WorldWideScience

Sample records for replica immunogold labeling

  1. Connexin composition in apposed gap junction hemiplaques revealed by matched double-replica freeze-fracture replica immunogold labeling.

    Science.gov (United States)

    Rash, John E; Kamasawa, Naomi; Davidson, Kimberly G V; Yasumura, Thomas; Pereda, Alberto E; Nagy, James I

    2012-06-01

    Despite the combination of light-microscopic immunocytochemistry, histochemical mRNA detection techniques and protein reporter systems, progress in identifying the protein composition of neuronal versus glial gap junctions, determination of the differential localization of their constituent connexin proteins in two apposing membranes and understanding human neurological diseases caused by connexin mutations has been problematic due to ambiguities introduced in the cellular and subcellular assignment of connexins. Misassignments occurred primarily because membranes and their constituent proteins are below the limit of resolution of light microscopic imaging techniques. Currently, only serial thin-section transmission electron microscopy and freeze-fracture replica immunogold labeling have sufficient resolution to assign connexin proteins to either or both sides of gap junction plaques. However, freeze-fracture replica immunogold labeling has been limited because conventional freeze fracturing allows retrieval of only one of the two membrane fracture faces within a gap junction, making it difficult to identify connexin coupling partners in hemiplaques removed by fracturing. We now summarize progress in ascertaining the connexin composition of two coupled hemiplaques using matched double-replicas that are labeled simultaneously for multiple connexins. This approach allows unambiguous identification of connexins and determination of the membrane "sidedness" and the identities of connexin coupling partners in homotypic and heterotypic gap junctions of vertebrate neurons.

  2. Immunogold labels: cell-surface markers in atomic force microscopy

    NARCIS (Netherlands)

    Putman, Constant A.J.; Grooth, de Bart G.; Hansma, Paul K.; Hulst, van Niek F.; Greve, Jan

    1993-01-01

    The feasibility of using immunogold labels as cell-surface markers in atomic force microscopy is shown in this paper. The atomic force microscope (AFM) was used to image the surface of immunogold-labeled human lymphocytes. The lymphocytes were isolated from whole blood and labeled by an indirect imm

  3. Immunogold labelling is a quantitative method as demonstrated by studies on aminopeptidase N in microvillar membrane vesicles

    DEFF Research Database (Denmark)

    Hansen, Gert Helge; Wetterberg, L L; Sjöström, H;

    1992-01-01

    Microvillar membrane vesicle preparations with varying content of aminopeptidase N were prepared from enterocytes of the pig small intestine. Postembedding immunogold labelling of aminopeptidase N was performed on these glutaraldehyde/paraformaldehyde-fixed, osmium tetroxide-treated and Epon-embe...... that postembedding immunogold labelling can be used quantitatively....

  4. Localization of viral antigens in leaf protoplasts and plants by immunogold labelling

    NARCIS (Netherlands)

    Lent, van J.W.M.

    1988-01-01

    This thesis describes the application of an immunocytochemical technique, immunogold labelling, new in the light and electron microscopic study of the plant viral infection. In Chapter 1 the present state of knowledge of the plant viral infection process, as revealed by in

  5. Localization of viral antigens in leaf protoplasts and plants by immunogold labelling.

    NARCIS (Netherlands)

    Lent, van J.W.M.

    1988-01-01

    This thesis describes the application of an immunocytochemical technique, immunogold labelling, new in the light and electron microscopic study of the plant viral infection. In Chapter 1 the present state of knowledge of the plant viral infection process, as revealed by insitu studies

  6. Localization of viral antigens in leaf protoplasts and plants by immunogold labelling

    NARCIS (Netherlands)

    Lent, van J.W.M.

    1988-01-01

    This thesis describes the application of an immunocytochemical technique, immunogold labelling, new in the light and electron microscopic study of the plant viral infection. In Chapter 1 the present state of knowledge of the plant viral infection process, as revealed by

  7. Immunogold labeling of stages of Cryptosporidium parvum recognized by immunoglobulins in hyperimmune bovine colostrum.

    Science.gov (United States)

    Fayer, R; Barta, J R; Guidry, A J; Blagburn, B L

    1991-06-01

    Ultrathin sections of mouse ileum infected with Cryptosporidium parvum were stained by immunogold techniques. Sections first were stained with polyvalent antibodies in whey from hyperimmune bovine colostrum (HBC), then stained by secondary antibodies in rabbit antibovine IgA, IgM, IgG1, and IgG2, and lastly labeled by goat anti-rabbit gold conjugate. Examination of the immunostained specimens by electron microscopy revealed that each bovine immunoglobulin isotype in the whey recognized antigens in meronts, merozoites, microgametocytes, microgametes, and macrogamonts. Based on these findings it is hypothesized that antigens in all stages of C. parvum provide targets of opportunity for the antiparasitic activity of HBC whey antibodies thereby accounting for its efficacy as an immunotherapeutic agent.

  8. Immunogold labeling reveals subcellular localisation of silica nanoparticles in a human blood-brain barrier model

    Science.gov (United States)

    Ye, Dong; Anguissola, Sergio; O'Neill, Tiina; Dawson, Kenneth A.

    2015-05-01

    Subcellular location of nanoparticles has been widely investigated with fluorescence microscopy, via fluorescently labeled antibodies to visualise target antigens in cells. However, fluorescence microscopy, such as confocal or live cell imaging, has generally limited 3D spatial resolution. Conventional electron microscopy can be useful in bridging resolution gap, but still not ideal in resolving subcellular organelle identities. Using the pre-embedding immunogold electron microscopic imaging, we performed accurate examination of the intracellular trafficking and gathered further evidence of transport mechanisms of silica nanoparticles across a human in vitro blood-brain barrier model. Our approach can effectively immunolocalise a variety of intracellular compartments and provide new insights into the uptake and subcellular transport of nanoparticles.Subcellular location of nanoparticles has been widely investigated with fluorescence microscopy, via fluorescently labeled antibodies to visualise target antigens in cells. However, fluorescence microscopy, such as confocal or live cell imaging, has generally limited 3D spatial resolution. Conventional electron microscopy can be useful in bridging resolution gap, but still not ideal in resolving subcellular organelle identities. Using the pre-embedding immunogold electron microscopic imaging, we performed accurate examination of the intracellular trafficking and gathered further evidence of transport mechanisms of silica nanoparticles across a human in vitro blood-brain barrier model. Our approach can effectively immunolocalise a variety of intracellular compartments and provide new insights into the uptake and subcellular transport of nanoparticles. Electronic supplementary information (ESI) available: Nanoparticle characterisation data, preservation of cellular structures, staining controls, optimisation of size amplification via the silver enhancement, and more imaging results from anti-clathrin and anti-caveolin 1

  9. The intensity of immunogold labeling of deplasticized acrylic sections compared to deplasticized epoxy sections-Theoretical deductions and experimental data.

    Science.gov (United States)

    Brorson, Sverre-Henning; Reinholt, Finn P

    2008-01-01

    The purpose of this study was to compare the level of immunogold labeling of deplasticized acrylic sections and deplasticized epoxy sections. Pure protein gels of IgG, albumin and thyroglobulin were produced by glutaraldehyde fixation and embedded in non-crosslinked acrylic resin (Technovit 9100) and epoxy resin (Epon 812), respectively. Ultrathin sections of acrylic and epoxy resin were separately deplasticized in 2-methoxyethyl acetate (MEA) and sodium ethoxide. Quantitative immunogold labeling was performed with anti-IgG, anti-albumin and anti-thyroglobulin antibodies on sections of the corresponding protein gels. For all antibodies tested, the intensity of labeling for deplasticized acrylic sections was significantly higher (two to four times) than for the corresponding deplasticized epoxy sections. The results fit with a theoretically deduced relation: the quotient of the labeling of two deplasticized sections of different resins is equivalent to the square root of the quotient of the labeling of the similar sections not exposed to any kind of pre-treatment. The practical significance of the results is that immunolabeling of deplasticized non-crosslinked acrylic resin results in more intense immunogold labeling than deplasticized epoxy sections. Deplasticizing is most useful when the requirements for ultrastructural preservation according to conventional criteria are moderate. Our theoretically deduced results also indicate that deplasticized Technovit (or other non-crosslinked acrylic resins) sections will be significantly better suited for immunolabeling at the light microscopic level than deplasticized epoxy sections.

  10. The mechanism of xylans removal during hydrothermal pretreatment of poplar fibers investigated by immunogold labeling.

    Science.gov (United States)

    Ma, Jing; Ji, Zhe; Chen, Jia C; Zhou, Xia; Kim, Yoon S; Xu, Feng

    2015-07-01

    Hydrothermal pretreatment initially removed the lignin-free xylan from the middle layer of secondary wall, followed by the lignin-bound xylan, but the cellulose-bound xylan was seldom removed by this pretreatment. An in-depth understanding of the mechanism of xylan removal during hydrothermal pretreatment (HTP) of wood is critical for cost-effective conversion of lignocellulosic biomass to biofuels. Several studies demonstrated the kinetics and mechanism of xylan removal during HTP on molecular scale, but the dissolution mechanism of xylan during HTP remains unclear at ultra-structural level. Our study investigated changes in the micro-distribution of xylan in poplar fiber cell walls during HTP by transmission electron microscopy (TEM) in combination with immunogold labeling. The study revealed that HTP caused greater decline in the density of xylan labeling in the S2 layer of fiber wall than in the S1 layer. There was a greater loss in the density of xylan labeling during HTP in the delignified and enzymatically treated fibers compared to untreated fibers. We propose that in the initial stages of HTP lignin-free xylan in the S2 layer was more readily hydrolyzed than in the S1 layer by hydronium ions. With increasing pretreatment time, the xylan covalently bound to lignin was also removed from the S2 layer due to the dissolution of lignin. The xylan tightly bound to cellulose was seldom removed during HTP, but was hydrolyzed in subsequent enzymatic treatment. This TEM-immunolabeling investigation reveals the manner in which different xylan fractions are removed from fiber cell wall during HTP, and we expect the information to be helpful in developing processes tailored for more effective conversion of cellulosic biomass into fermentable sugars.

  11. Native immunogold labeling of cell surface proteins and viral glycoproteins for cryo-electron microscopy and cryo-electron tomography applications.

    Science.gov (United States)

    Yi, Hong; Strauss, Joshua D; Ke, Zunlong; Alonas, Eric; Dillard, Rebecca S; Hampton, Cheri M; Lamb, Kristen M; Hammonds, Jason E; Santangelo, Philip J; Spearman, Paul W; Wright, Elizabeth R

    2015-10-01

    Numerous methods have been developed for immunogold labeling of thick, cryo-preserved biological specimens. However, most of the methods are permutations of chemical fixation and sample sectioning, which select and isolate the immunolabeled region of interest. We describe a method for combining immunogold labeling with cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) of the surface proteins of intact mammalian cells or the surface glycoproteins of assembling and budding viruses in the context of virus-infected mammalian cells cultured on EM grids. In this method, the cells were maintained in culture media at physiologically relevant temperatures while sequentially incubated with the primary and secondary antibodies. Subsequently, the immunogold-labeled specimens were vitrified and observed under cryo-conditions in the transmission electron microscope. Cryo-EM and cryo-ET examination of the immunogold-labeled cells revealed the association of immunogold particles with the target antigens. Additionally, the cellular structure was unaltered by pre-immunolabeling chemical fixation and retained well-preserved plasma membranes, cytoskeletal elements, and macromolecular complexes. We think this technique will be of interest to cell biologists for cryo-EM and conventional studies of native cells and pathogen-infected cells.

  12. Immunogold-labeled S-phase neoblasts, total neoblast number, their distribution, and evidence for arrested neoblasts in Macrostomum lignano (Platyhelminthes, Rhabditophora).

    Science.gov (United States)

    Bode, A; Salvenmoser, W; Nimeth, K; Mahlknecht, M; Adamski, Z; Rieger, R M; Peter, R; Ladurner, P

    2006-09-01

    Neoblasts in Platyhelminthes are the only cells to proliferate and differentiate into all cell types. In Macrostomum lignano, the incorporation of 5'-bromo-2'-deoxyuridine (BrdU) in neoblasts confirmed the distribution of S-phase cells in two lateral bands. BrdU labeling for light and for transmission electron microscopy (TEM) identified three populations of proliferating cells: somatic neoblasts located between the epidermis and gastrodermis (mesodermal neoblasts), neoblasts located within the gastrodermis (gastrodermal neoblasts), and gonadal S-phase cells. In adults, three stages of mesodermal neoblasts (2, 2-3, and 3) defined by their ultrastructure were found. Stage 1 neoblasts where only seen in hatchlings. These stages either were phases within the S-phase of one neoblast pool or were subsequent stages of differentiating neoblasts, each with its own cell cycle. Regular TEM and immunogold labeling provided the basis for calculating the total number of neoblasts and the ratio of labeled to non-labeled neoblasts. Somatic neoblasts represented 6.5% of the total number of cells. Of these, 27% were labeled in S-phase. Of this fraction, 33% were in stage 2, 46% in stage 2-3, and 21% in stage 3. Immunogold labeling substantiated results concerning the differentiation of neoblasts into somatic cells. Non-labeled stage 2 neoblasts were present, even after a 2-week BrdU exposure. Double labeling of mitoses and FMRF-amide revealed a close spatial relationship of mesodermal neoblasts with the nervous system. Immunogold-labeled sections showed that nearly 70% of S-phase cells were in direct contact or within 5 microm from nerve cords.

  13. Ultrastructure of the surface structures and electron immunogold labeling of peptide immunoreactivity in the nervous system of Pseudothoracocotyla indica (Polyopisthocotylea: Monogenea).

    Science.gov (United States)

    Brennan, G P; Ramasamy, P

    1996-01-01

    Transmission electron microscope studies of the tegument of the tropical marine fish monogenean parasite Pseudothoracocotyla indica describe surface specialisations and detail the ultrastructure of the tegument and the haptor. The tegument consists of a syncytium, numerous electron-dense granules, electron-lucent vesicles and large multivesicular bodies. The posterior tegumental syncytium is infolded to form tegumental ridges that are present on both the ventral and dorsal surfaces. A thin coat of glycocalyx is present on the tegument surface. In contrast, the tegumental syncytium of the haptor is relatively thin, containing electron-dense granules and various-sized electron-lucent vesicles. Exocytosis of the electron-dense and electron-lucent vesicles apparently occurs in the syncytium of the haptor and general body surface. Tegumental damage was observed on the dorsal surface in the mid-body region and may possibly have been due to natural mechanical forces. The haptor consists of electron-dense clamp sclerites embedded within a matrix covered by the tegumental syncytium. The sclerites are connected to each other and to the basal lamina by radially oriented muscle fibres. The haptor is richly supplied with non-myelinated nerve axons. Both uniciliated and non-ciliated presumed sensory structures are present on the body surface and haptor. Uniciliated sensory structures were found mainly around the oral sucker. Groups of neurons and nerve processes containing neurosecretory vesicles were frequently observed in the vicinity of the clamps. Electron immunogold labelling studies demonstrated that neuropeptide F [NPF (Moniezia expansa)] immunoreactivity was confined to electron-dense-cored neurosecretory vesicles in nerve fibres from the posterior and haptor regions of the fluke.

  14. Are Bosonic Replicas Faulty?

    CERN Document Server

    Osipov, Vladimir Al

    2007-01-01

    Motivated by the ongoing discussion about a seeming asymmetry in the performance of fermionic and bosonic replicas, we present an exact, nonperturbative approach to zero-dimensional replica field theories belonging to the broadly interpreted "beta=2" Dyson symmetry class. We then utilise the formalism developed to demonstrate that the bosonic replicas do correctly reproduce the microscopic spectral density in the QCD inspired chiral Gaussian unitary ensemble. This disproves the myth that the bosonic replica field theories are intrinsically faulty.

  15. Crystal Ball Replica

    Science.gov (United States)

    Ajamian, John

    2016-09-01

    The A2 collaboration of the Institute for Nuclear Physics of Johannes Gutenberg University performs research on (multiple) meson photoproduction and nucleon structure and dynamics using a high energy polarized photon beam at specific targets. Particles scattered from the target are detected in the Crystal Ball, or CB. The CB is composed of 672 NaI crystals that surround the target and can analyze particle type and energy of ejected particles. Our project was to create a replica of the CB that could display what was happening in real time on a 3 Dimensional scale replica. Our replica was constructed to help explain the physics to the general public, be used as a tool when calibrating each of the 672 NaI crystals, and to better analyze the electron showering of particles coming from the target. This poster will focus on the hardware steps necessary to construct the replica and wire the 672 programmable LEDS in such a way that they can be mapped to correspond to the Crystal Ball elements. George Washington NSF Grant.

  16. Immunogold-silver staining (IGSS) based U-bent fiberoptic sandwich biosensor

    Science.gov (United States)

    Ramakrishna, B.; Sai, V. V. R.

    2016-11-01

    An evanescent wave absorbance (EWA) based U-bent fiberoptic sandwich immunobiosensor with human IgG detection limits of 6.67 fM (1 pg/ml of human IgG) and 66.7 aM (10 fg/ml of HIgG) is demonstrated by exploiting immunogold labels and subsequently silver enhancement respectively. Such very low detection limits were achieved with the help of enhanced evanescent filed at the bend region of U-bent optical fiber probe that allows efficient interaction of light with 40 nm immunogold labels on the probe surface resulting in measurable optical absorbance changes. The other significant advantages of the demonstrated sensing scheme are low cost optoelectronic instrumentation consisting of an commercial green LED and a photodetector (S150C, Thorlabs Inc.), small volumes of sample and immunogold reagent each of 25 μl and rapid detection in 20 min. These results from the plasmonic fiberoptic biosensor demonstrate its huge potential for development of point-of-care diagnostic devices for sensitive and rapid detection of analytes.

  17. Immunogold quantification of amino acids and proteins in complex subcellular compartments.

    Science.gov (United States)

    Bergersen, Linda H; Storm-Mathisen, Jon; Gundersen, Vidar

    2008-01-01

    An increasing number of imaging techniques are in use to study the localization of molecules involved in cell-to-cell signaling. Here we describe the use of immunogold procedures to detect and quantify molecules on electron micrographs. To measure the areas of the subcellular compartments under investigation, the protocol uses an overlay screen with an array of regularly spaced points. On the basis of this, the densities of the gold-labeled molecules can be calculated. Despite the limited lateral resolution of the immunogold method as used by many investigators ( approximately 30 nm), it is possible to measure the content of molecules associated with tiny tissue compartments, e.g., synaptic vesicles and different types of membrane, such as plasma membranes and vesicle membranes. The quantification protocol can be carried out without using computer programs. The entire protocol can be completed in approximately 15 d.

  18. Hyper-V Replica essentials

    CERN Document Server

    Krstevski, Vangel

    2013-01-01

    a in various deployment scenarios.Hyper-V Replica Essentials is for Windows Server administrators who want to improve their system availability and speed up disaster recovery. You will need experience in Hyper-V deployment because Hyper-V Replica is built in the Hyper-V platform.

  19. Immunogold electron microscopy and confocal analyses reveal distinctive patterns of histone H3 phosphorylation during mitosis in MCF-7 cells.

    Science.gov (United States)

    Yan, Yitang; Cummings, Connie A; Sutton, Deloris; Yu, Linda; Castro, Lysandra; Moore, Alicia B; Gao, Xiaohua; Dixon, Darlene

    2016-04-01

    Histone phosphorylation has a profound impact on epigenetic regulation of gene expression, chromosome condensation and segregation, and maintenance of genome integrity. Histone H3 Serine 10 is evolutionally conserved and heavily phosphorylated during mitosis. To examine Histone H3 Serine 10 phosphorylation (H3S10ph) dynamics in mitosis, we applied immunogold labeling and confocal microscopy to visualize H3S10ph expression in MCF-7 cells. Confocal observations showed that MCF-7 cells had abundant H3S10ph expression in prophase and metaphase. In anaphase, the H3S10ph expression was significantly decreased and displayed only sparsely localized staining that mainly associated with the chromatid tips. We showed that immunogold bead density distribution followed the H3S10ph expression patterns observed in confocal analysis. At a higher magnification in metaphase, the immunogold beads were readily visible and the bead distribution along the condensed chromosomes was distinctive, indicating the specificity and reliability of the immunogold staining procedure. In anaphase, the beads were found to distribute focally in specific regions of chromatids, reinforcing the confocal observations of differential H3 phosphorylation. To our knowledge, this is the first report to show the specific H3S10ph expression with an immunogold technique and transmission electron microscopy. Additionally, with confocal microscopy, we analyzed H3S10ph expression in an immortalized cell line derived from benign uterine smooth muscle tumor cells. H3S10ph epitope was expressed more abundantly during anaphase in the benign tumor cells, and there was no dramatic differential expression within the condensed chromatid clusters as observed in MCF-7 cells. The differences in H3S10ph expression pattern and dynamics may contribute to the differential proliferative potential between benign tumor cells and MCF-7 cells.

  20. Replica trick for rare samples

    Science.gov (United States)

    Rizzo, Tommaso

    2014-05-01

    In the context of disordered systems with quenched Hamiltonians I address the problem of characterizing rare samples where the thermal average of a specific observable has a value different from the typical one. These rare samples can be selected through a variation of the replica trick which amounts to replicating the system and dividing the replicas intwo two groups containing, respectively, M and -M replicas. Replicas in the first (second) group experience a positive (negative) small field O (1/M) conjugate to the observable considered and the M →∞ limit is to be taken in the end. Applications to the random-field Ising model and to the Sherrington-Kirkpatrick model are discussed.

  1. Detection of human papilloma viruses in paraffin wax sections with biotinylated synthetic oligonucleotide probes and immunogold staining.

    Science.gov (United States)

    Cubie, H A; Norval, M

    1989-09-01

    Human papilloma virus was detected by in situ hybridisation in routinely processed paraffin wax sections using a synthetically produced oligonucleotide probe, end-labelled with biotin, and amplified with anti-biotin-immunogold silver staining (anti-biotin-IGSS). This system proved more sensitive than amplification with streptavidin-biotinylated alkaline phosphatase for detecting human papilloma virus type 16 in cervical tissues. The method was successfully combined with antigen staining for papilloma virus common antigens in skin and genital warts. This simple and quick method, using non-radioactively labelled synthetic probes, may be useful for the detection of other viruses in stored material and may be suitable for other double staining procedures.

  2. Replica trick and string winding

    Science.gov (United States)

    Prudenziati, Andrea; Trancanelli, Diego

    2017-07-01

    We apply the replica trick to compute the entropy of a cylinder amplitude in string theory. We focus on the contribution from nonperturbative winding modes and impose tadpole cancellation to understand the correct prescription for integrating over moduli. Choosing the entangling surface to cut longitudinally over the whole length of the cylinder, we obtain an answer that is interpreted as the entropy of a density matrix. We recast this result in target space language, in both the open and closed string picture.

  3. Subcellular distribution and relative expression of fibrocyte markers in the CD/1 mouse cochlea assessed by semiquantitative immunogold electron microscopy.

    Science.gov (United States)

    Mahendrasingam, Shanthini; Bebb, Catherine; Shepard, Ella; Furness, David N

    2011-11-01

    Spiral ligament fibrocytes function in cochlear homeostasis, maintaining the endocochlear potential by participating in potassium recycling, and fibrocyte degeneration contributes to hearing loss. Their superficial location makes them amenable to replacement by cellular transplantation. Fibrocyte cultures offer one source of transplantable cells, but determining what fibrocyte types they contain and what phenotype transplanted cells may adopt is problematic. Here, we use immunogold electron microscopy to assess the relative expression of markers in native fibrocytes of the CD/1 mouse spiral ligament. Caldesmon and aquaporin 1 are expressed more in type III fibrocytes than any other type. S-100 is strongly expressed in types I, II, and V fibrocytes, and α1Na,K-ATPase is expressed strongly only in types II and V. By combining caldesmon or aquaporin 1 with S-100 and α1Na,K-ATPase, a ratiometric analysis of immunogold density distinguishes all except type II and type V fibrocytes. Other putative markers (creatine kinase BB and connective tissue growth factor) did not provide additional useful analytical attributes. By labeling serial sections or by double or triple labeling with combinations of three antibodies, this technique could be used to distinguish all except type II and type V fibrocytes in culture or after cellular transplantation into the lateral wall.

  4. Replica trick and string winding

    CERN Document Server

    Prudenziati, Andrea

    2016-01-01

    We apply the replica trick to compute the entropy of a cylinder amplitude in string theory. We focus on the contribution from non-perturbative winding modes and impose tadpole cancellation to understand the correct prescription for integrating over moduli. Choosing the entangling surface to cut longitudinally over the whole length of the cylinder, we obtain an answer that is interpreted as the entropy of a density matrix. We recast this result in target space language, both in the open and closed string picture.

  5. File-based replica management

    CERN Document Server

    Kunszt, Peter Z; Stockinger, Heinz; Stockinger, Kurt

    2005-01-01

    Data replication is one of the best known strategies to achieve high levels of availability and fault tolerance, as well as minimal access times for large, distributed user communities using a world-wide Data Grid. In certain scientific application domains, the data volume can reach the order of several petabytes; in these domains, data replication and access optimization play an important role in the manageability and usability of the Grid. In this paper, we present the design and implementation of a replica management Grid middleware that was developed within the EDG project left bracket European Data Grid Project (EDG), http://www.eu-egee.org right bracket and is designed to be extensible so that user communities can adjust its detailed behavior according to their QoS requirements.

  6. Detection of alpha-helical coiled-coil dimer formation by spin-labeled synthetic peptides: a model parallel coiled-coil peptide and the antiparallel coiled coil formed by a replica of the ProP C-terminus.

    Science.gov (United States)

    Hillar, Alexander; Tripet, Brian; Zoetewey, David; Wood, Janet M; Hodges, Robert S; Boggs, Joan M

    2003-12-30

    Electron paramagnetic resonance spectroscopy was used to determine relative peptide orientation within homodimeric, alpha-helical coiled-coil structures. Introduction of cysteine (Cys) residues into peptides/proteins for spin labeling allows detection of their oligomerization from exchange broadening or dipolar interactions between residues within 25 A of each other. Two synthetic peptides containing Cys substitutions were used: a 35-residue model peptide and the 30-residue ProP peptide. The model peptide is known to form a stable, parallel homodimeric coiled coil, which is partially destabilized by Cys substitutions at heptad a and d positions (peptides C30a and C33d). The ProP peptide, a 30-residue synthetic peptide, corresponds to residues 468-497 of osmoregulatory transporter ProP from Escherichia coli. It forms a relatively unstable, homodimeric coiled coil that is predicted to be antiparallel in orientation. Cys was introduced in heptad g positions of the ProP peptide, near the N-terminus (K473C, creating peptide C473g) or closer to the center of the sequence (E480C, creating peptide C480g). In contrast to the destabilizing effect of Cys substitution at the core heptad a or d positions of model peptides C30a and C33d, circular dichroism spectroscopy showed that Cys substitutions at the heptad g positions of the ProP peptide had little or no effect on coiled-coil stability. Thermal denaturation analysis showed that spin labeling increased the stability of the coiled coil for all peptides. Strong exchange broadening was detected for both C30a and C33d, in agreement with a parallel structure. EPR spectra of C480g had a large hyperfine splitting of about 90 G, indicative of strong dipole-dipole interactions and a distance between spin-labeled residues of less than 9 A. Spin-spin interactions were much weaker for C473g. These results supported the hypothesis that the ProP peptide primarily formed an antiparallel coiled coil, since formation of a parallel dimer

  7. Study on the distribution of callose and β-1,3-D-glucanase in Chenopodium quinoa by immuno-gold labeling%免疫胶体金标记定位昆诺藜中的胼胝质和胼胝质降解酶

    Institute of Scientific and Technical Information of China (English)

    李云琴; 王华; 谢礼; 洪健

    2014-01-01

    运用免疫胶体金技术研究了感染蚕豆萎蔫病毒2号以及健康昆诺藜细胞中胼胝质和胼胝质降解酶的分布情况。电镜观察发现胶体金特异性标记在含有VP37小管的胞间运动通道周围,其余区域感病和健康细胞的胼胝质及胼胝质降解酶分布差别不大,胼胝质主要分布于细胞间隙的大块电子致密物质以及细胞壁结构发生较大变化的区域,胼胝质降解酶主要分布于筛板、维管束细胞紧贴细胞壁区域的大块电子致密物质上,在细胞壁结构发生较大改变的区域也有胼胝质降解酶的分布。推测胼胝质在昆诺藜细胞中的积累和降解可能与细胞壁结构成分改变有关。%The distribution of callose and β⁃1,3⁃D⁃glucanase in the Broad bean wilt virus 2 ( BBWV 2 ) infected and the healthy Chenopodium quinoa was investigated by using immuno⁃gold labeling with the antibody against callose and β⁃1, 3⁃D⁃glucanase, respectively. The results show that, except for the VP37 intercellular moving cell wall pathways, there is no obvious difference on the distribution of callose and β⁃1,3⁃D⁃glucanase between the infected and healthy cells. Callose is mainly distributed on the regions as bellow:the electron condensed material which located in the intercellular space, the structural altered region of cell wall and the cell wall broken region. Glucanase is mainly distributed on the regions as bellow:the sieve plate, the electron condensed material attached to cell wall in the vascular bundle and the structural altered region of cell wall. From these results, it can be deduced that the accumulation and degradation of callose in C. quinoa is related to the cell wall structural and component alteration.

  8. Replica symmetry breaking for anisotropic magnets with quenched disorder

    Science.gov (United States)

    Kogan, E.; Kaveh, M.

    2017-01-01

    We study critical behaviour of a magnet with cubic anisotropy and quenched scalar disorder which is taken into account by replica method. We derive to first order in ε approximation the renormalization group equations taking into account possible replica symmetry breaking. We study the stability of the replica symmetric fixed points with respect to perturbations without (in general case) replica symmetry. However, we find that if a fixed point is stable with respect to replica symmetric deviations, it is also stable with respect to deviations without replica symmetry.

  9. Replica symmetric spin glass field theory

    Energy Technology Data Exchange (ETDEWEB)

    Temesvari, T. [Research Group for Theoretical Physics of the Hungarian Academy of Sciences, Eoetvoes University, Pazmany Peter setany 1/A, H-1117 Budapest (Hungary)]. E-mail: temtam@helios.elte.hu

    2007-06-18

    A new powerful method to test the stability of the replica symmetric spin glass phase is proposed by introducing a replicon generator function g(v). Exact symmetry arguments are used to prove that its extremum is proportional to the inverse spin glass susceptibility. By the idea of independent droplet excitations a scaling form for g(v) can be derived, whereas it can be exactly computed in the mean field Sherrington-Kirkpatrick model. It is shown by a first order perturbative treatment that the replica symmetric phase is unstable down to dimensions d < or approx. 6, and the mean field scaling function proves to be very robust. Although replica symmetry breaking is escalating for decreasing dimensionality, a mechanism caused by the infrared divergent replicon propagator may destroy the mean field picture at some low enough dimension.

  10. Replica symmetric spin glass field theory

    Science.gov (United States)

    Temesvári, T.

    2007-06-01

    A new powerful method to test the stability of the replica symmetric spin glass phase is proposed by introducing a replicon generator function g(v). Exact symmetry arguments are used to prove that its extremum is proportional to the inverse spin glass susceptibility. By the idea of independent droplet excitations a scaling form for g(v) can be derived, whereas it can be exactly computed in the mean field Sherrington-Kirkpatrick model. It is shown by a first order perturbative treatment that the replica symmetric phase is unstable down to dimensions d≲6, and the mean field scaling function proves to be very robust. Although replica symmetry breaking is escalating for decreasing dimensionality, a mechanism caused by the infrared divergent replicon propagator may destroy the mean field picture at some low enough dimension.

  11. Replica Fourier Transform: Properties and applications

    Directory of Open Access Journals (Sweden)

    A. Crisanti

    2015-02-01

    Full Text Available The Replica Fourier Transform is the generalization of the discrete Fourier Transform to quantities defined on an ultrametric tree. It finds use in conjunction of the replica method used to study thermodynamics properties of disordered systems such as spin glasses. Its definition is presented in a systematic and simple form and its use illustrated with some representative examples. In particular we give a detailed discussion of the diagonalization in the Replica Fourier Space of the Hessian matrix of the Gaussian fluctuations about the mean field saddle point of spin glass theory. The general results are finally discussed for a generic spherical spin glass model, where the Hessian can be computed analytically.

  12. Two phase decision algorithm of replica allocation

    Institute of Scientific and Technical Information of China (English)

    Zuo Chaoshu; Liu Xinsong; Wang Zheng; Li Yi

    2006-01-01

    In distributed parallel server system, location and redundancy of replicas have great influence on availability and efficiency of the system. In order to improve availahility and efficiency of the system, two phase decision algorithm of replica allocation is proposed. The algorithm which makes use of auto-regression model dynamically predicts the future count of READ and WRITE operation, and then determines location and redundancy of replicas by considering availability, CPU and bands of the network. The algorithm can not only ensure the requirement of availability, but also reduce the system resources consumed by all the operations in a great scale. Analysis and test show that communication complexity and time complexity of the algorithm satisfy O( n ), resource optimizing scale increases with the increase of READ count.

  13. Generalized gravitational entropy without replica symmetry

    Science.gov (United States)

    Camps, Joan; Kelly, William R.

    2015-03-01

    We explore several extensions of the generalized entropy construction of Lewkowycz and Maldacena, including a formulation that does not rely on preserving replica symmetry in the bulk. We show that an appropriately general ansatz for the analytically continued replica metric gives us the flexibility needed to solve the gravitational field equations beyond general relativity. As an application of this observation we study EinsteinGauss-Bonnet gravity with a small Gauss-Bonnet coupling and derive the condition that the holographic entanglement entropy must be evaluated on a surface which extremizes the Jacobson-Myers entropy. We find that in both general relativity and Einstein-Gauss-Bonnet gravity replica symmetry breaking terms are permitted by the field equations, suggesting that they do not generically vanish.

  14. Generalized gravitational entropy without replica symmetry

    CERN Document Server

    Camps, Joan

    2014-01-01

    We explore several extensions of the generalized entropy construction of Lewkowycz and Maldacena, including a formulation that does not rely on preserving replica symmetry in the bulk. We show that an appropriately general ansatz for the analytically continued replica metric gives us the flexibility needed to solve the gravitational field equations beyond general relativity. As an application of this observation we study Einstein-Gauss-Bonnet gravity with a small Gauss-Bonnet coupling and derive the condition that the holographic entanglement entropy must be evaluated on a surface which extremizes the Jacobson-Myers entropy. We find that in both general relativity and Einstein-Gauss-Bonnet gravity replica symmetry breaking terms are permitted by the field equations, suggesting that they do not generically vanish.

  15. A simple asynchronous replica-exchange implementation

    CERN Document Server

    Bussi, Giovanni

    2008-01-01

    We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that different replicas are allowed to perform a different number of time-steps between subsequent attempts. The implementation is simple and based on the message-passing interface (MPI). We illustrate the advantages of our scheme with respect to the standard synchronous algorithm and we benchmark it for a model Lennard-Jones liquid on an IBM-LS21 blade center cluster.

  16. RRS: Replica Registration Service for Data Grids

    Energy Technology Data Exchange (ETDEWEB)

    Shoshani, Arie; Sim, Alex; Stockinger, Kurt

    2005-07-15

    Over the last few years various scientific experiments and Grid projects have developed different catalogs for keeping track of their data files. Some projects use specialized file catalogs, others use distributed replica catalogs to reference files at different locations. Due to this diversity of catalogs, it is very hard to manage files across Grid projects, or to replace one catalog with another. In this paper we introduce a new Grid service called the Replica Registration Service (RRS). It can be thought of as an abstraction of the concepts for registering files and their replicas. In addition to traditional single file registration operations, the RRS supports collective file registration requests and keeps persistent registration queues. This approach is of particular importance for large-scale usage where thousands of files are copied and registered. Moreover, the RRS supports a set of error directives that are triggered in case of registration failures. Our goal is to provide a single uniform interface for various file catalogs to support the registration of files across multiple Grid projects, and to make Grid clients oblivious to the specific catalog used.

  17. Immunogold localization of acyl carrier protein in plants and Escherichia coli: Evidence for membrane association in plants.

    Science.gov (United States)

    Slabas, A R; Smith, C G

    1988-08-01

    Immunogold labelling was used to study the distribution of acyl carrier protein (ACP) in Escherichia coli and a variety of plant tissues. In E. coli, ACP is distributed throughout the cytoplasm, confirming the observation of S. Jackowski et al. (1985, J. Bacteriol., 162, 5-8_. In the mesocarp of Avocado (Persea americana) and maturing seeds of oil-seed rape (Brassica napus cv. Jet Neuf), over 95% of the ACP is localised to plastids. The protein is almost exclusively located in the chloroplasts of leaf material from oil-seed rape. Approximately 80% of the gold particles associated with the ACP were further localized to the thylakoid membrane of the chloroplast. Since acetyl-CoA carboxylase has been reported to be localized to the thylakoid membrane (C.G. Kannangara and C.J. Jensen, 1975, Eur. J. Biochem., 54, 25-30), these results are consistent with the view that the two sequential enzymes in fatty-acid synthesis are in close spacial proximity.

  18. Novel algorithm for distributed replicas management based on dynamic programming

    Institute of Scientific and Technical Information of China (English)

    Wang Tao; Lu Xianliang; Hou Mengshu

    2006-01-01

    Replicas can improve the data reliability in distributed system. However, the traditional algorithms for replica management are based on the assumption that all replicas have the uniform reliability, which is inaccurate in some actual systems. To address such problem, a novel algorithm is proposed based on dynamic programming to manage the number and distribution of replicas in different nodes. By using Markov model, replicas management is organized as a multi-phase process, and the recursion equations are provided. In this algorithm, the heterogeneity of nodes, the expense for maintaining replicas and the engaged space have been considered. Under these restricted conditions, this algorithm realizes high data reliability in a distributed system. The results of case analysis prove the feasibility of the algorithm.

  19. An Adaptive Replica Allocation Algorithm in Mobile Ad Hoc Networks

    Institute of Scientific and Technical Information of China (English)

    JingZheng; JinshuSu; KanYang

    2004-01-01

    In mobile ad hoc networks (MANET), nodes move freely and the distribution of access requests changes dynamically. Replica allocation in such a dynamic environment is a significant challenge. In this paoer, a dynamic adaptive replica allocation algorithm that can adapt to the nodes motion is proposed to minimize the communication cost of object access. When changes occur in the access requests of the object or the network topology, each replica node collects access requests from its neighbors and makes decisions locally to expand replica to neighbors or to relinquish the replica. The algorithm dynamically adapts the replica allocation scheme to a local optimal one. Simulation results show that our algorithms efficiently reduce the communication cost of object access in MANET environment.

  20. An Arbitrary 2D Structured Replica Control Protocol

    OpenAIRE

    Basmadjian, Robert; Meer, Hermann,

    2011-01-01

    Traditional replication protocols that logically arrange the replicas into a specific structure have reasonable availability, lower communication cost as well as system load than those that do not require any logical organisation of replicas. We propose in this paper the A2DS protocol: a single protocol that, unlike the existing proposed protocols, can be adapted to any 2D structure. Its read operation is carried out on any replica of every level of the structure whereas write operations are ...

  1. Exchange frequency in replica exchange molecular dynamics

    Science.gov (United States)

    Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E.

    2008-01-01

    The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.

  2. Reliability of the impression replica technique.

    Science.gov (United States)

    Falk, Anders; Vult von Steyern, Per; Fransson, Håkan; Thorén, Margareta Molin

    2015-01-01

    The aim of this study was to evaluate the reliability of the impression replica technique with a four-unit zirconia fixed dental prosthesis (FDP). Marginal and internal fit were measured by repeatedly placing the FDP on an epoxy cast using light-body silicone material corresponding to cement. All measured marginal and internal fit points showed varying values. The greatest variations were seen at the most distal margin (33 μm) and at the distal abutment of the FDP (77 μm). The results showed that the technique gives moderate variations and is a useful method to evaluate marginal and internal fit.

  3. Spin Glass Field Theory with Replica Fourier Transforms

    Science.gov (United States)

    Pimentel, Iveta R.; De Dominicis, Cirano

    We develop a field theory for spin glasses using Replica Fourier Transforms (RFT). We present the formalism for the case of replica symmetry and the case of replica symmetry breaking on an ultrametric tree, with the number of replicas n and the number of replica symmetry breaking steps R generic integers. We show how the RFT applied to the two-replica fields allows to construct a new basis which block-diagonalizes the four-replica mass-matrix, into the replicon, anomalous and longitudinal modes. The eigenvalues are given in terms of the mass RFT and the propagators in the RFT space are obtained by inversion of the block-diagonal matrix. The formalism allows to express any i-replica vertex in the new RFT basis and hence enables to perform a standard perturbation expansion. We apply the formalism to calculate the contribution of the Gaussian fluctuations around the Parisi's solution for the free-energy of an Ising spin glass.

  4. Fret Replica Inspection Laser Scanner (FRILS)

    Energy Technology Data Exchange (ETDEWEB)

    Kretz, S.; Hanley, K., E-mail: steve.kretz@opg.com, E-mail: kelly.hanley@opg.com [Ontario Power Generation, Inspection Maintenance and Commercial Services, Pickering, Ontario (Canada)

    2008-07-01

    In the stress analysis of flaws and artifacts found in pressure tubes, it is crucial to have detailed knowledge of the flaw geometry. Fuel channel inspections by ultrasonic or eddy current inspection methods alone cannot provide the complete required geometry information. Replicas, which are a negative impression of surface pressure tube indications, are scanned with a laser system which will provide the additional detail required. FRILS was initially developed in 1993 to establish in-house capability of profiling indications on the inside diameter surface of pressure tubes. The need of this profiling was initially a response to the discovery of fuel bundle bearing pad fretting (FBBPF) caused by flow induced fuel bundle vibration. The benefits of the system were soon realized as a tool for profiling debris type indications. Although the primary use of FRILS is to profile FBBBF and Debris Fretting, since its inception the FRILS inspection system has become an instrumental tool in flaw assessment for: Fuel Bundle Bearing Pad Frets (FBBPF); Debris Frets; Scratches; Crevice Corrosion; Oxide Jacking; Areas of surface roughness; and, Weld Profiling. Replicas are collected via acquisition from tooling on both the Channel and Gauging Apparatus for Reactors (CIGAR) and the Advanced Non-Destructive Examination (ANDE) systems. The ANDE system is a high speed data acquisition system which includes both an ultrasonic inspection tool and a replication tool. Although both of these tools were designed to be delivered with the UDM, the platform for these tools was built with flexibility allowing for adoption to other delivery systems. These tools were based on the experience of the CIGAR inspection system. The CIGAR system has also undergone many system upgrades resulting in reduced inspection times. The FRILS system - Fret Replication Inspection Laser Scanner system was developed and has been upgraded to meet the demands of the improved inspection and replication systems. FRILS

  5. 77 FR 5767 - Application(s) for Duty-Free Entry of Scientific Instruments

    Science.gov (United States)

    2012-02-06

    ... refining the provisional localization of different calcium channel subunits from fluorescence microscopy initially by super resolution STED and then by immunogold freeze-fracture replica labeling. The objectives... structures, and optical characterization using high resolution spectroscopy. Justification for...

  6. Ultrastructural immunogold localization of major sperm protein (MSP) in spermatogenic cells of the nematode Acrobeles complexus (Nematoda, Rhabditida).

    Science.gov (United States)

    Yushin, Vladimir V; Claeys, Myriam; Bert, Wim

    2016-10-01

    The nematode spermatozoa represent a highly modified (aberrant) type of male gametes that lack a flagellum but for which the process of spermatogenesis culminates in the production of a crawling spermatozoon on the basis of the cytoskeletal component known as "major sperm protein", or MSP. MSP is also known as an important hormone triggering oocyte maturation and ovulation in the model nematode Caenorhabditis elegans, where this protein was first identified. However, direct evidence of MSP localization and of its fate in nematode spermatogenic cells is rare. In this study, the spermatogenesis and sperm structure in the rhabditid nematode Acrobeles complexus (Rhabditida: Tylenchina: Cephalobomorpha: Cephaloboidea: Cephalobidae) has been examined with electron microscopy. Morphological observations were followed by high-pressure freezing and freeze-substitution fixation which allows post-embedding immunogold localization of MSP in all stages of sperm development using antibodies raised for MSP of C. elegans. In spermatocytes, synthetic activity results in the development of specific cellular components, fibrous bodies (FB) and membranous organelles (MO), which appear as FB-MO complexes where the filamentous matter of FB has been MSP-labeled. The spermatids subdivide into a residual body with superfluous cytoplasm, and a main cell body which contains nucleus, mitochondria and FB-MO complexes. These complexes dissociate into individual components, MO and FB, with the MSP being localized in FB. Immature spermatozoa from testes are opaque cells where a centrally located nucleus is surrounded by mitochondria, MO and FB clustered together, the MSP still being localized only in FB. Cytoplasm of mature spermatozoa from spermatheca is segregated into external pseudopods lacking organelles and a central cluster of mitochondria with intact MO surrounding the central nucleus. The FB ultimately disappear, and the MSP labeling becomes concentrated in the filamentous content of

  7. Asynchronous replica exchange software for grid and heterogeneous computing

    Science.gov (United States)

    Gallicchio, Emilio; Xia, Junchao; Flynn, William F.; Zhang, Baofeng; Samlalsingh, Sade; Mentes, Ahmet; Levy, Ronald M.

    2015-11-01

    Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.

  8. Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing

    Science.gov (United States)

    Gallicchio, Emilio; Xia, Junchao; Flynn, William F.; Zhang, Baofeng; Samlalsingh, Sade; Mentes, Ahmet; Levy, Ronald M.

    2015-01-01

    Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices. PMID:27103749

  9. Response Time Optimization for Replica Selection Service in Data Grids

    Directory of Open Access Journals (Sweden)

    Husni H.E. AL-Mistarihi

    2008-01-01

    Full Text Available Problem Statement: Data Grid architecture provides a scalable infrastructure for grid services in order to manage data files and their corresponding replicas that were distributed across the globe. The grid services are designed to support a variety of data grid applications (jobs and projects. Replica selection is a high-level service that chooses a replica location from among many distributed replicas with the minimum response time for the users' jobs. Estimating the response time accurately in the grid environment is not an easy task. The current systems expose high response time in selecting the required replicas because the response time is estimated by considering the data transfer time only. Approach: We proposed a replica selection system that selects the best replica location for the users' running jobs in a minimum response time that can be estimated by considering new factors besides the data transfer time, namely, the storage access latency and the replica requests that waiting in the storage queue. Results: The performance of the proposed system was compared with a similar system that exists in the literature namely, SimpleOptimiser. The simulation results demonstrated that our system performed better than the SimpleOptimiser on an average of 6%. Conclusions: The proposed system can select the best replica location in a lesser response time than the SimpleOptimise. The efficiency of the proposed system is 6% higher than the SimpleOptimise. The efficiency level has a high impact on the quality of service that is perceived by grid users in a data grid environment where the data files are relatively big. For example, the data files produced from the scientific applications are of the size hundreds of Terabytes.

  10. Immunogold silver staining associated with epi-fluorescence for cucumber mosaic virus localisation on semi-thin sections of banana tissues

    Directory of Open Access Journals (Sweden)

    B Helliot

    2009-08-01

    Full Text Available The immunogold-silver staining (IGSS technique in combination with epi-fluorescence detection was used to localise cucumber mosaic virus (CMV particles within banana infected tissues. For this purpose, tissue samples (2 mm3 were excised from CMV-infected and highly proliferating meristem cultures of Williams BSJ banana (ITC. 0570, AAA, Cavendish subgroup. These samples were immediately fixed in a 2% paraformaldehyde/0.25% glutaraldehyde mixture, dehydrated in ethanol, and finally embedded in L.R.White resin. Semi-thin sections were cut, mounted on clean treated glass slides and immunostained for CMV particles using gold-labelled secondary antibodies and silver enhancement. Sections were counterstained with basic fuchsin and examined using laser scanning confocal microscopy. Negative controls included immuno-stained samples excised from non-virus infected material as well as infected material on which primary or secondary antibodies were not applied. Images of autofluorescence (in red and of epi-reflectance of silver-enhanced immunogold particles (in green were recorded separately and merged, allowing the specific localisation of CMV particles at the cellular level on semi-thin sections of aldehyde-fixed banana tissues. The main advantage of this analytical approach compared to previously published protocols is that it combines a fast staining procedure, stable preparation, a high resolution, and a narrow plane of focus with the flexibility in generation, processing and analysis of images offered by laser scanning confocal microscopy. Finally, the presence of numerous CMV particles within banana meristems constitutes a clear explanation of the very low CMV elimination efficiency when using meristem- tip culture alone.

  11. SRF Cavity Surface Topography Characterization Using Replica Techniques

    Energy Technology Data Exchange (ETDEWEB)

    C. Xu, M.J. Kelley, C.E. Reece

    2012-07-01

    To better understand the roll of topography on SRF cavity performance, we seek to obtain detailed topographic information from the curved practical cavity surfaces. Replicas taken from a cavity interior surface provide internal surface molds for fine Atomic Force Microscopy (AFM) and stylus profilometry. In this study, we confirm the replica resolution both on surface local defects such as grain boundary and etching pits and compare the surface uniform roughness with the aid of Power Spectral Density (PSD) where we can statistically obtain roughness parameters at different scales. A series of sampling locations are at the same magnetic field chosen at the same latitude on a single cell cavity to confirm the uniformity. Another series of sampling locations at different magnetic field amplitudes are chosen for this replica on the same cavity for later power loss calculation. We also show that application of the replica followed by rinsing does not adversely affect the cavity performance.

  12. Hamiltonian replica-exchange in GROMACS: a flexible implementation

    OpenAIRE

    Bussi, Giovanni

    2013-01-01

    A simple and general implementation of Hamiltonian replica exchange for the popular molecular-dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can be used for the different replicas without incurring in any significant performance penalty. The implementation was validated on a simple toy model - alanine dipeptide in water - and applied to study the rearrangement of an RNA tetraloop, where it was used to compare recently proposed force-field co...

  13. Hamiltonian replica-exchange in GROMACS: a flexible implementation

    CERN Document Server

    Bussi, Giovanni

    2013-01-01

    A simple and general implementation of Hamiltonian replica exchange for the popular molecular-dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can be used for the different replicas without incurring in any significant performance penalty. The implementation was validated on a simple toy model - alanine dipeptide in water - and applied to study the rearrangement of an RNA tetraloop, where it was used to compare recently proposed force-field corrections.

  14. Elastomer and resin replicas for sem observation of metallic materials

    OpenAIRE

    Palin-Luc, Thierry; Sellier, E.; D?Errico, F.; Vanhaeren, M.

    2002-01-01

    International audience; The replica technique is often used to study damage evolution at the surface of specimens or industrial components and understand the physicial phenomena responsible for fatigue crack initiation before failure. Replicas are usually made from acetate cellulose film. This paper presents an alternative technique generally used by archaeologists to study lithic use-wear and bone modification. A mold is made from a dental elastomer (silicon based impression material) and a ...

  15. JavaFIRE: A Replica and File System for Grids

    Science.gov (United States)

    Petek, Marko; da Silva Gomes, Diego; Resin Geyer, Claudio Fernando; Santoro, Alberto; Gowdy, Stephen

    2012-12-01

    The work is focused on the creation of a replica and file transfers system for Computational Grids inspired on the needs of the High Energy Physics (HEP). Due to the high volume of data created by the HEP experiments, an efficient file and dataset replica system may play an important role on the computing model. Data replica systems allow the creation of copies, distributed between the different storage elements on the Grid. In the HEP context, the data files are basically immutable. This eases the task of the replica system, because given sufficient local storage resources any dataset just needs to be replicated to a particular site once. Concurrent with the advent of computational Grids, another important theme in the distributed systems area that has also seen some significant interest is that of peer-to-peer networks (p2p). P2p networks are an important and evolving mechanism that eases the use of distributed computing and storage resources by end users. One common technique to achieve faster file download from possibly overloaded storage elements over congested networks is to split the files into smaller pieces. This way, each piece can be transferred from a different replica, in parallel or not, optimizing the moments when the network conditions are better suited to the transfer. The main tasks achieved by the system are: the creation of replicas, the development of a system for replicas transfer (RFT) and for replicas location (RLS) with a different architecture that the one provided by Globus and the development of a system for file transfer in pieces on computational grids with interfaces for several storage elements. The RLS uses a p2p overlay based on the Kademlia algorithm.

  16. Injection Compression Molding of Replica Molds for Nanoimprint Lithography

    Directory of Open Access Journals (Sweden)

    Keisuke Nagato

    2014-03-01

    Full Text Available As a breakthrough in the cost and durability of molds for nanoimprint lithography (NIL, replica molds are fabricated by injection compression molding (ICM. ICM is commonly used for optical disks such as DVDs or Blu-ray disks and is also a practical fabrication method for nanostructures. In this paper, I successfully demonstrated the fabrication of cycloolefin polymer replica molds with structures smaller than 60 nm by ICM. Furthermore, ultraviolet (UV-NIL using these replica molds was demonstrated. UV-cured resist was replicated over an area of 60 mm diameter. The degree of replication by UV-NIL in the first usage of each replica mold had good repeatability. Because ICM is a high-throughput, low-cost process, the replica mold can be disposed of after a certain time for UV-NIL. This method leads to a high-integrity UV-NIL process of patterned media because multiple large-area replica molds can be fabricated simultaneously.

  17. Bayesian ensemble refinement by replica simulations and reweighting.

    Science.gov (United States)

    Hummer, Gerhard; Köfinger, Jürgen

    2015-12-28

    We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

  18. Replica Fourier Tansforms on Ultrametric Trees, and Block-Diagonalizing Multi-Replica Matrices

    Science.gov (United States)

    de Dominicis, C.; Carlucci, D. M.; Temesvári, T.

    1997-01-01

    The analysis of objects living on ultrametric trees, in particular the block-diagonalization of 4-replica matrices M^{α β;γ^δ}, is shown to be dramatically simplified through the introduction of properly chosen operations on those objects. These are the Replica Fourier Transforms on ultrametric trees. Those transformations are defined and used in the present work. On montre que l'analyse d'objets vivant sur un arbre ultramétrique, en particulier, la diagonalisation par blocs d'une matrice M^{α β;γ^δ} dépendant de 4-répliques, se simplifie de façon dramatique si l'on introduit les opérations appropriées sur ces objets. Ce sont les Transformées de Fourier de Répliques sur un arbre ultramétrique. Ces transformations sont définies et utilisées dans le présent travail.

  19. Hamiltonian replica exchange molecular dynamics using soft-core interactions.

    Science.gov (United States)

    Hritz, Jozef; Oostenbrink, Chris

    2008-04-14

    To overcome the problem of insufficient conformational sampling within biomolecular simulations, we have developed a novel Hamiltonian replica exchange molecular dynamics (H-REMD) scheme that uses soft-core interactions between those parts of the system that contribute most to high energy barriers. The advantage of this approach over other H-REMD schemes is the possibility to use a relatively small number of replicas with locally larger differences between the individual Hamiltonians. Because soft-core potentials are almost the same as regular ones at longer distances, most of the interactions between atoms of perturbed parts will only be slightly changed. Rather, the strong repulsion between atoms that are close in space, which in many cases results in high energy barriers, is weakened within higher replicas of our proposed scheme. In addition to the soft-core interactions, we proposed to include multiple replicas using the same Hamiltonian/level of softness. We have tested the new protocol on the GTP and 8-Br-GTP molecules, which are known to have high energy barriers between the anti and syn conformation of the base with respect to the sugar moiety. During two 25 ns MD simulations of both systems the transition from the more stable to the less stable (but still experimentally observed) conformation is not seen at all. Also temperature REMD over 50 replicas for 1 ns did not show any transition at room temperature. On the other hand, more than 20 of such transitions are observed in H-REMD using six replicas (at three different Hamiltonians) during 6.8 ns per replica for GTP and 12 replicas (at six different Hamiltonians) during 8.7 ns per replica for 8-Br-GTP. The large increase in sampling efficiency was obtained from an optimized H-REMD scheme involving soft-core potentials, with multiple simulations using the same level of softness. The optimization of the scheme was performed by fast mimicking [J. Hritz and C. Oostenbrink, J. Chem. Phys. 127, 204104 (2007)].

  20. High-resolution immunogold localization of AMPA type glutamate receptor subunits at synaptic and non-synaptic sites in rat hippocampus.

    Science.gov (United States)

    Baude, A; Nusser, Z; Molnár, E; McIlhinney, R A; Somogyi, P

    1995-12-01

    particles for the GluRA, GluRB/C and GluRD subunits were present at type 1 synaptic membrane specializations on dendritic spines of pyramidal cells throughout all layers of the CA1 and CA3 areas. The most densely labelled synapses tended to be on the largest spines and many smaller spines remained unlabelled. Immunoparticle density at type 1 synapses on dendritic shafts of some non-principal cells was consistently higher than at labelled synapses of dendritic spines of pyramidal cells. Synapses established between dendritic spines and mossy fibre terminals, were immunoreactive for all studied subunits in stratum lucidum of the CA3 area. The postembedding immunogold method revealed that the AMPA type receptors are concentrated within the main body of the anatomically defined type 1 (asymmetrical) synaptic junction. Often only a part of the membrane specialization showed clustered immunoparticles. There was a sharp decrease in immunoreactive receptor density at the edge of the synaptic specialization. Immunolabelling was consistently demonstrated at extrasynaptic sites on dendrites, dendritic spines and somata. The results demonstrate that the GluRA, B/C and D subunits of the AMPA type glutamate receptor are present in many of the glutamatergic synapses formed by the entorhinal, CA3 pyramidal and mossy fibre terminals. Some interneurons have a higher density of AMPA type receptors in their asymmetrical afferent synapses than pyramidal cells. This may contribute to a lower activation threshold of interneurons as compared to principal cells by the same afferents in the hippocampal formation.

