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Sample records for antibody-antigen docking compensates

  1. Computational Docking of Antibody-Antigen Complexes, Opportunities and Pitfalls Illustrated by Influenza Hemagglutinin

    Directory of Open Access Journals (Sweden)

    Mattia Pedotti

    2011-01-01

    Full Text Available Antibodies play an increasingly important role in both basic research and the pharmaceutical industry. Since their efficiency depends, in ultimate analysis, on their atomic interactions with an antigen, studying such interactions is important to understand how they function and, in the long run, to design new molecules with desired properties. Computational docking, the process of predicting the conformation of a complex from its separated components, is emerging as a fast and affordable technique for the structural characterization of antibody-antigen complexes. In this manuscript, we first describe the different computational strategies for the modeling of antibodies and docking of their complexes, and then predict the binding of two antibodies to the stalk region of influenza hemagglutinin, an important pharmaceutical target. The purpose is two-fold: on a general note, we want to illustrate the advantages and pitfalls of computational docking with a practical example, using different approaches and comparing the results to known experimental structures. On a more specific note, we want to assess if docking can be successful in characterizing the binding to the same influenza epitope of other antibodies with unknown structure, which has practical relevance for pharmaceutical and biological research. The paper clearly shows that some of the computational docking predictions can be very accurate, but the algorithm often fails to discriminate them from inaccurate solutions. It is of paramount importance, therefore, to use rapidly obtained experimental data to validate the computational results.

  2. Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface

    Science.gov (United States)

    Chen, Ing-Chien; Lee, Yu-Ching; Chen, Jun-Bo; Tsai, Keng-Chang; Chen, Ching-Tai; Chang, Jeng-Yih; Yang, Ei-Wen; Hsu, Po-Chiang; Jian, Jhih-Wei; Hsu, Hung-Ju; Chang, Hung-Ju; Hsu, Wen-Lian; Huang, Kai-Fa; Ma, Alex Che; Yang, An-Suei

    2012-01-01

    Protein-protein interactions are critical determinants in biological systems. Engineered proteins binding to specific areas on protein surfaces could lead to therapeutics or diagnostics for treating diseases in humans. But designing epitope-specific protein-protein interactions with computational atomistic interaction free energy remains a difficult challenge. Here we show that, with the antibody-VEGF (vascular endothelial growth factor) interaction as a model system, the experimentally observed amino acid preferences in the antibody-antigen interface can be rationalized with 3-dimensional distributions of interacting atoms derived from the database of protein structures. Machine learning models established on the rationalization can be generalized to design amino acid preferences in antibody-antigen interfaces, for which the experimental validations are tractable with current high throughput synthetic antibody display technologies. Leave-one-out cross validation on the benchmark system yielded the accuracy, precision, recall (sensitivity) and specificity of the overall binary predictions to be 0.69, 0.45, 0.63, and 0.71 respectively, and the overall Matthews correlation coefficient of the 20 amino acid types in the 24 interface CDR positions was 0.312. The structure-based computational antibody design methodology was further tested with other antibodies binding to VEGF. The results indicate that the methodology could provide alternatives to the current antibody technologies based on animal immune systems in engineering therapeutic and diagnostic antibodies against predetermined antigen epitopes. PMID:22457753

  3. Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

    Science.gov (United States)

    Akiba, Hiroki; Tsumoto, Kouhei

    2015-07-01

    Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody-antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, thermodynamics of the contribution from aromatic, charged and hydrogen bond-forming amino acids are discussed, and their different characteristics have been elucidated. The information gives fundamental understanding of the antibody-antigen interaction. Furthermore, the consequences of antibody engineering are analysed from thermodynamic viewpoints: humanization to reduce immunogenicity and rational design to improve affinity. Amino acid residues outside hot-spots in the interface play important roles in these cases, and thus thermodynamic and kinetic parameters give much information about the antigen recognition. Thermodynamic analysis of mutant antibodies thus should lead to advanced strategies to design and select antibodies with high affinity. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  4. Characterization of ELISA Antibody-Antigen Interaction using Footprinting-Mass Spectrometry and Negative Staining Transmission Electron Microscopy

    Science.gov (United States)

    Lin, Margaret; Krawitz, Denise; Callahan, Matthew D.; Deperalta, Galahad; Wecksler, Aaron T.

    2018-03-01

    We describe epitope mapping data using multiple covalent labeling footprinting-mass spectrometry (MS) techniques coupled with negative stain transmission electron microscopy (TEM) data to analyze the antibody-antigen interactions in a sandwich enzyme-linked immunosorbant assay (ELISA). Our hydroxyl radical footprinting-MS data using fast photochemical oxidation of proteins (FPOP) indicates suppression of labeling across the antigen upon binding either of the monoclonal antibodies (mAbs) utilized in the ELISA. Combining these data with Western blot analysis enabled the identification of the putative epitopes that appeared to span regions containing N-linked glycans. An additional structural mapping technique, carboxyl group footprinting-mass spectrometry using glycine ethyl ester (GEE) labeling, was used to confirm the epitopes. Deglycosylation of the antigen resulted in loss of potency in the ELISA, supporting the FPOP and GEE labeling data by indicating N-linked glycans are necessary for antigen binding. Finally, mapping of the epitopes onto the antigen crystal structure revealed an approximate 90° relative spatial orientation, optimal for a noncompetitive binding ELISA. TEM data shows both linear and diamond antibody-antigen complexes with a similar binding orientation as predicted from the two footprinting-MS techniques. This study is the first of its kind to utilize multiple bottom-up footprinting-MS techniques and TEM visualization to characterize the monoclonal antibody-antigen binding interactions of critical reagents used in a quality control (QC) lot-release ELISA. [Figure not available: see fulltext.

  5. 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

  6. 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

  7. Prevalence of Helicobacter pylori and parasites in symptomatic children examined for Helicobacter pylori antibodies, antigens, and parasites in Yemen.

    Science.gov (United States)

    Bin Mohanna, Mabrook A; Al-Zubairi, Lutf M; Sallam, Abdul K

    2014-11-01

    To estimate the prevalence of Helicobacter pylori (H. pylori) and parasites in symptomatic children examined for H. pylori antibodies, antigens, and parasites in Yemen. A record-based study was carried out at Specialized Sam Pediatric Center in Sana'a, Yemen for 3 years between 2011-2013. Out of the 43,200 patients seen for different causes through that period, 1008 (2.3%) (females: 675 [67%]; males: 333 [33%]) had gastric complaints, and were subjected to an examination of blood and stool for H. pylori and parasites. Data regarding age and gender was also collected. The age of the patients ranged from 3-15 years. The prevalence of H. pylori among children examined for H. pylori was 65%, 30% of them were males, and 35% were females (chi square [I2]=142, p<0.01]). The prevalence in the 6-8 years age group was 83%, and it was 52% in the age group of 12-15 years. The prevalence of giardiasis was 10%, and amoebiasis was 25%. Prevalence of H. pylori infection among children was high, and was more prevalent in the age group of 6-8 years than in the other age groups. Females were more affected than males. Parasites (amoebiasis and giardiasis) infestation was less prevalent.

  8. Designing binding kinetic assay on the bio-layer interferometry (BLI) biosensor to characterize antibody-antigen interactions.

    Science.gov (United States)

    Kamat, Vishal; Rafique, Ashique

    2017-11-01

    The Octet biosensors provide a high-throughput alternative to the well-established surface plasmon resonance (SPR) and SPR imaging (SPRi) biosensors to characterize antibody-antigen interactions. However, the utility of the Octet biosensors for accurate and reproducible measurement of binding rate constants of monoclonal antibodies (mAbs) is limited due to challenges such as analyte rebinding, and mass transport limitation (MTL). This study focuses on addressing these challenges and provides experimental conditions to reliably measure kinetics of mAb-antigen interactions. The mAb capture density of less than 0.6 nm was found to be optimal to measure a wide range of binding affinities on Octet HTX biosensor. The titration kinetic and single cycle kinetic assays performed on Octet HTX generated reproducible binding kinetic parameters and correlated with the values measured on Biacore 4000 and MASS-1. Kinetic assays performed on 0.1 nm density mAb surfaces significantly reduced MTL and enabled characterization of picomolar affinity mAbs. Finally, kinetic analysis performed on 150 antibodies to 10 antigens with molecular weights ranging from 21kD to 105kD showed concordance between Octet HTX, Biacore 4000 and MASS-1 (R 2  > 0.90). The data presented in this study suggest that under optimal experimental conditions, Octet biosensor is capable of generating kinetic values comparable to SPR/SPRi biosensors. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  9. A new technique to detect antibody-antigen reaction (biological interactions) on a localized surface plasmon resonance (LSPR) based nano ripple gold chip

    Energy Technology Data Exchange (ETDEWEB)

    Saleem, Iram, E-mail: iiram.qau@gmail.com [Department of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX 77204 (United States); Widger, William, E-mail: widger@uh.edu [Department of Biology and Biochemistry and Texas Center for Superconductivity, University of Houston, Houston, TX 77204 (United States); Chu, Wei-Kan, E-mail: wkchu@uh.edu [Department of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX 77204 (United States)

    2017-07-31

    Highlights: • The nano ripple LSPR chip has monolayer molecule-coating sensitivity and specific selectivity. • Gold nano-ripple sensing chip is a low cost, and a label-free method for detecting the antibody-antigen reaction. • The plasmonic resonance shift depends upon the concentration of the biomolecules attached on the surface of the nano ripple pattern. - Abstract: We demonstrate that the gold nano-ripple localized surface plasmon resonance (LSPR) chip is a low cost and a label-free method for detecting the presence of an antigen. A uniform stable layer of an antibody was coated on the surface of a nano-ripple gold pattern chip followed by the addition of different concentrations of the antigen. A red shift was observed in the LSPR spectral peak caused by the change in the local refractive index in the vicinity of the nanostructure. The LSPR chip was fabricated using oblique gas cluster ion beam (GCIB) irradiation. The plasmon-resonance intensity of the scattered light was measured by a simple optical spectroscope. The gold nano ripple chip shows monolayer scale sensitivity and high selectivity. The LSPR substrate was used to detect antibody-antigen reaction of rabbit X-DENTT antibody and DENTT blocking peptide (antigen).

  10. 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.

  11. 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.

  12. Creative compensation

    International Nuclear Information System (INIS)

    Coll, D.

    1994-01-01

    A discussion is presented of executive compensation in Canada's petroleum industry. Mandatory disclosure of executive compensation and benefits is regulated by the Ontario Securities Commission. Examination of the compensation packages of 80 oilpatch CEOs shows a clear difference in philosophy between large and small companies. Larger companies pay larger salaries, offer pension plans, and reward long-term loyalty. Within smaller companies, compensation tends to be linked with stock performance. Trends in compensation are to lower base salaries with more variables such as bonuses, cash incentives and gain-sharing programs. Increasing shareholder scrutiny is prompting more stringent guidelines on stock option plans. Some companies place performance conditions on stock vesting. Another option is to grant premium priced options to executives, to increase the gains required for the executive to post a profit. Other comapanies are granting stock options to their field personnel, or are granting stock to all employees. Directors are playing an increasing role in executive compensation. 4 tabs

  13. Flexible Ligand Docking Using Differential Evolution

    DEFF Research Database (Denmark)

    Thomsen, René

    2003-01-01

    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...

  14. 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.)

  15. Remote docking apparatus

    International Nuclear Information System (INIS)

    Dent, T.H.; Sumpman, W.C.; Wilhelm, J.J.

    1981-01-01

    The remote docking apparatus comprises a support plate with locking devices mounted thereon. The locking devices are capable of being inserted into tubular members for suspending the support plate therefrom. A vertical member is attached to the support plate with an attachment mechanism attached to the vertical member. A remote access manipulator is capable of being attached to the attachment mechanism so that the vertical member can position the remote access manipulator so that the remote access manipulator can be initially attached to the tubular members in a well defined manner

  16. PatchDock and SymmDock: servers for rigid and symmetric docking

    OpenAIRE

    Schneidman-Duhovny, Dina; Inbar, Yuval; Nussinov, Ruth; Wolfson, Haim J.

    2005-01-01

    Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein–protein and protein–small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs to the servers are either protein PDB codes or uploaded protein structures. The services are available at . The methods behind the servers are very efficient, allowing large-scale...

  17. 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.

  18. PatchDock and SymmDock: servers for rigid and symmetric docking.

    Science.gov (United States)

    Schneidman-Duhovny, Dina; Inbar, Yuval; Nussinov, Ruth; Wolfson, Haim J

    2005-07-01

    Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein-protein and protein-small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs to the servers are either protein PDB codes or uploaded protein structures. The services are available at http://bioinfo3d.cs.tau.ac.il. The methods behind the servers are very efficient, allowing large-scale docking experiments.

  19. Employee Compensation.

    Science.gov (United States)

    Osif, Bonnie A.; Harwood, Richard L.

    1995-01-01

    Presents an overview of selected literature about employee compensation. Highlights include the foundations of reward and recognition systems, incentive plans, problems with merit pay, a historical perspective on performance pay, evaluation criteria and processes, self-rating, job motivation and satisfaction, employee attitudes, collective…

  20. Controlling docks by stubble cultivation

    OpenAIRE

    Dierauer, Hansueli; Siegrist, Franziska; Weidmann, Gilles

    2017-01-01

    The stubble cultivation cuts the dock roots below growth points. The vegetative plant parts are then cut off from the water and nutrient supply, and regrowth is inhibited. Practical recommendation • Summer dock treatment is especially worthwhile in dry summers with catch crop cultivation and after early maturing crops (winter barley, whole-crop silage) or with an early tillage of grass-clover. • After grass-clover lay or cereal harvest, undercut the dock plants at a depth of 12-15 cm...

  1. A python-based docking program utilizing a receptor bound ligand shape: PythDock.

    Science.gov (United States)

    Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi

    2011-09-01

    PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and docked pose, i.e., average root mean squared deviation values of the bound ligand were compared for fourteen protein-ligand complexes. Since the number of ligands' rotational flexibility is an important factor affecting the accuracy of a docking, the data set was chosen to have various degrees of flexibility. Although PythDock has a scoring function simpler than those of other programs (AutoDock and DOCK), our results showed that PythDock predicted more accurate poses than both AutoDock4.2 and DOCK6.2. This indicates that PythDock could be a useful tool to study ligand-receptor interactions and could also be beneficial in structure based drug design.

  2. 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

  3. 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

  4. A Hadoop-based Molecular Docking System

    Science.gov (United States)

    Dong, Yueli; Guo, Quan; Sun, Bin

    2017-10-01

    Molecular docking always faces the challenge of managing tens of TB datasets. It is necessary to improve the efficiency of the storage and docking. We proposed the molecular docking platform based on Hadoop for virtual screening, it provides the preprocessing of ligand datasets and the analysis function of the docking results. A molecular cloud database that supports mass data management is constructed. Through this platform, the docking time is reduced, the data storage is efficient, and the management of the ligand datasets is convenient.

  5. Reactive power compensating system

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Timothy J. (Redondo Beach, CA); El-Sharkawi, Mohamed A. (Renton, WA); Venkata, Subrahmanyam S. (Seattle, WA)

    1987-01-01

    The reactive power of an induction machine is compensated by providing fixed capacitors on each phase line for the minimum compensation required, sensing the current on one line at the time its voltage crosses zero to determine the actual compensation required for each phase, and selecting switched capacitors on each line to provide the balance of the compensation required.

  6. Dimerization of DOCK2 is essential for DOCK2-mediated Rac activation and lymphocyte migration.

    Directory of Open Access Journals (Sweden)

    Masao Terasawa

    Full Text Available The migratory properties of lymphocytes depend on DOCK2, an atypical Rac activator predominantly expressed in hematopoietic cells. Although DOCK2 does not contain the Dbl homology domain typically found in guanine nucleotide exchange factors (GEFs, DOCK2 mediates the GTP-GDP exchange reaction for Rac via its DOCK homology region (DHR-2 (also known as CZH2 or Docker domain. DOCK2 DHR-2 domain is composed of three lobes, and Rac binding site and catalytic center are generated entirely from lobes B and C. On the other hand, lobe A has been implicated in dimer formation, yet its physiological significance remains unknown. Here, we report that lobe A-mediated DOCK2 dimerization is crucial for Rac activation and lymphocyte migration. We found that unlike wild-type DOCK2, DOCK2 mutant lacking lobe A failed to restore motility and polarity when expressed in thymoma cells and primary T cells lacking endogenous expression of DOCK2. Similar results were obtained with the DOCK2 point mutant having a defect in dimerization. Deletion of lobe A from the DHR-2 domain did not affect Rac GEF activity in vitro. However, fluorescence resonance energy transfer analyses revealed that lobe A is required for DOCK2 to activate Rac effectively during cell migration. Our results thus indicate that DOCK2 dimerization is functionally important under the physiological condition where only limited amounts of DOCK2 and Rac are localized to the plasma membrane.

  7. 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 examin......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...

  8. Options in Compensation

    DEFF Research Database (Denmark)

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

    2014-01-01

    to motivate effort. If rewarding low outcomes is infeasible, compensation consisting of stocks and options is a near-efficient means of overcoming the manager's induced aversion to undertaking risky investments, whereas stock compensation is not. However, stock plus option compensation may induce excessively...

  9. Microgravity experiments of nano-satellite docking mechanism for final rendezvous approach and docking phase

    Science.gov (United States)

    Ui, Kyoichi; Matunaga, Saburo; Satori, Shin; Ishikawa, Tomohiro

    2005-09-01

    Laboratory for Space Systems (LSS), Tokyo Institute of Technology (Tokyo Tech) conducted three-dimensional microgravity environment experiments about a docking mechanism for mothership-daughtership (MS-DS) nano-satellite using the facility of Japan Micro Gravity Center (JAMIC) with Hokkaido Institute of Technology (HIT). LSS has studied and developed a docking mechanism for MS-DS nano-satellite system in final rendezvous approach and docking phase since 2000. Consideration of the docking mechanism is to mate a nano-satellite stably while remaining control error of relative velocity and attitude because it is difficult for nano-satellite to have complicated attitude control and mating systems. Objective of the experiments is to verify fundamental grasping function based on our proposed docking methodology. The proposed docking sequence is divided between approach/grasping phase and guiding phase. In the approach/grasping phase, the docking mechanism grasps the nano-satellite even though the nano-satellite has relative position and attitude control errors as well as relative velocity in a docking space. In the guiding function, the docking mechanism guides the nano-satellite to a docking port while adjusting its attitude in order to transfer electrical power and fuel to the nano-satellite. In the paper, we describe the experimental system including the docking mechanism, control system, the daughtership system and the release mechanism, and describe results of microgravity experiments in JAMIC.

  10. GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking

    Science.gov (United States)

    Baek, Minkyung; Shin, Woong-Hee; Chung, Hwan Won; Seok, Chaok

    2017-07-01

    Protein-ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein-ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein-ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.

  11. SwarmDock: a server for flexible protein-protein docking.

    Science.gov (United States)

    Torchala, Mieczyslaw; Moal, Iain H; Chaleil, Raphael A G; Fernandez-Recio, Juan; Bates, Paul A

    2013-03-15

    Protein-protein interactions are central to almost all biological functions, and the atomic details of such interactions can yield insights into the mechanisms that underlie these functions. We present a web server that wraps and extends the SwarmDock flexible protein-protein docking algorithm. After uploading PDB files of the binding partners, the server generates low energy conformations and returns a ranked list of clustered docking poses and their corresponding structures. The user can perform full global docking, or focus on particular residues that are implicated in binding. The server is validated in the CAPRI blind docking experiment, against the most current docking benchmark, and against the ClusPro docking server, the highest performing server currently available.

  12. 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.

  13. Rosetta Ligand docking with flexible XML protocols.

    Science.gov (United States)

    Lemmon, Gordon; Meiler, Jens

    2012-01-01

    RosettaLigand is premiere software for predicting how a protein and a small molecule interact. Benchmark studies demonstrate that 70% of the top scoring RosettaLigand predicted interfaces are within 2Å RMSD from the crystal structure [1]. The latest release of Rosetta ligand software includes many new features, such as (1) docking of multiple ligands simultaneously, (2) representing ligands as fragments for greater flexibility, (3) redesign of the interface during docking, and (4) an XML script based interface that gives the user full control of the ligand docking protocol.

  14. Developing fair compensation structures

    International Nuclear Information System (INIS)

    Trousdale, W.J.

    1998-01-01

    The issue of finding an effective way to incorporate Aboriginal values into the process of developing fair compensation structures was discussed. This paper discusses pricing intangible values using dollars, but it was emphasized that 'values' are whatever are important to us. Therefore, in order to achieve fair compensation, creative alternatives that are value-focused should be pursued. In addition to the more straight-forward monetary compensation, compensation could also be about avoiding losses, mitigating adverse impacts, achieving better communication, and promoting cultural understanding. 25 refs., 2 tabs

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

    DEFF Research Database (Denmark)

    Olsen, Lars; Pettersson, Ingrid; Hemmingsen, Lars

    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...

  16. 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,

  17. 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

  18. Simulation and Optimization of Space Docking Mechanism

    Science.gov (United States)

    Qu, Yanli; Zhang, Chongfeng; Xiao, Yuzhi; Zhao, Mingyang

    2002-01-01

    Space docking technique has been developed and applied quickly. The system used to implement two spacecrafts' docking mission is called as "Berthing and Docking Mechanism". During rendezvous, damping system in space docking mechanism arrests the relative motion of the two vehicles and prevents them from colliding. Therefore, damping mechanism is the most critical and complicated section of berthing mechanism in both function and structure. The research and development on the structural and functional capabilities of docking hardware is of great significance. Dynamics modeling, simulation and optimization are essential to the study of the docking mechanism, the dynamics simulation of docking process and the development of new design concepts for advanced docking unit. mission-the androgynous peripheral assembly system (APAS). Two simulation and analysis methods were used to evaluate/optimise APAS: Automatic Dynamic Analysis of Mechanical Systems (ADAMS), and Numerical Programming of the Dynamic Mathematical Models. In the ADAMS model, a virtual prototype of the docking mechanism was built on a SUN workstation, which consists of over one hundred three-dimensional parts and sub-assemblies. Except for the friction, clearance, etc., the prototype is almost as same as the actual mechanism. Meanwhile, based on the virtual work principle, a mathematical dynamic model of the system was developed where the momentum of the springs, electromagnetic dampers and friction clutch was converted to the equivalent forces acted on the ball screw/nut assemblies. Many analysis and tests were performed on both of the models, and the results helped to investigate how the two models correlate with each other. Because the ADAMS model was based on the three-dimensional models of all parts of the docking mechanism, the result was thought more accurate and used to revise the mathematical model to perform dynamic simulation of docking event. Various characteristics of the mechanism's response

  19. Indexing Executive Compensation Contracts

    NARCIS (Netherlands)

    I. Dittmann (Ingolf); E.G. Maug (Ernst); O.G. Spalt (Oliver)

    2013-01-01

    textabstractWe analyze the efficiency of indexing executive pay by calibrating the standard model of executive compensation to a large sample of US CEOs. The benefits from linking the strike price of stock options to an index are small and fully indexing all options would increase compensation costs

  20. Dockomatic - automated ligand creation and docking.

    Science.gov (United States)

    Bullock, Casey W; Jacob, Reed B; McDougal, Owen M; Hampikian, Greg; Andersen, Tim

    2010-11-08

    The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions. DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations. DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

  1. Dockomatic - automated ligand creation and docking

    Directory of Open Access Journals (Sweden)

    Hampikian Greg

    2010-11-01

    Full Text Available Abstract Background The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions. Results DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations. Conclusions DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

  2. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

    Science.gov (United States)

    Trott, Oleg; Olson, Arthur J

    2010-01-30

    AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user. Copyright 2009 Wiley Periodicals, Inc.

  3. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment.

    NARCIS (Netherlands)

    Kufareva, I.; Rueda, M.; Katritch, V.; Stevens, R.C.; Abagyan, R.; Vroling, B.; Sanders, M.P.A.

    2011-01-01

    The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule

  4. Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment

    NARCIS (Netherlands)

    Kufareva, I; Rueda, M; Katritch, V; Roumen, L.; de Esch, I.J.P.; Leurs, R.; de Graaf, C.; Stevens, R.C.; Abagyan, R

    2011-01-01

    The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    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...

  6. SwissDock, a protein-small molecule docking web service based on EADock DSS.

    Science.gov (United States)

    Grosdidier, Aurélien; Zoete, Vincent; Michielin, Olivier

    2011-07-01

    Most life science processes involve, at the atomic scale, recognition between two molecules. The prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. Docking programs have a wide range of applications ranging from protein engineering to drug design. This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. An efficient Ajax/HTML interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. A wiki and a forum are available to the community to promote interactions between users. The SwissDock web site is available online at http://www.swissdock.ch. We believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.

  7. Reactive Power Compensator.

    Science.gov (United States)

    El-Sharkawi, M.A.; Venkata, S.S.; Chen, M.; Andexler, G.; Huang, T.

    1992-07-28

    A system and method for determining and providing reactive power compensation for an inductive load. A reactive power compensator (50,50') monitors the voltage and current flowing through each of three distribution lines (52a, 52b, 52c), which are supplying three-phase power to one or more inductive loads. Using signals indicative of the current on each of these lines when the voltage waveform on the line crosses zero, the reactive power compensator determines a reactive power compensator capacitance that must be connected to the lines to maintain a desired VAR level, power factor, or line voltage. Alternatively, an operator can manually select a specific capacitance for connection to each line, or the capacitance can be selected based on a time schedule. The reactive power compensator produces control signals, which are coupled through optical fibers (102/106) to a switch driver (110, 110') to select specific compensation capacitors (112) for connections to each line. The switch driver develops triggering signals that are supplied to a plurality of series-connected solid state switches (350), which control charge current in one direction in respect to ground for each compensation capacitor. During each cycle, current flows from ground to charge the capacitors as the voltage on the line begins to go negative from its positive peak value. The triggering signals are applied to gate the solid state switches into a conducting state when the potential on the lines and on the capacitors reaches a negative peak value, thereby minimizing both the potential difference and across the charge current through the switches when they begin to conduct. Any harmonic distortion on the potential and current carried by the lines is filtered out from the current and potential signals used by the reactive power compensator so that it does not affect the determination of the required reactive compensation. 26 figs.

  8. Reactive power compensator

    Science.gov (United States)

    El-Sharkawi, Mohamed A.; Venkata, Subrahmanyam S.; Chen, Mingliang; Andexler, George; Huang, Tony

    1992-01-01

    A system and method for determining and providing reactive power compensation for an inductive load. A reactive power compensator (50,50') monitors the voltage and current flowing through each of three distribution lines (52a, 52b, 52c), which are supplying three-phase power to one or more inductive loads. Using signals indicative of the current on each of these lines when the voltage waveform on the line crosses zero, the reactive power compensator determines a reactive power compensator capacitance that must be connected to the lines to maintain a desired VAR level, power factor, or line voltage. Alternatively, an operator can manually select a specific capacitance for connection to each line, or the capacitance can be selected based on a time schedule. The reactive power compensator produces control signals, which are coupled through optical fibers (102/106) to a switch driver (110, 110') to select specific compensation capacitors (112) for connections to each line. The switch driver develops triggering signals that are supplied to a plurality of series-connected solid state switches (350), which control charge current in one direction in respect to ground for each compensation capacitor. During each cycle, current flows from ground to charge the capacitors as the voltage on the line begins to go negative from its positive peak value. The triggering signals are applied to gate the solid state switches into a conducting state when the potential on the lines and on the capacitors reaches a negative peak value, thereby minimizing both the potential difference and across the charge current through the switches when they begin to conduct. Any harmonic distortion on the potential and current carried by the lines is filtered out from the current and potential signals used by the reactive power compensator so that it does not affect the determination of the required reactive compensation.

  9. Reactive power compensator

    Energy Technology Data Exchange (ETDEWEB)

    El-Sharkawi, Mohamed A. (Renton, WA); Venkata, Subrahmanyam S. (Woodinville, WA); Chen, Mingliang (Kirkland, WA); Andexler, George (Everett, WA); Huang, Tony (Seattle, WA)

    1992-01-01

    A system and method for determining and providing reactive power compensation for an inductive load. A reactive power compensator (50,50') monitors the voltage and current flowing through each of three distribution lines (52a, 52b, 52c), which are supplying three-phase power to one or more inductive loads. Using signals indicative of the current on each of these lines when the voltage waveform on the line crosses zero, the reactive power compensator determines a reactive power compensator capacitance that must be connected to the lines to maintain a desired VAR level, power factor, or line voltage. Alternatively, an operator can manually select a specific capacitance for connection to each line, or the capacitance can be selected based on a time schedule. The reactive power compensator produces control signals, which are coupled through optical fibers (102/106) to a switch driver (110, 110') to select specific compensation capacitors (112) for connections to each line. The switch driver develops triggering signals that are supplied to a plurality of series-connected solid state switches (350), which control charge current in one direction in respect to ground for each compensation capacitor. During each cycle, current flows from ground to charge the capacitors as the voltage on the line begins to go negative from its positive peak value. The triggering signals are applied to gate the solid state switches into a conducting state when the potential on the lines and on the capacitors reaches a negative peak value, thereby minimizing both the potential difference and across the charge current through the switches when they begin to conduct. Any harmonic distortion on the potential and current carried by the lines is filtered out from the current and potential signals used by the reactive power compensator so that it does not affect the determination of the required reactive compensation.

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

    Directory of Open Access Journals (Sweden)

    Rezaul Chowdhury

    Full Text Available 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.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.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: http

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

    Directory of Open Access Journals (Sweden)

    Sankar Basu

    Full Text Available 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 (<3.0Å. This is also the reason why the so called CAPRI criteria for assessing the quality of docking models is defined by applying various ad-hoc cutoffs on these measures to classify a docking model into the four classes: Incorrect, Acceptable, Medium, or High quality. This classification has been useful in CAPRI, but since models are grouped in only four bins it is also rather limiting, making it difficult to rank models, correlate with scoring functions or use it as target function in machine learning algorithms. Here, we present DockQ, a continuous protein-protein docking model quality measure derived by combining Fnat, LRMS, and iRMS to a single score in the range [0, 1] that can be used to assess the quality of protein docking models. By using DockQ on CAPRI models it is possible to almost completely reproduce the original CAPRI classification into Incorrect, Acceptable, Medium and High quality. An average PPV of 94% at 90% Recall demonstrating that there is no need to apply predefined ad-hoc cutoffs to classify docking models. Since DockQ recapitulates the CAPRI classification almost perfectly, it can be viewed as a higher resolution version of the CAPRI classification, making it possible to estimate model quality in a more quantitative way using Z-scores or sum of top ranked models, which has been so valuable for the CASP community. The possibility to directly correlate a quality measure to a scoring function has been crucial for the development of scoring functions for

  12. Improved docking of polypeptides with Glide.

    Science.gov (United States)

    Tubert-Brohman, Ivan; Sherman, Woody; Repasky, Matt; Beuming, Thijs

    2013-07-22

    Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein-protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-α-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM-GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 Å for the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40% of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.

  13. Workers Compensation Claim Data -

    Data.gov (United States)

    Department of Transportation — This data set contains DOT employee workers compensation claim data for current and past DOT employees. Types of data include claim data consisting of PII data (SSN,...

  14. 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...

  15. Protein docking prediction using predicted protein-protein interface

    Directory of Open Access Journals (Sweden)

    Li Bin

    2012-01-01

    Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

  16. 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.

  17. Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system.

    Science.gov (United States)

    Kantardjiev, Alexander A

    2012-07-01

    Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments-the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein-ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html.

  18. Quantum.Ligand.Dock: protein–ligand docking with quantum entanglement refinement on a GPU system

    Science.gov (United States)

    Kantardjiev, Alexander A.

    2012-01-01

    Quantum.Ligand.Dock (protein–ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein–ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments—the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein–ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pKa values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html. PMID:22669908

  19. Proximity Operations and Docking Sensor Development

    Science.gov (United States)

    Howard, Richard T.; Bryan, Thomas C.; Brewster, Linda L.; Lee, James E.

    2009-01-01

    The Next Generation Advanced Video Guidance Sensor (NGAVGS) has been under development for the last three years as a long-range proximity operations and docking sensor for use in an Automated Rendezvous and Docking (AR&D) system. The first autonomous rendezvous and docking in the history of the U.S. Space Program was successfully accomplished by Orbital Express, using the Advanced Video Guidance Sensor (AVGS) as the primary docking sensor. That flight proved that the United States now has a mature and flight proven sensor technology for supporting Crew Exploration Vehicles (CEV) and Commercial Orbital Transport Systems (COTS) Automated Rendezvous and Docking (AR&D). NASA video sensors have worked well in the past: the AVGS used on the Demonstration of Autonomous Rendezvous Technology (DART) mission operated successfully in spot mode out to 2 km, and the first generation rendezvous and docking sensor, the Video Guidance Sensor (VGS), was developed and successfully flown on Space Shuttle flights in 1997 and 1998. 12 Parts obsolescence issues prevent the construction of more AVGS units, and the next generation sensor was updated to allow it to support the CEV and COTS programs. The flight proven AR&D sensor has been redesigned to update parts and add additional capabilities for CEV and COTS with the development of the Next Generation AVGS at the Marshall Space Flight Center. The obsolete imager and processor are being replaced with new radiation tolerant parts. In addition, new capabilities include greater sensor range, auto ranging capability, and real-time video output. This paper presents some sensor hardware trades, use of highly integrated laser components, and addresses the needs of future vehicles that may rendezvous and dock with the International Space Station (ISS) and other Constellation vehicles. It also discusses approaches for upgrading AVGS to address parts obsolescence, and concepts for minimizing the sensor footprint, weight, and power requirements

  20. 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.

  1. A New Scoring Function for Molecular Docking Based on AutoDock and AutoDock Vina.

    Science.gov (United States)

    Tanchuk, Vsevolod Yu; Tanin, Volodymyr O; Vovk, Andriy I; Poda, Gennady

    2015-01-01

    Molecular docking of small molecules in the protein binding sites is the most widely used computational technique in modern structure-based drug discovery. Although accurate prediction of binding modes of small molecules can be achieved in most cases, estimation of their binding affinities remains mediocre at best. As an attempt to improve the correlation between the inhibitory constants, pKi, and scoring, we created a new, hybrid scoring function. The new function is a linear combination of the terms of the scoring functions of AutoDock and AutoDock Vina. It was trained on 2,412 protein-ligand complexes from the PDBbind database (www.pdbbind.org.cn, version 2012) and validated on a set of 313 complexes released in the 2013 version as a test set. The new function was included in a modified version of AutoDock. The hybrid scoring function showed a statistically significant improvement in both training and test sets in terms of correlation with and root mean square and mean absolute errors in prediction of pKi values. It was also tested on the CSAR 2014 Benchmark Exercise dataset (team T) and produced reasonably good results.

  2. A Novel Docking System for Modular Self-Reconfigurable Robots

    Directory of Open Access Journals (Sweden)

    Tan Zhang

    2017-10-01

    Full Text Available Existing self-reconfigurable robots achieve connections and disconnections by a separate drive of the docking system. In this paper, we present a new docking system with which the connections and disconnections are driven by locomotion actuators, without the need for a separate drive, which reduces the weight and the complexity of the modules. This self-reconfigurable robot consists of two types of fundamental modules, i.e., active and passive modules. By the docking system, two types of connections are formed with the fundamental modules, and the docking and undocking actions are achieved through simple control with less sensory feedback. This paper describes the design of the robotic modules, the docking system, the docking process, and the docking force analysis. An experiment is performed to demonstrate the self-reconfigurable robot with the docking system.

  3. Digital compensation techniques for the effects of time lag in closed-loop simulation using the 6 DOF motion system

    Science.gov (United States)

    Brown, R.

    1982-01-01

    Efforts are continued to develop digital filter compensation schemes for the correction of momentum gains observed in the closed loop simulation of the docking of two satellites using the 6 DOF motion system. Several filters that work well for small delays ( .100ms) and a non-preloaded probe are discussed.

  4. Synthesis, anti-microbial activity and molecular docking studies on ...

    Indian Academy of Sciences (India)

    100, where I = Zone of inhibition. 2.6 Docking studies. The protein in complex with simocyclinone (PDB ID: 2Y3P) was used as the template for molecular docking studies. GLIDE 9.5 and IFD script from Schrödinger,. LLC (New York) was employed as our primary docking engine.20 A hierarchical search protocol was utilized ...

  5. 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...... (1.0±0.2 v. 0; Piron 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...

  6. Docking to flexible nicotinic acetylcholine receptors

    DEFF Research Database (Denmark)

    Sander, Tommy; Bruun, Anne T; Balle, Thomas

    2010-01-01

    Computational docking to nicotinic acetylcholine receptors (nAChRs) and other members of the Cys-loop receptor family is complicated by the flexibility of the so-called C-loop. As observed in the large number of published crystal structures of the acetylcholine binding protein (AChBP), a structural...

