In situ macromolecular crystallography using microbeams.

Science.gov (United States)

Axford, Danny; Owen, Robin L; Aishima, Jun; Foadi, James; Morgan, Ann W; Robinson, James I; Nettleship, Joanne E; Owens, Raymond J; Moraes, Isabel; Fry, Elizabeth E; Grimes, Jonathan M; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S; Stuart, David I; Evans, Gwyndaf

2012-05-01

Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams. © 2012 International Union of Crystallography

Design and application of a C++ macromolecular class library.

Science.gov (United States)

Chang, W; Shindyalov, I N; Pu, C; Bourne, P E

1994-01-01

PDBlib is an extensible object oriented class library written in C++ for representing the 3-dimensional structure of biological macromolecules. PDBlib forms the kernel of a larger software framework being developed for assiting in knowledge discovery from macromolecular structure data. The software design strategy used by PDBlib, how the library may be used and several prototype applications that use the library are summarized. PDBlib represents the structural features of proteins, DNA, RNA, and complexes thereof, at a level of detail on a par with that which can be parsed from a Protein Data Bank (PDB) entry. However, the memory resident representation of the macromolecule is independent of the PDB entry and can be obtained from other back-end data sources, for example, existing relational databases and our own object oriented database (OOPDB) built on top of the commercial object oriented database, ObjectStore. At the front-end are several prototype applications that use the library: Macromolecular Query Language (MMQL) is based on a separate class library (MMQLlib) for building complex queries pertaining to macromolecular structure; PDBtool is an interactive structure verification tool; and PDBview, is a structure rendering tool used either as a standalone tool or as part of another application. Each of these software components are described. All software is available via anonymous ftp from cuhhca.hhmi.columbia.edu.

Assembly and architecture of the EBV B cell entry triggering complex.

Directory of Open Access Journals (Sweden)

Karthik Sathiyamoorthy

2014-08-01

Full Text Available Epstein-Barr Virus (EBV is an enveloped double-stranded DNA virus of the gammaherpesvirinae sub-family that predominantly infects humans through epithelial cells and B cells. Three EBV glycoproteins, gH, gL and gp42, form a complex that targets EBV infection of B cells. Human leukocyte antigen (HLA class II molecules expressed on B cells serve as the receptor for gp42, triggering membrane fusion and virus entry. The mechanistic role of gHgL in herpesvirus entry has been largely unresolved, but it is thought to regulate the activation of the virally-encoded gB protein, which acts as the primary fusogen. Here we study the assembly and function of the reconstituted B cell entry complex comprised of gHgL, gp42 and HLA class II. The structure from negative-stain electron microscopy provides a detailed snapshot of an intermediate state in EBV entry and highlights the potential for the triggering complex to bring the two membrane bilayers into proximity. Furthermore, gHgL interacts with a previously identified, functionally important hydrophobic pocket on gp42, defining the overall architecture of the complex and playing a critical role in membrane fusion activation. We propose a macroscopic model of the initiating events in EBV B cell fusion centered on the formation of the triggering complex in the context of both viral and host membranes. This model suggests how the triggering complex may bridge the two membrane bilayers, orienting critical regions of the N- and C- terminal ends of gHgL to promote the activation of gB and efficient membrane fusion.

Isotope labeling for NMR studies of macromolecular structure and interactions

International Nuclear Information System (INIS)

Wright, P.E.

1994-01-01

Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform 13 C, 15 N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific 13 C and 15 N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions

Isotope labeling for NMR studies of macromolecular structure and interactions

Energy Technology Data Exchange (ETDEWEB)

Wright, P.E. [Scripps Research Institute, La Jolla, CA (United States)

1994-12-01

Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

In situ macromolecular crystallography using microbeams

International Nuclear Information System (INIS)

Axford, Danny; Owen, Robin L.; Aishima, Jun; Foadi, James; Morgan, Ann W.; Robinson, James I.; Nettleship, Joanne E.; Owens, Raymond J.; Moraes, Isabel; Fry, Elizabeth E.; Grimes, Jonathan M.; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S.; Stuart, David I.; Evans, Gwyndaf

2012-01-01

A sample environment for mounting crystallization trays has been developed on the microfocus beamline I24 at Diamond Light Source. The technical developments and several case studies are described. Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams

In situ macromolecular crystallography using microbeams

Energy Technology Data Exchange (ETDEWEB)

Axford, Danny; Owen, Robin L.; Aishima, Jun [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Morgan, Ann W.; Robinson, James I. [University of Leeds, Leeds LS9 7FT (United Kingdom); Nettleship, Joanne E.; Owens, Raymond J. [Research Complex at Harwell, Rutherford Appleton Laboratory R92, Didcot, Oxfordshire OX11 0DE (United Kingdom); Moraes, Isabel [Imperial College, London SW7 2AZ (United Kingdom); Fry, Elizabeth E.; Grimes, Jonathan M.; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S. [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Stuart, David I. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom)

2012-04-17

A sample environment for mounting crystallization trays has been developed on the microfocus beamline I24 at Diamond Light Source. The technical developments and several case studies are described. Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams.

ComplexViewer: visualization of curated macromolecular complexes.

Science.gov (United States)

Combe, Colin W; Sivade, Marine Dumousseau; Hermjakob, Henning; Heimbach, Joshua; Meldal, Birgit H M; Micklem, Gos; Orchard, Sandra; Rappsilber, Juri

2017-11-15

Proteins frequently function as parts of complexes, assemblages of multiple proteins and other biomolecules, yet network visualizations usually only show proteins as parts of binary interactions. ComplexViewer visualizes interactions with more than two participants and thereby avoids the need to first expand these into multiple binary interactions. Furthermore, if binding regions between molecules are known then these can be displayed in the context of the larger complex. freely available under Apache version 2 license; EMBL-EBI Complex Portal: http://www.ebi.ac.uk/complexportal; Source code: https://github.com/MICommunity/ComplexViewer; Package: https://www.npmjs.com/package/complexviewer; http://biojs.io/d/complexviewer. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js. colin.combe@ed.ac.uk or juri.rappsilber@ed.ac.uk. © The Author 2017. Published by Oxford University Press.

Practical macromolecular cryocrystallography

Energy Technology Data Exchange (ETDEWEB)

Pflugrath, J. W., E-mail: jim.pflugrath@gmail.com [Rigaku Americas Corp., 9009 New Trails Drive, The Woodlands, TX 77381 (United States)

2015-05-27

Current methods, reagents and experimental hardware for successfully and reproducibly flash-cooling macromolecular crystals to cryogenic temperatures for X-ray diffraction data collection are reviewed. Cryocrystallography is an indispensable technique that is routinely used for single-crystal X-ray diffraction data collection at temperatures near 100 K, where radiation damage is mitigated. Modern procedures and tools to cryoprotect and rapidly cool macromolecular crystals with a significant solvent fraction to below the glass-transition phase of water are reviewed. Reagents and methods to help prevent the stresses that damage crystals when flash-cooling are described. A method of using isopentane to assess whether cryogenic temperatures have been preserved when dismounting screened crystals is also presented.

The Joint Structural Biology Group beam lines at the ESRF: Modern macromolecular crystallography

CERN Document Server

Mitchell, E P

2001-01-01

Macromolecular crystallography has evolved considerably over the last decade. Data sets in under an hour are now possible on high throughput beam lines leading to electron density and, possibly, initial models calculated on-site. There are five beam lines currently dedicated to macromolecular crystallography: the ID14 complex and BM-14 (soon to be superseded by ID-29). These lines handle over five hundred projects every six months and demand is increasing. Automated sample handling, alignment and data management protocols will be required to work efficiently with this demanding load. Projects developing these themes are underway within the JSBG.

Macromolecular crystallography using synchrotron radiation

International Nuclear Information System (INIS)

Bartunik, H.D.; Phillips, J.C.; Fourme, R.

1982-01-01

The use of synchrotron X-ray sources in macromolecular crystallography is described. The properties of synchrotron radiation relevant to macromolecular crystallography are examined. The applications discussed include anomalous dispersion techniques, the acquisition of normal and high resolution data, and kinetic studies of structural changes in macromolecules; protein data are presented illustrating these applications. The apparatus used is described including information on the electronic detectors, the monitoring of the incident beam and crystal cooling. (U.K.)

Variationally optimal selection of slow coordinates and reaction coordinates in macromolecular systems

Science.gov (United States)

Noe, Frank

To efficiently simulate and generate understanding from simulations of complex macromolecular systems, the concept of slow collective coordinates or reaction coordinates is of fundamental importance. Here we will introduce variational approaches to approximate the slow coordinates and the reaction coordinates between selected end-states given MD simulations of the macromolecular system and a (possibly large) basis set of candidate coordinates. We will then discuss how to select physically intuitive order paremeters that are good surrogates of this variationally optimal result. These result can be used in order to construct Markov state models or other models of the stationary and kinetics properties, in order to parametrize low-dimensional / coarse-grained model of the dynamics. Deutsche Forschungsgemeinschaft, European Research Council.

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy.

Science.gov (United States)

Loquet, Antoine; Tolchard, James; Berbon, Melanie; Martinez, Denis; Habenstein, Birgit

2017-09-17

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13 C/ 15 N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

Recent Major Improvements to the ALS Sector 5 Macromolecular Crystallography Beamlines

International Nuclear Information System (INIS)

Morton, Simon A.; Glossinger, James; Smith-Baumann, Alexis; McKean, John P.; Trame, Christine; Dickert, Jeff; Rozales, Anthony; Dauz, Azer; Taylor, John; Zwart, Petrus; Duarte, Robert; Padmore, Howard; McDermott, Gerry; Adams, Paul

2007-01-01

Although the Advanced Light Source (ALS) was initially conceived primarily as a low energy (1.9GeV) 3rd generation source of VUV and soft x-ray radiation it was realized very early in the development of the facility that a multipole wiggler source coupled with high quality, (brightness preserving), optics would result in a beamline whose performance across the optimal energy range (5-15keV) for macromolecular crystallography (MX) would be comparable to, or even exceed, that of many existing crystallography beamlines at higher energy facilities. Hence, starting in 1996, a suite of three beamlines, branching off a single wiggler source, was constructed, which together formed the ALS Macromolecular Crystallography Facility. From the outset this facility was designed to cater equally to the needs of both academic and industrial users with a heavy emphasis placed on the development and introduction of high throughput crystallographic tools, techniques, and facilities--such as large area CCD detectors, robotic sample handling and automounting facilities, a service crystallography program, and a tightly integrated, centralized, and highly automated beamline control environment for users. This facility was immediately successful, with the primary Multiwavelength Anomalous Diffraction beamline (5.0.2) in particular rapidly becoming one of the foremost crystallographic facilities in the US--responsible for structures such as the 70S ribosome. This success in-turn triggered enormous growth of the ALS macromolecular crystallography community and spurred the development of five additional ALS MX beamlines all utilizing the newly developed superconducting bending magnets ('superbends') as sources. However in the years since the original Sector 5.0 beamlines were built the performance demands of macromolecular crystallography users have become ever more exacting; with growing emphasis placed on studying larger complexes, more difficult structures, weakly diffracting or smaller

Macromolecular crystallization in microgravity

International Nuclear Information System (INIS)

Snell, Edward H; Helliwell, John R

2005-01-01

Density difference fluid flows and sedimentation of growing crystals are greatly reduced when crystallization takes place in a reduced gravity environment. In the case of macromolecular crystallography a crystal of a biological macromolecule is used for diffraction experiments (x-ray or neutron) so as to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal then the greater the molecular structure detail that can be extracted. It is this structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences, with major potential in understanding disease pathologies. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyse the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural advances. Finally, limitations and alternatives to microgravity and future directions for this research are covered. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry and mathematics meet to enable insight to the fundamentals of life. As the reader will see, there is a great deal of physics involved when the microgravity environment is applied to crystallization, some of it known, and undoubtedly much yet to

Sequential recovery of macromolecular components of the nucleolus.

Science.gov (United States)

Bai, Baoyan; Laiho, Marikki

2015-01-01

The nucleolus is involved in a number of cellular processes of importance to cell physiology and pathology, including cell stress responses and malignancies. Studies of macromolecular composition of the nucleolus depend critically on the efficient extraction and accurate quantification of all macromolecular components (e.g., DNA, RNA, and protein). We have developed a TRIzol-based method that efficiently and simultaneously isolates these three macromolecular constituents from the same sample of purified nucleoli. The recovered and solubilized protein can be accurately quantified by the bicinchoninic acid assay and assessed by polyacrylamide gel electrophoresis or by mass spectrometry. We have successfully applied this approach to extract and quantify the responses of all three macromolecular components in nucleoli after drug treatments of HeLa cells, and conducted RNA-Seq analysis of the nucleolar RNA.

The complex portal--an encyclopaedia of macromolecular complexes.

Science.gov (United States)

Meldal, Birgit H M; Forner-Martinez, Oscar; Costanzo, Maria C; Dana, Jose; Demeter, Janos; Dumousseau, Marine; Dwight, Selina S; Gaulton, Anna; Licata, Luana; Melidoni, Anna N; Ricard-Blum, Sylvie; Roechert, Bernd; Skyzypek, Marek S; Tiwari, Manu; Velankar, Sameer; Wong, Edith D; Hermjakob, Henning; Orchard, Sandra

2015-01-01

The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/complex), through which protein complexes from major model organisms are being collated and made available for search, viewing and download. It has been built in close collaboration with other bioinformatics services and populated with data from ChEMBL, MatrixDB, PDBe, Reactome and UniProtKB. Each entry contains information about the participating molecules (including small molecules and nucleic acids), their stoichiometry, topology and structural assembly. Complexes are annotated with details about their function, properties and complex-specific Gene Ontology (GO) terms. Consistent nomenclature is used throughout the resource with systematic names, recommended names and a list of synonyms all provided. The use of the Evidence Code Ontology allows us to indicate for which entries direct experimental evidence is available or if the complex has been inferred based on homology or orthology. The data are searchable using standard identifiers, such as UniProt, ChEBI and GO IDs, protein, gene and complex names or synonyms. This reference resource will be maintained and grow to encompass an increasing number of organisms. Input from groups and individuals with specific areas of expertise is welcome. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

Directory of Open Access Journals (Sweden)

Anthony R Bradley

2017-06-01

Full Text Available Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis.

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm.

Science.gov (United States)

Zhang, Qing; Beard, Daniel A; Schlick, Tamar

2003-12-01

Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye-Hückel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a approximately 5.5% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK

The role of macromolecular stability in desiccation tolerance

NARCIS (Netherlands)

Wolkers, W.F.

1998-01-01

The work presented in this thesis concerns a study on the molecular interactions that play a role in the macromolecular stability of desiccation-tolerant higher plant organs. Fourier transform infrared microspectroscopy was used as the main experimental technique to assess macromolecular

[Macromolecular aromatic network characteristics of Chinese power coal analyzed by synchronous fluorescence and X-ray diffraction].

Science.gov (United States)

Ye, Cui-Ping; Feng, Jie; Li, Wen-Ying

2012-07-01

Coal structure, especially the macromolecular aromatic skeleton structure, has a strong influence on coke reactivity and coal gasification, so it is the key to grasp the macromolecular aromatic skeleton coal structure for getting the reasonable high efficiency utilization of coal. However, it is difficult to acquire their information due to the complex compositions and structure of coal. It has been found that the macromolecular aromatic network coal structure would be most isolated if small molecular of coal was first extracted. Then the macromolecular aromatic skeleton coal structure would be clearly analyzed by instruments, such as X-ray diffraction (XRD), fluorescence spectroscopy with synchronous mode (Syn-F), Gel permeation chromatography (GPC) etc. Based on the previous results, according to the stepwise fractional liquid extraction, two Chinese typical power coals, PS and HDG, were extracted by silica gel as stationary phase and acetonitrile, tetrahydrofuran (THF), pyridine and 1-methyl-2-pyrollidinone (NMP) as a solvent group for sequential elution. GPC, Syn-F and XRD were applied to investigate molecular mass distribution, condensed aromatic structure and crystal characteristics. The results showed that the size of aromatic layers (La) is small (3-3.95 nm) and the stacking heights (Lc) are 0.8-1.2 nm. The molecular mass distribution of the macromolecular aromatic network structure is between 400 and 1 130 amu, with condensed aromatic numbers of 3-7 in the structure units.

Optimizing Water Exchange Rates and Rotational Mobility for High-Relaxivity of a Novel Gd-DO3A Derivative Complex Conjugated to Inulin as Macromolecular Contrast Agents for MRI.

Science.gov (United States)

Granato, Luigi; Vander Elst, Luce; Henoumont, Celine; Muller, Robert N; Laurent, Sophie

2018-02-01

Thanks to the understanding of the relationships between the residence lifetime τ M of the coordinated water molecules to macrocyclic Gd-complexes and the rotational mobility τ R of these structures, and according to the theory for paramagnetic relaxation, it is now possible to design macromolecular contrast agents with enhanced relaxivities by optimizing these two parameters through ligand structural modification. We succeeded in accelerating the water exchange rate by inducing steric compression around the water binding site, and by removing the amide function from the DOTA-AA ligand [1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid mono(p-aminoanilide)] (L) previously designed. This new ligand 10[2(1-oxo-1-p-propylthioureidophenylpropyl]-1,4,7,10-tetraazacyclodecane-1,4,7-tetraacetic acid (L 1 ) was then covalently conjugated to API [O-(aminopropyl)inulin] to get the complex API-(GdL 1 )x with intent to slow down the rotational correlation time (τ R ) of the macromolecular complex. The evaluation of the longitudinal relaxivity at different magnetic fields and the study of the 17 O-NMR at variable temperature of the low-molecular-weight compound (GdL 1 ) showed a slight decrease of the τ M value (τM310 = 331 ns vs. τM310 = 450 ns for the GdL complex). Consequently to the increase of the size of the API-(GdL 1 )x complex, the rotational correlation time becomes about 360 times longer compared to the monomeric GdL 1 complex (τ R  = 33,700 ps), which results in an enhanced proton relaxivity. © 2018 Wiley-VHCA AG, Zurich, Switzerland.

The design of macromolecular crystallography diffraction experiments

International Nuclear Information System (INIS)

Evans, Gwyndaf; Axford, Danny; Owen, Robin L.

2011-01-01

Thoughts about the decisions made in designing macromolecular X-ray crystallography experiments at synchrotron beamlines are presented. The measurement of X-ray diffraction data from macromolecular crystals for the purpose of structure determination is the convergence of two processes: the preparation of diffraction-quality crystal samples on the one hand and the construction and optimization of an X-ray beamline and end station on the other. Like sample preparation, a macromolecular crystallography beamline is geared to obtaining the best possible diffraction measurements from crystals provided by the synchrotron user. This paper describes the thoughts behind an experiment that fully exploits both the sample and the beamline and how these map into everyday decisions that users can and should make when visiting a beamline with their most precious crystals

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

International Nuclear Information System (INIS)

Brockhauser, Sandor; Svensson, Olof; Bowler, Matthew W.; Nanao, Max; Gordon, Elspeth; Leal, Ricardo M. F.; Popov, Alexander; Gerring, Matthew; McCarthy, Andrew A.; Gotz, Andy

2012-01-01

A powerful and easy-to-use workflow environment has been developed at the ESRF for combining experiment control with online data analysis on synchrotron beamlines. This tool provides the possibility of automating complex experiments without the need for expertise in instrumentation control and programming, but rather by accessing defined beamline services. The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE

Macromolecular crystallography beamline X25 at the NSLS

Energy Technology Data Exchange (ETDEWEB)

Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L.; Dvorak, Joseph; Flaks, Leon; LaMarra, Steven; Myers, Stuart F.; Orville, Allen M.; Robinson, Howard H.; Roessler, Christian G.; Schneider, Dieter K.; Shea-McCarthy, Grace; Skinner, John M.; Skinner, Michael; Soares, Alexei S.; Sweet, Robert M.; Berman, Lonny E., E-mail: berman@bnl.gov [Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000 (United States)

2014-04-08

A description of the upgraded beamline X25 at the NSLS, operated by the PXRR and the Photon Sciences Directorate serving the Macromolecular Crystallography community, is presented. Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community.

Macromolecular crystallography beamline X25 at the NSLS

International Nuclear Information System (INIS)

Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L.; Dvorak, Joseph; Flaks, Leon; LaMarra, Steven; Myers, Stuart F.; Orville, Allen M.; Robinson, Howard H.; Roessler, Christian G.; Schneider, Dieter K.; Shea-McCarthy, Grace; Skinner, John M.; Skinner, Michael; Soares, Alexei S.; Sweet, Robert M.; Berman, Lonny E.

2014-01-01

A description of the upgraded beamline X25 at the NSLS, operated by the PXRR and the Photon Sciences Directorate serving the Macromolecular Crystallography community, is presented. Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community

A facile metal-free "grafting-from" route from acrylamide-based substrate toward complex macromolecular combs

KAUST Repository

Zhao, Junpeng

2013-01-01

High-molecular-weight poly(N,N-dimethylacrylamide-co-acrylamide) was used as a model functional substrate to investigate phosphazene base (t-BuP 4)-promoted metal-free anionic graft polymerization utilizing primary amide moieties as initiating sites. The (co)polymerization of epoxides was proven to be effective, leading to macromolecular combs with side chains being single- or double-graft homopolymer, block copolymer and statistical copolymer. © 2013 The Royal Society of Chemistry.

Event-triggered synchronization for reaction-diffusion complex networks via random sampling

Science.gov (United States)

Dong, Tao; Wang, Aijuan; Zhu, Huiyun; Liao, Xiaofeng

2018-04-01

In this paper, the synchronization problem of the reaction-diffusion complex networks (RDCNs) with Dirichlet boundary conditions is considered, where the data is sampled randomly. An event-triggered controller based on the sampled data is proposed, which can reduce the number of controller and the communication load. Under this strategy, the synchronization problem of the diffusion complex network is equivalently converted to the stability of a of reaction-diffusion complex dynamical systems with time delay. By using the matrix inequality technique and Lyapunov method, the synchronization conditions of the RDCNs are derived, which are dependent on the diffusion term. Moreover, it is found the proposed control strategy can get rid of the Zeno behavior naturally. Finally, a numerical example is given to verify the obtained results.

Macromolecular crowding directs extracellular matrix organization and mesenchymal stem cell behavior.

Directory of Open Access Journals (Sweden)

Adam S Zeiger

Full Text Available Microenvironments of biological cells are dominated in vivo by macromolecular crowding and resultant excluded volume effects. This feature is absent in dilute in vitro cell culture. Here, we induced macromolecular crowding in vitro by using synthetic macromolecular globules of nm-scale radius at physiological levels of fractional volume occupancy. We quantified the impact of induced crowding on the extracellular and intracellular protein organization of human mesenchymal stem cells (MSCs via immunocytochemistry, atomic force microscopy (AFM, and AFM-enabled nanoindentation. Macromolecular crowding in extracellular culture media directly induced supramolecular assembly and alignment of extracellular matrix proteins deposited by cells, which in turn increased alignment of the intracellular actin cytoskeleton. The resulting cell-matrix reciprocity further affected adhesion, proliferation, and migration behavior of MSCs. Macromolecular crowding can thus aid the design of more physiologically relevant in vitro studies and devices for MSCs and other cells, by increasing the fidelity between materials synthesized by cells in vivo and in vitro.

Macromolecular crowding directs extracellular matrix organization and mesenchymal stem cell behavior.

Science.gov (United States)

Zeiger, Adam S; Loe, Felicia C; Li, Ran; Raghunath, Michael; Van Vliet, Krystyn J

2012-01-01

Microenvironments of biological cells are dominated in vivo by macromolecular crowding and resultant excluded volume effects. This feature is absent in dilute in vitro cell culture. Here, we induced macromolecular crowding in vitro by using synthetic macromolecular globules of nm-scale radius at physiological levels of fractional volume occupancy. We quantified the impact of induced crowding on the extracellular and intracellular protein organization of human mesenchymal stem cells (MSCs) via immunocytochemistry, atomic force microscopy (AFM), and AFM-enabled nanoindentation. Macromolecular crowding in extracellular culture media directly induced supramolecular assembly and alignment of extracellular matrix proteins deposited by cells, which in turn increased alignment of the intracellular actin cytoskeleton. The resulting cell-matrix reciprocity further affected adhesion, proliferation, and migration behavior of MSCs. Macromolecular crowding can thus aid the design of more physiologically relevant in vitro studies and devices for MSCs and other cells, by increasing the fidelity between materials synthesized by cells in vivo and in vitro.

50th Anniversary Perspective: Polymers with Complex Architectures

KAUST Repository

Polymeropoulos, George

2017-02-09

The scope of this Perspective is to highlight innovative contributions in the synthesis of well-defined complex macromolecular architectures and to emphasize the importance of these materials to polymer physical chemistry, physics, theory, and applications. In addition, this Perspective tries to enlighten the past and show possible pathways for the future. Among the plethora of polymerization methods, we briefly report the impact of the truly living and controlled/living polymerization techniques focusing mainly on anionic polymerization, the mother of all living and controlled/living polymerizations. Through anionic polymerization well-defined model polymers with complex macromolecular architectures having the highest molecular weight, structural and compositional homogeneity can be achieved. The synthesized structures include star, comb/graft, cyclic, branched and hyberbranched, dendritic, and multiblock multicomponent polymers. In our opinion, in addition to the work needed on the synthesis, properties, and application of copolymers with more than three chemically different blocks and complex architecture, the polymer chemists in the future should follow closer the approaches Nature, the perfect chemist, uses to make functional complex macromolecular structures by noncovalent chemistry. Moreover, development of new analytical methods for the characterization/purification of polymers with complex macromolecular architectures is essential for the synthesis and properties study of this family of polymeric materials.

Nitrogen isotopic composition of macromolecular organic matter in interplanetary dust particles

Science.gov (United States)

Aléon, Jérôme; Robert, François; Chaussidon, Marc; Marty, Bernard

2003-10-01

Nitrogen concentrations and isotopic compositions were measured by ion microprobe scanning imaging in two interplanetary dust particles L2021 K1 and L2036 E22, in which imaging of D/H and C/H ratios has previously evidenced the presence of D-rich macromolecular organic components. High nitrogen concentrations of 10-20 wt% and δ 15N values up to +400‰ are observed in these D-rich macromolecular components. The previous study of D/H and C/H ratios has revealed three different D-rich macromolecular phases. The one previously ascribed to macromolecular organic matter akin the insoluble organic matter (IOM) from carbonaceous chondrites is enriched in nitrogen by one order of magnitude compared to the carbonaceous chondrite IOM, although its isotopic composition is still similar to what is known from Renazzo (δ 15N = +208‰). The correlation observed in macromolecular organic material between the D- and 15N-excesses suggests that the latter originate probably from chemical reactions typical of the cold interstellar medium. These interstellar materials preserved to some extent in IDPs are therefore macromolecular organic components with various aliphaticity and aromaticity. They are heavily N-heterosubstituted as shown by their high nitrogen concentrations >10 wt%. They have high D/H ratios >10 -3 and δ 15N values ≥ +400‰. In L2021 K1 a mixture is observed at the micron scale between interstellar and chondritic-like organic phases. This indicates that some IDPs contain organic materials processed at various heliocentric distances in a turbulent nebula. Comparison with observation in comets suggests that these molecules may be cometary macromolecules. A correlation is observed between the D/H ratios and δ 15N values of macromolecular organic matter from IDPs, meteorites, the Earth and of major nebular reservoirs. This suggests that most macromolecular organic matter in the inner solar system was probably issued from interstellar precursors and further processed

A saponification-triggered gelation of ester-based Zn(II) complex through conformational transformations.

Science.gov (United States)

Kumar, Ashish; Dubey, Mrigendra; Kumar, Amit; Pandey, Daya Shankar

2014-09-11

Novel saponification-triggered gelation in an ester-based bis-salen Zn(II) complex (1) is described. Strategic structural modifications induced by NaOH in 1 tune the dipolar-/π-interactions leading to J-aggregation and the creation of an inorganic gel material (IGM), which has been established by photophysical, DFT and rheological studies.

Analytical model for macromolecular partitioning during yeast cell division

International Nuclear Information System (INIS)

Kinkhabwala, Ali; Khmelinskii, Anton; Knop, Michael

2014-01-01

Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partitioning of the macromolecular content of the parent cell — which includes proteins, DNA, RNA, large proteinaceous assemblies and organelles — can be achieved by both passive (e.g. diffusion, localized retention sites) and active (e.g. motor-driven transport) processes operating in the presence of external polarity cues, internal asymmetries, spontaneous symmetry breaking, or stochastic effects. However, the quantitative contribution of different processes to the partitioning of macromolecular content is difficult to evaluate. Here we developed an analytical model that allows rapid quantitative assessment of partitioning as a function of various parameters in the budding yeast Saccharomyces cerevisiae. This model exposes quantitative degeneracies among the physical parameters that govern macromolecular partitioning, and reveals regions of the solution space where diffusion is sufficient to drive asymmetric partitioning and regions where asymmetric partitioning can only be achieved through additional processes such as motor-driven transport. Application of the model to different macromolecular assemblies suggests that partitioning of protein aggregates and episomes, but not prions, is diffusion-limited in yeast, consistent with previous reports. In contrast to computationally intensive stochastic simulations of particular scenarios, our analytical model provides an efficient and comprehensive overview of partitioning as a function of global and macromolecule-specific parameters. Identification of quantitative degeneracies among these parameters highlights the importance of their careful measurement for a given macromolecular species in order to understand the dominant processes responsible for its observed partitioning

What Macromolecular Crowding Can Do to a Protein

Science.gov (United States)

Kuznetsova, Irina M.; Turoverov, Konstantin K.; Uversky, Vladimir N.

2014-01-01

The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area. PMID:25514413

Macromolecular nanotheranostics for multimodal anticancer therapy

Science.gov (United States)

Huis in't Veld, Ruben; Storm, Gert; Hennink, Wim E.; Kiessling, Fabian; Lammers, Twan

2011-10-01

Macromolecular carrier materials based on N-(2-hydroxypropyl)methacrylamide (HPMA) are prototypic and well-characterized drug delivery systems that have been extensively evaluated in the past two decades, both at the preclinical and at the clinical level. Using several different imaging agents and techniques, HPMA copolymers have been shown to circulate for prolonged periods of time, and to accumulate in tumors both effectively and selectively by means of the Enhanced Permeability and Retention (EPR) effect. Because of this, HPMA-based macromolecular nanotheranostics, i.e. formulations containing both drug and imaging agents within a single formulation, have been shown to be highly effective in inducing tumor growth inhibition in animal models. In patients, however, as essentially all other tumor-targeted nanomedicines, they are generally only able to improve the therapeutic index of the attached active agent by lowering its toxicity, and they fail to improve the efficacy of the intervention. Bearing this in mind, we have recently reasoned that because of their biocompatibility and their beneficial biodistribution, nanomedicine formulations might be highly suitable systems for combination therapies. In the present manuscript, we briefly summarize several exemplary efforts undertaken in this regard in our labs in the past couple of years, and we show that long-circulating and passively tumor-targeted macromolecular nanotheranostics can be used to improve the efficacy of radiochemotherapy and of chemotherapy combinations.

Recent advances in macromolecular prodrugs

DEFF Research Database (Denmark)

Riber, Camilla Frich; Zelikin, Alexander N.

2017-01-01

Macromolecular prodrugs (MP) are high molar mass conjugates, typically carrying several copies of a drug or a drug combination, designed to optimize delivery of the drug, that is — its pharmacokinetics. From its advent several decades ago, design of MP has undergone significant development and es...

Status and prospects of macromolecular crystallography

Indian Academy of Sciences (India)

technique that could be completely automated in most cases. ... major challenge in macromolecular crystallography today is ... tial characterization of crystals in the home source and make a ... opportunities for a generation of structural biolo-.

Nucleic acid therapeutic carriers with on-demand triggered release.

Science.gov (United States)

Venkatesh, Siddarth; Wower, Jacek; Byrne, Mark E

2009-09-01

Biohybrid platforms such as synthetic polymer networks engineered from artificial and natural materials hold immense potential as drug and gene delivery vehicles. Here, we report the synthesis and characterization of novel polymer networks that release oligonucleotide sequences via enzymatic and physical triggers. Chemical monomers and acrylated oligonucleotides were copolymerized into networks, and phosphoimaging revealed that 70% of the oligonucleotides were incorporated into the networks. We observed that the immobilized oligonucleotides were readily cleaved when the networks were incubated with the type II restriction enzyme BamHI. The diffusion of the cleaved fragments through the macromolecular chains resulted in relatively constant release profiles very close to zero-order. To our knowledge, this is the first study which harnesses the sequence-specificity of restriction endonucleases as triggering agents for the cleavage and release of oligonucleotide sequences from a synthetic polymer network. The polymer networks exhibited an oligonucleotide diffusion coefficient of 5.6 x 10(-8) cm(2)/s and a diffusional exponent of 0.92. Sigmoidal temperature responsive characteristics of the networks matched the theoretical melting temperature of the oligonucleotides and indicated a cooperative melting transition of the oligonucleotides. The networks were also triggered to release a RNA-cleaving deoxyribozyme, which degraded a HIV-1 mRNA transcript in vitro. To tailor release profiles of the oligonucleotides, we controlled the structure of the macromolecular architecture of the networks by varying their cross-linking content. When incubated with DNase I, networks of cross-linking content 0.15%, 0.22%, and 0.45% exhibited oligonucleotide diffusion coefficients of 1.67 x 10(-8), 7.65 x 10(-9), and 2.7 x 10(-9) cm(2)/s, and diffusional exponents of 0.55, 0.8, and 0.8, respectively. The modular nature of our platform promises to open new avenues for the creation and

The trigger supervisor: Managing triggering conditions in a high energy physics experiment

International Nuclear Information System (INIS)

Wadsworth, B.; Lanza, R.; LeVine, M.J.; Scheetz, R.A.; Videbaek, F.

1987-01-01

A trigger supervisor, implemented in VME-bus hardware, is described, which enables the host computer to dynamically control and monitor the trigger configuration for acquiring data from multiple detector partitions in a complex experiment

Limited preemptive scheduling of mixed time-triggered and event-triggered tasks

NARCIS (Netherlands)

Heuvel, van den M.M.H.P.; Bril, R.J.; Zhang, X.; Abdullah, S.M.J.; Isovic, D.

2013-01-01

Many embedded systems have complex timing constraints and, at the same time, have flexibility requirements which prohibit offline planning of the entire system. To support a mixture of time-triggered and event-triggered tasks, some industrial systems deploy a table-driven dispatcher for

Automated data collection for macromolecular crystallography.

Science.gov (United States)

Winter, Graeme; McAuley, Katherine E

2011-09-01

An overview, together with some practical advice, is presented of the current status of the automation of macromolecular crystallography (MX) data collection, with a focus on MX beamlines at Diamond Light Source, UK. Copyright © 2011 Elsevier Inc. All rights reserved.

Celebrating macromolecular crystallography: A personal perspective

Directory of Open Access Journals (Sweden)

Abad-Zapatero, Celerino

2015-04-01

Full Text Available The twentieth century has seen an enormous advance in the knowledge of the atomic structures that surround us. The discovery of the first crystal structures of simple inorganic salts by the Braggs in 1914, using the diffraction of X-rays by crystals, provided the critical elements to unveil the atomic structure of matter. Subsequent developments in the field leading to macromolecular crystallography are presented with a personal perspective, related to the cultural milieu of Spain in the late 1950’s. The journey of discovery of the author, as he developed professionally, is interwoven with the expansion of macromolecular crystallography from the first proteins (myoglobin, hemoglobin to the ‘coming of age’ of the field in 1971 and the discoveries that followed, culminating in the determination of the structure of the ribosomes at the turn of the century. A perspective is presented exploring the future of the field and also a reflection about the future generations of Spanish scientists.El siglo XX ha sido testigo del increíble avance que ha experimentado el conocimiento de la estructura atómica de la materia que nos rodea. El descubrimiento de las primeras estructuras atómicas de sales inorgánicas por los Bragg en 1914, empleando difracción de rayos X con cristales, proporcionó los elementos clave para alcanzar tal conocimiento. Posteriores desarrollos en este campo, que condujeron a la cristalografía macromolecular, se presentan aquí desde una perspectiva personal, relacionada con el contexto cultural de la España de la década de los 50. La experiencia del descubrimiento científico, durante mi desarrollo profesional, se integra en el desarrollo de la cristalografía macromolecular, desde las primeras proteínas (míoglobina y hemoglobina, hasta su madurez en 1971 que, con los posteriores descubrimientos, culmina con la determinación del la estructura del ribosoma. Asimismo, se explora el futuro de esta disciplina y se

Structure studies of macromolecular systems

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich; Dohnálek, Jan; Skálová, Tereza; Dušková, Jarmila; Kolenko, Petr

2006-01-01

Roč. 13, č. 3 (2006), s. 136 ISSN 1211-5894. [Czech and Slovak Crystallographic Colloquium. 22.06.2006-24.06.2006, Grenoble] R&D Projects: GA AV ČR IAA4050811; GA MŠk 1K05008 Keywords : structure * X-ray diffraction * synchrotron Subject RIV: CD - Macromolecular Chemistry http://www. xray .cz/ms/default.htm

Orphan receptor GPR179 forms macromolecular complexes with components of metabotropic signaling cascade in retina ON-bipolar neurons.

Science.gov (United States)

Orlandi, Cesare; Cao, Yan; Martemyanov, Kirill A

2013-10-29

In the mammalian retina, synaptic transmission between light-excited rod photoreceptors and downstream ON-bipolar neurons is indispensable for dim vision, and disruption of this process leads to congenital stationary night blindness in human patients. The ON-bipolar neurons use the metabotropic signaling cascade, initiated by the mGluR6 receptor, to generate depolarizing responses to light-induced changes in neurotransmitter glutamate release from the photoreceptor axonal terminals. Evidence for the identity of the components involved in transducing these signals is growing rapidly. Recently, the orphan receptor, GPR179, a member of the G protein-coupled receptor (GPCR) superfamily, has been shown to be indispensable for the synaptic responses of ON-bipolar cells. In our study, we investigated the interaction of GPR179 with principle components of the signal transduction cascade. We used immunoprecipitation and proximity ligation assays in transfected cells and native retinas to characterize the protein-protein interactions involving GPR179. The influence of cascade components on GPR179 localization was examined through immunohistochemical staining of the retinas from genetic mouse models. We demonstrated that, in mouse retinas, GPR179 forms physical complexes with the main components of the metabotropic cascade, recruiting mGluR6, TRPM1, and the RGS proteins. Elimination of mGluR6 or RGS proteins, but not TRPM1, detrimentally affects postsynaptic targeting or GPR179 expression. These observations suggest that the mGluR6 signaling cascade is scaffolded as a macromolecular complex in which the interactions between the components ensure the optimal spatiotemporal characteristics of signal transduction.

Hypoxic tumor environments exhibit disrupted collagen I fibers and low macromolecular transport.

Directory of Open Access Journals (Sweden)

Samata M Kakkad

Full Text Available Hypoxic tumor microenvironments result in an aggressive phenotype and resistance to therapy that lead to tumor progression, recurrence, and metastasis. While poor vascularization and the resultant inadequate drug delivery are known to contribute to drug resistance, the effect of hypoxia on molecular transport through the interstitium, and the role of the extracellular matrix (ECM in mediating this transport are unexplored. The dense mesh of fibers present in the ECM can especially influence the movement of macromolecules. Collagen 1 (Col1 fibers form a key component of the ECM in breast cancers. Here we characterized the influence of hypoxia on macromolecular transport in tumors, and the role of Col1 fibers in mediating this transport using an MDA-MB-231 breast cancer xenograft model engineered to express red fluorescent protein under hypoxia. Magnetic resonance imaging of macromolecular transport was combined with second harmonic generation microscopy of Col1 fibers. Hypoxic tumor regions displayed significantly decreased Col1 fiber density and volume, as well as significantly lower macromolecular draining and pooling rates, than normoxic regions. Regions adjacent to severely hypoxic areas revealed higher deposition of Col1 fibers and increased macromolecular transport. These data suggest that Col1 fibers may facilitate macromolecular transport in tumors, and their reduction in hypoxic regions may reduce this transport. Decreased macromolecular transport in hypoxic regions may also contribute to poor drug delivery and tumor recurrence in hypoxic regions. High Col1 fiber density observed around hypoxic regions may facilitate the escape of aggressive cancer cells from hypoxic regions.

Macromolecular target prediction by self-organizing feature maps.

Science.gov (United States)

Schneider, Gisbert; Schneider, Petra

2017-03-01

Rational drug discovery would greatly benefit from a more nuanced appreciation of the activity of pharmacologically active compounds against a diverse panel of macromolecular targets. Already, computational target-prediction models assist medicinal chemists in library screening, de novo molecular design, optimization of active chemical agents, drug re-purposing, in the spotting of potential undesired off-target activities, and in the 'de-orphaning' of phenotypic screening hits. The self-organizing map (SOM) algorithm has been employed successfully for these and other purposes. Areas covered: The authors recapitulate contemporary artificial neural network methods for macromolecular target prediction, and present the basic SOM algorithm at a conceptual level. Specifically, they highlight consensus target-scoring by the employment of multiple SOMs, and discuss the opportunities and limitations of this technique. Expert opinion: Self-organizing feature maps represent a straightforward approach to ligand clustering and classification. Some of the appeal lies in their conceptual simplicity and broad applicability domain. Despite known algorithmic shortcomings, this computational target prediction concept has been proven to work in prospective settings with high success rates. It represents a prototypic technique for future advances in the in silico identification of the modes of action and macromolecular targets of bioactive molecules.

Using lanthanoid complexes to phase large macromolecular assemblies

International Nuclear Information System (INIS)

Talon, Romain; Kahn, Richard; Durá, M. Asunción; Maury, Olivier; Vellieux, Frédéric M. D.; Franzetti, Bruno; Girard, Eric

2011-01-01

A lanthanoid complex, [Eu(DPA) 3 ] 3− , was used to obtain experimental phases at 4.0 Å resolution of PhTET1-12s, a large self-compartmentalized homo-dodecameric protease complex of 444 kDa. Lanthanoid ions exhibit extremely large anomalous X-ray scattering at their L III absorption edge. They are thus well suited for anomalous diffraction experiments. A novel class of lanthanoid complexes has been developed that combines the physical properties of lanthanoid atoms with functional chemical groups that allow non-covalent binding to proteins. Two structures of large multimeric proteins have already been determined by using such complexes. Here the use of the luminescent europium tris-dipicolinate complex [Eu(DPA) 3 ] 3− to solve the low-resolution structure of a 444 kDa homododecameric aminopeptidase, called PhTET1-12s from the archaea Pyrococcus horikoshii, is reported. Surprisingly, considering the low resolution of the data, the experimental electron density map is very well defined. Experimental phases obtained by using the lanthanoid complex lead to maps displaying particular structural features usually observed in higher-resolution maps. Such complexes open a new way for solving the structure of large molecular assemblies, even with low-resolution data

Advancing complex explanatory conceptualizations of daily negative and positive affect: trigger and maintenance coping action patterns.

Science.gov (United States)

Dunkley, David M; Ma, Denise; Lee, Ihno A; Preacher, Kristopher J; Zuroff, David C

2014-01-01

The present study addressed a fundamental gap between research and clinical work by advancing complex explanatory conceptualizations of coping action patterns that trigger and maintain daily negative affect and (low) positive affect. One hundred ninety-six community adults completed measures of perfectionism, and then 6 months later completed questionnaires at the end of the day for 14 consecutive days to provide simultaneous assessments of appraisals, coping, and affect across different stressful situations in everyday life. Multilevel structural equation modeling (MSEM) supported complex explanatory conceptualizations that demonstrated (a) disengagement trigger patterns consisting of several distinct appraisals (e.g., event stress) and coping strategies (e.g., avoidant coping) that commonly operate together across many different stressors when the typical individual experiences daily increases in negative affect and drops in positive affect; and (b) disengagement maintenance patterns composed of different appraisal and coping maintenance factors that, in combination, can explain why individuals with higher levels of self-critical perfectionism have persistent daily negative affect and low positive mood 6 months later. In parallel, engagement patterns (triggers and maintenance) composed of distinct appraisals (e.g., perceived social support) and coping strategies (e.g., problem-focused coping) were linked to compensatory experiences of daily positive affect. These findings demonstrate the promise of using daily diary methodologies and MSEM to promote a shared understanding between therapists and clients of trigger and maintenance coping action patterns that explain what precipitates and perpetuates clients' difficulties, which, in turn, can help achieve the 2 overarching therapy goals of reducing clients' distress and bolstering resilience. (c) 2014 APA, all rights reserved.

Towards RTOS support for mixed time-triggered and event-triggered task sets

NARCIS (Netherlands)

Heuvel, van den M.M.H.P.; Bril, R.J.; Lukkien, J.J.; Isovic, D.; Sankar Ramachandran, G.

2012-01-01

Many embedded systems have complex timing constraints and, at the same time, have flexibility requirements which prohibit offline planning of the entire system. To support a mixture of time-triggered and event-triggered tasks, some industrial systems deploy a real-time operating system (RTOS) with a

UQlust: combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data.

Science.gov (United States)

Adamczak, Rafal; Meller, Jarek

2016-12-28

Advances in computing have enabled current protein and RNA structure prediction and molecular simulation methods to dramatically increase their sampling of conformational spaces. The quickly growing number of experimentally resolved structures, and databases such as the Protein Data Bank, also implies large scale structural similarity analyses to retrieve and classify macromolecular data. Consequently, the computational cost of structure comparison and clustering for large sets of macromolecular structures has become a bottleneck that necessitates further algorithmic improvements and development of efficient software solutions. uQlust is a versatile and easy-to-use tool for ultrafast ranking and clustering of macromolecular structures. uQlust makes use of structural profiles of proteins and nucleic acids, while combining a linear-time algorithm for implicit comparison of all pairs of models with profile hashing to enable efficient clustering of large data sets with a low memory footprint. In addition to ranking and clustering of large sets of models of the same protein or RNA molecule, uQlust can also be used in conjunction with fragment-based profiles in order to cluster structures of arbitrary length. For example, hierarchical clustering of the entire PDB using profile hashing can be performed on a typical laptop, thus opening an avenue for structural explorations previously limited to dedicated resources. The uQlust package is freely available under the GNU General Public License at https://github.com/uQlust . uQlust represents a drastic reduction in the computational complexity and memory requirements with respect to existing clustering and model quality assessment methods for macromolecular structure analysis, while yielding results on par with traditional approaches for both proteins and RNAs.

Diagnostic accuracy of sub-mSv prospective ECG-triggering cardiac CT in young infant with complex congenital heart disease.

Science.gov (United States)

Gao, Wei; Zhong, Yu Min; Sun, Ai Min; Wang, Qian; Ouyang, Rong Zhen; Hu, Li Wei; Qiu, Han Sheng; Wang, Shi Yu; Li, Jian Ying

2016-06-01

To explore the clinical value and evaluate the diagnostic accuracy of sub-mSv low-dose prospective ECG-triggering cardiac CT (CCT) in young infants with complex congenital heart disease (CHD). A total of 102 consecutive infant patients (53 boys and 49 girls with mean age of 2.9 ± 2.4 m and weight less than 5 kg) with complex CHD were prospectively enrolled. Scans were performed on a 64-slice high definition CT scanner with low dose prospective ECG-triggering mode and reconstructed with 80 % adaptive statistical iterative reconstruction algorithm. All studies were performed during free breathing with sedation. The subjective image quality was evaluated by 5-point grading scale and interobserver variability was calculated. The objective image noise (standard deviation, SD) and contrast to noise ratio (CNR) was calculated. The effective radiation dose from the prospective ECG-triggering mode was recorded and compared with the virtual conventional retrospective ECG-gating mode. The detection rate for the origin of coronary artery was calculated. All patients also underwent echocardiography before CCT examination. 81 patients had surgery and their preoperative CCT and echocardiography findings were compared with the surgical results and sensitivity, specificity, positive and negative predictive values and accuracy were calculated for separate cardiovascular anomalies. Heart rates were 70-161 beats per minute (bpm) with mean value of 129.19 ± 14.52 bpm. The effective dose of 0.53 ± 0.15 mSv in the prospective ECG-triggering cardiac CT was lower than the calculated value in a conventional retrospective ECG-gating mode (2.00 ± 0.35 mSv) (p ECG-triggering CCT with sub-mSv effective dose provides excellent imaging quality and high diagnostic accuracy for young infants with complex CHD.

Crowding-facilitated macromolecular transport in attractive micropost arrays.

Science.gov (United States)

Chien, Fan-Tso; Lin, Po-Keng; Chien, Wei; Hung, Cheng-Hsiang; Yu, Ming-Hung; Chou, Chia-Fu; Chen, Yeng-Long

2017-05-02

Our study of DNA dynamics in weakly attractive nanofabricated post arrays revealed crowding enhances polymer transport, contrary to hindered transport in repulsive medium. The coupling of DNA diffusion and adsorption to the microposts results in more frequent cross-post hopping and increased long-term diffusivity with increased crowding density. We performed Langevin dynamics simulations and found maximum long-term diffusivity in post arrays with gap sizes comparable to the polymer radius of gyration. We found that macromolecular transport in weakly attractive post arrays is faster than in non-attractive dense medium. Furthermore, we employed hidden Markov analysis to determine the transition of macromolecular adsorption-desorption on posts and hopping between posts. The apparent free energy barriers are comparable to theoretical estimates determined from polymer conformational fluctuations.

Data analysis at the CMS level-1 trigger: migrating complex selection algorithms from offline analysis and high-level trigger to the trigger electronics

CERN Document Server

Wulz, Claudia

2017-01-01

With ever increasing luminosity at the LHC, optimum online data selection is becoming more and more important. While in the case of some experiments (LHCb and ALICE) this task is being completely transferred to computer farms, the others -- ATLAS and CMS -- will not be able to do this in the medium-term future for technological, detector-related reasons. Therefore, these experiments pursue the complementary approach of migrating more and more of the offline and high-level trigger intelligence into the trigger electronics. The presentation illustrates how the level-1 trigger of the CMS experiment and in particular its concluding stage, the so-called ``Global Trigger", take up this challenge.

An acoustic on-chip goniometer for room temperature macromolecular crystallography.

Science.gov (United States)

Burton, C G; Axford, D; Edwards, A M J; Gildea, R J; Morris, R H; Newton, M I; Orville, A M; Prince, M; Topham, P D; Docker, P T

2017-12-05

This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.

Large branched self-assembled DNA complexes

International Nuclear Information System (INIS)

Tosch, Paul; Waelti, Christoph; Middelberg, Anton P J; Davies, A Giles

2007-01-01

Many biological molecules have been demonstrated to self-assemble into complex structures and networks by using their very efficient and selective molecular recognition processes. The use of biological molecules as scaffolds for the construction of functional devices by self-assembling nanoscale complexes onto the scaffolds has recently attracted significant attention and many different applications in this field have emerged. In particular DNA, owing to its inherent sophisticated self-organization and molecular recognition properties, has served widely as a scaffold for various nanotechnological self-assembly applications, with metallic and semiconducting nanoparticles, proteins, macromolecular complexes, inter alia, being assembled onto designed DNA scaffolds. Such scaffolds may typically contain multiple branch-points and comprise a number of DNA molecules selfassembled into the desired configuration. Previously, several studies have used synthetic methods to produce the constituent DNA of the scaffolds, but this typically constrains the size of the complexes. For applications that require larger self-assembling DNA complexes, several tens of nanometers or more, other techniques need to be employed. In this article, we discuss a generic technique to generate large branched DNA macromolecular complexes

Criticality and Connectivity in Macromolecular Charge Complexation

Energy Technology Data Exchange (ETDEWEB)

Qin, Jian; de Pablo, Juan J.

2016-11-04

We examine the role of molecular connectivity and architecture on the complexation of ionic macromolecules (polyelectrolytes) of finite size. A unified framework is developed and applied to evaluate the electrostatic correlation free energy for point-like, rod-like, and coil-like molecules. That framework is generalized to molecules of variable fractal dimensions, including dendrimers. Analytical expressions for the free energy, correlation length, and osmotic pressure are derived, thereby enabling consideration of the effects of charge connectivity, fractal dimension, and backbone stiffness on the complexation behavior of a wide range of polyelectrolytes. Results are presented for regions in the immediate vicinity of the critical region and far from it. A transparent and explicit expression for the coexistence curve is derived in order to facilitate analysis of experimentally observed phase diagrams.

Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents

Directory of Open Access Journals (Sweden)

Arghya Chakravorty

2018-03-01

Full Text Available Conventional modeling techniques to model macromolecular solvation and its effect on binding in the framework of Poisson-Boltzmann based implicit solvent models make use of a geometrically defined surface to depict the separation of macromolecular interior (low dielectric constant from the solvent phase (high dielectric constant. Though this simplification saves time and computational resources without significantly compromising the accuracy of free energy calculations, it bypasses some of the key physio-chemical properties of the solute-solvent interface, e.g., the altered flexibility of water molecules and that of side chains at the interface, which results in dielectric properties different from both bulk water and macromolecular interior, respectively. Here we present a Gaussian-based smooth dielectric model, an inhomogeneous dielectric distribution model that mimics the effect of macromolecular flexibility and captures the altered properties of surface bound water molecules. Thus, the model delivers a smooth transition of dielectric properties from the macromolecular interior to the solvent phase, eliminating any unphysical surface separating the two phases. Using various examples of macromolecular binding, we demonstrate its utility and illustrate the comparison with the conventional 2-dielectric model. We also showcase some additional abilities of this model, viz. to account for the effect of electrolytes in the solution and to render the distribution profile of water across a lipid membrane.

Macromolecular complexes of lysozyme with kappa carrageenan

NARCIS (Netherlands)

Antonov, Y.A.; Zhuravleva, I.L.; Cardinaels, R.; Moldenaers, P.

2018-01-01

We present a structural study of the complexation and binding of lysozyme (Lys) with kappa carrageenan (kCG) by means of turbidity measurements, phase analysis, dynamic and electrophoretic light scattering, differential scanning microcalorimetry (DSMC), confocal laser scanning (CLSM) microscopy,

A public database of macromolecular diffraction experiments.

Science.gov (United States)

Grabowski, Marek; Langner, Karol M; Cymborowski, Marcin; Porebski, Przemyslaw J; Sroka, Piotr; Zheng, Heping; Cooper, David R; Zimmerman, Matthew D; Elsliger, Marc André; Burley, Stephen K; Minor, Wladek

2016-11-01

The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics

Probing the hydration water diffusion of macromolecular surfaces and interfaces

International Nuclear Information System (INIS)

Ortony, Julia H; Cheng, Chi-Yuan; Franck, John M; Pavlova, Anna; Hunt, Jasmine; Han, Songi; Kausik, Ravinath

2011-01-01

We probe the translational dynamics of the hydration water surrounding the macromolecular surfaces of selected polyelectrolytes, lipid vesicles and intrinsically disordered proteins with site specificity in aqueous solutions. These measurements are made possible by the recent development of a new instrumental and methodological approach based on Overhauser dynamic nuclear polarization (DNP)-enhanced nuclear magnetic resonance (NMR) spectroscopy. This technique selectively amplifies 1 H NMR signals of hydration water around a spin label that is attached to a molecular site of interest. The selective 1 H NMR amplification within molecular length scales of a spin label is achieved by utilizing short-distance range (∼r -3 ) magnetic dipolar interactions between the 1 H spin of water and the electron spin of a nitroxide radical-based label. Key features include the fact that only minute quantities (<10 μl) and dilute (≥100 μM) sample concentrations are needed. There is no size limit on the macromolecule or molecular assembly to be analyzed. Hydration water with translational correlation times between 10 and 800 ps is measured within ∼10 A distance of the spin label, encompassing the typical thickness of a hydration layer with three water molecules across. The hydration water moving within this time scale has significant implications, as this is what is modulated whenever macromolecules or molecular assemblies undergo interactions, binding or conformational changes. We demonstrate, with the examples of polymer complexation, protein aggregation and lipid-polymer interaction, that the measurements of interfacial hydration dynamics can sensitively and site specifically probe macromolecular interactions.

Surface and permeability properties of membranes from polyelectrolyte complexes and polyelectrolyte surfactant complexes

Czech Academy of Sciences Publication Activity Database

Schwarz, H. H.; Lukáš, Jaromír; Richau, K.

2003-01-01

Roč. 218, 1-2 (2003), s. 1-9 ISSN 0376-7388 R&D Projects: GA AV ČR KSK4050111 Keywords : polyelectrolyte complex membranes * pervaporation * dehydration of organics Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.081, year: 2003

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.