  1. Standard practice for production and evaluation of field metallographic replicas

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2001-01-01

    1.1 This practice covers recognized methods for the preparation and evaluation of cellulose acetate or plastic film replicas which have been obtained from metallographically prepared surfaces. It is designed for the evaluation of replicas to ensure that all significant features of a metallographically prepared surface have been duplicated and preserved on the replica with sufficient detail to permit both LM and SEM examination with optimum resolution and sensitivity. 1.2 This practice may be used as a controlling document in commercial situations. 1.3 The values stated in SI units are to be regarded as the standard. Inch-pound units given in parentheses are for information only. 1.4 This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard to establish appropriate safety and health practices and determine the applicability of regulatory limitations prior to use.

  2. Time evolution of the autocorrelation function in dynamical replica theory

    Science.gov (United States)

    Sakata, A.

    2013-04-01

    Asynchronous dynamics given by the master equation in the Sherrington-Kirkpatrick (SK) spin-glass model is studied based on dynamical replica theory (DRT) with an extension to take into account the autocorrelation function. The dynamical behaviour of the system is approximately described by dynamical equations of the macroscopic quantities: magnetization, energy contributed by randomness and the autocorrelation function. The dynamical equations under the replica symmetry assumption are derived by introducing the subshell equipartitioning assumption and exploiting the replica method. The obtained dynamical equations are compared with Monte Carlo simulations, and it is demonstrated that the proposed formula describes well the time evolution of the autocorrelation function in some parameter regions. The study offers a reasonable description of the autocorrelation function in the SK spin-glass system.

  3. Fractographic ceramic failure analysis using the replica technique

    Science.gov (United States)

    Scherrer, Susanne S.; Quinn, Janet B.; Quinn, George D.; Anselm Wiskott, H. W.

    2007-01-01

    Objectives To demonstrate the effectiveness of in vivo replicas of fractured ceramic surfaces for descriptive fractography as applied to the analysis of clinical failures. Methods The fracture surface topography of partially failed veneering ceramic of a Procera Alumina molar and an In Ceram Zirconia premolar were examined utilizing gold-coated epoxy poured replicas viewed using scanning electron microscopy. The replicas were inspected for fractographic features such as hackle, wake hackle, twist hackle, compression curl and arrest lines for determination of the direction of crack propagation and location of the origin. Results For both veneering ceramics, replicas provided an excellent reproduction of the fractured surfaces. Fine details including all characteristic fracture features produced by the interaction of the advancing crack with the material's microstructure could be recognized. The observed features are indicators of the local direction of crack propagation and were used to trace the crack's progression back to its initial starting zone (the origin). Drawbacks of replicas such as artifacts (air bubbles) or imperfections resulting from inadequate epoxy pouring were noted but not critical for the overall analysis of the fractured surfaces. Significance The replica technique proved to be easy to use and allowed an excellent reproduction of failed ceramic surfaces. It should be applied before attempting to remove any failed part remaining in situ as the fracture surface may be damaged during this procedure. These two case studies are intended as an introduction for the clinical researcher in using qualitative (descriptive) fractography as a tool for understanding fracture processes in brittle restorative materials and, secondarily, to draw conclusions as to possible design inadequacies in failed restorations. PMID:17270267

  4. Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.

    Science.gov (United States)

    Zhang, Bin W; Dai, Wei; Gallicchio, Emilio; He, Peng; Xia, Junchao; Tan, Zhiqiang; Levy, Ronald M

    2016-08-25

    Replica exchange molecular dynamics is a multicanonical simulation technique commonly used to enhance the sampling of solvated biomolecules on rugged free energy landscapes. While replica exchange is relatively easy to implement, there are many unanswered questions about how to use this technique most efficiently, especially because it is frequently the case in practice that replica exchange simulations are not fully converged. A replica exchange cycle consists of a series of molecular dynamics steps of a set of replicas moving under different Hamiltonians or at different thermodynamic states followed by one or more replica exchange attempts to swap replicas among the different states. How the replica exchange cycle is constructed affects how rapidly the system equilibrates. We have constructed a Markov state model of replica exchange (MSMRE) using long molecular dynamics simulations of a host-guest binding system as an example, in order to study how different implementations of the replica exchange cycle can affect the sampling efficiency. We analyze how the number of replica exchange attempts per cycle, the number of MD steps per cycle, and the interaction between the two parameters affects the largest implied time scale of the MSMRE simulation. The infinite swapping limit is an important concept in replica exchange. We show how to estimate the infinite swapping limit from the diagonal elements of the exchange transition matrix constructed from MSMRE "simulations of simulations" as well as from relatively short runs of the actual replica exchange simulations.

  5. Replica calibration artefacts for optical 3D scanning of micro parts

    DEFF Research Database (Denmark)

    De Chiffre, Leonardo; Carmignato, S.; Cantatore, Angela

    2009-01-01

    This work deals with development of calibration artefacts produced by using hard replica materials, achieving high quality geometrical reproduction of suitable reference artefacts, high stability, and high surface cooperativeness. An investigation was carried out using a replica material for dental...

  6. Data-Replicas Scheduler for Heterogeneous MapReduce Cluster

    Directory of Open Access Journals (Sweden)

    Yang Yang

    2013-05-01

    Full Text Available Large scale data processing has rapidly increased in nowadays. MapReduce programming model, which is firstly mentioned in functional languages, appeared in distributed system and perform excellently in large scale data processing since 2006. Hadoop, which is the most popular framework of open-sourced MapReduce runtime environment, supplies reliable, scalable and distributed system processing large scale data across clusters of computers using this virtue programming model. In this system, files are split into many blocks and all blocks are replicated over several computers in clusters. To process these blocks efficiently, each job runs parallel and is divided into many tasks which deals with a file block. In order to fully take advantage of network bandwidth these systems, data locality is paid more and more attentions. Considering the existence of data-replica blocks, we propose a data-replicas scheduler which includes task scheduling and data allocation. The data-replicas scheduler takes fully advantage of data replicas in local Data node, reduce the costs of data transfer and improve the system performance. The results of experiments show that our scheduler not only improves the CPU ratio, but also reduces the packets that transfer in the network.

  7. Replicas in Caravaggio's paintings: the correct use of scientific analysis

    Science.gov (United States)

    Diana, Maurizio; Moioli, Pietro; Seccaroni, Claudio

    1998-05-01

    Painting techniques and materials employed by Caravaggio are analyzed by X-ray fluorescence and radiography of unquestioned genuine works and compared to replicas of his earlier work. This approach is important in the attribution of recently discovered paintings and copies from the XVII century.

  8. Replica-Based High-Performance Tuple Space Computing

    DEFF Research Database (Denmark)

    Andric, Marina; De Nicola, Rocco; Lluch Lafuente, Alberto

    2015-01-01

    We present the tuple-based coordination language RepliKlaim, which enriches Klaim with primitives for replica-aware coordination. Our overall goal is to offer suitable solutions to the challenging problems of data distribution and locality in large-scale high performance computing. In particular,...

  9. Amplification of resonant Rayleigh light scattering response using immunogold colloids for detection of lysozyme.

    Science.gov (United States)

    Truong, Phuoc Long; Choi, Seung Phill; Sim, Sang Jun

    2013-10-25

    A strategy for attomolar-level detection of small molecule-size proteins is reported based on Rayleigh light scattering spectroscopy of individual nanoplasmonic aptasensors by exploiting the outstanding characteristics of gold colloids to amplify the nontransparent resonant signal at ultralow analyte concentrations. The fabrication method utilizes thiol-mediated adsorption of a DNA aptamer on the immobilized Au nanoparticle surface, the interfacial binding characteristics of the aptamer with its target molecules, and the antibody-antigen interaction through plasmonic resonance coupling of the Au nanoparticles. Using lysozyme as a model analyte for disease detection, the detection limit of the aptasensor is ∼7 × 10(3) aM, corresponding to the LSPR λmax shift of ∼2.25 nm. Up to a 380% increase in the localized resonant λmax shift is demonstrated upon antibody binding to the analyte compared to the primary response during signal amplification using immunogold colloids. This enhancement leads to a limit of detection of ∼7 aM, which is an improvement of three orders of magnitude. The results demonstrate substantial promise for developing coupled plasmonic nanostructures for ultrasensitive detection of various biological and chemical analytes. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Spontaneous versus explicit replica symmetry breaking in the theory of disordered systems

    Science.gov (United States)

    Mouhanna, D.; Tarjus, G.

    2010-05-01

    We investigate the relation between spontaneous and explicit replica symmetry breaking in the theory of disordered systems. On general ground, we prove the equivalence between the replicon operator associated with the stability of the replica-symmetric solution in the standard replica scheme and the operator signaling a breakdown of the solution with analytic field dependence in a scheme in which replica symmetry is explicitly broken by applied sources. This opens the possibility to study, via the recently developed functional renormalization group, unresolved questions related to spontaneous replica symmetry breaking and spin-glass behavior in finite-dimensional disordered systems.

  11. Thiol synthetases of legumes: immunogold localization and differential gene regulation by phytohormones.

    Science.gov (United States)

    Clemente, Maria R; Bustos-Sanmamed, Pilar; Loscos, Jorge; James, Euan K; Pérez-Rontomé, Carmen; Navascués, Joaquín; Gay, Marina; Becana, Manuel

    2012-06-01

    In plants and other organisms, glutathione (GSH) biosynthesis is catalysed sequentially by γ-glutamylcysteine synthetase (γECS) and glutathione synthetase (GSHS). In legumes, homoglutathione (hGSH) can replace GSH and is synthesized by γECS and a specific homoglutathione synthetase (hGSHS). The subcellular localization of the enzymes was examined by electron microscopy in several legumes and gene expression was analysed in Lotus japonicus plants treated for 1-48 h with 50 μM of hormones. Immunogold localization studies revealed that γECS is confined to chloroplasts and plastids, whereas hGSHS is also in the cytosol. Addition of hormones caused differential expression of thiol synthetases in roots. After 24-48 h, abscisic and salicylic acids downregulated GSHS whereas jasmonic acid upregulated it. Cytokinins and polyamines activated GSHS but not γECS or hGSHS. Jasmonic acid elicited a coordinated response of the three genes and auxin induced both hGSHS expression and activity. Results show that the thiol biosynthetic pathway is compartmentalized in legumes. Moreover, the similar response profiles of the GSH and hGSH contents in roots of non-nodulated and nodulated plants to the various hormonal treatments indicate that thiol homeostasis is independent of the nitrogen source of the plants. The differential regulation of the three mRNA levels, hGSHS activity, and thiol contents by hormones indicates a fine control of thiol biosynthesis at multiple levels and strongly suggests that GSH and hGSH play distinct roles in plant development and stress responses.

  12. ATLAS Replica Management in Rucio: Replication Rules and Subscriptions

    CERN Document Server

    Barisits, M; The ATLAS collaboration; Garonne, V; Lassnig, M; Stewart, G; Beermann, T; Vigne, R; Goossens, L; Nairz, A; Molfetas, A

    2014-01-01

    The ATLAS Distributed Data Management system stores more than 150PB of physics data across 120 sites globally. To cope with the anticipated ATLAS workload of the coming decade, Rucio, the next-generation data management system has been developed. Replica management, as one of the keys aspects of the system, has to satisfy critical performance requirements in order to keep pace with the experiment’s high rate of continual data generation. The challenge lies in meeting these performance objectives while still giving the system users and applications a powerful toolkit to control their data workflows. In this work we present the concept, design and implementation of the replica management in Rucio. We will specifically introduce the workflows behind replication rules, their formal language definition, weighting and site selection. Furthermore we will present the subscription component, which offers functionality for users to proclaim interest in data that has not been created yet. This contribution describes t...

  13. ATLAS Replica Management in Rucio: Replication Rules and Subscriptions

    CERN Document Server

    Barisits, M; The ATLAS collaboration; Garonne, V; Lassnig, M; Stewart, G; Beermann, T; Vigne, R; Goossens, L; Nairz, A; Molfetas, A

    2013-01-01

    The ATLAS Distributed Data Management system stores more than 150PB of physics data across 120 sites globally. To cope with the anticipated ATLAS workload of the coming decade, Rucio, the next-generation data management system has been developed. Replica management, as one of the keys aspects of the system, has to satisfy critical performance requirements in order to keep pace with the experiment’s high rate of continual data generation. The challenge lies in meeting these performance objectives while still giving the system users and applications a powerful toolkit to control their data workflows. In this work we present the concept, design and implementation of the replica management in Rucio. We will specifically introduce the workflows behind replication rules, their formal language definition, weighting and site selection. Furthermore we will present the subscription component, which offers functionality for users to proclaim interest in data that has not been created yet. This contribution describes t...

  14. An adaptive range-query optimization technique with distributed replicas

    Institute of Scientific and Technical Information of China (English)

    Sayar Ahmet; Pierce Marlon; Fox C.Geoffrey

    2014-01-01

    Replication is an approach often used to speed up the execution of queries submitted to a large dataset. A compile-time/run-time approach is presented for minimizing the response time of 2-dimensional range when a distributed replica of a dataset exists. The aim is to partition the query payload (and its range) into subsets and distribute those to the replica nodes in a way that minimizes a client’s response time. However, since query size and distribution characteristics of data (data dense/sparse regions) in varying ranges are not known a priori, performing efficient load balancing and parallel processing over the unpredictable workload is difficult. A technique based on the creation and manipulation of dynamic spatial indexes for query payload estimation in distributed queries was proposed. The effectiveness of this technique was demonstrated on queries for analysis of archived earthquake-generated seismic data records.

  15. Replica symmetry breaking in cold atoms and spin glasses

    Science.gov (United States)

    Rotondo, P.; Tesio, E.; Caracciolo, S.

    2015-01-01

    We consider a system composed by N atoms trapped within a multimode cavity, whose theoretical description is captured by a disordered multimode Dicke model. We show that in the resonant, zero-field limit the system exactly realizes the Sherrington-Kirkpatrick model. Upon a redefinition of the temperature, the same dynamics is realized in the dispersive, strong-field limit. This regime also gives access to spin-glass observables which can be used to detect replica symmetry breaking.

  16. Replica inference approach to unsupervised multiscale image segmentation.

    Science.gov (United States)

    Hu, Dandan; Ronhovde, Peter; Nussinov, Zohar

    2012-01-01

    We apply a replica-inference-based Potts model method to unsupervised image segmentation on multiple scales. This approach was inspired by the statistical mechanics problem of "community detection" and its phase diagram. Specifically, the problem is cast as identifying tightly bound clusters ("communities" or "solutes") against a background or "solvent." Within our multiresolution approach, we compute information-theory-based correlations among multiple solutions ("replicas") of the same graph over a range of resolutions. Significant multiresolution structures are identified by replica correlations manifest by information theory overlaps. We further employ such information theory measures (such as normalized mutual information and variation of information), thermodynamic quantities such as the system entropy and energy, and dynamic measures monitoring the convergence time to viable solutions as metrics for transitions between various solvable and unsolvable phases. Within the solvable phase, transitions between contending solutions (such as those corresponding to segmentations on different scales) may also appear. With the aid of these correlations as well as thermodynamic measures, the phase diagram of the corresponding Potts model is analyzed at both zero and finite temperatures. Optimal parameters corresponding to a sensible unsupervised segmentations appear within the "easy phase" of the Potts model. Our algorithm is fast and shown to be at least as accurate as the best algorithms to date and to be especially suited to the detection of camouflaged images.

  17. Biomimetic zinc oxide replica with structural color using butterfly (Ideopsis similis) wings as templates.

    Science.gov (United States)

    Zhang, Wang; Zhang, Di; Fan, Tongxiang; Ding, Jian; Gu, Jiajun; Guo, Qixin; Ogawa, Hiroshi

    2006-09-01

    Nano-structured colorful zinc oxide (ZnO) replicas were produced using the wings of the Ideopsis similis butterfly as templates. The ZnO replicas we obtained exhibit iridescence, which was clearly observed under an optical microscope (OM). Field emission scanning electron microscope analysis shows that all the microstructure details are maintained faithfully in the ZnO replica. A computer model was established to simulate the diffraction spectral results, which agreed well with the OM images.

  18. Novel method of simultaneous multiple immunogold localization on resin sections in high resolution scanning electron microscopy.

    Science.gov (United States)

    Nebesarova, Jana; Wandrol, Petr; Vancova, Marie

    2016-01-01

    We present a new method of multiple immunolabeling that is suitable for a broad spectrum of biomedical applications. The general concept is to label both sides of the ultrathin section with the thickness of 70-80 nm with different antibodies conjugated to gold nanoparticles and to distinguish the labeled side by advanced imaging methods with high resolution scanning electron microscopy, such as by correlating images acquired at different energies of primary electrons using different signals. From the Clinical Editor: The use of transmission electron microscopy has become an indispensible tool in the detection of cellular proteins. In this short but interesting article, the authors described their new method of labeling and the identification of four different proteins simultaneously, which represents another advance in imaging technique.

  19. Replica location mechanism in data grid based on ED-Chord

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A peer-to-peer hierarchical replica location mechanism(PRLM)was designed for data grids to provide better load balancing capability and scalability.Global replica indexes of the PRLM are organized based on even distributed Chord(ED-Chord)structure.The locality can optimize queries on local replica indexes of virtual organizations.ED-Chord protocol collects the node identifiers information using a distributed method and assigns optimal identifiers for new nodes to make them more uniformly distributed in the entire identifier space.Theoretical analysis and simulations show that PRLM provides good performance,scalability and load balancing capability for replica location in data grids.

  20. Replica Analysis for Portfolio Optimization with Single-Factor Model

    Science.gov (United States)

    Shinzato, Takashi

    2017-06-01

    In this paper, we use replica analysis to investigate the influence of correlation among the return rates of assets on the solution of the portfolio optimization problem. We consider the behavior of an optimal solution for the case where the return rate is described with a single-factor model and compare the findings obtained from our proposed methods with correlated return rates with those obtained with independent return rates. We then analytically assess the increase in the investment risk when correlation is included. Furthermore, we also compare our approach with analytical procedures for minimizing the investment risk from operations research.

  1. REPLICA ORNSTEIN-ZERNIKE EQUATIONS FOR POSITIONALLY FROZEN HEISENBERG SYSTEMS

    Directory of Open Access Journals (Sweden)

    E.Lomba

    2003-01-01

    Full Text Available We present the formulation of the Replica Ornstein-Zernike equations for a model of positionally frozen disordered Heisenberg spin system. The results are obtained for various models, one in which the particle positions correspond to a frozen hard sphere fluid, another system in which the configurations are generated by a random insertion of hard spheres, a system of randomly distributed spins, and finally a system corresponding to a soft sphere fluid quenched at high and low temperatures. We will see that the orientational structure of the spin system is fairly well reproduced by the integral equation which, however, does not correctly account for the critical behaviour.

  2. Replica approach to mean-variance portfolio optimization

    Science.gov (United States)

    Varga-Haszonits, Istvan; Caccioli, Fabio; Kondor, Imre

    2016-12-01

    We consider the problem of mean-variance portfolio optimization for a generic covariance matrix subject to the budget constraint and the constraint for the expected return, with the application of the replica method borrowed from the statistical physics of disordered systems. We find that the replica symmetry of the solution does not need to be assumed, but emerges as the unique solution of the optimization problem. We also check the stability of this solution and find that the eigenvalues of the Hessian are positive for r  =  N/T  portfolio and T the length of the time series used to estimate the covariance matrix. At the critical point r  =  1 a phase transition is taking place. The out of sample estimation error blows up at this point as 1/(1  -  r), independently of the covariance matrix or the expected return, displaying the universality not only of the critical exponent, but also the critical point. As a conspicuous illustration of the dangers of in-sample estimates, the optimal in-sample variance is found to vanish at the critical point inversely proportional to the divergent estimation error.

  3. Generating Scaled Replicas of Real-World Complex Networks

    CERN Document Server

    Staudt, Christian L; Safro, Ilya; Gutfraind, Alexander; Meyerhenke, Henning

    2016-01-01

    Research on generative models plays a central role in the emerging field of network science, studying how statistical patterns found in real networks can be generated by formal rules. During the last two decades, a variety of models has been proposed with an ultimate goal of achieving comprehensive realism for the generated networks. In this study, we (a) introduce a new generator, termed ReCoN; (b) explore how models can be fitted to an original network to produce a structurally similar replica, and (c) aim for producing much larger networks than the original exemplar. In a comparative experimental study, we find ReCoN often superior to many other state-of-the-art network generation methods. Our design yields a scalable and effective tool for replicating a given network while preserving important properties at both micro- and macroscopic scales and (optionally) scaling the replica by orders of magnitude in size. We recommend ReCoN as a general practical method for creating realistic test data for the enginee...

  4. Immunogold identification of the somatotrophs of domestic fowl of different ages.

    Science.gov (United States)

    Malamed, S; Gibney, J A; Scanes, C G

    1988-03-01

    The somatotrophs of the pituitary gland of the male domestic fowl were identified by means of an immunoelectron-microscopic method based on gold as the electron-opaque label and an antibody to growth hormone. Gold particles indicating sites of growth hormone were restricted to cells in which virtually all of the granules were labelled. Little, if any, gold label was found outside the granules in these cells designated as somatotrophs, or at sites outside these cells. The size of these gold-labelled secretory granules presumed to contain growth hormone decreased with age, from a mean sectional diameter of 256 +/- 6.2 nm (SEM) at 4-6 weeks to 221 +/- 5.7 nm at 11-18 weeks and 205 +/- 8.6 nm at 24-30 weeks of age. On the basis of these values for mean sectional diameters the change between the first two periods represents a decrease in granule volume of about 36%. However, during the same period the growth hormone concentration of the granules increased. Accordingly, growth hormone content per granule changed little if at all. In contrast, from 11-18 weeks to 24-30 weeks of age there was a decrease of 31% in growth hormone content per granule. These data indicate that growth hormone packaging in the chicken somatotroph changes with age. The first change results in the production of smaller granules of higher growth hormone concentration. During this period growth hormone content per granule remains relatively constant. The later change results in the production of granules of lower growth hormone content than that of younger animals.

  5. Localization of human immunodeficiency virus antigens in infected cells by scanning/transmission-immunogold techniques

    Energy Technology Data Exchange (ETDEWEB)

    Herrera, M.I.; Santa Maria, I.; de Andres, R.; Najera, R.

    1988-01-01

    An application of high resolution scanning/transmission electron microscopy (STEM) and gold-labelling techniques for the rapid detection of human immunodeficiency virus (HIV) in infected cells has been developed. Experimental in vitro studies for detecting two HIV structural proteins, gp41 and p17, were performed following an indirect labeling procedure that uses monoclonal anti-p17 and anti-gp41 antibodies as primary antibodies and 40 nm gold-linked goat antimouse IgG as secondary antibodies. The cells were then studied by STEM in the scanning mode. Unambiguous localization of the viral antigens was possible by combining the three-dimensional image provided by the secondary electron image and the atomic number-dependent backscattered electron image for the identification of the gold marker. This technique combines both the morphological information and the rapid procedures of scanning electron microscopy with the precise and sensitive antigen detection provided by the use of STEM and immunological methods. The preliminary results of its application to the study of peripheral blood mononuclear cells from four anti-HIV-seropositive patients showing the presence of specific labeling in all of them suggest that it might prove useful for early detection of HIV infection before seroconversion, as well as for quantitative studies.

  6. Three-dimensional nanometrology of microstructures by replica molding and large-range atomic force microscopy

    DEFF Research Database (Denmark)

    Stöhr, Frederik; Michael-Lindhard, Jonas; Simons, Hugh

    2015-01-01

    We have used replica molding and large-range atomic force microscopy to characterize the threedimensional shape of high aspect ratio microstructures. Casting inverted replicas of microstructures using polydimethylsiloxane (PDMS) circumvents the inability of AFM probes to measure deep and narrow c...

  7. Finite size corrections in the random energy model and the replica approach

    Science.gov (United States)

    Derrida, Bernard; Mottishaw, Peter

    2015-01-01

    We present a systematic and exact way of computing finite size corrections for the random energy model, in its low temperature phase. We obtain explicit (though complicated) expressions for the finite size corrections of the overlap functions. In its low temperature phase, the random energy model is known to exhibit Parisi's broken symmetry of replicas. The finite size corrections given by our exact calculation can be reproduced using replicas if we make specific assumptions about the fluctuations (with negative variances!) of the number and sizes of the blocks when replica symmetry is broken. As an alternative we show that the exact expression for the non-integer moments of the partition function can be written in terms of coupled contour integrals over what can be thought of as ‘complex replica numbers’. Parisi's one step replica symmetry breaking arises naturally from the saddle point of these integrals without making any ansatz or using the replica method. The fluctuations of the ‘complex replica numbers’ near the saddle point in the imaginary direction correspond to the negative variances we observed in the replica calculation. Finally our approach allows one to see why some apparently diverging series or integrals are harmless.

  8. A Novel General Chemistry Laboratory: Creation of Biomimetic Superhydrophobic Surfaces through Replica Molding

    Science.gov (United States)

    Verbanic, Samuel; Brady, Owen; Sanda, Ahmed; Gustafson, Carolina; Donhauser, Zachary J.

    2014-01-01

    Biomimetic replicas of superhydrophobic lotus and taro leaf surfaces can be made using polydimethylsiloxane. These replicas faithfully reproduce the microstructures of the leaves' surface and can be analyzed using contact angle goniometry, self-cleaning experiments, and optical microscopy. These simple and adaptable experiments were used to…

  9. A Novel General Chemistry Laboratory: Creation of Biomimetic Superhydrophobic Surfaces through Replica Molding

    Science.gov (United States)

    Verbanic, Samuel; Brady, Owen; Sanda, Ahmed; Gustafson, Carolina; Donhauser, Zachary J.

    2014-01-01

    Biomimetic replicas of superhydrophobic lotus and taro leaf surfaces can be made using polydimethylsiloxane. These replicas faithfully reproduce the microstructures of the leaves' surface and can be analyzed using contact angle goniometry, self-cleaning experiments, and optical microscopy. These simple and adaptable experiments were used to…

  10. Fabrication of free-standing replicas of fragile, laminar, chitinous biotemplates.

    Science.gov (United States)

    Lakhtakia, Akhlesh; Martín-Palma, Raúl J; Motyka, Michael A; Pantano, Carlo G

    2009-09-01

    The conformal-evaporated-film-by-rotation technique, followed by the dissolution of chitin in an aqueous solution of orthophosphoric acid, can be used to fabricate free-standing replicas of fragile, laminar, chitinous biotemplates. This novel approach was demonstrated using butterfly wings as biotemplates and GeSeSb chalcogenide glass for replicas.

  11. Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.

    Science.gov (United States)

    Ostermeir, Katja; Zacharias, Martin

    2014-01-15

    A Hamiltonian Replica-Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two-dimensional backbone and one-dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions.

  12. Immunogold detection of L-glutamate and D-serine in small synaptic-like microvesicles in adult hippocampal astrocytes.

    Science.gov (United States)

    Bergersen, L H; Morland, C; Ormel, L; Rinholm, J E; Larsson, M; Wold, J F H; Røe, A T; Stranna, A; Santello, M; Bouvier, D; Ottersen, O P; Volterra, A; Gundersen, V

    2012-07-01

    Glutamate and the N-methyl-D-aspartate receptor ligand D-serine are putative gliotransmitters. Here, we show by immunogold cytochemistry of the adult hippocampus that glutamate and D-serine accumulate in synaptic-like microvesicles (SLMVs) in the perisynaptic processes of astrocytes. The estimated concentration of fixed glutamate in the astrocytic SLMVs is comparable to that in synaptic vesicles of excitatory nerve terminals (≈ 45 and ≈ 55 mM, respectively), whereas the D-serine level is about 6 mM. The vesicles are organized in small spaced clusters located near the astrocytic plasma membrane. Endoplasmic reticulum is regularly found in close vicinity to SLMVs, suggesting that astrocytes contain functional nanodomains, where a local Ca(2+) increase can trigger release of glutamate and/or D-serine.

  13. Replica analysis for the duality of the portfolio optimization problem

    Science.gov (United States)

    Shinzato, Takashi

    2016-11-01

    In the present paper, the primal-dual problem consisting of the investment risk minimization problem and the expected return maximization problem in the mean-variance model is discussed using replica analysis. As a natural extension of the investment risk minimization problem under only a budget constraint that we analyzed in a previous study, we herein consider a primal-dual problem in which the investment risk minimization problem with budget and expected return constraints is regarded as the primal problem, and the expected return maximization problem with budget and investment risk constraints is regarded as the dual problem. With respect to these optimal problems, we analyze a quenched disordered system involving both of these optimization problems using the approach developed in statistical mechanical informatics and confirm that both optimal portfolios can possess the primal-dual structure. Finally, the results of numerical simulations are shown to validate the effectiveness of the proposed method.

  14. Nontrivial Critical Fixed Point for Replica-Symmetry-Breaking Transitions

    Science.gov (United States)

    Charbonneau, Patrick; Yaida, Sho

    2017-05-01

    The transformation of the free-energy landscape from smooth to hierarchical is one of the richest features of mean-field disordered systems. A well-studied example is the de Almeida-Thouless transition for spin glasses in a magnetic field, and a similar phenomenon—the Gardner transition—has recently been predicted for structural glasses. The existence of these replica-symmetry-breaking phase transitions has, however, long been questioned below their upper critical dimension, du=6 . Here, we obtain evidence for the existence of these transitions in d

  15. Searching near-replicas of images via clustering

    Science.gov (United States)

    Chang, Edward Y.; Li, Chen; Wang, James Z.; Mork, Peter; Wiederhold, Gio

    1999-08-01

    Internet piracy has been one of the major concerns for Web publishing. In this study we present a system, RIME, that we have prototyped for detecting unauthorized image copying on the WWW. To speed up the copy detection, RIME uses a new clustering/hashing approach that first clusters similar images on adjacent disk cylinders and then builds indexes to access the clusters made in this way. Searching for the replicas of an image often takes just one IO to loop up the location of the cluster containing similar objects and one sequential file IO to read in this cluster. Our experimental results show that RIME can detect images copies both more efficiently and effectively than the traditional content- based image retrieval systems that use tree-like structures to index images. In addition, RIME copes well with image format conversion, resampling, requantization and geometric transformation.

  16. Replica exchange Monte Carlo applied to hard spheres.

    Science.gov (United States)

    Odriozola, Gerardo

    2009-10-14

    In this work a replica exchange Monte Carlo scheme which considers an extended isobaric-isothermal ensemble with respect to pressure is applied to study hard spheres (HSs). The idea behind the proposal is expanding volume instead of increasing temperature to let crowded systems characterized by dominant repulsive interactions to unblock, and so, to produce sampling from disjoint configurations. The method produces, in a single parallel run, the complete HS equation of state. Thus, the first order fluid-solid transition is captured. The obtained results well agree with previous calculations. This approach seems particularly useful to treat purely entropy-driven systems such as hard body and nonadditive hard mixtures, where temperature plays a trivial role.

  17. Scalable replica-exchange framework for Wang-Landau sampling.

    Science.gov (United States)

    Vogel, Thomas; Li, Ying Wai; Wüst, Thomas; Landau, David P

    2014-08-01

    We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we apply it to lattice spin models, the self-assembly process in amphiphilic solutions, and the adsorption of molecules on surfaces. While of general current interest, the latter phenomena are challenging to study computationally because of multiple structural transitions occurring over a broad temperature range. We show how the parallel framework facilitates simulations of such processes and, without any loss of accuracy or precision, gives a significant speedup and allows for the study of much larger systems and much wider temperature ranges than possible with single-walker methods.

  18. Scalable replica-exchange framework for Wang-Landau sampling

    Science.gov (United States)

    Vogel, Thomas; Li, Ying Wai; Wüst, Thomas; Landau, David P.

    2014-08-01

    We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we apply it to lattice spin models, the self-assembly process in amphiphilic solutions, and the adsorption of molecules on surfaces. While of general current interest, the latter phenomena are challenging to study computationally because of multiple structural transitions occurring over a broad temperature range. We show how the parallel framework facilitates simulations of such processes and, without any loss of accuracy or precision, gives a significant speedup and allows for the study of much larger systems and much wider temperature ranges than possible with single-walker methods.

  19. Scalable replica-exchange framework for Wang Landau sampling

    Energy Technology Data Exchange (ETDEWEB)

    Vogel, Thomas [University of Georgia, Athens, GA; Li, Ying Wai [ORNL; Wuest, Thomas [Swiss Federal Research Institute, Switzerland; Landau, David P [University of Georgia, Athens, GA

    2014-01-01

    We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we apply it to lattice spin models, the self-assembly process in amphiphilic solutions, and the adsorption of molecules on surfaces. While of general, current interest, the latter phenomena are challenging to study computationally because of multiple structural transitions occurring over a broad temperature range. We show how the parallel framework facilitates simulations of such processes and, without any loss of accuracy or precision, gives a significant speedup and allows for the study of much larger systems and much wider temperature ranges than possible with single-walker methods.

  20. Vertices from replica in a random matrix theory

    Energy Technology Data Exchange (ETDEWEB)

    Brezin, E [Laboratoire de Physique Theorique, Ecole Normale Superieure, 24 rue Lhomond 75231, Paris Cedex 05 (France); Hikami, S [Department of Basic Sciences, University of Tokyo, Meguro-ku, Komaba, Tokyo 153 (Japan)

    2007-11-09

    Kontsevich's work on Airy matrix integrals has led to explicit results for the intersection numbers of the moduli space of curves. In a subsequent work Okounkov rederived these results from the edge behavior of a Gaussian matrix integral. In our work we consider the correlation functions of vertices in a Gaussian random matrix theory, with an external matrix source. We deal with operator products of the form <{pi}{sub i=1}{sup n}1/N tr M{sup k{sub i}}>, in a 1/N expansion. For large values of the powers k{sub i}, in an appropriate scaling limit relating large k's to large N, universal scaling functions are derived. Furthermore, we show that the replica method applied to characteristic polynomials of the random matrices, together with a duality exchanging N and the number of points, provides a new way to recover Kontsevich's results on these intersection numbers.

  1. Beyond Virtual Replicas: 3D Modeling and Maltese Prehistoric Architecture

    Directory of Open Access Journals (Sweden)

    Filippo Stanco

    2013-01-01

    Full Text Available In the past decade, computer graphics have become strategic for the development of projects aimed at the interpretation of archaeological evidence and the dissemination of scientific results to the public. Among all the solutions available, the use of 3D models is particularly relevant for the reconstruction of poorly preserved sites and monuments destroyed by natural causes or human actions. These digital replicas are, at the same time, a virtual environment that can be used as a tool for the interpretative hypotheses of archaeologists and as an effective medium for a visual description of the cultural heritage. In this paper, the innovative methodology and aims and outcomes of a virtual reconstruction of the Borg in-Nadur megalithic temple, carried out by Archeomatica Project of the University of Catania, are offered as a case study for a virtual archaeology of prehistoric Malta.

  2. Food Labels

    Science.gov (United States)

    ... Surgery? Choosing the Right Sport for You Shyness Food Labels KidsHealth > For Teens > Food Labels Print A ... have at least 95% organic ingredients. continue Making Food Labels Work for You The first step in ...

  3. Internal structure analysis of particle-double network gels used in a gel organ replica

    Science.gov (United States)

    Abe, Mei; Arai, Masanori; Saito, Azusa; Sakai, Kazuyuki; Kawakami, Masaru; Furukawa, Hidemitsu

    2016-04-01

    In recent years, the fabrication of patient organ replicas using 3D printers has been attracting a great deal of attention in medical fields. However, the cost of these organ replicas is very high as it is necessary to employ very expensive 3D printers and printing materials. Here we present a new gel organ replica, of human kidney, fabricated with a conventional molding technique, using a particle-double network hydrogel (P-DN gel). The replica is transparent and has the feel of a real kidney. It is expected that gel organ replicas produced this way will be a useful tool for the education of trainee surgeons and clinical ultrasonography technologists. In addition to developing a gel organ replica, the internal structure of the P-DN gel used is also discussed. Because the P-DN gel has a complex structure comprised of two different types of network, it has not been possible to investigate them internally in detail. Gels have an inhomogeneous network structure. If it is able to get a more uniform structure, it is considered that this would lead to higher strength in the gel. In the present study we investigate the structure of P-DN gel, using the gel organ replica. We investigated the internal structure of P-DN gel using Scanning Microscopic Light Scattering (SMILS), a non-contacting and non-destructive.

  4. Fabrication of the replica templated from butterfly wing scales with complex light trapping structures

    Science.gov (United States)

    Han, Zhiwu; Li, Bo; Mu, Zhengzhi; Yang, Meng; Niu, Shichao; Zhang, Junqiu; Ren, Luquan

    2015-11-01

    The polydimethylsiloxane (PDMS) positive replica templated twice from the excellent light trapping surface of butterfly Trogonoptera brookiana wing scales was fabricated by a simple and promising route. The exact SiO2 negative replica was fabricated by using a synthesis method combining a sol-gel process and subsequent selective etching. Afterwards, a vacuum-aided process was introduced to make PDMS gel fill into the SiO2 negative replica, and the PDMS gel was solidified in an oven. Then, the SiO2 negative replica was used as secondary template and the structures in its surface was transcribed onto the surface of PDMS. At last, the PDMS positive replica was obtained. After comparing the PDMS positive replica and the original bio-template in terms of morphology, dimensions and reflectance spectra and so on, it is evident that the excellent light trapping structures of butterfly wing scales were inherited by the PDMS positive replica faithfully. This bio-inspired route could facilitate the preparation of complex light trapping nanostructure surfaces without any assistance from other power-wasting and expensive nanofabrication technologies.

  5. Immunogold study on lectin binding in the porcine zona pellucida and granulosa cells

    Directory of Open Access Journals (Sweden)

    F Parillo

    2009-06-01

    Full Text Available An ultrastructural localization of lectin receptors on the zona pellucida (ZP of porcine antral oocytes and on the granulosa cells was performed using a panel of horseradish peroxidase- labelled lectins in conjunction with antiperoxidase antibody and protein A-gold. In some cases, lectin incubation was preceded by sialidase digestion. WGA-, Con-A-, UEA-I-, RCA-I-, PNA- and SBA-reactive sites were distributed differently in the porcine ZP. Sialidase digestion increased the positivity obtained with RCA-I and it was necessary to promote PNA and SBA reactivity. These results indicated that the ZP contained N-acetylglucosamine, a-mannose, a- fucose, b-Gal-(1-4GlcNAc, b-Gal- (1-3GalNAc, b-GalNAc and sialic acid residues. We also observed the presence of vesicles in both the ooplasm and granulosa cells, showing a similar lectin binding pattern to that of the ZP, thus suggesting that the oocyte and granulosa cells are the site of synthesis of ZP glucidic determinants.

  6. Observation of immuno-labeled cells at high resolution using soft X-ray microscope at Ritsumeikan University SR Center

    Energy Technology Data Exchange (ETDEWEB)

    Yamamoto, A [Nagahama Institute of Bio-Science and Technology, 1266, Tamura-cho, Nagahama, Shiga, 526-0829 (Japan); Takemoto, K; Kihara, H [Department of Physics, Kansai Medical University, 18-89 Uyamahigashi, Hirakata, Osaka, 573-1136 (Japan); Fukui, T; Yoshimura, Y; Namba, H [Department of Physical Science, Ritsumeikan University, 1-1-1, Noji-Higashi, Kusatsu, Shiga, 525-8577 (Japan); Okuno, K, E-mail: takemoto@makino.kmu.ac.j [SR Center, Ritsumeikan University, 1-1-1, Noji-Higashi Kusatsu, Shiga, 525-8577 (Japan)

    2009-09-01

    Mouse fibroblast cell line NIH3T3 cells were labeled with the heavy metal (silver and gold) and observed intracellular structure under an X-ray microscope. Microtubules, Golgi apparatus and early endosomes of NIH3T3 cells were stained with immuno-gold nanoparticles, and immuno-staining was intensified by silver or gold enhancement procedure. Using a transmission soft X-ray microscope beamline (BL12) at Ritsumeikan University SR center, we observed immuno-stained NIH3T3 cells with several wavelengths just below and above oxygen edge ({lambda} = 2.32 nm). Using this method, cytoskeleton (microtubules) and organelles (Golgi apparatus and early endosomes) were successfully imaged with high resolution. Thus, immuno-gold silver and gold enhancement technique is useful for specific labeling of intracellular structure under an X-ray microscope.

  7. Observation of immuno-labeled cells at high resolution using soft X-ray microscope at Ritsumeikan University SR Center

    Science.gov (United States)

    Yamamoto, A.; Takemoto, K.; Fukui, T.; Yoshimura, Y.; Okuno, K.; Namba, H.; Kihara, H.

    2009-09-01

    Mouse fibroblast cell line NIH3T3 cells were labeled with the heavy metal (silver and gold) and observed intracellular structure under an X-ray microscope. Microtubules, Golgi apparatus and early endosomes of NIH3T3 cells were stained with immuno-gold nanoparticles, and immuno-staining was intensified by silver or gold enhancement procedure. Using a transmission soft X-ray microscope beamline (BL12) at Ritsumeikan University SR center, we observed immuno-stained NIH3T3 cells with several wavelengths just below and above oxygen edge (λ = 2.32 nm). Using this method, cytoskeleton (microtubules) and organelles (Golgi apparatus and early endosomes) were successfully imaged with high resolution. Thus, immuno-gold silver and gold enhancement technique is useful for specific labeling of intracellular structure under an X-ray microscope.

  8. Application of Replica Technique and SEM in Accuracy Measurement of Ceramic Crowns

    Science.gov (United States)

    Trifkovic, B.; Budak, I.; Todorovic, A.; Hodolic, J.; Puskar, T.; Jevremovic, D.; Vukelic, D.

    2012-01-01

    The paper presents a comparative study of the measuring values of the marginal gap related to the ceramic crowns made by dental CAD/CAM system using the replica technique and SEM. The study was conducted using three experimental groups, which consisted of ceramic crowns manufactured by the Cerec CAD/CAM system. The scanning procedure was carried out using three specialized dental 3D digitization systems from the Cerec family - two types of extraoral optical scanning systems and an intraoral optical scanner. Measurements of the marginal gap were carried out using the replica technique and SEM. The comparison of aggregate values of the marginal gap using the replica technique showed a statistically significant difference between the systems. The measured values of marginal gaps of ceramic crowns using the replica technique were significantly lower compared to those measured by SEM. The results indicate that the choice of technique for measuring the accuracy of ceramic crowns influences the final results of investigation.

  9. Automated magnification calibration in transmission electron microscopy using Fourier analysis of replica images.

    NARCIS (Netherlands)

    Laak, J.A.W.M. van der; Dijkman, H.B.P.M.; Pahlplatz, M.M.M.

    2006-01-01

    The magnification factor in transmission electron microscopy is not very precise, hampering for instance quantitative analysis of specimens. Calibration of the magnification is usually performed interactively using replica specimens, containing line or grating patterns with known spacing. In the pre

  10. Accelerating the convergence of replica exchange simulations using Gibbs sampling and adaptive temperature sets

    CERN Document Server

    Vogel, Thomas

    2015-01-01

    We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of relevant states through the whole ensemble of replicas. This mechanism depends on the knowledge of global thermodynamic functions which are measured during the simulation and not coupled to the heat bath temperatures driving the individual simulations. Therefore, this setup also allows for a continuous adaptation of the temperature set. In this paper, we will review the new scheme and demonstrate its capability. The method is particularly useful for the fast and reliable estimation of the microcanonical temperature T(U) or, equivalently, of the density of states g(U) over a wide range of energies.

  11. Rapid prototyping of replica knee implants for in vitro testing

    Directory of Open Access Journals (Sweden)

    Verjans Mark

    2016-09-01

    Full Text Available The understanding of the complex biomechanics of the knee is a key for an optimal implant design. To easily investigate the influence of prosthetic designs on knee biomechanics a rapid prototyping workflow for knee implants has been developed and evaluated. Therefore, different manufacturing technologies and post-treatment methods have been examined and overall seven different replica knee implants were manufactured. For evaluation, the manufacturing properties such as surface accuracy and roughness were determined and kinematic behaviour was investigated in a novel knee testing rig. It was carried out that PolyJet-Modelling with a sanded surface resulted in changed kinematic patterns compared to a usual CoCr-UHMWPE implant. However, fused deposition modelling using ABS and subsequent surface smoothening with acetone vapor showed the lowest roughness of the manufactured implants and only minor kinematic differences. For this reason this method constitutes a promising approach towards an optimal implant design for improved patient-satisfaction and long lifetime of the implant. Finally the workflow is not only limited to the knee.

  12. Critiques, replicas and proposals for the New Urbanism Vision

    Directory of Open Access Journals (Sweden)

    Alaide Retana

    2014-03-01

    Full Text Available The new urbanism (NU is a vision of planning and urban design emerged in 1993, which finds its basis in the design of traditional communities. This trend has had various criticisms and replicas, which were reviewed in relation to urban sprawl, transportation, re-densifying, mix of uses of land, design, gentrification, pedestrianization and safety, which were analyzed in the neighborhood of Santa Barbara in Toluca, Mexico. This area was chosen for being traditional and forming part of the historical center of the city, which even though it was not designed under the guidelines of the NU, it has the quality of traditional, from which the NU would theoretically has taken its essence. The objective of this analysis is to establish whether the NU has the essence of a traditional Mexican neighborhood, as well as to check if the criticisms of the NU are informed when applied to a space belonging to a Mexican historic center that has been abandoned by problems of insecurity and degradation. The general conclusion is that the traditional neighborhoods have provided design elements to the NU, which will refute some of the criticisms, however, proposals for NU in neighborhoods of his-toric centers have to be based on the community, the architecture and existing urbanism, since these elements are those that give the identity.

  13. Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

    Energy Technology Data Exchange (ETDEWEB)

    Kamberaj, Hiqmet, E-mail: hkamberaj@ibu.edu.mk [Department of Computer Engineering, International Balkan University, Tashko Karadza 11A, Skopje (Macedonia, The Former Yugoslav Republic of)

    2015-09-28

    In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4,  5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.

  14. Design of replica bit line control circuit to optimize power for SRAM

    Science.gov (United States)

    Pengjun, Wang; Keji, Zhou; Huihong, Zhang; Daohui, Gong

    2016-12-01

    A design of a replica bit line control circuit to optimize power for SRAM is proposed. The proposed design overcomes the limitations of the traditional replica bit line control circuit, which cannot shut off the word line in time. In the novel design, the delay of word line enable and disable paths are balanced. Thus, the word line can be opened and shut off in time. Moreover, the chip select signal is decomposed, which prevents feedback oscillations caused by the replica bit line and the replica word line. As a result, the switch power caused by unnecessary discharging of the bit line is reduced. A 2-kb SRAM is fully custom designed in an SMIC 65-nm CMOS process. The traditional replica bit line control circuit and the new replica bit line control circuit are used in the designed SRAM, and their performances are compared with each other. The experimental results show that at a supply voltage of 1.2 V, the switch power consumption of the memory array can be reduced by 53.7%. Project supported by the Zhejiang Provincial Natural Science Foundation of China (No. LQ14F040001), the National Natural Science Foundation of China (Nos. 61274132, 61234002, 61474068), and the K. C. Wong Magna Fund in Ningbo University.

  15. Preparation and optical scattering characterization of gold nanorods and their application to a dot-immunogold assay

    Science.gov (United States)

    Alekseeva, Anna V.; Bogatyrev, Vladimir A.; Dykman, Lev A.; Khlebtsov, Boris N.; Trachuk, Lyubov A.; Melnikov, Andrei G.; Khlebtsov, Nikolai G.

    2005-10-01

    We describe optical monitoring of the synthesis of gold nanorods (NRs) based on seed-mediated growth in the presence of the soft surfactant template cetyltrimethyilammonium bromide. To separate NRs from spheres and surfactants we fractionated samples in the density gradient of glycerol. The optical properties of NRs were characterized by extinction and differential light-scattering spectra (at 90°, 450-800 nm) and by the depolarization light-scattering ratio, I_vh/I_vv, measured at 90° with a helium-neon laser. Theoretical spectra and the I_vh/I_vv ratios were calculated by the T-matrix method as applied to randomly oriented NRs, which were modeled by right-circular cylinders with semispherical ends. The simulated data were fitted to experimental observations by use of particle length and width as adjustable parameters, which were close to the data yielded by transmission electron microscopy. The sensitivity of the long-wavelength resonance of NRs to the dielectric surroundings was examined both experimentally and theoretically by comparison of the extinction spectra of NRs in water and in a 25% glycerol solution. Finally, we discuss the application of NR-protein A conjugates to a dot-immunogold assay with the example of biospecific staining of human IgG molecules adsorbed onto small membrane spots.

  16. Human skulls with turquoise inlays: pre hispanic origin or replicas?; Craneos humanos con teselas de turquesa: origen prehispanico o replicas?

    Energy Technology Data Exchange (ETDEWEB)

    Silva V, Y. [FIME-UANL, Pedro A. del Alba s/n, Ciudad Universitaria, San Nicolas de los Garza, Nuevo Leon (Mexico); Castillo M, M.T.; Bautista M, J.P. [DRPMZA/INAH. Direccion de Registro Publico de Monumentos y Zonas Arqueologicas, Victoria 110, Copilco El Bajo, 04340 Mexico D.F. (Mexico); Arenas A, J. [IFUNAM, Circuito de la Investigacion Cientifica s/n, Ciudad Universitaria, 04510 Mexico D.F. (Mexico)]. e-mail: ysilva@fisica.unam.mx

    2006-07-01

    The lack of archaeological context determining if the manufacture of two human skulls adorned with turquoise inlays have pre-Columbian origin or not (replicas), led to perform other studies. Under these conditions, besides orthodox methodology commonly used to assign chronology and cultural aspects as form, style, decoration, iconography, etc., it was necessary to obtain more results based on the use of characterization techniques. The techniques employed were Scanning Electron Microscopy (SEM), X-Ray Energy Dispersive Spectroscopy (EDS), Transmission Electron Microscopy (TEM) and Fourier Transform Infrared Spectroscopy (FTIR), in order to determine the manufacture techniques and chemical composition of the materials used for the cementant. SEM analysis showed the presence of zones composed by Ca, O, C and Al. In some cases Mg, Cl, Fe and Pb were identified. High concentration of Cu was present in all samples, due to residues of turquoise inlays (CuAI{sub 6}(PO{sub 4}){sub 4}(OH){sub 8}(H{sub 2}O){sub 4}) with which the skulls were decorated. In the cementant was identified the Ca as base element of the cementant, as well as particles < 100 nm with irregular morphology and other amorphous zones. FTIR spectrums indicated the presence of organic substances that could be used as agglutinating in the cementant. The current work shows a progress identifying involved techniques in the manufacturing of two human skulls with turquoise inlays. (Author)

  17. An ingenious replica templated from the light trapping structure in butterfly wing scales

    Science.gov (United States)

    Han, Zhiwu; Niu, Shichao; Yang, Meng; Zhang, Junqiu; Yin, Wei; Ren, Luquan

    2013-08-01

    Although the physical mechanism of light trapping property of butterfly wings is well understood, it remains a challenge to create artificial replicas of these natural functional structures. Here, we synthesized a SiO2 inverse replica of a light trapping structure in butterfly wing scales using a method combining a sol-gel process and subsequent selective etching. First, the reflectance spectrum was taken to measure the reflectivity. Then, FESEM and TEM were used to observe the coupling structure of scales and the replicas. Afterwards, assisted by SEM and TEM data, 3D optimized models of the structures and fabrication process were generated by software. Finally, the parametric comparisons of the morphologies and structures between the original template and the inverse SiO2 replica were carefully conducted, and it was found that the original structures of bio-templates were well inherited by the structures of the inverse replica. This work would open up possibilities for an extensive study of mimicking novel bio-inspired functional materials, and the reported biomimetic technique confirms the feasibility of extending the functional structures in butterfly wings to particular optical devices in the field of space exploration, space equipment, photoelectrical devices and photo-induced sensors.Although the physical mechanism of light trapping property of butterfly wings is well understood, it remains a challenge to create artificial replicas of these natural functional structures. Here, we synthesized a SiO2 inverse replica of a light trapping structure in butterfly wing scales using a method combining a sol-gel process and subsequent selective etching. First, the reflectance spectrum was taken to measure the reflectivity. Then, FESEM and TEM were used to observe the coupling structure of scales and the replicas. Afterwards, assisted by SEM and TEM data, 3D optimized models of the structures and fabrication process were generated by software. Finally, the parametric

  18. Assessment of hydro/oleophobicity for shark skin replica with riblets.

    Science.gov (United States)

    Kim, Tae Wan

    2014-10-01

    The shark skin has a unique skin structure which enables the shark to swim faster and more efficiently due to an intriguing three-dimensional rib pattern. Shark skin has also known as having functional performances such as self cleaning and anti-fouling as well as excellent drag reduction due to a hierarchical structure built up by micro grooves and nano-long chain mucus drag reduction interface around the shark body. In this study, the wetting properties for the biomimetic surfaces that replicate shark skin are assessed. First of all, the shark skin replicas are obtained using the micro molding technique directly from a shark skin template. The quantitative replication precision of the shark skin replicas is evaluated comparing with the geometry of shark skin template using 3D and 2D surface profiles are measured. Then contact angles in the conditions of solid-air-water, solid-air-oil and solid-water-oil interfaces are evaluated for shark skin replicas. The effect of Teflon coating on the wetting properties of shark skin replicas is also observed. The results show the shark skin replica by the micro molding technique gives better effect on the wetting performance, and the micro riblets on shark skin improve the wettability feature.

  19. Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering.

    Science.gov (United States)

    Huang, Kun; García, Angel E

    2014-10-14

    The lateral heterogeneity of cellular membranes plays an important role in many biological functions such as signaling and regulating membrane proteins. This heterogeneity can result from preferential interactions between membrane components or interactions with membrane proteins. One major difficulty in molecular dynamics simulations aimed at studying the membrane heterogeneity is that lipids diffuse slowly and collectively in bilayers, and therefore, it is difficult to reach equilibrium in lateral organization in bilayer mixtures. Here, we propose the use of the replica exchange with solute tempering (REST) approach to accelerate lateral relaxation in heterogeneous bilayers. REST is based on the replica exchange method but tempers only the solute, leaving the temperature of the solvent fixed. Since the number of replicas in REST scales approximately only with the degrees of freedom in the solute, REST enables us to enhance the configuration sampling of lipid bilayers with fewer replicas, in comparison with the temperature replica exchange molecular dynamics simulation (T-REMD) where the number of replicas scales with the degrees of freedom of the entire system. We apply the REST method to a cholesterol and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer mixture and find that the lateral distribution functions of all molecular pair types converge much faster than in the standard MD simulation. The relative diffusion rate between molecules in REST is, on average, an order of magnitude faster than in the standard MD simulation. Although REST was initially proposed to study protein folding and its efficiency in protein folding is still under debate, we find a unique application of REST to accelerate lateral equilibration in mixed lipid membranes and suggest a promising way to probe membrane lateral heterogeneity through molecular dynamics simulation.

  20. Nutrition Labeling

    DEFF Research Database (Denmark)

    Grunert, Klaus G

    2013-01-01

    because consumers will avoid products that the label shows to be nutritionally deficient, but also because food producers will try to avoid marketing products that appear, according to the label, as nutritionally problematic, for example, because of a high content of saturated fat or salt. Nutrition......Nutrition labeling refers to the provision of information on a food product’s nutritional content on the package label. It can serve both public health and commercial purposes. From a public health perspective, the aim of nutrition labeling is to provide information that can enable consumers...... to make healthier choices when choosing food products. Nutrition labeling is thus closely linked to the notion of the informed consumer, that chooses products according to their aims, on the basis of the information at their disposal. Because many consumers are assumed to be interested in making healthy...

  1. Nutrition Labeling

    DEFF Research Database (Denmark)

    Grunert, Klaus G

    2013-01-01

    because consumers will avoid products that the label shows to be nutritionally deficient, but also because food producers will try to avoid marketing products that appear, according to the label, as nutritionally problematic, for example, because of a high content of saturated fat or salt. Nutrition......Nutrition labeling refers to the provision of information on a food product’s nutritional content on the package label. It can serve both public health and commercial purposes. From a public health perspective, the aim of nutrition labeling is to provide information that can enable consumers...... to make healthier choices when choosing food products. Nutrition labeling is thus closely linked to the notion of the informed consumer, that chooses products according to their aims, on the basis of the information at their disposal. Because many consumers are assumed to be interested in making healthy...

  2. Replica exchange simulations of the three-dimensional Ising spin glass: static and dynamic properties

    Science.gov (United States)

    Yucesoy, Burcu; Machta, Jonathan; Katzgraber, Helmut G.

    2012-02-01

    We present the results of a large-scale numerical study of the equilibrium three-dimensional Ising spin glass with Gaussian disorder. Using replica exchange (parallel tempering) Monte Carlo, we measure various static, as well as dynamical quantities, such as the autocorrelation times and round-trip times for the replica exchange Monte Carlo method. The correlation between static and dynamic observables for 5000 disorder realizations (N <=10^3 spins) down to very low temperatures (T 0.2Tc) is examined. Our results show that autocorrelation times are directly correlated with the roughness of the free energy landscape. We also discuss the size dependence of several static quantities.

  3. Implementation of replica-exchange umbrella sampling in the DFTB + semiempirical quantum chemistry package

    Science.gov (United States)

    Ito, Shingo; Irle, Stephan; Okamoto, Yuko

    2016-07-01

    The replica-exchange umbrella sampling (REUS) method combines replica-exchange and umbrella sampling methods and allows larger conformational sampling than conventional simulation methods. This method has been used in many studies to understand docking mechanisms and the functions of molecules. However, REUS has not been combined with quantum chemical codes. Therefore, we implemented the REUS simulation technique in the DFTB + quantum chemistry code utilizing approximate density functional theory. We performed REUS simulations of an intra-molecular proton transfer reaction of malonaldehyde and a formation of a phthalocyanine from four phthalonitriles and one iron atom to validate the reliability of our implemented REUS-DFTB + combination.

