ProQDock Contact: bjornw@ifm.liu.se Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307625

  15. Pointing compensation system for spacecraft instruments

    Science.gov (United States)

    Plescia, Carl T. (Inventor); Gamble, Donald W. (Inventor)

    1987-01-01

    A closed loop system reduces pointing errors in one or more spacecraft instruments. Associated with each instrument is a electronics package (3) for commanding motion in that instrument and a pointing control system (5) for imparting motion in that instrument in response to a command (4) from the commanding package (3). Spacecraft motion compensation logic (25) compensates for instrument pointing errors caused by instrument-motion-induced spacecraft motion. Any finite number of instruments can be so compensated, by providing each pointing control system (5) and each commanding package (3), for the instruments desired to be compensated, with a link to the spacecraft motion compensation logic (25). The spacecraft motion compensation logic (25) is an electronic manifestation of the algebraic negative of a model of the dynamics of motion of the spacecraft. An example of a suitable model, and computer-simulated results, are presented.

  16. How to avoid deferred-compensation troubles.

    Science.gov (United States)

    Freeman, Todd I

    2005-06-01

    Executive compensation packages have long included stock options and deferred compensation plans in order to compete for talent. Last year, Congress passed a law in response to the Enron debacle, in which executives were perceived to be protecting their deferred compensation at the expense of employees, creditors, and investors. The new law is designed to protect companies and their shareholders from being raided by the very executives that guided the company to financial ruin. Physicians who are part owners of medical practices need to know about the changes in the law regarding deferred compensation and how to avoid costly tax penalties. This article discusses how the changes affect medical practices as well as steps physician-owned clinics can take to avoid the risk of penalty, such as freezing deferred compensation and creating a new deferred compensation plan. PMID:16050311

  17. Engineering Compensations in Web Service Environment

    DEFF Research Database (Denmark)

    Schäfer, Micahel; Dolog, Peter; Nejdl, Wolfgang

    2007-01-01

    Business to business integration has recently been performed by employing Web service environments. Moreover, such environments are being provided by major players on the technology markets. Those environments are based on open specifications for transaction coordination. When a failure in such an...... compensations based on forward recovery principles. We extend the existing Web service transaction coordination architecture and infrastructure in order to support flexible compensation operations. A contract-based approach is being used, which allows the specification of permitted compensations at runtime. We...... introduce the abstract service and adapter components which allow us to separate the compensation logic from the coordination logic. In this way, we can easily plug in or plug out different compensation strategies based on a specification language defined on top of basic compensation activities and complex...

  18. Vertical vibration analysis for elevator compensating sheave

    International Nuclear Information System (INIS)

    Most elevators applied to tall buildings include compensating ropes to satisfy the balanced rope tension between the car and the counter weight. The compensating ropes receive tension by the compensating sheave, which is installed at the bottom space of the elevator shaft. The compensating sheave is only suspended by the compensating ropes, therefore, the sheave can move vertically while the car is traveling. This paper shows the elevator dynamic model to evaluate the vertical motion of the compensating sheave. Especially, behavior in emergency cases, such as brake activation and buffer strike, was investigated to evaluate the maximum upward motion of the sheave. The simulation results were validated by experiments and the most influenced factor for the sheave vertical motion was clarified

  19. A comparison of heuristic search algorithms for molecular docking.

    Science.gov (United States)

    Westhead, D R; Clark, D E; Murray, C W

    1997-05-01

    This paper describes the implementation and comparison of four heuristic search algorithms (genetic algorithm, evolutionary programming, simulated annealing and tabu search) and a random search procedure for flexible molecular docking. To our knowledge, this is the first application of the tabu search algorithm in this area. The algorithms are compared using a recently described fast molecular recognition potential function and a diverse set of five protein-ligand systems. Statistical analysis of the results indicates that overall the genetic algorithm performs best in terms of the median energy of the solutions located. However, tabu search shows a better performance in terms of locating solutions close to the crystallographic ligand conformation. These results suggest that a hybrid search algorithm may give superior results to any of the algorithms alone. PMID:9263849

  20. Robot Docking Based on Omnidirectional Vision and Reinforcement Learning

    Science.gov (United States)

    Muse, David; Weber, Cornelius; Wermter, Stefan

    We present a system for visual robotic docking using an omnidirectional camera coupled with the actor critic reinforcement learning algorithm. The system enables a PeopleBot robot to locate and approach a table so that it can pick an object from it using the pan-tilt camera mounted on the robot. We use a staged approach to solve this problem as there are distinct sub tasks and different sensors used. Starting with random wandering of the robot until the table is located via a landmark, and then a network trained via reinforcement allows the robot to rum to and approach the table. Once at the table the robot is to pick the object from it. We argue that our approach has a lot of potential allowing the learning of robot control for navigation removing the need for internal maps of the environment. This is achieved by allowing the robot to learn couplings between motor actions and the position of a landmark.

  1. Synthesis, Evaluation and Docking studies of Cholecalciferol Derivative

    Directory of Open Access Journals (Sweden)

    Sultanat

    2014-09-01

    Full Text Available Improved synthesis of 3b-acetoxy-9, 10-seco-19, 8(8-spiro-5(10, 6-cholestadiene has been reported after reacting cholecalciferol acetate with dimethylbutadiene by incorporating BF3·OEt2, SnCl4, ZnBr2, p-TsOH in toluene under Diels-Alder condition to get better yields. Agarose gel electrophoresis showed the potential in vitro DNA damaging nature while as the comet assay depicted the genotoxic nature by mobilizing the tail of the comet in lymphocytes. The molecular docking depicted the intercalation of steroid derivative with minor groove of the DNA molecule and in this configuration the phosphodiester bond of DNA stabilizes the acetoxy group. The bioactivity score and PASS software analysis confirmed the potential physicochemical features of the compound to act as active drug.

  2. Planification des opérations de cross-docking

    OpenAIRE

    Ladier, Anne-Laure; Alpan, Gülgün

    2014-01-01

    Les plateformes de cross-docking permettent d'accélérer les flux logistiques : les produits y sont déchargés, triés et rechargés dans les camions sans stockage intermédiaire. Nous nous intéressons à un problème de planification des opérations dans une telle plateforme, en supposant que les transporteurs communiquent à l'avance leurs créneaux de présence préférés. Outre la modélisation du problème par un programme linéaire, nous proposons deux heuristiques qui décomposent le problème et permet...

  3. SYNTHESIS, DOCKING STUDIES AND ANTIOXIDANT ACTIVITY OF TETRAPEPTIDE FGVY

    Directory of Open Access Journals (Sweden)

    Md. Abdulla

    2011-03-01

    Full Text Available A rational designing of linear Tetrapeptide FGVY was done and was synthesized by solution phase peptide synthesis. The docking studies of designed linear tetrapeptide FGVY was carried out by using Schrodinger Software Solutions, USA. Qikprop results show the ligand FGVY mostly act as antihypertensive and anti coagulant properties. The solution phase synthesis of FGVY is carried out by using Dicyclohexyl carbodiimide (DCC as coupling agents and triethyl amine as base. Structure of synthesized FGVY was confirmed by FTIR, 1H NMR and Mass spectral data, and evaluated for antioxidant property by using 1,1-diphenyl-2-picryl-hydrazil (DPPH. method and the synthesized peptides FGVY possess moderate antioxidant activity.

  4. FACILE SYNTHESIS, DOCKING STUDIES AND ANTIOXIDANT ACTIVITY OF FGVR

    Directory of Open Access Journals (Sweden)

    Himaja M

    2011-08-01

    Full Text Available A rational designing of linear Tetrapeptide FGVR was done and was synthesized by solution phase peptide synthesis. The docking studies of designed linear tetrapeptide FGVR was carried out by using Schrodinger Software Solutions, USA. Qikprop results show the ligand FGVR mostly act as antihypertensive and anti coagulant properties. The solution phase synthesis of FGVR is carried out by using 1-Ethyl-3-(3-dimethylaminopropyl carbodiimide (EDC as coupling agents and N-Methyl morpholine (NMM as base. Structure of synthesized FGVR was confirmed by FTIR, 1H NMR and Mass spectral data, and evaluated for antioxidant property by using 1,1-diphenyl-2-picryl-hydrazil (DPPH. method and the synthesized peptides FGVR possess moderate antioxidant activity.

  5. A New Interpretation of Compensate Effect

    CERN Document Server

    Shao, M X

    2000-01-01

    A new interpretation of compensate effect is presented. The Hawking effect in general space-time can be taken as a compensate effect of the scale transformation of coordinate time on the horizon in generalized tortoise coordinates transformation. It is proved that the Hawking temperature is the pure gauge of compensate field in tortoise coordinates. This interpretation does not refer to a zero-temperature space-time.

  6. Compensation consultants and CEO pay: UK evidence

    OpenAIRE

    Voulgaris, Georgios; Stathopoulos, Konstantinos; Walker, Martin

    2010-01-01

    International audience Manuscript type: Empirical Research Question/ Issue: This paper provides new evidence on the effect of compensation consultants on CEO pay. Research Findings/ Insights: We produce new evidence on the managerial power approach (MPA) to corporate governance by examining the influence of compensation consultants on CEO pay structures and the decision to hire a compensation consultant in the UK. We find evidence that is not consistent with the MPA. Contrary to the MPA pr...

  7. Compensation for earnings risk under worker heterogeneity

    OpenAIRE

    Berkhout, P.; Hartog, J.; Webbink, D.

    2006-01-01

    We use two large Dutch datasets to estimate the Risk Augmented Mincer equation and test for risk compensation in expected earnings. We replicate earlier findings of a positive premium for risk and a negative premium for skew and add confirmation of the key results if we control for individual ability. We find that immigrants have graduated in more risky educations but obtain identical risk compensation. Among recent graduates, women receive higher risk compensation than men, consistent with t...

  8. Securitization and Compensation in Financial Institutions

    OpenAIRE

    Inderst, Roman; Pfeil, Sebastian

    2010-01-01

    We analyze the interaction between financial institutions' internal compensation policy, the quality of loans, and their securitization decision. We also assess the case for requiring financial institutions to defer bonus pay so as to make incentives more commensurate with the longer-term risk of their transactions. While mandatory deferred compensation can improve the quality of loans, we also show when it has the opposite effect. We further analyze when mandatory deferred compensation can c...

  9. Loss Aversion, Stochastic Compensation, and Team Incentives

    OpenAIRE

    Kohei Daido; Takeshi Murooka

    2013-01-01

    We investigate moral-hazard problems with limited liability where agents have expectation-based reference-dependent preferences. We show that stochastic compensation for low performance can be optimal. Because of loss aversion, the agents have first-order risk aversion to wage uncertainty. This causes the agents to work harder when their low performance is stochastically compensated. We also examine team incentives for credibly employing such stochastic compensation. In an optimal contract, l...

  10. Extended frequency compensation of a diamagnetic loop

    International Nuclear Information System (INIS)

    A method of compensation for a diamagnetic loop that is magnetically coupled to a concentric stainless-steel vacuum vessel is presented. This compensation method accounts for imperfect magnetic coupling between the vessel eddy currents, the diamagnetic loop, and the plasma diamagnetic currents, and it also corrects for a finite loading resistance on the diamagnetic loop. A procedure for adjusting and calibrating the active-filter compensation circuit is presented. It can be applied to internal or external diamagnetic loops. (author)

  11. Enthalpy-entropy compensation in protein unfolding

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Enthalpy-entropy compensation was found to be a universal law in protein unfolding based on over 3 000 experimental data. Water molecular reorganization accompanying the protein unfolding was suggested as the origin of the enthalpy-entropy compensation in protein unfolding. It is indicated that the enthalpy-entropy compensation constitutes the physical foundation that satisfies the biological need of the small free energy changes in protein unfolding, without the sacrifice of the bio-diversity of proteins. The enthalpy-entropy compensation theory proposed herein also provides valuable insights into the Privalov's puzzle of enthalpy and entropy convergence in protein unfolding.

  12. Lithium compensation for full cell operation

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Jie; Zheng, Jianming; Chen, Xilin; Lu, Dongping; Liu, Jun; Jiguang, Jiguang

    2016-05-17

    Disclosed herein are embodiments of a lithium-ion battery system comprising an anode, an anode current collector, and a layer of lithium metal in contact with the current collector, but not in contact with the anode. The lithium compensation layer dissolves into the electrolyte to compensate for the loss of lithium ions during usage of the full cell. The specific placement of the lithium compensation layer, such that there is no direct physical contact between the lithium compensation layer and the anode, provides certain advantages.

  13. Dispersion compensation for attosecond electron pulses

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, Peter; Baumgarten, Cory; Batelaan, Herman; Centurion, Martin [Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588 (United States)

    2012-08-20

    We propose a device to compensate for the dispersion of attosecond electron pulses. The device uses only static electric and magnetic fields and therefore does not require synchronization to the pulsed electron source. Analogous to the well-known optical dispersion compensator, an electron dispersion compensator separates paths by energy in space. Magnetic fields are used as the dispersing element, while a Wien filter is used for compensation of the electron arrival times. We analyze a device with a size of centimeters, which can be applied to ultrafast electron diffraction and microscopy, and fundamental studies.

  14. Polarization-based compensation of astigmatism

    Science.gov (United States)

    Chowdhury, Dola Roy; Bhattacharya, Kallol; Chakraborty, Ajay K.; Ghosh, Raja

    2004-02-01

    One approach to aberration compensation of an imaging system is to introduce a suitable phase mask at the aperture plane of an imaging system. We utilize this principle for the compensation of astigmatism. A suitable polarization mask used on the aperture plane together with a polarizer-retarder combination at the input of the imaging system provides the compensating polarization-induced phase steps at different quadrants of the apertures masked by different polarizers. The aberrant phase can be considerably compensated by the proper choice of a polarization mask and suitable selection of the polarization parameters involved. The results presented here bear out our theoretical expectation.

  15. Undulator with dynamic compensation of magnetic forces

    Energy Technology Data Exchange (ETDEWEB)

    Gluskin, Efim; Trakhtenberg, Emil; Xu, Joseph Z.

    2016-05-31

    A method and apparatus for implementing dynamic compensation of magnetic forces for undulators are provided. An undulator includes a respective set of magnet arrays, each attached to a strongback, and placed on horizontal slides and positioned parallel relative to each other with a predetermined gap. Magnetic forces are compensated by a set of compensation springs placed along the strongback. The compensation springs are conical springs having exponential-force characteristics that substantially match undulator magnetic forces independently of the predetermined gap. The conical springs are positioned along the length of the magnets.

  16. Docking-complex-independent alignment of Chlamydomonas outer dynein arms with 24-nm periodicity in vitro.

    Science.gov (United States)

    Oda, Toshiyuki; Abe, Tatsuki; Yanagisawa, Haruaki; Kikkawa, Masahide

    2016-04-15

    The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to be a 24-nm molecular ruler because ODAs align along the DMTs with 24-nm periodicity. In this study, we rigorously tested this hypothesis using structural and genetic methods. We found that the ODAs can bind to DMTs and porcine microtubules with 24-nm periodicities even in the absence of the docking complexin vitro Using cryo-electron tomography and structural labeling, we observed that the docking complex took an unexpectedly flexible conformation and did not lie along the length of DMTs. In the absence of docking complex, ODAs were released from the DMT at relatively low ionic strength conditions, suggesting that the docking complex strengthens the electrostatic interactions between the ODA and DMT. Based on these results, we conclude that the docking complex serves as a flexible stabilizer of the ODA rather than as a molecular ruler. PMID:26933181

  17. NASA Docking System (NDS) Interface Definitions Document (IDD). Revision C, Nov. 2010

    Science.gov (United States)

    2010-01-01

    The NASA Docking System (NDS) mating system supports low approach velocity docking and provides a modular and reconfigurable standard interface, supporting crewed and autonomous vehicles during mating and assembly operations. The NDS is NASA's implementation for the emerging International Docking System Standard (IDSS) using low impact docking technology. All NDS configurations can mate with the configuration specified in the IDSS Interface Definition Document (IDD) released September 21, 2010. The NDS evolved from the Low Impact Docking System (LIDS). The acronym international Low Impact Docking System (iLIDS) is also used to describe this system. NDS and iLIDS may be used interchangeability. Some of the heritage documentation and implementations (e.g., software command names) used on NDS will continue to use the LIDS acronym. The NDS IDD defines the interface characteristics and performance capability of the NDS, including uses ranging from crewed to autonomous space vehicles and from low earth orbit to deep space exploration. The responsibility for developing space vehicles and for making them technically and operationally compatible with the NDS rests with the vehicle providers. Host vehicle examples include crewed/uncrewed spacecraft, space station modules, elements, etc. Within this document, any docking space vehicle will be referred to as the host vehicle. This document defines the NDS-to-NDS interfaces, as well as the NDS-to-host vehicle interfaces and performance capability.

  18. GPCR-Bench: A Benchmarking Set and Practitioners' Guide for G Protein-Coupled Receptor Docking.

    Science.gov (United States)

    Weiss, Dahlia R; Bortolato, Andrea; Tehan, Benjamin; Mason, Jonathan S

    2016-04-25

    Virtual screening is routinely used to discover new ligands and in particular new ligand chemotypes for G protein-coupled receptors (GPCRs). To prepare for a virtual screen, we often tailor a docking protocol that will enable us to select the best candidates for further screening. To aid this, we created GPCR-Bench, a publically available docking benchmarking set in the spirit of the DUD and DUD-E reference data sets for validation studies, containing 25 nonredundant high-resolution GPCR costructures with an accompanying set of diverse ligands and computational decoy molecules for each target. Benchmarking sets are often used to compare docking protocols; however, it is important to evaluate docking methods not by "retrospective" hit rates but by the actual likelihood that they will produce novel prospective hits. Therefore, docking protocols must not only rank active molecules highly but also produce good poses that a chemist will select for purchase and screening. Currently, no simple objective machine-scriptable function exists that can do this; instead, docking hit lists must be subjectively examined in a consistent way to compare between docking methods. We present here a case study highlighting considerations we feel are of importance when evaluating a method, intended to be useful as a practitioners' guide. PMID:26958710

  19. Reduced DOCK4 expression leads to erythroid dysplasia in myelodysplastic syndromes.

    Science.gov (United States)

    Sundaravel, Sriram; Duggan, Ryan; Bhagat, Tushar; Ebenezer, David L; Liu, Hui; Yu, Yiting; Bartenstein, Matthias; Unnikrishnan, Madhu; Karmakar, Subhradip; Liu, Ting-Chun; Torregroza, Ingrid; Quenon, Thomas; Anastasi, John; McGraw, Kathy L; Pellagatti, Andrea; Boultwood, Jacqueline; Yajnik, Vijay; Artz, Andrew; Le Beau, Michelle M; Steidl, Ulrich; List, Alan F; Evans, Todd; Verma, Amit; Wickrema, Amittha

    2015-11-17

    Anemia is the predominant clinical manifestation of myelodysplastic syndromes (MDS). Loss or deletion of chromosome 7 is commonly seen in MDS and leads to a poor prognosis. However, the identity of functionally relevant, dysplasia-causing, genes on 7q remains unclear. Dedicator of cytokinesis 4 (DOCK4) is a GTPase exchange factor, and its gene maps to the commonly deleted 7q region. We demonstrate that DOCK4 is underexpressed in MDS bone marrow samples and that the reduced expression is associated with decreased overall survival in patients. We show that depletion of DOCK4 levels leads to erythroid cells with dysplastic morphology both in vivo and in vitro. We established a novel single-cell assay to quantify disrupted F-actin filament network in erythroblasts and demonstrate that reduced expression of DOCK4 leads to disruption of the actin filaments, resulting in erythroid dysplasia that phenocopies the red blood cell (RBC) defects seen in samples from MDS patients. Reexpression of DOCK4 in -7q MDS patient erythroblasts resulted in significant erythropoietic improvements. Mechanisms underlying F-actin disruption revealed that DOCK4 knockdown reduces ras-related C3 botulinum toxin substrate 1 (RAC1) GTPase activation, leading to increased phosphorylation of the actin-stabilizing protein ADDUCIN in MDS samples. These data identify DOCK4 as a putative 7q gene whose reduced expression can lead to erythroid dysplasia. PMID:26578796

  20. Proposed docking interface between peptidoglycan and the target recognition domain of zoocin A

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yinghua [Department of Chemistry, University of Alabama, Tuscaloosa, AL 35487 (United States); Simmonds, Robin S. [Department of Microbiology and Immunology, University of Otago, Dunedin (New Zealand); Timkovich, Russell, E-mail: rtimkovi@bama.ua.edu [Department of Chemistry, University of Alabama, Tuscaloosa, AL 35487 (United States)

    2013-11-15

    Highlights: •Peptidoglycan added to zoocin rTRD perturbs NMR resonances around W115. •Simulations predict docking to a shallow surface groove near W115. •The docking interface is similar to mammalian antibody–antigen sites. •EDTA binds to a distinct surface site. -- Abstract: A docking model is proposed for the target recognition domain of the lytic exoenzyme zoocin A with the peptidoglycan on the outer cell surface of sensitive bacterial strains. Solubilized fragments from such peptidoglycans perturb specific backbone and side chain amide resonances in the recombinant form of the domain designated rTRD as detected in two-dimensional {sup 1}H–{sup 15}N correlation NMR spectra. The affected residues comprise a shallow surface cleft on the protein surface near W115, N53, N117, and Q105 among others, which interacts with the peptide portion of the peptidoglycan. Calculations with AutoDock Vina provide models of the docking interface. There is approximate homology between the rTDR-peptidoglycan docking site and the antigen binding site of Fab antibodies with the immunoglobin fold. EDTA was also found to bind to rTRD, but at a site distinct from the proposed peptidoglycan docking site.

  1. ASPDock: protein-protein docking algorithm using atomic solvation parameters model

    Directory of Open Access Journals (Sweden)

    Liu Shiyong

    2011-01-01

    Full Text Available Abstract Background Atomic Solvation Parameters (ASP model has been proven to be a very successful method of calculating the binding free energy of protein complexes. This suggests that incorporating it into docking algorithms should improve the accuracy of prediction. In this paper we propose an FFT-based algorithm to calculate ASP scores of protein complexes and develop an ASP-based protein-protein docking method (ASPDock. Results The ASPDock is first tested on the 21 complexes whose binding free energies have been determined experimentally. The results show that the calculated ASP scores have stronger correlation (r ≈ 0.69 with the binding free energies than the pure shape complementarity scores (r ≈ 0.48. The ASPDock is further tested on a large dataset, the benchmark 3.0, which contain 124 complexes and also shows better performance than pure shape complementarity method in docking prediction. Comparisons with other state-of-the-art docking algorithms showed that ASP score indeed gives higher success rate than the pure shape complementarity score of FTDock but lower success rate than Zdock3.0. We also developed a softly restricting method to add the information of predicted binding sites into our docking algorithm. The ASP-based docking method performed well in CAPRI rounds 18 and 19. Conclusions ASP may be more accurate and physical than the pure shape complementarity in describing the feature of protein docking.

  2. GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing.

    Directory of Open Access Journals (Sweden)

    Ye Fang

    Full Text Available Computational modeling of drug binding to proteins is an integral component of direct drug design. Particularly, structure-based virtual screening is often used to perform large-scale modeling of putative associations between small organic molecules and their pharmacologically relevant protein targets. Because of a large number of drug candidates to be evaluated, an accurate and fast docking engine is a critical element of virtual screening. Consequently, highly optimized docking codes are of paramount importance for the effectiveness of virtual screening methods. In this communication, we describe the implementation, tuning and performance characteristics of GeauxDock, a recently developed molecular docking program. GeauxDock is built upon the Monte Carlo algorithm and features a novel scoring function combining physics-based energy terms with statistical and knowledge-based potentials. Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU. First, we carried out a thorough performance tuning of the high-level framework and the docking kernel to produce a fast serial code, which was then ported to shared-memory multi-core CPUs yielding a near-ideal scaling. Further, using Xeon Phi gives 1.9× performance improvement over a dual 10-core Xeon CPU, whereas the best GPU accelerator, GeForce GTX 980, achieves a speedup as high as 3.5×. On that account, GeauxDock can take advantage of modern heterogeneous architectures to considerably accelerate structure-based virtual screening applications. GeauxDock is open-sourced and publicly available at www.brylinski.org/geauxdock and https://figshare.com/articles/geauxdock_tar_gz/3205249.