  7. Pharmacophore-based similarity scoring for DOCK.

    Science.gov (United States)

    Jiang, Lingling; Rizzo, Robert C

    2015-01-22

    Pharmacophore modeling incorporates geometric and chemical features of known inhibitors and/or targeted binding sites to rationally identify and design new drug leads. In this study, we have encoded a three-dimensional pharmacophore matching similarity (FMS) scoring function into the structure-based design program DOCK. Validation and characterization of the method are presented through pose reproduction, crossdocking, and enrichment studies. When used alone, FMS scoring dramatically improves pose reproduction success to 93.5% (∼20% increase) and reduces sampling failures to 3.7% (∼6% drop) compared to the standard energy score (SGE) across 1043 protein-ligand complexes. The combined FMS+SGE function further improves success to 98.3%. Crossdocking experiments using FMS and FMS+SGE scoring, for six diverse protein families, similarly showed improvements in success, provided proper pharmacophore references are employed. For enrichment, incorporating pharmacophores during sampling and scoring, in most cases, also yield improved outcomes when docking and rank-ordering libraries of known actives and decoys to 15 systems. Retrospective analyses of virtual screenings to three clinical drug targets (EGFR, IGF-1R, and HIVgp41) using X-ray structures of known inhibitors as pharmacophore references are also reported, including a customized FMS scoring protocol to bias on selected regions in the reference. Overall, the results and fundamental insights gained from this study should benefit the docking community in general, particularly researchers using the new FMS method to guide computational drug discovery with DOCK.

  8. Aeromagnetic Compensation for UAVs

    Science.gov (United States)

    Naprstek, T.; Lee, M. D.

    2017-12-01

    Aeromagnetic data is one of the most widely collected types of data in exploration geophysics. With the continuing prevalence of unmanned air vehicles (UAVs) in everyday life there is a strong push for aeromagnetic data collection using UAVs. However, apart from the many political and legal barriers to overcome in the development of UAVs as aeromagnetic data collection platforms, there are also significant scientific hurdles, primary of which is magnetic compensation. This is a well-established process in manned aircraft achieved through a combination of platform magnetic de-noising and compensation routines. However, not all of this protocol can be directly applied to UAVs due to fundamental differences in the platforms, most notably the decrease in scale causing magnetometers to be significantly closer to the avionics. As such, the methodology must be suitably adjusted. The National Research Council of Canada has collaborated with Aeromagnetic Solutions Incorporated to develop a standardized approach to de-noising and compensating UAVs, which is accomplished through a series of static and dynamic experiments. On the ground, small static tests are conducted on individual components to determine their magnetization. If they are highly magnetic, they are removed, demagnetized, or characterized such that they can be accounted for in the compensation. Dynamic tests can include measuring specific components as they are powered on and off to assess their potential effect on airborne data. The UAV is then flown, and a modified compensation routine is applied. These modifications include utilizing onboard autopilot current sensors as additional terms in the compensation algorithm. This process has been applied with success to fixed-wing and rotary-wing platforms, with both a standard manned-aircraft magnetometer, as well as a new atomic magnetometer, much smaller in scale.

  9. (statcom) in synchronous compensator

    African Journals Online (AJOL)

    eobe

    for adoption of advanced control technologies such as Flexible Alternating Current Transmission System (FACTS) with fast ... APPLICATION OF STATIC SYNCHRONOUS COMPENSATOR (STATCOM) IN IMPROVING POWER SYSTEM PERFORMANCE, R.A Jokojeje .... supply at bus i and is the reactive power demand at.

  10. Enthalpy–entropy compensation

    Indian Academy of Sciences (India)

    Enthalpy–entropy compensation is the name given to the correlation sometimes observed between the estimates of the enthalpy and entropy of a reaction obtained from temperature-dependence data. Although the mainly artefactual nature of this correlation has been known for many years, the subject enjoys periodical ...

  11. Coast Guard Compensation Alternatives.

    Science.gov (United States)

    1981-12-01

    allowances for quarters and subsistence (either in kind or cash), medical care, commissary and exchange priviledges , reenlistment bonuses, special...4t.17-.28] Another study indicated that women value pay less comparatively than do men. Women were found to value work atmosphere more highly than...compensation policies for active duty personnel. Specifically, policies concerning subsistence allowances, quarters allowances, commissary/exchange priviledges

  12. Teacher Compensation and Organization.

    Science.gov (United States)

    Kelley, Carolyn

    1997-01-01

    Examines changes in the conceptualization of schooling over time from an organizational perspective. Explores how compensation systems might be better designed to match alternative organizational designs, considering scientific management, effective schools, content-driven schooling, and high standards/high involvement schools as organizational…

  13. Reactive Power Compensating System.

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Timothy J.; El-Sharkawi, Mohamed A.; Venkata, Subrahmanyam S.

    1985-01-04

    The circuit was designed for the specific application of wind-driven induction generators. It has great potential for application in any situation where a varying reactive power load is present, such as with induction motors or generators, or for transmission network compensation.

  14. Structuring competitive physician compensation models.

    Science.gov (United States)

    Mobley, Kim; Turcotte, Claire

    2010-12-01

    When developing and reviewing their physician compensation programs, healthcare organizations should: Understand the market data. Test outcomes of incentive plans for fair market value. Check total compensation for fair market value and reasonableness.

  15. Center for Worker's Compensation Studies

    Data.gov (United States)

    Federal Laboratory Consortium — The mission of the NIOSH Center for Workers’ Compensation Studies (CWCS) is to use workers’ compensation data and systems to improve workplace safety and health....

  16. 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.

  17. 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

  18. 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.

  19. The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals.

    Science.gov (United States)

    Cho, Art E; Wendel, John A; Vaidehi, Nagarajan; Kekenes-Huskey, Peter M; Floriano, Wely B; Maiti, Prabal K; Goddard, William A

    2005-01-15

    To help improve the accuracy of protein-ligand docking as a useful tool for drug discovery, we developed MPSim-Dock, which ensures a comprehensive sampling of diverse families of ligand conformations in the binding region followed by an enrichment of the good energy scoring families so that the energy scores of the sampled conformations can be reliably used to select the best conformation of the ligand. This combines elements of DOCK4.0 with molecular dynamics (MD) methods available in the software, MPSim. We test here the efficacy of MPSim-Dock to predict the 64 protein-ligand combinations formed by starting with eight trypsin cocrystals, and crossdocking the other seven ligands to each protein conformation. We consider this as a model for how well the method would work for one given target protein structure. Using as a criterion that the structures within 2 kcal/mol of the top scoring include a conformation within a coordinate root mean square (CRMS) of 1 A of the crystal structure, we find that 100% of the 64 cases are predicted correctly. This indicates that MPSim-Dock can be used reliably to identify strongly binding ligands, making it useful for virtual ligand screening.

  20. 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.

  1. InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information

    Science.gov (United States)

    Yu, Jinchao; Vavrusa, Marek; Andreani, Jessica; Rey, Julien; Tufféry, Pierre; Guerois, Raphaël

    2016-01-01

    The structural modeling of protein–protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/. PMID:27131368

  2. Using graphics processors to accelerate protein docking calculations.

    Science.gov (United States)

    Ritchie, David W; Venkatraman, Vishwesh; Mavridis, Lazaros

    2010-01-01

    Protein docking is the computationally intensive task of calculating the three-dimensional structure of a protein complex starting from the individual structures of the constituent proteins. In order to make the calculation tractable, most docking algorithms begin by assuming that the structures to be docked are rigid. This article describes some recent developments we have made to adapt our FFT-based "Hex" rigid-body docking algorithm to exploit the computational power of modern graphics processors (GPUs). The Hex algorithm is very efficient on conventional central processor units (CPUs), yet significant further speed-ups have been obtained by using GPUs. Thus, FFT-based docking calculations which formerly took many hours to complete using CPUs may now be carried out in a matter of seconds using GPUs. The Hex docking program and access to a server version of Hex on a GPU-based compute cluster are both available for public use.

  3. NASA Docking System (NDS) Interface Definitions Document (IDD)

    Science.gov (United States)

    Tabakman, Alexander; England, Warren

    2013-01-01

    The contents of this document define the integrated performance and interface design for NASA Docking System (NDS) Block 1 and the International Docking Adapter. The intent of this IDD is to provide the interface design for using, installing, and interfacing to the NDS Block 1 that will enable successful docking to the IDA. This document is under the control of the ISS Development Projects Office (OG).

  4. 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.

  5. 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...

  6. 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

  7. Temperature compensated photovoltaic array

    Science.gov (United States)

    Mosher, Dan Michael

    1997-11-18

    A temperature compensated photovoltaic module (20) comprised of a series of solar cells (22) having a thermally activated switch (24) connected in parallel with several of the cells (22). The photovoltaic module (20) is adapted to charge conventional batteries having a temperature coefficient (TC) differing from the temperature coefficient (TC) of the module (20). The calibration temperatures of the switches (24) are chosen whereby the colder the ambient temperature for the module (20), the more switches that are on and form a closed circuit to short the associated solar cells (22). By shorting some of the solar cells (22) as the ambient temperature decreases, the battery being charged by the module (20) is not excessively overcharged at lower temperatures. PV module (20) is an integrated solution that is reliable and inexpensive.

  8. Temperature compensated photovoltaic array

    Science.gov (United States)

    Mosher, D.M.

    1997-11-18

    A temperature compensated photovoltaic module comprises a series of solar cells having a thermally activated switch connected in parallel with several of the cells. The photovoltaic module is adapted to charge conventional batteries having a temperature coefficient differing from the temperature coefficient of the module. The calibration temperatures of the switches are chosen whereby the colder the ambient temperature for the module, the more switches that are on and form a closed circuit to short the associated solar cells. By shorting some of the solar cells as the ambient temperature decreases, the battery being charged by the module is not excessively overcharged at lower temperatures. PV module is an integrated solution that is reliable and inexpensive. 2 figs.

  9. Layout and control policies for cross docking operations

    NARCIS (Netherlands)

    Vis, Iris F. A.; Roodbergen, Kees Jan

    2011-01-01

    Many supply chains strive to shorten the time between a customer's order and the actual delivery of the ordered goods. Cross docking is one of the options to reduce these response times. Cross docking facilities are dynamic environments where products arrive and leave the same day. To deal with

  10. Molecular docking and in silico ADMET studies of silibinin and ...

    African Journals Online (AJOL)

    Molecular docking and in silico ADMET studies of silibinin and glycyrrhetic acid anti-inflammatory activity. Arif Malik, Abdul Manan, Muhammad Usman Mirza. Abstract. Purpose: To use in silico docking analysis and ADMET prediction of silibinin and glycyrrhetic acid to determine their pharmacokinetic and pharmacodynamic ...

  11. Comparing Industry and Academic Perspectives on Cross-Docking Operations

    NARCIS (Netherlands)

    Buijs, Paul; Vis, Iris F. A.; Smith, J.; Ellis, K.; de Koster, R.; Montreuil, B.; Ogle, M.

    2014-01-01

    This paper performs a comparative analysis on the industry and academic perspectives on cross-docking operations. Detailed descriptions are provided for three typical cross-dock settings by means of case illustrations. The purpose of these descriptions is to inspire break-through innovations in

  12. Small-Angle X-ray Scattering Data in Combination with RosettaDock Improves the Docking Energy Landscape

    DEFF Research Database (Denmark)

    Sønderby, Pernille; Rinnan, Åsmund; Madsen, Jesper J.

    2017-01-01

    We have performed a benchmark to evaluate the relative success of using small-angle X-ray scattering (SAXS) data as constraints (hereafter termed SAXSconstrain) in the RosettaDock protocol (hereafter termed RosettaDockSAXS). For this purpose, we have chosen 38 protein complex structures, calculat...

  13. Takeovers and (Excess) CEO Compensation

    NARCIS (Netherlands)

    Feito Ruiz, Isabel; Renneboog, Luc

    2017-01-01

    We study if a CEO’s equity-based compensation affects the expected value generation in takeovers. When the objectives of management and shareholders are more aligned, as proxied by the use of equity-based compensation, more value-maximizing acquisitions are expected. Whereas in widely-held firms the

  14. 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

  15. Takeovers and (excess) CEO compensation

    NARCIS (Netherlands)

    Feito Ruiz, Isabel; Renneboog, Luc

    We study if a CEO’s equity-based compensation affects the expected value generation in takeovers. When the objectives of management and shareholders are more aligned, as proxied by the use of equity-based compensation, more value-maximizing acquisitions are expected. Whereas in widely-held firms the

  16. A New, Improved Hybrid Scoring Function for Molecular Docking and Scoring Based on AutoDock and AutoDock Vina.

    Science.gov (United States)

    Tanchuk, Vsevolod Yu; Tanin, Volodymyr O; Vovk, Andriy I; Poda, Gennady

    2016-04-01

    Automated docking is one of the most important tools for structure-based drug design that allows prediction of ligand binding poses and also provides an estimate of how well small molecules fit in the binding site of a protein. A new scoring function based on AutoDock and AutoDock Vina has been introduced. The new hybrid scoring function is a linear combination of the two scoring function components derived from a multiple linear regression fitting procedure. The scoring function was built on a training set of 2412 protein-ligand complexes from pdbbind database (www.pdbbind.org.cn, version 2012). A test set of 313 complexes that appeared in the 2013 version was used for validation purposes. The new hybrid scoring function performed better than the original functions, both on training and test sets of protein-ligand complexes, as measured by the non-parametric Pearson correlation coefficient, R, mean absolute error (MAE), and root-mean-square error (RMSE) between the experimental binding affinities and the docking scores. The function also gave one of the best results among more than 20 scoring functions tested on the core set of the pdbbind database. The new AutoDock hybrid scoring function will be implemented in modified version of AutoDock. © 2015 John Wiley & Sons A/S.

  17. KC-135 zero-G testing of a microsatellite docking mechanism

    Science.gov (United States)

    Pavlich, Jane C.; Tchoryk, Peter, Jr.; Hays, Anthony B.; Wassick, Gregory

    2003-08-01

    Michigan Aerospace Corporation has developed a mechanism for microsatellite docking, which has been successfully demonstrated in a microgravity environment. This docking mechanism is specifically designed for soft-docking capability, tolerance to misalignment, and scalability. The current Autonomous Microsatellite Docking System (AMDS) design resulted from modifications to an earlier docking mechanism prototype that was tested at the Marshall Space Flight Center (MSFC) Flat Floor Facility. The AMDS was tested in a microgravity environment through the NASA JSC Reduced Gravity Program, where a KC-135 turbo jet flies a series of parabolic maneuvers. The test objectives of the KC-135 flight were to determine the docking mechanism cable assembly behavior in zero-g, test the full range of the docking envelope in a six degree of freedom test setup and determine the undocking capability and stability. The nature of the Michigan Aerospace docking mechanism enabled the entire docking cycle, including soft dock, auto-alignment and hard dock, to be completed within the 20 seconds of 'zero-g' time. Complete end-to-end docking and undocking was performed under a variety of initial conditions and docking parameters. The data collected during the KC-135 testing will be used to validate dynamic simulation models of the docking mechanism. The intent of these dynamic models is to examine a number of docking scenarios between a chaser and target satellite. This paper will discuss the results of the KC-135 docking tests and docking simulations.

  18. Stabilized thermally compensated mirror

    International Nuclear Information System (INIS)

    Dunn, C. III; Tobin, R.D.; Bergstreser, N.E.; Heinz, T.A.

    1975-01-01

    A thermally compensated mirror is described that is formed by a laminated structure. The structure is comprised of a front plate having a reflective front surface and having a plurality of grooves formed in the rear surface for conducting coolant fluid in heat exchanging relation with said reflective surface, a rear plate having coolant inlet and coolant outlet openings extending therethrough, a minimum temperature plate interposed between said front and rear plates and formed with a plurality of coolant distribution passageways coupled to receive coolant fluid from said coolant inlet and oriented to distribute said coolant fluid in a manner to establish a minimum temperature plane parallel to said reflective surface, a temperature stabilization plate interposed between said front plate and said minimum temperature plate and formed with a plurality of coolant distribution channels coupled to receive said coolant fluid after said coolant fluid has passed in heat exchanging relation with said reflective surface and oriented to distribute said coolant fluid in a manner to establish a uniform temperature plane parallel to said reflective surface, and means for circulating said coolant fluid through said structure in a predetermined path. (U.S.)

  19. Apparent compensation effect

    Energy Technology Data Exchange (ETDEWEB)

    Schwab, G.M.

    1983-11-01

    It is shown that by linear extrapolation of low temperature Arrhenius lines to 1/T = 0 a phenomenon resembling the compensation effect is generated because the absolute position of those lines is raised by the entropy of activation energy distribution so that the lines have an intersection point. An equation first derived by O. K. Rice (Actication et Structures des Molecules, p. 304, Paris (1928); O. K. Rice and Ramsberger, J. Amer. Chem. Soc. 50, 617 (1928)) and C. N. Hinshelwood (Kinetics of Chemical Change in Gaseous Systems, 3rd ed., Oxford Clarendon Press (1933)) is used. For a well documented example it is shown graphically that the construction described fits the observations. From the rate equation used an expression is derived which gives for any reaction the number of degrees of freedom contributing to the activation of the critical complex as a function of the limiting activation energies and of the apparent isocatalytic temperature. It is applied to a number of catalyses by alloys, salts, supported and inverse supported catalysts for a variety of reactions. In all cases values around 10 to 20 result for the freedom numbers. The conductivity of several doped semiconductors follows the same rule. The results are briefly discussed. 21 references, 4 figures, 4 tables.

  20. Orion Handling Qualities During ISS Proximity Operations and Docking

    Science.gov (United States)

    Stephens, John-Paul; Vos, Gordon A.; Bilimoria, Karl D.; Mueller, Eric R.; Brazzel, Jack; Spehar, Pete

    2011-01-01

    NASA's Orion spacecraft is designed to autonomously rendezvous and dock with many vehicles including the International Space Station. However, the crew is able to assume manual control of the vehicle s attitude and flight path. In these instances, Orion must meet handling qualities requirements established by NASA. Two handling qualities assessments were conducted at the Johnson Space Center to evaluate preliminary designs of the vehicle using a six degree of freedom, high-fidelity guidance, navigation, and control simulation. The first assessed Orion s handling qualities during the last 20 ft before docking, and included both steady and oscillatory motions of the docking target. The second focused on manual acquisition of the docking axis during the proximity operations phase and subsequent station-keeping. Cooper-Harper handling qualities ratings, workload ratings and comments were provided by 10 evaluation pilots for the docking study and 5 evaluation pilots for the proximity operations study. For the docking task, both cases received 90% Level 1 (satisfactory) handling qualities ratings, exceeding NASA s requirement. All ratings for the ProxOps task were Level 1. These evaluations indicate that Orion is on course to meet NASA's handling quality requirements for ProxOps and docking.

  1. Sequence alignment reveals possible MAPK docking motifs on HIV proteins.

    Directory of Open Access Journals (Sweden)

    Perry Evans

    Full Text Available Over the course of HIV infection, virus replication is facilitated by the phosphorylation of HIV proteins by human ERK1 and ERK2 mitogen-activated protein kinases (MAPKs. MAPKs are known to phosphorylate their substrates by first binding with them at a docking site. Docking site interactions could be viable drug targets because the sequences guiding them are more specific than phosphorylation consensus sites. In this study we use multiple bioinformatics tools to discover candidate MAPK docking site motifs on HIV proteins known to be phosphorylated by MAPKs, and we discuss the possibility of targeting docking sites with drugs. Using sequence alignments of HIV proteins of different subtypes, we show that MAPK docking patterns previously described for human proteins appear on the HIV matrix, Tat, and Vif proteins in a strain dependent manner, but are absent from HIV Rev and appear on all HIV Nef strains. We revise the regular expressions of previously annotated MAPK docking patterns in order to provide a subtype independent motif that annotates all HIV proteins. One revision is based on a documented human variant of one of the substrate docking motifs, and the other reduces the number of required basic amino acids in the standard docking motifs from two to one. The proposed patterns are shown to be consistent with in silico docking between ERK1 and the HIV matrix protein. The motif usage on HIV proteins is sufficiently different from human proteins in amino acid sequence similarity to allow for HIV specific targeting using small-molecule drugs.

  2. Molecular docking study of Papaver alkaloids to some alkaloid receptors

    Directory of Open Access Journals (Sweden)

    A. Nofallah

    2017-11-01

    Full Text Available Background and objectives: More than 40 different alkaloids have been obtained from opium the most important of which are morphine, codeine, papaverine, noscapine and tabaine. Opioid alkaloids produce analgesia by affecting areas of the brain that have peptides with pharmacological pseudo-opioid properties. These alkaloids show important effects on some intracellular peptides like mu, delta, and kappa receptors. Therefore, studying the effects of these alkaloids on different receptors is essential. Methods: Molecular docking is a well-known method in exploring the protein-ligand interactions. In this research, five important alkaloids were docked to crystal structure of human mu opioid receptor (4DKL, human delta opioid receptor (4EJ4 and human kappa opioid receptor (4DJH which were retrieved from protein databank. The 3D-structures of alkaloids were drawn by chembiooffice2010 and minimized with hyperchem package and submitted to molecular docking utilizing autodock-vina. Flexibility of the proteins was considered. The docking studies were performed to compare the affinity of these five alkaloids to the mentioned receptors. Results: We computationally docked each alkaloid compound onto each receptor structure and estimated their binding affinity based on dock scores. Dock score is a criteria including binding energy which utilized here for prediction and comparison of the binding affinities. Binding interactions of the docked alkaloids in receptor pockets were also visually inspected and compared. Conclusion: In this approach, using docking study as a computational method provided a valuable insight of opioid receptor pocket structures which would be essential to design more efficient drugs in pain managements and addiction treatments.

  3. A primer for workers' compensation.

    Science.gov (United States)

    Bible, Jesse E; Spengler, Dan M; Mir, Hassan R

    2014-07-01

    A physician's role within a workers' compensation injury extends far beyond just evaluation and treatment with several socioeconomic and psychological factors at play compared with similar injuries occurring outside of the workplace. Although workers' compensation statutes vary among states, all have several basic features with the overall goal of returning the injured worker to maximal function in the shortest time period, with the least residual disability and shortest time away from work. To help physicians unfamiliar with the workers' compensation process accomplish these goals. Review. Educational review. The streamlined review addresses the topics of why is workers' compensation necessary; what does workers' compensation cover; progression after work injury; impairment and maximum medical improvement, including how to use the sixth edition of American Medical Association's (AMA) Guides to the evaluation of permanent impairment (Guides); completion of work injury claim after impairment rating; independent medical evaluation; and causation. In the "no-fault" workers' compensation system, physicians play a key role in progressing the claim along and, more importantly, getting the injured worker back to work as soon as safely possible. Physicians should remain familiar with the workers' compensation process, along with how to properly use the AMA Guides. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. International Docking Standard (IDSS) Interface Definition Document (IDD) . E; Revision

    Science.gov (United States)

    Kelly, Sean M.; Cryan, Scott P.

    2016-01-01

    This International Docking System Standard (IDSS) Interface Definition Document (IDD) is the result of a collaboration by the International Space Station membership to establish a standard docking interface to enable on-orbit crew rescue operations and joint collaborative endeavors utilizing different spacecraft. This IDSS IDD details the physical geometric mating interface and design loads requirements. The physical geometric interface requirements must be strictly followed to ensure physical spacecraft mating compatibility. This includes both defined components and areas that are void of components. The IDD also identifies common design parameters as identified in section 3.0, e.g., docking initial conditions and vehicle mass properties. This information represents a recommended set of design values enveloping a broad set of design reference missions and conditions, which if accommodated in the docking system design, increases the probability of successful docking between different spacecraft. This IDD does not address operational procedures or off-nominal situations, nor does it dictate implementation or design features behind the mating interface. It is the responsibility of the spacecraft developer to perform all hardware verification and validation, and to perform final docking analyses to ensure the needed docking performance and to develop the final certification loads for their application. While there are many other critical requirements needed in the development of a docking system such as fault tolerance, reliability, and environments (e.g. vibration, etc.), it is not the intent of the IDSS IDD to mandate all of these requirements; these requirements must be addressed as part of the specific developer's unique program, spacecraft and mission needs. This approach allows designers the flexibility to design and build docking mechanisms to their unique program needs and requirements. The purpose of the IDSS IDD is to provide basic common design parameters

  5. Astronaut Vance Brand practices operating Docking Module hatch for ASTP

    Science.gov (United States)

    1975-01-01

    Astronaut Vance D. Brand, command module pilot of the American Apollo Soyuz Test Project (ASTP) prime crew, practices operating a Docking Module hatch during ASTP pre-flight training at JSC. The Docking Module is designed to link the Apollo and Soyuz spacecraft during their docking in Earth orbit mission. Gary L. Doerre of JSC's Crew Training and Procedures Division is working with Brand. Doerre is wearing a face mask to help prevent possible exposure to Brand of disease prior to the ASTP launch.

  6. Compensative hypertrophy of the kidney

    International Nuclear Information System (INIS)

    Raynaud, C.

    1976-01-01

    Several measurement methods are available to practitioners to reveal a compensative hypertrophy. Mensuration of the kidney has the advantage of simplicity but is in fact an unreliable and inaccurate method. Separate clearances in their traditional form have never entered into routine use because of the disadvantages of ureteral catheterism. The use of radioactive tracers avoids this drawback, but clearances calculated in this way are only valid in the absence of obstructive urinary disorders. Solutions have been proposed, but the values obtained are no longer identical with the clearances. The Hg uptake test quantifies quite accurately the function of each kidney. From the results obtained a complete compensative hypertrophy developed on a healthy kidney and an incomplete compensative hypertrophy developed on the diseased kidney have been described. In each of these situations the degree to which compensative hypertrophy develops seems to be fixed at a given level peculiar to each patient [fr

  7. Motion Compensation on DCT Domain

    Directory of Open Access Journals (Sweden)

    K. J. Ray Liu

    2001-10-01

    Full Text Available Alternative fully DCT-based video codec architectures have been proposed in the past to address the shortcomings of the conventional hybrid motion compensated DCT video codec structures traditionally chosen as the basis of implementation of standard-compliant codecs. However, no prior effort has been made to ensure interoperability of these two drastically different architectures so that fully DCT-based video codecs are fully compatible with the existing video coding standards. In this paper, we establish the criteria for matching conventional codecs with fully DCT-based codecs. We find that the key to this interoperability lies in the heart of the implementation of motion compensation modules performed in the spatial and transform domains at both the encoder and the decoder. Specifically, if the spatial-domain motion compensation is compatiable with the transform-domain motion compensation, then the states in both the coder and the decoder will keep track of each other even after a long series of P-frames. Otherwise, the states will diverge in proportion to the number of P-frames between two I-frames. This sets an important criterion for the development of any DCT-based motion compensation schemes. We also discuss and develop some DCT-based motion compensation schemes as important building blocks of fully DCT-based codecs. For the case of subpixel motion compensation, DCT-based approaches allow more accurate interpolation without any increase in computation. Furthermore, a scare number of DCT coefficients after quantization significantly decreases the number of calculations required for motion compensation. Coupled with the DCT-based motion estimation algorithms, it is possible to realize fully DCT-based codecs to overcome the disadvantages of conventional hybrid codecs.

  8. Photonic correlator pattern recognition: Application to autonomous docking

    Science.gov (United States)

    Sjolander, Gary W.

    1991-01-01

    Optical correlators for real-time automatic pattern recognition applications have recently become feasible due to advances in high speed devices and filter formulation concepts. The devices are discussed in the context of their use in autonomous docking.

  9. Passive, Failure-Tolerant Docking and Undocking with Articulated Magnets

    Data.gov (United States)

    National Aeronautics and Space Administration — Current spacecraft docking relies on active movement (e.g. thrusters) to close the gap between participants, and to separate them when undocking. I intend to develop...

  10. Optimal Rendezvous and Docking Simulator for Elliptical Orbits, Phase I

    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...

  11. Companies hone in on radar-docking technology

    Science.gov (United States)

    Howell, Elizabeth

    2009-11-01

    As NASA prepares to retire the Space Shuttle next year, two private space firms have tested docking technology that could be used on the next generation of US spacecraft. In September, Canadian firm Neptec tested a new radar system on the Space Shuttle Discovery that allows spacecraft to dock more easily. Meanwhile, Space Exploration Technologies (SpaceX) based in California has revealed that it tested out a new proximity sensor, dubbed "Dragoneye", on an earlier shuttle mission in July.

  12. Exponential Repulsion Improves Structural Predictability of Molecular Docking

    Czech Academy of Sciences Publication Activity Database

    Bazgier, Václav; Berka, K.; Otyepka, M.; Banáš, P.

    2016-01-01

    Roč. 37, č. 28 (2016), s. 2485-2494 ISSN 0192-8651 Institutional support: RVO:61389030 Keywords : cyclin-dependent kinases * structure-based design * scoring functions * cdk2 inhibitors * force-field * ligand interactions * drug discovery * purine * potent * protein-kinase-2 * molecular docking * dock 6.6 * drug design * cyclin-dependent kinase 2 * directory of decoys Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.229, year: 2016

  13. A primer on wood as dock construction material

    Science.gov (United States)

    Stan Lebow

    2007-01-01

    To be a successful marina owner and operator, it’s important to understand all the facets of one’s facility, including the intricacies of one part of the marina that most boaters take for granted: the docks. When it comes to dock construction, marinas have a wide-range of materials to choose from, with one of the most commonly used materials being preservative-treated...

  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. Reactive Path Planning Approach for Docking Robots in Unknown Environment

    Directory of Open Access Journals (Sweden)

    Peng Cui

    2017-01-01

    Full Text Available Autonomous robots need to be recharged and exchange information with the host through docking in the long-distance tasks. Therefore, feasible path is required in the docking process to guide the robot and adjust its pose. However, when there are unknown obstacles in the work area, it becomes difficult to determine the feasible path for docking. This paper presents a reactive path planning approach named Dubins-APF (DAPF to solve the path planning problem for docking in unknown environment with obstacles. In this proposed approach the Dubins curves are combined with the designed obstacle avoidance potential field to plan the feasible path. Firstly, an initial path is planned and followed according to the configurations of the robot and the docking station. Then when the followed path is evaluated to be infeasible, the intermediate configuration is calculated as well as the replanned path based on the obstacle avoidance potential field. The robot will be navigated to the docking station with proper pose eventually via the DAPF approach. The proposed DAPF approach is efficient and does not require the prior knowledge about the environment. Simulation results are given to validate the effectiveness and feasibility of the proposed approach.

  16. Self-compensation in semiconductors

    Science.gov (United States)

    Tsur, Y.; Riess, I.

    1999-09-01

    The problem of self-compensation of charged dopants is analyzed. Special emphasis is given to dopants in binary oxides. It is shown that one can determine the degree of self-compensation from the properties of the host material and dopant concentration alone. It is further shown that for a native p-type semiconductor, donors are compensated, mostly, by native ionic defects. On the other hand, doping with acceptors allows us to increase significantly the hole concentration, i.e., self-compensation is low under high doping levels. For a native n-type semiconductor the opposite is true, namely, extrinsic acceptors are mainly compensated by native ionic defects. It is shown that the changes in concentration of all the charged defects are simply related by a single factor, the doping factor f, or its power fk where k depends solely on the defect's charge. Quantitative calculations of f and defect concentrations are presented for Cu2O, which was used as a model material. It is found that for p-type Cu2O doping with donors results in f within the range of 1-10, depending on the dopant concentration and P(O2). This means that the hole concentration decreases and the electron concentration increases at most by a factor of 10. Therefore one does not expect to obtain a changeover from p- to n-type cuprous oxide by doping, under equilibrium conditions. Most of the donors are compensated by negative ionic defects. Self-compensation in the presence of amphoteric defects and Fermi level stabilization are discussed, using the former formalism.

  17. 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 the...

  18. 29 CFR 525.6 - Compensable time.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Compensable time. 525.6 Section 525.6 Labor Regulations... WITH DISABILITIES UNDER SPECIAL CERTIFICATES § 525.6 Compensable time. Individuals employed subject to this part must be compensated for all hours worked. Compensable time includes not only those hours...

  19. Orion Handling Qualities During ISS Rendezvous and Docking

    Science.gov (United States)

    Hart, Jeremy J.; Stephens, J. P.; Spehar, P.; Bilimoria, K.; Foster, C.; Gonzalex, R.; Sullivan, K.; Jackson, B.; Brazzel, J.; Hart, J.

    2011-01-01

    The Orion spacecraft was designed to rendezvous with multiple vehicles in low earth orbit (LEO) and beyond. To perform the required rendezvous and docking task, Orion must provide enough control authority to perform coarse translational maneuvers while maintaining precision to perform the delicate docking corrections. While Orion has autonomous docking capabilities, it is expected that final approach and docking operations with the International Space Station (ISS) will initially be performed in a manual mode. A series of evaluations was conducted by NASA and Lockheed Martin at the Johnson Space Center to determine the handling qualities (HQ) of the Orion spacecraft during different docking and rendezvous conditions using the Cooper-Harper scale. This paper will address the specifics of the handling qualities methodology, vehicle configuration, scenarios flown, data collection tools, and subject ratings and comments. The initial Orion HQ assessment examined Orion docking to the ISS. This scenario demonstrates the Translational Hand Controller (THC) handling qualities of Orion. During this initial assessment, two different scenarios were evaluated. The first was a nominal docking approach to a stable ISS, with Orion initializing with relative position dispersions and a closing rate of approximately 0.1 ft/sec. The second docking scenario was identical to the first, except the attitude motion of the ISS was modeled to simulate a stress case ( 1 degree deadband per axis and 0.01 deg/sec rate deadband per axis). For both scenarios, subjects started each run on final approach at a docking port-to-port range of 20 ft. Subjects used the THC in pulse mode with cues from the docking camera image, window views, and range and range rate data displayed on the Orion display units. As in the actual design, the attitude of the Orion vehicle was held by the automated flight control system at 0.5 degree deadband per axis. Several error sources were modeled including Reaction

  20. The Performance of Several Docking Programs at Reproducing Protein–Macrolide-Like Crystal Structures

    Directory of Open Access Journals (Sweden)

    Alejandro Castro-Alvarez

    2017-01-01

    Full Text Available The accuracy of five docking programs at reproducing crystallographic structures of complexes of 8 macrolides and 12 related macrocyclic structures, all with their corresponding receptors, was evaluated. Self-docking calculations indicated excellent performance in all cases (mean RMSD values ≤ 1.0 and confirmed the speed of AutoDock Vina. Afterwards, the lowest-energy conformer of each molecule and all the conformers lying 0–10 kcal/mol above it (as given by Macrocycle, from MacroModel 10.0 were subjected to standard docking calculations. While each docking method has its own merits, the observed speed of the programs was as follows: Glide 6.6 > AutoDock Vina 1.1.2 > DOCK 6.5 >> AutoDock 4.2.6 > AutoDock 3.0.5. For most of the complexes, the five methods predicted quite correct poses of ligands at the binding sites, but the lower RMSD values for the poses of highest affinity were in the order: Glide 6.6 ≈ AutoDock Vina ≈ DOCK 6.5 > AutoDock 4.2.6 >> AutoDock 3.0.5. By choosing the poses closest to the crystal structure the order was: AutoDock Vina > Glide 6.6 ≈ DOCK 6.5 ≥ AutoDock 4.2.6 >> AutoDock 3.0.5. Re-scoring (AutoDock 4.2.6//AutoDock Vina, Amber Score and MM-GBSA improved the agreement between the calculated and experimental data. For all intents and purposes, these three methods are equally reliable.

  1. Crime victims‘ right to compensation

    Directory of Open Access Journals (Sweden)

    Mrvić-Petrović Nataša

    2012-01-01

    Full Text Available This paper analyzes the most important documents of the United Nations, Council of Europe and the European Union relating to rights to damage compensation (restitution from offender and state compensation. The analysis shows that there is a gradual move from the concept of exercising the rights of victims in favor of a solidaristic model that takes less into account the rights of victims, and more the need to satisfy their legitimate interests. The economic crisis that is undermining the foundations of the welfare state could jeopardize the realization of this concept, especially in those European countries where the criminal justice system focuses solely on the offender, as is the case in Serbia. In such circumstances, regulation which protects the right to compensation, other rights and interests of victims, shall apply only to the extent that serves crime prevention. So it happens that in spite of a suitable normative framework and developments regarding the protection of victims of domestic violence and trafficking, the right to compensation and other rights of the victims do not actually get actualized in practice. In order to overcome this, a systemic reform to the criminal justice system should be undertaken with the aim to redirect the system towards the victim of the offense. Within these reforms a public fund for compensation of the victims of violence should be established and the process of mediation between the victim and the offender with the goal to make a settlement should be regulated, because these mechanisms do not exist in Serbia.

  2. ARCADE small-scale docking mechanism for micro-satellites

    Science.gov (United States)

    Boesso, A.; Francesconi, A.

    2013-05-01

    The development of on-orbit autonomous rendezvous and docking (ARD) capabilities represents a key point for a number of appealing mission scenarios that include activities of on-orbit servicing, automated assembly of modular structures and active debris removal. As of today, especially in the field of micro-satellites ARD, many fundamental technologies are still missing or require further developments and micro-gravity testing. In this framework, the University of Padova, Centre of Studies and Activities for Space (CISAS), developed the Autonomous Rendezvous Control and Docking Experiment (ARCADE), a technology demonstrator intended to fly aboard a BEXUS stratospheric balloon. The goal was to design, build and test, in critical environment conditions, a proximity relative navigation system, a custom-made reaction wheel and a small-size docking mechanism. The ARCADE docking mechanism was designed against a comprehensive set of requirements and it can be classified as small-scale, central, gender mating and unpressurized. The large use of commercial components makes it low-cost and simple to be manufactured. Last, it features a good tolerance to off-nominal docking conditions and a by-design soft docking capability. The final design was extensively verified to be compliant with its requirements by means of numerical simulations and physical testing. In detail, the dynamic behaviour of the mechanism in both nominal and off-nominal conditions was assessed with the multibody dynamics analysis software MD ADAMS 2010 and functional tests were carried out within the fully integrated ARCADE experiment to ensure the docking system efficacy and to highlight possible issues. The most relevant results of the study will be presented and discussed in conclusion to this paper.