  4. Nickel replicas as calibration reference standards for industrial surface texture instruments

    DEFF Research Database (Denmark)

    Sammatini-Malberg, Maria-Pia

    The present report is a documentation of measurements carried out at DTU on Nickel replicas. The research is performed in the frame of the project with contract SMT4-CT97-2176 with title: Calibration Standards for Surface Topography Measuring Systems down to Nanometric Scale.......The present report is a documentation of measurements carried out at DTU on Nickel replicas. The research is performed in the frame of the project with contract SMT4-CT97-2176 with title: Calibration Standards for Surface Topography Measuring Systems down to Nanometric Scale....

  5. On the Application of Replica Molding Technology for the Indirect Measurement of Surface and Geometry of Micromilled Components

    DEFF Research Database (Denmark)

    Baruffi, Federico; Parenti, Paolo; Cacciatore, Francesco

    2017-01-01

    the replica molding technology. The method consists of obtaining a replica of the feature that is inaccessible for standard measurement devices and performing its indirect measurement. This paper examines the performance of a commercial replication media applied to the indirect measurement of micromilled...

  6. Sustainability Labeling

    NARCIS (Netherlands)

    Dam, van Y.K.

    2017-01-01

    Sustainability labeling originated from a need to protect the identity of alternative systems of food production and to increase market transparency. From the 1980s onwards sustainability labeling has changed into a policy instrument replacing direct government regulation of the food market, and a

  7. Studying the Early Stages of Protein Aggregation Using Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Shea, Joan-Emma; Levine, Zachary A

    2016-01-01

    The simulation of protein aggregation poses several computational challenges due to the disparate time and lengths scales that are involved. This chapter focuses on the use of atomistically detailed simulations to probe the initial steps of aggregation, with an emphasis on the Tau peptide as a model system, run under a replica exchange molecular dynamics protocol.

  8. Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.

    Science.gov (United States)

    Mishra, Sushil Kumar; Kara, Mahmut; Zacharias, Martin; Koca, Jaroslav

    2014-01-01

    Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.

  9. Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange.

    Science.gov (United States)

    Zacharias, Martin

    2008-03-01

    Coarse-grained elastic network models (ENM) of proteins can be used efficiently to explore the global mobility of a protein around a reference structure. A new Hamiltonian-replica exchange molecular dynamics (H-RexMD) method has been designed that effectively combines information extracted from an ENM analysis with atomic-resolution MD simulations. The ENM analysis is used to construct a distance-dependent penalty (flooding or biasing) potential that can drive the structure away from its current conformation in directions compatible with the ENM model. Various levels of the penalty or biasing potential are added to the force field description of the MD simulation along the replica coordinate. One replica runs at the original force field. By focusing the penalty potential on the relevant soft degrees of freedom the method avoids the rapid increase of the replica number with increasing system size to cover a desired temperature range in conventional (temperature) RexMD simulations. The application to domain motions in lysozyme of bacteriophage T4 and to peptide folding indicates significantly improved conformational sampling compared to conventional MD simulations.

  10. Nickel replicas as calibration reference standards for industrial surface texture instruments

    DEFF Research Database (Denmark)

    Sammatini-Malberg, Maria-Pia

    The present report is a documentation of measurements carried out at DTU on Nickel replicas. The research is performed in the frame of the project with contract SMT4-CT97-2176 with title: Calibration Standards for Surface Topography Measuring Systems down to Nanometric Scale....

  11. Investigation of the Airflow inside Realistic and Semi-Realistic Replicas of Human Airways

    Directory of Open Access Journals (Sweden)

    Lizal Frantisek

    2015-01-01

    Full Text Available Measurement of velocity in human lungs during breathing cycle is a challenging task for researchers, since the measuring location is accessible only with significant difficulties. A special measuring rig consisting of optically transparent replica of human lungs, breathing simulator, particle generator and Laser-Doppler anemometer was developed and used for investigation of the velocity in specific locations of lungs during simulated breathing cycle. Experiments were performed on two different replicas of human lungs in corresponding measuring points to facilitate the analysis of the influence of the geometry and its simplification on the flow. The analysis of velocity course and turbulence intensity revealed that special attention should be devoted to the modelling of vocal cords position during breathing, as the position of laryngeal jet created by vocal cords significantly influences velocity profiles in trachea. The shapes of velocity courses during expiration proved to be consistent for both replicas; however magnitudes of peak expiratory velocity differ between the corresponding measuring points in both the replicas.

  12. Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space

    Science.gov (United States)

    Valentim, Alexandra; Rocha, Julio C. S.; Tsai, Shan-Ho; Li, Ying Wai; Eisenbach, Markus; Fiore, Carlos E.; Landau, David P.

    2015-09-01

    We considered a higher-dimensional extension for the replica-exchange Wang- Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of Wang-Landau and Replica-Exchange algorithms, and the one-dimensional version of this approach has been shown to be very efficient and to scale well, up to several thousands of computing cores. This approach allows us to split the parameter space of the system to be simulated into several pieces and still perform a random walk over the entire parameter range, ensuring the ergodicity of the simulation. Previous work, in which a similar scheme of parallel simulation was implemented without using replica exchange and with a different way to combine the result from the pieces, led to discontinuities in the final density of states over the entire range of parameters. From our simulations, it appears that the replica-exchange Wang-Landau algorithm is able to overcome this difficulty, allowing exploration of higher parameter phase space by keeping track of the joint density of states.

  13. Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space

    Energy Technology Data Exchange (ETDEWEB)

    Valentim, Alexandra [University of Georgia, Athens, GA; Rocha, Julio C. S. [Universidade Federal de Minas Gerais; Tsai, Shan-Ho [University of Georgia, Athens, GA; Li, Ying Wai [ORNL; Eisenbach, Markus [ORNL; Fiore, Carlos E [University of Sao Paulo, BRAZIL; Landau, David P [University of Georgia, Athens, GA

    2015-01-01

    We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of Wang-Landau and Replica-Exchange algorithms, and the one-dimensional version of this approach has been shown to be very efficient and to scale well, up to several thousands of computing cores. This approach allows us to split the parameter space of the system to be simulated into several pieces and still perform a random walk over the entire parameter range, ensuring the ergodicity of the simulation. Previous work, in which a similar scheme of parallel simulation was implemented without using replica exchange and with a different way to combine the result from the pieces, led to discontinuities in the final density of states over the entire range of parameters. From our simulations, it appears that the replica-exchange Wang-Landau algorithm is able to overcome this diculty, allowing exploration of higher parameter phase space by keeping track of the joint density of states.

  14. Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space

    CERN Document Server

    Valentim, Alexandra; Tsai, Shan-Ho; Li, Ying Wai; Eisenbach, Markus; Fiore, Carlos E; Landau, David P

    2015-01-01

    We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of Wang-Landau and Replica-Exchange algorithms, and the one-dimensional version of this approach has been shown to be very efficient and to scale well, up to several thousands of computing cores. This approach allows us to split the parameter space of the system to be simulated into several pieces and still perform a random walk over the entire parameter range, ensuring the ergodicity of the simulation. Previous work, in which a similar scheme of parallel simulation was implemented without using replica exchange and with a different way to combine the result from the pieces, led to discontinuities in the final density of states over the entire range of parameters. From our simulations, it appears that the replica-exchange Wang-Landau algorithm is able to overcome this difficulty,...

  15. Fast Optimal Replica Placement with Exhaustive Search Using Dynamically Reconfigurable Processor

    Directory of Open Access Journals (Sweden)

    Hidetoshi Takeshita

    2011-01-01

    Full Text Available This paper proposes a new replica placement algorithm that expands the exhaustive search limit with reasonable calculation time. It combines a new type of parallel data-flow processor with an architecture tuned for fast calculation. The replica placement problem is to find a replica-server set satisfying service constraints in a content delivery network (CDN. It is derived from the set cover problem which is known to be NP-hard. It is impractical to use exhaustive search to obtain optimal replica placement in large-scale networks, because calculation time increases with the number of combinations. To reduce calculation time, heuristic algorithms have been proposed, but it is known that no heuristic algorithm is assured of finding the optimal solution. The proposed algorithm suits parallel processing and pipeline execution and is implemented on DAPDNA-2, a dynamically reconfigurable processor. Experiments show that the proposed algorithm expands the exhaustive search limit by the factor of 18.8 compared to the conventional algorithm search limit running on a Neumann-type processor.

  16. Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.

    Science.gov (United States)

    Itoh, Satoru G; Okumura, Hisashi

    2013-11-05

    We propose the Hamiltonian replica-permutation method (RPM) (or multidimensional RPM) for molecular dynamics and Monte Carlo simulations, in which parameters in the Hamiltonian are permuted among more than two replicas with the Suwa-Todo algorithm. We apply the Coulomb RPM, which is one of realization of the Hamiltonian RPM, to an alanine dipeptide and to two amyloid-β(29-42) molecules. The Hamiltonian RPM realizes more efficient sampling than the Hamiltonian replica-exchange method. We illustrate the protein misfolding funnel of amyloid-β(29-42) and reveal its dimerization pathways.

  17. Techniques of replica symmetry breaking and the storage problem of the McCulloch-Pitts neuron

    Science.gov (United States)

    Györgyi, G.

    2001-02-01

    In this article we review the framework for spontaneous replica symmetry breaking. Subsequently that is applied to the example of the statistical mechanical description of the storage properties of a McCulloch-Pitts neuron, i.e., simple perceptron. It is shown that in the neuron problem, the general formula that is at the core of all problems admitting Parisi's replica symmetry breaking ansatz with a one-component order parameter appears. The details of Parisi's method are reviewed extensively, with regard to the wide range of systems where the method may be applied. Parisi's partial differential equation and related differential equations are discussed, and the Green function technique is introduced for the calculation of replica averages, the key to determining the averages of physical quantities. The Green function of the Fokker-Planck equation due to Sompolinsky turns out to play the role of the statistical mechanical Green function in the graph rules for replica correlators. The subsequently obtained graph rules involve only tree graphs, as appropriate for a mean-field-like model. The lowest order Ward-Takahashi identity is recovered analytically and shown to lead to the Goldstone modes in continuous replica symmetry breaking phases. The need for a replica symmetry breaking theory in the storage problem of the neuron has arisen due to the thermodynamical instability of formerly given solutions. Variational forms for the neuron's free energy are derived in terms of the order parameter function x( q), for different prior distribution of synapses. Analytically in the high temperature limit and numerically in generic cases various phases are identified, among them is one similar to the Parisi phase in long-range interaction spin glasses. Extensive quantities like the error per pattern change slightly with respect to the known unstable solutions, but there is a significant difference in the distribution of non-extensive quantities like the synaptic overlaps and the

  18. How could the replica method improve accuracy of performance assessment of channel coding?

    Science.gov (United States)

    Kabashima, Yoshiyuki

    2009-12-01

    We explore the relation between the techniques of statistical mechanics and information theory for assessing the performance of channel coding. We base our study on a framework developed by Gallager in IEEE Trans. Inform. Theory IT-11, 3 (1965), where the minimum decoding error probability is upper-bounded by an average of a generalized Chernoff's bound over a code ensemble. We show that the resulting bound in the framework can be directly assessed by the replica method, which has been developed in statistical mechanics of disordered systems, whereas in Gallager's original methodology further replacement by another bound utilizing Jensen's inequality is necessary. Our approach associates a seemingly ad hoc restriction with respect to an adjustable parameter for optimizing the bound with a phase transition between two replica symmetric solutions, and can improve the accuracy of performance assessments of general code ensembles including low density parity check codes, although its mathematical justification is still open.

  19. Beyond Storage Capacity in a Single Model Neuron: Continuous Replica Symmetry Breaking

    Science.gov (United States)

    Györgyi, G.; Reimann, P.

    2000-10-01

    A single McCulloch-Pitts neuron, that is, the simple perceptron is studied, with focus on the region beyond storage capacity. It is shown that Parisi's hierarchical ansatz for the overlap matrix of the synaptic couplings with so called continuous replica symmetry breaking is a solution, and as we propose it is the exact one, to the equilibrium problem. We describe some of the most salient features of the theory and give results about the low temperature region. In particular, the basics of the Parisi technique and the way to calculate thermodynamical expectation values is explained. We have numerically extremized the replica free energy functional for some parameter settings, and thus obtained the order parameter function, i.e., the probability distribution of overlaps. That enabled us to evaluate the probability density of the local stability parameter. We also performed a simulation and found a local stability density closer to the theoretical curve than previous numerical results were.

  20. Water hexamer: Self-consistent phonons versus reversible scaling versus replica exchange molecular dynamics

    CERN Document Server

    Brown, Sandra E

    2014-01-01

    Classical free energies for the cage and prism isomers of water hexamer computed by the self- consistent phonons (SCP) method and reversible scaling (RS) method are presented for several flexible water potentials. Both methods have been augmented with a rotational correction for improved accuracy when working with clusters. Comparison of the SCP results with the RS results suggests a fairly broad temperature range over which the SCP approximation can be expected to give accurate results for systems of water clusters, and complements a previously reported assessment of SCP. Discrepancies between the SCP and RS results presented here, and recently published replica exchange molecular dynamics (REMD) results bring into question the convergence of the REMD and accompanying replica exchange path integral molecular dynamics results. In addition to the ever-present specter of unconverged results, several possible sources for the discrepancy are explored based on inherent characteristics of the methods used.

  1. Evaluation of generalized degrees of freedom for sparse estimation by replica method

    Science.gov (United States)

    Sakata, A.

    2016-12-01

    We develop a method to evaluate the generalized degrees of freedom (GDF) for linear regression with sparse regularization. The GDF is a key factor in model selection, and thus its evaluation is useful in many modelling applications. An analytical expression for the GDF is derived using the replica method in the large-system-size limit with random Gaussian predictors. The resulting formula has a universal form that is independent of the type of regularization, providing us with a simple interpretation. Within the framework of replica symmetric (RS) analysis, GDF has a physical meaning as the effective fraction of non-zero components. The validity of our method in the RS phase is supported by the consistency of our results with previous mathematical results. The analytical results in the RS phase are calculated numerically using the belief propagation algorithm.

  2. Virtual Replica of Matter in Bivacuum & Possible Mechanism of Distant Mind - Matter and Mind - Mind Interaction

    CERN Document Server

    Kaivarainen, A

    2001-01-01

    The original mechanism of bivacuum mediated Mind-Matter and Mind-Mind interaction, proposed here, is based on the following stages of long term efforts: New dynamic models of bivacuum, sub-elementary particles and corpuscle-wave [C-W] duality, as a background of Superunification; New Hierarchic theory of liquids and solids; New Hierarchic model of elementary act of consciousness; Virtual Replica (VR)of matter, including living organisms, in bivacuum; The distant resonant [Mind-Bivacuum-Matter] and [Mind-Bivacuum-Mind] interaction, mediated by Bivacuum oscillation (BvO, accompanied by virtual particles/antiparticles pressure oscillation. The latter factor is related to oscillation of vacuum permittivity and permeability. The virtual replica (VR) of condensed matter (living organisms in private case), may influence the properties of virtual pressure of bivacuum in following manner: 1) changing the amplitude of virtual pressure waves (VPW) in-phase with Bivacuum oscillations (BvO). This factor is dependent on fr...

  3. Performance of replica-exchange Wang-Landau sampling for the study of spin systems

    Science.gov (United States)

    Li, Ying Wai; Eisenbach, Markus; Vogel, Thomas; Wüst, Thomas; Landau, David P.

    2014-03-01

    The recently proposed replica-exchange Wang-Landau sampling (REWL) is a novel, massively parallel Monte Carlo method which allows for the parallelization of Wang-Landau sampling based on a replica-exchange framework. The robustness of the scheme is demonstrated by its broad applicability on a variety of spin systems: from the simplest models with discrete or continuous energy domains, to complex systems captured by large-scale first principles density functional theory calculations. The accuracy of REWL is studied by comparing the thermodynamic properties with exact solutions and results obtained by the original, serial Wang-Landau sampling. The principles for the speed-up, the strong and weak scaling behavior of REWL are also investigated when different parameter settings are employed. We will show, with the aid of selected spin systems, that the method accelerates the simulations significantly with a possible improved accuracy. Phys. Rev. Lett. 110, 210603 (2013)

  4. Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering

    CERN Document Server

    Gil-Ley, Alejandro

    2015-01-01

    The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strength of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.

  5. Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.

    Science.gov (United States)

    Roe, Daniel R; Bergonzo, Christina; Cheatham, Thomas E

    2014-04-03

    Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency.

  6. Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems.

    Science.gov (United States)

    Vreede, Jocelyne; Wolf, Maarten G; de Leeuw, Simon W; Bolhuis, Peter G

    2009-05-07

    Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states in molecular simulation methods. Previously, Wolf et al. showed that applying repulsive and attractive hydrogen bond biasing potentials in an alternating way significantly accelerates the folding process (Wolf, M. G.; de Leeuw, S. W. Biophys. J. 2008, 94, 3742). As the biasing potentials are only active during a fixed time interval, this alternating scheme does not represent a thermodynamic equilibrium. In this work, we present a Hamiltonian replica exchange molecular dynamics (REMD) scheme that aims to shuffle and reorder hydrogen bonds in the protein backbone. We therefore apply adapted hydrogen bond potentials in a Hamiltonian REMD scheme, which we call hydrogen bond switching (HS). To compare the performance of the HS to a standard REMD method, we performed HS and temperature REMD simulations of a beta-heptapeptide in methanol. Both methods sample the conformational space to a similar extent. As the HS simulation required only five replicas, while the REMD simulation required 20 replicas, the HS method is significantly more efficient. We tested the HS method also on a larger system, 16-residue polyalanine in water. Both of the simulations starting from a completely unfolded and a folded conformation resulted in an ensemble with, apart from the starting structure, similar conformational minima. We can conclude that the HS method provides an efficient way to sample the conformational space of a protein, without requiring knowledge of the folded states beforehand. In addition, these simulations revealed that convergence was hampered by replicas having a preference for specific biasing potentials. As this sorting effect is inherent to any Hamiltonian REMD method, finding a solution will result in an additional increase in the efficiency of Hamiltonian REMD methods in general.

  7. PHYSICAL DISABILITY, STIGMA, AND PHYSICAL ACTIVITY IN CHILDREN: A REPLICA STUDY

    OpenAIRE

    Gebhardt, Markus; MORA Julio G.; SCHWAB Susanne

    2016-01-01

    Introduction: Stereotypes can be reduced through positive descriptions. A stigma that able-bodied adults have towards children with physical disability can be reduced when the child is portrayed as being active. The study found out that a sporty active child, who uses a wheelchair, is perceived as more competent than the sporty active able-bodied child. Objective: This study is a replica study to support the hypotheses and to examine the stereotypes of able-bodied adults towards children w...

  8. Impact of Channel Estimation Errors on Multiuser Detection via the Replica Method

    Directory of Open Access Journals (Sweden)

    Li Husheng

    2005-01-01

    Full Text Available For practical wireless DS-CDMA systems, channel estimation is imperfect due to noise and interference. In this paper, the impact of channel estimation errors on multiuser detection (MUD is analyzed under the framework of the replica method. System performance is obtained in the large system limit for optimal MUD, linear MUD, and turbo MUD, and is validated by numerical results for finite systems.

  9. A new paradigm for petascale Monte Carlo simulation: Replica exchange Wang-Landau sampling

    CERN Document Server

    Li, Ying Wai; Wüst, Thomas; Landau, David P

    2014-01-01

    We introduce a generic, parallel Wang-Landau method that is naturally suited to implementation on massively parallel, petaflop supercomputers. The approach introduces a replica-exchange framework in which densities of states for overlapping sub-windows in energy space are determined iteratively by traditional Wang-Landau sampling. The advantages and general applicability of the method are demonstrated for several distinct systems that possess discrete or continuous degrees of freedom, including those with complex free energy landscapes and topological constraints.

  10. A new paradigm for petascale Monte Carlo simulation: Replica exchange Wang-Landau sampling

    Science.gov (United States)

    Li, Ying Wai; Vogel, Thomas; Wüst, Thomas; Landau, David P.

    2014-05-01

    We introduce a generic, parallel Wang-Landau method that is naturally suited to implementation on massively parallel, petaflop supercomputers. The approach introduces a replica-exchange framework in which densities of states for overlapping sub-windows in energy space are determined iteratively by traditional Wang-Landau sampling. The advantages and general applicability of the method are demonstrated for several distinct systems that possess discrete or continuous degrees of freedom, including those with complex free energy landscapes and topological constraints.

  11. A new paradigm for petascale Monte Carlo simulation: Replica exchange Wang Landau sampling

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ying Wai [ORNL; Vogel, Thomas [Los Alamos National Laboratory (LANL); Wuest, Thomas [Swiss Federal Research Institute, Switzerland; Landau, David P [University of Georgia, Athens, GA

    2014-01-01

    We introduce a generic, parallel Wang Landau method that is naturally suited to implementation on massively parallel, petaflop supercomputers. The approach introduces a replica-exchange framework in which densities of states for overlapping sub-windows in energy space are determined iteratively by traditional Wang Landau sampling. The advantages and general applicability of the method are demonstrated for several distinct systems that possess discrete or continuous degrees of freedom, including those with complex free energy landscapes and topological constraints.

  12. Protein-ligand docking using hamiltonian replica exchange simulations with soft core potentials.

    Science.gov (United States)

    Luitz, Manuel P; Zacharias, Martin

    2014-06-23

    Molecular dynamics (MD) simulations in explicit solvent allow studying receptor-ligand binding processes including full flexibility of the binding partners and an explicit inclusion of solvation effects. However, in MD simulations, the search for an optimal ligand-receptor complex geometry is frequently trapped in locally stable non-native binding geometries. A Hamiltonian replica-exchange (H-REMD)-based protocol has been designed to enhance the sampling of putative ligand-receptor complexes. It is based on softening nonbonded ligand-receptor interactions along the replicas and one reference replica under the control of the original force field. The efficiency of the method has been evaluated on two receptor-ligand systems and one protein-peptide complex. Starting from misplaced initial docking geometries, the H-REMD method reached in each case the known binding geometry significantly faster than a standard MD simulation. The approach could also be useful to identify and evaluate alternative binding geometries in a given binding region with small relative differences in binding free energy.

  13. General Formalism of Mass Scaling Approach for Replica-Exchange Molecular Dynamics and its Application

    Science.gov (United States)

    Nagai, Tetsuro

    2017-01-01

    Replica-exchange molecular dynamics (REMD) has demonstrated its efficiency by combining trajectories of a wide range of temperatures. As an extension of the method, the author formalizes the mass-manipulating replica-exchange molecular dynamics (MMREMD) method that allows for arbitrary mass scaling with respect to temperature and individual particles. The formalism enables the versatile application of mass-scaling approaches to the REMD method. The key change introduced in the novel formalism is the generalized rules for the velocity and momentum scaling after accepted replica-exchange attempts. As an application of this general formalism, the refinement of the viscosity-REMD (V-REMD) method [P. H. Nguyen, https://doi.org/10.1063/1.3369626" xlink:type="simple">J. Chem. Phys. 132, 144109 (2010)] is presented. Numerical results are provided using a pilot system, demonstrating easier and more optimized applicability of the new version of V-REMD as well as the importance of adherence to the generalized velocity scaling rules. With the new formalism, more sound and efficient simulations will be performed.

  14. Evaluation of internal adaptation in ceramic and composite resin inlays by silicon replica technique.

    Science.gov (United States)

    Karakaya, S; Sengun, A; Ozer, F

    2005-06-01

    This study was aimed at investigating the internal adaptation of a ceramic (Ceramco II) and two composite resin inlay materials (SureFil and 3M Filtek Z 250) using silicon replica technique as an indicator. Forty-five standard mesial-occlusal-distal (MOD) cavities were prepared into brass moulds by using computer numerically controlled system. Inlays were prepared according to manufacturers' instructions with indirect methods. Replicas of the prepared cavities and inlays were produced with a polyvinyl siloxane material (Elite H-D). The spaces between inlays and cavities were filled by different coloured light-body polyvinyl siloxane material. Two parallel slices (mesio-distally) were obtained from the replicas with a sharp blade. Different coloured polyvinyl siloxane material thickness between cavity and inlay was measured at seven points (mesial, occlusal and distal). The data were evaluated with anova and Tukey's honestly significantly different (HSD) statistical tests. In the SureFil and Ceramco II groups, the sizes of the contraction gaps at mesial and distal gingival floors were greater than that of the occlusal marginal walls. In comparison of gap formation at occlusal regions, while the 3M composite group showed highest gap values (204.33 +/- 75.45 microm), the Ceramco II group revealed the lowest (141.17 +/- 23.66 microm) (P 0.05). In conclusion, our results showed that ceramic inlays did not confer any big advantage for internal adaptation over the composite inlays.

  15. Recent advances in fabrication of monolayer colloidal crystals and their inverse replicas

    Institute of Scientific and Technical Information of China (English)

    YE XiaoZhou; QI LiMin

    2014-01-01

    Monolayer colloidal crystals(MCCs)are two-dimensional(2D)colloidal crystals consisting of a monolayer of monodisperse colloidal particles arrayed with a 2D periodic order.In recent years,MCCs have attracted intensive interest because they can act as 2D photonic crystals and be used as versatile templates for fabrication of various 2D nanostructure arrays.In this review,we provide an overview of the recent progress in the controllable fabrication of MCCs and their inverse replicas.First,some newly-developed methods for the self-assembly of MCCs based on different strategies including interfacial assembly and convective assembly are introduced.Second,some representative novel methods regarding the fabrication of various functional2D inverse replicas of MCCs,such as 2D arrays of nanobowls,nanocaps,and hollow spheres,as well as 2D monolayer inverse opals(MIOs),are described.In addition,the potential applications of MCCs and their inverse replicas are discussed.

  16. Characterization of Nb SRF cavity materials by white light interferometry and replica techniques

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Chen [Thomas Jefferson National Accelerator Facility, Newport News, VA 23606 (United States); The Applied Science Department, The College of William and Mary, Williamsburg, VA 23185 (United States); Reece, Charles [Thomas Jefferson National Accelerator Facility, Newport News, VA 23606 (United States); Kelley, Michael, E-mail: mkelley@jlab.org [Thomas Jefferson National Accelerator Facility, Newport News, VA 23606 (United States); The Applied Science Department, The College of William and Mary, Williamsburg, VA 23185 (United States)

    2013-06-01

    Much work has shown that the topography of the interior surface is an important contributor to the performance of Nb superconducting radiofrequency (SRF) accelerator cavities. Micron-scale topography is implicated in non-linear loss mechanisms that limit the useful accelerating gradient range and impact cryogenic cost. Aggressive final chemical treatments in cavity production seek to reliably obtain “smoothest” surfaces with superior performance. Process development suffers because the cavity interior surface cannot be viewed directly without cutting out pieces, rendering the cavities unavailable for further study. Here we explore replica techniques as an alternative, providing imprints of cavity internal surface that can be readily examined. A second matter is the topography measurement technique used. Atomic force microscopy (AFM) has proven successful, but too time intensive for routine use in this application. We therefore introduce white light interferometry (WLI) as an alternative approach. We examined real surfaces and their replicas, using AFM and WLI. We find that the replica/WLI is promising to provide the large majority of the desired information, recognizing that a trade-off is being made between best lateral resolution (AFM) and the opportunity to examine much more surface area (WLI).

  17. Biosynthesis of cathodoluminescent zinc oxide replicas using butterfly (Papilio paris) wing scales as templates

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Wang [State Key Lab of Metal Matrix Composites, Shanghai Jiao Tong University, 200240, Shanghai (China); Zhang Di [State Key Lab of Metal Matrix Composites, Shanghai Jiao Tong University, 200240, Shanghai (China)], E-mail: zhangdi@sjtu.edu.cn; Fan Tongxiang; Ding Jian; Gu Jiajun [State Key Lab of Metal Matrix Composites, Shanghai Jiao Tong University, 200240, Shanghai (China); Guo Qixin; Ogawa, Hiroshi [Department of Electrical and Electronic Engineering, Saga University, Saga 840-8502 (Japan)

    2009-01-01

    Papilio paris butterflies have an iridescent blue color patch on their hind wings which is visible over a wide viewing angle. Optical and scanning electron microscopy observations of scales from the wings show that the blue color scales have very different microstructure to the matt black ones which also populate the wings. Scanning electron micrographs of the blue scales show that their surfaces comprise a regular two-dimensional array of concavities. By contrast the matt black scales have fine, sponge-like structure, between the ridges and the cross ribs in the scales. Using both types of scale as bio-templates, we obtain zinc oxide (ZnO) replicas of the microstructures of the original scales. Room temperature (T = 300 K) cathodoluminescence spectra of these ZnO replicas have also been studied. Both spectra show a similar sharp near-band-edge emission, but have different green emission, which we associate with the different microstructures of the ZnO replicas.

  18. Food labels

    DEFF Research Database (Denmark)

    Selsøe Sørensen, Henrik; Clement, Jesper; Gabrielsen, Gorm

    2012-01-01

    The food industry develops tasty and healthy food but fails to deliver the message to all consumers. The consumers’ background knowledge is essential for how they find and decode relevant elements in the cocktail of signs which fight for attention on food labels. In this exploratory study, we find...... evidence for dividing consumers into two profiles: one relying on general food knowledge and another using knowledge related to signpost labels. In a combined eyetracking and questionnaire survey we analyse the influence of background knowledge and identify different patterns of visual attention...... for the two consumer profiles. This underlines the complexity in choosing and designing the ‘right’ elements for a food package that consumers actually look at and are able to make rational use of. In spite of any regulation of food information provided by authorities, consumers will still be confronted...

  19. Recommendations for replica testing of high temperature components in power plant; Rekommendationer foer replikprovning av hoegtemperaturkomponenter i kraftanlaeggningar

    Energy Technology Data Exchange (ETDEWEB)

    Storesund, Jan [Det Norske Veritas AB, Stockholm (Sweden)

    2000-08-01

    Replica testing is a non-destructive testing method where the microstructure of the surface of a component is replicated. This involves careful metallographical preparation which in some points also should be adapted to the aims of the investigation. There are published guidelines for replica testing of high temperature components in power plant, for instance by Nordtest, but these may be considered to be insufficient to assure the required quality and reproducibility of the replicas. There are no certification systems for the replica method in Sweden as well as abroad and the experience has shown that differences in the performance that existing praxis can involve may give significant influence on the results when the replicas are evaluated. In the present project recommendations have been compiled for replica testing with regard to creep damage on occurring heat resistant steel types in Swedish power plants. The recommendations consist of guidelines for metallographical replication in the field and cover: - Test positions at weldments and pipe bends; - Equipment; - Rough and fine grinding; - Macro-etching; - Electrolytic and mechanical polishing; - Etching; - Replication; - Documentation and storage; - Personnel. They describe differences in the testing of the different materials and the purpose is to assure replica testing of the highest quality and reproducibility. The recommendations have been compiled by use of guidelines and company standards as a starting point. Some points in the recommendations refer to trials for verification which have been carried out within the frame of the project. The trials have been focused on the appearance of creep damage and microstructure in different established methods for polishing and etching. Comments and closer descriptions for some points of the test procedures are given in an appendix to the recommendations.

  20. Introduction to Pesticide Labels

    Science.gov (United States)

    Pesticide product labels provide critical information about how to safely and legally handle and use pesticide products. Unlike most other types of product labels, pesticide labels are legally enforceable. Learn about pesticide product labels.

  1. Food Label and You

    Medline Plus

    Full Text Available ... Products Food Home Food Ingredients, Packaging & Labeling Labeling & Nutrition The Food Label and You — Video Share Tweet ... FDA has issued final changes to update the Nutrition Facts label for packaged foods. For more information, ...

  2. Ultrastructural Identification and Colocalization of Interacting Proteins in the Murine Cochlea by Post-Embedding Immunogold Transmission Electron Microscopy.

    Science.gov (United States)

    Harvey, Margaret C; Sokolowski, Bernd H A

    2016-01-01

    Verification of the presence and location of a protein within tissue can be accomplished by western blotting and immunohistochemistry, using either paraffin or frozen sections. Affinity purification by reciprocal coimmunoprecipitations using the tissue of interest can demonstrate the existence of an interacting pair of proteins. Ultimately, the ability to visualize the interaction at the cellular level is desired. Precise location(s) of interacting proteins in situ can be accomplished by ultrastructural localization with high-quality primary antibodies and small-particle-size Au-conjugated secondary antibodies. Visualization can be obtained with a transmission electron microscope fitted with a high-resolution camera permitting magnifications that exceed 2 × 10(5), and, to date, resolution capability of 20+ Mpixels, thus enabling localization of the target protein to within nanometers of the actual location. Here, we report the method by which immunolocalization at the level of the electron microscope is accomplished using the post-embedding technique, i.e., performing antibody labeling of proteins on ultrathin sections of tissue embedded in acrylic resin.

  3. Inferring predator behavior from attack rates on prey-replicas that differ in conspicuousness.

    Directory of Open Access Journals (Sweden)

    Yoel E Stuart

    Full Text Available Behavioral ecologists and evolutionary biologists have long studied how predators respond to prey items novel in color and pattern. Because a predatory response is influenced by both the predator's ability to detect the prey and a post-detection behavioral response, variation among prey types in conspicuousness may confound inference about post-prey-detection predator behavior. That is, a relatively high attack rate on a given prey type may result primarily from enhanced conspicuousness and not predators' direct preference for that prey. Few studies, however, account for such variation in conspicuousness. In a field experiment, we measured predation rates on clay replicas of two aposematic forms of the poison dart frog Dendrobates pumilio, one novel and one familiar, and two cryptic controls. To ask whether predators prefer or avoid a novel aposematic prey form independently of conspicuousness differences among replicas, we first modeled the visual system of a typical avian predator. Then, we used this model to estimate replica contrast against a leaf litter background to test whether variation in contrast alone could explain variation in predator attack rate. We found that absolute predation rates did not differ among color forms. Predation rates relative to conspicuousness did, however, deviate significantly from expectation, suggesting that predators do make post-detection decisions to avoid or attack a given prey type. The direction of this deviation from expectation, though, depended on assumptions we made about how avian predators discriminate objects from the visual background. Our results show that it is important to account for prey conspicuousness when investigating predator behavior and also that existing models of predator visual systems need to be refined.

  4. Multiple replica repulsion technique for efficient conformational sampling of biological systems.

    Science.gov (United States)

    Malevanets, Anatoly; Wodak, Shoshana J

    2011-08-17

    Here, we propose a technique for sampling complex molecular systems with many degrees of freedom. The technique, termed "multiple replica repulsion" (MRR), does not suffer from poor scaling with the number of degrees of freedom associated with common replica exchange procedures and does not require sampling at high temperatures. The algorithm involves creation of multiple copies (replicas) of the system, which interact with one another through a repulsive potential that can be applied to the system as a whole or to portions of it. The proposed scheme prevents oversampling of the most populated states and provides accurate descriptions of conformational perturbations typically associated with sampling ground-state energy wells. The performance of MRR is illustrated for three systems of increasing complexity. A two-dimensional toy potential surface is used to probe the sampling efficiency as a function of key parameters of the procedure. MRR simulations of the Met-enkephalin pentapeptide, and the 76-residue protein ubiquitin, performed in presence of explicit water molecules and totaling 32 ns each, investigate the ability of MRR to characterize the conformational landscape of the peptide, and the protein native basin, respectively. Results obtained for the enkephalin peptide reflect more closely the extensive conformational flexibility of this peptide than previously reported simulations. Those obtained for ubiquitin show that conformational ensembles sampled by MRR largely encompass structural fluctuations relevant to biological recognition, which occur on the microsecond timescale, or are observed in crystal structures of ubiquitin complexes with other proteins. MRR thus emerges as a very promising simple and versatile technique for modeling the structural plasticity of complex biological systems. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  5. Time-reversal focusing of an expanding soliton gas in disordered replicas

    KAUST Repository

    Fratalocchi, Andrea

    2011-05-31

    We investigate the properties of time reversibility of a soliton gas, originating from a dispersive regularization of a shock wave, as it propagates in a strongly disordered environment. An original approach combining information measures and spin glass theory shows that time-reversal focusing occurs for different replicas of the disorder in forward and backward propagation, provided the disorder varies on a length scale much shorter than the width of the soliton constituents. The analysis is performed by starting from a new class of reflectionless potentials, which describe the most general form of an expanding soliton gas of the defocusing nonlinear Schrödinger equation.

  6. Chiral-glass transition and replica symmetry breaking of a three-dimensional heisenberg spin glass

    Science.gov (United States)

    Hukushima; Kawamura

    2000-02-01

    Extensive equilibrium Monte Carlo simulations are performed for a three-dimensional Heisenberg spin glass with the nearest-neighbor Gaussian coupling to investigate its spin-glass and chiral-glass orderings. The occurrence of a finite-temperature chiral-glass transition without the conventional spin-glass order is established. Critical exponents characterizing the transition are different from those of the standard Ising spin glass. The calculated overlap distribution suggests the appearance of a peculiar type of replica-symmetry breaking in the chiral-glass ordered state.

  7. Replica symmetry breaking transition of the weakly anisotropic Heisenberg spin glass in magnetic fields.

    Science.gov (United States)

    Imagawa, Daisuke; Kawamura, Hikaru

    2004-02-20

    The spin and the chirality orderings of the three-dimensional Heisenberg spin glass with the weak random anisotropy are studied under applied magnetic fields by equilibrium Monte Carlo simulations. A replica symmetry breaking transition occurs in the chiral sector accompanied by the simultaneous spin-glass order. The ordering behavior differs significantly from that of the Ising spin glass, despite the similarity in the global symmetry. Our observation is consistent with the spin-chirality decoupling-recoupling scenario of a spin-glass transition.

  8. Investigation on a replica step gauge for optical 3D scanning of micro parts

    DEFF Research Database (Denmark)

    Cantatore, Angela; De Chiffre, Leonardo; Carmignato, S.

    2010-01-01

    . The stability over time of the step gauge was evaluated by repetitive measurement campaigns over a period of eight months, using measurements taken with a tactile CMM and with an optical scanner. Surface cooperativeness was investigated by measuring artefact grooves and pitch and comparing results with tactile......This work deals with investigation of the stability over time and surface cooperativeness of a calibration artefact intended for optical scanner verification. A replica step gauge with 11 grooves, made of bisacryl material for dental applications (luxabite) and previously fabricated was studied...

  9. Replica-exchange Wang Landau sampling: pushing the limits of Monte Carlo simulations in materials sciences

    Energy Technology Data Exchange (ETDEWEB)

    Perera, Meewanage Dilina N [ORNL; Li, Ying Wai [ORNL; Eisenbach, Markus [ORNL; Vogel, Thomas [Los Alamos National Laboratory (LANL); Landau, David P [University of Georgia, Athens

    2015-01-01

    We describe the study of thermodynamics of materials using replica-exchange Wang Landau (REWL) sampling, a generic framework for massively parallel implementations of the Wang Landau Monte Carlo method. To evaluate the performance and scalability of the method, we investigate the magnetic phase transition in body-centered cubic (bcc) iron using the classical Heisenberg model parameterized with first principles calculations. We demonstrate that our framework leads to a significant speedup without compromising the accuracy and precision and facilitates the study of much larger systems than is possible with its serial counterpart.

  10. Replica exchange molecular simulation of Lennard-Jones particles in a two-dimensional confined system

    Science.gov (United States)

    Doi, Hideo; Yasuoka, Kenji

    2017-05-01

    Confined systems exhibit interesting properties that are applied to the fields of lubrication, adhesion and nanotechnology. The replica exchange molecular simulation method was applied to calculate the phase equilibrium points of Lennard-Jones particles in a two-dimensional confined system. The liquid-solid phase equilibrium points and the solid structure with a dependency of the slit width were determined and the order parameter of the solid structure was analyzed. Such confined systems are shown to be favorable for manipulation of the phase equilibrium points.

  11. Anti-stiction coating of PDMS moulds for rapid microchannel fabrication by double replica moulding

    DEFF Research Database (Denmark)

    Zhuang, Guisheng; Kutter, Jörg Peter

    2011-01-01

    ), which resulted in an anti-stiction layer for the improved release after PDMS casting. The deposition of FDTS on an O2 plasma-activated surface of PDMS produced a reproducible and well-performing anti-stiction monolayer of fluorocarbon, and we used the FDTS-coated moulds as micro-masters for rapid......In this paper, we report a simple and precise method to rapidly replicate master structures for fast microchannel fabrication by double replica moulding of polydimethylsiloxane (PDMS). A PDMS mould was surface-treated by vapour phase deposition of 1H,1H,2H,2H-perfluorodecyltrichlorosilane (FDTS...

  12. Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

    Science.gov (United States)

    Ostermeir, Katja; Zacharias, Martin

    2014-12-01

    Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations.

  13. On Online Labeling with Polynomially Many Labels

    DEFF Research Database (Denmark)

    Babka, Martin; Bulánek, Jan; Cunat, Vladimír

    2012-01-01

    In the online labeling problem with parameters n and m we are presented with a sequence of nkeys from a totally ordered universe U and must assign each arriving key a label from the label set {1,2,…,m} so that the order of labels (strictly) respects the ordering on U. As new keys arrive it may be...

  14. A point-of-care testing system with Love-wave sensor and immunogold staining enhancement for early detection of lung cancer.

    Science.gov (United States)

    Zou, Yingchang; Zhang, Xi; An, Chao; Ran, Chunxue; Ying, Kejing; Wang, Ping

    2014-12-01

    It has been reported that detection of exhaled breath condensate (EBC) is available for studies of pulmonary diseases, especially lung disease. In order to detect lung cancer (LC) at early stage, a point-of-care testing system suitable for measurement of tumor markers in EBC is developed. The assay, based on gold nanoparticle sandwich immunoassay and subsequent gold staining, was performed on a Love-wave sensor packaged inside a chip cartridge. Benefit from high sensitivity of Love-wave sensor, oriented immobilization of coating antibodies and immunogold staining enhancement, the present immunosensor could provide a sensitive, specific and rapid measurement. Carcinoembryonic antigen (CEA), neuron specific enolase (NSE) and squamous cell carcinoma antigen (SCC) in EBC collected from 17 patients with LC and 13 healthy volunteers were detected by this system. Results were compared with commercial chemiluminescence immunoassay and showed high correlation between two methods. Additionally, it revealed significantly statistical differences existing between two groups of subjects. These results indicate that the present system is suitable for detection of tumor markers in EBC and could be used as assistant tools for early detection of LC.

  15. Photonic ferromagnetic-like spontaneous mode-locking phase transition with replica symmetry breaking in multimode Nd:YAG laser

    CERN Document Server

    Moura, André L; Raposo, Ernesto P; Gomes, Anderson S L; de Araújo, Cid B

    2016-01-01

    The recent reports of the replica symmetry breaking (RSB) phenomenon in photonic experiments [1-5] boosted the understanding of the role of disorder in multimode lasers, as well as helped to settle enlightening connections [6-13] with the statistical physics of complex systems. RSB manifests when identically-prepared system replicas reach distinct states, yielding different measures of observable quantities [14]. Here we demonstrate the RSB in the spontaneous mode-locking regime of a conventional multimode Nd:YAG laser in a closed cavity. The underlying mechanism is quite distinct from that of the RSB spinglass phase in cavityless random lasers with incoherently-oscillating modes. Here, a specific nonuniform distribution of the gain takes place in each pulse, and frustration is induced since the coherent oscillation of a given subset of longitudinal modes dominates and simultaneously inhibits the others. Nevertheless, when high losses are introduced only the replica-symmetric amplified stimulation emission is...

  16. Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.

    Science.gov (United States)

    Wang, Kai; Chodera, John D; Yang, Yanzhi; Shirts, Michael R

    2013-12-01

    We present a method to identify small molecule ligand binding sites and poses within a given protein crystal structure using GPU-accelerated Hamiltonian replica exchange molecular dynamics simulations. The Hamiltonians used vary from the physical end state of protein interacting with the ligand to an unphysical end state where the ligand does not interact with the protein. As replicas explore the space of Hamiltonians interpolating between these states, the ligand can rapidly escape local minima and explore potential binding sites. Geometric restraints keep the ligands from leaving the vicinity of the protein and an alchemical pathway designed to increase phase space overlap between intermediates ensures good mixing. Because of the rigorous statistical mechanical nature of the Hamiltonian exchange framework, we can also extract binding free energy estimates for all putative binding sites. We present results of this methodology applied to the T4 lysozyme L99A model system for three known ligands and one non-binder as a control, using an implicit solvent. We find that our methodology identifies known crystallographic binding sites consistently and accurately for the small number of ligands considered here and gives free energies consistent with experiment. We are also able to analyze the contribution of individual binding sites to the overall binding affinity. Our methodology points to near term potential applications in early-stage structure-guided drug discovery.

  17. Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.

    Science.gov (United States)

    Curuksu, Jeremy; Zacharias, Martin

    2009-03-14

    Although molecular dynamics (MD) simulations have been applied frequently to study flexible molecules, the sampling of conformational states separated by barriers is limited due to currently possible simulation time scales. Replica-exchange (Rex)MD simulations that allow for exchanges between simulations performed at different temperatures (T-RexMD) can achieve improved conformational sampling. However, in the case of T-RexMD the computational demand grows rapidly with system size. A Hamiltonian RexMD method that specifically enhances coupled dihedral angle transitions has been developed. The method employs added biasing potentials as replica parameters that destabilize available dihedral substates and was applied to study coupled dihedral transitions in nucleic acid molecules. The biasing potentials can be either fixed at the beginning of the simulation or optimized during an equilibration phase. The method was extensively tested and compared to conventional MD simulations and T-RexMD simulations on an adenine dinucleotide system and on a DNA abasic site. The biasing potential RexMD method showed improved sampling of conformational substates compared to conventional MD simulations similar to T-RexMD simulations but at a fraction of the computational demand. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions including explicit solvent and ions and can be easily extended to other types of molecules.

  18. Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations.

    Science.gov (United States)

    Meng, Yilin; Dashti, Danial Sabri; Roitberg, Adrian E

    2011-09-13

    Alchemical free energy calculations play a very important role in the field of molecular modeling. Efforts have been made to improve the accuracy and precision of those calculations. One of the efforts is to employ a Hamiltonian replica exchange molecular dynamics (H-REMD) method to enhance conformational sampling. In this paper, we demonstrated that HREMD method not only improves convergence in alchemical free energy calculations but also can be used to compute free energy differences directly via the Free Energy Perturbation (FEP)algorithm. We show a direct mapping between the H-REMD and the usual FEP equations, which are then used directly to compute free energies. The H-REMD alchemical free energy calculation (Replica exchange Free Energy Perturbation, REFEP) was tested on predicting the pK(a) value of the buried Asp26 in thioredoxin. We compare the results of REFEP with TI and regular FEP simulations. REFEP calculations converged faster than those from TI and regular FEP simulations. The final predicted pK(a) value from the H-REMD simulation was also very accurate, only 0.4 pK(a) unit above the experimental value. Utilizing the REFEP algorithm significantly improves conformational sampling, and this in turn improves the convergence of alchemical free energy simulations.

  19. Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.

    Science.gov (United States)

    Xia, Junchao; Flynn, William F; Gallicchio, Emilio; Zhang, Bin W; He, Peng; Tan, Zhiqiang; Levy, Ronald M

    2015-09-05

    We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these methods on NSF (National Science Foundation) XSEDE (Extreme Science and Engineering Discovery Environment) clusters and BOINC (Berkeley Open Infrastructure for Network Computing) distributed computing networks at Temple University and Brooklyn College at CUNY (the City University of New York). They are also being implemented on the IBM World Community Grid. To illustrate the methods, we have performed extensive (more than 60 ms in aggregate) simulations for the beta-cyclodextrin-heptanoate host-guest system in the context of one- and two-dimensional ASyncRE, and we used the results to estimate absolute binding free energies using the binding energy distribution analysis method. We propose ways to improve the efficiency of REMD simulations: these include increasing the number of exchanges attempted after a specified molecular dynamics (MD) period up to the fast exchange limit and/or adjusting the MD period to allow sufficient internal relaxation within each thermodynamic state. Although ASyncRE simulations generally require long MD periods (>picoseconds) per replica exchange cycle to minimize the overhead imposed by heterogeneous computing networks, we found that it is possible to reach an efficiency similar to conventional synchronous REMD, by optimizing the combination of the MD period and the number of exchanges attempted per cycle.

  20. Flow field analysis in a compliant acinus replica model using particle image velocimetry (PIV).

    Science.gov (United States)

    Berg, Emily J; Weisman, Jessica L; Oldham, Michael J; Robinson, Risa J

    2010-04-19

    Inhaled particles reaching the alveolar walls have the potential to cross the blood-gas barrier and enter the blood stream. Experimental evidence of pulmonary dosimetry, however, cannot be explained by current whole lung dosimetry models. Numerical and experimental studies shed some light on the mechanisms of particle transport, but realistic geometries have not been investigated. In this study, a three dimensional expanding model including two generations of respiratory bronchioles and five terminal alveolar sacs was created from a replica human lung cast. Flow visualization techniques were employed to quantify the fluid flow while utilizing streamlines to evaluate recirculation. Pathlines were plotted to track the fluid motion and estimate penetration depth of inhaled air. This study provides evidence that the two generations immediately proximal to the terminal alveolar sacs do not have recirculating eddies, even for intense breathing. Results of Peclet number calculations indicate that substantial convective motion is present in vivo for the case of deep breathing, which significantly increases particle penetration into the alveoli. However, particle diffusion remains the dominant mechanism of particle transport over convection, even for intense breathing because inhaled particles do not reach the alveolar wall in a single breath by convection alone. Examination of the velocity fields revealed significant uneven ventilation of the alveoli during a single breath, likely due to variations in size and location. This flow field data, obtained from replica model geometry with realistic breathing conditions, provides information to better understand fluid and particle behavior in the acinus region of the lung.

  1. Manufacture of patient-specific vascular replicas for endovascular simulation using fast, low-cost method

    Science.gov (United States)

    Kaneko, Naoki; Mashiko, Toshihiro; Ohnishi, Taihei; Ohta, Makoto; Namba, Katsunari; Watanabe, Eiju; Kawai, Kensuke

    2016-12-01

    Patient-specific vascular replicas are essential to the simulation of endovascular treatment or for vascular research. The inside of silicone replica is required to be smooth for manipulating interventional devices without resistance. In this report, we demonstrate the fabrication of patient-specific silicone vessels with a low-cost desktop 3D printer. We show that the surface of an acrylonitrile butadiene styrene (ABS) model printed by the 3D printer can be smoothed by a single dipping in ABS solvent in a time-dependent manner, where a short dip has less effect on the shape of the model. The vascular mold is coated with transparent silicone and then the ABS mold is dissolved after the silicone is cured. Interventional devices can pass through the inside of the smoothed silicone vessel with lower pushing force compared to the vessel without smoothing. The material cost and time required to fabricate the silicone vessel is about USD $2 and 24 h, which is much lower than the current fabrication methods. This fast and low-cost method offers the possibility of testing strategies before attempting particularly difficult cases, while improving the training of endovascular therapy, enabling the trialing of new devices, and broadening the scope of vascular research.

  2. PHYSICAL DISABILITY, STIGMA, AND PHYSICAL ACTIVITY IN CHILDREN: A REPLICA STUDY

    Directory of Open Access Journals (Sweden)

    Markus GEBHARDT

    2016-04-01

    Full Text Available Introduction: Stereotypes can be reduced through positive descriptions. A stigma that able-bodied adults have towards children with physical disability can be reduced when the child is portrayed as being active. The study found out that a sporty active child, who uses a wheelchair, is perceived as more competent than the sporty active able-bodied child. Objective: This study is a replica study to support the hypotheses and to examine the stereotypes of able-bodied adults towards children with and without (physical disabilities. Methods: This study presents two experimental replica studies using a 2 (physical activity x 2 (sporty activities. The dependent variables were the perception of competencies and warmth according to Stereotype Content Model (SCM. Study 1 is an online experiment with 355 students of the Open University of Hagen. Study 2 surveys 1176 participants (from Munich and Graz with a paper-pencil-questionnaire. Results: The significant interaction effect was not supported by our studies. The sporty able-bodied child was rated higher in competences than the sporty child, who use a wheelchair. Sporting activity only reduces the stigma towards children with a physical disability slightly. Conclusion: The stigma towards children with physical disability can be reduced when the child is portrayed as being active, but the effect was not strong enough to chance the original classification by the SCM.

  3. Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle.

    Science.gov (United States)

    Cavalli, Andrea; Camilloni, Carlo; Vendruscolo, Michele

    2013-03-07

    In order to characterise the dynamics of proteins, a well-established method is to incorporate experimental parameters as replica-averaged structural restraints into molecular dynamics simulations. Here, we justify this approach in the case of interproton distance information provided by nuclear Overhauser effects by showing that it generates ensembles of conformations according to the maximum entropy principle. These results indicate that the use of replica-averaged structural restraints in molecular dynamics simulations, given a force field and a set of experimental data, can provide an accurate approximation of the unknown Boltzmann distribution of a system.

  4. Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations : Application in the refinement of de novo models

    NARCIS (Netherlands)

    Fan, Hao; Periole, Xavier; Mark, Alan E.

    2012-01-01

    The efficiency of using a variant of Hamiltonian replica-exchange molecular dynamics (Chaperone H-replica-exchange molecular dynamics [CH-REMD]) for the refinement of protein structural models generated de novo is investigated. In CH-REMD, the interaction between the protein and its environment, spe

  5. Membrane topology of insulin receptors reconstituted into lipid vesicles

    DEFF Research Database (Denmark)

    Tranum-Jensen, Jørgen; Christiansen, K.; Carlsen, Jens;

    1994-01-01

    Anatomy, insulin receptors, membrane reconstitution, electron microscopy, quaternary structure, immunogold labeling......Anatomy, insulin receptors, membrane reconstitution, electron microscopy, quaternary structure, immunogold labeling...

  6. Food Label and You

    Medline Plus

    Full Text Available ... Vaccines, Blood & Biologics Animal & Veterinary Cosmetics Tobacco Products Food Home Food Ingredients, Packaging & Labeling Labeling & Nutrition The Food Label and You — Video Share Tweet Linkedin Pin ...

  7. Effects of Propyithiouracil (PTU) Administration on the Synthesis and Secretion of Thyroglobulin in the Rat Thyroid Gland: A Quantitative Immuno-electron Microscopic Study Using Immunogold Technique.

    Science.gov (United States)

    Yi, Xue; Yamamoto, Koichi; Shu, Lu; Katoh, Ryohei; Kawaoi, Akira

    1997-01-01

    To clarify the effects of an antithyroid drug on the kinetics of thyroglobulin synthesis, secretion, and reabsorption in the thyroid follicles, propylthiouracil (PTU) was administered to rats and the thyroid glands were examined by a refined post-embedding immunogold technique during and after withdrawal of PTU. Seven-wk-old male Wistar rats were administered with S mg of PTU/d through a gastric tube, and sacrificed at 1 and 2 wk of administration and at 1, 2, and 3 d, and 1, 2, 3, and 4 wk, after discontinuation. The administration of PTU caused a remarkable dilatation of the rER and Golgi apparatus, but these areas gradually recovered after withdrawal of PTU. During the experiment, no significant change in the density of thyroglobulin (Tg) was observed except for a transient increase immediately after withdrawal of PTU. The expression of Tg on subapical vesicles (SV) and follicular colloid took a relatively parallel course; increasing during administration of PTU and decreasing with a transient peak immediately after treatment was discontinued. In contrast to the remarkable changes in the morphology of compartments involved in Tg synthesis, the development of colloid droplets and formation of secondary lysosomes were suppressed during and after discontinuing administration of PTU. However, the basic pattern of the gradient of Tg density among the cellular compartments was essentially retained in the experimental group. Thus the present immunoelectron-microscopic study provided evidence that administration of PTU stimulates the synthesis and secretion of Tg in the follicular epithelium in vivo, and, also, suppresses reabsorption and degradation of Tg. Further, it was speculated that the density gradient of Tg among the compartments involved in Tg synthesis, secretion and storage is regulated by an unknown constitutive mechanism and not by the thyroid-stimulating hormone (TSH)-TSH receptor-mediated system.

  8. Instituto de Fisica, UFRGS, CP 15051, 91501-970, Porto Alegre RS, Brazil: Replica theory of granular media

    Science.gov (United States)

    Arenzon, Jeferson J.

    1999-03-01

    An infinite range spin-glass-like model for granular systems is introduced and studied through the replica mean-field formalism. Equilibrium, density-dependent properties under vibration and gravity are obtained that qualitatively resemble the results from real and numerical experiments.

  9. Validation of airway resistance models for predicting pressure loss through anatomically realistic conducting airway replicas of adults and children.

    Science.gov (United States)

    Borojeni, Azadeh A T; Noga, Michelle L; Martin, Andrew R; Finlay, Warren H

    2015-07-16

    This work describes in vitro measurement of the total pressure loss at varying flow rate through anatomically realistic conducting airway replicas of 10 children, 4 to 8 years old, and 5 adults. Experimental results were compared with analytical predictions made using published airway resistance models. For the adult replicas, the model proposed by van Ertbruggen et al. (2005. J. Appl. Physiol. 98, 970-980) most accurately predicted central conducting airway resistance for inspiratory flow rates ranging from 15 to 90 L/min. Models proposed by Pedley et al. (1970. J. Respir. Physiol. 9, 371-386) and by Katz et al. (2011. J. Biomech. 44, 1137-1143) also provided reasonable estimates, but with a tendency to over predict measured pressure loss for both models. For child replicas, the Pedley and Katz models both provided good estimation of measured pressure loss at flow rates representative of resting tidal breathing, but under predicted measured values at high inspiratory flow rate (60 L/min). The van Ertbruggen model, developed based on flow simulations performed in an adult airway model, tended to under predict measured pressure loss through the child replicas across the range of flow rates studied (2 to 60 L/min). These results are intended to provide guidance for selection of analytical pressure loss models for use in predicting airway resistance and ventilation distribution in adults and children. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Sealant retention is better assessed through colour photographs than through the replica and the visual examination methods

    NARCIS (Netherlands)

    Hu, X.; Fan, M.; Rong, W.; Lo, E.C.; Bronkhorst, E.M.; Frencken, J.E.F.M.