  3. GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing.

    Science.gov (United States)

    Fang, Ye; Ding, Yun; Feinstein, Wei P; Koppelman, David M; Moreno, Juana; Jarrell, Mark; Ramanujam, J; Brylinski, Michal

    2016-01-01

    Computational modeling of drug binding to proteins is an integral component of direct drug design. Particularly, structure-based virtual screening is often used to perform large-scale modeling of putative associations between small organic molecules and their pharmacologically relevant protein targets. Because of a large number of drug candidates to be evaluated, an accurate and fast docking engine is a critical element of virtual screening. Consequently, highly optimized docking codes are of paramount importance for the effectiveness of virtual screening methods. In this communication, we describe the implementation, tuning and performance characteristics of GeauxDock, a recently developed molecular docking program. GeauxDock is built upon the Monte Carlo algorithm and features a novel scoring function combining physics-based energy terms with statistical and knowledge-based potentials. Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU). First, we carried out a thorough performance tuning of the high-level framework and the docking kernel to produce a fast serial code, which was then ported to shared-memory multi-core CPUs yielding a near-ideal scaling. Further, using Xeon Phi gives 1.9× performance improvement over a dual 10-core Xeon CPU, whereas the best GPU accelerator, GeForce GTX 980, achieves a speedup as high as 3.5×. On that account, GeauxDock can take advantage of modern heterogeneous architectures to considerably accelerate structure-based virtual screening applications. GeauxDock is open-sourced and publicly available at www.brylinski.org/geauxdock and https://figshare.com/articles/geauxdock_tar_gz/3205249. PMID:27420300

  4. Temperature-compensated induction extensometer

    International Nuclear Information System (INIS)

    A linear displacement transducer, or extensometer, has been designed and constructed to measure displacements over a range of 0--150 mm. The transducer works by electromagnetic induction and consists of a bifilar coil coaxial with two conducting cylinders, one inside and the other outside the coil. The induction extensometer has been designed to eliminate errors caused by temperature changes from 00 to 10000C. Experimental measurements show an error of 1 mm over the 150-mm displacement range for a temperature change of 5000C, and the error should not be larger over the full 10000C temperature range. The displacement range can be varied from 2.5 to 250 mm by scaling the entire experiment up or down, and the temperature compensation can be made for any temperature range that is compatible with the constructional materials

  5. SIS junction reactance complete compensation

    International Nuclear Information System (INIS)

    SIS junction geometrical capacitance together with out of phase current Ikk impedance component forms sufficient junction reactance XSIS = (ωC + BQ)-1. This paper suggests the way to resonate out both ωC and BQ by using additional identical SIS junction connected to the first through a long line impedance inverter and RF + DC biased symmetrically to the first. Pumped IV curves without quantum reactance and frequency impedance patterns of the system were calculated. Calculations demonstrated the presence of high and even negative induced dynamic resistance regions at high order quasiparticle steps for the case of SIS junction reactance complete compensation. The suggested method may be used in SIS mixers and detectors for a better RF matching

  6. Compensated takings and negotiated solutions

    International Nuclear Information System (INIS)

    More than 30 year ago, the USA began protecting its environment with regulatory laws. However, this approach has progressed to the point where our economic health may have needlessly incurred long-term damage. The article explores the implications of a resurgent demand for legal guarantees for compensation when environmental regulations take individual property. What will happen when a price tag is attached to new or existing environmental laws? Some predict dire results; however, a more balanced and efficient policy may lie ahead. The discussion explores the implications of recent rulings, describes possible outcomes, and offers several alternatives to the traditional lobby-and-appeal tactics used in setting environmental policy. The authors conclude that as the concept of a regulatory taking is restored, more innovative negotiated solutions will take place between competing interests as they are given more equal legal footing

  7. Compensation for incoherent ground motion

    International Nuclear Information System (INIS)

    The power spectrum density and coherence function for ground motions are studied for the construction of the next generation electron-positron linear collider. It should provide a center of mass energy between 500 GeV-1 TeV with luminosity as high as 1033 to 1034 cm-2 sec-1. Since the linear collider has a relatively slow repetition rate, large number of particles and small sizes of the beam should be generated and preserved in the machine to obtain the required high luminosity. One of the most critical parameters is the extremely small vertical beam size at the interaction point, thus a proper alignment system for the focusing and accelerating elements of the machine is necessary to achieve the luminosity. We describe recent observed incoherent ground motions and an alignment system to compensate the distortion by the ground motions. (authors)

  8. A holistic molecular docking approach for predicting protein-protein complex structure

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

  9. Protein-protein docking using region-based 3D Zernike descriptors

    Directory of Open Access Journals (Sweden)

    Sael Lee

    2009-12-01

    Full Text Available Abstract Background Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. Results We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-αRMSD ≤ 2.5 Å within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. Conclusion We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for

  10. Docking System Design and Self-Assembly Control of Distributed Swarm Flying Robots

    Directory of Open Access Journals (Sweden)

    Hongxing Wei

    2012-11-01

    Full Text Available This paper presents a novel docking system design and the distributed self‐assembly control strategy for a Distributed Swarm Flying Robot (DSFR. The DSFR is a swarm robot comprising many identical robot modules that are able to move on the ground, dock with each other and fly coordinately once self‐assembled into a robotic structure. A generalized adjacency matrix method is proposed to describe the configurations of robotic structures. Based on the docking system and the adjacency matrix, experiments are performed to demonstrate and verify the self‐assembly control strategy.

  11. The Dock-in Model of music culture and cross-cultural perception

    OpenAIRE

    Fritz, T.

    2013-01-01

    This paper proposes a model that aims to illustrate how different human music cultures intersect and “dock in” to a set of music features that are universally perceived, while also displaying culture-specific features that must be learned. The model emphasizes that over historic time the music in a given culture can “dock into” and “dock out of” cues that are universally perceived, shifting its potential for cross-cultural perception and interaction. While this model accounts for music ethnol...

  12. JL-2: A Mobile Multi-robot System with Docking and Manipulating Capabilities

    OpenAIRE

    Wei Wang; Wenpeng Yu; Houxiang Zhang

    2010-01-01

    This paper presents a new version of the JL series reconfigurable multi-robot system called JL-2. By virtue of the docking manipulator composed of a parallel mechanism and a cam gripper, every mobile robot in the JL-2 system is able to not only perform tasks in parallel, e.g. moving and grasping, but also dock with each other even if there are large misalignments between two robots. A motorized spherical joint is formed between two docked robots to enhance the locomotion capability of JL-2. T...

  13. HexServer: an FFT-based protein docking server powered by graphics processors

    OpenAIRE

    Macindoe, Gary; Mavridis, Lazaros; Venkatraman, Vishwesh; Devignes, Marie-Dominique; Ritchie, David

    2010-01-01

    HexServer (http://hexserver.loria.fr/) is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical 6D docking run takes similar to 15 s, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions. The server requires two protein structures in PDB format to be uploaded, and it produces a ranked list of up to 1000...

  14. Vehicle Routing Problem for Fashion Supply Chains with Cross-Docking

    OpenAIRE

    Zhi-Hua Hu; Yingxue Zhao; Tsan-Ming Choi

    2013-01-01

    Cross-docking, as a strategy to reduce lead time and enhance the efficiency of the fashion supply chain, has attracted substantial attention from both the academy and the industry. Cross-docking is a critical part of many fashion and textiles supply chains in practice because it can help to achieve many supply chain strategies such as postponement. We consider a model where there are multiple suppliers and customers in a single cross-docking center. With such a model setting, the issue concer...

  15. Virtual screening of plant derived compounds for aldose reductase inhibition using molecular docking.

    Science.gov (United States)

    Muppalaneni, Naresh Babu; Rao, Allam Appa

    2012-01-01

    The role of the aldose reductase in type 2 diabetes is widely described. Therefore, it is of interest to identify plant derived compounds to inhibit its activity. We studied the protein-ligand interaction of 267 compounds from different parts of seven plants (Allium sativum, Coriandrum sativum, Dacus carota, Murrayyakoneigii, Eucalyptus, Calendula officinalis and Lycopersicon esculentum) with aldose reductase as the target protein. Molecular docking and re-scoring of top ten compounds (using GOLD, AutoDock Vina, eHiTS, PatchDock and MEDock) followed by rank-sum technique identified compound allium38 with high binding affinity for aldose reductase. PMID:23275691

  16. 38 CFR 3.351 - Special monthly dependency and indemnity compensation, death compensation, pension and spouse's...

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Special monthly dependency and indemnity compensation, death compensation, pension and spouse's compensation ratings. 3.351 Section 3.351 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS ADJUDICATION...

  17. 76 FR 49398 - Non-Discrimination in Compensation; Compensation Data Collection Tool

    Science.gov (United States)

    2011-08-10

    ... Compensation; Compensation Data Collection Tool AGENCY: Office of Federal Contract Compliance Programs. ACTION... on the development and implementation of a compensation data collection tool. Possible uses for the... from interested parties as early as possible in the development process of this new data...

  18. 75 FR 49595 - Performance of Functions; Claims for Compensation Under the Federal Employees' Compensation Act...

    Science.gov (United States)

    2010-08-13

    ... any comments by mail early. Comments on the proposed rule will be available for public inspection... regarding types and manner of transport allowed. Directed Medical Examinations Section 10.320 has been...; Claims for Compensation Under the Federal Employees' Compensation Act; Compensation for Disability...

  19. Multiple Compensation Consultants and CEO Pay

    NARCIS (Netherlands)

    Kabir, Rezaul; Minhat, Marizah

    2010-01-01

    The study examines the practice of employing multiple compensation consultants. Data for a sample of UK companies over the period 2003-2006 are analyzed using a variety of econometric methods. We find that CEOs receive higher equity-based pay when firms employ more than one compensation consultant.

  20. Tilt/Integral/Derivative Compensators For Controllers

    Science.gov (United States)

    Lurie, Boris J.

    1995-01-01

    Tilt/integral/derivative (TID) compensators for tunable feedback control systems offer advantages over proportional/integral/derivative compensators. Designed and adjusted more easily, and made to reject disturbances more strongly and less sensitive to variations in parameters of controlled system.

  1. Analytic compensation methods in dynamic tomography

    International Nuclear Information System (INIS)

    Recent progresses in X-ray tomography allow to study some organs dynamically. The aim of this work is to analyze the deformation compensation algorithms used to integrate dynamical evolution models into the image reconstruction processes. An exact and efficient analytical method of movement compensation is presented and applied to simulated data. Abstract only. (J.S.)

  2. A brief history of dosage compensation

    Indian Academy of Sciences (India)

    Stanley M. Gartler

    2014-08-01

    In 1914, H. J. Muller postulated the origin of the Y chromosome as having resulted from restricted recombination between homologous sex chromosomes in the male and the accumulation of deleterious mutations. This evolutionary process leads to dosage compensation. This article lays out a brief history of dosage compensation in genetics.

  3. Options in Compensation: Promises and Pitfalls

    DEFF Research Database (Denmark)

    Flor, Christian Riis; Frimor, Hans; Munk, Claus

    2014-01-01

    We derive the optimal compensation contract in a principal–agent setting in which outcome is used to provide incentives for both effort and risky investments. To motivate investment, optimal compensation entails rewards for high as well as low outcomes, and it is increasing at the mean outcome to...

  4. Reinventing Teacher Compensation Systems. CPRE Finance Briefs.

    Science.gov (United States)

    Kelley, Carolyn; Odden, Allan

    Other organizations in the United States have successfully implemented new compensation structures. This publication argues that it is time for education to join these successful efforts and revise teacher-pay systems. The brief provides a short history of changes in teacher compensation over the last century and a discussion of key organizational…

  5. Motion compensator for holographic motion picture camera

    Science.gov (United States)

    Kurtz, R. L.

    1973-01-01

    When reference beam strikes target it undergoes Doppler shift dependent upon target velocity. To compensate, object beam is first reflected from rotating cylinder that revolves in direction opposite to target but at same speed. When beam strikes target it is returned to original frequency and is in phase with reference beam. Alternatively this motion compensator may act on reference beam.

  6. Gravitational compensation for the LISA pathfinder

    International Nuclear Information System (INIS)

    This paper addresses the problem of compensating self-gravity for the LISA Technology Package. Massive components onboard the spacecraft produce a gravitational imbalance on the free-falling test masses. We present here a compensation scheme to reduce the gravitational forces, torques, stiffness and cross-talk to values within requirements. Gravitational analysis and subsequent compensation are needed to limit the gravitational imbalances in order to reduce the force noise and force gradients associated with the electrostatic actuation that must compensate any residual gravitational imbalances. Starting from an educated guess based on simple Newtonian arguments, we present the approximate shapes of a compensation block solution which minimizes the residual gravitational imbalance and stiffness while adding a minimum of mass

  7. Gravitational compensation for the LISA pathfinder

    Energy Technology Data Exchange (ETDEWEB)

    Armano, M [Dipartimento di Fisica, Universita di Trento and INFN, Sezione di Padova, Gruppo Collegato di Trento, I-38050, Povo, Trento (Italy); Dipartimento di Fisica, Universita degli Studi dell' Insubria, via Valleggio, 11, 22100 Como (Italy); Bortoluzzi, D [Dipartimento di Ingegneria Meccanica Strutturale, Universita di Trento, Mesiano, Trento (Italy); Hoyle, C D [Dipartimento di Fisica, Universita di Trento and INFN, Sezione di Padova, Gruppo Collegato di Trento, I-38050, Povo, Trento (Italy); Vitale, S [Dipartimento di Fisica, Universita di Trento and INFN, Sezione di Padova, Gruppo Collegato di Trento, I-38050, Povo, Trento (Italy)

    2005-05-21

    This paper addresses the problem of compensating self-gravity for the LISA Technology Package. Massive components onboard the spacecraft produce a gravitational imbalance on the free-falling test masses. We present here a compensation scheme to reduce the gravitational forces, torques, stiffness and cross-talk to values within requirements. Gravitational analysis and subsequent compensation are needed to limit the gravitational imbalances in order to reduce the force noise and force gradients associated with the electrostatic actuation that must compensate any residual gravitational imbalances. Starting from an educated guess based on simple Newtonian arguments, we present the approximate shapes of a compensation block solution which minimizes the residual gravitational imbalance and stiffness while adding a minimum of mass.

  8. Ownership Concentration, Top Management and Board Compensation

    Directory of Open Access Journals (Sweden)

    Marcos Barbosa Pinto

    2013-05-01

    Full Text Available The degree of ownership concentration may influence executive and board compensation (Bebchuk & Fried, 2003. This article analyzes this relationship. Detailed information about top management and board compensation became available starting in 2010 through new Securities Commission filings. Linear regression models applied to a sample of 315 Brazilian companies traded on the national exchange indicate a negative and statistically significant economic correlation between executive compensation and the degree of ownership concentration. Ceteris paribus, companies with a lower degree of ownership concentration pay higher compensation to top executives. Family controlled companies pay more to their chief executive, but not to the managerial team as a whole, and the compensation of directors increases with a greater proportion of control group members or their relatives on the board. There was support for the Managerial Power Hypothesis in companies with a lower degree of ownership concentration and for the extraction of private benefits in companies where it is greater.

  9. Rectangular Laser Resonators with Astigmatic Compensation

    DEFF Research Database (Denmark)

    Skettrup, Torben

    2005-01-01

    An investigation of rectangular resonators with a view to the compensation of astigmatism has been performed. In order to have beam waists placed at the same positions in the tangential and sagittal planes, pairs of equal mirrors were considered. It was found that at least two concave mirrors are...... necessary to obtain compensation. Four-concave-mirror systems are most stable close to the quadratic geometry, although the symmetric quadratic resonator itself cannot be compensated for astigmatism. Using four equal concave mirrors, compensation of astigmatism can be obtained in two arms at the same time....... Usually several stability ranges are found for four-mirror resonators with pair-wise equal mirrors, and it is possible with these systems to obtain small compensated beam waist radii suitable for frequency conversion. Relevant formulae are given and several relevant examples are shown using simulation...

  10. Docks and Piers, Fishing Piers in, Published in unknown, Manatee County Information Services Dept..

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Docks and Piers dataset as of unknown. It is described as 'Fishing Piers in'. Data by this publisher are often provided in State Plane coordinate system; in a...

  11. A Ground Testbed to Advance US Capability in Autonomous Rendezvous and Docking Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The entire Agency supports development of a Commodity for Autonomous Rendezvous and Docking (CARD) as outlined in the Agency-wide Community of Practice whitepaper...

  12. Actin- and Myosin-Dependent Vesicle Loading of Presynaptic Docking Sites Prior to Exocytosis.

    Science.gov (United States)

    Miki, Takafumi; Malagon, Gerardo; Pulido, Camila; Llano, Isabel; Neher, Erwin; Marty, Alain

    2016-08-17

    Variance analysis of postsynaptic current amplitudes suggests the presence of distinct docking sites (also called release sites) where vesicles pause before exocytosis. Docked vesicles participate in the readily releasable pool (RRP), but the relation between docking site number and RRP size remains unclear. It is also unclear whether all vesicles of the RRP are equally release competent, and what cellular mechanisms underlie RRP renewal. We address here these questions at single glutamatergic synapses, counting released vesicles using deconvolution. We find a remarkably low variance of cumulative vesicle counts during action potential trains. This, combined with Monte Carlo simulations, indicates that vesicles transit through two successive states before exocytosis, so that the RRP is up to 2-fold higher than the docking site number. The transition to the second state has a very rapid rate constant, and is specifically inhibited by latrunculin B and blebbistatin, suggesting the involvement of actin and myosin. PMID:27537485

  13. JL-2: A Mobile Multi-robot System with Docking and Manipulating Capabilities

    Directory of Open Access Journals (Sweden)

    Wei Wang

    2010-02-01

    Full Text Available This paper presents a new version of the JL series reconfigurable multi-robot system called JL-2. By virtue of the docking manipulator composed of a parallel mechanism and a cam gripper, every mobile robot in the JL-2 system is able to not only perform tasks in parallel, e.g. moving and grasping, but also dock with each other even if there are large misalignments between two robots. A motorized spherical joint is formed between two docked robots to enhance the locomotion capability of JL-2. To fulfill the demands of reconfiguration, a distributed control system and sonar based docking guidance system are designed for the JL-2 prototype. Based on the above design, the JL-2 prototype has been built and successfully demonstrated to confirm the validity and functionality of the proposed capabilities.

  14. Galaxy7TM: flexible GPCR-ligand docking by structure refinement.

    Science.gov (United States)

    Lee, Gyu Rie; Seok, Chaok

    2016-07-01

    G-protein-coupled receptors (GPCRs) play important physiological roles related to signal transduction and form a major group of drug targets. Prediction of GPCR-ligand complex structures has therefore important implications to drug discovery. With previously available servers, it was only possible to first predict GPCR structures by homology modeling and then perform ligand docking on the model structures. However, model structures generated without explicit consideration of specific ligands of interest can be inaccurate because GPCR structures can be affected by ligand binding. The Galaxy7TM server, freely accessible at http://galaxy.seoklab.org/7TM, improves an input GPCR structure by simultaneous ligand docking and flexible structure refinement using GALAXY methods. The server shows better performance in both ligand docking and GPCR structure refinement than commonly used programs AutoDock Vina and Rosetta MPrelax, respectively. PMID:27131365

  15. FlexAID: Revisiting Docking on Non-Native-Complex Structures.

    Science.gov (United States)

    Gaudreault, Francis; Najmanovich, Rafael J

    2015-07-27

    Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specific geometric criteria, based on surface complementarity. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. The prediction of binding poses is tested using the widely used Astex dataset as well as the HAP2 dataset, while performance in virtual screening is evaluated using a subset of the DUD dataset. We compare FlexAID to AutoDock Vina, FlexX, and rDock in an extensive number of scenarios to understand the strengths and limitations of the different programs as well as to reported results for Glide, GOLD, and DOCK6 where applicable. The most relevant among these scenarios is that of docking on flexible non-native-complex structures where as is the case in reality, the target conformation in the bound form is not known a priori. We demonstrate that FlexAID, unlike other programs, is robust against increasing structural variability. FlexAID obtains equivalent sampling success as GOLD and performs better than AutoDock Vina or FlexX in all scenarios against non-native-complex structures. FlexAID is better than rDock when there is at least one critical side-chain movement required upon ligand binding. In virtual screening, FlexAID results are lower on average than those of AutoDock Vina and rDock. The higher accuracy in flexible targets where critical movements are required, intuitive PyMOL-integrated graphical user interface and free source code as well as precompiled executables for Windows, Linux, and Mac OS make FlexAID a welcome addition to the arsenal of existing small-molecule protein docking methods. PMID

  16. Cultural methods for controlling docks in organically farmed grassland (extension 1998-99) (OFT0115T)

    OpenAIRE

    Hopkins, Alan

    1999-01-01

    Docks are considered to be one of the main weed problems of grassland. The absence of an effective non-chemical control may be a deterrent to organic-conversion for farmers accustomed to using herbicides for dock control. This work addresses this problem in the context of MAFF policy to encourage more farmers to adopt organic farming, and to encourage a reduction in the use of herbicides in farming generally. The project was based around hypotheses that physical techniques and management stra...

  17. DockAnalyse: an application for the analysis of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Cedano Juan

    2010-10-01

    Full Text Available Abstract Background Is it possible to identify what the best solution of a docking program is? The usual answer to this question is the highest score solution, but interactions between proteins are dynamic processes, and many times the interaction regions are wide enough to permit protein-protein interactions with different orientations and/or interaction energies. In some cases, as in a multimeric protein complex, several interaction regions are possible among the monomers. These dynamic processes involve interactions with surface displacements between the proteins to finally achieve the functional configuration of the protein complex. Consequently, there is not a static and single solution for the interaction between proteins, but there are several important configurations that also have to be analyzed. Results To extract those representative solutions from the docking output datafile, we have developed an unsupervised and automatic clustering application, named DockAnalyse. This application is based on the already existing DBscan clustering method, which searches for continuities among the clusters generated by the docking output data representation. The DBscan clustering method is very robust and, moreover, solves some of the inconsistency problems of the classical clustering methods like, for example, the treatment of outliers and the dependence of the previously defined number of clusters. Conclusions DockAnalyse makes the interpretation of the docking solutions through graphical and visual representations easier by guiding the user to find the representative solutions. We have applied our new approach to analyze several protein interactions and model the dynamic protein interaction behavior of a protein complex. DockAnalyse might also be used to describe interaction regions between proteins and, therefore, guide future flexible dockings. The application (implemented in the R package is accessible.

  18. ASTP crewmen in Docking Module trainer during training session at JSC

    Science.gov (United States)

    1975-01-01

    An interior view of the Docking Module trainer in bldg 35 during Apollo Soyuz Test Project (ASTP) joint crew training at JSC. Astronaut Thomas P. Stafford, commander of the American ASTP prime crew, is on the right. The other crewman is Cosmonaut Aleksey A. Leonov, commander of the Soviet ASTP prime crew. The training session simulated activities on the second day in Earth orbit. The Docking Module is designed to link the Apollo and Soyuz spacecraft.

  19. Automatic Docking System with Recharging and Battery Replacement for Surveillance Robot

    OpenAIRE

    M. Meena; Mrs. P. Thilagavathi*

    2012-01-01

    Most of the applications like industrial automation, home automation, hospitals, space exploration, military, etc, the surveillance robot are widely used. For that, continuous functioning of surveillance robot is necessary. In this paper, the development of automatic docking system with recharging and battery replacement process for surveillance robot is proposed. The robot can return to the docking station for recharging operations when the battery is low. The charging duration of the batter...

  20. International Low Impact Docking System (iLIDS) Project Technical Requirements Specification, Revision F

    Science.gov (United States)

    Lewis, James L.

    2011-01-01

    The NASA Docking System (NDS) is NASA's implementation for the emerging International Docking System Standard (IDSS) using low impact docking technology. The NASA Docking System Project (NDSP) is the International Space Station (ISS) Program's project to produce the NDS, Common Docking Adapter (CDA) and Docking Hub. The NDS design evolved from the Low Impact Docking System (LIDS). The acronym international Low Impact Docking System (iLIDS) is also used to describe this system as well as the Government Furnished Equipment (GFE) project designing the NDS for the NDSP. NDS and iLIDS may be used interchangeability. This document will use the acronym iLIDS. Some of the heritage documentation and implementations (e.g., software command names, requirement identification (ID), figures, etc.) used on NDS will continue to use the LIDS acronym. This specification defines the technical requirements for the iLIDS GFE delivered to the NDSP by the iLIDS project. This document contains requirements for two iLIDS configurations, SEZ29101800-301 and SEZ29101800-302. Requirements with the statement, iLIDS shall, are for all configurations. Examples of requirements that are unique to a single configuration may be identified as iLIDS (-301) shall or iLIDS (-302) shall. Furthermore, to allow a requirement to encompass all configurations with an exception, the requirement may be designated as iLIDS (excluding -302) shall. Verification requirements for the iLIDS project are identified in the Verification Matrix (VM) provided in the iLIDS Verification and Validation Document, JSC-63966. The following definitions differentiate between requirements and other statements: Shall: This is the only verb used for the binding requirements. Should/May: These verbs are used for stating non-mandatory goals. Will: This verb is used for stating facts or declaration of purpose. A Definition of Terms table is provided in Appendix B to define those terms with specific tailored uses in this document.

