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Sample records for macromolecular crowding tend

  1. Macromolecular crowding: Macromolecules friend or foe.

    Science.gov (United States)

    Mittal, Shruti; Chowhan, Rimpy Kaur; Singh, Laishram Rajendrakumar

    2015-09-01

    Cellular interior is known to be densely crowded due to the presence of soluble and insoluble macromolecules, which altogether occupy ~40% of the total cellular volume. This results in altered biological properties of macromolecules. Macromolecular crowding is observed to have both positive and negative effects on protein folding, structure, stability and function. Significant data has been accumulated so far on both the aspects. However, most of the review articles so far have focused on the positive aspect of macromolecular crowding and not much attention has been paid on the deleterious aspect of crowding on macromolecules. In order to have a complete knowledge of the effect of macromolecular crowding on proteins and enzymes, it is important to look into both the aspects of crowding to determine its precise role under physiological conditions. To fill the gap in the understanding of the effect of macromolecular crowding on proteins and enzymes, this review article focuses on the deleterious influence of crowding on macromolecules. Macromolecular crowding is not always good but also has several deleterious effects on various macromolecular properties. Taken together, the properties of biological macromolecules in vivo appears to be finely regulated by the nature and level of the intracellular crowdedness in order to perform their biological functions appropriately. The information provided here gives an understanding of the role played by the nature and level of cellular crowdedness in intensifying and/or alleviating the burden of various proteopathies. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Effects of macromolecular crowding on genetic networks.

    Science.gov (United States)

    Morelli, Marco J; Allen, Rosalind J; Wolde, Pieter Rein ten

    2011-12-21

    The intracellular environment is crowded with proteins, DNA, and other macromolecules. Under physiological conditions, macromolecular crowding can alter both molecular diffusion and the equilibria of bimolecular reactions and therefore is likely to have a significant effect on the function of biochemical networks. We propose a simple way to model the effects of macromolecular crowding on biochemical networks via an appropriate scaling of bimolecular association and dissociation rates. We use this approach, in combination with kinetic Monte Carlo simulations, to analyze the effects of crowding on a constitutively expressed gene, a repressed gene, and a model for the bacteriophage λ genetic switch, in the presence and absence of nonspecific binding of transcription factors to genomic DNA. Our results show that the effects of crowding are mainly caused by the shift of association-dissociation equilibria rather than the slowing down of protein diffusion, and that macromolecular crowding can have relevant and counterintuitive effects on biochemical network performance.

  3. An upper limit for macromolecular crowding effects

    Directory of Open Access Journals (Sweden)

    Miklos Andrew C

    2011-05-01

    Full Text Available Abstract Background Solutions containing high macromolecule concentrations are predicted to affect a number of protein properties compared to those properties in dilute solution. In cells, these macromolecular crowders have a large range of sizes and can occupy 30% or more of the available volume. We chose to study the stability and ps-ns internal dynamics of a globular protein whose radius is ~2 nm when crowded by a synthetic microgel composed of poly(N-isopropylacrylamide-co-acrylic acid with particle radii of ~300 nm. Results Our studies revealed no change in protein rotational or ps-ns backbone dynamics and only mild (~0.5 kcal/mol at 37°C, pH 5.4 stabilization at a volume occupancy of 70%, which approaches the occupancy of closely packing spheres. The lack of change in rotational dynamics indicates the absence of strong crowder-protein interactions. Conclusions Our observations are explained by the large size discrepancy between the protein and crowders and by the internal structure of the microgels, which provide interstitial spaces and internal pores where the protein can exist in a dilute solution-like environment. In summary, microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.

  4. The contrasting effect of macromolecular crowding on amyloid fibril formation.

    Directory of Open Access Journals (Sweden)

    Qian Ma

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

  5. What Macromolecular Crowding Can Do to a Protein

    Science.gov (United States)

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

    2014-01-01

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

  6. Stochastic reaction–diffusion algorithms for macromolecular crowding

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    Sturrock, Marc

    2016-06-01

    Compartment-based (lattice-based) reaction–diffusion algorithms are often used for studying complex stochastic spatio-temporal processes inside cells. In this paper the influence of macromolecular crowding on stochastic reaction–diffusion simulations is investigated. Reaction–diffusion processes are considered on two different kinds of compartmental lattice, a cubic lattice and a hexagonal close packed lattice, and solved using two different algorithms, the stochastic simulation algorithm and the spatiocyte algorithm (Arjunan and Tomita 2010 Syst. Synth. Biol. 4, 35–53). Obstacles (modelling macromolecular crowding) are shown to have substantial effects on the mean squared displacement and average number of molecules in the domain but the nature of these effects is dependent on the choice of lattice, with the cubic lattice being more susceptible to the effects of the obstacles. Finally, improvements for both algorithms are presented.

  7. Macromolecular crowding and the steady-state kinetics of malate dehydrogenase.

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    Poggi, Christopher G; Slade, Kristin M

    2015-01-20

    To understand how macromolecular crowding affects enzyme activity, we quantified the Michaelis-Menten kinetics of mitochondrial malate dehydrogenase (MDH) in the presence of hen egg white (HEW), lysozyme, bovine serum albumin (BSA), gum arabic, poly(vinylpyrrolidone) (PVP), and dextrans of various molecular weights. Although crowding tended to decrease Km and Vmax values, the magnitude depended on the crowding agent, reaction direction, and isozyme (mitochondrial porcine heart or thermophlic TaqMDH from Thermus flavus). Crowding slowed oxaloacetate reduction more significantly than malate oxidation, which may suggest that mitochondrial enzymes have evolved to function optimally under the crowded constraints in which they are immersed. Since direct comparisons of neutral to charged crowders are underrepresented in the literature, we performed these studies and found that neutral crowding agents lowered Vmax values more than charged crowders of similar size. The exception was hen egg white, a mixture of charged proteins that caused the largest observed decreases in both Km and Vmax. Finally, the data provide insight about the mechanism by corroborating MDH subunit dependence.

  8. Macromolecular Crowding Enhances Thermal Stability of Rabbit Muscle Creatine Kinase

    Institute of Scientific and Technical Information of China (English)

    ZHU Jiang; HE Huawei; LI Sen

    2008-01-01

    The effect of dextran on the conformation (or secondary structure) and thermal stability of creatine kinase (CK) was studied using the far-ultraviolet (UV) circular dichroism (CD) spectra.The results showed that lower concentrations of dextran (less than 60 g/L) induced formation of the secondary CK structures.However,the secondary structure content of CK decreased when the dextran concentrations exceeded 60 g/L.Thermally induced transition curves were measured for CK in the presence of different concentrations of dextran by far-UV CD.The thermal transition curves were fitted to a two-state model by a nonlinear,least-squares method to obtain the transition temperature of the unfolding transition.An increase in the tran- sition temperature was observed with the increase of the dextran concentration.These observations qualita-tively accord with predictions of a previously proposed model for the effect of intermolecular excluded volume (macromolecular crowding) on protein stability and conformation.These findings imply that the effects of macromolecular crowding can have an important influence on our understanding of how protein folding oc-curs in vivo.

  9. The effect of macromolecular crowding on the structure of the protein complex superoxide dismutase

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    Rajapaksha Mudalige, Ajith Rathnaweera

    Biological environments contain between 7 - 40% macromolecules by volume. This reduces the available volume for macromolecules and elevates the osmotic pressure relative to pure water. Consequently, biological macromolecules in their native environments tend to adopt more compact and dehydrated conformations than those in vitro. This effect is referred to as macromolecular crowding and constitutes an important physical difference between native biological environments and the simple solutions in which biomolecules are usually studied. We used small angle scattering (SAS) to measure the effects of macromolecular crowding on the size of a protein complex, superoxide dismutase (SOD). Crowding was induced using 400 MW polyethylene glycol (PEG), triethylene glycol (TEG), methyl-alpha-glucoside (alpha-MG) and trimethylamine N-oxide (TMAO). Parallel small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS) allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. SAS coupled with osmotic pressure measurements allowed us to estimate a compressibility modulus for SOD. We believe this to be the first time the osmotic compressibility of a protein complex was measured. Molecular Dynamics (MD) simulations are widely used to obtain insights on biomolecular processes. However, it is not clear whether MD is capable of predicting subtle effects of macromolecular crowding. We used our experimentally observed compressibility of SOD to evaluate the ability of MD to predict macromolecular crowding. Effects of macromolecular crowding due to PEG on SOD were modeled using an all atom MD simulation with the CHARMM forcefield and the crystallographically resolved structures of SOD and PEG. Two parallel MD simulations were performed for SOD in water and SOD in 40% PEG for over 150~ns. Over the period of the simulation the SOD structure in 40

  10. Macromolecular crowding for tailoring tissue-derived fibrillated matrices.

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    Magno, Valentina; Friedrichs, Jens; Weber, Heather M; Prewitz, Marina C; Tsurkan, Mikhail V; Werner, Carsten

    2017-06-01

    Tissue-derived fibrillated matrices can be instrumental for the in vitro reconstitution of multiphasic extracellular microenvironments. However, despite of several advantages, the obtained scaffolds so far offer a rather narrow range of materials characteristics only. In this work, we demonstrate how macromolecular crowding (MMC) - the supplementation of matrix reconstitution media with synthetic or natural macromolecules in ways to create excluded volume effects (EVE) - can be employed for tailoring important structural and biophysical characteristics of kidney-derived fibrillated matrices. Porcine kidneys were decellularized, ground and the obtained extracellular matrix (ECM) preparations were reconstituted under varied MMC conditions. We show that MMC strongly influences the fibrillogenesis kinetics and impacts the architecture and the elastic modulus of the reconstituted matrices, with diameters and relative alignment of fibrils increasing at elevated concentrations of the crowding agent Ficoll400, a nonionic synthetic polymer of sucrose. Furthermore, we demonstrate how MMC modulates the distribution of key ECM molecules within the reconstituted matrix scaffolds. As a proof of concept, we compared different variants of kidney-derived fibrillated matrices in cell culture experiments referring to specific requirements of kidney tissue engineering approaches. The results revealed that MMC-tailored matrices support the morphogenesis of human umbilical vein endothelial cells (HUVECs) into capillary networks and of murine kidney stem cells (KSCs) into highly branched aggregates. The established methodology is concluded to provide generally applicable new options for tailoring tissue-specific multiphasic matrices in vitro. Tissue-derived fibrillated matrices can be instrumental for the in vitro reconstitution of multiphasic extracellular microenvironments. However, despite of several advantages, the obtained scaffolds so far offer a rather narrow range of materials

  11. Macromolecular Crowding Modulates Folding Mechanism of α/β Protein Apoflavodoxin

    Science.gov (United States)

    Homouz, D.; Stagg, L.; Wittungstafshede, P.; Cheung, M.

    2009-01-01

    Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, here we have investigated the folding energy landscape of an alpha/beta protein, apoflavodoxin, in the presence of inert macromolecular crowding agents using in silico and in vitro approaches. By coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fraction of crowding agents (phi_c) as well as of crowding agent geometry (sphere or spherocylinder) at high phi_c. Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we have identified in silico crowding conditions that best enhance protein stability and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. The test-tube experiments confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. We propose that macromolecular crowding effects may be a tool for manipulation of protein folding and function in living cells.

  12. Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding

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    Wang, Po-hung; Yu, Isseki; Feig, Michael; Sugita, Yuji

    2017-03-01

    We investigate the effects of protein crowder sizes on hydration structure and dynamics in macromolecular crowded systems by all-atom MD simulations. The crowded systems consisting of only small proteins showed larger total surface areas than those of large proteins at the same volume fractions. As a result, more water molecules were trapped within the hydration shells, slowing down water diffusion. The simulation results suggest that the protein crowder size is another factor to determine the effect of macromolecular crowding and to explain the experimental kinetic data of proteins and DNAs in the presence of crowding agents.

  13. Effect of macromolecular crowding on the rate of diffusion-limited enzymatic reaction

    Indian Academy of Sciences (India)

    Manish Agrawal; S B Santra; Rajat Anand; Rajaram Swaminathan

    2008-08-01

    The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with increase in macromolecular crowding. Moreover, many cellular processes are dependent on molecular diffusion in the cell cytosol. The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model qualitatively explains some of the experimental observations.

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

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    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2013-06-01

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

  15. Synergy of DNA-bending nucleoid proteins and macromolecular crowd-condensing DNA

    NARCIS (Netherlands)

    Bessa Ramos, E.; Wintraecken, C.H.J.M.; Geerling, A.C.M.; Vries, de R.J.

    2007-01-01

    Many prokaryotic nucleoid proteins bend DNA and form extended helical protein-DNA fibers rather than condensed structures. On the other hand, it is known that such proteins (such as bacterial HU) strongly promote DNA condensation by macromolecular crowding. Using theoretical arguments, we show that

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

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    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2014-01-01

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

  17. Macromolecular crowding increases binding of DNA polymerase to DNA: an adaptive effect

    Energy Technology Data Exchange (ETDEWEB)

    Zimmerman, S.B.; Harrison, B.

    1987-05-01

    Macromolecular crowding extends the range of ionic conditions supporting high DNA polymerase reaction rates. Reactions tested were nick translation and gap-filling by DNA polymerase I of E. coli, nuclease and polymerase activities of the large fragment of that polymerase, and polymerization by the T4 DNA polymerase. For all of these reactions, high concentrations of nonspecific polymers increased enzymatic activity under otherwise inhibitory conditions resulting from relatively high ionic strength. The primary mechanism of the polymer effect seems to be to increase the binding of polymerase to DNA. They suggest that this effect of protein-DNA complexes is only one example of a general metabolic buffering action of crowded solutions on a variety of macromolecular interactions.

  18. The Differential Response of Proteins to Macromolecular Crowding

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    Candotti, Michela; Orozco, Modesto

    2016-01-01

    The habitat in which proteins exert their function contains up to 400 g/L of macromolecules, most of which are proteins. The repercussions of this dense environment on protein behavior are often overlooked or addressed using synthetic agents such as poly(ethylene glycol), whose ability to mimic protein crowders has not been demonstrated. Here we performed a comprehensive atomistic molecular dynamic analysis of the effect of protein crowders on the structure and dynamics of three proteins, namely an intrinsically disordered protein (ACTR), a molten globule conformation (NCBD), and a one-fold structure (IRF-3) protein. We found that crowding does not stabilize the native compact structure, and, in fact, often prevents structural collapse. Poly(ethylene glycol) PEG500 failed to reproduce many aspects of the physiologically-relevant protein crowders, thus indicating its unsuitability to mimic the cell interior. Instead, the impact of protein crowding on the structure and dynamics of a protein depends on its degree of disorder and results from two competing effects: the excluded volume, which favors compact states, and quinary interactions, which favor extended conformers. Such a viscous environment slows down protein flexibility and restricts the conformational landscape, often biasing it towards bioactive conformations but hindering biologically relevant protein-protein contacts. Overall, the protein crowders used here act as unspecific chaperons that modulate the protein conformational space, thus having relevant consequences for disordered proteins. PMID:27471851

  19. Role of solvent properties of aqueous media in macromolecular crowding effects.

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    Ferreira, Luisa A; Madeira, Pedro P; Breydo, Leonid; Reichardt, Christian; Uversky, Vladimir N; Zaslavsky, Boris Y

    2016-01-01

    Analysis of the macromolecular crowding effects in polymer solutions show that the excluded volume effect is not the only factor affecting the behavior of biomolecules in a crowded environment. The observed inconsistencies are commonly explained by the so-called soft interactions, such as electrostatic, hydrophobic, and van der Waals interactions, between the crowding agent and the protein, in addition to the hard nonspecific steric interactions. We suggest that the changes in the solvent properties of aqueous media induced by the crowding agents may be the root of these "soft" interactions. To check this hypothesis, the solvatochromic comparison method was used to determine the solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity of aqueous solutions of different polymers (dextran, poly(ethylene glycol), Ficoll, Ucon, and polyvinylpyrrolidone) with the polymer concentration up to 40% typically used as crowding agents. Polymer-induced changes in these features were found to be polymer type and concentration specific, and, in case of polyethylene glycol (PEG), molecular mass specific. Similarly sized polymers PEG and Ucon producing different changes in the solvent properties of water in their solutions induced morphologically different α-synuclein aggregates. It is shown that the crowding effects of some polymers on protein refolding and stability reported in the literature can be quantitatively described in terms of the established solvent features of the media in these polymers solutions. These results indicate that the crowding agents do induce changes in solvent properties of aqueous media in crowded environment. Therefore, these changes should be taken into account for crowding effect analysis.

  20. Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

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    Amninder S Virk

    2015-02-01

    Full Text Available Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction. Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

  1. Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects.

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    Vazquez, Alexei

    2010-05-21

    Macromolecules occupy between 34% and 44% of the cell cytoplasm, about half the maximum packing density of spheres in three dimension. Yet, there is no clear understanding of what is special about this value. To address this fundamental question we investigate the effect of macromolecular crowding on cell metabolism. We develop a cell scale flux balance model capturing the main features of cell metabolism at different nutrient uptakes and macromolecular densities. Using this model we show there are two metabolic regimes at low and high nutrient uptakes. The latter regime is characterized by an optimal cytoplasmatic density where the increase of reaction rates by confinement and the decrease by diffusion slow-down balance. More important, the predicted optimal density is in the range of the experimentally determined density of Escherichia coli.

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

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    Anne-Sophie Coquel

    2013-04-01

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

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

    Science.gov (United States)

    Coquel, Anne-Sophie; Jacob, Jean-Pascal; Primet, Mael; Demarez, Alice; Dimiccoli, Mariella; Julou, Thomas; Moisan, Lionel; Lindner, Ariel B; Berry, Hugues

    2013-04-01

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

  4. Structure of metaphase chromosomes: a role for effects of macromolecular crowding.

    Science.gov (United States)

    Hancock, Ronald

    2012-01-01

    In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.

  5. Structure of metaphase chromosomes: a role for effects of macromolecular crowding.

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    Ronald Hancock

    Full Text Available In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.

  6. The Effect of Attractive Interactions and Macromolecular Crowding on Crystallins Association.

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    Jiachen Wei

    Full Text Available In living systems proteins are typically found in crowded environments where their effective interactions strongly depend on the surrounding medium. Yet, their association and dissociation needs to be robustly controlled in order to enable biological function. Uncontrolled protein aggregation often causes disease. For instance, cataract is caused by the clustering of lens proteins, i.e., crystallins, resulting in enhanced light scattering and impaired vision or blindness. To investigate the molecular origins of cataract formation and to design efficient treatments, a better understanding of crystallin association in macromolecular crowded environment is needed. Here we present a theoretical study of simple coarse grained colloidal models to characterize the general features of how the association equilibrium of proteins depends on the magnitude of intermolecular attraction. By comparing the analytic results to the available experimental data on the osmotic pressure in crystallin solutions, we identify the effective parameters regimes applicable to crystallins. Moreover, the combination of two models allows us to predict that the number of binding sites on crystallin is small, i.e. one to three per protein, which is different from previous estimates. We further observe that the crowding factor is sensitive to the size asymmetry between the reactants and crowding agents, the shape of the protein clusters, and to small variations of intermolecular attraction. Our work may provide general guidelines on how to steer the protein interactions in order to control their association.

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

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    Iborra Francisco J

    2007-04-01

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

  8. Macromolecular crowding meets oxygen tension in human mesenchymal stem cell culture - A step closer to physiologically relevant in vitro organogenesis

    Science.gov (United States)

    Cigognini, Daniela; Gaspar, Diana; Kumar, Pramod; Satyam, Abhigyan; Alagesan, Senthilkumar; Sanz-Nogués, Clara; Griffin, Matthew; O’Brien, Timothy; Pandit, Abhay; Zeugolis, Dimitrios I.

    2016-01-01

    Modular tissue engineering is based on the cells’ innate ability to create bottom-up supramolecular assemblies with efficiency and efficacy still unmatched by man-made devices. Although the regenerative potential of such tissue substitutes has been documented in preclinical and clinical setting, the prolonged culture time required to develop an implantable device is associated with phenotypic drift and/or cell senescence. Herein, we demonstrate that macromolecular crowding significantly enhances extracellular matrix deposition in human bone marrow mesenchymal stem cell culture at both 20% and 2% oxygen tension. Although hypoxia inducible factor - 1α was activated at 2% oxygen tension, increased extracellular matrix synthesis was not observed. The expression of surface markers and transcription factors was not affected as a function of oxygen tension and macromolecular crowding. The multilineage potential was also maintained, albeit adipogenic differentiation was significantly reduced in low oxygen tension cultures, chondrogenic differentiation was significantly increased in macromolecularly crowded cultures and osteogenic differentiation was not affected as a function of oxygen tension and macromolecular crowding. Collectively, these data pave the way for the development of bottom-up tissue equivalents based on physiologically relevant developmental processes. PMID:27478033

  9. Macromolecular crowding meets oxygen tension in human mesenchymal stem cell culture - A step closer to physiologically relevant in vitro organogenesis

    Science.gov (United States)

    Cigognini, Daniela; Gaspar, Diana; Kumar, Pramod; Satyam, Abhigyan; Alagesan, Senthilkumar; Sanz-Nogués, Clara; Griffin, Matthew; O'Brien, Timothy; Pandit, Abhay; Zeugolis, Dimitrios I.

    2016-08-01

    Modular tissue engineering is based on the cells’ innate ability to create bottom-up supramolecular assemblies with efficiency and efficacy still unmatched by man-made devices. Although the regenerative potential of such tissue substitutes has been documented in preclinical and clinical setting, the prolonged culture time required to develop an implantable device is associated with phenotypic drift and/or cell senescence. Herein, we demonstrate that macromolecular crowding significantly enhances extracellular matrix deposition in human bone marrow mesenchymal stem cell culture at both 20% and 2% oxygen tension. Although hypoxia inducible factor - 1α was activated at 2% oxygen tension, increased extracellular matrix synthesis was not observed. The expression of surface markers and transcription factors was not affected as a function of oxygen tension and macromolecular crowding. The multilineage potential was also maintained, albeit adipogenic differentiation was significantly reduced in low oxygen tension cultures, chondrogenic differentiation was significantly increased in macromolecularly crowded cultures and osteogenic differentiation was not affected as a function of oxygen tension and macromolecular crowding. Collectively, these data pave the way for the development of bottom-up tissue equivalents based on physiologically relevant developmental processes.

  10. Macromolecular crowding gives rise to microviscosity, anomalous diffusion and accelerated actin polymerization

    Science.gov (United States)

    Rashid, Rafi; Chee, Stella Min Ling; Raghunath, Michael; Wohland, Thorsten

    2015-05-01

    Macromolecular crowding (MMC) has been used in various in vitro experimental systems to mimic in vivo physiology. This is because the crowded cytoplasm of cells contains many different types of solutes dissolved in an aqueous medium. MMC in the extracellular microenvironment is involved in maintaining stem cells in their undifferentiated state (niche) as well as in aiding their differentiation after they have travelled to new locations outside the niche. MMC at physiologically relevant fractional volume occupancies (FVOs) significantly enhances the adipogenic differentiation of human bone marrow-derived mesenchymal stem cells during chemically induced adipogenesis. The mechanism by which MMC produces this enhancement is not entirely known. In the context of extracellular collagen deposition, we have recently reported the importance of optimizing the FVO while minimizing the bulk viscosity. Two opposing properties will determine the net rate of a biochemical reaction: the negative effect of bulk viscosity and the positive effect of the excluded volume, the latter being expressed by the FVO. In this study we have looked more closely at the effect of viscosity on reaction rates. We have used fluorimetry to measure the rate of actin polymerization and fluorescence correlation spectroscopy (FCS) to measure diffusion of various probes in solutions containing the crowder Ficoll at physiological concentrations. Similar to its effect on collagen, Ficoll enhanced the actin polymerization rate despite increasing the bulk viscosity. Our FCS measurements reveal a relatively minor component of anomalous diffusion. In addition, our measurements do suggest that microviscosity becomes relevant in a crowded environment. We ruled out bulk viscosity as a cause of the rate enhancement by performing the actin polymerization assay in glycerol. These opposite effects of Ficoll and glycerol led us to conclude that microviscosity becomes relevant at the length scale of the reacting

  11. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

    Science.gov (United States)

    Foffi, G; Pastore, A; Piazza, F; Temussi, P A

    2013-08-02

    More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). [Formula: see text] Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international

  12. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012)

    Science.gov (United States)

    Foffi, G.; Pastore, A.; Piazza, F.; Temussi, P. A.

    2013-08-01

    More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). Figure 1. Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international conference

  13. CaMKII binding to GluN2B is differentially affected by macromolecular crowding reagents.

    Science.gov (United States)

    Goodell, Dayton J; Eliseeva, Tatiana A; Coultrap, Steven J; Bayer, K Ulrich

    2014-01-01

    Binding of the Ca2+/calmodulin(CaM)-dependent protein kinase II (CaMKII) to the NMDA-type glutamate receptor (NMDAR) subunit GluN2B controls long-term potentiation (LTP), a form of synaptic plasticity thought to underlie learning and memory. Regulation of this interaction is well-studied biochemically, but not under conditions that mimic the macromolecular crowding found within cells. Notably, previous molecular crowding experiments with lysozyme indicated an effect on the CaMKII holoenzyme conformation. Here, we found that the effect of molecular crowding on Ca2+/CaM-induced CaMKII binding to immobilized GluN2B in vitro depended on the specific crowding reagent. While binding was reduced by lysozyme, it was enhanced by BSA. The ATP content in the BSA preparation caused CaMKII autophosphorylation at T286 during the binding reaction; however, enhanced binding was also observed when autophosphorylation was blocked. Importantly, the positive regulation by nucleotide and BSA (as well as other macromolecular crowding reagents) did not alleviate the requirement for CaMKII stimulation to induce GluN2B binding. The differential effect of lysozyme (14 kDa) and BSA (66 kDa) was not due to size difference, as both dextran-10 and dextran-70 enhanced binding. By contrast, crowding with immunoglobulin G (IgG) reduced binding. Notably, lysozyme and IgG but not BSA directly bound to Ca2+/CaM in an overlay assay, suggesting a competition of lysozyme and IgG with the Ca2+/CaM-stimulus that induces CaMKII/GluN2B binding. However, lysozyme negatively regulated binding even when it was instead induced by CaMKII T286 phosphorylation. Alternative modes of competition would be with CaMKII or GluN2B, and the negative effects of lysozyme and IgG indeed also correlated with specific or non-specific binding to the immobilized GluN2B. Thus, the effect of any specific crowding reagent can differ, depending on its additional direct effects on CaMKII/GluN2B binding. However, the results of this

  14. CaMKII binding to GluN2B is differentially affected by macromolecular crowding reagents.

    Directory of Open Access Journals (Sweden)

    Dayton J Goodell

    Full Text Available Binding of the Ca2+/calmodulin(CaM-dependent protein kinase II (CaMKII to the NMDA-type glutamate receptor (NMDAR subunit GluN2B controls long-term potentiation (LTP, a form of synaptic plasticity thought to underlie learning and memory. Regulation of this interaction is well-studied biochemically, but not under conditions that mimic the macromolecular crowding found within cells. Notably, previous molecular crowding experiments with lysozyme indicated an effect on the CaMKII holoenzyme conformation. Here, we found that the effect of molecular crowding on Ca2+/CaM-induced CaMKII binding to immobilized GluN2B in vitro depended on the specific crowding reagent. While binding was reduced by lysozyme, it was enhanced by BSA. The ATP content in the BSA preparation caused CaMKII autophosphorylation at T286 during the binding reaction; however, enhanced binding was also observed when autophosphorylation was blocked. Importantly, the positive regulation by nucleotide and BSA (as well as other macromolecular crowding reagents did not alleviate the requirement for CaMKII stimulation to induce GluN2B binding. The differential effect of lysozyme (14 kDa and BSA (66 kDa was not due to size difference, as both dextran-10 and dextran-70 enhanced binding. By contrast, crowding with immunoglobulin G (IgG reduced binding. Notably, lysozyme and IgG but not BSA directly bound to Ca2+/CaM in an overlay assay, suggesting a competition of lysozyme and IgG with the Ca2+/CaM-stimulus that induces CaMKII/GluN2B binding. However, lysozyme negatively regulated binding even when it was instead induced by CaMKII T286 phosphorylation. Alternative modes of competition would be with CaMKII or GluN2B, and the negative effects of lysozyme and IgG indeed also correlated with specific or non-specific binding to the immobilized GluN2B. Thus, the effect of any specific crowding reagent can differ, depending on its additional direct effects on CaMKII/GluN2B binding. However, the

  15. The effect of macromolecular crowding on mobility of biomolecules, association kinetics and gene expression in living cells

    Science.gov (United States)

    Tabaka, Marcin; Kalwarczyk, Tomasz; Szymanski, Jedrzej; Hou, Sen; Hołyst, Robert

    2014-09-01

    We discuss a quantitative influence of macromolecular crowding on biological processes: motion, bimolecular reactions, and gene expression in prokaryotic and eukaryotic cells. We present scaling laws relating diffusion coefficient of an object moving in a cytoplasm of cells to a size of this object and degree of crowding. Such description leads to the notion of the length scale dependent viscosity characteristic for all living cells. We present an application of the length-scale dependent viscosity model to the description of motion in the cytoplasm of both eukaryotic and prokaryotic living cells. We compare the model with all recent data on diffusion of nanoscopic objects in HeLa, and E. coli cells. Additionally a description of the mobility of molecules in cell nucleus is presented. Finally we discuss the influence of crowding on the bimolecular association rates and gene expression in living cells.

  16. Effects of Macromolecular Crowding on Alcohol Dehydrogenase Activity Are Substrate-Dependent.

    Science.gov (United States)

    Wilcox, A E; LoConte, Micaela A; Slade, Kristin M

    2016-06-28

    Enzymes operate in a densely packed cellular environment that rarely matches the dilute conditions under which they are studied. To better understand the ramifications of this crowding, the Michaelis-Menten kinetics of yeast alcohol dehydrogenase (YADH) were monitored spectrophotometrically in the presence of high concentrations of dextran. Crowding decreased the maximal rate of the reaction by 40% for assays with ethanol, the primary substrate of YADH. This observation was attributed to slowed release of the reduced β-nicotinamide adenine dinucleotide product, which is rate-limiting. In contrast, when larger alcohols were used as the YADH substrate, the rate-limiting step becomes hydride transfer and crowding instead increased the maximal rate of the reaction by 20-40%. This work reveals the importance of considering enzyme mechanism when evaluating the ways in which crowding can alter kinetics.

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

    Directory of Open Access Journals (Sweden)

    Helena W Qi

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

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

    NARCIS (Netherlands)

    Wintraecken, C.H.J.M.

    2012-01-01

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

  19. Effects of macromolecular crowding on the structural stability of human α-lactalbumin

    Institute of Scientific and Technical Information of China (English)

    De-Lin Zhang; Ling-Jia Wu; Jie Chen; Yi Liang

    2012-01-01

    The folding of protein,an important process for protein to fulfill normal functions,takes place in crowded physiological environments.α-Lactaibumin,as a model system for protein-folding studies,has been used extensively because it can form stable molten globule states under a range of conditions.Here we report that the crowding agents Ficoll 70,dextran 70,and polyethylene glycol (PEG) 2000 have different effects on the structural stability of human α-lactalbumin (HLA) represented by the transition to a molten globule state: dextran 70 dramatically enhances the thermal stability of Ca2+-depleted HLA (apo-HLA) and Ficoll 70 enhances the thermal stability of apo-HLA to some extent,while PEG 2000 significantly decreases the thermal stability of apo-HLA.Ficoll 70 and dextran 70 have no obvious effects on trypsin degradation of apo-HLA but PEG 2000 accelerates apo-HLA degradation by trypsin and destabilizes the native conformation of apo-HLA.Furthermore,no interaction is observed between apo-HLA and Ficoll 70 or dextran 70,but a weak,non-specific interaction between the apo form of the protein and PEG 2000 is detected,and such a weak,non-specific interaction could overcome the excludedvolume effect of PEG 2000.Our data are consistent with the results of protein stability studies in cells and suggest that stabilizing excluded-volume effects of crowding agents can be ameliorated by non-specific interactions between proteins and crowders.

  20. A macromolecular crowding study of RNA folding and activity: polymer pore size matters! (Conference Presentation)

    Science.gov (United States)

    Börner, Richard; Fiorini, Erica; Paudel, Bishnu; Rueda, David; Sigel, Roland K. O.