    2014-01-01

    The aim of this study was to test the hypothesis that the colour photograph method has a higher level of validity for assessing sealant retention than the visual clinical examination and replica methods. Sealed molars were assessed by two evaluators. The scores for the three methods were compared ag

  11. Localization-Free Detection of Replica Node Attacks in Wireless Sensor Networks Using Similarity Estimation with Group Deployment Knowledge

    Science.gov (United States)

    Ding, Chao; Yang, Lijun; Wu, Meng

    2017-01-01

    Due to the unattended nature and poor security guarantee of the wireless sensor networks (WSNs), adversaries can easily make replicas of compromised nodes, and place them throughout the network to launch various types of attacks. Such an attack is dangerous because it enables the adversaries to control large numbers of nodes and extend the damage of attacks to most of the network with quite limited cost. To stop the node replica attack, we propose a location similarity-based detection scheme using deployment knowledge. Compared with prior solutions, our scheme provides extra functionalities that prevent replicas from generating false location claims without deploying resource-consuming localization techniques on the resource-constraint sensor nodes. We evaluate the security performance of our proposal under different attack strategies through heuristic analysis, and show that our scheme achieves secure and robust replica detection by increasing the cost of node replication. Additionally, we evaluate the impact of network environment on the proposed scheme through theoretic analysis and simulation experiments, and indicate that our scheme achieves effectiveness and efficiency with substantially lower communication, computational, and storage overhead than prior works under different situations and attack strategies. PMID:28098846

  12. Localization-Free Detection of Replica Node Attacks in Wireless Sensor Networks Using Similarity Estimation with Group Deployment Knowledge.

    Science.gov (United States)

    Ding, Chao; Yang, Lijun; Wu, Meng

    2017-01-15

    Due to the unattended nature and poor security guarantee of the wireless sensor networks (WSNs), adversaries can easily make replicas of compromised nodes, and place them throughout the network to launch various types of attacks. Such an attack is dangerous because it enables the adversaries to control large numbers of nodes and extend the damage of attacks to most of the network with quite limited cost. To stop the node replica attack, we propose a location similarity-based detection scheme using deployment knowledge. Compared with prior solutions, our scheme provides extra functionalities that prevent replicas from generating false location claims without deploying resource-consuming localization techniques on the resource-constraint sensor nodes. We evaluate the security performance of our proposal under different attack strategies through heuristic analysis, and show that our scheme achieves secure and robust replica detection by increasing the cost of node replication. Additionally, we evaluate the impact of network environment on the proposed scheme through theoretic analysis and simulation experiments, and indicate that our scheme achieves effectiveness and efficiency with substantially lower communication, computational, and storage overhead than prior works under different situations and attack strategies.

  13. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    CERN Document Server

    Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  14. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Andrzej Koliński

    2013-05-01

    Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  15. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    Science.gov (United States)

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  16. The 2003 Goddard Rocket Replica Project: A Reconstruction of the World's First Functional Liquid Rocket System

    Science.gov (United States)

    Farr, R. A.; Elam, S. K.; Hicks, G. D.; Sanders, T. M.; London, J. R.; Mayne, A. W.; Christensen, D. L.

    2003-01-01

    As a part of NASA s 2003 Centennial of Flight celebration, engineers and technicians at Marshall Space Flight Center (MSFC), Huntsville, Alabama, in cooperation with the Alabama-Mississippi AIAA Section, have reconstructed historically accurate, functional replicas of Dr. Robert H. Goddard s 1926 first liquid- fuel rocket. The purposes of this project were to clearly understand, recreate, and document the mechanisms and workings of the 1926 rocket for exhibit and educational use, creating a vital resource for researchers studying the evolution of liquid rocketry for years to come. The MSFC team s reverse engineering activity has created detailed engineering-quality drawings and specifications describing the original rocket and how it was built, tested, and operated. Static hot-fire tests, as well as flight demonstrations, have further defined and quantified the actual performance and engineering actual performance and engineering challenges of this major segment in early aerospace history.

  17. Statistical mechanics of the denatured state of a protein using replica-averaged metadynamics.

    Science.gov (United States)

    Camilloni, Carlo; Vendruscolo, Michele

    2014-06-25

    The characterization of denatured states of proteins is challenging because the lack of permanent structure in these states makes it difficult to apply to them standard methods of structural biology. In this work we use all-atom replica-averaged metadynamics (RAM) simulations with NMR chemical shift restraints to determine an ensemble of structures representing an acid-denatured state of the 86-residue protein ACBP. This approach has enabled us to reach convergence in the free energy landscape calculations, obtaining an ensemble of structures in relatively accurate agreement with independent experimental data used for validation. By observing at atomistic resolution the transient formation of native and non-native structures in this acid-denatured state of ACBP, we rationalize the effects of single-point mutations on the folding rate, stability, and transition-state structures of this protein, thus characterizing the role of the unfolded state in determining the folding process.

  18. Shear modulus of glasses: results from the full replica-symmetry-breaking solution.

    Science.gov (United States)

    Yoshino, Hajime; Zamponi, Francesco

    2014-08-01

    We compute the shear modulus of amorphous hard and soft spheres, using the exact solution in infinite spatial dimensions that has been developed recently. We characterize the behavior of this observable in the whole phase diagram, and in particular around the glass and jamming transitions. Our results are consistent with other theoretical approaches, which are unified within this general picture, and they are also consistent with numerical and experimental results. Furthermore, we discuss some properties of the out-of-equilibrium dynamics after a deep quench close to the jamming transition, and we show that a combined measure of the shear modulus and of the mean square displacement allows one to probe experimentally the complex structure of phase space predicted by the full replica-symmetry-breaking solution.

  19. Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation.

    Science.gov (United States)

    Xue, Xu; Yongjun, Wang; Zhihong, Li

    2015-01-21

    Riboswitches are cis-acting RNA fragments that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket, representing an inviting new class of biomolecular target for the development of antibiotics. To understand the folding mechanism of SAM-II riboswitch, occurring predominantly in proteobacteria, a 100ns replica-exchange molecular dynamics simulation in explicit solvent is performed. Our results show that this RNA pseudoknot has multiple folding pathways, and various intermediate structures. The resultant riboswitch conformational transition map is well consistent with the recent fluorescence measurement, which confirms the dynamical properties of this pseudoknot. Moreover, a novel transition pathway is predicted. The global folding dynamics is mainly coupled with the helix rather than the loop region. The potential folding pathways of the riboswitch presented here should lead to a deeper understanding of the folding mechanism of the riboswitch, as well as the conformational change of RNA pseudoknot.

  20. Coexistence of Replica Bands and Superconductivity in FeSe Monolayer Films

    Science.gov (United States)

    Rebec, S. N.; Jia, T.; Zhang, C.; Hashimoto, M.; Lu, D.-H.; Moore, R. G.; Shen, Z.-X.

    2017-02-01

    To elucidate the mechanisms behind the enhanced Tc in monolayer (1 ML) FeSe on SrTiO3 (STO), we grew highly strained 1 ML FeSe on the rectangular (100) face of rutile TiO2 , and observed the coexistence of replica bands and superconductivity with a Tc of 63 K. From the similar Tc between this system and 1ML FeSe on STO (001), we conclude that strain and dielectric constant are likely unimportant to the enhanced Tc in these systems. A systematic comparison of 1 ML FeSe on TiO2 with other systems in the FeSe family shows that while charge transfer alone can enhance Tc, it is only with the addition of interfacial electron-phonon coupling that Tc can be increased to the level seen in 1 ML FeSe on STO.

  1. Characterizing folding funnels with replica exchange Wang-Landau simulation of lattice proteins.

    Science.gov (United States)

    Shi, Guangjie; Wüst, Thomas; Landau, David P

    2016-11-01

    We have studied the folding of ribonuclease A by mapping it onto coarse-grained lattice protein models. With replica exchange Wang-Landau sampling, we calculated the free energy vs end-to-end distance as a function of temperature. A mapping to the famous hydrophobic-polar (HP) model shows a relatively shallow folding funnel and flat free energy minimum, reflecting the high degeneracy of the ground state. In contrast, extending the HP model with an additional "neutral" monomer type (i.e., a mapping to the three-letter H0P model) has a well developed, rough free energy funnel with a low degeneracy ground state. In both cases, folding funnels are asymmetric with temperature dependent shape.

  2. Replica-exchange Wang-Landau simulations of the H0P lattice protein model

    Science.gov (United States)

    Shi, Guangjie; Wüst, Thomas; Li, Ying Wai; Landau, David P.

    The hydrophobic-polar (HP) lattice protein model has been the subject of intensive investigation in an effort to aid our understanding of protein folding. However, the high ground state degeneracies caused by its simplification stands in contrast to the generally unique native states of natural proteins. Here we proposed a simple modification, by introducing a new type of ``neutral'' monomer, 0, i.e. neither hydrophobic nor polar, thus rendering the model more realistic without increasing the difficulties of sampling significantly. With the replica exchange Wang-Landau (REWL) scheme we investigated several widely studied HP proteins and their H0P counterparts. Dramatic differences in both ground state and thermodynamic properties have been found. For example, the H0P version of Crambin shows more clear two-step folding and 3 order of magnitudes less ground state degeneracy than its HP counterpart. Supported by NSF.

  3. Orientational glass: Full replica symmetry breaking in generalized spin glass-like models without reflection symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Tareyeva, E.E. [Institute for High Pressure Physics, Russian Academy of Sciences, 142190 Troitsk (Russian Federation); Schelkacheva, T.I., E-mail: tanschelk@gmail.com [Institute for High Pressure Physics, Russian Academy of Sciences, 142190 Troitsk (Russian Federation); Chtchelkatchev, N.M. [Institute for High Pressure Physics, Russian Academy of Sciences, 142190 Troitsk (Russian Federation); L.D. Landau Institute for Theoretical Physics, Russian Academy of Sciences, 117940 Moscow (Russian Federation); Department of Theoretical Physics, Moscow Institute of Physics and Technology, 141700 Moscow (Russian Federation)

    2013-02-15

    We investigate near the point of glass transition the expansion of the free energy corresponding to the generalized Sherrington–Kirkpatrick model with arbitrary diagonal operators U{sup -hat} standing instead of Ising spins. We focus on the case when U{sup -hat} is an operator with broken reflection symmetry. Such a consideration is important for understanding the behavior of spin glass-like phases in a number of real physical systems, mainly in orientational glasses in mixed molecular crystals which present just the case. We build explicitly a full replica symmetry breaking (FRSB) solution of the equations for the orientational glass order parameters when the nonsymmetric part of U{sup -hat} is small. This particular result presents a counterexample in the context of usually adopted conjecture of the absence of FRSB solution in systems with no reflection symmetry.

  4. Characterizing folding funnels with replica exchange Wang-Landau simulation of lattice proteins

    Science.gov (United States)

    Shi, Guangjie; Wüst, Thomas; Landau, David P.

    2016-11-01

    We have studied the folding of ribonuclease A by mapping it onto coarse-grained lattice protein models. With replica exchange Wang-Landau sampling, we calculated the free energy vs end-to-end distance as a function of temperature. A mapping to the famous hydrophobic-polar (HP) model shows a relatively shallow folding funnel and flat free energy minimum, reflecting the high degeneracy of the ground state. In contrast, extending the HP model with an additional "neutral" monomer type (i.e., a mapping to the three-letter H0P model) has a well developed, rough free energy funnel with a low degeneracy ground state. In both cases, folding funnels are asymmetric with temperature dependent shape.

  5. Behavioural responses of dogs to asymmetrical tail wagging of a robotic dog replica.

    Science.gov (United States)

    Artelle, K A; Dumoulin, L K; Reimchen, T E

    2011-03-01

    Recent evidence suggests that bilateral asymmetry in the amplitude of tail wagging of domestic dogs (Canis familiaris) is associated with approach (right wag) versus withdrawal (left wag) motivation and may be the by-product of hemispheric dominance. We consider whether such asymmetry in motion of the tail, a crucial appendage in intra-specific communication in all canids, provides visual information to a conspecific leading to differential behaviour. To evaluate this, we experimentally investigated the approach behaviour of free-ranging dogs to the asymmetric tail wagging of a life-size robotic dog replica. Our data, involving 452 separate interactions, showed a significantly greater proportion of dogs approaching the model continuously without stopping when the tail wagged to the left, compared with a right wag, which was more likely to yield stops. While the results indicate that laterality of a wagging tail provides behavioural information to conspecifics, the responses are not readily integrated into the predicted behaviour based on hemispheric dominance.

  6. Orientational glass: Full replica symmetry breaking in generalized spin glass-like models without reflection symmetry

    Science.gov (United States)

    Tareyeva, E. E.; Schelkacheva, T. I.; Chtchelkatchev, N. M.

    2013-02-01

    We investigate near the point of glass transition the expansion of the free energy corresponding to the generalized Sherrington-Kirkpatrick model with arbitrary diagonal operators Uˆ standing instead of Ising spins. We focus on the case when Uˆ is an operator with broken reflection symmetry. Such a consideration is important for understanding the behavior of spin glass-like phases in a number of real physical systems, mainly in orientational glasses in mixed molecular crystals which present just the case. We build explicitly a full replica symmetry breaking (FRSB) solution of the equations for the orientational glass order parameters when the nonsymmetric part of Uˆ is small. This particular result presents a counterexample in the context of usually adopted conjecture of the absence of FRSB solution in systems with no reflection symmetry.

  7. Pion emission from the T2K replica target: method, results and application

    CERN Document Server

    Abgrall, N; Anticic, T; Antoniou, N; Argyriades, J; Baatar, B; Blondel, A; Blumer, J; Bogomilov, M; Bravar, A; Brooks, W; Brzychczyk, J; Bubak, A; Bunyatov, S A; Busygina, O; Christakoglou, P; Chung, P; Czopowicz, T; Davis, N; Debieux, S; Di Luise, S; Dominik, W; Dumarchez, J; Dynowski, K; Engel, R; Ereditato, A; Esposito, L S; Feofilov, G A; Fodor, Z; Ferrero, A; Fulop, A; Gazdzicki, M; Golubeva, M; Grabez, B; Grebieszkow, K; Grzeszczuk, A; Guber, F; Haesler, A; Hakobyan, H; Hasegawa, T; Idczak, R; Igolkin, S; Ivanov, Y; Ivashkin, A; Kadija, K; Kapoyannis, A; Katrynska, N; Kielczewska, D; Kikola, D; Kirejczyk, M; Kisiel, J; Kiss, T; Kleinfelder, S; Kobayashi, T; Kochebina, O; Kolesnikov, V I; Kolev, D; Kondratiev, V P; Korzenev, A; Kowalski, S; Krasnoperov, A; Kuleshov, S; Kurepin, A; Lacey, R; Larsen, D; Laszlo, A; Lyubushkin, V V; Mackowiak-Pawlowska, M; Majka, Z; Maksiak, B; Malakhov, A I; Maletic, D; Marchionni, A; Marcinek, A; Maris, I; Marin, V; Marton, K; Matulewicz, T; Matveev, V; Melkumov, G L; Messina, M; Mrowczynski, St; Murphy, S; Nakadaira, T; Nishikawa, K; Palczewski, T; Palla, G; Panagiotou, A D; Paul, T; Peryt, W; Petukhov, O; Planeta, R; Pluta, J; Popov, B A; Posiadala, M; Pulawski, S; Puzovic, J; Rauch, W; Ravonel, M; Renfordt, R; Robert, A; Rohrich, D; Rondio, E; Rossi, B; Roth, M; Rubbia, A; Rustamov, A; Rybczynski, M; Sadovsky, A; Sakashita, K; Savic, M; Sekiguchi, T; Seyboth, P; Shibata, M; Sipos, M; Skrzypczak, E; Slodkowski, M; Staszel, P; Stefanek, G; Stepaniak, J; Strabel, C; Strobele, H; Susa, T; Szuba, M; Tada, M; Taranenko, A; Tereshchenko, V; Tolyhi, T; Tsenov, R; Turko, L; Ulrich, R; Unger, M; Vassiliou, M; Veberic, D; Vechernin, V V; Vesztergombi, G; Wilczek, A; Wlodarczyk, Z; Wojtaszek-Szwarc, A; Wyszynski, O; Zambelli, L; Zipper, W; Hartz, M; Ichikawa, A K; Kubo, H; Marino, A D; Matsuoka, K; Murakami, A; Nakaya, T; Suzuki, K; Yuan, T; Zimmerman, E D

    2013-01-01

    The T2K long-baseline neutrino oscillation experiment in Japan needs precise predictions of the initial neutrino flux. The highest precision can be reached based on detailed measurements of hadron emission from the same target as used by T2K exposed to a proton beam of the same kinetic energy of 30 GeV. The corresponding data were recorded in 2007-2010 by the NA61/SHINE experiment at the CERN SPS using a replica of the T2K graphite target. In this paper details of the experiment, data taking, data analysis method and results from the 2007 pilot run are presented. Furthermore, the application of the NA61/SHINE measurements to the predictions of the T2K initial neutrino flux is described and discussed.

  8. The replica symmetric solution for orthogonally constrained Heisenberg model on Bethe lattice

    Science.gov (United States)

    Concetti, Francesco

    2017-02-01

    In this paper, we study the thermodynamic properties of a system of D-components classical Heisenberg spins lying on the vertices of a random regular graph, with an unconventional first neighbor non-random interaction J{{≤ft({{\\mathbf{S}}i}\\centerdot {{\\mathbf{S}}k}\\right)}2} . We can consider this model as a continuum version of anti-ferromagnetic D-states Potts model. We compute the paramagnetic free energy, using a new approach, presented in this paper for the first time, based on the replica method. Through the linear stability analysis, we obtain an instability line on the temperature-connectivity plane that provides a bound to the appearance of a phase transition. We also argue about the character of the instability observed.

  9. Replica exchange molecular dynamics optimization of tensor network states for quantum many-body systems.

    Science.gov (United States)

    Liu, Wenyuan; Wang, Chao; Li, Yanbin; Lao, Yuyang; Han, Yongjian; Guo, Guang-Can; Zhao, Yong-Hua; He, Lixin

    2015-03-01

    Tensor network states (TNS) methods combined with the Monte Carlo (MC) technique have been proven a powerful algorithm for simulating quantum many-body systems. However, because the ground state energy is a highly non-linear function of the tensors, it is easy to get stuck in local minima when optimizing the TNS of the simulated physical systems. To overcome this difficulty, we introduce a replica-exchange molecular dynamics optimization algorithm to obtain the TNS ground state, based on the MC sampling technique, by mapping the energy function of the TNS to that of a classical mechanical system. The method is expected to effectively avoid local minima. We make benchmark tests on a 1D Hubbard model based on matrix product states (MPS) and a Heisenberg J1-J2 model on square lattice based on string bond states (SBS). The results show that the optimization method is robust and efficient compared to the existing results.

  10. How Is cis-trans Isomerization Controlled in Dronpa Mutants? A Replica Exchange Molecular Dynamics Study.

    Science.gov (United States)

    Moors, Samuel L C; Michielssens, Servaas; Flors, Cristina; Dedecker, Peter; Hofkens, Johan; Ceulemans, Arnout

    2008-06-01

    The reversibly photoactivatable green fluorescent protein analog Dronpa holds great promise as a marker for various new cellular imaging applications. Using a replica exchange method which combines both Hamiltonian and temperature exchanges, the ground-state dynamics of Dronpa and two mutants with increased switching kinetics, Val157Gly and Met159Thr, were compared. The dominant chromophore state was found to be the cis isomer in all three proteins. The simulation data suggest that both mutations strongly increase the chromophore flexibility and cis-trans isomerization rate. We identify three key amino acids, Val157, Met159, and Phe173, which are able to impede the bottom hula-twist transition path, depending on their position and rotameric state. We believe our insights will help to understand the switching process and provide useful information for the design of new variants with improved fluorescence properties.

  11. Long-time atomistic simulations with the Parallel Replica Dynamics method

    Science.gov (United States)

    Perez, Danny

    Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

  12. Deep Label Distribution Learning With Label Ambiguity

    Science.gov (United States)

    Gao, Bin-Bin; Xing, Chao; Xie, Chen-Wei; Wu, Jianxin; Geng, Xin

    2017-06-01

    Convolutional Neural Networks (ConvNets) have achieved excellent recognition performance in various visual recognition tasks. A large labeled training set is one of the most important factors for its success. However, it is difficult to collect sufficient training images with precise labels in some domains such as apparent age estimation, head pose estimation, multi-label classification and semantic segmentation. Fortunately, there is ambiguous information among labels, which makes these tasks different from traditional classification. Based on this observation, we convert the label of each image into a discrete label distribution, and learn the label distribution by minimizing a Kullback-Leibler divergence between the predicted and ground-truth label distributions using deep ConvNets. The proposed DLDL (Deep Label Distribution Learning) method effectively utilizes the label ambiguity in both feature learning and classifier learning, which help prevent the network from over-fitting even when the training set is small. Experimental results show that the proposed approach produces significantly better results than state-of-the-art methods for age estimation and head pose estimation. At the same time, it also improves recognition performance for multi-label classification and semantic segmentation tasks.

  13. Observation of Replica Symmetry Breaking in the 1D Anderson Localization Regime in an Erbium-Doped Random Fiber Laser

    CERN Document Server

    Gomes, Anderson S L; Pincheira, Pablo I R; Moura, André L; Gagné, Mathieu; Kashyap, Raman; Raposo, Ernesto P; de Araújo, Cid B

    2016-01-01

    The analogue of the paramagnetic to spin-glass phase transition in disordered magnetic systems, leading to the phenomenon of replica symmetry breaking, has been recently demonstrated in a two-dimensional random laser consisting of an organic-based amorphous solid-state thin film. We report here the first demonstration of replica symmetry breaking in a one-dimensional photonic system consisting of an erbium-doped random fiber laser operating in the continuous-wave regime based on a unique random fiber grating system, which plays the role of the random scatterers and operates in the Anderson localization regime. The clear transition from a photonic paramagnetic to a photonic spin glass phase, characterized by the probability distribution function of the Parisi overlap, was verified and characterized. In this unique system, the radiation field interacts only with the gain medium, and the fiber grating, which provides the disordered feedback mechanism, does not interfere with the pump.

  14. Synthetic fossilization of soft biological tissues and their shape-preserving transformation into silica or electron-conductive replicas.

    Science.gov (United States)

    Townson, Jason L; Lin, Yu-Shen; Chou, Stanley S; Awad, Yasmine H; Coker, Eric N; Brinker, C Jeffrey; Kaehr, Bryan

    2014-12-08

    Structural preservation of complex biological systems from the subcellular to whole organism level in robust forms, enabling dissection and imaging while preserving 3D context, represents an enduring grand challenge in biology. Here we report a simple immersion method for structurally preserving intact organisms via conformal stabilization within silica. This self-limiting process, which we refer to as silica bioreplication, occurs by condensation of water-soluble silicic acid proximally to biomolecular interfaces throughout the organism. Conformal nanoscopic silicification of all biomolecular features imparts structural rigidity enabling the preservation of shape and nano-to-macroscale dimensional features upon drying to form a biocomposite and further high temperature oxidative calcination to form silica replicas or reductive pyrolysis to form electrically conductive carbon replicas of complete organisms. The simplicity and generalizability of this approach should facilitate efforts in biological preservation and analysis and could enable the development of new classes of biomimetic composite materials.

  15. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

    Science.gov (United States)

    Jiang, Wei; Roux, Benoît

    2010-07-01

    Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

  16. Comparing 2D pictures with 3D replicas for the digital preservation and analysis of tangible heritage.

    OpenAIRE

    Galeazzi, Fabrizio; Di Giuseppantonio Di Franco, Paola; Matthews, Justin L.

    2015-01-01

    This is the author accepted manuscript. The final version is available from Taylor & Francis via http://dx.doi.org/10.1080/09647775.2015.1042515 In this paper, we present two experiments designed to compare 2D digital pictures and 3D digital replicas of artefacts, to understand how differently these media facilitate the perception and understanding of our past. Archaeologists and museum experts have commonly used 2D digital pictures to preserve and study artefacts. Recently these scholars ...

  17. Isobaric Molecular Dynamics Version of the Generalized Replica Exchange Method (gREM): Liquid-Vapor Equilibrium.

    Science.gov (United States)

    Małolepsza, Edyta; Secor, Maxim; Keyes, Tom

    2015-10-22

    A prescription for sampling isobaric generalized ensembles with molecular dynamics is presented and applied to the generalized replica exchange method (gREM), which was designed to simulate first-order phase transitions. The properties of the isobaric gREM ensemble are discussed, and a study is presented for the liquid-vapor equilibrium of the guest molecules given for gas hydrate formation with the mW water model. Phase diagrams, critical parameters, and a law of corresponding states are obtained.

  18. Multiple Replicas of Block Copolymer Thin Films from a Brushless Organosilicate Substrate

    Science.gov (United States)

    Suh, Hyo Seon; Yoon, Hyunsik; Char, Kookheon

    2011-03-01

    The chain end-grafted polymer brushes or cross-linked polymer mats have typically been utilized as the surface modification layers to induce the perpendicular orientation of block copolymer (BCP) thin films. Instead of such polymer-based approaches, we have recently introduced a new concept to control the BCP orientation using the brushless organosilicate (OS) substrates, whose surface energy can be finely tuned with thermal treatment. In this brushless case, the BCP chains do not penetrate into the underlying hard OS substrates during thermal annealing of BCP films, therefore, the BCP chains at the interface have no entangled structure with fairly weak adhesion of BCP films against the substrate. Owing to such weak adhesion of BCP films against the OS substrate, the perpendicularly oriented BCP film on a neutral OS substrate could be easily peeled off and transferred to a UV-curable resin applied onto the BCP film. The OS substrate after the peel-off process of a BCP film could regenerate the perpendicularly oriented BCP films since the surface energy of the OS substrate remains intact during the peel-off process. Furthermore, the direct-assembled BCP films on chemically patterned OS substrates could also be peeled off and transferred on to a UV-curable resin, allowing us to produce multiple replicas of direct-assembled BCP thin films from a single chemically patterned OS substrate.

  19. Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics.

    Science.gov (United States)

    Jo, Sunhwan; Chipot, Christophe; Roux, Benoît

    2015-05-12

    The performance and accuracy of different simulation schemes for estimating the entropy inferred from free energy calculations are tested. The results obtained from replica-exchange molecular dynamics (REMD) simulations based on a simplified toy model are compared to exact numerically derived ones to assess accuracy and convergence. It is observed that the error in entropy estimation decreases by at least an order of magnitude and the quantities of interest converge much faster when the simulations are coupled via a temperature REMD algorithm and the trajectories from different temperatures are combined. Simulations with the infinite-swapping method and its variants show some improvement over the traditional nearest-neighbor REMD algorithms, but they are more computationally expensive. To test the methodologies further, the free energy profile for the reversible association of two methane molecules in explicit water was calculated and decomposed into its entropic and enthalpic contributions. Finally, a strategy based on umbrella sampling computations carried out via simultaneous temperature and Hamiltonian REMD simulations is shown to yield the most accurate entropy estimation. The entropy profile between the two methane molecules displays the characteristic signature of a hydrophobic interaction.

  20. Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Nanyu Han

    Full Text Available Neuraminidase (NA of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1 was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147-150 of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus.

  1. Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Han, Nanyu; Mu, Yuguang

    2013-01-01

    Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147-150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus.

  2. Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations.

    Science.gov (United States)

    Zeller, Fabian; Zacharias, Martin

    2014-02-11

    The accurate calculation of potentials of mean force for ligand-receptor binding is one of the most important applications of molecular simulation techniques. Typically, the separation distance between ligand and receptor is chosen as a reaction coordinate along which a PMF can be calculated with the aid of umbrella sampling (US) techniques. In addition, restraints can be applied on the relative position and orientation of the partner molecules to reduce accessible phase space. An approach combining such phase space reduction with flattening of the free energy landscape and configurational exchanges has been developed, which significantly improves the convergence of PMF calculations in comparison with standard umbrella sampling. The free energy surface along the reaction coordinate is smoothened by iteratively adapting biasing potentials corresponding to previously calculated PMFs. Configurations are allowed to exchange between the umbrella simulation windows via the Hamiltonian replica exchange method. The application to a DNA molecule in complex with a minor groove binding ligand indicates significantly improved convergence and complete reversibility of the sampling along the pathway. The calculated binding free energy is in excellent agreement with experimental results. In contrast, the application of standard US resulted in large differences between PMFs calculated for association and dissociation pathways. The approach could be a useful alternative to standard US for computational studies on biomolecular recognition processes.

  3. Replica analysis of overfitting in regression models for time-to-event data

    Science.gov (United States)

    Coolen, A. C. C.; Barrett, J. E.; Paga, P.; Perez-Vicente, C. J.

    2017-09-01

    Overfitting, which happens when the number of parameters in a model is too large compared to the number of data points available for determining these parameters, is a serious and growing problem in survival analysis. While modern medicine presents us with data of unprecedented dimensionality, these data cannot yet be used effectively for clinical outcome prediction. Standard error measures in maximum likelihood regression, such as p-values and z-scores, are blind to overfitting, and even for Cox’s proportional hazards model (the main tool of medical statisticians), one finds in literature only rules of thumb on the number of samples required to avoid overfitting. In this paper we present a mathematical theory of overfitting in regression models for time-to-event data, which aims to increase our quantitative understanding of the problem and provide practical tools with which to correct regression outcomes for the impact of overfitting. It is based on the replica method, a statistical mechanical technique for the analysis of heterogeneous many-variable systems that has been used successfully for several decades in physics, biology, and computer science, but not yet in medical statistics. We develop the theory initially for arbitrary regression models for time-to-event data, and verify its predictions in detail for the popular Cox model.

  4. Replica exchange molecular dynamics study of the truncated amyloid beta (11-40) trimer in solution.

    Science.gov (United States)

    Ngo, Son Tung; Hung, Huynh Minh; Truong, Duc Toan; Nguyen, Minh Tho

    2017-01-18

    Amyloid beta (Aβ) oligomers are neurotoxic compounds that destroy the brain of Alzheimer's disease patients. Recent studies indicated that the trimer is one of the most cytotoxic forms of low molecular weight Aβ oligomers. As there was limited information about the structure of the Aβ trimer, either by experiment or by computation, we determined in this work the structure of the 3Aβ11-40 oligomer for the first time using the temperature replica exchange molecular dynamics simulations in the presence of an explicit solvent. More than 20.0 μs of MD simulations were performed. The probability of the β-content and random coil structure of the solvated trimer amounts to 42 ± 6 and 49 ± 7% which is in good agreement with experiments. Intermolecular interactions in central hydrophobic cores play a key role in stabilizing the oligomer. Intermolecular polar contacts between D23 and residues 24-29 replace the salt bridge D23-K28 to secure the loop region. The hydrophilic region of the N-terminus is maintained by the intermolecular polar crossing contacts H13A-Q15B and H13B-Q15C. The difference in the free energy of binding between the constituting monomers and the others amounts to -36 ± 8 kcal mol(-1). The collision cross section of the representative structures of the trimer was computed to be 1330 ± 47 Å(2), which is in good agreement with previous experiments.

  5. Optimization of the replica molding process of PDMS using pennate diatoms

    Science.gov (United States)

    Hlúbiková, D.; Luís, A. T.; Vaché, V.; Ector, L.; Hoffmann, L.; Choquet, P.

    2012-11-01

    Biomimetic fabrication of nanostructured materials has recently attracted the attention of researchers as a cost-effective and easily applicable method of nanotexturing. Different techniques and materials have been used in order to replicate natural patterns, among which polydimethylsiloxane (PDMS Sylgard 184®) was recently used to replicate the micro- and nanoscale patterns from centric diatoms. In this paper, we test the reproducibility and precision of this approach using various morphologically different diatom species trying to optimize the molding parameters. The optimization process is focused on immobilization of diatoms on the glass support, which serves as a master for templating, as well as on the parameters of PDMS fabrication such as the ratio of the curing agent and elastomer, use of vacuum, curing time and temperature. The results indicate that higher ratios of curing agent and elastomer, longer curing time and lower temperature are the most favorable conditions to obtain negative diatom replicas of good quality with features of 50 nm. Although this method can give very precise results producing high-resolution molds with all micro- and nanostructures replicated, we revealed some limitations regarding the size and morphology of the species used. These results indicate that large round and flat diatom species seem to be more suitable for the cast molding.

  6. Replica-moulded polydimethylsiloxane culture vessel lids attenuate osmotic drift in long-term cell cultures

    Indian Academy of Sciences (India)

    Axel Blau; Tanja Neumann; Christiane Ziegler; Fabio Benfenati

    2009-03-01

    An imbalance in medium osmolarity is a determinant that affects cell culture longevity. Even in humidified incubators, evaporation of water leads to a gradual increase in osmolarity overtime. We present a simple replica-moulding strategy for producing self-sealing lids adaptable to standard, small-size cell-culture vessels. They are made of polydimethylsiloxane (PDMS), a flexible, transparent and biocompatible material, which is gas-permeable but largely impermeable to water. Keeping cell cultures in a humidified 5% CO2 incubator at 37°C, medium osmolarity increased by +6.86 mosmol/kg/day in standard 35 mm Petri dishes, while PDMS lids attenuated its rise by a factor of four to changes of +1.72 mosmol/kg/ day. Depending on the lid membrane thickness, pH drifts at ambient CO2 levels were attenuated by a factor of 4 to 9. Comparative evaporation studies at temperatures below 60°C yielded a 10-fold reduced water vapour flux of 1.75 g/day/dm2 through PDMS lids as compared with 18.69 g/day/dm2 with conventional Petri dishes. Using such PDMS lids, about 2/3 of the cell cultures grew longer than 30 days in vitro. Among these, the average survival time was 69 days with the longest survival being 284 days under otherwise conventional cell culture conditions.

  7. Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics

    KAUST Repository

    Buin, Andrei

    2015-06-18

    © 2015 American Chemical Society. Organometal halide perovskites have recently attracted tremendous attention at both the experimental and theoretical levels. Much of this work has been dedicated to bulk material studies, yet recent experimental work has shown the formation of highly efficient quantum-confined nanocrystals with tunable band edges. Here we investigate perovskite quantum dots from theory, predicting an upper bound of the Bohr radius of 45 Å that agrees well with literature values. When the quantum dots are stoichiometric, they are trap-free and have nearly symmetric contributions to confinement from the valence and conduction bands. We further show that surface-associated conduction bandedge states in perovskite nanocrystals lie below the bulk states, which could explain the difference in Urbach tails between mesoporous and planar perovskite films. In addition to conventional molecular dynamics (MD), we implement an enhanced phase-space sampling algorithm, replica exchange molecular dynamics (REMD). We find that in simulation of methylammonium orientation and global minima, REMD outperforms conventional MD. To the best of our knowledge, this is the first REMD implementation for realistic-sized systems in the realm of DFT calculations.

  8. Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations.

    Science.gov (United States)

    de Ruiter, Anita; Oostenbrink, Chris

    2013-02-12

    The calculation of protein-ligand binding free energies is an important goal in the field of computational chemistry. Applying path-sampling methods for this purpose involves calculating the associated potential of mean force (PMF) and gives insight into the binding free energy along the binding process. Without a priori knowledge about the binding path, sampling reversible binding can be difficult to achieve. To alleviate this problem, we introduce the distancefield (DF) as a reaction coordinate for such calculations. DF is a grid-based method in which the shortest distance between the binding site and a ligand is determined avoiding routes that pass through the protein. Combining this reaction coordinate with Hamiltonian replica exchange molecular dynamics (HREMD) allows for the reversible binding of the ligand to the protein. A comparison is made between umbrella sampling using regular distance restraints and HREMD with DF restraints to study aspirin binding to the protein phospholipase A2. Although the free energies of binding are similar for both methods, the increased sampling with HREMD has a significant influence on the shape of the PMF. A remarkable agreement between the calculated binding free energies from the PMF and the experimental estimate is obtained.

  9. Replica Ornstein-Zernike self-consistent theory for mixtures in random pores.

    Science.gov (United States)

    Pellicane, G; Caccamo, C; Wilson, D S; Lee, L L

    2004-06-01

    We present a self-consistent integral equation theory for a binary liquid in equilibrium with a disordered medium, based on the formalism of the replica Ornstein-Zernike (ROZ) equations. Specifically, we derive direct formulas for the chemical potentials and the zero-separation theorems (the latter provide a connection between the chemical potentials and the fluid cavity distribution functions). Next we solve a modified-Verlet closure to ROZ equations, which has built-in parameters that can be adjusted to satisfy the zero-separation theorems. The degree of thermodynamic consistency of the theory is also kept under control. We model the binary fluid in random pores as a symmetrical binary mixture of nonadditive hard spheres in a disordered hard-sphere matrix and consider two different values of the nonadditivity parameter and of the quenched matrix packing fraction, at different mixture concentrations. We compare the theoretical structural properties as obtained through the present approach with Percus-Yevick and Martinov-Sarkisov integral equation theories, and assess both structural and thermodynamic properties by performing canonical standard and biased grand canonical Monte Carlo simulations. Our theory appears superior to the other integral equation schemes here examined and provides reliable estimates of the chemical potentials. This feature should be useful in studying the fluid phase behavior of model adsorbates in random pores in general.

  10. Enhancing dry adhesives and replica molding with ethyl cyano-acrylate

    Science.gov (United States)

    Bovero, E.; Menon, C.

    2014-08-01

    The use of cyano-acrylate to improve the performance of dry adhesives and their method of fabrication is investigated. Specifically, the contributions of this work are: (1) a new adhesion method to adhere to a large variety of surfaces, (2) a strategy to increase the compliance of dry adhesives, and (3) an improved fabrication process for micro-structured dry adhesives based on replica molding. For the first contribution, the adhesion method consists of anchoring a micro-structured dry adhesive to a surface through a layer of hardened ethyl cyano-acrylate (ECA). This method increases the adhesion of the orders of magnitude at the expense of leaving residue after detachment. However, this method preserves reusability. For the second contribution, a double-sided dry adhesive is obtained by introducing a substrate with a millimeter-sized pillar structure, which enabled further increasing adhesion. For the third contribution, an ECA layer is used as a mold for the fabrication of new adhesives. These new types of molds proved able to produce dry adhesives with high reproducibility and low degradation.

  11. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.

    Science.gov (United States)

    Chebaro, Yassmine; Dong, Xiao; Laghaei, Rozita; Derreumaux, Philippe; Mousseau, Normand

    2009-01-08

    Current approaches aimed at determining the free energy surface of all-atom medium-size proteins in explicit solvent are slow and are not sufficient to converge to equilibrium properties. To ensure a proper sampling of the configurational space, it is preferable to use reduced representations such as implicit solvent and/or coarse-grained protein models, which are much lighter computationally. Each model must be verified, however, to ensure that it can recover experimental structures and thermodynamics. Here we test the coarse-grained implicit solvent OPEP model with replica exchange molecular dynamics (REMD) on six peptides ranging in length from 10 to 28 residues: two alanine-based peptides, the second beta-hairpin from protein G, the Trp-cage and zinc-finger motif, and a dimer of a coiled coil peptide. We show that REMD-OPEP recovers the proper thermodynamics of the systems studied, with accurate structural description of the beta-hairpin and Trp-cage peptides (within 1-2 A from experiments). The light computational burden of REMD-OPEP, which enables us to generate many hundred nanoseconds at each temperature and fully assess convergence to equilibrium ensemble, opens the door to the determination of the free energy surface of larger proteins and assemblies.

  12. Diamond Opal-Replica Photonic Crystals and Graphitic Metallic Photonic Band Gap Structures: Fabrication and Properties

    Science.gov (United States)

    Zakhidov, A. A.; Baughman, R. H.; Iqbal, Z.; Khayrullin, I. I.; Ralchenko, V. G.

    1998-03-01

    We demonstrate a new method for the formation of photonic bandgap crystals that operate at optical wavelengths. This method involves the templating of a self-assempled SiO2 lattice with diamond, graphite, or amorphous forms of carbon, followed by the removal of the original SiO2 lattice matrix by chemical means. Such carbon opal replicas are the "air type" of photonic crystal (where air replaces silica spheres) that are most favourable for photonic bandgap formation. Surprisingly, the structure of the original opal lattice having a typical cubic lattice dimension of 250 nm) is reliably replicated down to the nanometer scale using either a diamond, graphite, or amorphous carbon templated material. The optical properties of these photonic bandgap crystals are reported and compared with both theory and experimental results on other types of opal-derived lattices that we have investigated. The graphitic reverse opal is the first example of a network type metallic photonic crystal for the optical domain, for which a large photonic bandgap have been predicted.

  13. From Dalek half balls to Daft Punk helmets: Mimetic fandom and the crafting of replicas

    Directory of Open Access Journals (Sweden)

    Matt Hills

    2014-06-01

    Full Text Available Mimetic fandom is a surprisingly understudied mode of (culturally masculinized fan activity in which fans research and craft replica props. Mimetic fandom can be considered as (inauthentic and (immaterial, combining noncommercial status with grassroots marketing or brand reinforcement as well as fusing an emphasis on material artifacts with Web 2.0 collective intelligence. Simply analyzing mimetic fandom as part of fannish material culture fails to adequately assess the nonmaterial aspects of this collaborative creativity. Two fan cultures are taken as case studies: Dalek building groups and Daft Punk helmet constructors. These diverse cases indicate that mimetic fandom has a presence and significance that moves across media fandoms and is not restricted to the science fiction, fantasy, and horror followings with which it is most often associated. Mimetic fandom may be theorized as an oscillatory activity that confuses binaries and constructions of (academic/fan authenticity. This fan practice desires and pursues a kind of ontological bridging or unity—from text to reality—that is either absent or less dominant in many other fan activities such as cosplay, screen-used prop collecting, and geographical pilgrimage. Fan studies may benefit from reassessing the place of mimesis, especially in order to theorize fan practices that are less clearly transformative in character.

  14. Replica-exchange Wang-Landau simulations of the H0P model of protein folding

    Science.gov (United States)

    Shi, Guangjie; Landau, David P.; Wüst, Thomas; Li, Ying Wai Li

    2015-03-01

    The hydrophobic-polar (HP) model has served as a coarse-grained lattice protein folding model attracting scientists from various disciplines. However, simplification into H and P monomers may yield high ground state degeneracies which stands in contrast to the generally unique native states of natural proteins. We propose a simple modification, by introducing a new type of ``neutral'' monomer, 0, i.e. neither hydrophobic nor polar, rendering the model more realistic without increasing the difficulties of sampling significantly. With the newly developed parallel Wang-Landau (replica exchange Wang-Landau) scheme and an innovative method of estimating the ground state degeneracies, we investigated some widely studied HP proteins and their H0P counterparts. Dramatic differences in ground state and thermodynamic properties have been observed, e.g. the estimation of ground state degeneracy for the 46mer is 460,000 for the HP version and only 20 for the H0P mapping. Similarly, the specific heat and structural properties: radius of gyration and etc. show more pronounced signals associated with folding. Supported by NSF.

  15. Replica of human dentin treated with different desensitizing agents: a methodological SEM study in vitro

    Directory of Open Access Journals (Sweden)

    Pereira Jose Carlos

    2002-01-01

    Full Text Available This is a preliminary study to determine a methodological sequence in vitro which may allow the reproduction of dentin for SEM analysis, after the use of different desensitizing agents. Dentin discs obtained from extracted human third molars were etched with 6% citric acid, an artificial smear layer was created and the surface dentin discs were divided into four quadrants. Quadrants 2, 3 and 4 of each disc were conditioned with 6% citric acid. The desensitizing agents (Oxa-Gel®, Gluma Desensitizer and an experimental agent were applied to quadrants 3 and 4. To evaluate the acid resistance of the treatment, quadrant 4 was etched again with 6% citric acid. An impression was then taken with Aquasil ULV. After a setting period of 6 min, each disc was removed from the impression and stored in a moist-free environment for 24 h at 37ºC. After that time, a low-viscosity epoxy resin (Araltec GY 1109 BR was poured into the impression and cured for 24 h. All specimens were metal-coated for SEM analysis. Comparison of the photomicrographs of dentin discs with their respective impressions and resin replicas showed that this technique can reproduce the characteristics of the dentin surface treated with desensitizing agents.

  16. Hydrogel Inverse Replicas of Breath Figures Exhibit Superoleophobicity Due to Patterned Surface Roughness.

    Science.gov (United States)

    Arora, Jaspreet Singh; Cremaldi, Joseph C; Holleran, Mary Kathleen; Ponnusamy, Thiruselvam; He, Jibao; Pesika, Noshir S; John, Vijay T

    2016-02-02

    The wetting behavior of a surface depends on both its surface chemistry and the characteristics of surface morphology and topography. Adding structure to a flat hydrophobic or oleophobic surface increases the effective contact angle and thus the hydrophobicity or oleophobicity of the surface, as exemplified by the lotus leaf analogy. We describe a simple strategy to introduce micropatterned roughness on surfaces of soft materials, utilizing the template of hexagonally packed pores of breath figures as molds. The generated inverse replicas represent micron scale patterned beadlike protrusions on hydrogel surfaces. This added roughness imparts superoleophobic properties (contact angle of the order of 150° and greater) to an inherently oleophobic flat hydrogel surface, when submerged. The introduced pattern on the hydrogel surface changes morphology as it swells in water to resemble morphologies remarkably analogous to the compound eye. Analysis of the wetting behavior using the Cassie-Baxter approximation leads to estimation of the contact angle in the superoleophobic regime and in agreement with the experimental value.

  17. Solid volume fraction estimation of bone:marrow replica models using ultrasound transit time spectroscopy.

    Science.gov (United States)

    Wille, Marie-Luise; Langton, Christian M

    2016-02-01

    The acceptance of broadband ultrasound attenuation (BUA) for the assessment of osteoporosis suffers from a limited understanding of both ultrasound wave propagation through cancellous bone and its exact dependence upon the material and structural properties. It has recently been proposed that ultrasound wave propagation in cancellous bone may be described by a concept of parallel sonic rays; the transit time of each ray defined by the proportion of bone and marrow propagated. A Transit Time Spectrum (TTS) describes the proportion of sonic rays having a particular transit time, effectively describing the lateral inhomogeneity of transit times over the surface aperture of the receive ultrasound transducer. The aim of this study was to test the hypothesis that the solid volume fraction (SVF) of simplified bone:marrow replica models may be reliably estimated from the corresponding ultrasound transit time spectrum. Transit time spectra were derived via digital deconvolution of the experimentally measured input and output ultrasonic signals, and compared to predicted TTS based on the parallel sonic ray concept, demonstrating agreement in both position and amplitude of spectral peaks. Solid volume fraction was calculated from the TTS; agreement between true (geometric calculation) with predicted (computer simulation) and experimentally-derived values were R(2)=99.9% and R(2)=97.3% respectively. It is therefore envisaged that ultrasound transit time spectroscopy (UTTS) offers the potential to reliably estimate bone mineral density and hence the established T-score parameter for clinical osteoporosis assessment.

  18. Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking.

    Science.gov (United States)

    Wang, Hongrui; Liu, Hongwei; Cai, Leixin; Wang, Caixia; Lv, Qiang

    2017-07-10

    In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein-small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (MC) and REMC sampling methods, these methods use multi-objective optimization Pareto front information to facilitate the selection of replicas for exchange. The Pareto front information generated to select lower energy conformations as representative conformation structure replicas can facilitate the convergence of the available conformational space, including available near-native structures. Furthermore, our approach directly provides min-min scenario Pareto optimal solutions, as well as a hybrid of the min-min and max-min scenario Pareto optimal solutions with lower energy conformations for use as structure templates in the REMC sampling method. These methods were validated based on a thorough analysis of a benchmark data set containing 16 benchmark test cases. An in-depth comparison between MC, REMC, multi-objective optimization-REMC (MO-REMC), and hybrid MO-REMC (HMO-REMC) sampling methods was performed to illustrate the differences between the four conformational search strategies. Our findings demonstrate that the MO-REMC and HMO-REMC conformational sampling methods are powerful approaches for obtaining protein-small molecule docking conformational predictions based on the binding energy of complexes in RosettaLigand.

  19. Pesticide Product Label System

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Pesticide Product Label System (PPLS) provides a collection of pesticide product labels (Adobe PDF format) that have been approved by EPA under Section 3 of the...

  20. Food Label and You

    Medline Plus

    Full Text Available ... has issued final changes to update the Nutrition Facts label for packaged foods. For more information, see Changes to the Nutrition Facts Label . FDA presents an entertaining and educational tool ...

  1. Semiotic labelled deductive systems

    Energy Technology Data Exchange (ETDEWEB)

    Nossum, R.T. [Imperial College of Science, Technology and Medicine, London (United Kingdom)

    1996-12-31

    We review the class of Semiotic Models put forward by Pospelov, as well as the Labelled Deductive Systems developed by Gabbay, and construct an embedding of Semiotic Models into Labelled Deductive Systems.

  2. Electronic Submission of Labels

    Science.gov (United States)

    Pesticide registrants can provide draft and final labels to EPA electronically for our review as part of the pesticide registration process. The electronic submission of labels by registrants is voluntary but strongly encouraged.

  3. Mental Labels and Tattoos

    Science.gov (United States)

    Hyatt, I. Ralph

    1977-01-01

    Discusses the ease with which mental labels become imprinted in our system, six basic axioms for maintaining negative mental tattoos, and psychological processes for eliminating mental tattoos and labels. (RK)

  4. A Label to Regulate

    DEFF Research Database (Denmark)

    Tricoire, Aurélie; Boxenbaum, Eva; Laurent, Brice

    This paper examines the role labelling plays in the government of the contemporary economy.1Drawing on a detailed study of BBC-Effinergy, a French label for sustainable construction, we showhow the adoption and evolution of voluntary labels can be seen as emblematic of a governmentthrough experim...... experiment engaging 4 operations: stimulating market anticipations, focussing politicalconsultations, producing collective expertise and containing the regulatory transcription of the label....

  5. Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search

    Directory of Open Access Journals (Sweden)

    Beukelaer Herman De

    2012-11-01

    Full Text Available Abstract Background Sampling core subsets from genetic resources while maintaining as much as possible the genetic diversity of the original collection is an important but computationally complex task for gene bank managers. The Core Hunter computer program was developed as a tool to generate such subsets based on multiple genetic measures, including both distance measures and allelic diversity indices. At first we investigate the effect of minimum (instead of the default mean distance measures on the performance of Core Hunter. Secondly, we try to gain more insight into the performance of the original Core Hunter search algorithm through comparison with several other heuristics working with several realistic datasets of varying size and allelic composition. Finally, we propose a new algorithm (Mixed Replica search for Core Hunter II with the aim of improving the diversity of the constructed core sets and their corresponding generation times. Results Our results show that the introduction of minimum distance measures leads to core sets in which all accessions are sufficiently distant from each other, which was not always obtained when optimizing mean distance alone. Comparison of the original Core Hunter algorithm, Replica Exchange Monte Carlo (REMC, with simpler heuristics shows that the simpler algorithms often give very good results but with lower runtimes than REMC. However, the performance of the simpler algorithms is slightly worse than REMC under lower sampling intensities and some heuristics clearly struggle with minimum distance measures. In comparison the new advanced Mixed Replica search algorithm (MixRep, which uses heterogeneous replicas, was able to sample core sets with equal or higher diversity scores than REMC and the simpler heuristics, often using less computation time than REMC. Conclusion The REMC search algorithm used in the original Core Hunter computer program performs well, sometimes leading to slightly better results

  6. Labeling Schemes with Queries

    OpenAIRE

    2006-01-01

    We study the question of ``how robust are the known lower bounds of labeling schemes when one increases the number of consulted labels''. Let $f$ be a function on pairs of vertices. An $f$-labeling scheme for a family of graphs $\\cF$ labels the vertices of all graphs in $\\cF$ such that for every graph $G\\in\\cF$ and every two vertices $u,v\\in G$, the value $f(u,v)$ can be inferred by merely inspecting the labels of $u$ and $v$. This paper introduces a natural generalization: the notion of $f$-...

  7. On the origin of the shallow and "replica" bands in FeSe monolayer superconductors

    Science.gov (United States)

    Nekrasov, I. A.; Pavlov, N. S.; Sadovskii, M. V.

    2017-03-01

    We compare the electronic structures of single FeSe layer films on SrTiO3 substrate (FeSe/STO) and K x Fe2- y Se2 superconductors obtained from extensive LDA and LDA + DMFT calculations with the results of ARPES experiments. It is demonstrated that correlation effects on Fe-3d states are sufficient in principle to explain the formation of the shallow electron-like bands at the M(X)-point. However, in FeSe/STO these effects alone are apparently insufficient for the simultaneous elimination of the hole-like Fermi surface around the Γ-point which is not observed in ARPES experiments. Detailed comparison of ARPES detected and calculated quasiparticle bands shows reasonable agreement between theory and experiment. Analysis of the bands with respect to their origin and orbital composition shows, that for FeSe/STO system the experimentally observed "replica" quasiparticle band at the M-point (usually attributed to forward scattering interactions with optical phonons in SrTiO3 substrate) can be reasonably understood just as the LDA calculated Fe-3d xy band, renormalized by electronic correlations. The only manifestation of the substrate reduces to lifting the degeneracy between Fe-3d xz and Fe-3d yz bands near M-point. For the case of K x Fe2- y Se2 most bands observed in ARPES can also be understood as correlation renormalized Fe-3d LDA calculated bands, with overall semi-quantitative agreement with LDA + DMFT calculations.

  8. FTIR study of ageing of fast drying oil colour (FDOC) alkyd paint replicas

    Science.gov (United States)

    Duce, Celia; Della Porta, Valentina; Tiné, Maria Rosaria; Spepi, Alessio; Ghezzi, Lisa; Colombini, Maria Perla; Bramanti, Emilia

    2014-09-01

    We propose ATR-FTIR spectroscopy for the characterization of the spectral changes in alkyd resin from the Griffin Alkyd Fast Drying Oil Colour range (Winsor & Newton), occurring over 550 days (∼18 months) of natural ageing and over six months of artificial ageing under an acetic acid atmosphere. Acetic acid is one of the atmospheric pollutants found inside museums in concentrations that can have a significant effect on the works exhibited. During natural ageing we observed an increase and broadening of the OH group band around 3300 cm-1 and an increase in bands in the region 1730-1680 cm-1 due to carbonyl stretching. We found a broad band around 1635 cm-1 likely due to Cdbnd O stretching vibrations of β dichetons. These spectral changes are the result of autooxidation reactions during natural ageing and crosslinking, which then form f alcohols and carbonyl species. The increase in absorbance at 1635 cm-1 was selected as a parameter to monitor the ageing process of paintings prepared with FDOC, without the need for any extractive procedure. FTIR spectra of paint replicas kept under an acetic acid atmosphere indicated the chemical groups involved in the reaction with acid, thus suggesting which spectral FTIR regions could be investigated in order to follow any degradation in real paintings. A red paint sample from a hyper-realistic artwork (“Racconta storie”, 2003) by the Italian painter Patrizia Zara was investigated by FTIR in order to evaluate the effects of 10 years natural ageing on alkyd colours. The results obtained suggested that after the end of chemical drying (autooxidation), alkyd colours are very stable.

  9. Immunogold Labelling to Localize Polyphenol Oxidase (PPO) During Wilting of Red Clover Leaf Tissue and the Effect of Removing Cellular Matrices on PPO Protection of Glycerol-Based Lipid in the Rumen

    Science.gov (United States)

    The enzyme polyphenol oxidase (PPO) reduces the extent of proteolysis and lipolysis within red clover fed to ruminants. PPO catalyses the conversion of phenols to quinones which can react with nucleophilic cellular constituents (e.g. proteins), forming protein-phenol complexes that may reduce protei...

  10. Micromorphological characterization and label-free quantitation of small rubber particle protein in natural rubber latex.

    Science.gov (United States)

    Wang, Sai; Liu, Jiahui; Wu, Yanxia; You, Yawen; He, Jingyi; Zhang, Jichuan; Zhang, Liqun; Dong, Yiyang

    2016-04-15

    Commercial natural rubber is traditionally supplied by Hevea brasiliensis, but now there is a big energy problem because of the limited resource and increasing demand. Intensive study of key rubber-related substances is urgently needed for further research of in vitro biosynthesis of natural rubber. Natural rubber is biosynthesized on the surface of rubber particles. A membrane protein called small rubber particle protein (SRPP) is a key protein associated closely with rubber biosynthesis; however, SRPP in different plants has been only qualitatively studied, and there are no quantitative reports so far. In this work, H. brasiliensis was chosen as a model plant. The microscopic distribution of SRPP on the rubber particles during the washing process was investigated by transmission electron microscopy-immunogold labeling. A label-free surface plasmon resonance (SPR) immunosensor was developed to quantify SRPP in H. brasiliensis for the first time. The immunosensor was then used to rapidly detect and analyze SRPP in dandelions and prickly lettuce latex samples. The label-free SPR immunosensor can be a desirable tool for rapid quantitation of the membrane protein SRPP, with excellent assay efficiency, high sensitivity, and high specificity. The method lays the foundation for further study of the functional relationship between SRPP and natural rubber content.