  1. Dock180 and ELMO1 proteins cooperate to promote evolutionarily conserved Rac-dependent cell migration.

    OpenAIRE

    Grimsley, C M; Kinchen, J M; Tosello-Trampont, A C; Brugnera, E.; Haney, L B; Lu, M; Chen, Q.; Klingele, D; Hengartner, M O; K.S.Ravichandran

    2004-01-01

    Cell migration is essential throughout embryonic and adult life. In numerous cell systems, the small GTPase Rac is required for lamellipodia formation at the leading edge and movement ability. However, the molecular mechanisms leading to Rac activation during migration are still unclear. Recently, a mammalian superfamily of proteins related to the prototype member Dock180 has been identified with homologues in Drosophila and Caenorhabditis elegans. Here, we addressed the role of Dock180 and E...

  2. Automated waste canister docking and emplacement using a sensor-based intelligent controller

    International Nuclear Information System (INIS)

    A sensor-based intelligent control system is described that utilizes a multiple degree-of-freedom robotic system for the automated remote manipulation and precision docking of large payloads such as waste canisters. Computer vision and ultrasonic proximity sensing are used to control the automated precision docking of a large object with a passive target cavity. Real-time sensor processing and model-based analysis are used to control payload position to a precision of ± 0.5 millimeter

  3. Situation Awareness for Improved Operational Control in Cross Docking: An Illustrative Case Study

    OpenAIRE

    Buijs, Paul; Szirbik, Nick; Meyer, Gerben; Wortmann, Johan

    2012-01-01

    This paper presents research in progress aimed at developing a conceptual framework for operational control at cross docks. The proposed framework contributes to cross docking literature by including situation awareness as an important concept of operational control. The implications of the proposed conceptual framework are explored in an illustrative case study. That case study reveals that despite the availability of real-time and detailed information about the on-going operations, the abil...

  4. Integrating atom-based and residue-based scoring functions for protein–protein docking

    OpenAIRE

    Vreven, Thom; Hwang, Howook; Weng, Zhiping

    2011-01-01

    Most scoring functions for protein–protein docking algorithms are either atom-based or residue-based, with the former being able to produce higher quality structures and latter more tolerant to conformational changes upon binding. Earlier, we developed the ZRANK algorithm for reranking docking predictions, with a scoring function that contained only atom-based terms. Here we combine ZRANK's atom-based potentials with five residue-based potentials published by other labs, as well as an atom-ba...

  5. A polynomial algorithm for a simple scheduling problem at cross docking terminals

    OpenAIRE

    Sadykov, Ruslan

    2009-01-01

    At cross docking terminals, products from incoming trucks are sorted according to there destinations and transferred to outgoing trucks using a temporary storage. Such terminals allow companies to reduce storage and transportation costs in supply chain. This paper focuses on the operational activities at cross docking terminals. We consider the trucks scheduling problem with the objective to minimise the storage usage during the product transfer. We show that a simplification of this NP-hard ...

  6. A New Method for Ligand Docking to Flexible Receptors by Dual Alanine Scanning and Refinement (SCARE)

    OpenAIRE

    Bottegoni, Giovanni; Kufareva, Irina; Totrov, Maxim; Abagyan, Ruben

    2008-01-01

    Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple conformations representing the variation of the pocket, or on a known bounding box for the ligand. Here we described a general induced fit docking protocol that requires only one initial pocket conformation and identifies most of the correct ligand positions as the lowest score. We expanded...

  7. Computational modelling of protein/protein and protein/DNA docking.

    OpenAIRE

    Moont, G.

    2005-01-01

    The docking problem is to start with unbound conformations for the components of a complex, and computationally model a near-native structure for the complex. This thesis describes work in developing computer programs to tackle both protein/protein and protein/DNA docking. Empirical pair potential functions are generated from datasets of residue/residue interactions. A scoring function was parameterised and then used to screen possible complexes, generated by the global search computer algori...

  8. A Multiobjective Iterated Greedy Algorithm for Truck Scheduling in Cross-Dock Problems

    OpenAIRE

    B. Naderi; Shadi Rahmani; Shabnam Rahmani

    2014-01-01

    The cross-docking system is a new distribution strategy which can reduce inventories, lead times, and improve responding time to customers. This paper considers biobjective problem of truck scheduling in cross-docking systems with temporary storage. The objectives are minimizing both makespan and total tardiness. For this problem, it proposes a multiobjective iterated greedy algorithm employing advance features such as modified crowding selection, restart phase, and local search. To evaluate ...

  9. Consistent improvement of cross docking results using binding site ensembles generated with Elastic Network Normal Modes

    OpenAIRE

    Rueda, Manuel; Bottegoni, Giovanni; Abagyan, Ruben

    2009-01-01

    The representation of protein flexibility is still a challenge for the state-of-the-art flexible ligand docking protocols. In this article we use a large and diverse benchmark to prove that is possible to improve consistently the cross docking performance against a single receptor conformation by using an equilibrium ensemble of binding site conformers. The benchmark contained 28 proteins, and the top ranked near native poses for the ligand were found 20% more efficiently than using a single ...

  10. Ranking multiple docking solutions based on the conservation of inter-residue contacts

    KAUST Repository

    Oliva, Romina M.

    2013-06-17

    Molecular docking is the method of choice for investigating the molecular basis of recognition in a large number of functional protein complexes. However, correctly scoring the obtained docking solutions (decoys) to rank native-like (NL) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First it calculates a conservation rate for each inter-residue contact, then it ranks decoys according to their ability to match the more frequently observed contacts. We applied CONSRANK to 102 targets from three different benchmarks, RosettaDock, DOCKGROUND, and Critical Assessment of PRedicted Interactions (CAPRI). The method performs consistently well, both in terms of NL solutions ranked in the top positions and of values of the area under the receiver operating characteristic curve. Its ideal application is to solutions coming from different docking programs and procedures, as in the case of CAPRI targets. For all the analyzed CAPRI targets where a comparison is feasible, CONSRANK outperforms the CAPRI scorers. The fraction of NL solutions in the top ten positions in the RosettaDock, DOCKGROUND, and CAPRI benchmarks is enriched on average by a factor of 3.0, 1.9, and 9.9, respectively. Interestingly, CONSRANK is also able to specifically single out the high/medium quality (HMQ) solutions from the docking decoys ensemble: it ranks 46.2 and 70.8% of the total HMQ solutions available for the RosettaDock and CAPRI targets, respectively, within the top 20 positions. © 2013 Wiley Periodicals, Inc.

  11. Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking

    Directory of Open Access Journals (Sweden)

    Tyagi Sadhna

    2009-06-01

    Full Text Available Abstract Background Previously, ways to adapt docking programs that were developed for modelling inhibitor-receptor interaction have been explored. Two main issues were discussed. First, when trying to model catalysis a reaction intermediate of the substrate is expected to provide more valid information than the ground state of the substrate. Second, the incorporation of protein flexibility is essential for reliable predictions. Results Here we present a predictive and robust method to model substrate specificity and enantioselectivity of lipases and esterases that uses reaction intermediates and incorporates protein flexibility. Substrate-imprinted docking starts with covalent docking of reaction intermediates, followed by geometry optimisation of the resulting enzyme-substrate complex. After a second round of docking the same substrate into the geometry-optimised structures, productive poses are identified by geometric filter criteria and ranked by their docking scores. Substrate-imprinted docking was applied in order to model (i enantioselectivity of Candida antarctica lipase B and a W104A mutant, (ii enantioselectivity and substrate specificity of Candida rugosa lipase and Burkholderia cepacia lipase, and (iii substrate specificity of an acetyl- and a butyrylcholine esterase toward the substrates acetyl- and butyrylcholine. Conclusion The experimentally observed differences in selectivity and specificity of the enzymes were reproduced with an accuracy of 81%. The method was robust toward small differences in initial structures (different crystallisation conditions or a co-crystallised ligand, although large displacements of catalytic residues often resulted in substrate poses that did not pass the geometric filter criteria.

  12. Histopathological Characterization of Tail Injury and Traumatic Neuroma Development after Tail Docking in Piglets.

    Science.gov (United States)

    Sandercock, D A; Smith, S H; Di Giminiani, P; Edwards, S A

    2016-07-01

    Tail docking of neonatal pigs is widely used as a measure to reduce the incidence of tail biting, a complex management problem in the pig industry. Concerns exist over the long-term consequences of tail docking for possible tail stump pain sensitivity due to the development of traumatic neuromas in injured peripheral nerves. Tail stumps were obtained post mortem from four female pigs at each of 1, 4, 8 and 16 weeks following tail amputation (approximately two-thirds removed) by a gas-heated docking iron on post natal day 3. Tissues were processed routinely for histopathological examination. Non-neural inflammatory and reparative epidermal and dermal changes associated with tissue thickening and healing were observed 1 to 4 months after docking. Mild neutrophilic inflammation was present in some cases, although this and other degenerative and non-neural reparative changes are not likely to have caused pain. Traumatic neuroma and neuromatous tissue development was not observed 1 week after tail docking, but was evident 1 month after tail docking. Over time there was marked nerve sheath and axonal proliferation leading to the formation of neuromata, which were either localized and circumscribed or comprised of multiple axons dispersed within granulation tissue. Four months after tail resection, neuroma formation was still incomplete, with possible implications for sensitivity of the tail stump. PMID:27302763

  13. Vehicle Routing Problem for Fashion Supply Chains with Cross-Docking

    Directory of Open Access Journals (Sweden)

    Zhi-Hua Hu

    2013-01-01

    Full Text Available Cross-docking, as a strategy to reduce lead time and enhance the efficiency of the fashion supply chain, has attracted substantial attention from both the academy and the industry. Cross-docking is a critical part of many fashion and textiles supply chains in practice because it can help to achieve many supply chain strategies such as postponement. We consider a model where there are multiple suppliers and customers in a single cross-docking center. With such a model setting, the issue concerning the coordinated routing between the inbound and outbound routes is much more complex than many traditional vehicle routing problems (VRPs. We formulate the optimal route selection problems from the suppliers to the cross-docking center and from the cross-docking center to the customers as the respective VRPs. Based on the relationships between the suppliers and the customers, we integrate the two VRP models to optimize the overall traveling time, distance, and waiting time at the cross-docking center. In addition, we propose a novel mixed 0/1 integer linear programming model by which the complexity of the problem can be reduced significantly. As demonstrated by the simulation analysis, our proposed model can be solved very efficiently by a commonly used optimization software package.

  14. Identification of Novel Smoothened Ligands Using Structure-Based Docking

    Science.gov (United States)

    Torosyan, Hayarpi; Parathaman, Pranavan; Irwin, John J.; Shoichet, Brian K.

    2016-01-01

    The seven transmembrane protein Smoothened is required for Hedgehog signaling during embryonic development and adult tissue homeostasis. Inappropriate activation of the Hedgehog signalling pathway leads to cancers such as basal cell carcinoma and medulloblastoma, and Smoothened inhibitors are now available clinically to treat these diseases. However, resistance to these inhibitors rapidly develops thereby limiting their efficacy. The determination of Smoothened crystal structures enables structure-based discovery of new ligands with new chemotypes that will be critical to combat resistance. In this study, we docked 3.2 million available, lead-like molecules against Smoothened, looking for those with high physical complementarity to its structure; this represents the first such campaign against the class Frizzled G-protein coupled receptor family. Twenty-one high-ranking compounds were selected for experimental testing, and four, representing three different chemotypes, were identified to antagonize Smoothened with IC50 values better than 50 μM. A screen for analogs revealed another six molecules, with IC50 values in the low micromolar range. Importantly, one of the most active of the new antagonists continued to be efficacious at the D473H mutant of Smoothened, which confers clinical resistance to the antagonist vismodegib in cancer treatment. PMID:27490099

  15. Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

    Directory of Open Access Journals (Sweden)

    Renata De Paris

    2015-01-01

    Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

  16. HERMES docking/berthing system pilot study. Quantitative assessment

    International Nuclear Information System (INIS)

    This study falls within the framework of the incorporation of quantitative risk assessment to the activities planned for the ESA-HERMES project (ESA/ CNES). The main objective behind the study was the analysis and evaluation of the potential contribution of so-called probabilistic or quantitative safety analysis to the optimization of the safety development process for the systems carrying out the safety functions required by the new and complex HERMES Space Vehicle. For this purpose, a pilot study was considered a good start in quantitative safety assessments (QSA), as this approach has been frequently used in the past to establish a solid base in large-scale QSA application programs while avoiding considerable economic risks. It was finally decided to select the HERMES docking/berthing system with Man Tender Free Flyer as the case-study. This report describes the different steps followed in the study, along with the main insights obtained and the general conclusions drawn from the study results. (author)

  17. Reducing Seal Adhesion in Low Impact Docking Systems

    Science.gov (United States)

    Banks, Bruce A.; Miller, Sharon K.

    2010-01-01

    Silicone elastomers, used in seals for airlocks or other sealing surfaces in space, are sticky in their as-received condition. Because of the sticking, a greater force may be needed to separate the mating surfaces. If the adhesion is sufficiently high, a sudden unpredicted movement of the spacecraft during undocking, vibration, or uneven release could pull off the seal, resulting in a damage that would have to be repaired before another docking. The damaged seal can result in significant gas leakage and possibly in a catastrophic mishap impacting the safety of the crew. It is also possible that a compromised seal could result in a delayed but sudden gas leak that could put the crew at unexpected risk. This is especially of concern for androgynous seals, which have identical mating surfaces on both sides for interchangeability and redundancy. Such seals typically have elastomer-on-elastomer sealing surfaces. To reduce sticking, one could use release agents such as powders and lubricants, but these can be easily removed and transferred to other surfaces, causing uneven sealing and contamination. Modification of the elastomer surface to make a more slippery and less sticky surface that is integral with the bulk elastomer would be more desirable.

  18. Noncatalytic docking domains of cellulosomes of anaerobic fungi.

    Science.gov (United States)

    Steenbakkers, P J; Li, X L; Ximenes, E A; Arts, J G; Chen, H; Ljungdahl, L G; Op Den Camp, H J

    2001-09-01

    A method is presented for the specific isolation of genes encoding cellulosome components from anaerobic fungi. The catalytic components of the cellulosome of anaerobic fungi typically contain, besides the catalytic domain, mostly two copies of a 40-amino-acid cysteine-rich, noncatalytic docking domain (NCDD) interspaced by short linkers. Degenerate primers were designed to anneal to the highly conserved region within the NCDDs of the monocentric fungus Piromyces sp. strain E2 and the polycentric fungus Orpinomyces sp. strain PC-2. Through PCR using cDNA from Orpinomyces sp. and genomic DNA from Piromyces sp. as templates, respectively, 9 and 19 PCR products were isolated encoding novel NCDD linker sequences. Screening of an Orpinomyces sp. cDNA library with four of these PCR products resulted in the isolation of new genes encoding cellulosome components. An alignment of the partial NCDD sequence information obtained and an alignment of database-accessible NCDD sequences, focusing on the number and position of cysteine residues, indicated the presence of three structural subfamilies within fungal NCDDs. Furthermore, evidence is presented that the NCDDs in CelC from the polycentric fungus Orpinomyces sp. strain PC-2 specifically recognize four proteins in a cellulosome preparation, indicating the presence of multiple scaffoldins. PMID:11514516

  19. Peptides Trapping Dioxins: A Docking-Based Inverse Screening Approach

    Directory of Open Access Journals (Sweden)

    German Perez

    2013-01-01

    Full Text Available A rapid and cost-effective computational methodology for designing and rationalizing the selection of small peptides as receptors for dioxin-like compounds was proposed. The backbone of the dioxin Ah receptor binding site was used to design a series of penta- and hexapeptide libraries, with 1400 elements in total. Peptide flexibility was considered and 10 conformers were found to be a good option to represent peptide conformational space with fair speed-accuracy ratio. Each peptide conformer was treated as a possible receptor, generating a dedicated box and then running a docking process using as ligands a family of 76 dibenzo-p-dioxins and 113 dibenzofurans mono- and polychlorinated. Significant predictions were confirmed by comparing primary structure of top and bottom ranked peptides binding dioxins confirming that scrambled positions of the same amino acids gave completely different predicted binding. The hexapeptide EWFQPW, with the best binding score, was chosen as selective sorbent material in solid-phase extraction. The retention performances were tested using the 2,3,7,8-tetrachlorodibenzo-p-dioxin and two polychlorinated biphenyls in order to verify the hexapeptide specificity. The solid-phase extraction experimental procedure was optimized, and analytical parameters of hexapeptide sorbent material were compared with the resin without hexapeptide and a commercial reversed phase cartridge.

  20. GVD compensation schemes with considering PMD

    Institute of Scientific and Technical Information of China (English)

    Aiying Yang(杨爱英); Anshi Xu(徐安士); Deming Wu(吴德明)

    2003-01-01

    Three group velocity dispersion (GVD) compensation schemes, i.e., the post-compensation, pre-compensation and hybrid-compensation schemes, are discussed with considering polarization mode disper-sion (PMD). In the 10- and 40-Gbit/s non-return-zero (NRZ) on-off-key (OOK) systems, three physicalfactors, Kerr effect, GVD and PMD are considered. The numerical results show that, when the impactof PMD is taken into account, the GVD pre-compensation scheme performs best with more than 1 dBbetter of average eye-opening penalty (EOP) when input power is up to 10 dBm in the 10-Gbit/s system.However the GVD post-compensation scheme perforns best for the case of 40 Gbit/s with input power lessthan 13 dBm, and GVD pre-compensation will be better if the input power increased beyond this range.The results are different from those already reported under the assumption that the impact of PMD isneglected. Therefore, the research in this paper provide a different insight into the system optimizationwhen PMD, Kerr effect and GVD are considered.

  1. Compensator configurations for load currents' symmetrization

    Science.gov (United States)

    Rusinaru, D.; Manescu, L. G.; Dinu, R. C.

    2016-02-01

    This paper approaches aspects regarding the mitigation effects of asymmetries in 3-phase 3-wire networks. The measure consisting in connecting of load current symmetrization devices at the load coupling point is presented. A time-variation of compensators parameters is determined as a function of the time-recorded electrical values. The general sizing principle of the load current symmetrization reactive components is based on a simple equivalent model of the unbalanced 3-phase loads. By using these compensators a certain control of the power components transits is ensured in the network. The control is based on the variations laws of the compensators parameters as functions of the recorded electrical values: [B] = [T]·[M]. The link between compensator parameters and measured values is ensured by a transformation matrix [T] for each operation conditions of the supply network. Additional conditions for improving of energy and efficiency performance of the compensator are considered: i.e. reactive power compensation. The compensator sizing algorithm was implemented into a MATLAB environment software, which generate the time-evolution of the parameters of load current symmetrization device. The input data of application takes into account time-recording of the electrical values. By using the compensator sizing software, some results were achieved for the case of a consumer connected at 20 kV busbar of a distribution substation, during 24 hours measurement session. Even the sizing of the compensators aimed some additional network operation aspects (power factor correction) correlated with the total or major load symmetrizations, the harmonics aspects of the network values were neglected.

  2. Advanced median method for timing jitter compensation

    Institute of Scientific and Technical Information of China (English)

    Wang Chen; Zhu Jiangmiao; Jan Verspecht; Liu Mingliang; Li Yang

    2008-01-01

    Timing jitter is one of the main factors that influence on the accuracy of time domain precision measurement. Timing jitter compensation is one of the problems people concern. Because of the flaws of median method, PDF deconvolution method and synthetic method, we put forward a new method for timing jitter compensation, which is called advanced median method. The theory of the advanced median method based on probability and statistics is analyzed, and the process of the advanced median method is summarized in this paper. Simulation and experiment show that compared with other methods, the new method could compensate timing jitter effectively.

  3. Zero energy buildings and mismatch compensation factors

    DEFF Research Database (Denmark)

    Lund, Henrik; Marszal, Anna Joanna; Heiselberg, Per

    2011-01-01

    individual buildings and an element of economy of scale. For these three reasons mismatches should be dealt with at the aggregated level and not at the individual level of each building. Instead, this paper suggests to compensate the mismatch of a building by increasing (or decreasing) the capacity of the...... energy production unit. Based on historical data for the electricity supply area in western Denmark, this paper makes a first attempt to quantify mismatch compensation factors. The results indicate that such compensation factors are a little below one for buildings with photovoltaics (PV) and a little...

  4. A Study on Compensation for Advertisement Translation

    Institute of Scientific and Technical Information of China (English)

    杨兰兰

    2012-01-01

    Considering the linguistic and cultural difference between English and Chinese, it is inevitable to lose the original musical beauty, visual beauty and original rhetorical devices in advertisements translation. So compensation measures are always taken to compensate the lost information. This paper focuses on the discussion of the features of advertisement, cultural and linguistic differences between English and Chinese advertisements, which result in the loss of information. And compensation strategies on words, musical beauty and rhetorical devices in advertisement translation are introduced in this paper.

  5. On the compensation effect in heterogeneous catalysis

    DEFF Research Database (Denmark)

    Pedersen, Thomas Bligaard; Honkala, Johanna Karoliina; Logadottir, Ashildur;

    2003-01-01

    to illustrate the effect. Both experiments and a detailed kinetic model show a compensation effect. Second, we use density functional theory calculations to show that the compensation effect is not only due to changes in the activation barrier and prefactor of the rate-determining step, N-2 dissociation. We......For a class of heterogeneously catalyzed reactions, we explain the compensation effect in terms of a switching of kinetic regimes leading to a concomitant change in the apparent activation energy and in the prefactor for the overall rate of the reaction. We first use the ammonia synthesis...

  6. Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.

    Science.gov (United States)

    Brylinski, Michal

    2013-11-25

    A common strategy for virtual screening considers a systematic docking of a large library of organic compounds into the target sites in protein receptors with promising leads selected based on favorable intermolecular interactions. Despite a continuous progress in the modeling of protein-ligand interactions for pharmaceutical design, important challenges still remain, thus the development of novel techniques is required. In this communication, we describe eSimDock, a new approach to ligand docking and binding affinity prediction. eSimDock employs nonlinear machine learning-based scoring functions to improve the accuracy of ligand ranking and similarity-based binding pose prediction, and to increase the tolerance to structural imperfections in the target structures. In large-scale benchmarking using the Astex/CCDC data set, we show that 53.9% (67.9%) of the predicted ligand poses have RMSD of <2 Å (<3 Å). Moreover, using binding sites predicted by recently developed eFindSite, eSimDock models ligand binding poses with an RMSD of 4 Å for 50.0-39.7% of the complexes at the protein homology level limited to 80-40%. Simulations against non-native receptor structures, whose mean backbone rearrangements vary from 0.5 to 5.0 Å Cα-RMSD, show that the ratio of docking accuracy and the estimated upper bound is at a constant level of ∼0.65. Pearson correlation coefficient between experimental and predicted by eSimDock Ki values for a large data set of the crystal structures of protein-ligand complexes from BindingDB is 0.58, which decreases only to 0.46 when target structures distorted to 3.0 Å Cα-RMSD are used. Finally, two case studies demonstrate that eSimDock can be customized to specific applications as well. These encouraging results show that the performance of eSimDock is largely unaffected by the deformations of ligand binding regions, thus it represents a practical strategy for across-proteome virtual screening using protein models. eSimDock is freely

  7. Compensating for estimation smoothing in kriging

    Science.gov (United States)

    Olea, R.A.; Pawlowsky, Vera

    1996-01-01

    Smoothing is a characteristic inherent to all minimum mean-square-error spatial estimators such as kriging. Cross-validation can be used to detect and model such smoothing. Inversion of the model produces a new estimator-compensated kriging. A numerical comparison based on an exhaustive permeability sampling of a 4-fr2 slab of Berea Sandstone shows that the estimation surface generated by compensated kriging has properties intermediate between those generated by ordinary kriging and stochastic realizations resulting from simulated annealing and sequential Gaussian simulation. The frequency distribution is well reproduced by the compensated kriging surface, which also approximates the experimental semivariogram well - better than ordinary kriging, but not as well as stochastic realizations. Compensated kriging produces surfaces that are more accurate than stochastic realizations, but not as accurate as ordinary kriging. ?? 1996 International Association for Mathematical Geology.

  8. Convention on supplementary compensation for nuclear damage

    International Nuclear Information System (INIS)

    The document reproduces the text of the Convention on Supplementary Compensation for Nuclear Damage which was adopted on 12 September 1997 by a Diplomatic Conference held between 8-12 September 1997 in Vienna

  9. Comprehensive Environmental Response, Compensation and Liability Act

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), commonly known as Superfund, provides a federal "superfund" to clean up...