Science.gov (United States)

Theobald, Douglas L; Wuttke, Deborah S

2006-09-01

THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.

Macromolecular organization of xyloglucan and cellulose in pea epicotyls

International Nuclear Information System (INIS)

Hayashi, T.; Maclachlan, G.

1984-01-01

Xyloglucan is known to occur widely in the primary cell walls of higher plants. This polysaccharide in most dicots possesses a cellulose-like main chain with three of every four consecutive residues substituted with xylose and minor addition of other sugars. Xyloglucan and cellulose metabolism is regulated by different processes; since different enzyme systems are probably required for the synthesis of their 1,4-β-linkages. A macromolecular complex composed of xyloglucan and cellulose only was obtained from elongating regions of etiolated pea stems. It was examined by light microscopy using iodine staining, by radioautography after labeling with [ 3 H]fructose, by fluorescence microscopy using a fluorescein-lectin (fructose-binding) as probe, and by electron microscopy after shadowing. The techniques all demonstrated that the macromolecule was present in files of cell shapes, referred to here as cell-wall ghosts, in which xyloglucan was localized both on and between the cellulose microfibrils

Macromolecular Networks Containing Fluorinated Cyclic Moieties

Science.gov (United States)

2015-12-12

Briefing Charts 3. DATES COVERED (From - To) 17 Nov 2015 – 12 Dec 2015 4. TITLE AND SUBTITLE Macromolecular Networks Containing Fluorinated Cyclic... FLUORINATED CYCLIC MOIETIES 12 December 2015 Andrew J. Guenthner,1 Scott T. Iacono,2 Cynthia A. Corley,2 Christopher M. Sahagun,3 Kevin R. Lamison,4...Reinforcements Good Flame, Smoke, & Toxicity Characteristics Low Water Uptake with Near Zero Coefficient of Hygroscopic Expansion ∆ DISTRIBUTION A

Stably engineered nanobubbles and ultrasound - An effective platform for enhanced macromolecular delivery to representative cells of the retina.

Directory of Open Access Journals (Sweden)

Sachin S Thakur

Full Text Available Herein we showcase the potential of ultrasound-responsive nanobubbles in enhancing macromolecular permeation through layers of the retina, ultimately leading to significant and direct intracellular delivery; this being effectively demonstrated across three relevant and distinct retinal cell lines. Stably engineered nanobubbles of a highly homogenous and echogenic nature were fully characterised using dynamic light scattering, B-scan ultrasound and transmission electron microscopy (TEM. The nanobubbles appeared as spherical liposome-like structures under TEM, accompanied by an opaque luminal core and darkened corona around their periphery, with both features indicative of efficient gas entrapment and adsorption, respectively. A nanobubble +/- ultrasound sweeping study was conducted next, which determined the maximum tolerated dose for each cell line. Detection of underlying cellular stress was verified using the biomarker heat shock protein 70, measured before and after treatment with optimised ultrasound. Next, with safety to nanobubbles and optimised ultrasound demonstrated, each human or mouse-derived cell population was incubated with biotinylated rabbit-IgG in the presence and absence of ultrasound +/- nanobubbles. Intracellular delivery of antibody in each cell type was then quantified using Cy3-streptavidin. Nanobubbles and optimised ultrasound were found to be negligibly toxic across all cell lines tested. Macromolecular internalisation was achieved to significant, yet varying degrees in all three cell lines. The results of this study pave the way towards better understanding mechanisms underlying cellular responsiveness to ultrasound-triggered drug delivery in future ex vivo and in vivo models of the posterior eye.

Extracting trends from two decades of microgravity macromolecular crystallization history.

Science.gov (United States)

Judge, Russell A; Snell, Edward H; van der Woerd, Mark J

2005-06-01

Since the 1980s hundreds of macromolecular crystal growth experiments have been performed in the reduced acceleration environment of an orbiting spacecraft. Significant enhancements in structural knowledge have resulted from X-ray diffraction of the crystals grown. Similarly, many samples have shown no improvement or degradation in comparison to those grown on the ground. A complex series of interrelated factors affect these experiments and by building a comprehensive archive of the results it was aimed to identify factors that result in success and those that result in failure. Specifically, it was found that dedicated microgravity missions increase the chance of success when compared with those where crystallization took place as a parasitic aspect of the mission. It was also found that the chance of success could not be predicted based on any discernible property of the macromolecule available to us.

CMS Trigger Performance

CERN Document Server

Donato, Silvio

2017-01-01

During its second run of operation (Run 2) which started in 2015, the LHC will deliver a peak instantaneous luminosity that may reach $2 \\cdot 10^{34}$ cm$^{-2}$s$^{-1}$ with an average pile-up of about 55, far larger than the design value. Under these conditions, the online event selection is a very challenging task. In CMS, it is realized by a two-level trigger system the Level-1 (L1) Trigger, implemented in custom-designed electronics, and the High Level Trigger (HLT), a streamlined version of the offline reconstruction software running on a computer farm. In order to face this challenge, the L1 trigger has been through a major upgrade compared to Run 1, whereby all electronic boards of the system have been replaced, allowing more sophisticated algorithms to be run online. Its last stage, the global trigger, is now able to perform complex selections and to compute high-level quantities, like invariant masses. Likewise, the algorithms that run in the HLT go through big improvements; in particular, new appr...

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

Science.gov (United States)

Maximova, Tatiana; Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth; Shehu, Amarda

2016-04-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.

Performance Analysis with Network-Enhanced Complexities: On Fading Measurements, Event-Triggered Mechanisms, and Cyber Attacks

Directory of Open Access Journals (Sweden)

Derui Ding

2014-01-01

Full Text Available Nowadays, the real-world systems are usually subject to various complexities such as parameter uncertainties, time-delays, and nonlinear disturbances. For networked systems, especially large-scale systems such as multiagent systems and systems over sensor networks, the complexities are inevitably enhanced in terms of their degrees or intensities because of the usage of the communication networks. Therefore, it would be interesting to (1 examine how this kind of network-enhanced complexities affects the control or filtering performance; and (2 develop some suitable approaches for controller/filter design problems. In this paper, we aim to survey some recent advances on the performance analysis and synthesis with three sorts of fashionable network-enhanced complexities, namely, fading measurements, event-triggered mechanisms, and attack behaviors of adversaries. First, these three kinds of complexities are introduced in detail according to their engineering backgrounds, dynamical characteristic, and modelling techniques. Then, the developments of the performance analysis and synthesis issues for various networked systems are systematically reviewed. Furthermore, some challenges are illustrated by using a thorough literature review and some possible future research directions are highlighted.

Outrunning free radicals in room-temperature macromolecular crystallography

International Nuclear Information System (INIS)

Owen, Robin L.; Axford, Danny; Nettleship, Joanne E.; Owens, Raymond J.; Robinson, James I.; Morgan, Ann W.; Doré, Andrew S.; Lebon, Guillaume; Tate, Christopher G.; Fry, Elizabeth E.; Ren, Jingshan; Stuart, David I.; Evans, Gwyndaf

2012-01-01

A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector. A significant increase in the lifetime of room-temperature macromolecular crystals is reported through the use of a high-brilliance X-ray beam, reduced exposure times and a fast-readout detector. This is attributed to the ability to collect diffraction data before hydroxyl radicals can propagate through the crystal, fatally disrupting the lattice. Hydroxyl radicals are shown to be trapped in amorphous solutions at 100 K. The trend in crystal lifetime was observed in crystals of a soluble protein (immunoglobulin γ Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A 2A adenosine G-protein coupled receptor). The observation of a similar effect in all three systems provides clear evidence for a common optimal strategy for room-temperature data collection and will inform the design of future synchrotron beamlines and detectors for macromolecular crystallography

Outrunning free radicals in room-temperature macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Owen, Robin L., E-mail: robin.owen@diamond.ac.uk; Axford, Danny [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Nettleship, Joanne E.; Owens, Raymond J. [Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Robinson, James I.; Morgan, Ann W. [University of Leeds, Leeds LS9 7FT (United Kingdom); Doré, Andrew S. [Heptares Therapeutics Ltd, BioPark, Welwyn Garden City AL7 3AX (United Kingdom); Lebon, Guillaume; Tate, Christopher G. [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom); Fry, Elizabeth E.; Ren, Jingshan [The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Stuart, David I. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Evans, Gwyndaf [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

2012-06-15

A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector. A significant increase in the lifetime of room-temperature macromolecular crystals is reported through the use of a high-brilliance X-ray beam, reduced exposure times and a fast-readout detector. This is attributed to the ability to collect diffraction data before hydroxyl radicals can propagate through the crystal, fatally disrupting the lattice. Hydroxyl radicals are shown to be trapped in amorphous solutions at 100 K. The trend in crystal lifetime was observed in crystals of a soluble protein (immunoglobulin γ Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A{sub 2A} adenosine G-protein coupled receptor). The observation of a similar effect in all three systems provides clear evidence for a common optimal strategy for room-temperature data collection and will inform the design of future synchrotron beamlines and detectors for macromolecular crystallography.

Macromolecular diffusion in crowded media beyond the hard-sphere model.

Science.gov (United States)

Blanco, Pablo M; Garcés, Josep Lluís; Madurga, Sergio; Mas, Francesc

2018-04-25

The effect of macromolecular crowding on diffusion beyond the hard-core sphere model is studied. A new coarse-grained model is presented, the Chain Entanglement Softened Potential (CESP) model, which takes into account the macromolecular flexibility and chain entanglement. The CESP model uses a shoulder-shaped interaction potential that is implemented in the Brownian Dynamics (BD) computations. The interaction potential contains only one parameter associated with the chain entanglement energetic cost (Ur). The hydrodynamic interactions are included in the BD computations via Tokuyama mean-field equations. The model is used to analyze the diffusion of a streptavidin protein among different sized dextran obstacles. For this system, Ur is obtained by fitting the streptavidin experimental long-time diffusion coefficient Dlongversus the macromolecular concentration for D50 (indicating their molecular weight in kg mol-1) dextran obstacles. The obtained Dlong values show better quantitative agreement with experiments than those obtained with hard-core spheres. Moreover, once parametrized, the CESP model is also able to quantitatively predict Dlong and the anomalous exponent (α) for streptavidin diffusion among D10, D400 and D700 dextran obstacles. Dlong, the short-time diffusion coefficient (Dshort) and α are obtained from the BD simulations by using a new empirical expression, able to describe the full temporal evolution of the diffusion coefficient.

A smooth and differentiable bulk-solvent model for macromolecular diffraction

Energy Technology Data Exchange (ETDEWEB)

Fenn, T. D. [Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford, California (United States); Schnieders, M. J. [Department of Chemistry, Stanford, California (United States); Brunger, A. T., E-mail: brunger@stanford.edu [Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford, California (United States); Departments of Neurology and Neurological Sciences, Structural Biology and Photon Science, Stanford, California (United States)

2010-09-01

A new method for modeling the bulk solvent in macromolecular diffraction data based on Babinet’s principle is presented. The proposed models offer the advantage of differentiability with respect to atomic coordinates. Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute–solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, R{sub free} and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography.

A smooth and differentiable bulk-solvent model for macromolecular diffraction

International Nuclear Information System (INIS)

Fenn, T. D.; Schnieders, M. J.; Brunger, A. T.

2010-01-01

A new method for modeling the bulk solvent in macromolecular diffraction data based on Babinet’s principle is presented. The proposed models offer the advantage of differentiability with respect to atomic coordinates. Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute–solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, R free and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography

The ATLAS trigger: high-level trigger commissioning and operation during early data taking

International Nuclear Information System (INIS)

Goncalo, R

2008-01-01

The ATLAS experiment is one of the two general-purpose experiments due to start operation soon at the Large Hadron Collider (LHC). The LHC will collide protons at a centre of mass energy of 14 TeV, with a bunch-crossing rate of 40 MHz. The ATLAS three-level trigger will reduce this input rate to match the foreseen offline storage capability of 100-200 Hz. This paper gives an overview of the ATLAS High Level Trigger focusing on the system design and its innovative features. We then present the ATLAS trigger strategy for the initial phase of LHC exploitation. Finally, we report on the valuable experience acquired through in-situ commissioning of the system where simulated events were used to exercise the trigger chain. In particular we show critical quantities such as event processing times, measured in a large-scale HLT farm using a complex trigger menu

A simple quantitative model of macromolecular crowding effects on protein folding: Application to the murine prion protein(121-231)

Science.gov (United States)

Bergasa-Caceres, Fernando; Rabitz, Herschel A.

2013-06-01

A model of protein folding kinetics is applied to study the effects of macromolecular crowding on protein folding rate and stability. Macromolecular crowding is found to promote a decrease of the entropic cost of folding of proteins that produces an increase of both the stability and the folding rate. The acceleration of the folding rate due to macromolecular crowding is shown to be a topology-dependent effect. The model is applied to the folding dynamics of the murine prion protein (121-231). The differential effect of macromolecular crowding as a function of protein topology suffices to make non-native configurations relatively more accessible.

Lessons from (triggered) tremor

Science.gov (United States)

Gomberg, Joan

2010-01-01

I test a “clock-advance” model that implies triggered tremor is ambient tremor that occurs at a sped-up rate as a result of loading from passing seismic waves. This proposed model predicts that triggering probability is proportional to the product of the ambient tremor rate and a function describing the efficacy of the triggering wave to initiate a tremor event. Using data mostly from Cascadia, I have compared qualitatively a suite of teleseismic waves that did and did not trigger tremor with ambient tremor rates. Many of the observations are consistent with the model if the efficacy of the triggering wave depends on wave amplitude. One triggered tremor observation clearly violates the clock-advance model. The model prediction that larger triggering waves result in larger triggered tremor signals also appears inconsistent with the measurements. I conclude that the tremor source process is a more complex system than that described by the clock-advance model predictions tested. Results of this and previous studies also demonstrate that (1) conditions suitable for tremor generation exist in many tectonic environments, but, within each, only occur at particular spots whose locations change with time; (2) any fluid flow must be restricted to less than a meter; (3) the degree to which delayed failure and secondary triggering occurs is likely insignificant; and 4) both shear and dilatational deformations may trigger tremor. Triggered and ambient tremor rates correlate more strongly with stress than stressing rate, suggesting tremor sources result from time-dependent weakening processes rather than simple Coulomb failure.

The Postgraduate Study of Macromolecular Sciences at the University of Zagreb (1971-1980

Directory of Open Access Journals (Sweden)

Kunst, B.

2008-07-01

Full Text Available The postgraduate study of macromolecular sciences (PSMS was established at the University of Zagreb in 1971 as a university study in the time of expressed interdisciplinary permeation of natural sciences - physics, chemistry and biology, and application of their achievements in technologicaldisciplines. PSMS was established by a group of prominent university professors from the schools of Science, Chemical Technology, Pharmacy and Medicine, as well as from the Institute of Biology. The study comprised basic fields of macromolecular sciences: organic chemistry of synthetic macromolecules, physical chemistry of macromolecules, physics of macromolecules, biological macromolecules and polymer engineering with polymer application and processing, and teaching was performed in 29 lecture courses lead by 30 professors with their collaborators. PSMS ceased to exist with the change of legislation in Croatia in 1980, when the attitude prevailed to render back postgraduate studies to the university schools. During 9 years of existence of PSMS the MSci grade was awarded to 37 macromolecular experts. It was assessed that the PSMS some thirty years ago was an important example of modern postgraduate education as compared with the international postgraduate development. In concordance with the recent introduction of similar interdisciplinary studies in macromolecular sciences elsewhere in the world, the establishment of a modern interdisciplinary study in the field would be of importance for further development of these sciences in Croatia.

Synthesis and characterization of macromolecular rhodamine tethers and their interactions with P-glycoprotein.

Science.gov (United States)

Crawford, Lindsey; Putnam, David

2014-08-20

Rhodamine dyes are well-known P-glycoprotein (P-gp) substrates that have played an important role in the detection of inhibitors and other substrates of P-gp, as well as in the understanding of P-gp function. Macromolecular conjugates of rhodamines could prove useful as tethers for further probing of P-gp structure and function. Two macromolecular derivatives of rhodamine, methoxypolyethylene glycol-rhodamine6G and methoxypolyethylene glycol-rhodamine123, were synthesized through the 2'-position of rhodamine6G and rhodamine123, thoroughly characterized, and then evaluated by inhibition with verapamil for their ability to interact with P-gp and to act as efflux substrates. To put the results into context, the P-gp interactions of the new conjugates were compared to the commercially available methoxypolyethylene glycol-rhodamineB. FACS analysis confirmed that macromolecular tethers of rhodamine6G, rhodamine123, and rhodamineB were accumulated in P-gp expressing cells 5.2 ± 0.3%, 26.2 ± 4%, and 64.2 ± 6%, respectively, compared to a sensitive cell line that does not overexpress P-gp. Along with confocal imaging, the efflux analysis confirmed that the macromolecular rhodamine tethers remain P-gp substrates. These results open potential avenues for new ways to probe the function of P-gp both in vitro and in vivo.

So how do you know you have a macromolecular complex?

International Nuclear Information System (INIS)

Dafforn, Timothy R.

2007-01-01

Structures of protein complexes offer some of the most interesting insights into biological processes. In this article, the methods required to show that the complex observed is the physiological one are investigated. Protein in crystal form is at an extremely high concentration and yet retains the complex secondary structure that defines an active protein. The protein crystal itself is made up of a repeating lattice of protein–protein and protein–solvent interactions. The problem that confronts any crystallographer is to identify those interactions that represent physiological interactions and those that do not. This review explores the tools that are available to provide such information using the original crystal liquor as a sample. The review is aimed at postgraduate and postdoctoral researchers who may well be coming up against this problem for the first time. Techniques are discussed that will provide information on the stoichiometry of complexes as well as low-resolution information on complex structure. Together, these data will help to identify the physiological complex

50th Anniversary Perspective: Polymers with Complex Architectures

KAUST Repository

Polymeropoulos, George; Zapsas, George; Ntetsikas, Konstantinos; Bilalis, Panayiotis; Gnanou, Yves; Hadjichristidis, Nikolaos

2017-01-01

The scope of this Perspective is to highlight innovative contributions in the synthesis of well-defined complex macromolecular architectures and to emphasize the importance of these materials to polymer physical chemistry, physics, theory

Diffusion accessibility as a method for visualizing macromolecular surface geometry.

Science.gov (United States)

Tsai, Yingssu; Holton, Thomas; Yeates, Todd O

2015-10-01

Important three-dimensional spatial features such as depth and surface concavity can be difficult to convey clearly in the context of two-dimensional images. In the area of macromolecular visualization, the computer graphics technique of ray-tracing can be helpful, but further techniques for emphasizing surface concavity can give clearer perceptions of depth. The notion of diffusion accessibility is well-suited for emphasizing such features of macromolecular surfaces, but a method for calculating diffusion accessibility has not been made widely available. Here we make available a web-based platform that performs the necessary calculation by solving the Laplace equation for steady state diffusion, and produces scripts for visualization that emphasize surface depth by coloring according to diffusion accessibility. The URL is http://services.mbi.ucla.edu/DiffAcc/. © 2015 The Protein Society.

A 3D Image Filter for Parameter-Free Segmentation of Macromolecular Structures from Electron Tomograms

Science.gov (United States)

Ali, Rubbiya A.; Landsberg, Michael J.; Knauth, Emily; Morgan, Garry P.; Marsh, Brad J.; Hankamer, Ben

2012-01-01

3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters—the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms. PMID:22479430

The dominating macromolecular complex of human gallbladder bile

NARCIS (Netherlands)

Verschure, J.C.M.; Mijnlieff, P.F.

The solutes of human gall bladder bile appear to exist mainly in the form of a complex macromolecule, formed around a nucleus of lipoprotein. The existence of this macromolecule was demonstrated by paper electrophoresis1, free electrophoresis and ultracentrifuge experiments. The molecular weight of

Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)

Science.gov (United States)

Bergasa-Caceres, Fernando; Rabitz, Herschel A.

2014-01-01

A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.

A programmable systolic trigger processor for FERA bus data

International Nuclear Information System (INIS)

Appelquist, G.; Hovander, B.; Sellden, B.; Bohm, C.

1992-09-01

A generic CAMAC based trigger processor module for fast processing of large amounts of ADC data, has been designed. This module has been realised using complex programmable gate arrays (LCAs from XILINX). The gate arrays have been connected to memories and multipliers in such a way that different gate array configurations can cover a wide range of module applications. Using this module, it is possible to construct complex trigger processors. The module uses both the fast ECL FERA bus and the CAMAC bus for inputs and outputs. The latter, however, is primarily used for set-up and control but may also be used for data output. Large numbers of ADCs can be served by a hierarchical arrangement of trigger processor modules, processing ADC data with pipe-line arithmetics producing the final result at the apex of the pyramid. The trigger decision will be transmitted to the data acquisition system via a logic signal while numeric results may be extracted by the CAMAC controller. The trigger processor was originally developed for the proposed neutral particle search experiment at CERN, NUMASS. There it was designed to serve as a second level trigger processor. It was required to correct all ADC raw data for efficiency and pedestal, calculate the total calorimeter energy, obtain the optimal time of flight data and calculate the particle mass. A suitable mass cut would then deliver the trigger decision. More complex triggers were also considered. (au)

Trigger chemistries for better industrial formulations.

Science.gov (United States)

Wang, Hsuan-Chin; Zhang, Yanfeng; Possanza, Catherine M; Zimmerman, Steven C; Cheng, Jianjun; Moore, Jeffrey S; Harris, Keith; Katz, Joshua S

2015-04-01

In recent years, innovations and consumer demands have led to increasingly complex liquid formulations. These growing complexities have provided industrial players and their customers access to new markets through product differentiation, improved performance, and compatibility/stability with other products. One strategy for enabling more complex formulations is the use of active encapsulation. When encapsulation is employed, strategies are required to effect the release of the active at the desired location and time of action. One particular route that has received significant academic research effort is the employment of triggers to induce active release upon a specific stimulus, though little has translated for industrial use to date. To address emerging industrial formulation needs, in this review, we discuss areas of trigger release chemistries and their applications specifically as relevant to industrial use. We focus the discussion on the use of heat, light, shear, and pH triggers as applied in several model polymeric systems for inducing active release. The goal is that through this review trends will emerge for how technologies can be better developed to maximize their value through industrial adaptation.

A trigger simulation framework for the ALICE experiment

International Nuclear Information System (INIS)

Antinori, F; Carminati, F; Gheata, A; Gheata, M

2011-01-01

A realistic simulation of the trigger system in a complex HEP experiment is essential for performing detailed trigger efficiency studies. The ALICE trigger simulation is evolving towards a framework capable of replaying the full trigger chain starting from the input to the individual trigger processors and ending with the decision mechanisms of the ALICE central trigger processor. This paper describes the new ALICE trigger simulation framework that is being tested and deployed. The framework handles details like trigger levels, signal delays and busy signals, implementing the trigger logic via customizable trigger device objects managed by a robust scheduling mechanism. A big advantage is the high flexibility of the framework, which is able to mix together components described with very different levels of detail. The framework is being gradually integrated within the ALICE simulation and reconstruction frameworks.

Macromolecular crystallography research at Trombay

International Nuclear Information System (INIS)

Kannan, K.K.; Chidamrabam, R.

1983-01-01

Neutron diffraction studies of hydrogen positions in small molecules of biological interest at Trombay have provided valuable information that has been used in protein and enzyme structure model-building and in developing hydrogen bond potential functions. The new R-5 reactor is expected to provide higher neutron fluxes and also make possible small-angle neutron scattering studies of large biomolecules and bio-aggregates. In the last few years infrastructure facilities have also been established for macromolecular x-ray crystallography research. Meanwhile, the refinement of carbonic hydrases and lyysozyme structures have been carried out and interesting results obtained on protein dynamics and structure-function relationships. Some interesting presynaptic toxin phospholipases have also taken up for study. (author)

Dexamethasone attenuates grain sorghum dust extract-induced increase in macromolecular efflux in vivo.

Science.gov (United States)

Akhter, S R; Ikezaki, H; Gao, X P; Rubinstein, I

1999-05-01

The purpose of this study was to determine whether dexamethasone attenuates grain sorghum dust extract-induced increase in macromolecular efflux from the in situ hamster cheek pouch and, if so, whether this response is specific. By using intravital microscopy, we found that an aqueous extract of grain sorghum dust elicited significant, concentration-dependent leaky site formation and increase in clearance of FITC-labeled dextran (FITC-dextran; mol mass, 70 kDa) from the in situ hamster cheek pouch (P grain sorghum dust extract- and substance P-induced increases in macromolecular efflux from the in situ hamster cheek pouch in a specific fashion.

A new paradigm for macromolecular crystallography beamlines derived from high-pressure methodology and results

Energy Technology Data Exchange (ETDEWEB)

Fourme, Roger, E-mail: roger.fourme@synchrotron-soleil.fr [Synchrotron SOLEIL, BP 48, Saint Aubin, 91192 Gif-sur-Yvette (France); Girard, Eric [IBS (UMR 5075 CEA-CNRS-UJF-PSB), 41 rue Jules Horowitz, 38027 Grenoble Cedex (France); Dhaussy, Anne-Claire [CRISMAT, ENSICAEN, 6 Boulevard du Maréchal Juin, 14000 Caen (France); Medjoubi, Kadda [Synchrotron SOLEIL, BP 48, Saint Aubin, 91192 Gif-sur-Yvette (France); Prangé, Thierry [LCRB (UMR 8015 CNRS), Université Paris Descartes, Faculté de Pharmacie, 4 avenue de l’Observatoire, 75270 Paris (France); Ascone, Isabella [ENSCP (UMR CNRS 7223), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Mezouar, Mohamed [ESRF, BP 220, 38043 Grenoble (France); Kahn, Richard [IBS (UMR 5075 CEA-CNRS-UJF-PSB), 41 rue Jules Horowitz, 38027 Grenoble Cedex (France)

2011-01-01

Macromolecular crystallography at high pressure (HPMX) is a mature technique. Shorter X-ray wavelengths increase data collection efficiency on cryocooled crystals. Extending applications and exploiting spin-off of HPMX will require dedicated synchrotron radiation beamlines based on a new paradigm. Biological structures can now be investigated at high resolution by high-pressure X-ray macromolecular crystallography (HPMX). The number of HPMX studies is growing, with applications to polynucleotides, monomeric and multimeric proteins, complex assemblies and even a virus capsid. Investigations of the effects of pressure perturbation have encompassed elastic compression of the native state, study of proteins from extremophiles and trapping of higher-energy conformers that are often of biological interest; measurements of the compressibility of crystals and macromolecules were also performed. HPMX results were an incentive to investigate short and ultra-short wavelengths for standard biocrystallography. On cryocooled lysozyme crystals it was found that the data collection efficiency using 33 keV photons is increased with respect to 18 keV photons. This conclusion was extended from 33 keV down to 6.5 keV by exploiting previously published data. To be fully exploited, the potential of higher-energy photons requires detectors with a good efficiency. Accordingly, a new paradigm for MX beamlines was suggested, using conventional short and ultra-short wavelengths, aiming at the collection of very high accuracy data on crystals under standard conditions or under high pressure. The main elements of such beamlines are outlined.

Macromolecular shape and interactions in layer-by-layer assemblies within cylindrical nanopores.

Science.gov (United States)

Lazzara, Thomas D; Lau, K H Aaron; Knoll, Wolfgang; Janshoff, Andreas; Steinem, Claudia

2012-01-01

Layer-by-layer (LbL) deposition of polyelectrolytes and proteins within the cylindrical nanopores of anodic aluminum oxide (AAO) membranes was studied by optical waveguide spectroscopy (OWS). AAO has aligned cylindrical, nonintersecting pores with a defined pore diameter d(0) and functions as a planar optical waveguide so as to monitor, in situ, the LbL process by OWS. The LbL deposition of globular proteins, i.e., avidin and biotinylated bovine serum albumin was compared with that of linear polyelectrolytes (linear-PEs), both species being of similar molecular weight. LbL deposition within the cylindrical AAO geometry for different pore diameters (d(0) = 25-80 nm) for the various macromolecular species, showed that the multilayer film growth was inhibited at different maximum numbers of LbL steps (n(max)). The value of n(max) was greatest for linear-PEs, while proteins had a lower value. The cylindrical pore geometry imposes a physical limit to LbL growth such that n(max) is strongly dependent on the overall internal structure of the LbL film. For all macromolecular species, deposition was inhibited in native AAO, having pores of d(0) = 25-30 nm. Both, OWS and scanning electron microscopy showed that LbL growth in larger AAO pores (d(0) > 25-30 nm) became inhibited when approaching a pore diameter of d(eff,n_max) = 25-35 nm, a similar size to that of native AAO pores, with d(0) = 25-30 nm. For a reasonable estimation of d(eff,n_max), the actual volume occupied by a macromolecular assembly must be taken into consideration. The results clearly show that electrostatic LbL allowed for compact macromolecular layers, whereas proteins formed loosely packed multilayers.

Tools for Trigger Aware Analyses in ATLAS

CERN Document Server

Krasznahorkay, A; The ATLAS collaboration; Stelzer, J

2010-01-01

In order to search for rare processes, all four LHC experiments have to use advanced triggering methods for selecting and recording the events of interest. At the expected nominal LHC operating conditions only about 0.0005% of the collision events can be kept for physics analysis in ATLAS. Therefore the understanding and evaluation of the trigger performance is one of the most crucial parts of any physics analysis. ATLAS’s first level trigger is composed of custom-built hardware, while the second and third levels are implemented using regular PCs running reconstruction and selection algorithms. Because of this split, accessing the results of the trigger execution for the two stages is different. The complexity of the software trigger presents further difficulties in accessing the trigger data. To make the job of the physicists easier when evaluating the trigger performance, multiple general-use tools are provided by the ATLAS Trigger Analysis Tools group. The TrigDecisionTool, a general tool, is provided to...

The DELPHI Trigger System at LEP2 Energies

CERN Document Server

Augustinus, A; Charpentier, P; De Wulf, J P; Fontanelli, F; Formenti, F; Gaspar, C; Gavillet, P; Goorens, R; Laugier, J P; Musico, P; Paganoni, M; Sannino, M; Valenti, G

2003-01-01

In this paper we describe the modifications carried out on the DELPHI trigger complex since the beginning of the high energy runs of LEP. The descriptions of the trigger configurations and performances for the 2000 data taking period are also presented.

Superhydrophobic hybrid membranes by grafting arc-like macromolecular bridges on graphene sheets: Synthesis, characterization and properties

Science.gov (United States)

Mo, Zhao-Hua; Luo, Zheng; Huang, Qiang; Deng, Jian-Ping; Wu, Yi-Xian

2018-05-01

Grafting single end-tethered polymer chains on the surface of graphene is a conventional way to modify the surface properties of graphene oxide. However, grafting arc-like macromolecular bridges on graphene surfaces has been barely reported. Herein, a novel arc-like polydimethylsiloxane (PDMS) macromolecular bridges grafted graphene sheets (GO-g-Arc PDMS) was successfully synthesized via a confined interface reaction at 90 °C. Both the hydrophilic α- and ω-amino groups of linear hydrophobic NH2-PDMS-NH2 macromolecular chains rapidly reacted with epoxy and carboxyl groups on the surfaces of graphene oxide in water suspension to form arc-like PDMS macromolecular bridges on graphene sheets. The grafting density of arc-like PDMS bridges on graphene sheets can reach up to 0.80 mmol g-1 or 1.32 arc-like bridges per nm2 by this confined interface reaction. The water contact angle (WCA) of the hybrid membrane could be increased with increasing both the grafting density and content of covalent arc-like bridges architecture. The superhydrophobic hybrid membrane with a WCA of 153.4° was prepared by grinding of the above arc-like PDMS bridges grafted graphene hybrid, dispersing in ethanol and filtrating by organic filter membrane. This superhydrophobic hybrid membrane shows good self-cleaning and complete oil-water separation properties, which provides potential applications in anticontamination coating and oil-water separation. To the best of our knowledge, this is the first report on the synthesis of functional hybrid membranes by grafting arc-like PDMS macromolecular bridges on graphene sheets via a confined interface reaction.

Tuning the properties of an anthracene-based PPE-PPV copolymer by fine variation of its macromolecular parameters

Czech Academy of Sciences Publication Activity Database

Tinti, F.; Sabir, F. K.; Gazzano, M.; Righi, S.; Ulbricht, C.; Usluer, Ö.; Pokorná, Veronika; Cimrová, Věra; Yohannes, T.; Egbe, D. A. M.; Camaioni, N.

2013-01-01

Roč. 3, č. 19 (2013), s. 6972-6980 ISSN 2046-2069 R&D Projects: GA ČR GAP106/12/0827; GA ČR(CZ) GA13-26542S Institutional support: RVO:61389013 Keywords : anthracene-containing PPE-PPV copolymer * macromolecular parameters * structural and transport properties Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.708, year: 2013

Metal Halide Perovskite Supercrystals: Gold-Bromide Complex Triggered Assembly of CsPbBr3 Nanocubes.

Science.gov (United States)

Wang, Kun-Hua; Yang, Jun-Nan; Ni, Qian-Kun; Yao, Hong-Bin; Yu, Shu-Hong

2018-01-16

Using nanocrystals as "artificial atoms" to construct supercrystals is an interesting process to explore the stacking style of nanoscale building blocks and corresponding collective properties. Various types of semiconducting supercrystals have been constructed via the assembly of nanocrystals driven by the entropic, electrostatic, or van der Waals interactions. We report a new type of metal halide perovskite supercrystals via the gold-bromide complex triggered assembly of newly emerged attractive CsPbBr 3 nanocubes. Through introducing gold-bromide (Au-Br) complexes into CsPbBr 3 nanocubes suspension, the self-assembly process of CsPbBr 3 nanocubes to form supercrystals was investigated with the different amount of Au-Br complexes added to the suspensions, which indicates that the driven force of the formation of CsPbBr 3 supercrystals included the van der Waals interactions among carbon chains and electrostatic interactions between Au-Br complexes and surfactants. Accordingly, the optical properties change with the assembly of CsPbBr 3 nanocubes and the variation of mesoscale structures of supercrystals with heating treatment was revealed as well, demonstrating the ionic characteristics of CsPbBr 3 nanocrystals. The fabricated CsPbBr 3 supercrystal presents a novel type of semiconducting supercrystals that will open an avenue for the assembly of ionic nanocrystals.

MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments

International Nuclear Information System (INIS)

Gabadinho, José; Beteva, Antonia; Guijarro, Matias; Rey-Bakaikoa, Vicente; Spruce, Darren

2010-01-01

MxCuBE is a beamline control environment optimized for the needs of macromolecular crystallography. This paper describes the design of the software and the features that MxCuBE currently provides. The design and features of a beamline control software system for macromolecular crystallography (MX) experiments developed at the European Synchrotron Radiation Facility (ESRF) are described. This system, MxCuBE, allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of a synchrotron beamline dedicated to experiments in MX. Additional functionality is provided through intuitive interfaces that enable the assessment of the diffraction characteristics of samples, experiment planning, automatic data collection and the on-line collection and analysis of X-ray emission spectra. The software can be run in a tandem client-server mode that allows for remote control and relevant experimental parameters and results are automatically logged in a relational database, ISPyB. MxCuBE is modular, flexible and extensible and is currently deployed on eight macromolecular crystallography beamlines at the ESRF. Additionally, the software is installed at MAX-lab beamline I911-3 and at BESSY beamline BL14.1

Making microenvironments: A look into incorporating macromolecular crowding into in vitro experiments, to generate biomimetic microenvironments which are capable of directing cell function for tissue engineering applications.

Science.gov (United States)

Benny, Paula; Raghunath, Michael

2017-01-01

Biomimetic microenvironments are key components to successful cell culture and tissue engineering in vitro. One of the most accurate biomimetic microenvironments is that made by the cells themselves. Cell-made microenvironments are most similar to the in vivo state as they are cell-specific and produced by the actual cells which reside in that specific microenvironment. However, cell-made microenvironments have been challenging to re-create in vitro due to the lack of extracellular matrix composition, volume and complexity which are required. By applying macromolecular crowding to current cell culture protocols, cell-made microenvironments, or cell-derived matrices, can be generated at significant rates in vitro. In this review, we will examine the causes and effects of macromolecular crowding and how it has been applied in several in vitro systems including tissue engineering.

Enzymes as Green Catalysts for Precision Macromolecular Synthesis.

Science.gov (United States)

Shoda, Shin-ichiro; Uyama, Hiroshi; Kadokawa, Jun-ichi; Kimura, Shunsaku; Kobayashi, Shiro

2016-02-24

The present article comprehensively reviews the macromolecular synthesis using enzymes as catalysts. Among the six main classes of enzymes, the three classes, oxidoreductases, transferases, and hydrolases, have been employed as catalysts for the in vitro macromolecular synthesis and modification reactions. Appropriate design of reaction including monomer and enzyme catalyst produces macromolecules with precisely controlled structure, similarly as in vivo enzymatic reactions. The reaction controls the product structure with respect to substrate selectivity, chemo-selectivity, regio-selectivity, stereoselectivity, and choro-selectivity. Oxidoreductases catalyze various oxidation polymerizations of aromatic compounds as well as vinyl polymerizations. Transferases are effective catalysts for producing polysaccharide having a variety of structure and polyesters. Hydrolases catalyzing the bond-cleaving of macromolecules in vivo, catalyze the reverse reaction for bond forming in vitro to give various polysaccharides and functionalized polyesters. The enzymatic polymerizations allowed the first in vitro synthesis of natural polysaccharides having complicated structures like cellulose, amylose, xylan, chitin, hyaluronan, and chondroitin. These polymerizations are "green" with several respects; nontoxicity of enzyme, high catalyst efficiency, selective reactions under mild conditions using green solvents and renewable starting materials, and producing minimal byproducts. Thus, the enzymatic polymerization is desirable for the environment and contributes to "green polymer chemistry" for maintaining sustainable society.

Atomic force microscopy applied to study macromolecular content of embedded biological material

Energy Technology Data Exchange (ETDEWEB)

Matsko, Nadejda B. [Electron Microscopy Centre, Institute of Applied Physics, HPM C 15.1, ETH-Hoenggerberg, CH-8093, Zurich (Switzerland)]. E-mail: matsko@iap.phys.ethz.ch

2007-02-15

We demonstrate that atomic force microscopy represents a powerful tool for the estimation of structural preservation of biological samples embedded in epoxy resin, in terms of their macromolecular distribution and architecture. The comparison of atomic force microscopy (AFM) and transmission electron microscopy (TEM) images of a biosample (Caenorhabditis elegans) prepared following to different types of freeze-substitution protocols (conventional OsO{sub 4} fixation, epoxy fixation) led to the conclusion that high TEM stainability of the sample results from a low macromolecular density of the cellular matrix. We propose a novel procedure aimed to obtain AFM and TEM images of the same particular organelle, which strongly facilitates AFM image interpretation and reveals new ultrastructural aspects (mainly protein arrangement) of a biosample in addition to TEM data.

Effect of macromolecular crowding on the rate of diffusion-limited ...

Indian Academy of Sciences (India)

The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model qualitatively explains some ...

New Paradigm for Macromolecular Crystallography Experiments at SSRL: Automated Crystal Screening And Remote Data Collection

International Nuclear Information System (INIS)

Soltis, S.M.; Cohen, A.E.; Deacon, A.; Eriksson, T.; Gonzalez, A.; McPhillips, S.; Chui, H.; Dunten, P.; Hollenbeck, M.; Mathews, I.; Miller, M.; Moorhead, P.; Phizackerley, R.P.; Smith, C.; Song, J.; Bedem, H. van dem; Ellis, P.; Kuhn, P.; McPhillips, T.; Sauter, N.; Sharp, K.

2009-01-01

Complete automation of the macromolecular crystallography experiment has been achieved at Stanford Synchrotron Radiation Lightsource (SSRL) through the combination of robust mechanized experimental hardware and a flexible control system with an intuitive user interface. These highly reliable systems have enabled crystallography experiments to be carried out from the researchers' home institutions and other remote locations while retaining complete control over even the most challenging systems. A breakthrough component of the system, the Stanford Auto-Mounter (SAM), has enabled the efficient mounting of cryocooled samples without human intervention. Taking advantage of this automation, researchers have successfully screened more than 200 000 samples to select the crystals with the best diffraction quality for data collection as well as to determine optimal crystallization and cryocooling conditions. These systems, which have been deployed on all SSRL macromolecular crystallography beamlines and several beamlines worldwide, are used by more than 80 research groups in remote locations, establishing a new paradigm for macromolecular crystallography experimentation.

In Vitro and In Vivo Evaluation of Microparticulate Drug Delivery Systems Composed of Macromolecular Prodrugs

Directory of Open Access Journals (Sweden)

Yoshiharu Machida

2008-08-01

Full Text Available Macromolecular prodrugs are very useful systems for achieving controlled drug release and drug targeting. In particular, various macromolecule-antitumor drug conjugates enhance the effectiveness and improve the toxic side effects. Also, polymeric micro- and nanoparticles have been actively examined and their in vivo behaviors elucidated, and it has been realized that their particle characteristics are very useful to control drug behavior. Recently, researches based on the combination of the concepts of macromolecular prodrugs and micro- or nanoparticles have been reported, although they are limited. Macromolecular prodrugs enable drugs to be released at a certain controlled release rate based on the features of the macromolecule-drug linkage. Micro- and nanoparticles can control in vivo behavior based on their size, surface charge and surface structure. These merits are expected for systems produced by the combination of each concept. In this review, several micro- or nanoparticles composed of macromolecule-drug conjugates are described for their preparation, in vitro properties and/or in vivo behavior.

Hydrogen-Bonding Interactions Trigger a Spin-Flip in Iron(III) Porphyrin Complexes**

Science.gov (United States)

Sahoo, Dipankar; Quesne, Matthew G; de Visser, Sam P; Rath, Sankar Prasad

2015-01-01

A key step in cytochrome P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure of a five-coordinate iron(III) octaethyltetraarylporphyrin chloride. The spin state of the metal was found to switch reversibly between high (S=5/2) and intermediate spin (S=3/2) with hydrogen bonding. Our study highlights the possible effects and importance of hydrogen-bonding interactions in heme proteins. This is the first example of a synthetic iron(III) complex that can reversibly change its spin state between a high and an intermediate state through weak external perturbations. PMID:26109743

Alkynyl gold(I) complex triggers necroptosis via ROS generation in colorectal carcinoma cells.

Science.gov (United States)

Mármol, Inés; Virumbrales-Muñoz, María; Quero, Javier; Sánchez-de-Diego, Cristina; Fernández, Luis; Ochoa, Ignacio; Cerrada, Elena; Yoldi, Mª Jesús Rodríguez

2017-11-01

Given the rise of apoptosis-resistant tumors, there exist a growing interest in developing new drugs capable of inducing different types of cell death to reduce colorectal cancer-related death rates. As apoptosis and necroptosis do not share cellular machinery, necroptosis induction may have a great therapeutic potential on those apoptosis-resistant cancers, despite the inflammatory effects associated with it. We have synthesized an alkynyl gold(I) complex [Au(CC-2-NC 5 H 4 )(PTA)] whose anticancer effect was tested on the colorectal adenocarcinoma Caco-2 cell line. With regard to its mechanism of action, this gold complex enters the mitochondria and disrupts its normal function, leading to an increase in ROS production, which triggers necroptosis. Necroptosis induction has been found dependent of TNF-α (Tumor necrosisfactor α) and TNFR1(Tumor necrosisfactor receptor 1) binding, RIP1(Receptor-Interacting Protein 1) activation and NF-κB (Nuclear Factor Kappa-Light-Chain-Enhancer of Activated B Cells) signaling. Moreover, the antitumor potential of [Au(CC-2-NC 5 H 4 )(PTA)] has also been confirmed on the 3D cancer model spheroid. Overall, the obtained data show firstly that gold complexes might have the ability of inducing necroptosis, and secondarily that our compound [Au(CC-2-NC 5 H 4 )(PTA)] is an interesting alternative to current chemotherapy drugs in cases of apoptosis resistance. Copyright © 2017. Published by Elsevier Inc.

TRIGGER

CERN Multimedia

Wesley Smith

Level-1 Trigger Hardware and Software The hardware of the trigger components has been mostly finished. The ECAL Endcap Trigger Concentrator Cards (TCC) are in production while Barrel TCC firmware has been upgraded, and the Trigger Primitives can now be stored by the Data Concentrator Card for readout by the DAQ. The Regional Calorimeter Trigger (RCT) system is complete, and the timing is being finalized. All 502 HCAL trigger links to RCT run without error. The HCAL muon trigger timing has been equalized with DT, RPC, CSC and ECAL. The hardware and firmware for the Global Calorimeter Trigger (GCT) jet triggers are being commissioned and data from these triggers is available for readout. The GCT energy sums from rings of trigger towers around the beam pipe beam have been changed to include two rings from both sides. The firmware for Drift Tube Track Finder, Barrel Sorter and Wedge Sorter has been upgraded, and the synchronization of the DT trigger is satisfactory. The CSC local trigger has operated flawlessly u...

Homogenization Theory for the Prediction of Obstructed Solute Diffusivity in Macromolecular Solutions.

Science.gov (United States)

Donovan, Preston; Chehreghanianzabi, Yasaman; Rathinam, Muruhan; Zustiak, Silviya Petrova

2016-01-01

The study of diffusion in macromolecular solutions is important in many biomedical applications such as separations, drug delivery, and cell encapsulation, and key for many biological processes such as protein assembly and interstitial transport. Not surprisingly, multiple models for the a-priori prediction of diffusion in macromolecular environments have been proposed. However, most models include parameters that are not readily measurable, are specific to the polymer-solute-solvent system, or are fitted and do not have a physical meaning. Here, for the first time, we develop a homogenization theory framework for the prediction of effective solute diffusivity in macromolecular environments based on physical parameters that are easily measurable and not specific to the macromolecule-solute-solvent system. Homogenization theory is useful for situations where knowledge of fine-scale parameters is used to predict bulk system behavior. As a first approximation, we focus on a model where the solute is subjected to obstructed diffusion via stationary spherical obstacles. We find that the homogenization theory results agree well with computationally more expensive Monte Carlo simulations. Moreover, the homogenization theory agrees with effective diffusivities of a solute in dilute and semi-dilute polymer solutions measured using fluorescence correlation spectroscopy. Lastly, we provide a mathematical formula for the effective diffusivity in terms of a non-dimensional and easily measurable geometric system parameter.

Homogenization Theory for the Prediction of Obstructed Solute Diffusivity in Macromolecular Solutions.

Directory of Open Access Journals (Sweden)

Preston Donovan

Full Text Available The study of diffusion in macromolecular solutions is important in many biomedical applications such as separations, drug delivery, and cell encapsulation, and key for many biological processes such as protein assembly and interstitial transport. Not surprisingly, multiple models for the a-priori prediction of diffusion in macromolecular environments have been proposed. However, most models include parameters that are not readily measurable, are specific to the polymer-solute-solvent system, or are fitted and do not have a physical meaning. Here, for the first time, we develop a homogenization theory framework for the prediction of effective solute diffusivity in macromolecular environments based on physical parameters that are easily measurable and not specific to the macromolecule-solute-solvent system. Homogenization theory is useful for situations where knowledge of fine-scale parameters is used to predict bulk system behavior. As a first approximation, we focus on a model where the solute is subjected to obstructed diffusion via stationary spherical obstacles. We find that the homogenization theory results agree well with computationally more expensive Monte Carlo simulations. Moreover, the homogenization theory agrees with effective diffusivities of a solute in dilute and semi-dilute polymer solutions measured using fluorescence correlation spectroscopy. Lastly, we provide a mathematical formula for the effective diffusivity in terms of a non-dimensional and easily measurable geometric system parameter.

Electrostatic assembly/disassembly of nanoscaled colloidosomes for light-triggered cargo release

KAUST Repository

Li, Song

2015-04-27

Colloidosome capsules possess the potential for the encapsulation and release of molecular and macromolecular cargos. However, the stabilization of the colloidosome shell usually requires an additional covalent crosslinking which irreversibly seals the capsules, and greatly limits their applications in large-cargos release. Herein we report nanoscaled colloidosomes designed by the electrostatic assembly of organosilica nanoparticles (NPs) with oppositely charged surfaces (rather than covalent bonds), arising from different contents of a bridged nitrophenylene-alkoxysilane [NB; 3-nitro-N-(3-(triethoxysilyl)propyl)-4-(((3-(triethoxysilyl)propyl)-amino)methyl)benzamid] derivative in the silica. The surface charge of the positively charged NPs was reversed by light irradiation because of a photoreaction in the NB moieties, which impacted the electrostatic interactions between NPs and disassembled the colloidosome nanosystems. This design was successfully applied for the encapsulation and light-triggered release of cargos. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PRIGo: a new multi-axis goniometer for macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Waltersperger, Sandro; Olieric, Vincent, E-mail: vincent.olieric@psi.ch; Pradervand, Claude [Paul Scherrer Institute, Villigen PSI (Switzerland); Glettig, Wayne [Centre Suisse d’Electronique et Microtechnique SA, Neuchâtel 2002 (Switzerland); Salathe, Marco; Fuchs, Martin R.; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias [Paul Scherrer Institute, Villigen PSI (Switzerland); Schulze-Briese, Clemens [Dectris Ltd, Baden 5400 (Switzerland); Wang, Meitian, E-mail: vincent.olieric@psi.ch [Paul Scherrer Institute, Villigen PSI (Switzerland)

2015-05-09

The design and performance of the new multi-axis goniometer PRIGo developed at the Swiss Light Source at Paul Scherrer Institute is described. The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0–90°), followed by a ϕ stage (0–360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.

Dendrimer-based Macromolecular MRI Contrast Agents: Characteristics and Application

Directory of Open Access Journals (Sweden)

Hisataka Kobayashi

2003-01-01

Full Text Available Numerous macromolecular MRI contrast agents prepared employing relatively simple chemistry may be readily available that can provide sufficient enhancement for multiple applications. These agents operate using a ~100-fold lower concentration of gadolinium ions in comparison to the necessary concentration of iodine employed in CT imaging. Herein, we describe some of the general potential directions of macromolecular MRI contrast agents using our recently reported families of dendrimer-based agents as examples. Changes in molecular size altered the route of excretion. Smaller-sized contrast agents less than 60 kDa molecular weight were excreted through the kidney resulting in these agents being potentially suitable as functional renal contrast agents. Hydrophilic and larger-sized contrast agents were found better suited for use as blood pool contrast agents. Hydrophobic variants formed with polypropylenimine diaminobutane dendrimer cores created liver contrast agents. Larger hydrophilic agents are useful for lymphatic imaging. Finally, contrast agents conjugated with either monoclonal antibodies or with avidin are able to function as tumor-specific contrast agents, which also might be employed as therapeutic drugs for either gadolinium neutron capture therapy or in conjunction with radioimmunotherapy.

Progress in rational methods of cryoprotection in macromolecular crystallography

International Nuclear Information System (INIS)

Alcorn, Thomas; Juers, Douglas H.

2010-01-01

Measurements of the average thermal contractions (294→72 K) of 26 different cryosolutions are presented and discussed in conjunction with other recent advances in the rational design of protocols for cryogenic cooling in macromolecular crystallography. Cryogenic cooling of macromolecular crystals is commonly used for X-ray data collection both to reduce crystal damage from radiation and to gather functional information by cryogenically trapping intermediates. However, the cooling process can damage the crystals. Limiting cooling-induced crystal damage often requires cryoprotection strategies, which can involve substantial screening of solution conditions and cooling protocols. Here, recent developments directed towards rational methods for cryoprotection are described. Crystal damage is described in the context of the temperature response of the crystal as a thermodynamic system. As such, the internal and external parts of the crystal typically have different cryoprotection requirements. A key physical parameter, the thermal contraction, of 26 different cryoprotective solutions was measured between 294 and 72 K. The range of contractions was 2–13%, with the more polar cryosolutions contracting less. The potential uses of these results in the development of cryocooling conditions, as well as recent developments in determining minimum cryosolution soaking times, are discussed

Collagen macromolecular drug delivery systems

International Nuclear Information System (INIS)

Gilbert, D.L.

1988-01-01

The objective of this study was to examine collagen for use as a macromolecular drug delivery system by determining the mechanism of release through a matrix. Collagen membranes varying in porosity, crosslinking density, structure and crosslinker were fabricated. Collagen characterized by infrared spectroscopy and solution viscosity was determined to be pure and native. The collagen membranes were determined to possess native vs. non-native quaternary structure and porous vs. dense aggregate membranes by electron microscopy. Collagen monolithic devices containing a model macromolecule (inulin) were fabricated. In vitro release rates were found to be linear with respect to t 1/2 and were affected by crosslinking density, crosslinker and structure. The biodegradation of the collagen matrix was also examined. In vivo biocompatibility, degradation and 14 C-inulin release rates were evaluated subcutaneously in rats

Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.

Science.gov (United States)

Ando, Tadashi; Yu, Isseki; Feig, Michael; Sugita, Yuji

2016-11-23

The cytoplasm of a cell is crowded with many different kinds of macromolecules. The macromolecular crowding affects the thermodynamics and kinetics of biological reactions in a living cell, such as protein folding, association, and diffusion. Theoretical and simulation studies using simplified models focus on the essential features of the crowding effects and provide a basis for analyzing experimental data. In most of the previous studies on the crowding effects, a uniform crowder size is assumed, which is in contrast to the inhomogeneous size distribution of macromolecules in a living cell. Here, we evaluate the free energy changes upon macromolecular association in a cell-like inhomogeneous crowding system via a theory of hard-sphere fluids and free energy calculations using Brownian dynamics trajectories. The inhomogeneous crowding model based on 41 different types of macromolecules represented by spheres with different radii mimics the physiological concentrations of macromolecules in the cytoplasm of Mycoplasma genitalium. The free energy changes of macromolecular association evaluated by the theory and simulations were in good agreement with each other. The crowder size distribution affects both specific and nonspecific molecular associations, suggesting that not only the volume fraction but also the size distribution of macromolecules are important factors for evaluating in vivo crowding effects. This study relates in vitro experiments on macromolecular crowding to in vivo crowding effects by using the theory of hard-sphere fluids with crowder-size heterogeneity.

Variable effects of soman on macromolecular secretion by ferret trachea

International Nuclear Information System (INIS)

McBride, R.K.; Zwierzynski, D.J.; Stone, K.K.; Culp, D.J.; Marin, M.G.

1991-01-01

The purpose of this study was to examine the effect of the anticholinesterase agent, soman, on macromolecular secretion by ferret trachea, in vitro. We mounted pieces of ferret trachea in Ussing-type chambers. Secreted sulfated macromolecules were radiolabeled by adding 500 microCi of 35 SO 4 to the submucosal medium and incubating for 17 hr. Soman added to the submucosal side produced a concentration-dependent increase in radiolabeled macromolecular release with a maximal secretory response (mean +/- SD) of 202 +/- 125% (n = 8) relative to the basal secretion rate at a concentration of 10 - 7 M. The addition of either 10 -6 M pralidoxime (acetylcholinesterase reactivator) or 10 -6 M atropine blocked the response to 10 -7 M soman. At soman concentrations greater than 10 -7 M, secretion rate decreased and was not significantly different from basal secretion. Additional experiments utilizing acetylcholine and the acetylcholinesterase inhibitor, physostigmine, suggest that inhibition of secretion by high concentrations of soman may be due to a secondary antagonistic effect of soman on muscarinic receptors

Data Management System at the Photon Factory Macromolecular Crystallography Beamline

International Nuclear Information System (INIS)

Yamada, Y; Matsugaki, N; Chavas, L M G; Hiraki, M; Igarashi, N; Wakatsuki, S

2013-01-01

Macromolecular crystallography is a very powerful tool to investigate three-dimensional structures of macromolecules at the atomic level, and is widely spread among structural biology researchers. Due to recent upgrades of the macromolecular crystallography beamlines at the Photon Factory, beamline throughput has improved, allowing more experiments to be conducted during a user's beam time. Although the number of beamlines has increased, so has the number of beam time applications. Consequently, both the experimental data from users' experiments and data derived from beamline operations have dramatically increased, causing difficulties in organizing these diverse and large amounts of data for the beamline operation staff and users. To overcome this problem, we have developed a data management system by introducing commercial middleware, which consists of a controller, database, and web servers. We have prepared several database projects using this system. Each project is dedicated to a certain aspect such as experimental results, beam time applications, beam time schedule, or beamline operation reports. Then we designed a scheme to link all the database projects.