  11. Succesful labelling schemes

    DEFF Research Database (Denmark)

    Juhl, Hans Jørn; Stacey, Julia

    2001-01-01

    It is usual practice to evaluate the success of a labelling scheme by looking at the awareness percentage, but in many cases this is not sufficient. The awareness percentage gives no indication of which of the consumer segments that are aware of and use labelling schemes and which do not. In the ......It is usual practice to evaluate the success of a labelling scheme by looking at the awareness percentage, but in many cases this is not sufficient. The awareness percentage gives no indication of which of the consumer segments that are aware of and use labelling schemes and which do not....... In the spring of 2001 MAPP carried out an extensive consumer study with special emphasis on the Nordic environmentally friendly label 'the swan'. The purpose was to find out how much consumers actually know and use various labelling schemes. 869 households were contacted and asked to fill in a questionnaire...... it into consideration when I go shopping. The respondent was asked to pick the most suitable answer, which described her use of each label. 29% - also called 'the labelling blind' - responded that they basically only knew the recycling label and the Government controlled organic label 'Ø-mærket'. Another segment of 6...

  12. Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.

    Science.gov (United States)

    Yang, Mingjun; Huang, Jing; MacKerell, Alexander D

    2015-06-09

    Replica exchange (REX) is a powerful computational tool for overcoming the quasi-ergodic sampling problem of complex molecular systems. Recently, several multidimensional extensions of this method have been developed to realize exchanges in both temperature and biasing potential space or the use of multiple biasing potentials to improve sampling efficiency. However, increased computational cost due to the multidimensionality of exchanges becomes challenging for use on complex systems under explicit solvent conditions. In this study, we develop a one-dimensional (1D) REX algorithm to concurrently combine the advantages of overall enhanced sampling from Hamiltonian solute scaling and the specific enhancement of collective variables using Hamiltonian biasing potentials. In the present Hamiltonian replica exchange method, termed HREST-BP, Hamiltonian solute scaling is applied to the solute subsystem, and its interactions with the environment to enhance overall conformational transitions and biasing potentials are added along selected collective variables associated with specific conformational transitions, thereby balancing the sampling of different hierarchical degrees of freedom. The two enhanced sampling approaches are implemented concurrently allowing for the use of a small number of replicas (e.g., 6 to 8) in 1D, thus greatly reducing the computational cost in complex system simulations. The present method is applied to conformational sampling of two nitrogen-linked glycans (N-glycans) found on the HIV gp120 envelope protein. Considering the general importance of the conformational sampling problem, HREST-BP represents an efficient procedure for the study of complex saccharides, and, more generally, the method is anticipated to be of general utility for the conformational sampling in a wide range of macromolecular systems.

  13. Replicon modes and stability of critical behaviour of disordered systems with respect to the continuous replica symmetry breaking

    Science.gov (United States)

    Fedorenko, A. A.

    2003-02-01

    A field-theory approach is used to investigate the 'spin-glass effects' on the critical behaviour of systems with weak temperature-like quenched disorder. The renormalization group (RG) analysis of the effective Hamiltonian of a model with replica symmetry breaking (RSB) potentials of a general type is carried out in the two-loop approximation. The fixed point (FP) stability, recently found within the one-step RSB RG treatment, is further explored in terms of replicon eigenvalues. We find that the traditional FPs, which are usually considered to describe the disorder-induced universal critical behaviour, remain stable when the continuous RSB modes are taken into account.

  14. Prediction of localized aerosol deposition in a realistic replica of human airways using experimental data and numerical simulation

    Science.gov (United States)

    Lizal, Frantisek; Elcner, Jakub; Belka, Miloslav; Jedelsky, Jan; Jicha, Miroslav

    2016-11-01

    The presence of aerosol deposition hot-spots in human airways presumably contributes to development of various diseases. The overall aerosol deposition in human lungs can be predicted with sufficient accuracy nowadays. However, the prediction of localized aerosol deposition poses arduous challenge, namely in diseased lungs. Numerical simulation is considered to be a promising tool for the successful prediction. Yet, the validation of such simulations is difficult to perform, as not enough experimental data acquired using realistic airway replicas is available. This paper presents a first comparison of localized deposition measurement and simulation performed on the identical realistic geometry. The analysis indicates that both approaches yield similar results for low Reynolds number flows.

  15. Evidence of a one-step replica symmetry breaking in a three-dimensional Potts glass model.

    Science.gov (United States)

    Takahashi, Takashi; Hukushima, Koji

    2015-02-01

    We study a seven-state Potts glass model in three dimensions with first-, second-, and third-nearest-neighbor interactions with a bimodal distribution of couplings by Monte Carlo simulations. Our results show the existence of a spin-glass transition at a finite temperature T(c), a discontinuous jump of an order parameter at T(c) without latent heat, and a nontrivial structure in the order parameter distribution below T(c). They are compatible with one-step replica symmetry breaking.

  16. A hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper.

    Science.gov (United States)

    Cukier, Robert I

    2011-01-28

    Leucine zippers consist of alpha helical monomers dimerized (or oligomerized) into alpha superhelical structures known as coiled coils. Forming the correct interface of a dimer from its monomers requires an exploration of configuration space focused on the side chains of one monomer that must interdigitate with sites on the other monomer. The aim of this work is to generate good interfaces in short simulations starting from separated monomers. Methods are developed to accomplish this goal based on an extension of a previously introduced [Su and Cukier, J. Phys. Chem. B 113, 9595, (2009)] hamiltonian temperature replica exchange method (HTREM), which scales the hamiltonian in both potential and kinetic energies that was used for the simulation of dimer melting curves. The new method, HTREM_MS (MS designates mean square), focused on interface formation, adds restraints to the hamiltonians for all but the physical system, which is characterized by the normal molecular dynamics force field at the desired temperature. The restraints in the nonphysical systems serve to prevent the monomers from separating too far, and have the dual aims of enhancing the sampling of close in configurations and breaking unwanted correlations in the restrained systems. The method is applied to a 31-residue truncation of the 33-residue leucine zipper (GCN4-p1) of the yeast transcriptional activator GCN4. The monomers are initially separated by a distance that is beyond their capture length. HTREM simulations show that the monomers oscillate between dimerlike and monomerlike configurations, but do not form a stable interface. HTREM_MS simulations result in the dimer interface being faithfully reconstructed on a 2 ns time scale. A small number of systems (one physical and two restrained with modified potentials and higher effective temperatures) are sufficient. An in silico mutant that should not dimerize because it lacks charged residues that provide electrostatic stabilization of the dimer

  17. Short-range Ising spin glasses: The metastate interpretation of replica symmetry breaking

    Science.gov (United States)

    Read, N.

    2014-09-01

    Parisi's formal replica-symmetry-breaking (RSB) scheme for mean-field spin glasses has long been interpreted in terms of many pure states organized ultrametrically. However, the early version of this interpretation, as applied to the short-range Edwards-Anderson model, runs into problems because as shown by Newman and Stein (NS) it does not allow for chaotic size dependence, and predicts non-self-averaging that cannot occur. NS proposed the concept of the metastate (a probability distribution over infinite-size Gibbs states in a given sample that captures the effects of chaotic size dependence) and a nonstandard interpretation of the RSB results in which the metastate is nontrivial and is responsible for what was called non-self-averaging. In this picture, each state drawn from the metastate has the ultrametric properties of the old theory, but when the state is averaged using the metastate, the resulting mixed state has little structure. This picture was constructed so as to agree both with the earlier RSB results and with rigorous results. Here we use the effective field theory of RSB, in conjunction with the rigorous definitions of pure states and the metastate in infinite-size systems, to show that the nonstandard picture follows directly from the RSB mean-field theory. In addition, the metastate-averaged state possesses power-law correlations throughout the low-temperature phase; the corresponding exponent ζ takes the value 4 according to the field theory in high dimensions d, and describes the effective fractal dimension of clusters of spins. Further, the logarithm of the number of pure states in the decomposition of the metastate-averaged state that can be distinguished if only correlations in a window of size W can be observed is of order Wd -ζ. These results extend the nonstandard picture quantitatively; we show that arguments against this scenario are inconclusive. More generally, in terms of Parisi's function q (x), if q(0)≠∫01dxq(x ), then the

  18. Seismic wavefield imaging based on the replica exchange Monte Carlo method

    Science.gov (United States)

    Kano, Masayuki; Nagao, Hiromichi; Ishikawa, Daichi; Ito, Shin-ichi; Sakai, Shin'ichi; Nakagawa, Shigeki; Hori, Muneo; Hirata, Naoshi

    2016-11-01

    Earthquakes sometimes cause serious disasters not only directly by ground motion itself but also secondarily by infrastructure damage, particularly in densely populated urban areas that have capital functions. To reduce the number and severity of secondary disasters, it is important to evaluate seismic hazards rapidly by analyzing the seismic responses of individual structures to input ground motions. We propose a method that integrates physics-based and data-driven approaches in order to obtain a seismic wavefield for use as input to a seismic response analysis. The new contribution of this study is the use of the replica exchange Monte Carlo (REMC) method, which is one of the Markov chain Monte Carlo (MCMC) methods, for estimation of a seismic wavefield, together with a one-dimensional (1-D) local subsurface structure and source information. Numerical tests were conducted to verify the proposed method, using synthetic observation data obtained from analytical solutions for two horizontally-layered subsurface structure models. The geometries of the observation sites were determined from the dense seismic observation array called the Metropolitan Seismic Observation network (MeSO-net), which has been in operation in the Tokyo metropolitan area in Japan since 2007. The results of the numerical tests show that the proposed method is able to search the parameters related to the source and the local subsurface structure in a broader parameter space than the Metropolis method, which is an ordinary MCMC method. The proposed method successfully reproduces a seismic wavefield consistent with a true wavefield. In contrast, ordinary kriging, which is a classical data-driven interpolation method for spatial data, is hardly able to reproduce a true wavefield, even in the low frequency bands. This suggests that it is essential to employ both physics-based and data-driven approaches in seismic wavefield imaging, utilizing seismograms from a dense seismic array. The REMC method

  19. A Hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper

    Science.gov (United States)

    Cukier, Robert I.

    2011-01-01

    Leucine zippers consist of alpha helical monomers dimerized (or oligomerized) into alpha superhelical structures known as coiled coils. Forming the correct interface of a dimer from its monomers requires an exploration of configuration space focused on the side chains of one monomer that must interdigitate with sites on the other monomer. The aim of this work is to generate good interfaces in short simulations starting from separated monomers. Methods are developed to accomplish this goal based on an extension of a previously introduced [Su and Cukier, J. Phys. Chem. B 113, 9595, (2009)] Hamiltonian temperature replica exchange method (HTREM), which scales the Hamiltonian in both potential and kinetic energies that was used for the simulation of dimer melting curves. The new method, HTREM_MS (MS designates mean square), focused on interface formation, adds restraints to the Hamiltonians for all but the physical system, which is characterized by the normal molecular dynamics force field at the desired temperature. The restraints in the nonphysical systems serve to prevent the monomers from separating too far, and have the dual aims of enhancing the sampling of close in configurations and breaking unwanted correlations in the restrained systems. The method is applied to a 31-residue truncation of the 33-residue leucine zipper (GCN4-p1) of the yeast transcriptional activator GCN4. The monomers are initially separated by a distance that is beyond their capture length. HTREM simulations show that the monomers oscillate between dimerlike and monomerlike configurations, but do not form a stable interface. HTREM_MS simulations result in the dimer interface being faithfully reconstructed on a 2 ns time scale. A small number of systems (one physical and two restrained with modified potentials and higher effective temperatures) are sufficient. An in silico mutant that should not dimerize because it lacks charged residues that provide electrostatic stabilization of the dimer

  20. Structure and thermodynamics of amylin dimer studied by Hamiltonian-temperature replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Laghaei, Rozita; Mousseau, Normand; Wei, Guanghong

    2011-03-31

    The loss of the insulin-producing β-cells in the pancreatic islets of Langerhans, responsible for type-II diabetes, is associated with islet amyloid deposits. The main component of these deposits is the amyloid fibrils formed by the 37-residue human islet amyloid polypeptide (hIAPP also known as amylin). Although the fibrils are well characterized by cross β structure, the structure of the transient oligomers formed in the early stage of aggregation remains elusive. In this study, we apply the Hamiltonian-temperature replica exchange molecular dynamics to characterize the structure and thermodynamics of a full-length hIAPP dimer in both the presence and the absence of the Cys2-Cys7 disulfide bond. We compare these results with those obtained on the monomeric and dimeric forms of rat IAPP (rIAPP) with a disulfide bridge which differ from the hIAPP by 6 amino acids in the C-terminal region, but it is unable to form fibrils. Using a coarse-grained protein force field (OPEP-the Optimized Potential for Efficient peptide structure Prediction) running for a total of 10-28 μs per system studied, we show that sequences sample α-helical structure in the N-terminal region but that the length of this secondary element is shorter and less stable for the chains without the disulfide bridge (residues 5-16 for hIAPP with the bridge vs 10-16 for hIAPP without the bridge). This α-helix is known to be an important transient stage in the formation of oligomers. In the C-terminal, the amyloidogenic region of hIAPP, β-strands are seen for residues 17-26 and 30-35. On the contrary, no significant β-sheet content in the C-terminal is observed for either the monomeric or the dimeric rIAPP. These numerical results are fully consistent with recent experimental findings that the N-terminal residues are not part of the fibril by forming α-helical structure but rather play a significant role in stabilizing the amyloidogenic region available for the fibrillation.

  1. Seismic wavefield imaging based on the replica exchange Monte Carlo method

    Science.gov (United States)

    Kano, Masayuki; Nagao, Hiromichi; Ishikawa, Daichi; Ito, Shin-ichi; Sakai, Shin'ichi; Nakagawa, Shigeki; Hori, Muneo; Hirata, Naoshi

    2017-01-01

    Earthquakes sometimes cause serious disasters not only directly by ground motion itself but also secondarily by infrastructure damage, particularly in densely populated urban areas that have capital functions. To reduce the number and severity of secondary disasters, it is important to evaluate seismic hazards rapidly by analysing the seismic responses of individual structures to input ground motions. We propose a method that integrates physics-based and data-driven approaches in order to obtain a seismic wavefield for use as input to a seismic response analysis. The new contribution of this study is the use of the replica exchange Monte Carlo (REMC) method, which is one of the Markov chain Monte Carlo (MCMC) methods, for estimation of a seismic wavefield, together with a 1-D local subsurface structure and source information. Numerical tests were conducted to verify the proposed method, using synthetic observation data obtained from analytical solutions for two horizontally layered subsurface structure models. The geometries of the observation sites were determined from the dense seismic observation array called the Metropolitan Seismic Observation network, which has been in operation in the Tokyo metropolitan area in Japan since 2007. The results of the numerical tests show that the proposed method is able to search the parameters related to the source and the local subsurface structure in a broader parameter space than the Metropolis method, which is an ordinary MCMC method. The proposed method successfully reproduces a seismic wavefield consistent with a true wavefield. In contrast, ordinary kriging, which is a classical data-driven interpolation method for spatial data, is hardly able to reproduce a true wavefield, even in the low frequency bands. This suggests that it is essential to employ both physics-based and data-driven approaches in seismic wavefield imaging, utilizing seismograms from a dense seismic array. The REMC method, which provides not only

  2. Ultrastructural localization of intracellular immunoglobulins in Epon-embedded human lymph nodes. An immunoelectron microscopic investigation using the immunogold staining (IGS) and the avidin-biotin-peroxidase complex (ABC) methods.

    Science.gov (United States)

    Viale, G; Dell'Orto, P; Braidotti, P; Coggi, G

    1985-05-01

    The ultrastructural localization of intracellular immunoglobulins on ultrathin sections of glutaraldehyde-fixed, postosmicated, and Epon-embedded human lymph nodes has been achieved using such highly sensitive immunocytochemical techniques as immunogold staining and avidin-biotin-peroxidase complex. These immunoelectron microscopic techniques allow the identification of intracellular immunoglobulins without affecting the ultrastructural morphology of the tissue, since they do not require any pretreatment of the sections with proteolytic enzymes or deresinating agents. Therefore, immunoglobulins can be precisely localized in the cell organelles; structures whose morphology is well preserved. The availability of a reliable postembedding staining procedure for the ultrastructural localization of immunoglobulins is of definite value for investigations on human lymphoid tissue, both normal and pathological.

  3. Food Label and You

    Medline Plus

    Full Text Available ... En Español Search FDA Submit search Popular Content Home Food Drugs Medical Devices Radiation-Emitting Products Vaccines, Blood & Biologics Animal & Veterinary Cosmetics Tobacco Products Food Home Food Ingredients, Packaging & Labeling Labeling & Nutrition The Food ...

  4. Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.

    Science.gov (United States)

    Mentes, Ahmet; Deng, Nan-Jie; Vijayan, R S K; Xia, Junchao; Gallicchio, Emilio; Levy, Ronald M

    2016-05-10

    Molecular dynamics modeling of complex biological systems is limited by finite simulation time. The simulations are often trapped close to local energy minima separated by high energy barriers. Here, we introduce Hamiltonian replica exchange (H-REMD) with torsional flattening in the Binding Energy Distribution Analysis Method (BEDAM), to reduce energy barriers along torsional degrees of freedom and accelerate sampling of intramolecular degrees of freedom relevant to protein-ligand binding. The method is tested on a standard benchmark (T4 Lysozyme/L99A/p-xylene complex) and on a library of HIV-1 integrase complexes derived from the SAMPL4 blind challenge. We applied the torsional flattening strategy to 26 of the 53 known binders to the HIV Integrase LEDGF site found to have a binding energy landscape funneled toward the crystal structure. We show that our approach samples the conformational space more efficiently than the original method without flattening when starting from a poorly docked pose with incorrect ligand dihedral angle conformations. In these unfavorable cases convergence to a binding pose within 2-3 Å from the crystallographic pose is obtained within a few nanoseconds of the Hamiltonian replica exchange simulation. We found that torsional flattening is insufficient in cases where trapping is due to factors other than torsional energy, such as the formation of incorrect intramolecular hydrogen bonds and stacking. Work is in progress to generalize the approach to handle these cases and thereby make it more widely applicable.

  5. Relationship between Rheological Behaviour and Final Structure of Al2O3 and YSZ Foams Produced by Replica

    Directory of Open Access Journals (Sweden)

    S. Y. Gómez

    2012-01-01

    Full Text Available Using rheological parameters of ceramic suspensions, it is possible to taylor the structure of the ceramic foams produced by replica. This method consists in the impregnation of a polymeric flexible template (polyurethane foam with a ceramic suspension (slurry containing the appropriate additives, followed by burning out organic compounds and additives and sintering the ceramic structure. In this work, ceramic foams were produced by the replica method from Al2O3 and 3% Y2O3-ZrO2. Rheological parameters of the ceramic suspensions were investigated to improve the mechanical performance of final structures. Different types and quantities of raw materials were combined in order to select the formulations for ceramic foams. The parameters that have a significant influence on the process are the binder type and the amount of solids. Significant changes on the hysteresis area of the suspensions resulted in a lower density of macrodefects in the material. Likewise, when the shear rate viscosity is enhanced, the thickness of the struts increased proportionally. Lastly, when the hysteresis area magnitude and the ceramic thickness increased, the material with higher uniformity was internally densified, and the stress concentration of the internal defects was smoothed

  6. A 10-bit 250 MSPS charge-domain pipelined ADC with replica controlled PVT insensitive BCT circuit

    Science.gov (United States)

    Songren, Huang; Hong, Zhang; Zhenhai, Chen; Shuang, Zhu; Zongguang, Yu; Hongwen, Qian; Yue, Hao

    2015-05-01

    A low power 10-bit 250 MSPS charge-domain (CD) pipelined analog-to-digital converter (ADC) is introduced. The ADC is implemented in MOS bucket-brigade devices (BBDs) based CD pipelined architecture. A replica controlled boosted charge transfer (BCT) circuit is introduced to reject the influence of PVT variations on the charge transfer process. Based on replica controlled BCT, the CD pipelined ADC is designed and realized in a 1P6M 0.18 μm CMOS process. The ADC achieves an SFDR of 64.4 dB, an SNDR of 56.9 dB and an ENOB of 9.2 for a 9.9 MHz input; and an SFDR of 63.1 dB, an SNR of 55.2 dB, an SNDR of 54.5 dB and an ENOB of 8.7 for a 220.5 MHz input at full sampling rate. The DNL is +0.5/ -0.55 LSB and INL is +0.8/ -0.85 LSB. The power consumption of the prototype ADC is only 45 mW at 1.8 V supply and it occupies an active die area of 1.56 mm2. Project supported by the National Natural Science Foundation of China (No. 61106027).

  7. 水稻受精前后胚囊内钙调素分布的变化:免疫金电镜观察%Changes of Calmodulin Distribution in the Embryo Sac of Oryza sativa Before and After Fertilization: an Immunogold Electron Microscope Study

    Institute of Scientific and Technical Information of China (English)

    杨军; 赵洁; 梁世平; 杨弘远

    2002-01-01

    Changes of calmodulin (CaM) distribution in the embryo sac of rice (Oryza sativa subsp. japonica) at various stages before and after fertilization have been investigated by using immunogold electron microscopy. Before pollination, both cytoplasm and vacuoles of the egg cell, synergids and central cell were labeled by gold particles. A small amount of gold particles were localized in the nucleus, endoplasmic reticulum, mitochondria and dictyosomes. From pollination to fertilization, CaM amount increased in these cells, especially rich in the starch of amyloplasts. Increase of gold particles in the central cell began about 2 h earlier than that in the egg cell. There was no distinct difference of CaM amount between the degenerated and the persistent synergids. It is interesting to observe an obvious change of CaM distribution form during pollination and fertilization from scattered single particles to clustered particles, and back again to single particles after the fertilization finished. CaM was also localized extracellularly in the embryo sac wall as well as in the wall and intercellular space of nucellus cells. The extracellular CaM also changes in its amount and form after pollination. These results suggest that CaM, either intra- or extra-cellular, may play important roles in fertilization and zygote formation.%用胶体金免疫电镜技术观察了水稻(Oryza sativa subsp. japonica)受精前后胚囊内钙调素的分布变化.授粉后,卵细胞、助细胞和中央细胞内的钙调素较授粉前均有所增加.中央细胞内钙调素的增加要比卵细胞中约早2 h,退化助细胞与宿存助细胞之间的钙调素含量无明显差异.授粉到受精期间,钙调素的主要分布形式由分散的单颗粒转变为聚集颗粒,受精完成后再变为分散的单颗粒形式.胚囊壁及珠心细胞的细胞壁和胞间隙中也观察到钙调素的分布和数量变化.初步讨论了胞内和胞外钙调素在水稻受精与合子形成中的作用.

  8. Número de replicações de inquéritos dietéticos para estimativa da ingestão de nutrientes em gestantes brasileiras

    Directory of Open Access Journals (Sweden)

    Daniela Saes Sartorelli

    2014-12-01

    Full Text Available Objetivos: determinar o número de replicações de inquéritos dietéticos necessários para estimar a ingestão usual de nutrientes e em categorias de consumo de gestantes no Brasil. Métodos: estudo prospectivo conduzido entre 82 gestantes, no qual as informações sobre energia e 18 nutrientes foram obtidas em três inquéritos recordatórios de 24 horas, sendo um em cada trimestre gestacional. Empregaram-se diferentes fórmulas para o cálculo do número de replicações do método necessárias para classificar as gestantes em categorias de ingestão, que considera a razão das variâncias intrapessoal/interpessoal, e para a estimativa da ingestão usual, baseado na variância intrapessoal. Resultados: para classificar as gestantes em categorias são necessárias entre 11 e 51 replicações do método, considerando-se coeficiente de correlação de 0,9. Admitindo coeficiente de correlação de 0,7, o número de replicações do método variou entre quatro e 19. Para a estimativa da ingestão usual são necessárias entre duas e 33 replicações, admitindo-se um erro de 10%. Considerando-se um erro de 20%, são necessárias entre uma e sete replicações de inquéritos dietéticos. Conclusões: é necessário um elevado número de replicações de inquéritos dietéticos na estimativa da ingestão de nutrientes na gestação e o emprego de um número reduzido de replicações poderá atenuar as associações entre a dieta e desfechos de saúde maternos e fetais.

  9. A replica exchange Monte Carlo algorithm for protein folding in the HP model

    Directory of Open Access Journals (Sweden)

    Shmygelska Alena

    2007-09-01

    Full Text Available Abstract Background The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of the most important and challenging problems in biochemistry, molecular biology and biophysics. The ab initio protein folding problem is computationally challenging and has been shown to be NP MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaat0uy0HwzTfgDPnwy1egaryqtHrhAL1wy0L2yHvdaiqaacqWFneVtcqqGqbauaaa@3961@-hard even when conformations are restricted to a lattice. In this work, we implement and evaluate the replica exchange Monte Carlo (REMC method, which has already been applied very successfully to more complex protein models and other optimization problems with complex energy landscapes, in combination with the highly effective pull move neighbourhood in two widely studied Hydrophobic Polar (HP lattice models. Results We demonstrate that REMC is highly effective for solving instances of the square (2D and cubic (3D HP protein folding problem. When using the pull move neighbourhood, REMC outperforms current state-of-the-art algorithms for most benchmark instances. Additionally, we show that this new algorithm provides a larger ensemble of ground-state structures than the existing state-of-the-art methods. Furthermore, it scales well with sequence length, and it finds significantly better conformations on long biological sequences and sequences with a provably unique ground-state structure, which is believed to be a characteristic of real proteins. We also present evidence that our REMC algorithm can fold sequences which exhibit significant interaction between termini in the hydrophobic core relatively easily. Conclusion We demonstrate that REMC utilizing the pull move

  10. From Label to Practice

    DEFF Research Database (Denmark)

    Byrkjeflot, Haldor; Strandgaard, Jesper; Svejenova, Silviya

    2013-01-01

    This article examines the process of creation of new Nordic cuisine (NNC) as a culinary innovation, focusing on the main stages, actors, and mechanisms that shaped the new label and its practices and facilitated its diffusion in the region and internationally. Fast-paced diffusion was possible...... because NNC was conceived as an identity movement, triggered by active involvement of entrepreneurial leaders from the culinary profession, high-profile political supporters, legitimating scientists, disseminating media, and interpreting audiences. It was facilitated by three mechanisms: First, the use...... actors and institutions to develop practices associated with the NNC label. Third, organized dissemination allowed the excitement and engagement with the new label to spread quickly....

  11. Capacitive label reader

    Science.gov (United States)

    Arlowe, H. Duane

    1985-01-01

    A capacitive label reader includes an outer ring transmitting portion, an inner ring transmitting portion, and a plurality of insulated receiving portions. A label is the mirror-image of the reader except that identifying portions corresponding to the receiving portions are insulated from only one of two coupling elements. Positive and negative pulses applied, respectively, to the two transmitting rings biased a CMOS shift register positively to either a 1 or 0 condition. The output of the CMOS may be read as an indication of the label.

  12. Food Label and You

    Medline Plus

    Full Text Available ... Sports show highlighting the importance of using the nutrition facts label to control portions, fat, calories and percent daily value. Two studio "sports announcers" describe the "game day" food action of ...

  13. FDA Online Label Repository

    Data.gov (United States)

    U.S. Department of Health & Human Services — The drug labels and other drug-specific information on this Web site represent the most recent drug listing information companies have submitted to the Food and Drug...

  14. Figuring Out Food Labels

    Science.gov (United States)

    ... usually appears on the back or side of packaging under the title "Nutrition Facts." It's also displayed in grocery stores near fresh foods, like fruits, vegetables, and fish. The nutrition facts label includes: a column of ...

  15. Food Label and You

    Medline Plus

    Full Text Available ... use the Nutrition Facts Label to make informed food choices. You can view the new video in its ... two sites, comparing serving sizes, ingredients and overall food choices in this "Battle of the Dueling Dinner Parties". ...

  16. Behind the Label "Alcoholic."

    Science.gov (United States)

    Wright, Deborah M.

    1989-01-01

    Relates individual's personal story of her childhood influenced by her parent's alcoholism, her own alcoholism as a young adult, and her experiences with counseling. Asks others not to reject her because of the label "alcoholic." (ABL)

  17. Food Label and You

    Medline Plus

    Full Text Available ... main page content Skip to search Skip to topics menu Skip to common links HHS U.S. Department ... a contestant in food label knowledge. Questions cover topics such as Calories, Serving Size, Servings per Container, ...

  18. Non-invasive Florentine Renaissance Panel Painting Replica Structures Investigation by Using Terahertz Time-Domain Imaging (THz-TDI) Technique

    DEFF Research Database (Denmark)

    Dandolo, Corinna Ludovica Koch; Picollo, Marcello; Cucci, Costanza

    2016-01-01

    The potentials of the Terahertz Time-Domain Imaging (THz-TDI) technique for a non-invasive inspection of panel paintings have been considered in detail. The THz-TD data acquired on a replica of a panel painting made in imitation of Italian Renaissance panel paintings were processed in order to pr...

  19. The conformational landscape of tartrate-based inhibitors of the TACE enzyme as revealed by Hamiltonian Replica Exchange simulation.

    Science.gov (United States)

    Guardiani, Carlo; Procacci, Piero

    2013-06-21

    The inhibitors of the Tumor Necrosis Factor-α Converting Enzyme represent promising tools for the treatment of Rheumatoid Arthritis, Multiple Sclerosis and other autoimmune diseases. In this work, using Hamiltonian Replica Exchange Molecular Dynamics simulations and atomistic force field we perform an accurate structural characterization of a group of tartrate-based inhibitors. The simulations highlight a correlation between the conformational landscape in bulk solvent and inhibition potency. Since the structures in bulk solvent are much more compact than the crystallographic bound state, we formulate the hypothesis of a two-step docking mechanism: (i) formation of an intermediate between the compact, hydroxyl exposing conformations in solution and the catalytic zinc ion; (ii) structural rearrangement in the active site of TACE of the zinc-tethered drug in the final binding conformation.

  20. Replica symmetry breaking in specially designed TiO$_{2}$ nanoparticles-based dye-colloidal random laser

    CERN Document Server

    Pincheira, Pablo I R; Carreño, Sandra J M; Fewo, Serge I; Moura, André L; Raposo, Ernesto P; Gomes, Anderson S L; de Araújo, Cid B

    2015-01-01

    Replica symmetry breaking (RSB) is a concept inherent to the theory of spin glasses and complex systems, which describes how identical systems prepared under identical initial conditions can reach different states. RSB was predicted and demonstrated, for the first time in any physical system, using random lasers (RLs) operating in the coherent feedback regime. However, attempts to show RSB in RLs operating in the incoherent feedback regime based on colloidal solution of dye and scatterer particles failed. In the present letter, by using specially designed nanoparticles scatterers which prevents photodegradation of the dye, we present clear evidence of RSB in a RL operating in the incoherent feedback regime based on ethanol solution of Rhodamine 6G and amorphous TiO$_{2}$ nanoparticles.

  1. Onsager-Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways.

    Science.gov (United States)

    Fujisaki, Hiroshi; Shiga, Motoyuki; Kidera, Akinori

    2010-04-07

    For sampling multiple pathways in a rugged energy landscape, we propose a novel action-based path sampling method using the Onsager-Machlup action functional. Inspired by the Fourier-path integral simulation of a quantum mechanical system, a path in Cartesian space is transformed into that in Fourier space, and an overdamped Langevin equation is derived for the Fourier components to achieve a canonical ensemble of the path at a finite temperature. To avoid "path trapping" around an initially guessed path, the path sampling method is further combined with a powerful sampling technique, the replica exchange method. The principle and algorithm of our method is numerically demonstrated for a model two-dimensional system with a bifurcated potential landscape. The results are compared with those of conventional transition path sampling and the equilibrium theory, and the error due to path discretization is also discussed.

  2. Fabrication of uniform DNA-conjugated hydrogel microparticles via replica molding for facile nucleic acid hybridization assays.

    Science.gov (United States)

    Lewis, Christina L; Choi, Chang-Hyung; Lin, Yan; Lee, Chang-Soo; Yi, Hyunmin

    2010-07-01

    We identify and investigate several critical parameters in the fabrication of single-stranded DNA conjugated poly(ethylene glycol) (PEG) microparticles based on replica molding (RM) for highly uniform and robust nucleic acid hybridization assays. The effects of PEG-diacrylate, probe DNA, and photoinitiator concentrations on the overall fluorescence and target DNA penetration depth upon hybridization are examined. Fluorescence and confocal microscopy results illustrate high conjugation capacity of the probe and target DNA, femtomole sensitivity, and sequence specificity. Combined, these findings demonstrate a significant step toward simple, robust, and scalable procedures to manufacture highly uniform and high-capacity hybridization assay particles in a well-controlled manner by exploiting many advantages that the batch processing-based RM technique offers. We envision that the results presented here may be readily applied to rapid and high-throughput hybridization assays for a wide variety of applications in bioprocess monitoring, food safety, and biological threat detection.

  3. Entropy generation in Gaussian quantum transformations: applying the replica method to continuous-variable quantum information theory

    Science.gov (United States)

    Gagatsos, Christos N.; Karanikas, Alexandros I.; Kordas, Georgios; Cerf, Nicolas J.

    2016-02-01

    In spite of their simple description in terms of rotations or symplectic transformations in phase space, quadratic Hamiltonians such as those modelling the most common Gaussian operations on bosonic modes remain poorly understood in terms of entropy production. For instance, determining the quantum entropy generated by a Bogoliubov transformation is notably a hard problem, with generally no known analytical solution, while it is vital to the characterisation of quantum communication via bosonic channels. Here we overcome this difficulty by adapting the replica method, a tool borrowed from statistical physics and quantum field theory. We exhibit a first application of this method to continuous-variable quantum information theory, where it enables accessing entropies in an optical parametric amplifier. As an illustration, we determine the entropy generated by amplifying a binary superposition of the vacuum and a Fock state, which yields a surprisingly simple, yet unknown analytical expression.

  4. Magnetic phase transition in coupled spin-lattice systems: A replica-exchange Wang-Landau study.

    Science.gov (United States)

    Perera, Dilina; Vogel, Thomas; Landau, David P

    2016-10-01

    Coupled, dynamical spin-lattice models provide a unique test ground for simulations investigating the finite-temperature magnetic properties of materials under the direct influence of the lattice vibrations. These models are constructed by combining a coordinate-dependent interatomic potential with a Heisenberg-like spin Hamiltonian, facilitating the treatment of both the atomic coordinates and the spins as explicit phase variables. Using a model parameterized for bcc iron, we study the magnetic phase transition in these complex systems via the recently introduced, massively parallel replica-exchange Wang-Landau Monte Carlo method. Comparison with the results obtained from rigid lattice (spin-only) simulations shows that the transition temperature as well as the amplitude of the peak in the specific heat curve is marginally affected by the lattice vibrations. Moreover, the results were found to be sensitive to the particular choice of interatomic potential.

  5. Magnetic phase transition in coupled spin-lattice systems: A replica-exchange Wang-Landau study

    Science.gov (United States)

    Perera, Dilina; Vogel, Thomas; Landau, David P.

    2016-10-01

    Coupled, dynamical spin-lattice models provide a unique test ground for simulations investigating the finite-temperature magnetic properties of materials under the direct influence of the lattice vibrations. These models are constructed by combining a coordinate-dependent interatomic potential with a Heisenberg-like spin Hamiltonian, facilitating the treatment of both the atomic coordinates and the spins as explicit phase variables. Using a model parameterized for bcc iron, we study the magnetic phase transition in these complex systems via the recently introduced, massively parallel replica-exchange Wang-Landau Monte Carlo method. Comparison with the results obtained from rigid lattice (spin-only) simulations shows that the transition temperature as well as the amplitude of the peak in the specific heat curve is marginally affected by the lattice vibrations. Moreover, the results were found to be sensitive to the particular choice of interatomic potential.

  6. A replica exchange transition interface sampling method with multiple interface sets for investigating networks of rare events

    Science.gov (United States)

    Swenson, David W. H.; Bolhuis, Peter G.

    2014-07-01

    The multiple state transition interface sampling (TIS) framework in principle allows the simulation of a large network of complex rare event transitions, but in practice suffers from convergence problems. To improve convergence, we combine multiple state TIS [J. Rogal and P. G. Bolhuis, J. Chem. Phys. 129, 224107 (2008)] with replica exchange TIS [T. S. van Erp, Phys. Rev. Lett. 98, 268301 (2007)]. In addition, we introduce multiple interface sets, which allow more than one order parameter to be defined for each state. We illustrate the methodology on a model system of multiple independent dimers, each with two states. For reaction networks with up to 64 microstates, we determine the kinetics in the microcanonical ensemble, and discuss the convergence properties of the sampling scheme. For this model, we find that the kinetics depend on the instantaneous composition of the system. We explain this dependence in terms of the system's potential and kinetic energy.

  7. Protein-Ligand Binding Potential of Mean Force Calculations with Hamiltonian Replica Exchange on Alchemical Interaction Grids

    CERN Document Server

    Minh, David D L

    2015-01-01

    A binding potential of mean force (BPMF) is a free energy of noncovalent association in which one binding partner is flexible and the other is rigid. I have developed a method to calculate BPMFs for protein-ligand systems. The method is based on replica exchange sampling from multiple thermodynamic states at different temperatures and protein-ligand interaction strengths. Protein-ligand interactions are represented by interpolating precomputed electrostatic and van der Waals grids. Using a simple estimator for thermodynamic length, thermodynamic states are initialized at approximately equal intervals. The method is demonstrated on the Astex diverse set, a database of 85 protein-ligand complexes relevant to pharmacy or agriculture. Fifteen independent simulations of each complex were started using poses from crystallography, docking, or the lowest-energy pose observed in the other simulations. Benchmark simulations completed within three days on a single processor. Overall, protocols initialized using the ther...

  8. Dimerization process of amyloid-β(29-42) studied by the Hamiltonian replica-permutation molecular dynamics simulations.

    Science.gov (United States)

    Itoh, Satoru G; Okumura, Hisashi

    2014-10-02

    The amyloid-β peptides form amyloid fibrils which are associated with Alzheimer's disease. Amyloid-β(29-42) is its C-terminal fragment and a critical determinant of the amyloid formation rate. This fragment forms the amyloid fibril by itself. However, the fragment conformation in the fibril has yet to be determined. The oligomerization process including the dimerization process is also still unknown. The dimerization process corresponds to an early process of the amyloidogenesis. In order to investigate the dimerization process and conformations, we applied the Hamiltonian replica-permutation method, which is a better alternative to the Hamiltonian replica-exchange method, to two amyloid-β(29-42) molecules in explicit water solvent. At the first step of the dimerization process, two amyloid-β(29-42) molecules came close to each other and had intermolecular side chain contacts. When two molecules had the intermolecular side chain contacts, the amyloid-β(29-42) tended to have intramolecular secondary structures, especially β-hairpin structures. The two molecules had intermolecular β-bridge structures by coming much closer at the second step of the dimerization process. Formation of these intermolecular β-bridge structures was induced by the β-hairpin structures. The intermolecular β-sheet structures elongated at the final step. Structures of the amyloid-β(29-42) in the monomer and dimer states are also shown with the free-energy landscapes, which were obtained by performing efficient sampling in the conformational space in our simulations.

  9. Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes.

    Science.gov (United States)

    Hudson, Phillip S; White, Justin K; Kearns, Fiona L; Hodoscek, Milan; Boresch, Stefan; Lee Woodcock, H

    2015-05-01

    Accurately modeling condensed phase processes is one of computation's most difficult challenges. Include the possibility that conformational dynamics may be coupled to chemical reactions, where multiscale (i.e., QM/MM) methods are needed, and this task becomes even more daunting. Free energy simulations (i.e., molecular dynamics), multiscale modeling, and reweighting schemes. Herein, we present two new approaches for mitigating the aforementioned challenges. The first is a new chain-of-replica method (off-path simulations, OPS) for computing potentials of mean force (PMFs) along an easily defined reaction coordinate. This development is coupled with a new distributed, highly-parallel replica framework (REPDstr) within the CHARMM package. Validation of these new schemes is carried out on two processes that undergo conformational changes. First is the simple torsional rotation of butane, while a much more challenging glycosidic rotation (in vacuo and solvated) is the second. Additionally, a new approach that greatly improves (i.e., possibly an order of magnitude) the efficiency of computing QM/MM PMFs is introduced and compared to standard schemes. Our efforts are grounded in the recently developed method for efficiently computing QM-based free energies (i.e., QM-Non-Boltzmann Bennett, QM-NBB). Again, we validate this new technique by computing the QM/MM PMF of butane's torsional rotation. The OPS-REPDstr method is a promising new approach that overcomes many limitations of standard pathway simulations in CHARMM. The combination of QM-NBB with pathway techniques is very promising as it offers significant advantages over current procedures. Efficiently computing potentials of mean force is a major, unresolved, area of interest. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

  10. Novel approach to the fabrication of an artificial small bone using a combination of sponge replica and electrospinning methods

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yang-Hee; Lee, Byong-Taek, E-mail: lbt@sch.ac.kr [Department of Biomedical Engineering and Materials, School of Medicine, Soonchunhyang University 366-1, Ssangyong-dong, Cheonan, Chungnam 330-090 (Korea, Republic of)

    2011-06-15

    In this study, a novel artificial small bone consisting of ZrO{sub 2}-biphasic calcium phosphate/polymethylmethacrylate-polycaprolactone-hydroxyapatite (ZrO{sub 2}-BCP/PMMA-PCL-HAp) was fabricated using a combination of sponge replica and electrospinning methods. To mimic the cancellous bone, the ZrO{sub 2}/BCP scaffold was composed of three layers, ZrO{sub 2}, ZrO{sub 2}/BCP and BCP, fabricated by the sponge replica method. The PMMA-PCL fibers loaded with HAp powder were wrapped around the ZrO{sub 2}/BCP scaffold using the electrospinning process. To imitate the Haversian canal region of the bone, HAp-loaded PMMA-PCL fibers were wrapped around a steel wire of 0.3 mm diameter. As a result, the bundles of fiber wrapped around the wires imitated the osteon structure of the cortical bone. Finally, the ZrO{sub 2}/BCP scaffold was surrounded by HAp-loaded PMMA-PCL composite bundles. After removal of the steel wires, the ZrO{sub 2}/BCP scaffold and bundles of HAp-loaded PMMA-PCL formed an interconnected structure resembling the human bone. Its diameter, compressive strength and porosity were approximately 12 mm, 5 MPa and 70%, respectively, and the viability of MG-63 osteoblast-like cells was determined to be over 90% by the MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay. This artificial bone shows excellent cytocompatibility and is a promising bone regeneration material.

  11. 云计算环境下的动态数据副本管理策略%Dynamic data replica management strategy in cloud computing environment

    Institute of Scientific and Technical Information of China (English)

    邓见光; 赵跃龙; 袁华强

    2015-01-01

    Focusing on the frequent single point of failure in cloud computer system ,a dynamic data replica management strategy was proposed in cloud computer environment .The replica placement de-cision of the proposed replica management strategy was made by specifically analyzing the state param-eters of target node ,including the current load condition ,the size of the current available storage ca-pacity ,the communication bandwidth ,the historical access record and its historical failure record . And at the same time ,a higher priority was provided to the bigger file replica in the decision-making of replica replacement .Experimental results illustrate that the proposed dynamic replica management strategy is stable in the criterion of average data access distance ,and w hich outperforms other several classic replica strategy in the measurements of the system load balance level and the average task exe-cution time .%针对云计算系统中的单点失效问题 ,提出一种云计算环境下的动态数据副本管理策略 .该管理策略通过综合考虑目标放置节点的当前负载状况、可用存储空间大小、通信带宽以及其历史访问记录和历史失效记录等状态参数来进行数据文件的副本放置决策 ,并在进行副本置换操作时给予大尺寸数据文件副本更高的优先权 .测试结果表明 :该管理策略具有较为稳定的平均数据访问距离 ,且在云计算系统的负载均衡水平和平均任务执行时间指标上优于另外几种经典的副本策略 .

  12. Atomic force microscopy recognition of protein A on Staphylococcus aureus cell surfaces by labelling with IgG–Au conjugates

    Directory of Open Access Journals (Sweden)

    Elena B. Tatlybaeva

    2013-11-01

    Full Text Available The labelling of functional molecules on the surface of bacterial cells is one way to recognize the bacteria. In this work, we have developed a method for the selective labelling of protein A on the cell surfaces of Staphylococcus aureus by using nanosized immunogold conjugates as cell-surface markers for atomic force microscopy (AFM. The use of 30-nm size Au nanoparticles conjugated with immunoglobulin G (IgG allowed the visualization, localization and distribution of protein A–IgG complexes on the surface of S. aureus. The selectivity of the labelling method was confirmed in mixtures of S. aureus with Bacillus licheniformis cells, which differed by size and shape and had no IgG receptors on the surface. A preferential binding of the IgG–Au conjugates to S. aureus was obtained. Thus, this novel approach allows the identification of protein A and other IgG receptor-bearing bacteria, which is useful for AFM indication of pathogenic microorganisms in poly-component associations.

  13. European consumers and nutrition labelling

    DEFF Research Database (Denmark)

    Wills, Josephine M.; Grunert, Klaus G.; Celemín, Laura Fernández

    2009-01-01

    Nutrition labelling of food in Europe is not compulsory, unless a nutrition or health claim is made for the product. The European Commission is proposing mandatory nutrition labelling, even front of pack labelling with nutrition information. Yet, how widespread is nutrition labelling in the EU...

  14. Distance labeling schemes for trees

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Gørtz, Inge Li; Bistrup Halvorsen, Esben;

    2016-01-01

    We consider distance labeling schemes for trees: given a tree with n nodes, label the nodes with binary strings such that, given the labels of any two nodes, one can determine, by looking only at the labels, the distance in the tree between the two nodes. A lower bound by Gavoille et al. [Gavoill...

  15. European consumers and nutrition labelling

    DEFF Research Database (Denmark)

    Wills, Josephine M.; Grunert, Klaus G.; Celemín, Laura Fernández

    2009-01-01

    Nutrition labelling of food in Europe is not compulsory, unless a nutrition or health claim is made for the product. The European Commission is proposing mandatory nutrition labelling, even front of pack labelling with nutrition information. Yet, how widespread is nutrition labelling in the EU...

  16. Distance labeling schemes for trees

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Gørtz, Inge Li; Bistrup Halvorsen, Esben

    2016-01-01

    We consider distance labeling schemes for trees: given a tree with n nodes, label the nodes with binary strings such that, given the labels of any two nodes, one can determine, by looking only at the labels, the distance in the tree between the two nodes. A lower bound by Gavoille et al. [Gavoille...... variants such as, for example, small distances in trees [Alstrup et al., SODA, 2003]. We improve the known upper and lower bounds of exact distance labeling by showing that 1/4 log2(n) bits are needed and that 1/2 log2(n) bits are sufficient. We also give (1 + ε)-stretch labeling schemes using Theta......(log(n)) bits for constant ε> 0. (1 + ε)-stretch labeling schemes with polylogarithmic label size have previously been established for doubling dimension graphs by Talwar [Talwar, STOC, 2004]. In addition, we present matching upper and lower bounds for distance labeling for caterpillars, showing that labels...

  17. Semantic Role Labeling

    CERN Document Server

    Palmer, Martha; Xue, Nianwen

    2011-01-01

    This book is aimed at providing an overview of several aspects of semantic role labeling. Chapter 1 begins with linguistic background on the definition of semantic roles and the controversies surrounding them. Chapter 2 describes how the theories have led to structured lexicons such as FrameNet, VerbNet and the PropBank Frame Files that in turn provide the basis for large scale semantic annotation of corpora. This data has facilitated the development of automatic semantic role labeling systems based on supervised machine learning techniques. Chapter 3 presents the general principles of applyin

  18. Labeling of Patient Specimens

    Science.gov (United States)

    2011-01-26

    noted during the event that the actu.al number of near miss incidmts reported monthly was low due to laboratory personnel performing rounds each...specimens never leaves label and if moved it is labeled), All orders in system and all near misses and errors reported to patient safety Purchase/Install...Meeting 14 Aug 09, 1400 in lab break room thru out Develop TICK sheet to track near misses .JDI Ms. Clark Clinics will provide toPS 1st working day of

  19. 云存储智能多数据副本放置机制��%Intelligent Multiple Data Replica Placement Scheme for Cloud Storage

    Institute of Scientific and Technical Information of China (English)

    张榜; 王兴伟; 黄敏

    2014-01-01

    The data replica management scheme is a critical component of cloud storage system. In order to improve its scalability and reliability at the same time shorten user access time, the multiple data replica scheme should be adopted and the proper placement for each replica should be determined. Thus, this paper proposes an intelligent multiple data replica placement scheme for cloud storage. This scheme is based on p-center model with minimizing user access cost as its optimization objective. It uses genetic algorithm (GA) to find the optimal data replica placement solution and uses biogeography-based optimization (BBO) algorithm to optimally assign user access request to the specific data replica. The proposed scheme has been implemented based on CloudSim and performance evaluation has been done. The simulation results show that it is both feasible and effective.%数据副本管理机制是云存储系统的重要组成部分。为了提高云存储系统的可伸缩性、可靠性,同时改善用户访问时间,通常采用多数据副本机制,并且需要解决数据副本放置问题。为此,提出了一种用于云存储系统的智能多数据副本放置机制。该机制基于p-中心模型,以最小化访问代价为优化目标,基于遗传算法(genetic algorithm,GA)确定优化的数据副本放置方案,基于生物地理学优化(biogeography-based optimization,BBO)算法确定用户访问请求对数据副本的优化分配。基于CloudSim进行了仿真实现和性能评价,结果表明,云存储智能多数据副本放置机制是可行和有效的。

  20. Labelled Execution Systems

    Science.gov (United States)

    2012-05-07

    This is most starkly evident in the classical example used to demonstrate that, in the case of infinitely branching systems, a transfinite number of... transfinite number of iterations to converge, what can be shown to fail by appropriately embedding the labelled transition systems of [46, prop. 10.5

  1. Waisda?: video labeling game

    NARCIS (Netherlands)

    Hildebrand, M.; Brinkerink, M.; Gligorov, R.; Steenbergen, M. van; Huijkman, J.; Oomen, J.

    2013-01-01

    The Waisda? video labeling game is a crowsourcing tool to collect user-generated metadata for video clips. It follows the paradigm of games-with-a-purpose, where two or more users play against each other by entering tags that describe the content of the video. Players score points by entering the sa

  2. Multi-label

    Directory of Open Access Journals (Sweden)

    Neda Abdelhamid

    2015-01-01

    Full Text Available Generating multi-label rules in associative classification (AC from single label data sets is considered a challenging task making the number of existing algorithms for this task rare. Current AC algorithms produce only the largest frequency class connected with a rule in the training data set and discard all other classes even though these classes have data representation with the rule’s body. In this paper, we deal with the above problem by proposing an AC algorithm called Enhanced Multi-label Classifiers based Associative Classification (eMCAC. This algorithm discovers rules associated with a set of classes from single label data that other current AC algorithms are unable to induce. Furthermore, eMCAC minimises the number of extracted rules using a classifier building method. The proposed algorithm has been tested on a real world application data set related to website phishing and the results reveal that eMCAC’s accuracy is highly competitive if contrasted with other known AC and classic classification algorithms in data mining. Lastly, the experimental results show that our algorithm is able to derive new rules from the phishing data sets that end-users can exploit in decision making.

  3. Food Label and You

    Medline Plus

    Full Text Available ... Label and You — Video Share Tweet Linkedin Pin it More sharing options Linkedin Pin it Email Print NOTE: FDA has issued final changes ... choices. You can view the new video in its entirety or select on any of the individual ...

  4. Health Labeling, and Consumption- Understanding Determinants To Health Label Use.

    OpenAIRE

    Hoyer, David; Dossing, Jens; Zhuravleva, Anna

    2013-01-01

    Consumer behavior was explored through the understanding, and use of health labeling. Government and business forces were discovered to influence the ability of consumers to use health labels for improved health and life expectancy, and reduce the negative health care costs of food related diseases. Our survey results were compared to other papers and experiments in the field of consumption and labeling. We discovered high usage of labels, especially nutrition information, and a desire for fr...

  5. Decode the Sodium Label Lingo

    Science.gov (United States)

    ... For Preschooler For Gradeschooler For Teen Decode the Sodium Label Lingo Published January 24, 2013 Print Email Reading food labels can help you slash sodium. Here's how to decipher them. "Sodium free" or " ...

  6. Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics.

    Science.gov (United States)

    Zheng, Weihua; Andrec, Michael; Gallicchio, Emilio; Levy, Ronald M

    2009-08-27

    We present an approach to recover kinetics from a simplified protein folding model at different temperatures using the combined power of replica exchange (RE), a kinetic network, and effective stochastic dynamics. While RE simulations generate a large set of discrete states with the correct thermodynamics, kinetic information is lost due to the random exchange of temperatures. We show how we can recover the kinetics of a 2D continuous potential with an entropic barrier by using RE-generated discrete states as nodes of a kinetic network. By choosing the neighbors and the microscopic rates between the neighbors appropriately, the correct kinetics of the system can be recovered by running a kinetic simulation on the network. We fine-tune the parameters of the network by comparison with the effective drift velocities and diffusion coefficients of the system determined from short-time stochastic trajectories. One of the advantages of the kinetic network model is that the network can be built on a high-dimensional discretized state space, which can consist of multiple paths not consistent with a single reaction coordinate.

  7. Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates

    Science.gov (United States)

    Iniesto, Miguel; Buscalioni, Ángela D.; Carmen Guerrero, M.; Benzerara, Karim; Moreira, David; López-Archilla, Ana I.

    2016-05-01

    Microbial mats have been hypothesized to improve the persistence and the preservation of organic remains during fossilization processes. We test this hypothesis with long-term experiments (up to 5.5 years) using invertebrate and vertebrate corpses. Once placed on mats, the microbial community coats the corpses and forms a three-dimensional sarcophagus composed of microbial cells and exopolymeric substances (EPS). This coverage provides a template for i) moulding superficial features, resulting in negative impressions, and ii) generating replicas. The impressions of fly setulae, fish scales and frog skin verrucae are shaped mainly by small cells in an EPS matrix. Microbes also replicate delicate structures such as the three successive layers that compose a fish eye. The sarcophagus protects the body integrity, allowing the persistence of inner organs such as the ovaries and digestive apparatus in flies, the swim bladder and muscles in fish, and the bone marrow in frog legs. This study brings strong experimental evidence to the idea that mats favour metazoan fossilization by moulding, replicating and delaying decay. Rapid burial has classically been invoked as a mechanism to explain exceptional preservation. However, mats may play a similar role during early fossilization as they can preserve complex features for a long time.

  8. Adsorption of a Hard Sphere Fluid in a Disordered Polymerized Matrix: Application of the Replica Ornstein-Zernike Equations

    Science.gov (United States)

    Pizio; Trokhymchuk; Henderson; Labik

    1997-07-01

    A model of hard spheres adsorbed in disordered porous media is studied using the associative replica Ornstein-Zernike (ROZ) equations. Extending previous studies of adsorption in a hard sphere matrices, we investigate a polymerized matrix. We consider an associating fluid of hard spheres with two intracore attractive sites per particle; consequently chains consisting of overlapping hard spheres can be formed due to the chemical association. This is the generalization of the model with sites on the surface of Wertheim that has been studied in the bulk by Chang and Sandler. The matrix structure is obtained in the polymer Percus-Yevick approximation. We solve the ROZ equations in the associative hypernetted chain approximation. The pair distribution functions, the fluid compressibility, the equation of state and chemical potential of the adsorbed fluid are obtained and discussed. It is shown that the adsorption of a hard sphere fluid in a matrix at given density, but consisting of longer chains of overlapping hard spheres, is higher than the adsorption of this fluid in a hard sphere matrix.

  9. Membrane insertion of fusion peptides from Ebola and Marburg viruses studied by replica-exchange molecular dynamics simulations.

    Science.gov (United States)

    Olson, Mark A; Lee, Michael S; Yeh, In-Chul

    2017-01-28

    This work presents replica-exchange molecular dynamics simulations of inserting a 16-residue Ebola virus fusion peptide into a membrane bilayer. A computational approach is applied for modeling the peptide at the explicit all-atom level and the membrane-aqueous bilayer by a generalized Born continuum model with a smoothed switching function (GBSW). We provide an assessment of the model calculations in terms of three metrics: (1) the ability to reproduce the NMR structure of the peptide determined in the presence of SDS micelles and comparable structural data on other fusion peptides; (2) determination of the effects of the mutation Trp-8 to Ala and sequence discrimination of the homologous Marburg virus; and (3) calculation of potentials of mean force for estimating the partitioning free energy and their comparison to predictions from the Wimley-White interfacial hydrophobicity scale. We found the GBSW implicit membrane model to produce results of limited accuracy in conformational properties of the peptide when compared to the NMR structure, yet the model resolution is sufficient to determine the effect of sequence differentiation on peptide-membrane integration. © 2016 Wiley Periodicals, Inc.

  10. Photovoltaic performance of nanoporous TiO2 replicas synthesized from mesoporous materials for dye-sensitized solar cells.

    Science.gov (United States)

    Hwang, Kyung-Jun; Yoo, Seung-Joon; Kim, Sung-Soo; Kim, Ji-Man; Shim, Wang-Geun; Kim, Sun-Il; Lee, Jae-Wook

    2008-10-01

    For dye-sensitized solar cell (DSSC), highly ordered nanoporous TiO2 materials with crystalline frameworks were successfully synthesized from different silica templates including SBA-15, KIT-6 and MSU-H. A photoelectrode in DSSC was fabricated by adsorbing cis-bis(isothiocyanato)bis(2,2'-bipyridyl-4,4'-dicarboxylato)-ruthenium(II)bis-tetrabutylammonium dye (N719) onto the prepared TiO2 nanoparticles. The samples were characterized by XRD, TEM, FE-SEM, AFM and Brunauer-Emmett-Teller (BET), and FT-IR analysis. An investigation of the influence of the bonding structure of N719 dye and nanoporous TiO2 on the photovoltaic performance of DSSC revealed that the bonding structure of N719 on TiO2 films is caused by the unidentate and bidentate linkage. Based on the overall conversion efficiency (eta), fill factor (FF), open-circuit voltage (V(oc)) and short-circuit current (/sc) from the I-V curves measured, it was observed that the photoelectric performance is strongly dependent on the dispersion properties of the nanoporous TiO2 replicas from mesoporous silica templates.