  3. Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges.

    Science.gov (United States)

    Huang, Sheng-You

    2017-03-14

    Protein-ligand docking has been playing an important role in modern drug discovery. To model drug-target binding in real systems, a number of flexible-ligand docking algorithms with different sampling strategies and scoring methods have been subsequently developed over the past three decades, while rigid-ligand docking is still being used because of its compelling computational efficiency. Here, a comprehensive assessment has been conducted to investigate the effectiveness of flexible-ligand docking versus rigid-ligand docking for three representative docking algorithms (global optimization, incremental construction and multi-conformer docking) in virtual screening and pose prediction on the Directory of Useful Decoys. It was found that overall flexible-ligand docking did not achieve a statistically significant improvement in enrichments over rigid-ligand docking in virtual screening, but all docking programs significantly improved the success rates when considering ligand flexibility in pose prediction. The worse effectiveness of flexible-ligand docking in virtual screening than in pose prediction suggests that the challenges of current docking algorithms exist in ranking more than docking, although the use of flexible-ligand docking in virtual screening was justified by its better effectiveness for more flexible ligand in virtual screening. Challenges for scoring, including internal energy, charge polarization, entropy and flexibility, were investigated and discussed. An empirical way was also proposed to consider loss of ligand conformational entropy for virtual screening. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. Arbitrary protein−protein docking targets biologically relevant interfaces

    International Nuclear Information System (INIS)

    Martin, Juliette; Lavery, Richard

    2012-01-01

    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

  9. A dynamic motion simulator for future European docking systems

    Science.gov (United States)

    Brondino, G.; Marchal, PH.; Grimbert, D.; Noirault, P.

    1990-01-01

    Europe's first confrontation with docking in space will require extensive testing to verify design and performance and to qualify hardware. For this purpose, a Docking Dynamics Test Facility (DDTF) was developed. It allows reproduction on the ground of the same impact loads and relative motion dynamics which would occur in space during docking. It uses a 9 degree of freedom, servo-motion system, controlled by a real time computer, which simulates the docking spacecraft in a zero-g environment. The test technique involves and active loop based on six axis force and torque detection, a mathematical simulation of individual spacecraft dynamics, and a 9 degree of freedom servomotion of which 3 DOFs allow extension of the kinematic range to 5 m. The configuration was checked out by closed loop tests involving spacecraft control models and real sensor hardware. The test facility at present has an extensive configuration that allows evaluation of both proximity control and docking systems. It provides a versatile tool to verify system design, hardware items and performance capabilities in the ongoing HERMES and COLUMBUS programs. The test system is described and its capabilities are summarized.

  10. 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.

  11. Optimal compensation for neuron loss

    Science.gov (United States)

    Barrett, David GT; Denève, Sophie; Machens, Christian K

    2016-01-01

    The brain has an impressive ability to withstand neural damage. Diseases that kill neurons can go unnoticed for years, and incomplete brain lesions or silencing of neurons often fail to produce any behavioral effect. How does the brain compensate for such damage, and what are the limits of this compensation? We propose that neural circuits instantly compensate for neuron loss, thereby preserving their function as much as possible. We show that this compensation can explain changes in tuning curves induced by neuron silencing across a variety of systems, including the primary visual cortex. We find that compensatory mechanisms can be implemented through the dynamics of networks with a tight balance of excitation and inhibition, without requiring synaptic plasticity. The limits of this compensatory mechanism are reached when excitation and inhibition become unbalanced, thereby demarcating a recovery boundary, where signal representation fails and where diseases may become symptomatic. DOI: http://dx.doi.org/10.7554/eLife.12454.001 PMID:27935480

  12. Addressing inadequate compensation | IDRC - International ...

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

    2016-08-12

    Aug 12, 2016 ... Communities' land and land use need to be fairly valuated for them to receive equitable compensation and a fair share of benefits and risks in land deals. Researchers in some projects are using “participatory valuation” processes with communities to help them appraise their lands' value and strengthening ...

  13. Rigid Molecule Docking: FPGA Reconfiguration for Alternative Force Laws

    Directory of Open Access Journals (Sweden)

    VanCourt Tom

    2006-01-01

    Full Text Available Molecular docking is one of the primary computational methods used by pharmaceutical companies to try to reduce the cost of drug discovery. A common docking technique, used for low-resolution screening or as an intermediate step, performs a three-dimensional correlation between two molecules to test for favorable interactions between them. We extend our previous work on FPGA-based docking accelerators, using reconfigurability for customization of the physical laws and geometric models that describe molecule interaction. Our approach, based on direct summation, allows straightforward combination of multiple forces and enables nonlinear force models; the latter, in particular, are incompatible with the transform-based techniques typically used. Our approach has the further advantage of supporting spatially oriented values in molecule models, as well as the detection of multiple positions representing favorable interactions. We report performance measurements on several different models of chemical behavior and show speedups of from to over a PC.

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

    DEFF Research Database (Denmark)

    Petersen, Hanne Løhmann; Røpke, Stefan

    2011-01-01

    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......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...

  15. 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.

  16. Parallel Evolutionary Optimization Algorithms for Peptide-Protein Docking

    Science.gov (United States)

    Poluyan, Sergey; Ershov, Nikolay

    2018-02-01

    In this study we examine the possibility of using evolutionary optimization algorithms in protein-peptide docking. We present the main assumptions that reduce the docking problem to a continuous global optimization problem and provide a way of using evolutionary optimization algorithms. The Rosetta all-atom force field was used for structural representation and energy scoring. We describe the parallelization scheme and MPI/OpenMP realization of the considered algorithms. We demonstrate the efficiency and the performance for some algorithms which were applied to a set of benchmark tests.

  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. Nuclear damage compensation and energy reform

    International Nuclear Information System (INIS)

    Yokemoto, Masafumi

    2013-01-01

    Nuclear damage compensation and energy reform were closely related. Nuclear damage compensation cost should be part of generation cost of nuclear power. Extend of nuclear damage compensation was limited by compensation standard of Tokyo Electric Power Co. (TEPCO) following guidelines of Dispute Reconciliation Committee for Nuclear Damage Compensation. TEPCO had already paid compensation of about two trillion yen until now, which was only a part of total damage compensation cost. TEPCO had been provided more than 3.4 trillion yen by Nuclear Damage Liability Facilitation Cooperation, which would be put back by nuclear operators including TEPCO. TEPCO could obtain present raising funds and try to reconstruct business with restart of nuclear power, which might disturb energy reform. Present nuclear damage compensation scheme had better be reformed with learning more from Minamata disease case in Japan. (T. Tanaka)

  19. Emittance compensation in split photoinjectors

    Directory of Open Access Journals (Sweden)

    Klaus Floettmann

    2017-01-01

    Full Text Available The compensation of correlated emittance contributions is of primary importance to optimize the performance of high brightness photoinjectors. While only extended numerical simulations can capture the complex beam dynamics of space-charge-dominated beams in sufficient detail to optimize a specific injector layout, simplified models are required to gain a deeper understanding of the involved dynamics, to guide the optimization procedure, and to interpret experimental results. In this paper, a slice envelope model for the emittance compensation process in a split photoinjector is presented. The emittance term is included in the analytical solution of the beam envelope in a drift, which is essential to take the emittance contribution due to a beam size mismatch into account. The appearance of two emittance minima in the drift is explained, and the matching into the booster cavity is discussed. A comparison with simulation results points out effects which are not treated in the envelope model, such as overfocusing and field nonlinearities.

  20. Kinesthetic compensation for sensorimotor rearrangements.

    Science.gov (United States)

    Ellis, Stephen R; Adelstein, Bernard D

    2009-11-01

    The authors report a new sensorimotor phenomenon in which participants use hand-sensed kinesthetic information to compensate for rotational sensorimotor rearrangements. This compensation benefits from conscious awareness and is related to hand posture. The technique can reduce control inefficiency with some misalignments by as much as 64%. The results support Y. Guiard's (1987) suggestion that in bimanual tasks one hand provides an operational frame of reference for the other hand as in a closed kinematic chain. Results with right-handed participants show that the right and left hands are equally effective at providing such a cue. A constant-angular-targeting-error model, similar to that used for hand movements by H. Cunningham and I. Vardi (1990) and for walking by S. K. Rushton, J. M. Harris, M. R. Lloyd, and J. P. Wann (1998), is used to model the trajectories of targeting hand movements demonstrating the phenomenon. The model provides a natural parameter of the error.

  1. Frequency Compensation of an Audio Power Amplifier

    NARCIS (Netherlands)

    van der Zee, Ronan A.R.; van Heeswijk, R.

    2006-01-01

    A car audio power amplifier is presented that uses a frequency compensation scheme which avoids large compensation capacitors around the MOS power transistors, while retaining the bandwidth and stable load range of nested miller compensation. THD is 0.005%@(1kHz, 10W), SNR is 108dB, and the

  2. Trends in VBA Disability Compensation Spending

    Science.gov (United States)

    2016-06-01

    Unemployability MCRMC Military Compensation and Retirement Modernization Commission PTSD Post -Traumatic Stress Disorder US United States VA...Defense Authorization Act of 2013 established the Military Compensation and Retirement Modernization Commission (MCRMC) to conduct a review of...military compensation and retirement systems and to make recommendations to modernize such programs. The Commission asked the Institute for Defense

  3. 33 CFR 136.217 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.217 Compensation... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Compensation allowable. 136.217...

  4. 33 CFR 136.205 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.205 Compensation... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Compensation allowable. 136.205...

  5. 33 CFR 136.223 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.223 Compensation... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Compensation allowable. 136.223...

  6. 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 PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT General Procedure § 136.113 Other compensation. A... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Other compensation. 136.113...

  7. Global Compensation Specialist | IDRC - International Development ...

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

    Job Summary. The Global Compensation Specialist provides advice and guidance regarding compensation and benefits by analysing trends, conducting studies, keeping up-to-date on new legislation, and developing strategies and tools to support corporate global compensation program. The incumbent supports the HR ...

  8. 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...

  9. 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...

  10. pso@autodock: a fast flexible molecular docking program based on Swarm intelligence.

    Science.gov (United States)

    Namasivayam, Vigneshwaran; Günther, Robert

    2007-12-01

    On the quest of novel therapeutics, molecular docking methods have proven to be valuable tools for screening large libraries of compounds determining the interactions of potential drugs with the target proteins. A widely used docking approach is the simulation of the docking process guided by a binding energy function. On the basis of the molecular docking program autodock, we present pso@autodock as a tool for fast flexible molecular docking. Our novel Particle Swarm Optimization (PSO) algorithms varCPSO and varCPSO-ls are suited for rapid docking of highly flexible ligands. Thus, a ligand with 23 rotatable bonds was successfully docked within as few as 100 000 computing steps (rmsd = 0.87 A), which corresponds to only 10% of the computing time demanded by autodock. In comparison to other docking techniques as gold 3.0, dock 6.0, flexx 2.2.0, autodock 3.05, and sodock, pso@autodock provides the smallest rmsd values for 12 in 37 protein-ligand complexes. The average rmsd value of 1.4 A is significantly lower then those obtained with the other docking programs, which are all above 2.0 A. Thus, pso@autodock is suggested as a highly efficient docking program in terms of speed and quality for flexible peptide-protein docking and virtual screening studies.

  11. 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

    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 ind...

  12. Synchronization in cross-docking networks : A research classification and framework

    NARCIS (Netherlands)

    Buijs, Paul; Vis, Iris F. A.; Carlo, Hector J.

    2014-01-01

    Cross-docking is a distribution strategy that enables the consolidation of less-than-truckload shipments into full truckloads without long-term storage. Due to the absence of a storage buffer inside a cross-dock, local and network-wide cross-docking operations need to be carefully synchronized. This

  13. 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.

  14. Compensation Techniques in Accelerator Physics

    International Nuclear Information System (INIS)

    Sayed, Hisham Kamal

    2011-01-01

    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

  15. An agent-based simulation model for autonomous trailer docking

    NARCIS (Netherlands)

    Gerrits, Berry; Mes, Martijn; Schuur, Peter Cornelis

    2018-01-01

    This paper presents a simulation model of a generic automated planning and control system for the pick-up and docking of semi-trailers by means of autonomous Yard Tractors (YTs) in a collision- and conflict free environment. To support the planning and control of the YTs, we propose a Multi-Agent

  16. Space Shuttle Discovery Docked to the Pressurized Mating Adapter

    Science.gov (United States)

    2007-01-01

    Space Shuttle Discovery, docked to the Pressurized Mating Adapter (PMA-2) on the International Space Station (ISS), is featured in this image photographed by a space walker during the second session of extravehicular activity (EVA) for the STS-120 mission on October 28, 2007.

  17. Molecular Dynamics and Docking of Biphenyl: A Potential ...

    African Journals Online (AJOL)

    Purpose: To develop a new drug that inhibits viral attachment and entry for the treatment of HIV/AIDS patients. Methods: Two Protein Databank (PDB) crystal structures of HIV-1 gp120-CD4 complexes, namely, 1RZK and 1G9N, were mutated at amino acid position 43 to a biphenylalanine (biPhe-43) residue. FireDock web ...

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

    Science.gov (United States)

    2010-04-01

    ..., boathouses, and all other residential water-use facilities shall not exceed a total footprint area of greater... 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 AUTHORITY...

  19. Application of the docking program SOL for CSAR benchmark.

    Science.gov (United States)

    Sulimov, Alexey V; Kutov, Danil C; Oferkin, Igor V; Katkova, Ekaterina V; Sulimov, Vladimir B

    2013-08-26

    This paper is devoted to results obtained by the docking program SOL and the post-processing program DISCORE at the CSAR benchmark. SOL and DISCORE programs are described. SOL is the original docking program developed on the basis of the genetic algorithm, MMFF94 force field, rigid protein, precalculated energy grid including desolvation in the frame of simplified GB model, vdW, and electrostatic interactions and taking into account the ligand internal strain energy. An important SOL feature is the single- or multi-processor performance for up to hundreds of CPUs. DISCORE improves the binding energy scoring by the local energy optimization of the ligand docked pose and a simple linear regression on the base of available experimental data. The docking program SOL has demonstrated a good ability for correct ligand positioning in the active sites of the tested proteins in most cases of CSAR exercises. SOL and DISCORE have not demonstrated very exciting results on the protein-ligand binding free energy estimation. Nevertheless, for some target proteins, SOL and DISCORE were among the first in prediction of inhibition activity. Ways to improve SOL and DISCORE are discussed.

  20. Synthesis, docking and anticancer activity studies of D-proline ...

    Indian Academy of Sciences (India)

    act as an anticancer drug. The collection of drug and receptor complex was identified via docking and their relative stabilities were evaluated using molecular dynamics and their binding affinities, using free energy simulations. Based on the total energy values, the anti- cancer activity of the compound was identified.

  1. 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.

  2. Molecular Dynamics and Docking of Biphenyl: A Potential ...

    African Journals Online (AJOL)

    by computational molecular modeling and docking is that it is a truthful and precise rational drug design approach. The present study serves as a motivation of pursue for an attachment inhibitor against HIV-1 gp120 glycoprotein to complement the currently. 0. 1. 2. 3. 4. 5. 6. 0. 1000. 2000. 3000. 4000. 5000. R. MSD. /Å.

  3. Synthesis and molecular docking of new hydrazones derived from ...

    African Journals Online (AJOL)

    Synthesis and molecular docking of new hydrazones derived from ethyl isonipecotate and their biological activities. A Munir, Aziz-ur Rehman, M.A. Abbasi, S.Z. Siddiqui, A Nasir, S.G. Khan, S Rasool, S.A.A. Shah ...

  4. Tail docking in dogs: can attitude change be achieved?

    Science.gov (United States)

    Bennett, P; Perini, E

    2003-05-01

    The debate about tail docking in domestic dogs continues to rage in many developed countries and attitudes expressed by different community groups remain diametrically opposed. Veterinary associations and welfare organisations typically want the practice banned, while many breeders and pure-bred dog associations just as vigorously oppose the introduction of anti-docking legislation. In recent years, much data have been accumulated concerning the welfare implications of tail docking. A recent evaluation of this literature suggests that the practice has little to recommend it and that, in the absence of reasonable case-by-case justification, it may constitute an unacceptable abuse of a sentient species. Given this situation, it is difficult to understand why many canine interest groups, presumably representing those people who care most about the welfare of companion dogs, should continue to hold such strong attitudes in favour of tail docking. In this review we attempt to explain why different community groups might espouse strong but opposing attitudes, despite having access to the same information. We argue that the theory of cognitive dissonance, popular among social psychologists, may provide a useful framework within which to understand, and attempt to alter, attitudes that persist even though they appear contrary to available empirical evidence.

  5. Functional and catalytic active sites prediction and docking analysis ...

    African Journals Online (AJOL)

    Bioinformatics

    2015-07-01

    Jul 1, 2015 ... African Journal of Biotechnology. Full Length Research Paper. Functional and catalytic active sites prediction and docking analysis of azoreductase enzyme in. Pseudomonas putida with a variety of commercially available azodyes. Bikash Thakuria, Chandra J Singha, Premchand Maisnam and Samrat ...

  6. 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 who...

  7. 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.

  8. 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.

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

    Directory of Open Access Journals (Sweden)

    Katelyn E Mills

    Full Text Available 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.

  10. A Practical Guide to Molecular Docking and Homology Modelling for Medicinal Chemists.

    Science.gov (United States)

    Lohning, Anna E; Levonis, Stephan M; Williams-Noonan, Billy; Schweiker, Stephanie S

    2017-01-01

    Elucidating details of the relationship between molecular structure and a particular biological end point is essential for successful, rational drug discovery. Molecular docking is a widely accepted tool for lead identification however, navigating the intricacies of the software can be daunting. Our objective was therefore to provide a step-by-step guide for those interested in incorporating contemporary basic molecular docking and homology modelling into their design strategy. Three molecular docking programs, AutoDock4, SwissDock and Surflex-Dock, were compared in the context of a case study where a set of steroidal and non-steroidal ligands were docked into the human androgen receptor (hAR) using both rigid and flexible target atoms. Metrics for comparison included how well each program predicted the X-ray structure orientation via root mean square deviation (rmsd), predicting known actives via ligand ranking and comparison to biological data where available. Benchmarking metrics were discussed in terms of identifying accurate and reliable results. For cases where no three dimensional structure exists, we provided a practical example for creating a homology model using Swiss-Model. Results showed an rmsd between X-ray ligands from wild-type and mutant receptors and docked poses were 4.15Å and 0.83Å (SwissDock), 2.69Å and 8.80Å (AutoDock4) and 0.39Å and 0.71Å (Surflex-Dock) respectively. Surflex-Dock performed consistently well in pose prediction (less than 2Å) while Auto- Dock4 predicted known active non-steroidal antiandrogens most accurately. Introducing flexibility into target atoms produced the largest degree of change in ligand ranking in Surflex-Dock. We produced a viable homology model of the P2X1 purireceptor for subsequent docking analysis. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  11. 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

  12. More tail lesions among undocked than tail docked pigs in a conventional herd

    DEFF Research Database (Denmark)

    Lahrmann, H. P.; Busch, M. E.; D'Eath, R. B.

    2017-01-01

    The vast majority of piglets reared in the European Union (EU) and worldwide is tail docked to reduce the risk of being tail bitten, even though EU animal welfare legislation bans routine tail docking. Many conventional herds experience low levels of tail biting among tail docked pigs, however...... it is not known, what the prevalence would have been had the pigs not been tail docked. The aim of this study was to compare the prevalence of tail lesions between docked and undocked pigs in a conventional piggery in Denmark with very low prevalence of tail biting among tail docked pigs. The study included 1922...... that housing pigs with intact tails in conventional herds with very low prevalence of tail biting among tail docked pigs, will increase the prevalence of pigs with tail lesions considerably, and pig producers will need more hospital pens. Abattoir data indicate that tail biting remarks from meat inspection...

  13. 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.

  14. 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

  15. International Oil Pollution Compensation Fund

    Energy Technology Data Exchange (ETDEWEB)

    1979-11-01

    The International Oil Pollution Compensation Fund was established under a 1971 Intergovernmental Maritime Consultative Organization Convention to supplement the 1969 Civil Liability Convention (CLC) under which shipowners were held liable for damage caused by oil spills up to $18 million per incident; the new fund increases the amount payable per incident to $57 million as of April 1979. A further increase up to about $76 million is now under consideration. During 1979, the Fund has been concerned in particular with claims arising out of oil spills in Japan and the Baltic Sea. In the former case, some 540 tons of oil was lost by Miya Maru No. 8 after a collision in March 1979 in the Japanese Inland Sea; cleanup costs and compensation to fishermen were about (pound sterling)400,000. In the latter phase, crude oil apparently coming from the Russian tanker Antonio Gramsci, which grounded off Ventspils in February 1979, drifted across the Baltic and was trapped in or under the ice. After the ice melted, it spread to more than 2000 islands in the Swedish Archipelaso; cleanup measures may result in claims as high as (pound sterling) 8 million.

  16. Risk compensation and bicycle helmets.

    Science.gov (United States)

    Phillips, Ross Owen; Fyhri, Aslak; Sagberg, Fridulv

    2011-08-01

    This study investigated risk compensation by cyclists in response to bicycle helmet wearing by observing changes in cycling behavior, reported experience of risk, and a possible objective measure of experienced risk. The suitability of heart rate variability (HRV) as an objective measure of experienced risk was assessed beforehand by recording HRV measures in nine participants watching a thriller film. We observed a significant decrease in HRV in line with expected increases in psychological challenge presented by the film. HRV was then used along with cycling pace and self-reported risk in a field experiment in which 35 cyclist volunteers cycled 0.4 km downhill, once with and once without a helmet. Routine helmet users reported higher experienced risk and cycled slower when they did not wear their helmet in the experiment than when they did wear their helmet, although there was no corresponding change in HRV. For cyclists not accustomed to helmets, there were no changes in speed, perceived risk, or any other measures when cycling with versus without a helmet. The findings are consistent with the notion that those who use helmets routinely perceive reduced risk when wearing a helmet, and compensate by cycling faster. They thus give some support to those urging caution in the use of helmet laws. © 2011 Society for Risk Analysis.

  17. Sensor-based automated docking of large waste canisters

    International Nuclear Information System (INIS)

    Drotning, W.D.

    1990-01-01

    Sensor-based programmable robots have the potential to speed up remote manipulation operations while protecting operators from exposure to radiation. Conventional master/slave manipulators have proven to be very slow in performing precision remote operations. In addition, inadvertent collisions of remotely manipulated objects with their environment increase the hazards associated with remote handling. This paper describes the development of a robotic system for the sensor-based automated remote manipulation and precision docking of large payloads. Computer vision and proximity sensing are used to control the precision docking of a large object with a passive target cavity. Specifically, a container of nuclear spent fuel on a transport vehicle is mated with an emplacement door on a vertical storage borehole at a waste repository

  18. Genetic, Clinical, and Laboratory Markers for DOCK8 Immunodeficiency Syndrome

    Directory of Open Access Journals (Sweden)

    Jeremiah C. Davis

    2010-01-01

    Full Text Available DOCK8 immunodeficiency syndrome (DIDS is a combined immunodeficiency characterized by recurrent viral infections, severe atopy, and early onset malignancy. Genetic studies revealed large, unique deletions in patients from different families and ethnic backgrounds. Clinical markers of DIDS include atopic dermatitis, allergies, cutaneous viral infections, recurrent respiratory tract infections, and malignancy. Immune assessments showed T cell lymphopenia, hyper-IgE, hypo-IgM, and eosinophilia. The impaired lymphocyte functions in DIDS patients appear central for disease pathogenesis.

  19. Docking Studies of Phthalimide Pharmacophore as a Sodium Channel Blocker

    Directory of Open Access Journals (Sweden)

    Maryam Iman

    2013-09-01

    Full Text Available   Objective(s: Recently, phthalimide derivatives were designed based on ameltolide and thalidomide as they possess a similar degree of anticonvulsant potency due to their phenytoin-like profile. The ability of phthalimide pharmacophore to interact with neuronal voltage-dependent sodium channels was studied in the batrachotoxin affinity assay. Therefore, in the present study, a series of 19 compounds of phthalimide pharmacophore possessing a variety of substituents (NO2, NH2 , Me, Cl, COOH, MeO at 2-, 3-, and 4- position of the N-phenyl ring and N-(3-amino-2-methylphenyl succinimide, were subjected to docking studies in order to inhibit voltage-gated sodium channels.   Materials and Methods : Chemical structures of all compounds were designed using HYPERCHEM program and Conformational studies were performed through semi-empirical molecular orbital calculations method followed by PM3 force field. Total energy gradient calculated as a root mean square (RMS value, until the RMS gradient was 0.01 kcal mol-1. Among all energy minima conformers, the global minimum of compounds was used in docking calculations. Using a model of the open pore of Na channels, docking study was performed by AUTODOCK4.2 program. Results : Docking studies have revealed that these types of ligands interacted mainly with II-S6 residues of NaV1.2 through making hydrogen bonds and have additional hydrophobic interactions with domain I, II, III and IV in the channel's inner pore. Conclusion   : These computational studies have displayed that these compounds are capable of inhibiting Na channel, efficiently.

  20. Terminal homing position estimation forAutonomous underwater vehicle docking

    Science.gov (United States)

    2017-06-01

    79  ix LIST OF FIGURES Figure 1.  NPS REMUS 100 with WHOI Docking Station. Source: [1...underwater missions were short and quick . Now, with advanced technology, underwater missions can be as long as the user desires. The new AUVs have...the full information problem. In order to use the MHE approach for real-time applications, the optimization process should be quick and accurate

  1. 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.

  2. CEO compensation and hospital financial performance.

    Science.gov (United States)

    Reiter, Kristin L; Sandoval, Guillermo A; Brown, Adalsteinn D; Pink, George H

    2009-12-01

    Growing interest in pay-for-performance and the level of chief executive officers' (CEOs') pay raises questions about the link between performance and compensation in the health sector. This study compares the compensation of nonprofit hospital CEOs in Ontario, Canada to the three longest reported and most used measures of hospital financial performance. Our sample consisted of 132 CEOs from 92 hospitals between 1999 and 2006. Unbalanced panel data were analyzed using fixed effects regression. Results suggest that CEO compensation was largely unrelated to hospital financial performance. Inflation-adjusted salaries appeared to increase over time independent of hospital performance, and hospital size was positively correlated with CEO compensation. The apparent upward trend in salary despite some declines in financial performance challenges the fundamental assumption underlying this article, that is, financial performance is likely linked to CEO compensation in Ontario. Further research is needed to understand long-term performance related to compensation incentives.

  3. Vertical vibration analysis for elevator compensating sheave

    International Nuclear Information System (INIS)

    Watanabe, Seiji; Nakazawa, Daisuke; Fukui, Daiki; Okawa, Takeya

    2013-01-01

    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

  4. Vertical vibration analysis for elevator compensating sheave

    Science.gov (United States)

    Watanabe, Seiji; Okawa, Takeya; Nakazawa, Daisuke; Fukui, Daiki

    2013-07-01

    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.

  5. 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.

  6. Rigid Body Energy Minimization on Manifolds for Molecular Docking.

    Science.gov (United States)

    Mirzaei, Hanieh; Beglov, Dmitri; Paschalidis, Ioannis Ch; Vajda, Sandor; Vakili, Pirooz; Kozakov, Dima

    2012-11-13

    Virtually all docking methods include some local continuous minimization of an energy/scoring function in order to remove steric clashes and obtain more reliable energy values. In this paper, we describe an efficient rigid-body optimization algorithm that, compared to the most widely used algorithms, converges approximately an order of magnitude faster to conformations with equal or slightly lower energy. The space of rigid body transformations is a nonlinear manifold, namely, a space which locally resembles a Euclidean space. We use a canonical parametrization of the manifold, called the exponential parametrization, to map the Euclidean tangent space of the manifold onto the manifold itself. Thus, we locally transform the rigid body optimization to an optimization over a Euclidean space where basic optimization algorithms are applicable. Compared to commonly used methods, this formulation substantially reduces the dimension of the search space. As a result, it requires far fewer costly function and gradient evaluations and leads to a more efficient algorithm. We have selected the LBFGS quasi-Newton method for local optimization since it uses only gradient information to obtain second order information about the energy function and avoids the far more costly direct Hessian evaluations. Two applications, one in protein-protein docking, and the other in protein-small molecular interactions, as part of macromolecular docking protocols are presented. The code is available to the community under open source license, and with minimal effort can be incorporated into any molecular modeling package.

  7. GPU Optimizations for a Production Molecular Docking Code*

    Science.gov (United States)

    Landaverde, Raphael; Herbordt, Martin C.

    2015-01-01

    Modeling molecular docking is critical to both understanding life processes and designing new drugs. In previous work we created the first published GPU-accelerated docking code (PIPER) which achieved a roughly 5× speed-up over a contemporaneous 4 core CPU. Advances in GPU architecture and in the CPU code, however, have since reduced this relalative performance by a factor of 10. In this paper we describe the upgrade of GPU PIPER. This required an entire rewrite, including algorithm changes and moving most remaining non-accelerated CPU code onto the GPU. The result is a 7× improvement in GPU performance and a 3.3× speedup over the CPU-only code. We find that this difference in time is almost entirely due to the difference in run times of the 3D FFT library functions on CPU (MKL) and GPU (cuFFT), respectively. The GPU code has been integrated into the ClusPro docking server which has over 4000 active users. PMID:26594667

  8. GPU Optimizations for a Production Molecular Docking Code.

    Science.gov (United States)

    Landaverde, Raphael; Herbordt, Martin C

    2014-09-01

    Modeling molecular docking is critical to both understanding life processes and designing new drugs. In previous work we created the first published GPU-accelerated docking code (PIPER) which achieved a roughly 5× speed-up over a contemporaneous 4 core CPU. Advances in GPU architecture and in the CPU code, however, have since reduced this relalative performance by a factor of 10. In this paper we describe the upgrade of GPU PIPER. This required an entire rewrite, including algorithm changes and moving most remaining non-accelerated CPU code onto the GPU. The result is a 7× improvement in GPU performance and a 3.3× speedup over the CPU-only code. We find that this difference in time is almost entirely due to the difference in run times of the 3D FFT library functions on CPU (MKL) and GPU (cuFFT), respectively. The GPU code has been integrated into the ClusPro docking server which has over 4000 active users.

  9. Advancements in design of an autonomous satellite docking system

    Science.gov (United States)

    Hays, Anthony B.; Tchoryk, Peter, Jr.; Pavlich, Jane C.; Ritter, Greg A.; Wassick, Gregory J.

    2004-08-01

    The past five years has witnessed a significant increase in the attention given to on-orbit satellite docking and servicing. Recent world events have proven how we have come to rely on our space assets, especially during times of crisis. It has become abundantly clear that the ability to autonomously rendezvous, dock, inspect and service both military and civilian assets is no longer a nicety, but a necessity. Reconnaissance and communications satellites, even the space shuttle and International Space Station, could benefit from this capability. Michigan Aerospace Corporation, with funding from the Defense Advanced Research Projects Agency (DARPA) and the Air Force Research Laboratory (AFRL), has been refining a compact, light, compliant soft-docking system. Earlier prototypes have been tested on the Marshall Space Flight Center (MSFC) flat-floor as well as on the Johnson Space Flight Center (JSC) KC-135 micro-gravity aircraft. Over the past year, refinements have been made to the mechanism based on the lessons learned from these tests. This paper discusses the optimal design that has resulted.

  10. Fragility of Floating Docks for Small Craft Marinas

    Science.gov (United States)

    Keen, A.; Eskijian, M.; Lynett, P. J.; Ayca, A.

    2015-12-01

    Because of the damage resulting from the 2010 Chile and 2011 Japanese tele-tsunamis, damage to the small craft marinas in California has become an important concern. This paper will explain the methodology and results used to simulate the demand and also the structural capacity of the floating dock system, composed of floating docks, fingers and moored vessels during tsunami events. The intent is to develop a predictive tool to understand the vulnerability of California's small craft harbors to tsunami events. To validate the methodology, the probabilistic model will be applied to Santa Cruz Harbor. Maps of maximum velocity and mean current direction from the 2011 Japan tsunami have been developed using a numerical model. Cleat and pile guide locations will be recorded and georeferenced from aerial images before the event. The fragility curves for each dock/finger system will be compared with damage reports and aerial images from just after the tsunami event. A discussion of how the fragility curves compare with the damage reports will be included. It is anticipated that these curves will be useful to marina operators to use as a tool to determine where rehabilitation might be necessary to mitigate some of the damage from the next event. Conclusions will focus on how results can be used by marina operators to reduce harbor vulnerability to tsunamis.

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

    DEFF Research Database (Denmark)

    Jørgensen, John Leif; Thuesen, Gøsta

    1999-01-01

    The phenomena and problems encountered when a rendezvous maneuver, 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 analyzed. So far, all solutions that have been brought into realization have bee...... timeliness and robustness of the system. Especially the pose information proved to be valuable for the human operator, and allows for implementation of automatic safety features such as proximity fuse and target rotation rate synchronization....... 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...... information to assist the human operator during the docking phase.The closed loop and operator assistance performance of the system have been assessed using a test bench including human operator, navigation module and high fidelity visualization module.The tests performed verified the general accuracy, real...

  12. The Rac-specific exchange factors Dock1 and Dock5 are dispensable for the establishment of the glomerular filtration barrier in vivo.

    Science.gov (United States)

    Laurin, Mélanie; Dumouchel, Annie; Fukui, Yoshinori; Côté, Jean-François

    2013-01-01

    Podocytes are specialized kidney cells that form the kidney filtration barrier through the connection of their foot processes. Nephrin and Neph family transmembrane molecules at the surface of podocytes interconnect to form a unique type of cell-cell junction, the slit diaphragm, which acts as a molecular sieve. The cytoplasmic tails of Nephrin and Neph mediate cytoskeletal rearrangement that contributes to the maintenance of the filtration barrier. Nephrin and Neph1 orthologs are essential to regulate cell-cell adhesion and Rac-dependent actin rearrangement during Drosophila myoblast fusion. We hypothesized here that molecules regulating myoblast fusion in Drosophila could contribute to signaling downstream of Nephrin and Neph1 in podocytes. We found that Nephrin engagement promoted recruitment of the Rac exchange factor Dock1 to the membrane. Furthermore, Nephrin overexpression led to lamellipodia formation that could be blocked by inhibiting Rac1 activity. We generated in vivo mouse models to investigate whether Dock1 and Dock5 contribute to the formation and maintenance of the kidney filtration barrier. Our results indicate that while Dock1 and Dock5 are expressed in podocytes, their functions are not essential for the development of the glomerular filtration barrier. Furthermore, mice lacking Dock1 were not protected from LPS-induced podocyte effacement. Our data suggest that Dock1 and Dock5 are not the important exchange factors regulating Rac activity during the establishment and maintenance of the glomerular barrier.

  13. DOCK8 is critical for the survival and function of NKT cells.

    Science.gov (United States)

    Crawford, Greg; Enders, Anselm; Gileadi, Uzi; Stankovic, Sanda; Zhang, Qian; Lambe, Teresa; Crockford, Tanya L; Lockstone, Helen E; Freeman, Alexandra; Arkwright, Peter D; Smart, Joanne M; Ma, Cindy S; Tangye, Stuart G; Goodnow, Christopher C; Cerundolo, Vincenzo; Godfrey, Dale I; Su, Helen C; Randall, Katrina L; Cornall, Richard J

    2013-09-19

    Patients with the dedicator of cytokinesis 8 (DOCK8) immunodeficiency syndrome suffer from recurrent viral and bacterial infections, hyper-immunoglobulin E levels, eczema, and greater susceptibility to cancer. Because natural killer T (NKT) cells have been implicated in these diseases, we asked if these cells were affected by DOCK8 deficiency. Using a mouse model, we found that DOCK8 deficiency resulted in impaired NKT cell development, principally affecting the formation and survival of long-lived, differentiated NKT cells. In the thymus, DOCK8-deficient mice lack a terminally differentiated subset of NK1.1(+) NKT cells expressing the integrin CD103, whereas in the liver, DOCK8-deficient NKT cells express reduced levels of the prosurvival factor B-cell lymphoma 2 and the integrin lymphocyte function-associated antigen 1. Although the initial NKT cell response to antigen is intact in the absence of DOCK8, their ongoing proliferative and cytokine responses are impaired. Importantly, a similar defect in NKT cell numbers was detected in DOCK8-deficient humans, highlighting the relevance of the mouse model. In conclusion, our data demonstrate that DOCK8 is required for the development and survival of mature NKT cells, consistent with the idea that DOCK8 mediates survival signals within a specialized niche. Accordingly, impaired NKT cell numbers and function are likely to contribute to the susceptibility of DOCK8-deficient patients to recurrent infections and malignant disease.