Recent Advances in the Analysis of Macromolecular Interactions Using the Matrix-Free Method of Sedimentation in the Analytical Ultracentrifuge

Directory of Open Access Journals (Sweden)

Stephen E. Harding

2015-03-01

Full Text Available Sedimentation in the analytical ultracentrifuge is a matrix free solution technique with no immobilisation, columns, or membranes required and can be used to study self-association and complex or “hetero”-interactions, stoichiometry, reversibility and interaction strength of a wide variety of macromolecular types and across a very large dynamic range (dissociation constants from 10−12 M to 10−1 M. We extend an earlier review specifically highlighting advances in sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge applied to protein interactions and mucoadhesion and to review recent applications in protein self-association (tetanus toxoid, agrin, protein-like carbohydrate association (aminocelluloses, carbohydrate-protein interactions (polysaccharide-gliadin, nucleic-acid protein (G-duplexes, nucleic acid-carbohydrate (DNA-chitosan and finally carbohydrate-carbohydrate (xanthan-chitosan and a ternary polysaccharide complex interactions.

TRIGGER

CERN Multimedia

Wesley Smith

Level-1 Trigger Hardware and Software The trigger synchronization procedures for running with cosmic muons and operating with the LHC were reviewed during the May electronics week. Firmware maintenance issues were also reviewed. Link tests between the new ECAL endcap trigger concentrator cards (TCC48) and the Regional Calorimeter Trigger have been performed. Firmware for the energy sum triggers and an upgraded tau trigger of the Global Calorimeter Triggers has been developed and is under test. The optical fiber receiver boards for the Track-Finder trigger theta links of the DT chambers are now all installed. The RPC trigger is being made more robust by additional chamber and cable shielding and also by firmware upgrades. For the CSC’s the front-end and trigger motherboard firmware have been updated. New RPC patterns and DT/CSC lookup tables taking into account phi asymmetries in the magnetic field configuration are under study. The motherboard for the new pipeline synchronizer of the Global Trigg...

The BTeV trigger and data acquisition system

Energy Technology Data Exchange (ETDEWEB)

Butler, Joel N.; /Fermilab

2004-10-01

The BTeV trigger inspects every beam crossing of the Fermilab Tevatron, running at a luminosity of 2 x 10{sup 32}/cm{sup 2}-s, and selects events that have ''detached vertices'' from B decays occurring downstream of the main interaction. The system uses a massively parallel system of FPGAs and microprocessors to produce a trigger decision on average every 396 ns. The trigger calculations are facilitated by the 23 Million channel pixel detector that provides the input to the trigger. Front end electronics sparsifies the remainder of event data and sends it to large, Tbyte, memory buffers that store it until the trigger decision can be made. This complex system presents special challenges in fault monitoring and power and cooling.

Combining triggers in HEP data analysis

International Nuclear Information System (INIS)

Lendermann, Victor; Herbst, Michael; Krueger, Katja; Schultz-Coulon, Hans-Christian; Stamen, Rainer; Haller, Johannes

2009-01-01

Modern high-energy physics experiments collect data using dedicated complex multi-level trigger systems which perform an online selection of potentially interesting events. In general, this selection suffers from inefficiencies. A further loss of statistics occurs when the rate of accepted events is artificially scaled down in order to meet bandwidth constraints. An offline analysis of the recorded data must correct for the resulting losses in order to determine the original statistics of the analysed data sample. This is particularly challenging when data samples recorded by several triggers are combined. In this paper we present methods for the calculation of the offline corrections and study their statistical performance. Implications on building and operating trigger systems are discussed. (orig.)

Combining triggers in HEP data analysis

Energy Technology Data Exchange (ETDEWEB)

Lendermann, Victor; Herbst, Michael; Krueger, Katja; Schultz-Coulon, Hans-Christian; Stamen, Rainer [Heidelberg Univ. (Germany). Kirchhoff-Institut fuer Physik; Haller, Johannes [Hamburg Univ. (Germany). Institut fuer Experimentalphysik

2009-01-15

Modern high-energy physics experiments collect data using dedicated complex multi-level trigger systems which perform an online selection of potentially interesting events. In general, this selection suffers from inefficiencies. A further loss of statistics occurs when the rate of accepted events is artificially scaled down in order to meet bandwidth constraints. An offline analysis of the recorded data must correct for the resulting losses in order to determine the original statistics of the analysed data sample. This is particularly challenging when data samples recorded by several triggers are combined. In this paper we present methods for the calculation of the offline corrections and study their statistical performance. Implications on building and operating trigger systems are discussed. (orig.)

Modeling the multi-scale mechanisms of macromolecular resource allocation

DEFF Research Database (Denmark)

Yang, Laurence; Yurkovich, James T; King, Zachary A

2018-01-01

As microbes face changing environments, they dynamically allocate macromolecular resources to produce a particular phenotypic state. Broad 'omics' data sets have revealed several interesting phenomena regarding how the proteome is allocated under differing conditions, but the functional consequen...... and detail how mathematical models have aided in our understanding of these processes. Ultimately, such modeling efforts have helped elucidate the principles of proteome allocation and hold promise for further discovery....

TRIGGER

CERN Multimedia

W. Smith

2012-01-01

  Level-1 Trigger The Level-1 Trigger group is ready to deploy improvements to the L1 Trigger algorithms for 2012. These include new high-PT patterns for the RPC endcap, an improved CSC PT assignment, a new PT-matching algorithm for the Global Muon Trigger, and new calibrations for ECAL, HCAL, and the Regional Calorimeter Trigger. These should improve the efficiency, rate, and stability of the L1 Trigger. The L1 Trigger group also is migrating the online systems to SLC5. To make the data transfer from the Global Calorimeter Trigger to the Global Trigger more reliable and also to allow checking the data integrity online, a new optical link system has been developed by the GCT and GT groups and successfully tested at the CMS electronics integration facility in building 904. This new system is now undergoing further tests at Point 5 before being deployed for data-taking this year. New L1 trigger menus have recently been studied and proposed by Emmanuelle Perez and the L1 Detector Performance Group...

Pi sampling: a methodical and flexible approach to initial macromolecular crystallization screening

International Nuclear Information System (INIS)

Gorrec, Fabrice; Palmer, Colin M.; Lebon, Guillaume; Warne, Tony

2011-01-01

Pi sampling, derived from the incomplete factorial approach, is an effort to maximize the diversity of macromolecular crystallization conditions and to facilitate the preparation of 96-condition initial screens. The Pi sampling method is derived from the incomplete factorial approach to macromolecular crystallization screen design. The resulting ‘Pi screens’ have a modular distribution of a given set of up to 36 stock solutions. Maximally diverse conditions can be produced by taking into account the properties of the chemicals used in the formulation and the concentrations of the corresponding solutions. The Pi sampling method has been implemented in a web-based application that generates screen formulations and recipes. It is particularly adapted to screens consisting of 96 different conditions. The flexibility and efficiency of Pi sampling is demonstrated by the crystallization of soluble proteins and of an integral membrane-protein sample

The CMS trigger in Run 2

CERN Document Server

Tosi, Mia

2018-01-01

During its second period of operation (Run 2) which started in 2015, the LHC will reach a peak instantaneous luminosity of approximately 2$\\times 10^{34}$~cm$^{-2}s^{-1}$ with an average pile-up of about 55, far larger than the design value. Under these conditions, the online event selection is a very challenging task. In CMS, it is realised by a two-level trigger system: the Level-1 (L1) Trigger, implemented in custom-designed electronics, and the High Level Trigger (HLT), a streamlined version of the offline reconstruction software running on a computer farm.\\\\ In order to face this challenge, the L1 trigger has undergone a major upgrade compared to Run 1, whereby all electronic boards of the system have been replaced, allowing more sophisticated algorithms to be run online. Its last stage, the global trigger, is now able to perform complex selections and to compute high-level quantities, like invariant masses. Likewise, the algorithms that run in the HLT went through big improvements; in particular, new ap...

TRIGGER

CERN Multimedia

Wesley Smith

Level-1 Trigger Hardware and Software The production of the trigger hardware is now basically finished, and in time for the turn-on of the LHC. The last boards produced are the Trigger Concentrator Cards for the ECAL Endcaps (TCC-EE). After the recent installation of the four EE Dees, the TCC-EE prototypes were used for their commissioning. Production boards are arriving and are being tested continuously, with the last ones expected in November. The Regional Calorimeter Trigger hardware is fully integrated after installation of the last EE cables. Pattern tests from the HCAL up to the GCT have been performed successfully. The HCAL triggers are fully operational, including the connection of the HCAL-outer and forward-HCAL (HO/HF) technical triggers to the Global Trigger. The HCAL Trigger and Readout (HTR) board firmware has been updated to permit recording of the tower “feature bit” in the data. The Global Calorimeter Trigger hardware is installed, but some firmware developments are still n...

Rapid automated superposition of shapes and macromolecular models using spherical harmonics.

Science.gov (United States)

Konarev, Petr V; Petoukhov, Maxim V; Svergun, Dmitri I

2016-06-01

A rapid algorithm to superimpose macromolecular models in Fourier space is proposed and implemented ( SUPALM ). The method uses a normalized integrated cross-term of the scattering amplitudes as a proximity measure between two three-dimensional objects. The reciprocal-space algorithm allows for direct matching of heterogeneous objects including high- and low-resolution models represented by atomic coordinates, beads or dummy residue chains as well as electron microscopy density maps and inhomogeneous multi-phase models ( e.g. of protein-nucleic acid complexes). Using spherical harmonics for the computation of the amplitudes, the method is up to an order of magnitude faster than the real-space algorithm implemented in SUPCOMB by Kozin & Svergun [ J. Appl. Cryst. (2001 ▸), 34 , 33-41]. The utility of the new method is demonstrated in a number of test cases and compared with the results of SUPCOMB . The spherical harmonics algorithm is best suited for low-resolution shape models, e.g . those provided by solution scattering experiments, but also facilitates a rapid cross-validation against structural models obtained by other methods.

Thermal behaviour of zinc(II) 5-chlorosalicylate complex compounds

Czech Academy of Sciences Publication Activity Database

Györyová, K.; Chomič, J.; Kovářová, Jana

2005-01-01

Roč. 80, č. 2 (2005), s. 375-380 ISSN 1388-6150 Grant - others:Slovak Ministry of Education(SK) VEGA 1/2474/05 Institutional research plan: CEZ:AV0Z40500505 Keywords : caffeine * chlorosalicylate complexes * nicotinamide Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.425, year: 2005

Evidence for functional pre-coupled complexes of receptor heteromers and adenylyl cyclase.

Science.gov (United States)

Navarro, Gemma; Cordomí, Arnau; Casadó-Anguera, Verónica; Moreno, Estefanía; Cai, Ning-Sheng; Cortés, Antoni; Canela, Enric I; Dessauer, Carmen W; Casadó, Vicent; Pardo, Leonardo; Lluís, Carme; Ferré, Sergi

2018-03-28

G protein-coupled receptors (GPCRs), G proteins and adenylyl cyclase (AC) comprise one of the most studied transmembrane cell signaling pathways. However, it is unknown whether the ligand-dependent interactions between these signaling molecules are based on random collisions or the rearrangement of pre-coupled elements in a macromolecular complex. Furthermore, it remains controversial whether a GPCR homodimer coupled to a single heterotrimeric G protein constitutes a common functional unit. Using a peptide-based approach, we here report evidence for the existence of functional pre-coupled complexes of heteromers of adenosine A 2A receptor and dopamine D 2 receptor homodimers coupled to their cognate Gs and Gi proteins and to subtype 5 AC. We also demonstrate that this macromolecular complex provides the necessary frame for the canonical Gs-Gi interactions at the AC level, sustaining the ability of a Gi-coupled GPCR to counteract AC activation mediated by a Gs-coupled GPCR.

TRIGGER

CERN Multimedia

by Wesley Smith

2010-01-01

Level-1 Trigger Hardware and Software The overall status of the L1 trigger has been excellent and the running efficiency has been high during physics fills. The timing is good to about 1%. The fine-tuning of the time synchronization of muon triggers is ongoing and will be completed after more than 10 nb-1 of data have been recorded. The CSC trigger primitive and RPC trigger timing have been refined. A new configuration for the CSC Track Finder featured modified beam halo cuts and improved ghost cancellation logic. More direct control was provided for the DT opto-receivers. New RPC Cosmic Trigger (RBC/TTU) trigger algorithms were enabled for collision runs. There is further work planned during the next technical stop to investigate a few of the links from the ECAL to the Regional Calorimeter Trigger (RCT). New firmware and a new configuration to handle trigger rate spikes in the ECAL barrel are also being tested. A board newly developed by the tracker group (ReTRI) has been installed and activated to block re...

Functionalization of Planet-Satellite Nanostructures Revealed by Nanoscopic Localization of Distinct Macromolecular Species

KAUST Repository

Rossner, Christian; Roddatis, Vladimir; Lopatin, Sergei; Vana, Philipp

2016-01-01

The development of a straightforward method is reported to form hybrid polymer/gold planet-satellite nanostructures (PlSNs) with functional polymer. Polyacrylate type polymer with benzyl chloride in its backbone as a macromolecular tracer

Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes.

Science.gov (United States)

Lee, Kenneth K; Sardiu, Mihaela E; Swanson, Selene K; Gilmore, Joshua M; Torok, Michael; Grant, Patrick A; Florens, Laurence; Workman, Jerry L; Washburn, Michael P

2011-07-05

Despite the availability of several large-scale proteomics studies aiming to identify protein interactions on a global scale, little is known about how proteins interact and are organized within macromolecular complexes. Here, we describe a technique that consists of a combination of biochemistry approaches, quantitative proteomics and computational methods using wild-type and deletion strains to investigate the organization of proteins within macromolecular protein complexes. We applied this technique to determine the organization of two well-studied complexes, Spt-Ada-Gcn5 histone acetyltransferase (SAGA) and ADA, for which no comprehensive high-resolution structures exist. This approach revealed that SAGA/ADA is composed of five distinct functional modules, which can persist separately. Furthermore, we identified a novel subunit of the ADA complex, termed Ahc2, and characterized Sgf29 as an ADA family protein present in all Gcn5 histone acetyltransferase complexes. Finally, we propose a model for the architecture of the SAGA and ADA complexes, which predicts novel functional associations within the SAGA complex and provides mechanistic insights into phenotypical observations in SAGA mutants.

Searching and Extracting Data from the EMBL-EBI Complex Portal.

Science.gov (United States)

Meldal, Birgit H M; Orchard, Sandra

2018-01-01

The Complex Portal ( www.ebi.ac.uk/complexportal ) is an encyclopedia of macromolecular complexes. Complexes are assigned unique, stable IDs, are species specific, and list all participating members with links to an appropriate reference database (UniProtKB, ChEBI, RNAcentral). Each complex is annotated extensively with its functions, properties, structure, stoichiometry, tissue expression profile, and subcellular location. Links to domain-specific databases allow the user to access additional information and enable data searching and filtering. Complexes can be saved and downloaded in PSI-MI XML, MI-JSON, and tab-delimited formats.

Thiomers for oral delivery of hydrophilic macromolecular drugs.

Science.gov (United States)

Bernkop-Schnürch, Andreas; Hoffer, Martin H; Kafedjiiski, Krum

2004-11-01

In recent years thiolated polymers (thiomers) have appeared as a promising new tool in oral drug delivery. Thiomers are obtained by the immobilisation of thio-bearing ligands to mucoadhesive polymeric excipients. By the formation of disulfide bonds with mucus glycoproteins, the mucoadhesive properties of thiomers are up to 130-fold improved compared with the corresponding unmodified polymers. Owing to the formation of inter- and intramolecular disulfide bonds within the thiomer itself, matrix tablets and particulate delivery systems show strong cohesive properties, resulting in comparatively higher stability, prolonged disintegration times and a more controlled drug release. The permeation of hydrophilic macromolecular drugs through the gastrointestinal (GI) mucosa can be improved by the use of thiomers. Furthermore, some thiomers exhibit improved inhibitory properties towards GI peptidases. The efficacy of thiomers in oral drug delivery has been demonstrated by various in vivo studies. A pharmacological efficacy of 1%, for example, was achieved in rats by oral administration of calcitonin tablets comprising a thiomer. Furthermore, tablets comprising a thiomer and pegylated insulin resulted in a pharmacological efficacy of 7% after oral application to diabetic mice. Low-molecular-weight heparin embedded in thiolated polycarbophil led to an absolute bioavailability of > or = 20% after oral administration to rats. In these studies, formulations comprising the corresponding unmodified polymer had only a marginal or no effect. These results indicate drug carrier systems based on thiomers appear to be a promising tool for oral delivery of hydrophilic macromolecular drugs.

TRIGGER

CERN Multimedia

Roberta Arcidiacono

2013-01-01

Trigger Studies Group (TSG) The Trigger Studies Group has just concluded its third 2013 workshop, where all POGs presented the improvements to the physics object reconstruction, and all PAGs have shown their plans for Trigger development aimed at the 2015 High Level Trigger (HLT) menu. The Strategy for Trigger Evolution And Monitoring (STEAM) group is responsible for Trigger menu development, path timing, Trigger performance studies coordination, HLT offline DQM as well as HLT release, menu and conditions validation – this last task in collaboration with PdmV (Physics Data and Monte Carlo Validation group). In the last months the group has delivered several HLT rate estimates and comparisons, using the available data and Monte Carlo samples. The studies were presented at the Trigger workshops in September and December, and STEAM has contacted POGs and PAGs to understand the origin of the discrepancies observed between 8 TeV data and Monte Carlo simulations. The most recent results show what the...

An 'attachment kinetics-based' volume of fraction method for organic crystallization: a fluid-dynamic approach to macromolecular-crystal engineering

International Nuclear Information System (INIS)

Lappa, Marcello

2003-01-01

This analysis exhibits a strong interdisciplinary nature and deals with advances in protein (crystal) engineering models and computational methods as well as with novel results on the relative importance of 'controlling forces' in macromolecular crystal growth. The attention is focused in particular on microgravity fluid-dynamic aspects. From a numerical point of view, the growing crystal gives rise to a moving boundary problem. A 'kinetic-coefficient-based' volume tracking method is specifically and carefully developed according to the complex properties and mechanisms of macromolecular protein crystal growth taking into account the possibility of anisotropic (faceted) surface-orientation-dependent growth. The method is used to shed some light on the interplay of surface attachment kinetics and mass transport (diffusive or convective) in liquid phase and on several mechanisms still poorly understood. It is shown that the size of a growing crystal plays a 'critical role' in the relative importance of surface effects and in determining the intensity of convection. Convective effects, in turn, are found to impact growth rates, macroscopic structures of precipitates, particle size and morphology as well as the mechanisms driving growth. The paper introduces a novel computational method (that simulates the growth due to the slow addition of solute molecules to a lattice and can handle the shape of organic growing crystals under the influence of natural convection) and, at the same time, represents a quite exhaustive attempt to help organic crystal growers to discern the complex interrelations among the various parameters under one's control (that are not independent of one another) and to elaborate rational guidelines relating to physical factors that can influence the probability of success in crystallizing protein substances

Fluid Physics and Macromolecular Crystal Growth in Microgravity

Science.gov (United States)

Helliwell, John R.; Snell, Edward H.; Chayen, Naomi E.; Judge, Russell A.; Boggon, Titus J.; Pusey, M. L.; Rose, M. Franklin (Technical Monitor)

2000-01-01

" is often historically used to describe these microgravity experiments. This is somewhat inaccurate as the field involves the study of many varied biological molecules including viruses, proteins, DNA, RNA and complexes of those structures. For this reason we use the term macromolecular crystal growth. In this chapter we review a series of diagnostic microgravity crystal growth experiments carried out principally using the European Space Agency (ESA) Advanced Protein Crystallization Facility (APCF). We also review related research, both experimental and theoretical, on the aspects of microgravity fluid physics that affect microgravity protein crystal growth. Our experiments have revealed some surprises that were not initially expected. We discuss them here in the context of practical lessons learnt and how to maximize the limited microgravity opportunities available.

ISPyB: an information management system for synchrotron macromolecular crystallography.

Science.gov (United States)

Delagenière, Solange; Brenchereau, Patrice; Launer, Ludovic; Ashton, Alun W; Leal, Ricardo; Veyrier, Stéphanie; Gabadinho, José; Gordon, Elspeth J; Jones, Samuel D; Levik, Karl Erik; McSweeney, Seán M; Monaco, Stéphanie; Nanao, Max; Spruce, Darren; Svensson, Olof; Walsh, Martin A; Leonard, Gordon A

2011-11-15

Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management. ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.

Macromolecular systems for vaccine delivery.

Science.gov (United States)

MuŽíková, G; Laga, R

2016-10-20

Vaccines have helped considerably in eliminating some life-threatening infectious diseases in past two hundred years. Recently, human medicine has focused on vaccination against some of the world's most common infectious diseases (AIDS, malaria, tuberculosis, etc.), and vaccination is also gaining popularity in the treatment of cancer or autoimmune diseases. The major limitation of current vaccines lies in their poor ability to generate a sufficient level of protective antibodies and T cell responses against diseases such as HIV, malaria, tuberculosis and cancers. Among the promising vaccination systems that could improve the potency of weakly immunogenic vaccines belong macromolecular carriers (water soluble polymers, polymer particels, micelles, gels etc.) conjugated with antigens and immunistumulatory molecules. The size, architecture, and the composition of the high molecular-weight carrier can significantly improve the vaccine efficiency. This review includes the most recently developed (bio)polymer-based vaccines reported in the literature.

Release of polyanions from polyelectrolyte complexes by selective degradation of the polycation

Czech Academy of Sciences Publication Activity Database

Etrych, Tomáš; Boustta, M.; Leclercq, L.; Vert, M.

2006-01-01

Roč. 21, č. 2 (2006), s. 89-105 ISSN 0883-9115 Institutional research plan: CEZ:AV0Z40500505 Keywords : polyelectrolyte complex * enzymatic degradation * hydrolytic degradation Subject RIV: CD - Macromolecular Chemistry Impact factor: 0.925, year: 2006

Synthesis of novel complexing macromolecular surfactants and study of their interactions with cobalt for the development of a decontamination process of textiles in dense CO2 medium

International Nuclear Information System (INIS)

Chirat, M.

2012-01-01

This study is about textile decontamination in dense CO 2 (liquid CO 2 or supercritical CO 2 ). The study is carried out in the framework of decontamination of textile used in the nuclear industry. The dense CO 2 offers an alternative to aqueous medium used in the current process which generates a huge quantity of contaminated aqueous effluent requiring a post-treatment. Cobalt is the targeted contamination and can be found as ionic species or particles. The cobalt extraction in dense CO 2 is achieved with an additive: a complexing CO 2 -philic/CO 2 -phobic macromolecular surfactant. Several types of additives were synthesized by controlled free radical polymerization: gradient copolymers made with CO 2 -philic groups (silicone-based or fluorinated moieties) and CO 2 -phobic complexing groups (aceto acetoxy, di-ethylphosphonate or phosphonic acid moieties). The copolymer behavior in dense CO 2 was determined by phase diagram measurements (cloud point method) and their self-assembly in dense CO 2 was investigated by small angle neutron scattering. The fluorinated copolymers were found advantageous in terms of solubility. Nevertheless, the silicone-based copolymers showed solubilities which are compatible with the process, therefore they are a good alternative to avoid fluorinated compounds which are unwanted in the conditioning of nuclear wastes. The study of cobalt complexation by the copolymers (UV-vis spectroscopy and inductively coupled plasma-mass spectroscopy) established relations between the type of complexing group and the affinity with the cobalt. The solubility of copolymer-cobalt complexes in dense CO 2 is similar to those of copolymers. Moreover, the self-assembly study of the complex revealed a low aggregation. Finally, the synthesized copolymers were used in particle or ionic decontamination processes. In the case of ionic decontamination process, a rate of 70% of decontamination was reached with the use of gradient copolymer poly(1

Functionalized active-nucleus complex sensor

Science.gov (United States)

Pines, Alexander; Wemmer, David E.; Spence, Megan; Rubin, Seth

2003-11-25

A functionalized active-nucleus complex sensor that selectively associates with one or more target species, and a method for assaying and screening for one or a plurality of target species utilizing one or a plurality of functionalized active-nucleus complexes with at least two of the functionalized active-nucleus complexes having an attraction affinity to different corresponding target species. The functionalized active-nucleus complex has an active-nucleus and a targeting carrier. The method involves functionalizing an active-nucleus, for each functionalized active-nucleus complex, by incorporating the active-nucleus into a macromolucular or molecular complex that is capable of binding one of the target species and then bringing the macromolecular or molecular complexes into contact with the target species and detecting the occurrence of or change in a nuclear magnetic resonance signal from each of the active-nuclei in each of the functionalized active-nucleus complexes.

TRIGGER

CERN Multimedia

W. Smith

2010-01-01

Level-1 Trigger Hardware and Software The Level-1 Trigger hardware has performed well during both the recent proton-proton and heavy ion running. Efforts were made to improve the visibility and handling of alarms and warnings. The tracker ReTRI boards that prevent fixed frequencies of Level-1 Triggers are now configured through the Trigger Supervisor. The Global Calorimeter Trigger (GCT) team has introduced a buffer cleanup procedure at stops and a reset of the QPLL during configuring to ensure recalibration in case of a switch from the LHC clock to the local clock. A device to test the cables between the Regional Calorimeter Trigger and the GCT has been manufactured. A wrong charge bit was fixed in the CSC Trigger. The ECAL group is improving crystal masking and spike suppression in the trigger primitives. New firmware for the Drift Tube Track Finder (DTTF) sorters was developed to improve fake track tagging and sorting. Zero suppression was implemented in the DT Sector Collector readout. The track finder b...

TRIGGER

CERN Multimedia

Wesley Smith

Trigger Hardware The status of the trigger components was presented during the September CMS Week and Annual Review and at the monthly trigger meetings in October and November. Procedures for cold and warm starts (e.g. refreshing of trigger parameters stored in registers) of the trigger subsystems have been studied. Reviews of parts of the Global Calorimeter Trigger (GCT) and the Global Trigger (GT) have taken place in October and November. The CERN group summarized the status of the Trigger Timing and Control (TTC) system. All TTC crates and boards are installed in the underground counting room, USC55. The central clock system will be upgraded in December (after the Global Run at the end of November GREN) to the new RF2TTC LHC machine interface timing module. Migration of subsystem's TTC PCs to SLC4/ XDAQ 3.12 is being prepared. Work is on going to unify the access to Local Timing Control (LTC) and TTC CMS interface module (TTCci) via SOAP (Simple Object Access Protocol, a lightweight XML-based messaging ...

The contrasting effect of macromolecular crowding on amyloid fibril formation.

Directory of Open Access Journals (Sweden)

Qian Ma

Full Text Available Amyloid fibrils associated with neurodegenerative diseases can be considered biologically relevant failures of cellular quality control mechanisms. It is known that in vivo human Tau protein, human prion protein, and human copper, zinc superoxide dismutase (SOD1 have the tendency to form fibril deposits in a variety of tissues and they are associated with different neurodegenerative diseases, while rabbit prion protein and hen egg white lysozyme do not readily form fibrils and are unlikely to cause neurodegenerative diseases. In this study, we have investigated the contrasting effect of macromolecular crowding on fibril formation of different proteins.As revealed by assays based on thioflavin T binding and turbidity, human Tau fragments, when phosphorylated by glycogen synthase kinase-3β, do not form filaments in the absence of a crowding agent but do form fibrils in the presence of a crowding agent, and the presence of a strong crowding agent dramatically promotes amyloid fibril formation of human prion protein and its two pathogenic mutants E196K and D178N. Such an enhancing effect of macromolecular crowding on fibril formation is also observed for a pathological human SOD1 mutant A4V. On the other hand, rabbit prion protein and hen lysozyme do not form amyloid fibrils when a crowding agent at 300 g/l is used but do form fibrils in the absence of a crowding agent. Furthermore, aggregation of these two proteins is remarkably inhibited by Ficoll 70 and dextran 70 at 200 g/l.We suggest that proteins associated with neurodegenerative diseases are more likely to form amyloid fibrils under crowded conditions than in dilute solutions. By contrast, some of the proteins that are not neurodegenerative disease-associated are unlikely to misfold in crowded physiological environments. A possible explanation for the contrasting effect of macromolecular crowding on these two sets of proteins (amyloidogenic proteins and non-amyloidogenic proteins has been

A readout buffer prototype for ATLAS high-level triggers

CERN Document Server

Calvet, D; Huet, M; Le Dû, P; Mandjavidze, I D; Mur, M

2001-01-01

Readout buffers are critical components in the dataflow chain of the ATLAS trigger/data-acquisition system. At up to 75 kHz, after each Level-1 trigger accept signal, these devices receive and store digitized data from groups of front-end electronic channels. Several readout buffers are grouped to form a readout buffer complex that acts as a data server for the high-level trigger selection algorithms and for the final data-collection system. This paper describes a functional prototype of a readout buffer based on a custom-made PCI mezzanine card that is designed to accept input data at up to 160 MB /s, to store up to 8 MB of data, and to distribute data chunks at the desired request rate. We describe the hardware of the card that is based on an Intel 1960 processor and complex programmable logic devices. We present the integration of several of these cards in a readout buffer complex. We measure various performance figures and discuss to which extent these can fulfil ATLAS needs. (5 refs).

A Novel in situ Trigger Combination Method

International Nuclear Information System (INIS)

Buzatu, Adrian; Warburton, Andreas; Krumnack, Nils; Yao, Wei-Ming

2012-01-01

Searches for rare physics processes using particle detectors in high-luminosity colliding hadronic beam environments require the use of multi-level trigger systems to reject colossal background rates in real time. In analyses like the search for the Higgs boson, there is a need to maximize the signal acceptance by combining multiple different trigger chains when forming the offline data sample. In such statistically limited searches, datasets are often amassed over periods of several years, during which the trigger characteristics evolve and their performance can vary significantly. Reliable production cross-section measurements and upper limits must take into account a detailed understanding of the effective trigger inefficiency for every selected candidate event. We present as an example the complex situation of three trigger chains, based on missing energy and jet energy, to be combined in the context of the search for the Higgs (H) boson produced in association with a W boson at the Collider Detector at Fermilab (CDF). We briefly review the existing techniques for combining triggers, namely the inclusion, division, and exclusion methods. We introduce and describe a novel fourth in situ method whereby, for each candidate event, only the trigger chain with the highest a priori probability of selecting the event is considered. The in situ combination method has advantages of scalability to large numbers of differing trigger chains and of insensitivity to correlations between triggers. We compare the inclusion and in situ methods for signal event yields in the CDF WH search.

In-vacuum long-wavelength macromolecular crystallography.

Science.gov (United States)

Wagner, Armin; Duman, Ramona; Henderson, Keith; Mykhaylyk, Vitaliy

2016-03-01

Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline.

Fourier-transform infrared spectroscopic study of a fractional-complexed polymer blend

Czech Academy of Sciences Publication Activity Database

Šturcová, Adriana; Kratochvíl, Jaroslav; Dybal, Jiří; Sikora, Antonín

2014-01-01

Roč. 59, October (2014), s. 200-207 ISSN 0014-3057 R&D Projects: GA ČR GAP108/12/0703 Institutional support: RVO:61389013 Keywords : miscible blend * inter-polymer complex * associative phase separation Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.005, year: 2014

Light-Triggered Release of DNA from Plasmon-Resonant Nanoparticles

Science.gov (United States)

Huschka, Ryan

Plasmon-resonant nanoparticle complexes show promising potential for lighttriggered, controllable delivery of deoxyribonucleic acids (DNA) for research and therapeutic purposes. For example, the approach of RNA interference (RNAi) . using antisense DNA or RNA oligonucleotides to silence activity of a specific pathogenic gene transcript and reduce expression of the encoded protein . is very useful in dissecting genetic function and holds promise as a molecular therapeutic. Herein, we investigate the mechanism and probe the in vitro therapeutic potential of DNA light-triggered release from plasmonic nanoparticles. First, we investigate the mechanism of light-triggered release by dehybridizing double-stranded (dsDNA) via laser illumination from two types of nanoparticle substrates: gold (Au) nanoshells and Au nanorods. Both light-triggered and thermally induced releases are distinctly observable from nanoshell-based complexes. Surprisingly, no analogous measurable light-triggered release was observable from nanorod-based complexes below the DNA melting temperature. These results suggest that a nonthermal mechanism may play a role in light-triggered DNA release. Second, we demonstrate the in vitro light-triggered release of molecules noncovalently attached within dsDNA bound to the Au nanoshell surface. DAPI (4',6- diamidino-2-phenylindole), a bright blue fluorescent molecule that binds reversibly to double-stranded DNA, was chosen to visualize this intracellular light-induced release process. Illumination through the cell membrane of the nanoshell-dsDNA-DAPI complexes dehybridizes the DNA and releases the DAPI molecules within living cells. The DAPI molecules diffuse to the nucleus and associate with the cell's endogenous DNA. This work could have future applications towards drug delivery of molecules that associate with dsDNA. Finally, we demonstrate an engineered Au nanoshell (AuNS)-based therapeutic oligonucleotide delivery vehicle, designed to release its cargo on

A real-time high level trigger system for CALIFA

Energy Technology Data Exchange (ETDEWEB)

Gernhaeuser, Roman; Heiss, Benjamin; Klenze, Philipp; Remmels, Patrick; Winkel, Max [Physik Department, Technische Universitaet Muenchen (Germany)

2016-07-01

The CALIFA calorimeter with its about 2600 scintillator crystals is a key component of the R{sup 3}B setup. For many experiments CALIFA will have to perform complex trigger decisions depending on the total energy deposition, γ multiplicities or geometrical patterns with a minimal latency. This selection is an essential tool for the accurate preselection of relevant events and provides a significant data reduction. The challenge is to aggregate local trigger information from up to 200 readout modules. The trigger tree transport protocol (T{sup 3}P) will use dedicated FPGA boards and bus systems to collect trigger information and perform hierarchical summations to ensure a trigger decision within 1 μs. The basic concept and implementation of T{sup 3}P are presented together with first tests on a prototype system.

Tracking at High Level Trigger in CMS

CERN Document Server

Tosi, Mia

2016-01-01

The trigger systems of the LHC detectors play a crucial role in determining the physics capabili- ties of the experiments. A reduction of several orders of magnitude of the event rate is needed to reach values compatible with detector readout, offline storage and analysis capability. The CMS experiment has been designed with a two-level trigger system: the Level-1 Trigger (L1T), implemented on custom-designed electronics, and the High Level Trigger (HLT), a stream- lined version of the CMS offline reconstruction software running on a computer farm. A software trigger system requires a trade-off between the complexity of the algorithms, the sustainable out- put rate, and the selection efficiency. With the computing power available during the 2012 data taking the maximum reconstruction time at HLT was about 200 ms per event, at the nominal L1T rate of 100 kHz. Track reconstruction algorithms are widely used in the HLT, for the reconstruction of the physics objects as well as in the identification of b-jets and ...

Electron-triggered chemistry in HNO3/H2O complexes

Czech Academy of Sciences Publication Activity Database

Lengyel, Jozef; Ončák, M.; Fedor, Juraj; Kočišek, Jaroslav; Pysanenko, Andriy; Beyer, M. K.; Fárník, Michal

2017-01-01

Roč. 19, č. 19 (2017), s. 11753-11758 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA15-12386S Institutional support: RVO:61388955 Keywords : electron-triggered chemistry * acid-water clusters * gas-phase reactions Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 4.123, year: 2016

Workshop on algorithms for macromolecular modeling. Final project report, June 1, 1994--May 31, 1995

Energy Technology Data Exchange (ETDEWEB)

Leimkuhler, B.; Hermans, J.; Skeel, R.D.

1995-07-01

A workshop was held on algorithms and parallel implementations for macromolecular dynamics, protein folding, and structural refinement. This document contains abstracts and brief reports from that workshop.

Structure of valinomycin and its complexes

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich; Makrlík, E.; Dušek, Michal; Císařová, I.; Dohnálek, Jan; Dušková, Jarmila; Skálová, Tereza

2009-01-01

Roč. 16, 2a (2009), s. 30-31 ISSN 1211-5894. [Struktura - Colloquium of Czech and Slovak Crystallographic Association. Hluboká nad Vltavou, 22.06.2009-25.06.2009] R&D Projects: GA ČR GA305/07/1073; GA AV ČR IAA500500701 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z10100521 Keywords : valinomycin * complex * structure 8 hydration Subject RIV: CD - Macromolecular Chemistry

MR lymphography with macromolecular Gd-DTPA compounds

International Nuclear Information System (INIS)

Hamm, B.; Wagner, S.; Branding, G.; Taupitz, M.; Wolf, K.J.

1990-01-01

This paper investigates the suitability of macromolecular Gd-DTPA compounds as signal-enhancing lymphographic agents in MR imaging. Two Gd-DTPA polylysin compounds and Gd-DTPA albumin, with molecular weights of 48,000,170,000, and 87,000 daltons, respectively, were tested in rabbits at gadolinium doses of 5 and 15 μmol per animal. Three animals were examined at each dose with T1-weighted sequences. The iliac lymph nodes were imaged prior to and during unilateral endolymphatic infusion into a femoral lymph vessel as well as over a period of 2 hours thereafter. All contrast media showed a homogeneous and pronounced signal enhancement in the lymph nodes during infusion at both doses

TRIGGER

CERN Multimedia

Wesley Smith

Level-1 Trigger Hardware and Software The final parts of the Level-1 trigger hardware are now being put in place. For the ECAL endcaps, more than half of the Trigger Concentrator Cards for the ECAL Endcap (TCC-EE) are now available at CERN, such that one complete endcap can be covered. The Global Trigger now correctly handles ECAL calibration sequences, without being influenced by backpressure. The Regional Calorimeter Trigger (RCT) hardware is complete and working in USC55. Intra-crate tests of all 18 RCT crates and the Global Calorimeter Trigger (GCT) are regularly taking place. Pattern tests have successfully captured data from HCAL through RCT to the GCT Source Cards. HB/HE trigger data are being compared with emulator results to track down the very few remaining hardware problems. The treatment of hot and dead cells, including their recording in the database, has been defined. For the GCT, excellent agreement between the emulator and data has been achieved for jets and HF ET sums. There is still som...

TRIGGER

CERN Multimedia

W. Smith

Level-1 Trigger Hardware and Software The trigger system has been constantly in use in cosmic and commissioning data taking periods. During CRAFT running it delivered 300 million muon and calorimeter triggers to CMS. It has performed stably and reliably. During the abort gaps it has also provided laser and other calibration triggers. Timing issues, namely synchronization and latency issues, have been solved. About half of the Trigger Concentrator Cards for the ECAL Endcap (TCC-EE) are installed, and the firmware is being worked on. The production of the other half has started. The HCAL Trigger and Readout (HTR) card firmware has been updated, and new features such as fast parallel zero-suppression have been included. Repairs of drift tube (DT) trigger mini-crates, optical links and receivers of sector collectors are under way and have been completed on YB0. New firmware for the optical receivers of the theta links to the drift tube track finder is being installed. In parallel, tests with new eta track finde...

TRIGGER

CERN Multimedia

R. Carlin with contributions from D. Acosta

2012-01-01

Level-1 Trigger Data-taking continues at cruising speed, with high availability of all components of the Level-1 trigger. We have operated the trigger up to a luminosity of 7.6E33, where we approached 100 kHz using the 7E33 prescale column.  Recently, the pause without triggers in case of an automatic "RESYNC" signal (the "settle" and "recover" time) was reduced in order to minimise the overall dead-time. This may become very important when the LHC comes back with higher energy and luminosity after LS1. We are also preparing for data-taking in the proton-lead run in early 2013. The CASTOR detector will make its comeback into CMS and triggering capabilities are being prepared for this. Steps to be taken include improved cooperation with the TOTEM trigger system and using the LHC clock during the injection and ramp phases of LHC. Studies are being finalised that will have a bearing on the Trigger Technical Design Report (TDR), which is to be rea...

Electron-triggered chemistry in HNO3/H2O complexes

Czech Academy of Sciences Publication Activity Database

Lengyel, Jozef; Ončák, M.; Fedor, Juraj; Kočišek, Jaroslav; Pysanenko, Andriy; Beyer, M. K.; Fárník, Michal

2017-01-01

Roč. 19, č. 19 (2017), s. 11753-11758 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA15-12386S Institutional support: RVO:61388955 Keywords : electron-triggered chemistry * acid-water clusters * gas-phase reaction s Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 4.123, year: 2016

Still more complexity in mammalian basement membranes

DEFF Research Database (Denmark)

Erickson, A C; Couchman, J R

2000-01-01

laminins, entactin-1/nidogen-1, Type IV collagen, and proteoglycans. However, within the past few years this complexity has increased as new components are described. The entactin/nidogen (E/N) family has expanded with the recent description of a new isoform, E/N-2/osteonidogen. Agrin and Type XVIII...... to be regulated through multiple, mostly domain-specific mechanisms. Understanding the functions of individual BM components and their assembly into macromolecular complexes is a considerable challenge that may increase as further BM and cell surface ligands are discovered for these proteins....

Complexation of Eu3+ with a macrocyclic lactam receptor: Experimental and theoretical study

Czech Academy of Sciences Publication Activity Database

Makrlík, E.; Záliš, Stanislav; Sedláková, Zdeňka; Vaňura, P.

2013-01-01

Roč. 1038, APR 2013 (2013), s. 216-219 ISSN 0022-2860 Institutional support: RVO:61388955 ; RVO:61389013 Keywords : europium * macrocyclic lactam receptor * complexation Subject RIV: CF - Physical ; Theoretical Chemistry; CD - Macromolecular Chemistry (UMCH-V) Impact factor: 1.599, year: 2013

Aging changes of macromolecular synthesis in the mitochondria of mouse hepatocytes as revealed by microscopic radioautography

Energy Technology Data Exchange (ETDEWEB)

Nagata, Tetsuji [Shinshu University, Matsumoto (Japan). Dept. of Anatomy and Cell Biology

2007-07-01

This mini-review reports aging changes of macromolecular synthesis in the mitochondria of mouse hepatocytes. We have observed the macromolecular synthesis, such as DNA, RNA and proteins, in the mitochondria of various mammalian cells by means of electron microscopic radioautography technique developed in our laboratory. The number of mitochondria per cell, number of labeled mitochondria per cell with 3H-thymidine, 3H-uridine and 3H-leucine, precursors for DNA, RNA and proteins, respectively, were counted and the labeling indices at various ages, from fetal to postnatal early days and several months to 1 and 2 years in senescence, were calculated, which showed variations due to aging. (author)

Signaling Mechanisms in Pattern-Triggered Immunity (PTI)

KAUST Repository

Bigeard, Jean; Colcombet, Jean; Hirt, Heribert

2015-01-01

In nature, plants constantly have to face pathogen attacks. However, plant disease rarely occurs due to efficient immune systems possessed by the host plants. Pathogens are perceived by two different recognition systems that initiate the so-called pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), both of which are accompanied by a set of induced defenses that usually repel pathogen attacks. Here we discuss the complex network of signaling pathways occurring during PTI, focusing on the involvement of mitogen-activated protein kinases. © 2015 The Author.

Macromolecular query language (MMQL): prototype data model and implementation.

Science.gov (United States)

Shindyalov, I N; Chang, W; Pu, C; Bourne, P E

1994-11-01

Macromolecular query language (MMQL) is an extensible interpretive language in which to pose questions concerning the experimental or derived features of the 3-D structure of biological macromolecules. MMQL portends to be intuitive with a simple syntax, so that from a user's perspective complex queries are easily written. A number of basic queries and a more complex query--determination of structures containing a five-strand Greek key motif--are presented to illustrate the strengths and weaknesses of the language. The predominant features of MMQL are a filter and pattern grammar which are combined to express a wide range of interesting biological queries. Filters permit the selection of object attributes, for example, compound name and resolution, whereas the patterns currently implemented query primary sequence, close contacts, hydrogen bonding, secondary structure, conformation and amino acid properties (volume, polarity, isoelectric point, hydrophobicity and different forms of exposure). MMQL queries are processed by MMQLlib; a C++ class library, to which new query methods and pattern types are easily added. The prototype implementation described uses PDBlib, another C(++)-based class library from representing the features of biological macromolecules at the level of detail parsable from a PDB file. Since PDBlib can represent data stored in relational and object-oriented databases, as well as PDB files, once these data are loaded they too can be queried by MMQL. Performance metrics are given for queries of PDB files for which all derived data are calculated at run time and compared to a preliminary version of OOPDB, a prototype object-oriented database with a schema based on a persistent version of PDBlib which offers more efficient data access and the potential to maintain derived information. MMQLlib, PDBlib and associated software are available via anonymous ftp from cuhhca.hhmi.columbia.edu.

TRIGGER

CERN Multimedia

W. Smith

At the March meeting, the CMS trigger group reported on progress in production, tests in the Electronics Integration Center (EIC) in Prevessin 904, progress on trigger installation in the underground counting room at point 5, USC55, the program of trigger pattern tests and vertical slice tests and planning for the Global Runs starting this summer. The trigger group is engaged in the final stages of production testing, systems integration, and software and firmware development. Most systems are delivering final tested electronics to CERN. The installation in USC55 is underway and integration testing is in full swing. A program of orderly connection and checkout with subsystems and central systems has been developed. This program includes a series of vertical subsystem slice tests providing validation of a portion of each subsystem from front-end electronics through the trigger and DAQ to data captured and stored. After full checkout, trigger subsystems will be then operated in the CMS Global Runs. Continuous...

TRIGGER

CERN Multimedia

Wesley Smith

2011-01-01

Level-1 Trigger Hardware and Software New Forward Scintillating Counters (FSC) for rapidity gap measurements have been installed and integrated into the Trigger recently. For the Global Muon Trigger, tuning of quality criteria has led to improvements in muon trigger efficiencies. Several subsystems have started campaigns to increase spares by recovering boards or producing new ones. The barrel muon sector collector test system has been reactivated, new η track finder boards are in production, and φ track finder boards are under revision. In the CSC track finder, an η asymmetry problem has been corrected. New pT look-up tables have also improved efficiency. RPC patterns were changed from four out of six coincident layers to three out of six in the barrel, which led to a significant increase in efficiency. A new PAC firmware to trigger on heavy stable charged particles allows looking for chamber hit coincidences in two consecutive bunch-crossings. The redesign of the L1 Trigger Emulator...

TRIGGER

CERN Multimedia

W. Smith from contributions of C. Leonidopoulos, I. Mikulec, J. Varela and C. Wulz.

Level-1 Trigger Hardware and Software Over the past few months, the Level-1 trigger has successfully recorded data with cosmic rays over long continuous stretches as well as LHC splash events, beam halo, and collision events. The L1 trigger hardware, firmware, synchronization, performance and readiness for beam operation were reviewed in October. All L1 trigger hardware is now installed at Point 5, and most of it is completely commissioned. While the barrel ECAL Trigger Concentrator Cards are fully operational, the recently delivered endcap ECAL TCC system is still being commissioned. For most systems there is a sufficient number of spares available, but for a few systems additional reserve modules are needed. It was decided to increase the overall L1 latency by three bunch crossings to increase the safety margin for trigger timing adjustments. In order for CMS to continue data taking during LHC frequency ramps, the clock distribution tree needs to be reset. The procedures for this have been tested. A repl...

Alternating ring-opening copolymerization of cyclohexene oxide with phthalic anhydride catalyzed by iron(III) salen complexes

Czech Academy of Sciences Publication Activity Database

Mundil, R.; Hošťálek, Z.; Šeděnková, Ivana; Merna, J.

2015-01-01

Roč. 23, č. 2 (2015), s. 161-166 ISSN 1598-5032 Institutional support: RVO:61389013 Keywords : polyesters * iron salen complexes * catalysis Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.357, year: 2015

Diagnostic Systems and Resources utilization of the ATLAS High Level Trigger

CERN Document Server

Sidoti, A; The ATLAS collaboration; Ospanov, R

2010-01-01

Since the LHC started colliding protons in December 2009, the ATLAS trigger has operated very successfully with a collision rate which has increased by several orders of magnitude. The trigger monitoring and data quality infrastructure was essential to this success. We describe the software tools used to monitor the trigger system performance and assess the overall quality of the trigger selection during collisions running. ATLAS has broad physics goals which require a large number of different active triggers due to complex event topology, requiring quite sophisticated software structures and concepts. The trigger of the ATLAS experiment is built as a three level system. The first level is realized in hardware while the high level triggers (HLT) are software based and run on large PC farms. The trigger reduces the bunch crossing rate of 40 MHz, at design, to an average event rate of about 200 Hz for storage. Since the ATLAS detector is a general purpose detector, the trigger must be sensitive to a large numb...

Flexible trigger menu implementation on the Global Trigger for the CMS Level-1 trigger upgrade

Science.gov (United States)

MATSUSHITA, Takashi; CMS Collaboration

2017-10-01

The CMS experiment at the Large Hadron Collider (LHC) has continued to explore physics at the high-energy frontier in 2016. The integrated luminosity delivered by the LHC in 2016 was 41 fb-1 with a peak luminosity of 1.5 × 1034 cm-2s-1 and peak mean pile-up of about 50, all exceeding the initial estimations for 2016. The CMS experiment has upgraded its hardware-based Level-1 trigger system to maintain its performance for new physics searches and precision measurements at high luminosities. The Global Trigger is the final step of the CMS Level-1 trigger and implements a trigger menu, a set of selection requirements applied to the final list of objects from calorimeter and muon triggers, for reducing the 40 MHz collision rate to 100 kHz. The Global Trigger has been upgraded with state-of-the-art FPGA processors on Advanced Mezzanine Cards with optical links running at 10 GHz in a MicroTCA crate. The powerful processing resources of the upgraded system enable implementation of more algorithms at a time than previously possible, allowing CMS to be more flexible in how it handles the available trigger bandwidth. Algorithms for a trigger menu, including topological requirements on multi-objects, can be realised in the Global Trigger using the newly developed trigger menu specification grammar. Analysis-like trigger algorithms can be represented in an intuitive manner and the algorithms are translated to corresponding VHDL code blocks to build a firmware. The grammar can be extended in future as the needs arise. The experience of implementing trigger menus on the upgraded Global Trigger system will be presented.

Triggered tremor sweet spots in Alaska

Science.gov (United States)

Gomberg, Joan; Prejean, Stephanie

2013-01-01

To better understand what controls fault slip along plate boundaries, we have exploited the abundance of seismic and geodetic data available from the richly varied tectonic environments composing Alaska. A search for tremor triggered by 11 large earthquakes throughout all of seismically monitored Alaska reveals two tremor “sweet spots”—regions where large-amplitude seismic waves repeatedly triggered tremor between 2006 and 2012. The two sweet spots locate in very different tectonic environments—one just trenchward and between the Aleutian islands of Unalaska and Akutan and the other in central mainland Alaska. The Unalaska/Akutan spot corroborates previous evidence that the region is ripe for tremor, perhaps because it is located where plate-interface frictional properties transition between stick-slip and stably sliding in both the dip direction and laterally. The mainland sweet spot coincides with a region of complex and uncertain plate interactions, and where no slow slip events or major crustal faults have been noted previously. Analyses showed that larger triggering wave amplitudes, and perhaps lower frequencies (tremor. However, neither the maximum amplitude in the time domain or in a particular frequency band, nor the geometric relationship of the wavefield to the tremor source faults alone ensures a high probability of triggering. Triggered tremor at the two sweet spots also does not occur during slow slip events visually detectable in GPS data, although slow slip below the detection threshold may have facilitated tremor triggering.

The Phase-1 Upgrade for the Level-1 Muon Barrel Trigger of the ATLAS Experiment at LHC

CERN Document Server

Izzo, Vincenzo; The ATLAS collaboration

2018-01-01

The Level-1 Barrel Trigger of the ATLAS Experiment is based on Resistive Plate Chambers (RPC) detectors. The on-detector trigger electronics identifies muons with specific values of transverse momentum (pT), by using coincidences between different layers of detectors. Trigger data is then transferred from on-detector to the off-detector trigger electronics boards. Data is processed by a complex system, which combines trigger data from the Barrel and the End-cap regions, and provides the combined muon candidate to the Central Trigger Processor (CTP). The system has been performing very well for almost a decade. However, in order to cope with continuously increasing LHC luminosity and more demanding requirements on trigger efficiency and performance, various upgrades for the full trigger system were already deployed, and others are foreseen in the next years. Most of the trigger upgrades are based on state-of-the-art technologies and allow designing more complex trigger menus, increasing processing power and da...

Experimental and DFT study on complexation of Eu3+ with a macrocyclic lactam receptor

Czech Academy of Sciences Publication Activity Database

Makrlík, E.; Záliš, Stanislav; Vaňura, P.; Sedláková, Zdeňka

2013-01-01

Roč. 24, č. 6 (2013), s. 2149-2153 ISSN 1040-0400 Institutional support: RVO:61388955 ; RVO:61389013 Keywords : europium * macrocyclic lactam receptor * complexation Subject RIV: CF - Physical ; Theoretical Chemistry; CD - Macromolecular Chemistry (UMCH-V) Impact factor: 1.900, year: 2013

TRIGGER

CERN Multimedia

W. Smith, from contributions of D. Acosta

2012-01-01

  The L1 Trigger group deployed several major improvements this year. Compared to 2011, the single-muon trigger rate has been reduced by a factor of 2 and the η coverage has been restored to 2.4, with high efficiency. During the current technical stop, a higher jet seed threshold will be applied in the Global Calorimeter Trigger in order to significantly reduce the strong pile-up dependence of the HT and multi-jet triggers. The currently deployed L1 menu, with the “6E33” prescales, has a total rate of less than 100 kHz and operates with detector readout dead time of less than 3% for luminosities up to 6.5 × 1033 cm–2s–1. Further prescale sets have been created for 7 and 8 × 1033 cm–2s–1 luminosities. The L1 DPG is evaluating the performance of the Trigger for upcoming conferences and publication. Progress on the Trigger upgrade was reviewed during the May Upgrade Week. We are investigating scenarios for stagin...

TRIGGER

CERN Multimedia

R. Arcidiacono

2013-01-01

  In 2013 the Trigger Studies Group (TSG) has been restructured in three sub-groups: STEAM, for the development of new HLT menus and monitoring their performance; STORM, for the development of HLT tools, code and actual configurations; and FOG, responsible for the online operations of the High Level Trigger. The Strategy for Trigger Evolution And Monitoring (STEAM) group is responsible for Trigger Menu development, path timing, trigger performance studies coordination, HLT offline DQM as well as HLT release, menu and conditions validation – in collaboration and with the technical support of the PdmV group. Since the end of proton-proton data taking, the group has started preparing for 2015 data taking, with collisions at 13 TeV and 25 ns bunch spacing. The reliability of the extrapolation to higher energy is being evaluated comparing the trigger rates on 7 and 8 TeV Monte Carlo samples with the data taken in the past two years. The effect of 25 ns bunch spacing is being studied on the d...

TRIGGER

CERN Multimedia

W. Smith

Level-1 Trigger Hardware and Software The road map for the final commissioning of the level-1 trigger system has been set. The software for the trigger subsystems is being upgraded to run under CERN Scientific Linux 4 (SLC4). There is also a new release for the Trigger Supervisor (TS 1.4), which implies upgrade work by the subsystems. As reported by the CERN group, a campaign to tidy the Trigger Timing and Control (TTC) racks has begun. The machine interface was upgraded by installing the new RF2TTC module, which receives RF signals from LHC Point 4. Two Beam Synchronous Timing (BST) signals, one for each beam, can now be received in CMS. The machine group will define the exact format of the information content shortly. The margin on the locking range of the CMS QPLL is planned for study for different subsystems in the next Global Runs, using a function generator. The TTC software has been successfully tested on SLC4. Some TTC subsystems have already been upgraded to SLC4. The TTCci Trigger Supervisor ...

Detection and cellular localisation of the synthetic soluble macromolecular drug carrier pHPMA

Czech Academy of Sciences Publication Activity Database

Kissel, M.; Peschke, P.; Šubr, Vladimír; Ulbrich, Karel; Strunz, A. M.; Kühnlein, R.; Debus, J.; Friedrich, E.