  11. A replica technique for extracting precipitates from neutron-irradiated or thermal-aged vanadium alloys for TEM analysis

    Energy Technology Data Exchange (ETDEWEB)

    Fukumoto, K., E-mail: fukumoto@u-fukui.ac.jp; Iwasaki, M.

    2014-06-01

    A carbon replica technique has been developed to extract precipitates from vanadium alloys. Using this technique, precipitation phases can be extracted from neutron-irradiated or thermal-aged V–4Cr–4Ti alloys. Precipitate identification using EDS X-ray analysis and electron diffraction was facilitated. Only NaCl type of Ti(OCN) precipitate was formed in the thermal-aged V–4Cr–4Ti alloys at 600 °C for 20 h and cation sub-lattice was only occupied by Ti atoms. However, the thin plate of precipitates with NaCl type of crystallographic structure could be seen in the V–4Cr–4Ti alloys irradiated at 593 °C in the JOYO fast reactor. The precipitate contained chromium and vanadium atoms on the cation sub-lattice as well as titanium atoms. It is considered that the phase of MX type (M = Ti, V, Cr and X = O, N, C) is a metastable phase under neutron irradiation.

  12. A replica technique for extracting precipitates from neutron-irradiated or thermal-aged vanadium alloys for TEM analysis

    Science.gov (United States)

    Fukumoto, K.; Iwasaki, M.

    2014-06-01

    A carbon replica technique has been developed to extract precipitates from vanadium alloys. Using this technique, precipitation phases can be extracted from neutron-irradiated or thermal-aged V-4Cr-4Ti alloys. Precipitate identification using EDS X-ray analysis and electron diffraction was facilitated. Only NaCl type of Ti(OCN) precipitate was formed in the thermal-aged V-4Cr-4Ti alloys at 600 °C for 20 h and cation sub-lattice was only occupied by Ti atoms. However, the thin plate of precipitates with NaCl type of crystallographic structure could be seen in the V-4Cr-4Ti alloys irradiated at 593 °C in the JOYO fast reactor. The precipitate contained chromium and vanadium atoms on the cation sub-lattice as well as titanium atoms. It is considered that the phase of MX type (M = Ti, V, Cr and X = O, N, C) is a metastable phase under neutron irradiation.

  13. A Hamiltonian replica exchange molecular dynamics (MD) method for the study of folding, based on the analysis of the stabilization determinants of proteins.

    Science.gov (United States)

    Meli, Massimiliano; Colombo, Giorgio

    2013-06-06

    Herein, we present a novel Hamiltonian replica exchange protocol for classical molecular dynamics simulations of protein folding/unfolding. The scheme starts from the analysis of the energy-networks responsible for the stabilization of the folded conformation, by means of the energy-decomposition approach. In this framework, the compact energetic map of the native state is generated by a preliminary short molecular dynamics (MD) simulation of the protein in explicit solvent. This map is simplified by means of an eigenvalue decomposition. The highest components of the eigenvector associated with the lowest eigenvalue indicate which sites, named "hot spots", are likely to be responsible for the stability and correct folding of the protein. In the Hamiltonian replica exchange protocol, we use modified force-field parameters to treat the interparticle non-bonded potentials of the hot spots within the protein and between protein and solvent atoms, leaving unperturbed those relative to all other residues, as well as solvent-solvent interactions. We show that it is possible to reversibly simulate the folding/unfolding behavior of two test proteins, namely Villin HeadPiece HP35 (35 residues) and Protein A (62 residues), using a limited number of replicas. We next discuss possible implications for the study of folding mechanisms via all atom simulations.

  14. A procedure to analyze surface profiles of the protein molecules visualized by quick-freeze deep-etch replica electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kimori, Yoshitaka [Division of Biomolecular Imaging, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan); Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502 (Japan); Oguchi, Yosuke [Department of Electric Engineering, Kogakuin University, Hachioji, Tokyo 192-0015 (Japan); Ichise, Norihiko [Department of Visual Communication, Komazawa Women' s University, Inagi, Tokyo 206-8511 (Japan); Baba, Norio [Department of Electric Engineering, Kogakuin University, Hachioji, Tokyo 192-0015 (Japan); Katayama, Eisaku [Division of Biomolecular Imaging, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan)]. E-mail: ekatayam@ims.u-tokyo.ac.jp

    2007-01-15

    Quick-freeze deep-etch replica electron microscopy gives high contrast snapshots of individual protein molecules under physiological conditions in vitro or in situ. The images show delicate internal pattern, possibly reflecting the rotary-shadowed surface profile of the molecule. As a step to build the new system for the 'Structural analysis of single molecules', we propose a procedure to quantitatively characterize the structural property of individual molecules; e.g. conformational type and precise view-angle of the molecules, if the crystallographic structure of the target molecule is available. This paper presents a framework to determine the observed face of the protein molecule by analyzing the surface profile of individual molecules visualized in freeze-replica specimens. A comprehensive set of rotary-shadowed views of the protein molecule was artificially generated from the available atomic coordinates using light-rendering software. Exploiting new mathematical morphology-based image filter, characteristic features were extracted from each image and stored as template. Similar features were extracted from the true replica image and the most likely projection angle and the conformation of the observed particle were determined by quantitative comparison with a set of archived images. The performance and the robustness of the procedure were examined with myosin head structure in defined configuration for actual application.

  15. A procedure to analyze surface profiles of the protein molecules visualized by quick-freeze deep-etch replica electron microscopy.

    Science.gov (United States)

    Kimori, Yoshitaka; Oguchi, Yosuke; Ichise, Norihiko; Baba, Norio; Katayama, Eisaku

    2007-01-01

    Quick-freeze deep-etch replica electron microscopy gives high contrast snapshots of individual protein molecules under physiological conditions in vitro or in situ. The images show delicate internal pattern, possibly reflecting the rotary-shadowed surface profile of the molecule. As a step to build the new system for the "Structural analysis of single molecules", we propose a procedure to quantitatively characterize the structural property of individual molecules; e.g. conformational type and precise view-angle of the molecules, if the crystallographic structure of the target molecule is available. This paper presents a framework to determine the observed face of the protein molecule by analyzing the surface profile of individual molecules visualized in freeze-replica specimens. A comprehensive set of rotary-shadowed views of the protein molecule was artificially generated from the available atomic coordinates using light-rendering software. Exploiting new mathematical morphology-based image filter, characteristic features were extracted from each image and stored as template. Similar features were extracted from the true replica image and the most likely projection angle and the conformation of the observed particle were determined by quantitative comparison with a set of archived images. The performance and the robustness of the procedure were examined with myosin head structure in defined configuration for actual application.

  16. A Hamiltonian Replica Exchange Molecular Dynamics (MD Method for the Study of Folding, Based on the Analysis of the Stabilization Determinants of Proteins

    Directory of Open Access Journals (Sweden)

    Massimiliano Meli

    2013-06-01

    Full Text Available Herein, we present a novel Hamiltonian replica exchange protocol for classical molecular dynamics simulations of protein folding/unfolding. The scheme starts from the analysis of the energy-networks responsible for the stabilization of the folded conformation, by means of the energy-decomposition approach. In this framework, the compact energetic map of the native state is generated by a preliminary short molecular dynamics (MD simulation of the protein in explicit solvent. This map is simplified by means of an eigenvalue decomposition. The highest components of the eigenvector associated with the lowest eigenvalue indicate which sites, named “hot spots”, are likely to be responsible for the stability and correct folding of the protein. In the Hamiltonian replica exchange protocol, we use modified force-field parameters to treat the interparticle non-bonded potentials of the hot spots within the protein and between protein and solvent atoms, leaving unperturbed those relative to all other residues, as well as solvent-solvent interactions. We show that it is possible to reversibly simulate the folding/unfolding behavior of two test proteins, namely Villin HeadPiece HP35 (35 residues and Protein A (62 residues, using a limited number of replicas. We next discuss possible implications for the study of folding mechanisms via all atom simulations.

  17. The use of rapid prototyped implants to simulate knee joint abnormalities for in vitro testing: a validation study with replica implants of the native trochlea.

    Science.gov (United States)

    Van Haver, Annemieke; De Roo, Karel; De Beule, Matthieu; Van Cauter, Sofie; Labey, Luc; De Baets, Patrick; Claessens, Tom; Verdonk, Peter

    2014-08-01

    To investigate the biomechanical effect of skeletal knee joint abnormalities, the authors propose to implant pathologically shaped rapid prototyped implants in cadaver knee specimens. This new method was validated by replacing the native trochlea by a replica implant on four cadaver knees with the aid of cadaver-specific guiding instruments. The accuracy of the guiding instruments was assessed by measuring the rotational errors of the cutting planes (on average 3.01° in extension and 1.18° in external/internal rotation). During a squat and open chain simulation, the patella showed small differences in its articulation with the native trochlea and the replica trochlea, which could partially be explained by the rotational errors of the implants. This study concludes that this method is valid to investigate the effect of knee joint abnormalities with a replica implant as a control condition to account for the influence of material properties and rotational errors of the implant. © IMechE 2014.

  18. Demonstration of characteristic skin surface contours of extramammary Paget's disease and parapsoriasis en plaque by image analysis of negative impression replicas.

    Science.gov (United States)

    Kikuchi, Katsuko; Aiba, Setsuya; O'Goshi, Ken-ichiro; Yanai, Motohiro; Takahashi, Motoji; Kasai, Hidefumi; Tagami, Hachiro

    2002-10-01

    The surface contours of lesional skin of certain skin diseases, such as parapsoriasis en plaque (PEP) and extramammary Paget's disease (EMPD), in which there is a massive infiltration by non-epidermal cells, looks somewhat different from that of the adjacent normal skin, needless to state that they are apparently different from that of ordinary chronic inflammatory dermatoses where we found acanthotic epidermis accompanied by hyperkeratosis. We attempted to objectively characterize these unique skin surface changes qualitatively and quantitatively using non-invasive methods. Negative impression replicas were taken from the lesional skin of patients with EMPD or PEP as well as from the adjacent uninvolved skin. The findings were confirmed histologically. The replicas were examined by using computerized image analysis. Several parameters were analyzed that correlate with the changes in the anisotropy of the skin furrows (VC1), average skin roughness (KSD), average length of skin furrows (LEN), and number of skin furrows (NUM). There were significant decreases in KSD and NUM in EMPD, indicating a smoother skin surface in the lesional skin than in the adjacent normal skin. In contrast, the PEP lesion had an increase in VC1 and LEN and a decrease in NUM, which suggests larger skin ridges in the lesional skin than in the uninvolved skin. Thus the unique skin surface of the cutaneous disorders accompanied by epidermal invasion by non-epidermal cells, such as EMPD and PEP, was characterized both qualitatively and quantitatively using computerized image analysis of negative impression replicas.

  19. A distinct group of CpG islands shows differential DNA methylation between replicas of the same cell line in vitro.

    Science.gov (United States)

    Cocozza, Sergio; Scala, Giovanni; Miele, Gennaro; Castaldo, Imma; Monticelli, Antonella

    2013-10-10

    CpG dinucleotide-rich genomic DNA regions, known as CpG islands (CGIs), can be methylated at their cytosine residues as an epigenetic mark that is stably inherited during cell mitosis. Differentially methylated regions (DMRs) are genomic regions showing different degrees of DNA methylation in multiple samples. In this study, we focused our attention on CGIs showing different DNA methylation between two culture replicas of the same cell line. We used methylation data of 35 cell lines from the Encyclopedia of DNA Elements (ENCODE) consortium to identify CpG islands that were differentially methylated between replicas of the same cell line and denoted them Inter Replicas Differentially Methylated CpG islands (IRDM-CGIs). We identified a group of IRDM-CGIs that was consistently shared by different cell lines, and denoted it common IRDM-CGIs. X chromosome CGIs were overrepresented among common IRDM-CGIs. Autosomal IRDM-CGIs were preferentially located in gene bodies and intergenic regions had a lower G + C content, a smaller mean length, and a reduced CpG percentage. Functional analysis of the genes associated with autosomal IRDM-CGIs showed that many of them are involved in DNA binding and development. Our results show that several specific functional and structural features characterize common IRDM-CGIs. They may represent a specific subset of CGIs that are more prone to being differentially methylated for their intrinsic characteristics.

  20. Labelling GM-free Products

    DEFF Research Database (Denmark)

    Punt, Maarten; Venus, Thomas; Wesseler, Justus

    2016-01-01

    Food suppliers in the EU must comply with labelling regulations for genetically modified organisms (GMOs). However, excluded from mandatory labelling are food products derived from animals fed with GM feed (mainly GM soybean in the EU). Because of this labelling exemption, consumers are unable to...

  1. Food Labels Tell the Story!

    Science.gov (United States)

    ... My World From the Label to the Table! Food Labels Tell the Story! What is in food? Food provides your body with all of the ... your food choices. Nutrition Facts—the Labels on Food Products Beginning in 1994, the US government began ...

  2. Modeling the effects of labeling

    DEFF Research Database (Denmark)

    Juhl, Hans Jørn; Fjord, Thomas Ahle; Poulsen, Carsten Stig

    A new approach to evaluate the consequences of labeling is presented and applied to test the potential effect of a label on fresh fish. Labeling effects on quality perceptions and overall quality are studied. The empirical study is based on an experimental design and nearly 500 respondents...

  3. Scaffolding Visitors' Learning through Labels

    Science.gov (United States)

    Wang, Joyce; Yoon, Susan

    2013-01-01

    In museum literature, labels have been found to increase visitor learning and contribute to greater cognitive gains. In this study, we seek to understand how various labels support the visitors' learning experience, and specifically in regards to conceptual and cognitive learning. We investigated the increasing use of three types of labels (visual…

  4. Map labeling and its generalizations

    Energy Technology Data Exchange (ETDEWEB)

    Doddi, S. [New Mexico Univ., Albuquerque, NM (United States). Dept. of Computer Science]|[Los Alamos National Lab., NM (United States); Marathe, M.V. [Los Alamos National Lab., NM (United States); Mirzaian, A. [York Univ., Toronto, ON (Canada). Dept. of Computer Science; Moret, B.M.E. [New Mexico Univ., Albuquerque, NM (United States). Dept. of Computer Science; Zhu, B. [City Univ. of Hong Kong (Hong Kong). Dept. of Computer Science]|[Los Alamos National Lab., NM (United States)

    1997-01-01

    Map labeling is of fundamental importance in cartography and geographical information systems and is one of the areas targeted for research by the ACM Computational Geometry Impact Task Force. Previous work on map labeling has focused on the problem of placing maximal uniform, axis-aligned, disjoint rectangles on the plane so that each point feature to be labeled lies at the corner of one rectangle. Here, we consider a number of variants of the map labeling problem. We obtain three general types of results. First, we devise constant-factor polynomial-time-approximation algorithms for labeling point features by rectangular labels, where the feature may lie anywhere on the boundary of its label region and where labeling rectangles may be placed in any orientation. These results generalize to the case of elliptical labels. Secondly, we consider the problem of labeling a map consisting of disjoint rectilinear fine segments. We obtain constant-factor polynomial-time approximation algorithms for the general problem and an optimal algorithm for the special case where all segments are horizontal. Finally, we formulate a bicriteria version of the map-labeling problem and provide bicriteria polynomial- time approximation schemes for a number of such problems.

  5. Linerless label device and method

    KAUST Repository

    Binladen, Abdulkari

    2016-01-14

    This apparatus and method for applying a linerless label to an end user product includes a device with a printer for printing on a face surface of a linerless label, and a release coat applicator for applying a release coat to the face surface of the label; another device including an unwinder unit (103) to unwind a roll of printed linerless label; a belt (108); a glue applicator (102) for applying glue to the belt; a nip roller (106) for contacting and applying pressure to the face surface of the linerless label such that the glue on the belt transfers to the back surface of the linerless label; at least one slitting knife 105) positioned downstream the belt and a rewinder unit (104) positioned downstream the slitting knife; and a third device which die cuts and applies the linerless label to an end user object.

  6. From Label to Practice

    DEFF Research Database (Denmark)

    Byrkjeflot, Haldor; Strandgaard, Jesper; Svejenova, Silviya

    2013-01-01

    This article examines the process of creation of new Nordic cuisine (NNC) as a culinary innovation, focusing on the main stages, actors, and mechanisms that shaped the new label and its practices and facilitated its diffusion in the region and internationally. Fast-paced diffusion was possible...... because NNC was conceived as an identity movement, triggered by active involvement of entrepreneurial leaders from the culinary profession, high-profile political supporters, legitimating scientists, disseminating media, and interpreting audiences. It was facilitated by three mechanisms: First, the use...

  7. Replica exchange molecular dynamics simulation of cross-fibrillation of IAPP and PrP106-126.

    Science.gov (United States)

    Chua, Khi Pin; Chew, Lock Yue; Mu, Yuguang

    2016-08-01

    Aggregation of proteins into amyloid is the central hallmark of a number of protein diseases. Most studies were carried out on the aggregation between proteins of similar species. However, it was observed that some patients with certain protein disease can easily acquire another unrelated protein disease. As such, it is also important to examine aggregation between proteins of different species. Usually aggregation between proteins of the same species can be attributed to the similarity between their respective amino acid sequences. In this article, we were motivated by an experimental study of aggregation between amylin (Islet Amyloid Polypeptide, IAPP) and prion106-126 (PrP106-126) fragment (JACS, 2013, 135, 13582-9). It was found that the two non-homologous peptides can aggregate quickly to form fibrils in the presence of negatively charged lipid bilayer. We attempted to elucidate the molecular mechanism of the early stage of dimerization of these two peptides through extensive replica exchange molecular dynamics simulations. Conformations consisting of various degrees of β-sheets structures, both intra-chain and inter-chain, were found in the simulations. The conformations of the aggregated complex are very diverse, which suggests that the cross-species fibrils formed between the two proteins are highly polymorphic. The driving forces are mainly hydrophobic interactions, including aromatic-aliphatic interactions. The palindromic region of PrP106-126 and SNNFGAIL region of IAPP were found to play important roles in the interaction. Our study sheds insight into the exciting research of protein cross-fibrillation. Proteins 2016; 84:1134-1146. © 2016 Wiley Periodicals, Inc.

  8. Conformation transitions of a single polyelectrolyte chain in a poor solvent: a replica-exchange lattice Monte-Carlo study.

    Science.gov (United States)

    Wang, Lang; Wang, Zheng; Jiang, Run; Yin, Yuhua; Li, Baohui

    2017-03-15

    The thermodynamic behaviors of a strongly charged polyelectrolyte chain in a poor solvent are studied using replica-exchange Monte-Carlo simulations on a lattice model, focusing on the effects of finite chain length and the solvent quality on the chain conformation and conformation transitions. The neutralizing counterions and solvent molecules are considered explicitly. The thermodynamic quantities that vary continuously with temperature over a wide range are computed using the multiple histogram reweighting method. Our results suggest that the strength of the short-range hydrophobic interaction, the chain length, and the temperature of the system, characterized by ε, N, and T, respectively, are important parameters that control the conformations of a charged chain. When ε is moderate, the competition between the electrostatic energy and the short-range hydrophobic interaction leads to rich conformations and conformation transitions for a longer chain with a fixed length. Our results have unambiguously demonstrated the stability of the n-pearl-necklace structures, where n has a maximum value and decreases with decreasing temperature. The maximum n value increases with increasing chain length. Our results have also demonstrated the first-order nature of the conformation transitions between the m-pearl and the (m-1)-pearl necklaces. With the increase of ε, the transition temperature increases and the first-order feature becomes more pronounced. It is deduced that at the thermodynamic limit of infinitely long chain length, the conformational transitions between the m-pearl and the (m-1)-pearl necklaces may remain first order when ε > 0 and m = 2 or 3. Pearl-necklace conformations cannot be observed when either ε is too large or N is too small. To observe a pearl-necklace conformation, the T value needs to be carefully chosen for simulations performed at only a single temperature.

  9. Towards Multi Label Text Classification through Label Propagation

    Directory of Open Access Journals (Sweden)

    Shweta C. Dharmadhikari

    2012-06-01

    Full Text Available Classifying text data has been an active area of research for a long time. Text document is multifaceted object and often inherently ambiguous by nature. Multi-label learning deals with such ambiguous object. Classification of such ambiguous text objects often makes task of classifier difficult while assigning relevant classes to input document. Traditional single label and multi class text classification paradigms cannot efficiently classify such multifaceted text corpus. Through our paper we are proposing a novel label propagation approach based on semi supervised learning for Multi Label Text Classification. Our proposed approach models the relationship between class labels and also effectively represents input text documents. We are using semi supervised learning technique for effective utilization of labeled and unlabeled data for classification. Our proposed approach promises better classification accuracy and handling of complexity and elaborated on the basis of standard datasets such as Enron, Slashdot and Bibtex.

  10. Radio labeling with pre-assigned frequencies

    NARCIS (Netherlands)

    Bodlaender, H.L.; Broersma, H.J.; Fomin, F.V.; Pyatkin, A.V.; Woeginer, G.J.

    2007-01-01

    A radio labeling of a graph G is an assignment of pairwise distinct, positive integer labels to the vertices of G such that labels of adjacent vertices differ by at least 2. The radio labeling problem (RL) consists in determining a radio labeling that minimizes the maximum label that is used (the so

  11. Radio labeling with pre-assigned frequencies

    NARCIS (Netherlands)

    Bodlaender, H.L.; Broersma, H.J.; Fomin, F.V.; Pyatkin, A.V.; Woeginer, G.J.

    2002-01-01

    A radio labeling of a graph G is an assignment of pairwise distinct, positive integer labels to the vertices of G such that labels of adjacent vertices differ by at least 2. The radio labeling problem (RL) consists in determining a radio labeling that minimizes the maximum label that is used (the

  12. Radio labeling with pre-assigned frequencies

    NARCIS (Netherlands)

    Bodlaender, H.L.; Broersma, Haitze J.; Fomin, F.V.; Pyatkin, A.V.; Woeginger, Gerhard

    2002-01-01

    A radio labeling of a graph $G$ is an assignment of pairwise distinct, positive integer labels to the vertices of $G$ such that labels of adjacent vertices differ by at least $2$. The radio labeling problem (\\mbox{\\sc RL}) consists in determining a radio labeling that minimizes the maximum label

  13. GEO label: The General Framework for Labeling and Certification

    Science.gov (United States)

    Bye, B. L.; McCallum, I.; Maso, J.

    2012-04-01

    The Group on Earth Observations (GEO) is coordinating efforts to build a Global Earth Observation System of Systems, or GEOSS. As part of a strategy to increase the involvement of the science and technology community in GEOSS, both as users and developers of GEOSS itself, GEO decided to develop a GEO label concept related to the scientific relevance, quality, acceptance and societal needs for services and data sets of GEOSS. The development of a GEO label is included in the GEO work plan and several projects address the challenges of developing a GEO label concept. Within the different projects developing the GEO label, various perspectives and approaches are being applied. In order to arrive at a generally accepted GEO label concept, a common understanding and basic knowledge of labeling is necessary. Assessment of quality of internationally standardized Earth observation data products implies possible certification. A general understanding of the framework for international standards and certification will also contribute to a more coherent discussion and more efficient development of a GEO label. We will describe the general labeling and certification framework emphasizing the relation to the three elements of the GEO label: quality, user acceptance and relevance. Based on a survey of international labels done by the EGIDA project, we have analyzed the legal framework and organization of labels and certification. We will discuss the frameworks for certification, user ratings, registration and analysis of user requirements. Quality assessment is a particular focus of the analysis and is based on the work done by the GeoViQua project. A GEO label will function both as a data distribution strategy and as a general management system for data. Through a label users can compare different data sets and get access to more information about the relevant data, including quality. A label will provide traceability of data both in the interest of users as well as data

  14. Sustainability labels on food products

    DEFF Research Database (Denmark)

    Grunert, Klaus G; Hieke, Sophie; Wills, Josephine

    2014-01-01

    This study investigates the relationship between consumer motivation, understanding and use of sustainability labels on food products (both environmental and ethical labels), which are increasingly appearing on food products. Data was collected by means of an online survey implemented in the UK......, human values as measured by the Schwartz value domains, and country differences. The results imply that sustainability labels currently do not play a major role in consumers’ food choices, and future use of these labels will depend on the extent to which consumers’ general concern about sustainability...

  15. 76 FR 75809 - Prior Label Approval System: Generic Label Approval

    Science.gov (United States)

    2011-12-05

    ... Food Standards and Labeling Policy Book; does not bear any special claims, such as quality claims... addition, deletion, or amendment of recipe suggestions for the product; j. Any change in punctuation; k... Policy Book, and questions and answers on various topics, such as irradiation and the labeling...

  16. Rapid Replica Copy Algorithm Based on Popularity in Hadoop%基于热度的Hadoop快速副本复制算法

    Institute of Scientific and Technical Information of China (English)

    张倩; 郑烇; 王嵩

    2015-01-01

    In cloud storage centers, replica of file may be lost because of the failure of nodes, which will affect the reliability of system, as well as the efficiency of file concurrent access. There are some deficiencies in the default replica copy algorithm in Hadoop, such as a concentration of data transfer process on a few DataNodes, load imbalance, low disk I/O throughput. To address this issue, this paper proposes a rapid replica copy algorithm based on popularity in Hadoop. It handles the popular block firstly, and chooses source and destination DataNodes properly. The simulation results show that the proposed algorithm improves the disk I/O throughput, load balance, and reduces average service response time significantly.%在云存储中心,由于节点失效带来的文件数据块副本丢失不仅会影响系统的可靠性,还会影响文件的并发访问效率。针对 Hadoop 中默认的副本复制方法存在的问题,即副本复制过程某些节点数据传输过于集中,负载不均衡,磁盘 I/O 吞吐率低,提出一种基于热度的快速副本复制算法。该算法优先复制热度高的数据块,合理选择数据块复制的源节点和目的节点。仿真结果表明,该算法平衡了系统的工作负载,提高了磁盘 I/O 吞吐率,显著降低用户请求平均响应时间。

  17. A novel approach to evaluating the reproducibility of a replication technique for the manufacture of electroconductive replicas for use in quantitative clinical dental wear studies.

    Science.gov (United States)

    Chadwick, R G; Mitchell, H L; Ward, S

    2004-04-01

    The assessment of the progression of tooth surface loss has until recently been limited to either the application of subjective ranking scales or visual comparison of sequential study casts. The development of quantitative measuring techniques offers the potential of greater accuracy and sensitivity. As direct intra-oral measurement is problematical such approaches often utilize impressions of the teeth, recorded at different epochs, to construct replicas for mapping and comparison. This in vitro investigation sought to determine the reproducibility of such an approach taking into account the total process chain. Two inlay cavities (one large, one small) were prepared in the palatal aspect of a plastic maxillary central incisor and restored with two flush fitting inlays. A series of impressions of this tooth were recorded, using a special tray and an addition cured light bodied silicone impression material (President, Coltene, Switzerland), with (a) both inlays in (b) both inlays out (c) large inlay out and small inlay in (d) large inlay in and small inlay out - a total of 16 impressions. Electroconductive replicas were fabricated from these and mapped using a computer controlled probe. Each series simulated wear of the tooth. A surface matching and difference detection algorithm was then used to compare each series of replicas and calculate the proportion of the surface undergoing simulated wear by a direct comparison of (a) matched to (b) or, indirectly as the summation of the results of matches of (a) with (c) and (a) with (d). The mean proportion of the surface with wear calculated directly was 26.6% (s.d.=0.6) and indirectly 26.1% (s.d. = 0.5). A one-way anova revealed no significant difference (P > 0.05). It is concluded that determining wear by this method is highly reproducible.

  18. Quality Evaluation Model for Map Labeling

    Institute of Scientific and Technical Information of China (English)

    FAN Hong; ZHANG Zuxun; DU Daosheng

    2005-01-01

    This paper discusses and sums up the basic criterions of guaranteeing the labeling quality and abstracts the four basic factors including the conflict for a label with a label, overlay for label with the features, position's priority and the association for a label with its feature. By establishing the scoring system, a formalized four-factors quality evaluation model is constructed. Last, this paper introduces the experimental result of the quality evaluation model applied to the automatic map labeling system-MapLabel.

  19. Non-invasive Florentine Renaissance Panel Painting Replica Structures Investigation by Using Terahertz Time-Domain Imaging (THz-TDI) Technique

    Science.gov (United States)

    Koch Dandolo, Corinna L.; Picollo, Marcello; Cucci, Costanza; Jepsen, Peter Uhd

    2016-11-01

    The potentials of the Terahertz Time-Domain Imaging (THz-TDI) technique for a non-invasive inspection of panel paintings have been considered in detail. The THz-TD data acquired on a replica of a panel painting made in imitation of Italian Renaissance panel paintings were processed in order to provide insights as to the limits and potentials of the technique in detecting different kinds of underdrawings and paint layers. Constituent layers, construction techniques, and anomalies were identified and localized by interpreting the extracted THz dielectric stratigraphy.

  20. Conductive polymer-mediated 2D and 3D arrays of Mn3O4 nanoblocks and mesoporous conductive polymers as their replicas.

    Science.gov (United States)

    Nakagawa, Yoshitaka; Kageyama, Hiroyuki; Matsumoto, Riho; Oaki, Yuya; Imai, Hiroaki

    2015-11-28

    Orientation-controlled 2D and 3D microarrays of Mn3O4 nanocuboids that were mediated by a conductive polymer were fabricated by evaporation-induced self-assembly of the oxide nanoblocks and subsequent polymerization of pyrrole in the interparticle spaces. Free-standing mesoporous polypyrroles (PPy) having chain- and square-grid-like nanovoid arrays were obtained as replicas of the composite assemblies by dissolving the oxide nanoblocks. The PPy-mediated manganese oxide arrays exhibited stable electrochemical performance as an ultrathin anode of a lithium-ion secondary battery.

  1. Seismic wavefield imaging in the Tokyo metropolitan area, Japan, based on the replica exchange Monte Carlo method

    Science.gov (United States)

    Kano, Masayuki; Nagao, Hiromichi; Nagata, Kenji; Ito, Shin-ichi; Sakai, Shin'ichi; Nakagawa, Shigeki; Hori, Muneo; Hirata, Naoshi

    2017-04-01

    Earthquakes sometimes cause serious disasters not only directly by ground motion itself but also secondarily by infrastructure damage, particularly in densely populated urban areas. To reduce these secondary disasters, it is important to rapidly evaluate seismic hazards by analyzing the seismic responses of individual structures due to the input ground motions. Such input motions are estimated utilizing an array of seismometers that are distributed more sparsely than the structures. We propose a methodology that integrates physics-based and data-driven approaches in order to obtain the seismic wavefield to be input into seismic response analysis. This study adopts the replica exchange Monte Carlo (REMC) method, which is one of the Markov chain Monte Carlo (MCMC) methods, for the estimation of the seismic wavefield together with one-dimensional local subsurface structure and source information. Numerical tests show that the REMC method is able to search the parameters related to the source and the local subsurface structure in broader parameter space than the Metropolis method, which is an ordinary MCMC method. The REMC method well reproduces the seismic wavefield consistent with the true one. In contrast, the ordinary kriging, which is a classical data-driven interpolation method for spatial data, is hardly able to reproduce the true wavefield even at low frequencies. This indicates that it is essential to take both physics-based and data-driven approaches into consideration for seismic wavefield imaging. Then the REMC method is applied to the actual waveforms observed by a dense seismic array MeSO-net (Metropolitan Seismic Observation network), in which 296 accelerometers are continuously in operation with several kilometer intervals in the Tokyo metropolitan area, Japan. The estimated wavefield within a frequency band of 0.10-0.20 Hz is absolutely consistent with the observed waveforms. Further investigation suggests that the seismic wavefield is successfully

  2. Expression and biological activity of double replica retrovirus carrier-mediated neurotrophin-3 in olfactory ensheathing cells

    Institute of Scientific and Technical Information of China (English)

    Shougang Guo; Yifeng Du; Feng Jin; Minzhong Wang

    2009-01-01

    : Recombinant double replica retrovirus NT-3 gene was stably and effectivelyexpressed in OECs, and the expressed NT-3 possessed biological activity that promoted neuronalsurvival.

  3. Source and replica calculations

    Energy Technology Data Exchange (ETDEWEB)

    Whalen, P.P.

    1994-02-01

    The starting point of the Hiroshima-Nagasaki Dose Reevaluation Program is the energy and directional distributions of the prompt neutron and gamma-ray radiation emitted from the exploding bombs. A brief introduction to the neutron source calculations is presented. The development of our current understanding of the source problem is outlined. It is recommended that adjoint calculations be used to modify source spectra to resolve the neutron discrepancy problem.

  4. Intervento di replica

    Directory of Open Access Journals (Sweden)

    Gianluigi Rossini

    2013-12-01

    Full Text Available Già dalla discussione che si sta sviluppando su questa rivista intorno al libro di Antonello credo si veda bene una contrapposizione che mi capita spesso di rilevare nel dibattito nostrano: da un lato la sacrosanta irritazione verso un certo conservatorismo di sinistra e verso la lamentosa condanna “crisologica” della contemporaneità, atteggiamenti tanto diffusi quanto sterili; dall’altro una condivisibile preoccupazione: non diventeremo, per dirla con Milan Kundera, gli «allegri alleati dei nostri stessi becchini»? Nell’affrancarci da posizioni che sembrano obsolete, cosa ci rimane da contrapporre al dominio dell’ideologia mercantile e brutalmente quantitativa del neoliberismo?

  5. A better carbon footprint label

    DEFF Research Database (Denmark)

    Thøgersen, John; Nielsen, Kristian S.

    2016-01-01

    , participants saw the original Carbon Trust label and in the other condition they saw the same label, but with traffic light colors added to communicate the product’s relative performance in terms of carbon footprint. All included attributes were found to have a significant impact on consumer choices...

  6. Nutrition Marketing on Food Labels

    Science.gov (United States)

    Colby, Sarah E.; Johnson, LuAnn; Scheett, Angela; Hoverson, Bonita

    2010-01-01

    Objective: This research sought to determine how often nutrition marketing is used on labels of foods that are high in saturated fat, sodium, and/or sugar. Design and Setting: All items packaged with food labels (N = 56,900) in all 6 grocery stores in Grand Forks, ND were surveyed. Main Outcome Measure(s): Marketing strategy, nutrient label…

  7. Nutrition Marketing on Food Labels

    Science.gov (United States)

    Colby, Sarah E.; Johnson, LuAnn; Scheett, Angela; Hoverson, Bonita

    2010-01-01

    Objective: This research sought to determine how often nutrition marketing is used on labels of foods that are high in saturated fat, sodium, and/or sugar. Design and Setting: All items packaged with food labels (N = 56,900) in all 6 grocery stores in Grand Forks, ND were surveyed. Main Outcome Measure(s): Marketing strategy, nutrient label…

  8. Distance labeling schemes for trees

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Gørtz, Inge Li; Bistrup Halvorsen, Esben

    2016-01-01

    variants such as, for example, small distances in trees [Alstrup et al., SODA, 2003]. We improve the known upper and lower bounds of exact distance labeling by showing that 1/4 log2(n) bits are needed and that 1/2 log2(n) bits are sufficient. We also give (1 + ε)-stretch labeling schemes using Theta...

  9. 16 CFR 460.12 - Labels.

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Labels. 460.12 Section 460.12 Commercial Practices FEDERAL TRADE COMMISSION TRADE REGULATION RULES LABELING AND ADVERTISING OF HOME INSULATION § 460.12 Labels. If you are a manufacturer, you must label all packages of your insulation. The labels...

  10. 21 CFR 201.71 - Magnesium labeling.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 4 2010-04-01 2010-04-01 false Magnesium labeling. 201.71 Section 201.71 Food and... LABELING Labeling Requirements for Over-the-Counter Drugs § 201.71 Magnesium labeling. (a) The labeling of over-the-counter (OTC) drug products intended for oral ingestion shall contain the magnesium...

  11. 21 CFR 610.60 - Container label.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Container label. 610.60 Section 610.60 Food and... GENERAL BIOLOGICAL PRODUCTS STANDARDS Labeling Standards § 610.60 Container label. (a) Full label. The following items shall appear on the label affixed to each container of a product capable of bearing a...

  12. Labeled Cocaine Analogs

    Science.gov (United States)

    Goodman, Mark M.; Shi, Bing Zhi; Keil, Robert N.

    1999-01-26

    Novel compounds having the structure: ##STR1## where X in .beta. configuration is phenyl, naphthyl; 2,3 or 4-iodophenyl; 2,3 or 4-(trimethylsilyl)phenyl; 3,4,5 or 6-iodonaphthyl; 3,4,5 or 6-(trimethylsilyl)naphthyl; 2,3 or 4-(trialkylstannyl)phenyl; or 3,4,5 or 6-(trialkylstannyl)naphthyl Y in .beta. configuration is Y.sub.1 or Y.sub.2, where Y.sub.1 is 2-fluoroethoxy, 3-fluoropropoxy, 4-fluorobutoxy, 2-fluorocyclopropoxy, 2 or 3-fluorocyclobutoxy, R,S 1'-fluoroisopropoxy, R 1'-fluoroisopropoxy, S 1'-fluoroisopropoxy, 1',3'-difluoroisopropoxy, R,S 1'-fluoroisobutoxy, R 1'-fluoroisobutoxy, S 1'-fluoroisobutoxy, R,S 4'-fluoroisobutoxy, R 4'-fluoroisobutoxy, S 4'-fluoroisobutoxy, or 1',1'-di(fluoromethyl)isobutoxy, and Y.sub.2 is 2-methanesulfonyloxy ethoxy, 3-methanesulfonyloxy propoxy, 4-methanesulfonyloxy butoxy, 2-methanesulfonyloxy cyclopropoxy, 2 or 3-methanesulfonyloxy cyclobutoxy, 1'methanesulfonyloxy isopropoxy, 1'-fluoro, 3'-methanesulfonyloxy isopropoxy, 1'-methanesulfonyloxy, 3'-fluoro isopropoxy, 1'-methanesulfonyloxy isobutoxy, or 4'-methanesulfonyloxy isobutoxy bind dopamine transporter protein and can be labeled with .sup.18 F or .sup.123 I for imaging.

  13. Synthesis Of Labeled Metabolites

    Science.gov (United States)

    Martinez, Rodolfo A.; Silks, III, Louis A.; Unkefer, Clifford J.; Atcher, Robert

    2004-03-23

    The present invention is directed to labeled compounds, for example, isotopically enriched mustard gas metabolites including: [1,1',2,2'-.sup.13 C.sub.4 ]ethane, 1,1'-sulfonylbis[2-(methylthio); [1,1',2,2'-.sup.13 C.sub.4 ]ethane, 1-[[2-(methylsulfinyl)ethyl]sulfonyl]-2-(methylthio); [1,1',2,2'-.sup.13 C.sub.4 ]ethane, 1,1'-sulfonylbis[2-(methylsulfinyl)]; and, 2,2'-sulfinylbis([1,2-.sup.13 C.sub.2 ]ethanol of the general formula ##STR1## where Q.sup.1 is selected from the group consisting of sulfide (--S--), sulfone (--S(O)--), sulfoxide (--S(O.sub.2)--) and oxide (--O--), at least one C* is .sup.13 C, X is selected from the group consisting of hydrogen and deuterium, and Z is selected from the group consisting of hydroxide (--OH), and --Q.sup.2 --R where Q.sup.2 is selected from the group consisting of sulfide (--S--), sulfone(--S(O)--), sulfoxide (--S(O.sub.2)--) and oxide (--O--), and R is selected from the group consisting of hydrogen, a C.sub.1 to C.sub.4 lower alkyl, and amino acid moieties, with the proviso that when Z is a hydroxide and Q.sup.1 is a sulfide, then at least one X is deuterium.

  14. Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic.

    Science.gov (United States)

    Mignon, David; Simonson, Thomas

    2016-07-15

    Computational protein design depends on an energy function and an algorithm to search the sequence/conformation space. We compare three stochastic search algorithms: a heuristic, Monte Carlo (MC), and a Replica Exchange Monte Carlo method (REMC). The heuristic performs a steepest-descent minimization starting from thousands of random starting points. The methods are applied to nine test proteins from three structural families, with a fixed backbone structure, a molecular mechanics energy function, and with 1, 5, 10, 20, 30, or all amino acids allowed to mutate. Results are compared to an exact, "Cost Function Network" method that identifies the global minimum energy conformation (GMEC) in favorable cases. The designed sequences accurately reproduce experimental sequences in the hydrophobic core. The heuristic and REMC agree closely and reproduce the GMEC when it is known, with a few exceptions. Plain MC performs well for most cases, occasionally departing from the GMEC by 3-4 kcal/mol. With REMC, the diversity of the sequences sampled agrees with exact enumeration where the latter is possible: up to 2 kcal/mol above the GMEC. Beyond, room temperature replicas sample sequences up to 10 kcal/mol above the GMEC, providing thermal averages and a solution to the inverse protein folding problem. © 2016 Wiley Periodicals, Inc.

  15. Evaluation of the marginal and internal gaps of three different dental prostheses: comparison of the silicone replica technique and three-dimensional superimposition analysis.

    Science.gov (United States)

    Park, Jin-Young; Bae, So-Yeon; Lee, Jae-Jun; Kim, Ji-Hwan; Kim, Hae-Young; Kim, Woong-Chul

    2017-06-01

    The purposes of this study were to evaluate the marginal and internal gaps, and the potential clinical applications of three different methods of dental prostheses fabrication, and to compare the prostheses prepared using the silicone replica technique (SRT) and those prepared using the three-dimensional superimposition analysis (3DSA). Five Pekkton, lithium disilicate, and zirconia crowns were each manufactured and tested using both the SRT and the two-dimensional section of the 3DSA. The data were analyzed with the nonparametric version of a two-way analysis of variance using rank-transformed values and the Tukey's post-hoc test (α = .05). Significant differences were observed between the fabrication methods in the marginal gap (P .350), deep chamfer (P > .719), and axial wall (P > .150). As the 3DSA method is three-dimensional, it allows for the measurement of arbitrary points. All of the three fabrication methods are valid for measuring clinical objectives because they produced prostheses within the clinically acceptable range. Furthermore, a three-dimensional superimposition analysis verification method such as the silicone replica technique is also applicable in clinical settings.

  16. 金标渗滤法快速检测血吸虫循环抗原的现场应用研究%THE FIELD TRIAL ON RAPID DETFCTION OF SCHISTOSOMA CIRCULATING ANTIGENS WITH DOT IMMUNOGOLD FILTRATION ASSAY (DIGFA)

    Institute of Scientific and Technical Information of China (English)

    干小仙; 沈丽英; 丁建祖; 沈慧英

    2000-01-01

    A total number of 2221sera collected from different kinds of subjects , i.e.patients with various stages of schistosomiasis. normal individuals, persons with other parasitic diseases or non-parasitic diseases, were detected with Dot Immunogold Filtration Assay (DIGFA) using anti-SVLBP IgG as capturig antibody. Positive rate of 70 sera from patients with acute schistosomiasis was 100%, and that of 307 sera with chronic schistosomiasis was 68.4% .None of 200 sera from normal individuals showed false positive reaction. No obvious cross reaction was found in sera from other parasitic/non-parasitic diseases except sera from patients with paragonimiasis.2 batches of sera were detected with DIGFA by single-blindness method. Results showed that sensitivities to chronic schistosomiasis were 69.4% and 68.9%, and 100% to acute schistosomiasis while specificities were 98.9%-99% .508 samples from residents in endemic areas were tested with DIGFA and Kato-Katz. Positive rate of circulating arrtigen was 20.9% with DIGFA while 65 samples were positive with stool examination.46 samples were positive both by DIGFA and by Kato-katz.The coincidental rate was 70.8% .These results indicated that DIGFA showed sensitive and specific in the detection of circulating antigen. It will be useful in mass application and vahuable in epidemiological stuvey.%将抗重组蛋白SVLBP-IgG用于DIGFA检测2221例血清中血吸虫循环抗原,其中急性血吸虫病人血清70份,慢性血吸虫病人血清307份,循环抗原检出率分别为100%和68.4%。非流行区健康人血清200份,未见阳性反应。除肺吸虫外,与其它寄生虫或非寄生虫感染病人血清无明显交叉反应。用DIGFA单盲法检测2批血清,结果 显示对急性血吸虫病人的敏感性均为100%;对慢性血吸虫病人的敏感性分别为69.4%和68.9%,非流行区体检人群血清的阴性率为99%和98.9%。检测血吸虫病流行区人群血清508

  17. 基于 Shamir 秘密共享的云端多副本审计%Multiple-replica auditing in clouds using Shamir secret sharing

    Institute of Scientific and Technical Information of China (English)

    田晖; 陈羽翔; 黄永峰

    2016-01-01

    For auditing the integrity of multiple-replica in clouds,a public auditing scheme based on Shamir secret sharing was presented.The scheme can generate diverse data tags for different replicas of a given file using Shamir-secret-sharing algorithm,which is helpful for avoiding possible attacks from cloud service provider (CSP)and locating errors while the CSP does not exactly store all required replicas.Further,the scheme support batch auditing for multiple-replicas using Boneh-Lynn-Shacham (BLS)signature and bilinear maps,which can cut down times of interactions between the CSP and the auditor,and reduce communication costs.Moreover,random masks were introduced in user′s data preprocessing and auditing process to avert conspiracy attack of the CSP and prevent privacy leakage. The security of the presented scheme was proved in theory,and the auditing performance was experi-mentally compared with that of the previous work.The experimental results demonstrate that the pro-posed scheme can effectively achieve secure auditing for multiple-replica in clouds,and outperforms the existing methods on both time and space costs.%针对云端多副本审计问题,提出了一种基于 Shamir 秘密共享的审计方案。该方案利用 Shamir 秘密共享算法为同一数据文件的所有副本生成不同的数据标签,以防范云服务提供商的多种攻击,且根据该算法特性生成的聚合标签能有助于实现云服务提供商未完全持有全部副本数据时的出错定位;利用 BLS (Boneh-Lynn-Shacham)签名和双线性映射技术实现了多副本的批量审计,避免了云服务提供商与审计者之间的多次交互,从而降低了审计过程中的通信开销;通过在用户数据预处理阶段引入随机掩码实现了对合谋攻击的防范,并在审计过程中应用随机掩码避免了用户隐私的泄漏。对提出方案的安全性进行了理论证明,并与已有方法在性能方面进行了比较和实

  18. Algorithms for Labeling Focus Regions.

    Science.gov (United States)

    Fink, M; Haunert, Jan-Henrik; Schulz, A; Spoerhase, J; Wolff, A

    2012-12-01

    In this paper, we investigate the problem of labeling point sites in focus regions of maps or diagrams. This problem occurs, for example, when the user of a mapping service wants to see the names of restaurants or other POIs in a crowded downtown area but keep the overview over a larger area. Our approach is to place the labels at the boundary of the focus region and connect each site with its label by a linear connection, which is called a leader. In this way, we move labels from the focus region to the less valuable context region surrounding it. In order to make the leader layout well readable, we present algorithms that rule out crossings between leaders and optimize other characteristics such as total leader length and distance between labels. This yields a new variant of the boundary labeling problem, which has been studied in the literature. Other than in traditional boundary labeling, where leaders are usually schematized polylines, we focus on leaders that are either straight-line segments or Bezier curves. Further, we present algorithms that, given the sites, find a position of the focus region that optimizes the above characteristics. We also consider a variant of the problem where we have more sites than space for labels. In this situation, we assume that the sites are prioritized by the user. Alternatively, we take a new facility-location perspective which yields a clustering of the sites. We label one representative of each cluster. If the user wishes, we apply our approach to the sites within a cluster, giving details on demand.

  19. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... las etiquetas de datos nutricionales (video) Most packaged foods come with a Nutrition Facts label. These labels ... Watch this video for tips on figuring out food labels so you can make healthy choices. For ...

  20. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... Under Control Figuring Out Food Labels Healthy Food Shopping If My Child Has Food Allergies, What Should ... for Parents Figuring Out Food Labels Smart Supermarket Shopping Figuring Out Fat and Calories Food Labels Contact ...

  1. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... las etiquetas de datos nutricionales (video) Most packaged foods come with a Nutrition Facts label. These labels ... Watch this video for tips on figuring out food labels so you can make healthy choices. For ...

  2. Labelling of benzocaine with tritium

    Energy Technology Data Exchange (ETDEWEB)

    Malik, Sohail (Washington Univ., Seattle, WA (United States))

    1994-10-01

    A convenient method is described to label a local anesthetic, benzocaine, with tritium. The bromoester of para-aminobenzoic acid (PABA) was prepared from para-nitrotoluene and was reduced with tritium. The generation of isotopic hydrogen and labelling of benzocaine was achieved in one-step. A mixture of sodium borohydride (NaB[sup 3]H[sub 4]) with cobalt (II) chloride was used to generate tritium gas. 5% Pd/C was used as a catalyst. This constitutes the first report of tritium labelled benzocaine. (author).

  3. New labels for radiation therapy

    Energy Technology Data Exchange (ETDEWEB)

    Kubota, Susumu; Mukai, Minoru; Kato, Hirotoshi (National Inst. of Radiological Sciences, Chiba (Japan))

    1992-12-01

    In simulating radiotherapy, the bone and trachea identified by plain X-P and the other organs, such as the esophagus and bladder, outlined by contrast medium have so far been used as labels. However, irradiation with a high therapeutic ratio is required for an intracorporeal insertion of artificial labels that are identified by X-ray fluoroscopy. For this purpose, metal clips and seed dummies are available, although they cause artifacts in CT scans. Therefore, the authors are using an acupuncture needle and lipiodol for tracing as new artificial labels, since both are identified by X-ray fluoroscopy and CT scan and create few artifacts. (J.P.N.).

  4. General Compact Labeling Schemes for Dynamic Trees

    OpenAIRE

    2006-01-01

    Let $F$ be a function on pairs of vertices. An {\\em $F$- labeling scheme} is composed of a {\\em marker} algorithm for labeling the vertices of a graph with short labels, coupled with a {\\em decoder} algorithm allowing one to compute $F(u,v)$ of any two vertices $u$ and $v$ directly from their labels. As applications for labeling schemes concern mainly large and dynamically changing networks, it is of interest to study {\\em distributed dynamic} labeling schemes. This paper investigates labelin...

  5. Mixed Electrical-Chemical Synapses in Adult Rat Hippocampus are Primarily Glutamatergic and Coupled by Connexin-36.

    Science.gov (United States)

    Hamzei-Sichani, Farid; Davidson, Kimberly G V; Yasumura, Thomas; Janssen, William G M; Wearne, Susan L; Hof, Patrick R; Traub, Roger D; Gutiérrez, Rafael; Ottersen, Ole P; Rash, John E

    2012-01-01

    Dendrodendritic electrical signaling via gap junctions is now an accepted feature of neuronal communication in mammalian brain, whereas axodendritic and axosomatic gap junctions have rarely been described. We present ultrastructural, immunocytochemical, and dye-coupling evidence for "mixed" (electrical/chemical) synapses on both principal cells and interneurons in adult rat hippocampus. Thin-section electron microscopic images of small gap junction-like appositions were found at mossy fiber (MF) terminals on thorny excrescences of CA3 pyramidal neurons (CA3pyr), apparently forming glutamatergic mixed synapses. Lucifer Yellow injected into weakly fixed CA3pyr was detected in MF axons that contacted four injected CA3pyr, supporting gap junction-mediated coupling between those two types of principal cells. Freeze-fracture replica immunogold labeling revealed diverse sizes and morphologies of connexin-36-containing gap junctions throughout hippocampus. Of 20 immunogold-labeled gap junctions, seven were large (328-1140 connexons), three of which were consistent with electrical synapses between interneurons; but nine were at axon terminal synapses, three of which were immediately adjacent to distinctive glutamate receptor-containing postsynaptic densities, forming mixed glutamatergic synapses. Four others were adjacent to small clusters of immunogold-labeled 10-nm E-face intramembrane particles, apparently representing extrasynaptic glutamate receptor particles. Gap junctions also were on spines in stratum lucidum, stratum oriens, dentate gyrus, and hilus, on both interneurons and unidentified neurons. In addition, one putative GABAergic mixed synapse was found in thin-section images of a CA3pyr, but none were found by immunogold labeling, suggesting the rarity of GABAergic mixed synapses. Cx36-containing gap junctions throughout hippocampus suggest the possibility of reciprocal modulation of electrical and chemical signals in diverse hippocampal neurons.

  6. Mixed electrical-chemical synapses in adult rat hippocampus are primarily glutamatergic and coupled by connexin-36

    Directory of Open Access Journals (Sweden)

    Farid eHamzei-Sichani

    2012-05-01

    Full Text Available Dendrodendritic electrical signaling via gap junctions is now an accepted feature of neuronal communication in the mammalian brain, whereas axodendritic and axosomatic gap junctions have rarely been described. We present ultrastructural, immunocytochemical, and dye-coupling evidence for mixed (electrical/chemical synapses in adult rat hippocampus on both principal cells and interneurons. Thin-section electron microscopic images of small gap junction-like appositions were found at mossy fiber (MF terminals on thorny excrescences of CA3 pyramidal neurons (CA3pyr, apparently forming glutamatergic mixed synapses. Lucifer Yellow injected into four weakly-fixed CA3pyr was detected in MF axons that contacted the injected CA3pyr, supporting gap junction-mediated coupling between those two types of principal cells. Freeze-fracture replica immunogold-labeling revealed diverse sizes and morphologies of connexin36-containing gap junctions throughout hippocampus. Of 20 immunogold-labeled gap junctions, seven were large (328-1140 connexons, three of which were consistent with electrical synapses between interneurons; but nine were at axon terminal synapses, three of which were immediately adjacent to distinctive glutamate receptor-containing postsynaptic densities, forming mixed glutamatergic synapses. Four others were adjacent to small clusters of immunogold-labeled 10-nm E-face intramembrane particles, apparently representing extrasynaptic glutamate receptor particles. Gap junctions also were on spines in stratum lucidum, stratum oriens, dentate gyrus, and hilus, on both interneurons and unidentified neurons. In addition, one putative GABAergic mixed synapse was found in thin section images of a CA3pyr, but none found by immunogold-labeling were at GABAergic mixed synapses, suggesting their rarity. Cx36-containing gap junctions throughout hippocampus suggest the possibility of reciprocal modulation of electrical and chemical signals in diverse hippocampal

  7. New Ideas on Labeling Schemes

    DEFF Research Database (Denmark)

    Rotbart, Noy Galil

    evaluation of fully dynamic labeling schemes. Due to a connection between adjacency labeling schemes and the graph theoretical study of induced universal graphs, we study these in depth and show novel results for bounded degree graphs and power-law graphs. We also survey and make progress on the related......With ever increasing size of graphs, many distributed graph systems emerged to store, preprocess and analyze them. While such systems ease up congestion on servers, they incur certain penalties compared to centralized data structure. First, the total storage required to store a graph...... in a distributed fashion increases. Second, attempting to answer queries on vertices of a graph stored in a distributed fashion can be significantly more complicated. In order to lay theoretical foundations to the first penalty mentioned a large body of work concentrated on labeling schemes. A labeling scheme...

  8. Off-Label Drug Use

    Science.gov (United States)

    ... it’s not legal for drug companies to market (advertise or promote) their drugs for off-label uses. ... Statistics Center Volunteer Learning Center Follow Us Twitter Facebook Instagram Cancer Information, Answers, and Hope. Available Every ...

  9. Sustainability labels on food products

    DEFF Research Database (Denmark)

    Grunert, Klaus G; Hieke, Sophie; Wills, Josephine

    2014-01-01

    of sustainability was limited, but understanding of four selected labels (Fair Trade, Rainforest Alliance, Carbon Footprint, and Animal Welfare) was better, as some of them seem to be self-explanatory. The results indicated a low level of use, no matter whether use was measured as self-reported use of different......This study investigates the relationship between consumer motivation, understanding and use of sustainability labels on food products (both environmental and ethical labels), which are increasingly appearing on food products. Data was collected by means of an online survey implemented in the UK...... types of information available on food labels or as use inferred from the results of a choice-based conjoint analysis. Hierarchical regression indicated that use is related to both motivation and understanding, and that both motivation, understanding and use are affected by demographic characteristics...

  10. 教育资源网格模型及副本创建策略%Education Resource Grid Model and Replica Creation Strategies

    Institute of Scientific and Technical Information of China (English)

    邢长明; 刘方爱; 杨林; 厉文

    2009-01-01

    教育资源网格是解决目前分布式教育资源共享问题的有效手段.针对中小学教育资源共享问题,提出了层次式的教育资源网格模型,定义了各层节点的功能.通过与欧洲数据网格对比,分析了教育资源网格的特点.基于层次式的教育资源网格,对影响副本创建策略性能的因素进行了分析,然后引入网络带宽和文件大小两个参数,提出了一种动态副本创建策略(dynamic replica creation strategy,简称EDRS).利用数据网格模拟工具OptorSim构建了教育资源网格虚拟环境,分析比较了EDRS策略与Caching-LRU策略、Caching-LFU策略和基于经济模型的副本创建策略的性能.最后,综合各项指标分析了不同策略对教育资源网格系统性能的影响.结果表明,EDRS策略在教育资源网格应用中有着更好的系统性能.%The education resource grid is an effective measure to solve the problem of sharing distributed education resources at present. First, with regard to the education resource sharing in secondary and elementary schools, a hierarchy model of education resource grid is proposed and the functions of nodes in each layer are defined in this paper. By comparing with the European Data Grid, the education resource grid is analyzed with its characteristics. Then based on the hierarchy grid model, some factors, which influence the performance of replica creation strategy, are analyzed and a dynamic replica creation strategy (EDRS) is proposed by introducing two parameters, i.e., the network bandwidth and file size. With the data grid simulation tool OptorSim, the performances of EDRS with Caching-LRU, Caching-LFU and the economic model strategy are compared respectively. At last, the influence of different strategies on the performance of the education resource grid system is analyzed by synthesizing each parameter. The result indicates that the EDRS has a better system performance in applications of the education resource

  11. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... Smart About Social Media How to Read a Nutrition Facts Label (Video) KidsHealth > For Parents > How to Read a Nutrition Facts Label (Video) Print A A A en ... nutricionales (video) Most packaged foods come with a Nutrition Facts label. These labels have a lot of ...