  14. DOCK8 is critical for the survival and function of NKT cells

    Science.gov (United States)

    Crawford, Greg; Enders, Anselm; Gileadi, Uzi; Stankovic, Sanda; Zhang, Qian; Lambe, Teresa; Crockford, Tanya L.; Lockstone, Helen E.; Freeman, Alexandra; Arkwright, Peter D.; Smart, Joanne M.; Ma, Cindy S.; Tangye, Stuart G.; Goodnow, Christopher C.; Cerundolo, Vincenzo; Godfrey, Dale I.; Su, Helen C.; Randall, Katrina L.

    2013-01-01

    Patients with the dedicator of cytokinesis 8 (DOCK8) immunodeficiency syndrome suffer from recurrent viral and bacterial infections, hyper–immunoglobulin E levels, eczema, and greater susceptibility to cancer. Because natural killer T (NKT) cells have been implicated in these diseases, we asked if these cells were affected by DOCK8 deficiency. Using a mouse model, we found that DOCK8 deficiency resulted in impaired NKT cell development, principally affecting the formation and survival of long-lived, differentiated NKT cells. In the thymus, DOCK8-deficient mice lack a terminally differentiated subset of NK1.1+ NKT cells expressing the integrin CD103, whereas in the liver, DOCK8-deficient NKT cells express reduced levels of the prosurvival factor B-cell lymphoma 2 and the integrin lymphocyte function-associated antigen 1. Although the initial NKT cell response to antigen is intact in the absence of DOCK8, their ongoing proliferative and cytokine responses are impaired. Importantly, a similar defect in NKT cell numbers was detected in DOCK8-deficient humans, highlighting the relevance of the mouse model. In conclusion, our data demonstrate that DOCK8 is required for the development and survival of mature NKT cells, consistent with the idea that DOCK8 mediates survival signals within a specialized niche. Accordingly, impaired NKT cell numbers and function are likely to contribute to the susceptibility of DOCK8-deficient patients to recurrent infections and malignant disease. PMID:23929855

  15. Compensated takings and negotiated solutions

    International Nuclear Information System (INIS)

    Thompson, R.P.

    1993-01-01

    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

  16. Compensation for incoherent ground motion

    Energy Technology Data Exchange (ETDEWEB)

    Shigeru, Takeda; Hiroshi, Matsumoto; Masakazu, Yoshioka; Yasunori, Takeuchi; Kikuo, Kudo [KEK, High Energy Alccelerator Research Organization (Japan); Tsuneya, Tsubokawa [National Astronomical Observatory, Mizusawa Astrogeodynamics Observatory (Japan); Mitsuaki, Nozaki; Kiyotomo, Kawagoe [Kobe Univ. (Japan). Dept. of Physics

    1999-07-01

    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 10{sup 33} to 10{sup 34} cm{sup -2} sec{sup -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)

  17. Ground Demonstration on the Autonomous Docking of Two 3U CubeSats Using a Novel Permanent-Magnet Docking Mechanism

    Science.gov (United States)

    Pei, Jing; Murchison, Luke; BenShabat, Adam; Stewart, Victor; Rosenthal, James; Follman, Jacob; Branchy, Mark; Sellers, Drew; Elandt, Ryan; Elliott, Sawyer; hide

    2017-01-01

    Small spacecraft autonomous rendezvous and docking is an essential technology for future space structure assembly missions. A novel magnetic capture and latching mechanism is analyzed that allows for docking of two CubeSats without precise sensors and actuators. The proposed magnetic docking hardware not only provides the means to latch the CubeSats but it also significantly increases the likelihood of successful docking in the presence of relative attitude and position errors. The simplicity of the design allows it to be implemented on many CubeSat rendezvous missions. A CubeSat 3-DOF ground demonstration effort is on-going at NASA Langley Research Center that enables hardware-in-the loop testing of the autonomous approach and docking of a follower CubeSat to an identical leader CubeSat. The test setup consists of a 3 meter by 4 meter granite table and two nearly frictionless air bearing systems that support the two CubeSats. Four cold-gas on-off thrusters are used to translate the follower towards the leader, while a single reaction wheel is used to control the attitude of each CubeSat. An innovative modified pseudo inverse control allocation scheme was developed to address interactions between control effectors. The docking procedure requires relatively high actuator precision, a novel minimal impulse bit mitigation algorithm was developed to minimize the undesirable deadzone effects of the thrusters. Simulation of the ground demonstration shows that the Guidance, Navigation, and Control system along with the docking subsystem leads to successful docking under 3-sigma dispersions for all key system parameters. Extensive simulation and ground testing will provide sufficient confidence that the proposed docking mechanism along with the choosen suite of sensors and actuators will perform successful docking in the space environment.

  18. 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 Pension...

  19. Molecular docking for thrombolytic activity of some isolated compounds from Clausena lansium.

    Directory of Open Access Journals (Sweden)

    Arkajyoti Paul

    2017-03-01

    Full Text Available Clausena lansium (Family- Rutaceae is commonly known as wampee, is found in fallow lands throughout Bangladesh. Our aim of the study to performed molecular docking studies to identify potential binding affinities of the phytocompounds from Clausena lansium, namely Clausemarin B, Clausenaline C, Clausenaline E, Murrayanine, vanillic acid and Xanthotoxol for searching of lead molecule for thrombolytic activity. A wide range of docking score found during molecular docking by Schrodinger. Clausemarin B , Clausenaline C , Clausenaline E, Murrayanine , vanillic acid and Xanthotoxol showed the docking score -6.926, -4.041, -4.889 , -4.356, -3.007 and -5.816 respectively. Among all the compounds Clausemarin B showed the best docking score. So, Clausemarin B is the best compounds for thrombolytic activity, as it possessed the best value in Molecular docking. Further in vivo investigation need to identify the thrombolytic activity of isolated compounds from Clausena lansium.

  20. Springback Compensation: Fundamental Topics and Practical Application

    NARCIS (Netherlands)

    Lingbeek, R.A.; Meinders, Vincent T.; Ohnimus, S.; Petzoldt, M.; Weiher, J.

    2006-01-01

    Now that the simulation of deep drawing processes has become more reliable the virtual compensation of the forming tools has become reality. In literature, the Displacement Adjustment (DA) algorithm has proved to be most effective. In this article it is shown how the compensation factor, required

  1. 33 CFR 136.211 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.211 Compensation... that amount required to accomplish the activities for which the claim was paid. Real or Personal...

  2. Compensation of oscillation coupling induced by solenoids

    International Nuclear Information System (INIS)

    Zelinskij, A.Yu.; Karnaukhov, I.M.; Shcherbakov, A.A.

    1988-01-01

    Methods for construction of various schemes of oscillation coupling compensation, induced by solenoids in charged particle storage rings, are described. Peculiarities of magnetic structure, enabling to localize oscillation coupling in wide energy range are discussed. Results of calculation of compensation schemes for design of NR-2000 storage ring spin rotation are presented

  3. 47 CFR 32.24 - Compensated absences.

    Science.gov (United States)

    2010-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES UNIFORM SYSTEM OF ACCOUNTS... shall record a liability and charge the appropriate expense accounts for compensated absences (vacations... liability that exists for compensated absences which is not yet recorded on the books as of the effective...

  4. 75 FR 22679 - Sound Incentive Compensation Guidance

    Science.gov (United States)

    2010-04-29

    ... information technology. We will summarize the comments that we receive and include them in the OTS request for... will promote the prompt improvement of incentive compensation practices in the banking industry by providing a common prudential foundation for incentive compensation arrangements across banking...

  5. 23 CFR 751.15 - Just compensation.

    Science.gov (United States)

    2010-04-01

    ... nonconforming junkyard as provided in § 751.11 must pertain at the time of the taking or removal in order to establish a right to just compensation. ... 23 Highways 1 2010-04-01 2010-04-01 false Just compensation. 751.15 Section 751.15 Highways...

  6. Rational automatic search method for stable docking models of protein and ligand.

    Science.gov (United States)

    Mizutani, M Y; Tomioka, N; Itai, A

    1994-10-21

    An efficient automatic method has been developed for docking a ligand molecule to a protein molecule. The method can construct energetically favorable docking models, considering specific interactions between the two molecules and conformational flexibility in the ligand. In the first stage of docking, likely binding modes are searched and estimated effectively in terms of hydrogen bonds, together with conformations in part of the ligand structure that includes hydrogen bonding groups. After that part is placed in the protein cavity and is optimized, conformations in the remaining part are also examined systematically. Finally, several stable docking models are obtained after optimization of the position, orientation and conformation of the whole ligand molecule. In all the screening processes, the total potential energy including intra- and intermolecular interaction energy, consisting of van der Waals, electrostatic and hydrogen bonding energies, is used as the index. The characteristics of our docking method are high accuracy of the results, fully automatic generation of models and short computational time. The efficiency of the method was confirmed by four docking trials using two enzyme systems. In two attempts to dock methotrexate to dihydrofolate reductase and 2'-GMP to ribonuclease T1, the exact structures of complexes in crystals were reproduced as the most stable docking models, without any assumptions concerning the binding modes and ligand conformations. The most stable docking models of dihydrofolate and trimethoprim, respectively, to dihydrofolate reductase were also in good agreement with those suggested by experiment. In all test cases, it was shown that our method can accurately predict the correct docking structures, discriminating the correct model from incorrect ones. The efficiency of our method was further tested from the viewpoint of ability to predict the relative stability of the docking structures of two triazine derivatives to

  7. Parallel side-docking technique for gynecologic procedures utilizing the da Vinci robot.

    Science.gov (United States)

    Silverman, Suzanne; Orbuch, Laurence; Orbuch, Iris

    2012-09-01

    Minimally invasive approaches to gynecologic surgery have quickly gained favor. The da Vinci surgical system robot as an option for minimally invasive surgery offers many advantages. As the placement of the system between the legs can be prohibitive, we propose a modification of the standard docking procedure by aligning the system parallel to the operating room table. Our experience is that parallel side-docking allows access to the perineum without compromising docking time and range of motion.

  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. Compensation of Disadvantages in University Examination Procedures

    Directory of Open Access Journals (Sweden)

    Ulrike Quapp

    2016-08-01

    Full Text Available Active social participation of disabled people is one of the major tasks of modern society. That also includes access to the academic community by higher education. Universities all over the world work hard to give handicapped students a chance to graduate. In this context, compensation of disadvantages in examination procedures is an important matter. But, also chronic illness may impair the student's examination performance. To ensure equal examination opportunities for all students, responsible university officials must be creative to find individual compensation solutions. The paper analyzes examination regulations at universities in different countries and offers solutions to compensate disabled and chronic ill students' disadvantages. It discusses the necessity of compensation for different types of disability and chronic illness. Finally, an overview of current German case law and solutions for compensation problems are provided.

  10. Comprehensive Monitor-Oriented Compensation Programming

    Directory of Open Access Journals (Sweden)

    Christian Colombo

    2014-04-01

    Full Text Available Compensation programming is typically used in the programming of web service compositions whose correct implementation is crucial due to their handling of security-critical activities such as financial transactions. While traditional exception handling depends on the state of the system at the moment of failure, compensation programming is significantly more challenging and dynamic because it is dependent on the runtime execution flow — with the history of behaviour of the system at the moment of failure affecting how to apply compensation. To address this dynamic element, we propose the use of runtime monitors to facilitate compensation programming, with monitors enabling the modeller to be able to implicitly reason in terms of the runtime control flow, thus separating the concerns of system building and compensation modelling. Our approach is instantiated into an architecture and shown to be applicable to a case study.

  11. Does CEO compensation impact patient satisfaction?

    Science.gov (United States)

    Akingbola, Kunle; van den Berg, Herman A

    2015-01-01

    This study examines the relationship between CEO compensation and patient satisfaction in Ontario, Canada. The purpose of this paper is to determine what impact hospital CEO compensation has on hospital patient satisfaction. The analyses in this study were based on data of 261 CEO-hospital-year observations in a sample of 103 nonprofit hospitals. A number of linear regressions were conducted, with patient satisfaction as the dependent variable and CEO compensation as the independent variable of interest. Controlling variables included hospital size, type of hospital, and frequency of adverse clinical outcomes. CEO compensation does not significantly influence hospital patient satisfaction. Both patient satisfaction and CEO compensation appear to be driven primarily by hospital size. Patient satisfaction decreases, while CEO compensation increases, with the number of acute care beds in a hospital. In addition, CEO compensation does not even appear to moderate the influence of hospital size on patient satisfaction. There are several limitations to this study. First, observations of CEO-hospital-years in which annual nominal CEO compensation was below $100,000 were excluded, as they were not publicly available. Second, this research was limited to a three-year range. Third, this study related the compensation of individual CEOs to a measure of performance based on a multitude of patient satisfaction surveys. Finally, this research is restricted to not-for-profit hospitals in Ontario, Canada. The findings seem to suggest that hospital directors seeking to improve patient satisfaction may find their efforts frustrated if they focus exclusively on the hospital CEO. The findings highlight the need for further research on how CEOs may, through leading and supporting those hospital clinicians and staff that interact more closely with patients, indirectly enhance patient satisfaction. To the best of the authors' knowledge, no research has examined the relationship between

  12. Biallelic loss-of-function variants in DOCK3 cause muscle hypotonia, ataxia, and intellectual disability.

    Science.gov (United States)

    Helbig, K L; Mroske, C; Moorthy, D; Sajan, S A; Velinov, M

    2017-10-01

    DOCK3 encodes the dedicator of cytokinesis 3 protein, a member of the DOCK180 family of proteins that are characterized by guanine-nucleotide exchange factor activity. DOCK3 is expressed exclusively in the central nervous system and plays an important role in axonal outgrowth and cytoskeleton reorganization. Dock3 knockout mice exhibit motor deficiencies with abnormal ataxic gait and impaired learning. We report 2 siblings with biallelic loss-of-function variants in DOCK3. Diagnostic whole-exome sequencing (WES) and chromosomal microarray were performed on a proband with severe developmental disability, hypotonia, and ataxic gait. Testing was also performed on the proband's similarly affected brother. A paternally inherited 458 kb deletion in chromosomal region 3p21.2 disrupting the DOCK3 gene was identified in both affected siblings. WES identified a nonsense variant c.382C>G (p.Gln128*) in the DOCK3 gene (NM_004947) on the maternal allele in both siblings. Common features in both affected individuals include severe developmental disability, ataxic gait, and severe hypotonia, which recapitulates the Dock3 knockout mouse phenotype. We show that complete DOCK3 deficiency in humans leads to developmental disability with significant hypotonia and gait ataxia, probably due to abnormal axonal development. © 2017 The Authors. Clinical Genetics published by John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  13. Hypomorphic function and somatic reversion of DOCK8 cause combined immunodeficiency without hyper-IgE.

    Science.gov (United States)

    Kienzler, Anne-Kathrin; van Schouwenburg, Pauline A; Taylor, John; Marwah, Ishita; Sharma, Richa U; Noakes, Charlotte; Thomson, Kate; Sadler, Ross; Segal, Shelley; Ferry, Berne; Taylor, Jenny C; Blair, Edward; Chapel, Helen; Patel, Smita Y

    2016-02-01

    Loss-of-function mutations in DOCK8 are linked to hyper-IgE syndrome. Patients typically present with recurrent sinopulmonary infections, severe cutaneous viral infections, food allergies and elevated serum IgE. Although patients may present with a spectrum of disease-related symptoms, molecular mechanisms explaining phenotypic variability in patients are poorly defined. Here we characterized a novel compound heterozygous mutation in DOCK8 in a patient diagnosed with primary combined immunodeficiency which was not typical of classical DOCK8 deficiency. In contrast to previously identified mutations in DOCK8 which result in complete loss of function, the newly identified single nucleotide insertion results in expression of a truncated DOCK8 protein. Functional evaluation of the truncated DOCK8 protein revealed its hypomorphic function. In addition we found somatic reversion of DOCK8 predominantly in T cells. The combination of somatic reversion and hypomorphic DOCK8 function explains the milder and atypical phenotype of the patient and further broadens the spectrum of DOCK8-associated disease. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  14. Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2

    Science.gov (United States)

    Salmaso, Veronica; Sturlese, Mattia; Cuzzolin, Alberto; Moro, Stefano

    2018-01-01

    Molecular docking is a powerful tool in the field of computer-aided molecular design. In particular, it is the technique of choice for the prediction of a ligand pose within its target binding site. A multitude of docking methods is available nowadays, whose performance may vary depending on the data set. Therefore, some non-trivial choices should be made before starting a docking simulation. In the same framework, the selection of the target structure to use could be challenging, since the number of available experimental structures is increasing. Both issues have been explored within this work. The pose prediction of a pool of 36 compounds provided by D3R Grand Challenge 2 organizers was preceded by a pipeline to choose the best protein/docking-method couple for each blind ligand. An integrated benchmark approach including ligand shape comparison and cross-docking evaluations was implemented inside our DockBench software. The results are encouraging and show that bringing attention to the choice of the docking simulation fundamental components improves the results of the binding mode predictions.

  15. Ligand pose and orientational sampling in molecular docking.

    Directory of Open Access Journals (Sweden)

    Ryan G Coleman

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

  16. 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.

  17. Synthesis, antiproliferative activity and molecular docking of Colchicine derivatives.

    Science.gov (United States)

    Huczyński, Adam; Majcher, Urszula; Maj, Ewa; Wietrzyk, Joanna; Janczak, Jan; Moshari, Mahshad; Tuszynski, Jack A; Bartl, Franz

    2016-02-01

    In order to create more potent anticancer agents, a series of five structurally different derivatives of Colchicine have been synthesised. These compounds were characterised spectroscopically and structurally and their antiproliferative activity against four human tumour cell lines (HL-60, HL-60/vinc, LoVo, LoVo/DX) was evaluated. Additionally the activity of the studied compounds was calculated using computational methods involving molecular docking of the Colchicine derivatives to β-tubulin. The experimental and computational results are in very good agreement indicating that the antimitotic activity of Colchicine derivatives can be readily predicted using computational modeling methods. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

  18. 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.

  19. 38 CFR 3.708 - Federal Employees' Compensation.

    Science.gov (United States)

    2010-07-01

    ... ADJUDICATION Pension, Compensation, and Dependency and Indemnity Compensation Concurrent Benefits and Elections..., hospitalization or hospital care, training, or compensated work therapy program. See §§ 3.358 and 3.361. (b...

  20. Inductive voltage compensation in superconducting magnet systems

    International Nuclear Information System (INIS)

    Yeh, H.T.; Goddard, J.S.; Shen, S.S.

    1979-01-01

    This paper details several techniques of inductive voltage compensation developed for quench detection in superconducting magnet systems with multiple coils and power supplies, with particular application for the Large Coil Test Facility (LCTF). Sources of noise, their magnitudes, and the sensitivity required for normal zone detection to avoid damage to the magnets are discussed. Two passive compensation schemes (second difference and central difference) are introduced and illustrated by parameters of LCTF; these take advantage of coil symmetries and other system characteristics. An active compensation scheme based on current rate input fom pickup coils and utilizing theory on ac loss voltage for calibration was tested, and the experimental setup and test results are discussed

  1. Health Insurance Costs and Employee Compensation: Evidence from the National Compensation Survey.

    Science.gov (United States)

    Anand, Priyanka

    2017-12-01

    This paper examines the relationship between rising health insurance costs and employee compensation. I estimate the extent to which total compensation decreases with a rise in health insurance costs and decompose these changes in compensation into adjustments in wages, non-health fringe benefits, and employee contributions to health insurance premiums. I examine this relationship using the National Compensation Survey, a panel dataset on compensation and health insurance for a sample of establishments across the USA. I find that total hourly compensation reduces by $0.52 for each dollar increase in health insurance costs. This reduction in total compensation is primarily in the form of higher employee premium contributions, and there is no evidence of a change in wages and non-health fringe benefits. These findings show that workers are absorbing at least part of the increase in health insurance costs through lower compensation and highlight the importance of examining total compensation, and not just wages, when examining the relationship between health insurance costs and employee compensation. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  2. Digitally compensated beam current transformer

    International Nuclear Information System (INIS)

    Kesselman, Martin

    2005-01-01

    The Spallation Neutron Source (SNS) is being built by a collaboration of six laboratories. Beam current monitors (BCMs) will be used to record the current of H-minus and H-plus beams ranging from 15 mA (tune-up in the Front End and Linac) to over 60A fully accumulated in the Ring and dumped to the load as a single pulse in the Ring to Beam Target (RTBT). The time structure of these beams ranges from 645 ns 'mini' bunches at the 1.05 MHz ring revolution rate, to an overall 1 ms long macro-pulse. The requirements for the BCMs will depend upon their location within the system. The need to measure individual mini-pulses, examine the characteristics of the chopper edge, as well as the longer average current pulse of the macropulse, or long duration pulses during Linac tuning place wide requirements upon the response of current transformers. To obtain the desired accuracy and resolution, current transformers must have <1 ns rise time and droops of 0.1%/ms. This places a significant design burden on the current transformer; such a design is almost impossible to achieve. Extremely large expensive cores are needed to meet the low droop, while leakage inductance increases with size, thereby reducing the achievable rise time. In this paper, I discuss a digital compensation approach [M. Kesselman, Spallation neutron source beam current monitor electronics, PAC2001 June 18-22, 2001, Chicago, IL.] that extends the lower cut-off frequency of the current transformer, optimized for high frequency response, so that it can be used in this application with improvements in droop of the order of 1000:1. Transformer saturation (current-time product) is a separate issue and the transformer must be designed to handle the current-time product of the signal to assure it does not saturate

  3. Waste Isolation Pilot Plant TruDock crane system analysis

    International Nuclear Information System (INIS)

    Morris, B.C.; Carter, M.

    1996-10-01

    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

  4. Transient ligand docking sites in Cerebratulus lacteus mini-hemoglobin.

    Science.gov (United States)

    Deng, Pengchi; Nienhaus, Karin; Palladino, Pasquale; Olson, John S; Blouin, George; Moens, Luc; Dewilde, Sylvia; Geuens, Eva; Nienhaus, G Ulrich

    2007-08-15

    The monomeric hemoglobin of the nemertean worm Cerebratulus lacteus functions as an oxygen storage protein to maintain neural activity under hypoxic conditions. It shares a large, apolar matrix tunnel with other small hemoglobins, which has been implicated as a potential ligand migration pathway. Here we explore ligand migration and binding within the distal heme pocket, to which the tunnel provides access to ligands from the outside. FTIR/TDS experiments performed at cryogenic temperatures reveal the presence of three transient ligand docking sites within the distal pocket, the primary docking site B on top of pyrrole C and secondary sites C and D. Site C is assigned to a cavity adjacent to the distal portion of the heme pocket, surrounded by the B and E helices. It has an opening to the apolar tunnel and is expected to be on the pathway for ligand entry and exit, whereas site D, circumscribed by TyrB10, GlnE7, and the CD corner, most likely is located on a side pathway of ligand migration. Flash photolysis experiments at ambient temperatures indicate that the rate-limiting step for ligand binding to CerHb is migration through the apolar channel to site C. Movement from C to B and iron-ligand bond formation involve low energy barriers and thus are very rapid processes in the wt protein.

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

    Indian Academy of Sciences (India)

    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 ...

  6. 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

  7. jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework.

    Science.gov (United States)

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

    2014-02-01

    Molecular docking is a method for structure-based drug design and structural molecular biology, which attempts to predict the position and orientation of a small molecule (ligand) in relation to a protein (receptor) to produce a stable complex with a minimum binding energy. One of the most widely used software packages for this purpose is AutoDock, which incorporates three metaheuristic techniques. We propose the integration of AutoDock with jMetalCpp, an optimization framework, thereby providing both single- and multi-objective algorithms that can be used to effectively solve docking problems. The resulting combination of AutoDock + jMetalCpp allows users of the former to easily use the metaheuristics provided by the latter. In this way, biologists have at their disposal a richer set of optimization techniques than those already provided in AutoDock. Moreover, designers of metaheuristic techniques can use molecular docking for case studies, which can lead to more efficient algorithms oriented to solving the target problems.  jMetalCpp software adapted to AutoDock is freely available as a C++ source code at http://khaos.uma.es/AutodockjMetal/.

  8. PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking.

    Science.gov (United States)

    Ng, Marcus C K; Fong, Simon; Siu, Shirley W I

    2015-06-01

    Protein-ligand docking is an essential step in modern drug discovery process. The challenge here is to accurately predict and efficiently optimize the position and orientation of ligands in the binding pocket of a target protein. In this paper, we present a new method called PSOVina which combined the particle swarm optimization (PSO) algorithm with the efficient Broyden-Fletcher-Goldfarb-Shannon (BFGS) local search method adopted in AutoDock Vina to tackle the conformational search problem in docking. Using a diverse data set of 201 protein-ligand complexes from the PDBbind database and a full set of ligands and decoys for four representative targets from the directory of useful decoys (DUD) virtual screening data set, we assessed the docking performance of PSOVina in comparison to the original Vina program. Our results showed that PSOVina achieves a remarkable execution time reduction of 51-60% without compromising the prediction accuracies in the docking and virtual screening experiments. This improvement in time efficiency makes PSOVina a better choice of a docking tool in large-scale protein-ligand docking applications. Our work lays the foundation for the future development of swarm-based algorithms in molecular docking programs. PSOVina is freely available to non-commercial users at http://cbbio.cis.umac.mo .

  9. 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) (a...

  10. Comprehensive Environmental Response, Compensation and Liability Act

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data represents geographic terms used within the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA). CERCLA, commonly known as...

  11. Convention on supplementary compensation for nuclear damage

    International Nuclear Information System (INIS)

    1998-01-01

    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

  12. 29 CFR 36.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... opposite sex for equal work on jobs the performance of which requires equal skill, effort, and... that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in...

  13. 7 CFR 15a.54 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... opposite sex for equal work on jobs the performance of which requires equal skill, effort, and... which, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in...

  14. 36 CFR 1211.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that... basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the payment...

  15. 44 CFR 19.515 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort... or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation...

  16. 10 CFR 5.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and..., on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the...

  17. HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

    Science.gov (United States)

    Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong

    2017-01-01

    Abstract Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein–protein and protein–DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10–20 min for a docking run. Tested on the cases with weakly homologous complexes of server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. PMID:28521030

  18. Increasing of AC compensation method accuracy

    Science.gov (United States)

    Havlíček, V.; Pokorný, M.

    2003-01-01

    The original MMF compensation method allows the magnetic properties of single sheets and strips to be measured in the same way as the closed specimen properties. The accuracy of the method is limited due to the finite gain of the feedback loop fulfilling the condition of its stability. Digitalisation of the compensation loop appropriate processing of the error signal can rapidly improve the accuracy. The basic ideas of this new approach and the experimental results are described in this paper.

  19. 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.

  20. [Biomechanic principles of the sagittal compensating curve].

    Science.gov (United States)

    Kubein-Meesenburg, D; Nägerl, H; Fanghänel, J

    1990-07-01

    The alignment of the buccal teeth along the compensating curve is of functional importance. It is closely related with the functional gear system of anterior and posterior guidance. Measurements have shown that individual differences between masticatory systems are mainly attributable to functional parameters. Purely skeletal parameters are of comparatively little variability. The compensating curve may be regarded as a guiding element within a master gear systems which includes the gear system of anterior and posterior guidance.

  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. Radiotherapy dose compensation for lung patients

    International Nuclear Information System (INIS)

    Piyaratna, N.; Arnold, A.; Metcalfe, P.

    1999-01-01

    The purpose of the present paper is to provide a more homogeneous dose distribution in the target volume from compensated anterior and posterior fields while the healthy lung is spared by de-weighting the lateral fields. A compensation computation which used linear iterations to compute the most homogeneous dose distribution across the target volume was applied to produce optimum compensator designs. The equivalent tissue-air ratio (E-TAR) inhomogeneity correction was applied for the computations using a GE target series 11 planning computer. The compensators designed were tested for accuracy in a modified water/lung phantom using a scanning diode and an anthropomorphic phantom using thermoluminescent dosimeters. A comparison has been made between the compensated and uncompensated plans for the first nine patients who we have treated with this technique. The dose profiles produced by the computation agreed with the prediction of the computed isodose plans to within ± 2% at the target depth. The thermoluminescent dosimeter (TLD)-measured results in the anthropomorphic phantom agreed with the planning computer within ± 3%. A comparison of nine compensated plans of radiotherapy patients for large-volume targets in the lung region showed a maximum variation in the target to be 19% uncompensated versus 10% compensated. By providing compensated treatment fields from anterior and posterior treatment portals, a homogeneous dose that conforms well to the target volume is provided. As an added bonus, this enables the lateral lung fields to be significantly de-weighted and the healthy lung is spared considerable dose. Copyright (1999) Blackwell Science Pty Ltd

  3. Fair compensation and the boomtown problem

    Energy Technology Data Exchange (ETDEWEB)

    O' Hare, M.

    1976-11-01

    While a variety of government responses to the boomtown problem (too-rapid growth due to energy facilities in rural communities) may be appropriate, those that pay subsidies to the residents or to local governments are likely to compensate the wrong parties. In particular, new arrivals should not be compensated for suffering boomtown conditions and conventional relief programs will probably benefit them at the expense of those who have a good claim to payments.

  4. 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.

  5. 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.

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    Jui-Le Chen

    2013-01-01

    Full Text Available 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 prediction algorithm (FCPLDPA, is presented to accelerate the docking prediction algorithm. The proposed algorithm works by leveraging two high-performance operators: (1 the novel migration (information exchange operator is designed specially for cloud-based environments to reduce the computation time; (2 the efficient operator is aimed at filtering out the worst search directions. Our simulation results illustrate that the proposed method outperforms the other docking algorithms compared in this paper in terms of both the computation time and the quality of the end result.

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

    Science.gov (United States)

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

    2015-06-01

    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.

  9. A novel approach for assesing macromolecular complexes combining soft-docking calculations with NMR data

    Science.gov (United States)

    Morelli, Xavier J.; Palma, P. Nuno; Guerlesquin, Françoise; Rigby, Alan C.

    2001-01-01

    We present a novel and efficient approach for assessing protein–protein complex formation, which combines ab initio docking calculations performed with the protein docking algorithm BiGGER and chemical shift perturbation data collected with heteronuclear single quantum coherence (HSQC) or TROSY nuclear magnetic resonance (NMR) spectroscopy. This method, termed "restrained soft-docking," is validated for several known protein complexes. These data demonstrate that restrained soft-docking extends the size limitations of NMR spectroscopy and provides an alternative method for investigating macromolecular protein complexes that requires less experimental time, effort, and resources. The potential utility of this novel NMR and simulated docking approach in current structural genomic initiatives is discussed. PMID:11567104

  10. Overcoming maladaptive plasticity through plastic compensation

    Directory of Open Access Journals (Sweden)

    Matthew R.J. MORRIS, Sean M. ROGERS

    2013-08-01

    Full Text Available 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 [Current Zoology 59 (4: 526–536, 2013].

  11. Goniometer crosstalk compensation for knee joint applications.

    Science.gov (United States)

    de Oliveira Sato, Tatiana; Hansson, Gert-Åke; Coury, Helenice Jane Cote Gil

    2010-01-01

    Electrogoniometers are prone to crosstalk errors related to endblocks rotation (general crosstalk) and to the characteristics of each sensor (individual crosstalk). The aim of this study was to assess the crosstalk errors due to endblock misalignments and to propose a procedure to compensate for these errors in knee applications. A precision jig was used to simulate pure ± 100° flexion/extension movements. A goniometer was mounted with various degrees of valgus/varus (± 20°) and rotation (± 30°) misalignments. For valgus/varus misalignments, although offset compensation eliminated the error in the valgus/varus recordings for 0° of flexion/extension and reduced it to a few degrees for small (± 30°) flexion/extension angles (root mean square error = 1.1°), the individual crosstalk caused pronounced errors for large (± 100°) angles (18.8°). Subsequent compensation for this crosstalk reduced these errors to 0.8° and 4.5°, respectively. For rotational misalignment, compensation for the general crosstalk by means of coordinate system rotation, in combination with compensation for the individual crosstalk, reduced the errors for small (± 30°) and large (± 100°) flexion/extension angles from 3.6° to 0.5° and from 15.5° to 2.4°, respectively. Crosstalk errors were efficiently compensated by the procedures applied, which might be useful in preprocessing of knee functional data, thereby substantially improving goniometer accuracy.

  12. Docking Validation Resources: Protein Family and Ligand Flexibility Experiments

    Science.gov (United States)

    Mukherjee, Sudipto; Balius, Trent E.; Rizzo, Robert C.

    2010-01-01

    A database consisting of 780 ligand-receptor complexes, termed SB2010, has been derived from the Protein Databank to evaluate the accuracy of docking protocols for regenerating bound ligand conformations. The goal is to provide easily accessible community resources for development of improved procedures to aid virtual screening for ligands with a wide range of flexibilities. Three core experiments using the program DOCK, which employ rigid (RGD), fixed anchor (FAD), and flexible (FLX) protocols, were used to gauge performance by several different metrics: (1) global results, (2) ligand flexibility, (3) protein family, and (4) crossdocking. Global spectrum plots of successes and failures vs rmsd reveal well-defined inflection regions, which suggest the commonly used 2 Å criteria is a reasonable choice for defining success. Across all 780 systems, success tracks with the relative difficulty of the calculations: RGD (82.3%) > FAD (78.1%) > FLX (63.8%). In general, failures due to scoring strongly outweigh those due to sampling. Subsets of SB2010 grouped by ligand flexibility (7-or-less, 8-to-15, and 15-plus rotatable bonds) reveal success degrades linearly for FAD and FLX protocols, in contrast to RGD which remains constant. Despite the challenges associated with FLX anchor orientation and on-the-fly flexible growth, success rates for the 7-or-less (74.5%), and in particular the 8-to-15 (55.2%) subset, are encouraging. Poorer results for the very flexible 15-plus set (39.3%) indicate substantial room for improvement. Family-based success appears largely independent of ligand flexibility suggesting a strong dependence on the binding site environment. For example, zinc-containing proteins are generally problematic despite moderately flexible ligands. Finally, representative crossdocking examples, for carbonic anhydrase, thermolysin, and neuraminidase families, show the utility of family-based analysis for rapid identification of particularly good or bad docking trends

  13. iLIDS Simulations and Videos for Docking TIM

    Science.gov (United States)

    Lewis, James L.

    2010-01-01

    The video shows various aspects of the International Low Impact Docking System, including team members, some production, configuration, mated androgynous iLIDS, SCS Lockdown system, thermal analysis, electrical engineering aspects, the iLIDS control box and emulator, radiation testing at BNL, component environmental testing, component vibration testing, 3G processor board delivery system, GTA vibe test, EMA testbed, hook and hook disassembly, flex shaftdrive assembly, GSE cradle MISSE-6 Columbus, MISSE 6 and 7 seal experiments, actuated full scale seal test rig, LIDS on Hubble, dynamics test prep, EDU 54 mass emulation and SCS, load ring characterization, 6DOF proof test, SCS at 6DOF, machining EEMS and inner ring assembly, APAS assembly, inner ring fitting, rotation stand assembly, EEMS mating, and EEMS proof of concept demonstration.

  14. Space vehicle with customizable payload and docking station

    Science.gov (United States)

    Judd, Stephen; Dallmann, Nicholas; McCabe, Kevin; Seitz, Daniel

    2018-01-30

    A "black box" space vehicle solution may allow a payload developer to define the mission space and provide mission hardware within a predetermined volume and with predetermined connectivity. Components such as the power module, radios and boards, attitude determination and control system (ADCS), command and data handling (C&DH), etc. may all be provided as part of a "stock" (i.e., core) space vehicle. The payload provided by the payload developer may be plugged into the space vehicle payload section, tested, and launched without custom development of core space vehicle components by the payload developer. A docking station may facilitate convenient development and testing of the space vehicle while reducing handling thereof.

  15. Vision Based Navigation Sensors for Spacecraft Rendezvous and Docking

    DEFF Research Database (Denmark)

    Benn, Mathias

    of this constellation, providing both position and pose information for the Target vehicle. This dissertation will describe the study, implementation and verification methods that has led to the realization of this optical Vision Based Sensor (VBS), which is used on the PRISMA mission. On June 15th 2010 the PRISMA....... Denmark has, with DTUs design of the Swarm mission, ESAs next Earth Observation Programme magnetic mapping mission, and DTUs participation in GRACE, ELISA and Alsat2, a leading role in designing and verifying sensor systems for this new class of spacecraft. The Swedish led PRISMA mission...... is a technological demonstration mission, where all aspects of space rendezvous and docking to both a cooperative and a non-cooperative target is researched, with the use of novel methods, instruments and technologies. Amongst other equipment, DTU has delivered a vision based sensor package to the Main spacecraft...

  16. Solving a molecular docking problem by the modified PSO method

    Directory of Open Access Journals (Sweden)

    A. P. Karpenko

    2014-01-01

    Full Text Available The paper presents an canonical method of the swarm particles in two modifications to raise this method efficiency in solving multi-extreme problems of high dimension optimization. The essence of PSO-M1 modification is to form two new points to attract swarm particles (along with the points which are responsible for inertial, cognitive, and social components of canonical method. These new points represent the best points of sets of particles-neighbours of a given point. The modification aims to diversify search. All free parameters of the PSO-M1 method (as well as an canonical method are static. In contrast, one of such parameters of PSO-M2 modification is dynamic. So this modification represents an example of a self-adaptive method of optimization. The modification aims to intensify search. A computing experiment to study the method efficiency and its abovementioned modifications at solving the test problems of optimization showed advantages of offered modifications in comparison with canonical method, revealed a superiority of PSO-M2 modification both over canonical method, and over PSO-M1 modification. Using the PSO-M2 method allows us to solve the 28-dimensional molecular docking problem of HIV1 protease and darunaviry 3U7S as the molecules of receptor and a ligand, respectively. Results of computing experiment have shown that the PSO-M2 method successfully finds the position of ligand close to native and can be recommended for solving the molecular docking problems as an alternative to genetic algorithm.