  10. Compensating fields and anomalies in supergravity

    International Nuclear Information System (INIS)

    We discuss the quantization of theories which are formulated using compensating fields. In particular, we discuss the relation between the components formulation and the superspace formulation of supergravity theories. The requirement that the compensating field can be eliminated at the quantum level gives rise to on-shell constraints on the operators of the theory. In some cases, the constraints turn out to be physically unacceptable. Using these considerations we show that new minimal supergravity is in general anomalous. (author). 17 refs

  11. Compensating Fields and Anomalies in Supergravity

    CERN Document Server

    Shamir, Y

    1993-01-01

    We discuss the quantization of theories which are formulated using compensating fields. In particular, we discuss the relation between the components formulation and the superspace formulation of supergravity theories. The requirement that the compensating field can be eliminated at the quantum level gives rise to on-shell constraints on the operators of the theory. In some cases, the constraints turn out to be physically unacceptable. Using these considerations we show that new minimal supergravity is in general anomalous.

  12. Stock Option Compensation and Managerial Turnover

    OpenAIRE

    Raluca Georgiana NASTASESCU

    2009-01-01

    This study examines the association between managerial turnover and equity-based compensation. I investigate whether stock options act to bond executives to their firms and whether retention of managers is a motivation of companies in designing CEO incentive contracts. The results show that stock options do negatively influence the probability of a CEO leaving the company. The monetary cost of losing the value of equity-based compensation package keeps the manager with his company. I also fin...

  13. Empirical Evidence of Recurring International Compensation Problems

    OpenAIRE

    Michael Harvey

    1993-01-01

    The expansion of international business necessitates an increased number of employees based in foreign markets. These expatriates, nationals and third-country nationals represent unique and complex compensation problems. This article addresses five of the recurring compensation problems reported by members of the Society for Human Resource Management International (SHRMI) in a recent survey.© 1993 JIBS. Journal of International Business Studies (1993) 24, 785–799

  14. Reversible thyristor converters of brushless synchronous compensators

    OpenAIRE

    А.М. Galynovskiy; E.М.Dubchak; E.А. Lenskaya

    2013-01-01

    Behavior of models of three-phase-to-single-phase rotary reversible thyristor converters of brushless synchronous compensators in a circuit simulation system is analyzed. It is shown that combined control mode of opposite-connected thyristors may result in the exciter armature winding short circuits both at the thyristor feed-forward and lagging current delay angles. It must be taken into consideration when developing brushless compensator excitation systems.

  15. Job Dispersion and Compensating Wage Differentials

    OpenAIRE

    Paul Sullivan; Ted To

    2013-01-01

    The empirical literature on compensating wage differentials has a mixed history. While there have been some successes, much of this literature finds weak support for the theory of equalizing differences. We argue that it is dispersion in total job values or "job dispersion" that leads to biased compensating wage differential estimates. We begin by demonstrating how job dispersion can lead to biased hedonic estimates. Then we take a partial equilibrium on-the-job search model with utility from...

  16. Temperature-Compensating Inactive Strain Gauge

    Science.gov (United States)

    Moore, Thomas C., Sr.

    1993-01-01

    Thermal contribution to output of active gauge canceled. High-temperature strain gauges include both active gauge wires sensing strains and inactive gauge wires providing compensation for thermal contributions to gauge readings. Inactive-gauge approach to temperature compensation applicable to commercially available resistance-type strain gauges operating at temperatures up to 700 degrees F and to developmental strain gauges operating at temperatures up to 2,000 degrees F.

  17. Executive compensation based on asset values

    OpenAIRE

    Hans Bystrom

    2012-01-01

    This paper describes how credit default swaps could be employed to create performance based executive compensation portfolios that reflect the value of a firm's debt as well as equity; i.e. the total value of all a firm's assets. We define so-called Asset Value Unit (AVU) compensation portfolios that work both for executive- and non-executive pay schemes in financial as well as non-financial firms.

  18. Executive Compensation and Misconduct: Environmental Harm

    OpenAIRE

    Minor, Dylan Blu

    2016-01-01

    We explore the relationship between managerial incentives and misconduct using the setting of environmental harm. We find that high powered executive compensation can increase the odds of environmental law-breaking by 40-60% and the magnitude of environmental harm by over 100%. We document similar results for the setting of executive compensation and illegal financial accounting. Finally, we outline some managerial and policy implications to blunt these adverse incentive effects.

  19. Environmental compensation is not for the birds

    OpenAIRE

    Cole, Scott

    2012-01-01

    The European Union (EU) recently implemented the Environmental Liability Directive (ELD), requiring that environmental damage be restored so that the affected environment returns to (or toward) its baseline condition and the public is compensated for the initial damage and the losses during the time it takes for the environment to recover (interim losses). Equivalency Analysis (EA) represents a method for scaling environmental compensation to offset interim losses. Ensuring appropriate compen...

  20. Compensation and Incentives in German Corporations

    OpenAIRE

    Moritz Heimes; Steffen Seemann

    2011-01-01

    In this paper we analyze executive compensation in Germany for the period 2005-2009. We use a self-collected dataset on compensation arrangements in German corporations to estimate the impact of firm performance and firm risk on executive pay. To be in line with earlier studies in this literature, we first measure firm performance and firm risk based on stock market returns. Our findings support the prediction from agency theory that incentive pay decreases with firm risk. We find, however, t...

  1. Reactive power compensation a practical guide

    CERN Document Server

    Hofmann, Wolfgang; Just, Wolfgang

    2012-01-01

    The comprehensive resource on reactive power compensation, presenting the design, application and operation of reactive power equipment and installations The area of reactive power compensation is gaining increasing importance worldwide. If suitably designed, it is capable of improving voltage quality significantly, meaning that losses in equipment and power systems are reduced, the permissible loading of equipment can be increased, and the over-all stability of system operation improved. Ultimately, energy use and CO2 emisson are reduced. This unique guide discusses the

  2. Improved charge amplifier using hybrid hysteresis compensation

    Science.gov (United States)

    Amin-Shahidi, Darya; Trumper, David L.

    2013-08-01

    We present a novel charge amplifier, with a robust feedback circuit and a method for compensating piezoelectric actuator's hysteresis at low frequencies. The amplifier uses a modified feedback circuit which improves robustness to the addition of series load impedance such as in cabling. We also describe a hybrid hysteresis compensation method for enabling the charge amplifier to reduce hysteresis at low frequencies. Experimental results demonstrate the utility of the new amplifier design.

  3. Reversible thyristor converters of brushless synchronous compensators

    Directory of Open Access Journals (Sweden)

    А.М.Galynovskiy

    2013-12-01

    Full Text Available Behavior of models of three-phase-to-single-phase rotary reversible thyristor converters of brushless synchronous compensators in a circuit simulation system is analyzed. It is shown that combined control mode of opposite-connected thyristors may result in the exciter armature winding short circuits both at the thyristor feed-forward and lagging current delay angles. It must be taken into consideration when developing brushless compensator excitation systems.

  4. Executive equity compensation and incentives: a survey

    OpenAIRE

    Core, John E.; Wayne R. Guay; David F. Larcker

    2003-01-01

    Stock and option compensation and the level of managerial equity incentives are aspects of corporate governance that are especially controversial to shareholders, institutional activists, and government regulators. Similar to much of the corporate finance and corporate governance literature, research on stock-based compensation and incentives has not only generated useful insights, but also produced many contradictory findings. Not surprisingly, many fundamental questions remain unanswered. I...

  5. Compensating Heterogeneous Salesforces: Some Explicit Solutions

    OpenAIRE

    Ram C. Rao

    1990-01-01

    This paper considers the question of how a sales manager should design the optimal compensation scheme for his salesforce when it consists of salespersons of varying selling skills, i.e., when the salesforce is heterogeneous. The manager's problem is to reward the salespersons based on observable, uncertain sales achieved by the salespersons. Under the assumption that both the manager and the salespersons are risk neutral, the optimal compensation scheme is derived. It consists of the manager...

  6. Executive Compensation as an Agency Problem

    OpenAIRE

    Lucian A. Bebchuk; Fried, Jesse M.

    2003-01-01

    This paper provides an overview of the main theoretical elements and empirical underpinnings of a "managerial power" approach to executive compensation. Under this approach, the design of executive compensation is viewed not only as an instrument for addressing the agency problem between managers and shareholders but also as part of the agency problem itself. Boards of publicly traded companies with dispersed ownership, we argue, cannot be expected to bargain at arm's length with managers. As...

  7. Crusader Automated Docking System: Technology support for the Crusader Resupply Team. Interim report, Ammunition Logistics Program

    Energy Technology Data Exchange (ETDEWEB)

    Kring, C.T.; Varma, V.K.; Jatko, W.B.

    1995-11-01

    The US Army and Team Crusader (United Defense, Lockheed Martin Armament Systems, etc.) are developing the next generation howitzer, the Crusader. The development program includes an advanced, self-propelled liquid propellant howitzer and a companion resupply vehicle. The resupply vehicle is intended to rendezvous with the howitzer near the battlefront and replenish ammunition, fuel, and other material. The Army has recommended that Crusader incorporate new and innovative technologies to improve performance and safety. One conceptual design proposes a robotic resupply boom on the resupply vehicle to upload supplies to the howitzer. The resupply boom would normally be retracted inside the resupply vehicle during transit. When the two vehicles are within range of the resupply boom, the boom would be extended to a receiving port on the howitzer. In order to reduce exposure to small arms fire or nuclear, biological, and chemical hazards, the crew would remain inside the resupply vehicle during the resupply operation. The process of extending the boom and linking with the receiving port is called docking. A boom operator would be designated to maneuver the boom into contact with the receiving port using a mechanical joystick. The docking operation depends greatly upon the skill of the boom operator to manipulate the boom into docking position. Computer simulations at the National Aeronautics and Space Administration have shown that computer-assisted or autonomous docking can improve the ability of the operator to dock safely and quickly. This document describes the present status of the Crusader Autonomous Docking System (CADS) implemented at Oak Ridge National laboratory (ORNL). The purpose of the CADS project is to determine the feasibility and performance limitations of vision systems to satisfy the autonomous docking requirements for Crusader and conduct a demonstration under controlled conditions.

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

    OpenAIRE

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

    2009-01-01

    Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and “noise” that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and mu...

  9. NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID

    OpenAIRE

    Gaudreault, Francis; Morency, Louis-Philippe; Najmanovich, Rafael J.

    2015-01-01

    Ligand protein docking simulations play a fundamental role in understanding molecular recognition. Herein we introduce the NRGsuite, a PyMOL plugin that permits the detection of surface cavities in proteins, their refinements, calculation of volume and use, individually or jointly, as target binding-sites for docking simulations with FlexAID. The NRGsuite offers the users control over a large number of important parameters in docking simulations including the assignment of flexible side-chain...

  10. Overcoming maladaptive plasticity through plastic compensation

    Institute of Scientific and Technical Information of China (English)

    Matthew R.J.MORRIS; Sean M.ROGERS

    2013-01-01

    Most species evolve within fluctuating environments,and have developed adaptations to meet the challenges posed by environmental heterogeneity.One such adaptation is phenotypic plasticity,or the ability of a single genotype to produce multiple environmentally-induced phenotypes.Yet,not all plasticity is adaptive.Despite the renewed interest in adaptive phenotypic plasticity and its consequences for evolution,much less is known about maladaptive plasticity.However,maladaptive plasticity is likely an important driver of phenotypic similarity among populations living in different environments.This paper traces four strategies for overcoming maladaptive plasticity that result in phenotypic similarity,two of which involve genetic changes (standing genetic variation,genetic compensation) and two of which do not (standing epigenetic variation,plastic compensation).Plastic compensation is defined as adaptive plasticity overcoming maladaptive plasticity.In particular,plastic compensation may increase the likelihood of genetic compensation by facilitating population persistence.We provide key terms to disentangle these aspects of phenotypic plasticity and introduce examples to reinforce the potential importance of plastic compensation for understanding evolutionary change.

  11. Cross Cutting Relative Navigation Technologies for Improved Landing Accuracy and Vehicle-to-Vehicle Rendezvous and Docking

    Science.gov (United States)

    Miller, K. L.; Masciarelli, J.; Rohrschneider, R. R.

    2012-06-01

    This presentation addresses recent development and test progress, as well as future technology advancement plans for precision landing and Autonomous Rendezvous, Proximity Operations and Docking (ARPOD).

  12. The relationship between tail biting in pigs, docking procedure and other management practices.

    Science.gov (United States)

    Hunter, E J; Jones, T A; Guise, H J; Penny, R H; Hoste, S

    2001-01-01

    The tail length (docked, tipped or undocked) and tail status (bitten or unbitten) of 27,870 pigs from 450 units was recorded at six UK abattoirs. A farm survey of the final finishing stage was used to investigate the relationship between management practice and tail biting. This showed that docking was the most important factor influencing the probability of being not bitten, with 2.4% of docked and 8.5% of long-tailed pigs being tail-bitten. The following factors reduced the probability of long-tailed pigs being tail-bitten; light straw provision, use of natural ventilation or artificially controlled natural ventilation (ACNV), mixed sex grouping, meal or liquid feeding, and use of double or multi-space feeders. Docked and long-tailed pigs provided with light straw and natural ventilation/ACNV had levels of tail biting of 1.2% and 4.3% respectively; 3.9% of docked pigs with artificial ventilation and no straw were tail-bitten. Long-tailed pigs fed via double or multi-space feeders also had 3.9% of tails bitten. PMID:11145831

  13. DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology

    Directory of Open Access Journals (Sweden)

    Michael-Rock Goldsmith

    2014-01-01

    Full Text Available We have developed DockScreen, a database of in silico biomolecular interactions designed to enable rational molecular toxicological insight within a computational toxicology framework. This database is composed of chemical/target (receptor and enzyme binding scores calculated by molecular docking of more than 1000 chemicals into 150 protein targets and contains nearly 135 thousand unique ligand/target binding scores. Obtaining this dataset was achieved using eHiTS (Simbiosys Inc., a fragment-based molecular docking approach with an exhaustive search algorithm, on a heterogeneous distributed high-performance computing framework. The chemical landscape covered in DockScreen comprises selected environmental and therapeutic chemicals. The target landscape covered in DockScreen was selected based on the availability of high-quality crystal structures that covered the assay space of phase I ToxCast in vitro assays. This in silico data provides continuous information that establishes a means for quantitatively comparing, on a structural biophysical basis, a chemical’s profile of biomolecular interactions. The combined minimum-score chemical/target matrix is provided.

  14. Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening

    Science.gov (United States)

    Villarreal, Marcos A.

    2016-01-01

    Autodock Vina is a very popular, and highly cited, open source docking program. Here we present a scoring function which we call Vinardo (Vina RaDii Optimized). Vinardo is based on Vina, and was trained through a novel approach, on state of the art datasets. We show that the traditional approach to train empirical scoring functions, using linear regression to optimize the correlation of predicted and experimental binding affinities, does not result in a function with optimal docking capabilities. On the other hand, a combination of scoring, minimization, and re-docking on carefully curated training datasets allowed us to develop a simplified scoring function with optimum docking performance. This article provides an overview of the development of the Vinardo scoring function, highlights its differences with Vina, and compares the performance of the two scoring functions in scoring, docking and virtual screening applications. Vinardo outperforms Vina in all tests performed, for all datasets analyzed. The Vinardo scoring function is available as an option within Smina, a fork of Vina, which is freely available under the GNU Public License v2.0 from http://smina.sf.net. Precompiled binaries, source code, documentation and a tutorial for using Smina to run the Vinardo scoring function are available at the same address. PMID:27171006

  15. Full structure building and docking of NifS from extremophile Acidithiobacillus ferrooxidans

    Institute of Scientific and Technical Information of China (English)

    LIU Yuan-dong; QIU Guan-zhou; WANG Hai-dong; JIANG Ying; ZHANG Cheng-gui; XIA Le-xia

    2008-01-01

    The gene iscS-2 from extremophile Acidithiobacillus ferrooxidans may play a crucial role in nitrogenase maturation. To investigate the protein encoded by this gene, a reliable integral three-dimensional molecular structure was built. The obtained structure was further used to search binding sites, carry out the flexible docking with cofactor pyridoxal 5′-phosphate(PLP) and substrate cysteine, and identify its key residues. The docking results of PLP reveal that the residues of Lys203, His100, Thr73, Ser200, His202, Asp177 and Gln180 have large interaction energies and/or hydrogen bonds fixation with PLP. The docking results of cysteine show that the amino group in cysteine is very near His100, Lys203 and PLP, and the interaction energies for cysteine with them are very big. These identified residues are in line with the experimental facts of NifS from other sources. Moreover, the four residues of Asn152, Val179, Ala102 and Met148 in the PLP docking and the two residues of Lys208 and Ala102 in the cysteine docking also have large interaction energies, which are fitly conserved in NifS from all kinds of sources but have not been identified before. According to these results, this gene encodes NifS protein, and the substrate cysteine can be effectively recruited into the active site. Furthermore, all of the above detected key residues are directly responsible for the binding and/or catalysis of PLP and cysteine.

  16. Structural determinants of resveratrol for cell proliferation inhibition potency: experimental and docking studies of new analogs.

    Science.gov (United States)

    Mazué, Frédéric; Colin, Didier; Gobbo, Jessica; Wegner, Maria; Rescifina, Antonio; Spatafora, Carmela; Fasseur, Dominique; Delmas, Dominique; Meunier, Philippe; Tringali, Corrado; Latruffe, Norbert

    2010-07-01

    Resveratrol is the subject of intense research because of the abundance of this compound in the human diet and as one of the most valuable natural chemopreventive agents. Further advances require new resveratrol analogs be used to identify the structural determinants of resveratrol for the inhibition potency of cell proliferation by comparing experimental and docking studies. Therefore, we synthesized new trans/(E)- and cis/(Z)-resveratrol - analogs not reported to date - by modifying the hydroxylation pattern of resveratrol and a double bond geometry. We included them in a larger panel of 14 molecules, including (Z)-3,5,4'-trimethoxystilbene, the most powerful molecule that is used as reference. Using a docking model complementary to experimental studies on the proliferation inhibition of the human colorectal tumor SW480 cell line, we show that methylation is the determinant substitution in inhibition efficacy, but only in molecules bearing a Z configuration. Most of the synthetic methylated derivatives (E or Z) stop mitosis at the M phase and lead to polyploid cells, while (E)-resveratrol inhibits cells at the S phase. Docking studies show that almost all of the docked structures of (Z)-polymethoxy isomers, but not most of the (E)-polymethoxy isomers substantially overlap the docked structure of combretastatin A-4, taken as reference ligand at the colchicine-tubulin binding site. PMID:20395019

  17. Effects of Low Earth Orbit on Docking Seal Materials

    Science.gov (United States)

    Imka, Emily C.; Asmar, Olivia C.; deGroh, Henry C., III; Banks, Bruce A.

    2014-01-01

    Spacecraft docking seals are typically made of silicone elastomers. When such seals are exposed to low Earth orbit (LEO) conditions, they can suffer damage from ultraviolet (UV) radiation and atomic oxygen (AO, or monoatomic oxygen, the predominant oxygen species in LEO). An experiment flew on the International Space Station (ISS) to measure the effects of LEO on seal materials S0383-70 and ELA-SA-401 and various mating counterface materials which included anodized aluminum. Samples flown in different orientations received different amounts of UV and AO. The hypotheses were that most of the damage would be from UV, and 10 days or more of exposure in LEO would badly damage the seals. Eighteen seals were exposed for 543 days in ram (windward), zenith (away from Earth), or wake (leeward) orientations, and 15 control samples (not flown) provided undamaged baseline leakage. To determine post-flight leak rates, each of the 33 seals were placed in an O-ring groove of a leak test fixture and pressure tested over time. Resistance temperature detectors (RTDs), pressure transducers, and LabVIEW (National Instruments) programs were used to measure and analyze the temperature and pressure and calculate leakage. Average leakage of control samples was 2.6 x 10(exp -7) lbs/day. LEO exposure did not considerably damage ELA-SA-401. The S0383-70 flight samples leaked at least 10 times more than ELA-SA-401 in all cases except one, demonstrating that ELA-SA-401 may be a more suitable sealing material in LEO. AO caused greater damage than UV; samples in ram orientation (receiving an AO fluence of 4.3 x 10(exp 21) atoms/(sq cm) and in wake (2.9x 10(exp 20) atoms/(sq cm)) leaked more than those in zenith orientation (1.58 x 10(exp 20) atoms/(sq cm)), whereas variations in UV exposure did not seem to affect the samples. Exposure to LEO did less damage to the seals than hypothesized, and the data did not support the conjecture that UV causes more damage than AO.

  18. Analytic compensation methods in dynamic tomography; Methodes analytiques de compensation des deformations en tomographie dynamique

    Energy Technology Data Exchange (ETDEWEB)

    Roux, S.; Desbat, L.; Koenig, A.; Grangeat, P. [Laboratoire TIMC-IMAG UMR CNRS 5525, Faculte de Medecine de Grenoble, 38 - La Tronche (France)]|[CEA Grenoble, Lab. Electronique et de Technologie de l' Informatique (LETI), 38 (France)

    2004-07-01

    Recent progresses in X-ray tomography allow to study some organs dynamically. The aim of this work is to analyze the deformation compensation algorithms used to integrate dynamical evolution models into the image reconstruction processes. An exact and efficient analytical method of movement compensation is presented and applied to simulated data. Abstract only. (J.S.)

  19. Risk compensation behaviours in construction workers' activities.

    Science.gov (United States)

    Feng, Yingbin; Wu, Peng

    2015-01-01

    The purpose of this study was to test whether the construction workers have the tendency of engaging in risk compensation behaviours, and identify the demographic variables, which may influence the extent to which the construction workers may show risk compensation behaviours. Both quantitative (survey) and qualitative (interviews) approaches were used in this study. A questionnaire survey was conducted with all the construction workers on three building construction sites of a leading construction company in Australia. Semi-structured interviews were then conducted to validate the findings of the quantitative research. The findings indicate that workers tend to show risk compensation behaviours in the construction environment. The workers with more working experience, higher education, or having never been injured at work before have a higher tendency to show risk compensation in their activities than the others. The implication is that contractors need to assess the potential influence of workers' risk compensation behaviours when evaluating the effect of risk control measures. It is recommended that supervisors pay more attention to the behavioural changes of those workers who have more experience, higher education, and have never been injured before after the implementation of new safety control measures on construction site. PMID:24134314

  20. Managerial Stock Compensation and Risky Investment

    Directory of Open Access Journals (Sweden)

    Raluca Georgiana Nastasescu

    2009-06-01

    Full Text Available This study analyzes the relationship between the mix of CEO equity-based compensation, namely stock options and restricted stock, and firms' risky investment. In general, the theory suggests that long-term compensation aligns CEOs' and shareholders' interests by inducing the managers to undertake risky investment, which has a positive impact on longterm well-being of the firm. However, as my results show, it is important to distinguish between types of awards since they can have different effects on the riskiness of the firm. In this respect, I answer the question how are different types of stock based compensation related to the executives' determination to increase or not the intensity of the firm's risky investment? I find that awarding the CEOs preponderantly with stock options positively affects the firm's level of R&D investment. Conversely, a higher proportion of restricted stock in the CEO's compensation is related to lower investment in (risky R&D. The inverse relation of causality also holds. Firms that make intensive R&D investments are more likely to award their CEOs with more stock options relative to restricted stock. Overall, the results are consistent with the theoretical prediction, in that the managerial compensation scheme plays an important role in determining the level of R&D investment.

  1. Temperature compensation and entrainment in circadian rhythms

    International Nuclear Information System (INIS)

    To anticipate daily variations in the environment and coordinate biological activities into a daily cycle many organisms possess a circadian clock. In the absence of external time cues the circadian rhythm persists with a period of approximately 24 h. The clock phase can be shifted by single pulses of light, darkness, chemicals, or temperature and this allows entrainment of the clock to exactly 24 h by cycles of these zeitgebers. On the other hand, the period of the circadian rhythm is kept relatively constant within a physiological range of constant temperatures, which means that the oscillator is temperature compensated. The mechanisms behind temperature compensation and temperature entrainment are not fully understood, neither biochemically nor mathematically. Here, we theoretically investigate the interplay of temperature compensation and entrainment in general oscillatory systems. We first give an analytical treatment for small temperature shifts and derive that every temperature-compensated oscillator is entrainable to external small-amplitude temperature cycles. Temperature compensation ensures that this entrainment region is always centered at the endogenous period regardless of possible seasonal temperature differences. Moreover, for small temperature cycles the entrainment region of the oscillator is potentially larger for rectangular pulses. For large temperature shifts we numerically analyze different circadian clock models proposed in the literature with respect to these properties. We observe that for such large temperature shifts sinusoidal or gradual temperature cycles allow a larger entrainment region than rectangular cycles. (paper)

  2. Do executives get appropriate compensation? : Evidence from intellectual capital perspective

    OpenAIRE

    Xie, Yamin

    2013-01-01

    This paper presents an empirical analysis of top executive compensation from intellectual capital perspective using data from US listed companies and aims to examine whether executives get appropriate compensation. I propose a pay-contribution compensation scheme and extend previous research on agency theory, by exploring how executive compensation contract design may be based on the firm’s intellectual capital (IC). Such features would serve the core purpose of compensation design, which is ...