  12. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... Games, and the Internet How to Read a Nutrition Facts Label (Video) KidsHealth > For Parents > How to Read a Nutrition Facts Label (Video) Print A A A en ... nutricionales (video) Most packaged foods come with a Nutrition Facts label. These labels have a lot of ...

  13. DSm Vector Spaces of Refined Labels

    CERN Document Server

    Kandasamy, W B Vasantha

    2011-01-01

    In this book the authors introduce the notion of DSm vector spaces of refined labels. They also realize the refined labels as a plane and a n-dimensional space. Further, using these refined labels, several algebraic structures are defined. Finally DSm semivector space or refined labels is described. Authors also propose some research problems.

  14. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... and the Internet How to Read a Nutrition Facts Label (Video) KidsHealth > For Parents > How to Read a Nutrition Facts Label (Video) Print A A A en español ... video) Most packaged foods come with a Nutrition Facts label. These labels have a lot of important ...

  15. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... to 2-Year-Old How to Read a Nutrition Facts Label (Video) KidsHealth > For Parents > How to Read a Nutrition Facts Label (Video) Print A A A en ... nutricionales (video) Most packaged foods come with a Nutrition Facts label. These labels have a lot of ...

  16. 21 CFR 606.121 - Container label.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Container label. 606.121 Section 606.121 Food and... Container label. (a) The container label requirements are designed to facilitate the use of a uniform container label for blood and blood components (except Source Plasma) by all blood establishments. (b)...

  17. Nanotechnology for forensic sciences: analysis of PDMS replica of the case head of spent cartridges by optical microscopy, SEM and AFM for the ballistic identification of individual characteristic features of firearms.

    Science.gov (United States)

    Valle, Francesco; Bianchi, Michele; Tortorella, Silvia; Pierini, Giovanni; Biscarini, Fabio; D'Elia, Marcello

    2012-10-10

    A novel application of replica molding to a forensic problem, viz. the accurate reproduction of the case head of gun and rifle cartridges, prior and after been shot, is presented. The fabrication of an arbitrary number of identical copies of the region hit by the firing pin and by the breech face is described. The replicas can be (i) handled without damaging the original evidence, (ii) distributed to different law enforcement agencies for comparison against other evidences found on crime scenes or ballistic tests of seized firearms, (iii) maintained on a file by the laboratories. A detailed analysis of the morphological features of the replicas has been carried out by standard microscopy techniques as well as by advanced microscopy such as scanning probe and scanning electron leading to a quantitative morphological characterization of the case heads down to the nanometer scale. The assignment of the cartridge replicas to the shooting weapon is demonstrated to hold below the micron scale, while it is hindered at the nanometer level both by the manufacturing differences and by eventual modifications occurring on the firing pin.

  18. SEM/EDX and vis spectrophotometry study of the stability of resin-bound mortars used for casting replicas and filling missing parts of historic stone fountains.

    Science.gov (United States)

    Roig-Salom, José-Luis; Doménech-Carbó, María-Teresa; de la Cruz-Cañizares, Juana; Bolívar-Galiano, Fernando; Pelufo-Carbonell, María-José; Peraza-Zurita, Yaiza

    2003-04-01

    A study by SEM/EDX and spectrophotometry in the visible region attempting to assess the stability of new resin-bound mortars used for casting replicas of marble historic fountains is presented in this paper. Different accelerating tests such as thermal ageing, UV light ageing, ageing in an SO(2) pollutant chamber, freezing cycles ageing, salt crystallisation ageing, natural ageing and biological attack have been applied to a series of test specimens prepared with polyester-, epoxy- and gel-coat-bound mortars. Examination of morphology, measurement of chemical composition and chromatic coordinates before and after ageing treatments establish the higher stability and resistance properties of these resin-bound mortars by comparison to those from the natural marbles.

  19. Oligomer Formation of Amyloid-β(29-42) from Its Monomers Using the Hamiltonian Replica-Permutation Molecular Dynamics Simulation.

    Science.gov (United States)

    Itoh, Satoru G; Okumura, Hisashi

    2016-07-14

    Oligomers of amyloid-β peptides (Aβ) are formed during the early stage of the amyloidogenesis process and exhibit neurotoxicity. The oligomer formation process of Aβ and even that of Aβ fragments are still poorly understood, though understanding of these processes is essential for remedying Alzheimer's disease. In order to better understand the oligomerization process of the C-terminal Aβ fragment Aβ(29-42) at the atomic level, we performed the Hamiltonian replica-permutation molecular dynamics simulation with Aβ(29-42) molecules using the explicit water solvent model. We observed that oligomers increased in size through the sequential addition of monomers to the oligomer, rather than through the assembly of small oligomers. Moreover, solvent effects played an important role in this oligomerization process.

  20. Skylab 3600 groove/mm replica grating with a scandium-silicon multilayer coating and high normal-incidence efficiency at 38-nm wavelength.

    Science.gov (United States)

    Seely, John F; Uspenskii, Yu A; Pershin, Yu P; Kondratenko, V V; Vinogradov, A V

    2002-04-01

    A Sc-Si multilayer coating was applied to a replica of the 3600 groove/mm grating, developed for the SO82A spectroheliograph that flew on the Skylab mission, for the purpose of enhancing the normal-incidence efficiency in the extreme-ultraviolet region. The efficiency, measured at an angle of incidence of 6 degrees with synchrotron radiation, had a maximum value of 7.2% at a wavelength of 38 nm and was a factor of 3 higher than the efficiency of the gold-coated Skylab grating. The measured efficiency of the Sc-Si grating was in good agreement with the efficiency calculated by use of the modified integral method.

  1. Replica symmetry breaking in the critical behavior in the m-component ferromagnetic spin systems with a short-range disorder

    Science.gov (United States)

    Wu, Xin-tian

    We investigate the replica symmetry breaking (RSB) in m-component ferromagnetic spin systems with a short-range disorder. Using ε-expansion the Landau-Ginzburg Hamiltonian with a RSB quartic interaction term is studied, where ε=4- d, d is the spatial dimension. The differential recursion relations of renormalization group (RG) are derived to the second order of ε. The replicon eigenvalue, which is a simple way to investigate the stability with respect to the continuous RSB modes, is defined. The fixed points and their eigenvalues are obtained. For m mc, we find a stable fixed point, which is not only stable in the one-step RSB subspace but also stable with respect to the continuous RSB. However, it is unphysical. For m> mc only the pure fixed point is physical and stable.

  2. Hierarchical control of porous silica by pH adjustment: Alkyl polyamines as surfactants for bimodal silica synthesis and its carbon replica

    Science.gov (United States)

    Abellán, G.; Carrillo, A. I.; Linares, N.; Serrano, E.; García-Martínez, J.

    2009-08-01

    Bimodal macro-mesoporous silica networks have been prepared in a simple one-pot synthesis using an inexpensive tetramine surfactant and tetraethoxysilane as a silica precursor. These novel materials show high pore volumes and templated mesopores (average pore size 3.0 nm) embedded in 20 nm thick walls forming interparticle large meso/macropores. The judicious control of the pH during the silica formation allows for the precise control of the interparticle condensation, likely due to the change in the interaction between the tetramine surfactant and the silica precursors. Finally, a highly porous carbon replica with bimodal porosity was prepared by using the bimodal silica as a hard sacrificial template. The microstructure of the silica template was accurately transferred to the carbon material obtaining high surface areas (up to 1300 m 2 g -1) and total pore volumes ≥2 cm 3 g -1.

  3. Interface free-energy exponent in the one-dimensional Ising spin glass with long-range interactions in both the droplet and broken replica symmetry regions

    Science.gov (United States)

    Aspelmeier, T.; Wang, Wenlong; Moore, M. A.; Katzgraber, Helmut G.

    2016-08-01

    The one-dimensional Ising spin-glass model with power-law long-range interactions is a useful proxy model for studying spin glasses in higher space dimensions and for finding the dimension at which the spin-glass state changes from having broken replica symmetry to that of droplet behavior. To this end we have calculated the exponent that describes the difference in free energy between periodic and antiperiodic boundary conditions. Numerical work is done to support some of the assumptions made in the calculations and to determine the behavior of the interface free-energy exponent of the power law of the interactions. Our numerical results for the interface free-energy exponent are badly affected by finite-size problems.

  4. The use of 3D laser imaging and a new breast replica cast as a method to optimize autologous breast reconstruction after mastectomy.

    Science.gov (United States)

    Ahcan, Uros; Bracun, Drago; Zivec, Katarina; Pavlic, Rok; Butala, Peter

    2012-04-01

    Aesthetically pleasing and symmetrical breasts are the goal of reconstructive breast surgery. Sometimes, however, multiple procedures are needed to improve a reconstructed breast's symmetry and appearance. In order to avoid additional corrective procedures, we have developed a new method that uses a reverse engineering technique to produce what we call a new breast replica cast (NBRC). The NBRC is a mould of the contralateral healthy breast, designed according to preoperative laser 3D images. During surgery, the mould is used to help shape the new breast. With this method, we are able to achieve breast symmetry in terms of volume, projection, contour, and position on the chest wall more accurately, more quickly, and more safely than before. Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. A brief history of cell labelling

    Energy Technology Data Exchange (ETDEWEB)

    Peters, A.M. [Royal Sussex Country Hospital, Brighton (United Kingdom)

    2005-12-15

    The term cell labelling is usually used in the context of labelled leukocytes for imaging inflammation and labelled platelets for imaging thrombosis. Erythrocyte labelling for in vitro measurements of red cell life span, in vivo measurements of splenic red cell pooling, radionuclide ventriculography and imaging sites of bleeding has developed rather separately and has a different history. Labelled platelets and leukocytes were originally developed for cell kinetic studies. Since the current-day applications of labelled platelets and leukocytes depend on a clear understanding of cell kinetics, these classical studies are important and relevant to the history of cell labelling.

  6. An Optimal Labeling Scheme for Ancestry Queries

    OpenAIRE

    2009-01-01

    An ancestry labeling scheme assigns labels (bit strings) to the nodes of rooted trees such that ancestry queries between any two nodes in a tree can be answered merely by looking at their corresponding labels. The quality of an ancestry labeling scheme is measured by its label size, that is the maximal number of bits in a label of a tree node. In addition to its theoretical appeal, the design of efficient ancestry labeling schemes is motivated by applications in web search engines. For this p...

  7. Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models.

    Science.gov (United States)

    Fan, Hao; Periole, Xavier; Mark, Alan E

    2012-07-01

    The efficiency of using a variant of Hamiltonian replica-exchange molecular dynamics (Chaperone H-replica-exchange molecular dynamics [CH-REMD]) for the refinement of protein structural models generated de novo is investigated. In CH-REMD, the interaction between the protein and its environment, specifically, the electrostatic interaction between the protein and the solvating water, is varied leading to cycles of partial unfolding and refolding mimicking some aspects of folding chaperones. In 10 of the 15 cases examined, the CH-REMD approach sampled structures in which the root-mean-square deviation (RMSD) of secondary structure elements (SSE-RMSD) with respect to the experimental structure was more than 1.0 Å lower than the initial de novo model. In 14 of the 15 cases, the improvement was more than 0.5 Å. The ability of three different statistical potentials to identify near-native conformations was also examined. Little correlation between the SSE-RMSD of the sampled structures with respect to the experimental structure and any of the scoring functions tested was found. The most effective scoring function tested was the DFIRE potential. Using the DFIRE potential, the SSE-RMSD of the best scoring structures was on average 0.3 Å lower than the initial model. Overall the work demonstrates that targeted enhanced-sampling techniques such as CH-REMD can lead to the systematic refinement of protein structural models generated de novo but that improved potentials for the identification of near-native structures are still needed.

  8. Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution

    Institute of Scientific and Technical Information of China (English)

    Zanxia Cao; Lei Liu; Ping Wu; Jihua Wang

    2011-01-01

    The structural and thermodynamics characters of α-syn12 (residues 1-12 of the human α-synuclein protein) peptide in aqueous solution were investigated through temperature replica-exchange molecular dynamics (T-REMD) simulations with the GROMOS 43A1 force field. The two independent T-REMD simulations were completed starting from an initial conformational α-helix and an irregular structure,respectively. Each replica was run for 300ns. The structural and thermodynamics characters were studied based on parameters such as distributions of backbone dihedral angles, free energy surface, stability of folded β-hairpin structure, and favorite conformations. The results showed that the isolated α-syn12 peptide in water adopted four different conformational states: the first state was a β-hairpin ensemble with Turno-6 and four hydrogen bonds, the second state was a β-hairpin ensemble with two turns (Turn9-6 and Turn5-2) and three hydrogen bonds, the third state was a disordered structure with both Turn8-5 and Turn5-2, and the last state was a π-helix ensemble. Meanwhile, we studied the free energy change of α-syn12 peptide from the unfolded state to the β-hairpin state, which was in good agreement with the experiments and molecular dynamics simulations for some other peptides. We also analyzed the driving force of the peptide transition.The results indicated that the driving forces were high solvent exposure of hydrophobic Leu8 and hydrophobic residues in secondary structure. To our knowledge, this was the first report to study the isolated α-syn12 peptide in water by T-REMD.

  9. Photoaffinity Labeling of Plasma Proteins

    Directory of Open Access Journals (Sweden)

    Masaki Otagiri

    2013-11-01

    Full Text Available Photoaffinity labeling is a powerful technique for identifying a target protein. A high degree of labeling specificity can be achieved with this method in comparison to chemical labeling. Human serum albumin (HSA and α1-acid glycoprotein (AGP are two plasma proteins that bind a variety of endogenous and exogenous substances. The ligand binding mechanism of these two proteins is complex. Fatty acids, which are known to be transported in plasma by HSA, cause conformational changes and participate in allosteric ligand binding to HSA. HSA undergoes an N-B transition, a conformational change at alkaline pH, that has been reported to result in increased ligand binding. Attempts have been made to investigate the impact of fatty acids and the N-B transition on ligand binding in HSA using ketoprofen and flunitrazepam as photolabeling agents. Meanwhile, plasma AGP is a mixture of genetic variants of the protein. The photolabeling of AGP with flunitrazepam has been utilized to shed light on the topology of the protein ligand binding site. Furthermore, a review of photoaffinity labeling performed on other major plasma proteins will also be discussed. Using a photoreactive natural ligand as a photolabeling agent to identify target protein in the plasma would reduce non-specific labeling.

  10. 49 CFR 172.430 - POISON label.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false POISON label. 172.430 Section 172.430... SECURITY PLANS Labeling § 172.430 POISON label. (a) Except for size and color, the POISON label must be as follows: EC02MR91.029 (b) In addition to complying with § 172.407, the background on the POISON label...

  11. 基于小世界的物联网中副本定位算法%Replica Location Algorithm Approach Based on the Small World in the Internet of Things

    Institute of Scientific and Technical Information of China (English)

    高辉; 张冬悦; 赵俊涛; 吴吉红

    2012-01-01

    Internet of Things has a large amount of data,heterogeneous node,extensive distribution,etc.Replica can improve data access performance.According to the requirements of fast and efficient replica location for the Internet of things,a replica location method based on the class of small world-the class level and the domain level in the Internet of Things is presented.From the local clustering of data access in the Internet of Things,nodes are divided into the class level and domain level.Given the class-domain data access characteristics,two-way circular message diffusion mechanism to achieve replica of the local and global location is proposed to increase the replica location efficiency.%物联网具有数据量大,节点异构且分布广泛等特点。采用副本存储可以提高数据访问性能。针对物联网中对副本定位快速高效要求的问题,提出一种基于小世界的类-域层次的物联网中副本定位方法。从物联网中数据访问的局部聚类性考虑,将节点划分为类层次和域层次,分别采用根据类-域数据访问特点的双向环形消息扩散机制,实现副本的局部和全局定位,从而提高副本定位的效率。

  12. Fibrinogen labelling with I-131

    Energy Technology Data Exchange (ETDEWEB)

    Seminario, C.; Capillo, T.; Montanez, J. (Instituto Peruano de Energia Nuclear, Lima)

    1983-05-01

    Of the different techniques of labelling liophylized human fibrinogen, the technique of mono-chloride with modified iodine was selected. The labelling of the molecule was performed in alkali media of buffalo glycine in which the solution of stable iodine will react as well as on a later stage will the radioactive isotope. The labelling processes which were undertaken with different activities had an efficiency of over 40%; when purification with resins amberlite was carried through, in none of the cases were the impurities over 5%. Daily controls till the seventh day showed that the average values of radiochemical purity decrease were lower than 1%. The specific activity as well as the concentration of I/sup 131/, the fibrinogen and other characteristics come up to the norms of the pharmacopoeia which are applied.

  13. Learning With Auxiliary Less-Noisy Labels.

    Science.gov (United States)

    Duan, Yunyan; Wu, Ou

    2016-04-06

    Obtaining a sufficient number of accurate labels to form a training set for learning a classifier can be difficult due to the limited access to reliable label resources. Instead, in real-world applications, less-accurate labels, such as labels from nonexpert labelers, are often used. However, learning with less-accurate labels can lead to serious performance deterioration because of the high noise rate. Although several learning methods (e.g., noise-tolerant classifiers) have been advanced to increase classification performance in the presence of label noise, only a few of them take the noise rate into account and utilize both noisy but easily accessible labels and less-noisy labels, a small amount of which can be obtained with an acceptable added time cost and expense. In this brief, we propose a learning method, in which not only noisy labels but also auxiliary less-noisy labels, which are available in a small portion of the training data, are taken into account. Based on a flipping probability noise model and a logistic regression classifier, this method estimates the noise rate parameters, infers ground-truth labels, and learns the classifier simultaneously in a maximum likelihood manner. The proposed method yields three learning algorithms, which correspond to three prior knowledge states regarding the less-noisy labels. The experiments show that the proposed method is tolerant to label noise, and outperforms classifiers that do not explicitly consider the auxiliary less-noisy labels.

  14. 78 FR 66826 - Prior Label Approval System: Generic Label Approval

    Science.gov (United States)

    2013-11-07

    ... product as ``organic'' or containing organic ingredients; (3) claims that are undefined in FSIS... labeling errors resulted from production mistakes, such as packaging the product in the wrong box. More... poultry products inspection regulations to expand the circumstances in which FSIS will generically...

  15. Denture labeling: A new approach

    Directory of Open Access Journals (Sweden)

    Pardeep K Bansal

    2011-01-01

    Full Text Available The need for denture labeling is important for forensic and social reasons in case patients need to be identified individually. The importance of denture marking has long been acknowledged by the dental profession. Over the years, various denture marking systems have been reported in the literature, but none till date fulfills all the prescribed ADA specifications. A simple, easy, inexpensive procedure for marking accurate identification marks on dentures with a lead foil is described here. The label caring the patient information is incorporated in the acrylic resin during the denture processing.

  16. Connected Component Labeling Using Components Neighbors-Scan Labeling Approach

    Directory of Open Access Journals (Sweden)

    Akmal Rakhmadi

    2010-01-01

    Full Text Available Problem statement: Many approaches have been proposed in previous such as the classic sequential connected components labeling algorithm which is relies on two subsequent raster-scans of a binary image. This method produced good performance in terms of accuracy, but because of the implementation of the image processing systems now requires faster process of the computer, the speed of this technique’s process has become an important issue. Approach: A computational approach, called components neighbors-scan labeling algorithm for connected component labeling was presented in this study. This algorithm required scanning through an image only once to label connected components. The algorithm started by scanning from the head of the component’s group, before tracing all the components neighbors by using the main component’s information. This algorithm had desirable characteristics, it is simple while promoted accuracy and low time consuming. By using a table of components, this approach also gave other advantages as the information for the next higher process. Results: The approach had been tested with a collection of binary images. In practically all cases, the technique had successfully given the desired result. Averagely, from the results the algorithm increased the speed around 67.4% from the two times scanning method. Conclusion: Conclusion from the comparison with the previous method, the approach of components neighbors-scan for connected component labeling promoted speed, accuracy and simplicity. The results showed that the approach has a good performance in terms of accuracy, the time consumed and the simplicity of the algorithm.

  17. Food quality labels from the producers’ perspective

    Directory of Open Access Journals (Sweden)

    Šárka Velčovská

    2016-09-01

    Full Text Available The paper deals with analysing the food producer attitudes towards quality labels. The Klasa label, as the most known and the most frequently used food quality label in the Czech Republic, have become the subject of investigation. The aim of the research was to identify the benefits and problems arising from the certification process and the label use. Primary data were collected in online survey based on standardized questionnaire. In census, 86 respondents from the total 218 producers with the Klasa label in the Czech Republic completed the questionnaire. The most of producers (72% have a longer experience with the label, they are using the label for more than four years. The producers’ expectations from the label were fulfilled only partially. A poor state marketing support and missing marketing strategy were identified as general problems of the label. Specific perceived problems are formalities connected with the certification process and certification of poor-quality products. Correlation analysis, t-test and Pearson chi-square test were calculated to discover relations between variables. The results of the study can be beneficial to both, food producers as well as administrator of the label. Identified problems could help them to improve marketing strategy of the label in order to manage the label in effective way and use all benefits arising from the certification. Administrator of the label should make the certification process more effective and transparent, promotion should be focused on the explanation to consumers what the Klasa label guarantees.

  18. Improving the energy labelling scheme

    DEFF Research Database (Denmark)

    Gram-Hanssen, Kirsten; Christensen, Toke Haunstrup

    This report summarises the main results of an EU project on consumer response to energy labels in buildings. This report is mainly directed at Danish policy makers. The main focus is therefore on results that are relevant from a Danish point of view and on how they can be used to further strengthen...

  19. The Labelling Approach to Deviance.

    Science.gov (United States)

    Rains, Prudence M.; Kitsuse, John L.; Duster, Troy; Freidson, Eliot

    2003-01-01

    This reprint of one chapter from the 1975 text, "Issues in the Classification of Children" by Nicholas Hobbs and others, addresses the theoretical, methodological, and empirical issues involved in the "labeling" approach to the sociology of deviance. It examines the social process of classification, the use of classification in social agencies,…

  20. When Diagnostic Labels Mask Trauma

    Science.gov (United States)

    Foltz, Robert; Dang, Sidney; Daniels, Brian; Doyle, Hillary; McFee, Scott; Quisenberry, Carolyn

    2013-01-01

    A growing body of research shows that many seriously troubled children and adolescents are reacting to adverse life experiences. Yet traditional diagnostic labels are based on checklists of surface symptoms. Distracted by disruptive behavior, the common response is to medicate, punish, or exclude rather than respond to needs of youth who have…

  1. Psychological effectiveness of carbon labelling

    Science.gov (United States)

    Beattie, Geoffrey

    2012-04-01

    Despite the decision by supermarket-giant Tesco to delay its plan to add carbon-footprint information onto all of its 70,000 products, carbon labelling, if carefully designed, could yet change consumer behaviour. However, it requires a new type of thinking about consumers and much additional work.

  2. Labelling schemes: From a consumer perspective

    DEFF Research Database (Denmark)

    Juhl, Hans Jørn; Stacey, Julia

    2000-01-01

    . A recent MAPP study has investigated the value consumers attach the Government-controlled labels 'Ø-mærket' and 'Den Blå Lup' and the private supermarket label 'Mesterhakket' when they purchase minced meat. The results reveal four consumer segments that use labelling schemes for food products very....... The remaining consumers, about 55%, trust the institutions guaranteeing the labels and they use the labels as a signal without actually knowing the content of each label. Segment composition will probably change depending on the food group studied. It is therefore recommended that the different consumer types...

  3. Precise localization of the voltage-gated potassium channel subunits Kv3.1b and Kv3.3 revealed in the molecular layer of the rat cerebellar cortex by a pre-embedding immunogold method.

    Science.gov (United States)

    Puente, Nagore; Mendizabal-Zubiaga, Juan; Elezgarai, Izaskun; Reguero, Leire; Buceta, Ianire; Grandes, Pedro

    2010-10-01

    A proper motor activity relies on a correct cerebellar function. The Kv3.1 and Kv3.3 voltage-gated potassium channels are key proteins involved in cerebellar function and dysfunction, as the lack of these causes severe motor deficits. Both channel subunits are coexpressed in granule cells and are rapidly activated at relatively positive potentials to support the generation of fast action potentials. However, the contribution of each subunit to the molecular architecture of the parallel fibers, the granule cell axons, is so far unknown. The goal of this study was to elucidate the relative distribution of Kv3.1b and Kv3.3 in specific compartments of the rat parallel fibers by using a pre-embedding immunocytochemical method for electron microscopy. Numerous Kv3.1b and Kv3.3 silver-intensified gold particles were associated with membranes of parallel fiber synaptic terminals and their intervaricose segments. Kv3.1b was found in about 85% of parallel fiber synaptic terminals and in about 47% of their intervaricose portions. However, only 28% of intervaricosities and 23% of parallel fiber presynaptic boutons were Kv3.3 immunopositive. The analysis also revealed that 54% of Purkinje cell dendritic spines localized Kv3.3. Although both potassium channel subunits share localization in the same presynaptic parallel fiber compartments, the present results with the method used indicate that there are a higher percentage of parallel fibers labeled for Kv3.1b than for Kv3.3, and that the labeling intensity for each subunit is higher in specific subcompartments analyzed than in others.

  4. Ivabradine: A Review of Labeled and Off-Label Uses.

    Science.gov (United States)

    Oliphant, Carrie S; Owens, Ryan E; Bolorunduro, Oluwaseyi B; Jha, Sunil K

    2016-10-01

    Ivabradine is a unique medication recently approved in the USA for the treatment of select heart failure patients. It was first approved for use in several countries around the world over a decade ago as an anti-anginal agent, with subsequent approval for use in heart failure patients. Since ivabradine has selective activity blocking the I f currents in the sinus node, it can reduce heart rate without appreciable effects on blood pressure. Given this heart-rate-specific effect, it has been investigated in many off-label indications as an alternative to traditional heart-rate-reducing medications such as beta blockers and calcium channel blockers. We conducted searches of PubMed and Google Scholar for ivabradine, heart failure, HFrEF, HFpEF, angina, coronary artery disease, inappropriate sinus tachycardia, postural orthostatic hypotension, coronary computed tomography angiography and atrial fibrillation. We reviewed and included studies, case reports, and case series published between 1980 and June 2016 if they provided information relevant to the practicing clinician. In many cases, larger clinical trials are needed to solidify the benefit of ivabradine, although studies indicate benefit in most therapeutic areas explored to date. The purpose of this paper is to review the current labeled and off-label uses of ivabradine, with a focus on clinical trial data.

  5. Statistical Model to Analyze Quantitative Proteomics Data Obtained by 18O/16O Labeling and Linear Ion Trap Mass Spectrometry

    Science.gov (United States)

    Jorge, Inmaculada; Navarro, Pedro; Martínez-Acedo, Pablo; Núñez, Estefanía; Serrano, Horacio; Alfranca, Arántzazu; Redondo, Juan Miguel; Vázquez, Jesús

    2009-01-01

    Statistical models for the analysis of protein expression changes by stable isotope labeling are still poorly developed, particularly for data obtained by 16O/18O labeling. Besides large scale test experiments to validate the null hypothesis are lacking. Although the study of mechanisms underlying biological actions promoted by vascular endothelial growth factor (VEGF) on endothelial cells is of considerable interest, quantitative proteomics studies on this subject are scarce and have been performed after exposing cells to the factor for long periods of time. In this work we present the largest quantitative proteomics study to date on the short term effects of VEGF on human umbilical vein endothelial cells by 18O/16O labeling. Current statistical models based on normality and variance homogeneity were found unsuitable to describe the null hypothesis in a large scale test experiment performed on these cells, producing false expression changes. A random effects model was developed including four different sources of variance at the spectrum-fitting, scan, peptide, and protein levels. With the new model the number of outliers at scan and peptide levels was negligible in three large scale experiments, and only one false protein expression change was observed in the test experiment among more than 1000 proteins. The new model allowed the detection of significant protein expression changes upon VEGF stimulation for 4 and 8 h. The consistency of the changes observed at 4 h was confirmed by a replica at a smaller scale and further validated by Western blot analysis of some proteins. Most of the observed changes have not been described previously and are consistent with a pattern of protein expression that dynamically changes over time following the evolution of the angiogenic response. With this statistical model the 18O labeling approach emerges as a very promising and robust alternative to perform quantitative proteomics studies at a depth of several thousand proteins

  6. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... General Health Growth & Development Infections Diseases & Conditions Pregnancy & ... leer las etiquetas de datos nutricionales (video) Most packaged foods come with a Nutrition Facts label. These labels ...

  7. 99mTc: Labeling Chemistry and Labeled Compounds

    Science.gov (United States)

    Alberto, R.; Abram, U.

    This chapter reviews the radiopharmaceutical chemistry of technetium related to the synthesis of perfusion agents and to the labeling of receptor-binding biomolecules. To understand the limitations of technetium chemistry imposed by future application of the complexes in nuclear medicine, an introductory section analyzes the compulsory requirements to be considered when facing the incentive of introducing a novel radiopharmaceutical into the market. Requirements from chemistry, routine application, and market are discussed. In a subsequent section, commercially available 99mTc-based radiopharmaceuticals are treated. It covers the complexes in use for imaging the most important target organs such as heart, brain, or kidney. The commercially available radiopharmaceuticals fulfill the requirements outlined earlier and are discussed with this background. In a following section, the properties and perspectives of the different generations of radiopharmaceuticals are described in a general way, covering characteristics for perfusion agents and for receptor-specific molecules. Technetium chemistry for the synthesis of perfusion agents and the different labeling approaches for target-specific biomolecules are summarized. The review comprises a general introduction to the common approaches currently in use, employing the N x S4-x , [3+1] and 2-hydrazino-nicotinicacid (HYNIC) method as well as more recent strategies such as the carbonyl and the TcN approach. Direct labeling without the need of a bifunctional chelator is briefly reviewed as well. More particularly, recent developments in the labeling of concrete targeting molecules, the second generation of radiopharmaceuticals, is then discussed and prominent examples with antibodies/peptides, neuroreceptor targeting small molecules, myocardial imaging agents, vitamins, thymidine, and complexes relevant to multidrug resistance are given. In addition, a new approach toward peptide drug development is described. The section

  8. Automatic Labelling of Topics with Neural Embeddings

    OpenAIRE

    Bhatia, Shraey; Lau, Jey Han; Baldwin, Timothy

    2016-01-01

    Topics generated by topic models are typically represented as list of terms. To reduce the cognitive overhead of interpreting these topics for end-users, we propose labelling a topic with a succinct phrase that summarises its theme or idea. Using Wikipedia document titles as label candidates, we compute neural embeddings for documents and words to select the most relevant labels for topics. Compared to a state-of-the-art topic labelling system, our methodology is simpler, more efficient, and ...

  9. SOME ECONOMIC IMPLICATIONS OF PUBLIC LABELING

    OpenAIRE

    2003-01-01

    This article discusses economic issues related to public labeling. The main contributions in both the empirical and theoretical literatures are presented in order to motivate responses to the questions, when should a regulator promote public labeling, and what are the limits to and the possible market distortions from public labeling? Although the issues are complicated, there is already much economic guidance that can be given to inform the policy debate over food labeling.

  10. ANTIMAGIC LABELING OF GENERALIZED SAUSAGE GRAPHS

    Directory of Open Access Journals (Sweden)

    Oudone Phanalasy

    2014-10-01

    Full Text Available An antimagic labeling of a graph with q edges is a bijection from the set of edges to the set of positive integers {1,2,...,q} such that all vertex weights are pairwise distinct, where the vertex weight of a vertex is the sum of the labels of all the edges incident with that vertex. A graph is antimagic if it has an antimagic labeling. In this paper we construct antimagic labeling for the family of generalized sausage graphs.

  11. White Label Space GLXP Mission

    Science.gov (United States)

    Barton, A.

    2012-09-01

    This poster presents a lunar surface mission concept and corresponding financing approach developed by the White Label Space team, an official competitor in the Google Lunar X PRIZE. The White Label Space team's origins were in the European Space Agency's ESTEC facility in the Netherlands. Accordingly the team's technical headquarters are located just outside ESTEC in the Space Business Park. The team has active partners in Europe, Japan and Australia. The team's goal is to provide a unique publicity opportunity for global brands to land on the moon and win the prestigious Google Lunar X PRIZE. The poster presents the main steps to achieve this goal, the cost estimates for the mission, describes the benefits to the potential sponsors and supporters, and details the progress achieved to date.

  12. Labeling nuclear DNA using DAPI.

    Science.gov (United States)

    Chazotte, Brad

    2011-01-01

    A number of fluorescent stains are available that label DNA and allow easy visualization of the nucleus in interphase cells and chromosomes in mitotic cells, including Hoechst, 4',6-diamidino-2-phenylindole (DAPI), ethidium bromide, propidium iodide, and acridine orange. Although not as bright as the vital Hoechst stains for DNA, DAPI has greater photostability. It is believed that DAPI associates with the minor groove of double-stranded DNA, with a preference for the adenine-thymine clusters. Cells must be permeabilized and/or fixed for DAPI to enter the cell and to bind DNA. Fluorescence increases approximately 20-fold when DAPI is bound to double-stranded DNA. This protocol describes the use of DAPI to label nuclear DNA of cells grown in culture.

  13. Tissue Specific Labeling in Proteomics

    Directory of Open Access Journals (Sweden)

    Evelyn Ramberger

    2017-07-01

    Full Text Available Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed. These tools facilitate the selective labeling of proteins, their interactome, or of specific cell types within a tissue or an organism, while avoiding the difficult and contamination-prone biochemical separation of cells from the tissue. In this review, we give an overview of existing techniques and their application in cell culture models and whole animals.

  14. POS Tagging Using Relaxation Labelling

    CERN Document Server

    Padro, L

    1995-01-01

    Relaxation labelling is an optimization technique used in many fields to solve constraint satisfaction problems. The algorithm finds a combination of values for a set of variables such that satisfies -to the maximum possible degree- a set of given constraints. This paper describes some experiments performed applying it to POS tagging, and the results obtained. It also ponders the possibility of applying it to word sense disambiguation.

  15. 16 CFR 1209.9 - Labeling requirement.

    Science.gov (United States)

    2010-01-01

    ... SAFETY STANDARD FOR CELLULOSE INSULATION The Standard § 1209.9 Labeling requirement. (a) Manufacturers, importers, and private labelers of cellulose insulation shall place on all containers of cellulose... corrosiveness of cellulose insulation. To meet this requirement manufacturers, importers, and private labelers...

  16. Politique de label et commerce international

    OpenAIRE

    2001-01-01

    This article investigates the effects of a public labelling system in a context of international trade. A simple framework allows to present some distortions linked to such a policy. A trade liberalisation situation may lead to a change in the label policy, where the foreign seller incurs the label cost. Classification JEL : F1, D8

  17. What determines consumer attention to nutrition labels?

    NARCIS (Netherlands)

    Bialkova, S.E.; Trijp, van J.C.M.

    2010-01-01

    To identify the key determinants of consumer attention to nutrition labels, visual search tasks (present – absent; one – two targets) were used as an effective experimental tool. The main manipulation concerned: set size (number of labels on front of pack); label characteristics (display size, posit

  18. DYNAMIC LABELING BASED FPGA DELAY OPTIMIZATION ALGORITHM

    Institute of Scientific and Technical Information of China (English)

    吕宗伟; 林争辉; 张镭

    2001-01-01

    DAG-MAP is an FPGA technology mapping algorithm for delay optimization and the labeling phase is the algorithm's kernel. This paper studied the labeling phase and presented an improved labeling method. It is shown through the experimental results on MCNC benchmarks that the improved method is more effective than the original method while the computation time is almost the same.

  19. Fluorescent Labeling of Nanometer Hydroxyapatite

    Institute of Scientific and Technical Information of China (English)

    Yuan ZHANG; Yuan YUAN; Changsheng LIU

    2008-01-01

    A novel surface treatment method using 3-aminopropyltriethoxysilane (AMPTES), was developed to immobilize the fluorescein molecule on nano-HAP (nanometer hydroxyapatite) powders. By pretreating the nano-HAP powders surface with AMPTES, fluorescein, chosen on the basis of the chemical structure of the nano- HAP powders, could be bound to the nano-HAP powders surface. The chemical compositions of nano-HAP before and after being labeled were characterized by Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). The morphology, phase composition, and the fluorescence characteristics of the nano-HAP powders with and without staining were also investigated. The FTIR and XPS results revealed that fiuorescein had been successfully immobilized on the surface of AMPTES-bound nano-HAP powders via the acylamide bond formation between the -COOH of fluorescein and the -NH2 of AMPTES. The labeled nano-HAP powders possessed strong fluorescent intensity with a little deviation from the maximum emission wavelength of fluorescein. But the morphology and phase composition had no obvious alteration. Under fluorescence microscopy, the labeled nano-HAP powders., even after 24 h cell incubation, exhibited strong fluorescence.

  20. Nutrition marketing on food labels.

    Science.gov (United States)

    Colby, Sarah E; Johnson, LuAnn; Scheett, Angela; Hoverson, Bonita

    2010-01-01

    This research sought to determine how often nutrition marketing is used on labels of foods that are high in saturated fat, sodium, and/or sugar. All items packaged with food labels (N = 56,900) in all 6 grocery stores in Grand Forks, ND were surveyed. Marketing strategy, nutrient label information, if the product was fruit/or milk based, and target age. Frequency distributions were computed. Forty-nine percent of all products contained nutrition marketing and of those, 48% had both nutrition marketing and were high in saturated fat, sodium and/or sugar (11%, 17%, and 31% respectively). Seventy-one percent of products marketed to children had nutrition marketing. Of those, 59% were high in saturated fat, sodium and/or sugar content, with more than half being high in sugar. The most commonly used nutrition marketing statements were "good source of calcium", "reduced/low/fat free", and "food company's health symbol". Nutrition marketing is commonly used on products high in saturated fat, sodium and/or sugar and is more often used on products marketed toward children than products marketed toward adults. Current food industry symbols may not be helping consumers select foods low in saturated fat, sodium or sugar. Published by Elsevier Inc.

  1. Measurements of π{sup ±} differential yields from the surface of the T2K replica target for incoming 31 GeV/c protons with the NA61/SHINE spectrometer at the CERN SPS

    Energy Technology Data Exchange (ETDEWEB)

    Abgrall, N.; Ajaz, M.; Blondel, A.; Bravar, A.; Debieux, S.; Haesler, A.; Korzenev, A.; Ravonel, M. [University of Geneva, Geneva (Switzerland); Aduszkiewicz, A.; Dominik, W.; Kuich, M.; Matulewicz, T.; Posiadala-Zezula, M. [University of Warsaw, Warsaw (Poland); Ali, Y. [Jagiellonian University, Cracow (Poland); COMSATS Institute of Information Technology, Department of Physics, Islamabad (Pakistan); Andronov, E.; Feofilov, G.A.; Igolkin, S.; Kondratiev, V.P.; Seryakov, A.; Vechernin, V.V.; Vinogradov, L. [St. Petersburg State University, Saint Petersburg (Russian Federation); Anticic, T.; Kadija, K.; Susa, T. [Ruder Boskovic Institute, Zagreb (Croatia); Antoniou, N.; Christakoglou, P.; Davis, N.; Diakonos, F.; Kapoyannis, A.; Panagiotou, A.D.; Vassiliou, M. [University of Athens, Athens (Greece); Baatar, B.; Bunyatov, S.A.; Kolesnikov, V.I.; Krasnoperov, A.; Lyubushkin, V.V.; Malakhov, A.I.; Matveev, V.; Melkumov, G.L.; Tereshchenko, V. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Bay, F.; Di Luise, S.; Rubbia, A.; Sgalaberna, D. [ETH Zuerich, Zuerich (Switzerland); Bluemer, J.; Dembinski, H.; Engel, R.; Herve, A.E.; Mathes, H.J.; Roth, M.; Szuba, M.; Ulrich, R.; Unger, M.; Veberic, D. [Karlsruhe Institute of Technology, Karlsruhe (Germany); Bogomilov, M.; Kolev, D.; Tsenov, R. [University of Sofia, Faculty of Physics, Sofia (Bulgaria); Brandin, A.; Selyuzhenkov, I.; Taranenko, A. [National Research Nuclear University ' ' MEPhI' ' (Moscow Engineering Physics Institute), Moscow (Russian Federation); Brzychczyk, J.; Larsen, D.; Planeta, R.; Richter-Was, E.; Staszel, P.; Wyszynski, O. [Jagiellonian University, Cracow (Poland); Busygina, O.; Golubeva, M.; Guber, F.; Ivashkin, A.; Kurepin, A.; Sadovsky, A. [Institute for Nuclear Research, Moscow (Russian Federation); Cirkovic, M.; Manic, D.; Puzovic, J. [University of Belgrade, Belgrade (Serbia); Czopowicz, T.; Dynowski, K.; Grebieszkow, K.; Mackowiak-Pawlowska, M.; Maksiak, B.; Sarnecki, R.; Slodkowski, M.; Tefelska, A.; Tefelski, D. [Warsaw University of Technology, Warsaw (Poland); Deveaux, M.; Koziel, M.; Renfordt, R.; Stroebele, H. [University of Frankfurt, Frankfurt (Germany); Dumarchez, J.; Robert, A. [LPNHE, University of Paris VI and VII, Paris (France); Ereditato, A.; Hierholzer, M.; Nirkko, M.; Pistillo, C.; Redij, A. [University of Bern, Bern (Switzerland); Fodor, Z. [Wigner Research Centre for Physics of the Hungarian Academy of Sciences, Budapest (Hungary); University of Wroclaw, Wroclaw (Poland); Garibov, A. [National Nuclear Research Center, Baku (Azerbaijan); Gazdzicki, M. [University of Frankfurt, Frankfurt (Germany); Jan Kochanowski University in Kielce, Kielce (Poland); Grzeszczuk, A.; Kaptur, E.; Kisiel, J.; Kowalski, S.; Pulawski, S.; Schmidt, K.; Wilczek, A. [University of Silesia, Katowice (Poland); Hasegawa, T.; Kobayashi, T.; Nakadaira, T.; Nishikawa, K.; Sakashita, K.; Sekiguchi, T.; Shibata, M.; Tada, M.; Friend, M. [Institute for Particle and Nuclear Studies, Tsukuba (Japan); Johnson, S.R.; Marino, A.D.; Rumberger, B.T.; Zimmerman, E.D. [University of Colorado, Boulder (United States); Kowalik, K.; Rondio, E.; Stepaniak, J. [National Centre for Nuclear Research, Warsaw (Poland); Laszlo, A.; Marton, K.; Vesztergombi, G. [Wigner Research Centre for Physics of the Hungarian Academy of Sciences, Budapest (Hungary); Lewicki, M.; Naskret, M.; Turko, L. [University of Wroclaw, Wroclaw (Poland); Marcinek, A. [Jagiellonian University, Cracow (Poland); University of Wroclaw, Wroclaw (PL); Messerly, B.; Nagai, Y.; Paolone, V. [University of Pittsburgh, Pittsburgh (US); Mills, G.B.; Yarritu, K. [Los Alamos National Laboratory, Los Alamos (US); Morozov, S.; Petukhov, O. [Institute for Nuclear Research, Moscow (RU); National Research Nuclear University ' ' MEPhI' ' (Moscow Engineering Physics Institute), Moscow (RU); Mrowczynski, S.; Rybczynski, M.; Seyboth, P.; Stefanek, G.; Wlodarczyk, Z.; Wojtaszek-Szwarc, A. [Jan Kochanowski University in Kielce, Kielce (PL); Pavin, M. [Ruder Boskovic Institute, Zagreb (HR); LPNHE, University of Paris VI and VII, Paris (FR); Popov, B.A. [LPNHE, University of Paris VI and VII, Paris (FR); Joint Institute for Nuclear Research, Dubna (RU); Rauch, W. [Fachhochschule Frankfurt, Frankfurt (DE); Roehrich, D. [University of Bergen, Bergen (NO); Rustamov, A. [National Nuclear Research Center, Baku (AZ); University of Frankfurt, Frankfurt (DE); Zambelli, L. [LPNHE, University of Paris VI and VII, Paris (FR); Institute for Particle and Nuclear Studies, Tsukuba (JP); Galymov, V. [IPNL, University of Lyon, Villeurbanne (FR); Hartz, M. [Kavli Institute for the Physics and Mathematics of the Universe (WPI), The University of Tokyo Institutes for Advanced Study, University of Tokyo, Kashiwa, Chiba (JP); TRIUMF, Vancouver, BC (CA); Hiraki, T.; Ichikawa, A.; Kubo, H.; Matsuoka, K.; Murakami, A.; Nakaya, T.; Suzuki, K. [Kyoto University, Department of Physics, Kyoto (JP); Tzanov, M. [Louisiana State University, Department of Physics and Astronomy, Baton Rouge, LA (US); Yu, M. [York University, Department of Physics and Astronomy, Toronto, ON (CA); Collaboration: NA61/SHINE Collaboration

    2016-11-15

    Measurements of particle emission from a replica of the T2K 90 cm-long carbon target were performed in the NA61/SHINE experiment at CERN SPS, using data collected during a high-statistics run in 2009. An efficient use of the long-target measurements for neutrino flux predictions in T2K requires dedicated reconstruction and analysis techniques. Fully-corrected differential yields of π{sup ±}-mesons from the surface of the T2K replica target for incoming 31 GeV/c protons are presented. A possible strategy to implement these results into the T2K neutrino beam predictions is discussed and the propagation of the uncertainties of these results to the final neutrino flux is performed. (orig.)

  2. Measurements of charged pion differential yields from the surface of the T2K replica target for incoming 31 GeV/c protons with the NA61/SHINE spectrometer at the CERN SPS

    CERN Document Server

    Abgrall, N; Ajaz, M; Ali, Y; Andronov, E; Anticic, T; Antoniou, N; Baatar, B; Bay, F; Blondel, A; Blümer, J; Bogomilov, M; Brandin, A; Bravar, A; Brzychczyk, J; Bunyatov, S A; Busygina, O; Christakoglou, P; Cirkovic, M; Czopowicz, T; Davis, N; Debieux, S; Dembinski, H; Deveaux, M; Diakonos, F; Di Luise, S; Dominik, W; Dumarchez, J; Dynowski, K; Engel, R; Ereditato, A; Feofilov, G A; Fodor, Z; Garibov, A; Gazdzicki, M; Golubeva, M; Grebieszkow, K; Grzeszczuk, A; Guber, F; Haesler, A; Hasegawa, T; Hervé, A E; Hierholzer, M; Igolkin, S; Ivashkin, A; Johnson, S R; Kadija, K; Kapoyannis, A; Kaptur, E; Kisiel, J; Kobayashi, T; Kolesnikov, V I; Kolev, D; Kondratiev, V P; Korzenev, A; Kowalik, K; Kowalski, S; Koziel, M; Krasnoperov, A; Kuich, M; Kurepin, A; Larsen, D; László, A; Lewicki, M; Lyubushkin, V V; Mackowiak-Pawłowska, M; Maksiak, B; Malakhov, A I; Manic, D; Marcinek, A; Marino, A D; Marton, K; Mathes, H -J; Matulewicz, T; Matveev, V; Melkumov, G L; Messerly, B; Mills, G B; Morozov, S; Mrówczynski, S; Nagai, Y; Nakadaira, T; Naskret, M; Nirkko, M; Nishikawa, K; Panagiotou, A D; Paolone, V; Pavin, M; Petukhov, O; Pistillo, C; Płaneta, R; Popov, B A; Posiadała-Zezula, M; Puławski, S; Puzovic, J; Rauch, W; Ravonel, M; Redij, A; Renfordt, R; Richter-Was, E; Robert, A; Röhrich, D; Rondio, E; Roth, M; Rubbia, A; Rumberger, B T; Rustamov, A; Rybczynski, M; Sadovsky, A; Sakashita, K; Sarnecki, R; Schmidt, K; Sekiguchi, T; Selyuzhenkov, I; Seryakov, A; Seyboth, P; Sgalaberna, D; Shibata, M; Słodkowski, M; Staszel, P; Stefanek, G; Stepaniak, J; Ströbele, H; Šuša, T; Szuba, M; Tada, M; Taranenko, A; Tefelska, A; Tefelski, D; Tereshchenko, V; Tsenov, R; Turko, L; Ulrich, R; Unger, M; Vassiliou, M; Veberic, D; Vechernin, V V; Vesztergombi, G; Vinogradov, L; Wilczek, A; Włodarczyk, Z; Wojtaszek-Szwarc, A; Wyszynski, O; Yarritu, K; Zambelli, L; Zimmerman, E D; Friend, M; Galymov, V; Hartz, M; Hiraki, T; Ichikawa, A; Kubo, H; Matsuoka, K; Murakami, A; Nakaya, T; Suzuki, K; Tzanov, M; Yu, M

    2016-01-01

    Measurements of particle emission from a replica of the T2K 90 cm-long carbon target were performed in the NA61/SHINE experiment at CERN SPS, using data collected during a high-statistics run in 2009. An efficient use of the long-target measurements for neutrino flux predictions in T2K requires dedicated reconstruction and analysis techniques. Fully-corrected differential yields of charged pions from the surface of the T2K replica target for incoming 31 GeV/c protons are presented. A possible strategy to implement these results into the T2K neutrino beam predictions is discussed and the propagation of the uncertainties of these results to the final neutrino flux is performed

  3. Measurements of π ^± differential yields from the surface of the T2K replica target for incoming 31 GeV/ c protons with the NA61/SHINE spectrometer at the CERN SPS

    Science.gov (United States)

    Abgrall, N.; Aduszkiewicz, A.; Ajaz, M.; Ali, Y.; Andronov, E.; Antićić, T.; Antoniou, N.; Baatar, B.; Bay, F.; Blondel, A.; Blümer, J.; Bogomilov, M.; Brandin, A.; Bravar, A.; Brzychczyk, J.; Bunyatov, S. A.; Busygina, O.; Christakoglou, P.; Ćirković, M.; Czopowicz, T.; Davis, N.; Debieux, S.; Dembinski, H.; Deveaux, M.; Diakonos, F.; Di Luise, S.; Dominik, W.; Dumarchez, J.; Dynowski, K.; Engel, R.; Ereditato, A.; Feofilov, G. A.; Fodor, Z.; Garibov, A.; Gaździcki, M.; Golubeva, M.; Grebieszkow, K.; Grzeszczuk, A.; Guber, F.; Haesler, A.; Hasegawa, T.; Hervé, A. E.; Hierholzer, M.; Igolkin, S.; Ivashkin, A.; Johnson, S. R.; Kadija, K.; Kapoyannis, A.; Kaptur, E.; Kisiel, J.; Kobayashi, T.; Kolesnikov, V. I.; Kolev, D.; Kondratiev, V. P.; Korzenev, A.; Kowalik, K.; Kowalski, S.; Koziel, M.; Krasnoperov, A.; Kuich, M.; Kurepin, A.; Larsen, D.; László, A.; Lewicki, M.; Lyubushkin, V. V.; Maćkowiak-Pawłowska, M.; Maksiak, B.; Malakhov, A. I.; Manić, D.; Marcinek, A.; Marino, A. D.; Marton, K.; Mathes, H.-J.; Matulewicz, T.; Matveev, V.; Melkumov, G. L.; Messerly, B.; Mills, G. B.; Morozov, S.; Mrówczyński, S.; Nagai, Y.; Nakadaira, T.; Naskręt, M.; Nirkko, M.; Nishikawa, K.; Panagiotou, A. D.; Paolone, V.; Pavin, M.; Petukhov, O.; Pistillo, C.; Płaneta, R.; Popov, B. A.; Posiadała-Zezula, M.; Puławski, S.; Puzović, J.; Rauch, W.; Ravonel, M.; Redij, A.; Renfordt, R.; Richter-Wąs, E.; Robert, A.; Röhrich, D.; Rondio, E.; Roth, M.; Rubbia, A.; Rumberger, B. T.; Rustamov, A.; Rybczynski, M.; Sadovsky, A.; Sakashita, K.; Sarnecki, R.; Schmidt, K.; Sekiguchi, T.; Selyuzhenkov, I.; Seryakov, A.; Seyboth, P.; Sgalaberna, D.; Shibata, M.; Słodkowski, M.; Staszel, P.; Stefanek, G.; Stepaniak, J.; Ströbele, H.; Šuša, T.; Szuba, M.; Tada, M.; Taranenko, A.; Tefelska, A.; Tefelski, D.; Tereshchenko, V.; Tsenov, R.; Turko, L.; Ulrich, R.; Unger, M.; Vassiliou, M.; Veberič, D.; Vechernin, V. V.; Vesztergombi, G.; Vinogradov, L.; Wilczek, A.; Włodarczyk, Z.; Wojtaszek-Szwarc, A.; Wyszyński, O.; Yarritu, K.; Zambelli, L.; Zimmerman, E. D.; Friend, M.; Galymov, V.; Hartz, M.; Hiraki, T.; Ichikawa, A.; Kubo, H.; Matsuoka, K.; Murakami, A.; Nakaya, T.; Suzuki, K.; Tzanov, M.; Yu, M.

    2016-11-01

    Measurements of particle emission from a replica of the T2K 90 cm-long carbon target were performed in the NA61/SHINE experiment at CERN SPS, using data collected during a high-statistics run in 2009. An efficient use of the long-target measurements for neutrino flux predictions in T2K requires dedicated reconstruction and analysis techniques. Fully-corrected differential yields of π ^± -mesons from the surface of the T2K replica target for incoming 31 GeV/ c protons are presented. A possible strategy to implement these results into the T2K neutrino beam predictions is discussed and the propagation of the uncertainties of these results to the final neutrino flux is performed.

  4. 78 FR 24211 - Draft Guidance for Industry on Safety Considerations for Container Labels and Carton Labeling...

    Science.gov (United States)

    2013-04-24

    ... Container Labels and Carton Labeling Design To Minimize Medication Errors; Availability AGENCY: Food and... the availability of a draft guidance for industry entitled ``Safety Considerations for Container... aspects of the container label and carton labeling design for prescription drug and biological...

  5. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus.

    Science.gov (United States)

    Rubio, María E; Fukazawa, Yugo; Kamasawa, Naomi; Clarkson, Cheryl; Molnár, Elek; Shigemoto, Ryuichi

    2014-12-15

    We examined the synaptic structure, quantity, and distribution of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)- and N-methyl-D-aspartate (NMDA)-type glutamate receptors (AMPARs and NMDARs, respectively) in rat cochlear nuclei by a highly sensitive freeze-fracture replica labeling technique. Four excitatory synapses formed by two distinct inputs, auditory nerve (AN) and parallel fibers (PF), on different cell types were analyzed. These excitatory synapse types included AN synapses on bushy cells (AN-BC synapses) and fusiform cells (AN-FC synapses) and PF synapses on FC (PF-FC synapses) and cartwheel cell spines (PF-CwC synapses). Immunogold labeling revealed differences in synaptic structure as well as AMPAR and NMDAR number and/or density in both AN and PF synapses, indicating a target-dependent organization. The immunogold receptor labeling also identified differences in the synaptic organization of FCs based on AN or PF connections, indicating an input-dependent organization in FCs. Among the four excitatory synapse types, the AN-BC synapses were the smallest and had the most densely packed intramembrane particles (IMPs), whereas the PF-CwC synapses were the largest and had sparsely packed IMPs. All four synapse types showed positive correlations between the IMP-cluster area and the AMPAR number, indicating a common intrasynapse-type relationship for glutamatergic synapses. Immunogold particles for AMPARs were distributed over the entire area of individual AN synapses; PF synapses often showed synaptic areas devoid of labeling. The gold-labeling for NMDARs occurred in a mosaic fashion, with less positive correlations between the IMP-cluster area and the NMDAR number. Our observations reveal target- and input-dependent features in the structure, number, and organization of AMPARs and NMDARs in AN and PF synapses. © 2014 Wiley Periodicals, Inc.

  6. Stigma of a label: educational expectations for high school students labeled with learning disabilities.

    Science.gov (United States)

    Shifrer, Dara

    2013-01-01

    Poorer outcomes for youth labeled with learning disabilities (LDs) are often attributed to the student's own deficiencies or cumulative disadvantage; but the more troubling possibility is that special education placement limits rather than expands these students' opportunities. Labeling theory partially attributes the poorer outcomes of labeled persons to stigma related to labels. This study uses data on approximately 11,740 adolescents and their schools from the Education Longitudinal Survey of 2002 to determine if stigma influences teachers' and parents' educational expectations for students labeled with LDs and labeled adolescents' expectations for themselves. Supporting the predictions of labeling theory, teachers and parents are more likely to perceive disabilities in, and hold lower educational expectations for labeled adolescents than for similarly achieving and behaving adolescents not labeled with disabilities. The negative effect of being labeled with LDs on adolescents' educational expectations is partially mechanized through parents' and particularly teachers' lower expectations.

  7. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Tong Zhang

    Full Text Available Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III Hexamine ions or Mg(2+ ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III Hexamine ions were found to bind stronger with the loop than Mg(2+ ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III Hexamine ions on CorA ions transportation.