    2016-03-01

    Catalytic RNAs, like the group IIB intron ribozyme of S. cerevesiae, require a high magnesium(II) concentration to show folding and function in vitro [1]. In contrast, in vivo conditions are characterized by a highly crowded cellular environment and much lower ion concentration. Molecular crowding agents are a widespread tool to mimic cellular crowding [2]. However, particular physical/chemical properties explaining the crowders influence are mostly not understood. In this study, we gain new insights on how polymer properties like viscosity, pore size etc. influence the activity and folding of a large RNA. We combined bulk activity assays and single-molecule Förster Resonance Energy Transfer experiments, screening the PEG volume fraction (%) and molecular weight (MW). Our results revealed that upon the influence of crowding agents, a compaction of the underlying structure depends on the PEG % and the presence of different PEG MW and % unveiled an optimal pore size in terms of catalytic activity. In summary, an increasing density of the crowding environment shifts the RNA towards the most compact state, but the ribozyme is only active if the crowders network matches its size [4]. We interpret the most compact state as necessary, but not sufficient, to keep the ribozyme active. Financial support from the European Research Council (MIRNA N° 259092, to RKOS), the Swiss National Fund (SNF), and the Forschungskredit Grant of the University of Zürich (FK-14-096 and 15-092 to RB) are gratefully acknowledged. [1] Swisher J.F., Su L.J., Brenowitz M., Anderson V.E., Pyle A.M., J. Mol. Bio., 315, 297-310 (2002). [2] Kilburn D., Roh J.H., Guo L., Briber R.M., Woodson S.A., JACS, 132, 8690-6 (2010). [3] Steiner M., Karunatilaka K.S., Sigel R.K.O., Rueda D., Proc. Natl. Acad. Sci. U.S.A.,105, 13853-8 (2008). [4] aBörner R, Fiorini E, Sigel R.K.O., Chimia, 69, 207-212 (2015).; bFiorini E., Paudel B., Börner R., Rueda D., Sigel R.K.O., submitted. [5] König S.L.B., Hadzic M

  1. Effects of macromolecular crowding on amyloid beta (16-22) aggregation using coarse-grained simulations.

    Science.gov (United States)

    Latshaw, David C; Cheon, Mookyung; Hall, Carol K

    2014-11-26

    To examine the effect of crowding on protein aggregation, discontinuous molecular dynamics (DMD) simulations combined with an intermediate resolution protein model, PRIME20, were applied to a peptide/crowder system. The systems contained 192 Aβ(16-22) peptides and crowders of diameters 5, 20, and 40 Å, represented here by simple hard spheres, at crowder volume fractions of 0.00, 0.10, and 0.20. Results show that both crowder volume fraction and crowder diameter have a large impact on fibril and oligomer formation. The addition of crowders to a system of peptides increases the rate of oligomer formation, shifting from a slow ordered formation of oligomers in the absence of crowders, similar to nucleated polymerization, to a fast collapse of peptides and subsequent rearrangement characteristic of nucleated conformational conversion with a high maximum in the number of peptides in oligomers as the total crowder surface area increases. The rate of conversion from oligomers to fibrils also increases with increasing total crowder surface area, giving rise to an increased rate of fibril growth. In all cases, larger volume fractions and smaller crowders provide the greatest aggregation enhancement effects. We also show that the size of the crowders influences the formation of specific oligomer sizes. In our simulations, the 40 Å crowders enhance the number of dimers relative to the numbers of trimers, hexamers, pentamers, and hexamers, while the 5 Å crowders enhance the number of hexamers relative to the numbers of dimers, trimers, tetramers, and pentamers. These results are in qualitative agreement with previous experimental and theoretical work.

  2. Effects of Macromolecular Crowding on Human Adipose Stem Cell Culture in Fetal Bovine Serum, Human Serum, and Defined Xeno-Free/Serum-Free Conditions

    Directory of Open Access Journals (Sweden)

    Mimmi Patrikoski

    2017-01-01

    Full Text Available Microenvironment plays an important role for stem cell proliferation and differentiation. Macromolecular crowding (MMC was recently shown to assist stem cells in forming their own matrix microenvironment in vitro. The ability of MMC to support adipose stem cell (ASC proliferation, metabolism, and multilineage differentiation was studied under different conditions: fetal bovine serum- (FBS- and human serum- (HS- based media and xeno- and serum-free (XF/SF media. Furthermore, the immunophenotype of ASCs under MMC was evaluated. The proliferative capacity of ASCs under MMC was attenuated in each condition. However, osteogenic differentiation was enhanced under MMC, shown by increased deposition of mineralized matrix in FBS and HS cultures. Likewise, significantly greater lipid droplet accumulation and increased collagen IV deposition indicated enhanced adipogenesis under MMC in FBS and HS cultures. In contrast, chondrogenic differentiation was attenuated in ASCs expanded under MMC. The ASC immunophenotype was maintained under MMC with significantly higher expression of CD54. However, MMC impaired metabolic activity and differentiation capacity of ASCs in XF/SF conditions. Both the supportive and inhibitory effects of MMC on ASC are culture condition dependent. In the presence of serum, MMC maintains ASC immunophenotype and enhances adipogenic and osteogenic differentiation at the cost of reduced proliferation.

  3. The Role of Crowding Forces in Juxtaposing β-Globin Gene Domain Remote Regulatory Elements in Mouse Erythroid Cells.

    Directory of Open Access Journals (Sweden)

    Arkadiy K Golov

    Full Text Available The extremely high concentration of macromolecules in a eukaryotic cell nucleus indicates that the nucleoplasm is a crowded macromolecular solution in which large objects tend to gather together due to crowding forces. It has been shown experimentally that crowding forces support the integrity of various nuclear compartments. However, little is known about their role in control of chromatin dynamics in vivo. Here, we experimentally addressed the possible role of crowding forces in spatial organization of the eukaryotic genome. Using the mouse β-globin domain as a model, we demonstrated that spatial juxtaposition of the remote regulatory elements of this domain in globin-expressing cells may be lost and restored by manipulation of the level of macromolecular crowding. In addition to proving the role of crowding forces in shaping interphase chromatin, our results suggest that the folding of the chromatin fiber is a major determinant in juxtaposing remote genomic elements.

  4. Attentional priming releases crowding.

    Science.gov (United States)

    Kristjánsson, Arni; Heimisson, Pétur Rúnar; Róbertsson, Gunnar Freyr; Whitney, David

    2013-10-01

    Views of natural scenes unfold over time, and objects of interest that were present a moment ago tend to remain present. While visual crowding places a fundamental limit on object recognition in cluttered scenes, most studies of crowding have suffered from the limitation that they typically involved static scenes. The role of temporal continuity in crowding has therefore been unaddressed. We investigated intertrial effects upon crowding in visual scenes, showing that crowding is considerably diminished when objects remain constant on consecutive visual search trials. Repetition of both the target and distractors decreases the critical distance for crowding from flankers. More generally, our results show how object continuity through between-trial priming releases objects that would otherwise be unidentifiable due to crowding. Crowding, although it is a significant bottleneck on object recognition, can be mitigated by statistically likely temporal continuity of the objects. Crowding therefore depends not only on what is momentarily present, but also on what was previously attended.

  5. THE OPEP COARSE-GRAINED PROTEIN MODEL: FROM SINGLE MOLECULES, AMYLOID FORMATION, ROLE OF MACROMOLECULAR CROWDING AND HYDRODYNAMICS TO RNA/DNA COMPLEXES

    OpenAIRE

    Sterpone, Fabio; Melchionna, Simone; Tuffery, Pierre; Pasquali, Samuela; Mousseau, Normand; Cragnolini, Tristan; Chebaro, Yassmine; Saint-Pierre, Jean-Francois; Kalimeri, Maria; Barducci, Alessandro; Laurin, Yohan; Tek, Alex; Baaden, Marc; Nguyen, Phuong Hoang; Derreumaux, Philippe

    2014-01-01

    The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows studying single protein properties, DNA/RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then presen...

  6. 基于大分子拥挤原理的介孔二氧化硅中青霉素酰化酶的共价组装%Covalent Assembly of Penicillin Acylase in Mesoporous Silica Based on Macromolecular Crowding Theory

    Institute of Scientific and Technical Information of China (English)

    王安明; 周成; 王华; 沈树宝; 薛建跃; 欧阳平凯

    2007-01-01

    To improve the covalent immobilization of penicillin acylase (PA),macromolecular crowding theory was applied to its immobilization. Influence of mass ratio of enzyme to the silica,as well as,activation time with glutaraldehyde on the activity of assembled PA,was studied. In the mesopores,the effect of β-cyclodextrin (β-CD)on the immobilization of the enzyme was also investigated. It was remarkable that the coupled yield and relative activity reached 99.5% and 92.3%,respectively,when penicillin acylase assembled covalently in the mesopores. The results here indicate that mimicked macromolecule crowding could significantly ameliorate the performance of covalently immobilized PA.

  7. THE OPEP COARSE-GRAINED PROTEIN MODEL: FROM SINGLE MOLECULES, AMYLOID FORMATION, ROLE OF MACROMOLECULAR CROWDING AND HYDRODYNAMICS TO RNA/DNA COMPLEXES

    Science.gov (United States)

    Sterpone, Fabio; Melchionna, Simone; Tuffery, Pierre; Pasquali, Samuela; Mousseau, Normand; Cragnolini, Tristan; Chebaro, Yassmine; Saint-Pierre, Jean-Francois; Kalimeri, Maria; Barducci, Alessandro; Laurin, Yohan; Tek, Alex; Baaden, Marc; Nguyen, Phuong Hoang; Derreumaux, Philippe

    2015-01-01

    The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows studying single protein properties, DNA/RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the on-going developments. PMID:24759934

  8. Associative Interactions in Crowded Solutions of Biopolymers Counteract Depletion Effects

    NARCIS (Netherlands)

    Groen, Joost; Foschepoth, David; te Brinke, Esra; Boersma, Arnold J; Imamura, Hiromi; Rivas, Germán; Heus, Hans A; Huck, Wilhelm T S

    2015-01-01

    The cytosol of Escherichia coli is an extremely crowded environment, containing high concentrations of biopolymers which occupy 20-30% of the available volume. Such conditions are expected to yield depletion forces, which strongly promote macromolecular complexation. However, crowded macromolecule s

  9. Crowding in polymer-nanoparticle mixtures.

    Science.gov (United States)

    Denton, Alan R

    2014-01-01

    The cell nucleus is a highly crowded environment, filled with a multicomponent, polydisperse mixture of biopolymers and nuclear bodies dispersed in a viscous solvent. With volume fractions approaching 20%, excluded-volume interactions play a key role in determining the structure, dynamics, and function of macromolecules in vivo. Under such constraints, the ensembles of macromolecular conformations can differ substantially from those prevailing in dilute solutions. Crowding thus can affect protein and RNA folding, conformational stability, and reaction kinetics, as well as phase stability of macromolecular mixtures. From the perspective of soft matter physics, this chapter reviews recent studies on crowding in polymer-nanoparticle mixtures, seeking to demonstrate the utility of simple physical models for addressing challenging issues in cell biology. The focus is on applications of free-volume theory and Monte Carlo simulation, based on geometrical models of polymers as fluctuating spheres or ellipsoids. Ideal polymer coils respond to hard-sphere crowding agents by compactifying, reducing their radius of gyration, and becoming more spherical. At sufficiently high concentrations, polymers and crowders phase-separate. The goal of this review is to identify universal principles governing macromolecular crowding and to establish a general framework for future explorations of more realistic models that may include nonsteric (e.g., electrostatic) interactions. © 2014 Elsevier Inc. All rights reserved.

  10. Object crowding.

    Science.gov (United States)

    Wallace, Julian M; Tjan, Bosco S

    2011-05-25

    Crowding occurs when stimuli in the peripheral fields become harder to identify when flanked by other items. This phenomenon has been demonstrated extensively with simple patterns (e.g., Gabors and letters). Here, we characterize crowding for everyday objects. We presented three-item arrays of objects and letters, arranged radially and tangentially in the lower visual field. Observers identified the central target, and we measured contrast energy thresholds as a function of target-to-flanker spacing. Object crowding was similar to letter crowding in spatial extent but was much weaker. The average elevation in threshold contrast energy was in the order of 1 log unit for objects as compared to 2 log units for letters and silhouette objects. Furthermore, we examined whether the exterior and interior features of an object are differentially affected by crowding. We used a circular aperture to present or exclude the object interior. Critical spacings for these aperture and "donut" objects were similar to those of intact objects. Taken together, these findings suggest that crowding between letters and objects are essentially due to the same mechanism, which affects equally the interior and exterior features of an object. However, for objects defined with varying shades of gray, it is much easier to overcome crowding by increasing contrast.

  11. Associative Interactions in Crowded Solutions of Biopolymers Counteract Depletion Effects.

    Science.gov (United States)

    Groen, Joost; Foschepoth, David; te Brinke, Esra; Boersma, Arnold J; Imamura, Hiromi; Rivas, Germán; Heus, Hans A; Huck, Wilhelm T S

    2015-10-14

    The cytosol of Escherichia coli is an extremely crowded environment, containing high concentrations of biopolymers which occupy 20-30% of the available volume. Such conditions are expected to yield depletion forces, which strongly promote macromolecular complexation. However, crowded macromolecule solutions, like the cytosol, are very prone to nonspecific associative interactions that can potentially counteract depletion. It remains unclear how the cytosol balances these opposing interactions. We used a FRET-based probe to systematically study depletion in vitro in different crowded environments, including a cytosolic mimic, E. coli lysate. We also studied bundle formation of FtsZ protofilaments under identical crowded conditions as a probe for depletion interactions at much larger overlap volumes of the probe molecule. The FRET probe showed a more compact conformation in synthetic crowding agents, suggesting strong depletion interactions. However, depletion was completely negated in cell lysate and other protein crowding agents, where the FRET probe even occupied slightly more volume. In contrast, bundle formation of FtsZ protofilaments proceeded as readily in E. coli lysate and other protein solutions as in synthetic crowding agents. Our experimental results and model suggest that, in crowded biopolymer solutions, associative interactions counterbalance depletion forces for small macromolecules. Furthermore, the net effects of macromolecular crowding will be dependent on both the size of the macromolecule and its associative interactions with the crowded background.

  12. Crowd Sourcing.

    Science.gov (United States)

    Baum, Neil

    2016-01-01

    The Internet has contributed new words and slang to our daily vernacular. A few terms, such as tweeting, texting, sexting, blogging, and googling, have become common in most vocabularies and in many languages, and are now included in the dictionary. A new buzzword making the rounds in industry is crowd sourcing, which involves outsourcing an activity, task, or problem by sending it to people or groups outside a business or a practice. Crowd sourcing allows doctors and practices to tap the wisdom of many instead of relying only on the few members of their close-knit group. This article defines "crowd sourcing," offers examples, and explains how to get started with this approach that can increase your ability to finish a task or solve problems that you don't have the time or expertise to accomplish.

  13. Crowd Theory and the Management of Crowds

    DEFF Research Database (Denmark)

    Borch, Christian

    2013-01-01

    Sociologists of policing and collective protest have made a plea for eradicating from police literature and training programmes which aim to provide guidelines for crowd management any references to classical crowd theory where crowds are depicted as irrational entities. Instead, these scholars...... suggest, rational conceptions of crowds should inform contemporary crowd management. This article questions this plea on two grounds. First, it demonstrates that there is no unidirectional connection between sociological crowd theory (whatever its content) and practical strategies for governing crowds....... The tactical polyvalence of crowd theory is illustrated by showing how the irrational conception of crowds has given rise to very different strategies for the management of crowds (urban reform programmes in the Progressive Era and Hitler’s mobilization strategies, respectively). Second, the article argues...

  14. Rigidity of a spherical capsule switches the localization of encapsulated particles between inner and peripheral regions under crowding condition: Simple model on cellular architecture

    Energy Technology Data Exchange (ETDEWEB)

    Shew, Chwen-Yang, E-mail: chwenyang.shew@csi.cuny.edu; Kondo, Kenta [Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314 (United States); Yoshikawa, Kenichi [Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394 (Japan)

    2014-01-14

    We have investigated the inhomogeneous interior of confined spherical cavities as capsules containing encapsulated binary hard sphere mixtures for different compositions and cavity wall rigidity. Such a greatly simplified model manifests the effects of macromolecular crowding arising from excluded volume interactions in a tiny cell or a cellular nucleus. By fixing the number of large particles, the level of crowding is adjusted by changing the amount of small hard spheres in the cavity. For a rigid cavity, large spheres tend to pack in liquid-like order apart from the surface to the center of the cavity as the crowding level is increased. Whereas, for a soft cavity, larger spheres tend to blend with small spheres in the peripheral region at near the boundary of the cavity, and are susceptible to be depleted from the interior of the cavity as the cavity becomes more crowded. These results may help future elucidation of the thermodynamic pathways to stabilize the inhomogeneous structure of mixtures confined in cavities, such as the derepression of genome materials around the interior rim of the nucleus in a cancerous cell.

  15. Look into Crowds.

    Science.gov (United States)

    Christian Education Movement, London (England).

    This booklet is designed to help British teachers introduce concepts of crowds to young students. Elementary school students will better understand issues of crowd behavior such as rural to urban migration and crowding in urban areas if they realize that all crowds are composed of individual human beings. Teachers can help students become familiar…

  16. Macromolecular Prodrugs of Ribavirin

    DEFF Research Database (Denmark)

    Riber, Camilla Frich; Hinton, Tracey M; Gajda, Paulina

    2017-01-01

    The requirement for new antiviral therapeutics is an ever present need. Particularly lacking are broad spectrum antivirals that have low toxicity. We develop such agents based on macromolecular prodrugs whereby both the polymer chain and the drug released from the polymer upon cell entry have ant...

  17. Macromolecular Crystallization in Microgravity

    Science.gov (United States)

    Snell, Edward H.; Helliwell, John R.

    2004-01-01

    The key concepts that attracted crystal growers, macromolecular or solid state, to microgravity research is that density difference fluid flows and sedimentation of the growing crystals are greatly reduced. Thus, defects and flaws in the crystals can be reduced, even eliminated, and crystal volume can be increased. Macromolecular crystallography differs from the field of crystalline semiconductors. For the latter, crystals are harnessed for their electrical behaviors. A crystal of a biological macromolecule is used instead for diffraction experiments (X-ray or neutron) to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal of a biological macromolecule then the more molecular structure detail that can be extracted. This structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences with major potential in understanding disease pathologies. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry, and mathematics meet to enable insight to the basic fundamentals of life. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment, and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyze the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural

  18. Macromolecular crystallization in microgravity

    Energy Technology Data Exchange (ETDEWEB)

    Snell, Edward H [Biophysics Group, NASA Marshall Space Flight Center, Code XD42, Huntsville, AL 35812 (United States); Helliwell, John R [Department of Chemistry, The University of Manchester, Manchester, M13 9PL (United Kingdom)

    2005-04-01

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

  19. Uncovering foveal crowding?

    Science.gov (United States)

    Lev, Maria; Yehezkel, Oren; Polat, Uri

    2014-02-12

    Visual crowding, as context modulation, reduce the ability to recognize objects in clutter, sets a fundamental limit on visual perception and object recognition. It's considered that crowding does not exist in the fovea and extensive efforts explored crowding in the periphery revealed various models that consider several aspects of spatial processing. Studies showed that spatial and temporal crowding are correlated, suggesting a tradeoff between spatial and temporal processing of crowding. We hypothesized that limiting stimulus availability should decrease object recognition in clutter. Here we show, for the first time, that robust contour interactions exist in the fovea for much larger target-flanker spacing than reported previously: participants overcome crowded conditions for long presentations times but exhibit contour interaction effects for short presentation times. Thus, by enabling enough processing time in the fovea, contour interactions can be overcome, enabling object recognition. Our results suggest that contemporary models of context modulation should include both time and spatial processing.

  20. Perceived positions determine crowding.

    Science.gov (United States)

    Maus, Gerrit W; Fischer, Jason; Whitney, David

    2011-01-01

    Crowding is a fundamental bottleneck in object recognition. In crowding, an object in the periphery becomes unrecognizable when surrounded by clutter or distractor objects. Crowding depends on the positions of target and distractors, both their eccentricity and their relative spacing. In all previous studies, position has been expressed in terms of retinal position. However, in a number of situations retinal and perceived positions can be dissociated. Does retinal or perceived position determine the magnitude of crowding? Here observers performed an orientation judgment on a target Gabor patch surrounded by distractors that drifted toward or away from the target, causing an illusory motion-induced position shift. Distractors in identical physical positions led to worse performance when they drifted towards the target (appearing closer) versus away from the target (appearing further). This difference in crowding corresponded to the difference in perceived positions. Further, the perceptual mislocalization was necessary for the change in crowding, and both the mislocalization and crowding scaled with drift speed. The results show that crowding occurs after perceived positions have been assigned by the visual system. Crowding does not operate in a purely retinal coordinate system; perceived positions need to be taken into account.

  1. Perceived positions determine crowding.

    Directory of Open Access Journals (Sweden)

    Gerrit W Maus

    Full Text Available Crowding is a fundamental bottleneck in object recognition. In crowding, an object in the periphery becomes unrecognizable when surrounded by clutter or distractor objects. Crowding depends on the positions of target and distractors, both their eccentricity and their relative spacing. In all previous studies, position has been expressed in terms of retinal position. However, in a number of situations retinal and perceived positions can be dissociated. Does retinal or perceived position determine the magnitude of crowding? Here observers performed an orientation judgment on a target Gabor patch surrounded by distractors that drifted toward or away from the target, causing an illusory motion-induced position shift. Distractors in identical physical positions led to worse performance when they drifted towards the target (appearing closer versus away from the target (appearing further. This difference in crowding corresponded to the difference in perceived positions. Further, the perceptual mislocalization was necessary for the change in crowding, and both the mislocalization and crowding scaled with drift speed. The results show that crowding occurs after perceived positions have been assigned by the visual system. Crowding does not operate in a purely retinal coordinate system; perceived positions need to be taken into account.

  2. Microgravity and Macromolecular Crystallography

    Science.gov (United States)

    Kundrot, Craig E.; Judge, Russell A.; Pusey, Marc L.; Snell, Edward H.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    Macromolecular crystal growth has been seen as an ideal experiment to make use of the reduced acceleration environment provided by an orbiting spacecraft. The experiments are small, simply operated and have a high potential scientific and economic impact. In this review we examine the theoretical reasons why microgravity should be a beneficial environment for crystal growth and survey the history of experiments on the Space Shuttle Orbiter, on unmanned spacecraft, and on the Mir space station. Finally we outline the direction for optimizing the future use of orbiting platforms.

  3. Dependence of Protein Folding Stability and Dynamics on the Density and Composition of Macromolecular Crowders

    Science.gov (United States)

    Mittal, Jeetain; Best, Robert B.

    2010-01-01

    We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the variation in folding stability with crowder size for typical α-, β-, and α/β-proteins is well described by an adaptation of the scaled particle theory. The native state, the transition state, and the unfolded protein are treated as effective hard spheres, with the folded and transition state radii independent of the size and concentration of the crowders. Remarkably, we find that, as the effective unfolded state radius is very weakly dependent on the crowder concentration, it can also be approximated by a single size. The same model predicts the effect of crowding on the folding barrier and therefore refolding rates with no adjustable parameters. A simple extension of the scaled-particle theory model, assuming additivity, can also describe the behavior of mixtures of crowding particles. PMID:20338853

  4. Cities, Crowding and Crime

    Science.gov (United States)

    Trotter, Robert J.

    1974-01-01

    This article considers the effects of human crowding in light of recent tests and observations. Factors such as sex, age, culture, socio-economic standing, frustration, and interpersonal physical distance are examined. Results indicate that crowding contributes to social problems and crime. (TK)

  5. Crowding and Density

    Science.gov (United States)

    Design and Environment, 1972

    1972-01-01

    Three-part report pinpointing problems and uncovering solutions for the dual concepts of density (ratio of people to space) and crowding (psychological response to density). Section one, A Primer on Crowding,'' reviews new psychological and social findings; section two, Density in the Suburbs,'' shows conflict between status quo and increased…

  6. Crowding as appropriation

    DEFF Research Database (Denmark)

    Thelle, Mikkel

    2016-01-01

    This article seeks to address the relation between crowds andpublic space as a question of appropriation. With the newliberal constitutions in Europe, several phenomena of crowdingemerge in major cities, of which Copenhagen is taken as anexample. By focusing on the crowd as an agglomeration ofbod...

  7. Crowds and Speculation

    DEFF Research Database (Denmark)

    Bondo Hansen, Kristian

    , the dissertation offers a broad, yet rigorously focused, historical perspective on crowd phenomena in financial markets. Furthermore, it explores how ideas about crowd action, imitation, herding and contagion were introduced to and became integral parts of the discourses on financial markets. Reiterations......This dissertation undertakes an explorative historical analysis of problems associated with crowd phenomena in the U.S. financial markets between 1890 and 1940. While a study of crowd-related problems in the financial markets invariably involves examinations of panics and crises, the dissertation...... shows that crowds were not exclusively seen as crisis phenomena, but were considered by many financial writers to be of much broader significance to the organisation and functioning of markets. The dissertation claims that it is necessary to explore the close connections between financial markets...

  8. Dynamics of crowd disasters: An empirical study

    Science.gov (United States)

    Helbing, Dirk; Johansson, Anders; Al-Abideen, Habib Zein

    2007-04-01

    Many observations of the dynamics of pedestrian crowds, including various self-organization phenomena, have been successfully described by simple many-particle models. For ethical reasons, however, there is a serious lack of experimental data regarding crowd panic. Therefore, we have analyzed video recordings of the crowd disaster in Mina/Makkah during the Hajj in 1426H on 12 January 2006. They reveal two subsequent, sudden transitions from laminar to stop-and-go and “turbulent” flows, which question many previous simulation models. While the transition from laminar to stop-and-go flows supports a recent model of bottleneck flows [D. Helbing , Phys. Rev. Lett. 97, 168001 (2006)], the subsequent transition to turbulent flow is not yet well understood. It is responsible for sudden eruptions of pressure release comparable to earthquakes, which cause sudden displacements and the falling and trampling of people. The insights of this study into the reasons for critical crowd conditions are important for the organization of safer mass events. In particular, they allow one to understand where and when crowd accidents tend to occur. They have also led to organizational changes, which have ensured a safe Hajj in 1427H.

  9. Effects of Crowding in Prisons.

    Science.gov (United States)

    Paulus, Paul B.; And Others

    Research on crowding in prisons is reviewed. Studies have shown that crowding in prisons can increase blood pressure, palmar sweat, illness complaints, and aggression. The number of people per housing unit appears to be more important than space per person. Tolerance for crowding was found to decrease with the experience of crowding. Research on…

  10. Taming Crowded Visual Scenes

    Science.gov (United States)

    2014-08-12

    movements  and  behaviors  of  “ crowds ”  of  people.  This   interest  spans  several  scientific... movement  in  dense,  heterogeneous   crowds .  The  monograph   is  organized  into  different  parts  that  consolidate...project. We developed solutions to a number of important and challenging problems related to visual analysis of crowds and modeling of

  11. Crowd Control Plan

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This Crowd Control Plan for Swan Lake National Wildlife Refuge outlines operational procedures in the event of a civil disorder on the Refuge. An inventory of...

  12. CrowdFilter

    DEFF Research Database (Denmark)

    Mortensen, Michael Lind; Wallace, Byron C.; Kraska, Tim

    for complex multi-criteria search problems through crowdsourcing. The CrowdFilter system is capable of supporting both criteria-level labels and n-gram rationales, capturing the human decision making process behind each filtering choice. Using the data provided through CrowdFilter we also introduce a novel......Multi-criteria filtering of mixed open/closed-world data is a time-consuming task, requiring significant manual effort when latent open-world attributes are present. In this work we introduce a novel open-world filtering framework CrowdFilter, enabling automatic UI generation and label elicitation...... multi-criteria active learning method; capable of incorporating labels and n-gram rationales per inclusion criteria, and thus capable of determining both clear includes/excludes, as well as complex borderline cases. By incorporating the active learning approach into the elicitation process of Crowd...

  13. Crowds and Crisis

    DEFF Research Database (Denmark)

    Borch, Christian

    of crowds and their alleged revolutionary aspirations. Interestingly, the sociological interest in crowds took off in the late nineteenth century as a reflection on modern political (dis)order, with the French Revolution and in particular the Paris Commune serving as key points of reference. This early......The November Revolution in 1918 made manifest and further unleashed a political crisis in Germany, the consequences of which have been thoroughly examined. What has attracted less attention is how the Revolution also triggered a semantic crisis within sociology, namely with regard to conceptions...... semantics of crowds associated collective behaviour with irrationality, contagion and hypnotic suggestibility. Precisely this semantic repertoire was called into question after the November revolution: Weimar sociologists, with Theodor Geiger in a lead role, argued for an alternative conception of crowds...

  14. Polymer crowding and shape distributions in polymer-nanoparticle mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Wei Kang; Denton, Alan R., E-mail: alan.denton@ndsu.edu [Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050 (United States)

    2014-09-21

    Macromolecular crowding can influence polymer shapes, which is important for understanding the thermodynamic stability of polymer solutions and the structure and function of biopolymers (proteins, RNA, DNA) under confinement. We explore the influence of nanoparticle crowding on polymer shapes via Monte Carlo simulations and free-volume theory of a coarse-grained model of polymer-nanoparticle mixtures. Exploiting the geometry of random walks, we model polymer coils as effective penetrable ellipsoids, whose shapes fluctuate according to the probability distributions of the eigenvalues of the gyration tensor. Accounting for the entropic cost of a nanoparticle penetrating a larger polymer coil, we compute the crowding-induced shift in the shape distributions, radius of gyration, and asphericity of ideal polymers in a theta solvent. With increased nanoparticle crowding, we find that polymers become more compact (smaller, more spherical), in agreement with predictions of free-volume theory. Our approach can be easily extended to nonideal polymers in good solvents and used to model conformations of biopolymers in crowded environments.

  15. Crowding by invisible flankers.

    Directory of Open Access Journals (Sweden)

    Cristy Ho

    Full Text Available BACKGROUND: Human object recognition degrades sharply as the target object moves from central vision into peripheral vision. In particular, one's ability to recognize a peripheral target is severely impaired by the presence of flanking objects, a phenomenon known as visual crowding. Recent studies on how visual awareness of flanker existence influences crowding had shown mixed results. More importantly, it is not known whether conscious awareness of the existence of both the target and flankers are necessary for crowding to occur. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that crowding persists even when people are completely unaware of the flankers, which are rendered invisible through the continuous flash suppression technique. Contrast threshold for identifying the orientation of a grating pattern was elevated in the flanked condition, even when the subjects reported that they were unaware of the perceptually suppressed flankers. Moreover, we find that orientation-specific adaptation is attenuated by flankers even when both the target and flankers are invisible. CONCLUSIONS: These findings complement the suggested correlation between crowding and visual awareness. What's more, our results demonstrate that conscious awareness and attention are not prerequisite for crowding.

  16. Strategies in crowd and crowd structure

    CERN Document Server

    Gawronski, P; Krawczyk, M J; Malinowski, J; Kupczak, A; Sikora, W; Kulakowski, K; Was, J; Kantelhardt, J

    2012-01-01

    In an emergency situation, imitation of strategies of neighbours can lead to an order-disorder phase transition, where spatial clusters of pedestrians adopt the same strategy. We assume that there are two strategies, cooperating and competitive, which correspond to a smaller or larger desired velocity. The results of our simulations within the Social Force Model indicate that the ordered phase can be detected as an increase of spatial order of positions of the pedestrians in the crowd.

  17. An escape from crowding.

    Science.gov (United States)

    Freeman, Jeremy; Pelli, Denis G

    2007-10-26

    Crowding occurs when nearby flankers jumble the appearance of a target object, making it hard to identify. Crowding is feature integration over an inappropriately large region. What determines the size of that region? According to bottom-up proposals, the size is that of an anatomically determined isolation field. According to top-down proposals, the size is that of the spotlight of attention. Intriligator and Cavanagh (2001) proposed the latter, but we show that their conclusion rests on an implausible assumption. Here we investigate the role of attention in crowding using the change blindness paradigm. We measure capacity for widely and narrowly spaced letters during a change detection task, both with and without an interstimulus cue. We find that standard crowding manipulations-reducing spacing and adding flankers-severely impair uncued change detection but have no effect on cued change detection. Because crowded letters look less familiar, we must use longer internal descriptions (less compact representations) to remember them. Thus, fewer fit into working memory. The memory limit does not apply to the cued condition because the observer need remember only the cued letter. Cued performance escapes the effects of crowding, as predicted by a top-down account. However, our most parsimonious account of the results is bottom-up: Cued change detection is so easy that the observer can tolerate feature degradation and letter distortion, making the observer immune to crowding. The change detection task enhances the classic partial report paradigm by making the test easier (same/different instead of identifying one of many possible targets), which increases its sensitivity, so it can reveal degraded memory traces.