  17. 28 CFR 104.21 - Filing for compensation.

    Science.gov (United States)

    2010-07-01

    ... “Personal Injury Compensation Form” or a “Death Compensation Form.” A claim shall be deemed “filed” for... filing either a “Personal Injury Compensation Form” or a “Death Compensation Form,” the claim shall be..., when a Claims Evaluator determines that both the Eligibility Form and either a Personal Injury...

  18. 50 CFR 296.4 - Claims eligible for compensation.

    Science.gov (United States)

    2010-10-01

    ... compensation. (a) Claimants. Damage or loss eligible for Fund compensation must be suffered by a commercial fisherman. (b) Damage or loss of fishing gear. Damage or loss is eligible for Fund compensation if it was... is not eligible for Fund compensation: (1) If the damage or loss was caused by the negligence or...

  19. 28 CFR 104.41 - Amount of compensation.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Amount of compensation. 104.41 Section 104.41 Judicial Administration DEPARTMENT OF JUSTICE (CONTINUED) SEPTEMBER 11TH VICTIM COMPENSATION FUND OF 2001 Amount of Compensation for Eligible Claimants. § 104.41 Amount of compensation. As...

  20. 20 CFR 226.62 - Computing average monthly compensation.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Computing average monthly compensation. 226... RETIREMENT ACT COMPUTING EMPLOYEE, SPOUSE, AND DIVORCED SPOUSE ANNUITIES Years of Service and Average Monthly Compensation § 226.62 Computing average monthly compensation. The employee's average monthly compensation is...

  1. Defining Compensable Injury in Biomedical Research.

    Science.gov (United States)

    Larkin, Megan E

    2015-01-01

    Biomedical research provides a core social good by enabling medical progress. In the twenty-first century alone, this includes reducing transmission of HIV/AIDS, developing innovative therapies for cancer patients, and exploring the possibilities of personalized medicine. In order to continue to advance medical science, research relies on the voluntary participation of human subjects. Because research is inherently uncertain, unintended harm is an inevitable part of the research enterprise. Currently, injured research participants in the United States must turn to the “litigation lottery” of the tort system in search of compensation. This state of affairs fails research participants, who are too often left uncompensated for devastating losses, and makes the United States an outlier in the international community. In spite of forty years’ worth of Presidential Commissions and other respected voices calling for the development of a no-fault compensation system, no progress has been made to date. One of the reasons for this lack of progress is the failure to develop a coherent ethical basis for an obligation to provide compensation for research related injuries. This problem is exacerbated by the lack of a clear definition of “compensable injury” in the biomedical research context. This article makes a number of important contributions to the scholarship in this growing field. To begin, it examines compensation systems already in existence and concludes that there are four main definitional elements that must be used to define “compensable injury.” Next, it examines the justifications that have been put forth as the basis for an ethical obligation to provide compensation, and settles on retrospective nonmaleficence and distributive and compensatory justice as the most salient and persuasive. Finally, it uses the regulatory elements and the justifications discussed in the first two sections to develop a well-rounded definition of “compensable injury

  2. DOVIS: an implementation for high-throughput virtual screening using AutoDock

    Directory of Open Access Journals (Sweden)

    Wallqvist Anders

    2008-02-01

    Full Text Available Abstract Background Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial. Results We have developed an application termed DOVIS that uses AutoDock (version 3 as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions of small molecules (ligands to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried. Conclusion DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.

  3. Pharmacophore Modeling and Molecular Docking Studies on Pinus roxburghii as a Target for Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    Pawan Kaushik

    2014-01-01

    Full Text Available The present study attempts to establish a relationship between ethnopharmacological claims and bioactive constituents present in Pinus roxburghii against all possible targets for diabetes through molecular docking and to develop a pharmacophore model for the active target. The process of molecular docking involves study of different bonding modes of one ligand with active cavities of target receptors protein tyrosine phosphatase 1-beta (PTP-1β, dipeptidyl peptidase-IV (DPP-IV, aldose reductase (AR, and insulin receptor (IR with help of docking software Molegro virtual docker (MVD. From the results of docking score values on different receptors for antidiabetic activity, it is observed that constituents, namely, secoisoresinol, pinoresinol, and cedeodarin, showed the best docking results on almost all the receptors, while the most significant results were observed on AR. Then, LigandScout was applied to develop a pharmacophore model for active target. LigandScout revealed that 2 hydrogen bond donors pointing towards Tyr 48 and His 110 are a major requirement of the pharmacophore generated. In our molecular docking studies, the active constituent, secoisoresinol, has also shown hydrogen bonding with His 110 residue which is a part of the pharmacophore. The docking results have given better insights into the development of better aldose reductase inhibitor so as to treat diabetes related secondary complications.

  4. Fast and accurate grid representations for atom-based docking with partner flexibility.

    Science.gov (United States)

    de Vries, Sjoerd J; Zacharias, Martin

    2017-06-30

    Macromolecular docking methods can broadly be divided into geometric and atom-based methods. Geometric methods use fast algorithms that operate on simplified, grid-like molecular representations, while atom-based methods are more realistic and flexible, but far less efficient. Here, a hybrid approach of grid-based and atom-based docking is presented, combining precalculated grid potentials with neighbor lists for fast and accurate calculation of atom-based intermolecular energies and forces. The grid representation is compatible with simultaneous multibody docking and can tolerate considerable protein flexibility. When implemented in our docking method ATTRACT, grid-based docking was found to be ∼35x faster. With the OPLSX forcefield instead of the ATTRACT coarse-grained forcefield, the average speed improvement was >100x. Grid-based representations may allow atom-based docking methods to explore large conformational spaces with many degrees of freedom, such as multiple macromolecules including flexibility. This increases the domain of biological problems to which docking methods can be applied. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  5. Development and evaluation of a generic evolutionary method for protein-ligand docking.

    Science.gov (United States)

    Yang, Jinn-Moon

    2004-04-30

    We have developed a generic evolutionary method with an empirical scoring function for the protein-ligand docking, which is a problem of paramount importance in structure-based drug design. This approach, referred to as the GEMDOCK (Generic Evolutionary Method for molecular DOCKing), combines both continuous and discrete search mechanisms. We tested our approach on seven protein-ligand complexes, and the docked lowest energy structures have root-mean-square derivations ranging from 0.32 to 0.99 A with respect to the corresponding crystal ligand structures. In addition, we evaluated GEMDOCK on crossdocking experiments, in which some complexes with an identical protein used for docking all crystallized ligands of these complexes. GEMDOCK yielded 98% docked structures with RMSD below 2.0 A when the ligands were docked into foreign protein structures. We have reported the validation and analysis of our approach on various search spaces and scoring functions. Experimental results show that our approach is robust, and the empirical scoring function is simple and fast to recognize compounds. We found that if GEMDOCK used the RMSD scoring function, then the prediction accuracy was 100% and the docked structures had RMSD below 0.1 A for each test system. These results suggest that GEMDOCK is a useful tool, and may systematically improve the forms and parameters of a scoring function, which is one of major bottlenecks for molecular recognition. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 843-857, 2004

  6. 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.

  7. 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.

  8. 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.

  9. 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

  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. istar: A Web Platform for Large-Scale Protein-Ligand Docking

    Science.gov (United States)

    Li, Hongjian; Leung, Kwong-Sak; Ballester, Pedro J.; Wong, Man-Hon

    2014-01-01

    Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. istar

  12. Predicting receptor functionality of signaling lymphocyte activation molecule for measles virus hemagglutinin by docking simulation.

    Science.gov (United States)

    Suzuki, Yoshiyuki

    2017-05-01

    Predicting susceptibility of various species to a virus assists assessment of risk of interspecies transmission. Evaluation of receptor functionality may be useful in screening for susceptibility. In this study, docking simulation was conducted for measles virus hemagglutinin (MV-H) and immunoglobulin-like variable domain of signaling lymphocyte activation molecule (SLAM-V). It was observed that the docking scores for MV-H and SLAM-V correlated with the activity of SLAM as an MV receptor. These results suggest that the receptor functionality may be predicted from the docking scores of virion surface proteins and cellular receptor molecules. © 2017 The Societies and John Wiley & Sons Australia, Ltd.

  13. 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

  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. Institutional directors and board compensation: Spanish evidence

    Directory of Open Access Journals (Sweden)

    Felix López-Iturriaga

    2015-07-01

    Full Text Available We address the influence of directors who represent institutional investors in three aspects of board compensation policies: level of compensation, composition, and performance sensitivity. We differentiate pressure-sensitive directors (i.e., with business links and pressure-resistant directors (i.e., without business links. Our results show that pressure-resistant directors decrease total board compensation and its fixed proportion, whereas they increase the variable proportion of total remuneration and the pay-for-performance sensitivity. By contrast, pressure-sensitive directors offer the opposite results. These findings are consistent with the view that institutional investors are not a homogeneous group and that pressure-resistant directors fulfill a more thorough monitoring role.

  16. 'Compensation neurosis': a review of the literature.

    Science.gov (United States)

    Weighill, V E

    1983-01-01

    This review examines the literature on psychological reactions, often referred to as 'compensation neurosis', which occur after an accident and which are thought to be produced or maintained by a compensation claim. Theories and research are examined. The area is complicated and research so far is limited in scope and design. Few accident cases involve compensation claims and the incidence of psychological difficulties across the whole range of cases is unknown. Researchers have considered a number of background factors--severity of injury, pre-existing neurotic traits, social class, sex and age--but there has been little investigation of attitudinal, family, social and employment factors or of progress of the condition and follow-up after settlement. The review identifies a major research need for more adequate screening and sampling of cases and for more systematic investigation of personal and family factors.

  17. (Crime Victims’ Compensation: The Emergence of Convergence

    Directory of Open Access Journals (Sweden)

    Renée S.B. Kool

    2014-07-01

    Full Text Available Crime victims’ compensation has become a major issue within Dutch criminal policy. Legal procedures have been subject to change, leading towards the convergence of tort law and criminal law. Such a convergence calls for a reflection (on the application of the core concepts of responsibility, accountability and liability. Moreover, the current pursuit of victims’ compensation affects procedural issues, specifically with regard to the issue of enforcement. Leaving aside the issue of the legitimacy of victims’ compensation, this convergence raises the question of how to preserve the delicate balance that flows from the use of the law as an instrument to preserve social order. The topical question is not whether convergence is occurring, but how we must deal with it in order to find a (new equilibrium between the public interest and the interest of the individual who has experienced a harmful wrong.

  18. Software compensation in Particle Flow reconstruction

    CERN Document Server

    Lan Tran, Huong; Sefkow, Felix; Green, Steven; Marshall, John; Thomson, Mark; Simon, Frank

    2017-01-01

    The Particle Flow approach to calorimetry requires highly granular calorimeters and sophisticated software algorithms in order to reconstruct and identify individual particles in complex event topologies. The high spatial granularity, together with analog energy information, can be further exploited in software compensation. In this approach, the local energy density is used to discriminate electromagnetic and purely hadronic sub-showers within hadron showers in the detector to improve the energy resolution for single particles by correcting for the intrinsic non-compensation of the calorimeter system. This improvement in the single particle energy resolution also results in a better overall jet energy resolution by improving the energy measurement of identified neutral hadrons and improvements in the pattern recognition stage by a more accurate matching of calorimeter energies to tracker measurements. This paper describes the software compensation technique and its implementation in Particle Flow reconstruct...

  19. 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.

  20. Compensation: Will it provide a waste site?

    International Nuclear Information System (INIS)

    Pulsipher, A.G.

    1993-01-01

    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

  1. Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

    Science.gov (United States)

    Lam, Polo C.-H.; Abagyan, Ruben; Totrov, Maxim

    2018-01-01

    Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.

  2. Phase alteration compensation in reflection digital holography

    International Nuclear Information System (INIS)

    Rincon, O; Amezquita, R; Monroy, F

    2011-01-01

    The phase maps obtained from digital holographic microscopy techniques carry information about the axial lengths of the object under study. Additionally, these phase maps have information of tilt and curvatures with origin in the off-axis geometry and the magnification lenses system, respectively. Only a complete compensation of these extra phases allows a correct interpretation of the phase information. In this article a numerical strategy to compensate for these alterations is designed, using a phase mask located in different planes. This strategy is applied in the measurement of a phase steps plate using a digital holography setup.

  3. Individual Hearing Loss: Characterization, Modelling, Compensation Strategies

    DEFF Research Database (Denmark)

    Santurette, Sébastien; Dau, Torsten; Christensen-Dalsgaard, Jakob

    2016-01-01

    It is well-established that hearing loss does not only lead to a reduction of hearing sensitivity. Large individual differences are typically observed among listeners with hearing impairment in a wide range of suprathreshold auditory measures. In many cases, audiometric thresholds cannot fully...... account for such individual differences, which make it challenging to find adequate compensation strategies in hearing devices. How to characterize, model, and compensate for individual hearing loss were the main topics of the fifth International Symposium on Auditory and Audiological Research (ISAAR...

  4. 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

  5. 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

  6. Adaptive motion compensation without blocking artifacts

    Science.gov (United States)

    Terriberry, Timothy B.

    2015-03-01

    The Block Matching Algorithms used in most popular video codec standards introduce blocking artifacts which must be removed via residual coding or deblocking filters. Alternative transform stages that do not cause blocking artifacts, such as lapped transforms or wavelets, require motion compensation methods that do not produce blocking artifacts, since they are expensive to remove. We design a new Overlapped Block Motion Compensation (OBMC) scheme that avoids these artifacts while allowing adaptive blending window sizes. This has the potential to show significant visual quality improvements over traditional OBMC.

  7. Digital, electromagnetic rod position indicator with compensation

    International Nuclear Information System (INIS)

    Feilchenfeld, M.M.; Geis, C.G.

    1985-01-01

    A digital rod position indicator having discrete coils L 0 , L 1 , L 2 ..... spaced along the travel path of an elongate magnetically permeable member stores in digital form compensation signals for automatically adjusting the location relative to the coils at which a digital output signal representative of the position of the end of the elongate member transitions from one code to the next. The appropriate compensation signal is addressed using the digital output signal and a correction factor which takes into account the direction of movement including reversals. Reference is made to the positioning of the control rods in a pressurized water reactor. (author)

  8. Compensation systems for low temperature applications

    CERN Document Server

    Skoczen, Balzej T

    2004-01-01

    The book is dedicated to the behaviour of ductile materials at cryogenic temperatures, structural stability issues and reliability oriented parametric optimisation of compensation systems containing the corrugated bellows. The problems of local and global stability of systems containing bellows, coupling between the low-cycle fatigue and stability as well as evolution of plastic strain fields, micro-damage and strain induced phase transformation in the corrugated shells at cryogenic temperatures are presented. As a special feature reliability oriented optimum design of compensation systems under strength, stability, fatigue and geometrical constraints is discussed. The relevant applications in the particle accelerators and cryogenic transfer lines are shown.

  9. Radiation damage effects on calorimeter compensation

    International Nuclear Information System (INIS)

    Gabriel, T.A.; Handler, T.

    1990-01-01

    An important consideration in the design of a detector that is to be used at the Superconducting Super Collider (SSC) is the response of the calorimeter to electromagnetic and hadronic particles and the equality of those responses for different types of particles at equal incident energies, i.e. compensation. However, as the simulations that are reported show, the compensation characteristics of a calorimeter can be seriously compromised over a relatively short period of time due to the large radiation levels that are expected in the SSC environment. 6 refs., 3 figs

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

    Science.gov (United States)

    Lee, Gyu Rie; Seok, Chaok

    2016-07-08

    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. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Data.gov (United States)

    National Aeronautics and Space Administration — This project will advance the Autonomous Rendezvous and Docking (AR&D) GNC system by testing it on hardware, particularly in a flight processor, with a goal of...

  12. HIGA: A Running History Information Guided Genetic Algorithm for Protein–Ligand Docking

    Directory of Open Access Journals (Sweden)

    Boxin Guan

    2017-12-01

    Full Text Available Protein-ligand docking is an essential part of computer-aided drug design, and it identifies the binding patterns of proteins and ligands by computer simulation. Though Lamarckian genetic algorithm (LGA has demonstrated excellent performance in terms of protein-ligand docking problems, it can not memorize the history information that it has accessed, rendering it effort-consuming to discover some promising solutions. This article illustrates a novel optimization algorithm (HIGA, which is based on LGA for solving the protein-ligand docking problems with an aim to overcome the drawback mentioned above. A running history information guided model, which includes CE crossover, ED mutation, and BSP tree, is applied in the method. The novel algorithm is more efficient to find the lowest energy of protein-ligand docking. We evaluate the performance of HIGA in comparison with GA, LGA, EDGA, CEPGA, SODOCK, and ABC, the results of which indicate that HIGA outperforms other search algorithms.

  13. Boring crustaceans damage polystyrene floats under docks polluting marine waters with microplastic.

    Science.gov (United States)

    Davidson, Timothy M

    2012-09-01

    Boring isopods damage expanded polystyrene floats under docks and, in the process, expel copious numbers of microplastic particles. This paper describes the impacts of boring isopods in aquaculture facilities and docks, quantifies and discusses the implications of these microplastics, and tests if an alternate foam type prevents boring. Floats from aquaculture facilities and docks were heavily damaged by thousands of isopods and their burrows. Multiple sites in Asia, Australia, Panama, and the USA exhibited evidence of isopod damage. One isopod creates thousands of microplastic particles when excavating a burrow; colonies can expel millions of particles. Microplastics similar in size to these particles may facilitate the spread of non-native species or be ingested by organisms causing physical or toxicological harm. Extruded polystyrene inhibited boring, suggesting this foam may prevent damage in the field. These results reveal boring isopods cause widespread damage to docks and are a novel source of microplastic pollution. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. AggieSat: Autonomous Rendezvous and Docking Technology Demonstrator, Phase I

    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...

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

    Science.gov (United States)

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

    2010-07-01

    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 approximately 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 docking predictions. Knowledge of one or both protein binding sites may be used to focus and shorten the calculation when such information is available. The first 20 predictions may be accessed individually, and a single file of all predicted orientations may be downloaded as a compressed multi-model PDB file. The server is publicly available and does not require any registration or identification by the user.

  16. In Silico Molecular Docking Analysis of Natural Pyridoacridines as Anticancer Agents

    Directory of Open Access Journals (Sweden)

    Vikas Sharma

    2016-01-01

    Full Text Available Docking studies are proved to be an essential tool that facilitates the structural diversity of natural products to be harnessed in an organized manner. In this study, pyridoacridines containing natural anticancer pigments were subjected to docking studies using Glide (Schrodinger. Investigations were carried out to find out the potential molecular targets for these selected pigments. The docking was carried out on different cancer macromolecules involved in different cell cycle pathways, that is, CDK-2, CDK-6, Bcl-2, VEGFR-2, IGF-1R kinase, and G-Quadruplexes. CDK-6 was found to be the most suitable anticancer target for the pyridoacridines. In addition, effectiveness of the study was further evaluated by performing docking of known inhibitors against their respective selected macromolecules. However, the results are preliminary and experimental evaluation will be carried out in near future.

  17. AggieSat: Autonomous Rendezvous and Docking Technology Demonstrator, Phase II

    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...

  18. Molecular docking of γ-sitosterol with some targets related to diabetes.

    Science.gov (United States)

    Balamurugan, Rangachari; Stalin, Antony; Ignacimuthu, Savarimuthu

    2012-01-01

    γ-sitosterol isolated from Lippia nodiflora was taken as ligand for molecular docking. The molecular targets, glucokinase, Fructose 1, 6- bisphosphatase 1, Human multidrug resistance protein 1 and Cytochromes P450 whose crystallographic structures are available on the PDB database as 1V4S, 2JJK, 3LC4, 2CBZ respectively, were used for the docking analysis using the Autodock tool v 4.2 and ADT v1.5.4 programs. The docking studies of the ligand γ- sitosterol with four different target proteins showed that this is a good molecule which docks well with various targets related to diabetes mellitus. Hence γ-sitosterol can be considered for developing into a potent antidiabetic drug. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  19. Fault-Tolerant Relative Navigation System (RNS) for Docking, Phase I

    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...

  20. The Compensation Act 2006 and School Trips

    Science.gov (United States)

    Hunter-Jones, John

    2006-01-01

    The Compensation Act 2006 received its Royal Assent on 25 July 2006. The Act allows the courts to have regard to the social utility of "desirable activities", including school trips, in considering negligence claims. The article reviews the law of negligence as it affects teachers of the very young and considers the possible impact of…

  1. 77 FR 58469 - Plum Pox Compensation

    Science.gov (United States)

    2012-09-21

    ... Animal and Plant Health Inspection Service 7 CFR Part 301 RIN 0579-AD58 Plum Pox Compensation AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Affirmation of interim rule. SUMMARY: We are... Washington, DC, this 17th day of September 2012. Kevin Shea, Acting Administrator, Animal and Plant Health...

  2. Compensation-device for a magnetic field

    NARCIS (Netherlands)

    Kruit, P.; Ferreira, J.A.

    2007-01-01

    The invention relates to compensation device for a magnetic field generated through electric traction in a tram or train transport system that comprises an overhead line and rails, the overhead line and rails during operation being live, wherein a predetermined section of the overhead line and rails

  3. A brief history of dosage compensation

    Indian Academy of Sciences (India)

    know that the random X inactivation system of placental mammals likely evolved from the nonrandom paternal X in- activation dosage compensation system characteristic of marsupials (Brown and Chandra 1973) and that the XIST gene evolved from a marsupial protein coding gene (Duret et al. 2006). It seems likely that ...

  4. Compensation of coupling in the SSC complex

    International Nuclear Information System (INIS)

    Pilat, F.; Bourianoff, G.

    1991-10-01

    This paper will describe a study of the coupling effects and their compensation by means of local depending techniques for some of the accelerators in the SSC Complex. Results concerning corrections and decoupling for the Low Energy and Medium Energy Boosters will be compared to results obtained for the Collider Ring. Some preliminary experimental data about measurement of coupling quantities will also be presented

  5. Evaluation of the implementation of Employees Compensation ...

    African Journals Online (AJOL)

    Since the passage into law of the Employees Compensation Act in 2011, countless cases of workplace accidents have occurred in Nigeria. Yet there seems to be no succour for the Nigerian worker as many state governments have either refused to register with or do not have the will power to implement the legislation in ...

  6. Software compensation in particle flow reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Tran, Huong Lan; Krueger, Katja; Sefkow, Felix [Deutsches Elektronen-Synchrotron DESY, Hamburg (Germany); Green, Steven; Marshall, John; Thomson, Mark [Cavendish Laboratory, Cambridge (United Kingdom); Simon, Frank [Max-Planck-Institut fuer Physik, Muenchen (Germany)

    2017-10-15

    The particle flow approach to calorimetry benefits from highly granular calorimeters and sophisticated software algorithms in order to reconstruct and identify individual particles in complex event topologies. The high spatial granularity, together with analogue energy information, can be further exploited in software compensation. In this approach, the local energy density is used to discriminate electromagnetic and purely hadronic sub-showers within hadron showers in the detector to improve the energy resolution for single particles by correcting for the intrinsic non-compensation of the calorimeter system. This improvement in the single particle energy resolution also results in a better overall jet energy resolution by improving the energy measurement of identified neutral hadrons and improvements in the pattern recognition stage by a more accurate matching of calorimeter energies to tracker measurements. This paper describes the software compensation technique and its implementation in particle flow reconstruction with the Pandora Particle Flow Algorithm (PandoraPFA). The impact of software compensation on the choice of optimal transverse granularity for the analogue hadronic calorimeter option of the International Large Detector (ILD) concept is also discussed. (orig.)

  7. Software compensation in particle flow reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Tran, Huong Lan; Krueger, Katja; Sefkow, Felix [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Green, Steven; Marshall, John; Thomson, Mark [Cavendish Laboratory, Cambridge (United Kingdom); Simon, Frank [Max-Planck-Institut fuer Physik, Muenchen (Germany)

    2017-10-15

    The particle flow approach to calorimetry benefits from highly granular calorimeters and sophisticated software algorithms in order to reconstruct and identify individual particles in complex event topologies. The high spatial granularity, together with analogue energy information, can be further exploited in software compensation. In this approach, the local energy density is used to discriminate electromagnetic and purely hadronic sub-showers within hadron showers in the detector to improve the energy resolution for single particles by correcting for the intrinsic non-compensation of the calorimeter system. This improvement in the single particle energy resolution also results in a better overall jet energy resolution by improving the energy measurement of identified neutral hadrons and improvements in the pattern recognition stage by a more accurate matching of calorimeter energies to tracker measurements. This paper describes the software compensation technique and its implementation in particle flow reconstruction with the Pandora Particle Flow Algorithm (PandoraPFA). The impact of software compensation on the choice of optimal transverse granularity for the analogue hadronic calorimeter option of the International Large Detector (ILD) concept is also discussed.

  8. Arc -furnace Flicker Compensation in Ethiopia.

    African Journals Online (AJOL)

    series capacitors nor the translater scheme is appli- cable where more ... The arc furnace is of conventional design. The furnace ... power of the furnace. This reactor had three tappings and a short-circuiting switch. REQUIREMENTS OF THE COMPENSATOR. The fluctuations could be caused by the furnace on whichever ...

  9. Lossless Compression of Video using Motion Compensation

    DEFF Research Database (Denmark)

    Martins, Bo; Forchhammer, Søren

    1998-01-01

    using one or multiple previous images, predictor dependent error modelling, and selection of motion field by code length. For slow pan or slow zoom sequences, coding methods that use multiple previous images are up to 20% better than motion compensation using a single previous image and up to 40% better...

  10. 12 CFR 2.5 - Bank compensation.

    Science.gov (United States)

    2010-01-01

    ... shareholder who holds an insurance agent's license from agreeing to compensate the bank for the use of its... be credited to an affiliate operating under the Bank Holding Company Act of 1956, 12 U.S.C. 1841 et seq., or to a trust for the benefit of all shareholders, provided that the bank receives reasonable...

  11. Compensation techniques for operational amplifier bias current

    International Nuclear Information System (INIS)

    Silva, M.S.

    1981-01-01

    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) [pt

  12. Annual compensation for pipelines in Alberta

    International Nuclear Information System (INIS)

    2008-11-01

    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

  13. ARCC Teacher Compensation Initiative: Literature Review

    Science.gov (United States)

    Appalachia Regional Comprehensive Center, 2014

    2014-01-01

    In February 2014, the Tennessee State Board of Education (SBE) requested that the Appalachia Regional Comprehensive Center (ARCC) provide assistance to the SBE's Basic Education Program (BEP) Review Committee. The SBE requested additional information on the use and effectiveness of market-based teacher compensation and market-based incentives by…

  14. Granulate of stainless steel as compensator material

    NARCIS (Netherlands)

    J.P.C. van Santvoort (J. P C)

    1995-01-01

    textabstractCompensators produced with computer controlled milling devices usually consist of a styrofoam mould, filled with an appropriate material. We investigated granulate of stainless steel as filling material. This cheap, easy to use, clean and re-usable material can be obtained with an

  15. A brief history of dosage compensation

    Indian Academy of Sciences (India)

    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 ...

  16. T1 VSAT Fade Compensation Statistical Results

    Science.gov (United States)

    Johnson, Sandra K.; Acosta, Roberto; Ugweje, Oke

    2000-01-01

    New satellite communication systems are steadily seeking to use higher frequency bands to accommodate the requirements for additional capacity. At these higher frequencies, propagation impairments that did not significantly affect the signal at lower frequencies begin to have considerable impact. In Ka-band. the next logical commercial frequency band to be used for satellite communication, attenuation of the signal due to rain is a primary concern. An experimental satellite built by NASA, the Advanced Communication Technology Satellite (ACTS). launched in September 1993, is the first U.S. communication satellite operating in the Ka-band. In addition to higher carrier frequencies, a number of other new technologies, including on-board baseband processing. multiple beam antennas, and rain fade detection and compensation techniques, were designed into the ACTS. Verification experiments have been conducted since the launch to characterize the new technologies. The focus of this paper is to characterize the method used by the ACTS TI Very Small Aperture Terminal (TI VSAT) ground stations in detecting the presence of fade in the communication signal and to adaptively compensate for it by the addition of burst rate reduction and forward error correction. Measured data obtained from the ACTS program was used to validate the compensation technique. A software process was developed and demonstrated to statistically characterize the increased availability achieved by the compensation techniques in terms of the bit error rate time enhancement factor. Several improvements to the ACTS technique are discussed and possible implementations for future Ka band system are offered.

  17. Women's Experience in the Workers' Compensation System.

    Science.gov (United States)

    Guthrie, Robert; Jansz, Janis

    2006-09-01

    Gender differences is a question of major importance within workers' compensation given the increased role of women in the workforce over the past several decades. This article reviews literature relating to women's experiences following work injury. An Australian study is used as background to exploring the broad issue of the question of gender equity in workers' compensation. In doing so it takes account of historical, legal and medical issues. Women's experience in the workers' compensation system is different to that of men due to a range of factors. It is heavily influenced by the industrial environment in which they work. Women are paid less than men in many instances and work in gender-segregated circumstances, which often reduces their industrial bargaining power. Women also suffer different forms of injury and disease to men because of the different nature of their work. The Australian experience suggests that as a consequence of the combination of lesser industrial bargaining power, lower wages and differing forms of injury and disease women often receive less than men in compensation payments, struggle to obtain equity in the dispute resolution process and experience greater difficulties in returning to work following injury or disease.

  18. 28 CFR 54.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar working conditions. ...

  19. 38 CFR 23.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar...

  20. 24 CFR 3.515 - Compensation.

    Science.gov (United States)

    2010-04-01

    ... distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar...

  1. 45 CFR 86.54 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and which are performed under similar working conditions...

  2. 45 CFR 2555.515 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar...

  3. 34 CFR 106.54 - Compensation.

    Science.gov (United States)

    2010-07-01

    ...) Makes distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and which are performed...

  4. 14 CFR 1253.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar working...

  5. 32 CFR 196.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar...

  6. 15 CFR 8a.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar working conditions. ...

  7. 40 CFR 5.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar working conditions. ...

  8. 6 CFR 17.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar working conditions. ...

  9. 13 CFR 113.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar...

  10. 18 CFR 1317.515 - Compensation.

    Science.gov (United States)

    2010-04-01

    ... distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar...

  11. 41 CFR 101-4.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar working conditions. ...

  12. 45 CFR 618.515 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar...

  13. 31 CFR 28.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... in rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar...

  14. 43 CFR 41.515 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid to employees of the opposite sex for equal work on jobs the performance of which requires equal skill, effort, and responsibility, and that are performed under similar working conditions. ...

  15. Mandatory Compensation to Commercial Agents upon Termination ...

    African Journals Online (AJOL)

    Kamil Abdu Oumer

    Abstract. The Ethiopian Commercial Code recognizes mandatory compensation if agency agreement for an indefinite period of time is terminated due to the fault of the principal; and the Draft Commercial Code is likely to maintain this approach. This comment examines the status and functions of a commercial agent as well ...

  16. 76 FR 27959 - Investment Adviser Performance Compensation

    Science.gov (United States)

    2011-05-13

    ... 3235-AK71 Investment Adviser Performance Compensation AGENCY: Securities and Exchange Commission... under the Investment Advisers Act of 1940 that permits investment advisers to charge performance based..., Office of Regulatory Policy, Division of Investment Management, Securities and Exchange Commission, 100 F...

  17. Disclosed Values of Option-Based Compensation

    DEFF Research Database (Denmark)

    Bechmann, Ken L.; Hjortshøj, Toke Lilhauge

    New accounting standards require firms to expense the costs of option-based compensation (OBC), but the associated valuations offer many challenges for firms. Earlier research has documented that firms in the U.S. generally underreport the values of OBC by manipulating the inputs used for valuation...

  18. Wire compensation: Performance, SPS MDs, pulsed system

    CERN Document Server

    Dorda, U

    2008-01-01

    A wire compensation (BBLR) scheme has been proposed in order to improve the long range beam-beam performance of the nominal LHC and its phase 1 and phase 2 upgrades[1]. In this paper we present experimental experience of the CERN SPS wires (BBLR) and report on progress with the RF BBLR.

  19. 1979-1980 Administrative Compensation Survey.

    Science.gov (United States)

    Bryan, James; And Others

    Results of the 1979-80 Administrative Compensation Survey Report conducted by the College and University Personnel Association are presented. The survey is based on 1,383 responses and covers 77 positions. Salary data are indicated for the median and interquartile range for each position. Data are provided by type of institution, by size of…

  20. 1981-1982 Administrative Compensation Survey.

    Science.gov (United States)

    Miller, Jan P.; And Others

    Results of the College and University Personnel Association's 1981-1982 Administrative Compensation Survey, which provides data on 94 positions, is presented. Questionnaires were sent to 2,770 higher education institutions, and 1,391 usable responses were obtained. Salary data indicate the median and the interquartile range for each position and…

  1. Administrative Compensation Survey, 1983-84.

    Science.gov (United States)

    Benedict, Forest C.; And Others

    Results of the College and University Personnel Association's 1983-1984 Administrative Compensation Survey, which provides data on 99 positions, is presented. Questionnaires were sent to 2,856 higher education institutions, and 1,515 usable responses were obtained. Salary data indicate the median and the interquartile range for each position and…

  2. Manager, Global Compensation | IDRC - International Development ...

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

    Provide corporate HR leadership with regards to strategy, policy, design, development, implementation and continuous improvement of the areas related to the mandate of the work unit, ensuring that the frameworks, ... Develop, plan and evaluate IDRC's benefit program and its integration with the cash compensation policy.

  3. Software compensation in particle flow reconstruction

    International Nuclear Information System (INIS)

    Tran, Huong Lan; Krueger, Katja; Sefkow, Felix; Green, Steven; Marshall, John; Thomson, Mark; Simon, Frank

    2017-10-01

    The particle flow approach to calorimetry benefits from highly granular calorimeters and sophisticated software algorithms in order to reconstruct and identify individual particles in complex event topologies. The high spatial granularity, together with analogue energy information, can be further exploited in software compensation. In this approach, the local energy density is used to discriminate electromagnetic and purely hadronic sub-showers within hadron showers in the detector to improve the energy resolution for single particles by correcting for the intrinsic non-compensation of the calorimeter system. This improvement in the single particle energy resolution also results in a better overall jet energy resolution by improving the energy measurement of identified neutral hadrons and improvements in the pattern recognition stage by a more accurate matching of calorimeter energies to tracker measurements. This paper describes the software compensation technique and its implementation in particle flow reconstruction with the Pandora Particle Flow Algorithm (PandoraPFA). The impact of software compensation on the choice of optimal transverse granularity for the analogue hadronic calorimeter option of the International Large Detector (ILD) concept is also discussed.

  4. Hybrid VAR compensator with improved efficiency

    Directory of Open Access Journals (Sweden)

    V. V. Burlaka

    2015-03-01

    Full Text Available In modern electrical networks thyristor-switched capacitors (TSC are most used devices for VAR compensation. These devices don’t contain rotating parts and mechanical contacts, provide a stepwise control of reactive power and no generation of harmonics to the network. However, with the help of TSC it’s not possible to ensure smooth control of reactive power and capacitor banks (CB are exposed to the negative impact of higher harmonic components of the network voltage. Hybrid VAR compensator don’t have such drawbacks. It consists of active filter (AF and capacitor bank with discrete regulation. The main drawback of such systems is the necessity of accessing all six terminals of CB, while most of them are manufactured with three terminals, internally delta-connected. In the article, the topology and control system of hybrid VAR compensator free from beforementioned drawback, is proposed. The control system provides operating modes of overcompensation or undercompensation reactive power. VAR distribution regulator performs redistribution of reactive power between active filter and capacitor banks with the condition to minimize active filter’s power. Scheme of the hybrid VAR compensator, which includes a three-phase three-terminal delta-connected capacitor banks, is shown. Proposed approach allows to provide smooth control of reactive power, isolate the capacitor bank from harmonic currents and use a more effective low-voltage power components

  5. 77 FR 5381 - Plum Pox Compensation

    Science.gov (United States)

    2012-02-03

    ... United States where plum pox has been detected and restrict the interstate movement of regulated articles... articles within the nursery in order to control plum pox. The compensation provisions of Sec. 301.74-5 were... panel composed of APHIS and State representatives, industry representatives, and university scientists...

  6. On the compensation effect in heterogeneous catalysis

    DEFF Research Database (Denmark)

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

    2003-01-01

    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...

  7. A brief history of dosage compensation

    Indian Academy of Sciences (India)

    to dosage compensation and their citation numbers would therefore not be relevant. Also supportive of the lack of interest in dosage compensa- tion at the time is the fact ..... Received 4 October 2013, in revised form 28 November 2013; accepted 3 December 2013. Published on the Web: 11 July 2014. Journal of Genetics ...