  8. Structure, dynamics, and function of the hammerhead ribozyme in bulk water and at a clay mineral surface from replica exchange molecular dynamics.

    Science.gov (United States)

    Swadling, Jacob B; Wright, David W; Suter, James L; Coveney, Peter V

    2015-03-01

    Compared with proteins, the relationship between structure, dynamics, and function of RNA enzymes (known as ribozymes) is far less well understood, despite the fact that ribozymes are found in many organisms and are often conceived as "molecular fossils" of the first self-replicating molecules to have arisen on Earth. To investigate how ribozymal function is governed by structure and dynamics, we study the full hammerhead ribozyme in bulk water and in an aqueous clay mineral environment by computer simulation using replica-exchange molecular dynamics. Through extensive sampling of the major conformational states of the hammerhead ribozyme, we are able to show that the hammerhead manifests a free-energy landscape reminiscent of that which is well known in proteins, exhibiting a "funnel" topology that guides the ribozyme into its globally most stable conformation. The active-site geometry is found to be closely correlated to the tertiary structure of the ribozyme, thereby reconciling conflicts between previously proposed mechanisms for the self-scission of the hammerhead. The conformational analysis also accounts for the differences reported experimentally in the catalytic activity of the hammerhead ribozyme, which is reduced when interacting with clay minerals as compared with bulk water.

  9. Effect of cross sectional geometry on PDMS micro peristaltic pump performance: comparison of SU-8 replica molding vs. micro injection molding.

    Science.gov (United States)

    Graf, Neil J; Bowser, Michael T

    2013-10-07

    Two different fabrication methods were employed to fabricate micropumps with different cross-sectional channel geometries. The first was to fabricate rectangular cross-sectional microchannel geometries using the well known fabrication method of replica molding (REM). The second, and far less utilized fabrication technique, was to create microchannel molds using an in-house fabricated handheld micro injection molding apparatus. The injection mold apparatus was designed for use with elastomeric room temperature vulcanization (RTV) polymers, as opposed to most other injection molding machines, which are designed for use with thermoplastic polymers. The injection mold's bottom plate was used as a microchannel molding template. The molding template was created by threading a small-diameter wire (150 μm or less) through the injection mold's bottom plate, with subsequent adhesion and smoothing of a thin piece of aluminum foil over the wire-raised injection mold template. When molded against, the template produced a rounded/Gaussian-shaped PDMS microchannel. The design of the injection mold will be presented, along with a direct comparison for micropump performance metrics such as flow rate, valving characteristics, and maximum backpressures attainable for each of the respective micropump channel geometries.

  10. Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

    Science.gov (United States)

    De Simone, Alfonso; Derreumaux, Philippe

    2010-04-01

    The self-assembly of proteins and peptides into amyloid fibrils is connected to over 40 pathological conditions including neurodegenerative diseases and systemic amyloidosis. Diffusible, low molecular weight protein and peptide oligomers that form in the early steps of aggregation appear to be the harmful cytotoxic species in the molecular etiology of these diseases. So far, the structural characterization of these oligomers has remained elusive owing to their transient and dynamic features. We here address, by means of full atomistic replica exchange molecular dynamics simulations, the energy landscape of heptamers of the amyloidogenic peptide NHVTLSQ from the beta-2 microglobulin protein. The simulations totaling 5 μs show that low molecular weight oligomers in explicit solvent consist of β-barrels in equilibrium with amorphous states and fibril-like assemblies. The results, also accounting for the influence of the pH on the conformational properties, provide a strong evidence of the formation of transient β-barrel assemblies in the early aggregation steps of amyloid-forming systems. Our findings are discussed in terms of oligomers cytotoxicity.

  11. Folding Thermodynamics and Mechanism of Five Trp-Cage Variants from Replica-Exchange MD Simulations with RSFF2 Force Field.

    Science.gov (United States)

    Zhou, Chen-Yang; Jiang, Fan; Wu, Yun-Dong

    2015-11-10

    To test whether our recently developed residue-specific force field RSFF2 can reproduce the mutational effect on the thermal stability of Trp-cage mini-protein and decipher its detailed folding mechanism, we carried out long-time replica-exchange molecular dynamics (REMD) simulations on five Trp-cage variants, including TC5b and TC10b. Initiated from their unfolded structures, the simulations not only well-reproduce their experimental structures but also their melting temperatures and folding enthalpies reasonably well. For each Trp-cage variant, the overall folding free energy landscape is apparently two-state, but some intermediate states can be observed when projected on more detailed coordinates. We also found different variants have the same major folding pathway, including the well formed PII-helix in the unfolded state, the formation of W6-P12/P18/P19 contacts and the α-helix before the transition state, the following formation of most native contacts, and the final native loop formation. The folding mechanism derived here is consistent with many previous simulations and experiments.

  12. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    Science.gov (United States)

    Zhang, Tong; Mu, Yuguang

    2012-01-01

    Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg(2+) ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg(2+) ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+) ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation.

  13. Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods.

    Science.gov (United States)

    Gai, Lili; Vogel, Thomas; Maerzke, Katie A; Iacovella, Christopher R; Landau, David P; Cummings, Peter T; McCabe, Clare

    2013-08-07

    Two different techniques - replica-exchange Wang-Landau (REWL) and statistical temperature molecular dynamics (STMD) - were applied to systematically study the phase transition behavior of self-assembling lipids as a function of temperature using an off-lattice lipid model. Both methods allow the direct calculation of the density of states with improved efficiency compared to the original Wang-Landau method. A 3-segment model of amphiphilic lipids solvated in water has been studied with varied particle interaction energies (ε) and lipid concentrations. The phase behavior of the lipid molecules with respect to bilayer formation has been characterized through the calculation of the heat capacity as a function of temperature, in addition to various order parameters and general visual inspection. The simulations conducted by both methods can go to very low temperatures with the whole system exhibiting well-ordered structures. With optimized parameters, several bilayer phases are observed within the temperature range studied, including gel phase bilayers with frozen water, mixed water (i.e., frozen and liquid water), and liquid water, and a more fluid bilayer with liquid water. The results obtained from both methods, STMD and REWL, are consistently in excellent agreement with each other, thereby validating both the methods and the results.

  14. Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods

    Science.gov (United States)

    Gai, Lili; Vogel, Thomas; Maerzke, Katie A.; Iacovella, Christopher R.; Landau, David P.; Cummings, Peter T.; McCabe, Clare

    2013-08-01

    Two different techniques - replica-exchange Wang-Landau (REWL) and statistical temperature molecular dynamics (STMD) - were applied to systematically study the phase transition behavior of self-assembling lipids as a function of temperature using an off-lattice lipid model. Both methods allow the direct calculation of the density of states with improved efficiency compared to the original Wang-Landau method. A 3-segment model of amphiphilic lipids solvated in water has been studied with varied particle interaction energies (ɛ) and lipid concentrations. The phase behavior of the lipid molecules with respect to bilayer formation has been characterized through the calculation of the heat capacity as a function of temperature, in addition to various order parameters and general visual inspection. The simulations conducted by both methods can go to very low temperatures with the whole system exhibiting well-ordered structures. With optimized parameters, several bilayer phases are observed within the temperature range studied, including gel phase bilayers with frozen water, mixed water (i.e., frozen and liquid water), and liquid water, and a more fluid bilayer with liquid water. The results obtained from both methods, STMD and REWL, are consistently in excellent agreement with each other, thereby validating both the methods and the results.

  15. An Optimal Labeling Scheme for Ancestry Queries

    CERN Document Server

    Fraigniaud, Pierre

    2009-01-01

    An ancestry labeling scheme assigns labels (bit strings) to the nodes of rooted trees such that ancestry queries between any two nodes in a tree can be answered merely by looking at their corresponding labels. The quality of an ancestry labeling scheme is measured by its label size, that is the maximal number of bits in a label of a tree node. In addition to its theoretical appeal, the design of efficient ancestry labeling schemes is motivated by applications in web search engines. For this purpose, even small improvements in the label size are important. In fact, the literature about this topic is interested in the exact label size rather than just its order of magnitude. As a result, following the proposal of a simple interval-based ancestry scheme with label size $2\\log_2 n$ bits (Kannan et al., STOC '88), a considerable amount of work was devoted to improve the bound on the size of a label. The current state of the art upper bound is $\\log_2 n + O(\\sqrt{\\log n})$ bits (Abiteboul et al., SODA '02) which is...

  16. Eye tracking and nutrition label use

    DEFF Research Database (Denmark)

    Graham, Dan J.; Orquin, Jacob Lund; Visschers, Vivianne H.M.

    2012-01-01

    Nutrition labels on food packages are among the most prominent and far-reaching policy measures related to diet and have the capacity to promote healthy eating. Unfortunately, certain nutrition label characteristics may impede consumer detection and comprehension of labels. Research using precise...... cameras monitoring consumer visual attention (i.e., eye tracking) has begun to identify ways in which label design could be modified to improve consumers’ ability to locate and effectively utilize nutrition information. The present paper reviews all published studies of nutrition label use that have...... utilized eye tracking methodology, identifies directions for further research in this growing field, and makes research-based recommendations for ways in which labels could be modified to improve consumers’ ability to use nutrition labels to select healthful foods....

  17. Hemoglobin Labeled by Radioactive Lysine

    Science.gov (United States)

    Bale, W. F.; Yuile, C. L.; DeLaVergne, L.; Miller, L. L.; Whipple, G. H.

    1949-12-08

    This paper reports on the utilization of tagged epsilon carbon of DL-lysine by a dog both anemic and hypoproteinemic due to repeated bleeding plus a diet low in protein. The experiment extended over period of 234 days, a time sufficient to indicate an erythrocyte life span of at least 115 days based upon the rate of replacement of labeled red cell proteins. The proteins of broken down red cells seem not to be used with any great preference for the synthesis of new hemoglobin.

  18. Chemical kin label in seabirds

    Science.gov (United States)

    Célérier, Aurélie; Bon, Cécile; Malapert, Aurore; Palmas, Pauline; Bonadonna, Francesco

    2011-01-01

    Chemical signals yield critical socio-ecological information in many animals, such as species, identity, social status or sex, but have been poorly investigated in birds. Recent results showed that chemical signals are used to recognize their nest and partner by some petrel seabirds whose olfactory anatomy is well developed and which possess a life-history propitious to olfactory-mediated behaviours. Here, we investigate whether blue petrels (Halobaena caerulea) produce some chemical labels potentially involved in kin recognition and inbreeding avoidance. To overcome methodological constraints of chemical analysis and field behavioural experiments, we used an indirect behavioural approach, based on mice olfactory abilities in discriminating odours. We showed that mice (i) can detect odour differences between individual petrels, (ii) perceive a high odour similarity between a chick and its parents, and (iii) perceive this similarity only before fledging but not during the nestling developmental stage. Our results confirm the existence of an individual olfactory signature in blue petrels and show for the first time, to our knowledge, that birds may exhibit an olfactory kin label, which may have strong implications for inbreeding avoidance. PMID:21525047

  19. Link Label Prediction in Signed Citation Network

    KAUST Repository

    Akujuobi, Uchenna

    2016-04-12

    Link label prediction is the problem of predicting the missing labels or signs of all the unlabeled edges in a network. For signed networks, these labels can either be positive or negative. In recent years, different algorithms have been proposed such as using regression, trust propagation and matrix factorization. These approaches have tried to solve the problem of link label prediction by using ideas from social theories, where most of them predict a single missing label given that labels of other edges are known. However, in most real-world social graphs, the number of labeled edges is usually less than that of unlabeled edges. Therefore, predicting a single edge label at a time would require multiple runs and is more computationally demanding. In this thesis, we look at link label prediction problem on a signed citation network with missing edge labels. Our citation network consists of papers from three major machine learning and data mining conferences together with their references, and edges showing the relationship between them. An edge in our network is labeled either positive (dataset relevant) if the reference is based on the dataset used in the paper or negative otherwise. We present three approaches to predict the missing labels. The first approach converts the label prediction problem into a standard classification problem. We then, generate a set of features for each edge and then adopt Support Vector Machines in solving the classification problem. For the second approach, we formalize the graph such that the edges are represented as nodes with links showing similarities between them. We then adopt a label propagation method to propagate the labels on known nodes to those with unknown labels. In the third approach, we adopt a PageRank approach where we rank the nodes according to the number of incoming positive and negative edges, after which we set a threshold. Based on the ranks, we can infer an edge would be positive if it goes a node above the

  20. Effect of the disulfide bond on the monomeric structure of human amylin studied by combined Hamiltonian and temperature replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Laghaei, Rozita; Mousseau, Normand; Wei, Guanghong

    2010-05-27

    The human Islet amyloid polypeptide (hIAPP or amylin) is a 37-residue peptide hormone that is normally cosecreted with insulin by the pancreatic beta-cells. In patients with type 2 diabetes, hIAPP deposits as amyloid fibrils in the extracellular spaces of the pancreatic islets. Recent experimental studies show that the intramolecular disulfide bond between Cys2 and Cys7 plays a central role in the process of fibril formation. However, the effect of the disulfide bond on the intrinsic structural properties of monomeric hIAPP is yet to be determined. In this study, we characterize the atomic structure and the thermodynamics of full-length hIAPP in the presence and absence of a disulfide bond using extensive combined Hamiltonian and temperature replica exchange molecular dynamics simulations (HT-REMD) with a coarse grained protein force field. Our simulations show that HT-REMD is more efficient in sampling than temperature REMD. On the basis of a total simulation time of 28 mus, we find that, although native hIAPP (in the presence of a disulfide bond) essentially adopts a disordered conformation in solution, consistent with the signal measured by ultraviolet-circular dichroism (UV-CD) spectroscopy, it also transiently samples alpha-helical structure for residues 5-16. In comparison with the N-terminal region, the C-terminal region is highly disordered and populates a much lesser content of isolated beta-strand conformation for residues 22-26 and 30-35. Moreover, the absence of the disulfide bond greatly decreases the extent of helix formed throughout residues 5-9 in favor of random coil and beta-sheet structure. Implications of the stabilization of N-terminal helical structure by disulfide bond on the initialization of hIAPP amyloid formation are discussed.

  1. Jendl-3.1 iron validation on the PCA-REPLICA (H{sub 2}O/Fe) shielding benchmark experiment

    Energy Technology Data Exchange (ETDEWEB)

    Pescarini, M.; Borgia, M. G. [ENEA, Centro Ricerche ``Ezio Clementel``, Bologna (Italy). Dipt. Energia

    1997-03-01

    The PCA-REPLICA (H{sub 2}O/Fe) neutron shielding benchmarks experiment is analysed using the SN 2-D DOT 3.5-E code and the 3-D-equivalent flux synthesis method. This engineering benchmark reproduces the ex-core radial geometry of a PWR, including a mild steel reactor pressure vessel (RPV) simulator, and is designed to test the accuracy of the calculation of the in-vessel neutron exposure parameters. This accuracy is strongly dependent on the quality of the iron neutron cross sections used to describe the nuclear reactions within the RPV simulator. In particular, in this report, the cross sections based on the JENDL-3.1 iron data files are tested, through a comparison of the calculated integral and spectral results with the corresponding experimental data. In addition, the present results are compared, on the same benchmark experiment, with those of a preceding ENEA-Bologna validation of the ENDF/B VI iron cross sections. The integral result comparison indicates that, for all the threshold detectors considered (Rh-103 (n, n`) Rh-103m, In-115 (n, n`) In-115m and S-32 (n, p) P-32), the JENDL-3.1 natural iron data produce satisfactory results similar to those obtained with the ENDF/B VI iron data. On the contrary, when the JENDL/3.1 Fe-56 data file is used, strongly underestimated results are obtained for the lower energy threshold detectors, Rh-103 and In-115. This fact, in particular, becomes more evident with increasing the neutron penetration depth in the RPV simulator.

  2. Extending Modal Transition Systems with Structured Labels

    DEFF Research Database (Denmark)

    Bauer, Sebastian S.; Juhl, Line; Larsen, Kim Guldstrand

    2012-01-01

    We introduce a novel formalism of label-structured modal transition systems that combines the classical may/must modalities on transitions with structured labels that represent quantitative aspects of the model. On the one hand, the specification formalism is general enough to include models like...... study modal and thorough refinement, determinization, parallel composition, conjunction, quotient, and logical characterization of label-structured modal transition systems....

  3. Functional alterations of human platelets following indium-111 labelling using different incubation media and labelling agents

    Energy Technology Data Exchange (ETDEWEB)

    Isaka, Yoshinari; Imaizumi, Masatoshi (Osaka National Hospital (Japan). Dept. of Cardiovascular Medicine and Radiological Science); Kimura, Kazufumi (Osaka Univ. (Japan). Dept. of Nuclear Medicine); Matsumoto, Masayasu; Kamada, Takenobu (Osaka Univ. (Japan). 1. Dept. of Internal Medicine)

    1991-05-01

    Human platelets were labelled in the absence of presence of plasma using {sup 111}In-labelled oxine sulphate, tropolone or 2-mercaptopyridine-N-oxide (MPO). Under in vitro and in vivo conditions, platelet functions were evaluated by measuring their aggregability, survival, recovery and early distribution. High labelling efficiency was achieved in saline labelling, whereas with plasma labelling, it was necessary to concentrate the platelet-rich plasma to 4.8x10{sup 6} platelets/{mu}l. The aggregation of platelets labelled in plasma or saline was compared with that of controls; platelets labelled in saline showed lower aggregability in 2 {mu}M ADP but not in 5 {mu}M ADP nor with collagen. No significant differences in platelet survival and recovery were noted between platelets labelled in plasma and those labelled in saline. Our results indicate that partial loss of ADP aggregability in vitro does not influence the in vivo viability of platelets labelled in saline. Scintigraphic studies showed that platelets labelled in a saline medium were temporarily sequestrated in the liver but not in the spleen or heart. Thus, platelet labelling in saline does not affect platelet function adversely, but platelets labelled in plasma are more desirable for assessing the early distribution of platelets in the reticuloendothelial system. (orig.).

  4. ML-MG: Multi-label Learning with Missing Labels Using a Mixed Graph

    KAUST Repository

    Wu, Baoyuan

    2015-12-07

    This work focuses on the problem of multi-label learning with missing labels (MLML), which aims to label each test instance with multiple class labels given training instances that have an incomplete/partial set of these labels (i.e. some of their labels are missing). To handle missing labels, we propose a unified model of label dependencies by constructing a mixed graph, which jointly incorporates (i) instance-level similarity and class co-occurrence as undirected edges and (ii) semantic label hierarchy as directed edges. Unlike most MLML methods, We formulate this learning problem transductively as a convex quadratic matrix optimization problem that encourages training label consistency and encodes both types of label dependencies (i.e. undirected and directed edges) using quadratic terms and hard linear constraints. The alternating direction method of multipliers (ADMM) can be used to exactly and efficiently solve this problem. To evaluate our proposed method, we consider two popular applications (image and video annotation), where the label hierarchy can be derived from Wordnet. Experimental results show that our method achieves a significant improvement over state-of-the-art methods in performance and robustness to missing labels.

  5. Optimal design of isotope labeling experiments.

    Science.gov (United States)

    Yang, Hong; Mandy, Dominic E; Libourel, Igor G L

    2014-01-01

    Stable isotope labeling experiments (ILE) constitute a powerful methodology for estimating metabolic fluxes. An optimal label design for such an experiment is necessary to maximize the precision with which fluxes can be determined. But often, precision gained in the determination of one flux comes at the expense of the precision of other fluxes, and an appropriate label design therefore foremost depends on the question the investigator wants to address. One could liken ILE to shadows that metabolism casts on products. Optimal label design is the placement of the lamp; creating clear shadows for some parts of metabolism and obscuring others.An optimal isotope label design is influenced by: (1) the network structure; (2) the true flux values; (3) the available label measurements; and, (4) commercially available substrates. The first two aspects are dictated by nature and constrain any optimal design. The second two aspects are suitable design parameters. To create an optimal label design, an explicit optimization criterion needs to be formulated. This usually is a property of the flux covariance matrix, which can be augmented by weighting label substrate cost. An optimal design is found by using such a criterion as an objective function for an optimizer. This chapter uses a simple elementary metabolite units (EMU) representation of the TCA cycle to illustrate the process of experimental design of isotope labeled substrates.

  6. Synthesis of tritium labelled 24-epibrassinolide

    Energy Technology Data Exchange (ETDEWEB)

    Kolbe, A.; Marquardt, V.; Adam, G. (Inst. of Plant Biochemistry Halle, Halle/Saale (Germany))

    1992-10-01

    Deuterium and tritium 5,7,7-tris-labelled 24-epibrassinolide were prepared by base catalyzed exchange reaction using 24-epicastasterone tetraacetate 1 or bis-isopropylidenedioxy-24-epicastasterone 8 and labelled water. Baeyer-Villiger oxidation of the obtained labelled 6-ketones 2 and 3 with CF[sub 3]CO[sub 3]H gave after alkaline deacetylation of the resulting 4 and 5 the desired tris-labelled 24-epibrassinolides 6 and 7, respectively, or starting from 9 under simultaneous oxidation and deprotection in one step the same final products. (author).

  7. METHOD AND MODULE FOR OPTICAL SUBCARRIER LABELLING

    DEFF Research Database (Denmark)

    2004-01-01

    ) transmitters. The payload and the label are encoded independently on optical carrier and subcarrier signals respectively, using electro-optical modulators. The invention applies single or double sideband carrier-suppressed modulation to generate subcarrier signals for encoding of the label. Thereby the payload......The present invention relates to optical labelling in WDM networks, in that it provides a method and a module to be used in subcarrier label generation and switching in network edge nodes and core switch nodes. The methods and modules are typically employed in Optical Subcarrier Multiplexing (OSCM...

  8. Organic labeling influences food valuation and choice.

    Science.gov (United States)

    Linder, N S; Uhl, G; Fliessbach, K; Trautner, P; Elger, C E; Weber, B

    2010-10-15

    Everyday we choose between a variety of different food items trying to reach a decision that fits best our needs. These decisions are highly dependent on the context in which the alternatives are presented (e.g. labeling). We investigate the influence of cognition on food evaluation, using an fMRI experiment in which subjects saw and bid on different foods labeled with (or without) a widely known German emblem for organically produced food. Increased activity in the ventral striatum was found for foods labeled "organic" in comparison to conventionally labeled food. Between-subject differences in activity were related to actual everyday consumption behavior of organic food.

  9. Simultaneous Segmentation and Statistical Label Fusion.

    Science.gov (United States)

    Asman, Andrew J; Landmana, Bennett A

    2012-02-23

    Labeling or segmentation of structures of interest in medical imaging plays an essential role in both clinical and scientific understanding. Two of the common techniques to obtain these labels are through either fully automated segmentation or through multi-atlas based segmentation and label fusion. Fully automated techniques often result in highly accurate segmentations but lack the robustness to be viable in many cases. On the other hand, label fusion techniques are often extremely robust, but lack the accuracy of automated algorithms for specific classes of problems. Herein, we propose to perform simultaneous automated segmentation and statistical label fusion through the reformulation of a generative model to include a linkage structure that explicitly estimates the complex global relationships between labels and intensities. These relationships are inferred from the atlas labels and intensities and applied to the target using a non-parametric approach. The novelty of this approach lies in the combination of previously exclusive techniques and attempts to combine the accuracy benefits of automated segmentation with the robustness of a multi-atlas based approach. The accuracy benefits of this simultaneous approach are assessed using a multi-label multi- atlas whole-brain segmentation experiment and the segmentation of the highly variable thyroid on computed tomography images. The results demonstrate that this technique has major benefits for certain types of problems and has the potential to provide a paradigm shift in which the lines between statistical label fusion and automated segmentation are dramatically blurred.

  10. Synthesis and labelling of epidepride

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    S-(-)-N-[(1-ethyl-2-pyrrolidinyl)methyl]-5-iodo-2,3-dimethoxybenzamide (proposed generic name, epidepride) is a very potent dopamine D2 antagonist. It was synthesized by five steps from 3-methoxysalicylic acid. [131I]epidepride was obtained in 97.3% radiochemical yields from the corresponding 5-(tributyltin) derivative using hydrogen peroxide as the oxidant. The aryltin precursor was prepared from non-labelled epidepride by palladium-catalyzed stannylation using bis(tri-n-butyltin) in triethylamine. [131I]epidepride was stable under 4℃, and partition coefficient was 72.3 at pH 7.40. The biodistribution study in rats exihibited high localization in the striatum of the brain with the striatum/cerebellum ratio reaching 237/1 at 320 min postinjection.All these results suggest that[131I]epidepride may be usedd widely as a useful dopamineD2 receptor imaging agent for SPECT.

  11. Principles of food product labelling

    Directory of Open Access Journals (Sweden)

    Krystyna Krysztofiak

    2011-09-01

    Full Text Available The purpose of the label of the food product is to provide information on ingredients and additionally on its origin, production method, storage conditions, date tagging, as well as to enable to identify the producer or distributor of this product. Legal regulations precisely give instructions on the range and the way of the presentation of these data, so they could be clear and understandable for the average consumer. Since 25th of November 2005, the information about allergens’ presence must be placed on the label, regardless of their content in the product (Directive 2003/89/WE... 2003 – Off. J. L 308: 15-18. The Regulation (WE No 1924/2006 about placing the nutritional information and medicinal claims concerning foods (Regulation (WE No 1924/2006... 2006 a is valid in all countries of European Union since 1st of July 2007 (Off. J. L 404: 9-25. It coordinates the legislative, executive and administrative regulations connected with this labelling. According to these regulations, “nutritional information” states, suggests or gives to understand that the food product has special properties concerning its ingredients. Those statements are of type: “the source of...”, “no... content”, “high content of...”, “low content of...”, “reduced content of...” with reference to calorie or selected ingredients’ content. “Medicinal claims” state, suggest or give to understand, that there is a connection between the food product or one of its ingredients and the health condition of the consumer. First type of these medicinal claims refers to the influence of the ingredient on the physiology. Such a statement is based on generally accepted scientific conclusions and could be properly understood by the average consumer, e.g. “calcium takes part in the process of building of strong bones”. “Statements about decreasing the risk of a disease” give information, that food product or one of its ingredients efficiently

  12. F-18 labeled 3-fluorodiazepam

    Energy Technology Data Exchange (ETDEWEB)

    Luxen, A.; Barrio, J.R.; Bida, G.T.; Satyamurthy, N.; Phelps, M.E.

    1985-05-01

    3-Fluorodiazepam is a new and potent antianxiety agent with prolonged action. The authors found that molecular fluorine (0.5% in Ne) reacts cleanly with diazepam in freon or chloroform at room temperature to produce 3-fluorodiazepam in good yields. Successful syntheses have employed 2:1 to 5:1 molar ratios diazepam: fluorine to minimize the formation of byproducts. (/sup 18/F) 3-Fluorodiazepam, a potential candidate for PET studies, (specific activity 3-5 Ci/mmol) has been synthesized from /sup 18/F-F/sub 2/ using the same procedure, followed by column chromatographic purification (Silicagel, dichloromethane: ethyl acetate, 5:1) with a radiochemical yield of 12-20% (50% maximum) and a chemical and radiochemical purity >99% as judged by reversed-phase high pressure liquid chromatography analysis (Ultrasyl octyl column, 10 ..mu.. m, 4.6 x 250 mm i.d., 60% MeOH 40% water; flow rate, 1.0 ml/min; retention time for (/sup 18/F) fluorodiazepam, 11.4 min; for diazepam, 13.5 min; radioactivity and ultraviolet detectors). Lower radiochemical yields (5-7%), and significant formation of by-products were observed when (/sup 18/F)acetylhypofluorite, prepared in the gasphase, was used as the reagent. Readily accessible routes to /sup 18/F-labeled benzodiazepines of higher specific activity were also investigated. Approaches to the synthesis of high specific activity (>200 Ci/mmol) (/sup 18/F)3-fluorodiazepam involve nucleophilic displacement at carbon-3 (e.g. from 3-chlorodiazepam) with (/sup 18/F)fluoride ion. The results presented here demonstrate the synthetic accessibility of /sup 18/F-labeled benzodiazepines for application in neurotransmitter ligand studies with PET.

  13. Chain store management through private labels strategy

    Directory of Open Access Journals (Sweden)

    Martina Sopta

    2007-07-01

    Full Text Available The purpose of this paper is to examine the market shares of private labels in the European Union and on the global market, and to compare the results of the analysis with the level of presence of private labels on the Croatian market. Moreover, through the application of macro and microeconomic tools, the author tried to estimate the future trends of private labels in Croatia.For the purpose of the paper secondary and primary data was used in the research. Relevant scientific and professional literature of local and foreign authors was analyzed. In addition, a few recent research studies were analyzed and their results compared. Field research has been conducted by the survey method, with 225 respondents included in the intentional sample.The main hypothesis of the paper based on research is that, in total sales, private labels are gaining a growing share in all markets, regardless of the development level of those markets. Alongside the main hypothesis of the work, three supporting hypotheses were tested to see which private labels are a good alternative to other brands on the world market. Private labels are generally developed on generic products. The third supporting hypothesis starts from the assumption that the investments in the promotion of private labels are negligible, resulting in lower prices of thoseproducts. The results of research and analyses in the work indicate that the position of private labels will strengthen internationally, as part of the process of liberalization and globalization of trade flows. In the process of purchase of private labels the positioning of the point of sale and price have an increasing contribution. With the concentration of commerce in chain stores, the share of private labels grows, approaching a half of the total sales in some countries. Considering the Croatian market, according to the international product life cycle theory, the share of private labels in the total sales will grow in the future

  14. 76 FR 46671 - Food Labeling; Gluten-Free Labeling of Foods; Reopening of the Comment Period

    Science.gov (United States)

    2011-08-03

    ... HUMAN SERVICES Food and Drug Administration 21 CFR Part 101 RIN 0910-ZA26 Food Labeling; Gluten-Free... the comment period for the proposed rule on the ``gluten-free'' labeling of foods, published in the... ``gluten- free,'' for voluntary use in the labeling of foods, to mean that the food does not contain...

  15. Label Space Reduction in MPLS Networks: How Much Can A Single Stacked Label Do?

    DEFF Research Database (Denmark)

    Solano, Fernando; Stidsen, Thomas K.; Fabregat, Ramon

    2008-01-01

    Most network operators have considered reducing LSR label spaces (number of labels used) as a way of simplifying management of underlaying virtual private networks (VPNs) and therefore reducing operational expenditure (OPEX). The IETF outlined the label merging feature in MPLS-allowing the config...

  16. Portion Size Labeling and Intended Soft Drink Consumption: The Impact of Labeling Format and Size Portfolio

    Science.gov (United States)

    Vermeer, Willemijn M.; Steenhuis, Ingrid H. M.; Leeuwis, Franca H.; Bos, Arjan E. R.; de Boer, Michiel; Seidell, Jacob C.

    2010-01-01

    Objective: To assess what portion size labeling "format" is most promising in helping consumers selecting appropriate soft drink sizes, and whether labeling impact depends on the size portfolio. Methods: An experimental study was conducted in fast-food restaurants in which 2 labeling formats (ie, reference portion size and small/medium/large…

  17. Portion Size Labeling and Intended Soft Drink Consumption: The Impact of Labeling Format and Size Portfolio

    Science.gov (United States)

    Vermeer, Willemijn M.; Steenhuis, Ingrid H. M.; Leeuwis, Franca H.; Bos, Arjan E. R.; de Boer, Michiel; Seidell, Jacob C.

    2010-01-01

    Objective: To assess what portion size labeling "format" is most promising in helping consumers selecting appropriate soft drink sizes, and whether labeling impact depends on the size portfolio. Methods: An experimental study was conducted in fast-food restaurants in which 2 labeling formats (ie, reference portion size and small/medium/large…

  18. Multi-label Dictionary Learning for Image Annotation.

    Science.gov (United States)

    Jing, Xiao-Yuan; Wu, Fei; Li, Zhiqiang; Hu, Ruimin; Zhang, David

    2016-03-31

    Image annotation has attracted lots of research interest, and multi-label learning is an effective technique for image annotation. How to effectively exploit the underlying correlation among labels is a crucial task for multi-label learning. Most existing multi-label learning methods exploit the label correlation only in the output label space, leaving the connection between label and features of images untouched. Although recently some methods attempt towards exploiting the label correlation in the input feature space by using the label information, they cannot effectively conduct the learning process in both spaces simultaneously, and there still exists much room for improvement. In this paper, we propose a novel multi-label learning approach, named Multi-Label Dictionary Learning with label consistency regularization and partial-identical label embedding (MLDL), which conducts multi-label dictionary learning and partial-identical label embedding simultaneously. In the input feature space, we incorporate the dictionary learning technique into multi-label learning and design the label consistency regularization term to learn better representation of features. In the output label space, we design the partial-identical label embedding, in which samples with the exactly same label set can cluster together, and samples with partial-identical label sets can collaboratively represent each other. Experimental results on three widely used image datasets including Corel 5K, IAPR TC12 and ESP Game demonstrate the effectiveness of the proposed approach.

  19. 78 FR 2200 - Energy Labeling Rule

    Science.gov (United States)

    2013-01-10

    ... ensure consumers can view the labels when they are shopping online. In particular, it will provide retail... From the Federal Register Online via the Government Publishing Office FEDERAL TRADE COMMISSION 16..., clarifying testing requirements and enforcement provisions, improving online energy label disclosures, and...

  20. 40 CFR 1042.830 - Labeling.

    Science.gov (United States)

    2010-07-01

    ... EMISSIONS FROM NEW AND IN-USE MARINE COMPRESSION-IGNITION ENGINES AND VESSELS Special Provisions for Remanufactured Marine Engines § 1042.830 Labeling. (a) At the time of remanufacture, affix a permanent and...) Written in English. (b) The label must— (1) Include the heading “EMISSION CONTROL INFORMATION”....

  1. 78 FR 8362 - Energy Labeling Rule

    Science.gov (United States)

    2013-02-06

    ... EnergyGuide label.\\19\\ For example, ACCA stated that the new labels will facilitate compliance with the... Conditioning Contractors of America (ACCA) ( 560904-00011); Air-Conditioning, Heating, and Refrigeration...://www.ftc.gov/os/comments/regionaldisclosurenprm/index.shtm . \\20\\ ACCA also supported the proposed...

  2. Synthesis of deuterium labeled plant ethylene precursor

    Energy Technology Data Exchange (ETDEWEB)

    Nam, K.C. [Chonnam National Univ., Kwangju (Korea, Republic of). Dept. of Chemistry; Rapoport, H. [California Univ., Berkeley, CA (United States). Dept. of Chemistry

    1995-12-31

    Synthetic methods for the preparation of {beta}-deuterium labeled 2-keto-4-methylbutyric acid were investigated. Vinyl chloride was first reacted with the ethyl oxalyl chloride moiety using aluminum chloride as condensing agent and the addition of methyl mercaptan followed. Deuterium labeling was achieved by using NaBD{sub 4} reduction in pyridine. (author).

  3. The anatomy of a laser label

    Science.gov (United States)

    Laser labeling of fruits and vegetables is an efficient alternative to adhesive tags. The advantages of this system are numerous. In general the label consists of alphanumerical characters formed by laser generated pinhole depressions that penetrate the produce’s surface creating visible markings. H...

  4. China Cotton label to be generalized

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    "China Cotton"authorization press conference was held in Beijing on October 11. China Cotton Association granted authorization to the first four enterprises, allowing them to use the label of China Cotton on their qualified products. Shandong Lanyan Group, Beijing Miantian Textile Co., Ltd are among the fi rst companies authorized to use China Cotton label.

  5. 78 FR 18272 - Energy Labeling Rule

    Science.gov (United States)

    2013-03-26

    ... CFR Part 305 Energy Labeling Rule AGENCY: Federal Trade Commission (``FTC'' or ``Commission''). ACTION... in the SUPPLEMENTARY INFORMATION section below. Write ``Energy Label Ranges, Matter No. R611004'' on... Proposed Rulemaking (NPRM) until April 1, 2013. In the NPRM, the Commission proposed to amend the...

  6. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... 1- to 2-Year-Old How to Read a Nutrition Facts Label (Video) KidsHealth > For Parents > How to Read a Nutrition Facts Label (Video) Print A A A en español Cómo leer las etiquetas ...

  7. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... Watch this video for tips on figuring out food labels so you can make healthy choices. For Teens For Kids For Parents MORE ON THIS TOPIC Keeping Portions Under Control Figuring Out Food Labels Healthy Food Shopping If My Child Has ...

  8. On the Complexity of Labeled Oriented Trees

    Indian Academy of Sciences (India)

    Stephan Rosebrock

    2010-02-01

    We define a notion of complexity for labeled oriented trees (LOTs) related to the bridge number in knot theory and prove that LOTs of complexity 2 are aspherical. We also present a class of LOTs of higher complexity which is aspherical, give an upper bound for the complexity of labeled oriented intervals and study the complexity of torus knots.

  9. Do European consumers use nutrition labels?

    DEFF Research Database (Denmark)

    Wills, Josephine M.; Grunert, Klaus G.; Celemín, Laura Fernández

    2009-01-01

    Nutrition labelling on food packages becomes more and more widespread in the European Union. Such information is not compulsory, unless a nutrition or health claim is made. However, how do consumers use nutrition information? Two European studies are currently assessing whether nutrition...... knowledge about nutrition and are able to use nutrition labels to identify healthier products within a category....

  10. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... Watch this video for tips on figuring out food labels so you can make healthy choices. For Teens For Kids For Parents MORE ON THIS TOPIC Keeping Portions Under Control Figuring Out Food Labels Healthy Food Shopping If My Child Has ...

  11. 7 CFR 65.400 - Labeling.

    Science.gov (United States)

    2010-01-01

    ... AGRICULTURAL MARKETING ACT OF 1946 AND THE EGG PRODUCTS INSPECTION ACT (CONTINUED) COUNTRY OF ORIGIN LABELING..., PEANUTS, AND GINSENG General Provisions Country of Origin Notification § 65.400 Labeling. (a) Country of... country of origin of a product may be in the form of a statement such as “Product of USA,” “Produce of the...

  12. 9 CFR 101.4 - Labeling terminology.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Labeling terminology. 101.4 Section 101.4 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF... Labeling terminology. Terms pertaining to identification and packaging of biological products shall...

  13. Private labels : The brands of the future

    NARCIS (Netherlands)

    Keller, Kristopher

    2017-01-01

    This dissertation consists of three essays that study private labels’ evolution from private labels as brand class to individual private-label brands from three different perspectives. In the second chapter of this dissertation (essay 1), I study the antecedents and performance implications of

  14. Influence of Food Labels on Adolescent Diet.

    Science.gov (United States)

    Misra, Ranjita

    2002-01-01

    Provides information on food nutrition labels and discusses the benefits of adolescents' using them to plan healthy diets. Suggests that teachers and educators should encourage appropriate label reading education for adolescents to promote healthy eating practices. Provides definitions of nutrient content claims. (SG)

  15. How to Read a Nutrition Facts Label

    Medline Plus

    Full Text Available ... Be Smart About Social Media How to Read a Nutrition Facts Label (Video) KidsHealth > For Parents > How to Read a Nutrition Facts Label (Video) Print A A A en español Cómo leer las etiquetas ...

  16. 9 CFR 116.3 - Label records.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Label records. 116.3 Section 116.3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE VIRUSES... labeling a product. (Approved by the Office of Management and Budget under control number 0579-0013)...

  17. 21 CFR 201.64 - Sodium labeling.

    Science.gov (United States)

    2010-04-01

    ... paragraph (b) of this section). (e) The term very low sodium may be used in the labeling of OTC drug... milligrams or less. (f) The term low sodium may be used in the labeling of OTC drug products intended for... substituted for the term sodium. (h) The terms sodium free, very low sodium, and low sodium shall be in print...

  18. Do European consumers use nutrition labels?

    DEFF Research Database (Denmark)

    Wills, Josephine M.; Grunert, Klaus G.; Celemín, Laura Fernández

    2009-01-01

    Nutrition labelling on food packages becomes more and more widespread in the European Union. Such information is not compulsory, unless a nutrition or health claim is made. However, how do consumers use nutrition information? Two European studies are currently assessing whether nutrition...... knowledge about nutrition and are able to use nutrition labels to identify healthier products within a category....

  19. Alternatives to radioimmunoassay: labels and methods

    Energy Technology Data Exchange (ETDEWEB)

    Schall, R.F. Jr.; Tenoso, H.J.

    1981-07-01

    The following labels used as substitutes for radioisotopes in immunoassay systems are reviewed bacteriophages, chemiluminescence precursors, fluorochromes, fluorogens, fluorescence quenchers, enzymes, coenzymes, inhibitors, substrates, various particulates, metal atoms, and stable free radicals. New methods for performing immunoassays with these labels are described where appropriate. Methods that require no separation steps and offer special promise for easy automation are noted. 69 references cited.

  20. Recent developments in blood cell labeling research

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, S.C.; Straub, R.F.; Meinken, G.E.

    1988-09-07

    A number of recent developments in research on blood cell labeling techniques are presented. The discussion relates to three specific areas: (1) a new in vitro method for red blood cell labeling with /sup 99m/Tc; (2) a method for labeling leukocytes and platelets with /sup 99m/Tc; and (3) the use of monoclonal antibody technique for platelet labeling. The advantages and the pitfalls of these techniques are examined in the light of available mechanistic information. Problems that remain to be resolved are reviewed. An assessment is made of the progress as well as prospects in blood cell labeling methodology including that using the monoclonal antibody approach. 37 refs., 4 figs.

  1. Labeling of creatinine with technetium-99m

    Energy Technology Data Exchange (ETDEWEB)

    Yurt Lambrecht, F. [Ege Univ., Bornova, Izmir (Turkey). Dept. of Nuclear Applications, Inst. of Nuclear Sciences; Durkan, K. [Dokuz Eylul Univ., Buca, Izmir (Turkey). Chemistry Technicianship Program, Izmir Vocational School; Soylu, A. [Dokuz Eylul Univ., Narlidere, Izmir (Turkey). Dept. of Pediatrics, Medical Faculty

    2004-07-01

    Creatinine is a clinically important index of renal glomerular filtration rate. Urine creatinine levels can be used as a screening test to evaluate kidney function or can be part of the creatinine clearance test. In case of kidney dysfunction or muscle disorders the creatinine concentration in serum/plasma may rise to a higher value than in healthy body. Technetium- 99m has been used in nuclear medicine and in biomedical research to label molecular and cellular structures employed as radiotracers. {sup 99m}Tc is utilized to label molecules and cells, used as radiopharmaceuticals, and also to label biological species. It presents many desirable characteristics. SnCl{sub 2} method is frequently used as a reducing agent in the {sup 99m}Tc- labeling process. Creatinine metabolism might be investigated by using labeled {sup 99m}Tc- creatinine in healthy or uremic rats. (orig.)

  2. 16 CFR 300.14 - Substitute label requirement.

    Science.gov (United States)

    2010-01-01

    ... AND REGULATIONS UNDER THE WOOL PRODUCTS LABELING ACT OF 1939 Labeling § 300.14 Substitute label... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Substitute label requirement. 300.14 Section... product appearing on the stamp, tag, label, or other mark of identification affixed to such product shall...

  3. A Note on Prime and Sequential Labelings of Finite Graphs

    OpenAIRE

    Mathew Varkey T.K; Sunoj. B.S

    2015-01-01

    A labeling or valuation of a graph G is an assignment f of labels to the vertices of G that induces for each edge xy a label depending on the vertex labels f(x) and f(y). In this paper, we study some classes of graphs and their corresponding labelings.

  4. 49 CFR 172.416 - POISON GAS label.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false POISON GAS label. 172.416 Section 172.416... SECURITY PLANS Labeling § 172.416 POISON GAS label. (a) Except for size and color, the POISON GAS label... POISON GAS label and the symbol must be white. The background of the upper diamond must be black and...

  5. Universality class of replica symmetry breaking, scaling behavior, and the low-temperature fixed-point order function of the Sherrington-Kirkpatrick model.

    Science.gov (United States)

    Oppermann, R; Schmidt, M J

    2008-12-01

    A scaling theory of replica symmetry breaking (RSB) in the Sherrington-Kirkpatrick (SK) model is presented in the framework of critical phenomena for the scaling regime of large RSB orders kappa , small temperatures T , and small (homogeneous) magnetic fields H . We employ the pseudodynamical picture [R. Oppermann, M. J. Schmidt, and D. Sherrington, Phys. Rev. Lett. 98, 127201 (2007)], where two critical points CP1 and CP2 are associated with the order function's pseudodynamical limits lim_{a-->infinity}q(a)=1 and lim_{a-->0}q(a)=0 at (T=0 , H=0 , 1kappa=0) . CP1 - and CP2 -dominated contributions to the free energy functional F[q(a)] require an unconventional scaling hypothesis. We determine the scaling contributions in accordance with detailed numerical self-consistent solutions for up to 200 orders of RSB. Power laws, scaling functions, and crossover lines are obtained. CP1 -dominated behavior is found for the nonequilibrium susceptibility, which decays like chi_{1}=kappa;{-53}f_{1}(Tkappa;{-53}) , for the entropy, which obeys S(T=0) approximately chi_{1};{2} , and for the subclass of diverging parameters a_{i}=kappa;{53}f_{a_{i}}(Tkappa;{-53}) [describing Parisi box sizes m_{i}(T) identical witha_{i}(T)T ], with f_{1}(zeta) approximately zeta and f_{a_{i}}(zeta) approximately 1zeta for zeta-->infinity , while f(0) is finite. CP2 -dominated behavior, controlled by the magnetic field H while temperature is irrelevant, is retrieved in the plateau height (or width) of the order function q(a) according to q_{pl}(H)=kappa;{-1}f_{pl}(H;{23}kappa;{-1}) with f_{pl}mid R:(zeta)mid R:_{zeta-->infinity} approximately zeta and f_{pl}(0) finite. Divergent characteristic RSB orders kappa_{CP1}(T) approximately T;{-35} and kappa_{CP2}(H) approximately H;{-23} , respectively, describe the crossover from mean field SK- to RSB-critical behavior with rational-valued exponents extracted with high precision from our RSB data. The order function q(a) is obtained as a fixed

  6. Aerospace devices for magnetic replicas

    Science.gov (United States)

    Weinstein, Roy

    1993-05-01

    Retained persistent magnetic field has been studied and improved in the superconductor YBa2Cu3O7 (Y123). During the study, trapped magnetic field, B(t), has been increased by over a factor of 10(exp 5). Methods used to improve magnetic field trapping were principally: (1) the adoption of the Melt Texturing process to increase grain size; (2) the addition of excess Y to disperse deposits of Y2BaCuO5 (Y211) and again increase grain size; (3) irradiation with high energy particles including 1H+, 3He++, 4He++, and fission fragments; and (4) utilizing temperatures below 77 K has also been quantified as a way to increase trapped field. In addition, in our study of B(t), we have found laws governing creep, activation, temperature dependence, creep vs. current flow, etc. In the range 20 K less than or equal to T less than or equal to 65 K, and for B less than 10 Tesla, a simple empirical relationship was found: B(trap) (T2) = B(trap) (T1) ((Tc - T2)/(Tc - T1))squared where Tc is the critical temperature. The highest experimental trapped field was B(trap) = 3.96 Tesla, at 65 K. We believe this to be the highest persistent field ever produced, by any method. A two component model of the persistent currents has been developed. This accurately reproduces the data, using as parameters only the magnitude of a constant surface current, J(s), and a constant volume current J(v). The model successfully predicts B(t) (xyz) for the case of maximum trapped field, for all samples observed. It has also been extended to describe the unsaturated case either zero field cooled, or field cooled. Loss of strap with time has been studied for the critical state (Bt,max), and non critical state (Bt less than Bt,max), for times from a few minutes to a few months, for unirradiated material, for irradiation by 1H+, 3He++, 4He++, high z projectiles, and neutrons, and for all materials used in the overall study. We conclude that: (1) multi Tesla trapped fields are attained; (2) fields over 10 T are achievable; (3) creep is not a large problem; (4) application is feasible to motors, generators, magnets for particle beam optics, separators, levitating bearings, energy storage, shielding, and transportation.

  7. On Labeled Traveling Salesman Problems

    DEFF Research Database (Denmark)

    Couetoux, Basile; Gourves, Laurent; Monnot, Jerome

    2008-01-01

    We consider labeled Traveling Salesman Problems, defined upon a complete graph of n vertices with colored edges. The objective is to find a tour of maximum (or minimum) number of colors. We derive results regarding hardness of approximation, and analyze approximation algorithms for both versions...... of the problem. For the maximization version we give a -approximation algorithm and show that it is APX-hard. For the minimization version, we show that it is not approximable within n 1 − ε for every ε> 0. When every color appears in the graph at most r times and r is an increasing function of n the problem...... is not O(r 1 − ε )-approximable. For fixed constant r we analyze a polynomial-time (r + H r )/2-approximation algorithm (H r is the r-th harmonic number), and prove APX-hardness. Analysis of the studied algorithms is shown to be tight....

  8. ORGANIC FOOD LABELING AND CERTIFICATION

    Directory of Open Access Journals (Sweden)

    NICOLETA-ANDREEA NEACSU

    2011-04-01

    Full Text Available In the rush to produce more and more crops to satisfy growing demand producers have had to resort to using a lethal cocktail of pesticides to control disease and insect attack. This has lead to numerous international debates about unhealthy food, the effects of it and the measures that must be taken in order to avoid the harmful effects of genetically modified food consumption demonstrated by specialists. These debates evolve around the benefits of the organic products versus the pure trade trick outlined by some. The organic food movement has earned its well deserved place in many markets around the world. Its prestige is lately being widespread to vast parts of Eastern-Europe as well. Based on data collected from specialized reports and articles on organic products, the aim of this paper is to present the importance of organic products, the regulations on organic food and different labels used around the world in order to certify the organic food products.

  9. 99Tcm direct labeling of angiostatin

    Institute of Scientific and Technical Information of China (English)

    张金赫; 徐海峰; 邵秋菊; 袁梦晖; 周润锁; 周亮飞

    2004-01-01

    Objective: To explore the method of 99Tcm direct labeling of angiostatin (AS) and investigate the stability and bioactivity of the 99Tcm-labeled AS in vitro. Methods: AS was extracted, validated, and then labeled with 99Tcm after having been reduced by 2-ME or SnCl2. The best labeling condition was screened by cross design. The labeling efficiency was measured by TLC and column chromatography. The stability of 99Tcm-AS was observed and compared when BSA, saline and different molar ratios of Cys∶AS were separately added. The bioactivity of 99Tcm-AS was observed in human umbilical vein endothelial cell (CEV304). Results: The labeling efficiency can reach (97±1.5)% for the 2-ME-reducing approach. Its best experimental condition was as follows: AS 100 μg,PB(0.5 mol/L, pH 7.3)1 ml, 2-ME 100 μg, MDP (dissolved in 1 ml saline) 10 μl, and 99TcmO4- 185 MBq. The labeling efficiency using SnCl2-reducing method can reach (90±3.0)%. The best experimental procedure was as follows: AS 100 μg,boric acid buffer(0.1 mol/L, pH 9.0)1 ml, 2%SnCl2 (dissolved in 1 mol/L hydrochloric acid) 20 μl, was added into MDP, which was diluted with 1 ml deoxygenized water, and then 20 μl, 99TcmO4- 185 MBq was added. The product of 99Tcm labeled AS was stable in vitro and had the same bioactivity as AS. Conclusion: 99Tcm direct labeling of AS is simple and efficient. And the bioactivity of 99Tcm-AS has no significant change compared with AS.

  10. 7 CFR 205.306 - Labeling of livestock feed.

    Science.gov (United States)

    2010-01-01

    ... Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) ORGANIC FOODS PRODUCTION ACT PROVISIONS NATIONAL ORGANIC PROGRAM Labels, Labeling, and Market Information § 205.306 Labeling of...

  11. 27 CFR 16.21 - Mandatory label information.

    Science.gov (United States)

    2010-04-01

    ... the brand label or separate front label, or on a back or side label, separate and apart from all other... of alcoholic beverages impairs your ability to drive a car or operate machinery, and may cause...

  12. 21 CFR 1230.13 - Labeling of “poison”.

    Science.gov (United States)

    2010-04-01

    ... FEDERAL CAUSTIC POISON ACT Labeling § 1230.13 Labeling of “poison”. The following are styles of...-point size are required on a label in stating the word “poison” they must not be smaller than...

  13. Sublinear distance labeling for sparse graphs

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Dahlgaard, Søren; Knudsen, Mathias Bæk Tejs;

    2015-01-01

    between pairs of nodes that are at distance at least $D$ from each other. In this paper we consider distance labeling schemes for the classical case of unweighted and undirected graphs. We present the first distance labeling scheme of size $o(n)$ for sparse graphs (and hence bounded degree graphs......). This addresses an open problem by Gavoille et. al. [J. Algo. 2004], hereby separating the complexity from general graphs which require $\\Omega(n)$ size Moon [Proc. of Glasgow Math. Association 1965]. As an intermediate result we give a $O(\\frac{n}{D}\\log^2 D)$ $D$-preserving distance labeling scheme, improving...

  14. The antibody approach of labeling blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, S.C.

    1991-12-31

    Although the science of blood cell labeling using monoclonal antibodies directed against specific cellular antigens is still in its early stages, considerable progress has recently been accomplished in this area. The monoclonal antibody approach offers the promise of greater selectivity and enhanced convenience since specific cell types can be labeled in vivo, thus eliminating the need for complex and damaging cell separation procedures. This article focuses on these developments with primary emphasis on antibody labeling of platelets and leukocytes. The advantages and the shortcomings of the recently reported techniques are criticality assessed and evaluated.

  15. The antibody approach of labeling blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, S.C.

    1991-01-01

    Although the science of blood cell labeling using monoclonal antibodies directed against specific cellular antigens is still in its early stages, considerable progress has recently been accomplished in this area. The monoclonal antibody approach offers the promise of greater selectivity and enhanced convenience since specific cell types can be labeled in vivo, thus eliminating the need for complex and damaging cell separation procedures. This article focuses on these developments with primary emphasis on antibody labeling of platelets and leukocytes. The advantages and the shortcomings of the recently reported techniques are criticality assessed and evaluated.

  16. The antibody approach of labeling blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, S.C.

    1992-12-31

    Although the science of blood cell labeling using monoclonal antibodies directed against specific cellular antigens is still in its early stages, considerable progress has recently been accomplished in this area. The monoclonal antibody approach offers the promise of greater selectivity and enhanced convenience since specific cell types can be labeled in vivo, thus eliminating the need for complex and damaging cell separation procedures. This article focuses on these developments with primary emphasis on antibody labeling of platelets and leukocytes. The advantages and the shortcomings of the recently reported techniques are critically assessed and evaluated.

  17. Valuing labelling attributes with hedonic price analysis:

    DEFF Research Database (Denmark)

    Steiner, Bodo

    2004-01-01

    The market share of New World wines sold in many European countries has increased dramatically over the past decade. More aggressive marketing, together with a more distinct and recognizable labeling scheme, are often regarded as the keys to the marketing success of these new wines. This article...... that consumers consider regions jointly with grape varieties as proxies for brands. This contrasts with the general observation that grape varietal labeling is the distinctive feature of New World wines. Marketing implications are examined by considering the revenue impact of changes in labeling at the retail...

  18. The antibody approach of labeling blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, S.C.

    1991-01-01

    Although the science of blood cell labeling using monoclonal antibodies directed against specific cellular antigens is still in its early stages, considerable progress has recently been accomplished in this area. The monoclonal antibody approach offers the promise of greater selectivity and enhanced convenience since specific cell types can be labeled in vivo, thus eliminating the need for complex and damaging cell separation procedures. This article focuses on these developments with primary emphasis on antibody labeling of platelets and leukocytes. The advantages and the shortcomings of the recently reported techniques are criticality assessed and evaluated.

  19. The antibody approach of labeling blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, S.C.

    1991-12-31

    Although the science of blood cell labeling using monoclonal antibodies directed against specific cellular antigens is still in its early stages, considerable progress has recently been accomplished in this area. The monoclonal antibody approach offers the promise of greater selectivity and enhanced convenience since specific cell types can be labeled in vivo, thus eliminating the need for complex and damaging cell separation procedures. This article focuses on these developments with primary emphasis on antibody labeling of platelets and leukocytes. The advantages and the shortcomings of the recently reported techniques are criticality assessed and evaluated.

  20. Imaging Cytoskeleton Components by Electron Microscopy

    Science.gov (United States)

    Svitkina, Tatyana

    2016-01-01

    The cytoskeleton is a complex of detergent-insoluble components of the cytoplasm playing critical roles in cell motility, shape generation, and mechanical properties of a cell. Fibrillar polymers—actin filaments, microtubules, and intermediate filaments—are major constituents of the cytoskeleton, which constantly change their organization during cellular activities. The actin cytoskeleton is especially polymorphic, as actin filaments can form multiple higher order assemblies performing different functions. Structural information about cytoskeleton organization is critical for understanding its functions and mechanisms underlying various forms of cellular activity. Because of the nanometer-scale thickness of cytoskeletal fibers, electron microscopy (EM) is a key tool to determine the structure of the cytoskeleton. This article describes application of rotary shadowing (or metal replica) EM for visualization of the cytoskeleton. The procedure is applicable to thin cultured cells growing on glass coverslips and consists of detergent extraction of cells to expose their cytoskeleton, chemical fixation to provide stability, ethanol dehydration and critical point drying to preserve three-dimensionality, rotary shadowing with platinum to create contrast, and carbon coating to stabilize replicas. This technique provides easily interpretable three-dimensional images, in which individual cytoskeletal fibers are clearly resolved, and individual proteins can be identified by immunogold labeling. More importantly, replica EM is easily compatible with live cell imaging, so that one can correlate the dynamics of a cell or its components, e.g., expressed fluorescent proteins, with high resolution structural organization of the cytoskeleton in the same cell. PMID:26498781