  3. WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking.

    Science.gov (United States)

    Murphy, Robert B; Repasky, Matthew P; Greenwood, Jeremy R; Tubert-Brohman, Ivan; Jerome, Steven; Annabhimoju, Ramakrishna; Boyles, Nicholas A; Schmitz, Christopher D; Abel, Robert; Farid, Ramy; Friesner, Richard A

    2016-05-12

    We have developed a new methodology for protein-ligand docking and scoring, WScore, incorporating a flexible description of explicit water molecules. The locations and thermodynamics of the waters are derived from a WaterMap molecular dynamics simulation. The water structure is employed to provide an atomic level description of ligand and protein desolvation. WScore also contains a detailed model for localized ligand and protein strain energy and integrates an MM-GBSA scoring component with these terms to assess delocalized strain of the complex. Ensemble docking is used to take into account induced fit effects on the receptor conformation, and protein reorganization free energies are assigned via fitting to experimental data. The performance of the method is evaluated for pose prediction, rank ordering of self-docked complexes, and enrichment in virtual screening, using a large data set of PDB complexes and compared with the Glide SP and Glide XP models; significant improvements are obtained. PMID:27054459

  4. Discovery of Anti-SARS Coronavirus Drug Based on Molecular Docking and Database Screening

    Institute of Scientific and Technical Information of China (English)

    CHEN,Hai-Feng(陈海峰); YAO,Jian-Hua(姚建华); SUN,Jing(孙晶); LI,Qiang(李强); LI,Feng(李丰); FAN,Bo-Tao(范波涛); YUAN,Shen-Gang(袁身刚)

    2004-01-01

    The active site of 3CL proteinase (3CLpro) for coronavirus was identified by comparing the crystal structures of human and porcine coronavirus. The inhibitor of the main protein of rhinovirus (Ag7088) could bind with 3CLpro of human coronavirus, then it was selected as the reference for molecular docking and database screening. The ligands from two databases were used to search potential lead structures with molecular docking. Several structures from natural products and ACD-SC databases were found to have lower binding free energy with 3CLpro than that of Ag7088. These structures have similar hydrophobicity to Ag7088. They have complementary electrostatic potential and hydrogen bond acceptor and donor with 3CLpro, showing that the strategy of anti-SARS drug design based on molecular docking and database screening is feasible.

  5. What in silico molecular docking can do for the `bench-working biologists'

    Indian Academy of Sciences (India)

    Marius Mihăşan

    2012-12-01

    Required by an increasing amount of scientists, the in silico docking field is in full expansion, new algorithms and methods appearing at an exponential rate. The sheer range of available programs is overwhelming for the bench-working biologist, which is often discouraging by the lack of a graphical user interface, good user manual or literature to validate a given program. This mini-review attempts to present the docking problem and available solutions from a non-bioinformatician point of view and makes a selection of the available servers and programs. These tools are evaluated from several points of view, as numbers of citations, ease of usage and computer requirements. Finally, the capabilities and limitations as well as specific applications of in silico docking techniques are presented.

  6. Modulation of current through a nanopore induced by a charged globule: implications for DNA-docking

    CERN Document Server

    Chinappi, Mauro; Cecconi, Fabio; Marconi, Umberto Marini Bettolo; Melchionna, Simone

    2015-01-01

    The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of the two events. However, at low voltages a clear distinction of the two phases is lost. By using numerical simulations we clarify how the current signature associated to the docking events depends on the applied voltage. The simulations show that at small voltage the DNA globule enhances the pore conductance due to an enrichment of charge carriers. At high voltage, the globule drains substantial charge carriers from the pore region, thereby reducing the overall conductance. The results provide a new interpretation to the experimental data on conductance and show how docking interferes with the translocation signal, of potential interest for sequencing applications.

  7. Exploration of the binding mode between (-)-zampanolide and tubulin using docking and molecular dynamics simulation.

    Science.gov (United States)

    Liao, Si-Yan; Mo, Guang-Quan; Chen, Jin-Can; Zheng, Kang-Cheng

    2014-02-01

    The binding mode of (-)-zampanolide (ZMP) to tubulin was investigated using docking, molecular dynamics (MD) simulation, and binding free-energy calculations. The docking studies validated the experimental results indicating that the paclitaxel site is the binding site for (-)-ZMP. The 18 ns MD simulation shows the docking mode has changed a lot, whereas it offers more reliable binding data. MM-PBSA binding free-energy calculations further confirmed the results of the MD simulation. The study revealed that hydrophobic interactions play an important role in stabilizing the binding, and the strong hydrogen bond formed with Asp224 enhances the affinity for tubulin. Meanwhile, the results support the assumption that (-)-ZMP can be attacked by His227, leading to a nucleophilic reaction and covalent binding. These theoretical results lead to a greater understanding of the mechanism of action of binding to tubulin, and will therefore aid the design of new compounds with higher affinities for tubulin. PMID:24478043

  8. Synthesis of hydrazine based novel HMG coA inhibitor and its docking studies

    Directory of Open Access Journals (Sweden)

    Saravanan. B

    2013-12-01

    Full Text Available Heart attack is the recent attention to the medical sciences and cardiac low density cholesterol (LDL has a significant role in inhibiting the arrest. Various pathways having the keypoints which can interrupt the synthesis of bad cholesterol. In this study Hydrazine based compound is choosen due to its wide applications, the 1,2-Bis (2-hydroxy-5-methylbenzylidene - hydrazine crystals were synthesized. It was taken as a ligand for molecular docking. The target receptor used for docking is HMG-CoA reductase whose crystal structure is available on the PDB database as PDB ID: 1DQ8. For docking analysis, Autodock tool v4. 2 program used. The synthesized crystals are subjected to single crystal X-ray studies in order to investigate their molecular structure.

  9. Development of Algorithms for Approaching and Docking Underwater Vehicle with Underwater Station

    Directory of Open Access Journals (Sweden)

    Gurenko B.V.

    2015-01-01

    Full Text Available Underwater vehicles (UV are widely spread nowadays. Their efficient application requires accompanying base ships or net of stations for technical servicing. Fast and energy-efficient docking is one of the key requirements for trouble-free operation. In this paper authors describe the research and development of algorithms for UV control system that allows docking with underwater station. The process is divided in two steps: moving to docking zone and vehicle positioning of station. First task includes development of path regulator. The proposed one features separation of control channels for simple adjustment and gives best results when multicoupling influence is low. Second task was solved on the basis of UV mathematical model. Developed control values were tested in simulation and proved themselves to be efficient. Authors give results of coordinate changes, control force modifications and deviation of velocity and orientation angles from the required values.

  10. Using RosettaLigand for small molecule docking into comparative models.

    Directory of Open Access Journals (Sweden)

    Kristian W Kaufmann

    Full Text Available Computational small molecule docking into comparative models of proteins is widely used to query protein function and in the development of small molecule therapeutics. We benchmark RosettaLigand docking into comparative models for nine proteins built during CASP8 that contain ligands. We supplement the study with 21 additional protein/ligand complexes to cover a wider space of chemotypes. During a full docking run in 21 of the 30 cases, RosettaLigand successfully found a native-like binding mode among the top ten scoring binding modes. From the benchmark cases we find that careful template selection based on ligand occupancy provides the best chance of success while overall sequence identity between template and target do not appear to improve results. We also find that binding energy normalized by atom number is often less than -0.4 in native-like binding modes.

  11. Carbon Dioxide Removal Troubleshooting aboard the International Space Station (ISS) during Space Shuttle (STS) Docked Operations

    Science.gov (United States)

    Matty, Christopher M.; Cover, John M.

    2009-01-01

    The International Space Station (ISS) represents a largely closed-system habitable volume which requires active control of atmospheric constituents, including removal of exhaled Carbon Dioxide (CO2). The ISS provides a unique opportunity to observe system requirements for (CO2) removal. CO2 removal is managed by the Carbon Dioxide Removal Assembly (CDRA) aboard the US segment of ISS and by Lithium Hydroxide (LiOH) aboard the Space Shuttle (STS). While the ISS and STS are docked, various methods are used to balance the CO2 levels between the two vehicles, including mechanical air handling and management of general crew locations. Over the course of ISS operation, several unexpected anomalies have occurred which have required troubleshooting, including possible compromised performance of the CDRA and LiOH systems, and possible imbalance in CO2 levels between the ISS and STS while docked. This paper will cover efforts to troubleshoot the CO2 removal systems aboard the ISS and docked STS.

  12. Comparative docking and CoMFA analysis of curcumine derivatives as HIV-1 integrase inhibitors.

    Science.gov (United States)

    Gupta, Pawan; Garg, Prabha; Roy, Nilanjan

    2011-08-01

    The docking studies and comparative molecular field analysis (CoMFA) were performed on highly active molecules of curcumine derivatives against 3' processing activity of HIV-1 integrase (IN) enzyme. The optimum CoMFA model was selected with statistically significant cross-validated r(2) value of 0.815 and non-cross validated r (2) value of 0.99. The common pharmacophore of highly active molecules was used for screening of HIV-1 IN inhibitors. The high contribution of polar interactions in pharmacophore mapping is well supported by docking and CoMFA results. The results of docking, CoMFA, and pharmacophore mapping give structural insights as well as important binding features of curcumine derivatives as HIV-1 IN inhibitors which can provide guidance for the rational design of novel HIV-1 IN inhibitors. PMID:21327540

  13. Differential regulation of synaptic vesicle tethering and docking by UNC-18 and TOM-1

    Directory of Open Access Journals (Sweden)

    Elena O Gracheva

    2010-10-01

    Full Text Available The assembly of SNARE complexes between syntaxin, SNAP-25 and synaptobrevin is required to prime synaptic vesicles for fusion. Since Munc18 and tomosyn compete for syntaxin interactions, the interplay between these proteins is predicted to be important in regulating synaptic transmission. We explored this possibility, by examining genetic interactions between C. elegans unc-18(Munc18, unc-64(syntaxin and tom-1(tomosyn. We have previously demonstrated that unc-18 mutants have reduced synaptic transmission, whereas tom-1 mutants exhibit enhanced release. Here we show that the unc-18 mutant release defect is associated with loss of two morphologically distinct vesicle pools; those tethered within 25nm of the plasma membrane and those docked with the plasma membrane. In contrast, priming defective unc-13 mutants accumulate tethered vesicles, while docked vesicles are greatly reduced, indicating tethering is UNC-18-dependent and occurs in the absence of priming. C. elegans unc-64 mutants phenocopy unc-18 mutants, losing both tethered and docked vesicles, whereas overexpression of open syntaxin preferentially increases vesicle docking, suggesting UNC-18/closed syntaxin interactions are responsible for vesicle tethering. Given the competition between vertebrate tomosyn and Munc18, for syntaxin binding, we hypothesized that C. elegans TOM-1 may inhibit both UNC-18-dependent vesicle targeting steps. Consistent with this hypothesis, tom-1 mutants exhibit enhanced UNC-18 plasma membrane localization and a concomitant increase in both tethered and docked synaptic vesicles. Furthermore, in tom-1;unc-18 double mutants the docked, primed vesicle pool is preferentially rescued relative to unc-18 single mutants. Together these data provide evidence for the differential regulation of two vesicle targeting steps by UNC-18 and TOM-1 through competitive interactions with syntaxin

  14. Meteoroid and Orbital Debris Threats to NASA's Docking Seals: Initial Assessment and Methodology

    Science.gov (United States)

    deGroh, Henry C., III; Gallo, Christopher A.; Nahra, Henry K.

    2009-01-01

    The Crew Exploration Vehicle (CEV) will be exposed to the Micrometeoroid Orbital Debris (MMOD) environment in Low Earth Orbit (LEO) during missions to the International Space Station (ISS) and to the micrometeoroid environment during lunar missions. The CEV will be equipped with a docking system which enables it to connect to ISS and the lunar module known as Altair; this docking system includes a hatch that opens so crew and supplies can pass between the spacecrafts. This docking system is known as the Low Impact Docking System (LIDS) and uses a silicone rubber seal to seal in cabin air. The rubber seal on LIDS presses against a metal flange on ISS (or Altair). All of these mating surfaces are exposed to the space environment prior to docking. The effects of atomic oxygen, ultraviolet and ionizing radiation, and MMOD have been estimated using ground based facilities. This work presents an initial methodology to predict meteoroid and orbital debris threats to candidate docking seals being considered for LIDS. The methodology integrates the results of ground based hypervelocity impacts on silicone rubber seals and aluminum sheets, risk assessments of the MMOD environment for a variety of mission scenarios, and candidate failure criteria. The experimental effort that addressed the effects of projectile incidence angle, speed, mass, and density, relations between projectile size and resulting crater size, and relations between crater size and the leak rate of candidate seals has culminated in a definition of the seal/flange failure criteria. The risk assessment performed with the BUMPER code used the failure criteria to determine the probability of failure of the seal/flange system and compared the risk to the allotted risk dictated by NASA s program requirements.

  15. Automatic Transaction Compensation for Reliable Grid Applications

    Institute of Scientific and Technical Information of China (English)

    Fei-Long Tang; Ming-Lu Li; Joshua Zhexue Huang

    2006-01-01

    As grid technology is expanding from scientific computing to business applications, service oriented grid computing is aimed at providing reliable services for users and hiding complexity of service processes from them. The grid services for coordinating long-lived transactions that occur in business applications play an important role in reliable grid applications. In this paper, the grid transaction service (GridTS) is proposed for dealing with long-lived business transactions. We present a compensation-based long-lived transaction coordination algorithm that enables users to select results from committed sub-transactions. Unlike other long-lived transaction models that require application programmers to develop corresponding compensating transactions, GridTS can automatically generate compensating transactions on execution of a long-lived grid transaction. The simulation result has demonstrated the feasibility of GridTS and effectiveness of the corresponding algorithm.

  16. Compensation: Will it provide a waste site?

    International Nuclear Information System (INIS)

    Offering an attractive compensation package to persuade a community to voluntarily accept an otherwise undesirable facility may work in some cases, but it's not likely to work for high-level nuclear-waste disposal. The public perception of the risks involved and the public distrust of the institutions responsible for managing those risks are just too great. Much of the controversy stems from public perceptions that the site-selection process itself is unfair. Resentment builds when this occurs, and offers of compensation come to be labeled bribes or blood money. The driving force behind current nuclear-waste policy is intergenerational equity - the moral concept that the generation that produced the waste should dispose of it, permanently. Regardless of the moral appeal, doubts have been raised about the technical feasibility of this approach. Alternatives featuring intergenerational monetary compensation may better honor the commitment hor-ellipsis and reduce pressure to try to do what may be impossible

  17. Incomplete and imperfect information for sales compensation

    Directory of Open Access Journals (Sweden)

    Raluca Valeanu

    2010-12-01

    Full Text Available Sales force compensation represents the fix and / or variable payment by the company. To compensate agents based on the results, the company set a goal which is brought to their attention through the compensation plan. Applying the model of moral hazard, where the agent behavior cannot be verified, it cannot be specified in the contract what is the expected behavior of the agent. In order to make an offer to contract principal should know the effort that the agent will submit it to define the payment and the contract is determined optimally in trade between the two conflicting objectives of the two participants in the contract. Although agent behavior cannot be verified, the result of this behavior should be measurable at the end of the contract so that the employer may make the contract contingent on effort commission agent for sale of which is measured by the amount of earnings to the company.

  18. Supersymmetric composite gauge fields with compensators

    Science.gov (United States)

    Nishino, Hitoshi; Rajpoot, Subhash

    2016-06-01

    We study supersymmetric composite gauge theory, supplemented with compensator mechanism. As our first example, we give the formulation of N = 1 supersymmetric non-Abelian composite gauge theory without the kinetic term of a non-Abelian gauge field. The important ingredient is the Proca-Stueckelberg-type compensator scalar field that makes the gauge-boson field equation non-singular, i.e., the field equation can be solved for the gauge field algebraically as a perturbative expansion. As our second example, we perform the gauging of chiral-symmetry for N = 1 supersymmetry in four dimensions by a composite gauge field. These results provide supporting evidence for the consistency of the mechanism that combines the composite gauge field formulations and compensator formulations, all unified under supersymmetry.

  19. Histopathological Characterization of Tail Injury and Traumatic Neuroma Development after Tail Docking in Piglets

    OpenAIRE

    Sandercock, D A; Smith, S H; Di Giminiani, P.; Edwards, S. A.

    2016-01-01

    Tail docking of neonatal pigs is widely used as a measure to reduce the incidence of tail biting, a complex management problem in the pig industry. Concerns exist over the long-term consequences of tail docking for possible tail stump pain sensitivity due to the development of traumatic neuromas in injured peripheral nerves. Tail stumps were obtained post mortem from four female pigs at each of 1, 4, 8 and 16 weeks following tail amputation (approximately two-thirds removed) by a gas-heated d...

  20. Concepts to Automate Fluid Transfer Capability of Low Impact Docking System (LIDS)

    Science.gov (United States)

    Miernik, Janie H.; Lukens, Scott; Robertson, Jeff

    2005-01-01

    The capability to transfer mass between spacecraft is necessary for many mission scenarios. Docking and berthing operations have enabled fluid, electrical, crew and equipment transfers to some degree on all manned space operations since the Gemini program. The Apollo program performed some sophisticated docking maneuvers to land men on the moon and return them safely to Earth. These programs primarily transferred crew, equipment, and pressurized atmosphere between docked spacecraft. The International Space Station (ISS) U.S. modules are connected by Common Berthing Mechanism (CBM) portals. They provide many feed-through ports for electrical, and fluid transfer between modules, as well as a large diameter crew and equipment tunnel. Fluid and electrical jumpers are manually installed after the CBM sealing surfaces have been securely mated to maintain the pressurized cabin environment. CBM berthing and subsequent fluid transfer capability requires a lengthy manual process involving an active interface that mates with a passive half. The Androgynous Peripheral Attach System (MAS) a Russian technology that docked the Russian Zarya module to Unity, or Node 1, is a more complex system that also is capable of fuel transfer, enabling refueling of the Russian re-boost engines on ISS. For several years, a Low Impact Docking System (LIDS) has been under development at Johnson Space Center (JSC). This docking technology has a requirement to be androgynous in order to allow the fabrication of a single configuration that can dock with all other LIDS units. It is desired to make electrical and fluid coupling mating an automated process to enable routine docking and undocking operations to support future exploration missions. It is envisioned that modular design and vehicle assembly will require an efficient LIDS for fuel, electrical, crew, and equipment transfer. Marshall Space Flight Center (MSFC) has joined the LIDS development effort and plans to employ fluid transfer concepts

  1. Interaction of CTX­M­15 enzyme with cefotaxime: a molecular modelling and docking study

    OpenAIRE

    Shakil, Shazi; Khan, Asad Ullah

    2010-01-01

    Extended­spectrum β­lactamases (ESBLs) are the bacterial enzymes that make them resistant to advanced-generation cephalosporins. CTXM enzymes (the most prevalent ESBL­type) target cefotaxime. Aims of the study were: Modelling of CTX­M enzyme from bla CTX­M sequences of clinical Escherichia coli isolates Docking of cefotaxime with modelled CTX­M enzymes to identify amino acid residues crucial to their interaction To hypothesize a possible relationship between ’interaction energy of the docked ...

  2. Docking stability and electronic structure of azurin-cytochrome c551 complex system

    Science.gov (United States)

    Sugiyama, Ayumu; Takamatsu, Yuichiro; Nishikawa, Keigo; Nagao, Hidemi; Nishikawa, Kiyoshi

    We investigate the docking structure between cytochrome c551 and azurin proteins by quantum mechanical calculation and molecular dynamics (MD). A model for the docking structure of the cytochrome-azurin complex is presented. We calculate the charge distribution around the active site for each protein and force field parameters to simulate the complex system by MD. We estimate some physical properties, such as binding free energy and the dynamical cross-correlation map. We discuss the stability of the cytochrome c551-azurin complex system.

  3. Synthesis, anti-inflammatory evaluation and docking studies of some new fluorinated fused quinazolines.

    Science.gov (United States)

    Balakumar, C; Lamba, P; Kishore, D Pran; Narayana, B Lakshmi; Rao, K Venkat; Rajwinder, K; Rao, A Raghuram; Shireesha, B; Narsaiah, B

    2010-11-01

    A series of novel 8/10-trifluoromethyl-substituted-imidazo[1,2-c] quinazolines have been synthesized and evaluated in vivo (rat paw edema) for their anti-inflammatory activity and in silico (docking studies) to recognize the hypothetical binding motif of the title compounds with the cyclooxygenase isoenzymes (COX-1 and COX-2) employing GOLD (CCDC, 4.0.1 version) software. The compounds, 9b and 10b, were found to have good anti-inflammatory activity [around 80% of the standard: indomethacin]. The binding mode of the title compounds has been proposed based on the docking studies. PMID:20800934

  4. Post-docking virtual screening of diverse binding pockets: comparative study using DOCK, AMMOS, X-Score and FRED scoring functions.

    Science.gov (United States)

    Pencheva, Tania; Soumana, Oumarou Samna; Pajeva, Ilza; Miteva, Maria A

    2010-06-01

    Most of the benchmark studies on docking-scoring methods reported in the last decade conclude that no single scoring function performs well across different protein targets. In this study a comparison of thirteen commonly used force field and empirical scoring functions as implemented in DOCK, AMMOS, X-Score and FRED is carried out on five proteins with diverse binding pockets. The performance is analyzed in relation to the physicochemical properties of the binding sites. The solvation effects are considered via the Generalized Born/Surface Area (GBSA) solvation method for one of the assessed scoring functions. We examined the ability of these scoring functions to discriminate between active and inactive compounds over receptor-based focused libraries. Our results demonstrated that the employed here empirical scoring functions were more appropriate for the pocket of predominant hydrophobic nature while the force field scoring functions performed better on the mixed or polar pockets. PMID:20227800

  5. 9 CFR 355.15 - Inedible material operating and storage rooms; outer premises, docks, driveways, etc.; fly...

    Science.gov (United States)

    2010-01-01

    ... storage rooms; outer premises, docks, driveways, etc.; fly-breeding material; nuisances. 355.15 Section....15 Inedible material operating and storage rooms; outer premises, docks, driveways, etc.; fly... any material in which flies may breed, or the maintenance of any nuisance on the premises shall not...

  6. Design of an I-Shaped Less-Than-Truckload Cross-Dock: A Simulation Experiment Study

    Science.gov (United States)

    Leng, Kaijun; Shi, Wen; Chen, Jinbo; Lv, Zhihan

    2015-12-01

    The most important decision in cross-docking design is the number of unloading and loading doors. This paper focuses on the design issues of unloading and loading doors of symmetric-I-shaped (I-LTL) cross-docks pervasive in the Chinese auto-part supplying chain which is obviously a very complex system. First of all, this paper analyzes the operation process of I-LTL cross-docking in detail and completes the construction of discrete event simulation that conforms to I-LTL cross-docking operation on the basis of practical details in reality through ARENA platform. In the simulation analysis, this paper selects the physical flow of parts (supporting for arrival frequency and loading capacity of transport vehicles) and I-LTL cross-docking as the simulation experimental factors and applies multilevel factorial design to carry out a large-scale simulation experiment. The results suggest that the required number of receiving dock doors is determined by the arrival frequency of storage vehicles and loading capacity. Moreover, the effect of arrival frequency index is far greater than the loading capacity index. On the other hand, the required number of shipping dock doors primarily depends on the cross-docking consolidation rate and vehicle arrival frequency. Moreover, the index action of consolidation rate is greater than the effect of arriving frequency linearity.

  7. Ligand similarity guided receptor selection enhances docking accuracy and recall for non-nucleoside HIV reverse transcriptase inhibitors.