2002-01-01

Roč. 29, č. 8 (2002), s. 1055-1062 ISSN 1619-7070 R&D Projects: GA ČR GV307/96/K226 Institutional research plan: CEZ:AV0Z4050913 Keywords : EPR effect * Radiolabelled macromolecules * Pharmacokinetic Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.568, year: 2002

Predictive Mechanical Characterization of Macro-Molecular Material Chemistry Structures of Cement Paste at Nano Scale - Two-phase Macro-Molecular Structures of Calcium Silicate Hydrate, Tri-Calcium Silicate, Di-Calcium Silicate and Calcium Hydroxide

Science.gov (United States)

Padilla Espinosa, Ingrid Marcela

Concrete is a hierarchical composite material with a random structure over a wide range of length scales. At submicron length scale the main component of concrete is cement paste, formed by the reaction of Portland cement clinkers and water. Cement paste acts as a binding matrix for the other components and is responsible for the strength of concrete. Cement paste microstructure contains voids, hydrated and unhydrated cement phases. The main crystalline phases of unhydrated cement are tri-calcium silicate (C3S) and di-calcium silicate (C2S), and of hydrated cement are calcium silicate hydrate (CSH) and calcium hydroxide (CH). Although efforts have been made to comprehend the chemical and physical nature of cement paste, studies at molecular level have primarily been focused on individual components. Present research focuses on the development of a method to model, at molecular level, and analysis of the two-phase combination of hydrated and unhydrated phases of cement paste as macromolecular systems. Computational molecular modeling could help in understanding the influence of the phase interactions on the material properties, and mechanical performance of cement paste. Present work also strives to create a framework for molecular level models suitable for potential better comparisons with low length scale experimental methods, in which the sizes of the samples involve the mixture of different hydrated and unhydrated crystalline phases of cement paste. Two approaches based on two-phase cement paste macromolecular structures, one involving admixed molecular phases, and the second involving cluster of two molecular phases are investigated. The mechanical properties of two-phase macromolecular systems of cement paste consisting of key hydrated phase CSH and unhydrated phases C3S or C2S, as well as CSH with the second hydrated phase CH were calculated. It was found that these cement paste two-phase macromolecular systems predicted an isotropic material behavior. Also

The CMS Trigger Supervisor: Control and Hardware Monitoring System of the CMS Level-1 Trigger at CERN

CERN Document Server

Ildefons Magrans de Abril

2008-01-01

The experiments CMS (Compact Muon Solenoid) and ATLAS (A Toroidal LHC ApparatuS) at the LargeHadron Collider (LHC) are the greatest exponents of the rising complexity in High Energy Physics (HEP) datahandling instrumentation. Tens of millions of readout channels, tens of thousands of hardware boards and thesame order of connections are figures of merit. However, the hardware volume is not the only complexitydimension, the unprecedented large number of research institutes and scientists that form the internationalcollaborations, and the long design, development, commissioning and operational phases are additional factorsthat must be taken into account.The Level-1 (L1) trigger decision loop is an excellent example of these difficulties. This system is based on apipelined logic destined to analyze without deadtime the data from each LHC bunch crossing occurring every25_ns, using special coarsely segmented trigger data from the detectors. The L1 trigger is responsible forreducing the rate of accepted crossings to...

Implementation of BES-III TOF trigger system in programmable logic devices

International Nuclear Information System (INIS)

Zheng Wei; Liu Shubin; Liu Xuzong; An Qi

2009-01-01

The TOF trigger sub-system on the upgrading Beijing Spectrometer is designed to receive 368 bits fast hit signals from the front end electronics module to yield 7 bits trigger information according to the physical requirement. It sends the processed real time trigger information to the Global-Trigger-Logic to generate the primal trigger signal L1, and sends processed 136 bits real time position information to the Track-Match-Logic to calculate the particle flight tracks. The sub-system also packages the valid events for the DAQ system to read out. Following the reconfigurable concept, a large number of programmable logic devices are employed to increase the flexibility and reliability of the system, and decrease the complexity and the space requirement of PCB layout. This paper describes the implementation of the kernel trigger logic in a programmable logic device. (authors)

TRIGGER

CERN Multimedia

by Wesley Smith

2011-01-01

Level-1 Trigger Hardware and Software After the winter shutdown minor hardware problems in several subsystems appeared and were corrected. A reassessment of the overall latency has been made. In the TTC system shorter cables between TTCci and TTCex have been installed, which saved one bunch crossing, but which may have required an adjustment of the RPC timing. In order to tackle Pixel out-of-syncs without influencing other subsystems, a special hardware/firmware re-sync protocol has been introduced in the Global Trigger. The link between the Global Calorimeter Trigger and the Global Trigger with the new optical Global Trigger Interface and optical receiver daughterboards has been successfully tested in the Electronics Integration Centre in building 904. New firmware in the GCT now allows a setting to remove the HF towers from energy sums. The HF sleeves have been replaced, which should lead to reduced rates of anomalous signals, which may allow their inclusion after this is validated. For ECAL, improvements i...

TRIGGER

CERN Multimedia

W. Smith from contributions of C. Leonidopoulos

2010-01-01

Level-1 Trigger Hardware and Software Since nearly all of the Level-1 (L1) Trigger hardware at Point 5 has been commissioned, activities during the past months focused on the fine-tuning of synchronization, particularly for the ECAL and the CSC systems, on firmware upgrades and on improving trigger operation and monitoring. Periodic resynchronizations or hard resets and a shortened luminosity section interval of 23 seconds were implemented. For the DT sector collectors, an automatic power-off was installed in case of high temperatures, and the monitoring capabilities of the opto-receivers and the mini-crates were enhanced. The DTTF and the CSCTF now have improved memory lookup tables. The HCAL trigger primitive logic implemented a new algorithm providing better stability of the energy measurement in the presence of any phase misalignment. For the Global Calorimeter Trigger, additional Source Cards have been manufactured and tested. Testing of the new tau, missing ET and missing HT algorithms is underw...

Interplay between the bacterial nucleoid protein H-NS and macromolecular crowding in compacting DNA

NARCIS (Netherlands)

Wintraecken, C.H.J.M.

2012-01-01

In this dissertation we discuss H-NS and its connection to nucleoid compaction and organization. Nucleoid formation involves a dramatic reduction in coil volume of the genomic DNA. Four factors are thought to influence coil volume: supercoiling, DNA charge neutralization, macromolecular

Insights from LGI1 and CASPR2 potassium channel complex autoantibody subtyping.

Science.gov (United States)

Klein, Christopher J; Lennon, Vanda A; Aston, Paula A; McKeon, Andrew; O'Toole, Orna; Quek, Amy; Pittock, Sean J

2013-02-01

To determine, in patients identified as seropositive for neuronal voltage-gated potassium channel (VGKC) complex autoantibodies, the spectrum of clinical presentations and frequency of leucine-rich glioma-inactivated protein 1 (LGI1) and contactin-associated protein-like 2 (CASPR2) as defined antigenic neuronal targets in the VGKC macromolecular complex. Retrospective cohort study. Clinical practice, Mayo Clinic Neuroimmunology Laboratory and Department of Neurology. A total of 54 853 patients were evaluated, of whom 1992 were found to be VGKC complex IgG positive. From June 1, 2008, to June 30, 2010, comprehensive service serologic evaluation performed on 54853 patients with unexplained neurologic symptoms identified 1992 patients (4%) who were positive for VGKC complex IgG (values ≥ 0.03 nmol/L). Among 316 seropositive patients evaluated clinically at our institution, 82 (26%) were seropositive for LGI1 IgG and/or CASPR2 IgG. Of these 82 patients, 27% had low (0.03-0.09 nmol/L), 51% had medium (0.10-0.99 nmol/L), and 22% had high (≥ 1.00 nmol/L) VGKC complex IgG values. Leucine-rich glioma-inactivated protein 1 IgG positivity was associated with higher VGKC complex IgG values (PVGKC complex IgG values and varying LGI1 IgG and CASPR2 IgG specificities. The frequent occurrence of LGI1 IgG and CASPR2 IgG in serum samples with low and medium VGKC complex IgG values supports the clinical significance of low values in clinical evaluation. Additional antigenic components of VGKC macromolecular complexes remain to be defined.

Bringing macromolecular machinery to life using 3D animation.

Science.gov (United States)

Iwasa, Janet H

2015-04-01

Over the past decade, there has been a rapid rise in the use of three-dimensional (3D) animation to depict molecular and cellular processes. Much of the growth in molecular animation has been in the educational arena, but increasingly, 3D animation software is finding its way into research laboratories. In this review, I will discuss a number of ways in which 3d animation software can play a valuable role in visualizing and communicating macromolecular structures and dynamics. I will also consider the challenges of using animation tools within the research sphere. Copyright © 2015. Published by Elsevier Ltd.

Fractional complexation in a miscible polymer blend. Calorimetry and size exclusion chromatography

Czech Academy of Sciences Publication Activity Database

Kratochvíl, Jaroslav; Šturcová, Adriana; Sikora, Antonín; Dybal, Jiří

2014-01-01

Roč. 63, č. 8 (2014), s. 1406-1413 ISSN 0959-8103 R&D Projects: GA AV ČR IAA200500903; GA ČR GAP108/12/0703 Institutional support: RVO:61389013 Keywords : miscible blend * interpolymer complex * residual phase Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.409, year: 2014

Thermo-Responsive Complexes of c-Myc Antisense Oligonucleotide with Block Copolymer of Poly(OEGMA) and Quaternized Poly(4-Vinylpyridine).

Science.gov (United States)

Topuzogullari, Murat; Elalmis, Yeliz Basaran; Isoglu, Sevil Dincer

2017-04-01

Solution behavior of thermo-responsive polymers and their complexes with biological macromolecules may be affected by environmental conditions, such as the concentration of macromolecular components, pH, ion concentration, etc. Therefore, a thermo-responsive polymer and its complexes should be characterized in detail to observe their responses against possible environments under physiological conditions before biological applications. To briefly indicate this important issue, thermo-responsive block copolymer of quaternized poly(4-vinylpyridine) and poly(oligoethyleneglycol methyl ether methacrylate) as a potential nonviral vector has been synthesized. Polyelectrolyte complexes of this copolymer with the antisense oligonucleotide of c-Myc oncogene are also thermo-responsive but, have lower LCST (lower critical solution temperature) values compared to individual copolymer. LCST values of complexes decrease with molar ratio of macromolecular components and presence of salt. Dilution of solutions also affects solution behavior of complexes and causes a significant decrease in size and an increase in LCST, which indicates possible effects of severe dilutions in the blood stream. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interaction of cesium ions with calix[2]furan[4]pyrrole and its fluoride complex

Czech Academy of Sciences Publication Activity Database

Kříž, Jaroslav; Dybal, Jiří; Makrlík, E.; Kohnke, F. H.

2012-01-01

Roč. 541, 10 July (2012), s. 27-31 ISSN 0009-2614 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : calix[2]furan[4]pyrrole * Cs complex * NMR Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.145, year: 2012

Macromolecular and dendrimer-based magnetic resonance contrast agents

Energy Technology Data Exchange (ETDEWEB)

Bumb, Ambika; Brechbiel, Martin W. (Radiation Oncology Branch, National Cancer Inst., National Inst. of Health, Bethesda, MD (United States)), e-mail: pchoyke@mail.nih.gov; Choyke, Peter (Molecular Imaging Program, National Cancer Inst., National Inst. of Health, Bethesda, MD (United States))

2010-09-15

Magnetic resonance imaging (MRI) is a powerful imaging modality that can provide an assessment of function or molecular expression in tandem with anatomic detail. Over the last 20-25 years, a number of gadolinium-based MR contrast agents have been developed to enhance signal by altering proton relaxation properties. This review explores a range of these agents from small molecule chelates, such as Gd-DTPA and Gd-DOTA, to macromolecular structures composed of albumin, polylysine, polysaccharides (dextran, inulin, starch), poly(ethylene glycol), copolymers of cystamine and cystine with GD-DTPA, and various dendritic structures based on polyamidoamine and polylysine (Gadomers). The synthesis, structure, biodistribution, and targeting of dendrimer-based MR contrast agents are also discussed

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

International Nuclear Information System (INIS)

Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L.; Armour, Wes; Waterman, David G.; Iwata, So; Evans, Gwyndaf

2013-01-01

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Aller, Pierre [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz; Cameron, Alex [Imperial College, London SW7 2AZ (United Kingdom); Axford, Danny; Owen, Robin L. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Armour, Wes [Oxford e-Research Centre (OeRC), Keble Road, Oxford OX1 3QG (United Kingdom); Waterman, David G. [Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom)

2013-08-01

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

Macromolecularly crowded in vitro microenvironments accelerate the production of extracellular matrix-rich supramolecular assemblies.

Science.gov (United States)

Kumar, Pramod; Satyam, Abhigyan; Fan, Xingliang; Collin, Estelle; Rochev, Yury; Rodriguez, Brian J; Gorelov, Alexander; Dillon, Simon; Joshi, Lokesh; Raghunath, Michael; Pandit, Abhay; Zeugolis, Dimitrios I

2015-03-04

Therapeutic strategies based on the principles of tissue engineering by self-assembly put forward the notion that functional regeneration can be achieved by utilising the inherent capacity of cells to create highly sophisticated supramolecular assemblies. However, in dilute ex vivo microenvironments, prolonged culture time is required to develop an extracellular matrix-rich implantable device. Herein, we assessed the influence of macromolecular crowding, a biophysical phenomenon that regulates intra- and extra-cellular activities in multicellular organisms, in human corneal fibroblast culture. In the presence of macromolecules, abundant extracellular matrix deposition was evidenced as fast as 48 h in culture, even at low serum concentration. Temperature responsive copolymers allowed the detachment of dense and cohesive supramolecularly assembled living substitutes within 6 days in culture. Morphological, histological, gene and protein analysis assays demonstrated maintenance of tissue-specific function. Macromolecular crowding opens new avenues for a more rational design in engineering of clinically relevant tissue modules in vitro.

Long-wavelength macromolecular crystallography - First successful native SAD experiment close to the sulfur edge

Science.gov (United States)

Aurelius, O.; Duman, R.; El Omari, K.; Mykhaylyk, V.; Wagner, A.

2017-11-01

Phasing of novel macromolecular crystal structures has been challenging since the start of structural biology. Making use of anomalous diffraction of natively present elements, such as sulfur and phosphorus, for phasing has been possible for some systems, but hindered by the necessity to access longer X-ray wavelengths in order to make most use of the anomalous scattering contributions of these elements. Presented here are the results from a first successful experimental phasing study of a macromolecular crystal structure at a wavelength close to the sulfur K edge. This has been made possible by the in-vacuum setup and the long-wavelength optimised experimental setup at the I23 beamline at Diamond Light Source. In these early commissioning experiments only standard data collection and processing procedures have been applied, in particular no dedicated absorption correction has been used. Nevertheless the success of the experiment demonstrates that the capability to extract phase information can be even further improved once data collection protocols and data processing have been optimised.

The In-Situ One-Step Synthesis of a PDC Macromolecular Pro-Drug and the Fabrication of a Novel Core-Shell Micell.

Science.gov (United States)

Yu, Cui-Yun; Yang, Sa; Li, Zhi-Ping; Huang, Can; Ning, Qian; Huang, Wen; Yang, Wen-Tong; He, Dongxiu; Sun, Lichun

2016-01-01

The development of slow release nano-sized carriers for efficient antineoplastic drug delivery with a biocompatible and biodegradable pectin-based macromolecular pro-drug for tumor therapy has been reported in this study. Pectin-doxorubicin conjugates (PDC), a macromolecular pro-drug, were prepared via an amide condensation reaction, and a novel amphiphilic core-shell micell based on a PDC macromolecular pro-drug (PDC-M) was self-assembled in situ, with pectin as the hydrophilic shell and doxorubicin (DOX) as the hydrophobic core. Then the chemical structure of the PDC macromolecular pro-drug was identified by both Fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance spectroscopy ((1)H-NMR), and proved that doxorubicin combined well with the pectin and formed macromolecular pro-drug. The PDC-M were observed to have an unregularly spherical shape and were uniform in size by scanning electron microscopy (SEM). The average particle size of PDC-M, further measured by a Zetasizer nanoparticle analyzer (Nano ZS, Malvern Instruments), was about 140 nm. The encapsulation efficiency and drug loading were 57.82% ± 3.7% (n = 3) and 23.852% ±2.3% (n = 3), respectively. The in vitro drug release behaviors of the resulting PDC-M were studied in a simulated tumor environment (pH 5.0), blood (pH 7.4) and a lysosome media (pH 6.8), and showed a prolonged slow release profile. Assays for antiproliferative effects and flow cytometry of the resulting PDC-M in HepG2 cell lines demonstrated greater properties of delayed and slow release as compared to free DOX. A cell viability study against endothelial cells further revealed that the resulting PDC-M possesses excellent cell compatibilities and low cytotoxicities in comparison with that of the free DOX. Hemolysis activity was investigated in rabbits, and the results also demonstrated that the PDC-M has greater compatibility in comparison with free DOX. This shows that the resulting PDC-M can ameliorate the

Complex Non-volcanic Tremor in Guerrero Mexico Triggered by the 2010 Mw 8.8 Chilean Earthquake

Science.gov (United States)

Zigone, D.; Campillo, M.; Husker, A. L.; Kostoglodov, V.; Payero, J. S.; Frank, W.; Shapiro, N. M.; Voisin, C.; Cougoulat, G.; Cotte, N.

2010-12-01

In this study we analyze the tremors triggered in Guerrero region (Mexico) by the 2010 magnitude 8.8 Chilean Earthquake using mini-seismic array data from the French-Mexican G-GAP project and broadband data from the Servicio Sismologico Nacional of Mexico. The strong dynamic shaking by the earthquake produced the first observed triggered non-volcanic tremors (NVT) in Mexico so far with at least 3 different types of tremors at different time scales. There was a slow slip event (SSE) occurring at the time of the earthquake, which may have increased the probability of tremor triggering in the region. The first type of observed triggered tremors occurred during the S waves, Love waves and Rayleigh waves as already reported in other subductions zones and continental faults (Miyazawa and Mori, 2005, 2006; Rubinstein et al., 2007; Gomberg et al., 2008; Peng et al, 2009…). The greatest amount of energy and duration accompanies the long-period Rayleigh waves, with smaller bursts during the S and Love waves. For this particular tremor we observed the dispersion of Rayleigh waves in the envelopes of triggered tremors, which indicates a very strong modulation of the source by the passing surface wave. An unexpected short-term tremor occurred approximately one hour later of the arrival of the surface waves on the coastal stations. The NVT has only been previously observed at distances > 100 km inland. It also has a shorter frequency range (3-6 Hz) than other NVT (1-10 Hz) observed in the region. Finally, we observed a significant increase of so-called ambient tremor activity with higher intensity than all triggered NVT during the days after the earthquake. This study adds new types of tremors to the lexicon of triggered NVT observed in the world.

TRIGGER

CERN Multimedia

W. Smith

2011-01-01

Level-1 Trigger Hardware and Software Overall the L1 trigger hardware has been running very smoothly during the last months of proton running. Modifications for the heavy-ion run have been made where necessary. The maximal design rate of 100 kHz can be sustained without problems. All L1 latencies have been rechecked. The recently installed Forward Scintillating Counters (FSC) are being used in the heavy ion run. The ZDC scintillators have been dismantled, but the calorimeter itself remains. We now send the L1 accept signal and other control signals to TOTEM. Trigger cables from TOTEM to CMS will be installed during the Christmas shutdown, so that the TOTEM data can be fully integrated within the CMS readout. New beam gas triggers have been developed, since the BSC-based trigger is no longer usable at high luminosities. In particular, a special BPTX signal is used after a quiet period with no collisions. There is an ongoing campaign to provide enough spare modules for the different subsystems. For example...

TRIGGER

CERN Multimedia

J. Alimena

2013-01-01

Trigger Strategy Group The Strategy for Trigger Evolution And Monitoring (STEAM) group is responsible for the development of future High-Level Trigger menus, as well as of its DQM and validation, in collaboration and with the technical support of the PdmV group. Taking into account the beam energy and luminosity expected in 2015, a rough estimate of the trigger rates indicates a factor four increase with respect to 2012 conditions. Assuming that a factor two can be tolerated thanks to the increase in offline storage and processing capabilities, a toy menu has been developed using the new OpenHLT workflow to estimate the transverse energy/momentum thresholds that would halve the current trigger rates. The CPU time needed to run the HLT has been compared between data taken with 25 ns and 50 ns bunch spacing, for equivalent pile-up: no significant difference was observed on the global time per event distribution at the only available data point, corresponding to a pile-up of about 10 interactions. Using th...

Advantages of video trigger in problem-based learning.

Science.gov (United States)

Chan, Lap Ki; Patil, Nivritti G; Chen, Julie Y; Lam, Jamie C M; Lau, Chak S; Ip, Mary S M

2010-01-01

Traditionally, paper cases are used as 'triggers' to stimulate learning in problem-based learning (PBL). However, video may be a better medium because it preserves the original language, encourages the active extraction of information, avoids depersonalization of patients and allows direct observation of clinical consultations. In short, it exposes the students to the complexity of actual clinical problems. The study aims to find out whether students and facilitators who are accustomed to paper cases would prefer video triggers or paper cases and the reasons for their preference. After students and facilitators had completed a video PBL tutorial, their responses were measured by a structured questionnaire using a modified Likert scale. A total of 257 students (92%) and 26 facilitators (100%) responded. The majority of students and facilitators considered that using video triggers could enhance the students' observational powers and clinical reasoning, help them to integrate different information and better understand the cases and motivate them to learn. They found PBL using video triggers more interesting and preferred it to PBL using paper cases. Video triggers are preferred by both students and facilitators over paper cases in PBL.

Using Simple Manipulatives to Improve Student Comprehension of a Complex Biological Process: Protein Synthesis

Science.gov (United States)

Guzman, Karen; Bartlett, John

2012-01-01

Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article…

Macrophage triggering by aggregated immunoglobulins. II. Comparison of IgE and IgG aggregates or immune complexes.

Science.gov (United States)

Pestel, J; Dessaint, J P; Joseph, M; Bazin, H; Capron, A

1984-01-01

Macrophages incubated with complexed or aggregated IgE released beta-glucuronidase (beta-G) within 30 min. In contrast in the presence of aggregated or complexed IgG, macrophages liberated equivalent amount of beta-G only after 6 h incubation. In addition the rapid macrophage stimulation induced by aggregated IgE was also followed by a faster 3H-glucosamine incorporation when compared to the delayed activation caused by aggregated IgG. However, macrophages stimulated either by IgG or by IgE oligomers produced the same percentage of plasminogen activator at 24 h. In contrast, while the interaction between macrophages and aggregated IgE was only followed by a peak of cyclic GMP and a beta-G release during the first 30 min of incubation, the interaction between macrophages and IgG oligomers was accompanied by a simultaneous increase of cyclic GMP and AMP nucleotides and by an absence of beta-G exocytosis. Moreover, the beta-G release induced by aggregated IgE was increased when macrophages were preincubated with aggregated IgG. This additive effect was not observed in the reverse situation. Finally macrophages activated by IgG oligomers were demonstrated to exert a cytotoxic effect on tumour cells and to kill schistosomula in the presence of a low level of complement. Taken together these results underline the peculiar ability of aggregated or complexed IgE to trigger rapidly the macrophage activation compared to aggregated IgG and can explain the important role of complexed IgE in some macrophage dependent cytotoxicity mechanisms (i.e. in parasitic diseases). PMID:6088135

MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron

International Nuclear Information System (INIS)

Cowieson, Nathan Philip; Aragao, David; Clift, Mark; Ericsson, Daniel J.; Gee, Christine; Harrop, Stephen J.; Mudie, Nathan; Panjikar, Santosh; Price, Jason R.; Riboldi-Tunnicliffe, Alan; Williamson, Rachel; Caradoc-Davies, Tom

2015-01-01

The macromolecular crystallography beamline MX1 at the Australian Synchrotron is described. MX1 is a bending-magnet crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range from 8 to 18 keV to a focal spot at the sample position of 120 µm FWHM. The beamline endstation and ancillary equipment facilitate local and remote access for both chemical and biological macromolecular crystallography. Here, the design of the beamline and endstation are discussed. The beamline has enjoyed a full user program for the last seven years and scientific highlights from the user program are also presented

Synthesis of branched polymers under continuous-flow microprocess: an improvement of the control of macromolecular architectures.

Science.gov (United States)

Bally, Florence; Serra, Christophe A; Brochon, Cyril; Hadziioannou, Georges

2011-11-15

Polymerization reactions can benefit from continuous-flow microprocess in terms of kinetics control, reactants mixing or simply efficiency when high-throughput screening experiments are carried out. In this work, we perform for the first time the synthesis of branched macromolecular architecture through a controlled/'living' polymerization technique, in tubular microreactor. Just by tuning process parameters, such as flow rates of the reactants, we manage to generate a library of polymers with various macromolecular characteristics. Compared to conventional batch process, polymerization kinetics shows a faster initiation step and more interestingly an improved branching efficiency. Due to reduced diffusion pathway, a characteristic of microsystems, it is thus possible to reach branched polymers exhibiting a denser architecture, and potentially a higher functionality for later applications. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural analysis of nanoparticulate carriers for encapsulation of macromolecular drugs

Czech Academy of Sciences Publication Activity Database

Angelov, Borislav; Garamus, V.M.; Drechsler, M.; Angelova, A.

2017-01-01

Roč. 235, Jun (2017), s. 83-89 ISSN 0167-7322 R&D Projects: GA MŠk EF15_003/0000447; GA MŠk EF15_008/0000162 Grant - others:OP VVV - ELIBIO(XE) CZ.02.1.01/0.0/0.0/15_003/0000447; ELI Beamlines(XE) CZ.02.1.01/0.0/0.0/15_008/0000162 Institutional support: RVO:68378271 Keywords : self-assembled nanocarriers * liquid crystalline phase transitions * cationic lipids * macromolecular drugs Subject RIV: BO - Biophysics OBOR OECD: Biophysics Impact factor: 3.648, year: 2016

Protein crystal growth studies at the Center for Macromolecular Crystallography

International Nuclear Information System (INIS)

DeLucas, Lawrence J.; Long, Marianna M.; Moore, Karen M.; Harrington, Michael; McDonald, William T.; Smith, Craig D.; Bray, Terry; Lewis, Johanna; Crysel, William B.; Weise, Lance D.

2000-01-01

The Center for Macromolecular Crystallography (CMC) has been involved in fundamental studies of protein crystal growth (PCG) in microgravity and in our earth-based laboratories. A large group of co-investigators from academia and industry participated in these experiments by providing protein samples and by performing the x-ray crystallographic analysis. These studies have clearly demonstrated the usefulness of a microgravity environment for enhancing the quality and size of protein crystals. Review of the vapor diffusion (VDA) PCG results from nineteen space shuttle missions is given in this paper

Subsumed complexity: abiogenesis as a by-product of complex energy transduction

Science.gov (United States)

Adam, Z. R.; Zubarev, D.; Aono, M.; Cleaves, H. James

2017-11-01

The origins of life bring into stark relief the inadequacy of our current synthesis of thermodynamic, chemical, physical and information theory to predict the conditions under which complex, living states of organic matter can arise. Origins research has traditionally proceeded under an array of implicit or explicit guiding principles in lieu of a universal formalism for abiogenesis. Within the framework of a new guiding principle for prebiotic chemistry called subsumed complexity, organic compounds are viewed as by-products of energy transduction phenomena at different scales (subatomic, atomic, molecular and polymeric) that retain energy in the form of bonds that inhibit energy from reaching the ground state. There is evidence for an emergent level of complexity that is overlooked in most conceptualizations of abiogenesis that arises from populations of compounds formed from atomic energy input. We posit that different forms of energy input can exhibit different degrees of dissipation complexity within an identical chemical medium. By extension, the maximum capacity for organic chemical complexification across molecular and macromolecular scales subsumes, rather than emerges from, the underlying complexity of energy transduction processes that drive their production and modification. This article is part of the themed issue 'Reconceptualizing the origins of life'.

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

Science.gov (United States)

Boutselakis, H; Dimitropoulos, D; Fillon, J; Golovin, A; Henrick, K; Hussain, A; Ionides, J; John, M; Keller, P A; Krissinel, E; McNeil, P; Naim, A; Newman, R; Oldfield, T; Pineda, J; Rachedi, A; Copeland, J; Sitnov, A; Sobhany, S; Suarez-Uruena, A; Swaminathan, J; Tagari, M; Tate, J; Tromm, S; Velankar, S; Vranken, W

2003-01-01

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

The ATLAS Level-1 Topological Trigger Design and Operation in Run-2

CERN Document Server

Igonkina, Olga; The ATLAS collaboration

2018-01-01

The ATLAS Level-1 Trigger system performs initial event selection using data from calorimeters and the muon spectrometer to reduce the LHC collision event rate down to about 100 kHz. Trigger decisions from the different sub-systems are combined in the Central Trigger Processor for the final Level-1 decision. A new FPGAs-based AdvancedTCA sub-system was introduced to calculate in real time complex kinematic observables: the Topological Processor System. It was installed during the shutdown and commissioning started in 2015 and continued during 2016. The design and operation of the Level-1 Topological Trigger in Run-2 will be illustrated.

Macromolecular Engineering: New Routes Towards the Synthesis of Well-??Defined Polyethers/Polyesters Co/Terpolymers with Different Architectures

KAUST Repository

Alamri, Haleema

2016-01-01

Macromolecular engineering (as discussed in the first chapter) of homo/copolymers refers to the specific tailoring of these materials for achieving an easy and reproducible synthesis that results in precise molecular

Flexible trigger menu implementation on the Global Trigger for the CMS Level-1 trigger upgrade

CERN Document Server

Matsushita, Takashi

2017-01-01

The CMS experiment at the Large Hadron Collider (LHC) has continued to explore physics at the high-energy frontier in 2016. The integrated luminosity delivered by the LHC in 2016 was 41~fb$^{-1}$ with a peak luminosity of 1.5 $\\times$ 10$^{34}$ cm$^{-2}$s$^{-1}$ and peak mean pile-up of about 50, all exceeding the initial estimations for 2016. The CMS experiment has upgraded its hardware-based Level-1 trigger system to maintain its performance for new physics searches and precision measurements at high luminosities. The Global Trigger is the final step of the CMS \\mbox{Level-1} trigger and implements a trigger menu, a set of selection requirements applied to the final list of objects from calorimeter and muon triggers, for reducing the 40 MHz collision rate to 100 kHz. The Global Trigger has been upgraded with state-of-the-art FPGA processors on Advanced Mezzanine Cards with optical links running at 10 GHz in a MicroTCA crate. The powerful processing resources of the upgraded system enable implemen...

Method of triggering the vacuum arc in source with a resistor

International Nuclear Information System (INIS)

Zheng Le; Lan Zhaohui; Long Jidong; Peng Yufei; Li Jie; Yang Zhen; Dong Pan; Shi Jinshui

2014-01-01

Background: The metal vapor vacuum arc (MEVVA) ion source is a common source which provides strong metal ion flow. To trigger this ion source, a high-voltage trigger pulse generator and a high-voltage isolation pulse transformer are needed, which makes the power supply system complex. Purpose: To simplify the power supply system, a trigger method with a resistor was introduced, and some characteristics of this method were studied. Methods: The ion flow provided by different main arc current was measured, as well as the trigger current. The main arc current and the ion current were recorded with different trigger resistances. Results: Experimental results showed that, within a certain range of resistances, the larger the resistance value, the more difficult it was to success fully trigger the source. Meanwhile, the main arc rising edge became slower on the increasing in the trigger time. However, the resistance value increment had hardly impact on the intensity of ion flow extracted in the end, The ion flow became stronger with the increasing main arc current. Conclusion: The power supply system of ion source is simplified by using the trigger method with a resistor. Only a suitable resistor was needed to complete the conversion process from trigger to arc initiating. (authors)

Time-efficient, high-resolution, whole brain three-dimensional macromolecular proton fraction mapping.

Science.gov (United States)

Yarnykh, Vasily L

2016-05-01

Macromolecular proton fraction (MPF) mapping is a quantitative MRI method that reconstructs parametric maps of a relative amount of macromolecular protons causing the magnetization transfer (MT) effect and provides a biomarker of myelination in neural tissues. This study aimed to develop a high-resolution whole brain MPF mapping technique using a minimal number of source images for scan time reduction. The described technique was based on replacement of an actually acquired reference image without MT saturation by a synthetic one reconstructed from R1 and proton density maps, thus requiring only three source images. This approach enabled whole brain three-dimensional MPF mapping with isotropic 1.25 × 1.25 × 1.25 mm(3) voxel size and a scan time of 20 min. The synthetic reference method was validated against standard MPF mapping with acquired reference images based on data from eight healthy subjects. Mean MPF values in segmented white and gray matter appeared in close agreement with no significant bias and small within-subject coefficients of variation (maps demonstrated sharp white-gray matter contrast and clear visualization of anatomical details, including gray matter structures with high iron content. The proposed synthetic reference method improves resolution of MPF mapping and combines accurate MPF measurements with unique neuroanatomical contrast features. © 2015 Wiley Periodicals, Inc.

Boosted decision trees in the CMS Level-1 endcap muon trigger

CERN Document Server

Low, Jia Fu; Busch, Elena Laura; Carnes, Andrew Mathew; Furic, Ivan-Kresimir; Gleyzer, Sergei; Kotov, Khristian; Madorsky, Alexander; Rorie, Jamal Tildon; Scurlock, Bobby; Shi, Wei; Acosta, Darin Edward

2017-01-01

The first implementation of Boosted Decision Trees (BDTs) inside a Level-1 trigger system at the LHC is presented. The Endcap Muon Track Finder (EMTF) at CMS uses BDTs to infer the momentum of muons in the forward region of the detector, based on 25 different variables. Combinations of these variables are evaluated offline using regression BDTs, whose output is stored in 1.2 GB look-up tables (LUTs) in the EMTF hardware. These BDTs take advantage of complex correlations between variables, the inhomogeneous magnetic field, and non-linear effects such as inelastic scattering to distinguish high-momentum signal muons from the overwhelming low-momentum background. The LUTs are used to turn the complex BDT evaluation into a simple look-up operation in fixed low latency. The new momentum assignment algorithm has reduced the trigger rate by a factor of 3 at the 25 GeV trigger threshold with respect to the legacy system, with further improvements foreseen in the coming year.

The Phase-1 Upgrade of the ATLAS First Level Calorimeter Trigger

CERN Document Server

Andrei, George Victor; The ATLAS collaboration

2017-01-01

The ATLAS Level-1 calorimeter trigger is planning a series of upgrades in order to face the challenges posed by the upcoming increase of the LHC luminosity. The hardware built for the Phase-1 upgrade will be installed during the long shutdown of the LHC starting in 2019, with the aim of being fully commissioned before the restart in 2021. The upgrade will benefit from new front end electronics for parts of the calorimeter which provide the trigger system with digital data with a tenfold increase in granularity. This makes possible the use of more complex algorithms than currently used and while maintaining low trigger thresholds under much harsher collision conditions. Of principal significance among these harsher conditions will be the increased number interactions per bunch crossing, known as pile-up. The Level-1 calorimeter system upgrade consists of an active and a passive system for digital data distribution and three different Feature EXtraction systems (FEXs) which run complex algorithms to identify el...

A read-out buffer prototype for ATLAS high level triggers

CERN Document Server

Calvet, D; Huet, M; Le Dû, P; Mandjavidze, I D; Mur, M

2000-01-01

Read-Out Buffers are critical components in the dataflow chain of the ATLAS Trigger/DAQ system. At up to 75 kHz, after each Level-1 trigger accept signal, these devices receive and store digitized data from groups of front-end electronic channels. Several Read-Out Buffers are grouped to form a Read-Out Buffer Complex that acts as a data server for the High Level Triggers selection algorithms and for the final data collection system. This paper describes a functional prototype of a Read-Out Buffer based on a custom made PCI mezzanine card that is designed to accept input data at up to 160 MB/s, to store up to 8 MB of data and to distribute data chunks at the desired request rate. We describe the hardware of the card that is based on an Intel I960 processor and CPLDs. We present the integration of several of these cards in a Read-Out Buffer Complex. We measure various performance figures and we discuss to which extent these can fulfill ATLAS needs. 5 Refs.

Generalized Born Models of Macromolecular Solvation Effects

Science.gov (United States)

Bashford, Donald; Case, David A.

2000-10-01

It would often be useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.

The LHCb trigger

International Nuclear Information System (INIS)

Korolko, I.

1998-01-01

This paper describes progress in the development of the LHCb trigger system since the letter of intent. The trigger philosophy has significantly changed, resulting in an increase of trigger efficiency for signal B events. It is proposed to implement a level-1 vertex topology trigger in specialised hardware. (orig.)

TRIGGER

CERN Multimedia

W. Smith

At the December meeting, the CMS trigger group reported on progress in production, tests in the Electronics Integration Center (EIC) in Prevessin 904, progress on trigger installation in the underground counting room at point 5, USC55, and results from the Magnet Test and Cosmic Challenge (MTCC) phase II. The trigger group is engaged in the final stages of production testing, systems integration, and software and firmware development. Most systems are delivering final tested electronics to CERN. The installation in USC55 is underway and moving towards integration testing. A program of orderly connection and checkout with subsystems and central systems has been developed. This program includes a series of vertical subsystem slice tests providing validation of a portion of each subsystem from front-end electronics through the trigger and DAQ to data captured and stored. This is combined with operations and testing without beam that will continue until startup. The plans for start-up, pilot and early running tri...

Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography

Energy Technology Data Exchange (ETDEWEB)

Wall, Michael E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-10-16

X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins.

The structural biology center at the APS: an integrated user facility for macromolecular crystallography

International Nuclear Information System (INIS)

Rosenbaum, G.; Westbrook, E.M.

1997-01-01

The Structural Biology Center (SBC) has developed and operates a sector (undulator and bending magnet) of the APS as a user facility for macromolecular crystallography. Crystallographically determined structures of proteins, nucleic acids and their complexes with proteins, viruses, and complexes between macromolecules and small ligands have become of central importance in molecular and cellular biology. Major design goals were to make the extremely high brilliance of the APS available for brilliance limited studies, and to achieve a high throughput of less demanding studies, as well as optimization for MAS-phasing. Crystal samples will include extremely small crystals, crystals with large unit cells (viruses, ribosomes, etc.) and ensembles of closely similar crystal structures for drug design, protein engineering, etc. Data are recorded on a 3000x3000 pixel CCD-area detector (optionally on image plates). The x-ray optics of both beamlines has been designed to produce a highly demagnified image of the source in order to match the focal size with the sizes of the sample and the resolution element of the detector. Vertical focusing is achieved by a flat, cylindrically bent mirror. Horizontal focusing is achieved by sagitally bending the second crystal of the double crystal monochromator. Monochromatic fluxes of 1.3 * 10 13 ph/s into focal sizes of 0.08 mm (horizontal)x0.04 mm (vertical) FWHM (flux density 3.5 * 10 15 ph/s/mm 2 ) have been recorded.copyright 1997 American Institute of Physics

Proceedings of a one-week course on exploiting anomalous scattering in macromolecular structure determination (EMBO'07)

International Nuclear Information System (INIS)

Weiss, M.S.; Shepard, W.; Dauter, Z.; Leslie, A.; Diederichs, K.; Evans, G.; Svensson, O.; Schneider, T.; Bricogne, G.; Dauter, Z.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Leslie, A.; Kabsch, W.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Read, R.; Panjikar, S.; Pannu, N.S.; Dauter, Z.; Weiss, M.S.; McSweeney, S.

2007-01-01

This course, which was directed to young scientists, illustrated both theoretical and practical aspects of macromolecular crystal structure solution using synchrotron radiation. Some software dedicated to data collection, processing and analysis were presented. This document gathers only the slides of the presentations

Proceedings of a one-week course on exploiting anomalous scattering in macromolecular structure determination (EMBO'07)

Energy Technology Data Exchange (ETDEWEB)

Weiss, M S; Shepard, W; Dauter, Z; Leslie, A; Diederichs, K; Evans, G; Svensson, O; Schneider, T; Bricogne, G; Dauter, Z; Flensburg, C; Terwilliger, T; Lamzin, V; Leslie, A; Kabsch, W; Flensburg, C; Terwilliger, T; Lamzin, V; Read, R; Panjikar, S; Pannu, N S; Dauter, Z; Weiss, M S; McSweeney, S

2007-07-01

This course, which was directed to young scientists, illustrated both theoretical and practical aspects of macromolecular crystal structure solution using synchrotron radiation. Some software dedicated to data collection, processing and analysis were presented. This document gathers only the slides of the presentations.

BAT Triggering Performance

Science.gov (United States)

McLean, Kassandra M.; Fenimore, E. E.; Palmer, D. M.; BAT Team

2006-09-01

The Burst Alert Telescope (BAT) onboard Swift has detected and located about 160 gamma-ray bursts (GRBs) in its first twenty months of operation. BAT employs two triggering systems to find GRBs: image triggering, which looks for a new point source in the field of view, and rate triggering, which looks for a significant increase in the observed counts. The image triggering system looks at 1 minute, 5 minute, and full pointing accumulations of counts in the detector plane in the energy range of 15-50 keV, with about 50 evaluations per pointing (about 40 minutes). The rate triggering system looks through 13 different time scales (from 4ms to 32s), 4 overlapping energy bins (covering 15-350 keV), 9 regions of the detector plane (from the full plane to individual quarters), and two background sampling models to search for GRBs. It evaluates 27000 trigger criteria in a second, for close to 1000 criteria. The image triggering system looks at 1, 5, and 40 minute accumulations of counts in the detector plane in the energy range of 15-50 keV. Both triggering systems are working very well with the settings from before launch and after we turned on BAT. However, we now have more than a year and a half of data to evaluate these triggering systems and tweak them for optimal performance, as well as lessons learned from these triggering systems.

Polycapillary x-ray optics for macromolecular crystallography

International Nuclear Information System (INIS)

Owens, S.M.; Gibson, W.M.; Carter, D.C.; Sisk, R.C.; Ho, J.X.

1996-01-01

Polycapillary x-ray optics have found potential application in many different fields, including antiscatter and magnification in mammography, radiography, x-ray fluorescence, x-ray lithography, and x-ray diffraction techniques. In x-ray diffraction, an optic is used to collect divergent x-rays from a point source and redirect them into a quasi-parallel, or slightly focused beam. Monolithic polycapillary optics have been developed recently for macromolecular crystallography and have already shown considerable gains in diffracted beam intensity over pinhole collimation. Development is being pursued through a series of simulations and prototype optics. Many improvements have been made over the stage 1 prototype reported previously, which include better control over the manufacturing process, reducing the diameter of the output beam, and addition of a slight focusing at the output of the optic to further increase x-ray flux at the sample. The authors report the characteristics and performance of the stage 1 and stage 2 optics

TRIGGER

CERN Multimedia

W. Smith

Level-1 Trigger Hardware The CERN group is working on the TTC system. Seven out of nine sub-detector TTC VME crates with all fibers cabled are installed in USC55. 17 Local Trigger Controller (LTC) boards have been received from production and are in the process of being tested. The RF2TTC module replacing the TTCmi machine interface has been delivered and will replace the TTCci module used to mimic the LHC clock. 11 out of 12 crates housing the barrel ECAL off-detector electronics have been installed in USC55 after commissioning at the Electronics Integration Centre in building 904. The cabling to the Regional Calorimeter Trigger (RCT) is terminated. The Lisbon group has completed the Synchronization and Link mezzanine board (SLB) production. The Palaiseau group has fully tested and installed 33 out of 40 Trigger Concentrator Cards (TCC). The seven remaining boards are being remade. The barrel TCC boards have been tested at the H4 test beam, and good agreement with emulator predictions were found. The cons...

Study of physicochemical properties of zinc(II) butyrate complex compounds with some heterocyclic ligands

Czech Academy of Sciences Publication Activity Database

Szakácsová, M.; Györová, K.; Szunyogová, E.; Kovářová, Jana

2002-01-01

Roč. 96, - (2002), s. 383 ISSN 0009-2770. [Meeting of Chemical Societies /54./. 30.06.2002-04.07.2002, Brno] R&D Projects: GA AV ČR KSK4050111; GA MŠk VEGA 1/9247/02; GA MŠk VEGA 047/074 Keywords : butyrate complex compounds * heterocyclic ligands Subject RIV: CD - Macromolecular Chemistry

The Complex Role of Store Operated Calcium Entry Pathways and Related Proteins in the Function of Cardiac, Skeletal and Vascular Smooth Muscle Cells

Directory of Open Access Journals (Sweden)

Javier Avila-Medina

2018-03-01

Full Text Available Cardiac, skeletal, and smooth muscle cells shared the common feature of contraction in response to different stimuli. Agonist-induced muscle's contraction is triggered by a cytosolic free Ca2+ concentration increase due to a rapid Ca2+ release from intracellular stores and a transmembrane Ca2+ influx, mainly through L-type Ca2+ channels. Compelling evidences have demonstrated that Ca2+ might also enter through other cationic channels such as Store-Operated Ca2+ Channels (SOCCs, involved in several physiological functions and pathological conditions. The opening of SOCCs is regulated by the filling state of the intracellular Ca2+ store, the sarcoplasmic reticulum, which communicates to the plasma membrane channels through the Stromal Interaction Molecule 1/2 (STIM1/2 protein. In muscle cells, SOCCs can be mainly non-selective cation channels formed by Orai1 and other members of the Transient Receptor Potential-Canonical (TRPC channels family, as well as highly selective Ca2+ Release-Activated Ca2+ (CRAC channels, formed exclusively by subunits of Orai proteins likely organized in macromolecular complexes. This review summarizes the current knowledge of the complex role of Store Operated Calcium Entry (SOCE pathways and related proteins in the function of cardiac, skeletal, and vascular smooth muscle cells.

The Postgraduate Study of Macromolecular Sciences at the University of Zagreb (1971-1980)

OpenAIRE

Kunst, B.; Dezelic, D.; Veksli, Z.

2008-01-01

The postgraduate study of macromolecular sciences (PSMS) was established at the University of Zagreb in 1971 as a university study in the time of expressed interdisciplinary permeation of natural sciences - physics, chemistry and biology, and application of their achievements in technologicaldisciplines. PSMS was established by a group of prominent university professors from the schools of Science, Chemical Technology, Pharmacy and Medicine, as well as from the Institute of Biology. The study...

A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF

International Nuclear Information System (INIS)

McCarthy, Andrew A.; Brockhauser, Sandor; Nurizzo, Didier; Theveneau, Pascal; Mairs, Trevor; Spruce, Darren; Guijarro, Matias; Lesourd, Marc; Ravelli, Raimond B. G.; McSweeney, Sean

2009-01-01

The improvement of the X-ray beam quality achieved on ID14-4 by the installation of new X-ray optical elements is described. ID14-4 at the ESRF is the first tunable undulator-based macromolecular crystallography beamline that can celebrate a decade of user service. During this time ID14-4 has not only been instrumental in the determination of the structures of biologically important molecules but has also contributed significantly to the development of various instruments, novel data collection schemes and pioneering radiation damage studies on biological samples. Here, the evolution of ID14-4 over the last decade is presented, and some of the major improvements that were carried out in order to maintain its status as one of the most productive macromolecular crystallography beamlines are highlighted. The experimental hutch has been upgraded to accommodate a high-precision diffractometer, a sample changer and a large CCD detector. More recently, the optical hutch has been refurbished in order to improve the X-ray beam quality on ID14-4 and to incorporate the most modern and robust optical elements used at other ESRF beamlines. These new optical elements will be described and their effect on beam stability discussed. These studies may be useful in the design, construction and maintenance of future X-ray beamlines for macromolecular crystallography and indeed other applications, such as those planned for the ESRF upgrade

MolProbity: all-atom structure validation for macromolecular crystallography

International Nuclear Information System (INIS)

Chen, Vincent B.; Arendall, W. Bryan III; Headd, Jeffrey J.; Keedy, Daniel A.; Immormino, Robert M.; Kapral, Gary J.; Murray, Laura W.; Richardson, Jane S.; Richardson, David C.

2010-01-01

MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction. MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors’ contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database

In-situ complex with by-product HCl and release chloride ions to dissolve aramid.

Science.gov (United States)

Dai, Yu; Cheng, Zheng; Yuan, Yihao; Meng, Chenbo; Qin, Jiaqiang; Liu, Xiangyang

2018-06-20

Because of the strong hydrogen-bond interaction among macromolecular chains, addition of chloride salts is generally needed to offer Cl- ions for dissolution of aromatic polyamides. In this paper, poly-(benzimidazole-terephthalamide) which complexed with by-product HCl during polymerization (PABI-HCl) was prepared and imidazole compound as cosolvent was added into dimethylacetamide (DMAc) to dissolve PABI-HCl. Due to stronger affinity to protons, imidazole compound could in-situ complex with HCl of PABI-HCl and form imidazolium hydrochloride. Then imidazolium hydrochloride would ionize and produce much free Cl- ions which acted as stronger hydrogen-bond acceptor to disrupt interaction among macromolecular chains. As a result, solubility of PABI-HCl in DMAc was improved significantly in existence of small amount of imidazole compound. Moreover, DMAc-imidazole mixture was utlized for synthesis of different kinds of aramids and no precipitation was observed with progress of the reaction. So the mixture was suitable to be utlized as solvent for polymerization of aramid. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Distribution and enzymatic activity of heterotrophic bacteria decomposing selected macromolecular compounds in a Baltic Sea sandy beach

Science.gov (United States)

Podgórska, B.; Mudryk, Z. J.

2003-03-01

The potential capability to decompose macromolecular compounds, and the level of extracellular enzyme activities were determined in heterotrophic bacteria isolated from a sandy beach in Sopot on the Southern Baltic Sea coast. Individual isolates were capable of hydrolysing a wide spectrum of organic macromolecular compounds. Lipids, gelatine, and DNA were hydrolyzed most efficiently. Only a very small percentage of strains were able to decompose cellulose, and no pectinolytic bacteria were found. Except for starch-hydrolysis, no significant differences in the intensity of organic compound decomposition were recorded between horizontal and vertical profiles of the studied beach. Of all the studied extracellular enzymes, alkaline phosphatase, esterase lipase, and leucine acrylaminidase were most active; in contrast, the activity α-fucosidase, α-galactosidase and β-glucouronidase was the weakest. The level of extracellular enzyme activity was similar in both sand layers.

Phase-Separated Liposomes Enhance the Efficiency of Macromolecular Delivery to the Cellular Cytoplasm.

Science.gov (United States)

Imam, Zachary I; Kenyon, Laura E; Ashby, Grant; Nagib, Fatema; Mendicino, Morgan; Zhao, Chi; Gadok, Avinash K; Stachowiak, Jeanne C

2017-10-01

From viruses to organelles, fusion of biological membranes is used by diverse biological systems to deliver macromolecules across membrane barriers. Membrane fusion is also a potentially efficient mechanism for the delivery of macromolecular therapeutics to the cellular cytoplasm. However, a key shortcoming of existing fusogenic liposomal systems is that they are inefficient, requiring a high concentration of fusion-promoting lipids in order to cross cellular membrane barriers. Toward addressing this limitation, our experiments explore the extent to which membrane fusion can be amplified by using the process of lipid membrane phase separation to concentrate fusion-promoting lipids within distinct regions of the membrane surface. We used confocal fluorescence microscopy to investigate the integration of fusion-promoting lipids into a ternary lipid membrane system that separated into liquid-ordered and liquid-disordered membrane phases. Additionally, we quantified the impact of membrane phase separation on the efficiency with which liposomes transferred lipids and encapsulated macromolecules to cells, using a combination of confocal fluorescence imaging and flow cytometry. Here we report that concentrating fusion-promoting lipids within phase-separated lipid domains on the surfaces of liposomes significantly increases the efficiency of liposome fusion with model membranes and cells. In particular, membrane phase separation enhanced the delivery of lipids and model macromolecules to the cytoplasm of tumor cells by at least 4-fold in comparison to homogenous liposomes. Our findings demonstrate that phase separation can enhance membrane fusion by locally concentrating fusion-promoting lipids on the surface of liposomes. This work represents the first application of lipid membrane phase separation in the design of biomaterials-based delivery systems. Additionally, these results lay the ground work for developing fusogenic liposomes that are triggered by physical and

Macromolecular contrast agents for MR mammography: current status

International Nuclear Information System (INIS)

Daldrup-Link, Heike E.; Brasch, Robert C.

2003-01-01

Macromolecular contrast media (MMCM) encompass a new class of diagnostic drugs that can be applied with dynamic MRI to extract both physiologic and morphologic information in breast lesions. Kinetic analysis of dynamic MMCM-enhanced MR data in breast tumor patients provides useful estimates of tumor blood volume and microvascular permeability, typically increased in cancer. These tumor characteristics can be applied to differentiate benign from malignant lesions, to define the angiogenesis status of cancers, and to monitor tumor response to therapy. The most immediate challenge to the development of MMCM-enhanced mammography is the identification of those candidate compounds that demonstrate the requisite long intravascular distribution and have the high tolerance necessary for clinical use. Potential mammographic applications and limitations of various MMCM, defined by either experimental animal testing or clinical testing in patients, are reviewed in this article. (orig.)

A Fast Hardware Tracker for the ATLAS Trigger System

CERN Document Server

Neubauer, M; The ATLAS collaboration

2009-01-01

As the LHC luminosity is ramped up to the design level of 10^{34} cm^{-2} s^{-1} and beyond, the high rates, multiplicities, and energies of particles seen by the detectors will pose a unique challenge. Only a tiny fraction of the produced collisions can be stored on tape and immense real-time data reduction is needed. An effective trigger system must maintain high trigger efficiencies for the physics we are most interested in, and at the same time suppress the enormous QCD backgrounds. This requires massive computing power to minimize the online execution time of complex algorithms. A multi-level trigger is an effective solution for an otherwise impossible problem. The Fast Tracker (FTK) is a proposed upgrade to the ATLAS trigger system that will operate at full Level-1 output rates and provide high quality tracks reconstructed over the entire detector by the start of processing in Level-2. FTK solves the combinatorial challenge inherent to tracking by exploiting the massive parallelism of Associative Memori...

Whistler Triggered Upper Band Chorus Observed in Alaska

Science.gov (United States)

Hosseini, P.; Golkowski, M.

2017-12-01

VLF radiation from lightning discharges is one of several sources of energy injection into the inner magnetosphere from the Earth. Lightning discharges initially produce a broadband impulse or `sferic' but after propagation in the dispersive magnetosphere this waveform soon becomes quasi narrow band with the characteristic spectrographic form of the whistler. Most of the lightning induced VLF wave energy injected into the magnetosphere will be unducted with a k-vector which becomes increasingly oblique. Although unducted radiation is ubiquitous throughout the inner magnetosphere, it is generally of a low amplitude due to Landau damping and is not expected to produce strong nonlinear phenomena such as triggered emissions and chorus waves. However, VLF wave energy ducted or trapped in field-aligned plasma density enhancements can have relatively large amplitudes due to focusing and also linear cyclotron resonance growth. Therefore high amplitude ducted whistler waves can trigger a number of complex nonlinear phenomena. These include the triggering of VLF emissions and triggering of VLF hiss or chorus. Such phenomena are generally considered to result from nonlinear electron cyclotron phase trapping. Observation of such VLF emissions triggered by natural whistlers have been reported since the 1970s in Antarctica. We present observations of whistlers triggered upper band chorus emission from Alaska. Dispersion analyze of whistlers determine the L-shell range to be 4.5 clear frequency band gap between upper and lower band of the observed chorus emissions. The observations point to ducted chorus generation in the vicinity of the plasmapause boundary.

NOMAD Trigger Studies

International Nuclear Information System (INIS)

Varvell, K.

1995-01-01

The author reports on the status of an offline study of the NOMAD triggers, which has several motivations. Of primary importance is to demonstrate, using offline information recorded by the individual subdetectors comprising NOMAD, that the online trigger system is functioning as expected. Such an investigation serves to complement the extensive monitoring which is already carried out online. More specific to the needs of the offline software and analysis, the reconstruction of tracks and vertices in the detector requires some knowledge of the time at which the trigger has occurred, in order to locate relevant hits in the drift chambers and muon chambers in particular. The fact that the different triggers allowed by the MIOTRINO board take varying times to form complicates this task. An offline trigger algorithm may serve as a tool to shed light on situations where the online trigger status bits have not been recorded correctly, as happens in a small number of cases, or as an aid to studies with the aim of further refinement of the online triggers themselves

ISOTDAQ: another successful trigger and data acquisition school

CERN Multimedia

Antonella Del Rosso

2013-01-01

The fourth ISOTDAQ school was held at the Aristotle University of Thessaloniki (Greece) from 1 to 8 February.   This year, the school received over 70 applications from which the organisers selected 51 participants of 17 different nationalities. The photo shows a tutor and some of the students during the practical exercises. The school, which consists 50% of lectures and 50% of exercises, is a unique opportunity for students to learn how to implement a good trigger and to design a data-acquisition system for today’s increasingly complex experiments. Thanks to the tutored exercises, students can gain hands-on experience of trigger systems, data-acquisition hardware and software, and data-transfer technologies.