  8. Attitudes toward the dubious compensation claim.

    Science.gov (United States)

    LEGGO, C

    1951-07-01

    Laws providing for compensation of workmen for occupational injury are a powerful socio-economic force. In settlement of compensation claims the goal, difficult to achieve, is fairness to employee, employer and insurance carrier. Often, medical, legal, economic and social considerations conflict with one another. A "fact" in one field may not be considered so in another. Since medical data and testimony often guide the ultimate decision of a compensation claim, the physician's attitude is a large factor not only immediately and directly in determination of the case at hand but, perhaps more important, in the ultimate direction of the socio-economic forces which spring from the sum of all such determinations. To perpetuate the good in workmen's compensation laws, the next generation of physicians-and of lawyers and business administrators as well, for they, too, are involved-ought to have basic training in the social sciences in order that they may have a broad rather than a segmental view of the problems with which they deal.

  9. Temperature-Compensated Clock Skew Adjustment

    Directory of Open Access Journals (Sweden)

    Joaquín Olivares

    2013-08-01

    Full Text Available This work analyzes several drift compensation mechanisms in wireless sensor networks (WSN. Temperature is an environmental factor that greatly affects oscillators shipped in every WSN mote. This behavior creates the need of improving drift compensation mechanisms in synchronization protocols. Using the Flooding Time Synchronization Protocol (FTSP, this work demonstrates that crystal oscillators are affected by temperature variations. Thus, the influence of temperature provokes a low performance of FTSP in changing conditions of temperature. This article proposes an innovative correction factor that minimizes the impact of temperature in the clock skew. By means of this factor, two new mechanisms are proposed in this paper: the Adjusted Temperature (AT and the Advanced Adjusted Temperature (A2T. These mechanisms have been combined with FTSP to produce AT-FTSP and A2T-FTSP. Both have been tested in a network of TelosB motes running TinyOS. Results show that both AT-FTSP and A2T-FTSP improve the average synchronization errors compared to FTSP and other temperature-compensated protocols (Environment-Aware Clock Skew Estimation and Synchronization for WSN (EACS and Temperature Compensated Time Synchronization (TCTS.

  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. CrossDocker: a tool for performing cross-docking using Autodock Vina.

    Science.gov (United States)

    Shamsara, Jamal

    2016-01-01

    Cross-docking is an approach to find the best holo structures among multiple structures available for a target protein. CrossDocker significantly decreases the time needed for setting parameters and inputs for performing multiple dockings, data collection and subsequent analysis. CrossDocker was written in Python language and is available as executable binary for Windows operating system. It is available at http://www.pharm-sbg.com. Some example data sets were also provided.

  12. DETERMINING A SUFFICIENT DEPTH OF PILE FOUNDATION ON THE PERTAMINA GRAVING DOCK DESIGN SORONG PAPUA

    Directory of Open Access Journals (Sweden)

    Franto Novico

    2017-07-01

    Full Text Available Engineering geological aspect and bearing capacity of pile foundation are significant for safety of upper structure, especially for substantial constructions such as a docking ship. Moreover, it provides effectiveness and cost efficiency when applies in rural areas of Indonesia. This is due to lack of docking ship appropriately built at rural areas particularly in eastern areas of Indonesia. Karim island of Papua even though is a small island yet is very strategic as Pertamina place its transitory function on that island connecting its oil supply route to Sorong. Appropriate docking ship construction is required to aim the effective and efficient port management. Choosing the most suitable structure for a docking is also the key. Graving dock structure has been chosen by Pertamina as the most appropriate type of structure for the docking ship in Karim Island. The structure of graving dock planned to be built in Karim island Papua, is projected to be able to serve the maximum 7500 DWT ship capacity, with approximately dimension is 125 x 25 x 8 meters. Therefore, to support the plan, type and design of the best foundation is the key. There are two methods could be done in determining the type and bearing capacity foundation. Field and laboratory test applied ASTM, field observation result by applying Meyerhoff theory and laboratorial analysis derived from Tarzaghi theory. Those observation and analysis has confirmed that the soil layer at the graving dock design consists of three layers, those are; cover layer, silt-clay layer and clay rock unit. Therefore, the most suitable foundation to be constructed in that area is a pile massive foundation, with depth of pile foundation approximately -20 m below the land surface, and the ultimate point load pile massive for 30x30 cm - 75x75 cm dimension approximately 79.76 – 406.25 ton, and frictional resistance value approximately 24.59-61.48 ton.

  13. American and Soviet engineers examine Soyuz docking system prior to tests

    Science.gov (United States)

    1974-01-01

    Three Apollo Soyuz Test Project (ASTP) engineers look over a Soyuz spacecraft docking system prior to an ASTP docking mechanism fitness test conducted in bldg 13 at JSC. They are, left to right, Robert White, Vladimir Syromyatnikov and Yevgeniy Bobrov. White is the American Chairman of ASTP Working Group No.3, and Syromyatnikov is his Soviet counterpart. Bobrov is a junior researcher with the Institute of Machine Building.

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

    International Nuclear Information System (INIS)

    Drotning, W.D.

    1992-08-01

    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

  15. Cooperative Rendezvous and Docking for Underwater Robots Using Model Predictive Control and Dual Decomposition

    DEFF Research Database (Denmark)

    Nielsen, Mikkel Cornelius; Johansen, Tor Arne; Blanke, Mogens

    2018-01-01

    This paper considers the problem of rendezvous and docking with visual constraints in the context of underwater robots with camera-based navigation. The objective is the convergence of the vehicles to a common point while maintaining visual contact. The proposed solution includes the design of a ...... of a distributed model predictive controller based on dual decomposition, which allows for optimization in a decentralized fashion. The proposed distributed controller enables rendezvous and docking between vehicles while maintaining visual contact....

  16. Vision Based Navigation for Autonomous Cooperative Docking of CubeSats

    Science.gov (United States)

    Pirat, Camille; Ankersen, Finn; Walker, Roger; Gass, Volker

    2018-05-01

    A realistic rendezvous and docking navigation solution applicable to CubeSats is investigated. The scalability analysis of the ESA Autonomous Transfer Vehicle Guidance, Navigation & Control (GNC) performances and the Russian docking system, shows that the docking of two CubeSats would require a lateral control performance of the order of 1 cm. Line of sight constraints and multipath effects affecting Global Navigation Satellite System (GNSS) measurements in close proximity prevent the use of this sensor for the final approach. This consideration and the high control accuracy requirement led to the use of vision sensors for the final 10 m of the rendezvous and docking sequence. A single monocular camera on the chaser satellite and various sets of Light-Emitting Diodes (LEDs) on the target vehicle ensure the observability of the system throughout the approach trajectory. The simple and novel formulation of the measurement equations allows differentiating unambiguously rotations from translations between the target and chaser docking port and allows a navigation performance better than 1 mm at docking. Furthermore, the non-linear measurement equations can be solved in order to provide an analytic navigation solution. This solution can be used to monitor the navigation filter solution and ensure its stability, adding an extra layer of robustness for autonomous rendezvous and docking. The navigation filter initialization is addressed in detail. The proposed method is able to differentiate LEDs signals from Sun reflections as demonstrated by experimental data. The navigation filter uses a comprehensive linearised coupled rotation/translation dynamics, describing the chaser to target docking port motion. The handover, between GNSS and vision sensor measurements, is assessed. The performances of the navigation function along the approach trajectory is discussed.

  17. Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms.

    Science.gov (United States)

    Sulimov, Alexey V; Zheltkov, Dmitry A; Oferkin, Igor V; Kutov, Danil C; Katkova, Ekaterina V; Tyrtyshnikov, Eugene E; Sulimov, Vladimir B

    2017-01-01

    We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters. The conformation space of the system coordinates is formed by translations and rotations of the ligand as a whole, by the ligand torsions and also by Cartesian coordinates of the selected target protein atoms. Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally. The algorithm is realized in the novel parallel docking SOL-P program and results of its performance for a set of 30 protein-ligand complexes are presented. Dependence of the docking positioning accuracy is investigated as a function of parameters of the docking algorithm and the number of protein moveable atoms. It is shown that mobility of the protein atoms improves docking positioning accuracy. The SOL-P program is able to perform docking of a flexible ligand into the active site of the target protein with several dozens of protein moveable atoms: the native crystallized ligand pose is correctly found as the global energy minimum in the search space with 157 dimensions using 4700 CPU ∗ h at the Lomonosov supercomputer.

  18. 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

  19. Spectroscopic, structural and drug docking studies of carbocysteine

    Science.gov (United States)

    Manivannan, M.; Rajeshwaran, K.; Govindhan, R.; Karthikeyan, B.

    2017-09-01

    Carbocysteine or carbocisteine having the empirical formula C5H9NO4S,is one of the most therapeutically prescribed expectorant, sold under the brand name viz., Mucodyne (UK and India), Rhinathiol and Mucolite. In pediatric respiratory pathology, it can relieve the symptoms of obstructive pulmonary disease (COPD) and bronchiectasis. On the consideration of its extensive pharmaceutical usage and medicinal value, we have investigated its chemical structure and composition by employing various spectral techniques like 1H, 13C NMR, FT-IR,Raman, UV-Visible spectroscopy and powder X-ray diffraction method. Density Functional Theoretical (DFT) studies on its electronic structure is also carried out. Drug docking studies were carried out to ascertain the nature of molecular interaction with the biological protein system. Furthermore theoretical Raman spectrum of this molecule has been computed and compared with the experimental Raman spectrum. The forbidden energy gap between its frontier molecular orbitals, viz., HOMO-LUMO is calculated and correlated with its observed λmax value. Atomic orbitals which are mainly contributes to the frontier molecular orbitals were identified. Molecular electrostatic potential diagram has been mapped to explain its chemical activity. Based on the results, a suitable mechanism of its protein binding mode and drug action has been discussed.

  20. 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

  1. Molecular docking, spectroscopic studies and quantum calculations on nootropic drug.

    Science.gov (United States)

    Uma Maheswari, J; Muthu, S; Sundius, Tom

    2014-04-05

    A systematic vibrational spectroscopic assignment and analysis of piracetam [(2-oxo-1-pyrrolidineacetamide)] have been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G++(d,p) basis set. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, and harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption wavelengths λmax were determined by the time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PED) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. Molecular docking studies have been carried out in the active site of piracetam by using Argus Lab. In addition, the potential energy surface, HOMO and LUMO energies, first-order hyperpolarizability and the molecular electrostatic potential have been computed. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Steroid-Functionalized Titanocenes: Docking Studies with Estrogen Receptor Alpha

    Directory of Open Access Journals (Sweden)

    Li Ming Gao

    2016-11-01

    Full Text Available Estrogen receptor alpha (ERα is a transcription factor that is activated by hormones, with 17β-estradiol being its most active agonist endogenous ligand. ERα is also activated or inactivated by exogenous ligands. ER is overexpressed in hormone-dependent breast cancer, and one of the treatments for this type of cancer is the use of an ER antagonist to halt cell proliferation. We have previously reported four steroid-functionalized titanocenes: pregnenolone, dehydroepiandrosterone (DHEA, trans-androsterone, and androsterone. These steroids have hormonal activity as well as moderate antiproliferative activity, thus these steroids could act as vectors for the titanocene dichloride to target hormone-dependent cancers. Also, these steroids could increase the antiproliferative activity of the resulting titanocenes based on synergism. In order to elucidate which factors contribute to the enhanced antiproliferative activity of these steroid-functionalized titanocenes, we performed docking studies between ERα and the titanocenes and the steroids. The binding affinities and type of bonding interactions of the steroid-functionalized titanocenes with ERα are herein discussed.

  3. 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.

  4. Hippeastrum reticulatum (Amaryllidaceae: Alkaloid Profiling, Biological Activities and Molecular Docking

    Directory of Open Access Journals (Sweden)

    Luciana R. Tallini

    2017-12-01

    Full Text Available The Amaryllidaceae family has proven to be a rich source of active compounds, which are characterized by unique skeleton arrangements and a broad spectrum of biological activities. The aim of this work was to perform the first detailed study of the alkaloid constituents of Hippeastrum reticulatum (Amaryllidaceae and to determine the anti-parasitological and cholinesterase (AChE and BuChE inhibitory activities of the epimers (6α-hydroxymaritidine and 6β-hydroxymaritidine. Twelve alkaloids were identified in H. reticulatum: eight known alkaloids by GC-MS and four unknown (6α-hydroxymaritidine, 6β-hydroxymaritidine, reticulinine and isoreticulinine by NMR. The epimer mixture (6α-hydroxymaritidine and 6β-hydroxymaritidine showed low activity against all protozoan parasites tested and weak AChE-inhibitory activity. Finally, a molecular docking analysis of AChE and BuChE proteins showed that isoreticulinine may be classified as a potential inhibitory molecule since it can be stabilized in the active site through hydrogen bonds, π-π stacking and hydrophobic interactions.

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

    International Nuclear Information System (INIS)

    Munoz Blasco, J.; Goicoechea Sanchez, F.J.

    1993-01-01

    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)

  6. Dynamic compensation in the central Pacific Ocean

    Science.gov (United States)

    Hinojosa, Juan Homero; Marsh, Bruce D.

    1988-01-01

    The intermediate-wavelength geoid (lambda similar to 2000 km) and sea-floor topography fields in the central Pacific Ocean were studied in terms of static and dynamic compensation models. Topographic features on the sea-floor with lambda less than 1000 km were found to be compensated both regionally, by the elastic strength of the lithosphere, and locally, by displacing mantle material to reach isostatic adjustment. The larger-scale sea-floor topography and the corresponding geoid anomalies with lambda similar to 2000 km cannot be explained by either local or regional compensation. The topography and the resulting geoid anomaly at this wavelength were modeled by considering the dynamic effects arising from viscous stresses in a layer of fluid with a highly temperature-dependent viscosity for the cases of: (1) surface cooling, and (2) basal heating. In this model, the mechanical properties of the elastic part of the lithosphere were taken into account by considering an activation energy of about 520 kJ/mol in the Arrhenius law for the viscosity. Numerical predictions of the topography, total geoid anomaly, and admittance were obtained, and the results show that the thermal perturbation in the layer, which accounts for the mass deficit, must be located close to the surface to compensate the gravitational effect of the surface deformation. For the case of basal heating, the temperature dependence of viscosity results in a separation of the upper, quasi-rigid lid from the lower mobile fluid, hence inhibiting the development of a compensating thermal perturbation at shallow depths. The results clearly rule out small-scale, upper-mantle convection as the source of these anomalies. Instead, the geophysical observables can be well explained by a shallow, transient thermal perturbation.

  7. Assessment of the transmembrane domain structures in GPCR Dock 2013 models.

    Science.gov (United States)

    Wang, Ting; Liu, Haiguang; Duan, Yong

    2018-03-01

    The community-wide blind prediction of G-protein coupled receptor (GPCR) structures and ligand docking has been conducted three times and the quality of the models was primarily assessed by the accuracy of ligand binding modes. The seven transmembrane (TM) helices of the receptors were taken as a whole; thus the model quality within the 7TM domains has not been evaluated. Here we evaluate the 7TM domain structures in the models submitted for the last round of prediction - GPCR Dock 2013. Applying the 7 × 7 RMSD matrix analysis described in our prior work, we show that the models vary widely in prediction accuracy of the 7TM structures, exhibiting diverse structural differences from the targets. For the prediction of the 5-hydroxytryptamine receptors, the top 7TM models are rather close to the targets, which however are not ranked top by ligand-docking. On the other hand, notable deviations of the TMs are found in in the previously identified top docking models that closely resemble other receptors. We further reveal reasons of success and failure in ligand docking for the models. This current assessment not only complements the previous assessment, but also provides important insights into the current status of GPCR modeling and ligand docking. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. 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.

  9. A cross docking pipeline for improving pose prediction and virtual screening performance

    Science.gov (United States)

    Kumar, Ashutosh; Zhang, Kam Y. J.

    2018-01-01

    Pose prediction and virtual screening performance of a molecular docking method depend on the choice of protein structures used for docking. Multiple structures for a target protein are often used to take into account the receptor flexibility and problems associated with a single receptor structure. However, the use of multiple receptor structures is computationally expensive when docking a large library of small molecules. Here, we propose a new cross-docking pipeline suitable to dock a large library of molecules while taking advantage of multiple target protein structures. Our method involves the selection of a suitable receptor for each ligand in a screening library utilizing ligand 3D shape similarity with crystallographic ligands. We have prospectively evaluated our method in D3R Grand Challenge 2 and demonstrated that our cross-docking pipeline can achieve similar or better performance than using either single or multiple-receptor structures. Moreover, our method displayed not only decent pose prediction performance but also better virtual screening performance over several other methods.

  10. Targeting Ras-Driven Cancer Cell Survival and Invasion through Selective Inhibition of DOCK1

    Directory of Open Access Journals (Sweden)

    Hirotada Tajiri

    2017-05-01

    Full Text Available Oncogenic Ras plays a key role in cancer initiation but also contributes to malignant phenotypes by stimulating nutrient uptake and promoting invasive migration. Because these latter cellular responses require Rac-mediated remodeling of the actin cytoskeleton, we hypothesized that molecules involved in Rac activation may be valuable targets for cancer therapy. We report that genetic inactivation of the Rac-specific guanine nucleotide exchange factor DOCK1 ablates both macropinocytosis-dependent nutrient uptake and cellular invasion in Ras-transformed cells. By screening chemical libraries, we have identified 1-(2-(3′-(trifluoromethyl-[1,1′-biphenyl]-4-yl-2-oxoethyl-5-pyrrolidinylsulfonyl-2(1H-pyridone (TBOPP as a selective inhibitor of DOCK1. TBOPP dampened DOCK1-mediated invasion, macropinocytosis, and survival under the condition of glutamine deprivation without impairing the biological functions of the closely related DOCK2 and DOCK5 proteins. Furthermore, TBOPP treatment suppressed cancer metastasis and growth in vivo in mice. Our results demonstrate that selective pharmacological inhibition of DOCK1 could be a therapeutic approach to target cancer cell survival and invasion.

  11. Starfish ApDOCK protein essentially functions in larval defense system operated by mesenchyme cells.

    Science.gov (United States)

    Furukawa, Ryohei; Funabashi, Hiromi; Matsumoto, Midori; Kaneko, Hiroyuki

    2012-11-01

    In larvae of the starfish, Asterina pectinifera, mesenchyme cells operate in the defense system through various behaviors. We have investigated mesenchyme cell dynamics during the immune response by identifying ApDOCK, a new member of the DOCK180 superfamily protein. In 4-day-old bipinnaria larvae processed for morpholino oligonucleotide-mediated knockdown of ApDOCK, injection of inorganic foreign substances revealed that (1) mesenchyme cells fail to undergo either directed migration toward a large oil-droplet or persistent spreading on the oil-droplet after contact; (2) neither uptake of micro-beads nor cell-to-cell fusion on the large oil-droplet differed from that of mesenchyme cells from control larvae. Similar behaviors were also recorded in experiments where bacteria were injected. Under culture conditions, the expression level of ApDOCK mRNA was significantly associated with the immunological behavior of mesenchyme cells. Apparently, the mesenchyme cells from ApDOCK loss-of-function larvae exhibited insufficient lamellipodium formation via lack of fibrous form of actin organization at the leading edge. These results suggest that the migratory congregation and persistence of encapsulation of larval mesenchyme cells are intracellularly regulated by ApDOCK protein, and this regulation is associated with organization of cytoskeletal actin.

  12. Quantitative Structure-activity Relationship (QSAR) Models for Docking Score Correction.

    Science.gov (United States)

    Fukunishi, Yoshifumi; Yamasaki, Satoshi; Yasumatsu, Isao; Takeuchi, Koh; Kurosawa, Takashi; Nakamura, Haruki

    2017-01-01

    In order to improve docking score correction, we developed several structure-based quantitative structure activity relationship (QSAR) models by protein-drug docking simulations and applied these models to public affinity data. The prediction models used descriptor-based regression, and the compound descriptor was a set of docking scores against multiple (∼600) proteins including nontargets. The binding free energy that corresponded to the docking score was approximated by a weighted average of docking scores for multiple proteins, and we tried linear, weighted linear and polynomial regression models considering the compound similarities. In addition, we tried a combination of these regression models for individual data sets such as IC 50 , K i , and %inhibition values. The cross-validation results showed that the weighted linear model was more accurate than the simple linear regression model. Thus, the QSAR approaches based on the affinity data of public databases should improve docking scores. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  13. Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina.

    Directory of Open Access Journals (Sweden)

    Max W Chang

    Full Text Available BACKGROUND: The AutoDock family of software has been widely used in protein-ligand docking research. This study compares AutoDock 4 and AutoDock Vina in the context of virtual screening by using these programs to select compounds active against HIV protease. METHODOLOGY/PRINCIPAL FINDINGS: Both programs were used to rank the members of two chemical libraries, each containing experimentally verified binders to HIV protease. In the case of the NCI Diversity Set II, both AutoDock 4 and Vina were able to select active compounds significantly better than random (AUC = 0.69 and 0.68, respectively; p<0.001. The binding energy predictions were highly correlated in this case, with r = 0.63 and iota = 0.82. For a set of larger, more flexible compounds from the Directory of Universal Decoys, the binding energy predictions were not correlated, and only Vina was able to rank compounds significantly better than random. CONCLUSIONS/SIGNIFICANCE: In ranking smaller molecules with few rotatable bonds, AutoDock 4 and Vina were equally capable, though both exhibited a size-related bias in scoring. However, as Vina executes more quickly and is able to more accurately rank larger molecules, researchers should look to it first when undertaking a virtual screen.

  14. Exploring the importance of different items as reasons for leaving emergency medical services between fully compensated, partially compensated, and non-compensated/volunteer samples.

    Science.gov (United States)

    Blau, Gary; Chapman, Susan; Gibson, Gregory; Bentley, Melissa A

    2011-01-01

    The purpose of our study was to investigate the importance of different items as reasons for leaving the Emergency Medical Service (EMS) profession. An exit survey was returned by three distinct EMS samples: 127 full compensated, 45 partially compensated and 72 non-compensated/volunteer respondents, who rated the importance of 17 different items for affecting their decision to leave EMS. Unfortunately, there were a high percentage of "not applicable" responses for 10 items. We focused on those seven items that had a majority of useable responses across the three samples. Results showed that the desire for better pay and benefits was a more important reason for leaving EMS for the partially compensated versus fully compensated respondents. Perceived lack of advancement opportunity was a more important reason for leaving for the partially compensated and volunteer groups versus the fully compensated group. Study limitations are discussed and suggestions for future research offered.

  15. Re-Planning for Compensator-Based IMRT with Original Compensators

    International Nuclear Information System (INIS)

    Zhang, Geoffrey; Feygelman, Vladimir; Stevens, Craig; Li Weiqi; Leuthold, Susan; Springett, Gregory; Hoffe, Sarah

    2011-01-01

    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.

  16. Torque compensation technology for the geostationary meteorological satellite

    Science.gov (United States)

    Wang, Zhigang; Wang, Lusha; Chen, Shilu; Li, Qing

    2009-12-01

    To acquire high quality image, the new generation Geostationary Meteorological Satellite in China (GMSC) adopts three-axis stabilized attitude control mode, besides an advanced control system is required to be designed to get higher pointing precision and degree of stability of the satellite. However, the ability of the control system is limited. Torque compensation technology is studied in this paper aiming at rejecting the disturbance factors, which cannot be absorbed by the control system. In the research of torque compensation technology, the main factors that influence the degree of stability of satellite are analyzed; the objects compensated are confirmed through analysis of simulation; the system technical concept of torque compensation is designed; the mathematical models of the compensated objects and compensation devices are founded; the torque compensation arithmetic is designed; the valid arithmetic of torque compensation is proved through simulation. The research provides theoretical principles to develop the new generation GMSC.

  17. US-LHC IR magnet error analysis and compensation

    International Nuclear Information System (INIS)

    Wei, J.; Ptitsin, V.; Pilat, F.; Tepikian, S.; Gelfand, N.; Wan, W.; Holt, J.

    1998-01-01

    This paper studies the impact of the insertion-region (IR) magnet field errors on LHC collision performance. Compensation schemes including magnet orientation optimization, body-end compensation, tuning shims, and local nonlinear correction are shown to be highly effective

  18. 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.

  19. Hybrid compensation arrangement in dispersed generation systems

    DEFF Research Database (Denmark)

    Chen, Zhe; Blaabjerg, Frede; Pedersen, John Kim

    2005-01-01

    This paper presents a hybrid compensation system consisting of an active filter and distributed passive filters. In the system, each individual passive filter is connected to a distortion source and designed to eliminate main harmonics and supply reactive power for the distortion source, while...... the active filter is responsible for the correction of the system unbalance and the cancellation of the remaining harmonics. The paper also analyzes the effects of the circuit configuration on the system impedance characteristics and consequently the effectiveness of the filter system. Simulation studies...... are performed for a power system including the dispersed generation units connected into the system through power electronic converters and diode rectifier loads, which produce the distorted waveforms. The simulation results have demonstrated that good compensation effects can be achieved by using the combined...

  20. Phase Noise Compensation for OFDM Systems

    Science.gov (United States)

    Leshem, Amir; Yemini, Michal

    2017-11-01

    We describe a low complexity method for time domain compensation of phase noise in OFDM systems. We extend existing methods in several respects. First we suggest using the Karhunen-Lo\\'{e}ve representation of the phase noise process to estimate the phase noise. We then derive an improved datadirected choice of basis elements for LS phase noise estimation and present its total least square counterpart problem. The proposed method helps overcome one of the major weaknesses of OFDM systems. We also generalize the time domain phase noise compensation to the multiuser MIMO context. Finally we present simulation results using both simulated and measured phased noise. We quantify the tracking performance in the presence of residual carrier offset.

  1. Compensating for telecommunication delays during robotic telerehabilitation.

    Science.gov (United States)

    Consoni, Leonardo J; Siqueira, Adriano A G; Krebs, Hermano I

    2017-07-01

    Rehabilitation robotic systems may afford better care and telerehabilitation may extend the use and benefits of robotic therapy to the home. Data transmissions over distance are bound by intrinsic communication delays which can be significant enough to deem the activity unfeasible. Here we describe an approach that combines unilateral robotic telerehabilitation and serious games. This approach has a modular and distributed design that permits different types of robots to interact without substantial code changes. We demonstrate the approach through an online multiplayer game. Two users can remotely interact with each other with no force exchanges, while a smoothing and prediction algorithm compensates motions for the delay in the Internet connection. We demonstrate that this approach can successfully compensate for data transmission delays, even when testing between the United States and Brazil. This paper presents the initial experimental results, which highlight the performance degradation with increasing delays as well as improvements provided by the proposed algorithm, and discusses planned future developments.

  2. An EMTDC Model of a Three Level four MVAR Compensator

    DEFF Research Database (Denmark)

    Rasmussen, Tonny Wederberg

    1997-01-01

    The paper discusses the dynamic characteristics of a three level ±4mvar solid state var compensator which is built and will be used for dynamic reactive power compensation in a wind farm. An investigation has been carried out of the influence of the compensator reactor, the DC intermediate voltag...

  3. 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 governance...

  4. Wildlife Damage and Agriculture: A Dynamic Analysis of Compensation Schemes

    NARCIS (Netherlands)

    Bulte, E.H.; Rondeau, D.

    2007-01-01

    We study the environmental and economic consequences of introducing a program to compensate peasants for damages caused by wildlife. We show that the widely held belief that compensation induces wildlife conservation may be erroneous. In a partially open economy, compensation can lower the wildlife

  5. Critical Issues in Assessing Teacher Compensation. Backgrounder. No. 2638

    Science.gov (United States)

    Richwine, Jason; Biggs, Andrew G.

    2012-01-01

    A November 2011 Heritage Foundation report--"Assessing the Compensation of Public-School Teachers"--presented data on teacher salaries and benefits in order to inform debates about teacher compensation reform. The report concluded that public-school teacher compensation is far ahead of what comparable private-sector workers enjoy, and that…

  6. 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 beginning...

  7. 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 accordance...

  8. 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 Elections...

  9. 39 CFR 3.2 - Compensation of Board.

    Science.gov (United States)

    2010-07-01

    ... 39 Postal Service 1 2010-07-01 2010-07-01 false Compensation of Board. 3.2 Section 3.2 Postal Service UNITED STATES POSTAL SERVICE THE BOARD OF GOVERNORS OF THE U.S. POSTAL SERVICE BOARD OF GOVERNORS (ARTICLE III) § 3.2 Compensation of Board. Section 202(a)(1) of title 39 provides for the compensation of...

  10. Assessment of Wetland Valuation Processes for Compensation in ...

    African Journals Online (AJOL)

    The issue of compensation has been debated in various fora; however compensation on wetland resources has not been given the primary place. Wetland valuation like any other type of valuation requires going through stages, which may be more complex than real estate valuation for compensation. This study therefore ...

  11. 14 CFR 250.8 - Denied boarding compensation.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 4 2010-01-01 2010-01-01 false Denied boarding compensation. 250.8 Section... PROCEEDINGS) ECONOMIC REGULATIONS OVERSALES § 250.8 Denied boarding compensation. (a) Every carrier shall tender to a passenger eligible for denied boarding compensation, on the day and place the denied boarding...

  12. 34 CFR 75.519 - Dual compensation of staff.

    Science.gov (United States)

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Dual compensation of staff. 75.519 Section 75.519... by a Grantee? Project Staff § 75.519 Dual compensation of staff. A grantee may not use its grantee to pay a project staff member for time or work for which that staff member is compensated from some other...

  13. Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase

    Science.gov (United States)

    Birch, Louise; Murray, Christopher W.; Hartshorn, Michael J.; Tickle, Ian J.; Verdonk, Marcel L.

    2002-12-01

    Many proteins undergo small side chain or even backbone movements on binding of different ligands into the same protein structure. This is known as induced fit and is potentially problematic for virtual screening of databases against protein targets. In this report we investigate the limits of the rigid protein approximation used by the docking program, GOLD, through cross-docking using protein structures of influenza neuraminidase. Neuraminidase is known to exhibit small but significant induced fit effects on ligand binding. Some neuraminidase crystal structures caused concern due to the bound ligand conformation and GOLD performed poorly on these complexes. A `clean' set, which contained unique, unambiguous complexes, was defined. For this set, the lowest energy structure was correctly docked (i.e. RMSD < 1.5 Å away from the crystal reference structure) in 84% of proteins, and the most promiscuous protein (1mwe) was able to dock all 15 ligands accurately including those that normally required an induced fit movement. This is considerably better than the 70% success rate seen with GOLD against general validation sets. Inclusion of specific water molecules involved in water-mediated hydrogen bonds did not significantly improve the docking performance for ligands that formed water-mediated contacts but it did prevent docking of ligands that displaced these waters. Our data supports the use of a single protein structure for virtual screening with GOLD in some applications involving induced fit effects, although care must be taken to identify the protein structure that performs best against a wide variety of ligands. The performance of GOLD was significantly better than the GOLD implementation of ChemScore and the reasons for this are discussed. Overall, GOLD has shown itself to be an extremely good, robust docking program for this system.

  14. 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.

  15. Compensation for gravitational sag of bent mirror

    International Nuclear Information System (INIS)

    Mao, Chengwen; Jiang, Hui; He, Yan; Liang, Dongxu; Lan, Xuying; Yan, Shuai; Shu, De-ming; Li, Aiguo

    2017-01-01

    The gravitational sag of aspheric bent mirrors with face-up or face-down geometry produces a nonnegligible optical error. As an effective compensation, width optimization is used to match the combined effects of the gravitational and bending moments. This method is described by analytical expressions and two calculation algorithms. The results of theoretical simulations and finite element analysis have proved that this method can reduce the slope error resulting from gravitational sag to the level of nano radians.

  16. Compensation for gravitational sag of bent mirror

    Energy Technology Data Exchange (ETDEWEB)

    Mao, Chengwen; Jiang, Hui; He, Yan; Liang, Dongxu; Lan, Xuying; Yan, Shuai [Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, CAS, Shanghai 201800 (China); Shu, De-ming [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States); Li, Aiguo, E-mail: aiguo.li@sinap.ac.cn [Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, CAS, Shanghai 201800 (China)

    2017-05-01

    The gravitational sag of aspheric bent mirrors with face-up or face-down geometry produces a nonnegligible optical error. As an effective compensation, width optimization is used to match the combined effects of the gravitational and bending moments. This method is described by analytical expressions and two calculation algorithms. The results of theoretical simulations and finite element analysis have proved that this method can reduce the slope error resulting from gravitational sag to the level of nano radians.

  17. Environmental Regulation, Industrial Heterogeneity and Value Compensation

    OpenAIRE

    Chen Lisha; Ding Changqing

    2017-01-01

    This article divided environmental regulation tools into market-oriented environmental regulation, environmental administrative control and environmental pollution regulation, divided enterprises into pollution intensive and clean production enterprises. Take Chinese manufacturing listed companies as research object, through panel data analysis, this article measured short-term and long-term value compensation effect and the possible existence of the threshold effect and cumulative effect of ...

  18. Compensation for Combat Deaths: Policy Considerations

    Science.gov (United States)

    2012-01-01

    receive $100,000 if the 10-percent risk of a loss of $100,000 actually came to pass. Tort law generally uses an ex post approach to compensation and...through the courts for deaths resulting from other parties’ negligence or criminal behavior; a key difference between the tort system and many other...Bookstore Make a charitable contribution Limited Electronic Distribution Rights This document and trademark(s) contained herein are protected by law

  19. Compensation and Honesty: Gender Differences in Lying

    OpenAIRE

    Nieken, Petra; Dato, Simon

    2016-01-01

    We compare gender differences in lying under two incentive schemes that are widely used in companies: individual performance-pay and tournament incentives. While we do not observe significantly different behavior of males and females given individual performance-pay, females lie significantly less than males if the compensation scheme is switched to tournament incentives. This result is mainly driven by a decrease in the propensity to lie of females in a competitive environment. The gender ga...

  20. Doppler Shift Compensation Schemes in VANETs

    Directory of Open Access Journals (Sweden)

    F. Nyongesa

    2015-01-01

    Full Text Available Over the last decade vehicle-to-vehicle (V2V communication has received a lot of attention as it is a crucial issue in intravehicle communication as well as in Intelligent Transportation System (ITS. In ITS the focus is placed on integration of communication between mobile and fixed infrastructure to execute road safety as well as nonsafety information dissemination. The safety application such as emergence alerts lays emphasis on low-latency packet delivery rate (PDR, whereas multimedia and infotainment call for high data rates at low bit error rate (BER. The nonsafety information includes multimedia streaming for traffic information and infotainment applications such as playing audio content, utilizing navigation for driving, and accessing Internet. A lot of vehicular ad hoc network (VANET research has focused on specific areas including channel multiplexing, antenna diversity, and Doppler shift compensation schemes in an attempt to optimize BER performance. Despite this effort few surveys have been conducted to highlight the state-of-the-art collection on Doppler shift compensation schemes. Driven by this cause we survey some of the recent research activities in Doppler shift compensation schemes and highlight challenges and solutions as a stock-taking exercise. Moreover, we present open issues to be further investigated in order to address the challenges of Doppler shift in VANETs.

  1. Lossless Compression of Video using Motion Compensation

    DEFF Research Database (Denmark)

    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 estimati......, 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 motion field as one of choosing among a number of predictors. This way, we can incorporate 3D......-predictors and intra-frame predictors as well. As proposed by Ribas-Corbera (see PhD thesis, University of Michigan, 1996), we use bi-linear interpolation in order to achieve sub-pixel precision of the motion field. Using more reference images is another way of achieving higher accuracy of the match. The motion...... information is coded with the same algorithm as is used for the data. For slow pan or slow zoom sequences, coding methods that use multiple previous images perform up to 20% better than motion compensation using a single previous image and up to 40% better than coding that does not utilize motion compensation...

  2. Installation of the sag compensator for HANARO

    International Nuclear Information System (INIS)

    Kim, H. K.; Jung, H. S.; Ahn, G. H.; Lim, I. C.