  18. Airborne Crowd Density Estimation

    Science.gov (United States)

    Meynberg, O.; Kuschk, G.

    2013-10-01

    This paper proposes a new method for estimating human crowd densities from aerial imagery. Applications benefiting from an accurate crowd monitoring system are mainly found in the security sector. Normally crowd density estimation is done through in-situ camera systems mounted on high locations although this is not appropriate in case of very large crowds with thousands of people. Using airborne camera systems in these scenarios is a new research topic. Our method uses a preliminary filtering of the whole image space by suitable and fast interest point detection resulting in a number of image regions, possibly containing human crowds. Validation of these candidates is done by transforming the corresponding image patches into a low-dimensional and discriminative feature space and classifying the results using a support vector machine (SVM). The feature space is spanned by texture features computed by applying a Gabor filter bank with varying scale and orientation to the image patches. For evaluation, we use 5 different image datasets acquired by the 3K+ aerial camera system of the German Aerospace Center during real mass events like concerts or football games. To evaluate the robustness and generality of our method, these datasets are taken from different flight heights between 800 m and 1500 m above ground (keeping a fixed focal length) and varying daylight and shadow conditions. The results of our crowd density estimation are evaluated against a reference data set obtained by manually labeling tens of thousands individual persons in the corresponding datasets and show that our method is able to estimate human crowd densities in challenging realistic scenarios.

  19. Amblyopic reading is crowded.

    Science.gov (United States)

    Levi, Dennis M; Song, Shuang; Pelli, Denis G

    2007-10-26

    We measure acuity, crowding, and reading in amblyopic observers to answer four questions. (1) Is reading with the amblyopic eye impaired because of larger required letter size (i.e., worse acuity) or larger required spacing (i.e., worse crowding)? The size or spacing required to read at top speed is called "critical". For each eye of seven amblyopic observers and the preferred eyes of two normal observers, we measure reading rate as a function of the center-to-center spacing of the letters in central and peripheral vision. From these results, we estimate the critical spacing for reading. We also measured traditional acuity for an isolated letter and the critical spacing for identifying a letter among other letters, which is the classic measure of crowding. For both normals and amblyopes, in both central and peripheral vision, we find that the critical spacing for reading equals the critical spacing for crowding. The identical critical spacings, and very different critical sizes, show that crowding, not acuity, limits reading. (2) Does amblyopia affect peripheral reading? No. We find that amblyopes read normally with their amblyopic eye except that abnormal crowding in the fovea prevents them from reading fine print. (3) Is the normal periphery a good model for the amblyopic fovea? No. Reading centrally, the amblyopic eye has an abnormally large critical spacing but reads all larger spacings at normal rates. This is unlike the normal periphery, in which both critical spacing and maximum reading rate are severely impaired relative to the normal fovea. (4) Can the uncrowded-span theory of reading rate explain amblyopic reading? Yes. The case of amblyopia shows that crowding limits reading solely by determining the uncrowded span: the number of characters that are not crowded. Characters are uncrowded if and only if their spacing is more than critical. The text spacing may be uniform, but the observer's critical spacing increases with distance from fixation, so the

  20. Using the crowd as an innovation partner.

    Science.gov (United States)

    Boudreau, Kevin J; Lakhani, Karim R

    2013-04-01

    From Apple to Merck to Wikipedia, more and more organizations are turning to crowds for help in solving their most vexing innovation and research questions, but managers remain understandably cautious. It seems risky and even unnatural to push problems out to vast groups of strangers distributed around the world, particularly for companies built on a history of internal innovation. How can intellectual property be protected? How can a crowd-sourced solution be integrated into corporate operations? What about the costs? These concerns are all reasonable, the authors write, but excluding crowdsourcing from the corporate innovation tool kit means losing an opportunity. After a decade of study, they have identified when crowds tend to outperform internal organizations (or not). They outline four ways to tap into crowd-powered problem solving--contests, collaborative communities, complementors, and labor markets--and offer a system for picking the best one in a given situation. Contests, for example, are suited to highly challenging technical, analytical, and scientific problems; design problems; and creative or aesthetic projects. They are akin to running a series of independent experiments that generate multiple solutions--and if those solutions cluster at some extreme, a company can gain insight into where a problem's "technical frontier" lies. (Internal R&D may generate far less information.)

  1. Evidence for Categorical Crowding

    Directory of Open Access Journals (Sweden)

    J Reuther

    2014-08-01

    Full Text Available An object easily recognised in isolation is hampered when other objects are situated close to it. This phenomenon is called crowding. It is generally thought that crowding affects object recognition only at the level of feature combination. However, recent studies have shown that if flankers and targets belong to different categories crowding is weaker, calling into question the above assertion. Nevertheless, these results can be explained in terms of featural-differences between categories. The current study tests if category-level (i.e., high-level interference in crowding occurs when featural-differences are controlled for. The first experiment used letters and numbers as targets and flankers in a two-by-two study design. We found lower critical spacing when targets and flankers belonged to different categories, replicating previous results. In a second experiment, using a font that ensured that both categories had the same feature-set, we observed the same, albeit weaker, category-dependent effect. This suggests that although featural differences can account partly for the reduction, category-level effects persist even when featural differences are fully controlled for. We conclude that crowding results from not only the well-documented feature-level interactions but also additional interactions at a level where objects are grouped by meaning.

  2. Firms, crowds, and innovation.

    Science.gov (United States)

    Felin, Teppo; Lakhani, Karim R; Tushman, Michael L

    2017-05-01

    The purpose of this article is to suggest a (preliminary) taxonomy and research agenda for the topic of "firms, crowds, and innovation" and to provide an introduction to the associated special issue. We specifically discuss how various crowd-related phenomena and practices-for example, crowdsourcing, crowdfunding, user innovation, and peer production-relate to theories of the firm, with particular attention on "sociality" in firms and markets. We first briefly review extant theories of the firm and then discuss three theoretical aspects of sociality related to crowds in the context of strategy, organizations, and innovation: (1) the functions of sociality (sociality as extension of rationality, sociality as sensing and signaling, sociality as matching and identity), (2) the forms of sociality (independent/aggregate and interacting/emergent forms of sociality), and (3) the failures of sociality (misattribution and misapplication). We conclude with an outline of future research directions and introduce the special issue papers and essays.

  3. Entropic Geometry of Crowd Dynamics

    CERN Document Server

    Ivancevic, Vladimir G

    2008-01-01

    We propose an entropic geometrical model of psycho-physical crowd dynamics (with dissipative crowd kinematics), using Feynman action-amplitude formalism that operates on three synergetic levels: macro, meso and micro. Its most natural statistical descriptor is crowd entropy $S$ that satisfies the Prigogine's extended second law of thermodynamics, $\\partial_tS \\geq 0$ (for any nonisolated multicomponent system). Qualitative similarities and superpositions between individual and crowd configuration manifolds motivate our claim that goal-directed crowd movement operates under entropy conservation, $\\partial_tS = 0$, while natural crowd dynamics operates under (monotonically) increasing entropy function, $\\partial_tS > 0$. Between these two distinct topological phases lies a phase transition with a chaotic inter-phase. Both inertial crowd dynamics and its dissipative kinematics represent diffusion processes on the crowd manifold governed by the Ricci flow, with the associated Perelman entropy-action. Keywords: Cr...

  4. Crowding and Family Relations

    Science.gov (United States)

    Booth, Alan; Edwards, John N.

    1976-01-01

    The effect of household and neighborhood crowding on the relations between spouses, those between parents and children, and the relations among children are examined; a sample of urban families residing in conditions ranging from open to highly compressed provided the data for the investigation and multiple regression was used to analyze the…

  5. Brownian dynamics simulations of an idealized chemical reaction network under spatial confinement and crowding conditions

    CERN Document Server

    Bellesia, Giovanni

    2015-01-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a simple, non-linear chemical network (the Willamowski-Rossler network) under spatial confinement and crowding conditions. Our results show that the presence of inert crowders has a non-nontrivial effect on the dynamics of the network and, consequently, that effective modeling efforts aiming at a general understanding of the behavior of biochemical networks in vivo should be stochastic in nature and based on an explicit representation of both spatial confinement and macromolecular crowding.

  6. Identification of macromolecular complexes in cryoelectron tomograms of phantom cells

    Science.gov (United States)

    Frangakis, Achilleas S.; Böhm, Jochen; Förster, Friedrich; Nickell, Stephan; Nicastro, Daniela; Typke, Dieter; Hegerl, Reiner; Baumeister, Wolfgang

    2002-01-01

    Electron tomograms of intact frozen-hydrated cells are essentially three-dimensional images of the entire proteome of the cell, and they depict the whole network of macromolecular interactions. However, this information is not easily accessible because of the poor signal-to-noise ratio of the tomograms and the crowded nature of the cytoplasm. Here, we describe a template matching algorithm that is capable of detecting and identifying macromolecules in tomographic volumes in a fully automated manner. The algorithm is based on nonlinear cross correlation and incorporates elements of multivariate statistical analysis. Phantom cells, i.e., lipid vesicles filled with macromolecules, provide a realistic experimental scenario for an assessment of the fidelity of this approach. At the current resolution of ≈4 nm, macromolecules in the size range of 0.5–1 MDa can be identified with good fidelity. PMID:12391313

  7. Niching method using clustering crowding

    Institute of Scientific and Technical Information of China (English)

    GUO Guan-qi; GUI Wei-hua; WU Min; YU Shou-yi

    2005-01-01

    This study analyzes drift phenomena of deterministic crowding and probabilistic crowding by using equivalence class model and expectation proportion equations. It is proved that the replacement errors of deterministic crowding cause the population converging to a single individual, thus resulting in premature stagnation or losing optional optima. And probabilistic crowding can maintain equilibrium multiple subpopulations as the population size is adequate large. An improved niching method using clustering crowding is proposed. By analyzing topology of fitness landscape using hill valley function and extending the search space for similarity analysis, clustering crowding determines the locality of search space more accurately, thus greatly decreasing replacement errors of crowding. The integration of deterministic and probabilistic replacement increases the capacity of both parallel local hill climbing and maintaining multiple subpopulations. The experimental results optimizing various multimodal functions show that,the performances of clustering crowding, such as the number of effective peaks maintained, average peak ratio and global optimum ratio are uniformly superior to those of the evolutionary algorithms using fitness sharing, simple deterministic crowding and probabilistic crowding.

  8. Crowding by a repeating pattern.

    Science.gov (United States)

    Rosen, Sarah; Pelli, Denis G

    2015-01-01

    Theinability to recognize a peripheral target among flankers is called crowding. For a foveal target, crowding can be distinguished from overlap masking by its sparing of detection, linear scaling with eccentricity, and invariance with target size.Crowding depends on the proximity and similarity of the flankers to the target. Flankers that are far from or dissimilar to the target do not crowd it. On a gray page, text whose neighboring letters have different colors, alternately black and white, has enough dissimilarity that it might escape crowding. Since reading speed is normally limited by crowding, escape from crowding should allow faster reading. Yet reading speed is unchanged (Chung & Mansfield, 2009). Why? A recent vernier study found that using alternating-color flankers produces strong crowding (Manassi, Sayim, & Herzog, 2012). Might that effect occur with letters and reading? Critical spacing is the minimum center-to-center target-flanker spacing needed to correctly identify the target. We measure it for a target letter surrounded by several equidistant flanker letters of the same polarity, opposite polarity, or mixed polarity: alternately white and black. We find strong crowding in the alternating condition, even though each flanker letter is beyond its own critical spacing (as measured in a separate condition). Thus a periodic repeating pattern can produce crowding even when the individual elements do not. Further, in all conditions we find that, once a periodic pattern repeats (two cycles), further repetition does not affect critical spacing of the innermost flanker.

  9. The Crowd Energy Concept

    Institute of Scientific and Technical Information of China (English)

    Stephanie Teufel; Bernd Teufel

    2014-01-01

    ⎯After the Fukushima disaster, European politicians began to reassess the energy strategy for their countries. The focus is now on renewable energy sources and as a result on decentralization. The decentralized generation, storage, and of course the consumption of energy is the central point. Now with the new develop-ments under the roof of energy turnaround the way back from the centralized architecture of our energy system to a more decentralized one is predetermined. Decentralization implies the change in the role of today’s consumers. They become energy prosumers. This is the basis for the crowd energy concept. In this position paper the crowd energy concept is introduced and necessary research fields are identified.

  10. Unpaid Crowd Complementors

    DEFF Research Database (Denmark)

    Boudreau, Kevin J.; Jeppesen, Lars Bo

    2014-01-01

    on network effects and strategies to attract large numbers of complementors remain advisable in such contexts? We test hypotheses related to these issues using data from 85 online multi-player game platforms with unpaid complementors. We find that complementor development responds to platform growth even...... without sales incentives, but that attracting complementors has a net zero effect on on-going development and fails to stimulate network effects. We discuss conditions under which a strategy of using unpaid crowd complementors remains advantageous....

  11. Firms, crowds, and innovation

    Science.gov (United States)

    Felin, Teppo; Lakhani, Karim R; Tushman, Michael L

    2017-01-01

    The purpose of this article is to suggest a (preliminary) taxonomy and research agenda for the topic of “firms, crowds, and innovation” and to provide an introduction to the associated special issue. We specifically discuss how various crowd-related phenomena and practices—for example, crowdsourcing, crowdfunding, user innovation, and peer production—relate to theories of the firm, with particular attention on “sociality” in firms and markets. We first briefly review extant theories of the firm and then discuss three theoretical aspects of sociality related to crowds in the context of strategy, organizations, and innovation: (1) the functions of sociality (sociality as extension of rationality, sociality as sensing and signaling, sociality as matching and identity), (2) the forms of sociality (independent/aggregate and interacting/emergent forms of sociality), and (3) the failures of sociality (misattribution and misapplication). We conclude with an outline of future research directions and introduce the special issue papers and essays. PMID:28690428

  12. Temporal crowding and its interplay with spatial crowding.

    Science.gov (United States)

    Yeshurun, Yaffa; Rashal, Einat; Tkacz-Domb, Shira

    2015-03-18

    Spatial crowding refers to impaired target identification when the target is surrounded by other stimuli in space temporal crowding refers to impaired target identification when the target is surrounded by other stimuli in time previously, when spatial and temporal crowding were measured in the fovea they were interrelated with amblyopic observers but almost absent with normal observers bonneh, sagi, & polat, 2007. In the current study we examined whether reliable temporal crowding can be found for normal observers with peripheral presentation 9° of eccentricity, and whether similar relations between temporal and spatial crowding will emerge to that end, we presented a sequence of three displays separated by a varying interstimulus interval (ISI). Each display included either one letter : experiments 1a ,: 1b ,: 1c or three letters separated by a varying interletter spacing: Experiments 2a ,: 2b). One of these displays included an oriented T. Observers indicated the T's orientation. As expected, we found spatial crowding: accuracy improved as the interletter spacing increased. Critically, we also found temporal crowding: in all experiments accuracy increased as the ISI increased, even when only stimulus-onset asynchronies (SOAs) larger than 150 ms were included, ensuring this effect does not reflect mere ordinary masking. Thus, with peripheral presentation, temporal crowding also emerged for normal observers. However, only a weak interaction between temporal and spatial crowding was found.

  13. CrowdPhase: crowdsourcing the phase problem.

    Science.gov (United States)

    Jorda, Julien; Sawaya, Michael R; Yeates, Todd O

    2014-06-01

    The human mind innately excels at some complex tasks that are difficult to solve using computers alone. For complex problems amenable to parallelization, strategies can be developed to exploit human intelligence in a collective form: such approaches are sometimes referred to as `crowdsourcing'. Here, a first attempt at a crowdsourced approach for low-resolution ab initio phasing in macromolecular crystallography is proposed. A collaborative online game named CrowdPhase was designed, which relies on a human-powered genetic algorithm, where players control the selection mechanism during the evolutionary process. The algorithm starts from a population of `individuals', each with a random genetic makeup, in this case a map prepared from a random set of phases, and tries to cause the population to evolve towards individuals with better phases based on Darwinian survival of the fittest. Players apply their pattern-recognition capabilities to evaluate the electron-density maps generated from these sets of phases and to select the fittest individuals. A user-friendly interface, a training stage and a competitive scoring system foster a network of well trained players who can guide the genetic algorithm towards better solutions from generation to generation via gameplay. CrowdPhase was applied to two synthetic low-resolution phasing puzzles and it was shown that players could successfully obtain phase sets in the 30° phase error range and corresponding molecular envelopes showing agreement with the low-resolution models. The successful preliminary studies suggest that with further development the crowdsourcing approach could fill a gap in current crystallographic methods by making it possible to extract meaningful information in cases where limited resolution might otherwise prevent initial phasing.

  14. Molecular crowding causes narrowing of population heterogeneity and restricts internal dynamics in a protein

    Science.gov (United States)

    Mondal, Samsuzzoha; Kallianpur, Mamata V.; Udgaonkar, Jayant B.; Krishnamoorthy, G.

    2016-03-01

    Macromolecular crowding is a distinguishing property of intracellular media. Knowledge on the structure and dynamics of a protein in a crowded environment is essential for a complete understanding of its function. Reduction in intermolecular space could cause structural and functional alterations. Here, we have studied a model protein barstar to see how polyethylene glycol (PEG)-induced crowding affects its various structural states (native, unfolded and molten-globule-like) with different extents of change in conformational heterogeneity. Intramolecular distances and distance distributions were determined by time-resolved Förster resonance energy transfer from Trp53 to several acceptor sites by analysis of fluorescence decay kinetics using the Maximum Entropy Method. We observed PEG-induced narrowing of population distributions along with shifting of populations towards more compact states. Structural compactness also resulted in the slowing down of internal dynamics of the protein as revealed by fluorescence anisotropy decay kinetics of the fluorophore IAEDANS attached at several sites.

  15. Colour, Luminance and Crowding

    Directory of Open Access Journals (Sweden)

    BJ Jennings

    2013-10-01

    Full Text Available Three experiments were performed to assess the effect backgrounds have on object discrimination. Experiment 1 investigated the discrimination of foveally presented Gaborised objects and non-objects with and without a surrounding background. Thresholds were obtained by modulating the Gabor patches in 7 different directions, either isolating the L-M, S-(L+M and L+M geniculate mechanisms, or stimulating these mechanisms in combination. The spacing between background Gabor elements and the object contour was chosen so as to not cause crowding, on the basis of previously published work with luminance stimuli. No differences were found between the Michelson contrasts required for threshold with or without a background, except when signals in the S-(L+M and L+M were combined. The signals were combined at an elevation of 30° in DKL colour space, which resulted in a mixture with a proportionally strong chromatic signal. Experiment 2 investigated this finding further using three background conditions: no background, a sparse background and a densely populated background. Object vs. non-object discrimination thresholds were obtained for the L+M and S-(L+M isolating directions, along with two conditions that combined them at DKL luminance elevations of 30° and 60°. In the 60° combination, the proportion of the chromatic signal was lower than in the 30° combination. Thresholds were found to be largely stable across chromatic and luminance conditions and background class, again with the exception of the combination at 30° elevation. The final experiment examined Gabor orientation discrimination over the same conditions as experiment 2 using a classical crowding paradigm, with a peripheral target and a set of three target-flanker separations. Crowding was most pronounced in the 30° combination. We conclude that when S-(L+M signals above a certain level are combined with luminance signals, an increase in crowding results. This is likely to underlie the

  16. Crowd simulation and visualization

    OpenAIRE

    Perez, Hugo; Rudomin, Isaac; Ayguadé Parra, Eduard; Hernandez, Benjamin; Espinosa-Oviedo, Javier A.; Vargas-Solar, Genoveva

    2015-01-01

    This paper presents a methodology to simulate and visualize crowds. Our goal is to represent the most realistic possible scenarios in a city. Due to the high demand of resources a GPU Cluster is used. We use real data from which we identify the behavior of the masses applying statistical and artificial intelligence techniques. In order to take advantge of the processing power of the GPU cluster we use the following programming models during the characters simulation: MPI, OmpSs and CUDA. We d...

  17. Advances in electron microscopy: A qualitative view of instrumentation development for macromolecular imaging and tomography.

    Science.gov (United States)

    Schröder, Rasmus R

    2015-09-01

    Macromolecular imaging and tomography of ice embedded samples has developed into a mature imaging technology, in structural biology today widely referred to simply as cryo electron microscopy.(1) While the pioneers of the technique struggled with ill-suited instruments, state-of-the-art cryo microscopes are now readily available and an increasing number of groups are producing excellent high-resolution structural data of macromolecular complexes, of cellular organelles, or the morphology of whole cells. Instrumentation developers, however, are offering yet more novel electron optical devices, such as energy filters and monochromators, aberration correctors or physical phase plates. Here we discuss how current instrumentation has already changed cryo EM, and how newly available instrumentation - often developed in other fields of electron microscopy - may further develop the use and applicability of cryo EM to the imaging of single isolated macromolecules of smaller size or molecules embedded in a crowded cellular environment.

  18. Holistic crowding of Mooney faces.

    Science.gov (United States)

    Farzin, Faraz; Rivera, Susan M; Whitney, David

    2009-06-29

    An object or feature is generally more difficult to identify when other objects are presented nearby, an effect referred to as crowding. Here, we used Mooney faces to examine whether crowding can also occur within and between holistic face representations (C. M. Mooney, 1957). Mooney faces are ideal stimuli for this test because no cues exist to distinguish facial features in a Mooney face; to find any facial feature, such as an eye or a nose, one must first holistically perceive the image as a face. Through a series of six experiments we tested the effect of crowding on Mooney face recognition. Our results demonstrate crowding between and within Mooney faces and fulfill the diagnostic criteria for crowding, including eccentricity dependence and lack of crowding in the fovea, critical flanker spacing consistent with less than half the eccentricity of the target, and inner-outer flanker asymmetry. Further, our results show that recognition of an upright Mooney face is more strongly impaired by upright Mooney face flankers than inverted ones. Taken together, these results suggest crowding can occur selectively between high-level representations of faces and that crowding must occur at multiple levels in the visual system.

  19. Macaque monkeys experience visual crowding.

    Science.gov (United States)

    Crowder, Erin A; Olson, Carl R

    2015-01-01

    In peripheral vision, objects that are easily discriminated on their own become less discriminable in the presence of surrounding clutter. This phenomenon is known as crowding.The neural mechanisms underlying crowding are not well understood. Better insight might come from single-neuron recording in nonhuman primates, provided they exhibit crowding; however, previous demonstrations of crowding have been confined to humans. In the present study, we set out to determine whether crowding occurs in rhesus macaque monkeys. We found that animals trained to identify a target letter among flankers displayed three hallmarks of crowding as established in humans. First, at a given eccentricity, increasing the spacing between the target and the flankers improved recognition accuracy. Second, the critical spacing, defined as the minimal spacing at which target discrimination was reliable, was proportional to eccentricity. Third, the critical spacing was largely unaffected by object size. We conclude that monkeys, like humans, experience crowding. These findings open the door to studies of crowding at the neuronal level in the monkey visual system.

  20. Illusory contour formation survives crowding.

    Science.gov (United States)

    Lau, Jonathan Siu Fung; Cheung, Sing-Hang

    2012-06-12

    Flanked objects are difficult to identify using peripheral vision due to visual crowding, which limits conscious access to target identity. Nonetheless, certain types of visual information have been shown to survive crowding. Such resilience to crowding provides valuable information about the underlying neural mechanism of crowding. Here we ask whether illusory contour formation survives crowding of the inducers. We manipulated the presence of illusory contours through the (mis)alignment of the four inducers of a Kanizsa square. In the inducer-aligned condition, the observers judged the perceived shape (thin vs. fat) of the illusory Kanizsa square, manipulated by small rotations of the inducers. In the inducer-misaligned condition, three of the four inducers (all except the upper-left) were rotated 90°. The observers judged the orientation of the upper-left inducer. Crowding of the inducers worsened observers' performance significantly only in the inducer-misaligned condition. Our findings suggest that information for illusory contour formation survives crowding of the inducers. Crowding happens at a stage where the low-level featural information is integrated for inducer orientation discrimination, but not at a stage where the same information is used for illusory contour formation.

  1. Pedestrian, Crowd, and Evacuation Dynamics

    CERN Document Server

    Helbing, Dirk

    2013-01-01

    This contribution describes efforts to model the behavior of individual pedestrians and their interactions in crowds, which generate certain kinds of self-organized patterns of motion. Moreover, this article focusses on the dynamics of crowds in panic or evacuation situations, methods to optimize building designs for egress, and factors potentially causing the breakdown of orderly motion.

  2. Crowd funding voor juridische fijnproevers

    NARCIS (Netherlands)

    I. van der Vlies

    2012-01-01

    Crowd funding is een eigentijds instrument om geld van goede gevers te verzamelen via de sociale media. Bij crowd funding hoeft de ‘crowd’ niet als groep of gemeenschap te bestaan. Het gaat om een verzameling personen die één ding gemeen heeft: geld geven voor een bepaald doel. De oude media speelde

  3. Gender differences in crowd perception.

    Science.gov (United States)

    Bai, Yang; Leib, Allison Y; Puri, Amrita M; Whitney, David; Peng, Kaiping

    2015-01-01

    In this study, we investigated whether the first impression of a crowd of faces-crowd perception-is influenced by social background and cognitive processing. Specifically, we explored whether males and females, two groups that are distinct biologically and socially, differ in their ability to extract ensemble characteristics from crowds of faces that were comprised of different identities. Participants were presented with crowds of similar faces and were instructed to scroll through a morphed continuum of faces until they found a face that was representative of the average identity of each crowd. Consistent with previous research, females were more precise in single face perception. Furthermore, the results showed that females were generally more accurate in estimating the average identity of a crowd. However, the correlation between single face discrimination and crowd averaging differed between males and females. Specifically, male subjects' ensemble integration slightly compensated for their poor single face perception; their performance on the crowd perception task was not as poor as would be expected from their single face discrimination ability. Overall, the results suggest that group perception is not an isolated or uniform cognitive mechanism, but rather one that interacts with biological and social processes.

  4. Effects of molecular crowding on the dynamics of intrinsically disordered proteins.

    Directory of Open Access Journals (Sweden)

    Elio A Cino

    Full Text Available Inside cells, the concentration of macromolecules can reach up to 400 g/L. In such crowded environments, proteins are expected to behave differently than in vitro. It has been shown that the stability and the folding rate of a globular protein can be altered by the excluded volume effect produced by a high density of macromolecules. However, macromolecular crowding effects on intrinsically disordered proteins (IDPs are less explored. These proteins can be extremely dynamic and potentially sample a wide ensemble of conformations under non-denaturing conditions. The dynamic properties of IDPs are intimately related to the timescale of conformational exchange within the ensemble, which govern target recognition and how these proteins function. In this work, we investigated the macromolecular crowding effects on the dynamics of several IDPs by measuring the NMR spin relaxation parameters of three disordered proteins (ProTα, TC1, and α-synuclein with different extents of residual structures. To aid the interpretation of experimental results, we also performed an MD simulation of ProTα. Based on the MD analysis, a simple model to correlate the observed changes in relaxation rates to the alteration in protein motions under crowding conditions was proposed. Our results show that 1 IDPs remain at least partially disordered despite the presence of high concentration of other macromolecules, 2 the crowded environment has differential effects on the conformational propensity of distinct regions of an IDP, which may lead to selective stabilization of certain target-binding motifs, and 3 the segmental motions of IDPs on the nanosecond timescale are retained under crowded conditions. These findings strongly suggest that IDPs function as dynamic structural ensembles in cellular environments.

  5. Macromolecular architectures for organic photovoltaics.

    Science.gov (United States)

    Popere, Bhooshan C; Della Pelle, Andrea M; Poe, Ambata; Thayumanavan, S

    2012-03-28

    Research in the field of organic photovoltaics has gained considerable momentum in the last two decades owing to the need for developing low-cost and efficient energy harvesting systems. Elegant molecular architectures have been designed, synthesized and employed as active materials for photovoltaic devices thereby leading to a better molecular structure-device property relationship understanding. In this perspective, we outline new macromolecular scaffolds that have been designed within the purview of each of the three fundamental processes involving light harvesting, charge separation and charge transport.

  6. Emergent Property in Macromolecular Motion

    Institute of Scientific and Technical Information of China (English)

    吴嘉麟

    2003-01-01

    In this paper, the model of inverse cascade fractal super-blocks along one direction (in the positive or negative) in the 3-dimensional space is developed to describe the self-similar motion in macromolecular system. Microscopically the cohesive and dispersed states of the motion blocks are co-existent states with vastly different probability of occurrence.Experimental results and theoretical analysis show that the microscopic cohesive state energy and dispersed state energy of each motion block are respectively equal to the macroscopic glassy state energy kT8 and molten state energy kTm of the system. This singularity unveils topologically the nonintegrability, mathematically the anholonomy, and macroscopically the emergent property. This singularity also reveals that the glass, viscoelastic and melt states are three distinct emergent properties of macromolecular motion from a macroscopic viewpoint. The fractal concept of excluded volume is introduced to depict the random motion at various scales in the system. The Hausdorff dimensions of the excluded volune and the motion blocks are both found equal to 3/2.

  7. Data Mining of Macromolecular Structures.

    Science.gov (United States)

    van Beusekom, Bart; Perrakis, Anastassis; Joosten, Robbie P

    2016-01-01

    The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.

  8. Macromolecular mimicry of nucleic acid and protein

    DEFF Research Database (Denmark)

    Nautrup Pedersen, Gitte; Nyborg, Jens; Clark, Brian F

    1999-01-01

    of the concept of macromolecular mimicry. Macromolecular mimicry has further been proposed among initiation and release factors, thereby adding a new element to the description of protein synthesis in bacteria. Such mimicry has also been observed in other biological processes such as autoimmunity, DNA repair......, and gene regulation, at both transcriptional and translational levels. Udgivelsesdato: 1999-Jul...

  9. The walking behaviour of pedestrian social groups and its impact on crowd dynamics

    CERN Document Server

    Moussaid, Mehdi; Garnier, Simon; Helbing, Dirk; Theraulaz, Guy

    2010-01-01

    Human crowd motion is mainly driven by self-organized processes based on local interactions among pedestrians. While most studies of crowd behavior consider only interactions among isolated individuals, it turns out that up to 70% of people in a crowd are actually moving in groups, such as friends, couples, or families walking together. These groups constitute medium-scale aggregated structures and their impact on crowd dynamics is still largely unknown. In this work, we analyze the motion of approximately 1500 pedestrian groups under natural condition, and show that social interactions among group members generate typical group walking patterns that influence crowd dynamics. At low density, group members tend to walk side by side, forming a line perpendicular to the walking direction. As the density increases, however, the linear walking formation is bent forward, turning it into a V-like pattern. These spatial patterns can be well described by a model based on social communication between group members. We ...

  10. Liver-targeting macromolecular MRI contrast agents

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Macromolecular ligands with liver-targeting group (pyridoxamine, PM) PHEA-DTPA-PM and PAEA-DTPA-PM were prepared by the incorporation of different amount of diethylenetriaminepentaacetic acid monopyridoxamine group (DTPA-PM) into poly-a, b-[N-(2-hydroxyethyl)-L- aspartamide] (PHEA) and poly-a, b-[N-(2-aminoethyl)-L-aspartamide] (PAEA). The macromolecular ligands thus obtained were further complexed with gadolinium chloride to give macromolecular MRI contrast agents with different Gd(Ⅲ) contents. These macromolecular ligands and their gadolinium complexes were characterized by 1H NMR, IR, UV and elementary analysis. Relaxivity studies showed that these polyaspartamide gadolinium complexes possess higher relaxation effectiveness than that of the clinically used Gd-DTPA. Magnetic resonance imaging of the liver in rats and experimental data of biodistribution in mice indicate that these macromolecular MRI contrast agents containing pyridoxamine exhibit liver-targeting property.