Moessbauer spectroscopic characterization of macromolecule-metallochlorophyll complexes

International Nuclear Information System (INIS)

Inoue, H.; Fukuda, K.; Nonomura, Y.; Fluck, E.

1993-01-01

The bis-adducts of iron chlorophylls with poly(4-vinylpyridine-costyrene) (PVP) have been prepared and characterized by 57 Fe Moessbauer spectroscopy. The Moessbauer parameters of the PVP-adducts of iron chlorophylls are typical of low-spin iron(II) complexes. The central iron(III) ion is spontaneously reduced upon the axial coordination of PVP to iron(III) chlorophylls. The general tendency in the spontaneous reduction of the iron(III) chlorophylls has been interpreted in terms of the σ-donor and π-acceptor power of the axial macromolecular ligand. (orig.)

Triggering at high luminosity: fake triggers from pile-up

International Nuclear Information System (INIS)

Johnson, R.

1983-01-01

Triggers based on a cut in transverse momentum (p/sub t/) have proved to be useful in high energy physics both because they indicte that a hard constituent scattering has occurred and because they can be made quickly enough to gate electronics. These triggers will continue to be useful at high luminosities if overlapping events do not cause an excessive number of fake triggers. In this paper, I determine if this is indeed a problem at high luminosity machines

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

Directory of Open Access Journals (Sweden)

Shane Ó Conchúir

Full Text Available The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a "best practice" set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available.

Macromolecular crowding compacts unfolded apoflavodoxin and causes severe aggregation of the off-pathway intermediate during apoflavodoxin folding

NARCIS (Netherlands)

Engel, R.; Westphal, A.H.; Huberts, D.; Nabuurs, S.M.; Lindhoud, S.; Visser, A.J.W.G.; Mierlo, van C.P.M.

2008-01-01

To understand how proteins fold in vivo, it is important to investigate the effects of macromolecular crowding on protein folding. Here, the influence of crowding on in vitro apoflavodoxin folding, which involves a relatively stable off-pathway intermediate with molten globule characteristics, is

Proceedings of a one-week course on exploiting anomalous scattering in macromolecular structure determination (EMBO'07)

Energy Technology Data Exchange (ETDEWEB)

Weiss, M.S.; Shepard, W.; Dauter, Z.; Leslie, A.; Diederichs, K.; Evans, G.; Svensson, O.; Schneider, T.; Bricogne, G.; Dauter, Z.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Leslie, A.; Kabsch, W.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Read, R.; Panjikar, S.; Pannu, N.S.; Dauter, Z.; Weiss, M.S.; McSweeney, S

2007-07-01

This course, which was directed to young scientists, illustrated both theoretical and practical aspects of macromolecular crystal structure solution using synchrotron radiation. Some software dedicated to data collection, processing and analysis were presented. This document gathers only the slides of the presentations.

Probing the Interplay of Size, Shape, and Solution Environment in Macromolecular Diffusion Using a Simple Refraction Experiment

Science.gov (United States)

Mankidy, Bijith D.; Coutinho, Cecil A.; Gupta, Vinay K.

2010-01-01

The diffusion coefficient of polymers is a critical parameter in biomedicine, catalysis, chemical separations, nanotechnology, and other industrial applications. Here, measurement of macromolecular diffusion in solutions is described using a visually instructive, undergraduate-level optical refraction experiment based on Weiner's method. To…

ATLAS Trigger Monitoring and Operation in Proton Proton Collisions at 900 GeV

CERN Document Server

zur Nedden, M; The ATLAS collaboration

2010-01-01

The trigger of the ATLAS-experiment is build as a three level system. The first level is realized in hardware while the higher levels (HLT) are pure software implemented triggers based on large PC farms. According to the LHC bunch crossing frequency of 40 MHz and the expectation of up to 23 interactions per bunch crossing at design luminosity, the trigger system must be able to deal with an input rate of 1 GHz whereas the maximum storage rate is 200 Hz. This complex data acquisition and trigger system requires a reliable and redundant diagnostic and monitoring system. This is inevitable for a successful commissioning and stable running of the whole experiment. The main aspects of trigger monitoring are the rate measurements at each step of the trigger decision at each level, the determination of the quality of the physics objects candidates to be selected at trigger level (as candidates for electrons, muons, taus, gammas, jets, b-jets and missing energy) and the supervision of the system's behavior during the...

Grain sorghum dust increases macromolecular efflux from the in situ nasal mucosa.

Science.gov (United States)

Gao, X P

1998-04-01

The purpose of this study was to determine whether an aqueous extract of grain sorghum dust increases macromolecular efflux from the nasal mucosa in vivo and, if so, whether this response is mediated, in part, by substance P. Suffusion of grain sorghum dust extract on the in situ nasal mucosa of anesthetized hamsters elicits a significant increase in clearance of fluorescein isothiocyanate-labeled dextran (FITC-dextran; mol mass, 70 kDa; P grain sorghum dust elicits neurogenic plasma exudation from the in situ nasal mucosa.

Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

Energy Technology Data Exchange (ETDEWEB)

A Soares; D Schneider; J Skinner; M Cowan; R Buono; H Robinson; A Heroux; M Carlucci-Dayton; A Saxena; R Sweet

2011-12-31

The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

International Nuclear Information System (INIS)

Soares, A.; Schneider, D.; Skinner, J.; Cowan, M.; Buono, R.; Robinson, H.; Heroux, A.; Carlucci-Dayton, M.; Saxena, A.; Sweet, R.

2008-01-01

The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

Trigger finger

Science.gov (United States)

... digit; Trigger finger release; Locked finger; Digital flexor tenosynovitis ... cut or hand Yellow or green drainage from the cut Hand pain or discomfort Fever If your trigger finger returns, call your surgeon. You may need another surgery.

The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study.

Directory of Open Access Journals (Sweden)

Helena W Qi

Full Text Available Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders, this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered "effective" solvent dielectric to account for crowding, although the "best" effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the

Tinnitus-provoking salicylate treatment triggers social impairments in mice.

Science.gov (United States)

Guitton, Matthieu J

2009-09-01

Tinnitus (perception of sound in silence) strongly affects the quality of life of sufferers. Tinnitus sufferers and their relatives frequently complain about major social impairments. However, it is not known whether this impairment directly results from the occurrence of tinnitus or is the indirect expression of a preexisting psychological vulnerability. Using the well-characterized animal model of salicylate-induced tinnitus, we investigate in mice whether the occurrence of tinnitus can trigger social impairments. Experiments were performed on 32 male Balb/C mice. Tinnitus was induced in mice using salicylate treatment. Social behavior was assessed in experimental and control animals using social interaction paradigm. Interaction time, number of social events, and number of nonsocial events were assessed in all animals. We demonstrate for the first time that treatment known to induce tinnitus triggers complex social impairments in mice. While salicylate-treated animals present a massive decrease in their overall social interactions compared to control untreated animals, they also display a paradoxal increase in the number of conspecific followings. Tinnitus can thus trigger a complex set of modifications of behavior, which will not only find their expression at the individual level, but also at the social level. Our results suggest that tinnitus can directly be a cause of psychosocial impairment in human and have strong implications for the clinical management of tinnitus sufferers.

Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data

International Nuclear Information System (INIS)

Dosset, Patrice; Hus, Jean-Christophe; Blackledge, Martin; Marion, Dominique

2000-01-01

A novel program has been developed for the interpretation of 15 N relaxation rates in terms of macromolecular anisotropic rotational diffusion. The program is based on a highly efficient simulated annealing/minimization algorithm, designed specifically to search the parametric space described by the isotropic, axially symmetric and fully anisotropic rotational diffusion tensor models. The high efficiency of this algorithm allows extensive noise-based Monte Carlo error analysis. Relevant statistical tests are systematically applied to provide confidence limits for the proposed tensorial models. The program is illustrated here using the example of the cytochrome c' from Rhodobacter capsulatus, a four-helix bundle heme protein, for which data at three different field strengths were independently analysed and compared

An R&D programme on alternative technologies for the ATLAS level-1 calorimeter trigger

CERN Document Server

Appelquist, G; Bohm, C; Engström, M; Hellman, S; Holmgren, S O; Johansson, E; Yamdagni, N; Zhao, X; Sundblad, R; Ödmark, A; Bodo, P; Elderstig, H; Hentzell, H; Lindgren, S; Tober, M; Johansson, H; Svensson, C; Yuan, J R; Mohktari, M; Ellis, Nick

1995-01-16

This note describes a first-level calorimeter trigger processor designed to take advantage of new possibilities that arise as a consequence of modern design techniques and components such as optical interconnections, application specific integrated circuits (ASICs) and multi-chip modules (MCMs). The design is homogeneous down to the trigger cell level. This means that no boundary effects occur due to the system partitioning. The construction presented relies mainly on two different types of highly complex ASICs for processing and an MCM for opto-electrical conversion of input data. The trigger processor performs electron/photon identification, jet detection and missing ET calculations for the central first-level trigger and region of interest (RoI) selection for the second-level trigger. Exploring the possibilities given by advanced technologies leads to a first-level trigger architecture with advantages over more traditional designs, allowing, for example, higher precision calculations. Remaining degrees of ...

¹²⁹ Xe NMR Relaxation-Based Macromolecular Sensing

Energy Technology Data Exchange (ETDEWEB)

Gomes, Muller D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Dao, Phuong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Jeong, Keunhong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Slack, Clancy C. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Vassiliou, Christophoros C. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Finbloom, Joel A. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Francis, Matthew B. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Wemmer, David E. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; Pines, Alexander [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

2016-07-29

A ¹²⁹Xe NMR relaxation-based sensing approach is reported on that exploits changes in the bulk xenon relaxation rate induced by slowed tumbling of a cryptophane-based sensor upon target binding. The amplification afforded by detection of the bulk dissolved xenon allows sensitive detection of targets. The sensor comprises a xenon-binding cryptophane cage, a target interaction element, and a metal chelating agent. Xenon associated with the target-bound cryptophane cage is rapidly relaxed and then detected after exchange with the bulk. Here we show that large macromolecular targets increase the rotational correlation time of xenon, increasing its relaxation rate. Upon binding of a biotin-containing sensor to avidin at 1.5 μM concentration, the free xenon T₂ is reduced by a factor of 4.

Do reflex seizures and spontaneous seizures form a continuum? - triggering factors and possible common mechanisms.

Science.gov (United States)

Irmen, Friederike; Wehner, Tim; Lemieux, Louis

2015-02-01

Recent changes in the understanding and classification of reflex seizures have fuelled a debate on triggering mechanisms of seizures and their conceptual organization. Previous studies and patient reports have listed extrinsic and intrinsic triggers, albeit their multifactorial and dynamic nature is poorly understood. This paper aims to review literature on extrinsic and intrinsic seizure triggers and to discuss common mechanisms among them. Among self-reported seizure triggers, emotional stress is most frequently named. Reflex seizures are typically associated with extrinsic sensory triggers; however, intrinsic cognitive or proprioceptive triggers have also been assessed. The identification of a trigger underlying a seizure may be more difficult if it is intrinsic and complex, and if triggering mechanisms are multifactorial. Therefore, since observability of triggers varies and triggers are also found in non-reflex seizures, the present concept of reflex seizures may be questioned. We suggest the possibility of a conceptual continuum between reflex and spontaneous seizures rather than a dichotomy and discuss evidence to the notion that to some extent most seizures might be triggered. Copyright © 2014 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

Control, Test and Monitoring Software Framework for the ATLAS Level-1 Calorimeter Trigger

CERN Document Server

Achenbach, R; Aharrouche, M; Andrei, V; Åsman, B; Barnett, B M; Bauss, B; Bendel, M; Bohm, C; Booth, J R A; Bracinik, J; Brawn, I P; Charlton, D G; Childers, J T; Collins, N J; Curtis, C J; Davis, A O; Eckweiler, S; Eisenhandler, E F; Faulkner, P J W; Fleckner, J; Föhlisch, F; Gee, C N P; Gillman, A R; Goringer, C; Groll, M; Hadley, D R; Hanke, P; Hellman, S; Hidvegi, A; Hillier, S J; Johansen, M; Kluge, E E; Kühl, T; Landon, M; Lendermann, V; Lilley, J N; Mahboubi, K; Mahout, G; Meier, K; Middleton, R P; Moa, T; Morris, J D; Müller, F; Neusiedl, A; Ohm, C; Oltmann, B; Perera, V J O; Prieur, D P F; Qian, W; Rieke, S; Rühr, F; Sankey, D P C; Schäfer, U; Schmitt, K; Schultz-Coulon, H C; Silverstein, S; Sjölin, J; Staley, R J; Stamen, R; Stockton, M C; Tan, C L A; Tapprogge, S; Thomas, J P; Thompson, P D; Watkins, P M; Watson, A; Weber, P; Wessels, M; Wildt, M

2008-01-01

The ATLAS first-level calorimeter trigger is a hardware-based system designed to identify high-pT jets, electron/photon and tau candidates and to measure total and missing ET in the ATLAS calorimeters. The complete trigger system consists of over 300 customdesignedVME modules of varying complexity. These modules are based around FPGAs or ASICs with many configurable parameters, both to initialize the system with correct calibrations and timings and to allow flexibility in the trigger algorithms. The control, testing and monitoring of these modules requires a comprehensive, but well-designed and modular, software framework, which we will describe in this paper.

The Phase-1 Upgrade for the Level-1 Muon Barrel Trigger of the ATLAS Experiment at LHC

CERN Document Server

Izzo, Vincenzo; The ATLAS collaboration

2018-01-01

The Level-1 Muon Barrel Trigger of the ATLAS Experiment at LHC makes use of Resistive Plate Chamber (RPC) detectors. The on-detector trigger electronics modules are able to identify muons with predefined transverse momentum values (pT) by executing a coincidence logic on signals coming from the various detector layers. On-detector trigger boards then transfer trigger data to the off-detector electronics. A complex trigger system processes the incoming data by combining trigger information from the barrel and the endcap regions, and providing the combined muon candidate to the Central Trigger Processor (CTP). For almost a decade, the Level-1 Trigger system operated very well, despite the challenging requirements on trigger efficiency and performance, and the continuously increasing LHC luminosity. In order to cope with these constraints, various upgrades for the full trigger system were already deployed, and others have been designed to be installed in the next years. Most of the upgrades to the trigger system...

Topological Trigger Developments

CERN Multimedia

Likhomanenko, Tatiana

2015-01-01

The main b-physics trigger algorithm used by the LHCb experiment is the so-called topological trigger. The topological trigger selects vertices which are a) detached from the primary proton-proton collision and b) compatible with coming from the decay of a b-hadron. In the LHC Run 1, this trigger utilized a custom boosted decision tree algorithm, selected an almost 100% pure sample of b-hadrons with a typical efficiency of 60-70%, and its output was used in about 60% of LHCb papers. This talk presents studies carried out to optimize the topological trigger for LHC Run 2. In particular, we have carried out a detailed comparison of various machine learning classifier algorithms, e.g., AdaBoost, MatrixNet and uBoost. The topological trigger algorithm is designed to select all "interesting" decays of b-hadrons, but cannot be trained on every such decay. Studies have therefore been performed to determine how to optimize the performance of the classification algorithm on decays not used in the training. These inclu...

Gd-DTPA L-cystine bisamide copolymers as novel biodegradable macromolecular contrast agents for MR blood pool imaging.

Science.gov (United States)

Kaneshiro, Todd L; Ke, Tianyi; Jeong, Eun-Kee; Parker, Dennis L; Lu, Zheng-Rong

2006-06-01

The purpose of this study was to synthesize biodegradable Gd-DTPA L-cystine bisamide copolymers (GCAC) as safe and effective, macromolecular contrast agents for magnetic resonance imaging (MRI) and to evaluate their biodegradability and efficacy in MR blood pool imaging in an animal model. Three new biodegradable GCAC with different substituents at the cystine bisamide [R = H (GCAC), CH2CH2CH3 (Gd-DTPA L-cystine bispropyl amide copolymers, GCPC), and CH(CH3)2 (Gd-DTPA cystine bisisopropyl copolymers, GCIC)] were prepared by the condensation copolymerization of diethylenetriamine pentaacetic acid (DTPA) dianhydride with cystine bisamide or bisalkyl amides, followed by complexation with gadolinium triacetate. The degradability of the agents was studied in vitro by incubation in 15 microM cysteine and in vivo with Sprague-Dawley rats. The kinetics of in vivo contrast enhancement was investigated in Sprague-Dawley rats on a Siemens Trio 3 T scanner. The apparent molecular weight of the polydisulfide Gd(III) chelates ranged from 22 to 25 kDa. The longitudinal (T1) relaxivities of GCAC, GCPC, and GCIC were 4.37, 5.28, and 5.56 mM(-1) s(-1) at 3 T, respectively. The polymeric ligands and polymeric Gd(III) chelates readily degraded into smaller molecules in incubation with 15 microM cysteine via disulfide-thiol exchange reactions. The in vitro degradation rates of both the polymeric ligands and macromolecular Gd(III) chelates decreased as the steric effect around the disulfide bonds increased. The agents readily degraded in vivo, and the catabolic degradation products were detected in rat urine samples collected after intravenous injection. The agents showed strong contrast enhancement in the blood pool, major organs, and tissues at a dose of 0.1 mmol Gd/kg. The difference of their in vitro degradability did not significantly alter the kinetics of in vivo contrast enhancement of the agents. These novel GCAC are promising contrast agents for cardiovascular and tumor MRI

The fast tracker processor for hadronic collider triggers

CERN Document Server

Annovi, A; Bardi, A; Carosi, R; Dell'Orso, Mauro; D'Onofrio, M; Giannetti, P; Iannaccone, G; Morsani, F; Pietri, M; Varotto, G

2000-01-01

Perspective for precise and fast track reconstruction in future hadronic collider experiments are addressed. We discuss the feasibility of a pipelined highly parallelized processor dedicated to the implementation of a very fast algorithm. The algorithm is based on the use of a large bank of pre-stored combinations of trajectory points (patterns) for extremely complex tracking systems. The CMS experiment at LHC is used as a benchmark. Tracking data from the events selected by the level-1 trigger are sorted and filtered by the Fast Tracker processor at a rate of 100 kHz. This data organization allows the level-2 trigger logic to reconstruct full resolution traces with transverse momentum above few GeV and search secondary vertexes within typical level-2 times. 15 Refs.

The Central Trigger Processor (CTP)

CERN Multimedia

Franchini, Matteo

2016-01-01

The Central Trigger Processor (CTP) receives trigger information from the calorimeter and muon trigger processors, as well as from other sources of trigger. It makes the Level-1 decision (L1A) based on a trigger menu.

Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect.

Directory of Open Access Journals (Sweden)

Anne-Sophie Coquel

2013-04-01

Full Text Available Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian. Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of "soft" intracellular structuring (based on

The Trigger Processor and Trigger Processor Algorithms for the ATLAS New Small Wheel Upgrade

CERN Document Server

Lazovich, Tomo; The ATLAS collaboration

2015-01-01

The ATLAS New Small Wheel (NSW) is an upgrade to the ATLAS muon endcap detectors that will be installed during the next long shutdown of the LHC. Comprising both MicroMegas (MMs) and small-strip Thin Gap Chambers (sTGCs), this system will drastically improve the performance of the muon system in a high cavern background environment. The NSW trigger, in particular, will significantly reduce the rate of fake triggers coming from track segments in the endcap not originating from the interaction point. We will present an overview of the trigger, the proposed sTGC and MM trigger algorithms, and the hardware implementation of the trigger. In particular, we will discuss both the heart of the trigger, an ATCA system with FPGA-based trigger processors (using the same hardware platform for both MM and sTGC triggers), as well as the full trigger electronics chain, including dedicated cards for transmission of data via GBT optical links. Finally, we will detail the challenges of ensuring that the trigger electronics can ...

Macromolecular synthesis in algal cells

International Nuclear Information System (INIS)

Ishida, M.R.; Kikuchi, Tadatoshi

1980-01-01

The present paper is a review of our experimental results obtained previously on the macromolecular biosyntheses in the cells of blue-green alga Anacystis nidulans as a representative species of prokaryote, and also in those of three species of eukaryotic algae, i.e. Euglena gracilis strain Z, Chlamydomonas reinhardi, and Cyanidium caldarium. In these algal cells, the combined methods consisting of pulse-labelling using 32 P, 3 H- and 14 C-labelled precursors for macromolecules, of their chasing and of the use of inhibitors which block specifically the syntheses of macromolecules such as proteins, RNA and DNA in living cells were very effectively applied for the analyses of the regulatory mechanism in biosyntheses of macromolecules and of the mode of their assembly into the cell structure, especially organelle constituents. Rased on the results obtained thus, the following conclusions are reached: (1) the metabolic pool for syntheses of macromolecules in the cells of prokaryotic blue-green alga is limited to the small extent and such activities couple largely with the photosynthetic mechanism; (2) 70 S ribosomes in the blue-green algal cells are assembled on the surface of thylakoid membranes widely distributed in their cytoplasm; and (3) the cells of eukaryotic unicellular algae used here have biochemical characters specific for already differentiated enzyme system involving in transcription and translation machineries as the same as in higher organisms, but the control mechanism concerning with such macromolecule syntheses are different among each species. (author)

Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density

International Nuclear Information System (INIS)

Terwilliger, Thomas C.; Berendzen, Joel

1999-01-01

The correlation of local r.m.s. density is shown to be a good measure of the presence of distinct solvent and macromolecule regions in macromolecular electron-density maps. It has recently been shown that the standard deviation of local r.m.s. electron density is a good indicator of the presence of distinct regions of solvent and protein in macromolecular electron-density maps [Terwilliger & Berendzen (1999 ▶). Acta Cryst. D55, 501–505]. Here, it is demonstrated that a complementary measure, the correlation of local r.m.s. density in adjacent regions on the unit cell, is also a good measure of the presence of distinct solvent and protein regions. The correlation of local r.m.s. density is essentially a measure of how contiguous the solvent (and protein) regions are in the electron-density map. This statistic can be calculated in real space or in reciprocal space and has potential uses in evaluation of heavy-atom solutions in the MIR and MAD methods as well as for evaluation of trial phase sets in ab initio phasing procedures

ISOTDAQ - where students learn about trigger and data acquisition

CERN Multimedia

CERN Bulletin

2011-01-01

Where can students learn to implement a good trigger and to design the data acquisition system for today’s increasingly complex experiments? Universities rarely include classes on such specific topics. The ISOTDAQ School trains students and helps them gain hands-on experience of trigger systems, data-acquisition hardware and software, and data-transfer technologies.   One of the commercially available FPGA development boards from Altera. This was used in one of the practical exercises at ISOTDAQ2011 to teach students the principles of FPGA programming. The second International School of Trigger and Data Acquisition (ISOTDAQ) was held from 9 to 16 February at the Physics Department of Rome University, ‘La Sapienza’. The School was jointly organised and sponsored by CERN, INFN, ACEOLE (a Marie Curie Initial Training Network at CERN), and National Instruments. This year almost fifty students took part in the School. “Leading experts in the field gave lectures ...

The Phase-1 Upgrade for the Level-1 Muon Barrel Trigger of the ATLAS Experiment at LHC

CERN Document Server

Izzo, Vincenzo; The ATLAS collaboration

2018-01-01

The Level-1 Muon Barrel Trigger of the ATLAS Experiment at LHC makes use of Resistive Plate Chamber (RPC) detectors. The on-detector trigger electronics modules are able to identify muons with predefined transverse momentum values (pT) by executing a coincidence logic on signals coming from the various detector layers. Then, on-detector trigger boards transfer trigger data to the off-detector electronics. A complex trigger system processes the incoming data by combining trigger information from the Barrel and the End-cap regions, and by providing the combined muon candidate to the Central Trigger Processor (CTP). For almost a decade, the Level-1 Trigger system has been operating very well, despite the challenging requirements on trigger efficiency and performance, and the continuously increasing LHC luminosity. In order to cope with these constraints, various upgrades for the full trigger system were already deployed, and others have been designed to be installed in the next years. Most of the upgrades to the...

From precision polymers to complex materials and systems

Science.gov (United States)

Lutz, Jean-François; Lehn, Jean-Marie; Meijer, E. W.; Matyjaszewski, Krzysztof

2016-05-01

Complex chemical systems, such as living biological matter, are highly organized structures based on discrete molecules in constant dynamic interactions. These natural materials can evolve and adapt to their environment. By contrast, man-made materials exhibit simpler properties. In this Review, we highlight that most of the necessary elements for the development of more complex synthetic matter are available today. Using modern strategies, such as controlled radical polymerizations, supramolecular polymerizations or stepwise synthesis, polymers with precisely controlled molecular structures can be synthesized. Moreover, such tailored polymers can be folded or self-assembled into defined nanoscale morphologies. These self-organized macromolecular objects can be at thermal equilibrium or can be driven out of equilibrium. Recently, in the latter case, interesting dynamic materials have been developed. However, this is just a start, and more complex adaptive materials are anticipated.

A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits.

Science.gov (United States)

Jaskolski, Mariusz; Dauter, Zbigniew; Wlodawer, Alexander

2014-09-01

As a contribution to the celebration of the year 2014, declared by the United Nations to be 'The International Year of Crystallography', the FEBS Journal is dedicating this issue to papers showcasing the intimate union between macromolecular crystallography and structural biology, both in historical perspective and in current research. Instead of a formal editorial piece, by way of introduction, this review discusses the most important, often iconic, achievements of crystallographers that led to major advances in our understanding of the structure and function of biological macromolecules. We identified at least 42 scientists who received Nobel Prizes in Physics, Chemistry or Medicine for their contributions that included the use of X-rays or neutrons and crystallography, including 24 who made seminal discoveries in macromolecular sciences. Our spotlight is mostly, but not only, on the recipients of this most prestigious scientific honor, presented in approximately chronological order. As a summary of the review, we attempt to construct a genealogy tree of the principal lineages of protein crystallography, leading from the founding members to the present generation. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ.

Science.gov (United States)

Xia, Hongwei; Fu, Hailin; Zhang, Yanfeng; Shih, Kuo-Chih; Ren, Yuan; Anuganti, Murali; Nieh, Mu-Ping; Cheng, Jianjun; Lin, Yao

2017-08-16

Supramolecular polymerization or assembly of proteins or large macromolecular units by a homogeneous nucleation mechanism can be quite slow and require specific solution conditions. In nature, protein assembly is often regulated by molecules that modulate the electrostatic interactions of the protein subunits for various association strengths. The key to this regulation is the coupling of the assembly process with a reversible or irreversible chemical reaction that occurs within the constituent subunits. However, realizing this complex process by the rational design of synthetic molecules or macromolecules remains a challenge. Herein, we use a synthetic polypeptide-grafted comb macromolecule to demonstrate how the in situ modulation of interactions between the charged macromolecules affects their resulting supramolecular structures. The kinetics of structural formation was studied and can be described by a generalized model of nucleated polymerization containing secondary pathways. Basic thermodynamic analysis indicated the delicate role of the electrostatic interactions between the charged subunits in the reaction-induced assembly process. This approach may be applicable for assembling a variety of ionic soft matters that are amenable to chemical reactions in situ.

Evaluation of quantum-chemical methods of radiolysis stability for macromolecular structures

International Nuclear Information System (INIS)

Postolache, Cristian; Matei, Lidia

2005-01-01

The behavior of macromolecular structures in ionising fields was analyzed by quantum-chemical methods. In this study the primary radiolytic effect was analyzed using a two-step radiolytic mechanism: a) ionisation of molecule and spatial redistribution of atoms in order to reach a minimum value of energy, characteristic to the quantum state; b) neutralisation of the molecule by electron capture and its rapid dissociation into free radicals. Chemical bonds suspected to break are located in the distribution region of LUMO orbital and have minimal homolytic dissociation energies. Representative polymer structures (polyethylene, polypropylene, polystyrene, poly α and β polystyrene, polyisobutylene, polytetrafluoroethylene, poly methylsiloxanes) were analyzed. (authors)

The Postgraduate Study of Macromolecular Sciences at the University of Zagreb (1971– 1980)

OpenAIRE

Deželić, D.; Kunst, B.; Veksli, Zorica

2008-01-01

The postgraduate study of macromolecular sciences (PSMS) was established at the University of Zagreb in 1971 as a university study in the time of expressed interdisciplinary permeation of natural sciences - physics, chemistry and biology, and application of their achievements in technological disciplines. PSMS was established by a group of prominent university professors from the schools of Science, Chemical Technology, Pharmacy and Medicine, as well as from the Institute of Biology. The s...

Hydrogen-Bonding Interactions Trigger a Spin-Flip in Iron(III) Porphyrin Complexes**

OpenAIRE

Sahoo, Dipankar; Quesne, Matthew G; de?Visser, Sam P; Rath, Sankar Prasad

2015-01-01

A key step in cytochrome?P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure ...

Hydrogen-Bonding Interactions Trigger a Spin-Flip in Iron(III) Porphyrin Complexes**

OpenAIRE

Sahoo, Dipankar; Quesne, Matthew G; de Visser, Sam P; Rath, Sankar Prasad

2015-01-01

A key step in cytochrome P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure ...

Daily Stress, Coping, and Negative and Positive Affect in Depression: Complex Trigger and Maintenance Patterns.

Science.gov (United States)

Dunkley, David M; Lewkowski, Maxim; Lee, Ihno A; Preacher, Kristopher J; Zuroff, David C; Berg, Jody-Lynn; Foley, J Elizabeth; Myhr, Gail; Westreich, Ruta

2017-05-01

Major depressive disorder is characterized by emotional dysfunction, but mood states in daily life are not well understood. This study examined complex explanatory models of daily stress and coping mechanisms that trigger and maintain daily negative affect and (lower) positive affect in depression. Sixty-three depressed patients completed perfectionism measures, and then completed daily questionnaires of stress appraisals, coping, and affect for 7 consecutive days. Multilevel structural equation modeling (MSEM) demonstrated that, across many stressors, when the typical individual with depression perceives more criticism than usual, he/she uses more avoidant coping and experiences higher event stress than usual, and this is connected to daily increases in negative affect as well as decreases in positive affect. In parallel, results showed that perceived control, less avoidant coping, and problem-focused coping commonly operate together when daily positive affect increases. MSEM also showed that avoidant coping tendencies and ongoing stress, in combination, explain why people with depression and higher self-critical perfectionism maintain daily negative affect and lower positive affect. These findings advance a richer and more detailed understanding of specific stress and coping patterns to target in order to more effectively accomplish the two predominant therapy goals of decreasing patients' distress and strengthening resilience. Copyright © 2016. Published by Elsevier Ltd.

Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry

Science.gov (United States)

Belov, Arseniy M.; Viner, Rosa; Santos, Marcia R.; Horn, David M.; Bern, Marshall; Karger, Barry L.; Ivanov, Alexander R.

2017-12-01

Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). [Figure not available: see fulltext.

Macromolecular Crystallization in Microfluidics for the International Space Station

Science.gov (United States)

Monaco, Lisa A.; Spearing, Scott

2003-01-01

At NASA's Marshall Space Flight Center, the Iterative Biological Crystallization (IBC) project has begun development on scientific hardware for macromolecular crystallization on the International Space Station (ISS). Currently ISS crystallization research is limited to solution recipes that were prepared on the ground prior to launch. The proposed hardware will conduct solution mixing and dispensing on board the ISS, be fully automated, and have imaging functions via remote commanding from the ground. Utilizing microfluidic technology, IBC will allow for on orbit iterations. The microfluidics LabChip(R) devices that have been developed, along with Caliper Technologies, will greatly benefit researchers by allowing for precise fluid handling of nano/pico liter sized volumes. IBC will maximize the amount of science return by utilizing the microfluidic approach and be a valuable tool to structural biologists investigating medically relevant projects.

The monitoring system for macromolecular crystallography beamlines at BSRF

International Nuclear Information System (INIS)

Guo Xian; Chang Guangcai; Gan Quan; Shi Hong; Liu Peng; Sun Gongxing

2012-01-01

The monitoring system for macromolecular crystallography beamlines at BSRF (Beijing Synchrotron Radiation Facility) based on LabVIEW is introduced. In order to guarantee a safe, stable, and reliable running for the beamline devices, the system monitors the state of vacuum, cooling-water, optical components, beam, Liquid nitrogen in the beamlines in real time, detects faults and gives the alarm timely. System underlying uses the driver developed for the field devices for data acquisition, Data of collection is uploaded to the data-sharing platform makes it accessible via a network share. The upper system divides modules according to the actual function, and establishes the main interface of the monitoring system of beamline. To Facilitate data storage, management and inquiry, the system use LabSQL toolkit to achieve the interconnection with MySQL database which data of collection is sent to. (authors)

GPU Enhancement of the Trigger to Extend Physics Reach at the LHC

CERN Document Server

Lujan, P.; Hunt, A.; Jindal, P.; LeGresley, P.

2014-01-01

At the Large Hadron Collider (LHC), the trigger systems for the detectors must be able to process a very large amount of data in a very limited amount of time, so that the nominal collision rate of 40 MHz can be reduced to a data rate that can be stored and processed in a reasonable amount of time. This need for high performance places very stringent requirements on the complexity of the algorithms that can be used for identifying events of interest in the trigger system, which potentially limits the ability to trigger on signatures of various new physics models. In this paper, we present an alternative tracking algorithm, based on the Hough transform, which avoids many of the problems associated with the standard combinatorial track finding currently used. The Hough transform is also well-adapted for Graphics Processing Unit (GPU)-based computing, and such GPU-based systems could be easily integrated into the existing High-Level Trigger (HLT). This algorithm offers the ability to trigger on topological signa...

Kobuvirus VP3 protein restricts the IFN-β-triggered signaling pathway by inhibiting STAT2-IRF9 and STAT2-STAT2 complex formation

Energy Technology Data Exchange (ETDEWEB)

Peng, Qianqian; Lan, Xi; Wang, Chen [State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046 (China); Ren, Yujie; Yue, Ningning [College of Life Sciences, Wuhan University, Wuhan 430072 (China); Wang, Junyong [State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046 (China); Zhong, Bo [College of Life Sciences, Wuhan University, Wuhan 430072 (China); Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071 (China); Zhu, Qiyun, E-mail: zhuqiyun@caas.cn [State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046 (China)

2017-07-15

Emerged porcine kobuvirus (PKV) has adversely affected the global swine industry since 2008, but the etiological biology of PKV is unclear. Screening PKV-encoded structural and non-structural proteins with a type I IFN-responsive luciferase reporter showed that PKV VP3 protein inhibited the IFN-β-triggered signaling pathway, resulting in the decrease of VSV-GFP replication. QPCR data showed that IFN-β downstream cytokine genes were suppressed without cell-type specificity as well. The results from biochemical experiments indicated that PKV VP3 associated with STAT2 and IRF9, and interfered with the formation of the STAT2-IRF9 and STAT2-STAT2 complex, impairing nuclear translocation of STAT2 and IRF9. Taken together, these data reveal a new mechanism for immune evasion of PKV. - Highlights: •PKV VP3 inhibits the IFN-β-triggered signaling pathway. •VP3 associates with STAT2 and IRF9. •VP3 blocks the STAT2-IRF9 nuclear translocation. •VP3 utilizes a novel strategy for innate immune evasion.

Performance Evaluation and Robustness Testing of Advanced Oscilloscope Triggering Schemes

Directory of Open Access Journals (Sweden)

Shakeb A. KHAN

2010-01-01

Full Text Available In this paper, performance and robustness of two advanced oscilloscope triggering schemes is evaluated. The problem of time period measurement of complex waveforms can be solved using the algorithms, which utilize the associative memory network based weighted hamming distance (Whd and autocorrelation based techniques. Robustness of both the advanced techniques, are then evaluated by simulated addition of random noise of different levels to complex test signals waveforms, and minimum value of Whd (Whd min and peak value of coefficient of correlation(COCmax are computed over 10000 cycles of the selected test waveforms. The distance between mean value of second lowest value of Whd and Whd min and distance between second highest value of coefficient of correlation (COC and COC max are used as parameters to analyze the robustness of considered techniques. From the results, it is found that both the techniques are capable of producing trigger pulses efficiently; but correlation based technique is found to be better from robustness point of view.

The 2D Structure of the T. brucei Preedited RPS12 mRNA Is Not Affected by Macromolecular Crowding

Directory of Open Access Journals (Sweden)

W.-Matthias Leeder

2017-01-01

Full Text Available Mitochondrial transcript maturation in African trypanosomes requires RNA editing to convert sequence-deficient pre-mRNAs into translatable mRNAs. The different pre-mRNAs have been shown to adopt highly stable 2D folds; however, it is not known whether these structures resemble the in vivo folds given the extreme “crowding” conditions within the mitochondrion. Here, we analyze the effects of macromolecular crowding on the structure of the mitochondrial RPS12 pre-mRNA. We use high molecular mass polyethylene glycol as a macromolecular cosolute and monitor the structure of the RNA globally and with nucleotide resolution. We demonstrate that crowding has no impact on the 2D fold and we conclude that the MFE structure in dilute solvent conditions represents a good proxy for the folding of the pre-mRNA in its mitochondrial solvent context.

Macromolecular Engineering: New Routes Towards the Synthesis of Well-??Defined Polyethers/Polyesters Co/Terpolymers with Different Architectures

KAUST Repository

Alamri, Haleema

2016-05-18

The primary objective of this research was to develop a new and efficient pathway for well-defined multicomponent homo/co/terpolymers of cyclic esters/ethers using an organocatalytic approach with an emphasis on the macromolecular engineering aspects of the overall synthesis. Macromolecular engineering (as discussed in the first chapter) of homo/copolymers refers to the specific tailoring of these materials for achieving an easy and reproducible synthesis that results in precise molecular characteristics, i.e. molecular weight and polydispersity, as well as specific structure and end?group choices. Precise control of these molecular characteristics will provide access to new materials that can be used for pre-targeted purposes such as biomedical applications. Among the most commonly used engineering materials are polyesters (biocompatible and biodegradable) and polyethers (biocompatible), either as homopolymers or when or copolymers with linear structures. The ability to create non-linear structures, for example stars, will open new horizons in the applications of these important polymeric materials. The second part of this thesis describes the synthesis of aliphatic polyesters, particularly polycaprolactone and polylactide, using a metal-free initiator/catalyst system. A phosphazene base (t?BuP2) was used as the catalyst for the ring-opening copolymerization of ?-aprolactone (??CL) and L,Lactide (LLA) at room temperature with a variety of protic initiators in different solvents. These studies provided important information for the design of a metal-free route toward the synthesis of polyester?based (bio) materials. The third part of the thesis describes a novel route for the one?pot synthesis of polyether-b polyester block copolymers with either a linear or a specific macromolecular architecture. Poly (styrene oxide)?b?poly(caprolactone)?b?poly(L,lactide) was prepared using this method with the goal of synthesizing poly(styrene oxide)-based materials since this

Reliability model analysis and primary experimental evaluation of laser triggered pulse trigger

International Nuclear Information System (INIS)

Chen Debiao; Yang Xinglin; Li Yuan; Li Jin

2012-01-01

High performance pulse trigger can enhance performance and stability of the PPS. It is necessary to evaluate the reliability of the LTGS pulse trigger, so we establish the reliability analysis model of this pulse trigger based on CARMES software, the reliability evaluation is accord with the statistical results. (authors)

Interconnection test framework for the CMS level-1 trigger system

International Nuclear Information System (INIS)

Hammer, J.; Magrans de Abril, M.; Wulz, C.E.

2012-01-01

The Level-1 Trigger Control and Monitoring System is a software package designed to configure, monitor and test the Level-1 Trigger System of the Compact Muon Solenoid (CMS) experiment at CERN's Large Hadron Collider. It is a large and distributed system that runs over 50 PCs and controls about 200 hardware units. The objective of this paper is to describe and evaluate the architecture of a distributed testing framework - the Interconnection Test Framework (ITF). This generic and highly flexible framework for creating and executing hardware tests within the Level-1 Trigger environment is meant to automate testing of the 13 major subsystems interconnected with more than 1000 links. Features include a web interface to create and execute tests, modeling using finite state machines, dependency management, automatic configuration, and loops. Furthermore, the ITF will replace the existing heterogeneous testing procedures and help reducing both maintenance and complexity of operation tasks. (authors)

Stay away from asthma triggers

Science.gov (United States)

Asthma triggers - stay away from; Asthma triggers - avoiding; Reactive airway disease - triggers; Bronchial asthma - triggers ... clothes. They should leave the coat outside or away from your child. Ask people who work at ...

The fast tracker processor for hadron collider triggers

CERN Document Server

Annovi, A; Bardi, A; Carosi, R; Dell'Orso, Mauro; D'Onofrio, M; Giannetti, P; Iannaccone, G; Morsani, E; Pietri, M; Varotto, G

2001-01-01

Perspectives for precise and fast track reconstruction in future hadron collider experiments are addressed. We discuss the feasibility of a pipelined highly parallel processor dedicated to the implementation of a very fast tracking algorithm. The algorithm is based on the use of a large bank of pre-stored combinations of trajectory points, called patterns, for extremely complex tracking systems. The CMS experiment at LHC is used as a benchmark. Tracking data from the events selected by the level-1 trigger are sorted and filtered by the Fast Tracker processor at an input rate of 100 kHz. This data organization allows the level-2 trigger logic to reconstruct full resolution tracks with transverse momentum above a few GeV and search for secondary vertices within typical level-2 times. (15 refs).

Multi-signal sedimentation velocity analysis with mass conservation for determining the stoichiometry of protein complexes.

Directory of Open Access Journals (Sweden)

Chad A Brautigam

Full Text Available Multi-signal sedimentation velocity analytical ultracentrifugation (MSSV is a powerful tool for the determination of the number, stoichiometry, and hydrodynamic shape of reversible protein complexes in two- and three-component systems. In this method, the evolution of sedimentation profiles of macromolecular mixtures is recorded simultaneously using multiple absorbance and refractive index signals and globally transformed into both spectrally and diffusion-deconvoluted component sedimentation coefficient distributions. For reactions with complex lifetimes comparable to the time-scale of sedimentation, MSSV reveals the number and stoichiometry of co-existing complexes. For systems with short complex lifetimes, MSSV reveals the composition of the reaction boundary of the coupled reaction/migration process, which we show here may be used to directly determine an association constant. A prerequisite for MSSV is that the interacting components are spectrally distinguishable, which may be a result, for example, of extrinsic chromophores or of different abundances of aromatic amino acids contributing to the UV absorbance. For interacting components that are spectrally poorly resolved, here we introduce a method for additional regularization of the spectral deconvolution by exploiting approximate knowledge of the total loading concentrations. While this novel mass conservation principle does not discriminate contributions to different species, it can be effectively combined with constraints in the sedimentation coefficient range of uncomplexed species. We show in theory, computer simulations, and experiment, how mass conservation MSSV as implemented in SEDPHAT can enhance or even substitute for the spectral discrimination of components. This should broaden the applicability of MSSV to the analysis of the composition of reversible macromolecular complexes.

Implementation and synchronisation of the First Level Global Trigger for the CMS experiment at LHC

International Nuclear Information System (INIS)

Taurok, A.; Bergauer, H.; Padrta, M.

2001-01-01

The hardware implementation of the First Level Global Trigger for the Compact Muon Solenoid experiment at the CERN Large Hadron Collider is described. Special emphasis is given to the algorithm logic and the synchronisation procedure. Up to 128 different trigger algorithms are calculated in parallel by the Global Trigger (GT) for every beam crossing taking place at 25 ns intervals. Already, at the first trigger level the GT is able to select complex topological event configurations by performing fast calculations. The electronics is based on VME and relies completely on Field Programmable Gate Arrays (FPGA) technology. The electronic circuits are optimised for speed by exploiting, to a great extent, the small look-up tables provided in the FPGA chips

Effects of far-ultraviolet radiation and oxygen on macromolecular synthesis and protein induction in Bacteroides fragilis BF-2

International Nuclear Information System (INIS)

Schumann, J.P.

1983-11-01

The study deals with the effects of far-UV radiation, oxygen and hydrogen peroxide on macromolecular synthesis and viability in the obligate anaerobe, Bacteroides fragilis, as well as the specific proteins induced in this organism by these different DNA damaging agents. Irradiation of Bacteroides fragilis cells with far-UV light (254 nm) under anaerobic conditions resulted in the immediate, rapid and extensive degradation of DNA which continued for 40 to 60 min after irradiation. DNA degradation after irradiation was inhibited by chloramphenicol and caffeine. RNA and protein synthesis were decreased by UV irradiation and the degree of inhibition was proportional to the UV dose. Colony formation was not affected immediately by UV irradiation and continued for a dose-dependent period prior to inhibition. The relationship between the DNA damage-induced proteins, macromolecular synthesis in damaged B. fragilis cells and the observed physiological responses and inducible repair phenomena after the different DNA damaging treatments in this anaerobe are discussed

Can visco-elastic phase separation, macromolecular crowding and colloidal physics explain nuclear organisation?

Directory of Open Access Journals (Sweden)

Iborra Francisco J

2007-04-01

Full Text Available Abstract Background The cell nucleus is highly compartmentalized with well-defined domains, it is not well understood how this nuclear order is maintained. Many scientists are fascinated by the different set of structures observed in the nucleus to attribute functions to them. In order to distinguish functional compartments from non-functional aggregates, I believe is important to investigate the biophysical nature of nuclear organisation. Results The various nuclear compartments can be divided broadly as chromatin or protein and/or RNA based, and they have very different dynamic properties. The chromatin compartment displays a slow, constrained diffusional motion. On the other hand, the protein/RNA compartment is very dynamic. Physical systems with dynamical asymmetry go to viscoelastic phase separation. This phase separation phenomenon leads to the formation of a long-lived interaction network of slow components (chromatin scattered within domains rich in fast components (protein/RNA. Moreover, the nucleus is packed with macromolecules in the order of 300 mg/ml. This high concentration of macromolecules produces volume exclusion effects that enhance attractive interactions between macromolecules, known as macromolecular crowding, which favours the formation of compartments. In this paper I hypothesise that nuclear compartmentalization can be explained by viscoelastic phase separation of the dynamically different nuclear components, in combination with macromolecular crowding and the properties of colloidal particles. Conclusion I demonstrate that nuclear structure can satisfy the predictions of this hypothesis. I discuss the functional implications of this phenomenon.

Glycogen-graft-poly(2-alkyl-2-oxazolines) - the new versatile biopolymer-based thermoresponsive macromolecular toolbox

Czech Academy of Sciences Publication Activity Database

Pospíšilová, Aneta; Filippov, Sergey K.; Bogomolova, Anna; Turner, S.; Sedláček, Ondřej; Matushkin, Nikolai; Černochová, Zulfiya; Štěpánek, Petr; Hrubý, Martin

2014-01-01

Roč. 4, č. 106 (2014), s. 61580-61588 ISSN 2046-2069 R&D Projects: GA ČR GA13-08336S; GA MŠk(CZ) LH14079 Grant - others:AV ČR(CZ) M200501201; AV ČR(CZ) ASCR/CONICET 2012CZ006 Program:M Institutional support: RVO:61389013 Keywords : glycogen * poly(2-alkyl-2-oxazoline) * hybrid copolymer Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.840, year: 2014

Triggered creep as a possible mechanism for delayed dynamic triggering of tremor and earthquakes

Science.gov (United States)

Shelly, David R.; Peng, Zhigang; Hill, David P.; Aiken, Chastity

2011-01-01

The passage of radiating seismic waves generates transient stresses in the Earth's crust that can trigger slip on faults far away from the original earthquake source. The triggered fault slip is detectable in the form of earthquakes and seismic tremor. However, the significance of these triggered events remains controversial, in part because they often occur with some delay, long after the triggering stress has passed. Here we scrutinize the location and timing of tremor on the San Andreas fault between 2001 and 2010 in relation to distant earthquakes. We observe tremor on the San Andreas fault that is initiated by passing seismic waves, yet migrates along the fault at a much slower velocity than the radiating seismic waves. We suggest that the migrating tremor records triggered slow slip of the San Andreas fault as a propagating creep event. We find that the triggered tremor and fault creep can be initiated by distant earthquakes as small as magnitude 5.4 and can persist for several days after the seismic waves have passed. Our observations of prolonged tremor activity provide a clear example of the delayed dynamic triggering of seismic events. Fault creep has been shown to trigger earthquakes, and we therefore suggest that the dynamic triggering of prolonged fault creep could provide a mechanism for the delayed triggering of earthquakes. ?? 2011 Macmillan Publishers Limited. All rights reserved.

Polyelectrolyte complex formation and stability when mixing polyanions and polycations in salted media: A model study related to the case of body fluids

Czech Academy of Sciences Publication Activity Database

Etrych, Tomáš; Leclercq, L.; Boustta, M.; Vert, M.

2005-01-01

Roč. 25, 1-2 (2005), s. 281-288 ISSN 0928-0987 EU Projects: European Commission(XE) 512087 - GIANT Institutional research plan: CEZ:AV0Z40500505 Keywords : polyelectrolyte complex * selectivity * light scattering Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.347, year: 2005

The NA27 trigger

International Nuclear Information System (INIS)

Bizzarri, R.; Di Capua, E.; Falciano, S.; Iori, M.; Marel, G.; Piredda, G.; Zanello, L.; Haupt, L.; Hellman, S.; Holmgren, S.O.; Johansson, K.E.

1985-05-01

We have designed and implemented a minimum bias trigger together with a fiducial volume trigger for the experiment NA27, performed at the CERN SPS. A total of more than 3 million bubble chamber pictures have been taken with a triggered cross section smaller than 75% of the total inelastic cross section. Events containing charm particles were triggered with an efficiency of 98 +2 sub(-3)%. With the fiducial volume trigger, the probability for a picture to contain an interaction in the visible hydrogen increased from 47.3% to 59.5%, reducing film cost and processing effort with about 20%. The improvement in data taking rate is shown to be negligible. (author)

Tidal triggering of earthquakes suggests poroelastic behavior on the San Andreas Fault

International Nuclear Information System (INIS)

Delorey, Andrew A.; Elst, Nicholas J. van der; Johnson, Paul Allan

2016-01-01

Tidal triggering of earthquakes is hypothesized to provide quantitative information regarding the fault's stress state, poroelastic properties, and may be significant for our understanding of seismic hazard. To date, studies of regional or global earthquake catalogs have had only modest successes in identifying tidal triggering. We posit that the smallest events that may provide additional evidence of triggering go unidentified and thus we developed a technique to improve the identification of very small magnitude events. We identify events applying a method known as inter-station seismic coherence where we prioritize detection and discrimination over characterization. Here we show tidal triggering of earthquakes on the San Andreas Fault. We find the complex interaction of semi-diurnal and fortnightly tidal periods exposes both stress threshold and critical state behavior. Lastly, our findings reveal earthquake nucleation processes and pore pressure conditions – properties of faults that are difficult to measure, yet extremely important for characterizing earthquake physics and seismic hazards.

Tidal triggering of earthquakes suggests poroelastic behavior on the San Andreas Fault

Science.gov (United States)

Delorey, Andrew; Van Der Elst, Nicholas; Johnson, Paul

2017-01-01

Tidal triggering of earthquakes is hypothesized to provide quantitative information regarding the fault's stress state, poroelastic properties, and may be significant for our understanding of seismic hazard. To date, studies of regional or global earthquake catalogs have had only modest successes in identifying tidal triggering. We posit that the smallest events that may provide additional evidence of triggering go unidentified and thus we developed a technique to improve the identification of very small magnitude events. We identify events applying a method known as inter-station seismic coherence where we prioritize detection and discrimination over characterization. Here we show tidal triggering of earthquakes on the San Andreas Fault. We find the complex interaction of semi-diurnal and fortnightly tidal periods exposes both stress threshold and critical state behavior. Our findings reveal earthquake nucleation processes and pore pressure conditions – properties of faults that are difficult to measure, yet extremely important for characterizing earthquake physics and seismic hazards.

Triggers of oral lichen planus flares and the potential role of trigger avoidance in disease management.

Science.gov (United States)

Chen, Hannah X; Blasiak, Rachel; Kim, Edwin; Padilla, Ricardo; Culton, Donna A

2017-09-01

Many patients with oral lichen planus (OLP) report triggers of flares, some of which overlap with triggers of other oral diseases, including oral allergy syndrome and oral contact dermatitis. The purpose of this study was to evaluate the prevalence of commonly reported triggers of OLP flares, their overlap with triggers of other oral diseases, and the potential role of trigger avoidance as a management strategy. Questionnaire-based survey of 51 patients with biopsy-proven lichen planus with oral involvement seen in an academic dermatology specialty clinic and/or oral pathology clinic between June 2014 and June 2015. Of the participants, 94% identified at least one trigger of their OLP flares. Approximately half of the participants (51%) reported at least one trigger that overlapped with known triggers of oral allergy syndrome, and 63% identified at least one trigger that overlapped with known triggers of oral contact dermatitis. Emotional stress was the most commonly reported trigger (77%). Regarding avoidance, 79% of the study participants reported avoiding their known triggers in daily life. Of those who actively avoided triggers, 89% reported an improvement in symptoms and 70% reported a decrease in the frequency of flares. Trigger identification and avoidance can play a potentially effective role in the management of OLP. Copyright © 2017 Elsevier Inc. All rights reserved.

In silico prediction of harmful effects triggered by drugs and chemicals

International Nuclear Information System (INIS)

Vedani, Angelo; Dobler, Max; Lill, Markus A.

2005-01-01

While the computer-assisted discovery and optimization of drug candidates based on the known three-dimensional structure of the macromolecular target (structure-based design) or a binding-site surrogate (receptor modeling) is doubtless one of the more potent approaches in rational drug design, the simulation and quantification of side effects triggered by drugs and chemicals are still in their infancy. Major obstacles include the often not available 3D structure of the molecular target, the low specificity of the involved bioregulators and the identification of the controlling metabolic pathways. In the recent past, our laboratory has explored concepts allowing to simulate receptor-mediated toxic phenomena by developing algorithms, allowing to construct realistic 3D binding-site surrogates of receptors known or assumed triggering adverse effects and validating them against large batches of molecular data. The underlying technology (software Quasar and Raptor, respectively) specifically allows for induced fit, solvation phenomena and entropic effects. It has been applied to various systems both of pharmacological and toxicological interest including the neurokinin-1, chemokine-3, bradykinin B 2 , steroid, 5 HT 2A , aryl hydrocarbon, estrogen and androgen receptor, respectively. In this account, we describe the design of a virtual laboratory allowing for a reliable estimation of harmful effects triggered by drugs, chemicals and their metabolites in silico. In the recent past, the Biographics Laboratory 3R has compiled a 3D database including the surrogates of three major receptor systems known to mediate adverse effects (the aryl hydrocarbon, the estrogen and the androgen receptor, respectively) and validated them against a total of 345 compounds (drugs, chemicals, toxins) using multidimensional QSAR technologies. Within this pilot project, we could demonstrate that our virtual laboratory is able to both recognize toxic compounds substantially different from those

Identification of the Mitochondrial Heme Metabolism Complex.

Science.gov (United States)

Medlock, Amy E; Shiferaw, Mesafint T; Marcero, Jason R; Vashisht, Ajay A; Wohlschlegel, James A; Phillips, John D; Dailey, Harry A

2015-01-01

Heme is an essential cofactor for most organisms and all metazoans. While the individual enzymes involved in synthesis and utilization of heme are fairly well known, less is known about the intracellular trafficking of porphyrins and heme, or regulation of heme biosynthesis via protein complexes. To better understand this process we have undertaken a study of macromolecular assemblies associated with heme synthesis. Herein we have utilized mass spectrometry with coimmunoprecipitation of tagged enzymes of the heme biosynthetic pathway in a developing erythroid cell culture model to identify putative protein partners. The validity of these data obtained in the tagged protein system is confirmed by normal porphyrin/heme production by the engineered cells. Data obtained are consistent with the presence of a mitochondrial heme metabolism complex which minimally consists of ferrochelatase, protoporphyrinogen oxidase and aminolevulinic acid synthase-2. Additional proteins involved in iron and intermediary metabolism as well as mitochondrial transporters were identified as potential partners in this complex. The data are consistent with the known location of protein components and support a model of transient protein-protein interactions within a dynamic protein complex.