    Science.gov (United States)

    Stanton, Richard A; Nettles, James H; Schinazi, Raymond F

    2015-11-01

    Non-nucleoside reverse transcriptase inhibitors (NNRTI) are allosteric inhibitors of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), a viral polymerase essential to infection. Despite the availability of >150 NNRTI-bound RT crystal structures, rational design of new NNRTI remains challenging because of the variability of their induced fit, hydrophobic binding patterns. Docking NNRTI yields inconsistent results that vary markedly depending on the receptor structure used, as only 27% of the >20k cross-docking calculations we performed using known NNRTI were accurate. In order to determine if a hospitable receptor for docking could be selected a priori, we evaluated more than 40 chemical descriptors for their ability to pre-select a best receptor for NNRTI cross-docking. The receptor selection was based on similarity scores between the bound- and target-ligands generated by each descriptor. The top descriptors were able to double the probability of cross-docking accuracy over random receptor selection. Additionally, recall of known NNRTI from a large library of similar decoys was increased using the same approach. The results demonstrate the utility of pre-selecting receptors when docking into difficult targets. Graphical Abstract Cross-docking accuracy increases when using chemical descriptors to determine the NNRTI with maximum similarity to the new compound and then docking into its respective receptor. PMID:26450349

  8. Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.

    Science.gov (United States)

    Gagnon, Jessica K; Law, Sean M; Brooks, Charles L

    2016-03-30

    Protein-ligand docking is a commonly used method for lead identification and refinement. While traditional structure-based docking methods represent the receptor as a rigid body, recent developments have been moving toward the inclusion of protein flexibility. Proteins exist in an interconverting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a well-appreciated computational challenge. To this end, we have developed the Flexible CDOCKER method as an extension of the family of complete docking solutions available within CHARMM. This method integrates atomically detailed side chain flexibility with grid-based docking methods, maintaining efficiency while allowing the protein and ligand configurations to explore their conformational space simultaneously. This is in contrast to existing approaches that use induced-fit like sampling, such as Glide or Autodock, where the protein or the ligand space is sampled independently in an iterative fashion. Presented here are developments to the CHARMM docking methodology to incorporate receptor flexibility and improvements to the sampling protocol as demonstrated with re-docking trials on a subset of the CCDC/Astex set. These developments within CDOCKER achieve docking accuracy competitive with or exceeding the performance of other widely utilized docking programs. PMID:26691274

  9. Reactive Power Compensation using a Matrix Converter

    OpenAIRE

    Holtsmark, Nathalie Marie-Anna

    2010-01-01

    This Master's thesis investigates a new application for the matrix converter: Shunt reactive power compensation. The suggested Matrix Converter-based Reactive power Compensation (MCRC) device is composed of a matrix converter, which input is connected to the grid and an electric machine at the output of the converter. The reactive power flowing in or out of the grid can be regulated with the matrix converter by controlling the magnitude and/or phase angle of the current at the input of the co...

  10. Convention on supplementary compensation for nuclear damage

    International Nuclear Information System (INIS)

    The Contracting parties recognize the importance of the measures provided in the Vienna Convention on Civil Liability for Nuclear Damage and the Paris Convention on Third party liability in the Field of Nuclear Energy as well as in national legislation on compensation for nuclear damage consistent with the principles of these conventions. The Contracting parties desire to establish a worldwide liability regime to supplement and enhance these measures with a view to increasing the amount of compensation for nuclear damage and encourage regional and global co-operation to promote a higher level of nuclear safety in accordance with the principle of international partnership and solidarity

  11. Security careers skills, compensation, and career paths

    CERN Document Server

    Walker, Stephen W

    2014-01-01

    The third edition of Security Careers is the authoritative reference for current job descriptions and pay practices of security, compliance, ethics, environmental, health and safety occupations. The job descriptions and compensation ranges in this report are drawn from research from the Foushée Group, which has been conducting this research since 1980. Security Careers includes more than 75 job descriptions for security-related positions, which range from the entry-level security guard to the top global corporate executive. It also provides four years of compensation trend data to give a th

  12. Beam loading compensation in the NLCTA

    International Nuclear Information System (INIS)

    In the design of the Next Linear Collider (NLC), multi-bunch operation is employed to improve efficiency at the cost of substantial beam loading. The RF pulse that powers the accelerator structures will be shaped to compensate for the effect of the transient loading along the bunch train. This scheme has been implemented in the Next Linear Collider Test Accelerator (NLCTA), a facility built to test the key accelerator technology of the NLC. In this paper the authors describe the compensation method, the techniques used to measure the energy variation along the bunch train, and results from tests with NLC-like beam currents

  13. Static compensators (STATCOMs) in power systems

    CERN Document Server

    Shahnia, Farhad; Ghosh, Arindam

    2014-01-01

    A static compensator (STATCOM), also known as static synchronous compensator, is a member of the flexible alternating current transmission system (FACTS) devices. It is a power-electronics based regulating device which is composed of a voltage source converter (VSC) and is shunt-connected to alternating current electricity transmission and distribution networks. The voltage source is created from a DC capacitor and the STATCOM can exchange reactive power with the network. It can also supply some active power to the network, if a DC source of power is connected across the capacitor. A STATCOM

  14. Application of fuzzy logic-neural network based reinforcement learning to proximity and docking operations: Special approach/docking testcase results

    Science.gov (United States)

    Jani, Yashvant

    1993-01-01

    As part of the RICIS project, the reinforcement learning techniques developed at Ames Research Center are being applied to proximity and docking operations using the Shuttle and Solar Maximum Mission (SMM) satellite simulation. In utilizing these fuzzy learning techniques, we use the Approximate Reasoning based Intelligent Control (ARIC) architecture, and so we use these two terms interchangeably to imply the same. This activity is carried out in the Software Technology Laboratory utilizing the Orbital Operations Simulator (OOS) and programming/testing support from other contractor personnel. This report is the final deliverable D4 in our milestones and project activity. It provides the test results for the special testcase of approach/docking scenario for the shuttle and SMM satellite. Based on our experience and analysis with the attitude and translational controllers, we have modified the basic configuration of the reinforcement learning algorithm in ARIC. The shuttle translational controller and its implementation in ARIC is described in our deliverable D3. In order to simulate the final approach and docking operations, we have set-up this special testcase as described in section 2. The ARIC performance results for these operations are discussed in section 3 and conclusions are provided in section 4 along with the summary for the project.

  15. Compensations in the Shapley value and the compensation solutions for graph games

    OpenAIRE

    Béal, Sylvain; Rémila, Eric; Solal, Philippe

    2010-01-01

    We consider an alternative expression of the Shapley value that reveals a system of compensations: each player receives an equal share of the worth of each coalition he belongs to, and has to compensate an equal share of the worth of any coalition he does not belong to. We give an interpretation in terms of formation of the grand coalition according to an ordering of the players and define the corresponding compensation vector. Then, we generalize this idea to cooperative games with a communi...

  16. Compensation for forest ecological services in China

    Institute of Scientific and Technical Information of China (English)

    Liu Can; Wang Sen; Zhang Wei; Liang Dan

    2007-01-01

    The paper discusses methods to compensate for the costs incurred in the supply of forest ecological services (FES), i.e.government dominated and market-based instruments as well as progress made so far in China. Factors which constrain the supply of these services and potential policy improvements are presented.

  17. A multiportal compensator system for IMRT delivery

    International Nuclear Information System (INIS)

    We have developed a multiportal compensator system for IMRT delivery, comprising a rotational compensator mount for a linac head, cylindrical compensator enclosures positioned in the mount, a vacuum-formed thermoplastic sheet with heavy alloy granules inside the enclosure, and a vacuum thermoforming device. The mount rotates like a revolver by a stepping motor, thus allowing automatic multiportal IMRT without exchanging compensators by human operators during treatment. The thermoforming device has servo-motor-driven 10x10 metal rod elements to actualize an arbitrary intensity profile. The thermoplastic sheet is preheated by a built-in biplanar heater and then it is placed over the rod elements. Subsequently, vacuum forming is performed through corner cut-outs of the rod elements. After forced cooling down, the heavy alloy granules are fed into the formed sheet. Preliminary experiment using solid water phantoms and an x-ray film has shown that the intensity profile on the film agrees reasonably well with the desired profile

  18. Compensation techniques for operational amplifier bias current

    International Nuclear Information System (INIS)

    Two techniques are proposed for the compensation of the input current on operational amplifiers that can be used on inverting and non-inverting configurations. A qualitative analysis of temperature drift problems is made, and as a practical application, the construction of a voltage follower for high impedance measurements is presented. (Author)

  19. Wavefront compensation applied to AVLIS laser systems

    International Nuclear Information System (INIS)

    The efficiency of an AVLIS system depends upon the power density and uniformity of the laser system. Because of wavefront aberrations the realized beam quality is not ideal. Wavefront compensation provides a means to improve beam quality and system efficiency. (author)

  20. The cost and compensability of trauma patients.

    Science.gov (United States)

    Curtis, Kate; Dickson, Cara; Black, Deborah; Nau, Thomas

    2009-02-01

    Injury in Australia was responsible for 400 000 hospitalisations in 2002. This study aimed to examine the direct costs of trauma patients in a Level 1 trauma centre and determine the compensability of those patients. Data on all admitted patients (206) filling trauma criteria were collected prospectively over a 3-month period (November 2006 to January 2007). A 10-question survey was completed on each patient to record mechanism of injury, third party private health insurance or workers compensation, and direct costs were also obtained. 30% of trauma admissions had an injury severity score (ISS)> 15 (n = 62; median ISS =9; range, 1-56). Median length of stay was 3 days (range, 1-126). Almost half (47%) of the patients were involved in road trauma, and 29% in falls. More than half (53.4%) were eligible for compensation (21.8% of patients had full hospital health insurance cover, 21.4% third party insurance and 9.2% workers compensation). The mechanism of injury with the highest median cost per patient was assault, followed by pedal cyclists, pedestrians then motor vehicle collisions. PMID:19203337

  1. A slow gravity compensated atom laser

    DEFF Research Database (Denmark)

    Kleine Büning, G.; Will, J.; Ertmer, W.;

    2010-01-01

    We report on a slow guided atom laser beam outcoupled from a Bose–Einstein condensate of 87Rb atoms in a hybrid trap. The acceleration of the atom laser beam can be controlled by compensating the gravitational acceleration and we reach residual accelerations as low as 0.0027 g. The outcoupling me...

  2. PRECISELY COMPENSATED EFFICIENT COMPONENT MODE SYNTHESIS METHOD

    Institute of Scientific and Technical Information of China (English)

    Zhu Yutian; Ichiro Hagiwara

    2004-01-01

    Based on the improved mode superposition method proposed by Z.D.Ma and I.Hagiwara, a precisely compensated efficient mode synthesis method is developed.The calculation procedure is discussed in detail and the truncation error is also analyzed.By comparison, it is shown that this method has a higher accuracy and a less calculation time than the general used ones.

  3. On compensation in multidimensional response modeling

    NARCIS (Netherlands)

    Linden, van der W.J.

    2012-01-01

    The issue of compensation in multidimensional response modeling is addressed. We show that multidimensional response models are compensatory in their ability parameters if and only if they are monotone. In addition, a minimal set of assumptions is presented under which the MLEs of the ability parame

  4. Annual compensation for pipelines in Alberta

    International Nuclear Information System (INIS)

    The Surface Rights Board (SRB) in Alberta held a hearing in November 2007 to address three issues involving a pipeline for Enbridge Pipelines (Athabasca) Inc. as well as several land owner issues in Townships 66-68 and Ranges 17-19, all west of the 4th Meridian. The issues the SRB examined were the appropriate amount (i.e. magnitude) of compensation payable under right of entry orders under consideration; the appropriate structure of the compensation award; and to whom the compensation was payable. This document presented a review by the Farmer's Advocate Office (FAO) of the published decision of the SRB. The verbatim decision and rationale used by the SRB to award annual compensation for loss and/or ongoing nuisance and inconvenience was presented. The document could be useful to landowners as they determine their negotiation strategy when faced with considering future pipeline access agreements. The document included a discussion of the context for the decision and a case review. Specific topics that were covered included the rationale for the decision; long term effects of pipeline arguments and SRB commentary; the award and determination; and what still needs to be done. It was concluded that the SRB requires evidence in order to answer several questions regarding the magnitude of any losses, and to what degree, if any, had the nuisance, inconvenience, and loss of rights already been anticipated and factored into the operator's final offer

  5. Dispersion Compensation with a Prism-pair

    CERN Document Server

    Shaked, Yaakov; Pe'er, Avi

    2014-01-01

    We present a detailed calculation of the total dispersion (spectral phase) from a pair of Brewster-cut prisms. This paper aims to aid advanced students in tracking the operation of this major configuration for dispersion-compensation and phase-control of ultra-short pulses.

  6. Filament stretching rheometer: inertia compensation revisited

    DEFF Research Database (Denmark)

    Szabo, Peter; McKinley, Gareth H.

    2003-01-01

    The necessary inertia compensation used in the force balance for the filament stretching rheometer is derived for an arbitrary frame of reference. This enables the force balance to be used to extract correctly the extensional viscosity from measurements of the tensile force at either end of the...

  7. 13 CFR 113.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Compensation. 113.515 Section 113.515 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NONDISCRIMINATION IN FINANCIAL... of which requires equal skill, effort, and responsibility, and that are performed under...

  8. Large Capacity SMES for Voltage Dip Compensation

    Science.gov (United States)

    Iwatani, Yu; Saito, Fusao; Ito, Toshinobu; Shimada, Mamoru; Ishida, Satoshi; Shimanuki, Yoshio

    Voltage dips of power grids due to thunderbolts, snow damage, and so on, cause serious damage to production lines of precision instruments, for example, semiconductors. In recent years, in order to solve this problem, uninterruptible power supply systems (UPS) are used. UPS, however, has small capacity, so a great number of UPS are needed in large factories. Therefore, we have manufactured the superconducting magnetic energy storage (SMES) system for voltage dip compensation able to protect loads with large capacity collectively. SMES has advantages such as space conservation, long lifetime and others. In field tests, cooperating with CHUBU Electric Power Co., Inc. we proved that SMES is valuable for compensating voltage dips. Since 2007, 10MVA SMES improved from field test machines has been running in a domestic liquid crystal display plant, and in 2008, it protected plant loads from a number of voltage dips. In this paper, we report the action principle and components of the improved SMES for voltage dip compensation, and examples of waveforms when 10MVA SMES compensated voltage dips.

  9. 7 CFR 301.74-5 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... marketers. Orchard owners eligible for compensation under this paragraph who market all fruit they produce...) Direct marketers. Owners of commercial stone fruit orchards who APHIS has determined meet the eligibility... marketers. The completed application must be accompanied by: (i) A copy of the emergency action...

  10. Active Wireline Heave Compensation for Ocean Drilling

    Science.gov (United States)

    Goldberg, D.; Liu, T.; Swain, K.; Furman, C.; Iturrino, G. J.

    2014-12-01

    The up-and-down heave motion of a ship causes a similar motion on any instruments tethered on wireline cable below it. If the amplitude of this motion is greater than a few tens of cm, significant discrepancy in the depth below the ship is introduced, causing uncertainty in the acquired data. Large and irregular cabled motions also increase the risk of damaging tethered instruments, particularly those with relatively delicate sensors. In 2005, Schlumberger and Deep Down, Inc built an active wireline heave compensator (AHC) system for use onboard the JOIDES Resolution to compensate for heave motion on wireline logging tools deployed in scientific drill holes. The goals for the new AHC system were to (1) design a reliable heave compensation system; and (2) devise a robust and quantitative methodology for routine assessment of compensation efficiency (CE) during wireline operations. Software programs were developed to monitor CE and the dynamics of logging tools in real-time, including system performance under variable parameters such as water depth, sea state, cable length, logging speed and direction. We present the CE results from the AHC system on the JOIDES Resolution during a 5-year period of recent IODP operations and compare the results to those from previous compensation systems deployed during ODP and IODP. Based on new data under heave conditions of ±0.2-2.0 m and water depths of 300-4,800 m in open holes, the system reduces 65-80% of downhole tool displacement under stationary conditions and 50-60% during normal logging operations. Moreover, down/up tool motion at low speeds (300-600 m/h) reduces the system's CE values by 15-20%, and logging down at higher speeds (1,000-1,200 m/h) reduces CE values by 55-65%. Furthermore, the system yields slightly lower CE values of 40-50% without tension feedback of the downhole cable while logging. These results indicate that the new system's compensation efficiency is comparable to or better than previous systems

  11. S/W concept for an autonomous rendezvous and docking mission

    Science.gov (United States)

    Sommer, J.

    The onboard software required for a typical rendezvous and docking mission profile is discussed. The mission profiles for the MATRA and MBB/ERNO satellites are given along with corresponding satellite configurations. The navigational algorithms used in the individual mission phases are briefly explained, and the corresponding structure of the application software and the related service software are addressed.

  12. Occurrence of Potato virus X on hybrid dock in Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Petrzik, Karel

    2009-01-01

    Roč. 53, č. 1 (2009), s. 49-52. ISSN 0001-723X R&D Projects: GA AV ČR(CZ) 1QS500510558 Institutional research plan: CEZ:AV0Z50510513 Keywords : hybrid dock * potato virus X * Radish mosaic virus * Turnip yellow mosaic virus Subject RIV: EE - Microbiology, Virology Impact factor: 0.746, year: 2009

  13. An Insight into the Anticancer Activities of Ru(II-Based Metallocompounds Using Docking Methods

    Directory of Open Access Journals (Sweden)

    Peter A. Ajibade

    2013-09-01

    Full Text Available Unlike organic molecules, reports on docking of metal complexes are very few; mainly due to the inadequacy of force fields in docking packages to appropriately characterize the metal atoms that consequentially hinder the rational design of metal-based drug complexes. In this study we have made used Molegro and Autodock to predict the anticancer activities of selected Ru(II complexes against twelve anticancer targets. We observed that introducing the quantum calculated atomic charges of the optimized geometries significantly improved the docking predictions of these anticancer metallocompounds. Despite several limitations in the docking of metal-based complexes, we obtained results that are highly correlated with the available experimental results. Most of our newly proposed metallocompounds are found theoretically to be better anticancer metallocompounds than all the experimentally proposed RAPTA complexes. An interesting features of a strong interactions of new modeled of metallocompounds against the two base edges of DNA strands suggest similar mechanisms of anticancer activities similar to that of cisplatin. There is possibility of covalent bonding between the metal center of the metallocompounds and the residues of the receptors DNA-1, DNA-2, HDAC7, HIS and RNR. However, the general results suggest the possibility of metals positioning the coordinated ligands in the right position for optimal receptor interactions and synergistic effects, rather than forming covalent bonds.

  14. Conceptual design of the hot cell facility universal docking station at ITER

    International Nuclear Information System (INIS)

    Between main shutdowns of the ITER machine, in-vessel components and Iter Remote Maintenance System (IRMS) are transferred between the Tokamak complex and the Hot Cell Facility using different types of sealed casks. Transfer Casks have different physical interfaces with the Vacuum Vessel, which need to be the same at the docking stations of the HCF. It means that in-vessel components and IRMS are cleaned in the same cells, which is in fact not convenient. Furthermore, logistic studies showed that the use rate of the cells is very inhomogeneous. In order to have dedicated cell for decontamination of Remote Handling tools, in order to increase the operability efficiency and to removes the hot cell docking operation from the critical path, the concept of a universal docking station has been investigated. Based on an existing design, the work was focused on a review of requirements, the re-design and the integration within the HCF layout. The universal docking station has been proposed and is now integrated in HCF design.

  15. Conceptual design of the hot cell facility universal docking station at ITER

    Energy Technology Data Exchange (ETDEWEB)

    Dammann, A., E-mail: alexis.dammann@iter.org [ITER Organization, CS 90 046, 13067 St Paul Lez Durance Cedex (France); Benchikhoune, M.; Friconneau, J.P.; Ivanov, V. [ITER Organization, CS 90 046, 13067 St Paul Lez Durance Cedex (France); Lemee, A. [SOGETI High Tech, 180 Rue Rene Descartes, 13851 Aix en Provence (France); Martins, J.P. [ITER Organization, CS 90 046, 13067 St Paul Lez Durance Cedex (France); Tamassy, G. [SOGETI High Tech, 180 Rue Rene Descartes, 13851 Aix en Provence (France)

    2011-10-15

    Between main shutdowns of the ITER machine, in-vessel components and Iter Remote Maintenance System (IRMS) are transferred between the Tokamak complex and the Hot Cell Facility using different types of sealed casks. Transfer Casks have different physical interfaces with the Vacuum Vessel, which need to be the same at the docking stations of the HCF. It means that in-vessel components and IRMS are cleaned in the same cells, which is in fact not convenient. Furthermore, logistic studies showed that the use rate of the cells is very inhomogeneous. In order to have dedicated cell for decontamination of Remote Handling tools, in order to increase the operability efficiency and to removes the hot cell docking operation from the critical path, the concept of a universal docking station has been investigated. Based on an existing design, the work was focused on a review of requirements, the re-design and the integration within the HCF layout. The universal docking station has been proposed and is now integrated in HCF design.

  16. Demonstration of Self-Training Autonomous Neural Networks in Space Vehicle Docking Simulations

    Science.gov (United States)

    Patrick, M. Clinton; Thaler, Stephen L.; Stevenson-Chavis, Katherine

    2006-01-01

    Neural Networks have been under examination for decades in many areas of research, with varying degrees of success and acceptance. Key goals of computer learning, rapid problem solution, and automatic adaptation have been elusive at best. This paper summarizes efforts at NASA's Marshall Space Flight Center harnessing such technology to autonomous space vehicle docking for the purpose of evaluating applicability to future missions.

  17. Overview of Carbon Dioxide Control Issues During International Space Station/Space Shuttle Joint Docked Operations

    Science.gov (United States)

    Matty, Christopher M.; Hayley, Elizabeth P.

    2009-01-01

    Manned space vehicles have a common requirement to remove the Carbon Dioxide (CO2) created by the metabolic processes of the crew. The Space Shuttle and International Space Station (ISS) each have systems in place to allow control and removal of CO2 from the habitable cabin environment. During periods where the Space Shuttle is docked to ISS, known as joint docked operations, the Space Shuttle and ISS share a common atmosphere environment. During this period there is an elevated production of CO2 caused by the combined metabolic activity of the Space Shuttle and ISS crew. This elevated CO2 production, combined with the large effective atmosphere created by the collective volumes of the docked vehicles, creates a unique set of requirements for CO2 removal. This paper will describe the individual CO2 control plans implemented by the Space Shuttle and ISS engineering teams, as well as the integrated plans used when both vehicles are docked. In addition, the paper will discuss some of the issues and anomalies experienced by both engineering teams.

  18. A robot to detect and control broad-leaved dock (Rumex obtusifolius L.) in grassland

    NARCIS (Netherlands)

    Evert, van F.K.; Samsom, J.; Polder, G.; Vijn, M.P.; Dooren, van H.J.C.; Lamaker, E.J.J.; Heijden, van der G.W.A.M.; Kempenaar, C.; Zalm, van der A.J.A.; Lotz, L.A.P.

    2011-01-01

    Broad-leaved dock is a common and troublesome grassland weed with a wide geographic distribution. In conventional farming the weed is normally controlled by using a selective herbicide, but in organic farming manual removal is the best option to control this weed. The objective of our work was to de

  19. Drug targets for cell cycle dysregulators in leukemogenesis: in silico docking studies.

    Directory of Open Access Journals (Sweden)

    Archana Jayaraman

    Full Text Available Alterations in cell cycle regulating proteins are a key characteristic in neoplastic proliferation of lymphoblast cells in patients with Acute Lymphoblastic Leukemia (ALL. The aim of our study was to investigate whether the routinely administered ALL chemotherapeutic agents would be able to bind and inhibit the key deregulated cell cycle proteins such as--Cyclins E1, D1, D3, A1 and Cyclin Dependent Kinases (CDK 2 and 6. We used Schrödinger Glide docking protocol to dock the chemotherapeutic drugs such as Doxorubicin and Daunorubicin and others which are not very common including Clofarabine, Nelarabine and Flavopiridol, to the crystal structures of these proteins. We observed that the drugs were able to bind and interact with cyclins E1 and A1 and CDKs 2 and 6 while their docking to cyclins D1 and D3 were not successful. This binding proved favorable to interact with the G1/S cell cycle phase proteins that were examined in this study and may lead to the interruption of the growth of leukemic cells. Our observations therefore suggest that these drugs could be explored for use as inhibitors for these cell cycle proteins. Further, we have also highlighted residues which could be important in the designing of pharmacophores against these cell cycle proteins. This is the first report in understanding the mechanism of action of the drugs targeting these cell cycle proteins in leukemia through the visualization of drug-target binding and molecular docking using computational methods.