  11. Crowding alone cannot account for cosolute effect on amyloid aggregation.

    Directory of Open Access Journals (Sweden)

    Shahar Sukenik

    Full Text Available Amyloid fiber formation is a specific form of protein aggregation, often resulting from the misfolding of native proteins. Aimed at modeling the crowded environment of the cell, recent experiments showed a reduction in fibrillation halftimes for amyloid-forming peptides in the presence of cosolutes that are preferentially excluded from proteins and peptides. The effect of excluded cosolutes has previously been attributed to the large volume excluded by such inert cellular solutes, sometimes termed "macromolecular crowding". Here, we studied a model peptide that can fold to a stable monomeric β-hairpin conformation, but under certain solution conditions aggregates in the form of amyloid fibrils. Using Circular Dichroism spectroscopy (CD, we found that, in the presence of polyols and polyethylene glycols acting as excluded cosolutes, the monomeric β-hairpin conformation was stabilized with respect to the unfolded state. Stabilization free energy was linear with cosolute concentration, and grew with molecular volume, as would also be predicted by crowding models. After initiating the aggregation process with a pH jump, fibrillation in the presence and absence of cosolutes was followed by ThT fluorescence, transmission electron microscopy, and CD spectroscopy. Polyols (glycerol and sorbitol increased the lag time for fibril formation and elevated the amount of aggregated peptide at equilibrium, in a cosolute size and concentration dependent manner. However, fibrillation rates remained almost unaffected by a wide range of molecular weights of soluble polyethylene glycols. Our results highlight the importance of other forces beyond the excluded volume interactions responsible for crowding that may contribute to the cosolute effects acting on amyloid formation.

  12. Crowding and the Educational Process

    Science.gov (United States)

    Baron, Reuben M.

    1975-01-01

    Important conceptual and practical problems are involved in specifying the conditions under which individuals or groups are likely to experience a sense of crowding. An ecological/environmental perspective can help educators determine humane space utilization. (Author/DW)

  13. Mobility, Fertility, and Residential Crowding

    Science.gov (United States)

    Morris, Earl W.

    1977-01-01

    Regression analyses predicting fertility and mobility in a sample of a metropolitan county in New York State indicate that residential mobility serves to release the negative pressure that residential crowding might exert on fertility behavior. (Author)

  14. Crowding effects in vehicular traffic.

    Science.gov (United States)

    Combinido, Jay Samuel L; Lim, May T

    2012-01-01

    While the impact of crowding on the diffusive transport of molecules within a cell is widely studied in biology, it has thus far been neglected in traffic systems where bulk behavior is the main concern. Here, we study the effects of crowding due to car density and driving fluctuations on the transport of vehicles. Using a microscopic model for traffic, we found that crowding can push car movement from a superballistic down to a subdiffusive state. The transition is also associated with a change in the shape of the probability distribution of positions from a negatively-skewed normal to an exponential distribution. Moreover, crowding broadens the distribution of cars' trap times and cluster sizes. At steady state, the subdiffusive state persists only when there is a large variability in car speeds. We further relate our work to prior findings from random walk models of transport in cellular systems.

  15. Crowding effects in vehicular traffic

    CERN Document Server

    Combinido, Jay Samuel L

    2012-01-01

    While the impact of crowding on the diffusive transport of molecules within a cell is widely studied in biology, it has thus far been neglected in traffic systems where bulk behavior is the main concern. Here, we study the effects of crowding due to car density and driving fluctuations on the transport of vehicles. Using a microscopic model for traffic, we found that crowding can push car movement from a superballistic down to a subdiffusive state. The transition is also associated with a change in the shape of the probability distribution of positions from negatively-skewed normal to an exponential distribution. Moreover, crowding broadens the distribution of cars' trap times and cluster sizes. At steady state, the subdiffusive state persists only when there is a large variability in car speeds. We further relate our work to prior findings from random walk models of transport in cellular systems.

  16. Peculiarities of the Super-Folder GFP Folding in a Crowded Milieu

    Directory of Open Access Journals (Sweden)

    Olesya V. Stepanenko

    2016-10-01

    Full Text Available The natural cellular milieu is crowded by large quantities of various biological macromolecules. This complex environment is characterized by a limited amount of unoccupied space, limited amounts of free water, and changed solvent properties. Obviously, such a tightly packed cellular environment is poorly mimicked by traditional physiological conditions, where low concentrations of a protein of interest are analyzed in slightly salted aqueous solutions. An alternative is given by the use of a model crowded milieu, where a protein of interest is immersed in a solution containing high concentrations of various polymers that serve as model crowding agents. An expected outcome of the presence of such macromolecular crowding agents is their ability to increase conformational stability of a globular protein due to the excluded volume effects. In line with this hypothesis, the behavior of a query protein should be affected by the hydrodynamic size and concentration of an inert crowder (i.e., an agent that does not interact with the protein, whereas the chemical nature of a macromolecular crowder should not play a role in its ability to modulate conformational properties. In this study, the effects of different crowding agents (polyethylene glycols (PEGs of various molecular masses (PEG-600, PEG-8000, and PEG-12000, Dextran-70, and Ficoll-70 on the spectral properties and unfolding–refolding processes of the super-folder green fluorescent protein (sfGFP were investigated. sfGFP is differently affected by different crowders, suggesting that, in addition to the expected excluded volume effects, there are some changes in the solvent properties.

  17. Analysis of Tagish Lake macromolecular organic material

    OpenAIRE

    Gilmour, I; Pearson, V. K.; Sephton, M.A.

    2001-01-01

    Macromolecular material is, by far, the major organic component of meteorites. Flash pyrolysis GCMS has been used to investigate this organic component in Tagish Lake. It is more condensed, less susbtituted than Murchson.

  18. Automated data collection for macromolecular crystallography.

    Science.gov (United States)

    Winter, Graeme; McAuley, Katherine E

    2011-09-01

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

  19. Energy transfer in macromolecular arrays

    Science.gov (United States)

    Andrews, David L.; Jenkins, Robert D.

    2003-11-01

    Macromolecular systems comprised of many light-sensitive centres (the photosynthetic unit, dendrimers, and other highly symmetric multichromophore arrays) are important structures offering challenges to theoreticians and synthetic chemists alike. Here we outline novel photophysical interactions predicted and observed in such arrays. Using the tools of molecular quantum electrodynamics (QED) we present quantum amplitudes for a variety of higher-order resonance energy transfer (RET) schemes associated with well-known nonlinear optical effects such as two- and three-photon absorption. The initial analysis is extended to account for situations where the participant donor species are identical and exist in a highly symmetric environment, leading to the possible formation of excitons. It emerges from the QED theory that such excitons are closely associated with the higher-order RET processes. General results are interpreted by analyzing particular molecular architectures which offer interesting features such as rate enhancement or limitation and exciton pathway quenching. Applications in the areas of photosynthesis, molecular logic gates and low-intensity fluorescence energy transfer are predicted.

  20. How odgcrnwi becomes crowding: stimulus-specific learning reduces crowding.

    Science.gov (United States)

    Huckauf, Anke; Nazir, Tatjana A

    2007-08-16

    Processes underlying crowding in visual letter recognition were examined by investigating effects of training. Experiment 1 revealed that training reduces crowding mainly for trained strings. This was corroborated in Experiment 2, where no training effects were obvious after 3 days of training when strings changed from trial to trial. Experiment 3 specified that after a short amount of training, learning effects remained specific to trained strings and also to the trained retinal eccentricity and the interletter spacing used in training. Transfer to other than trained conditions was observed only after further training. Experiment 4 showed that transfer occurred earlier when words were used as stimuli. These results thus demonstrate that part of crowding results from the absence of higher level representations of the stimulus. Such representations can be acquired through learning visual properties of the stimulus.

  1. Crowd science user contribution patterns and their implications

    Science.gov (United States)

    Sauermann, Henry; Franzoni, Chiara

    2015-01-01

    Scientific research performed with the involvement of the broader public (the crowd) attracts increasing attention from scientists and policy makers. A key premise is that project organizers may be able to draw on underused human resources to advance research at relatively low cost. Despite a growing number of examples, systematic research on the effort contributions volunteers are willing to make to crowd science projects is lacking. Analyzing data on seven different projects, we quantify the financial value volunteers can bring by comparing their unpaid contributions with counterfactual costs in traditional or online labor markets. The volume of total contributions is substantial, although some projects are much more successful in attracting effort than others. Moreover, contributions received by projects are very uneven across time-a tendency toward declining activity is interrupted by spikes typically resulting from outreach efforts or media attention. Analyzing user-level data, we find that most contributors participate only once and with little effort, leaving a relatively small share of users who return responsible for most of the work. Although top contributor status is earned primarily through higher levels of effort, top contributors also tend to work faster. This speed advantage develops over multiple sessions, suggesting that it reflects learning rather than inherent differences in skills. Our findings inform recent discussions about potential benefits from crowd science, suggest that involving the crowd may be more effective for some kinds of projects than others, provide guidance for project managers, and raise important questions for future research.

  2. Quantifying error distributions in crowding.

    Science.gov (United States)

    Hanus, Deborah; Vul, Edward

    2013-03-22

    When multiple objects are in close proximity, observers have difficulty identifying them individually. Two classes of theories aim to account for this crowding phenomenon: spatial pooling and spatial substitution. Variations of these accounts predict different patterns of errors in crowded displays. Here we aim to characterize the kinds of errors that people make during crowding by comparing a number of error models across three experiments in which we manipulate flanker spacing, display eccentricity, and precueing duration. We find that both spatial intrusions and individual letter confusions play a considerable role in errors. Moreover, we find no evidence that a naïve pooling model that predicts errors based on a nonadditive combination of target and flankers explains errors better than an independent intrusion model (indeed, in our data, an independent intrusion model is slightly, but significantly, better). Finally, we find that manipulating trial difficulty in any way (spacing, eccentricity, or precueing) produces homogenous changes in error distributions. Together, these results provide quantitative baselines for predictive models of crowding errors, suggest that pooling and spatial substitution models are difficult to tease apart, and imply that manipulations of crowding all influence a common mechanism that impacts subject performance.

  3. Protein Crowding in Lipid Bilayers Gives Rise to Non-Gaussian Anomalous Lateral Diffusion of Phospholipids and Proteins

    Science.gov (United States)

    Jeon, Jae-Hyung; Javanainen, Matti; Martinez-Seara, Hector; Metzler, Ralf; Vattulainen, Ilpo

    2016-04-01

    Biomembranes are exceptionally crowded with proteins with typical protein-to-lipid ratios being around 1 ∶50 -1 ∶100 . Protein crowding has a decisive role in lateral membrane dynamics as shown by recent experimental and computational studies that have reported anomalous lateral diffusion of phospholipids and membrane proteins in crowded lipid membranes. Based on extensive simulations and stochastic modeling of the simulated trajectories, we here investigate in detail how increasing crowding by membrane proteins reshapes the stochastic characteristics of the anomalous lateral diffusion in lipid membranes. We observe that correlated Gaussian processes of the fractional Langevin equation type, identified as the stochastic mechanism behind lipid motion in noncrowded bilayer, no longer adequately describe the lipid and protein motion in crowded but otherwise identical membranes. It turns out that protein crowding gives rise to a multifractal, non-Gaussian, and spatiotemporally heterogeneous anomalous lateral diffusion on time scales from nanoseconds to, at least, tens of microseconds. Our investigation strongly suggests that the macromolecular complexity and spatiotemporal membrane heterogeneity in cellular membranes play critical roles in determining the stochastic nature of the lateral diffusion and, consequently, the associated dynamic phenomena within membranes. Clarifying the exact stochastic mechanism for various kinds of biological membranes is an important step towards a quantitative understanding of numerous intramembrane dynamic phenomena.

  4. Anomalous transport in the crowded world of biological cells.

    Science.gov (United States)

    Höfling, Felix; Franosch, Thomas

    2013-04-01

    A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important

  5. Normative Mediation of Reactions to Crowding

    Science.gov (United States)

    Karlin, Robert A.; And Others

    1976-01-01

    This study manipulated norms governing interaction levels in crowded groups of women. Results indicated norms influenced reactions to crowding as predicted. Women reacted most positively when interaction levels were high and most negatively when interaction levels were low. (Author)

  6. The Walking Behaviour of Pedestrian Social Groups and Its Impact on Crowd Dynamics

    Science.gov (United States)

    Moussaïd, Mehdi; Perozo, Niriaska; Garnier, Simon; Helbing, Dirk; Theraulaz, Guy

    2010-01-01

    Human crowd motion is mainly driven by self-organized processes based on local interactions among pedestrians. While most studies of crowd behaviour consider only interactions among isolated individuals, it turns out that up to 70% of people in a crowd are actually moving in groups, such as friends, couples, or families walking together. These groups constitute medium-scale aggregated structures and their impact on crowd dynamics is still largely unknown. In this work, we analyze the motion of approximately 1500 pedestrian groups under natural condition, and show that social interactions among group members generate typical group walking patterns that influence crowd dynamics. At low density, group members tend to walk side by side, forming a line perpendicular to the walking direction. As the density increases, however, the linear walking formation is bent forward, turning it into a V-like pattern. These spatial patterns can be well described by a model based on social communication between group members. We show that the V-like walking pattern facilitates social interactions within the group, but reduces the flow because of its “non-aerodynamic” shape. Therefore, when crowd density increases, the group organization results from a trade-off between walking faster and facilitating social exchange. These insights demonstrate that crowd dynamics is not only determined by physical constraints induced by other pedestrians and the environment, but also significantly by communicative, social interactions among individuals. PMID:20383280

  7. The walking behaviour of pedestrian social groups and its impact on crowd dynamics.

    Directory of Open Access Journals (Sweden)

    Mehdi Moussaïd

    Full Text Available Human crowd motion is mainly driven by self-organized processes based on local interactions among pedestrians. While most studies of crowd behaviour consider only interactions among isolated individuals, it turns out that up to 70% of people in a crowd are actually moving in groups, such as friends, couples, or families walking together. These groups constitute medium-scale aggregated structures and their impact on crowd dynamics is still largely unknown. In this work, we analyze the motion of approximately 1500 pedestrian groups under natural condition, and show that social interactions among group members generate typical group walking patterns that influence crowd dynamics. At low density, group members tend to walk side by side, forming a line perpendicular to the walking direction. As the density increases, however, the linear walking formation is bent forward, turning it into a V-like pattern. These spatial patterns can be well described by a model based on social communication between group members. We show that the V-like walking pattern facilitates social interactions within the group, but reduces the flow because of its "non-aerodynamic" shape. Therefore, when crowd density increases, the group organization results from a trade-off between walking faster and facilitating social exchange. These insights demonstrate that crowd dynamics is not only determined by physical constraints induced by other pedestrians and the environment, but also significantly by communicative, social interactions among individuals.

  8. Space and time in masking and crowding.

    Science.gov (United States)

    Lev, Maria; Polat, Uri

    2015-01-01

    Masking and crowding are major phenomena associated with contextual modulations, but the relationship between them remains unclear. We have recently shown that crowding is apparent in the fovea when the time available for processing is limited, pointing to the strong relationship between crowding in the spatial and temporal domains. Models of crowding emphasize the size (acuity) of the target and the spacing between the target and flankers as the main determinants that predict crowding. Our model, which is based on lateral interactions, posits that masking and crowding are related in the spatial and temporal domains at the fovea and periphery and that both can be explained by the increasing size of the human perceptive field (PF) with increasing eccentricity. We explored the relations between masking and crowding using letter identification and contrast detection by correlating the crowding effect with the estimated size of the PF and with masking under different spatiotemporal conditions. We found that there is a large variability in PF size and crowding effects across observers. Nevertheless, masking and crowding were both correlated with the estimated size of the PF in the fovea and periphery under a specific range of spatiotemporal parameters. Our results suggest that under certain conditions, crowding and masking share common neural mechanisms that underlie the spatiotemporal properties of these phenomena in both the fovea and periphery. These results could explain the transfer of training gains from spatiotemporal Gabor masking to letter acuity, reading, and reduced crowding.

  9. Comparing crowding in human and ideal observers

    NARCIS (Netherlands)

    van den Berg, Ronald; Johnson, Addie; Anton, Angela Martinez; Schepers, Anne L.; Cornelissen, Frans W.

    2012-01-01

    A visual target is more difficult to recognize when it is surrounded by other, similar objects. This breakdown in object recognition is known as crowding. Despite a long history of experimental work, computational models of crowding are still sparse. Specifically, few studies have examined crowding

  10. Emergency department crowding: Factors influencing flow

    NARCIS (Netherlands)

    van der Linden, M.C.

    2015-01-01

    This thesis focuses on emergency department (ED) crowding. In the first part (ED crowding in the Netherlands) the current state of EDs regarding patients’ length of stay and ED managers’ experiences of crowding are described. Part two (input factors) contains three studies which describe the case lo

  11. External vibration enhances macromolecular crowding for construction of aligned three-dimensional collagen fibril scaffolds.

    Science.gov (United States)

    Hsu, Hsiao-Ting; Rau, Lih-Rou; Zeng, Yao-Nan; Kang, Yi-Lin; Tsai, Shiao-Wen; Wu, Min-Hsien

    2015-04-17

    There are many techniques for preparing two-dimensional aligned fibril matrices. However, the critical problem associated with these techniques is the destruction of the native structure (e.g., the α-helix) of the proteins. Moreover, most of these techniques cannot create a three-dimensional (3D), aligned reconstituted collagen fibril matrix in one step. In this study, we used a simple device composed of a pneumatic membrane that generates a tunable vibration frequency to apply physical stimulation to fabricate a 3D, aligned collagen fibril matrix with the characteristic D-period structure of collagen in one step. Using second harmonic images, we demonstrated that the aligned, reconstituted collagen fibrils preserve the native collagen D-period structure. The average angular deviation of fibril alignment was reduced to 25.01 ± 4.2° compared with the 39.7 ± 2.19° of alignment observed for the randomly distributed fibril matrix. In addition, the ultimate tensile strength of the aligned matrix when force was applied in the direction parallel to the fiber orientation was higher than that of the randomly oriented matrix. The aligned reconstituted collagen fibril matrix also enhanced the expression of smoothelin (a specific marker of contractile phenotype) of thoracic aortic smooth muscle cell (A7r5) relative to the randomly distributed collagen fibril matrix.

  12. Protein Coevolution and Isoexpression in Yeast Macromolecular Complexes

    Directory of Open Access Journals (Sweden)

    Laurence Ettwiller

    2007-01-01

    Full Text Available Previous studies in the yeast Saccharomyces cerevisiae have shown that genes encoding subunits of macromolecular complexes have similar evolutionary rates (K and expression levels (E. Besides, it is known that the expression of a gene is a strong predictor of its rate of evolution (i.e., E and K are correlated. Here we show that intracomplex variation of subunit expression correlates with intracomplex variation of their evolutionary rates (using two different measures of dispersion. However, a similar trend was observed for randomized complexes. Therefore, using a mathematical transformation, we created new variables capturing intracomplex variation of both E and K. The values of these new compound variables were smaller for real complexes than for randomized ones. This shows that proteins in complexes tend to have closer expressivities (E and K's simultaneously than in the randomly grouped genes. We speculate about the possible implications of this finding.

  13. Eye movements, search and crowding

    NARCIS (Netherlands)

    Vlaskamp, B.N.S.

    2006-01-01

    If you fixate a single letter in a text, you will notice that it is impossible to identify a letter that is only a few letters away. This is caused by letters that flank this target letter. This is an example of the 'crowding' phenomenon, i.e. items that are close enough to each other interfere with

  14. Macromolecular mimicry of nucleic acid and protein

    DEFF Research Database (Denmark)

    Nautrup Pedersen, Gitte; Nyborg, Jens; Clark, Brian F

    1999-01-01

    of the concept of macromolecular mimicry. Macromolecular mimicry has further been proposed among initiation and release factors, thereby adding a new element to the description of protein synthesis in bacteria. Such mimicry has also been observed in other biological processes such as autoimmunity, DNA repair......Although proteins and nucleic acids consist of different chemical components, proteins can mimic structures and possibly also functions of nucleic acids. Recently, structural mimicry was observed between two elongation factors in bacterial protein biosynthesis leading to the introduction...

  15. Crowd Art: Density and Flow Based Crowd Motion Design

    OpenAIRE

    Jordao, Kevin; Charalambous, Panayiotis; Christie, Marc; Pettré, Julien; Cani, Marie-Paule

    2015-01-01

    International audience; Artists, animation and game designers are in demand for solutions to easily populate large virtual environments with crowds that satisfy desired visual features. This paper presents a method to intuitively populate virtual environments by specifying two key features: localized density, being the amount of agents per unit of surface, and localized flow, being the direction in which agents move through a unit of surface. The technique we propose is also time-independant,...

  16. A Tale of Two Crowds

    Science.gov (United States)

    Robinson, K. L.; Luo, J. Y.; Guigand, C.; Sponaugle, S.; Cowen, R. K.

    2016-02-01

    `Big biological data' sets are becoming common in oceanography with the advent of sampling technologies that can generate high-frequency observations for multiple data streams simultaneously. Identifying and implementing robust and efficient approaches to manage and analyze these big biological data (BBD) sets has become a primary challenge facing many biological oceanographers and marine ecologists alike. Using a large plankton imagery dataset generated by the "Deep Focus Plankton Imager-2" (formerly the ISIIS-2) system as an example, we present two `crowd-sourcing' approaches applied to the problem of efficiently classifying tens of millions of images of individual plankters. The first approach uses `crowd sourcing'' in its typical format by asking members of the general public to identify groups of plankton via a web-interface hosted by Zooniverse. The second approach engaged members of the data science community via a partnership with Kaggle and Booz Allen Hamilton, two data science industry leaders. We discuss how academic-industry partnerships were established, the questions we sought to answer via crowd-sourcing as well as the success, the pit-falls, and the surprising outcomes that were generated by each approach.

  17. The Wisdom of e-crowds: Can Masses Create Value?

    Directory of Open Access Journals (Sweden)

    Wieczerzycki Marcin

    2016-09-01

    Full Text Available With the rising popularity of the Internet, interactions between companies and their consumers have become more common and meaningful. Researchers often tend to apply the metaphor of community to these on-line networks of B2C relationships. However, this term implies durability and a long-term orientation. It does not cover more incidental, short-lived groups of consumers, who therefore should not be treated as communities. The purpose of this paper is to explore the ability of these short-term, collective consumer phenomena (addressed as e-crowds within the scope of this paper to create value. Based on a critical literature analysis that considers works from several different fields of knowledge (including management, economics, psychology and media studies and empirical examples, we argue that while lacking a complex internal organization, e-crowds are capable of creating use, exchange and sign value when certain conditions are met. However, they are equally likely to perform value-destroying activities, which present real risks for companies that interact with e-crowds.

  18. Release of crowding by pattern completion.

    Science.gov (United States)

    Manassi, Mauro; Hermens, Frouke; Francis, Gregory; Herzog, Michael H

    2015-01-01

    In crowding, target perception deteriorates in the presence of flanking elements. Crowding is classically explained by low-level mechanisms such as pooling or feature substitution. However, we have previously shown that perceptual grouping between the target and flankers, rather than low-level mechanisms, determines crowding. There are many grouping cues that can determine crowding, such as low- and high-level feature similarity, low- and high-level pattern regularity, and good Gestalt. Here we show that pattern completion, another grouping cue that is important for crowding in foveal vision, is also important in peripheral vision. We also describe computer simulations that show how pattern completion, and crowding in general, can be partly explained by recurrent processing.

  19. International perspectives on emergency department crowding.

    Science.gov (United States)

    Pines, Jesse M; Hilton, Joshua A; Weber, Ellen J; Alkemade, Annechien J; Al Shabanah, Hasan; Anderson, Philip D; Bernhard, Michael; Bertini, Alessio; Gries, André; Ferrandiz, Santiago; Kumar, Vijaya Arun; Harjola, Veli-Pekka; Hogan, Barbara; Madsen, Bo; Mason, Suzanne; Ohlén, Gunnar; Rainer, Timothy; Rathlev, Niels; Revue, Eric; Richardson, Drew; Sattarian, Mehdi; Schull, Michael J

    2011-12-01

    The maturation of emergency medicine (EM) as a specialty has coincided with dramatic increases in emergency department (ED) visit rates, both in the United States and around the world. ED crowding has become a public health problem where periodic supply and demand mismatches in ED and hospital resources cause long waiting times and delays in critical treatments. ED crowding has been associated with several negative clinical outcomes, including higher complication rates and mortality. This article describes emergency care systems and the extent of crowding across 15 countries outside of the United States: Australia, Canada, Denmark, Finland, France, Germany, Hong Kong, India, Iran, Italy, The Netherlands, Saudi Arabia, Catalonia (Spain), Sweden, and the United Kingdom. The authors are local emergency care leaders with knowledge of emergency care in their particular countries. Where available, data are provided about visit patterns in each country; however, for many of these countries, no national data are available on ED visits rates or crowding. For most of the countries included, there is both objective evidence of increases in ED visit rates and ED crowding and also subjective assessments of trends toward higher crowding in the ED. ED crowding appears to be worsening in many countries despite the presence of universal health coverage. Scandinavian countries with robust systems to manage acute care outside the ED do not report crowding is a major problem. The main cause for crowding identified by many authors is the boarding of admitted patients, similar to the United States. Many hospitals in these countries have implemented operational interventions to mitigate crowding in the ED, and some countries have imposed strict limits on ED length of stay (LOS), while others have no clear plan to mitigate crowding. An understanding of the causes and potential solutions implemented in these countries can provide a lens into how to mitigate ED crowding in the United States

  20. GPU Generation of Large Varied Animated Crowds

    OpenAIRE

    Isaac Rudomin; Benjamín Hernández; Oriam de Gyves; Leonel Toledo; Ivan Rivalcoba; Sergio Ruiz

    2013-01-01

    ..We discuss several steps in the process of simulating and visualizing large and varied crowds in real time for consumer-level computers and graphic cards (GPUs). Animating varied crowds using a diversity of models and animations (assets) is complex and costly. One has to use models that are expensive if bought, take a long time to model, and consume too much memory and computing resources. We discuss methods for simulating, generating, animating and rendering crowds of varied aspect and a d...

  1. On the generality of crowding: visual crowding in size, saturation, and hue compared to orientation.

    Science.gov (United States)

    van den Berg, Ronald; Roerdink, Jos B T M; Cornelissen, Frans W

    2007-07-17

    Perception of peripherally viewed shapes is impaired when surrounded by similar shapes. This phenomenon is commonly referred to as "crowding". Although studied extensively for perception of characters (mainly letters) and, to a lesser extent, for orientation, little is known about whether and how crowding affects perception of other features. Nevertheless, current crowding models suggest that the effect should be rather general and thus not restricted to letters and orientation. Here, we report on a series of experiments investigating crowding in the following elementary feature dimensions: size, hue, and saturation. Crowding effects in these dimensions were benchmarked against those in the orientation domain. Our primary finding is that all features studied show clear signs of crowding. First, identification thresholds increase with decreasing mask spacing. Second, for all tested features, critical spacing appears to be roughly half the viewing eccentricity and independent of stimulus size, a property previously proposed as the hallmark of crowding. Interestingly, although critical spacings are highly comparable, crowding magnitude differs across features: Size crowding is almost as strong as orientation crowding, whereas the effect is much weaker for saturation and hue. We suggest that future theories and models of crowding should be able to accommodate these differences in crowding effects.

  2. Statistics of Multiscale Fluctuations in Macromolecular Systems

    CERN Document Server

    Yukalov, V I

    2012-01-01

    An approach is suggested for treating multiscale fluctuations in macromolecular systems. The emphasis is on the statistical properties of such fluctuations. The approach is illustrated by a macromolecular system with mesoscopic fluctuations between the states of atomic orbitals. Strong-orbital and weak-orbital couplings fluctuationally arise, being multiscale in space and time. Statistical properties of the system are obtained by averaging over the multiscale fluctuations. The existence of such multiscale fluctuations causes phase transitions between strong-coupling and weak-coupling states. These transitions are connected with structure and size transformations of macromolecules. An approach for treating density and size multiscale fluctuations by means of classical statistical mechanics is also advanced.

  3. In situ macromolecular crystallography using microbeams.

    Science.gov (United States)

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

    2012-05-01

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

  4. Growth and dissolution of macromolecular Markov chains

    CERN Document Server

    Gaspard, Pierre

    2016-01-01

    The kinetics and thermodynamics of free living copolymerization are studied for processes with rates depending on k monomeric units of the macromolecular chain behind the unit that is attached or detached. In this case, the sequence of monomeric units in the growing copolymer is a kth-order Markov chain. In the regime of steady growth, the statistical properties of the sequence are determined analytically in terms of the attachment and detachment rates. In this way, the mean growth velocity as well as the thermodynamic entropy production and the sequence disorder can be calculated systematically. These different properties are also investigated in the regime of depolymerization where the macromolecular chain is dissolved by the surrounding solution. In this regime, the entropy production is shown to satisfy Landauer's principle.

  5. Growth and Dissolution of Macromolecular Markov Chains

    Science.gov (United States)

    Gaspard, Pierre

    2016-07-01

    The kinetics and thermodynamics of free living copolymerization are studied for processes with rates depending on k monomeric units of the macromolecular chain behind the unit that is attached or detached. In this case, the sequence of monomeric units in the growing copolymer is a kth-order Markov chain. In the regime of steady growth, the statistical properties of the sequence are determined analytically in terms of the attachment and detachment rates. In this way, the mean growth velocity as well as the thermodynamic entropy production and the sequence disorder can be calculated systematically. These different properties are also investigated in the regime of depolymerization where the macromolecular chain is dissolved by the surrounding solution. In this regime, the entropy production is shown to satisfy Landauer's principle.

  6. Crowdedness mediates the effect of social identification on positive emotion in a crowd: a survey of two crowd events.

    Directory of Open Access Journals (Sweden)

    David Novelli

    Full Text Available Exposure to crowding is said to be aversive, yet people also seek out and enjoy crowded situations. We surveyed participants at two crowd events to test the prediction of self-categorization theory that variable emotional responses to crowding are a function of social identification with the crowd. In data collected from participants who attended a crowded outdoor music event (n = 48, identification with the crowd predicted feeling less crowded; and there was an indirect effect of identification with the crowd on positive emotion through feeling less crowded. Identification with the crowd also moderated the relation between feeling less crowded and positive emotion. In data collected at a demonstration march (n = 112, identification with the crowd predicted central (most dense location in the crowd; and there was an indirect effect of identification with the crowd on positive emotion through central location in the crowd. Positive emotion in the crowd also increased over the duration of the crowd event. These findings are in line with the predictions of self-categorization theory. They are inconsistent with approaches that suggest that crowding is inherently aversive; and they cannot easily be explained through the concept of 'personal space'.

  7. Crowding, reading, and developmental dyslexia.

    Science.gov (United States)

    Martelli, Marialuisa; Di Filippo, Gloria; Spinelli, Donatella; Zoccolotti, Pierluigi

    2009-04-17

    We tested the hypothesis that crowding effects are responsible for the reading slowness characteristic of developmental dyslexia. A total of twenty-nine Italian dyslexics and thirty-three age-matched controls participated in various parts of the study. In Experiment 1, we measured contrast thresholds for identifying letters and words as a function of stimulus duration. Thresholds were higher in dyslexics than controls for words (at a limited time exposure) but not for single letters. Adding noise to the stimuli produced comparable effects in dyslexics and controls. At the long time exposure thresholds were comparable in the two groups. In Experiment 2, we measured the spacing between a target letter and two flankers at a fixed level of performance as a function of eccentricity and size. With eccentricity, the critical spacing (CS) scaled in the control group with 0.62 proportionality (a value of b close to Bouma's law, 0.50) and with a greater proportionality (0.95) in the dyslexic group. CS was independent of size in both groups. In Experiment 3, we examined the critical print size (CPS), that is, the increase in reading rate up to a critical character size (S. T. Chung, J. S. Mansfield, & G. E. Legge, 1998). CPS of dyslexic children was greater than that of controls. Individual maximal reading speed was predicted by individual bs (from Experiment 2). The maximal reading rate achieved by dyslexics at CPS (and also for larger print sizes) was below the values observed in controls. We conclude that word analysis in dyslexics is slowed because of greater crowding effects, which limit letter identification in multi-letter arrays across the visual field. We propose that the peripheral reading of normal readers might constitute a model for dyslexic reading. The periphery model accounts for 60% of dyslexics' slowness. After compensating for crowding, the dyslexics' reading rate remains slower than that of proficient readers. This failure is discussed in terms of a

  8. Crowd Simulation and Its Applications:Recent Advances

    Institute of Scientific and Technical Information of China (English)

    徐明亮; 蒋浩; 金小刚; 邓志刚

    2014-01-01

    This article surveys the state-of-the-art crowd simulation techniques and their selected applications, with its focus on our recent research advances in this rapidly growing research field. We first give a categorized overview on the mainstream methodologies of crowd simulation. Then, we describe our recent research advances on crowd evacuation, pedestrian crowds, crowd formation, traffic simulation, and swarm simulation. Finally, we offer our viewpoints on open crowd simulation research challenges and point out potential future directions in this field.