    2008-01-01

    Electric power is essential for all industrial plants and also for nuclear facilities. HANARO is a research reactor which produces a 30MW thermal power. HANARO is designed to be tripped automatically when interruptions or some extents of sags occur. HANARO has the reactor regulation system (RRS) and reactor protection system (RPS). HANARO is designed so as to tripped automatically by insertion of control absorber rods (CAR) and shut-off rods (SOR). When voltage or momentary interruption occurs, the reactor has an unwanted trip by insertion of CARs and SORs even though the process systems are still in operation. HANARO was experienced in a nuisance trip as often as the unexpected voltage sag and/or momentary interruption occurs. We installed the voltage sag compensator on the power supply for CARs and SORs so as to prevent an unwanted trip. We undertook voltage sag assessment of the AC coil contactor which is a component of the power supply unit for the SORs. The compensation time is determined to be less than 1 sec in consideration of the reactor safety. This paper is concerned with the impact of the momentary interruption on the reactor and the effect of the voltage sag compensator

  3. Installation of the sag compensator for HANARO

    International Nuclear Information System (INIS)

    Kim, Hyung Kyoo; Jung, Hoan Sung; Lim, In Cheol; Ahn, Guk Hoon

    2008-01-01

    Electric power is essential for all industrial plants and also for nuclear facilities. HANARO is a research reactor which produces a 30MW thermal power. HANARO is designed to be tripped automatically when interruptions or some extent of sags occur. HANARO has the reactor regulation system(RRs) and reactor protection system(RPS). HANARO is designed so as to be tripped automatically by insertion of control absorber rods(CAR) and shut off rods(SOR). When voltage sag or momentary interruption occurs, the reactor has an unwanted trip by insertion of CARs and SORs even though the process systems are still in operation. HANARO was experienced in a nuisance trip as often as the unexpected voltage sag and/or momentary interruption occurs. We installed the voltage sag compensator voltage sag assessment of the AC coil contactor which is a component of the power supply unit for the SORs. The compensation time is determined to be less than 1 sec in consideration of the reactor safety. This paper is concerned with the impact of the momentary interruption on the reactor and the effect of the voltage sag compensator

  4. Installation of the sag compensator for HANARO

    International Nuclear Information System (INIS)

    Kim, Hyungkyoo; Jung, Hoansung; Lim, Incheol; Ahn, Gukhoon

    2008-01-01

    Electric power is essential for all industrial plants and also for nuclear facilities. HANARO is a research reactor which produces a 30 MW thermal power. HANARO is designed to be tripped automatically when interruptions or some extent of sags occur. HANARO has the reactor regulation system(RRS) and reactor protection system(RPS). HANARO is designed so as to be tripped automatically by insertion of control absorber rods(CAR) and shut-off rods(SOR). When voltage sag or momentary interruption occurs, the reactor has an unwanted trip by insertion of CARs and SORs even though the process systems are still in operation. HANARO was experienced in a nuisance trip as often as the unexpected voltage sag and/or momentary interruption occurs. We installed the voltage sag compensator on the power supply for CARs and SORs so as to prevent an unwanted trip. We undertook voltage sag assessment of the AC coil contactor which is a component of the power supply unit for the SORs. The compensation time is determined to be less than 1 sec in consideration of the reactor safety. This paper is concerned with the impact of the momentary interruption on the reactor and the effect of the voltage sag compensator. (author)

  5. Direct Lorentz force compensation flowmeter for electrolytes

    International Nuclear Information System (INIS)

    Vasilyan, S.; Froehlich, Th.

    2014-01-01

    A simplified method of contactless Lorentz force (LF) measurements for flow meters on electrolytes is described and realized. Modification and comparative representation are discussed against recently well-developed methods. Based on the catapult effect, that current carrying conductor experiences a repulsive force in a magnetic field, we demonstrate force measurement method of LF velocimetry applications by commonly known “electromagnetic force” compensation principle. Measurement approach through zero point stability is considered to minimize mechanical influences and avoid gravimetric uncertainties. Here, the current carrying wires are static fixed in the vicinity of magnet system at zero point stable position, while occurring deflection of magnets by electrolyte flow is compensated by external applied current within wires. Measurements performed by developed servo-system which drives control loop by means of optical position sensor for simplified (i) single wire and (ii) coil-like extended compensation schemes. Guided by experiments on electrolyte flow, we demonstrate the applicability of adopted principle for conductivities ranging from 2 to 20 S/m. Further improvements are discussed in agreement with the parameters of demonstration setup, straightforward theory, and experimental results. We argue that this method is potentially suitable for: (a) applications with higher conductivity like molten metal (order of 10 6  S/m) assuming spatial configuration of setup and (b) for lower range of conductivity (below 1 S/m) while this is strongly subject to stiffness of system and noise mainly mechanical and thermal radiations

  6. Direct Lorentz force compensation flowmeter for electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Vasilyan, S., E-mail: suren.vasilyan@tu-ilmenau.de; Froehlich, Th. [Institute of Process Measurement and Sensor Technology, Ilmenau University of Technology, 98684 Ilmenau (Germany)

    2014-12-01

    A simplified method of contactless Lorentz force (LF) measurements for flow meters on electrolytes is described and realized. Modification and comparative representation are discussed against recently well-developed methods. Based on the catapult effect, that current carrying conductor experiences a repulsive force in a magnetic field, we demonstrate force measurement method of LF velocimetry applications by commonly known “electromagnetic force” compensation principle. Measurement approach through zero point stability is considered to minimize mechanical influences and avoid gravimetric uncertainties. Here, the current carrying wires are static fixed in the vicinity of magnet system at zero point stable position, while occurring deflection of magnets by electrolyte flow is compensated by external applied current within wires. Measurements performed by developed servo-system which drives control loop by means of optical position sensor for simplified (i) single wire and (ii) coil-like extended compensation schemes. Guided by experiments on electrolyte flow, we demonstrate the applicability of adopted principle for conductivities ranging from 2 to 20 S/m. Further improvements are discussed in agreement with the parameters of demonstration setup, straightforward theory, and experimental results. We argue that this method is potentially suitable for: (a) applications with higher conductivity like molten metal (order of 10{sup 6 }S/m) assuming spatial configuration of setup and (b) for lower range of conductivity (below 1 S/m) while this is strongly subject to stiffness of system and noise mainly mechanical and thermal radiations.

  7. Gravity compensation of an upper extremity exoskeleton.

    Science.gov (United States)

    Moubarak, S; Pham, M T; Moreau, R; Redarce, T

    2010-01-01

    This paper presents a new gravity compensation method for an upper extremity exoskeleton mounted on a wheel chair. This new device is dedicated to regular and efficient rehabilitation training for post-stroke and injured people without the continuous presence of a therapist. The exoskeleton is a wearable robotic device attached to the human arm. The user provides information signals to the controller by means of the force sensors around the wrist and the arm, and the robot controller generates the appropriate control signals for different training strategies and paradigms. This upper extremity exoskeleton covers four basic degrees of freedom of the shoulder and the elbow joints with three additional adaptability degrees of freedom in order to match the arm anatomy of different users. For comfortable and efficient rehabilitation, a new heuristic method have been studied and applied on our prototype in order to calculate the gravity compensation model without the need to identify the mass parameters. It is based on the geometric model of the robot and accurate torque measurements of the prototype's actuators in a set of specifically chosen joint positions. The weight effect has been successfully compensated so that the user can move his arm freely while wearing the exoskeleton without feeling its mass.

  8. Compensating for the harms of family violence: statutory barriers in Australian victims of crime compensation schemes.

    Science.gov (United States)

    Forster, Christine

    2014-09-01

    This article considers the compensative capacity of the victims of crime statutory schemes that are present in all eight Australian jurisdictions for primary victims of family violence. It argues that the recommendations of the Final Report on Family Violence conducted jointly by the Australian Law Reform Commission and the New South Wales Law Reform Commission in 2010, although a positive step, are insufficient to facilitate meaningful compensation to victims of family violence. In addition to the primary limitations identified by the Commissions--a requirement to report the crime to the police within a reasonable time and a requirement for multiple acts of violence to be reduced to a single act if they are related--there are other statutory barriers that disproportionately disadvantage victims of family violence. These include time limitation provisions, a requirement to report the crime to police, the restriction of compensation to prescribed categories of loss which exclude many of the social, vocational, emotional and psychological harms suffered by victims of family violence, and significant cut-backs on the non-economic component of the schemes. This article further argues that the statutory barriers cumulatively contribute to the perception of a crime as an isolated event perpetrated by a deviant individual. The article recommends that specific provisions for family violence victims should be introduced into all schemes including three categories of compensation not tied to criminal offences but rather the different forms of family violence, with a generous compensation range, and no requirement for proof of injury.

  9. Executive compensation and firm performance: Evidence from Indian firms

    Directory of Open Access Journals (Sweden)

    Mehul Raithatha

    2016-09-01

    Full Text Available The study examines the relationship between executive compensation and firm performance among Indian firms. The evidence suggests that firm performance measured by accounting, as well as market-based measures, significantly affects executive compensation. We also test for the presence of persistence in executive compensation by employing the system-generalised methods of moments (GMM estimator. We find significant persistence in executive compensation among the sample firms. Further, we report the absence of pay–performance relationship among the smaller sample firms and business group affiliated firms. Thus, our findings cast doubts over the performance-based executive compensation practices of Indian business group affiliated firms.

  10. Synthesis of 4-aminophenyl substituted indole derivatives for the instrumental analysis and molecular docking evaluation studies

    Science.gov (United States)

    Singh, Navneet; Kumar, Keshav

    2017-07-01

    The Indole has been known to maintain celebrity status since so many decades and has been a centre point at the spectrum of pharmacological research. The present work stimulates an idea of generating a pool of library of lead compounds. The data collected can be used for the mapping of biologically active compounds. The reported derivatives of 4-aminophenyl substituted Indole were prepared by the methods of Fischer Indole synthesis and Vilsemeier reaction followed by screening for instrumental analysis and molecular docking studies. The synthesized compounds 4-(1-(2-phenylhydrazono)ethyl)aniline, 1, 4-(1H-indol-2-yl)aniline, 2 and 2-(4-aminophenyl)-1H-indole-3-carbaldehyde, 3 were found to have remarkable yield and instrumental data analysis and also showed remarkable docked characteristic. The molecular docking studies revealed that ligand (amino acids) of comp. 1, 2 and 3 had been docked successfully on the binding site of the 3JUS protein selected from PDB with H bonding. The molecular docking data showed that compound 1, would possess remarkable biological activity and compd. 2 and 3 would possess mild to moderate biological activity. Thus this research work paves the way to synthesize new derivatives and thus to develop new compounds in future with accurate prediction.

  11. Use of industrial robots for hardware-in-the-loop simulation of satellite rendezvous and docking

    Science.gov (United States)

    Ma, Ou; Flores-Abad, Angel; Boge, Toralf

    2012-12-01

    One of the most challenging and risky operations for spacecraft is to perform rendezvous and docking autonomously in space. To ensure a safe and reliable operation, such a mission must be carefully designed and thoroughly verified before a real space mission can be launched. This paper describes the control strategy for achieving high fidelity contact dynamics simulation of a new, robotics-based, hardware-in-the-loop (HIL) rendezvous and docking simulation facility that uses two industrial robots to physically simulate the 6-DOF dynamic maneuvering of two docking satellites. The facility is capable of physically simulating the final approaching within a 25-meter range and the entire docking/capturing process for a satellite on-orbit servicing mission. The key difficulties of using industrial robots for high-fidelity HIL contact dynamics simulation were found and different solution techniques were investigated in the presented project. An admittance control method was proposed to achieve the goal of making the robots in the HIL simulation process match the impedance of the two docking satellites. Simulation study showed the effectiveness and performance of the proposed solution method.

  12. 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.

  13. PyGOLD: a python based API for docking based virtual screening workflow generation.

    Science.gov (United States)

    Patel, Hitesh; Brinkjost, Tobias; Koch, Oliver

    2017-08-15

    Molecular docking is one of the successful approaches in structure based discovery and development of bioactive molecules in chemical biology and medicinal chemistry. Due to the huge amount of computational time that is still required, docking is often the last step in a virtual screening approach. Such screenings are set as workflows spanned over many steps, each aiming at different filtering task. These workflows can be automatized in large parts using python based toolkits except for docking using the docking software GOLD. However, within an automated virtual screening workflow it is not feasible to use the GUI in between every step to change the GOLD configuration file. Thus, a python module called PyGOLD was developed, to parse, edit and write the GOLD configuration file and to automate docking based virtual screening workflows. The latest version of PyGOLD, its documentation and example scripts are available at: http://www.ccb.tu-dortmund.de/koch or http://www.agkoch.de. PyGOLD is implemented in Python and can be imported as a standard python module without any further dependencies. oliver.koch@agkoch.de, oliver.koch@tu-dortmund.de. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  14. Dock/Nck facilitates PTP61F/PTP1B regulation of insulin signalling.

    Science.gov (United States)

    Wu, Chia-Lun; Buszard, Bree; Teng, Chun-Hung; Chen, Wei-Lin; Warr, Coral G; Tiganis, Tony; Meng, Tzu-Ching

    2011-10-01

    PTP1B (protein tyrosine phosphatase 1B) is a negative regulator of IR (insulin receptor) activation and glucose homoeostasis, but the precise molecular mechanisms governing PTP1B substrate selectivity and the regulation of insulin signalling remain unclear. In the present study we have taken advantage of Drosophila as a model organism to establish the role of the SH3 (Src homology 3)/SH2 adaptor protein Dock (Dreadlocks) and its mammalian counterpart Nck in IR regulation by PTPs. We demonstrate that the PTP1B orthologue PTP61F dephosphorylates the Drosophila IR in S2 cells in vitro and attenuates IR-induced eye overgrowth in vivo. Our studies indicate that Dock forms a stable complex with PTP61F and that Dock/PTP61F associate with the IR in response to insulin. We report that Dock is required for effective IR dephosphorylation and inactivation by PTP61F in vitro and in vivo. Furthermore, we demonstrate that Nck interacts with PTP1B and that the Nck/PTP1B complex inducibly associates with the IR for the attenuation of IR activation in mammalian cells. Our studies reveal for the first time that the adaptor protein Dock/Nck attenuates insulin signalling by recruiting PTP61F/PTP1B to its substrate, the IR.

  15. DOCK2 confers immunity and intestinal colonization resistance to Citrobacter rodentium infection.

    Science.gov (United States)

    Liu, Zhiping; Man, Si Ming; Zhu, Qifan; Vogel, Peter; Frase, Sharon; Fukui, Yoshinori; Kanneganti, Thirumala-Devi

    2016-06-13

    Food poisoning is one of the leading causes of morbidity and mortality in the world. Citrobacter rodentium is an enteric pathogen which attaches itself to enterocytes and induces attachment and effacing (A/E) lesions. The ability of the bacterium to cause infection requires subversion of the host actin cytoskeleton. Rac-dependent actin polymerization is activated by a guanine nucleotide exchange factor known as Dedicator of cytokinesis 2 (DOCK2). However, the role of DOCK2 in infectious disease is largely unexplored. Here, we found that mice lacking DOCK2 were susceptible to C. rodentium infection. These mice harbored increased levels of C. rodentium bacteria, showed more pronounced weight loss and inflammation-associated pathology, and were prone to bacterial dissemination to the systemic organs compared with wild-type mice. We found that mice lacking DOCK2 were more susceptible to C. rodentium attachment to intestinal epithelial cells. Therefore, our results underscored an important role of DOCK2 for gastrointestinal immunity to C. rodentium infection.

  16. 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.

  17. "No compensation" or "pro compensation": Moore v. Regents and default rules for human tissue donations.

    Science.gov (United States)

    Korobkin, Russell

    2007-01-01

    The much studied case of Moore v. Regents of the University of California is often considered important in property law for denying property rights in human tissue. This widespread misunderstanding of Moore has not only misplaced the legal emphasis of human tissue donations on property law instead of contract law, but has also hindered the creation of a much-needed default rule governing the issue of compensation for donated tissue. While it is possible that the majority of donors rarely consider compensation as an incentive to donate, without a legally recognized default rule the law remains blurred as to what contractual provisions apply to the exchange between donor and researcher. This Article argues that the solution is a weak default rule of no compensation that may be overridden by evidence that the parties intended otherwise.

  18. Compensation for oil pollution damage caused by oil spills from ships and the International Oil Pollution Compensation Fund

    International Nuclear Information System (INIS)

    Jacobsson, M.

    1994-01-01

    Liability and compensation for pollution damage caused by oil spills from laden tankers is governed by two international conventions: the 1969 Civil Liability Convention and the 1971 Fund Convention. The Civil Liability Convention established a system of strict liability for tanker owners and introduced compulsory liability insurance. The Fund Convention created a system of supplementary compensation administered by an intergovernmental organization, the International Oil Pollution Compensation Fund (IOPC Fund), which at present has 56 member states (August 1993). The IOPC Fund pays compensation to victims of oil pollution in member states when the compensation from the ship owner and his insurer is insufficient. (author)

  19. Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions.

    Science.gov (United States)

    Peterson, Lenna X; Kim, Hyungrae; Esquivel-Rodriguez, Juan; Roy, Amitava; Han, Xusi; Shin, Woong-Hee; Zhang, Jian; Terashi, Genki; Lee, Matt; Kihara, Daisuke

    2017-03-01

    We report the performance of protein-protein docking predictions by our group for recent rounds of the Critical Assessment of Prediction of Interactions (CAPRI), a community-wide assessment of state-of-the-art docking methods. Our prediction procedure uses a protein-protein docking program named LZerD developed in our group. LZerD represents a protein surface with 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. The appropriate soft representation of protein surface with 3DZD makes the method more tolerant to conformational change of proteins upon docking, which adds an advantage for unbound docking. Docking was guided by interface residue prediction performed with BindML and cons-PPISP as well as literature information when available. The generated docking models were ranked by a combination of scoring functions, including PRESCO, which evaluates the native-likeness of residues' spatial environments in structure models. First, we discuss the overall performance of our group in the CAPRI prediction rounds and investigate the reasons for unsuccessful cases. Then, we examine the performance of several knowledge-based scoring functions and their combinations for ranking docking models. It was found that the quality of a pool of docking models generated by LZerD, that is whether or not the pool includes near-native models, can be predicted by the correlation of multiple scores. Although the current analysis used docking models generated by LZerD, findings on scoring functions are expected to be universally applicable to other docking methods. Proteins 2017; 85:513-527. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  20. Experimental evaluation of model predictive control and inverse dynamics control for spacecraft proximity and docking maneuvers

    Science.gov (United States)

    Virgili-Llop, Josep; Zagaris, Costantinos; Park, Hyeongjun; Zappulla, Richard; Romano, Marcello

    2018-03-01

    An experimental campaign has been conducted to evaluate the performance of two different guidance and control algorithms on a multi-constrained docking maneuver. The evaluated algorithms are model predictive control (MPC) and inverse dynamics in the virtual domain (IDVD). A linear-quadratic approach with a quadratic programming solver is used for the MPC approach. A nonconvex optimization problem results from the IDVD approach, and a nonlinear programming solver is used. The docking scenario is constrained by the presence of a keep-out zone, an entry cone, and by the chaser's maximum actuation level. The performance metrics for the experiments and numerical simulations include the required control effort and time to dock. The experiments have been conducted in a ground-based air-bearing test bed, using spacecraft simulators that float over a granite table.

  1. Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures

    Science.gov (United States)

    2015-01-01

    Background The hardware accelerators will provide solutions to computationally complex problems in bioinformatics fields. However, the effect of acceleration depends on the nature of the application, thus selection of an appropriate accelerator requires some consideration. Results In the present study, we compared the effects of acceleration using graphics processing unit (GPU) and many integrated core (MIC) on the speed of fast Fourier transform (FFT)-based protein-protein docking calculation. The GPU implementation performed the protein-protein docking calculations approximately five times faster than the MIC offload mode implementation. The MIC native mode implementation has the advantage in the implementation costs. However, the performance was worse with larger protein pairs because of memory limitations. Conclusion The results suggest that GPU is more suitable than MIC for accelerating FFT-based protein-protein docking applications. PMID:25707855

  2. Domain requirements for the Dock adapter protein in growth- cone signaling.

    Science.gov (United States)

    Rao, Y; Zipursky, S L

    1998-03-03

    Tyrosine phosphorylation has been implicated in growth-cone guidance through genetic, biochemical, and pharmacological studies. Adapter proteins containing src homology 2 (SH2) domains and src homology 3 (SH3) domains provide a means of linking guidance signaling through phosphotyrosine to downstream effectors regulating growth-cone motility. The Drosophila adapter, Dreadlocks (Dock), the homolog of mammalian Nck containing three N-terminal SH3 domains and a single SH2 domain, is highly specialized for growth-cone guidance. In this paper, we demonstrate that Dock can couple signals in either an SH2-dependent or an SH2-independent fashion in photoreceptor (R cell) growth cones, and that Dock displays different domain requirements in different neurons.

  3. 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.

  4. 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.

  5. 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.

  6. Redesigning reservoir compensation releases for ecological beenfit

    Science.gov (United States)

    Maynard, Carly

    2010-05-01

    River regulation is commonplace in England and much of the UK. Regulation for the purposes of public water supply causes flows downstream of a reservoir to be attenuated and the flow regime of the channel to be altered. The impact of channel impoundment on a small, upland UK river, has been assessed and methods for mitigation of ecological impacts explored. The method utilised a unique macroinvertebrate data set for pre- and post-impoundment periods to quantify the impact of Derwent Reservoir and the steady, continuous compensation release into the River Derwent, Northumberland. Impacts on the hydrological regime were also investigated and links drawn between changes in flow regime and changes in macroinvertebrate richness and diversity as a result of impoundment. In response to the claim that the impoundment has caused a change in flow regime and had deleterious effects on fish and macroinvertebrates, a compensation redesign tool (CRAB: Compensation Release Assessment at the Broad scale) was employed to design new compensation release regimes from the reservoir which account for the seasonal flow requirements of a number of key fish species. The impact of impoundment on the current flow regime was modelled and the impacts of predicted new regimes were predicted, using a 1D hydrodynamic model (HEC-RAS), as part of a modelling process known as CRAM (Compensation Release Assessment at the Meso-scale). Depth and velocity were the foci of the analysis as they are the two habitat requirements most well documented for the fish species in question, they could be modelled using HEC-RAS and they can act as surrogates for other habitat parameters such as temperature and substrate. The suitability of the depth and velocity combinations predicted using the HEC-RAS model were assessed using fuzzy-rule based modelling, which allowed the habitat quality of a given parameter combination to be quantified. Based on the results of the investigation it was concluded that there has

  7. Illumination compensation in ground based hyperspectral imaging

    Science.gov (United States)

    Wendel, Alexander; Underwood, James

    2017-07-01

    Hyperspectral imaging has emerged as an important tool for analysing vegetation data in agricultural applications. Recently, low altitude and ground based hyperspectral imaging solutions have come to the fore, providing very high resolution data for mapping and studying large areas of crops in detail. However, these platforms introduce a unique set of challenges that need to be overcome to ensure consistent, accurate and timely acquisition of data. One particular problem is dealing with changes in environmental illumination while operating with natural light under cloud cover, which can have considerable effects on spectral shape. In the past this has been commonly achieved by imaging known reference targets at the time of data acquisition, direct measurement of irradiance, or atmospheric modelling. While capturing a reference panel continuously or very frequently allows accurate compensation for illumination changes, this is often not practical with ground based platforms, and impossible in aerial applications. This paper examines the use of an autonomous unmanned ground vehicle (UGV) to gather high resolution hyperspectral imaging data of crops under natural illumination. A process of illumination compensation is performed to extract the inherent reflectance properties of the crops, despite variable illumination. This work adapts a previously developed subspace model approach to reflectance and illumination recovery. Though tested on a ground vehicle in this paper, it is applicable to low altitude unmanned aerial hyperspectral imagery also. The method uses occasional observations of reference panel training data from within the same or other datasets, which enables a practical field protocol that minimises in-field manual labour. This paper tests the new approach, comparing it against traditional methods. Several illumination compensation protocols for high volume ground based data collection are presented based on the results. The findings in this paper are

  8. The Drosophila DOCK family protein Sponge is required for development of the air sac primordium

    Energy Technology Data Exchange (ETDEWEB)

    Morishita, Kazushge; Anh Suong, Dang Ngoc; Yoshida, Hideki; Yamaguchi, Masamitsu, E-mail: myamaguc@kit.ac.jp

    2017-05-15

    Dedicator of cytokinesis (DOCK) family genes are known as DOCK1-DOCK11 in mammals. DOCK family proteins mainly regulate actin filament polymerization and/or depolymerization and are GEF proteins, which contribute to cellular signaling events by activating small G proteins. Sponge (Spg) is a Drosophila counterpart to mammalian DOCK3/DOCK4, and plays a role in embryonic central nervous system development, R7 photoreceptor cell differentiation, and adult thorax development. In order to conduct further functional analyses on Spg in vivo, we examined its localization in third instar larval wing imaginal discs. Immunostaining with purified anti-Spg IgG revealed that Spg mainly localized in the air sac primordium (ASP) in wing imaginal discs. Spg is therefore predicted to play an important role in the ASP. The specific knockdown of Spg by the breathless-GAL4 driver in tracheal cells induced lethality accompanied with a defect in ASP development and the induction of apoptosis. The monitoring of ERK signaling activity in wing imaginal discs by immunostaining with anti-diphospho-ERK IgG revealed reductions in the ERK signal cascade in Spg knockdown clones. Furthermore, the overexpression of D-raf suppressed defects in survival and the proliferation of cells in the ASP induced by the knockdown of Spg. Collectively, these results indicate that Spg plays a critical role in ASP development and tracheal cell viability that is mediated by the ERK signaling pathway. - Highlights: • Spg mainly localizes in the air sac primordium in wing imaginal discs. • Spg plays a critical role in air sac primordium development. • Spg positively regulates the ERK signal cascade.

  9. Differential Regulation of Synaptic Vesicle Tethering and Docking by UNC-18 and TOM-1.

    Science.gov (United States)

    Gracheva, Elena O; Maryon, Ed B; Berthelot-Grosjean, Martine; Richmond, Janet E

    2010-01-01

    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 25 nm 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.

  10. 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

  11. The Rac Activator DOCK2 Mediates Plasma Cell Differentiation and IgG Antibody Production

    Directory of Open Access Journals (Sweden)

    Miho Ushijima

    2018-02-01

    Full Text Available A hallmark of humoral immune responses is the production of antibodies. This process involves a complex cascade of molecular and cellular interactions, including recognition of specific antigen by the B cell receptor (BCR, which triggers activation of B cells and differentiation into plasma cells (PCs. Although activation of the small GTPase Rac has been implicated in BCR-mediated antigen recognition, its precise role in humoral immunity and the upstream regulator remain elusive. DOCK2 is a Rac-specific guanine nucleotide exchange factor predominantly expressed in hematopoietic cells. We found that BCR-mediated Rac activation was almost completely lost in DOCK2-deficient B cells, resulting in defects in B cell spreading over the target cell-membrane and sustained growth of BCR microclusters at the interface. When wild-type B cells were stimulated in vitro with anti-IgM F(ab′2 antibody in the presence of IL-4 and IL-5, they differentiated efficiently into PCs. However, BCR-mediated PC differentiation was severely impaired in the case of DOCK2-deficient B cells. Similar results were obtained in vivo when DOCK2-deficient B cells expressing a defined BCR specificity were adoptively transferred into mice and challenged with the cognate antigen. In addition, by generating the conditional knockout mice, we found that DOCK2 expression in B-cell lineage is required to mount antigen-specific IgG antibody. These results highlight important role of the DOCK2–Rac axis in PC differentiation and IgG antibody responses.

  12. 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.

  13. 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

  14. Hybrid compensation arrangement in dispersed generation systems

    DEFF Research Database (Denmark)

    Chen, Zhe; Blaabjerg, Frede; Pedersen, John Kim

    2005-01-01

    This paper presents a hybrid compensation system consisting of an active filter and distributed passive filters. In the system, each individual passive filter is connected to a distortion source and designed to eliminate main harmonics and supply reactive power for the distortion source, while...... filter system consisting of distributed passive filters and an active filter....... the active filter is responsible for the correction of the system unbalance and the cancellation of the remaining harmonics. The paper also analyzes the effects of the circuit configuration on the system impedance characteristics and consequently the effectiveness of the filter system. Simulation studies...

  15. Excess density compensation of island herpetofaunal assemblages

    Science.gov (United States)

    Rodda, G.H.; Dean-Bradley, K.

    2002-01-01

    Aim Some species reach extraordinary densities on islands. Island assemblages have fewer species, however, and it is possible that island species differ from their mainland counterparts in average mass. Island assemblages could be partitioned differently (fewer species or smaller individuals) from mainland sites without differing in aggregate biomass (density compensation). Our objective was to determine the generality of excess density compensation in island herpetofaunal assemblages.Location Our bounded removal plot data were obtained from Pacific Island sites (Guam, Saipan and Rota), the West Indies (British Virgin Islands), and the Indian Ocean (Ile aux Aigrettes off Mauritius). The literature values were taken from several locales. Other island locations included Barro Colorado Island, Bonaire, Borneo, Philippine Islands, Seychelle Islands, Barrow Island (Australia), North Brother Island (New Zealand), Dominica and Puerto Rico. Mainland sites included Costa Rica, Ivory Coast, Cameroon, Australia, Thailand, Peru, Brazil, Panama and the USA.Method We added our thirty-nine bounded total removal plots from sixteen island habitats to fifteen literature records to obtain seventy-five venues with estimable density and biomass of arboreal or terrestrial herpetofaunal assemblages. These biomass estimates were evaluated geographically and in relation to sampling method, insularity, latitude, disturbance regime, seasonality, community richness, vegetative structure and climate. Direct data on trophic interactions (food availability, parasitism and predation pressure) were generally unavailable. Sampling problems were frequent for arboreal, cryptic and evasive species.Results and main conclusions We found strong evidence that herpetofaunal assemblages on small islands (mostly lizards) exhibit a much greater aggregate density of biomass (kg ha−1) than those of larger islands or mainland assemblages (small islands show excess density compensation). High aggregate biomass

  16. Spectroscopic and molecular docking studies on the interaction of antiviral drug nevirapine with calf thymus DNA.

    Science.gov (United States)

    Moghadam, Neda Hosseinpour; Salehzadeh, Sadegh; Shahabadi, Nahid

    2017-09-02

    The interaction of calf thymus DNA with nevirapine at physiological pH was studied by using absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, salt effect studies and computational methods. The drug binds to ct-DNA in a groove binding mode, as shown by slight variation in the viscosity of ct-DNA. Furthermore, competitive fluorimetric studies with Hoechst 33258 indicate that nevirapine binds to DNA via groove binding. Moreover, the structure of nevirapine was optimized by DFT calculations and was used for the molecular docking calculations. The molecular docking results suggested that nevirapine prefers to bind on the minor groove of ct-DNA.

  17. An ensemble docking calculation of lysozyme and HyHEL-10: Insight into the binding mechanism

    Science.gov (United States)

    Yamashita, Takefumi; Takamatsu, Yuichiro

    2017-11-01

    Although many computational methods have been proposed for predicting protein-protein complex structures, the prediction remains difficult at the atomic level. In this study, we applied a simple ensemble docking method to the complex of hen egg white lysozyme and its antibody (HyHEL-10). Although this method took into account the protein conformational ensemble, the result was not better than that of a typical rigid docking calculation. In the decomposition analysis, however, we found energetic minima near the crystal structure for a few conformation pairs. This may imply that conformational selection is essential during the early stage of binding.

  18. Optimització del disseny i operativa en magatzems de cross-docking

    OpenAIRE

    Castany Fontanet, Xavier

    2016-01-01

    En el present document es realitza un anàlisi de les terminals de les xarxes de distribució de mercaderies. Aquests punts de la xarxa és on produeixen més operacions que tenen afecte directes sobre l’eficàcia de la xarxa. Concretament l’anàlisi es centre en magatzem de tipus cross-docking. L’anàlisi es realitza mitjançant simulació discreta amb el software ARENA. Es crea i es calibra un model d’un magatzem cross-docking a partir d’un real. Posteriorment se li apliquen d...

  19. Synthesis and characterization of curcumin-sulfonamide hybrids: Biological evaluation and molecular docking studies

    Science.gov (United States)

    Banuppriya, Govindharasu; Sribalan, Rajendran; Padmini, Vediappen

    2018-03-01

    Curcumin-sulfonamide hybrids (4a-e) were synthesized and their in vitro antioxidant, anti-inflammatory and anticancer activities were studied. The synthesized compounds showed a very good potent activity towards antioxidant and anti-inflammatory studies rather than its parent as well as standard. These compounds have exhibited an excellent toxicity effect to the cancer cell lines such as A549 and AGS. The compounds 4a and 4c have showed good anticancer activity than curcumin. The molecular docking studies were also performed against various Epidermal Growth Factor Receptor (EGFR) enzymes. The DFT calculations were also done in order to support the docking results.

  20. Report of the working group for nuclear damage compensation system

    International Nuclear Information System (INIS)

    1989-01-01

    The Working Group for Nuclear Damage Compensation System was established within the Atomic Energy Commision of Japan on August 2, 1988. The Group has held five meetings to make a study on the revision of the reserve for nuclear damage compensation. The nuclear damage compensation system in Japan has been established under the Law Concerning Compensation for Nuclear Damages and the Law Concerning Contract for Compensation for Nuclear Damages. The former law requires the nuclear power plant operators to set up a reserve for damage compensation to ensure positive and quick payment of compensation in the event of an accident. The reserve is currently rely on liability insurance and a government compensation contract. The Working Group has concluded that the total reserve should be increased from the current yen10 bill. to yen30 bill. The amount of the reserve specified in the enforcement law for the Law Concerning Compensation for Nuclear Damages should also be increased accordingly. The Law Concerning compensation for Nuclear damage will also be applied to damage which occurs overseas as a result of an accident in Japan. (N.K.)

  1. Predictors of Energy Compensation during Exercise Interventions: A Systematic Review

    Directory of Open Access Journals (Sweden)

    Marie-Ève Riou

    2015-05-01

    Full Text Available Weight loss from exercise-induced energy deficits is usually less than expected. The objective of this systematic review was to investigate predictors of energy compensation, which is defined as body energy changes (fat mass and fat-free mass over the total amount of exercise energy expenditure. A search was conducted in multiple databases without date limits. Of 4745 studies found, 61 were included in this systematic review with a total of 928 subjects. The overall mean energy compensation was 18% ± 93%. The analyses indicated that 48% of the variance of energy compensation is explained by the interaction between initial fat mass, age and duration of exercise interventions. Sex, frequency, intensity and dose of exercise energy expenditure were not significant predictors of energy compensation. The fitted model suggested that for a shorter study duration, lower energy compensation was observed in younger individuals with higher initial fat mass (FM. In contrast, higher energy compensation was noted for younger individuals with lower initial FM. From 25 weeks onward, energy compensation was no longer different for these predictors. For studies of longer duration (about 80 weeks, the energy compensation approached 84%. Lower energy compensation occurs with short-term exercise, and a much higher level of energy compensation accompanies long-term exercise interventions.

  2. The focal adhesion-associated proteins DOCK5 and GIT2 comprise a rheostat in control of epithelial invasion

    DEFF Research Database (Denmark)

    Frank, Scott R; Köllmann, C P; van Lidth de Jeude, J F

    2017-01-01

    protrusions and nascent cell-substratum adhesions. We further demonstrate that GIT2 inhibits the interaction of DOCK5 with Crk. Moreover, we show that depletion of GIT2 promotes DOCK5-dependent activation of the Crk-p130Cas signaling cascade to promote Rac1-mediated lamellipodial protrusion and FA turnover...

  3. 18 CFR 1304.206 - Requirements for community docks, piers, boathouses, or other water-use facilities.

    Science.gov (United States)

    2010-04-01

    ... community docks, piers, boathouses, or other water-use facilities. 1304.206 Section 1304.206 Conservation of....206 Requirements for community docks, piers, boathouses, or other water-use facilities. (a) Community facilities where individual facilities are not allowed: (1) TVA may limit water-use facilities to community...

  4. A Multidomain Flexible Docking Approach to Deal with Large Conformational Changes in the Modeling of Biomolecular Complexes

    NARCIS (Netherlands)

    Karaca, E.|info:eu-repo/dai/nl/315554789; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238

    2011-01-01

    Binding-induced backbone and large-scale conformational changes represent one of the major challenges in the modeling of biomolecular complexes by docking. To address this challenge, we have developed a flexible multidomain docking protocol that follows a “divide-and-conquer” approach to model both

  5. HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.

    Science.gov (United States)

    Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong; Huang, Sheng-You

    2017-07-03

    Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. 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.

  7. Instability of compensated beam-beam collisions

    International Nuclear Information System (INIS)

    Rosenzweig, J.B.; Autin, B.; Chen, Pisin.

    1989-01-01

    The beam-beam disruption phenomena in linear colliders are increasingly seen as a source of serious problems for these machines. A plasma compensation scheme, in which the motion of the plasma electrons in the presence of the colliding beams provides neutralizing charge and current densities, has been proposed and studied. But natural alternative to this scheme is to consider the overlapping of nearly identical high energy e + and e/sup /minus// bunches, and the collision of two such pairs - in other words, collision of two opposing relativistic positronium plasmas. It should be noticed that while the luminosity for all collisions is increased by a factor of four in this scheme, the event rate for e + e/sup /minus// collisions is only increased by a factor of two. The other factor of two corresponds to the addition of e + e + and e/sup /minus//e/sup /minus// collisions to the interaction point. This beam compensation scheme, which has been examined through computer simulation by Balakin and Solyak in the Soviet Union, promises full neutralization of beam charges and currents. These numerical investigations have shown that plasma instabilities exist in this nominally neutral system. Although the implementation of this idea seems technically daunting, the potential benefits (beamstrahlung and disruption suppression, relaxation of final focus system constraints) are such that we should consider the physics of these collisions further. In the remainder of this paper, we theoretically analyze the issues of stability and bunch parameter tolerances in this scheme. 11 refs

  8. Modelling, Measuring and Compensating Color Weak Vision.

    Science.gov (United States)

    Oshima, Satoshi; Mochizuki, Rika; Lenz, Reiner; Chao, Jinhui

    2016-03-08

    We use methods from Riemann geometry to investigate transformations between the color spaces of color-normal and color weak observers. The two main applications are the simulation of the perception of a color weak observer for a color normal observer and the compensation of color images in a way that a color weak observer has approximately the same perception as a color normal observer. The metrics in the color spaces of interest are characterized with the help of ellipsoids defined by the just-noticable-differences between color which are measured with the help of color-matching experiments. The constructed mappings are isometries of Riemann spaces that preserve the perceived color-differences for both observers. Among the two approaches to build such an isometry, we introduce normal coordinates in Riemann spaces as a tool to construct a global color-weak compensation map. Compared to previously used methods this method is free from approximation errors due to local linearizations and it avoids the problem of shifting locations of the origin of the local coordinate system. We analyse the variations of the Riemann metrics for different observers obtained from new color matching experiments and describe three variations of the basic method. The performance of the methods is evaluated with the help of semantic differential (SD) tests.