  20. Resident CAPS on dense-core vesicles docks and primes vesicles for fusion.

    Science.gov (United States)

    Kabachinski, Greg; Kielar-Grevstad, D Michelle; Zhang, Xingmin; James, Declan J; Martin, Thomas F J

    2016-02-15

    The Ca(2+)-dependent exocytosis of dense-core vesicles in neuroendocrine cells requires a priming step during which SNARE protein complexes assemble. CAPS (aka CADPS) is one of several factors required for vesicle priming; however, the localization and dynamics of CAPS at sites of exocytosis in live neuroendocrine cells has not been determined. We imaged CAPS before, during, and after single-vesicle fusion events in PC12 cells by TIRF micro-scopy. In addition to being a resident on cytoplasmic dense-core vesicles, CAPS was present in clusters of approximately nine molecules near the plasma membrane that corresponded to docked/tethered vesicles. CAPS accompanied vesicles to the plasma membrane and was present at all vesicle exocytic events. The knockdown of CAPS by shRNA eliminated the VAMP-2-dependent docking and evoked exocytosis of fusion-competent vesicles. A CAPS(ΔC135) protein that does not localize to vesicles failed to rescue vesicle docking and evoked exocytosis in CAPS-depleted cells, showing that CAPS residence on vesicles is essential. Our results indicate that dense-core vesicles carry CAPS to sites of exocytosis, where CAPS promotes vesicle docking and fusion competence, probably by initiating SNARE complex assembly. PMID:26700319

  1. Structure prediction of protein complexes by an NMR-based protein docking algorithm

    International Nuclear Information System (INIS)

    Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lengthy process of experimental structure elucidation of protein complexes by proposing potential structures. In this paper, we are discussing a variant of the protein-protein docking problem, where the input consists of the tertiary structures of proteins A and B plus an unassigned one-dimensional 1H-NMR spectrum of the complex AB. We present a new scoring function for evaluating and ranking potential complex structures produced by a docking algorithm. The scoring function computes a 'theoretical' 1H-NMR spectrum for each tentative complex structure and subtracts the calculated spectrum from the experimental one. The absolute areas of the difference spectra are then used to rank the potential complex structures. In contrast to formerly published approaches (e.g. [Morelli et al. (2000) Biochemistry, 39, 2530-2537]) we do not use distance constraints (intermolecular NOE constraints). We have tested the approach with four protein complexes whose three-dimensional structures are stored in the PDB data bank [Bernstein et al. (1977)] and whose 1H-NMR shift assignments are available from the BMRB database. The best result was obtained for an example, where all standard scoring functions failed completely. Here, our new scoring function achieved an almost perfect separation between good approximations of the true complex structure and false positives

  2. Virtual Screening and Docking Studies of Synthesized Chalcones: Potent Anti-Malarial Drug

    Directory of Open Access Journals (Sweden)

    Prashant Singh

    2016-03-01

    Full Text Available A novel series of Chalcones were synthesized targets asexual blood stages of Plasmodium falciparum has been analyzed by utilizing a combination of molecular modeling techniques. Statistically significant structure-based quantitative structure activity relationships models were generated and validated through acceptable predictive ability to support internal and external set of compounds. Screening of most valuable drug among of pre-synthesized drug on the basis of binding efficiency to target receptor was carried out by docking view. Prior this pre-computed Mean IC50 and MIC value were also taken in consideration. The most effective compound on the basis all consideration was found. Previous studies have suggested that Ca2+-ATPase (PfATP6 of P. falciparum is the target of many anti-malarial drugs. However, the mechanism of inhibition of Ca2+- ATPase (PfATP6 is not known. Here we address this issue using bioinformatics tools. We generated a molecular model of Ca2+-ATPase (PfATP6 of P. falciparum and performed molecular docking of all chalcones. Molecular docking programme Glide iGEMDock was used to determine binding feasibility of 52 analogues of chalcones. The comparison of docking parameters showed, more than 5 analogues are better ligands of PfATP6. The binding of chalocones to PFATP6 is mediated by both hydrogen bonding, hydrophobic and polar interactions. Our results suggest that chalcones analogues are promising lead compounds for the development of anti-malarial drugs

  3. Synthesis, Docking Study and β-Adrenoceptor Activity of Some New Oxime Ether Derivatives

    Directory of Open Access Journals (Sweden)

    Hazem A. Ghabbour

    2014-03-01

    Full Text Available A new series of oxime ethers 4a–z was designed and synthesized to test the blocking activity against β1 and β2-adrenergic receptors. Docking of these ether derivatives into the active site of the identified 3D structures of β1 and β2-adrenergic receptors showed MolDock scores comparable to those of reference compounds. Biological results revealed that the inhibition effects on the heart rate and contractility are less than those of propranolol. Nevertheless, the two compounds 4p and 4q that displayed the highest negative MolDock score with β2-adrenergic receptors showed β2-antagonistic activity by decreasing salbutamol relaxation of precontracted tracheal strips, which indicates the importance of a chlorothiophene moiety in the hydrophobic region for best complementarity with β2 receptors. On other hand, the presence of a homoveratryl moiety increases the MolDock score of the tested compounds with the β1 receptor.

  4. Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand

    Science.gov (United States)

    DeLuca, Samuel; Khar, Karen; Meiler, Jens

    2015-01-01

    RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand) making it unfeasible for use in virtual High Throughput Screening (vHTS). To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial ‘low-resolution’ docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10–15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the ‘high-resolution’ full atom refinement step. PMID:26207742

  5. Study on dock nuclear emergency decision-making model based on theory of bayes risk decision

    International Nuclear Information System (INIS)

    Considering the characteristics of nuclear power ship dock and in order to reduce the effect brought about by the uncertainty of wind field, optimization model has been established based on Bayes risk decision theory. The model compartmentalizes a whole area into several subfields and further takes into account the restriction of public acceptability and international intervention principle. An example analysis is also provided. (authors)

  6. Quantum mechanical/molecular mechanical (QM/MM) docking: an evaluation for known test systems

    Science.gov (United States)

    Beierlein, Frank; Lanig, Harald; Schürer, Gudrun; Horn, Anselm H. C.; Clark, Timothy

    A combined quantum mechanical/molecular mechanical (QM/MM) docking approach for the investigation of protein-inhibitor complexes is presented. Starting points for QM/MM optimizations are generated with AutoDock. The subsequent semiempirical AM1 QM/MM optimization of the complex obtained by the docking procedure gives a more detailed description of the binding mode and the electronic properties of the ligand. As we use a flexible protein environment in the QM/MM optimizations, we are able to simulate limited structural changes of the enzyme upon binding a ligand, even within a simple geometry optimization. The method was validated using a set of structurally known protein-inhibitor complexes, whose crystallographic data were taken from the Protein Data Bank. In addition to protein structures taken directly from complexes with the inhibitors, structures of uncomplexed HIV-1-protease and thrombin were also used successfully for QM/MM docking experiments. By comparing the resulting structures with those obtained using protein structures from protein-inhibitor complexes, we find that the method is able to simulate the effect of the induced fit when a simple optimization is adequate to reproduce the protein movement. Describing the ligand quantum mechanically gives a detailed view of its electronic properties, for example its polarization within the active site of the enzyme. This study suggests strongly that a QM/MM molecular dynamics approach will be able to simulate the induced fit in general cases.

  7. Overview of Carbon Dioxide Control Issues During International Space Station/Space Shuttle Joint Docked Operations

    Science.gov (United States)

    Matty, Christopher M.

    2010-01-01

    Crewed space vehicles have a common requirement to remove the carbon dioxide (CO2) created by the metabolic processes of the crew. The space shuttle [Space Transportation System (STS)] and International Space Station (ISS) each have systems in place that allow control and removal of CO2 from the habitable cabin environment. During periods in which the space shuttle is docked to the ISS, known as "joint docked operations," the space shuttle and ISS share a common atmosphere environment. During this period, an elevated amount of CO2 is produced through the combined metabolic activity of the STS and ISS crews. This elevated CO2 production, together with the large effective atmosphere created by collective volumes of the docked vehicles, creates a unique set of requirements for CO2 removal. This paper will describe individual CO2 control plans implemented by STS and ISS engineering teams, as well as the integrated plans used when both vehicles are docked. The paper will also discuss some of the issues and anomalies experienced by both engineering teams.

  8. An Experimental Investigation of Leak Rate Performance of a Subscale Candidate Elastomer Docking Space Seal

    Science.gov (United States)

    Garafolo, Nicholas G.; Daniels, Christopher C.

    2011-01-01

    A novel docking seal was developed for the main interface seal of NASA s Low Impact Docking System (LIDS). This interface seal was designed to maintain acceptable leak rates while being exposed to the harsh environmental conditions of outer space. In this experimental evaluation, a candidate docking seal assembly called Engineering Development Unit (EDU58) was characterized and evaluated against the Constellation Project leak rate requirement. The EDU58 candidate seal assembly was manufactured from silicone elastomer S0383-70 vacuum molded in a metal retainer ring. Four seal designs were considered with unique characteristic heights. The leak rate performance was characterized through a mass point leak rate method by monitoring gas properties within an internal control volume. The leakage performance of the seals were described herein at representative docking temperatures of -50, +23, and +50 C for all four seal designs. Leak performance was also characterized at 100, 74, and 48 percent of full closure. For all conditions considered, the candidate seal assemblies met the Constellation Project leak rate requirement.

  9. Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design

    Directory of Open Access Journals (Sweden)

    Sam Z. Grinter

    2014-07-01

    Full Text Available The docking methods used in structure-based virtual database screening offer the ability to quickly and cheaply estimate the affinity and binding mode of a ligand for the protein receptor of interest, such as a drug target. These methods can be used to enrich a database of compounds, so that more compounds that are subsequently experimentally tested are found to be pharmaceutically interesting. In addition, like all virtual screening methods used for drug design, structure-based virtual screening can focus on curated libraries of synthesizable compounds, helping to reduce the expense of subsequent experimental verification. In this review, we introduce the protein-ligand docking methods used for structure-based drug design and other biological applications. We discuss the fundamental challenges facing these methods and some of the current methodological topics of interest. We also discuss the main approaches for applying protein-ligand docking methods. We end with a discussion of the challenging aspects of evaluating or benchmarking the accuracy of docking methods for their improvement, and discuss future directions.

  10. 48 CFR 47.303-12 - Ex dock, pier, or warehouse, port of importation.

    Science.gov (United States)

    2010-10-01

    ... warehouse, port of importation. 47.303-12 Section 47.303-12 Federal Acquisition Regulations System FEDERAL..., pier, or warehouse, port of importation. (a) Explanation of delivery term. Ex dock, pier, or warehouse... in the warehouse at the specified port of importation. (b) Contractor responsibilities....

  11. The DOCK protein sponge binds to ELMO and functions in Drosophila embryonic CNS development.

    Directory of Open Access Journals (Sweden)

    Bridget Biersmith

    Full Text Available Cell morphogenesis, which requires rearrangement of the actin cytoskeleton, is essential to coordinate the development of tissues such as the musculature and nervous system during normal embryonic development. One class of signaling proteins that regulate actin cytoskeletal rearrangement is the evolutionarily conserved CDM (C. elegansCed-5, human DOCK180, DrosophilaMyoblast city, or Mbc family of proteins, which function as unconventional guanine nucleotide exchange factors for the small GTPase Rac. This CDM-Rac protein complex is sufficient for Rac activation, but is enhanced upon the association of CDM proteins with the ELMO/Ced-12 family of proteins. We identified and characterized the role of Drosophila Sponge (Spg, the vertebrate DOCK3/DOCK4 counterpart as an ELMO-interacting protein. Our analysis shows Spg mRNA and protein is expressed in the visceral musculature and developing nervous system, suggesting a role for Spg in later embryogenesis. As maternal null mutants of spg die early in development, we utilized genetic interaction analysis to uncover the role of Spg in central nervous system (CNS development. Consistent with its role in ELMO-dependent pathways, we found genetic interactions with spg and elmo mutants exhibited aberrant axonal defects. In addition, our data suggests Ncad may be responsible for recruiting Spg to the membrane, possibly in CNS development. Our findings not only characterize the role of a new DOCK family member, but help to further understand the role of signaling downstream of N-cadherin in neuronal development.

  12. Improving protein-ligand docking with flexible interfacial water molecules using SWRosettaLigand.

    Science.gov (United States)

    Li, Linqing; Xu, Weiwei; Lü, Qiang

    2015-11-01

    Computational protein-ligand docking is of great importance in drug discovery and design. Conformational changes greatly affect the results of protein-ligand docking, especially when water molecules take part in mediating protein ligand interactions or when large conformational changes are observed in the receptor backbone interface. We have developed an improved protocol, SWRosettaLigand, based on the RosettaLigand protocol. This approach incorporates the flexibility of interfacial water molecules and modeling of the interface of the receptor into the original RosettaLigand. In a coarse sampling step, SWRosettaLigand pre-optimizes the initial position of the water molecules, docks the ligand to the receptor with explicit water molecules, and minimizes the predicted structure with water molecules. The receptor backbone interface is treated as a loop and perturbed and refined by kinematic closure, or cyclic coordinate descent algorithm, with the presence of the ligand. In two cross-docking test sets, it was identified that for 8 out of 14, and 16 out of 22, test instances, the top-ranked structures by SWRosettaLigand achieved better accuracy than other protocols. PMID:26515196

  13. A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI.

    Science.gov (United States)

    Gong, Xin Qi; Chang, Shan; Zhang, Qing Hua; Li, Chun Hua; Shen, Long Zhu; Ma, Xiao Hui; Wang, Ming Hui; Liu, Bin; He, Hong Qiu; Chen, Wei Zu; Wang, Cun Xin

    2007-12-01

    Protein-protein docking is usually exploited with a two-step strategy, i.e., conformational sampling and decoy scoring. In this work, a new filter enhanced sampling scheme was proposed and added into the RosettaDock algorithm to improve the conformational sampling efficiency. The filter term is based on the statistical result that backbone hydrogen bonds in the native protein structures are wrapped by more than nine hydrophobic groups to shield them from attacks of water molecules (Fernandez and Scheraga, Proc Natl Acad Sci USA 2003;100:113-118). A combinatorial scoring function, ComScore, specially designed for the other-type protein-protein complexes was also adopted to select the near native docked modes. ComScore was composed of the atomic contact energy, van der Waals, and electrostatic interaction energies, and the weight of each item was fit through the multiple linear regression approach. To analyze our docking results, the filter enhanced sampling scheme was applied to targets T12, T20, and T21 after the CAPRI blind test, and improvements were obtained. The ligand least root mean square deviations (L_rmsds) were reduced and the hit numbers were increased. ComScore was used in the scoring test for CAPRI rounds 9-12 with good success in rounds 9 and 11. PMID:17803223

  14. Docking simulation analysis of range data requirements for the orbital maneuvering vehicle

    Science.gov (United States)

    Micheal, J. D.; Vinz, F. L.

    1985-01-01

    The results of an initial study are reported assess the controllability of the Orbital Maneuvering Vehicle (OMV) for terminal closure and docking are reported. The vehicle characteristics used in this study are those of the Marshall Space Flight Center (MSFC) baseline OMV which were published with the request for proposals for preliminary design of this vehicle. This simulation was conducted at MSFC using the Target Motion Simulator. The study focused on the OMV manual mode capability to accommodate both stabilized and tumbling target engagements with varying complements of range and range rate data displayed to the OMV operator. Four trained test subjects performed over 400 simulated orbital dockings during this study. A firm requirement for radar during the terminal closure and dock phase of the OMV mission was not established by these simulations. Fifteen pound thrusters recommended in the MSFC baseline design were found to be advantageous for initial rate matching maneuvers with unstabilized targets; however, lower thrust levels were desirable for making the final docking maneuvers.

  15. Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics.

    Science.gov (United States)

    Iakovou, Georgios; Hayward, Steven; Laycock, Stephen D

    2015-09-01

    Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500Hz to 1kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates. PMID:26186491

  16. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment

    DEFF Research Database (Denmark)

    Kufareva, Irina; Katritch, Vsevolod; Biggin, Phil;

    2014-01-01

    Despite tremendous successes of GPCR crystallography, the receptors with available structures represent only a small fraction of human GPCRs. An important role of the modeling community is to maximize structural insights for the remaining receptors and complexes. The community-wide GPCR Dock asse...

  17. Implementation of Statistical Process Control: Evaluating the Mechanical Performance of a Candidate Silicone Elastomer Docking Seal

    Science.gov (United States)

    Oravec, Heather Ann; Daniels, Christopher C.

    2014-01-01

    The National Aeronautics and Space Administration has been developing a novel docking system to meet the requirements of future exploration missions to low-Earth orbit and beyond. A dynamic gas pressure seal is located at the main interface between the active and passive mating components of the new docking system. This seal is designed to operate in the harsh space environment, but is also to perform within strict loading requirements while maintaining an acceptable level of leak rate. In this study, a candidate silicone elastomer seal was designed, and multiple subscale test articles were manufactured for evaluation purposes. The force required to fully compress each test article at room temperature was quantified and found to be below the maximum allowable load for the docking system. However, a significant amount of scatter was observed in the test results. Due to the stochastic nature of the mechanical performance of this candidate docking seal, a statistical process control technique was implemented to isolate unusual compression behavior from typical mechanical performance. The results of this statistical analysis indicated a lack of process control, suggesting a variation in the manufacturing phase of the process. Further investigation revealed that changes in the manufacturing molding process had occurred which may have influenced the mechanical performance of the seal. This knowledge improves the chance of this and future space seals to satisfy or exceed design specifications.

  18. Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power.

    Science.gov (United States)

    Wang, Zhe; Sun, Huiyong; Yao, Xiaojun; Li, Dan; Xu, Lei; Li, Youyong; Tian, Sheng; Hou, Tingjun

    2016-05-14

    As one of the most popular computational approaches in modern structure-based drug design, molecular docking can be used not only to identify the correct conformation of a ligand within the target binding pocket but also to estimate the strength of the interaction between a target and a ligand. Nowadays, as a variety of docking programs are available for the scientific community, a comprehensive understanding of the advantages and limitations of each docking program is fundamentally important to conduct more reasonable docking studies and docking-based virtual screening. In the present study, based on an extensive dataset of 2002 protein-ligand complexes from the PDBbind database (version 2014), the performance of ten docking programs, including five commercial programs (LigandFit, Glide, GOLD, MOE Dock, and Surflex-Dock) and five academic programs (AutoDock, AutoDock Vina, LeDock, rDock, and UCSF DOCK), was systematically evaluated by examining the accuracies of binding pose prediction (sampling power) and binding affinity estimation (scoring power). Our results showed that GOLD and LeDock had the best sampling power (GOLD: 59.8% accuracy for the top scored poses; LeDock: 80.8% accuracy for the best poses) and AutoDock Vina had the best scoring power (rp/rs of 0.564/0.580 and 0.569/0.584 for the top scored poses and best poses), suggesting that the commercial programs did not show the expected better performance than the academic ones. Overall, the ligand binding poses could be identified in most cases by the evaluated docking programs but the ranks of the binding affinities for the entire dataset could not be well predicted by most docking programs. However, for some types of protein families, relatively high linear correlations between docking scores and experimental binding affinities could be achieved. To our knowledge, this study has been the most extensive evaluation of popular molecular docking programs in the last five years. It is expected that our work

  19. On docking, scoring and assessing protein-DNA complexes in a rigid-body framework.

    Directory of Open Access Journals (Sweden)

    Marc Parisien

    Full Text Available We consider the identification of interacting protein-nucleic acid partners using the rigid body docking method FTdock, which is systematic and exhaustive in the exploration of docking conformations. The accuracy of rigid body docking methods is tested using known protein-DNA complexes for which the docked and undocked structures are both available. Additional tests with large decoy sets probe the efficacy of two published statistically derived scoring functions that contain a huge number of parameters. In contrast, we demonstrate that state-of-the-art machine learning techniques can enormously reduce the number of parameters required, thereby identifying the relevant docking features using a miniscule fraction of the number of parameters in the prior works. The present machine learning study considers a 300 dimensional vector (dependent on only 15 parameters, termed the Chemical Context Profile (CCP, where each dimension reflects a specific type of protein amino acid-nucleic acid base interaction. The CCP is designed to capture the chemical complementarities of the interface and is well suited for machine learning techniques. Our objective function is the Chemical Context Discrepancy (CCD, which is defined as the angle between the native system's CCP vector and the decoy's vector and which serves as a substitute for the more commonly used root mean squared deviation (RMSD. We demonstrate that the CCP provides a useful scoring function when certain dimensions are properly weighted. Finally, we explore how the amino acids on a protein's surface can help guide DNA binding, first through long-range interactions, followed by direct contacts, according to specific preferences for either the major or minor grooves of the DNA.

  20. Assessment of Spatial Navigation and Docking Performance During Simulated Rover Tasks

    Science.gov (United States)

    Wood, S. J.; Dean, S. L.; De Dios, Y. E.; Moore, S. T.

    2010-01-01

    INTRODUCTION: Following long-duration exploration transits, pressurized rovers will enhance surface mobility to explore multiple sites across Mars and other planetary bodies. Multiple rovers with docking capabilities are envisioned to expand the range of exploration. However, adaptive changes in sensorimotor and cognitive function may impair the crew s ability to safely navigate and perform docking tasks shortly after transition to the new gravitoinertial environment. The primary goal of this investigation is to quantify post-flight decrements in spatial navigation and docking performance during a rover simulation. METHODS: Eight crewmembers returning from the International Space Station will be tested on a motion simulator during four pre-flight and three post-flight sessions over the first 8 days following landing. The rover simulation consists of a serial presentation of discrete tasks to be completed within a scheduled 10 min block. The tasks are based on navigating around a Martian outpost spread over a 970 sq m terrain. Each task is subdivided into three components to be performed as quickly and accurately as possible: (1) Perspective taking: Subjects use a joystick to indicate direction of target after presentation of a map detailing current orientation and location of the rover with the task to be performed. (2) Navigation: Subjects drive the rover to the desired location while avoiding obstacles. (3) Docking: Fine positioning of the rover is required to dock with another object or align a camera view. Overall operator proficiency will be based on how many tasks the crewmember can complete during the 10 min time block. EXPECTED RESULTS: Functionally relevant testing early post-flight will develop evidence regarding the limitations to early surface operations and what countermeasures are needed. This approach can be easily adapted to a wide variety of simulated vehicle designs to provide sensorimotor assessments for other operational and civilian populations.

  1. Compensation of errors in robot machining with a parallel 3D-piezo compensation mechanism

    OpenAIRE

    Schneider, Ulrich; Drust, Manuel; Puzik, Arnold; Verl, Alexander

    2013-01-01

    This paper proposes an approach for a 3D-Piezo Compensation Mechanism unit that is capable of fast and accurate adaption of the spindle position to enhance machining by robots. The mechanical design is explained which focuses on low mass, good stiffness and high bandwidth in order to allow compensating for errors beyond the bandwidth of the robot. In addition to previous works [7] and [9], an advanced actuation design is presented enabling movements in three translational axes allowing a work...

  2. Re-Planning for Compensator-Based IMRT with Original Compensators

    International Nuclear Information System (INIS)

    Compared with multileaf collimator (MLC)-based intensity-modulated radiotherapy (IMRT) for moving targets, compensator-based IMRT has advantages such as shorter beam-on time, fewer monitor units with potentially decreased secondary carcinogenesis risk, better optimization-to-deliverable dose conversion, and often better dose conformity. Some of the disadvantages include additional time for the compensators to be built and delivered, as well as extra cost. Patients undergoing treatment of abdominal cancers often experience weight loss. It would be necessary to account for this change in weight with a new plan and a second set of compensators. However, this would result in treatment delays and added costs. We have developed a method to re-plan the patient using the same set of compensators. Because the weight changes seen with the treatment of abdominal cancers are usually relatively small, a new 4D computed tomography (CT) acquired in the treatment position with markers on the original isocenter tattoos can be registered to the original planning scan. The contours of target volumes from the original scans are copied to the new scan after fusion. The original compensator set can be used together with a few field-in-field (FiF) beams defined by the MLC (or beams with cerrobend blocks for accelerators not equipped with a MLC). The weights of the beams with compensators are reduced so that the FiF or blocked beams can be optimized to mirror the original plan and dose distribution. Seven abdominal cancer cases are presented using this technique. The new plan on the new planning CT images usually has the same dosimetric quality as the original. The target coverage and dose uniformity are improved compared with the plan without FiF/block modification. Techniques combining additional FiF or blocked beams with the original compensators optimize the treatment plans when patients lose weight and save time and cost compared with generating plans with a new set of compensators.

  3. Deformation compensation in dynamic tomography; Compensation de deformations en tomographie dynamique

    Energy Technology Data Exchange (ETDEWEB)

    Desbat, L. [Universite Joseph Fourier, UMR CNRS 5525, 38 - Grenoble (France); Roux, S. [Universite Joseph Fourier, TIMC-IMAG, In3S, Faculte de Medecine, 38 - Grenoble (France)]|[CEA Grenoble, Lab. d' Electronique et de Technologie de l' Informatique (LETI), 38 (France); Grangeat, P. [CEA Grenoble, Lab. d' Electronique et de Technologie de l' Informatique (LETI), 38 (France)

    2005-07-01

    This work is a contribution to the compensation of motion in tomography. New classes of deformation are proposed, that compensates analytically by an algorithm of a F.B.P. type reconstruction. This work makes a generalisation of the known results for affine deformations, in parallel geometry and fan-beam, to deformation classes of infinite dimension able to include strong non linearities. (N.C.)