  9. Dextran: A promising macromolecular drug carrier

    Directory of Open Access Journals (Sweden)

    Dhaneshwar Suneela

    2006-01-01

    Full Text Available Over the past three decades intensive efforts have been made to design novel systems able to deliver the drug more effectively to the target site. The ongoing intense search for novel and innovative drug delivery systems is predominantly a consequence of the well-established fact that the conventional dosage forms are not sufficiently effective in conveying the drug compound to its site of action and once in the target area, in releasing the active agent over a desired period of time. The potential use of macromolecular prodrugs as a means of achieving targeted drug delivery has attracted considerable interest in recent years. Macromolecules such as antibodies, lipoproteins, lectins, proteins, polypeptides, polysaccharides, natural as well as synthetic polymers offer potential applicabilities as high molecular weight carriers for various therapeutically active compounds. Dextrans serve as one of the most promising macromolecular carrier candidates for a wide variety of therapeutic agents due to their excellent physico-chemical properties and physiological acceptance. The present contribution attempts to review various features of the dextran carrier like its source, structural and physico-chemical characteristics, pharmacokinetic fate and its applications as macromolecular carrier with special emphasis on dextran prodrugs.

  10. Bibliotecas escolares: tendências globais

    Directory of Open Access Journals (Sweden)

    Kelley Cristine Gonçalves Dias Gasque

    2016-09-01

    Full Text Available Este artigo aborda as transformações do processo de ensinoaprendizagem e das tecnologias e o impacto dessas nas bibliotecas escolares, especificamente, na formação do acervo, na configuração do espaço e no papel dos bibliotecários. A análise da literatura mostra tendência à adoção de modelos de aprendizagem baseados na construção colaborativa do conhecimento, com ênfase na aprendizagem compreensiva e atividades de ensino em ambientes diversificados. As bibliotecas escolares podem acolher e subsidiar atividades de ensino variadas, transformando-se em locais não apenas de apropriação da informação, mas também de produção do conhecimento por meio de atividades colaborativas, conectadas e diversificadas. O bibliotecário precisa fortalecer o domínio de tecnologias para obtenção, gerenciamento, produção e compartilhamento de informações. O fomento à leitura continua a ser importante, mas precisa ser ampliado para diferentes suportes e formatos.

  11. Function of metabolic and organelle networks in crowded and organized media

    Directory of Open Access Journals (Sweden)

    Miguel A Aon

    2015-01-01

    Full Text Available (Macromolecular crowding and the ability of the ubiquitous cytoskeleton to dynamically polymerize-depolymerize are prevalent cytoplasmic conditions in prokaryotic and eukaryotic cells. Protein interactions, enzymatic or signaling reactions - single, sequential or in complexes - whole metabolic pathways and organelles can be affected by crowding, the type and polymeric status of cytoskeletal proteins (e.g. tubulin, actin, and their imparted organization. The self-organizing capability of the cytoskeleton can orchestrate metabolic fluxes through entire pathways while its fractal organization can frame the scaling of activities in several levels of organization. The intracellular environment dynamics (e.g. biochemical reactions is dominated by the orderly cytoskeleton and the intrinsic randomness of molecular crowding. Existing evidence underscores the inherent capacity of intracellular organization to generate emergent global behavior. Yet unknown is the relative impact on cell function provided by organelle or functional compartmentation based on transient proteins association driven by weak interactions (quinary structures under specific environmental challenges or functional conditions (e.g. hypoxia, division, differentiation. We propose a qualitative, integrated structural-functional model of cytoplasmic organization based on a modified version of the Sierspinsky-Menger-Mandelbrot sponge, a 3D representation of a percolation cluster, and examine its capacity to accommodate established experimental facts.

  12. Comparing crowding in human and ideal observers.

    Science.gov (United States)

    van den Berg, Ronald; Johnson, Addie; Martinez Anton, Angela; Schepers, Anne L; Cornelissen, Frans W

    2012-06-12

    A visual target is more difficult to recognize when it is surrounded by other, similar objects. This breakdown in object recognition is known as crowding. Despite a long history of experimental work, computational models of crowding are still sparse. Specifically, few studies have examined crowding using an ideal-observer approach. Here, we compare crowding in ideal observers with crowding in humans. We derived an ideal-observer model for target identification under conditions of position and identity uncertainty. Simulations showed that this model reproduces the hallmark of crowding, namely a critical spacing that scales with viewing eccentricity. To examine how well the model fits quantitatively to human data, we performed three experiments. In Experiments 1 and 2, we measured observers' perceptual uncertainty about stimulus positions and identities, respectively, for a target in isolation. In Experiment 3, observers identified a target that was flanked by two distractors. We found that about half of the errors in Experiment 3 could be accounted for by the perceptual uncertainty measured in Experiments 1 and 2. The remainder of the errors could be accounted for by assuming that uncertainty (i.e., the width of internal noise distribution) about stimulus positions and identities depends on flanker proximity. Our results provide a mathematical restatement of the crowding problem and support the hypothesis that crowding behavior is a sign of optimality rather than a perceptual defect.

  13. Cohort Crowding and Nonresident College Enrollment

    Science.gov (United States)

    Winters, John V.

    2012-01-01

    This study uses a fixed effects panel data framework to examine the effects of cohort crowding and other variables on nonresident enrollment at four-year public colleges and universities. The results suggest that larger cohorts of resident students crowd out nonresident students at flagship universities, but there is inconsistent evidence of crowd…

  14. Image correlates of crowding in natural scenes.

    Science.gov (United States)

    Wallis, Thomas S A; Bex, Peter J

    2012-07-13

    Visual crowding is the inability to identify visible features when they are surrounded by other structure in the peripheral field. Since natural environments are replete with structure and most of our visual field is peripheral, crowding represents the primary limit on vision in the real world. However, little is known about the characteristics of crowding under natural conditions. Here we examine where crowding occurs in natural images. Observers were required to identify which of four locations contained a patch of "dead leaves'' (synthetic, naturalistic contour structure) embedded into natural images. Threshold size for the dead leaves patch scaled with eccentricity in a manner consistent with crowding. Reverse correlation at multiple scales was used to determine local image statistics that correlated with task performance. Stepwise model selection revealed that local RMS contrast and edge density at the site of the dead leaves patch were of primary importance in predicting the occurrence of crowding once patch size and eccentricity had been considered. The absolute magnitudes of the regression weights for RMS contrast at different spatial scales varied in a manner consistent with receptive field sizes measured in striate cortex of primate brains. Our results are consistent with crowding models that are based on spatial averaging of features in the early stages of the visual system, and allow the prediction of where crowding is likely to occur in natural images.

  15. No priming for global motion in crowding.

    Science.gov (United States)

    Pavan, Andrea; Gall, Martin G; Manassi, Mauro; Greenlee, Mark W

    2015-01-01

    There is psychophysical evidence that low-level priming, e.g., from oriented gratings, as well as high-level semantic priming, survives crowding. We investigated priming for global translational motion in crowded and noncrowded conditions. The results indicated that reliable motion priming occurs in the noncrowded condition, but motion priming does not survive crowding. Crowding persisted despite variations in the direction of the flankers with respect to the prime's direction. Motion priming was still absent under crowding when 85% of the flankers moved in the same direction as the prime. Crowding also persisted despite variations in the speed of the flankers relative to the prime even when the flankers' speed was four times slower than the speed of the prime. However, a priming effect was evident when the prime's spatial location was precued and its distance to the flankers increased, suggesting a release from crowding. These results suggest that transient attention induced by precueing the spatial location of the prime may improve subjects' ability to discriminate its direction. Spatial cueing could act to decrease the integration field, thereby diminishing the influence of nearby distracters. In an additional experiment in which we used fewer flankers, we found a priming effect under conditions in which the interelement distance varied between flankers and prime. Overall, the results suggest that motion priming is strongly affected by crowding, but transient attention can partially retrieve such facilitation.

  16. How crowded is the prokaryotic cytoplasm?

    NARCIS (Netherlands)

    Spitzer, Jan; Poolman, Bert; Ferguson, Stuart

    2013-01-01

    We consider biomacromolecular crowding within the cytoplasm of prokaryotic cells as a two-phase system of 'supercrowded' cytogel and 'dilute' cytosol; we simplify and quantify this model for a coccoid cell over a wide range of biomacromolecular crowding. The key result shows that the supercrowded

  17. Socialization of Social Anxiety in Adolescent Crowds

    Science.gov (United States)

    Van Zalk, Nejra; Van Zalk, Maarten Herman Walter; Kerr, Margaret

    2011-01-01

    In this study, we looked at whether social anxiety is socialized, or influenced by peers' social anxiety, more in some peer crowds than others. Adolescents in crowds with eye-catching appearances such as Goths and Punks (here termed "Radical"), were compared with three comparison groups. Using data from 796 adolescents (353 girls and 443 boys; M…

  18. Perceptions of Emergency Department Crowding in Pennsylvania

    Directory of Open Access Journals (Sweden)

    Pines, Jesse M

    2013-02-01

    Full Text Available Introduction: The state of emergency department (ED crowding in Pennsylvania has not previously been reported.Methods: We assessed perceptions of ED crowding by surveying medical directors/chairs from Pennsylvania EDs in the spring of 2008.Results: A total of 106 completed the questionnaire (68% response rate. A total of 83% (86/104 agreed that ED crowding was a problem; 26% (27/105 reported that at least half of admitted patients boarded for more than 4 hours. Ninety-eight percent (102/104 agreed that patient satisfaction suffers during crowding and 79% (84/106 stated that quality suffers. Sixty-five percent (68/105 reported that crowding had worsened during the past 2 years. Several hospital interventions were used to alleviate crowding: expediting discharges, 81% (86/106; prioritizing ED patients for inpatient beds, 79% (84/ 106; and ambulance diversion, 55% (57/105. Almost all respondents who had improved ED operations reported that it had reduced crowding.Conclusion: ED crowding is a common problem in Pennsylvania and is worsening in the majority of hospitals, despite the implementation of a variety of interventions. [West J EmergMed. 2013;14(1:1–10.

  19. Shadow obstacle model for realistic corner-turning behavior in crowd simulation

    Institute of Scientific and Technical Information of China (English)

    Gao-qi HE; Yi JIN; Qi CHEN; Zhen LIU; Wen-hui YUE; Xing-jian LU

    2016-01-01

    This paper describes a novel model known as the shadow obstacle model to generate a realistic corner-turning be-havior in crowd simulation. The motivation for this model comes from the observation that people tend to choose a safer route rather than a shorter one when turning a corner. To calculate a safer route, an optimization method is proposed to generate the corner-turning rule that maximizes the viewing range for the agents. By combining psychological and physical forces together, a full crowd simulation framework is established to provide a more realistic crowd simulation. We demonstrate that our model produces a more realistic corner-turning behavior by comparison with real data obtained from the experiments. Finally, we per-form parameter analysis to show the believability of our model through a series of experiments.

  20. Pervasive Adaptation in Car Crowds

    Science.gov (United States)

    Ferscha, Alois; Riener, Andreas

    Advances in the miniaturization and embedding of electronics for microcomputing, communication and sensor/actuator systems, have fertilized the pervasion of technology into literally everything. Pervasive computing technology is particularly flourishing in the automotive domain, exceling the “smart car”, embodying intelligent control mechanics, intelligent driver assistance, safety and comfort systems, navigation, tolling, fleet management and car-to-car interaction systems, as one of the outstanding success stories of pervasive computing. This paper raises the issue of the socio-technical phenomena emerging from the reciprocal interrelationship between drivers and smart cars, particularly in car crowds. A driver-vehicle co-model (DVC-model) is proposed, expressing the complex interactions between the human driver and the in-car and on-car technologies. Both explicit (steering, shifting, overtaking), as well as implicit (body posture, respiration) interactions are considered, and related to the drivers vital state (attentive, fatigue, distracted, aggressive). DVC-models are considered as building blocks in large scale simulation experiments, aiming to analyze and understand adaptation phenomena rooted in the feed-back loops among individual driver behavior and car crowds.

  1. Crowd and environmental management during mass gatherings.

    Science.gov (United States)

    Johansson, Anders; Batty, Michael; Hayashi, Konrad; Al Bar, Osama; Marcozzi, David; Memish, Ziad A

    2012-02-01

    Crowds are a feature of large cities, occurring not only at mass gatherings but also at routine events such as the journey to work. To address extreme crowding, various computer models for crowd movement have been developed in the past decade, and we review these and show how they can be used to identify health and safety issues. State-of-the-art models that simulate the spread of epidemics operate on a population level, but the collection of fine-scale data might enable the development of models for epidemics that operate on a microscopic scale, similar to models for crowd movement. We provide an example of such simulations, showing how an individual-based crowd model can mirror aggregate susceptible-infected-recovered models that have been the main models for epidemics so far.

  2. Motor-free actin bundle contractility driven by molecular crowding

    CERN Document Server

    Schnauß, Jörg; Schuldt, Carsten; Schmidt, B U Sebastian; Glaser, Martin; Strehle, Dan; Heussinger, Claus; Käs, Josef A

    2015-01-01

    Modeling approaches of suspended, rod-like particles and recent experimental data have shown that depletion forces display different signatures depending on the orientation of these particles. It has been shown that axial attraction of two rods yields contractile forces of 0.1pN that are independent of the relative axial shift of the two rods. Here, we measured depletion-caused interactions of actin bundles extending the phase space of single pairs of rods to a multi-particle system. In contrast to a filament pair, we found forces up to 3pN . Upon bundle relaxation forces decayed exponentially with a mean decay time of 3.4s . These different dynamics are explained within the frame of a mathematical model by taking pairwise interactions to a multi-filament scale. The macromolecular content employed for our experiments is well below the crowding of cells. Thus, we propose that arising forces can contribute to biological force generation without the need to convert chemical energy into mechanical work.

  3. Avenues for crowd science in Hydrology.

    Science.gov (United States)

    Koch, Julian; Stisen, Simon

    2016-04-01

    Crowd science describes research that is conducted with the participation of the general public (the crowd) and gives the opportunity to involve the crowd in research design, data collection and analysis. In various fields, scientists have already drawn on underused human resources to advance research at low cost, with high transparency and large acceptance of the public due to the bottom up structure and the participatory process. Within the hydrological sciences, crowd research has quite recently become more established in the form of crowd observatories to generate hydrological data on water quality, precipitation or river flow. These innovative observatories complement more traditional ways of monitoring hydrological data and strengthen a community-based environmental decision making. However, the full potential of crowd science lies in internet based participation of the crowd and it is not yet fully exploited in the field of Hydrology. New avenues that are not primarily based on the outsourcing of labor, but instead capitalize the full potential of human capabilities have to emerge. In multiple realms of solving complex problems, like image detection, optimization tasks, narrowing of possible solutions, humans still remain more effective than computer algorithms. The most successful online crowd science projects Foldit and Galaxy Zoo have proven that the collective of tens of thousands users could clearly outperform traditional computer based science approaches. Our study takes advantage of the well trained human perception to conduct a spatial sensitivity analysis of land-surface variables of a distributed hydrological model to identify the most sensitive spatial inputs. True spatial performance metrics, that quantitatively compare patterns, are not trivial to choose and their applicability is often not universal. On the other hand humans can quickly integrate spatial information at various scales and are therefore a trusted competence. We selected

  4. Smoothing techniques for macromolecular global optimization

    Energy Technology Data Exchange (ETDEWEB)

    More, J.J.; Wu, Zhijun

    1995-09-01

    We study global optimization problems that arise in macromolecular modeling, and the solution of these problems via continuation and smoothing. Our results unify and extend the theory associated with the use of the Gaussian transform for smoothing. We show that the, Gaussian transform can be viewed as a special case of a generalized transform and that these generalized transforms share many of the properties of the Gaussian transform. We also show that the smoothing behavior of the generalized transform can be studied in terms of the Fourier transform and that these results indicate that the Gaussian transform has superior smoothing properties.

  5. Celebrating macromolecular crystallography: A personal perspective

    Directory of Open Access Journals (Sweden)

    Abad-Zapatero, Celerino

    2015-04-01

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

  6. The Behavioral Effects of Crowding: Definitions and Methods.

    Science.gov (United States)

    Dean, Larry M.; And Others

    Crews of 18 U.S. Navy combat vessels rated their living and working conditions aboard ship, including degree of crowding. In order to better understand the behavioral effects of crowding, three different types of measures, corresponding to different definitions of crowding, were constructed. These separate crowding measures correlated uniquely…

  7. Real-Time Density-Based Crowd Simulation

    NARCIS (Netherlands)

    van Toll, W.G.; Cook IV, A.F.; Geraerts, R.J.

    2012-01-01

    Virtual characters in games and simulations often need to plan visually convincing paths through a crowded environment. This paper describes how crowd density information can be used to guide a large number of characters through a crowded environment. Crowd density information helps characters avoid

  8. Realistic Crowd Simulation with Density-Based Path Planning

    NARCIS (Netherlands)

    van Toll, W.G.; Cook IV, A.F.; Geraerts, R.J.

    2012-01-01

    Virtual characters in games and simulations often need to plan visually convincing paths through a crowded environment. This paper describes how crowd density information can be used to guide a large number of characters through a crowded environment. Crowd density information helps characters avoid

  9. Realistic Crowd Simulation with Density-Based Path Planning

    NARCIS (Netherlands)

    van Toll, W.G.; Cook IV, A.F.; Geraerts, R.J.

    2012-01-01

    Virtual characters in games and simulations often need to plan visually convincing paths through a crowded environment. This paper describes how crowd density information can be used to guide a large number of characters through a crowded environment. Crowd density information helps characters avoid

  10. Real-Time Density-Based Crowd Simulation

    NARCIS (Netherlands)

    van Toll, W.G.; Cook IV, A.F.; Geraerts, R.J.

    2012-01-01

    Virtual characters in games and simulations often need to plan visually convincing paths through a crowded environment. This paper describes how crowd density information can be used to guide a large number of characters through a crowded environment. Crowd density information helps characters avoid

  11. An Energy based Method to Measure the Crowd Safety

    NARCIS (Netherlands)

    Yin, H.; Li, D.; Zheng, X.

    2014-01-01

    How to evaluate crowd safety in crowded areas is a tough, but important, problem. According to accident-causing theory, uncontrolled release of hazardous energy among overcrowded pedestrians is the basic cause of crowd disaster. Therefore, crowd energy is modeled in this paper, which takes both

  12. Multiscale macromolecular simulation: role of evolving ensembles.

    Science.gov (United States)

    Singharoy, A; Joshi, H; Ortoleva, P J

    2012-10-22

    Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin time step is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers.

  13. Macromolecular recognition in the Protein Data Bank

    Energy Technology Data Exchange (ETDEWEB)

    Janin, Joël, E-mail: joel.janin@ibbmc.u-psud.fr [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Rodier, Francis [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Chakrabarti, Pinak [Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Bahadur, Ranjit P. [Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France)

    2007-01-01

    X-ray structures in the PDB illustrate both the specific recognition of two polypeptide chains in protein–protein complexes and dimeric proteins and their nonspecific interaction at crystal contacts. Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein–protein and protein–DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200–2000 Å{sup 2} of protein surface occur in protease–inhibitor and antigen–antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes.

  14. Rotation-Induced Macromolecular Spooling of DNA

    Directory of Open Access Journals (Sweden)

    Tyler N. Shendruk

    2017-07-01

    Full Text Available Genetic information is stored in a linear sequence of base pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we discover that rotation-induced macromolecular spooling of DNA around a rotating microwire can monotonically order genomic bases, overcoming this challenge. We use single-molecule fluorescence microscopy to directly visualize long DNA strands deforming and elongating in shear flow near a rotating microwire, in agreement with numerical simulations. While untethered DNA is observed to elongate substantially, in agreement with our theory and numerical simulations, strong extension of DNA becomes possible by introducing tethering. For the case of tethered polymers, we show that increasing the rotation rate can deterministically spool a substantial portion of the chain into a fully stretched, single-file conformation. When applied to DNA, the fraction of genetic information sequentially ordered on the microwire surface will increase with the contour length, despite the increased entropy. This ability to handle long strands of DNA is in contrast to modern DNA sample preparation technologies for sequencing and mapping, which are typically restricted to comparatively short strands, resulting in challenges in reconstructing the genome. Thus, in addition to discovering new rotation-induced macromolecular dynamics, this work inspires new approaches to handling genomic-length DNA strands.

  15. Rotation-Induced Macromolecular Spooling of DNA

    Science.gov (United States)

    Shendruk, Tyler N.; Sean, David; Berard, Daniel J.; Wolf, Julian; Dragoman, Justin; Battat, Sophie; Slater, Gary W.; Leslie, Sabrina R.

    2017-07-01

    Genetic information is stored in a linear sequence of base pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we discover that rotation-induced macromolecular spooling of DNA around a rotating microwire can monotonically order genomic bases, overcoming this challenge. We use single-molecule fluorescence microscopy to directly visualize long DNA strands deforming and elongating in shear flow near a rotating microwire, in agreement with numerical simulations. While untethered DNA is observed to elongate substantially, in agreement with our theory and numerical simulations, strong extension of DNA becomes possible by introducing tethering. For the case of tethered polymers, we show that increasing the rotation rate can deterministically spool a substantial portion of the chain into a fully stretched, single-file conformation. When applied to DNA, the fraction of genetic information sequentially ordered on the microwire surface will increase with the contour length, despite the increased entropy. This ability to handle long strands of DNA is in contrast to modern DNA sample preparation technologies for sequencing and mapping, which are typically restricted to comparatively short strands, resulting in challenges in reconstructing the genome. Thus, in addition to discovering new rotation-induced macromolecular dynamics, this work inspires new approaches to handling genomic-length DNA strands.

  16. The role of macromolecular stability in desiccation tolerance

    NARCIS (Netherlands)

    Wolkers, W.F.

    1998-01-01

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

  17. The role of macromolecular stability in desiccation tolerance.

    NARCIS (Netherlands)

    Wolkers, W.

    1998-01-01

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

  18. Technology for Simulating Crowd Evacuation Behaviors

    Institute of Scientific and Technical Information of China (English)

    Wen-Hu Qin; Guo-Hui Su; Xiao-Na Li

    2009-01-01

    This paper presents a model for simulating crowd evacuation and investigates three widely recognized problems. For the space continuity problem, this paper presents two computation algorithms: one uses grid space to evaluate the coordinates of the obstacle's bounding box and the other employs the geometry rule to establish individual evacuation routes. For the problem of collision, avoidance, and excess among the individuals, this paper computes the generalized force and friction force and then modifies the direction of march to obtain a speed model based on the crowd density and real time speed. For the exit selection problem, this paper establishes a method of selecting the exits by combining the exit's crowd state with the individuals. Finally, a particle system is used to simulate the behavior of crowd evacuation and produces useful test results.

  19. NIH Abroad: Pictures Are Crowd Pullers

    Science.gov (United States)

    ... Pictures Are Crowd Pullers …" Art, culture, and the Internet combine to intervene against malaria in Uganda NLM's ... Services Division collaborated on the project through the Internet. "We wanted to see if such a 'health ...

  20. Towards a South African crowd control model

    CSIR Research Space (South Africa)

    Modise, M

    2013-03-01

    Full Text Available With the escalating number of incidents of service delivery, labour related protests and the increasingly violent nature of protests; crowd control is one of the major challenges facing South Africa today. Often these protests are characterized...

  1. Spatio-temporal properties of letter crowding

    Science.gov (United States)

    Chung, Susana T. L.

    2016-01-01

    Crowding between adjacent letters has been investigated primarily as a spatial effect. The purpose of this study was to investigate the spatio-temporal properties of letter crowding. Specifically, we examined the systematic changes in the degradation effects in letter identification performance when adjacent letters were presented with a temporal asynchrony, as a function of letter separation and between the fovea and the periphery. We measured proportion-correct performance for identifying the middle target letter in strings of three lowercase letters at the fovea and 10° in the inferior visual field, for a range of center-to-center letter separations and a range of stimulus onset asynchronies (SOA) between the target and flanking letters (positive SOAs: target preceded flankers). As expected, the accuracy for identifying the target letters reduces with decreases in letter separation. This crowding effect shows a strong dependency on SOAs, such that crowding is maximal between 0 and ∼100 ms (depending on conditions) and diminishes for larger SOAs (positive or negative). Maximal crowding does not require the target and flanking letters to physically coexist for the entire presentation duration. Most importantly, crowding can be minimized even for closely spaced letters if there is a large temporal asynchrony between the target and flankers. The reliance of letter identification performance on SOAs and how it changes with letter separations imply that the crowding effect can be traded between space and time. Our findings are consistent with the notion that crowding should be considered as a spatio-temporal, and not simply a spatial, effect. PMID:27088895

  2. Spatio-temporal properties of letter crowding.

    Science.gov (United States)

    Chung, Susana T L

    2016-01-01

    Crowding between adjacent letters has been investigated primarily as a spatial effect. The purpose of this study was to investigate the spatio-temporal properties of letter crowding. Specifically, we examined the systematic changes in the degradation effects in letter identification performance when adjacent letters were presented with a temporal asynchrony, as a function of letter separation and between the fovea and the periphery. We measured proportion-correct performance for identifying the middle target letter in strings of three lowercase letters at the fovea and 10° in the inferior visual field, for a range of center-to-center letter separations and a range of stimulus onset asynchronies (SOA) between the target and flanking letters (positive SOAs: target preceded flankers). As expected, the accuracy for identifying the target letters reduces with decreases in letter separation. This crowding effect shows a strong dependency on SOAs, such that crowding is maximal between 0 and ∼100 ms (depending on conditions) and diminishes for larger SOAs (positive or negative). Maximal crowding does not require the target and flanking letters to physically coexist for the entire presentation duration. Most importantly, crowding can be minimized even for closely spaced letters if there is a large temporal asynchrony between the target and flankers. The reliance of letter identification performance on SOAs and how it changes with letter separations imply that the crowding effect can be traded between space and time. Our findings are consistent with the notion that crowding should be considered as a spatio-temporal, and not simply a spatial, effect.

  3. Crowd Behavior Algorithm Development for COMBAT XXI

    Science.gov (United States)

    2017-05-30

    time to scenario development for CXXI scenario integraters. Report Organization This report is organized into literature review, analysis, results, and...TRAC-M-TR-17-027 30 May 2017 Crowd Behavior Algorithm Development for COMBATXXI TRADOC Analysis Center 700 Dyer Road Monterey, California 93943-0692...30 May 2017 Crowd Behavior Algorithm Development for COMBATXXI LTC Casey Connors Dr. Steven Hall Dr. Imre Balogh Terry Norbraten TRADOC Analysis

  4. Predicting Molecular Crowding Effects in Ion-RNA Interactions.

    Science.gov (United States)

    Yu, Tao; Zhu, Yuhong; He, Zhaojian; Chen, Shi-Jie

    2016-09-01

    We develop a new statistical mechanical model to predict the molecular crowding effects in ion-RNA interactions. By considering discrete distributions of the crowders, the model can treat the main crowder-induced effects, such as the competition with ions for RNA binding, changes of electrostatic interaction due to crowder-induced changes in the dielectric environment, and changes in the nonpolar hydration state of the crowder-RNA system. To enhance the computational efficiency, we sample the crowder distribution using a hybrid approach: For crowders in the close vicinity of RNA surface, we sample their discrete distributions; for crowders in the bulk solvent away from the RNA surface, we use a continuous mean-field distribution for the crowders. Moreover, using the tightly bound ion (TBI) model, we account for ion fluctuation and correlation effects in the calculation for ion-RNA interactions. Applications of the model to a variety of simple RNA structures such as RNA helices show a crowder-induced increase in free energy and decrease in ion binding. Such crowding effects tend to contribute to the destabilization of RNA structure. Further analysis indicates that these effects are associated with the crowder-ion competition in RNA binding and the effective decrease in the dielectric constant. This simple ion effect model may serve as a useful framework for modeling more realistic crowders with larger, more complex RNA structures.

  5. Categorical membership modulates crowding: evidence from characters.

    Science.gov (United States)

    Reuther, Josephine; Chakravarthi, Ramakrishna

    2014-10-16

    Visual crowding is generally thought to affect recognition mostly or only at the level of feature combination. Calling this assertion into question, recent studies have shown that if a target object and its flankers belong to different categories crowding is weaker than if they belong to the same category. Nevertheless, these results can be explained in terms of featural differences between categories. The current study tests if category-level (i.e., high-level) interference in crowding occurs when featural differences are controlled for. First, replicating previous results, we found lower critical spacing for targets and flankers belonging to different categories. Second, we observed the same, albeit weaker, category-specific effect when objects in both categories had the exact same feature set, suggesting that category-specific effects persist even when featural differences are fully controlled for. Third, we manipulated the semantic content of the flankers while keeping their feature set constant, by using upright or rotated objects, and found that meaning modulated crowding. An exclusively feature-based account of crowding would predict no differences due to such changes in meaning. We conclude that crowding results from not only the well-documented feature-level interactions but also additional interactions at a level where objects are grouped by meaning.

  6. Crowding in the S-cone pathway.

    Science.gov (United States)

    Coates, Daniel R; Chung, Susana T L

    2016-05-01

    The spatial extent of interference from nearby object or contours (the critical spacing of "crowding") has been thoroughly characterized across the visual field, typically using high contrast achromatic stimuli. However, attempts to link this measure with known properties of physiological pathways have been inconclusive. The S-cone pathway, with its ease of psychophysical isolation and known anatomical characteristics, offers a unique tool to gain additional insights into crowding. In this study, we measured the spatial extent of crowding in the S-cone pathway at several retinal locations using a chromatic adaptation paradigm. S-cone crowding was evident and extensive, but its spatial extent changed less markedly as a function of retinal eccentricity than the extent found using traditional achromatic stimuli. However, the spatial extent agreed with that of low contrast achromatic stimuli matched for isolated resolvability. This suggests that common cortical mechanisms mediate the crowding effect in the S-cone and achromatic pathway, but contrast is an important factor. The low contrast of S-cone stimuli makes S-cone vision more acuity-limited than crowding-limited.

  7. Acuity, crowding, reading and fixation stability.

    Science.gov (United States)

    Falkenberg, Helle K; Rubin, Gary S; Bex, Peter J

    2007-01-01

    People with age-related macular disease frequently experience reading difficulty that could be attributed to poor acuity, elevated crowding or unstable fixation associated with peripheral visual field dependence. We examine how the size, location, spacing and instability of retinal images affect the visibility of letters and words at different eccentricities. Fixation instability was simulated in normally sighted observers by randomly jittering single or crowded letters or words along a circular arc of fixed eccentricity. Visual performance was assessed at different levels of instability with forced choice measurements of acuity, crowding and reading speed in a rapid serial visual presentation paradigm. In the periphery: (1) acuity declined; (2) crowding increased for acuity- and eccentricity-corrected targets; and (3), the rate of reading fell with acuity-, crowding- and eccentricity-corrected targets. Acuity and crowding were unaffected by even high levels of image instability. However, reading speed decreased with image instability, even though the visibility of the component letters was unaffected. The results show that reading performance cannot be standardised across the visual field by correcting the size, spacing and eccentricity of letters or words. The results suggest that unstable fixation may contribute to reading difficulties in people with low vision and therefore that rehabilitation may benefit from fixation training.

  8. A Hierarchical Bayesian Model for Crowd Emotions

    Science.gov (United States)

    Urizar, Oscar J.; Baig, Mirza S.; Barakova, Emilia I.; Regazzoni, Carlo S.; Marcenaro, Lucio; Rauterberg, Matthias

    2016-01-01

    Estimation of emotions is an essential aspect in developing intelligent systems intended for crowded environments. However, emotion estimation in crowds remains a challenging problem due to the complexity in which human emotions are manifested and the capability of a system to perceive them in such conditions. This paper proposes a hierarchical Bayesian model to learn in unsupervised manner the behavior of individuals and of the crowd as a single entity, and explore the relation between behavior and emotions to infer emotional states. Information about the motion patterns of individuals are described using a self-organizing map, and a hierarchical Bayesian network builds probabilistic models to identify behaviors and infer the emotional state of individuals and the crowd. This model is trained and tested using data produced from simulated scenarios that resemble real-life environments. The conducted experiments tested the efficiency of our method to learn, detect and associate behaviors with emotional states yielding accuracy levels of 74% for individuals and 81% for the crowd, similar in performance with existing methods for pedestrian behavior detection but with novel concepts regarding the analysis of crowds. PMID:27458366

  9. Adaptively Learning the Crowd Kernel

    CERN Document Server

    Tamuz, Omer; Belongie, Serge; Shamir, Ohad; Kalai, Adam Tauman

    2011-01-01

    We introduce an algorithm that, given n objects, learns a similarity matrix over all n^2 pairs, from crowdsourced data alone. The algorithm samples responses to adaptively chosen triplet-based relative-similarity queries. Each query has the form "is object 'a' more similar to 'b' or to 'c'?" and is chosen to be maximally informative given the preceding responses. The output is an embedding of the objects into Euclidean space (like MDS); we refer to this as the "crowd kernel." The runtime (empirically observed to be linear) and cost (about $0.15 per object) of the algorithm are small enough to permit its application to databases of thousands of objects. The distance matrix provided by the algorithm allows for the development of an intuitive and powerful sequential, interactive search algorithm which we demonstrate for a variety of visual stimuli. We present quantitative results that demonstrate the benefit in cost and time of our approach compared to a nonadaptive approach. We also show the ability of our appr...