  9. Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design.

    Science.gov (United States)

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

    2018-01-01

    Docking simulations help us understand molecular interactions. Here we present a hands-on tutorial to utilize FlexAID (Flexible Artificial Intelligence Docking), an open source molecular docking software between ligands such as small molecules or peptides and macromolecules such as proteins and nucleic acids. The tutorial uses the NRGsuite PyMOL plugin graphical user interface to set up and visualize docking simulations in real time as well as detect and refine target cavities. The ease of use of FlexAID and the NRGsuite combined with its superior performance relative to widely used docking software provides nonexperts with an important tool to understand molecular interactions with direct applications in structure-based drug design and virtual high-throughput screening.

  10. Performance of a docking/molecular dynamics protocol for virtual screening of nutlin-class inhibitors of Mdmx.

    Science.gov (United States)

    Bharatham, Nagakumar; Finch, Kristin E; Min, Jaeki; Mayasundari, Anand; Dyer, Michael A; Guy, R Kiplin; Bashford, Donald

    2017-06-01

    A virtual screening protocol involving docking and molecular dynamics has been tested against the results of fluorescence polarization assays testing the potency of a series of compounds of the nutlin class for inhibition of the interaction between p53 and Mdmx, an interaction identified as a driver of certain cancers. The protocol uses a standard docking method (AutoDock) with a cutoff based on the AutoDock score (ADscore), followed by molecular dynamics simulation with a cutoff based on root-mean-square-deviation (RMSD) from the docked pose. An analysis of the experimental and computational results shows modest performance of ADscore alone, but dramatically improved performance when RMSD is also used. Published by Elsevier Inc.

  11. Analysis of car-following model with cascade compensation strategy

    Science.gov (United States)

    Zhu, Wen-Xing; Zhang, Li-Dong

    2016-05-01

    Cascade compensation mechanism was designed to improve the dynamical performance of traffic flow system. Two compensation methods were used to study unit step response in time domain and frequency characteristics with different parameters. The overshoot and phase margins are proportional to the compensation parameter in an underdamped condition. Through the comparison we choose the phase-lead compensation method as the main strategy in suppressing the traffic jam. The simulations were conducted under two boundary conditions to verify the validity of the compensator. The conclusion can be drawn that the stability of the system is strengthened with increased phase-lead compensation parameter. Moreover, the numerical simulation results are in good agreement with analytical results.

  12. Theoretical Study of Watershed Eco-Compensation Standards

    Science.gov (United States)

    Yan, Dandan; Fu, Yicheng; Liu, Biu; Sha, Jinxia

    2018-01-01

    Watershed eco-compensation is an effective way to solve conflicts over water allocation and ecological destruction problems in the exploitation of water resources. Despite an increasing interest in the topic, the researches has neglected the effect of water quality and lacked systematic calculation method. In this study we reviewed and analyzed the current literature and proposedatheoretical framework to improve the calculation of co-compensation standard.Considering the perspectives of the river ecosystems, forest ecosystems and wetland ecosystems, the benefit compensation standard was determined by the input-output corresponding relationship. Based on the opportunity costs related to limiting development and water conservation loss, the eco-compensation standard was calculated.In order to eliminate the defects of eco-compensation implementation, the improvement suggestions were proposed for the compensation standard calculation and implementation.

  13. Fringe Benefits Compensation of Real Estate Agents and Brokers

    OpenAIRE

    Daniel T. Winkler; W. Keener Hughen

    2012-01-01

    Fringe benefits compensation offered by employers has grown rapidly over the past 50 years. Research in this area has been primarily limited to hourly and salaried employees. This study examines employer-based fringe benefits compensation of real estate agents and brokers. A model is developed that jointly estimates the income, hours worked, and fringe benefits compensation. The findings indicate that fringe benefits increase according to hours worked and the sales professional¡¦s contributio...

  14. The compensation culture: cliché or cause for concern?

    OpenAIRE

    Hand, James

    2010-01-01

    The 'compensation culture' has featured frequently in the popular press over the last decade. There have, however, been comparatively few academic studies and such studies as there have been have largely focused on personal injury claims. A compensation culture, if it exists, could extend much wider than that. This article compares the exponential increase in the use of the term `compensation culture' in the national printed media since 1995 with available statistics relating to the Queen's B...

  15. The compensation culture: cliché or cause for concern?

    OpenAIRE

    Hand, James

    2010-01-01

    The 'compensation culture' has featured frequently in the popular press over the last decade. There have, however, been comparatively few academic studies and such studies as there have been have largely focused on personal injury claims. A compensation culture, if it exists, could extend much wider than that. This article compares the exponential increase in the use of the term 'compensation culture' in the national printed media since 1995 with available statistics relating to the Queen's B...

  16. Error Analysis and Compensation Method Of 6-axis Industrial Robot

    OpenAIRE

    Zhang, Jianhao; Cai, Jinda

    2017-01-01

    A method of compensation is proposed based on the error model with the robot's parameters of kinematic structure and the joint angle. Using the robot kinematics equation depending on D-H algorithm, a kinematic error model is deduced relative to the end actuator of the robot, a comprehensive compensation method of kinematic parameters' error by mapping structural parameters to the joint angular parameter is proposed. In order to solve the angular error problem in the compensation process of ea...

  17. Enthalpy?entropy compensation: the role of solvation

    OpenAIRE

    Dragan, Anatoliy I.; Read, Christopher M.; Crane-Robinson, Colyn

    2016-01-01

    Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy-entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e. a compensating conformational entropy reduct...

  18. Adaptive Beam Loading Compensation in Room Temperature Bunching Cavities

    Energy Technology Data Exchange (ETDEWEB)

    Edelen, J. P. [Fermilab; Chase, B. E. [Fermilab; Cullerton, E. [Fermilab; Varghese, P. [Fermilab

    2017-10-01

    In this paper we present the design, simulation, and proof of principle results of an optimization based adaptive feedforward algorithm for beam-loading compensation in a high impedance room temperature cavity. We begin with an overview of prior developments in beam loading compensation. Then we discuss different techniques for adaptive beam loading compensation and why the use of Newton?s Method is of interest for this application. This is followed by simulation and initial experimental results of this method.

  19. Forest ecosystem services and eco-compensation mechanisms in China.

    Science.gov (United States)

    Deng, Hongbing; Zheng, Peng; Liu, Tianxing; Liu, Xin

    2011-12-01

    Forests are a major terrestrial ecosystem providing multiple ecosystem services. However, the importance of forests is frequently underestimated from an economic perspective because of the externalities and public good properties of these services. Forest eco-compensation is a transfer mechanism that serves to internalize the externalities of forest ecosystem services by compensating individuals or companies for the losses or costs resulting from the provision of these services. China's current forest eco-compensation system is centered mainly on noncommercial forest. The primary measures associated with ecosystem services are (1) a charge on destructive activities, such as indiscriminate logging, and (2) compensation for individual or local activities and investments in forest conservation. The Compensation Fund System for Forest Ecological Benefits was first listed in the Forest Law of the People's Republic of China in 1998. In 2004, the Central Government Financial Compensation Fund, an important source for the Compensation Fund for Forest Ecological Benefits, was formally established. To improve the forest eco-compensation system, it is crucial to design and establish compensation criteria for noncommercial forests. These criteria should take both theoretical and practical concerns into account, and they should be based on the quantitative valuation of ecosystem services. Although some initial headway has been made on this task, the implementation of an effective forest eco-compensation system in China still has deficiencies and still faces problems. Implementing classification-based and dynamic management for key noncommercial forests and establishing an eco-compensation mechanism with multiple funding sources in the market economy are the key measures needed to conquer these problems and improve the forest eco-compensation system and China's forestry development in sequence.

  20. Direct correlation between potentiometric and impedance biosensing of antibody-antigen interactions using an integrated system

    Science.gov (United States)

    Tsai, Meng-Yen; Creedon, Niamh; Brightbill, Eleanor; Pavlidis, Spyridon; Brown, Billyde; Gray, Darren W.; Shields, Niall; Sayers, Ríona; Mooney, Mark H.; O'Riordan, Alan; Vogel, Eric M.

    2017-08-01

    A fully integrated system that combines extended gate field-effect transistor (EGFET)-based potentiometric biosensors and electrochemical impedance spectroscopy (EIS)-based biosensors has been demonstrated. This integrated configuration enables the sequential measurement of the same immunological binding event on the same sensing surface and consequently sheds light on the fundamental origins of sensing signals produced by FET and EIS biosensors, as well as the correlation between the two. Detection of both the bovine serum albumin (BSA)/anti-BSA model system in buffer solution and bovine parainfluenza antibodies in complex blood plasma samples was demonstrated using the integrated biosensors. Comparison of the EGFET and EIS sensor responses reveals similar dynamic ranges, while equivalent circuit modeling of the EIS response shows that the commonly reported total impedance change (ΔZtotal) is dominated by the change in charge transfer resistance (Rct) rather than surface capacitance (Csurface). Using electrochemical kinetics and the Butler-Volmer equation, we unveil that the surface potential and charge transfer resistance, measured by potentiometric and impedance biosensors, respectively, are, in fact, intrinsically linked. This observation suggests that there is no significant gain in using the FET/EIS integrated system and leads to the demonstration that low-cost EGFET biosensors are sufficient as a detection tool to resolve the charge information of biomolecules for practical sensing applications.

  1. Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms

    OpenAIRE

    Yang, Danlin; Singh, Ajit; Wu, Helen; Kroe-Barrett, Rachel

    2017-01-01

    Label-free optical biosensors are powerful tools in drug discovery for the characterization of biomolecular interactions. In this study, we describe the use of four routinely used biosensor platforms in our laboratory to evaluate the binding affinity and kinetics of ten high-affinity monoclonal antibodies (mAbs) against human proprotein convertase subtilisin kexin type 9 (PCSK9). While both Biacore T100 and ProteOn XPR36 are derived from the well-established Surface Plasmon Resonance (SPR) te...

  2. Extending the throughput of Biacore 4000 biosensor to accelerate kinetic analysis of antibody-antigen interaction.

    Science.gov (United States)

    Kamat, Vishal; Rafique, Ashique

    2017-08-01

    The surface plasmon resonance (SPR) biosensors are being routinely used in different stages of drug discovery and development. However, the lack of high throughput SPR biosensors continues to be a primary bottleneck for the rapid kinetic screening of large panels of monoclonal antibodies (mAbs). To further increase the throughput of the Biacore 4000 biosensor, we have developed three kinetic screening assays to characterize mAb-antigen interactions - (i) 16-mAb capture kinetic, (ii) single cycle kinetic (SCK), and (iii) parallel kinetic (PK). The performance of all three kinetic assays was evaluated by characterizing the binding of kinetically diverse human mAbs to four antigens with molecular weights of 14kD, 29kD, 38kD, and 48kD and binding affinities ranging from 130pM to 200 nM. The binding rate constants measured using all three kinetic assays were reproducible across multiple experiments and correlated with the values generated using the conventional 8-mAb capture kinetic assay on the Biacore 4000 (R 2  > 0.94). Moreover, the 16-mAb capture assay decreased experiment time and analyte consumption by 35% and 50%, respectively. This work illustrates the significance of the 16-mAb capture kinetic, SCK, and PK assays to increase the throughput of Biacore 4000 and to support rapid kinetic screening of mAbs. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  3. MOTIVATION AND COMPENSATION IN HEALTH SYSTEM

    Directory of Open Access Journals (Sweden)

    K. N. Borisov

    2014-01-01

    Full Text Available By the defi nition accepted by WHO, «health» it is not simple absence of an illness, but a condition of full physical, moral, mental and social wellbeing. By this defi nition forms of behavior and a way of life of the people, allowing prolonging the period of active, creative and happy life are meant. Health of each person – the main value for modern society. A crisis state of population as open social system, it is shown by its indignation in reply to stressful infl uences of negative socio-economic factors. It is accompanied by change of a condition of the public health which level refl ects depth of occurring changes. In the conditions of market managing also, the policy in the fi eld of compensation, material encouragement and social support of medical workers essentially changes. A certain level of compensation regardless of should be guaranteed to the medical worker, whether mechanisms of economic incentives of its work are used or not. At the same time, the desire of the worker to hold a position with higher salary and desire to work on it is productive and is qualitative – far not same. Increase of material compensation not always leads to increase of labor motivation and aspiration it is better to work. Socially psychological bases of labor motivation of medical workers are those new approaches that will allow solving problems of increase of labor motivation more eff ectively. In article the assessment of labor motivation is analyzed by medical workers, measures for increase of labor motivation and according to improvement of quality of medical care are off ered. The majority of the western experts ineffi ciency of management recognize as the main problem of health care ofRussia. The conclusion that medical institutes, academies and institutes of a post degree obrazoyovaniye, professional development faculties, and, probably, and institutes an upravleyoniya, should adapt foreign experience (motivational, conceptual, technological

  4. MOTIVATION AND COMPENSATION IN HEALTH SYSTEM

    Directory of Open Access Journals (Sweden)

    K. N. Borisov

    2015-01-01

    Full Text Available By the definition accepted by WHO, «health» it is not simple absence of an illness, but a condition of full physical, moral, mental and social wellbeing. By this definition forms of behavior and a way of life of the people, allowing prolonging the period of active, creative and happy life are meant. Health of each person – the main value for modern society. A crisis state of population as open social system, it is shown by its indignation in reply to stressful influences of negative socio-economic factors. It is accompanied by change of a condition of the public health which level refl ects depth of occurring changes. In the conditions of market managing also, the policy in the field of compensation, material encouragement and social support of medical workers essentially changes. A certain level of compensation regardless of should be guaranteed to the medical worker, whether mechanisms of economic incentives of its work are used or not. At the same time, the desire of the worker to hold a position with higher salary and desire to work on it is productive and is qualitative – far not same. Increase of material compensation not always leads to increase of labor motivation and aspiration it is better to work. Socially psychological bases of labor motivation of medical workers are those new approaches that will allow solving problems of increase of labor motivation more effectively. In article the assessment of labor motivation is analyzed by medical workers, measures for increase of labor motivation and according to improvement of quality of medical care are off ered. The majority of the western experts inefficiency of management recognize as the main problem of health care ofRussia. The conclusion that medical institutes, academies and institutes of a post degree obrazoyovaniye, professional development faculties, and, probably, and institutes an upravleyoniya, should adapt foreign experience (motivational, conceptual, technological and

  5. Secondary control for voltage unbalance compensation in an islanded microgrid

    DEFF Research Database (Denmark)

    Savaghebi, Mehdi; Guerrero, Josep M.; Jalilian, Alireza

    2011-01-01

    In this paper, the concept of secondary control is applied for voltage unbalance compensation in an islanded microgrid. The aim of the proposed control approach is to enhance the voltage quality at the point of common coupling (PCC). Unbalance compensation is achieved by proper control of distrib......In this paper, the concept of secondary control is applied for voltage unbalance compensation in an islanded microgrid. The aim of the proposed control approach is to enhance the voltage quality at the point of common coupling (PCC). Unbalance compensation is achieved by proper control...

  6. Research on the Mechanism of Cross Regional Grassland Ecological Compensation

    Science.gov (United States)

    Yang, Ran; Ma, Jun

    2018-01-01

    In recent years, grassland environmental damage has become serious, and grassland resources protection task has become heavy, grassland ecological compensation has become an effective way to solve this problem; but the current grassland ecological compensation standards were low, the effect is poor. The fundamental reason is the model of administrative division destroys the integrity of grassland. Based on the analysis of the status quo of grassland compensation, this paper tries to protect the grassland integrity, breaks the administrative division restriction, implements the space regulation, constructs the framework of cross-regional grassland ecological compensation mechanism, describes its operation process. It provides new way to realize the sustainable development of the grassland environment.

  7. A Novel Time-Varying Friction Compensation Method for Servomechanism

    Directory of Open Access Journals (Sweden)

    Bin Feng

    2015-01-01

    Full Text Available Friction is an inevitable nonlinear phenomenon existing in servomechanisms. Friction errors often affect their motion and contour accuracies during the reverse motion. To reduce friction errors, a novel time-varying friction compensation method is proposed to solve the problem that the traditional friction compensation methods hardly deal with. This problem leads to an unsatisfactory friction compensation performance and the motion and contour accuracies cannot be maintained effectively. In this method, a trapezoidal compensation pulse is adopted to compensate for the friction errors. A generalized regression neural network algorithm is used to generate the optimal pulse amplitude function. The optimal pulse duration function and the pulse amplitude function can be established by the pulse characteristic parameter learning and then the optimal friction compensation pulse can be generated. The feasibility of friction compensation method was verified on a high-precision X-Y worktable. The experimental results indicated that the motion and contour accuracies were improved greatly with reduction of the friction errors, in different working conditions. Moreover, the overall friction compensation performance indicators were decreased by more than 54% and this friction compensation method can be implemented easily on most of servomechanisms in industry.

  8. Recycler model magnet test on temperature compensation for strontium ferrite

    International Nuclear Information System (INIS)

    Yamada, R.; Foster, W.; Ostiguy, F.; Wake, M.

    1995-10-01

    The Recycler ring magnet will be made of Strontium ferrite permanent magnets. A strontium ferrite permanent magnet without compensation has a temperature coefficient of -0.2 % in dB/dT. To compensate this effect, we are utilizing 30 % Ni 70 % Fe alloy, a temperature compensation ferromagnetic material with a low Curie point. To search for optimum commercially available material and optimum condition, we made a couple of simple model magnets, and tested with several different compensating material. The test results are reported and its optimal conditions are shown. Several different configurations were tested including a possible 2 kG magnet configuration

  9. A framework of psychological compensation in attention deficit hyperactivity disorder.

    Science.gov (United States)

    Merkt, Julia; Reinelt, Tilman; Petermann, Franz

    2015-01-01

    The term compensation is widely used in the context of attention deficit hyperactivity disorder (ADHD), yet, it is neither defined nor theory driven. Adapting a model of psychological compensation (Bäckman and Dixon, 1992) to fit ADHD research is the aim of this review: we will (1) introduce the existing theoretical framework of psychological compensation, (2) discuss its applicability to ADHD and adapt the model to fit ADHD research, and (3) set up requirements for research on psychological compensation in ADHD. According to the framework psychological compensation can be inferred if a deficit (i.e., a mismatch between skill and environmental demand) is counterbalanced by the investment of more effort, the utilization of latent skills, or the acquisition of new skills. The framework has to be adapted because ADHD deficits are developmental and in individuals with ADHD compensation can appear independent of awareness of the deficit. A better understanding of psychological compensation in ADHD could foster diagnosis and interventions. Therefore, we suggest that future studies should follow a research design incorporating independent measures of deficit, compensation, and outcome as well as include individuals who compensate for their ADHD related deficits.

  10. A framework of psychological compensation in attention deficit hyperactivity disorder

    Directory of Open Access Journals (Sweden)

    Julia eMerkt

    2015-10-01

    Full Text Available The term compensation is widely used in the context of Attention Deficit Hyperactivity Disorder (ADHD, yet, it is neither defined nor theory driven. Adapting a model of psychological compensation (Bäckman and Dixon, 1992 to fit ADHD research is the aim of this review: We will (1 introduce the existing theoretical framework of psychological compensation, (2 discuss its applicability to ADHD and adapt the model to fit ADHD research, and (3 set up requirements for research on psychological compensation in ADHD. According to the framework psychological compensation can be inferred if a deficit (i.e., a mismatch between skill and environmental demand is counterbalanced by the investment of more effort, the utilization of latent skills, or the acquisition of new skills. The framework has to be adapted because ADHD deficits are developmental and in individuals with ADHD compensation can appear independent of awareness of the deficit. A better understanding of psychological compensation in ADHD could foster diagnosis and interventions. Therefore, we suggest that future studies should follow a research design incorporating independent measures of deficit, compensation and outcome as well as include individuals who compensate for their ADHD related deficits.

  11. 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.

  12. Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment : Meeting New Challenges

    NARCIS (Netherlands)

    Kufareva, I.; Katritch, V.; Westen, van G.J.P.; Lenselink, E.B.; Overington, J.P.; Participants, of GPCR Dock 2013; Stevens, RC Abagyan R

    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

  13. Simulation of a multi-agent system for autonomous trailer docking

    NARCIS (Netherlands)

    Gerrits, Berry; Mes, Martijn R.K.; Schuur, Peter

    2016-01-01

    This paper presents a simulation model of a generic automated planning and control system for the pick-up and docking of semi-trailers by means of autonomous Yard Tractors (YTs) in a collision- and con flict free environment. To support the planning and control of the YTs, we propose a Multi-Agent

  14. Comparative docking studies of CYP1b1 and its PCG-associated ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    Keywords. CYP1b1; molecular docking; molecular dynamics; oestradiol. Abbreviations used: AA, amino acid; CYP, cytochrome p450; E2, estradiol or oestradiol ; FIR, functionally important region; GA, genetic algorithm; HB, hydrogen bond; HBR, haem-binding region; MD, molecular dynamics; MT, mutant; Nb, non-bonded; ...

  15. Just-in-Time Retail Distribution : A Systems Perspective on Cross-Docking

    NARCIS (Netherlands)

    Buijs, Paul; Danhof, Hans W.; Wortmann, J.(Hans) C.

    2016-01-01

    Cross-docking is a just-in-time strategy for distribution logistics. It is aimed at reducing inventory levels and distribution lead times by creating a seamless flow of products from suppliers to customers. Prior supply chain literature has argued that creating such a seamless product flows requires

  16. Control of industrial robots for hardware-in-the-loop simulation of satellite docking

    Science.gov (United States)

    Ma, Ou; Zebenay, Melak; Boge, Toralf

    2011-06-01

    One of the most challenging and risky missions for spacecraft is to perform Rendezvous and Docking (RvD) autonomously in space. To ensure a safe and reliable operation, such a mission must be carefully designed and thoroughly verified before a real space mission can be launched. This paper describes the impact-contact dynamics simulation capability of a new, robotics-based, hardware-in-the-loop (HIL) RvD simulation facility which uses two industrial robots to simulate 6-DOF dynamic maneuvering of two docking satellites. The facility is capable of physically simulating the final approaching within 25-meter range and the entire docking/capturing process in a satellite on-orbit servicing mission. The paper briefly discusses the difficulties of using industrial robots for HIL contact dynamics simulation and how these problems are solved. Admittance control strategy is proposed to control the robotic system to make the robot dynamically behave like the spacecraft during a physical interception. The control strategy works as an outer loop on the top of the existing control system of the industrial robot and hence, it does not require altering the joint control hardware and software which are inaccessible for an industrial robot. A simulation study has shown that the methodology can accurately simulate the impact-contact dynamics behavior of the spacecraft in a docking operation.

  17. [Screening of anti-aging active ingredients and mechanism analysis based on molecular docking technology].

    Science.gov (United States)

    Du, Ran-Feng; Zhang, Xiao-Hua; Ye, Xiao-Tong; Yu, Wen-Kang; Wang, Yun

    2016-07-01

    Dampness evil is the source of all diseases, which is easy to cause disease and promote aging, while aging could also promote the occurence and development of diseases. In this paper, the relationship between the dampness evil and aging would be discussed, to find the anti-aging active ingredients in traditional Chinese medicine (TCM), and analyze the anti-aging mechanism of dampness eliminating drug. Molecular docking technology was used, with aging-related mammalian target of rapamycin as the docking receptors, and chemical components of Fuling, Sangzhi, Mugua, Yiyiren and Houpo as the docking molecules, to preliminarily screen the anti-aging active ingredients in dampness eliminating drug. Through the comparison with active drugs already on the market (temsirolimus and everolimus), 12 kinds of potential anti-aging active ingredients were found, but their drug gability still needs further study. The docking results showed that various components in the dampness eliminating drug can play anti-aging activities by acting on mammalian target of rapamycin. This result provides a new thought and direction for the method of delaying aging by eliminating dampness. Copyright© by the Chinese Pharmaceutical Association.

  18. 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...

  19. 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

  20. 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

  1. Rendezvous and Docking Strategy for Crewed Segment of the Asteroid Redirect Mission

    Science.gov (United States)

    Hinkel, Heather D.; Cryan, Scott P.; D'Souza, Christopher; Dannemiller, David P.; Brazzel, Jack P.; Condon, Gerald L.; Othon, William L.; Williams, Jacob

    2014-01-01

    This paper will describe the overall rendezvous, proximity operations and docking (RPOD) strategy in support of the Asteroid Redirect Crewed Mission (ARCM), as part of the Asteroid Redirect Mission (ARM). The focus of the paper is on the crewed mission phase of ARM, starting with the establishment of Orion in the Distant Retrograde Orbit (DRO) and ending with docking to the Asteroid Redirect Vechicle (ARV). The paper will detail the sequence of maneuvers required to execute the rendezvous and proximity operations mission phases along with the on-board navigation strategies, including the final approach phase. The trajectories to be considered will include target vehicles in a DRO. The paper will also discuss the sensor requirements for rendezvous and docking and the various trade studies associated with the final sensor selection. Building on the sensor requirements and trade studies, the paper will include a candidate sensor concept of operations, which will drive the selection of the sensor suite; concurrently, it will be driven by higher level requirements on the system, such as crew timeline constraints and vehicle consummables. This paper will address how many of the seemingly competing requirements will have to be addressed to create a complete system and system design. The objective is to determine a sensor suite and trajectories that enable Orion to successfully rendezvous and dock with a target vehicle in trans lunar space. Finally, the paper will report on the status of a NASA action to look for synergy within RPOD, across the crewed and robotic asteroid missions.

  2. Numerical modeling of seawater flow through the flooding system of dry docks

    Directory of Open Access Journals (Sweden)

    A. Najafi-Jilani

    2009-12-01

    Full Text Available Numerical simulations have been carried out on the flooding system of a dry dock in design stage and to be located at the south coasts of Iran. The main goals of the present investigation are to evaluate the flooding time as well as the seawater flow characteristics in the intake channels of the dock. The time dependent upstream and downstream boundary conditions of the flooding system are imposed in the modeling. The upstream boundary condition is imposed in accordance with the tidal fluctuations of sea water level. At the downstream, the gradually rising water surface elevation in the dry dock is described in a transient boundary condition. The numerical results are compared with available laboratory measured data and a good agreement is obtained. The seawater discharge through the flooding system and the required time to filling up the dry dock is determined at the worst case. The water current velocity and pressure on the rigid boundaries are also calculated and discussed.

  3. Exploring the binding site of the human muscarinic M3 receptor: Homology modeling and docking study

    Science.gov (United States)

    Ostopovici, Liliana; Mracec, Maria; Mracec, Mircea; Borota, Ana

    The human muscarinic M3 receptor (hM3) and its interactions with selective agonists and antagonists were investigated by means of combined homology and docking approach. Also, two pharmacophoric models for the hM3 agonist and antagonist binding sites were proposed. The three-dimensional (3D) structure of hM3 receptor was modeled based on the high-resolution X-ray structure of bovine rhodopsin from the Protein Data Bank (PDB). To validate the reliability of the model obtained, the main chain torsion angles phi (?) and psi (?) were examined in a Ramachandran plot, and all omega angles were measured for peptidic bond planarity. The characteristics of the active site, the position, and the orientation of ligands in situ, as well as the binding modes of the representative agonists and antagonists, were analyzed by applying a molecular docking technique using the AutoDock 3.0.5 program. Specific interactions responsible for recognition of the hM3 receptor, like ionic bond formed between protonated amine of the ligands and the Asp3.6 side chain were identified. Structure-reactivity relationships have been explained by analyzing the 3D structure of the hM3 model and the ligand conformations resulted from molecular docking simulation.

  4. 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.

  5. Discovery of potential cholesterol esterase inhibitors using in silico docking studies

    Directory of Open Access Journals (Sweden)

    Thirumalaisamy Sivashanmugam

    2013-08-01

    Full Text Available New drug discovery is considered broadly in terms of two kinds of investiga-tional activities such as exploration and exploitation. This study deals with the evaluation of the cholesterol esterase inhibitory activity of flavonoids apigenin, biochanin, curcumin, diosmetin, epipervilline, glycitein, okanin, rhamnazin and tangeritin using in silico docking studies. In silico docking studies were carried out using AutoDock 4.2, based on the Lamarckian genetic algorithm principle. The results showed that all the selected flavonoids showed binding energy ranging between -7.08 kcal/mol to -5.64 kcal/mol when compared with that of the standard compound gallic acid (-4.11 kcal/mol. Intermolecular energy (-9.13 kcal/mol to -7.09 kcal/mol and inhibition constant (6.48 µM to 73.18 µM of the ligands also coincide with the binding energy. All the selected flavonoids contributed cholesterol esterase inhibitory activity, these molecular docking analyses could lead to the further develop-ment of potent cholesterol esterase inhibitors for the treatment of obesity.

  6. What in silico molecular docking can do for the 'bench-working ...

    Indian Academy of Sciences (India)

    BD http://autodock.scripps.edu/. Free, command line program available for Linux, OSX, Windows, Solaris. A very god graphical user interface is also available from the program developers: AutoDockTools (ADT); it allows the user to select which atoms of the ligand and the protein are able to be joined by a covalent bound.

  7. Application of Numerical Optimization Methods to Perform Molecular Docking on Graphics Processing Units

    Directory of Open Access Journals (Sweden)

    M. A. Farkov

    2014-01-01

    Full Text Available An analysis of numerical optimization methods for solving a problem of molecular docking has been performed. Some additional requirements for optimization methods according to GPU architecture features were specified. A promising method for implementation on GPU was selected. Its implementation was described and performance and accuracy tests were performed.

  8. A Memetic Algorithm for the Vehicle Routing Problem with Cross Docking

    Directory of Open Access Journals (Sweden)

    Sanae Larioui

    2015-11-01

    Full Text Available In this paper we address the VRPCD, in which a set of homogeneous vehicles are used to transport products from the suppliers to customers via a cross-dock. The products can be consolidated at the cross-dock but cannot be stored for very long as the cross-dock does not have long-term inventory-holding capabilities. The objective of the VRPCD is to minimize the total traveled distance while respecting time window constraints of suppliers and customers and a time horizon for the whole transportation operation. Rummaging through all the work of literature on vehicle routing problems with cross-docking, there is no work that considers that customer will receive its requests from several suppliers; this will be the point of innovation of this work. A heuristic and a memetic algorithm are used to solve the problem. The proposed algorithms are implemented and tested on data sets involving up to 200 nodes (customers and suppliers. The first results show that the memetic algorithm can produce high quality solutions.

  9. What in silico molecular docking can do for the 'bench-working ...

    Indian Academy of Sciences (India)

    ... 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.

  10. Data of the molecular dynamics simulations of mutations in the human connexin46 docking interface

    Directory of Open Access Journals (Sweden)

    Patrik Schadzek

    2016-06-01

    The data described here are related to the research article entitled “The cataract related mutation N188T in human connexin46 (hCx46 revealed a critical role for residue N188 in the docking process of gap junction channels” (Schadzek et al., 2015 [1].

  11. Molecular Docking of Enzyme Inhibitors: A Computational Tool for Structure-Based Drug Design

    Science.gov (United States)

    Rudnitskaya, Aleksandra; Torok, Bela; Torok, Marianna

    2010-01-01

    Molecular docking is a frequently used method in structure-based rational drug design. It is used for evaluating the complex formation of small ligands with large biomolecules, predicting the strength of the bonding forces and finding the best geometrical arrangements. The major goal of this advanced undergraduate biochemistry laboratory exercise…

  12. 19 CFR 4.1 - Boarding of vessels; cutter and dock passes.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Boarding of vessels; cutter and dock passes. 4.1... OF THE TREASURY VESSELS IN FOREIGN AND DOMESTIC TRADES Arrival and Entry of Vessels § 4.1 Boarding of... regulations. (4) The master of any vessel shall not authorize the boarding or leaving of his vessel by any...

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

    Indian Academy of Sciences (India)

    WINTEC

    Abstract. The interaction of pres1 region of hepatitis B virus B-cell epitope antigen with specific hepa- titis B neutralizing monoclonal antibody was examined by docking study. We modelled the 3D complex structure of B-cell epitope antigen residues CTTPAQGNSMFPSCCCTKPTDGNCY by homology model- ling and ...

  14. 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.

  15. What in silico molecular docking can do for the 'bench-working ...

    Indian Academy of Sciences (India)

    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 ...

  16. Evaluation of multiple protein docking structures using correctly predicted pairwise subunits

    Directory of Open Access Journals (Sweden)

    Esquivel-Rodríguez Juan

    2012-03-01

    Full Text Available Abstract Background Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development of multiple protein docking methods, it is important to establish a metric for evaluating prediction results in a reasonable and practical fashion. However, since there are only few works done in developing methods for multiple protein docking, there is no study that investigates how accurate structural models of multiple protein complexes should be to allow scientists to gain biological insights. Methods We generated a series of predicted models (decoys of various accuracies by our multiple protein docking pipeline, Multi-LZerD, for three multi-chain complexes with 3, 4, and 6 chains. We analyzed the decoys in terms of the number of correctly predicted pair conformations in the decoys. Results and conclusion We found that pairs of chains with the correct mutual orientation exist even in the decoys with a large overall root mean square deviation (RMSD to the native. Therefore, in addition to a global structure similarity measure, such as the global RMSD, the quality of models for multiple chain complexes can be better evaluated by using the local measurement, the number of chain pairs with correct mutual orientation. We termed the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0Å as fpair and propose to use it for evaluation of the accuracy of multiple protein docking.

  17. What in silico molecular docking can do for the 'bench-working ...

    Indian Academy of Sciences (India)

    RB, FL http://www.biosolveit.de/FlexX/. Commercial program available for Linux and Windows, part of the LeadIT software solution. Good user interface. Takes account of the metal coordination. It allows the user to select which atoms of the ligand and the protein are able to be joined by a covalent bound. Dock 6 (Kuntz et al.

  18. Meta-server for automatic analysis, scoring and ranking of docking models.

    Science.gov (United States)

    Anashkina, Anastasia A; Kravatsky, Yuri; Kuznetsov, Eugene; Makarov, Alexander A; Adzhubei, Alexei A

    2017-09-18

    Modelling with multiple servers that use different algorithms for docking results in more reliable predictions of interaction sites. However, the scoring and comparison of all models by an expert is time-consuming and is not feasible for large volumes of data generated by such modelling. QASDOM Server (Quality ASsessment of DOcking Models) is a simple and efficient tool for real-time simultaneous analysis, scoring and ranking of datasets of receptor-ligand complexes built by a range of docking techniques. This meta-server is designed to analyse large datasets of docking models and rank them by scoring criteria developed in this study. It produces two types of output showing the likelihood of specific residues and clusters of residues to be involved in receptor-ligand interactions, and the ranking of models. The server also allows visualising residues that form interaction sites in the receptor and ligand sequence, and displays three-dimensional model structures of the receptor-ligand complexes. http://qasdom.eimb.ru. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  19. The pepATTRACT web server for blind, large-scale peptide-protein docking.

    Science.gov (United States)

    de Vries, Sjoerd J; Rey, Julien; Schindler, Christina E M; Zacharias, Martin; Tuffery, Pierre

    2017-07-03

    Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. In various stages of its development, pepATTRACT has participated in CAPRI, making successful predictions for five out of seven protein-peptide targets. Its performance is similar or better than state-of-the-art local docking protocols that do require binding site information. Here we present a novel web server that carries out the rigid-body stage of pepATTRACT. On the peptiDB benchmark, the web server generates a correct model in the top 50 in 34% of the cases. Compared to the full pepATTRACT protocol, this leads to some loss of performance, but the computation time is reduced from ∼18 h to ∼10 min. Combined with the fact that it is fully blind, this makes the web server well-suited for large-scale in silico protein-peptide docking experiments. The rigid-body pepATTRACT server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Activated Cdc42 kinase regulates Dock localization in male germ cells during Drosophila spermatogenesis.

    Science.gov (United States)

    Abdallah, Abbas M; Zhou, Xin; Kim, Christine; Shah, Kushani K; Hogden, Christopher; Schoenherr, Jessica A; Clemens, James C; Chang, Henry C

    2013-06-15

    Deregulation of the non-receptor tyrosine kinase ACK1 (Activated Cdc42-associated kinase) correlates with poor prognosis in cancers and has been implicated in promoting metastasis. To further understand its in vivo function, we have characterized the developmental defects of a null mutation in Drosophila Ack, which bears a high degree of sequence similarity to mammalian ACK1 but lacks a CRIB domain. We show that Ack, while not essential for viability, is critical for sperm formation. This function depends on Ack tyrosine kinase activity and is required cell autonomously in differentiating male germ cells at or after the spermatocyte stage. Ack associates predominantly with endocytic clathrin sites in spermatocytes, but disruption of Ack function has no apparent effect on clathrin localization and receptor-mediated internalization of Boss (Bride of sevenless) protein in eye discs. Instead, Ack is required for the subcellular distribution of Dock (dreadlocks), the Drosophila homolog of the SH2- and SH3-containing adaptor protein Nck. Moreover, Dock forms a complex with Ack, and the localization of Dock in male germ cells depends on its SH2 domain. Together, our results suggest that Ack-dependent tyrosine phosphorylation recruits Dock to promote sperm differentiation. Copyright © 2013 Elsevier Inc. All rights reserved.