A simulation framework for the CMS Track Trigger electronics

International Nuclear Information System (INIS)

Amstutz, C.; Weber, M.; Magazzù, G.; Palla, F.

2015-01-01

A simulation framework has been developed to test and characterize algorithms, architectures and hardware implementations of the vastly complex CMS Track Trigger for the high luminosity upgrade of the CMS experiment at the Large Hadron Collider in Geneva. High-level SystemC models of all system components have been developed to simulate a portion of the track trigger. The simulation of the system components together with input data from physics simulations allows evaluating figures of merit, like delays or bandwidths, under realistic conditions. The use of SystemC for high-level modelling allows co-simulation with models developed in Hardware Description Languages, e.g. VHDL or Verilog. Therefore, the simulation framework can also be used as a test bench for digital modules developed for the final system

A simulation framework for the CMS Track Trigger electronics

Science.gov (United States)

Amstutz, C.; Magazzù, G.; Weber, M.; Palla, F.

2015-03-01

A simulation framework has been developed to test and characterize algorithms, architectures and hardware implementations of the vastly complex CMS Track Trigger for the high luminosity upgrade of the CMS experiment at the Large Hadron Collider in Geneva. High-level SystemC models of all system components have been developed to simulate a portion of the track trigger. The simulation of the system components together with input data from physics simulations allows evaluating figures of merit, like delays or bandwidths, under realistic conditions. The use of SystemC for high-level modelling allows co-simulation with models developed in Hardware Description Languages, e.g. VHDL or Verilog. Therefore, the simulation framework can also be used as a test bench for digital modules developed for the final system.

AR-NE3A, a New Macromolecular Crystallography Beamline for Pharmaceutical Applications at the Photon Factory

International Nuclear Information System (INIS)

Yamada, Yusuke; Hiraki, Masahiko; Sasajima, Kumiko; Matsugaki, Naohiro; Igarashi, Noriyuki; Kikuchi, Takashi; Mori, Takeharu; Toyoshima, Akio; Kishimoto, Shunji; Wakatsuki, Soichi; Amano, Yasushi; Warizaya, Masaichi; Sakashita, Hitoshi

2010-01-01

Recent advances in high-throughput techniques for macromolecular crystallography have highlighted the importance of structure-based drug design (SBDD), and the demand for synchrotron use by pharmaceutical researchers has increased. Thus, in collaboration with Astellas Pharma Inc., we have constructed a new high-throughput macromolecular crystallography beamline, AR-NE3A, which is dedicated to SBDD. At AR-NE3A, a photon flux up to three times higher than those at existing high-throughput beams at the Photon Factory, AR-NW12A and BL-5A, can be realized at the same sample positions. Installed in the experimental hutch are a high-precision diffractometer, fast-readout, high-gain CCD detector, and sample exchange robot capable of handling more than two hundred cryo-cooled samples stored in a Dewar. To facilitate high-throughput data collection required for pharmaceutical research, fully automated data collection and processing systems have been developed. Thus, sample exchange, centering, data collection, and data processing are automatically carried out based on the user's pre-defined schedule. Although Astellas Pharma Inc. has a priority access to AR-NE3A, the remaining beam time is allocated to general academic and other industrial users.

Organ specific acute toxicity of the carcinogen trans-4-acetylaminostilbene is not correlated with macromolecular binding.

Science.gov (United States)

Pfeifer, A; Neumann, H G

1986-09-01

trans-4-Acetylaminostilbene (trans-AAS) is acutely toxic in rats and lesions are produced specifically in the glandular stomach. Toxicity is slightly increased by pretreating the animals with phenobarbital (PB) and is completely prevented by pretreatment with methylcholanthrene (MC). The prostaglandin inhibitors, indomethacin and acetyl salicylic acid, do not reduce toxicity. The high efficiency of MC suggested that toxicity is caused by reactive metabolites. trans-[3H]-AAS was administered orally to untreated and to PB- or MC-pretreated female Wistar rats and target doses in different tissues were measured by means of covalent binding to proteins, RNA and DNA. Macromolecular binding in the target tissue of poisoned animals was significantly lower than in liver and kidney and comparable to other non-target tissues. Pretreatment with MC lowered macromolecular binding in all extrahepatic tissues but not in liver. These findings are not in line with tissue specific metabolic activation. The only unique property of the target tissue, glandular stomach, that we observed was a particular affinity for the systemically available parent compound. In the early phase of poisoning, tissue concentrations were exceedingly high and the stomach function was impaired.

Complexation of the cesium cation with 1,3-alternate-25,27-bis(1-octyloxy)calix[4]arene-crown-6

Czech Academy of Sciences Publication Activity Database

Makrlík, E.; Dybal, Jiří; Vaňura, P.

2013-01-01

Roč. 295, č. 2 (2013), s. 1299-1303 ISSN 0236-5731 R&D Projects: GA ČR GA203/09/1478 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : cesium cation * substituted calix[4]arene-crown-6 * complexation Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.415, year: 2013

Fully automated data collection and processing system on macromolecular crystallography beamlines at the PF

International Nuclear Information System (INIS)

Yamada, Yusuke; Hiraki, Masahiko; Matsugaki, Naohiro; Chavas, Leonard M.G.; Igarashi, Noriyuki; Wakatsuki, Soichi

2012-01-01

Fully automated data collection and processing system has been developed on macromolecular crystallography beamlines at the Photon Factory. In this system, the sample exchange, centering and data collection are sequentially performed for all samples stored in the sample exchange system at a beamline without any manual operations. Data processing of collected data sets is also performed automatically. These results are stored into the database system, and users can monitor the progress and results of automated experiment via a Web browser. (author)

Minimum Bias Trigger in ATLAS

International Nuclear Information System (INIS)

Kwee, Regina

2010-01-01

Since the restart of the LHC in November 2009, ATLAS has collected inelastic pp collisions to perform first measurements on charged particle densities. These measurements will help to constrain various models describing phenomenologically soft parton interactions. Understanding the trigger efficiencies for different event types are therefore crucial to minimize any possible bias in the event selection. ATLAS uses two main minimum bias triggers, featuring complementary detector components and trigger levels. While a hardware based first trigger level situated in the forward regions with 2.2 < |η| < 3.8 has been proven to select pp-collisions very efficiently, the Inner Detector based minimum bias trigger uses a random seed on filled bunches and central tracking detectors for the event selection. Both triggers were essential for the analysis of kinematic spectra of charged particles. Their performance and trigger efficiency measurements as well as studies on possible bias sources will be presented. We also highlight the advantage of these triggers for particle correlation analyses. (author)

Causality and headache triggers

Science.gov (United States)

Turner, Dana P.; Smitherman, Todd A.; Martin, Vincent T.; Penzien, Donald B.; Houle, Timothy T.

2013-01-01

Objective The objective of this study was to explore the conditions necessary to assign causal status to headache triggers. Background The term “headache trigger” is commonly used to label any stimulus that is assumed to cause headaches. However, the assumptions required for determining if a given stimulus in fact has a causal-type relationship in eliciting headaches have not been explicated. Methods A synthesis and application of Rubin’s Causal Model is applied to the context of headache causes. From this application the conditions necessary to infer that one event (trigger) causes another (headache) are outlined using basic assumptions and examples from relevant literature. Results Although many conditions must be satisfied for a causal attribution, three basic assumptions are identified for determining causality in headache triggers: 1) constancy of the sufferer; 2) constancy of the trigger effect; and 3) constancy of the trigger presentation. A valid evaluation of a potential trigger’s effect can only be undertaken once these three basic assumptions are satisfied during formal or informal studies of headache triggers. Conclusions Evaluating these assumptions is extremely difficult or infeasible in clinical practice, and satisfying them during natural experimentation is unlikely. Researchers, practitioners, and headache sufferers are encouraged to avoid natural experimentation to determine the causal effects of headache triggers. Instead, formal experimental designs or retrospective diary studies using advanced statistical modeling techniques provide the best approaches to satisfy the required assumptions and inform causal statements about headache triggers. PMID:23534872

The D0 calorimeter trigger

International Nuclear Information System (INIS)

Guida, J.

1992-12-01

The D0 calorimeter trigger system consists of many levels to make physics motivated trigger decisions. The Level-1 trigger uses hardware techniques to reduce the trigger rate from ∼ 100kHz to 200Hz. It forms sums of electromagnetic and hadronic energy, globally and in towers, along with finding the missing transverse energy. A minimum energy is set on these energy sums to pass the event. The Level-2 trigger is a set of software filters, operating in a parallel-processing microvax farm which further reduces the trigger rate to a few Hertz. These filters will reject events which lack electron candidates, jet candidates, or missing transverse energy in the event. The performance of these triggers during the early running of the D0 detector will also be discussed

ATLAS calorimetry: Trigger, simulation and jet calibration

CERN Document Server

Weber, Pavel

2008-01-01

The Pre-Processor system of the ATLAS Level-1 Calorimeter Trigger performs complex processing of analog trigger tower signals from electromagnetic and hadronic calorimeters. The main processing block of the Pre-Processor System is the Multi-Chip Module (MCM). The first part of this thesis describes MCM quality assurance tests that have been developed, their use in the MCM large scale production and the results that have been obtained. In the second part of the thesis a validation of a shower parametrisation model for the ATLAS fast simulation package ATLFAST based on QCD dijet events is performed. A detailed comparison of jet response and jet energy resolution between the fast and the full simulation is presented. The uniformity of the calorimeter response has a significant impact on the accuracy of the jet energy measurement. A study of the calorimeter intercalibration using QCD dijet events is presented in the last part of the thesis. The intercalibration study is performed in azimuth angle phi and in pseud...

Development of an online UV–visible microspectrophotometer for a macromolecular crystallography beamline

Energy Technology Data Exchange (ETDEWEB)

Shimizu, Nobutaka, E-mail: nobutaka.shimizu@kek.jp [SPring-8/JASRI, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Shimizu, Tetsuya [RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Baba, Seiki; Hasegawa, Kazuya [SPring-8/JASRI, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Yamamoto, Masaki [RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Kumasaka, Takashi [SPring-8/JASRI, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

2013-11-01

An online UV–visible microspectrophotometer has been developed for the macromolecular crystallography beamline at SPring-8. Details of this spectrophotometer are reported. Measurement of the UV–visible absorption spectrum is a convenient technique for detecting chemical changes of proteins, and it is therefore useful to combine spectroscopy and diffraction studies. An online microspectrophotometer for the UV–visible region was developed and installed on the macromolecular crystallography beamline, BL38B1, at SPring-8. This spectrophotometer is equipped with a difference dispersive double monochromator, a mercury–xenon lamp as the light source, and a photomultiplier as the detector. The optical path is mostly constructed using mirrors, in order to obtain high brightness in the UV region, and the confocal optics are assembled using a cross-slit diaphragm like an iris to eliminate stray light. This system can measure optical densities up to a maximum of 4.0. To study the effect of radiation damage, preliminary measurements of glucose isomerase and thaumatin crystals were conducted in the UV region. Spectral changes dependent on X-ray dose were observed at around 280 nm, suggesting that structural changes involving Trp or Tyr residues occurred in the protein crystal. In the case of the thaumatin crystal, a broad peak around 400 nm was also generated after X-ray irradiation, suggesting the cleavage of a disulfide bond. Dose-dependent spectral changes were also observed in cryo-solutions alone, and these changes differed with the composition of the cryo-solution. These responses in the UV region are informative regarding the state of the sample; consequently, this device might be useful for X-ray crystallography.

Macromolecular pHPMA-based nanoparticles with cholesterol for solid tumor targeting: behavior in HSA protein environment

Czech Academy of Sciences Publication Activity Database

Zhang, X.; Niebuur, B.-J.; Chytil, Petr; Etrych, Tomáš; Filippov, Sergey K.; Kikhney, A.; Wieland, D. C. F.; Svergun, D. I.; Papadakis, C. M.

2018-01-01

Roč. 19, č. 2 (2018), s. 470-480 ISSN 1525-7797 R&D Projects: GA ČR(CZ) GC15-10527J; GA MZd(CZ) NV16-28594A; GA MŠk(CZ) LO1507 Institutional support: RVO:61389013 Keywords : polymer carriers * N-(2-hydroxypropyl)methacrylamide * tumor targeting Subject RIV: CD - Macromolecular Chemistry OBOR OECD: Polymer science Impact factor: 5.246, year: 2016

Environmental triggers in IBD: a review of progress and evidence.

Science.gov (United States)

Ananthakrishnan, Ashwin N; Bernstein, Charles N; Iliopoulos, Dimitrios; Macpherson, Andrew; Neurath, Markus F; Ali, Raja A Raja; Vavricka, Stephan R; Fiocchi, Claudio

2018-01-01

A number of environmental factors have been associated with the development of IBD. Alteration of the gut microbiota, or dysbiosis, is closely linked to initiation or progression of IBD, but whether dysbiosis is a primary or secondary event is unclear. Nevertheless, early-life events such as birth, breastfeeding and exposure to antibiotics, as well as later childhood events, are considered potential risk factors for IBD. Air pollution, a consequence of the progressive contamination of the environment by countless compounds, is another factor associated with IBD, as particulate matter or other components can alter the host's mucosal defences and trigger immune responses. Hypoxia associated with high altitude is also a factor under investigation as a potential new trigger of IBD flares. A key issue is how to translate environmental factors into mechanisms of IBD, and systems biology is increasingly recognized as a strategic tool to unravel the molecular alterations leading to IBD. Environmental factors add a substantial level of complexity to the understanding of IBD pathogenesis but also promote the fundamental notion that complex diseases such as IBD require complex therapies that go well beyond the current single-agent treatment approach. This Review describes the current conceptualization, evidence, progress and direction surrounding the association of environmental factors with IBD.

A general-purpose trigger processor system and its application to fast vertex trigger

International Nuclear Information System (INIS)

Hazumi, M.; Banas, E.; Natkaniec, Z.; Ostrowicz, W.

1997-12-01

A general-purpose hardware trigger system has been developed. The system comprises programmable trigger processors and pattern generator/samplers. The hardware design of the system is described. An application as a prototype of the very fast vertex trigger in an asymmetric B-factory at KEK is also explained. (author)

BTeV Trigger

International Nuclear Information System (INIS)

Gottschalk, Erik E.

2006-01-01

BTeV was designed to conduct precision studies of CP violation in BB-bar events using a forward-geometry detector in a hadron collider. The detector was optimized for high-rate detection of beauty and charm particles produced in collisions between protons and antiprotons. The trigger was designed to take advantage of the main difference between events with beauty and charm particles and more typical hadronic events-the presence of detached beauty and charm decay vertices. The first stage of the BTeV trigger was to receive data from a pixel vertex detector, reconstruct tracks and vertices for every beam crossing, reject at least 98% of beam crossings in which neither beauty nor charm particles were produced, and trigger on beauty events with high efficiency. An overview of the trigger design and its evolution to include commodity networking and computing components is presented

Triggering trigeminal neuralgia

DEFF Research Database (Denmark)

Di Stefano, Giulia; Maarbjerg, Stine; Nurmikko, Turo

2018-01-01

Introduction Although it is widely accepted that facial pain paroxysms triggered by innocuous stimuli constitute a hallmark sign of trigeminal neuralgia, very few studies to date have systematically investigated the role of the triggers involved. In the recently published diagnostic classification...

LHCb Topological Trigger Reoptimization

CERN Document Server

INSPIRE-00400931; Ilten, Philip; Khairullin, Egor; Rogozhnikov, Alex; Ustyuzhanin, Andrey; Williams, Michael

2015-12-23

The main b-physics trigger algorithm used by the LHCb experiment is the so-called topological trigger. The topological trigger selects vertices which are a) detached from the primary proton-proton collision and b) compatible with coming from the decay of a b-hadron. In the LHC Run 1, this trigger, which utilized a custom boosted decision tree algorithm, selected a nearly 100% pure sample of b-hadrons with a typical efficiency of 60-70%; its output was used in about 60% of LHCb papers. This talk presents studies carried out to optimize the topological trigger for LHC Run 2. In particular, we have carried out a detailed comparison of various machine learning classifier algorithms, e.g., AdaBoost, MatrixNet and neural networks. The topological trigger algorithm is designed to select all "interesting" decays of b-hadrons, but cannot be trained on every such decay. Studies have therefore been performed to determine how to optimize the performance of the classification algorithm on decays not used in the training. ...

The TOTEM modular trigger system

Energy Technology Data Exchange (ETDEWEB)

Bagliesi, M.G., E-mail: mg.bagliesi@pi.infn.i [University of Siena and INFN Pisa (Italy); Berretti, M.; Cecchi, R.; Greco, V.; Lami, S.; Latino, G.; Oliveri, E.; Pedreschi, E.; Scribano, A.; Spinella, F.; Turini, N. [University of Siena and INFN Pisa (Italy)

2010-05-21

The TOTEM experiment will measure the total cross-section with the luminosity independent method and study elastic and diffractive scattering at the LHC. We are developing a modular trigger system, based on programmable logic, that will select meaningful events within 2.5{mu}s. The trigger algorithm is based on a tree structure in order to obtain information compression. The trigger primitive is generated directly on the readout chip, VFAT, that has a specific fast output that gives low resolution hits information. In two of the TOTEM detectors, Roman Pots and T2, a coincidence chip will perform track recognition directly on the detector readout boards, while for T1 the hits are transferred from the VFATs to the trigger hardware. Starting from more than 2000 bits delivered by the detector electronics, we extract, in a first step, six trigger patterns of 32 LVDS signals each; we build, then, on a dedicated board, a 1-bit (L1) trigger signal for the TOTEM experiment and 16 trigger bits to the CMS experiment global trigger system for future common data taking.

The TOTEM modular trigger system

International Nuclear Information System (INIS)

Bagliesi, M.G.; Berretti, M.; Cecchi, R.; Greco, V.; Lami, S.; Latino, G.; Oliveri, E.; Pedreschi, E.; Scribano, A.; Spinella, F.; Turini, N.

2010-01-01

The TOTEM experiment will measure the total cross-section with the luminosity independent method and study elastic and diffractive scattering at the LHC. We are developing a modular trigger system, based on programmable logic, that will select meaningful events within 2.5μs. The trigger algorithm is based on a tree structure in order to obtain information compression. The trigger primitive is generated directly on the readout chip, VFAT, that has a specific fast output that gives low resolution hits information. In two of the TOTEM detectors, Roman Pots and T2, a coincidence chip will perform track recognition directly on the detector readout boards, while for T1 the hits are transferred from the VFATs to the trigger hardware. Starting from more than 2000 bits delivered by the detector electronics, we extract, in a first step, six trigger patterns of 32 LVDS signals each; we build, then, on a dedicated board, a 1-bit (L1) trigger signal for the TOTEM experiment and 16 trigger bits to the CMS experiment global trigger system for future common data taking.

LEGO-NMR spectroscopy: a method to visualize individual subunits in large heteromeric complexes.

Science.gov (United States)

Mund, Markus; Overbeck, Jan H; Ullmann, Janina; Sprangers, Remco

2013-10-18

Seeing the big picture: Asymmetric macromolecular complexes that are NMR active in only a subset of their subunits can be prepared, thus decreasing NMR spectral complexity. For the hetero heptameric LSm1-7 and LSm2-8 rings NMR spectra of the individual subunits of the complete complex are obtained, showing a conserved RNA binding site. This LEGO-NMR technique makes large asymmetric complexes accessible to detailed NMR spectroscopic studies. © 2013 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of Creative Commons the Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Characterizing time series: when Granger causality triggers complex networks

Science.gov (United States)

Ge, Tian; Cui, Yindong; Lin, Wei; Kurths, Jürgen; Liu, Chong

2012-08-01

In this paper, we propose a new approach to characterize time series with noise perturbations in both the time and frequency domains by combining Granger causality and complex networks. We construct directed and weighted complex networks from time series and use representative network measures to describe their physical and topological properties. Through analyzing the typical dynamical behaviors of some physical models and the MIT-BIHMassachusetts Institute of Technology-Beth Israel Hospital. human electrocardiogram data sets, we show that the proposed approach is able to capture and characterize various dynamics and has much potential for analyzing real-world time series of rather short length.

Characterizing time series: when Granger causality triggers complex networks

International Nuclear Information System (INIS)

Ge Tian; Cui Yindong; Lin Wei; Liu Chong; Kurths, Jürgen

2012-01-01

In this paper, we propose a new approach to characterize time series with noise perturbations in both the time and frequency domains by combining Granger causality and complex networks. We construct directed and weighted complex networks from time series and use representative network measures to describe their physical and topological properties. Through analyzing the typical dynamical behaviors of some physical models and the MIT-BIH human electrocardiogram data sets, we show that the proposed approach is able to capture and characterize various dynamics and has much potential for analyzing real-world time series of rather short length. (paper)

LHCb Topological Trigger Reoptimization

International Nuclear Information System (INIS)

Likhomanenko, Tatiana; Khairullin, Egor; Rogozhnikov, Alex; Ustyuzhanin, Andrey; Ilten, Philip; Williams, Michael

2015-01-01

The main b-physics trigger algorithm used by the LHCb experiment is the so- called topological trigger. The topological trigger selects vertices which are a) detached from the primary proton-proton collision and b) compatible with coming from the decay of a b-hadron. In the LHC Run 1, this trigger, which utilized a custom boosted decision tree algorithm, selected a nearly 100% pure sample of b-hadrons with a typical efficiency of 60-70%; its output was used in about 60% of LHCb papers. This talk presents studies carried out to optimize the topological trigger for LHC Run 2. In particular, we have carried out a detailed comparison of various machine learning classifier algorithms, e.g., AdaBoost, MatrixNet and neural networks. The topological trigger algorithm is designed to select all ’interesting” decays of b-hadrons, but cannot be trained on every such decay. Studies have therefore been performed to determine how to optimize the performance of the classification algorithm on decays not used in the training. Methods studied include cascading, ensembling and blending techniques. Furthermore, novel boosting techniques have been implemented that will help reduce systematic uncertainties in Run 2 measurements. We demonstrate that the reoptimized topological trigger is expected to significantly improve on the Run 1 performance for a wide range of b-hadron decays. (paper)

Error detection, handling and recovery at the High Level Trigger of the ATLAS experiment at the LHC

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00223972; The ATLAS collaboration

2016-01-01

The complexity of the ATLAS High Level Trigger (HLT) requires a robust system for error detection and handling during online data-taking; it also requires an offline system for the recovery of events where no trigger decision could be made online. The error detection and handling ensure smooth operation of the trigger system and provide debugging information necessary for offline analysis and diagnosis. In this presentation, we give an overview of the error detection, handling and recovery of problematic events at the HLT of ATLAS.

Subunit Organisation of In Vitro Reconstituted HOPS and CORVET Multisubunit Membrane Tethering Complexes

Science.gov (United States)

Guo, Zhong; Johnston, Wayne; Kovtun, Oleksiy; Mureev, Sergey; Bröcker, Cornelia; Ungermann, Christian; Alexandrov, Kirill

2013-01-01

Biochemical and structural analysis of macromolecular protein assemblies remains challenging due to technical difficulties in recombinant expression, engineering and reconstitution of multisubunit complexes. Here we use a recently developed cell-free protein expression system based on the protozoan Leishmania tarentolae to produce in vitro all six subunits of the 600 kDa HOPS and CORVET membrane tethering complexes. We demonstrate that both subcomplexes and the entire HOPS complex can be reconstituted in vitro resulting in a comprehensive subunit interaction map. To our knowledge this is the largest eukaryotic protein complex in vitro reconstituted to date. Using the truncation and interaction analysis, we demonstrate that the complex is assembled through short hydrophobic sequences located in the C-terminus of the individual Vps subunits. Based on this data we propose a model of the HOPS and CORVET complex assembly that reconciles the available biochemical and structural data. PMID:24312556

A simulation framework for the CMS Track Trigger electronics

CERN Document Server

Amstutz, Christian; Weber, Marc; Palla, Fabrizio

2014-01-01

A simulation framework has been developed to test and characterize algorithms, architectures and hardware implementations of the vastly complex CMS Track Trigger for the high luminosity upgrade of the CMS experiment at the Large Hadron Collider in Geneva. High-level SystemC models of all system components have been developed to simulate a portion of the track trigger. The simulation of the system components together with input data from physics simulations allows evaluating figures of merit, like delays or bandwidths, under realistic conditions. The use of SystemC for high-level modelling allows \\mbox{co-simulation} with models developed in Hardware Description Languages, e.g.~VHDL or Verilog. Therefore, the simulation framework can also be used as a test bench for digital modules developed for the final system.

New methods for trigger electronics development

Energy Technology Data Exchange (ETDEWEB)

Cleland, W.E.; Stern, E.G. [Univ. of Pittsburgh, PA (United States)

1991-12-31

The large and complex nature of RHIC experiments and the tight time schedule for their construction requires that new techniques for designing the electronics should be employed. This is particularly true of the trigger and data acquisition electronics which has to be ready for turn-on of the experiment. We describe the use of the Workview package from VIEWlogic Inc. for design, simulation, and verification of a flash ADC readout system. We also show how field-programmable gate arrays such as the Xilinx 4000 might be employed to construct or prototype circuits with a large number of gates while preserving flexibility.

Higher-Order Structure in Bacterial VapBC Toxin-Antitoxin Complexes

DEFF Research Database (Denmark)

Bendtsen, Kirstine L; Brodersen, Ditlev E

2017-01-01

Toxin-antitoxin systems are widespread in the bacterial kingdom, including in pathogenic species, where they allow rapid adaptation to changing environmental conditions through selective inhibition of key cellular processes, such as DNA replication or protein translation. Under normal growth...... that allow auto-regulation of transcription by direct binding to promoter DNA. In this chapter, we review our current understanding of the structural characteristics of type II toxin-antitoxin complexes in bacterial cells, with a special emphasis on the staggering variety of higher-order architecture...... conditions, type II toxins are inhibited through tight protein-protein interaction with a cognate antitoxin protein. This toxin-antitoxin complex associates into a higher-order macromolecular structure, typically heterotetrameric or heterooctameric, exposing two DNA binding domains on the antitoxin...

Headache triggers in the US military.

Science.gov (United States)

Theeler, Brett J; Kenney, Kimbra; Prokhorenko, Olga A; Fideli, Ulgen S; Campbell, William; Erickson, Jay C

2010-05-01

Headaches can be triggered by a variety of factors. Military service members have a high prevalence of headache but the factors triggering headaches in military troops have not been identified. The objective of this study is to determine headache triggers in soldiers and military beneficiaries seeking specialty care for headaches. A total of 172 consecutive US Army soldiers and military dependents (civilians) evaluated at the headache clinics of 2 US Army Medical Centers completed a standardized questionnaire about their headache triggers. A total of 150 (87%) patients were active-duty military members and 22 (13%) patients were civilians. In total, 77% of subjects had migraine; 89% of patients reported at least one headache trigger with a mean of 8.3 triggers per patient. A wide variety of headache triggers was seen with the most common categories being environmental factors (74%), stress (67%), consumption-related factors (60%), and fatigue-related factors (57%). The types of headache triggers identified in active-duty service members were similar to those seen in civilians. Stress-related triggers were significantly more common in soldiers. There were no significant differences in trigger types between soldiers with and without a history of head trauma. Headaches in military service members are triggered mostly by the same factors as in civilians with stress being the most common trigger. Knowledge of headache triggers may be useful for developing strategies that reduce headache occurrence in the military.

Sensory determinants of the autonomous sensory meridian response (ASMR): understanding the triggers.

Science.gov (United States)

Barratt, Emma L; Spence, Charles; Davis, Nick J

2017-01-01

The autonomous sensory meridian response (ASMR) is an atypical sensory phenomenon involving electrostatic-like tingling sensations in response to certain sensory, primarily audio-visual, stimuli. The current study used an online questionnaire, completed by 130 people who self-reported experiencing ASMR. We aimed to extend preliminary investigations into the experience, and establish key multisensory factors contributing to the successful induction of ASMR through online media. Aspects such as timing and trigger load, atmosphere, and characteristics of ASMR content, ideal spatial distance from various types of stimuli, visual characteristics, context and use of ASMR triggers, and audio preferences are explored. Lower-pitched, complex sounds were found to be especially effective triggers, as were slow-paced, detail-focused videos. Conversely, background music inhibited the sensation for many respondents. These results will help in designing media for ASMR induction.

Sensory determinants of the autonomous sensory meridian response (ASMR: understanding the triggers

Directory of Open Access Journals (Sweden)

Emma L. Barratt

2017-10-01

Full Text Available The autonomous sensory meridian response (ASMR is an atypical sensory phenomenon involving electrostatic-like tingling sensations in response to certain sensory, primarily audio-visual, stimuli. The current study used an online questionnaire, completed by 130 people who self-reported experiencing ASMR. We aimed to extend preliminary investigations into the experience, and establish key multisensory factors contributing to the successful induction of ASMR through online media. Aspects such as timing and trigger load, atmosphere, and characteristics of ASMR content, ideal spatial distance from various types of stimuli, visual characteristics, context and use of ASMR triggers, and audio preferences are explored. Lower-pitched, complex sounds were found to be especially effective triggers, as were slow-paced, detail-focused videos. Conversely, background music inhibited the sensation for many respondents. These results will help in designing media for ASMR induction.

The LHCb trigger

CERN Document Server

Hernando Morata, Jose Angel

2006-01-01

The LHCb experiment relies on an efficient trigger to select a rate up to 2 kHz of events useful for physics analysis from an initial rate of 10 MHz of visible collisions. In this contribution, we describe the different LHCb trigger algorithms and present their expected performance.

Children with migraine: Provocation of headache via pressure to myofascial trigger points in the trapezius muscle? - A prospective controlled observational study.

Science.gov (United States)

Landgraf, M N; Biebl, J T; Langhagen, T; Hannibal, I; Eggert, T; Vill, K; Gerstl, L; Albers, L; von Kries, R; Straube, A; Heinen, F

2018-02-01

The objective was to evaluate a supposed clinical interdependency of myofascial trigger points and migraine in children. Such interdependency would support an interaction of spinal and trigeminal afferences in the trigemino-cervical complex as a contributing factor in migraine. Children ≤18 years with the confirmed diagnosis of migraine were prospectively investigated. Comprehensive data on medical history, clinical neurological and psychological status were gathered. Trigger points in the trapezius muscle were identified by palpation and the threshold of pressure pain at these points was measured. Manual pressure was applied to the trigger points, and the occurrence and duration of induced headache were recorded. At a second consultation (4 weeks after the first), manual pressure with the detected pressure threshold was applied to non-trigger points within the same trapezius muscle (control). Headache and related parameters were again recorded and compared to the results of the first consultation. A total of 13 girls and 13 boys with migraine and a median age of 14.5 (Range 6.3-17.8) years took part in the study. Manual pressure to trigger points in the trapezius muscle led to lasting headache after termination of the manual pressure in 13 patients while no patient experienced headache when manual pressure was applied to non-trigger points at the control visit (p complex, especially in adolescents. In children with migraine headache can often be induced by pressure to myofascial trigger points, but not by pressure to non-trigger points in the trapezius muscle. This supports the hypothesis of a trigemino-cervical-complex in the pathophysiology of migraine, which might have implications for innovative therapies in children with migraine. © 2017 European Pain Federation - EFIC®.

The ATLAS High Level Trigger Steering Framework and the Trigger 
Configuration System.

CERN Document Server

Pérez Cavalcanti, Tiago; The ATLAS collaboration

2011-01-01

The ATLAS High Level Trigger Steering Framework and the Trigger 
Configuration System.
 
The ATLAS detector system installed in the Large Hadron Collider (LHC) 
at CERN is designed to study proton-proton and nucleus-nucleus 
collisions with a maximum center of mass energy of 14 TeV at a bunch 
collision rate of 40MHz.  In March 2010 the four LHC experiments saw 
the first proton-proton collisions at 7 TeV. Still within the year a 
collision rate of nearly 10 MHz is expected. At ATLAS, events of 
potential interest for ATLAS physics are selected by a three-level 
trigger system, with a final recording rate of about 200 Hz. The first 
level (L1) is implemented in custom hardware; the two levels of 
the high level trigger (HLT) are software triggers, running on large 
farms of standard computers and network devices. 

Within the ATLAS physics program more than 500 trigger signatures are 
defined. The HLT tests each signature on each L1-accepted event; the 
test outcome is recor...

A track reconstructing low-latency trigger processor for high-energy physics

International Nuclear Information System (INIS)

Cuveland, Jan de

2009-01-01

The detection and analysis of the large number of particles emerging from high-energy collisions between atomic nuclei is a major challenge in experimental heavy-ion physics. Efficient trigger systems help to focus the analysis on relevant events. A primary objective of the Transition Radiation Detector of the ALICE experiment at the LHC is to trigger on high-momentum electrons. In this thesis, a trigger processor is presented that employs massive parallelism to perform the required online event reconstruction within 2 μs to contribute to the Level-1 trigger decision. Its three-stage hierarchical architecture comprises 109 nodes based on FPGA technology. Ninety processing nodes receive data from the detector front-end at an aggregate net bandwidth of 2.16 Tbit/s via 1080 optical links. Using specifically developed components and interconnections, the system combines high bandwidth with minimum latency. The employed tracking algorithm three-dimensionally reassembles the track segments found in the detector's drift chambers based on explicit value comparisons, calculates the momentum of the originating particles from the course of the reconstructed tracks, and finally leads to a trigger decision. The architecture is capable of processing up to 20 000 track segments in less than 2 μs with high detection efficiency and reconstruction precision for high-momentum particles. As a result, this thesis shows how a trigger processor performing complex online track reconstruction within tight real-time requirements can be realized. The presented hardware has been built and is in continuous data taking operation in the ALICE experiment. (orig.)

A track reconstructing low-latency trigger processor for high-energy physics

Energy Technology Data Exchange (ETDEWEB)

Cuveland, Jan de

2009-09-17

The detection and analysis of the large number of particles emerging from high-energy collisions between atomic nuclei is a major challenge in experimental heavy-ion physics. Efficient trigger systems help to focus the analysis on relevant events. A primary objective of the Transition Radiation Detector of the ALICE experiment at the LHC is to trigger on high-momentum electrons. In this thesis, a trigger processor is presented that employs massive parallelism to perform the required online event reconstruction within 2 {mu}s to contribute to the Level-1 trigger decision. Its three-stage hierarchical architecture comprises 109 nodes based on FPGA technology. Ninety processing nodes receive data from the detector front-end at an aggregate net bandwidth of 2.16 Tbit/s via 1080 optical links. Using specifically developed components and interconnections, the system combines high bandwidth with minimum latency. The employed tracking algorithm three-dimensionally reassembles the track segments found in the detector's drift chambers based on explicit value comparisons, calculates the momentum of the originating particles from the course of the reconstructed tracks, and finally leads to a trigger decision. The architecture is capable of processing up to 20 000 track segments in less than 2 {mu}s with high detection efficiency and reconstruction precision for high-momentum particles. As a result, this thesis shows how a trigger processor performing complex online track reconstruction within tight real-time requirements can be realized. The presented hardware has been built and is in continuous data taking operation in the ALICE experiment. (orig.)

The Phase-I Upgrade of the ATLAS First Level Calorimeter Trigger

CERN Document Server

Andrei, George Victor; The ATLAS collaboration

2017-01-01

The ATLAS Level-1 calorimeter trigger is planning a series of upgrades in order to face the challenges posed by the upcoming increase of the LHC luminosity. The upgrade will benefit from new front-end electronics for parts of the calorimeter that provide the trigger system with digital data with a tenfold increase in granularity. This makes possible the implementation of more efficient algorithms than currently used to maintain the low trigger thresholds at much harsher LHC collision conditions. The Level-1 calorimeter system upgrade consists of an active and a passive system for digital data distribution, and three different Feature Extractor systems which run complex algorithms to identify various physics object candidates. The algorithms are implemented in firmware on custom electronics boards with up to four high speed processing FPGAs. The main characteristics of the electronic boards are a high input bandwidth, up to several TB/s per module, implemented through optical receivers, and a large number of o...

Topological trigger device using scintillating fibers and position-sensitive photomultipliers

Energy Technology Data Exchange (ETDEWEB)

Kuroda, Keiichi; Dufournaud, J; Sillou, D [Laboratoire d' Annecy-le-Vieux de Physique des Particules (LAPP), 74 (France); Agoritsas, V [European Organization for Nuclear Research, Geneva (Switzerland); Bystricky, G; Lehar, F; Lesquen, A de [CEN-Saclay, 91 - Gif-sur-Yvette (France); Giacomich, R; Pauletta, G; Penzo, A; Salvato, G; Schiavon, P; Villari, A [INFN, Messina (Italy) INFN, Trieste (Italy) INFN, Udine (Italy); Gorin, A M; Meschanin, A P; Nurushev, S B; Rakhmatov, V E; Rykalin, V L; Solovyanov, V L; Vasiliev, A N; Vasil' chencko, V G [Institute for High Energy Physics, Serpukhov (USSR); Oshima, N; Yamada, R [Fermi National Accelerator Lab., Batavia, IL (USA); Takeutchi, F [Kyoto-Sanyo Univ., Kyoto (Japan); Yoshida, T [Osaka City Univ. (Japan); Akchurin, N; Onel, Y; Newsom, C

1991-07-01

An approach to a high quality of the Level-1 Trigger is investigated on the basis of a topological trigger device. It will be realized by using scintillating fibers and position-sensitive photomultipliers, both considered as potential candidates of new detector-components thanks to their excellent time characteristics and high radiation resistances. The device is characterized in particular by its simple concept and reliable operation supported by the mature technologies emploied. The major interests of such a scheme under LHC environments reside in its capability of selcting high pperpendicular to tracks in real time, its optional immunity against low pperpendicular to tracks and loopers, as well as its effective links to other associated devices in the complex of a vertex detector. (orig.).

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography.

Science.gov (United States)

Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L; Armour, Wes; Waterman, David G; Iwata, So; Evans, Gwyndaf

2013-08-01

The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

The ATLAS muon trigger performance in pp collisions at sqrt(s) = 8 TeV in year 2012 runs

CERN Document Server

Nobe, T; The ATLAS collaboration

2012-01-01

Events with muons in the final state are an important signature for many physics topics at Large Hadron Collider (LHC), for instance, searches for Higgs boson production or new phenomena, measurements on the standard model processes like top-quark, W, Z production. Thus, efficient trigger on muons in data taking and understanding its performance are crucial to perform these physics studies. At LHC high rejection power against large backgrounds, while maintaining high efficiency for rare signal events, is required for online selection at the trigger level. The ATLAS experiment employs a multi-level trigger architecture that selects the events in three sequential steps of increasing complexity and accuracy to cope with this challenging task. The L1 muon trigger system gets its input from fast muon trigger detectors. Fast sector logic boards select muon candidates, which are passed via an interface board to the central trigger processor and then to the High Level Trigger (HLT). The Muon HLT is purely software ba...

Detailed Investigation of the Structural, Thermal, and Electronic Properties of Gold Isocyanide Complexes with Mechano-Triggered Single-Crystal-to-Single-Crystal Phase Transitions.

Science.gov (United States)

Seki, Tomohiro; Sakurada, Kenta; Muromoto, Mai; Seki, Shu; Ito, Hajime

2016-02-01

Mechano-induced phase transitions in organic crystalline materials, which can alter their properties, have received much attention. However, most mechano-responsive molecular crystals exhibit crystal-to-amorphous phase transitions, and the intermolecular interaction patterns in the daughter phase are difficult to characterize. We have investigated phenyl(phenylisocyanide)gold(I) (1) and phenyl(3,5-dimethylphenylisocyanide)gold(I) (2) complexes, which exhibit a mechano-triggered single-crystal-to-single-crystal phase transition. Previous reports of complexes 1 and 2 have focused on the relationships between the crystalline structures and photoluminescence properties; in this work we have focused on other aspects. The face index measurements of complexes 1 and 2 before and after the mechano-induced phase transitions have indicated that they undergo non-epitaxial phase transitions without a rigorous orientational relationship between the mother and daughter phases. Differential scanning calorimetry analyses revealed the phase transition of complex 1 to be enthalpically driven by the formation of new aurophilic interactions. In contrast, the phase transition of complex 2 was found to be entropically driven, with the closure of an empty void in the mother phase. Scanning electron microscopy observation showed that the degree of the charging effect of both complexes 1 and 2 was changed by the phase transitions, which suggests that the formation of the aurophilic interactions affords more effective conductive pathways. Moreover, flash-photolysis time-resolved microwave conductivity measurements revealed that complex 1 increased in conductivity after the phase change, whereas the conductivity of complex 2 decreased. These contrasting results were explained by the different patterns in the aurophilic interactions. Finally, an intriguing disappearing polymorphism of complex 2 has been reported, in which a polymorph form could not be obtained again after some period of time

Near-infrared remotely triggered drug-release strategies for cancer treatment

Science.gov (United States)

Goodman, Amanda M.; Neumann, Oara; Nørregaard, Kamilla; Henderson, Luke; Choi, Mi-Ran; Clare, Susan E.; Halas, Naomi J.

2017-11-01

Remotely controlled, localized drug delivery is highly desirable for potentially minimizing the systemic toxicity induced by the administration of typically hydrophobic chemotherapy drugs by conventional means. Nanoparticle-based drug delivery systems provide a highly promising approach for localized drug delivery, and are an emerging field of interest in cancer treatment. Here, we demonstrate near-IR light-triggered release of two drug molecules from both DNA-based and protein-based hosts that have been conjugated to near-infrared-absorbing Au nanoshells (SiO2 core, Au shell), each forming a light-responsive drug delivery complex. We show that, depending upon the drug molecule, the type of host molecule, and the laser illumination method (continuous wave or pulsed laser), in vitro light-triggered release can be achieved with both types of nanoparticle-based complexes. Two breast cancer drugs, docetaxel and HER2-targeted lapatinib, were delivered to MDA-MB-231 and SKBR3 (overexpressing HER2) breast cancer cells and compared with release in noncancerous RAW 264.7 macrophage cells. Continuous wave laser-induced release of docetaxel from a nanoshell-based DNA host complex showed increased cell death, which also coincided with nonspecific cell death from photothermal heating. Using a femtosecond pulsed laser, lapatinib release from a nanoshell-based human serum albumin protein host complex resulted in increased cancerous cell death while noncancerous control cells were unaffected. Both methods provide spatially and temporally localized drug-release strategies that can facilitate high local concentrations of chemotherapy drugs deliverable at a specific treatment site over a specific time window, with the potential for greatly minimized side effects.

NATO Advanced Study Institute on Evolving Methods for Macromolecular Gystallography

CERN Document Server

Read, Randy J

2007-01-01

X-ray crystallography is the pre-eminent technique for visualizing the structures of macromolecules at atomic resolution. These structures are central to understanding the detailed mechanisms of biological processes, and to discovering novel therapeutics using a structure-based approach. As yet, structures are known for only a small fraction of the proteins encoded by human and pathogenic genomes. To counter the myriad modern threats of disease, there is an urgent need to determine the structures of the thousands of proteins whose structure and function remain unknown. This volume draws on the expertise of leaders in the field of macromolecular crystallography to illuminate the dramatic developments that are accelerating progress in structural biology. Their contributions span the range of techniques from crystallization through data collection, structure solution and analysis, and show how modern high-throughput methods are contributing to a deeper understanding of medical problems.

The ATLAS Muon and Tau Trigger

CERN Document Server

Dell'Asta, L; The ATLAS collaboration

2013-01-01

[Muon] The ATLAS experiment at CERN's Large Hadron Collider (LHC) deploys a three-levels processing scheme for the trigger system. The level-1 muon trigger system gets its input from fast muon trigger detectors. Fast sector logic boards select muon candidates, which are passed via an interface board to the central trigger processor and then to the High Level Trigger (HLT). The muon HLT is purely software based and encompasses a level-2 (L2) trigger followed by an event filter (EF) for a staged trigger approach. It has access to the data of the precision muon detectors and other detector elements to refine the muon hypothesis. Trigger-specific algorithms were developed and are used for the L2 to increase processing speed for instance by making use of look-up tables and simpler algorithms, while the EF muon triggers mostly benefit from offline reconstruction software to obtain most precise determination of the track parameters. There are two algorithms with different approaches, namely inside-out and outside-in...

Performance of the ATLAS Muon Trigger and Phase-1 Upgrade of Level-1 Endcap Muon Trigger

CERN Document Server

Mizukami, Atsushi; The ATLAS collaboration

2017-01-01

The ATLAS experiment utilises a trigger system to efficiently record interesting events. It consists of first-level and high-level triggers. The first-level trigger is implemented with custom-built hardware to reduce the event rate from 40 MHz to100 kHz. Then the software-based high-level triggers refine the trigger decisions reducing the output rate down to 1 kHz. Events with muons in the final state are an important signature for many physics topics at the LHC. An efficient trigger on muons and a detailed understanding of its performance are required. Trigger efficiencies are, for example, obtained from the muon decay of Z boson, with a Tag&Probe method, using proton-proton collision data collected in 2016 at a centre-of-mass energy of 13 TeV. The LHC is expected to increase its instantaneous luminosity to $3\\times10^{34} \\rm{cm^{-2}s^{-1}}$ after the phase-1 upgrade between 2018-2020. The upgrade of the ATLAS trigger system is mandatory to cope with this high-luminosity. In the phase-1 upgrade, new det...

ATLAS calorimetry. Trigger, simulation and jet calibration

Energy Technology Data Exchange (ETDEWEB)

Weber, P

2007-02-06

The Pre-Processor system of the ATLAS Level-1 Calorimeter Trigger performs complex processing of analog trigger tower signals from electromagnetic and hadronic calorimeters. The main processing block of the Pre-Processor System is the Multi-Chip Module (MCM). The first part of this thesis describes MCM quality assurance tests that have been developed, their use in the MCM large scale production and the results that have been obtained. In the second part of the thesis a validation of a shower parametrisation model for the ATLAS fast simulation package ATLFAST based on QCD dijet events is performed. A detailed comparison of jet response and jet energy resolution between the fast and the full simulation is presented. The uniformity of the calorimeter response has a significant impact on the accuracy of the jet energy measurement. A study of the calorimeter intercalibration using QCD dijet events is presented in the last part of the thesis. The intercalibration study is performed in azimuth angle {phi} and in pseudorapidity {eta}. The performance of the calibration methods including possible systematic and statistical effects is described. (orig.)

Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures.

Science.gov (United States)

Viswanath, Shruthi; Chemmama, Ilan E; Cimermancic, Peter; Sali, Andrej

2017-12-05

Modeling of macromolecular structures involves structural sampling guided by a scoring function, resulting in an ensemble of good-scoring models. By necessity, the sampling is often stochastic, and must be exhaustive at a precision sufficient for accurate modeling and assessment of model uncertainty. Therefore, the very first step in analyzing the ensemble is an estimation of the highest precision at which the sampling is exhaustive. Here, we present an objective and automated method for this task. As a proxy for sampling exhaustiveness, we evaluate whether two independently and stochastically generated sets of models are sufficiently similar. The protocol includes testing 1) convergence of the model score, 2) whether model scores for the two samples were drawn from the same parent distribution, 3) whether each structural cluster includes models from each sample proportionally to its size, and 4) whether there is sufficient structural similarity between the two model samples in each cluster. The evaluation also provides the sampling precision, defined as the smallest clustering threshold that satisfies the third, most stringent test. We validate the protocol with the aid of enumerated good-scoring models for five illustrative cases of binary protein complexes. Passing the proposed four tests is necessary, but not sufficient for thorough sampling. The protocol is general in nature and can be applied to the stochastic sampling of any set of models, not just structural models. In addition, the tests can be used to stop stochastic sampling as soon as exhaustiveness at desired precision is reached, thereby improving sampling efficiency; they may also help in selecting a model representation that is sufficiently detailed to be informative, yet also sufficiently coarse for sampling to be exhaustive. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

DUMAND data acquisition with triggering

International Nuclear Information System (INIS)

Brenner, A.E.; Theriot, D.; March, R.H.

1980-01-01

A data acquisition scheme for the standard DUMAND array that includes a simple triggering scheme as a fundamental part of the system is presented. Although there are a number of not yet fully understood parameters, it is assumed that thresholds can be set in such a manner as to give rise to a triggered signal that is not so dominated by randoms that it gives a substantial decrease in the data acquisition rate over that which would be required by a nontriggered system. It is also assumed that the triggering logic is relatively simple and does not need major computational capabilities for a trigger logic decision. With these assumptions, it is possible to generate the trigger at the array and restrict the data transfer to shore. However, with a not unreasonable delay of 200 microseconds, it is even possible to transmit the information for the trigger to shore and perform all that logic on the shore. The critical point is to send the minimum amount of information necessary to construct the trigger such that one need not send all the possible information in all detectors of the array continuously to shore. 1 figure

The ATLAS hadronic tau trigger

CERN Document Server

Black, C; The ATLAS collaboration

2012-01-01

With the high luminosities of proton-proton collisions achieved at the LHC, the strategies for triggering have become more important than ever for physics analysis. The naive inclusive single tau lepton triggers now suffer from severe rate limitations. To allow for a large program of physics analyses with taus, the development of topological triggers that combine tau signatures with other measured quantities in the event is required. These combined triggers open many opportunities to study new physics beyond the Standard Model and to search for the Standard Model Higgs. We present the status and performance of the hadronic tau trigger in ATLAS. We demonstrate that the ATLAS tau trigger ran remarkably well over 2011, and how the lessons learned from 2011 led to numerous improvements in the preparation of the 2012 run. These improvements include the introduction of tau selection criteria that are robust against varying pileup scenarios, and the implementation of multivariate selection techniques in the tau trig...

The ATLAS hadronic tau trigger

CERN Document Server

Black, C; The ATLAS collaboration

2012-01-01

With the high luminosities of proton-proton collisions achieved at the LHC, the strategies for triggering have become more important than ever for physics analysis. The naïve inclusive single tau lepton triggers now suffer from severe rate limitations. To allow for a large program of physics analyses with taus, the development of topological triggers that combine tau signatures with other measured quantities in the event is required. These combined triggers open many opportunities to study new physics beyond the Standard Model and to search for the Standard Model Higgs. We present the status and performance of the hadronic tau trigger in ATLAS. We demonstrate that the ATLAS tau trigger ran remarkably well over 2011, and how the lessons learned from 2011 led to numerous improvements in the preparation of the 2012 run. These improvements include the introduction of tau selection criteria that are robust against varying pileup scenarios, and the implementation of multivariate selection techniques in the tau tri...

Proteomics analysis suggests broad functional changes in potato leaves triggered by phosphites and a complex indirect mode of action against Phytophthora infestans.

Science.gov (United States)

Lim, Sanghyun; Borza, Tudor; Peters, Rick D; Coffin, Robert H; Al-Mughrabi, Khalil I; Pinto, Devanand M; Wang-Pruski, Gefu

2013-11-20

Phosphite (salts of phosphorous acid; Phi)-based fungicides are increasingly used in controlling oomycete pathogens, such as the late blight agent Phytophthora infestans. In plants, low amounts of Phi induce pathogen resistance through an indirect mode of action. We used iTRAQ-based quantitative proteomics to investigate the effects of phosphite on potato plants before and after infection with P. infestans. Ninety-three (62 up-regulated and 31 down-regulated) differentially regulated proteins, from a total of 1172 reproducibly identified proteins, were identified in the leaf proteome of Phi-treated potato plants. Four days post-inoculation with P. infestans, 16 of the 31 down-regulated proteins remained down-regulated and 42 of the 62 up-regulated proteins remained up-regulated, including 90% of the defense proteins. This group includes pathogenesis-related, stress-responsive, and detoxification-related proteins. Callose deposition and ultrastructural analyses of leaf tissues after infection were used to complement the proteomics approach. This study represents the first comprehensive proteomics analysis of the indirect mode of action of Phi, demonstrating broad effects on plant defense and plant metabolism. The proteomics data and the microscopy study suggest that Phi triggers a hypersensitive response that is responsible for induced resistance of potato leaves against P. infestans. Phosphie triggers complex functional changes in potato leaves that are responsible for the induced resistance against Phytophthora infestans. This article is part of a Special Issue entitled: Translational Plant Proteomics. Copyright © 2013 Elsevier B.V. All rights reserved.

Permeability to macromolecular contrast media quantified by dynamic MRI correlates with tumor tissue assays of vascular endothelial growth factor (VEGF)

International Nuclear Information System (INIS)

Cyran, Clemens C.; Sennino, Barbara; Fu, Yanjun; Rogut, Victor; Shames, David M.; Chaopathomkul, Bundit; Wendland, Michael F.; McDonald, Donald M.; Brasch, Robert C.; Raatschen, Hans-Juergen

2012-01-01

Purpose: To correlate dynamic MRI assays of macromolecular endothelial permeability with microscopic area–density measurements of vascular endothelial growth factor (VEGF) in tumors. Methods and material: This study compared tumor xenografts from two different human cancer cell lines, MDA-MB-231 tumors (n = 5), and MDA-MB-435 (n = 8), reported to express respectively higher and lower levels of VEGF. Dynamic MRI was enhanced by a prototype macromolecular contrast medium (MMCM), albumin-(Gd-DTPA)35. Quantitative estimates of tumor microvascular permeability (K PS ; μl/min × 100 cm 3 ), obtained using a two-compartment kinetic model, were correlated with immunohistochemical measurements of VEGF in each tumor. Results: Mean K PS was 2.4 times greater in MDA-MB-231 tumors (K PS = 58 ± 30.9 μl/min × 100 cm 3 ) than in MDA-MB-435 tumors (K PS = 24 ± 8.4 μl/min × 100 cm 3 ) (p < 0.05). Correspondingly, the area–density of VEGF in MDA-MB-231 tumors was 2.6 times greater (27.3 ± 2.2%, p < 0.05) than in MDA-MB-435 cancers (10.5 ± 0.5%, p < 0.05). Considering all tumors without regard to cell type, a significant positive correlation (r = 0.67, p < 0.05) was observed between MRI-estimated endothelial permeability and VEGF immunoreactivity. Conclusion: Correlation of MRI assays of endothelial permeability to a MMCM and VEGF immunoreactivity of tumors support the hypothesis that VEGF is a major contributor to increased macromolecular permeability in cancers. When applied clinically, the MMCM-enhanced MRI approach could help to optimize the appropriate application of VEGF-inhibiting therapy on an individual patient basis.

Nonlinear dynamical triggering of slow slip

Energy Technology Data Exchange (ETDEWEB)

Johnson, Paul A [Los Alamos National Laboratory; Knuth, Matthew W [WISCONSIN; Kaproth, Bryan M [PENN STATE; Carpenter, Brett [PENN STATE; Guyer, Robert A [Los Alamos National Laboratory; Le Bas, Pierre - Yves [Los Alamos National Laboratory; Daub, Eric G [Los Alamos National Laboratory; Marone, Chris [PENN STATE

2010-12-10

Among the most fascinating, recent discoveries in seismology have been the phenomena of triggered slip, including triggered earthquakes and triggered-tremor, as well as triggered slow, silent-slip during which no seismic energy is radiated. Because fault nucleation depths cannot be probed directly, the physical regimes in which these phenomena occur are poorly understood. Thus determining physical properties that control diverse types of triggered fault sliding and what frictional constitutive laws govern triggered faulting variability is challenging. We are characterizing the physical controls of triggered faulting with the goal of developing constitutive relations by conducting laboratory and numerical modeling experiments in sheared granular media at varying load conditions. In order to simulate granular fault zone gouge in the laboratory, glass beads are sheared in a double-direct configuration under constant normal stress, while subject to transient perturbation by acoustic waves. We find that triggered, slow, silent-slip occurs at very small confining loads ({approx}1-3 MPa) that are smaller than those where dynamic earthquake triggering takes place (4-7 MPa), and that triggered slow-slip is associated with bursts of LFE-like acoustic emission. Experimental evidence suggests that the nonlinear dynamical response of the gouge material induced by dynamic waves may be responsible for the triggered slip behavior: the slip-duration, stress-drop and along-strike slip displacement are proportional to the triggering wave amplitude. Further, we observe a shear-modulus decrease corresponding to dynamic-wave triggering relative to the shear modulus of stick-slips. Modulus decrease in response to dynamical wave amplitudes of roughly a microstrain and above is a hallmark of elastic nonlinear behavior. We believe that the dynamical waves increase the material non-affine elastic deformation during shearing, simultaneously leading to instability and slow-slip. The inferred

ATLAS: triggers for B-physics

International Nuclear Information System (INIS)

George, Simon

2000-01-01

The LHC will produce bb-bar events at an unprecedented rate. The number of events recorded by ATLAS will be limited by the rate at which they can be stored offline and subsequently analysed. Despite the huge number of events, the small branching ratios mean that analysis of many of the most interesting channels for CP violation and other measurements will be limited by statistics. The challenge for the Trigger and Data Acquisition (DAQ) system is therefore to maximise the fraction of interesting B decays in the B-physics data stream. The ATLAS Trigger/DAQ system is split into three levels. The initial B-physics selection is made in the first-level trigger by an inclusive low-p T muon trigger (∼6 GeV). The second-level trigger strategy is based on identifying classes of final states by their partial reconstruction. The muon trigger is confirmed before proceeding to a track search. Electron/hadron separation is given by the transition radiation tracking detector and the Electromagnetic calorimeter. Muon identification is possible using the muon detectors and the hadronic calorimeter. From silicon strips, pixels and straw tracking, precise track reconstruction is used to make selections based on invariant mass, momentum and impact parameter. The ATLAS trigger group is currently engaged in algorithm development and performance optimisation for the B-physics trigger. This is closely coupled to the R and D programme for the higher-level triggers. Together the two programmes of work will optimise the hardware, architecture and algorithms to meet the challenging requirements. This paper describes the current status and progress of this work

Designing signal-enriched triggers for boosted jets.