  10. Analysis on Forest Tending Subsidies Policy in China

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The shortage of forest tending funds in China has caused the retarded thinning for those forests that need urgently the tending thinning, which in turn has a negative impact on the implementation of forest management activities and results in the poor state of forest quality, function and healthy. This paper analyzed the necessity to implement forest tending subsidies, concluded the experience abroad, and proposed some policy recommendations on how to implement forest tending subsidies in China. It was indi...

  11. Innovative funding solution for special projects: Crowd funding

    Directory of Open Access Journals (Sweden)

    Sentot Imam Wahjono

    2015-06-01

    Full Text Available The aim of this paper is to examine the influence of crowd funding knowledge, applica-tion, platform, and project initiator toward successful crowd funding. This study conducted by quantitative approach, data have been collected with web-based ques-tionnaires via Kickstarter.com direct message and e-mail to 200 successful crowd funding project initiators as a sample and as much 152 sets questionnaire returned by a complete answer and should be analyzed further. Deployment and data collection take 3 month from October to December 2013. This study found evidence that crowd funding knowledge, crowd funding application, crowd funding platform, and project initiator has positive and significant relationship toward the success of crowd funding. The implication from this research is crowd funding can be a source of capital to finance the projects, not just rely on traditional sources of financing just like banking and capital markets. Crowd funding can be innovative funding solution.

  12. CrowdAidRepair: A Crowd-Aided Interactive Data Repairing Method

    KAUST Repository

    Zhou, Jian

    2016-03-25

    Data repairing aims at discovering and correcting erroneous data in databases. Traditional methods relying on predefined quality rules to detect the conflict between data may fail to choose the right way to fix the detected conflict. Recent efforts turn to use the power of crowd in data repairing, but the crowd power has its own drawbacks such as high human intervention cost and inevitable low efficiency. In this paper, we propose a crowd-aided interactive data repairing method which takes the advantages of both rule-based method and crowd-based method. Particularly, we investigate the interaction between crowd-based repairing and rule-based repairing, and show that by doing crowd-based repairing to a small portion of values, we can greatly improve the repairing quality of the rule-based repairing method. Although we prove that the optimal interaction scheme using the least number of values for crowd-based repairing to maximize the imputation recall is not feasible to be achieved, still, our proposed solution identifies an efficient scheme through investigating the inconsistencies and the dependencies between values in the repairing process. Our empirical study on three data collections demonstrates the high repairing quality of CrowdAidRepair, as well as the efficiency of the generated interaction scheme over baselines.

  13. A 3D image filter for parameter-free segmentation of macromolecular structures from electron tomograms.

    Directory of Open Access Journals (Sweden)

    Rubbiya A Ali

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

  14. A 3D image filter for parameter-free segmentation of macromolecular structures from electron tomograms.

    Science.gov (United States)

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

    2012-01-01

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

  15. Functional Sub-states by High-pressure Macromolecular Crystallography.

    Science.gov (United States)

    Dhaussy, Anne-Claire; Girard, Eric

    2015-01-01

    At the molecular level, high-pressure perturbation is of particular interest for biological studies as it allows trapping conformational substates. Moreover, within the context of high-pressure adaptation of deep-sea organisms, it allows to decipher the molecular determinants of piezophily. To provide an accurate description of structural changes produced by pressure in a macromolecular system, developments have been made to adapt macromolecular crystallography to high-pressure studies. The present chapter is an overview of results obtained so far using high-pressure macromolecular techniques, from nucleic acids to virus capsid through monomeric as well as multimeric proteins.

  16. Sequential recovery of macromolecular components of the nucleolus.

    Science.gov (United States)

    Bai, Baoyan; Laiho, Marikki

    2015-01-01

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

  17. Structure and Conformational Properties of d-Glucose/d-Galactose-Binding Protein in Crowded Milieu

    Directory of Open Access Journals (Sweden)

    Alexander V. Fonin

    2017-02-01

    Full Text Available Conformational changes of d-glucose/d-galactose-binding protein (GGBP were studied under molecular crowding conditions modeled by concentrated solutions of polyethylene glycols (PEG-12000, PEG-4000, and PEG-600, Ficoll-70, and Dextran-70, addition of which induced noticeable structural changes in the GGBP molecule. All PEGs promoted compaction of GGBP and lead to the increase in ordering of its structure. Concentrated solutions of PEG-12000 and PEG-4000 caused GGBP aggregation. Although Ficoll-70 and Dextran-70 also promoted increase in the GGBP ordering, the structural outputs were different for different crowders. For example, in comparison with the GGBP in buffer, the intrinsic fluorescence spectrum of this protein was shifted to short-wave region in the presence of PEGs but was red-shifted in the presence of Ficoll-70 and Dextran-70. It was hypothesized that this difference could be due to the specific interaction of GGBP with the sugar-based polymers (Ficoll-70 and Dextran-70, indicating that protein can adopt different conformations in solutions containing molecular crowders of different chemical nature. It was also shown that all tested crowding agents were able to stabilize GGBP structure shifting the GGBP guanidine hydrochloride (GdnHCl-induced unfolding curves to higher denaturant concentrations, but their stabilization capabilities did not depend on the hydrodynamic dimensions of the polymers molecules. Refolding of GGBP was complicated by protein aggregation in all tested solutions of crowding agents. The lowest yield of refolded protein was achieved in the highly concentrated solutions of PEG-12000. These data support the previous notion that the influence of macromolecular crowders on proteins is rather complex phenomenon that extends beyond the excluded volume effects.

  18. The crowding factor method applied to parafoveal vision

    Science.gov (United States)

    Ghahghaei, Saeideh; Walker, Laura

    2016-01-01

    Crowding increases with eccentricity and is most readily observed in the periphery. During natural, active vision, however, central vision plays an important role. Measures of critical distance to estimate crowding are difficult in central vision, as these distances are small. Any overlap of flankers with the target may create an overlay masking confound. The crowding factor method avoids this issue by simultaneously modulating target size and flanker distance and using a ratio to compare crowded to uncrowded conditions. This method was developed and applied in the periphery (Petrov & Meleshkevich, 2011b). In this work, we apply the method to characterize crowding in parafoveal vision (crowding than in the periphery, yet radial/tangential asymmetries are clearly preserved. There are considerable idiosyncratic differences observed between participants. The crowding factor method provides a powerful tool for examining crowding in central and peripheral vision, which will be useful in future studies that seek to understand visual processing under natural, active viewing conditions. PMID:27690170

  19. Station Crowd Control Plan: Shiawassee National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This Crowd Control Plan for Shiawassee NWR outlines the operations for crowd control on the Refuge. An inventory of resources, a summary of communications...

  20. Grouping, pooling, and when bigger is better in visual crowding.

    Science.gov (United States)

    Manassi, Mauro; Sayim, Bilge; Herzog, Michael H

    2012-01-01

    In crowding, perception of a target is strongly deteriorated by nearby elements. Crowding is often explained by pooling models predicting that adding flankers increases crowding. In contrast, the centroid hypothesis proposes that adding flankers decreases crowding--"bigger is better." In foveal vision, we have recently shown that adding flankers can increase or decrease crowding depending on whether the target groups or ungroups from the flankers. We have further shown how configural effects, such as good and global Gestalt, determine crowding. Foveal and peripheral crowding do not always reveal the same characteristics. Here, we show that the very same grouping and Gestalt results of foveal vision are also found in the periphery. These results can neither be explained by simple pooling nor by centroid models. We discuss when bigger is better and how grouping might shape crowding.

  1. The neural correlates of crowding-induced changes in appearance

    National Research Council Canada - National Science Library

    Anderson, Elaine J; Dakin, Steven C; Schwarzkopf, D Samuel; Rees, Geraint; Greenwood, John A

    2012-01-01

    .... Despite its severity, little is known about the cortical locus of crowding. Here, we examined the neural correlates of crowding by combining event-related fMRI adaptation with a change-detection paradigm...

  2. EMOTIONAL CONTAGION AND MOOD IN CROWD SERVING AS AUDIENCE

    Directory of Open Access Journals (Sweden)

    Beno Arnejcic

    2015-06-01

    Full Text Available The global world is gradually becoming a world of separated crowds despite the artificial wire and wireless connection through television and the Internet. Crowds remain a prevailing subject of research in different social studies, and the research of changes in the psychological structure of crowds and their characteristics is still of primary interest. The main focus of the research is on the interpretation of the results of the research paper about a special separated crowd called audience. It was observed how students, constituting the crowd, perceive a crowd on video. The observation was focused on the research of emotional contagion and mood in the crowd serving as audience. While watching a mass event on a big screen, the crowd serving as audience emotionally converges with someone else, in our case with public speakers.

  3. Factors influencing experience in crowds - The participant perspective.

    Science.gov (United States)

    Filingeri, Victoria; Eason, Ken; Waterson, Patrick; Haslam, Roger

    2017-03-01

    Humans encounter crowd situations on a daily basis, resulting in both negative and positive experiences. Understanding how to optimise the participant experience of crowds is important. In the study presented in this paper, 5 focus groups were conducted (35 participants, age range: 21-71 years) and 55 crowd situations observed (e.g. transport hubs, sport events, retail situations). Influences on participant experience in crowds identified by the focus groups and observations included: physical design of crowd space and facilities (layout, queuing strategies), crowd movement (monitoring capacity, pedestrian flow), communication and information (signage, wayfinding), comfort and welfare (provision of facilities, environmental comfort), and public order. It was found that important aspects affecting participant experience are often not considered systematically in the planning of events or crowd situations. The findings point to human factors aspects of crowds being overlooked, with the experiences of participants often poor.

  4. Crowding during restricted and free viewing.

    Science.gov (United States)

    Wallace, Julian M; Chiu, Michael K; Nandy, Anirvan S; Tjan, Bosco S

    2013-05-24

    Crowding impairs the perception of form in peripheral vision. It is likely to be a key limiting factor of form vision in patients without central vision. Crowding has been extensively studied in normally sighted individuals, typically with a stimulus duration of a few hundred milliseconds to avoid eye movements. These restricted testing conditions do not reflect the natural behavior of a patient with central field loss. Could unlimited stimulus duration and unrestricted eye movements change the properties of crowding in any fundamental way? We studied letter identification in the peripheral vision of normally sighted observers in three conditions: (i) a fixation condition with a brief stimulus presentation of 250 ms, (ii) another fixation condition but with an unlimited viewing time, and (iii) an unrestricted eye movement condition with an artificial central scotoma and an unlimited viewing time. In all conditions, contrast thresholds were measured as a function of target-to-flanker spacing, from which we estimated the spatial extent of crowding in terms of critical spacing. We found that presentation duration beyond 250 ms had little effect on critical spacing with stable gaze. With unrestricted eye movements and a simulated central scotoma, we found a large variability in critical spacing across observers, but more importantly, the variability in critical spacing was well correlated with the variability in target eccentricity. Our results assure that the large body of findings on crowding made with briefly presented stimuli remains relevant to conditions where viewing time is unconstrained. Our results further suggest that impaired oculomotor control associated with central vision loss can confound peripheral form vision beyond the limits imposed by crowding.

  5. A field study on real-time self-reported emotions in crowds

    NARCIS (Netherlands)

    Li, J.; Erkin, Z.; De Ridder, H.; Vermeeren, A.P.O.S.

    2013-01-01

    Crowd experience is inevitable in daily life. Crowd managers need tools to accurately estimate the psychological aspects of crowds, an important one being crowd emotion. In this study, we explore the feasibility of obtaining a real-time, dynamic map of crowd emotions through self-reporting by crowd

  6. Modelling asymmetric growth in crowded plant communities

    DEFF Research Database (Denmark)

    Damgaard, Christian

    2010-01-01

    A class of models that may be used to quantify the effect of size-asymmetric competition in crowded plant communities by estimating a community specific degree of size-asymmetric growth for each species in the community is suggested. The model consists of two parts: an individual size-asymmetric ......A class of models that may be used to quantify the effect of size-asymmetric competition in crowded plant communities by estimating a community specific degree of size-asymmetric growth for each species in the community is suggested. The model consists of two parts: an individual size...

  7. How crowded is the prokaryotic cytoplasm?

    Science.gov (United States)

    Spitzer, Jan; Poolman, Bert

    2013-07-11

    We consider biomacromolecular crowding within the cytoplasm of prokaryotic cells as a two-phase system of 'supercrowded' cytogel and 'dilute' cytosol; we simplify and quantify this model for a coccoid cell over a wide range of biomacromolecular crowding. The key result shows that the supercrowded cytogel extends the vectorial character of the plasma membrane deeper into the cytoplasm by about 20-70 nm. We discuss useful physiological insights that this model gives into the functioning of a prokaryotic cell on the micrometer scale. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  8. Virtual Crowds Methods, Simulation, and Control

    CERN Document Server

    Pelechano, Nuria; Allbeck, Jan

    2008-01-01

    There are many applications of computer animation and simulation where it is necessary to model virtual crowds of autonomous agents. Some of these applications include site planning, education, entertainment, training, and human factors analysis for building evacuation. Other applications include simulations of scenarios where masses of people gather, flow, and disperse, such as transportation centers, sporting events, and concerts. Most crowd simulations include only basic locomotive behaviors possibly coupled with a few stochastic actions. Our goal in this survey is to establish a baseline o

  9. Preparation of imprinted monolithic column under molecular crowding conditions

    Institute of Scientific and Technical Information of China (English)

    Xiao Xia Li; Xin Liu; Li Hong Bai; Hong Quan Duan; Yan Ping Huang; Zhao Sheng Liu

    2011-01-01

    Molecular crowding is a new concept to obtain molecularly imprinted polymers (MIPs) with greater capacity and selectivity. In this work, molecular crowding agent was firstly applied to the preparation of MIPs monolithic column. A new polymerization system based on molecular crowding surrounding was developed to prepare enrofloxacin-imprinted monolith, which was composed of polystyrene and tetrahydrofuran. The result showed that the monolithic MIPs under molecular crowding conditions presented good molecular recognition for enrofloxacin with an imprinting factor of 3.03.

  10. EMOTIONAL CONTAGION AND MOOD IN CROWD SERVING AS AUDIENCE

    OpenAIRE

    2015-01-01

    The global world is gradually becoming a world of separated crowds despite the artificial wire and wireless connection through television and the Internet. Crowds remain a prevailing subject of research in different social studies, and the research of changes in the psychological structure of crowds and their characteristics is still of primary interest. The main focus of the research is on the interpretation of the results of the research paper about a special separated crowd called audience...

  11. Macromolecular components of tomato fruit pectin.

    Science.gov (United States)

    Fishman, M L; Gross, K C; Gillespie, D T; Sondey, S M

    1989-10-01

    Chelate and alkaline-soluble pectin extracted from cell walls of pericarp tissue from mature green, turning, and red ripe (Lycopersicon esculentum Mill.) fruit (cv. Rutgers), were studied by high-performance size-exclusion chromatography. Computer-aided curve fitting of the chromatograms to a series of Gaussian-shaped components revealed that pectin from all fractions was composed of a linear combination of five macromolecular-sized species. The relative sizes of these macromolecules as obtained from their radii of gyration were 1:2:4:8:16. Dialysis against 0.05 M NaCl induced partial dissociation of the biopolymers. Apparently, the weight fraction of smaller sized species increased at the expense of larger ones. Also, the dissociation produced low-molecular-weight fragments. Behavior in the presence of 0.05 M NaCl led to the conclusion that cell wall pectin acted as if it were an aggregated mosaic, held together at least partially through noncovalent interactions.

  12. The solvent component of macromolecular crystals

    Energy Technology Data Exchange (ETDEWEB)

    Weichenberger, Christian X. [European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, Bozen/Bolzano, I-39100 Südtirol/Alto Adige (Italy); Afonine, Pavel V. [Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mail Stop 64R0121, Berkeley, CA 94720 (United States); Kantardjieff, Katherine [California State University, San Marcos, CA 92078 (United States); Rupp, Bernhard, E-mail: br@hofkristallamt.org [k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084 (United States); Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck (Austria)

    2015-04-30

    On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.

  13. Stress and Incongruity Theory: Effects of Crowding,

    Science.gov (United States)

    1981-01-01

    Nogami, G. Y. Crowding: Effects of group size, room size or density. Journal of Applied Social Psychology , 1976, 6, 105-125. Osgood, C. E. and...perceived control and behavioral effects. Journal of Applied Social Psychology , 1974, 4, 171-186. -43- Sommer, R. Personal space: The behavioral

  14. Intact crowding and temporal masking in dyslexia.

    Science.gov (United States)

    Doron, Adi; Manassi, Mauro; Herzog, Michael H; Ahissar, Merav

    2015-01-01

    Phonological deficits in dyslexia are well documented. However, there is an ongoing discussion about whether visual deficits limit the reading skills of people with dyslexia. Here, we investigated visual crowding and backward masking. We presented a Vernier (i.e., two vertical bars slightly offset to the left or right) and asked observers to indicate the offset direction. Vernier stimuli are visually similar to letters and are strongly affected by crowding, even in the fovea. To increase task difficulty, Verniers are often followed by a mask (i.e., backward masking). We measured Vernier offset discrimination thresholds for the basic Vernier task, under crowding, and under backward masking, in students with dyslexia (n = 19) and age and intelligence matched students (n = 27). We found no group differences in any of these conditions. Controls with fast visual processing (good backward masking performance), were faster readers. By contrast, no such correlation was found among the students with dyslexia, suggesting that backward masking does not limit their reading efficiency. These findings indicate that neither elevated crowding nor elevated backward masking pose a bottleneck to reading skills of people with dyslexia.

  15. Crowding Affects Letters and Symbols Differently

    Science.gov (United States)

    Grainger, Jonathan; Tydgat, Ilse; Issele, Joanna

    2010-01-01

    Five experiments examined crowding effects with letter and symbol stimuli. Experiments 1 through 3 compared 2-alternative forced-choice (2AFC) identification accuracy for isolated targets presented left and right of fixation with targets flanked either by 2 other items of the same category or a single item situated to the right or left of targets.…

  16. Crowd-sourcing with Uncertain Quality

    DEFF Research Database (Denmark)

    Papakonstantinou, Athanasios; Bogetoft, Peter

    This article addresses two important issues in crowd-sourcing: ex ante uncertainty about the quality and cost of different workers and strategic behaviour. We present a novel multi-dimensional auction that incentivises the workers to make partial enquiry into the task and to honestly report quality...

  17. Diabetes market grows ever more crowded.

    Science.gov (United States)

    Gohil, Kunj; Enhoffer, Devin

    2014-12-01

    Global prevalence of type-2 diabetes is expected to reach 330 million cases by 2022, with medication sales of $67.7 billion. The market is crowded with generic medications, and most products now in the development pipeline are "me-too" drugs.

  18. Diabetes Market Grows Ever More Crowded

    OpenAIRE

    Gohil, Kunj; Enhoffer, Devin

    2014-01-01

    Global prevalence of type-2 diabetes is expected to reach 330 million cases by 2022, with medication sales of $67.7 billion. The market is crowded with generic medications, and most products now in the development pipeline are “me-too” drugs.

  19. The crowd in the Occupy movement

    NARCIS (Netherlands)

    Ossewaarde, Marinus R.R.

    2013-01-01

    In this article, I recast Elias Canetti's notion of crowds by placing it in the framework provided by Friedrich Nietzsche's Heraclitean dialectic of Apollonian and Dionysian opposites. The argument is introduced that, in European societies, the forms of social existence are mainly Apollonian,

  20. Network Science and Crowd Behavior Metrics

    Science.gov (United States)

    2008-12-01

    pressures (Asch 1951; Festinger 1954), group structure and processes, and communication (Bavelas 1968), and intergroup conflict (Deutsch 1973...development of a crowd dynamics model., Fire Safety Jo Festinger , L., 1954: A theory of social comparison processes. Human Relations 7: 117-140. dquarters

  1. The crowd in the Occupy movement

    NARCIS (Netherlands)

    Ossewaarde, M.R.R.

    2013-01-01

    In this article, I recast Elias Canetti's notion of crowds by placing it in the framework provided by Friedrich Nietzsche's Heraclitean dialectic of Apollonian and Dionysian opposites. The argument is introduced that, in European societies, the forms of social existence are mainly Apollonian, wherea

  2. Understanding the crowd - how to construct the crowd and manage participants in customer co-creation

    OpenAIRE

    Bilgram, Volker

    2017-01-01

    The dissertation investigates the participants in co-creation initiatives referred to as the ‘crowd’ of customers, who get involved in firm-led creative and social processes designed to co-create value. In a general introduction, the theoretical background is outlined considering co-creation, service-dominant logic and consumer empowerment literature. In four individual papers, the thesis provides a more granular perspective on the members of the crowd and investigate how the crowd can be con...

  3. CrowdWater: a new smartphone app for crowd-based data collection in hydrology

    Science.gov (United States)

    Seibert, Jan; Strobl, Barbara; Etter, Simon; Vis, Marc; (Ilja) van Meerveld, H. J.

    2017-04-01

    The project CrowdWater (www.crowdwater.ch) explores opportunities for public involvement in hydrological observations. The project uses a "geocaching" type approach with the help of smartphones. Citizens can find existing sites and participate in the collection of hydrological data (stream water level, streamflow and soil moisture) using a smartphone app. The app also allows citizens to set up new sites. On this poster we present and discuss the first version of the CrowdWater app.

  4. Modelling crowd-bridge dynamic interaction with a discretely defined crowd

    Science.gov (United States)

    Carroll, S. P.; Owen, J. S.; Hussein, M. F. M.

    2012-05-01

    This paper presents a novel method of modelling crowd-bridge interaction using discrete element theory (DET) to model the pedestrian crowd. DET, also known as agent-based modelling, is commonly used in the simulation of pedestrian movement, particularly in cases where building evacuation is critical or potentially problematic. Pedestrians are modelled as individual elements subject to global behavioural rules. In this paper a discrete element crowd model is coupled with a dynamic bridge model in a time-stepping framework. Feedback takes place between both models at each time-step. An additional pedestrian stimulus is introduced that is a function of bridge lateral dynamic behaviour. The pedestrians' relationship with the vibrating bridge as well as the pedestrians around them is thus simulated. The lateral dynamic behaviour of the bridge is modelled as a damped single degree of freedom (SDoF) oscillator. The excitation and mass enhancement of the dynamic system is determined as the sum of individual pedestrian contributions at each time-step. Previous crowd-structure interaction modelling has utilised a continuous hydrodynamic crowd model. Limitations inherent in this modelling approach are identified and results presented that demonstrate the ability of DET to address these limitations. Simulation results demonstrate the model's ability to consider low density traffic flows and inter-subject variability. The emergence of the crowd's velocity-density relationship is also discussed.

  5. Macromolecular networks and intelligence in microorganisms

    Directory of Open Access Journals (Sweden)

    Hans V Westerhoff

    2014-07-01

    Full Text Available Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of Information and Communication Technology (ICT: they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity – particularly activity of the human brain – with a phenomenon we call intelligence. Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as human and brain out of the defining features of intelligence, all forms of life – from microbes to humans – exhibit some or all characteristics consistent with intelligence. We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo.

  6. Macromolecular networks and intelligence in microorganisms

    Science.gov (United States)

    Westerhoff, Hans V.; Brooks, Aaron N.; Simeonidis, Evangelos; García-Contreras, Rodolfo; He, Fei; Boogerd, Fred C.; Jackson, Victoria J.; Goncharuk, Valeri; Kolodkin, Alexey

    2014-01-01

    Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of information and communication technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity – particularly activity of the human brain – with a phenomenon we call “intelligence.” Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as “human” and “brain” out of the defining features of “intelligence,” all forms of life – from microbes to humans – exhibit some or all characteristics consistent with “intelligence.” We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo. PMID:25101076

  7. Macromolecular Topography Leaps into the Digital Age

    Science.gov (United States)

    Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

    2003-01-01

    A low-cost, real-time digital topography system is under development which will replace x-ray film and nuclear emulsion plates. The imaging system is based on an inexpensive surveillance camera that offers a 1000x1000 array of 8 im square pixels, anti-blooming circuitry, and very quick read out. Currently, the system directly converts x-rays to an image with no phosphor. The system is small and light and can be easily adapted to work with other crystallographic equipment. Preliminary images have been acquired of cubic insulin at the NSLS x26c beam line. NSLS x26c was configured for unfocused monochromatic radiation. Six reflections were collected with stills spaced from 0.002 to 0.001 degrees apart across the entire oscillation range that the reflections were in diffracting condition. All of the reflections were rotated to the vertical to reduce Lorentz and beam related effects. This particular CCD is designed for short exposure applications (much less than 1 sec) and so has a relatively high dark current leading to noisy raw images. The images are processed to remove background and other system noise with a multi-step approach including the use of wavelets, histogram, and mean window filtering. After processing, animations were constructed with the corresponding reflection profile to show the diffraction of the crystal volume vs. the oscillation angle as well as composite images showing the parts of the crystal with the strongest diffraction for each reflection. The final goal is to correlate features seen in reflection profiles captured with fine phi slicing to those seen in the topography images. With this development macromolecular topography finally comes into the digital age.

  8. Molecular crowding and protein enzymatic dynamics.

    Science.gov (United States)

    Echeverria, Carlos; Kapral, Raymond

    2012-05-21

    The effects of molecular crowding on the enzymatic conformational dynamics and transport properties of adenylate kinase are investigated. This tridomain protein undergoes large scale hinge motions in the course of its enzymatic cycle and serves as prototype for the study of crowding effects on the cyclic conformational dynamics of proteins. The study is carried out at a mesoscopic level where both the protein and the solvent in which it is dissolved are treated in a coarse grained fashion. The amino acid residues in the protein are represented by a network of beads and the solvent dynamics is described by multiparticle collision dynamics that includes effects due to hydrodynamic interactions. The system is crowded by a stationary random array of hard spherical objects. Protein enzymatic dynamics is investigated as a function of the obstacle volume fraction and size. In addition, for comparison, results are presented for a modification of the dynamics that suppresses hydrodynamic interactions. Consistent with expectations, simulations of the dynamics show that the protein prefers a closed conformation for high volume fractions. This effect becomes more pronounced as the obstacle radius decreases for a given volume fraction since the average void size in the obstacle array is smaller for smaller radii. At high volume fractions for small obstacle radii, the average enzymatic cycle time and characteristic times of internal conformational motions of the protein deviate substantially from their values in solution or in systems with small density of obstacles. The transport properties of the protein are strongly affected by molecular crowding. Diffusive motion adopts a subdiffusive character and the effective diffusion coefficients can change by more than an order of magnitude. The orientational relaxation time of the protein is also significantly altered by crowding.

  9. The effect of spacing regularity on visual crowding.

    Science.gov (United States)

    Saarela, T P; Westheimer, G; Herzog, M H

    2010-08-18

    Crowding limits peripheral visual discrimination and recognition: a target easily identified in isolation becomes impossible to recognize when surrounded by other stimuli, often called flankers. Most accounts of crowding predict less crowding when the target-flanker distance increases. On the other hand, the importance of perceptual organization and target-flanker coherence in crowding has recently received more attention. We investigated the effect of target-flanker spacing on crowding in multi-element stimulus arrays. We show that increasing the average distance between the target and the flankers does not always decrease the amount of crowding but can even sometimes increase it. We suggest that the regularity of inter-element spacing plays an important role in determining the strength of crowding: regular spacing leads to the perception of a single, coherent, texture-like stimulus, making judgments about the individual elements difficult.

  10. Macromolecular Antioxidants and Dietary Fiber in Edible Seaweeds.

    Science.gov (United States)

    Sanz-Pintos, Nerea; Pérez-Jiménez, Jara; Buschmann, Alejandro H; Vergara-Salinas, José Rodrigo; Pérez-Correa, José Ricardo; Saura-Calixto, Fulgencio

    2017-02-01

    Seaweeds are rich in different bioactive compounds with potential uses in drugs, cosmetics and the food industry. The objective of this study was to analyze macromolecular antioxidants or nonextractable polyphenols, in several edible seaweed species collected in Chile (Gracilaria chilensis, Callophyllis concepcionensis, Macrocystis pyrifera, Scytosyphon lomentaria, Ulva sp. and Enteromorpha compressa), including their 1st HPLC characterization. Macromolecular antioxidants are commonly ignored in studies of bioactive compounds. They are associated with insoluble dietary fiber and exhibit significant biological activity, with specific features that are different from those of both dietary fiber and extractable polyphenols. We also evaluated extractable polyphenols and dietary fiber, given their relationship with macromolecular antioxidants. Our results show that macromolecular antioxidants are a major polyphenol fraction (averaging 42% to total polyphenol content), with hydroxycinnamic acids, hydroxybenzoic acids and flavonols being the main constituents. This fraction also showed remarkable antioxidant capacity, as determined by 2 complementary assays. The dietary fiber content was over 50% of dry weight, with some samples exhibiting the target proportionality between soluble and insoluble dietary fiber for adequate nutrition. Overall, our data show that seaweed could be an important source of commonly ignored macromolecular antioxidants. © 2017 Institute of Food Technologists®.

  11. Crowding and eccentricity determine reading rate.

    Science.gov (United States)

    Pelli, Denis G; Tillman, Katharine A; Freeman, Jeremy; Su, Michael; Berger, Tracey D; Majaj, Najib J

    2007-10-26

    Bouma's law of crowding predicts an uncrowded central window through which we can read and a crowded periphery through which we cannot. The old discovery that readers make several fixations per second, rather than a continuous sweep across the text, suggests that reading is limited by the number of letters that can be acquired in one fixation, without moving one's eyes. That "visual span" has been measured in various ways, but remains unexplained. Here we show (1) that the visual span is simply the number of characters that are not crowded and (2) that, at each vertical eccentricity, reading rate is proportional to the uncrowded span. We measure rapid serial visual presentation (RSVP) reading rate for text, in both original and scrambled word order, as a function of size and spacing at central and peripheral locations. As text size increases, reading rate rises abruptly from zero to maximum rate. This classic reading rate curve consists of a cliff and a plateau, characterized by two parameters, critical print size and maximum reading rate. Joining two ideas from the literature explains the whole curve. These ideas are Bouma's law of crowding and Legge's conjecture that reading rate is proportional to visual span. We show that Legge's visual span is the uncrowded span predicted by Bouma's law. This result joins Bouma and Legge to explain reading rate's dependence on letter size and spacing. Well-corrected fluent observers reading ordinary text with adequate light are limited by letter spacing (crowding), not size (acuity). More generally, it seems that this account holds true, independent of size, contrast, and luminance, provided only that text contrast is at least four times the threshold contrast for an isolated letter. For any given spacing, there is a central uncrowded span through which we read. This uncrowded span model explains the shape of the reading rate curve. We test the model in several ways. We use a "silent substitution" technique to measure the

  12. Complex Macromolecular Architectures by Living Cationic Polymerization

    KAUST Repository

    Alghamdi, Reem D.