  4. Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.

    Science.gov (United States)

    Hanawa-Suetsugu, Kyoko; Kukimoto-Niino, Mutsuko; Mishima-Tsumagari, Chiemi; Akasaka, Ryogo; Ohsawa, Noboru; Sekine, Shun-ichi; Ito, Takuhiro; Tochio, Naoya; Koshiba, Seizo; Kigawa, Takanori; Terada, Takaho; Shirouzu, Mikako; Nishikimi, Akihiko; Uruno, Takehito; Katakai, Tomoya; Kinashi, Tatsuo; Kohda, Daisuke; Fukui, Yoshinori; Yokoyama, Shigeyuki

    2012-02-28

    DOCK2, a hematopoietic cell-specific, atypical guanine nucleotide exchange factor, controls lymphocyte migration through ras-related C3 botulinum toxin substrate (Rac) activation. Dedicator of cytokinesis 2-engulfment and cell motility protein 1 (DOCK2•ELMO1) complex formation is required for DOCK2-mediated Rac signaling. In this study, we identified the N-terminal 177-residue fragment and the C-terminal 196-residue fragment of human DOCK2 and ELMO1, respectively, as the mutual binding regions, and solved the crystal structure of their complex at 2.1-Å resolution. The C-terminal Pro-rich tail of ELMO1 winds around the Src-homology 3 domain of DOCK2, and an intermolecular five-helix bundle is formed. Overall, the entire regions of both DOCK2 and ELMO1 assemble to create a rigid structure, which is required for the DOCK2•ELMO1 binding, as revealed by mutagenesis. Intriguingly, the DOCK2•ELMO1 interface hydrophobically buries a residue which, when mutated, reportedly relieves DOCK180 from autoinhibition. We demonstrated that the ELMO-interacting region and the DOCK-homology region 2 guanine nucleotide exchange factor domain of DOCK2 associate with each other for the autoinhibition, and that the assembly with ELMO1 weakens the interaction, relieving DOCK2 from the autoinhibition. The interactions between the N- and C-terminal regions of ELMO1 reportedly cause its autoinhibition, and binding with a DOCK protein relieves the autoinhibition for ras homolog gene family, member G binding and membrane localization. In fact, the DOCK2•ELMO1 interface also buries the ELMO1 residues required for the autoinhibition within the hydrophobic core of the helix bundle. Therefore, the present complex structure reveals the structural basis by which DOCK2 and ELMO1 mutually relieve their autoinhibition for the activation of Rac1 for lymphocyte chemotaxis. PMID:22331897

  5. Dosimetric evaluation of compensation in radiotherapy of the breast: MLC intensity modulation and physical compensators

    International Nuclear Information System (INIS)

    Background and purpose: Electronic portal images may be used to design the compensation required to maximise dose uniformity in the breast from opposed tangential beams. Materials and methods: Four methods of implementing the desired compensation have been studied: a simple wedge, a physical compensator in conjunction with a wedge; one open field plus four shaped multi-leaf-collimated (MLC) fields, and one wedged field in conjunction with three shaped MLC fields. Evaluation was performed using thermoluminescent dosimeters (TLDs) placed inside a phantom which was designed to mimic the human breast. The measured results are compared with both the prediction of the in-house compensation design software and with the dose predicted by the GE Target II planning system. The implications of each method for the time taken to plan and deliver treatment were analysed. Results: The dose inhomogeneity, as measured at seven points in the central plane was greatest for the simple wedge (root mean square (rms) = 4.5%) compared to an open field plus four shaped MLC fields (rms = 2.2%), a wedged field plus three shaped MLC fields (rms = 3.3%), and the physical compensator (rms = 2.4%). The times required to plan and prepare these treatments varied considerably. The standard wedged treatment required under 15 min; both MLC-based and the physical compensator treatments required = 50 min. Differences of treatment delivery times were up to 8 min. Conclusions: These results indicate that the dose inhomogeneity can be reduced by beam intensity modulation designed using EPIDs

  6. The RhoG/ELMO1/Dock180 signaling module is required for spine morphogenesis in hippocampal neurons.

    Science.gov (United States)

    Kim, Jeong-Yoon; Oh, Mi Hee; Bernard, Laura P; Macara, Ian G; Zhang, Huaye

    2011-10-28

    Dendritic spines are actin-rich structures, the formation and plasticity of which are regulated by the Rho GTPases in response to synaptic input. Although several guanine nucleotide exchange factors (GEFs) have been implicated in spine development and plasticity in hippocampal neurons, it is not known how many different Rho GEFs contribute to spine morphogenesis or how they coordinate the initiation, establishment, and maintenance of spines. In this study, we screened 70 rat Rho GEFs in cultured hippocampal neurons by RNA interference and identified a number of candidates that affected spine morphogenesis. Of these, Dock180, which plays a pivotal role in a variety of cellular processes including cell migration and phagocytosis, was further investigated. We show that depletion of Dock180 inhibits spine morphogenesis, whereas overexpression of Dock180 promotes spine morphogenesis. ELMO1, a protein necessary for in vivo functions of Dock180, functions in a complex with Dock180 in spine morphogenesis through activating the Rac GTPase. Moreover, RhoG, which functions upstream of the ELMO1/Dock180 complex, is also important for spine formation. Together, our findings uncover a role for the RhoG/ELMO1/Dock180 signaling module in spine morphogenesis in hippocampal neurons. PMID:21900250

  7. Pharmacophore modeling, 3D-QSAR and docking study of 2-phenylpyrimidine analogues as selective PDE4B inhibitors.

    Science.gov (United States)

    Tripuraneni, Naga Srinivas; Azam, Mohammed Afzal

    2016-04-01

    Pharmacophore modeling, molecular docking, and molecular dynamics (MD) simulation studies have been performed, to explore the putative binding modes of 2-phenylpyrimidine series as PDE4B selective inhibitors. A five point pharmacophore model was developed using 87 molecules having pIC50 ranging from 8.52 to 5.07. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2)=0.918), cross validation coefficient (Q(2)=0.852), and F value (175) at 4 component PLS factor. The external validation indicated that our QSAR model possessed high predictive power (R(2)=0.70). The generated model was further validated by enrichment studies using the decoy test. To evaluate the effectiveness of docking protocol in flexible docking, we have selected crystallographic bound compound to validate our docking procedure as evident from root mean square deviation. A 10ns molecular dynamics simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Further, similar orientation was observed between the superposition of the conformations of 85 after MD simulation and best XP-docking pose; MD simulation and 3D-QSAR pose; best XP-docking and 3D-QSAR poses. Outcomes of the present study provide insight in designing novel molecules with better PDE4B selective inhibitory activity. PMID:26804643

  8. Method for Analysis of an Offshore Heave Compensator

    Directory of Open Access Journals (Sweden)

    Gwi-Nam Kim

    2016-02-01

    Full Text Available A heave compensation system consists of a drill string compensator (DSC and an active heave compensator (AHC cylinder, which together produce control force over an oil pressure system suitable for transmission of considerable power and compensating for heaving motion of the hull during drilling work. In this study, a heave compensator of an oil pressure system was simulated to draw a conclusion, which was verified by comparison with the result of a test conducted using an actual miniature model. The compensation rate was 95%, based on which the dynamic behaviors of an actual-size heave compensator were presumed. Furthermore, the speed of each cylinder and the acceleration of heave can be determined and used to fabricate an actual-size heave compensator.

  9. 48 CFR 970.2803-1 - Workers' Compensation Insurance.

    Science.gov (United States)

    2010-10-01

    ... SUPPLEMENTARY REGULATIONS DOE MANAGEMENT AND OPERATING CONTRACTS Bonds and Insurance 970.2803-1 Workers... apply where management and operating contractors purchase workers' compensation insurance. With respect... workers' compensation insurance programs of management and operating contractors in the light...

  10. MTB-USDH Compensation Tracking System (MTB-CTS)

    Data.gov (United States)

    US Agency for International Development — MTB-USDH Compensation Tracking System: is the USDH Compensation Tracking System (MTB-CTS) to assist managers in monitoring their payroll costs for U.S. direct...

  11. The economic consequences of executive compensation disclosure: evidence from Germany

    OpenAIRE

    Lofruthe, Hendrik

    2011-01-01

    PURPOSE OF THE STUDY Executive compensation frequently makes headlines in both academic journals and the yellow press. From the academic point of view, executive compensation has its grounds in agency theory. Effective compensation schemes align the interests of managers and owners and motivate managers to maximize shareholder value. Disclosure of compensation schemes enables shareholders to evaluate the remuneration contracts’ adequacy. In 2005, the German legislator created a natural exp...

  12. A General Theoretical Model of Enthalpy-EntropyCompensation

    Institute of Scientific and Technical Information of China (English)

    LIU,Lei; GUO, Qing-Xiang

    2001-01-01

    Enthalpy-entropy compensation remains a mystery in chemistry and biophysics.recent study suggested that the solventreorganization might constitute the physical orihin of the compensation, which was unforumstely not wisely applicable because compensation was also observeserved in solid phade reactions.In this study,a general theoretical model based upon strictmathematical deduction was presented,which indicated thatthe redistribution of the distinguishable subspecies might bethe physical origin of the enthalpy-intropy compensations in solvation and surface adsorption weue discussed.

  13. Design and prototype of Variable Gravity Compensation Mechanism (VGCM)

    OpenAIRE

    Takesue, Naoyuki; Ikematsu, Takashi; Murayama, Hideyuki; Fujimoto, Hideo

    2011-01-01

    A machine moving vertically requires strong gravitational resistance. Gravity compensation mechanisms devised to reduce actuator force mostly compensate for constant weight, but practical use requires that the mechanism compensate for weight variations. This paper presents a Variable Gravity Compensation Mechanism (VGCM) that uses two types of linear springs and changes the equilibrium position of one. The mechanism principle is described and the prototype is designed. Performance is experime...

  14. Work-Related Musculoskeletal Diseases and the Workers' Compensation

    OpenAIRE

    Jang, Tae-Won; KOO, Jung-Wan; Kwon, Soon-Chan; Song, Jaechul

    2014-01-01

    The Industrial Accident Compensation Insurance Act (IACIA) regulates the workers' compensation insurance system and the standards for the recognition of occupational diseases (ODs). Since its establishment in 1994, the IACIA has been amended several times. Before 2008, the approval of compensation for work-related musculoskeletal diseases (WMSDs) was decided based on the recommendation of consultants of the Korea Workers' Compensation and Welfare Service (COMWEL). The IACIA was amended in 200...

  15. Sales compensation governance: the last frontier of corporate reform.

    Science.gov (United States)

    Gundy, Peter R; Gaeta, Elizabeth C

    2004-01-01

    The area of sales compensation has remained relatively untouched by recent pressures for compensation reform. This article highlights some of the ways that sales organizations stumble in managing their compensation programs, and why it takes more than a simple tactical fix to address these problems effectively. The authors describe a more structured governance framework that not only identifies and resolves key sales compensation issues, but ultimately safeguards the effectiveness and financial integrity of the sales organization itself. PMID:15015424

  16. Video Coding with Motion-Compensated Lifted Wavelet Transforms

    OpenAIRE

    Flierl, M; Girod, B.

    2004-01-01

    This article explores the efficiency of motion-compensated three-dimensional transform coding, a compression scheme that employs a motion-compensated transform for a group of pictures. We investigate this coding scheme experimentally and theoretically. The practical coding scheme employs in temporal direction a wavelet decomposition with motion-compensated lifting steps. Further, we compare the experimental results to that of a predictive video codec with single-hypothesis motion compensation...

  17. 26 CFR 1.85-1 - Unemployment compensation.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 2 2010-04-01 2010-04-01 false Unemployment compensation. 1.85-1 Section 1.85-1...) INCOME TAXES (CONTINUED) Items Specifically Included in Gross Income § 1.85-1 Unemployment compensation... unemployment compensation (as defined in paragraph (b)(1) of this section) paid in taxable years...

  18. 45 CFR 302.65 - Withholding of unemployment compensation.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 2 2010-10-01 2010-10-01 false Withholding of unemployment compensation. 302.65... HUMAN SERVICES STATE PLAN REQUIREMENTS § 302.65 Withholding of unemployment compensation. The State plan... State agency charged with the administration of the State unemployment compensation laws in...

  19. 12 CFR 918.2 - Annual directors' compensation policy.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 7 2010-01-01 2010-01-01 false Annual directors' compensation policy. 918.2... HOME LOAN BANKS BANK DIRECTOR COMPENSATION AND EXPENSES § 918.2 Annual directors' compensation policy. Beginning in 2000 and annually thereafter, each Bank's board of directors shall adopt by resolution...

  20. 38 CFR 3.701 - Elections of pension or compensation.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Elections of pension or compensation. 3.701 Section 3.701 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS ADJUDICATION Pension, Compensation, and Dependency and Indemnity Compensation Concurrent Benefits and...

  1. 20 CFR 211.15 - Verification of compensation claimed.

    Science.gov (United States)

    2010-04-01

    ... employee, which is not credited in the records of the Board, must be verified to the satisfaction of the Board before it may be credited. An employee's claim to compensation not credited shall be processed as... employee that the compensation claimed is not creditable. (b) If the compensation is claimed within...

  2. 29 CFR 553.221 - Compensable hours of work.

    Science.gov (United States)

    2010-07-01

    ... Compensable hours of work. (a) The general rules on compensable hours of work are set forth in 29 CFR part 785... 29 Labor 3 2010-07-01 2010-07-01 false Compensable hours of work. 553.221 Section 553.221 Labor... OF THE FAIR LABOR STANDARDS ACT TO EMPLOYEES OF STATE AND LOCAL GOVERNMENTS Fire Protection and...

  3. Executive Compensation and Financial Performance in the Real Estate Industry

    OpenAIRE

    Davis, Barbara J.; Roger M. Shelor

    1995-01-01

    The purpose of this study is to examine the relationships between financial performance, firm size, and executive compensation among firms in the real estate industry. Previous analyses of compensation have not been industry specific. The findings indicate that there is a significant relationship between executive compensation and measures of financial performance, firm size, and age of the highest paid executive.

  4. 29 CFR 541.601 - Highly compensated employees.

    Science.gov (United States)

    2010-07-01

    ... Salary Requirements § 541.601 Highly compensated employees. (a) An employee with total annual... compensation” must include at least $455 per week paid on a salary or fee basis. Total annual compensation may... total annual compensation does not total at least the minimum amount established in paragraph (a)...

  5. 31 CFR 30.0 - Executive compensation and corporate governance.

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Executive compensation and corporate governance. 30.0 Section 30.0 Money and Finance: Treasury Office of the Secretary of the Treasury TARP STANDARDS FOR COMPENSATION AND CORPORATE GOVERNANCE § 30.0 Executive compensation and corporate...

  6. 10 CFR 39.53 - Energy compensation source.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Energy compensation source. 39.53 Section 39.53 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.53 Energy compensation source. The licensee may use an energy compensation source (ECS) which...

  7. 39 CFR 3050.27 - Workers' Compensation Report.

    Science.gov (United States)

    2010-07-01

    ... 39 Postal Service 1 2010-07-01 2010-07-01 false Workers' Compensation Report. 3050.27 Section 3050.27 Postal Service POSTAL REGULATORY COMMISSION PERSONNEL PERIODIC REPORTING § 3050.27 Workers' Compensation Report. The Workers' Compensation Report, including summary workpapers, shall be provided by...

  8. Temperature compensation of resonant cavities with a teflon post

    OpenAIRE

    Bará Temes, Francisco Javier

    1982-01-01

    The negative temperature coefficient of E for teflon is used to compensate the frequency drift of a metal cavity due to thermal expansion. An experimental X-band transmission resonator was compensated in this way with a 10 mm teflon post. The results are considered of great interest for the compensation of waveguide millimiter wave oscillators. Peer Reviewed

  9. Load positioning system with gravity compensation

    Science.gov (United States)

    Hollow, R. H.

    1984-01-01

    A load positioning system with gravity compensation has a servomotor, position sensing feedback potentiometer and velocity sensing tachometer in a conventional closed loop servo arrangement to cause a lead screw and a ball nut to vertically position a load. Gravity compensating components comprise the DC motor, gears, which couple torque from the motor to the lead screw, and constant current power supply. The constant weight of the load applied to the lead screw via the ball nut tend to cause the lead screw to rotate, the constant torque of which is opposed by the constant torque produced by the motor when fed from the constant current source. The constant current is preset as required by the potentiometer to effect equilibration of the load which thereby enables the positioning servomotor to see the load as weightless under both static and dynamic conditions. Positioning acceleration and velocity performance are therefore symmetrical.

  10. Intonation and Compensation of Fretted String Instruments

    CERN Document Server

    Varieschi, Gabriele U

    2009-01-01

    In this paper we present mathematical models and we analyze the physics related to the problem of intonation of musical instruments such as guitars, mandolins and similar, i.e., we study how to produce perfectly in tune notes on these instruments. This analysis begins with the correct fret placement on the instrument fingerboard, following precise mathematical laws, but then it becomes increasingly complicated due to the geometrical deformation of the strings when these instruments are played, and also due to the inharmonic characteristics of the same strings. As a consequence of these factors, perfect intonation of all the notes on the instrument can never be achieved, but complex compensation procedures are introduced and studied to minimize the problem. To test the validity of these compensation procedures, we have performed extensive measurements using standard monochord sonometers and other basic acoustical devices, which confirm the correctness of our theoretical models. In particular, these experimenta...

  11. Vibration Compensation for Scanning Tunneling Microscope

    Institute of Scientific and Technical Information of China (English)

    LI Meng-chao; FU Xing; WEI Xiao-lei; HU Xiao-tang

    2003-01-01

    The influence of vibration is already one of main obstacles for improving the nano measuring accuracy.The techniques of anti-vibration,vibration isolation and vibration compensation become an important branch in nano measuring field.Starting with the research of sensitivity to vibration of scanning tunneling microscope(STM),the theory,techniques and realization methods of nano vibration sensor based on tunnel effect are initially investigated,followed by developing the experimental devices.The experiments of the vibration detection and vibration compensation are carried out.The experimental results show that vibration sensor based on tunnel effect is characterized by high sensitivity,good frequency characteristic and the same vibratory response characteristic consistent with STM.

  12. Aberration compensation in charged particle projection lithography

    International Nuclear Information System (INIS)

    Projection systems offer the opportunity to increase the throughput for charged particle lithography, because such systems image a large area of a mask directly on to a wafer as a single shot. Shots have to be imaged over a certain range of off-axis distances at the wafer to increase the writing speed, because shot sizes are limited to about 0.25x0.25 mm2 due to aberrations. In a projection system with only lenses, however, the aberrations for off-axis shots are still very large, and some aberration compensation elements need to be introduced. In this paper, three aberration compensation elements (deflectors, stigmators and dynamic focus lenses) are first discussed, a suite of newly developed software, called PROJECTION, based on this principle and our unified aberration theory is then described, and an illustrative example computed with the software is finally given

  13. Integrating structure- and ligand-based virtual screening: comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets.

    Science.gov (United States)

    Tan, Lu; Geppert, Hanna; Sisay, Mihiret T; Gütschow, Michael; Bajorath, Jürgen

    2008-10-01

    Similarity searching is often used to preselect compounds for docking, thereby decreasing the size of screening databases. However, integrated structure- and ligand-based screening schemes are rare at present. Docking and similarity search calculations using 2D fingerprints were carried out in a comparative manner on nine target enzymes, for which significant numbers of diverse inhibitors could be obtained. In the absence of knowledge-based docking constraints and target-directed parameter optimisation, fingerprint searching displayed a clear preference over docking calculations. Alternative combinations of docking and similarity search results were investigated and found to further increase compound recall of individual methods in a number of instances. When the results of similarity searching and docking were combined, parallel selection of candidate compounds from individual rankings was generally superior to rank fusion. We suggest that complementary results from docking and similarity searching can be captured by integrated compound selection schemes. PMID:18651695

  14. Lossless Compression of Video using Motion Compensation

    OpenAIRE

    Martins, Bo; Forchhammer, Søren

    1998-01-01

    Summary form only given. We investigate lossless coding of video using predictive coding and motion compensation. The new coding methods combine state-of-the-art lossless techniques as JPEG (context based prediction and bias cancellation, Golomb coding), with high resolution motion field estimation, 3D predictors, prediction using one or multiple (k) previous images, predictor dependent error modelling, and selection of motion field by code length. We treat the problem of precision of the mot...

  15. REACTIVE POWER COMPENSATION IN ASYNCHRONOUS ELECTRIC DRIVES

    Directory of Open Access Journals (Sweden)

    V.S. Malyar

    2013-10-01

    Full Text Available A problem of calculating capacity of cosine capacitors for individual compensation of reactive power in asynchronous electric drives in stationary and transient operation modes is considered. The algorithm introduced employs a high-adequacy mathematical model of asynchronous motor developed on the theory of representing vectors which takes into account both the magnetic core saturation and the current displacement in the rotor bars.

  16. Power Compensation for ICRF Heating in EAST

    Science.gov (United States)

    Chen, Gen; Qin, Chengming; Mao, Yuzhou; Zhao, Yanping; Yuan, Shuai; Zhang, Xinjun

    2016-08-01

    The source system covering a working frequency range of 24 MHz to 70 MHz with a total maximum output power of 12 MW has already been fabricated for Ion Cyclotron Range of Frequency (ICRF) heating in EAST from 2012. There are two continuous wave (CW) antennas consisting of four launching elements each fed by a separate 1.5 MW transmitter. Due to the strong mutual coupling among the launching elements, the injection power for launching elements should be imbalance to keep the k‖ (parallel wave number) spectrum of the launcher symmetric for ICRF heating. Cross power induced by the mutual coupling will also induce many significant issues, such as an uncontrollable phase of currents in launching elements, high voltage standing wave ratio (VSWR), and impedance mismatching. It is necessary to develop a power compensation system for antennas to keep the power balance between the feed points. The power balance system consists of two significant parts: a decoupler and phase control. The decoupler helps to achieve ports isolation to make the differential phase controllable and compensate partly cross power. After that, the differential phase of 0 or π will keep the power balance of two feed points completely. The first power compensation system consisting of four decouplers was assembled and tested for the port B antenna at the working frequency of 35 MHz. With the application of the power compensation system, the power balance, phase feedback control, and voltage standing wave ratio (VSWR) had obviously been improved in the 2015 EAST campaign. supported by the National Magnetic Confinement Fusion Science Program of China (No. 2015GB101001) and National Natural Science Foundation of China (Nos. 11575237, 11375235, 11375236)

  17. Board Independence, CEO Pay, and Camouflaged Compensation

    OpenAIRE

    Ruiz-Verdú, Pablo; Singh, Ravi

    2014-01-01

    We study how directors' reputational concerns influence executive compensation and the use ofcamouflaged forms of pay. We show that, in order to signal their independence to investors,boards lower managers' pay, but may also pay managers in hidden ways or structure compensationinefficiently. We also show that independent boards are more likely to make use of hiddencompensation than manager-friendly boards. We apply our model to study the costs and benefitsof greater pay transparency and of me...

  18. Board Committees, CEO Compensation, and Earnings Management

    OpenAIRE

    Laux, Christian; Laux, Volker

    2007-01-01

    We analyze the effect of committee formation on how corporate boards perform two main functions: setting CEO pay and overseeing the financial reporting process. The use of performance-based pay schemes induces the CEO to manipulate earnings, which leads to an increased need for board oversight. If the whole board is responsible for both functions, it is inclined to provide the CEO with a compensation scheme that is relatively insensitive to performance in order to reduce the burden of subsequ...

  19. Motion compensation of Synthetic Aperture Radar

    OpenAIRE

    Duncan, David; Long, David

    2003-01-01

    Synthetic aperture radar (SAR) is a digital signal processing technique which enhances the azimuth resolution of a radar image using the target doppler history created by the motion of the radar platform. If the platform deviates from a constant velocity, straight-line path then image quality is lost and image details become unfocused. Motion compensation (MOCO) is a technique in which the position and attitude of the platform is recorded or estimated and then used to correct the scene's dopp...

  20. Passive heave compensation of heavy modules

    OpenAIRE

    Jakobsen, Sten Magne Eng

    2008-01-01

    New subsea technology has increased size and weight of installed modules significantly. This thesis looks at heavy module installation from barge, through moonpool with use of passive heave compensation. An installation barge is designed with moonpool used as working platform for installation. Motion responses for barge are analyzed with use of marine engineering software MOSES. Responses found shows a significantly impact from moonpool, and it doubtingly if software is capa...