CERN Document Server

Toumazou, Marina

2017-01-01

Triggers designed to favour the selection of hadronically decaying massive particles have been studied. Both triggers using solely ET and mass cuts (similar to new 2017 triggers) and triggers exploiting polarization information have been studied. The mass cut triggers show substantial gains in rate reduction, while the benefits of polarization triggers are less obvious. The final conclusion is that it is more useful to identify and trigger on generic boosted decays, irrespective of the polarization of the decaying particle

Embodied social robots trigger gaze following in real-time

OpenAIRE

Wiese, Eva; Weis, Patrick; Lofaro, Daniel

2018-01-01

In human-human interaction, we use information from gestures, facial expressions and gaze direction to make inferences about what interaction partners think, feel or intend to do next. Observing changes in gaze direction triggers shifts of attention to gazed-at locations and helps establish shared attention between gazer and observer - a prerequisite for more complex social skills like mentalizing, action understanding and joint action. The ability to follow others’ gaze develops early in lif...

Macromolecular crowding-assisted fabrication of liquid-crystalline imprinted polymers.

Science.gov (United States)

Zhang, Chen; Zhang, Jing; Huang, Yan-Ping; Liu, Zhao-Sheng

2015-04-01

A macromolecular crowding-assisted liquid-crystalline molecularly imprinted monolith (LC-MIM) was prepared successfully for the first time. The imprinted stationary phase was synthesized with polymethyl methacrylate (PMMA) or polystyrene (PS) as the crowding agent, 4-cyanophenyl dicyclohexyl propylene (CPCE) as the liquid-crystal monomer, and hydroquinidine as the pseudo-template for the chiral separation of cinchona alkaloids in HPLC. A low level of cross-linker (26%) has been found to be sufficient to achieve molecular recognition on the crowding-assisted LC-MIM due to the physical cross-linking of mesogenic groups in place of chemical cross-linking, and baseline separation of quinidine and quinine could be achieved with good resolution (R(s) = 2.96), selectivity factor (α = 2.16), and column efficiency (N = 2650 plates/m). In contrast, the LC-MIM prepared without crowding agents displayed the smallest diastereoselectivity (α = 1.90), while the crowding-assisted MIM with high level of cross-linker (80%) obtained the greatest selectivity factor (α = 7.65), but the lowest column efficiency (N = 177 plates/m).

On macromolecular refinement at subatomic resolution with interatomic scatterers

Energy Technology Data Exchange (ETDEWEB)

Afonine, Pavel V., E-mail: pafonine@lbl.gov; Grosse-Kunstleve, Ralf W.; Adams, Paul D. [Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720 (United States); Lunin, Vladimir Y. [Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290 (Russian Federation); Urzhumtsev, Alexandre [IGMBC, 1 Rue L. Fries, 67404 Illkirch and IBMC, 15 Rue R. Descartes, 67084 Strasbourg (France); Faculty of Sciences, Nancy University, 54506 Vandoeuvre-lès-Nancy (France); Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720 (United States)

2007-11-01

Modelling deformation electron density using interatomic scatters is simpler than multipolar methods, produces comparable results at subatomic resolution and can easily be applied to macromolecules. A study of the accurate electron-density distribution in molecular crystals at subatomic resolution (better than ∼1.0 Å) requires more detailed models than those based on independent spherical atoms. A tool that is conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8–1.0 Å, the number of experimental data is insufficient for full multipolar model refinement. As an alternative, a simpler model composed of conventional independent spherical atoms augmented by additional scatterers to model bonding effects has been proposed. Refinement of these mixed models for several benchmark data sets gave results that were comparable in quality with the results of multipolar refinement and superior to those for conventional models. Applications to several data sets of both small molecules and macromolecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package.

Peptidoglycan from Fermentation By-Product Triggers Defense Responses in Grapevine

Science.gov (United States)

Chen, Yang; Takeda, Taito; Aoki, Yoshinao; Fujita, Keiko; Suzuki, Shunji; Igarashi, Daisuke

2014-01-01

Plants are constantly under attack from a variety of microorganisms, and rely on a series of complex detection and response systems to protect themselves from infection. Here, we found that a by-product of glutamate fermentation triggered defense responses in grapevine, increasing the expression of defense response genes in cultured cells, foliar chitinase activity, and resistance to infection by downy mildew in leaf explants. To identify the molecule that triggered this innate immunity, we fractionated and purified candidates extracted from Corynebacterium glutamicum, a bacterium used in the production of amino acids by fermentation. Using hydrolysis by lysozyme, a silkworm larva plasma detection system, and gel filtration analysis, we identified peptidoglycan as inducing the defense responses. Peptidoglycans of Escherichia coli, Bacillus subtilis, and Staphylococcus aureus also generated similar defensive responses. PMID:25427192

The Run-2 ATLAS Trigger System

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00222798; The ATLAS collaboration

2016-01-01

The ATLAS trigger successfully collected collision data during the first run of the LHC between 2009-2013 at different centre-of-mass energies between 900 GeV and 8 TeV. The trigger system consists of a hardware Level-1 and a software-based high level trigger (HLT) that reduces the event rate from the design bunch-crossing rate of 40 MHz to an average recording rate of a few hundred Hz. In Run-2, the LHC will operate at centre-of-mass energies of 13 and 14 TeV and higher luminosity, resulting in roughly five times higher trigger rates. A brief review of the ATLAS trigger system upgrades that were implemented between Run-1 and Run-2, allowing to cope with the increased trigger rates while maintaining or even improving the efficiency to select physics processes of interest, will be given. This includes changes to the Level-1 calorimeter and muon trigger systems, the introduction of a new Level-1 topological trigger module and the merging of the previously two-level HLT system into a single event filter farm. A ...

The LVL2 trigger goes online

CERN Multimedia

David Berge

On Friday, the 9th of February, the ATLAS TDAQ community reached an important milestone. In a successful integration test, cosmic-ray muons were recorded with parts of the muon spectrometer, the central-trigger system and a second-level trigger algorithm. This was actually the first time that a full trigger slice all the way from the first-level trigger muon chambers up to event building after event selection by the second-level trigger ran online with cosmic rays. The ATLAS trigger and data acquisition system has a three-tier structure that is designed to cope with the enormous demands of proton-proton collisions at a bunch-crossing frequency of 40 MHz, with a typical event size of 1-2 MB. The online event selection has to reduce the incoming rate by a factor of roughly 200,000 to 200 Hz, a rate digestible by the archival-storage and offline-processing facilities. ATLAS has a mixed system: the first-level trigger (LVL1) is in hardware, while the other two consecutive levels, the second-level trigger (LVL2)...

The Database Driven ATLAS Trigger Configuration System

CERN Document Server

Martyniuk, Alex; The ATLAS collaboration

2015-01-01

This contribution describes the trigger selection configuration system of the ATLAS low- and high-level trigger (HLT) and the upgrades it received in preparation for LHC Run 2. The ATLAS trigger configuration system is responsible for applying the physics selection parameters for the online data taking at both trigger levels and the proper connection of the trigger lines across those levels. Here the low-level trigger consists of the already existing central trigger (CT) and the new Level-1 Topological trigger (L1Topo), which has been added for Run 2. In detail the tasks of the configuration system during the online data taking are Application of the selection criteria, e.g. energy cuts, minimum multiplicities, trigger object correlation, at the three trigger components L1Topo, CT, and HLT On-the-fly, e.g. rate-dependent, generation and application of prescale factors to the CT and HLT to adjust the trigger rates to the data taking conditions, such as falling luminosity or rate spikes in the detector readout ...

DT Local Trigger performance in 2015

CERN Document Server

CMS Collaboration

2015-01-01

The Local Trigger system of the CMS Drift Tube chambers (DT) was checked applying similar methods as in the LHC Run 1 (2012). The main variables shown in this note are the trigger efficiency, the trigger quality and the fraction of trigger ghosts. The performance was found to be comparable or better than in Run 1.

Timely deposition of macromolecular structures is necessary for peer review

International Nuclear Information System (INIS)

Joosten, Robbie P.; Soueidan, Hayssam; Wessels, Lodewyk F. A.; Perrakis, Anastassis

2013-01-01

Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature

Timely deposition of macromolecular structures is necessary for peer review

Energy Technology Data Exchange (ETDEWEB)

Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Soueidan, Hayssam; Wessels, Lodewyk F. A. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam (Netherlands); Perrakis, Anastassis, E-mail: a.perrakis@nki.nl [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands)

2013-12-01

Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature.

A beamline for macromolecular crystallography at the Advanced Light Source

International Nuclear Information System (INIS)

Padmore, H.A.; Earnest, T.; Kim, S.H.; Thompson, A.C.; Robinson, A.L.

1994-08-01

A beamline for macromolecular crystallography has been designed for the ALS. The source will be a 37-pole wiggler with a, 2-T on-axis peak field. The wiggler will illuminate three beamlines, each accepting 3 mrad of horizontal aperture. The central beamline will primarily be used for multiple-wavelength anomalous dispersion measurements in the wavelength range from 4 to 0.9 angstrom. The beamline optics will comprise a double-crystal monochromator with a collimating pre-mirror and a double-focusing mirror after the monochromator. The two side stations will be used for fixed-wavelength experiments within the wavelength range from 1.5 to 0.95 angstrom. The optics will consist of a conventional vertically focusing cylindrical mirror followed by an asymmetrically cut curved-crystal monochromator. This paper presents details of the optimization of the wiggler source for crystallography, gives a description of the beamline configuration, and discusses the reasons for the choices made

GPU Enhancement of the Trigger to Extend Physics Reach at the LHC

CERN Document Server

Halyo, V; Jindal, P; LeGresley, P; Lujan, P

2013-01-01

Significant new challenges are continuously confronting the High Energy Physics (HEP) experiments, in particular the two detectors at the Large Hadron Collider (LHC) at CERN, where nominal conditions deliver proton-proton collisions to the detectors at a rate of 40 MHz. This rate must be significantly reduced to comply with both the performance limitations of the mass storage hardware and the capabilities of the computing resources to process the collected data in a timely fashion for physics analysis. At the same time, the physics signals of interest must be retained with high efficiency. The quest for rare new physics phenomena at the LHC leads us to evaluate a Graphics Processing Unit (GPU) enhancement of the existing High-Level Trigger (HLT), made possible by the current flexibility of the trigger system, which not only provides faster and more efficient event selection, but also includes the possibility of new complex triggers that were not previously feasible. A new tracking algorithm is evaluated on a ...

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

Science.gov (United States)

Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L.; Armour, Wes; Waterman, David G.; Iwata, So; Evans, Gwyndaf

2013-01-01

The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein. PMID:23897484

Comparison of two self-assembled macromolecular prodrug micelles with different conjugate positions of SN38 for enhancing antitumor activity

Directory of Open Access Journals (Sweden)

Liu Y

2015-03-01

Full Text Available Yi Liu,1 Hongyu Piao,1 Ying Gao,1 Caihong Xu,2 Ye Tian,1 Lihong Wang,1 Jinwen Liu,1 Bo Tang,1 Meijuan Zou,1 Gang Cheng1 1Department of Pharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, People’s Republic of China; 2Department of Food Science, Shenyang Normal University, Shenyang, Liaoning Province, People’s Republic of China Abstract: 7-Ethyl-10-hydroxycamptothecin (SN38, an active metabolite of irinotecan (CPT-11, is a remarkably potent antitumor agent. The clinical application of SN38 has been extremely restricted by its insolubility in water. In this study, we successfully synthesized two macromolecular prodrugs of SN38 with different conjugate positions (chitosan-(C10-OHSN38 and chitosan-(C20-OHSN38 to improve the water solubility and antitumor activity of SN38. These prodrugs can self-assemble into micelles in aqueous medium. The particle size, morphology, zeta potential, and in vitro drug release of SN38 and its derivatives, as well as their cytotoxicity, pharmacokinetics, and in vivo antitumor activity in a xenograft BALB/c mouse model were studied. In vitro, chitosan-(C10-OHSN38 (CS-(10sSN38 and chitosan-(C20-OHSN38 (CS-(20sSN38 were 13.3- and 25.9-fold more potent than CPT-11 in the murine colon adenocarcinoma cell line CT26, respectively. The area under the curve (AUC0–24 of SN38 after intravenously administering CS-(10sSN38 and CS-(20sSN38 to Sprague Dawley rats was greatly improved when compared with CPT-11 (both P<0.01. A larger AUC0–24 of CS-(20sSN38 was observed when compared to CS-(10sSN38 (P<0.05. Both of the novel self-assembled chitosan-SN38 prodrugs demonstrated superior anticancer activity to CPT-11 in the CT26 xenograft BALB/c mouse model. We have also investigated the differences between these macromolecular prodrug micelles with regards to enhancing the antitumor activity of SN38. CS-(20sSN38 exhibited better in vivo antitumor activity than CS-(10sSN38 at a dose of 2.5 mg/kg (P<0

Errors in macromolecular synthesis after stress. A study of the possible protective role of the small heat shock proteinsBiochemistry

NARCIS (Netherlands)

Marin Vinader, L.

2006-01-01

The general goal of this thesis was to gain insight in what small heat shock proteins (sHsps) do with respect to macromolecular synthesis during a stressful situation in the cell. It is known that after a non-lethal heat shock, cells are better protected against a subsequent more severe heat shock,

Probing the Cosmic Gamma-Ray Burst Rate with Trigger Simulations of the Swift Burst Alert Telescope

Science.gov (United States)

Lien, Amy; Sakamoto, Takanori; Gehrels, Neil; Palmer, David M.; Barthelmy, Scott D.; Graziani, Carlo; Cannizzo, John K.

2013-01-01

The gamma-ray burst (GRB) rate is essential for revealing the connection between GRBs, supernovae and stellar evolution. Additionally, the GRB rate at high redshift provides a strong probe of star formation history in the early universe. While hundreds of GRBs are observed by Swift, it remains difficult to determine the intrinsic GRB rate due to the complex trigger algorithm of Swift. Current studies of the GRB rate usually approximate the Swift trigger algorithm by a single detection threshold. However, unlike the previously own GRB instruments, Swift has over 500 trigger criteria based on photon count rate and additional image threshold for localization. To investigate possible systematic biases and explore the intrinsic GRB properties, we develop a program that is capable of simulating all the rate trigger criteria and mimicking the image threshold. Our simulations show that adopting the complex trigger algorithm of Swift increases the detection rate of dim bursts. As a result, our simulations suggest bursts need to be dimmer than previously expected to avoid over-producing the number of detections and to match with Swift observations. Moreover, our results indicate that these dim bursts are more likely to be high redshift events than low-luminosity GRBs. This would imply an even higher cosmic GRB rate at large redshifts than previous expectations based on star-formation rate measurements, unless other factors, such as the luminosity evolution, are taken into account. The GRB rate from our best result gives a total number of 4568 +825 -1429 GRBs per year that are beamed toward us in the whole universe.

The Run-2 ATLAS Trigger System

CERN Document Server

Ruiz-Martinez, Aranzazu; The ATLAS collaboration

2016-01-01

The ATLAS trigger has been successfully collecting collision data during the first run of the LHC between 2009-2013 at a centre-of-mass energy between 900 GeV and 8 TeV. The trigger system consists of a hardware Level-1 (L1) and a software based high-level trigger (HLT) that reduces the event rate from the design bunch-crossing rate of 40 MHz to an average recording rate of a few hundred Hz. In Run-2, the LHC will operate at centre-of-mass energies of 13 and 14 TeV resulting in roughly five times higher trigger rates. We will briefly review the ATLAS trigger system upgrades that were implemented during the shutdown, allowing us to cope with the increased trigger rates while maintaining or even improving our efficiency to select relevant physics processes. This includes changes to the L1 calorimeter and muon trigger systems, the introduction of a new L1 topological trigger module and the merging of the previously two-level HLT system into a single event filter farm. At hand of a few examples, we will show the ...

Triggering soft bombs at the LHC

Science.gov (United States)

Knapen, Simon; Griso, Simone Pagan; Papucci, Michele; Robinson, Dean J.

2017-08-01

Very high multiplicity, spherically-symmetric distributions of soft particles, with p T ˜ few×100 MeV, may be a signature of strongly-coupled hidden valleys that exhibit long, efficient showering windows. With traditional triggers, such `soft bomb' events closely resemble pile-up and are therefore only recorded with minimum bias triggers at a very low efficiency. We demonstrate a proof-of-concept for a high-level triggering strategy that efficiently separates soft bombs from pile-up by searching for a `belt of fire': a high density band of hits on the innermost layer of the tracker. Seeding our proposed high-level trigger with existing jet, missing transverse energy or lepton hardware-level triggers, we show that net trigger efficiencies of order 10% are possible for bombs of mass several × 100 GeV. We also consider the special case that soft bombs are the result of an exotic decay of the 125 GeV Higgs. The fiducial rate for `Higgs bombs' triggered in this manner is marginally higher than the rate achievable by triggering directly on a hard muon from associated Higgs production.

Survey of large protein complexes D. vulgaris reveals great structural diversity

Energy Technology Data Exchange (ETDEWEB)

Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

2009-08-15

An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

Calorimetry triggering in ATLAS

CERN Document Server

Igonkina, O; Adragna, P; Aharrouche, M; Alexandre, G; Andrei, V; Anduaga, X; Aracena, I; Backlund, S; Baines, J; Barnett, B M; Bauss, B; Bee, C; Behera, P; Bell, P; Bendel, M; Benslama, K; Berry, T; Bogaerts, A; Bohm, C; Bold, T; Booth, J R A; Bosman, M; Boyd, J; Bracinik, J; Brawn, I, P; Brelier, B; Brooks, W; Brunet, S; Bucci, F; Casadei, D; Casado, P; Cerri, A; Charlton, D G; Childers, J T; Collins, N J; Conde Muino, P; Coura Torres, R; Cranmer, K; Curtis, C J; Czyczula, Z; Dam, M; Damazio, D; Davis, A O; De Santo, A; Degenhardt, J; Delsart, P A; Demers, S; Demirkoz, B; Di Mattia, A; Diaz, M; Djilkibaev, R; Dobson, E; Dova, M, T; Dufour, M A; Eckweiler, S; Ehrenfeld, W; Eifert, T; Eisenhandler, E; Ellis, N; Emeliyanov, D; Enoque Ferreira de Lima, D; Faulkner, P J W; Ferland, J; Flacher, H; Fleckner, J E; Flowerdew, M; Fonseca-Martin, T; Fratina, S; Fhlisch, F; Gadomski, S; Gallacher, M P; Garitaonandia Elejabarrieta, H; Gee, C N P; George, S; Gillman, A R; Goncalo, R; Grabowska-Bold, I; Groll, M; Gringer, C; Hadley, D R; Haller, J; Hamilton, A; Hanke, P; Hauser, R; Hellman, S; Hidvgi, A; Hillier, S J; Hryn'ova, T; Idarraga, J; Johansen, M; Johns, K; Kalinowski, A; Khoriauli, G; Kirk, J; Klous, S; Kluge, E-E; Koeneke, K; Konoplich, R; Konstantinidis, N; Kwee, R; Landon, M; LeCompte, T; Ledroit, F; Lei, X; Lendermann, V; Lilley, J N; Losada, M; Maettig, S; Mahboubi, K; Mahout, G; Maltrana, D; Marino, C; Masik, J; Meier, K; Middleton, R P; Mincer, A; Moa, T; Monticelli, F; Moreno, D; Morris, J D; Mller, F; Navarro, G A; Negri, A; Nemethy, P; Neusiedl, A; Oltmann, B; Olvito, D; Osuna, C; Padilla, C; Panes, B; Parodi, F; Perera, V J O; Perez, E; Perez Reale, V; Petersen, B; Pinzon, G; Potter, C; Prieur, D P F; Prokishin, F; Qian, W; Quinonez, F; Rajagopalan, S; Reinsch, A; Rieke, S; Riu, I; Robertson, S; Rodriguez, D; Rogriquez, Y; Rhr, F; Saavedra, A; Sankey, D P C; Santamarina, C; Santamarina Rios, C; Scannicchio, D; Schiavi, C; Schmitt, K; Schultz-Coulon, H C; Schfer, U; Segura, E; Silverstein, D; Silverstein, S; Sivoklokov, S; Sjlin, J; Staley, R J; Stamen, R; Stelzer, J; Stockton, M C; Straessner, A; Strom, D; Sushkov, S; Sutton, M; Tamsett, M; Tan, C L A; Tapprogge, S; Thomas, J P; Thompson, P D; Torrence, E; Tripiana, M; Urquijo, P; Urrejola, P; Vachon, B; Vercesi, V; Vorwerk, V; Wang, M; Watkins, P M; Watson, A; Weber, P; Weidberg, T; Werner, P; Wessels, M; Wheeler-Ellis, S; Whiteson, D; Wiedenmann, W; Wielers, M; Wildt, M; Winklmeier, F; Wu, X; Xella, S; Zhao, L; Zobernig, H; de Seixas, J M; dos Anjos, A; Asman, B; Özcan, E

2009-01-01

The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2 105 to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule–Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs

Science.gov (United States)

Bujalowski, Wlodzimierz; Jezewska, Maria J.

2011-01-01

Analysis of thermodynamically rigorous binding isotherms provides fundamental information about the energetics of the ligand–macromolecule interactions and often an invaluable insight about the structure of the formed complexes. The Macromolecular Competition Titration (MCT) method enables one to quantitatively obtain interaction parameters of protein–nucleic acid interactions, which may not be available by other methods, particularly for the unmodified long polymer lattices and specific nucleic acid substrates, if the binding is not accompanied by adequate spectroscopic signal changes. The method can be applied using different fluorescent nucleic acids or fluorophores, although the etheno-derivatives of nucleic acid are especially suitable as they are relatively easy to prepare, have significant blue fluorescence, their excitation band lies far from the protein absorption spectrum, and the modification eliminates the possibility of base pairing with other nucleic acids. The MCT method is not limited to the specific size of the reference nucleic acid. Particularly, a simple analysis of the competition titration experiments is described in which the fluorescent, short fragment of nucleic acid, spanning the exact site-size of the protein–nucleic acid complex, and binding with only a 1:1 stoichiometry to the protein, is used as a reference macromolecule. Although the MCT method is predominantly discussed as applied to studying protein–nucleic acid interactions, it can generally be applied to any ligand–macromolecule system by monitoring the association reaction using the spectroscopic signal originating from the reference macromolecule in the presence of the competing macromolecule, whose interaction parameters with the ligand are to be determined. PMID:21195223

Macromolecular competition titration method accessing thermodynamics of the unmodified macromolecule-ligand interactions through spectroscopic titrations of fluorescent analogs.

Science.gov (United States)

Bujalowski, Wlodzimierz; Jezewska, Maria J

2011-01-01

Analysis of thermodynamically rigorous binding isotherms provides fundamental information about the energetics of the ligand-macromolecule interactions and often an invaluable insight about the structure of the formed complexes. The Macromolecular Competition Titration (MCT) method enables one to quantitatively obtain interaction parameters of protein-nucleic acid interactions, which may not be available by other methods, particularly for the unmodified long polymer lattices and specific nucleic acid substrates, if the binding is not accompanied by adequate spectroscopic signal changes. The method can be applied using different fluorescent nucleic acids or fluorophores, although the etheno-derivatives of nucleic acid are especially suitable as they are relatively easy to prepare, have significant blue fluorescence, their excitation band lies far from the protein absorption spectrum, and the modification eliminates the possibility of base pairing with other nucleic acids. The MCT method is not limited to the specific size of the reference nucleic acid. Particularly, a simple analysis of the competition titration experiments is described in which the fluorescent, short fragment of nucleic acid, spanning the exact site-size of the protein-nucleic acid complex, and binding with only a 1:1 stoichiometry to the protein, is used as a reference macromolecule. Although the MCT method is predominantly discussed as applied to studying protein-nucleic acid interactions, it can generally be applied to any ligand-macromolecule system by monitoring the association reaction using the spectroscopic signal originating from the reference macromolecule in the presence of the competing macromolecule, whose interaction parameters with the ligand are to be determined. Copyright © 2011 Elsevier Inc. All rights reserved.

Wired and Wireless Camera Triggering with Arduino

Science.gov (United States)

Kauhanen, H.; Rönnholm, P.

2017-10-01

Synchronous triggering is an important task that allows simultaneous data capture from multiple cameras. Accurate synchronization enables 3D measurements of moving objects or from a moving platform. In this paper, we describe one wired and four wireless variations of Arduino-based low-cost remote trigger systems designed to provide a synchronous trigger signal for industrial cameras. Our wireless systems utilize 315 MHz or 434 MHz frequencies with noise filtering capacitors. In order to validate the synchronization accuracy, we developed a prototype of a rotating trigger detection system (named RoTriDeS). This system is suitable to detect the triggering accuracy of global shutter cameras. As a result, the wired system indicated an 8.91 μs mean triggering time difference between two cameras. Corresponding mean values for the four wireless triggering systems varied between 7.92 and 9.42 μs. Presented values include both camera-based and trigger-based desynchronization. Arduino-based triggering systems appeared to be feasible, and they have the potential to be extended to more complicated triggering systems.

Triggering for charm, beauty, and truth

International Nuclear Information System (INIS)

Appel, J.A.

1982-02-01

As the search for more and more rare processes accelerates, the need for more and more effective event triggers also accelerates. In the earliest experiments, a simple coincidence often sufficed not only as the event trigger, but as the complete record of an event of interest. In today's experiments, not only has the fast trigger become more sophisticated, but one or more additional level of trigger processing precedes writing event data to magnetic tape for later analysis. Further search experiments will certainly require further expansion in the number of trigger levels required to filter those rare events of particular interest

AIDS radio triggers.

Science.gov (United States)

Elias, A M

1991-07-01

In April 1991, the Ethnic Communities' Council of NSW was granted funding under the Community AIDS Prevention and Education Program through the Department of Community Services and Health, to produce a series of 6x50 second AIDS radio triggers with a 10-second tag line for further information. The triggers are designed to disseminate culturally-sensitive information about HIV/AIDS in English, Italian, Greek, Spanish, Khmer, Turkish, Macedonian, Serbo-Croatian, Arabic, Cantonese, and Vietnamese, with the goal of increasing awareness and decreasing the degree of misinformation about HIV/AIDS among people of non-English-speaking backgrounds through radio and sound. The 6 triggers cover the denial that AIDS exists in the community, beliefs that words and feelings do not protect one from catching HIV, encouraging friends to be compassionate, compassion within the family, AIDS information for a young audience, and the provision of accurate and honest information on HIV/AIDS. The triggers are slated to be completed by the end of July 1991 and will be broadcast on all possible community, ethnic, and commercial radio networks across Australia. They will be available upon request in composite form with an information kit for use by health care professionals and community workers.

Application of Vector Triggering Random Decrement

DEFF Research Database (Denmark)

Asmussen, J. C.; Ibrahim, S. R.; Brincker, Rune

result is a Random Decrement function from each measurement. In traditional Random Decrement estimation the triggering condition is a scalar condition, which should only be fulfilled in a single measurement. In vector triggering Random Decrement the triggering condition is a vector condition......This paper deals with applications of the vector triggering Random Decrement technique. This technique is new and developed with the aim of minimizing estimation time and identification errors. The theory behind the technique is discussed in an accompanying paper. The results presented...... in this paper should be regarded as a further documentation of the technique. The key point in Random Decrement estimation is the formulation of a triggering condition. If the triggering condition is fulfilled a time segment from each measurement is picked out and averaged with previous time segments. The final...

Application of Vector Triggering Random Decrement

DEFF Research Database (Denmark)

Asmussen, J. C.; Ibrahim, S. R.; Brincker, Rune

1997-01-01

result is a Random Decrement function from each measurement. In traditional Random Decrement estimation the triggering condition is a scalar condition, which should only be fulfilled in a single measurement. In vector triggering Random Decrement the triggering condition is a vector condition......This paper deals with applications of the vector triggering Random Decrement technique. This technique is new and developed with the aim of minimizing estimation time and identification errors. The theory behind the technique is discussed in an accompanying paper. The results presented...... in this paper should be regarded as a further documentation of the technique. The key point in Random Decrement estimation is the formulation of a triggering condition. If the triggering condition is fulfilled a time segment from each measurement is picked out and averaged with previous time segments. The final...

Geometrical Acceptance Analysis for RPC PAC Trigger

CERN Document Server

Seo, Eunsung

2010-01-01

The CMS(Compact Muon Solenoid) is one of the four experiments that will analyze the collision results of the protons accelerated by the Large Hardron Collider(LHC) at CERN(Conseil Europen pour la Recherche Nuclaire). In case of the CMS experiment, the trigger system is divided into two stages : The Level-1 Trigger and High Level Trigger. The RPC(Resistive Plate Chamber) PAC(PAttern Comparator) Trigger system, which is a subject of this thesis, is a part of the Level-1 Muon Trigger System. Main task of the PAC Trigger is to identify muons, measures transverse momenta and select the best muon candidates for each proton bunch collision occurring every 25 ns. To calculate the value of PAC Trigger efficiency for triggerable muon, two terms of different efficiencies are needed ; acceptance efficiency and chamber efficiency. Main goal of the works described in this thesis is obtaining the acceptance efficiency of the PAC Trigger in each logical cone. Acceptance efficiency is a convolution of the chambers geometry an...

The ATLAS High Level Trigger Steering Framework and the Trigger Configuration System.

CERN Document Server

Perez Cavalcanti, Tiago; The ATLAS collaboration

2011-01-01

The ATLAS detector system installed in the Large Hadron Collider (LHC) at CERN is designed to study proton-proton and nucleus-nucleus collisions with a maximum centre of mass energy of 14 TeV at a bunch collision rate of 40MHz. In March 2010 the four LHC experiments saw the first proton-proton collisions at 7 TeV. Still within the year a collision rate of nearly 10 MHz is expected. At ATLAS, events of potential interest for ATLAS physics are selected by a three-level trigger system, with a final recording rate of about 200 Hz. The first level (L1) is implemented in custom hardware; the two levels of the high level trigger (HLT) are software triggers, running on large farms of standard computers and network devices. Within the ATLAS physics program more than 500 trigger signatures are defined. The HLT tests each signature on each L1-accepted event; the test outcome is recorded for later analysis. The HLT-Steering is responsible for this. It foremost ensures the independent test of each signature, guarantying u...

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

International Nuclear Information System (INIS)

Tsai, Yingssu; McPhillips, Scott E.; González, Ana; McPhillips, Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David; Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson, Keith O.; Soltis, S. Michael

2013-01-01

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully

Triggering the GRANDE array

International Nuclear Information System (INIS)

Wilson, C.L.; Bratton, C.B.; Gurr, J.; Kropp, W.; Nelson, M.; Sobel, H.; Svoboda, R.; Yodh, G.; Burnett, T.; Chaloupka, V.; Wilkes, R.J.; Cherry, M.; Ellison, S.B.; Guzik, T.G.; Wefel, J.; Gaidos, J.; Loeffler, F.; Sembroski, G.; Goodman, J.; Haines, T.J.; Kielczewska, D.; Lane, C.; Steinberg, R.; Lieber, M.; Nagle, D.; Potter, M.; Tripp, R.

1990-01-01

A brief description of the Gamma Ray And Neutrino Detector Experiment (GRANDE) is presented. The detector elements and electronics are described. The trigger logic for the array is then examined. The triggers for the Gamma Ray and the Neutrino portions of the array are treated separately. (orig.)

Calorimetry triggering in ATLAS

International Nuclear Information System (INIS)

Igonkina, O; Achenbach, R; Andrei, V; Adragna, P; Aharrouche, M; Bauss, B; Bendel, M; Alexandre, G; Anduaga, X; Aracena, I; Backlund, S; Bogaerts, A; Baines, J; Barnett, B M; Bee, C; P, Behera; Bell, P; Benslama, K; Berry, T; Bohm, C

2009-01-01

The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2 | 10 5 to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

Calorimetry Triggering in ATLAS

International Nuclear Information System (INIS)

Igonkina, O.; Achenbach, R.; Adragna, P.; Aharrouche, M.; Alexandre, G.; Andrei, V.; Anduaga, X.; Aracena, I.; Backlund, S.; Baines, J.; Barnett, B.M.; Bauss, B.; Bee, C.; Behera, P.; Bell, P.; Bendel, M.; Benslama, K.; Berry, T.; Bogaerts, A.; Bohm, C.; Bold, T.; Booth, J.R.A.; Bosman, M.; Boyd, J.; Bracinik, J.; Brawn, I.P.; Brelier, B.; Brooks, W.; Brunet, S.; Bucci, F.; Casadei, D.; Casado, P.; Cerri, A.; Charlton, D.G.; Childers, J.T.; Collins, N.J.; Conde Muino, P.; Coura Torres, R.; Cranmer, K.; Curtis, C.J.; Czyczula, Z.; Dam, M.; Damazio, D.; Davis, A.O.; De Santo, A.; Degenhardt, J.

2011-01-01

The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2/10 5 to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

Calorimetry triggering in ATLAS

Energy Technology Data Exchange (ETDEWEB)

Igonkina, O [Nikhef National Institute for Subatomic Physics, Amsterdam (Netherlands); Achenbach, R; Andrei, V [Kirchhoff Institut fuer Physik, Universitaet Heidelberg, Heidelberg (Germany); Adragna, P [Physics Department, Queen Mary, University of London, London (United Kingdom); Aharrouche, M; Bauss, B; Bendel, M [Institut fr Physik, Universitt Mainz, Mainz (Germany); Alexandre, G [Section de Physique, Universite de Geneve, Geneva (Switzerland); Anduaga, X [Universidad Nacional de La Plata, La Plata (Argentina); Aracena, I [Stanford Linear Accelerator Center (SLAC), Stanford (United States); Backlund, S; Bogaerts, A [European Laboratory for Particle Physics (CERN), Geneva (Switzerland); Baines, J; Barnett, B M [STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon (United Kingdom); Bee, C [Centre de Physique des Particules de Marseille, IN2P3-CNRS, Marseille (France); P, Behera [Iowa State University, Ames, Iowa (United States); Bell, P [School of Physics and Astronomy, University of Manchester, Manchester (United Kingdom); Benslama, K [University of Regina, Regina (Canada); Berry, T [Department of Physics, Royal Holloway and Bedford New College, Egham (United Kingdom); Bohm, C [Fysikum, Stockholm University, Stockholm (Sweden)

2009-04-01

The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2 | 10{sup 5} to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

The Run-2 ATLAS Trigger System

International Nuclear Information System (INIS)

Martínez, A Ruiz

2016-01-01

The ATLAS trigger successfully collected collision data during the first run of the LHC between 2009-2013 at different centre-of-mass energies between 900 GeV and 8TeV. The trigger system consists of a hardware Level-1 and a software-based high level trigger (HLT) that reduces the event rate from the design bunch-crossing rate of 40 MHz to an average recording rate of a few hundred Hz. In Run-2, the LHC will operate at centre-of-mass energies of 13 and 14 TeV and higher luminosity, resulting in up to five times higher rates of processes of interest. A brief review of the ATLAS trigger system upgrades that were implemented between Run-1 and Run-2, allowing to cope with the increased trigger rates while maintaining or even improving the efficiency to select physics processes of interest, will be given. This includes changes to the Level-1 calorimeter and muon trigger systems, the introduction of a new Level-1 topological trigger module and the merging of the previously two-level HLT system into a single event processing farm. A few examples will be shown, such as the impressive performance improvements in the HLT trigger algorithms used to identify leptons, hadrons and global event quantities like missing transverse energy. Finally, the status of the commissioning of the trigger system and its performance during the 2015 run will be presented. (paper)

The ATLAS Electron and Photon Trigger

CERN Document Server

Jones, Samuel David; The ATLAS collaboration

2017-01-01

Electron and photon triggers covering transverse energies from 5 GeV to several TeV are essential for signal selection in a wide variety of ATLAS physics analyses to study Standard Model processes and to search for new phenomena. Final states including leptons and photons had, for example, an important role in the discovery and measurement of the Higgs boson. Dedicated triggers are also used to collect data for calibration, efficiency and fake rate measurements. The ATLAS trigger system is divided in a hardware-based Level-1 trigger and a software-based high-level trigger, both of which were upgraded during the LHC shutdown in preparation for Run-2 operation. To cope with the increasing luminosity and more challenging pile-up conditions at a center-of-mass energy of 13 TeV, the trigger selections at each level are optimized to control the rates and keep efficiencies high. To achieve this goal multivariate analysis techniques are used. The ATLAS electron and photon triggers and their performance with Run 2 dat...

The ATLAS Electron and Photon Trigger

CERN Document Server

Jones, Samuel David; The ATLAS collaboration

2018-01-01

Electron and photon triggers covering transverse energies from 5 GeV to several TeV are essential for signal selection in a wide variety of ATLAS physics analyses to study Standard Model processes and to search for new phenomena. Final states including leptons and photons had, for example, an important role in the discovery and measurement of the Higgs boson. Dedicated triggers are also used to collect data for calibration, efficiency and fake rate measurements. The ATLAS trigger system is divided in a hardware-based Level-1 trigger and a software-based high-level trigger, both of which were upgraded during the LHC shutdown in preparation for Run-2 operation. To cope with the increasing luminosity and more challenging pile-up conditions at a center-of-mass energy of 13 TeV, the trigger selections at each level are optimized to control the rates and keep efficiencies high. To achieve this goal multivariate analysis techniques are used. The ATLAS electron and photon triggers and their performance with Run 2 dat...

The DOe Silicon Track Trigger

International Nuclear Information System (INIS)

Steinbrueck, Georg

2003-01-01

We describe a trigger preprocessor to be used by the DOe experiment for selecting events with tracks from the decay of long-lived particles. This Level 2 impact parameter trigger utilizes information from the Silicon Microstrip Tracker to reconstruct tracks with improved spatial and momentum resolutions compared to those obtained by the Level 1 tracking trigger. It is constructed of VME boards with much of the logic existing in programmable processors. A common motherboard provides the I/O infrastructure and three different daughter boards perform the tasks of identifying the roads from the tracking trigger data, finding the clusters in the roads in the silicon detector, and fitting tracks to the clusters. This approach provides flexibility for the design, testing and maintenance phases of the project. The track parameters are provided to the trigger framework in 25 μs. The effective impact parameter resolution for high-momentum tracks is 35 μm, dominated by the size of the Tevatron beam

Review Document: Full Software Trigger

CERN Document Server

Albrecht, J; Raven, G

2014-01-01

This document presents a trigger system for the upgraded LHCb detector, scheduled to begin operation in 2020. This document serves as input for the internal review towards the "DAQ, online and trigger TDR". The proposed trigger system is implemented entirely in software. In this document we show that track reconstruction of a similar quality to that available in the offline algorithms can be performed on the full inelastic $pp$-collision rate, without prior event selections implemented in custom hardware and without relying upon a partial event reconstruction. A track nding eciency of 98.8 % relative to oine can be achieved for tracks with $p_T >$ 500 MeV/$c$. The CPU time required for this reconstruction is about 40 % of the available budget. Proof-of-principle selections are presented which demonstrate that excellent performance is achievable using an inclusive beauty trigger, in addition to exclusive beauty and charm triggers. Finally, it is shown that exclusive beauty and charm selections that do not intr...

Macromolecular Crystal Growth by Means of Microfluidics

Science.gov (United States)

vanderWoerd, Mark; Ferree, Darren; Spearing, Scott; Monaco, Lisa; Molho, Josh; Spaid, Michael; Brasseur, Mike; Curreri, Peter A. (Technical Monitor)

2002-01-01

We have performed a feasibility study in which we show that chip-based, microfluidic (LabChip(TM)) technology is suitable for protein crystal growth. This technology allows for accurate and reliable dispensing and mixing of very small volumes while minimizing bubble formation in the crystallization mixture. The amount of (protein) solution remaining after completion of an experiment is minimal, which makes this technique efficient and attractive for use with proteins, which are difficult or expensive to obtain. The nature of LabChip(TM) technology renders it highly amenable to automation. Protein crystals obtained in our initial feasibility studies were of excellent quality as determined by X-ray diffraction. Subsequent to the feasibility study, we designed and produced the first LabChip(TM) device specifically for protein crystallization in batch mode. It can reliably dispense and mix from a range of solution constituents into two independent growth wells. We are currently testing this design to prove its efficacy for protein crystallization optimization experiments. In the near future we will expand our design to incorporate up to 10 growth wells per LabChip(TM) device. Upon completion, additional crystallization techniques such as vapor diffusion and liquid-liquid diffusion will be accommodated. Macromolecular crystallization using microfluidic technology is envisioned as a fully automated system, which will use the 'tele-science' concept of remote operation and will be developed into a research facility for the International Space Station as well as on the ground.

Mix and Inject: Reaction Initiation by Diffusion for Time-Resolved Macromolecular Crystallography

Directory of Open Access Journals (Sweden)

Marius Schmidt

2013-01-01

Full Text Available Time-resolved macromolecular crystallography unifies structure determination with chemical kinetics, since the structures of transient states and chemical and kinetic mechanisms can be determined simultaneously from the same data. To start a reaction in an enzyme, typically, an initially inactive substrate present in the crystal is activated. This has particular disadvantages that are circumvented when active substrate is directly provided by diffusion. However, then it is prohibitive to use macroscopic crystals because diffusion times become too long. With small micro- and nanocrystals diffusion times are adequately short for most enzymes and the reaction can be swiftly initiated. We demonstrate here that a time-resolved crystallographic experiment becomes feasible by mixing substrate with enzyme nanocrystals which are subsequently injected into the X-ray beam of a pulsed X-ray source.

Structure analysis of molecular systems in the Institute of Macromolecular Chemistry of the Czech Academy of Sciences

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich

2010-01-01

Roč. 17, 2a (2010), k32-k34 ISSN 1211-5894. [Struktura 2010. Soláň, 14.06.2010-17.06.2010] R&D Projects: GA AV ČR IAA500500701; GA ČR GA305/07/1073 Institutional research plan: CEZ:AV0Z40500505 Keywords : Academy of Sciences of the Czech Republic * X-ray structure analysis * crystallography Subject RIV: CD - Macromolecular Chemistry http:// xray .cz/ms/bul2010-2a/hasek.pdf

The ATLAS hadronic tau trigger

International Nuclear Information System (INIS)

Shamim, Mansoora

2012-01-01

The extensive tau physics programs of the ATLAS experiment relies heavily on trigger to select hadronic decays of tau lepton. Such a trigger is implemented in ATLAS to efficiently collect signal events, while keeping the rate of multi-jet background within the allowed bandwidth. This contribution summarizes the performance of the ATLAS hadronic tau trigger system during 2011 data taking period and improvements implemented for the 2012 data collection.

Involvement of Prohibitin Upregulation in Abrin-Triggered Apoptosis

Directory of Open Access Journals (Sweden)

Yu-Huei Liu

2012-01-01

Full Text Available Abrin (ABR, a protein purified from the seeds of Abrus precatorius, induces apoptosis in various types of cancer cells. However, the detailed mechanism remains largely uncharacterized. By using a cDNA microarray platform, we determined that prohibitin (PHB, a tumor suppressor protein, is significantly upregulated in ABR-triggered apoptosis. ABR-induced upregulation of PHB is mediated by the stress-activated protein kinase/c-Jun NH2-terminal kinase (SAPK/JNK pathway, as demonstrated by chemical inhibitors. In addition, ABR significantly induced the expression of Bax as well as the activation of caspase-3 and poly(ADP-ribose polymerase (PARP in Jurkat T cells, whereas the reduction of PHB by specific RNA interference delayed ABR-triggered apoptosis through the proapoptotic genes examined. Moreover, our results also indicated that nuclear translocation of the PHB-p53 complex may play a role in the transcription of Bax. Collectively, our data show that PHB plays a role in ABR-induced apoptosis, which may be helpful for the development of diagnostic or therapeutic agents.

pH-controlled self-assembling of meso-tetrakis(4-sulfonatophenyl)porphyrin-chitosan complexes

Czech Academy of Sciences Publication Activity Database

Synytsya, A.; Synytsya, Andriy.; Blafková, P.; Ederová, J.; Spěváček, Jiří; Slepička, P.; Král, V.; Volka, K.

2009-01-01

Roč. 10, č. 5 (2009), s. 1067-1076 ISSN 1525-7797 R&D Projects: GA ČR GA525/05/0273 Grant - others:GA AV ČR(CZ) KAN400480701; GA AV ČR(CZ) KAN200100801; GA AV ČR(CZ) KAN200200651; GA MŠk(CZ) LC06041; GA ČR(CZ) GA203/02/0420 Program:KA; KA; KA; LC; GA Institutional research plan: CEZ:AV0Z40500505 Keywords : self-assembling * meso-tetrakis(4-sulfonatophenyl)porphyrin- chitosan complex * spectroscopy Subject RIV: CD - Macromolecular Chemistry Impact factor: 4.502, year: 2009

Global search of triggered non-volcanic tremor

Science.gov (United States)

Chao, Tzu-Kai Kevin

Deep non-volcanic tremor is a newly discovered seismic phenomenon with low amplitude, long duration, and no clear P- and S-waves as compared with regular earthquake. Tremor has been observed at many major plate-boundary faults, providing new information about fault slip behaviors below the seismogenic zone. While tremor mostly occurs spontaneously (ambient tremor) or during episodic slow-slip events (SSEs), sometimes tremor can also be triggered during teleseismic waves of distance earthquakes, which is known as "triggered tremor". The primary focus of my Ph.D. work is to understand the physical mechanisms and necessary conditions of triggered tremor by systematic investigations in different tectonic regions. In the first chapter of my dissertation, I conduct a systematic survey of triggered tremor beneath the Central Range (CR) in Taiwan for 45 teleseismic earthquakes from 1998 to 2009 with Mw ≥ 7.5. Triggered tremors are visually identified as bursts of high-frequency (2-8 Hz), non-impulsive, and long-duration seismic energy that are coherent among many seismic stations and modulated by the teleseismic surface waves. A total of 9 teleseismic earthquakes has triggered clear tremor in Taiwan. The peak ground velocity (PGV) of teleseismic surface waves is the most important factor in determining tremor triggering potential, with an apparent threshold of ˜0.1 cm/s, or 7-8 kPa. However, such threshold is partially controlled by the background noise level, preventing triggered tremor with weaker amplitude from being observed. In addition, I find a positive correlation between the PGV and the triggered tremor amplitude, which is consistent with the prediction of the 'clock-advance' model. This suggests that triggered tremor can be considered as a sped-up occurrence of ambient tremor under fast loading from the passing surface waves. Finally, the incident angles of surface waves also play an important rule in controlling the tremor triggering potential. The next

HACE1 Negatively Regulates Virus-Triggered Type I IFN Signaling by Impeding the Formation of the MAVS-TRAF3 Complex

Directory of Open Access Journals (Sweden)

He-Ting Mao

2016-05-01

Full Text Available During virus infection, the cascade signaling pathway that leads to the production of proinflammatory cytokines is controlled at multiple levels to avoid detrimental overreaction. HACE1 has been characterized as an important tumor suppressor. Here, we identified HACE1 as an important negative regulator of virus-triggered type I IFN signaling. Overexpression of HACE1 inhibited Sendai virus- or poly (I:C-induced signaling and resulted in reduced IFNB1 production and enhanced virus replication. Knockdown of HACE1 expression exhibited the opposite effects. Ubiquitin E3 ligase activity of the dead mutant HACE1/C876A had a comparable inhibitory function as WT HACE1, suggesting that the suppressive function of HACE1 on virus-induced signaling is independent of its E3 ligase activity. Further study indicated that HACE1 acted downstream of MAVS and upstream of TBK1. Mechanistic studies showed that HACE1 exerts its inhibitory role on virus-induced signaling by disrupting the MAVS-TRAF3 complex. Therefore, we uncovered a novel function of HACE1 in innate immunity regulation.

The CLEO-III Trigger: Decision and gating

International Nuclear Information System (INIS)

Bergfeld, T.J.; Gollin, G.D.; Haney, M.J.

1996-01-01

The CLEO-III Trigger provides a trigger decision every 42ns, with a latency of approximately 2.5μs. This paper describes the free-running, pipelined trigger decision logic, the throttling mechanism whereby the data acquisition system can modulate the trigger rate to maximize throughput without buffer overrun, and the subsequent signal distribution mechanism for delivering the trigger decision to the front-end electronics. This paper also describes the multilevel simulation methods employed to allow detailed low-level models of trigger components to be co-simulated with more abstract system models, thus allowing full system modeling without incurring prohibitive computational overheads

Triggers in UA2 and UA1

International Nuclear Information System (INIS)

Dorenbosch, J.

1985-01-01

The UA2 and UA1 trigger systems are described as they will be used after the upgrade of the CERN SPPS. The luminosity of the collider will increase to 3x10 30 . The bunch spacing is 4 microseconds, comparable to the time available for a second level trigger at the SSC. The first level triggers are very powerful and deliver trigger rates of about 100 Hz. The UA1 second level trigger operates on the final digitizings with a combination of special and general purpose processors. At the highest trigger levels a small farm of processors performs the final reduction. (orig.)

Concept of the CMS Trigger Supervisor

CERN Document Server

Magrans de Abril, Ildefons; Varela, Joao

2006-01-01

The Trigger Supervisor is an online software system designed for the CMS experiment at CERN. Its purpose is to provide a framework to set up, test, operate and monitor the trigger components on one hand and to manage their interplay and the information exchange with the run control part of the data acquisition system on the other. The Trigger Supervisor is conceived to provide a simple and homogeneous client interface to the online software infrastructure of the trigger subsystems. This document specifies the functional and non-functional requirements, design and operational details, and the components that will be delivered in order to facilitate a smooth integration of the trigger software in the context of CMS.

Stretchable All-Gel-State Fiber-Shaped Supercapacitors Enabled by Macromolecularly Interconnected 3D Graphene/Nanostructured Conductive Polymer Hydrogels.

Science.gov (United States)

Li, Panpan; Jin, Zhaoyu; Peng, Lele; Zhao, Fei; Xiao, Dan; Jin, Yong; Yu, Guihua

2018-05-01

Nanostructured conductive polymer hydrogels (CPHs) have been extensively applied in energy storage owing to their advantageous features, such as excellent electrochemical activity and relatively high electrical conductivity, yet the fabrication of self-standing and flexible electrode-based CPHs is still hampered by their limited mechanical properties. Herein, macromolecularly interconnected 3D graphene/nanostructured CPH is synthesized via self-assembly of CPHs and graphene oxide macrostructures. The 3D hybrid hydrogel shows uniform interconnectivity and enhanced mechanical properties due to the strong macromolecular interaction between the CPHs and graphene, thus greatly reducing aggregation in the fiber-shaping process. A proof-of-concept all-gel-state fibrous supercapacitor based on the 3D polyaniline/graphene hydrogel is fabricated to demonstrate the outstanding flexibility and mouldability, as well as superior electrochemical properties enabled by this 3D hybrid hydrogel design. The proposed device can achieve a large strain (up to ≈40%), and deliver a remarkable volumetric energy density of 8.80 mWh cm -3 (at power density of 30.77 mW cm -3 ), outperforming many fiber-shaped supercapacitors reported previously. The all-hydrogel design opens up opportunities in the fabrication of next-generation wearable and portable electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Implementation of fast macromolecular proton fraction mapping on 1.5 and 3 Tesla clinical MRI scanners: preliminary experience

Science.gov (United States)

Yarnykh, V.; Korostyshevskaya, A.

2017-08-01

Macromolecular proton fraction (MPF) is a biophysical parameter describing the amount of macromolecular protons involved into magnetization exchange with water protons in tissues. MPF represents a significant interest as a magnetic resonance imaging (MRI) biomarker of myelin for clinical applications. A recent fast MPF mapping method enabled clinical translation of MPF measurements due to time-efficient acquisition based on the single-point constrained fit algorithm. However, previous MPF mapping applications utilized only 3 Tesla MRI scanners and modified pulse sequences, which are not commonly available. This study aimed to test the feasibility of MPF mapping implementation on a 1.5 Tesla clinical scanner using standard manufacturer’s sequences and compare the performance of this method between 1.5 and 3 Tesla scanners. MPF mapping was implemented on 1.5 and 3 Tesla MRI units of one manufacturer with either optimized custom-written or standard product pulse sequences. Whole-brain three-dimensional MPF maps obtained from a single volunteer were compared between field strengths and implementation options. MPF maps demonstrated similar quality at both field strengths. MPF values in segmented brain tissues and specific anatomic regions appeared in close agreement. This experiment demonstrates the feasibility of fast MPF mapping using standard sequences on 1.5 T and 3 T clinical scanners.

Macromolecular refinement by model morphing using non-atomic parameterizations.

Science.gov (United States)

Cowtan, Kevin; Agirre, Jon

2018-02-01

Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.

Structural changes in the ordering processes of macromolecular compounds

International Nuclear Information System (INIS)

Kobayashi, M.; Tashiro, K.

1998-01-01

In order to clarify the microscopically-viewed relationship between the conformational ordering process and the aggregation process of the macromolecular chains in the phase transitions from melt to solid or from solution to gel, the time-resolved Fourier-transform infrared spectra and small-angle X-ray or neutron scattering data have been analyzed in an organized manner. Two concrete examples were presented. (1) In the gelation phenomenon of syndiotactic polystyrene-organic solvent system, the ordered TTGG conformation is formed and develops with time. This conformational ordering is accelerated by the aggregation of these chain segments, resulting in the formation of macroscopic gel network. (2) In the isothermal crystallization process from the melt of polyethylene, the following ordering mechanism was revealed. The conformationally-disordered short trans conformers appear at first in the random coils of the melt. These disordered trans sequences grow to longer and more regular trans sequences of the orthorhombic-type crystal and then the isolated lamellae are formed. Afterwards, the stacked lamellar structure is developed without change of lamellar thickness but with small decrease in the long period, indicating an insertion of new lamellae between the already produced lamellar layers

The ZEUS calorimeter first level trigger

International Nuclear Information System (INIS)

Smith, W.H.; Ali, I.; Behrens, B.; Fordham, C.; Foudas, C.; Goussiou, A.; Jaworski, M.; Kinnel, T.; Lackey, J.; Robl, P.; Silverstein, S.; Dawson, J.W.; Krakauer, D.A.; Talaga, R.L.; Schlereth, J.L.

1994-10-01

The design of the ZEUS Calorimeter First Level Trigger (CFLT) is presented. The CFLT utilizes a pipelined architecture to provide trigger data for a global first leel trigger decision 5 μsec after each beam crossing, occurring every 96 nsec. The charges from 13K phototubes are summed into 1792 trigger tower pulseheights which are digitized by flash ADC's. The digital values are linearized, stored and used for sums and pattern tests. Summary data is forwarded to the Global First Level Trigger for each crossing 2 μsec after the crossing occurred. The CFLT determines the total energy, the total transverse energy, the missing energy, and the energy and number of isolated electrons and muons. It also provides information on the electromagnetic and hadronic energy deposited in various regions of the calorimeter. The CFLT has kept the experimental trigger rate below ∼200 Hz at the highest luminosity experienced at HERA. Performance studies suggest that the CFLT will keep the trigger rate below 1 kHZ against a rate of proton-beam gas interactions on the order of the 100 kHz expected at design luminosity. (orig.)