    2015-05-01

    Poly (vinyl ether)-based graft polymers have been synthesized by the combination of living cationic polymerization of vinyl ethers with other living or controlled/ living polymerization techniques (anionic and ATRP). The process involves the synthesis of well-defined homopolymers (PnBVE) and co/terpolymers [PnBVE-b-PCEVE-b-PSiDEGVE (ABC type) and PSiDEGVE-b-PnBVE-b-PSiDEGVE (CAC type)] by sequential living cationic polymerization of n-butyl vinyl ether (nBVE), 2-chloroethyl vinyl ether (CEVE) and tert-butyldimethylsilyl ethylene glycol vinyl ether (SiDEGVE), using mono-functional {[n-butoxyethyl acetate (nBEA)], [1-(2-chloroethoxy) ethyl acetate (CEEA)], [1-(2-(2-(t-butyldimethylsilyloxy)ethoxy) ethoxy) ethyl acetate (SiDEGEA)]} or di-functional [1,4-cyclohexanedimethanol di(1-ethyl acetate) (cHMDEA), (VEMOA)] initiators. The living cationic polymerizations of those monomers were conducted in hexane at -20 0C using Et3Al2Cl3 (catalyst) in the presence of 1 M AcOEt base.[1] The PCEVE segments of the synthesized block terpolymers were then used to react with living macroanions (PS-DPE-Li; poly styrene diphenyl ethylene lithium) to afford graft polymers. The quantitative desilylation of PSiDEGVE segments by n-Bu4N+F- in THF at 0 °C led to graft co- and terpolymers in which the polyalcohol is the outer block. These co-/terpolymers were subsequently subjected to “grafting-from” reactions by atom transfer radical polymerization (ATRP) of styrene to afford more complex macromolecular architectures. The base assisted living cationic polymerization of vinyl ethers were also used to synthesize well-defined α-hydroxyl polyvinylether (PnBVE-OH). The resulting polymers were then modified into an ATRP macro-initiator for the synthesis of well-defined block copolymers (PnBVE-b-PS). Bifunctional PnBVE with terminal malonate groups was also synthesized and used as a precursor for more complex architectures such as H-shaped block copolymer by “grafting-from” or

  13. Systematic review of emergency department crowding: causes, effects, and solutions.

    Science.gov (United States)

    Hoot, Nathan R; Aronsky, Dominik

    2008-08-01

    Emergency department (ED) crowding represents an international crisis that may affect the quality and access of health care. We conducted a comprehensive PubMed search to identify articles that (1) studied causes, effects, or solutions of ED crowding; (2) described data collection and analysis methodology; (3) occurred in a general ED setting; and (4) focused on everyday crowding. Two independent reviewers identified the relevant articles by consensus. We applied a 5-level quality assessment tool to grade the methodology of each study. From 4,271 abstracts and 188 full-text articles, the reviewers identified 93 articles meeting the inclusion criteria. A total of 33 articles studied causes, 27 articles studied effects, and 40 articles studied solutions of ED crowding. Commonly studied causes of crowding included nonurgent visits, "frequent-flyer" patients, influenza season, inadequate staffing, inpatient boarding, and hospital bed shortages. Commonly studied effects of crowding included patient mortality, transport delays, treatment delays, ambulance diversion, patient elopement, and financial effect. Commonly studied solutions of crowding included additional personnel, observation units, hospital bed access, nonurgent referrals, ambulance diversion, destination control, crowding measures, and queuing theory. The results illustrated the complex, multifaceted characteristics of the ED crowding problem. Additional high-quality studies may provide valuable contributions toward better understanding and alleviating the daily crisis. This structured overview of the literature may help to identify future directions for the crowding research agenda.

  14. Diffusion and reaction in crowded environments

    Energy Technology Data Exchange (ETDEWEB)

    EcheverIa, Carlos [Laboratorio de Fisica Aplicada y Computacional, Departamento de Matematica y Fisica, Universidad Nacional Experimental del Tachira, San Cristobal 5001 (Venezuela); Tucci, Kay [Centro de Fisica Fundamental, Universidad de Los Andes, Merida 5101 (Venezuela); Kapral, Raymond [Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6 (Canada)

    2007-02-14

    The effects of molecular crowding on small molecule diffusion and chemical reaction rate coefficients are investigated. The systems considered comprise a random distribution of stationary spherical obstacles occupying a volume fraction {phi} of the system and a large number of small molecules whose dynamics are followed. Chemical reactions are studied in such crowded systems where, in addition to the obstacles, a large reactive sphere C is present that catalyses the reaction A+C {yields} B+C. Using a mesoscopic description of the dynamics employing multiparticle collisions among the small molecules, the {phi} dependence of the diffusion and reaction rate coefficients is computed. Both the diffusion and reaction rate coefficients decrease with increase of the obstacle volume fraction as expected but variations of these quantities with {phi} are not predicted by simple models of the dynamics.

  15. The foveal 'crowding' effect: physics or physiology?

    Science.gov (United States)

    Hess, R F; Dakin, S C; Kapoor, N

    2000-01-01

    It has been known for some time that both foveal and peripheral visual acuity is higher for single letters than for letters in a row. Early work showed that this was due to the destructive interaction of adjacent contours (termed 'crowding' or contour interaction). It has been assumed to have a neural basis and a number of competing explanations have been advanced which implicate either high-level or low-level stages of visual processing. Our results suggest a much simpler explanation, one primarily determined by the physics of the stimulus rather than the physiology of the visual system. We show that, under conditions of contour interaction or 'crowding', the most relevant physical spatial frequency band of the letter is displaced to higher spatial frequencies and that foveal vision tracks this change in spatial scale.

  16. PROBABILISTIC CATALOGS FOR CROWDED STELLAR FIELDS

    Energy Technology Data Exchange (ETDEWEB)

    Brewer, Brendon J. [Department of Statistics, University of Auckland, Private Bag 92019, Auckland 1142 (New Zealand); Foreman-Mackey, Daniel; Hogg, David W., E-mail: bj.brewer@auckland.ac.nz [Center for Cosmology and Particle Physics, Department of Physics, New York University, Washington Place, New York, NY 10003 (United States)

    2013-07-01

    We present and implement a probabilistic (Bayesian) method for producing catalogs from images of stellar fields. The method is capable of inferring the number of sources N in the image and can also handle the challenges introduced by noise, overlapping sources, and an unknown point-spread function. The luminosity function of the stars can also be inferred, even when the precise luminosity of each star is uncertain, via the use of a hierarchical Bayesian model. The computational feasibility of the method is demonstrated on two simulated images with different numbers of stars. We find that our method successfully recovers the input parameter values along with principled uncertainties even when the field is crowded. We also compare our results with those obtained from the SExtractor software. While the two approaches largely agree about the fluxes of the bright stars, the Bayesian approach provides more accurate inferences about the faint stars and the number of stars, particularly in the crowded case.

  17. Macromolecular crystallography beamline X25 at the NSLS.

    Science.gov (United States)

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

    2014-05-01

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

  18. Effect of serial extraction alone on crowding: relationships between tooth width, arch length, and crowding.

    Science.gov (United States)

    Yoshihara, T; Matsumoto, Y; Suzuki, J; Sato, N; Oguchi, H

    1999-12-01

    In this study, we examined the effect of serial extraction alone on crowding. We also investigated the relationships between tooth width, arch length, and irregularity index. Maxillary dental casts from 32 subjects who had undergone only serial extraction were analyzed at 3 stages: before deciduous canines extraction, after first premolars extraction, and at the end of the observation period. The mean of the irregularity index decreased significantly as serial extraction proceeded and further decreased during the observation period. In cases where the width of the incisor was more than 2 standard deviations above the means for the control subjects, there was a significant correlation between tooth width of the lateral incisors and irregularity index before extraction as well as a significant correlation between the summation of tooth widths of the central and lateral incisors and irregularity index at that time. There was a significant negative correlation between arch length discrepancy and irregularity index before extraction and also a significant correlation between arch length discrepancy and correction of the irregularity index from before deciduous canines extraction to after first premolars extraction. These results suggest that tooth width and arch length discrepancy might preferentially affect the degree of anterior crowding in cases of severe crowding. There was no aggravation of the average crowding level during the observation period in the present study. The present study quantitatively suggested that serial extraction was useful for the purpose of correcting crowding in most cases.

  19. Do agricultural subsidies crowd out or stimulate rural credit market institutions? The case of EU Common Agricultural Policy

    Directory of Open Access Journals (Sweden)

    Jan and Katarina Szegenyova Pokrivcak

    2012-11-01

    Full Text Available In this paper we estimate the impact of agricultural subsidies granted under the European Union’s Common Agricultural Policy (CAP on bank loans extended to farms. According to our theoretical analysis, subsidies may either stimulate or crowd out bank loans depending on the timing of subsidies, severity of credit constraint, type of subsidies and bank loans, and the relative cost of internal and external financing. In empirical analysis we use the Farm Accountancy Data Network (FADN farm level panel data for the period 1995-2007. We employ the fixed effects and generalised method of moment (GMM models. The estimated results suggest that (i big farms tend to use subsidies to increase long-term loans, whereas small farms tend to use subsidies to obtain short-term loans; (ii subsidies tend to crowd out short-term loans for big farms and long-term loans for small farms; (iii when controlling for the endogeneity, the crowding out effect becomes smaller, but the positive causal effect of subsidies on bank loans remains significant.

  20. Verification Games: Crowd-Sourced Formal Verification

    Science.gov (United States)

    2016-03-01

    Government drawings, specifications, or other data included in this document for any purpose other than Government procurement does not in any way...information exchange, and its publication does not constitute the Government’s approval or disapproval of its ideas or findings. REPORT DOCUMENTATION ...DATES COVERED (From - To) JUN 2012 – SEP 2015 4. TITLE AND SUBTITLE VERIFICATION GAMES: CROWD-SOURCED FORMAL VERIFICATION 5a. CONTRACT NUMBER FA8750

  1. Personalized recommendation against crowd's popular selection

    CERN Document Server

    Zhu, Xuzhen; Liu, Haifeng

    2014-01-01

    The problem of personalized recommendation in an ocean of data attracts more and more attention recently. Most traditional researches ignore the popularity of the recommended object, which resulting in low personality and accuracy. In this Letter, we proposed a personalized recommendation method based on weighted object network, punishing the recommended object that is the crowd's popular selection, namely, Anti-popularity index(AP), which can give enhanced personality, accuracy and diversity in contrast to mainstream baselines with a low computational complexity.

  2. Is the crowd's wisdom biased? A quantitative asessment of three online communities

    CERN Document Server

    Kostakos, Vassilis

    2009-01-01

    This paper presents a study of user voting on three websites: Imdb, Amazon and BookCrossings. It reports on an expert evaluation of the voting mechanisms of each website and a quantitative data analysis of users' aggregate voting behavior. The results suggest that voting follows different patterns across the websites, with higher barrier to vote introducing a more of one-off voters and attracting mostly experts. The results also show that that one-off voters tend to vote on popular items, while experts mostly vote for obscure, low-rated items. The study concludes with design suggestions to address the "wisdom of the crowd" bias.

  3. Transport in active systems crowded by obstacles

    Science.gov (United States)

    Huang, Mu-Jie; Schofield, Jeremy; Kapral, Raymond

    2017-02-01

    The reactive and diffusive dynamics of a single chemically powered Janus motor in a crowded medium of moving but passive obstacles is investigated using molecular simulation. It is found that the reaction rate of the catalytic motor reaction decreases in a crowded medium as the volume fraction of obstacles increases as a result of a reduction in the Smoluchowski diffusion-controlled reaction rate coefficient that contributes to the overall reaction rate. A continuum model is constructed and analyzed to interpret the dependence of the steady-state reaction rate observed in simulations on the volume fraction of obstacles in the system. The steady-state concentration fields of reactant and product are shown to be sensitive to the local structure of obstacles around the Janus motor. It is demonstrated that the active motor exhibits enhanced diffusive motion at long times with a diffusion constant that decreases as the volume fraction of crowding species increases. In addition, the dynamical properties of a passive tracer particle in a system containing many active Janus motors is studied to investigate how an active environment influences the transport of non-active species. The diffusivity of a passive tracer particle in an active medium is found to be enhanced in systems with forward-moving Janus motors due to the cooperative dynamics of these motors.

  4. The simulation and analysis of small group effect in crowd evacuation

    Science.gov (United States)

    You, Lei; Hu, Jun; Gu, Musong; Fan, Wenjie; Zhang, Hong

    2016-10-01

    A crowd usually tends to move in small groups during evacuation. Small group has a large proportion in crowd evacuation, and small group effect affects crowd evacuation significantly. In this work, we propose a novel methodology for calculating movement profit based on cellular automaton model. Specifically, this methodology calculates the movement profit for a target at the next moment by comprehensively combining distance profit, density profit, and average velocity profit. In particular, this paper defines three types of small-group formation with totally six different forms of small group in terms of the size, and sets the corresponding movement velocity. At last, we simulate the evacuation process of small groups, and discuss the relationship among evacuation time, average movement velocity, and pedestrian density, and analyze the efficiency of small group evacuation in terms of evacuation strategies. As the simulation results demonstrated, the evacuation efficiency of different types of small groups is greatly different, and the same type of small groups with different forms is also different.

  5. A field study on real-time self-reported emotions in crowds

    NARCIS (Netherlands)

    Li, J.; Erkin, Z.; De Ridder, H.; Vermeeren, A.P.O.S.

    2013-01-01

    Crowd experience is inevitable in daily life. Crowd managers need tools to accurately estimate the psychological aspects of crowds, an important one being crowd emotion. In this study, we explore the feasibility of obtaining a real-time, dynamic map of crowd emotions through self-reporting by

  6. Towards an Integrated Approach to Crowd Analysis and Crowd Synthesis: a Case Study and First Results

    CERN Document Server

    Bandini, Stefania; Vizzari, Giuseppe

    2013-01-01

    Studies related to crowds of pedestrians, both those of theoretical nature and application oriented ones, have generally focused on either the analysis or the synthesis of the phenomena related to the interplay between individual pedestrians, each characterised by goals, preferences and potentially relevant relationships with others, and the environment in which they are situated. The cases in which these activities have been systematically integrated for a mutual benefit are still very few compared to the corpus of crowd related literature. This paper presents a case study of an integrated approach to the definition of an innovative model for pedestrian and crowd simulation (on the side of synthesis) that was actually motivated and supported by the analyses of empirical data acquired from both experimental settings and observations in real world scenarios. In particular, we will introduce a model for the adaptive behaviour of pedestrians that are also members of groups, that strive to maintain their cohesion...

  7. The hierarchical sparse selection model of visual crowding.

    Science.gov (United States)

    Chaney, Wesley; Fischer, Jason; Whitney, David

    2014-01-01

    Because the environment is cluttered, objects rarely appear in isolation. The visual system must therefore attentionally select behaviorally relevant objects from among many irrelevant ones. A limit on our ability to select individual objects is revealed by the phenomenon of visual crowding: an object seen in the periphery, easily recognized in isolation, can become impossible to identify when surrounded by other, similar objects. The neural basis of crowding is hotly debated: while prevailing theories hold that crowded information is irrecoverable - destroyed due to over-integration in early stage visual processing - recent evidence demonstrates otherwise. Crowding can occur between high-level, configural object representations, and crowded objects can contribute with high precision to judgments about the "gist" of a group of objects, even when they are individually unrecognizable. While existing models can account for the basic diagnostic criteria of crowding (e.g., specific critical spacing, spatial anisotropies, and temporal tuning), no present model explains how crowding can operate simultaneously at multiple levels in the visual processing hierarchy, including at the level of whole objects. Here, we present a new model of visual crowding-the hierarchical sparse selection (HSS) model, which accounts for object-level crowding, as well as a number of puzzling findings in the recent literature. Counter to existing theories, we posit that crowding occurs not due to degraded visual representations in the brain, but due to impoverished sampling of visual representations for the sake of perception. The HSS model unifies findings from a disparate array of visual crowding studies and makes testable predictions about how information in crowded scenes can be accessed.

  8. Simulating and Visualizing Real-Time Crowds on GPU Clusters

    OpenAIRE

    Benjamín Hernández; Hugo Pérez; Isaac Rudomin; Sergio Ruiz; Oriam de Gyves; Leonel Toledo

    2014-01-01

    We present a set of algorithms for simulating and visualizing real-time crowds in GPU (Graphics Processing Units) clusters. First we present crowd simulation and rendering techniques that take advantage of single GPU machines. Then, using as an example a wandering crowd behavior simulation algorithm, we explain how this kind of algorithms can be extended for their use in GPU cluster environments. We also present a visualization architecture that renders the simulation results using detailed 3...

  9. Workshop on Populations & Crowds: Dynamics, Disruptions and their Computational Models

    Science.gov (United States)

    2015-01-01

    behavior and, ultimately, what can be done to block contagion of hostile behavior in both population and crowd contexts. The workshop was organized at the...powerful in their ability to spread information and rapidly alter their collective behavior . Crowds can transition from loosely to tightly organized and...7 September, 2012 concentrating on organization , dynamics and disruption of populations and crowds. The purpose of this workshop was to bring

  10. Generating triangulated macromolecular surfaces by Euclidean Distance Transform.

    Directory of Open Access Journals (Sweden)

    Dong Xu

    Full Text Available Macromolecular surfaces are fundamental representations of their three-dimensional geometric shape. Accurate calculation of protein surfaces is of critical importance in the protein structural and functional studies including ligand-protein docking and virtual screening. In contrast to analytical or parametric representation of macromolecular surfaces, triangulated mesh surfaces have been proved to be easy to describe, visualize and manipulate by computer programs. Here, we develop a new algorithm of EDTSurf for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface, using the technique of fast Euclidean Distance Transform (EDT. The triangulated surfaces are constructed directly from volumetric solids by a Vertex-Connected Marching Cube algorithm that forms triangles from grid points. Compared to the analytical result, the relative error of the surface calculations by EDTSurf is <2-4% depending on the grid resolution, which is 1.5-4 times lower than the methods in the literature; and yet, the algorithm is faster and costs less computer memory than the comparative methods. The improvements in both accuracy and speed of the macromolecular surface determination should make EDTSurf a useful tool for the detailed study of protein docking and structure predictions. Both source code and the executable program of EDTSurf are freely available at http://zhang.bioinformatics.ku.edu/EDTSurf.

  11. Two-center-multipole expansion method: application to macromolecular systems

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.;

    2007-01-01

    We propose a theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an alternative to the well-known fast multipole method. Its...

  12. 30 CFR 56.7012 - Tending drills in operation.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Tending drills in operation. 56.7012 Section 56.7012 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE SAFETY AND HEALTH SAFETY AND HEALTH STANDARDS-SURFACE METAL AND NONMETAL MINES Drilling and...

  13. 30 CFR 57.7012 - Tending drills in operation.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Tending drills in operation. 57.7012 Section 57.7012 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE SAFETY AND HEALTH SAFETY AND HEALTH STANDARDS-UNDERGROUND METAL AND NONMETAL MINES Drilling...

  14. Two-stage perceptual learning to break visual crowding.

    Science.gov (United States)

    Zhu, Ziyun; Fan, Zhenzhi; Fang, Fang

    2016-01-01

    When a target is presented with nearby flankers in the peripheral visual field, it becomes harder to identify, which is referred to as crowding. Crowding sets a fundamental limit of object recognition in peripheral vision, preventing us from fully appreciating cluttered visual scenes. We trained adult human subjects on a crowded orientation discrimination task and investigated whether crowding could be completely eliminated by training. We discovered a two-stage learning process with this training task. In the early stage, when the target and flankers were separated beyond a certain distance, subjects acquired a relatively general ability to break crowding, as evidenced by the fact that the breaking of crowding could transfer to another crowded orientation, even a crowded motion stimulus, although the transfer to the opposite visual hemi-field was weak. In the late stage, like many classical perceptual learning effects, subjects' performance gradually improved and showed specificity to the trained orientation. We also found that, when the target and flankers were spaced too finely, training could only reduce, rather than completely eliminate, the crowding effect. This two-stage learning process illustrates a learning strategy for our brain to deal with the notoriously difficult problem of identifying peripheral objects in clutter. The brain first learned to solve the "easy and general" part of the problem (i.e., improving the processing resolution and segmenting the target and flankers) and then tackle the "difficult and specific" part (i.e., refining the representation of the target).

  15. Crowding, grouping, and object recognition: A matter of appearance.

    Science.gov (United States)

    Herzog, Michael H; Sayim, Bilge; Chicherov, Vitaly; Manassi, Mauro

    2015-01-01

    In crowding, the perception of a target strongly deteriorates when neighboring elements are presented. Crowding is usually assumed to have the following characteristics. (a) Crowding is determined only by nearby elements within a restricted region around the target (Bouma's law). (b) Increasing the number of flankers can only deteriorate performance. (c) Target-flanker interference is feature-specific. These characteristics are usually explained by pooling models, which are well in the spirit of classic models of object recognition. In this review, we summarize recent findings showing that crowding is not determined by the above characteristics, thus, challenging most models of crowding. We propose that the spatial configuration across the entire visual field determines crowding. Only when one understands how all elements of a visual scene group with each other, can one determine crowding strength. We put forward the hypothesis that appearance (i.e., how stimuli look) is a good predictor for crowding, because both crowding and appearance reflect the output of recurrent processing rather than interactions during the initial phase of visual processing.

  16. Grouping and crowding affect target appearance over different spatial scales.

    Directory of Open Access Journals (Sweden)

    Bilge Sayim

    Full Text Available Crowding is the impairment of peripheral target perception by nearby flankers. A number of recent studies have shown that crowding shares many features with grouping. Here, we investigate whether effects of crowding and grouping on target perception are related by asking whether they operate over the same spatial scale. A target letter T had two sets of flanking Ts of varying orientations. The first set was presented close to the target, yielding strong crowding. The second set was either close enough to cause crowding on their own or too far to cause crowding on their own. The Ts of the second set had the same orientation that either matched the target's orientation (Grouped condition or not (Ungrouped condition. In Experiment 1, the Grouped flankers reduced crowding independently of their distance from the target, suggesting that grouping operated over larger distances than crowding. In Experiments 2 and 3 we found that grouping did not affect sensitivity but produced a strong bias to report that the grouped orientation was present at the target location whether or not it was. Finally, we investigated whether this bias was a response or perceptual bias, rejecting the former in favor of a perceptual grouping explanation. We suggest that the effect of grouping is to assimilate the target to the identity of surrounding flankers when they are all the same, and that this shape assimilation effect differs in its spatial scale from the integration effect of crowding.

  17. A generic method for evaluating crowding in the emergency department

    DEFF Research Database (Denmark)

    Eiset, Andreas Halgreen; Erlandsen, Mogens; Møllekær, Anders Brøns;

    2016-01-01

    Background Crowding in the emergency department (ED) has been studied intensively using complicated non-generic methods that may prove difficult to implement in a clinical setting. This study sought to develop a generic method to describe and analyse crowding from measurements readily available......, a ‘carry over’ effect was shown between shifts and days. Conclusions The presented method offers an easy and generic way to get detailed insight into the dynamics of crowding in an ED. Keywords Crowding, Emergency department, ED, Generic, Method, Model, Queue, Patient flow...

  18. Effect of molecular crowding on the enzymes of glycogenolysis.

    Science.gov (United States)

    Chebotareva, N A

    2007-12-01

    Cell cytoplasm contains high concentrations of macromolecules occupying a significant part of the cell volume (crowding conditions). According to modern concepts, crowding has a pronounced effect on the rate and equilibrium of biochemical reactions and stimulates the formation of more compact structures. This review considers different aspects of the crowding effect in vivo and in vitro, its role in regulation of cell volume, the effect of crowding on various interactions, such as protein-ligand and protein-protein interactions, as well as on protein denaturation, conformation transitions of macromolecules, and supramolecular structure formation. The influence of crowding arising from the presence of high concentrations of osmolytes on the interactions of the enzymes of glycogenolysis has been demonstrated. It has been established that, in accordance with predictions of crowding theory, trimethylamine N-oxide (TMAO) and betaine highly stimulate the association of phosphorylase kinase (PhK) and its interaction with glycogen. However, high concentrations of proline, betaine, and TMAO completely suppress the formation of PhK complex with phosphorylase b (Phb). The protective effect of osmolyte-induced molecular crowding on Phb denaturation by guanidine hydrochloride is shown. The influence of crowding on the interaction of Phb with allosteric inhibitor FAD has been revealed. The results show that, under crowding conditions, the equilibrium of the isomerization of Phb shifts towards a more compact dimeric state with decreased affinity for FAD.

  19. Simulation of Cognitive Pedestrian Agents Crowds in Crisis Situations

    Directory of Open Access Journals (Sweden)

    Margaret Lyell

    2006-06-01

    Full Text Available In crisis situations in an urban environment, first responder teams often must deal with crowds of people. Consider the case of a building fire in a dense city environment. People may be injured; walkways may be blocked, with fire equipment attempting to reach the scene. Crowd behavior can become an issue when trying to reach the injured, ensure safety and restore conditions to normal. The motivations of pedestrians that form the crowd can vary. Some are there because they are curious about the crisis situation. Others, attending to their individual concerns, may have found themselves in the 'wrong' location. They may be trying to leave the area, but the density of people as well as the spatial layout of the walkways may be impeding their progress. Other individuals, unaware of the fire, may be attempting to reach their intended destinations that happen to be near the crisis area, thus adding to crowd congestion. With a model of crowd behavior, effective strategies for resource usage in managing crowd behavior can be developed. Our approach to this problem is that of agent-based modeling and simulation. We develop a cognitive pedestrian agent model. Utilizing this model, we simulate crowd behavior in a 'city fire' scenario. Characteristics of crowd behavior with different pedestrian personality mixes and a strategy for crowd management are investigated

  20. Time-Resolved Linear Dichroism Measurements of Carbonmonoxy Myoglobin as a Probe of the Microviscosity in Crowded Environments.

    Science.gov (United States)

    Chen, Eefei; Kliger, David S

    2017-07-27

    The distribution of viscosities in living cells is heterogeneous because of the different sizes and natures of macromolecular components. When thinking about protein folding/function processes in such an environment, the relevant (micro)viscosity at the micrometer length scale is necessarily distinguished from the bulk (macro)viscosity. The concentration dependencies of microviscosities are determined by a number of factors, such as electrostatic interactions, van der Waals forces, and excluded volume effects. To explore such factors, the rotational diffusion time of myoglobin in the presence of varying concentrations of macromolecules that differ in molecular weight (dextran 6000, 10 000, and 70 000), shape (dextran versus Ficoll), size, and surface charge is measured with time-resolved linear dichroism spectroscopy. The results of these studies offer simple empirically determined linear and exponential functions useful for predicting microviscosities as a function of concentration for these macromolecular crowders that are typically used to study crowding effects on protein folding. To understand how relevant these microviscosity measurements are to intracellular environments, the TRLD results are discussed in the context of studies that measure viscosity in cells.

  1. On the generality of crowding : Visual crowding in size, saturation, and hue compared to orientation

    NARCIS (Netherlands)

    Berg, Ronald van den; Roerdink, Jos B.T.M.; Cornelissen, Frans W.

    2007-01-01

    Perception of peripherally viewed shapes is impaired when surrounded by similar shapes. This phenomenon is commonly referred to as "crowding". Although studied extensively for perception of characters ( mainly letters) and, to a lesser extent, for orientation, little is known about whether and how c

  2. The Hierarchical Sparse Selection Model of Visual Crowding

    Directory of Open Access Journals (Sweden)

    Wesley eChaney

    2014-09-01

    Full Text Available Because the environment is cluttered, objects rarely appear in isolation. The visual system must therefore attentionally select behaviorally relevant objects from among many irrelevant ones. A limit on our ability to select individual objects is revealed by the phenomenon of visual crowding: an object seen in the periphery, easily recognized in isolation, can become impossible to identify when surrounded by other, similar objects. The neural basis of crowding is hotly debated: while prevailing theories hold that crowded information is irrecoverable – destroyed due to over-integration in early-stage visual processing – recent evidence demonstrates otherwise. Crowding can occur between high-level, configural object representations, and crowded objects can contribute with high precision to judgments about the gist of a group of objects, even when they are individually unrecognizable. While existing models can account for the basic diagnostic criteria of crowding (e.g. specific critical spacing, spatial anisotropies, and temporal tuning, no present model explains how crowding can operate simultaneously at multiple levels in the visual processing hierarchy, including at the level of whole objects. Here, we present a new model of visual crowding— the hierarchical sparse selection (HSS model, which accounts for object-level crowding, as well as a number of puzzling findings in the recent literature. Counter to existing theories, we posit that crowding occurs not due to degraded visual representations in the brain, but due to impoverished sampling of visual representations for the sake of perception. The HSS model unifies findings from a disparate array of visual crowding studies and makes testable predictions about how information in crowded scenes can be accessed.

  3. Crowding follows the binding of relative position and orientation.

    Science.gov (United States)

    Greenwood, John A; Bex, Peter J; Dakin, Steven C

    2012-03-21

    Crowding--the deleterious influence of clutter on object recognition--disrupts the identification of visual features as diverse as orientation, motion, and color. It is unclear whether this occurs via independent feature-specific crowding processes (preceding the feature binding process) or via a singular (late) mechanism tuned for combined features. To examine the relationship between feature binding and crowding, we measured interactions between the crowding of relative position and orientation. Stimuli were a target cross and two flanker crosses (each composed of two near-orthogonal lines), 15 degrees in the periphery. Observers judged either the orientation (clockwise/counterclockwise) of the near-horizontal target line, its position (up/down relative to the stimulus center), or both. For single-feature judgments, crowding affected position and orientation similarly: thresholds were elevated and responses biased in a manner suggesting that the target appeared more like the flankers. These effects were tuned for orientation, with near-orthogonal elements producing little crowding. This tuning allowed us to separate the predictions of independent (feature specific) and combined (singular) models: for an independent model, reduced crowding for one feature has no effect on crowding for other features, whereas a combined process affects either all features or none. When observers made conjoint judgments, a reduction of orientation crowding (by increasing target-flanker orientation differences) increased the rate of correct responses for both position and orientation, as predicted by our combined model. In contrast, our independent model incorrectly predicted a high rate of position errors, since the probability of positional crowding would be unaffected by changes in orientation. Thus, at least for these features, crowding is a singular process that affects bound position and orientation values in an all-or-none fashion.

  4. The Financial Impact of Emergency Department Crowding

    Directory of Open Access Journals (Sweden)

    Foley, Mathew

    2011-05-01

    Full Text Available Objective: The economic benefits of reducing emergency department (ED crowding are potentially substantial as they may decrease hospital length of stay. Hospital administrators and public officials may therefore be motivated to implement crowding protocols. We sought to identify a potential cost of ED crowding by evaluating the contribution of excess ED length of stay (LOS to overall hospital length of stay. Methods: We performed a retrospective review of administrative data of adult patients from two urban hospitals (one county and one university in Brooklyn, New York from 2006-2007. Data was provided by each facility. Extrapolating from prior research (Krochmal and Riley, 2005, we determined the increase in total hospital LOS due to extended ED lengths of stay, and applied cost and charge analyses for the two separate facilities. Results: We determined that 6,205 (5.0% admitted adult patients from the county facility and 3,017 (3.4% patients from the university facility were held in the ED greater than one day over a one-year period. From prior research, it has been estimated that each of these patient’s total hospital length of stay was increased on average by 11.7% (0.61 days at the county facility, and 0.71 days at the university facility. The increased charges over one year at the county facility due to the extended ED LOS was therefore approximately $9.8 million, while the increased costs at the university facility were approximately $3.9 million. Conclusion: Based on extrapolations from Krochmal and Riley applied to two New York urban hospitals, the county hospital could potentially save $9.8 million in charges and the university hospital $3.9 million in costs per year if they eliminate ED boarding of adult admitted patients by improving movement to the inpatient setting. [West J Emerg Med. 2011;12(2:192-197.

  5. Nonlocal Crowd Dynamics Models for several Populations

    CERN Document Server

    Colombo, Rinaldo M

    2011-01-01

    This paper develops the basic analytical theory related to some recently introduced crowd dynamics models. Where well posedness was known only locally in time, it is here extended to all of $\\reali^+$. The results on the stability with respect to the equations are improved. Moreover, here the case of several populations is considered, obtaining the well posedness of systems of multi-D non-local conservation laws. The basic analytical tools are provided by the classical Kruzkov theory of scalar conservation laws in several space dimensions.

  6. NONLOCAL CROWD DYNAMICS MODELS FOR SEVERAL POPULATIONS

    Institute of Scientific and Technical Information of China (English)

    Rinaldo M. Colombo; Magali Lécureux-Mercier

    2012-01-01

    This paper develops the basic analytical theory related to some recently introduced crowd dynamics models.Where well posedness was known only locally in time,it is here extended to all of R+.The results on the stability with respect to the equations are improved.Moreover,here the case of several populations is considered,obtaining the well posedness of systems of multi-D non-local conservation laws.The basic analytical tools are provided by the classical Kru(z)kov theory of scalar conservation laws in several space dimensions.