Trigger Menu in 2017

CERN Document Server

The ATLAS collaboration

2018-01-01

This document summarises the trigger menu deployed by the ATLAS experiment during 2017 data taking at proton-proton collision centre-of-mass energies of $\\sqrt{s}=13$ TeV and $\\sqrt{s}=5$ TeV at the LHC and describes the improvements with respect to the trigger system and menu used in 2016 data taking.

Intelligent trigger processor for the crystal box

International Nuclear Information System (INIS)

Sanders, G.H.; Butler, H.S.; Cooper, M.D.

1981-01-01

A large solid angle modular NaI(Tl) detector with 432 phototubes and 88 trigger scintillators is being used to search simultaneously for three lepton flavor changing decays of muon. A beam of up to 10 6 muons stopping per second with a 6% duty factor would yield up to 1000 triggers per second from random triple coincidences. A reduction of the trigger rate to 10 Hz is required from a hardwired primary trigger processor described in this paper. Further reduction to < 1 Hz is achieved by a microprocessor based secondary trigger processor. The primary trigger hardware imposes voter coincidence logic, stringent timing requirements, and a non-adjacency requirement in the trigger scintillators defined by hardwired circuits. Sophisticated geometric requirements are imposed by a PROM-based matrix logic, and energy and vector-momentum cuts are imposed by a hardwired processor using LSI flash ADC's and digital arithmetic loci. The secondary trigger employs four satellite microprocessors to do a sparse data scan, multiplex the data acquisition channels and apply additional event filtering

The ATLAS Level-1 Topological Trigger Performance

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00371751; The ATLAS collaboration

2016-01-01

The LHC will collide protons in the ATLAS detector with increasing luminosity through 2016, placing stringent operational and physical requirements to the ATLAS trigger system in order to reduce the 40 MHz collision rate to a manageable event storage rate of 1 kHz, while not rejecting interesting physics events. The Level-1 trigger is the first rate-reducing step in the ATLAS trigger system with an output rate of 100 kHz and decision latency smaller than 2.5 μs. It consists of a calorimeter trigger, muon trigger and a central trigger processor. During the LHC shutdown after the Run 1 finished in 2013, the Level-1 trigger system was upgraded including hardware, firmware and software updates. In particular, new electronics modules were introduced in the real-time data processing path: the Topological Processor System (L1Topo). It consists of a single AdvancedCTA shelf equipped with two Level-1 topological processor blades. They receive real-time information from the Level-1 calorimeter and muon triggers, which...

The ATLAS trigger high-level trigger commissioning and operation during early data taking

CERN Document Server

Goncalo, R

2008-01-01

The ATLAS experiment is one of the two general-purpose experiments due to start operation soon at the Large Hadron Collider (LHC). The LHC will collide protons at a centre of mass energy of 14~TeV, with a bunch-crossing rate of 40~MHz. The ATLAS three-level trigger will reduce this input rate to match the foreseen offline storage capability of 100-200~Hz. After the Level 1 trigger, which is implemented in custom hardware, the High-Level Trigger (HLT) further reduces the rate from up to 100~kHz to the offline storage rate while retaining the most interesting physics. The HLT is implemented in software running in commercially available computer farms and consists of Level 2 and Event Filter. To reduce the network data traffic and the processing time to manageable levels, the HLT uses seeded, step-wise reconstruction, aiming at the earliest possible rejection. Data produced during LHC commissioning will be vital for calibrating and aligning sub-detectors, as well as for testing the ATLAS trigger and setting up t...

Investigation of index finger triggering force using a cadaver experiment: Effects of trigger grip span, contact location, and internal tendon force.

Science.gov (United States)

Chang, Joonho; Freivalds, Andris; Sharkey, Neil A; Kong, Yong-Ku; Mike Kim, H; Sung, Kiseok; Kim, Dae-Min; Jung, Kihyo

2017-11-01

A cadaver study was conducted to investigate the effects of triggering conditions (trigger grip span, contact location, and internal tendon force) on index finger triggering force and the force efficiency of involved tendons. Eight right human cadaveric hands were employed, and a motion simulator was built to secure and control the specimens. Index finger triggering forces were investigated as a function of different internal tendon forces (flexor digitorum profundus + flexor digitorum superficialis = 40, 70, and 100 N), trigger grip spans (40, 50, and 60 mm), and contact locations between the index finger and a trigger. Triggering forces significantly increased when internal tendon forces increased from 40 to 100 N. Also, trigger grip spans and contact locations had significant effects on triggering forces; maximum triggering forces were found at a 50 mm span and the most proximal contact location. The results revealed that only 10-30% of internal tendon forces were converted to their external triggering forces. Copyright © 2017 Elsevier Ltd. All rights reserved.

Macromolecular crystallography with a large format CMOS detector

Energy Technology Data Exchange (ETDEWEB)

Nix, Jay C., E-mail: jcnix@lbl.gov [Molecular Biology Consortium 12003 S. Pulaski Rd. #166 Alsip, IL 60803 U.S.A (United States)

2016-07-27

Recent advances in CMOS technology have allowed the production of large surface area detectors suitable for macromolecular crystallography experiments [1]. The Molecular Biology Consortium (MBC) Beamline 4.2.2 at the Advanced Light Source in Berkeley, CA, has installed a 2952 x 2820 mm RDI CMOS-8M detector with funds from NIH grant S10OD012073. The detector has a 20nsec dead pixel time and performs well with shutterless data collection strategies. The sensor obtains sharp point response and minimal optical distortion by use of a thin fiber-optic plate between the phosphor and sensor module. Shutterless data collections produce high-quality redundant datasets that can be obtained in minutes. The fine-sliced data are suitable for processing in standard crystallographic software packages (XDS, HKL2000, D*TREK, MOSFLM). Faster collection times relative to the previous CCD detector have resulted in a record number of datasets collected in a calendar year and de novo phasing experiments have resulted in publications in both Science and Nature [2,3]. The faster collections are due to a combination of the decreased overhead requirements of shutterless collections combined with exposure times that have decreased by over a factor of 2 for images with comparable signal to noise of the NOIR-1 detector. The overall increased productivity has allowed the development of new beamline capabilities and data collection strategies.

Hierarchical trigger of the ALICE calorimeters

CERN Document Server

Muller, Hans; Novitzky, Norbert; Kral, Jiri; Rak, Jan; Schambach, Joachim; Wang, Ya-Ping; Wang, Dong; Zhou, Daicui

2010-01-01

The trigger of the ALICE electromagnetic calorimeters is implemented in 2 hierarchically connected layers of electronics. In the lower layer, level-0 algorithms search shower energy above threshold in locally confined Trigger Region Units (TRU). The top layer is implemented as a single, global trigger unit that receives the trigger data from all TRUs as input to the level-1 algorithm. This architecture was first developed for the PHOS high pT photon trigger before it was adopted by EMCal also for the jet trigger. TRU units digitize up to 112 analogue input signals from the Front End Electronics (FEE) and concentrate their digital stream in a single FPGA. A charge and time summing algorithm is combined with a peakfinder that suppresses spurious noise and is precise to single LHC bunches. With a peak-to-peak noise level of 150 MeV the linear dynamic range above threshold spans from MIP energies at 215 up to 50 GeV. Local level-0 decisions take less than 600 ns after LHC collisions, upon which all TRUs transfer ...

Level-1 Calorimeter Trigger starts firing

CERN Multimedia

Stephen Hillier

2007-01-01

L1Calo is one of the major components of ATLAS First Level trigger, along with the Muon Trigger and Central Trigger Processor. It forms all of the first-level calorimeter-based triggers, including electron, jet, tau and missing ET. The final system consists of over 250 custom designed 9U VME boards, most containing a dense array of FPGAs or ASICs. It is subdivided into a PreProcessor, which digitises the incoming trigger signals from the Liquid Argon and Tile calorimeters, and two separate processor systems, which perform the physics algorithms. All of these are highly flexible, allowing the possibility to adapt to beam conditions and luminosity. All parts of the system are read out through Read-Out Drivers, which provide monitoring data and Region of Interest (RoI) information for the Level-2 trigger. Production of the modules is now essentially complete, and enough modules exist to populate the full scale system in USA15. Installation is proceeding rapidly - approximately 90% of the final modules are insta...

The molecular complex associated with the Galactic H II region Sh2-90: a possible site of triggered star formation

Science.gov (United States)

Samal, M. R.; Zavagno, A.; Deharveng, L.; Molinari, S.; Ojha, D. K.; Paradis, D.; Tigé, J.; Pandey, A. K.; Russeil, D.

2014-06-01

Aims: We investigate the star formation activity in the molecular complex associated with the Galactic H ii region Sh2-90. Methods: We obtain the distribution of the ionized and cold neutral gas using radio-continuum and Herschel observations. We use near-infrared and Spitzer data to investigate the stellar content of the complex. We discuss the evolutionary status of embedded massive young stellar objects (MYSOs) using their spectral energy distribution. Results: The Sh2-90 region presents a bubble morphology in the mid-infrared. Radio observations suggest it is an evolved H ii region with an electron density ~144 cm-3, emission measure ~ 6.7 × 104 cm-6 pc and an ionized mass ~55 M⊙. From Herschel and CO (J = 3 - 2) observations we found that the H ii region is part of an elongated extended molecular cloud (H2 column density ≥ 3 × 1021 cm-2 and dust temperature 18-27 K) of total mass ≥ 1 × 104 M⊙. We identify the ionizing cluster of Sh2-90, the main exciting star being an O8-O9 V star. Five cold dust clumps, four mid-IR blobs around B stars, and a compact H ii region are found at the edge of the bubble. The velocity information derived from CO data cubes suggest that most of them are associated with the Sh2-90 region. One hundred and twenty-nine low mass (≤3 M⊙) YSOs have been identified, and they are found to be distributed mostly in the regions of high column density. Four candidate Class 0/I MYSOs have been found. We suggest that multi-generation star formation is present in the complex. From evidence of interaction, time scales involved, and evolutionary status of stellar/protostellar sources, we argue that the star formation at the edges of Sh2-90 might have been triggered. However, several young sources in this complex are probably formed by some other processes. Full Table 5 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/566/A122

Warning Triggers in Environmental Hazards: Who Should Be Warned to Do What and When?

Science.gov (United States)

Cova, Thomas J; Dennison, Philip E; Li, Dapeng; Drews, Frank A; Siebeneck, Laura K; Lindell, Michael K

2017-04-01

Determining the most effective public warnings to issue during a hazardous environmental event is a complex problem. Three primary questions need to be answered: Who should take protective action? What is the best action? and When should this action be initiated? Warning triggers provide a proactive means for emergency managers to simultaneously answer these questions by recommending that a target group take a specified protective action if a preset environmental trigger condition occurs (e.g., warn a community to evacuate if a wildfire crosses a proximal ridgeline). Triggers are used to warn the public across a wide variety of environmental hazards, and an improved understanding of their nature and role promises to: (1) advance protective action theory by unifying the natural, built, and social themes in hazards research into one framework, (2) reveal important information about emergency managers' risk perception, situational awareness, and threat assessment regarding threat behavior and public response, and (3) advance spatiotemporal models for representing the geography and timing of disaster warning and response (i.e., a coupled natural-built-social system). We provide an overview and research agenda designed to advance our understanding and modeling of warning triggers. © 2016 Society for Risk Analysis.

The CDF level-3 trigger

International Nuclear Information System (INIS)

Devlin, T.

1993-01-01

The Collider Detector at Fermilab (CDF) has been operating at the Tevatron and collecting data on proton-antiproton interactions with collision rates above 250,000 Hz. Three levels of filtering select events for data logging at a rate of about 4 Hz. The Level 3 trigger provides most of the capabilities of the offline production programs for event reconstruction and physics analysis. The type of physics triggers, application of cuts, and combinations of logical requirements for event selection are controlled at run time by a trigger table using a syntax fully integrated with the Level 1 and Level 2 hardware triggers. The level 3 software operates in 48 RISC/UNIX processors (over 1000 mips) served by four 20-MByte/sec data buses for input, output and control. The system architecture, debugging, code validation, error reporting, analysis capabilities and performance will be described

Pathogen-triggered ethylene signaling mediates systemic-induced susceptibility to herbivory in Arabidopsis.

Science.gov (United States)

Groen, Simon C; Whiteman, Noah K; Bahrami, Adam K; Wilczek, Amity M; Cui, Jianping; Russell, Jacob A; Cibrian-Jaramillo, Angelica; Butler, Ian A; Rana, Jignasha D; Huang, Guo-Hua; Bush, Jenifer; Ausubel, Frederick M; Pierce, Naomi E

2013-11-01

Multicellular eukaryotic organisms are attacked by numerous parasites from diverse phyla, often simultaneously or sequentially. An outstanding question in these interactions is how hosts integrate signals induced by the attack of different parasites. We used a model system comprised of the plant host Arabidopsis thaliana, the hemibiotrophic bacterial phytopathogen Pseudomonas syringae, and herbivorous larvae of the moth Trichoplusia ni (cabbage looper) to characterize mechanisms involved in systemic-induced susceptibility (SIS) to T. ni herbivory caused by prior infection by virulent P. syringae. We uncovered a complex multilayered induction mechanism for SIS to herbivory. In this mechanism, antiherbivore defenses that depend on signaling via (1) the jasmonic acid-isoleucine conjugate (JA-Ile) and (2) other octadecanoids are suppressed by microbe-associated molecular pattern-triggered salicylic acid (SA) signaling and infection-triggered ethylene signaling, respectively. SIS to herbivory is, in turn, counteracted by a combination of the bacterial JA-Ile mimic coronatine and type III virulence-associated effectors. Our results show that SIS to herbivory involves more than antagonistic signaling between SA and JA-Ile and provide insight into the unexpectedly complex mechanisms behind a seemingly simple trade-off in plant defense against multiple enemies.

MR imaging findings of trigger thumb

Energy Technology Data Exchange (ETDEWEB)

Chang, Eric Y.; Chen, Karen C.; Chung, Christine B. [VA San Diego Healthcare System, Radiology Service, San Diego, CA (United States); University of California, San Diego Medical Center, Department of Radiology, San Diego, CA (United States)

2015-08-15

Trigger finger (or trigger thumb), also known as sclerosing tenosynovitis, is a common clinical diagnosis that rarely presents for imaging. Because of this selection bias, many radiologists may not be familiar with the process. Furthermore, patients who do present for imaging frequently have misleading examination indications. To our knowledge, magnetic resonance (MR) imaging findings of trigger thumb have not been previously reported in the literature. In this article, we review the entity of trigger thumb, the anatomy involved, and associated imaging findings, which include flexor pollicis longus tendinosis with a distinct nodule, A1 pulley thickening, and tenosynovitis. In addition, in some cases, an abnormal Av pulley is apparent. In the rare cases of trigger finger that present for MR imaging, accurate diagnosis by the radiologist can allow initiation of treatment and avoid further unnecessary workup. (orig.)

MR imaging findings of trigger thumb

International Nuclear Information System (INIS)

Chang, Eric Y.; Chen, Karen C.; Chung, Christine B.

2015-01-01

Trigger finger (or trigger thumb), also known as sclerosing tenosynovitis, is a common clinical diagnosis that rarely presents for imaging. Because of this selection bias, many radiologists may not be familiar with the process. Furthermore, patients who do present for imaging frequently have misleading examination indications. To our knowledge, magnetic resonance (MR) imaging findings of trigger thumb have not been previously reported in the literature. In this article, we review the entity of trigger thumb, the anatomy involved, and associated imaging findings, which include flexor pollicis longus tendinosis with a distinct nodule, A1 pulley thickening, and tenosynovitis. In addition, in some cases, an abnormal Av pulley is apparent. In the rare cases of trigger finger that present for MR imaging, accurate diagnosis by the radiologist can allow initiation of treatment and avoid further unnecessary workup. (orig.)

Elastic Network Model of a Nuclear Transport Complex

Science.gov (United States)

Ryan, Patrick; Liu, Wing K.; Lee, Dockjin; Seo, Sangjae; Kim, Young-Jin; Kim, Moon K.

2010-05-01

The structure of Kap95p was obtained from the Protein Data Bank (www.pdb.org) and analyzed RanGTP plays an important role in both nuclear protein import and export cycles. In the nucleus, RanGTP releases macromolecular cargoes from importins and conversely facilitates cargo binding to exportins. Although the crystal structure of the nuclear import complex formed by importin Kap95p and RanGTP was recently identified, its molecular mechanism still remains unclear. To understand the relationship between structure and function of a nuclear transport complex, a structure-based mechanical model of Kap95p:RanGTP complex is introduced. In this model, a protein structure is simply modeled as an elastic network in which a set of coarse-grained point masses are connected by linear springs representing biochemical interactions at atomic level. Harmonic normal mode analysis (NMA) and anharmonic elastic network interpolation (ENI) are performed to predict the modes of vibrations and a feasible pathway between locked and unlocked conformations of Kap95p, respectively. Simulation results imply that the binding of RanGTP to Kap95p induces the release of the cargo in the nucleus as well as prevents any new cargo from attaching to the Kap95p:RanGTP complex.

Trigger processing using reconfigurable logic in the CMS calorimeter trigger

Energy Technology Data Exchange (ETDEWEB)

Brooke, J J; Cussans, D G; Heath, G P; Maddox, A J; Newbold, D M; Rabbetts, P D

2001-04-01

We present the design of the Global Calorimeter Trigger processor for the CMS detector at LHC. This is a fully pipelined processor system which collects data from all the CMS calorimeters and produces summary information used in forming the Level-1 trigger decision for each event. The design in based on the use of state-of-the-art reconfigurable logic devices (FPGAs) and fast data links. We present the results of device testing using a low-latency pipelined sort algorithm, which demonstrate that an FPGA can be used to perform processing previously foreseen to require custom ASICs. Our design approach results in a powerful, flexible and compact processor system.

Trigger Finger

Science.gov (United States)

... in a bent position. People whose work or hobbies require repetitive gripping actions are at higher risk ... developing trigger finger include: Repeated gripping. Occupations and hobbies that involve repetitive hand use and prolonged gripping ...

The primed SNARE–complexin–synaptotagmin complex for neuronal exocytosis

Energy Technology Data Exchange (ETDEWEB)

Zhou, Qiangjun; Zhou, Peng; Wang, Austin L.; Wu, Dick; Zhao, Minglei; Südhof, Thomas C.; Brunger, Axel T.

2017-08-16

Synaptotagmin, complexin, and neuronal SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) proteins mediate evoked synchronous neurotransmitter release, but the molecular mechanisms mediating the cooperation between these molecules remain unclear. Here we determine crystal structures of the primed pre-fusion SNARE–complexin–synaptotagmin-1 complex. These structures reveal an unexpected tripartite interface between synaptotagmin-1 and both the SNARE complex and complexin. Simultaneously, a second synaptotagmin-1 molecule interacts with the other side of the SNARE complex via the previously identified primary interface. Mutations that disrupt either interface in solution also severely impair evoked synchronous release in neurons, suggesting that both interfaces are essential for the primed pre-fusion state. Ca2+ binding to the synaptotagmin-1 molecules unlocks the complex, allows full zippering of the SNARE complex, and triggers membrane fusion. The tripartite SNARE–complexin–synaptotagmin-1 complex at a synaptic vesicle docking site has to be unlocked for triggered fusion to start, explaining the cooperation between complexin and synaptotagmin-1 in synchronizing evoked release on the sub-millisecond timescale.

High energy physics experiment triggers and the trustworthiness of software

International Nuclear Information System (INIS)

Nash, T.

1991-10-01

For all the time and frustration that high energy physicists expend interacting with computers, it is surprising that more attention is not paid to the critical role computers play in the science. With large, expensive colliding beam experiments now dependent on complex programs working at startup, questions of reliability -- the trustworthiness of software -- need to be addressed. This issue is most acute in triggers, used to select data to record -- and data to discard -- in the real time environment of an experiment. High level triggers are built on codes that now exceed 2 million source lines -- and for the first time experiments are truly dependent on them. This dependency will increase at the accelerators planned for the new millennium (SSC and LHC), where cost and other pressures will reduce tolerance for first run problems, and the high luminosities will make this on-line data selection essential. A sense of this incipient crisis motivated the unusual juxtaposition to topics in these lectures. 37 refs., 1 fig

The ATLAS High Level Trigger Infrastructure, Performance and Future Developments

CERN Document Server

The ATLAS collaboration

2009-01-01

The ATLAS High Level Trigger (HLT) is a distributed real-time software system that performs the final online selection of events produced during proton-proton collisions at the Large Hadron Collider (LHC). It is designed as a two-stage event filter running on a farm of commodity PC hardware. Currently the system consists of about 850 multi-core processing nodes that will be extended incrementally following the increasing luminosity of the LHC to about 2000 nodes depending on the evolution of the processor technology. Due to the complexity and similarity of the algorithms a large fraction of the software is shared between the online and offline event reconstruction. The HLT Infrastructure serves as the interface between the two domains and provides common services for the trigger algorithms. The consequences of this design choice will be discussed and experiences from the operation of the ATLAS HLT during cosmic ray data taking and first beam in 2008 will be presented. Since the event processing time at the HL...

Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components

DEFF Research Database (Denmark)

Jensen, Kaj Frank; Pedersen, Steen

1990-01-01

In this paper, the Escherichia coli cell is considered as a system designed for rapid growth, but limited by the medium. We propose that this very design causes the cell to become subsaturated with precursors and catalytic components at all levels of macromolecular biosynthesis and leads to a mol...

Real-time track-less Cherenkov ring fitting trigger system based on Graphics Processing Units

Science.gov (United States)

Ammendola, R.; Biagioni, A.; Chiozzi, S.; Cretaro, P.; Cotta Ramusino, A.; Di Lorenzo, S.; Fantechi, R.; Fiorini, M.; Frezza, O.; Gianoli, A.; Lamanna, G.; Lo Cicero, F.; Lonardo, A.; Martinelli, M.; Neri, I.; Paolucci, P. S.; Pastorelli, E.; Piandani, R.; Piccini, M.; Pontisso, L.; Rossetti, D.; Simula, F.; Sozzi, M.; Vicini, P.

2017-12-01

The parallel computing power of commercial Graphics Processing Units (GPUs) is exploited to perform real-time ring fitting at the lowest trigger level using information coming from the Ring Imaging Cherenkov (RICH) detector of the NA62 experiment at CERN. To this purpose, direct GPU communication with a custom FPGA-based board has been used to reduce the data transmission latency. The GPU-based trigger system is currently integrated in the experimental setup of the RICH detector of the NA62 experiment, in order to reconstruct ring-shaped hit patterns. The ring-fitting algorithm running on GPU is fed with raw RICH data only, with no information coming from other detectors, and is able to provide more complex trigger primitives with respect to the simple photodetector hit multiplicity, resulting in a higher selection efficiency. The performance of the system for multi-ring Cherenkov online reconstruction obtained during the NA62 physics run is presented.

State-of-the-art Versus Time-triggered Object Tracking in Advanced Driver Assistance Systems

Directory of Open Access Journals (Sweden)

Moritz Koplin

2013-04-01

Full Text Available Most state-of-the-art driver assistance systems cannot guarantee that real-time images of object states are updated within a given time interval, because the object state observations are typically sampled by uncontrolled sensors and transmitted via an indeterministic bus system such as CAN. To overcome this shortcoming, a paradigm shift toward time-triggered advanced driver assistance systems based on a deterministic bus system, such as FlexRay, is under discussion. In order to prove the feasibility of this paradigm shift, this paper develops different models of a state-of-the-art and a time-triggered advanced driver assistance system based on multi-sensor object tracking and compares them with regard to their mean performance. The results show that while the state-of-the-art model is advantageous in scenarios with low process noise, it is outmatched by the time-triggered model in the case of high process noise, i.e., in complex situations with high dynamic.

Macromolecular peroxo complexes of Vanadium(V) and ...

Indian Academy of Sciences (India)

Molybdenum(VI): Catalytic activities and biochemical relevance. NASHREEN S ISLAM∗ and ... already been identified as an important pathway for the action of inorganic drugs and .... chain or network. Physical incorporation of metals or.

Triggers for a high sensitivity charm experiment

International Nuclear Information System (INIS)

Christian, D.C.

1994-07-01

Any future charm experiment clearly should implement an E T trigger and a μ trigger. In order to reach the 10 8 reconstructed charm level for hadronic final states, a high quality vertex trigger will almost certainly also be necessary. The best hope for the development of an offline quality vertex trigger lies in further development of the ideas of data-driven processing pioneered by the Nevis/U. Mass. group

Functionalization of Planet-Satellite Nanostructures Revealed by Nanoscopic Localization of Distinct Macromolecular Species

KAUST Repository

Rossner, Christian

2016-09-26

The development of a straightforward method is reported to form hybrid polymer/gold planet-satellite nanostructures (PlSNs) with functional polymer. Polyacrylate type polymer with benzyl chloride in its backbone as a macromolecular tracer is synthesized to study its localization within PlSNs by analyzing the elemental distribution of chlorine. The functionalized nanohybrid structures are analyzed by scanning transmission electron microscopy, electron energy loss spectroscopy, and spectrum imaging. The results show that the RAFT (reversible addition-fragmentation chain transfer) polymers\\' sulfur containing end groups are colocalized at the gold cores, both within nanohybrids of simple core-shell morphology and within higher order PlSNs, providing microscopic evidence for the affinity of the RAFT group toward gold surfaces. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA., Weinheim.

OCTOPUS: an innovative multimodal diffractometer for neutron macromolecular crystallography across the length scales

International Nuclear Information System (INIS)

Blakeley, M.P.; Andersen, K.; Kreuz, M.; Giroud, B.; McSweeney, S.; Mitchell, E.; Teixeira, S.C.M.; Forsyth, V.T.

2011-01-01

We propose to construct a novel protein diffractometer at position H112B. The new instrument will deliver major efficiency gains, as well as offering greatly extended flexibility through the option of several easily interchangeable modes of operation. This proposal builds on the demonstrable need to extend ILL's capacity for high resolution structural studies of protein systems, as well as a need to widen the scope of biological crystallography - in particular for monochromatic studies at both high and low resolution. The development will be carried out in close collaboration with structural biologists at the ESRF, and engineered in such a way that the user interface of the instrument (from sample to software) will be transparently identifiable to a large, dynamic, and driven community of European synchrotron X-ray macromolecular crystallographers. (authors)

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

DEFF Research Database (Denmark)

Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.

2017-01-01

orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME......Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many...... models have 70,000 constraints and variables and will grow larger). We have developed a quadrupleprecision version of our linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging...

A neutral polydisulfide containing Gd(III) DOTA monoamide as a redox-sensitive biodegradable macromolecular MRI contrast agent.

Science.gov (United States)

Ye, Zhen; Zhou, Zhuxian; Ayat, Nadia; Wu, Xueming; Jin, Erlei; Shi, Xiaoyue; Lu, Zheng-Rong

2016-01-01

This work aims to develop safe and effective gadolinium (III)-based biodegradable macromolecular MRI contrast agents for blood pool and cancer imaging. A neutral polydisulfide containing macrocyclic Gd-DOTA monoamide (GOLS) was synthesized and characterized. In addition to studying the in vitro degradation of GOLS, its kinetic stability was also investigated in an in vivo model. The efficacy of GOLS for contrast-enhanced MRI was examined with female BALB/c mice bearing 4T1 breast cancer xenografts. The pharmacokinetics, biodistribution, and metabolism of GOLS were also determined in mice. GOLS has an apparent molecular weight of 23.0 kDa with T1 relaxivities of 7.20 mM(-1) s(-1) per Gd at 1.5 T, and 6.62 mM(-1) s(-1) at 7.0 T. GOLS had high kinetic inertness against transmetallation with Zn(2+) ions, and its polymer backbone was readily cleaved by L-cysteine. The agent showed improved efficacy for blood pool and tumor MR imaging. The structural effect on biodistribution and in vivo chelation stability was assessed by comparing GOLS with Gd(HP-DO3A), a negatively charged polydisulfide containing Gd-DOTA monoamide GODC, and a polydisulfide containing Gd-DTPA-bisamide (GDCC). GOLS showed high in vivo chelation stability and minimal tissue deposition of gadolinium. The biodegradable macromolecular contrast agent GOLS is a promising polymeric contrast agent for clinical MR cardiovascular imaging and cancer imaging. Copyright © 2015 John Wiley & Sons, Ltd.

The effect of complex fault rupture on the distribution of landslides triggered by the 12 January 2010, Haiti earthquake

Science.gov (United States)

Harp, Edwin L.; Jibson, Randall W.; Dart, Richard L.; Margottini, Claudio; Canuti, Paolo; Sassa, Kyoji

2013-01-01

The MW 7.0, 12 January 2010, Haiti earthquake triggered more than 7,000 landslides in the mountainous terrain south of Port-au-Prince over an area that extends approximately 50 km to the east and west from the epicenter and to the southern coast. Most of the triggered landslides were rock and soil slides from 25°–65° slopes within heavily fractured limestone and deeply weathered basalt and basaltic breccia. Landslide volumes ranged from tens of cubic meters to several thousand cubic meters. Rock slides in limestone typically were 2–5 m thick; slides within soils and weathered basalt typically were less than 1 m thick. Twenty to thirty larger landslides having volumes greater than 10,000 m3 were triggered by the earthquake; these included block slides and rotational slumps in limestone bedrock. Only a few landslides larger than 5,000 m3 occurred in the weathered basalt. The distribution of landslides is asymmetric with respect to the fault source and epicenter. Relatively few landslides were triggered north of the fault source on the hanging wall. The densest landslide concentrations lie south of the fault source and the Enriquillo-Plantain-Garden fault zone on the footwall. Numerous landslides also occurred along the south coast west of Jacmél. This asymmetric distribution of landsliding with respect to the fault source is unusual given the modeled displacement of the fault source as mainly thrust motion to the south on a plane dipping to the north at approximately 55°; landslide concentrations in other documented thrust earthquakes generally have been greatest on the hanging wall. This apparent inconsistency of the landslide distribution with respect to the fault model remains poorly understood given the lack of any strong-motion instruments within Haiti during the earthquake.

Commissioning the ATLAS Level-1 Central Trigger System

CERN Document Server

Sherman, Daniel

2010-01-01

The ATLAS Level-1 central trigger is a critical part of ATLAS operation. It receives the 40 MHz bunch clock from the LHC and distributes it to all sub-detectors. It initiates their read-out by forming the Level-1 Accept decision, which is based on information from the calorimeter and muon trigger processors and a variety of additional trigger inputs from detectors in the forward region. It also provides trigger summary information to the data acquisition system and the Level-2 trigger system. In this paper, we present the completion of the installed central trigger system, its performance during cosmic-ray data taking and the experience gained with triggering on the first LHC beams.

D0 triggering and data acquisition

International Nuclear Information System (INIS)

Gibbard, B.

1992-10-01

The trigger for D0 is a multi-tier system. Within the 3.5 μsec bunch crossing interval, custom electronics select interesting event candidates based on electromagnetic and hadronic energy deposits in the calorimeter and on indications of tracks in the muon system. Subsequent hardware decisions use refined calculations of electron and muon characteristics. The highest level trigger occurs in one element of a farm of microprocessors, where fully developed algorithms for electrons, muons, jets, or missing E t are executed. This highest level trigger also provides the assembly of the event into its final data structure. Performance of this trigger and data acquisition system in collider operation is described

The STAR Level-3 trigger system

International Nuclear Information System (INIS)

Adler, C.; Berger, J.; Demello, M.; Dietel, T.; Flierl, D.; Landgraf, J.; Lange, J.S.; LeVine, M.J.; Ljubicic, A.; Nelson, J.; Roehrich, D.; Stock, R.; Struck, C.; Yepes, P.

2003-01-01

The STAR Level-3 trigger issues a trigger decision upon a complete online reconstruction of Au+Au collisions at relativistic heavy ion collider energies. Central interactions are processed up to a rate of 50 s -1 including a simple analysis of physics observables. The setup of the processor farm and the event reconstruction as well as experiences and the proposed trigger algorithms are described

Polyelectrolyte-surfactant complexes formed by poly[3,5-bis(trimethylammoniummethyl)4-hydroxystyrene iodide]-block-poly(ethylene oxide) and sodium dodecyl sulfate in aqueous solutions

Czech Academy of Sciences Publication Activity Database

Štěpánek, M.; Matějíček, P.; Procházka, K.; Filippov, Sergey K.; Angelov, Borislav; Šlouf, Miroslav; Mountrichas, G.; Pispas, S.

2011-01-01

Roč. 27, č. 9 (2011), s. 5275-5281 ISSN 0743-7463 R&D Projects: GA MŠk ME09059; GA ČR GCP205/11/J043; GA ČR GAP208/10/0353 Institutional research plan: CEZ:AV0Z40500505 Keywords : polyelectrolyte-surfactant complexes * sodium dodecyl sulfate * small-angle X-ray scattering Subject RIV: CD - Macromolecular Chemistry Impact factor: 4.186, year: 2011

Discrete element modeling of triggered slip in faults with granular gouge: application to dynamic earthquake triggering

International Nuclear Information System (INIS)

Ferdowsi, B.

2014-01-01

Recent seismological observations based on new, more sensitive instrumentation show that seismic waves radiated from large earthquakes can trigger other earthquakes globally. This phenomenon is called dynamic earthquake triggering and is well-documented for over 30 of the largest earthquakes worldwide. Granular materials are at the core of mature earthquake faults and play a key role in fault triggering by exhibiting a rich nonlinear response to external perturbations. The stick-slip dynamics in sheared granular layers is analogous to the seismic cycle for earthquake fault systems. In this research effort, we characterize the macroscopic scale statistics and the grain-scale mechanisms of triggered slip in sheared granular layers. We model the granular fault gouge using three dimensional discrete element method simulations. The modeled granular system is put into stick-slip dynamics by applying a conning pressure and a shear load. The dynamic triggering is simulated by perturbing the spontaneous stick-slip dynamics using an external vibration applied to the boundary of the layer. The influences of the triggering consist in a frictional weakening during the vibration interval, a clock advance of the next expected large slip event and long term effects in the form of suppression and recovery of the energy released from the granular layer. Our study suggests that above a critical amplitude, vibration causes a significant clock advance of large slip events. We link this clock advance to a major decline in the slipping contact ratio as well as a decrease in shear modulus and weakening of the granular gouge layer. We also observe that shear vibration is less effective in perturbing the stick-slip dynamics of the granular layer. Our study suggests that in order to have an effective triggering, the input vibration must also explore the granular layer at length scales about or less than the average grain size. The energy suppression and the subsequent recovery and increased

Upgrade of the CMS Global Muon Trigger

CERN Document Server

Jeitler, Manfred; Rabady, Dinyar; Sakulin, Hannes; Stahl, Achim

2015-01-01

The increase in center-of-mass energy and luminosity for Run-II of the Large Hadron Collider poses new challenges for the trigger systems of the experiments. To keep triggering with a similar performance as in Run-I, the CMS muon trigger is currently being upgraded. The new algorithms will provide higher resolution, especially for the muon transverse momentum and will make use of isolation criteria that combine calorimeter with muon information already in the level-1 trigger. The demands of the new algorithms can only be met by upgrading the level-1 trigger system to new powerful FPGAs with high bandwidth I/O. The processing boards will be based on the new μTCA standard. We report on the planned algorithms for the upgraded Global Muon Trigger (μGMT) which sorts and removes duplicates from boundaries of the muon trigger sub-systems. Furthermore, it determines how isolated the muon candidates are based on calorimetric energy deposits. The μGMT will be implemented using a processing board that features a larg...

Upgrade of the CMS Global Muon Trigger

CERN Document Server

Lingemann, Joschka; Sakulin, Hannes; Jeitler, Manfred; Stahl, Achim

2015-01-01

The increase in center-of-mass energy and luminosity for Run 2 of the Large Hadron Collider pose new challenges for the trigger systems of the experiments. To keep triggering with a similar performance as in Run 1, the CMS muon trigger is currently being upgraded. The new algorithms will provide higher resolution, especially for the muon transverse momentum and will make use of isolation criteria that combine calorimeter with muon information already in the level-1 trigger. The demands of the new algorithms can only be met by upgrading the level-1 trigger system to new powerful FPGAs with high bandwidth I/O. The processing boards will be based on the new microTCA standard. We report on the planned algorithms for the upgraded Global Muon Trigger (GMT) which combines information from the muon trigger sub-systems and assigns the isolation variable. The upgraded GMT will be implemented using a Master Processor 7 card, built by Imperial College, that features a large Xilinx Virtex 7 FPGA. Up to 72 optical links at...

Upgrade trigger: Biannual performance update

CERN Document Server

Aaij, Roel; Couturier, Ben; Esen, Sevda; De Cian, Michel; De Vries, Jacco Andreas; Dziurda, Agnieszka; Fitzpatrick, Conor; Fontana, Marianna; Grillo, Lucia; Hasse, Christoph; Jones, Christopher Rob; Le Gac, Renaud; Matev, Rosen; Neufeld, Niko; Nikodem, Thomas; Polci, Francesco; Del Buono, Luigi; Quagliani, Renato; Schwemmer, Rainer; Seyfert, Paul; Stahl, Sascha; Szumlak, Tomasz; Vesterinen, Mika Anton; Wanczyk, Joanna; Williams, Mark Richard James; Yin, Hang; Zacharjasz, Emilia Anna

2017-01-01

This document presents the performance of the LHCb Upgrade trigger reconstruction sequence, incorporating changes to the underlying reconstruction algorithms and detector description since the Trigger and Online Upgrade TDR. An updated extrapolation is presented using the most recent example of an Event Filter Farm node.

Triggered Release from Polymer Capsules

Energy Technology Data Exchange (ETDEWEB)

Esser-Kahn, Aaron P. [Univ. of Illinois, Urbana, IL (United States). Beckman Inst. for Advanced Science and Technology and Dept. of Chemistry; Odom, Susan A. [Univ. of Illinois, Urbana, IL (United States). Beckman Inst. for Advanced Science and Technology and Dept. of Chemistry; Sottos, Nancy R. [Univ. of Illinois, Urbana, IL (United States). Beckman Inst. for Advanced Science and Technology and Dept. of Materials Science and Engineering; White, Scott R. [Univ. of Illinois, Urbana, IL (United States). Beckman Inst. for Advanced Science and Technology and Dept. of Aerospace Engineering; Moore, Jeffrey S. [Univ. of Illinois, Urbana, IL (United States). Beckman Inst. for Advanced Science and Technology and Dept. of Chemistry

2011-07-06

Stimuli-responsive capsules are of interest in drug delivery, fragrance release, food preservation, and self-healing materials. Many methods are used to trigger the release of encapsulated contents. Here we highlight mechanisms for the controlled release of encapsulated cargo that utilize chemical reactions occurring in solid polymeric shell walls. Triggering mechanisms responsible for covalent bond cleavage that result in the release of capsule contents include chemical, biological, light, thermal, magnetic, and electrical stimuli. We present methods for encapsulation and release, triggering methods, and mechanisms and conclude with our opinions on interesting obstacles for chemically induced activation with relevance for controlled release.

The ATLAS Trigger System: Ready for Run-2

CERN Document Server

Maeda, Junpei; The ATLAS collaboration

2015-01-01

The ATLAS trigger has been successfully collecting collision data during the first run of the LHC between 2009-2013 at a centre-of-mass energy between 900 GeV and 8 TeV. The trigger system consists of a hardware Level-1 and a software based high-level trigger that reduces the event rate from the design bunch-crossing rate of 40 MHz to an average recording rate of a few hundred Hz. During the data-taking period of Run-2 the LHC will operate at a centre-of-mass energy of about 13 TeV resulting in roughly five times higher trigger rates. In these proceedings, we briefly review the ATLAS trigger system upgrades that were implemented during the shutdown, allowing us to cope with the increased trigger rates while maintaining or even improving our efficiency to select relevant physics processes. This includes changes to the Level-1 calorimeter and muon trigger system, the introduction of a new Level-1 topological trigger module and themerging of the previously two-level higher-level trigger system into a single even...

First level trigger of the DIRAC experiment

International Nuclear Information System (INIS)

Afanas'ev, L.G.; Karpukhin, V.V.; Kulikov, A.V.; Gallas, M.

2001-01-01

The logic of the first level trigger of the DIRAC experiment at CERN is described. A parallel running of different trigger modes with tagging of events and optional independent prescaling is realized. A CAMAC-based trigger system is completely computer controlled

Performance of ATLAS RPC Level-1 Muon trigger during the 2015 data taking

CERN Document Server

Corradi, Massimo; The ATLAS collaboration

2016-01-01

The Level-1 Muon Barrel Trigger is one of the main elements of the event selection of the ATLAS experiment at the Large Hadron Collider. Its input stage consists of an array of processors receiving the full granularity of data from Resistive Plate Chambers in the central area of the ATLAS detector ("Barrel"). The trigger efficiency and the level of synchronisation of its elements with the rest of ATLAS and the LHC clock are crucial figures of this system: many parameters of the constituent RPC detector and the trigger electronics have to be constantly and carefully checked to assure a correct functioning of the Level-1 selection. Notwithstanding the complexity of such a large array of integrated RPC detectors, the ATLAS Level-1 system has resumed operations successfully after the past 2 year shutdown, with levels similar to those of Run 1. We present the inclusive monitoring of the RPC+L1 system that we have developed to characterise the behaviour of the system, using reconstructed muons in events selected by...

The ATLAS Level-1 Central Trigger Processor (CTP)

CERN Document Server

Spiwoks, Ralf; Ellis, Nick; Farthouat, P; Gällnö, P; Haller, J; Krasznahorkay, A; Maeno, T; Pauly, T; Pessoa-Lima, H; Resurreccion-Arcas, I; Schuler, G; De Seixas, J M; Torga-Teixeira, R; Wengler, T

2005-01-01

The ATLAS Level-1 Central Trigger Processor (CTP) combines information from calorimeter and muon trigger processors and makes the final Level-1 Accept (L1A) decision on the basis of lists of selection criteria (trigger menus). In addition to the event-selection decision, the CTP also provides trigger summary information to the Level-2 trigger and the data acquisition system. It further provides accumulated and bunch-by-bunch scaler data for monitoring of the trigger, detector and beam conditions. The CTP is presented and results are shown from tests with the calorimeter adn muon trigger processors connected to detectors in a particle beam, as well as from stand-alone full-system tests in the laboratory which were used to validate the CTP.

CMS Triggers for the LHC Startup

CERN Document Server

Nhan Nguyen, Chi

2009-01-01

The LHC will collide proton beams at a bunch-crossing rate of 40 MHz. At the design luminosity of $10^{34}$ cm$^{-2}$s$^{-1}$ each crossing results in an average of about 20 inelastic pp events. The CMS trigger system is designed to reduce the input rate to about 100 Hz. This task is carried out in two steps, namely the Level-1 (L1) and the High-Level trigger (HLT). The L1 trigger is built of customized fast electronics and is designed to reduce the rate to 100 kHz. The HLT is implemented in a filter farm running on hundreds of CPUs and is designed to reduce the rate by another factor of ~1000. It combines the traditional L2 and L3 trigger components in a novel way and allows the coherent tuning of the HLT algorithms to accommodate multiple physics channels. We will discuss the strategies for optimizing triggers covering the experiment`s early physics program.

The ATLAS Level-1 Calorimeter Trigger

International Nuclear Information System (INIS)

Achenbach, R; Andrei, V; Adragna, P; Apostologlou, P; Barnett, B M; Brawn, I P; Davis, A O; Edwards, J P; Asman, B; Bohm, C; Ay, C; Bauss, B; Bendel, M; Dahlhoff, A; Eckweiler, S; Booth, J R A; Thomas, P Bright; Charlton, D G; Collins, N J; Curtis, C J

2008-01-01

The ATLAS Level-1 Calorimeter Trigger uses reduced-granularity information from all the ATLAS calorimeters to search for high transverse-energy electrons, photons, τ leptons and jets, as well as high missing and total transverse energy. The calorimeter trigger electronics has a fixed latency of about 1 μs, using programmable custom-built digital electronics. This paper describes the Calorimeter Trigger hardware, as installed in the ATLAS electronics cavern

The ATLAS Level-1 Calorimeter Trigger

Energy Technology Data Exchange (ETDEWEB)

Achenbach, R; Andrei, V [Kirchhoff-Institut fuer Physik, University of Heidelberg, D-69120 Heidelberg (Germany); Adragna, P [Physics Department, Queen Mary, University of London, London E1 4NS (United Kingdom); Apostologlou, P; Barnett, B M; Brawn, I P; Davis, A O; Edwards, J P [STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX (United Kingdom); Asman, B; Bohm, C [Fysikum, Stockholm University, SE-106 91 Stockholm (Sweden); Ay, C; Bauss, B; Bendel, M; Dahlhoff, A; Eckweiler, S [Institut fuer Physik, University of Mainz, D-55099 Mainz (Germany); Booth, J R A; Thomas, P Bright; Charlton, D G; Collins, N J; Curtis, C J [School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom)], E-mail: e.eisenhandler@qmul.ac.uk (and others)

2008-03-15

The ATLAS Level-1 Calorimeter Trigger uses reduced-granularity information from all the ATLAS calorimeters to search for high transverse-energy electrons, photons, {tau} leptons and jets, as well as high missing and total transverse energy. The calorimeter trigger electronics has a fixed latency of about 1 {mu}s, using programmable custom-built digital electronics. This paper describes the Calorimeter Trigger hardware, as installed in the ATLAS electronics cavern.

Software trigger for the TOPAZ detector at TRISTAN

International Nuclear Information System (INIS)

Tsukamoto, T.; Yamauchi, M.; Enomoto, R.

1990-01-01

A new software trigger system was developed and installed at the TOPAZ detector to the trigger system for the TRISTAN e + e - collider to take data efficiently in the scheduled high luminosity experiment. This software trigger requires two or more charged tracks originated at the interaction point by examining the timing of signals from the time projection chamber. To execute the vertex finding very quickly, four microprocessors are used in parallel. By this new trigger the rate of the track trigger was reduced down to 30-40% with very small inefficiency. The additional dead time by this trigger is negligible. (orig.)

The Trigger for Early Running

CERN Document Server

The ATLAS Collaboration

2009-01-01

The ATLAS trigger and data acquisition system is based on three levels of event selection designed to capture the physics of interest with high efficiency from an initial bunch crossing rate of 40 MHz. The selections in the three trigger levels must provide sufficient rejection to reduce the rate to 200 Hz, compatible with offline computing power and storage capacity. The LHC is expected to begin its operation with a peak luminosity of 10^31 with a relatively small number of bunches, but quickly ramp up to higher luminosities by increasing the number of bunches, and thus the overall interaction rate. Decisions must be taken every 25 ns during normal LHC operations at the design luminosity of 10^34, where the average bunch crossing will contain more than 20 interactions. Hence, trigger selections must be deployed that can adapt to the changing beam conditions while preserving the interesting physics and satisfying varying detector requirements. In this paper, we provide a menu of trigger selections that can be...

BTeV detached vertex trigger

International Nuclear Information System (INIS)

Gottschalk, E.E.

2001-01-01

BTeV is a collider experiment that has been approved to run in the Tevatron at Fermilab. The experiment will conduct precision studies of CP violation using a forward-geometry detector. The detector will be optimized for high-rate detection of beauty and charm particles produced in collisions between protons and anti-protons. BTeV will trigger on beauty and charm events by taking advantage of the main difference between these heavy quark events and more typical hadronic events - the presence of detached beauty and charm decay vertices. The first stage of the BTeV trigger will receive data from a pixel vertex detector at a rate of 100 gb s -1 , reconstruct tracks and vertices for every beam crossing, reject 99% of beam crossings that do not produce beauty or charm particles, and trigger on beauty events with high efficiency. An overview of the trigger design and its influence on the design of the pixel vertex detector is presented

Rate Predictions and Trigger/DAQ Resource Monitoring in ATLAS

CERN Document Server

Schaefer, D M; The ATLAS collaboration

2012-01-01

Since starting in 2010, the Large Hadron Collider (LHC) has pro- duced collisions at an ever increasing rate. The ATLAS experiment successfully records the collision data with high eciency and excel- lent data quality. Events are selected using a three-level trigger system, where each level makes a more re ned selection. The level-1 trigger (L1) consists of a custom-designed hardware trigger which seeds two higher software based trigger levels. Over 300 triggers compose a trig- ger menu which selects physics signatures such as electrons, muons, particle jets, etc. Each trigger consumes computing resources of the ATLAS trigger system and oine storage. The LHC instantaneous luminosity conditions, desired physics goals of the collaboration, and the limits of the trigger infrastructure determine the composition of the ATLAS trigger menu. We describe a trigger monitoring frame- work for computing the costs of individual trigger algorithms such as data request rates and CPU consumption. This framework has been used...

Convergent and Divergent Signaling in PAMP-Triggered Immunity and Effector-Triggered Immunity.

Science.gov (United States)

Peng, Yujun; van Wersch, Rowan; Zhang, Yuelin

2018-04-01

Plants use diverse immune receptors to sense pathogen attacks. Recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors localized on the plasma membrane leads to PAMP-triggered immunity (PTI). Detection of pathogen effectors by intracellular or plasma membrane-localized immune receptors results in effector-triggered immunity (ETI). Despite the large variations in the magnitude and duration of immune responses triggered by different PAMPs or pathogen effectors during PTI and ETI, plasma membrane-localized immune receptors activate similar downstream molecular events such as mitogen-activated protein kinase activation, oxidative burst, ion influx, and increased biosynthesis of plant defense hormones, indicating that defense signals initiated at the plasma membrane converge at later points. On the other hand, activation of ETI by immune receptors localized to the nucleus appears to be more directly associated with transcriptional regulation of defense gene expression. Here, we review recent progress in signal transductions downstream of different groups of plant immune receptors, highlighting the converging and diverging molecular events.

The Trigger System of the CMS Experiment

OpenAIRE

Felcini, Marta

2008-01-01

We give an overview of the main features of the CMS trigger and data acquisition (DAQ) system. Then, we illustrate the strategies and trigger configurations (trigger tables) developed for the detector calibration and physics program of the CMS experiment, at start-up of LHC operations, as well as their possible evolution with increasing luminosity. Finally, we discuss the expected CPU time performance of the trigger algorithms and the CPU requirements for the event filter farm at start-up.

Smart trigger logic for focal plane arrays

Science.gov (United States)

Levy, James E; Campbell, David V; Holmes, Michael L; Lovejoy, Robert; Wojciechowski, Kenneth; Kay, Randolph R; Cavanaugh, William S; Gurrieri, Thomas M

2014-03-25

An electronic device includes a memory configured to receive data representing light intensity values from pixels in a focal plane array and a processor that analyzes the received data to determine which light values correspond to triggered pixels, where the triggered pixels are those pixels that meet a predefined set of criteria, and determines, for each triggered pixel, a set of neighbor pixels for which light intensity values are to be stored. The electronic device also includes a buffer that temporarily stores light intensity values for at least one previously processed row of pixels, so that when a triggered pixel is identified in a current row, light intensity values for the neighbor pixels in the previously processed row and for the triggered pixel are persistently stored, as well as a data transmitter that transmits the persistently stored light intensity values for the triggered and neighbor pixels to a data receiver.

UA1 upgrade first-level calorimeter trigger processor

International Nuclear Information System (INIS)

Bains, N.; Charlton, D.; Ellis, N.; Garvey, J.; Gregory, J.; Jimack, M.P.; Jovanovic, P.; Kenyon, I.R.; Baird, S.A.; Campbell, D.; Cawthraw, M.; Coughlan, J.; Flynn, P.; Galagedera, S.; Grayer, G.; Halsall, R.; Shah, T.P.; Stephens, R.; Eisenhandler, E.; Fensome, I.; Landon, M.

1989-01-01

A new first-level trigger processor has been built for the UA1 experiment on the Cern SppS Collider. The processor exploits the fine granularity of the new UA1 uranium-TMP calorimeter to improve the selectivity of the trigger. The new electron trigger has improved hadron jet rejection, achieved by requiring low energy deposition around the electromagnetic cluster. A missing transverse energy trigger and a total energy trigger have also been implemented. (orig.)

Astrocyte-to-neuron communication through integrin-engaged Thy-1/CBP/Csk/Src complex triggers neurite retraction via the RhoA/ROCK pathway.

Science.gov (United States)

Maldonado, H; Calderon, C; Burgos-Bravo, F; Kobler, O; Zuschratter, W; Ramirez, O; Härtel, S; Schneider, P; Quest, A F G; Herrera-Molina, R; Leyton, L

2017-02-01

Two key proteins for cellular communication between astrocytes and neurons are αvβ3 integrin and the receptor Thy-1. Binding of these molecules in the same (cis) or on adjacent (trans) cellular membranes induces Thy-1 clustering, triggering actin cytoskeleton remodeling. Molecular events that could explain how the Thy-1-αvβ3 integrin interaction signals have only been studied separately in different cell types, and the detailed transcellular communication and signal transduction pathways involved in neuronal cytoskeleton remodeling remain unresolved. Using biochemical and genetic approaches, single-molecule tracking, and high-resolution nanoscopy, we provide evidence that upon binding to αvβ3 integrin, Thy-1 mobility decreased while Thy-1 nanocluster size increased. This occurred concomitantly with inactivation and exclusion of the non-receptor tyrosine kinase Src from the Thy-1/C-terminal Src kinase (Csk)-binding protein (CBP)/Csk complex. The Src inactivation decreased the p190Rho GTPase activating protein phosphorylation, promoting RhoA activation, cofilin, and myosin light chain II phosphorylation and, consequently, neurite shortening. Finally, silencing the adaptor CBP demonstrated that this protein was a key transducer in the Thy-1 signaling cascade. In conclusion, these data support the hypothesis that the Thy-1-CBP-Csk-Src-RhoA-ROCK axis transmitted signals from astrocytic integrin-engaged Thy-1 (trans) to the neuronal actin cytoskeleton. Importantly, the β3 integrin in neurons (cis) was not found to be crucial for neurite shortening. This is the first study to detail the signaling pathway triggered by αvβ3, the endogenous Thy-1 ligand, highlighting the role of membrane-bound integrins as trans acting ligands in astrocyte-neuron communication. Copyright © 2016 Elsevier B.V. All rights reserved.

The ATLAS Trigger: Recent Experience and Future Plans

CERN Document Server

The ATLAS collaboration

2009-01-01

This paper will give an overview of the ATLAS trigger design and its innovative features. It will describe the valuable experience gained in running the trigger reconstruction and event selection in the fastchanging environment of the detector commissioning during 2008. It will also include a description of the trigger selection menu and its 2009 deployment plan from first collisions to the nominal luminosity. ATLAS is one of the two general-purpose detectors at the Large Hadron Collider (LHC). The trigger system needs to efficiently reject a large rate of background events and still select potentially interesting ones with high efficiency. After a first level trigger implemented in custom electronics, the trigger event selection is made by the High Level Trigger (HLT) system, implemented in software. To reduce the processing time to manageable levels, the HLT uses seeded, step-wise and fast selection algorithms, aiming at the earliest possible rejection of background events. The ATLAS trigger event selection...

CMS Level-1 Upgrade Calorimeter Trigger Prototype Development

CERN Document Server

Klabbers, Pamela Renee

2013-01-01

As the LHC increases luminosity and energy, it will become increasingly difficult to select interesting physics events and remain within the readout bandwidth limitations. An upgrade to the CMS Calorimeter Trigger implementing more complex algorithms is proposed. It utilizes AMC cards with Xilinx FPGAs running in micro-TCA crate with card interconnections via crate backplanes and optical links operating at up to 10 Gbps. Prototype cards with Virtex-6 and Virtex-7 FPGAs have been built and software frameworks for operation and monitoring developed. The physics goals, hardware architectures, and software will be described in this talk. More details can be found in a separate poster at this conference.

JBluIce-EPICS control system for macromolecular crystallography

International Nuclear Information System (INIS)

Stepanov, S.; Makarov, O.; Hilgart, M.; Pothineni, S.; Urakhchin, A.; Devarapalli, S.; Yoder, D.; Becker, M.; Ogata, C.; Sanishvili, R.; Nagarajan, V.; Smith, J.L.; Fischetti, R.F.

2011-01-01

The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline component. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallographic experiments, especially in the field of microcrystallography.

Increasing the sensitivity of NMR diffusion measurements by paramagnetic longitudinal relaxation enhancement, with application to ribosome–nascent chain complexes

International Nuclear Information System (INIS)