  7. The supermarket model with arrival rate tending to one

    CERN Document Server

    Brightwell, Graham

    2012-01-01

    In the supermarket model, there are $n$ queues, each with a single server. Customers arrive in a Poisson process with arrival rate $\\lambda n$, where $\\lambda = \\lambda (n) \\in (0,1)$. Upon arrival, a customer selects $d=d(n)$ servers uniformly at random, and joins the queue of a least-loaded server amongst those chosen. Service times are independent exponentially distributed random variables with mean~1. In this paper, we analyse the behaviour of the supermarket model in a regime where $\\lambda(n)$ tends to~1, and $d(n)$ tends to infinity, as $n \\to \\infty$. For suitable triples $(n,d,\\lambda)$, we identify a subset ${\\cal N}$ of the state space where the process remains for a long time in equilibrium. We further show that the process is rapidly mixing when started in ${\\cal N}$, and give bounds on the speed of mixing for more general initial conditions.

  8. PREFACE: Complex dynamics of fluids in disordered and crowded environments Complex dynamics of fluids in disordered and crowded environments

    Science.gov (United States)

    Coslovich, Daniele; Kahl, Gerhard; Krakoviack, Vincent

    2011-06-01

    Over the past two decades, the dynamics of fluids under nanoscale confinement has attracted much attention. Motivation for this rapidly increasing interest is based on both practical and fundamental reasons. On the practical and rather applied side, problems in a wide range of scientific topics, such as polymer and colloidal sciences, rheology, geology, or biophysics, benefit from a profound understanding of the dynamical behaviour of confined fluids. Further, effects similar to those observed in confinement are expected in fluids whose constituents have strong size or mass asymmetry, and in biological systems where crowding and obstruction phenomena in the cytosol are responsible for clear separations of time scales for macromolecular transport in the cell. In fundamental research, on the other hand, the interest focuses on the complex interplay between confinement and structural relaxation, which is responsible for the emergence of new phenomena in the dynamics of the system: in confinement, geometric constraints associated with the pore shape are imposed to the adsorbed fluids and an additional characteristic length scale, i.e. the pore size, comes into play. For many years, the topic has been mostly experimentally driven. Indeed, a broad spectrum of systems has been investigated by sophisticated experimental techniques, while theoretical and simulation studies were rather scarce due to conceptual and computational issues. In the past few years, however, theory and simulations could largely catch up with experiments. On one side, new theories have been put forward that duly take into account the porosity, the connectivity, and the randomness of the confinement. On the other side, the ever increasing available computational power now allows investigations that were far out of reach a few years ago. Nowadays, instead of isolated state points, systematic investigations on the dynamics of confined fluids, covering a wide range of system parameters, can be realized

  9. A Unifying Model of Orientation Crowding in Peripheral Vision.

    Science.gov (United States)

    Harrison, William J; Bex, Peter J

    2015-12-21

    Peripheral vision is fundamentally limited not by the visibility of features, but by the spacing between them [1]. When too close together, visual features can become "crowded" and perceptually indistinguishable. Crowding interferes with basic tasks such as letter and face identification and thus informs our understanding of object recognition breakdown in peripheral vision [2]. Multiple proposals have attempted to explain crowding [3], and each is supported by compelling psychophysical and neuroimaging data [4-6] that are incompatible with competing proposals. In general, perceptual failures have variously been attributed to the averaging of nearby visual signals [7-10], confusion between target and distractor elements [11, 12], and a limited resolution of visual spatial attention [13]. Here we introduce a psychophysical paradigm that allows systematic study of crowded perception within the orientation domain, and we present a unifying computational model of crowding phenomena that reconciles conflicting explanations. Our results show that our single measure produces a variety of perceptual errors that are reported across the crowding literature. Critically, a simple model of the responses of populations of orientation-selective visual neurons accurately predicts all perceptual errors. We thus provide a unifying mechanistic explanation for orientation crowding in peripheral vision. Our simple model accounts for several perceptual phenomena produced by crowding of orientation and raises the possibility that multiple classes of object recognition failures in peripheral vision can be accounted for by a single mechanism.

  10. Emergency department crowding and risk of preventable medical errors.

    Science.gov (United States)

    Epstein, Stephen K; Huckins, David S; Liu, Shan W; Pallin, Daniel J; Sullivan, Ashley F; Lipton, Robert I; Camargo, Carlos A

    2012-04-01

    The objective of the study is to determine the association between emergency department (ED) crowding and preventable medical errors (PME). This was a retrospective cohort study of 533 ED patients enrolled in the National ED Safety Study (NEDSS) in four Massachusetts EDs. Individual patients' average exposure to ED crowding during their ED visit was compared with the occurrence of a PME (yes/no) for the three diagnostic categories in NEDSS: acute myocardial infarction, asthma exacerbation, and dislocation requiring procedural sedation. To accommodate site-to-site differences in available administrative data, ED crowding was measured using one of three previously validated crowding metrics (ED Work Index, ED Workscore, and ED Occupancy). At each site, the continuous measure was placed into site-specific quartiles, and these quartiles then were combined across sites. We found that 46 (8.6%; 95% confidence interval, 6.4-11.3%) of the 533 patients experienced a PME. For those seen during higher levels of ED crowding (quartile 4 vs. quartile 1), the occurrence of PMEs was more than twofold higher, both on unadjusted analysis and adjusting for two potential confounders (diagnosis, site). The association appeared non-linear, with most PMEs occurring at the highest crowding level. We identified a direct association between high levels of ED crowding and risk of preventable medical errors. Further study is needed to determine the generalizability of these results. Should such research confirm our findings, we would suggest that mitigating ED crowding may reduce the occurrence of preventable medical errors.

  11. Perceptions of emergency department crowding in the commonwealth of pennsylvania.

    Science.gov (United States)

    Pines, Jesse M; Isserman, Joshua A; Kelly, John J

    2013-02-01

    The state of emergency department (ED) crowding in Pennsylvania has not previously been reported. We assessed perceptions of ED crowding by surveying medical directors/chairs from Pennsylvania EDs in the spring of 2008. A total of 106 completed the questionnaire (68% response rate). A total of 83% (86/104) agreed that ED crowding was a problem; 26% (27/105) reported that at least half of admitted patients boarded for more than 4 hours. Ninety-eight percent (102/104) agreed that patient satisfaction suffers during crowding and 79% (84/106) stated that quality suffers. Sixty-five percent (68/105) reported that crowding had worsened during the past 2 years. Several hospital interventions were used to alleviate crowding: expediting discharges, 81% (86/106); prioritizing ED patients for inpatient beds, 79% (84/106); and ambulance diversion, 55% (57/105). Almost all respondents who had improved ED operations reported that it had reduced crowding. ED crowding is a common problem in Pennsylvania and is worsening in the majority of hospitals, despite the implementation of a variety of interventions.

  12. Emergency department crowding in The Netherlands: managers’ experiences

    NARCIS (Netherlands)

    C. van der Linden (Christien); R. Reijnen (Resi); R. Derlet (Robert); N. van der Linden (Naomi); R. Lindeboom (Robert); C. Lucas (Cees); J. Richards (John)

    2013-01-01

    markdownabstract__Abstract__ __Background__ In The Netherlands, the state of emergency department (ED) crowding is unknown. Anecdotal evidence suggests that current ED patients experience a longer length of stay (LOS) compared to some years ago, which is indicative of ED crowding. However, no multi

  13. Designing for crowd well-being: needs and design suggestions

    NARCIS (Netherlands)

    Li, J.; De Ridder, H.; Vermeeren, A.P.O.S.; Conrado, C.; Martella, C.

    2013-01-01

    This paper investigates the needs or criteria for sustaining well-being in crowded situations through two focus group discussions with a total of ten participants. We conclude that pursuing crowd well-being could be divided into two different cases: one is obtaining the enhancement of the current st

  14. Eye movement targets are released from visual crowding.

    Science.gov (United States)

    Harrison, William J; Mattingley, Jason B; Remington, Roger W

    2013-02-13

    Our ability to recognize objects in peripheral vision is impaired when other objects are nearby (Bouma, 1970). This phenomenon, known as crowding, is often linked to interactions in early visual processing that depend primarily on the retinal position of visual stimuli (Pelli, 2008; Pelli and Tillman, 2008). Here we tested a new account that suggests crowding is influenced by spatial information derived from an extraretinal signal involved in eye movement preparation. We had human observers execute eye movements to crowded targets and measured their ability to identify those targets just before the eyes began to move. Beginning ∼50 ms before a saccade toward a crowded object, we found that not only was there a dramatic reduction in the magnitude of crowding, but the spatial area within which crowding occurred was almost halved. These changes in crowding occurred despite no change in the retinal position of target or flanking stimuli. Contrary to the notion that crowding depends on retinal signals alone, our findings reveal an important role for eye movement signals. Eye movement preparation effectively enhances object discrimination in peripheral vision at the goal of the intended saccade. These presaccadic changes may enable enhanced recognition of visual objects in the periphery during active search of visually cluttered environments.

  15. On the relations between crowding and visual masking.

    Science.gov (United States)

    Huckauf, Anke; Heller, Dieter

    2004-05-01

    To study the question of which processes contribute to crowding and whether these are comparable to those of visual temporal masking, we varied the stimulus onset asynchrony (SOA) between target and flankers in a crowding setting. Monotonically increasing Type A masking functions observedfor small spacings and large eccentricities indicate that the integration of information from target and flankers underlies crowding. Decreasing masking functions obtained for large spacings and small eccentricities relate processes of crowding to those contributing to Type B masking. In addition, Type B masking was more frequent with letter-like nonletter flankers than with letter flankers, suggesting that Type B masking, just like crowding over large areas, is due to higher level interactions. The rapid decrease of the effects of interletter spacing and eccentricity with increasing SOA indicates that positional information is transient.

  16. Designing interactive technology for crowd experiences - beyond sanitization

    DEFF Research Database (Denmark)

    Veerasawmy, Rune

    2014-01-01

    This dissertation concerns the topic on designing interactive technology for crowd expe- riences. It takes the outset in the experience-oriented design approach within interaction design, exploring the research question how can we conceptually understand and design interactive technology for crowd...... in a conceptual model of social experiences that presents crowd experiences as a distinct type of social experience. This is different from what previously have been explored within experi- ence-oriented design. This dissertation is composed of four research papers framed by an overview that summarizes...... experience within interaction design. This dissertation introduces an understanding of crowd experience as a distinct type of social experiences driven by non-rational behavior. This conceptual understanding is established in the intersection between sociological crowd theory and a pragmatist perspective...

  17. Wandering crowd simulation based on space syntax theory

    Institute of Scientific and Technical Information of China (English)

    ZHENG Liping; SUN Chen; LIU Li; WANG Lin

    2012-01-01

    Space syntax has proven there appears to be a fundamental process that informs human and social usage of an environ- ment, and the effects of spatial configuration on movement patterns are consistent with a model of individual decision behavior. In- troducing space syntax to crowd simulation will enable space structure guide the random movement of the crowd with no specific targets. This paper proposes a simulation method of the wandering crowd, which calculates the crowd distribution corresponding to the space through space syntax and uses a hybrid path planning algorithm to dynamically navigate the crowd to conform to the dis- tribution. Experiments show the presented method can obtain reasonable and vision-realistic simulation results.

  18. German crowd-investing platforms: Literature review and survey

    Directory of Open Access Journals (Sweden)

    David Grundy

    2016-12-01

    Full Text Available This article presents a comprehensive overview of the current German crowd-investing market drawing on a data-set of 31 crowd-investing platforms including the analysis of 265 completed projects. While crowd-investing market still only represents a niche in the German venture capital market, there is potential for an increase in both market volume and in average project investment. The market share is distributed among a few crowd-investing platforms with high entry barriers for new platforms although platforms that specialise in certain sectors have managed to successfully enter the market. German crowd-investing platforms are found to promote mainly internet-based enterprises (36% followed by projects in real estate (24% and green projects (19%, with the median money raised 100,000 euro.

  19. Crowd Energy Management:New Paradigm for Electricity Market

    Institute of Scientific and Technical Information of China (English)

    Mario Gstrein; Stephanie Teufel

    2015-01-01

    Abstract-The traditionally centralized approach of electricity networks is progressively undergoing a shift towards a decentralized, distributed structure. The local and crowd-based principle is transforming the existing supply chain and related activities into a value network (VN). Previous researches on crowd value network concepts focus on the activities of infrastructure and load management and neglect activities that generate collaboration. Collaboration with and within crowds particularly demands a different mindset and management of sharing values, information, benefit, and risks. Furthermore, these concepts must integrate technical, processual, and social aspects. Thus, this article proposes a holistic framework of electricity VN management for crowd energy. It redefines VN activities for infrastructure and load management while appending VN activities for social electricity handling. Additionally, the framework illustrates the interactions among these three elements and concludes with an adaption cycle for the crowd value network.

  20. Crowd Analysis by Using Optical Flow and Density Based Clustering

    DEFF Research Database (Denmark)

    Santoro, Francesco; Pedro, Sergio; Tan, Zheng-Hua;

    2010-01-01

    , it is applied a crowd tracker in every frame, allowing us to detect and track the crowds. Our system gives the output as a graphic overlay, i.e it adds arrows and colors to the original frame sequence, in order to identify crowds and their movements. For the evaluation, we check when our system detect certains......In this paper, we present a system to detect and track crowds in a video sequence captured by a camera. In a first step, we compute optical flows by means of pyramidal Lucas-Kanade feature tracking. Afterwards, a density based clustering is used to group similar vectors. In the last step...... events on the crowds, such as merging, splitting and collision....

  1. A bivalent scale for measuring crowding among deer hunters

    Science.gov (United States)

    Gigliotti, Larry M.; Chase, Loren

    2014-01-01

    One factor that may influence satisfaction in outdoor recreation is crowding, which historically has been defined as a negative evaluation of the density of other participants. While this definition is suitable for most scenarios, there are circumstances where encounters with others in the area are evaluated positively and thus contribute to the satisfaction of the participant. To adequately describe this phenomenon we suggest a more inclusive measurement of crowding that allows for both positive and negative evaluations of participant density to more accurately explore the relationship between crowding and satisfaction. We identified a sub-group of deer hunters who negatively evaluated the low density of other hunters, which reduced their satisfaction with their overall hunting experience. The methodology for measuring crowding in recreation research may have an important effect in identifying the relationship crowding has with other relevant variables as well as management implications.

  2. Private Giving Crowding Government Funding in Public Higher Education

    Directory of Open Access Journals (Sweden)

    G. Thomas Sav

    2010-01-01

    Full Text Available Problem statement: Private giving and government funding are critical revenue sources for public colleges and universities. If increased private giving reduces government funding, then that type and extent of crowding out carries important managerial and public policy implications. Approach: The study used a government funding reaction function and an instrumental variable approach to empirically estimate the potential for crowding out. Results: The study examined the extent to which private giving reduces or crowds out state government funding of public colleges and universities. Government free riding was at question and investigated to determine how active it is in terms of private donations partially or wholly displacing state government funding. The findings suggested that the rate of crowding out was 43% on the dollar. That compares to the 45% political substitution of the 1960’s but is much diminished from the 1980’s dollar for dollar crowding out. Those are aggregate comparisons for all public institutions. A disaggregated approach in this study additionally revealed that doctoral universities were victims of the same 43% crowd out but that at two other levels, master degree granting and associate degree granting colleges, there was the opposite effect of crowding in. Those colleges received state funding augmentations of 32-92% on their dollar of privately provided donations. Conclusion/Recommendations: The study’s finding of the existence of both crowding out and crowding in can carry important policy implications for college and university funding. Future managerial and public policy decision making should take that into account. However, political sustainability and economy wide and localized effects over time of crowding out and in could prove fruitful avenues of inquiry for future research.

  3. Controlled architecture for improved macromolecular memory within polymer networks.

    Science.gov (United States)

    DiPasquale, Stephen A; Byrne, Mark E

    2016-08-01

    This brief review analyzes recent developments in the field of living/controlled polymerization and the potential of this technique for creating imprinted polymers with highly structured architecture with macromolecular memory. As a result, it is possible to engineer polymers at the molecular level with increased homogeneity relating to enhanced template binding and transport. Only recently has living/controlled polymerization been exploited to decrease heterogeneity and substantially improve the efficiency of the imprinting process for both highly and weakly crosslinked imprinted polymers. Living polymerization can be utilized to create imprinted networks that are vastly more efficient than similar polymers produced using conventional free radical polymerization, and these improvements increase the role that macromolecular memory can play in the design and engineering of new drug delivery and sensing platforms.

  4. Isotope labeling for NMR studies of macromolecular structure and interactions

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-01

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

  5. Temperature-dependent macromolecular X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Weik, Martin, E-mail: martin.weik@ibs.fr; Colletier, Jacques-Philippe [CEA, IBS, Laboratoire de Biophysique Moléculaire, F-38054 Grenoble (France); CNRS, UMR5075, F-38027 Grenoble (France); Université Joseph Fourier, F-38000 Grenoble (France)

    2010-04-01

    The dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100 K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15 K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography.

  6. Refinement of macromolecular structures against neutron data with SHELXL2013.

    Science.gov (United States)

    Gruene, Tim; Hahn, Hinrich W; Luebben, Anna V; Meilleur, Flora; Sheldrick, George M

    2014-02-01

    Some of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to use SHELXL for refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst. (1991), A47, 392-400] restraints to H atoms and discusses several of the features of SHELXL that make the program particularly useful for the investigation of H atoms with neutron diffraction. SHELXL2013 is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures.

  7. The vibron dressing in α-helicoidal macromolecular chains

    Institute of Scientific and Technical Information of China (English)

    D.(C)evizovi(c); S.Galovi(c); A.Reshetnyak; Z.Ivi(c)

    2013-01-01

    We present a study of the physical properties of the vibrational excitation in α-helicoidal macromolecular chains,caused by the interaction with acoustical and optical phonon modes.The influence of the temperature and the basic system parameters on the vibron dressing have been analyzed by employing the simple mean-field approach based on the variational extension of the Lang-Firsov unitary transformation.The applied approach predicts a region in system parameter space where one has an abrupt transition from a partially dressed (light and mobile) to a fully dressed (immobile) vibron state.We found that the boundary of this region depends on system temperature and the type of bond among structural elements in the macromolecular chain.

  8. A macromolecular model for the endothelial surface layer

    Science.gov (United States)

    Harden, James; Danova-Okpetu, Darina; Grest, Gary

    2006-03-01

    The endothelial surface layer (ESL) is a micron-scale macromolecular lining of the luminal side of blood vessels composed of proteoglycans, glycoproteins, polysaccharides and associated plasma proteins all in dynamic equilibrium. It has numerous physiological roles including the regulation of blood flow and microvascular permeability, and active participation in mechanotransduction and stress regulation, coagulation, cell adhesion, and inflammatory response. The dynamic structure and the mechanical properties of the ESL are crucial for many of its physiological properties. We present a topological model for the ESL composed of three basic macromolecular elements: branched proteoglycans, linear polysaccharide chains, and small plasma proteins. The model was studied using non-equilibrium molecular dynamics simulations and compared with scaling theories for associating tethered polymers. We discuss the observed dynamical and mechanical properties of the ESL captured by this model, and the possible physical insight it provides into the physiological behavior of the ESL.

  9. Eyes on crowding : Crowding is preserved when responding by eye and similarly affects identity and position accuracy

    NARCIS (Netherlands)

    Yildirim, Funda; Meyer, Vincent; Cornelissen, Frans W.

    2015-01-01

    Peripheral vision guides recognition and selection of targets for eye movements. Crowding-a decline in recognition performance that occurs when a potential target is surrounded by other, similar, objects-influences peripheral object recognition. A recent model study suggests that crowding may be due

  10. A systematic review on 'Foveal Crowding' in visually impaired children and perceptual learning as a method to reduce Crowding.

    NARCIS (Netherlands)

    Huurneman, B.; Boonstra, F.N.; Cox, R.F.; Cillessen, A.H.; Rens, G. van

    2012-01-01

    BACKGROUND: This systematic review gives an overview of foveal crowding (the inability to recognize objects due to surrounding nearby contours in foveal vision) and possible interventions. Foveal crowding can have a major effect on reading rate and deciphering small pieces of information from busy v

  11. A systematic review on 'Foveal Crowding' in visually impaired children and perceptual learning as a method to reduce Crowding

    NARCIS (Netherlands)

    Huurneman, B.; Boonstra, F.N.; Cox, R.F.A.; Cillessen, A.H.N.; Rens, G.H.M.B. van

    2012-01-01

    Background - This systematic review gives an overview of foveal crowding (the inability to recognize objects due to surrounding nearby contours in foveal vision) and possible interventions. Foveal crowding can have a major effect on reading rate and deciphering small pieces of information from busy

  12. A systematic review on 'Foveal Crowding' in visually impaired children and perceptual learning as a method to reduce Crowding

    NARCIS (Netherlands)

    Huurneman, Bianca; Boonstra, F. Nienke; Cox, Ralf F. A.; Cillessen, Antonius H. N.; van Rens, Ger

    2012-01-01

    Background: This systematic review gives an overview of foveal crowding (the inability to recognize objects due to surrounding nearby contours in foveal vision) and possible interventions. Foveal crowding can have a major effect on reading rate and deciphering small pieces of information from busy v

  13. Orlando, ou a tendência social da androginia

    OpenAIRE

    Alvarenga,Nízia Maria

    1997-01-01

    Este artigo analisa o filme Orlando por ser expressão de uma das tendências que vêm despontando no processo atual de mudanças sociais no conjunto das sociedades capitalistas ocidentais. A dimensão simbólica destas sociedades abrange representações tais como racionalidade, objetividade, pragmatismo, impessoalidade, utilitarismo, disciplina e neutralidade afetiva, que constituem o cerne do sistema de valores sociais predominantes. Uma alteração desta dimensão significa uma revolução em seu modo...

  14. A Strategy for the Development of Macromolecular Nonlinear Optical Materials

    Science.gov (United States)

    1990-01-01

    obsolete. SECURITY CLASSIFICATION OF THIS PAGE STRATEGY FOR THE DEVELOPMENT OF MACROMOLECULAR NONLINEAR OPTICAL MATERIALS Braja K. Mandala , Jan-Chan...materials is significantly different from the conventional inorganic NLO materials. The extent of second order (quadratic) NLO effect such as second...is a criterion of paramount importance for a large second order electro-optic effect in organic materials 8 ,9 . The most common approach to obtain

  15. Facilitating structure determination: workshop on robotics andautomation in macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Ralston, Corie; Cork, C.W.; McDermott, G.; Earnest, T.N.

    2006-03-28

    As part of the annual Advanced Light Source (ALS) andStanford Synchrotron Radiation Laboratory (SSRL) Users' Meeting inOctober of this year, the macromolecular crystallography staff at bothsynchrotrons held a joint hands-on workshop to address automation issuesin crystal mounting and data collection at the beamline. This paperdescribes the ALS portion of the workshop, while the accompanying paperreviews the SSRL workshop.

  16. Single-particle cryo-electron microscopy of macromolecular assemblies

    OpenAIRE

    Cheng, Kimberley

    2009-01-01

    In this thesis, single-particle cryo-electron microscopy (cryo-EM) was used to study the structure of three macromolecular assemblies: the two hemocyanin isoforms from Rapana thomasiana, the Pyrococcus furiosus chaperonin, and the ribosome from Escherichia coli. Hemocyanins are large respiratory proteins in arthropods and molluscs. Most molluscan hemocyanins exist as two distinct isoforms composed of related polypeptides. In most species the two isoforms differ in terms of their oligomeric st...

  17. Relationship among Lower Arch Length, Arch Width and Arch Perimeter in Crowding and Non-Crowding Groups

    Directory of Open Access Journals (Sweden)

    Selmani Mimoza

    2015-03-01

    Full Text Available Crowding is one of the causes of class I malocclusion. The purpose of the present study was to examine the relationship between arch length, arch width and arch perimeter in crowded and non-crowded arches, as well as to made comparison of the right and left sides between them and to find out the contributing factor in lower arch crowding. The study groups consisted of 60 subjects aged 16 to 21 years. First group consisted of 30 pairs of dental study models with class I normal occlusion. The second group consisted of 30 pairs of study models with class I crowding. Measurements of arch length and width were made as defined by Lavelle and Foster, using Korkhaus callipers. Arch perimeter was measured by Lundstrom method’s using manual calliper with sharp points. Differences between these measurements were made by Mann-Whitney U test (Z/U.

  18. REFMAC5 for the refinement of macromolecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Murshudov, Garib N., E-mail: garib@ysbl.york.ac.uk [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Skubák, Pavol [Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden (Netherlands); Lebedev, Andrey A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Pannu, Navraj S. [Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden (Netherlands); Steiner, Roberto A. [Randall Division of Cell and Molecular Biophysics, New Hunt’s House, King’s College London, London (United Kingdom); Nicholls, Robert A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Winn, Martyn D. [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Long, Fei; Vagin, Alexei A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom)

    2011-04-01

    The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described. This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.

  19. Macromolecular amplification of binding response in superaptamer hydrogels.

    Science.gov (United States)

    Bai, Wei; Gariano, Nicholas A; Spivak, David A

    2013-05-08

    It is becoming more important to detect ultralow concentrations of analytes for biomedical, environmental, and national security applications. Equally important is that new methods should be easy to use, inexpensive, portable, and if possible allow detection by the naked eye. By and large, detection of low concentrations of analytes cannot be achieved directly but requires signal amplification by catalysts, macromolecules, metal surfaces, or supramolecular aggregates. The rapidly progressing field of macromolecular signal amplification has been advanced using conjugated polymers, chirality in polymers, solvating polymers, and polymerization/depolymerization strategies. A new type of aptamer-based hydrogel with specific response to target proteins presented in this report demonstrates an additional category of macromolecular signal amplification. This superaptamer assembly provides the first example of using protein-specific aptamers to create volume-changing hydrogels with amplified response to the target protein. A remarkable aspect of these superaptamer hydrogels is that volume shrinking is visible to the naked eye down to femtomolar concentrations of protein. This extraordinary macromolecular amplification is attributed to a complex interplay between protein-aptamer supramolecular cross-links and the consequential reduction of excluded volume in the hydrogel. Specific recognition is even maintained in biological matrices such as urine and tears. Furthermore, the gels can be dried for long-term storage and regenerated for use without loss of activity. In practice, the ease of this biomarker detection method offers an alternative to traditional analytical techniques that require sophisticated instrumentation and highly trained personnel.

  20. Macromolecular Assemblage in the Design of a Synthetic AIDS Vaccine

    Science.gov (United States)

    Defoort, Jean-Philippe; Nardelli, Bernardetta; Huang, Wolin; Ho, David D.; Tam, James P.

    1992-05-01

    We describe a peptide vaccine model based on the mimicry of surface coat protein of a pathogen. This model used a macromolecular assemblage approach to amplify peptide antigens in liposomes or micelles. The key components of the model consisted of an oligomeric lysine scaffolding to amplify peptide antigens covalently 4-fold and a lipophilic membrane-anchoring group to further amplify noncovalently the antigens many-fold in liposomal or micellar form. A peptide antigen derived from the third variable domain of glycoprotein gp120 of human immunodeficiency virus type 1 (HIV-1), consisting of neutralizing, T-helper, and T-cytotoxic epitopes, was used in a macromolecular assemblage model (HIV-1 linear peptide amino acid sequence 308-331 in a tetravalent multiple antigen peptide system linked to tripalmitoyl-S-glycerylcysteine). The latter complex, in liposome or micelle, was used to immunize mice and guinea pigs without any adjuvant and found to induce gp120-specific antibodies that neutralize virus infectivity in vitro, elicit cytokine production, and prime CD8^+ cytotoxic T lymphocytes in vivo. Our results show that the macromolecular assemblage approach bears immunological mimicry of the gp120 of HIV virus and may lead to useful vaccines against HIV infection.

  1. Crowded: a crowd-sourced perspective of events as they happen

    Science.gov (United States)

    Brantingham, Richard; Hossain, Aleem

    2013-05-01

    `Crowded' is a web-based application developed by the Defence Science & Technology Laboratory (Dstl) that collates imagery of a particular location from a variety of media sources to provide an operator with real-time situational awareness. Emergency services and other relevant agencies have detected or become aware of an event - a riot or an explosion, for instance - and its location or text associated with it. The ubiquity of mobile devices allows people to collect and upload media of the incident to the Internet, in real time. Crowded manages the interactions with online sources of media: Flickr; Instagram; YouTube; Twitter; and Transport for London traffic cameras, to retrieve imagery that is being uploaded at that point in time. In doing so, it aims to provide human operators with near-instantaneous `eyes-on' from a variety of different perspectives. The first instantiation of Crowded was implemented as a series of integrated web-services with the aim of rapidly understanding whether the approach was viable. In doing so, it demonstrated how non-traditional, open sources can be used to provide a richer current intelligence picture than can be obtained alone from classified sources. The development of Crowded also explored how open source technology and cloud-based services can be used in the modern intelligence and security environment to provide a multi-agency Common Operating Picture to help achieve a co-ordinated response. The lessons learned in building the prototype are currently being used to design and develop a second version, and identify options and priorities for future development.

  2. Global crowd data to understand risk taking behavior: Understanding the costs of crowd sourcing

    Science.gov (United States)

    Hendrikx, J.; Johnson, J.

    2016-12-01

    Crowd sourcing is an increasingly common approach to collect data from a large number of places, people, or both, for a given phenomenon or observation. It is often thought of as a very cost effective approach to collect data from large spatial domains, or from difficult to reach areas, or for spatially discrete observations. While crowd sourcing data can provide a wealth of data beyond that which most research teams can collect themselves, there are many associated, and sometime unexpected costs with this approach. We present a case study of a crowd-sourced data collection campaign to collect GPS tracks of back country recreationalists in avalanche terrain. We ask the volunteers to track their outings using the GPS on their smart phone using a free application, and on the completion of their trip email us their track. On receipt of this track we automatically reply with a link to a decision making survey. In this way we collect data on both the physical attributes of their trip, as well as the social, psychological and demographic data about the person. While this approach has been very successful, it has come at a high cost time-wise. Much like the role of an online course instructor, instructor (or in this case researcher) presence is essential. Replying to emails, updating webpages, posting on social media, and connecting with your volunteer data collectors can become a full time job - and that's even before you start the data analysis. We encourage future researchers to plan ahead for this when starting a crowd sourcing project involving the general public, and seek advice and training in social media, web site development and communication techniques like semi-automated email.

  3. Tendências da ética profissional na modernidade

    Directory of Open Access Journals (Sweden)

    Elizete Silva Passos

    1993-03-01

    Full Text Available Identifica-se no momento presente uma crise de valores morais, fazendo com que os cidadãos clamem por justiça, respeitabilidade e compromisso social. Também os profissionais refletem essa situação e passam a investir na criação de valores que possam regulamentar as suas relações. Tal situação decorre da importância que a subjetividade passou a ter a partir da Modernidade, assim como, de algumas alterações ocorridas nas esferas política, econômica e social, fazendo com que os homens ganhassem uma grande confiança em si mesmos, a ponto de negarem a necessidade de seguirem valores estabelecidos socialmente. Assim, a ética na modernidade estrutura-se, basicamente, em três direções: uma de tradição teológica, outra que reconhece a situação de crise e tem consciência que precisa modificá-la, e a última que nega a necessidade de qualquer código moral. Em consonância com os valores vividos na sociedade, também, os códigos de ética profissional seguem tendências divergentes. Podemos identificá-los ora como um mero exercício tautológico, comprometido em sacramentar as práticas exercidas, ora como um falso enfrentamento das práticas cristalizadas e em outros momentos como uma tendência questionadora, voltada para a superação do egoísmo, do individualismo e do corporativismo. Acreditamos que esta última deveria ser a tendência a ser seguida, pois caracteriza-se como uma verdadeira orientação deontológica e não como subterfúgio de práticas desonestas e comportamentos moralmente inadequados.

  4. Supercrowding: weakly masking a target expands the range of crowding.

    Science.gov (United States)

    Vickery, Timothy J; Shim, Won Mok; Chakravarthi, Ramakrishna; Jiang, Yuhong V; Luedeman, Robert

    2009-02-10

    Crowding is impairment of peripheral object identification by nearby objects. Critical spacing (the minimum target-flanker distance that does not produce crowding) scales with target eccentricity and is consistently reported as roughly equal to or less than 50% of target eccentricity (0.5e). This study demonstrates that crowding occurs far beyond the typical critical spacing when the target is weakly masked by a surrounding contour or backwards pattern mask. A target was presented at a peripheral location on every trial and participants reported its orientation. Flankers appeared at target-flanker distances of 0.3-0.7e, or were absent. The target was presented with or without a mask. When flankers were absent, the masks only mildly impaired performance. When flankers were present but the mask was absent, target identification was nearly perfect at wide target-flanker distances (0.5e-0.7e). However, when flankers were present and the target was masked, performance dropped significantly, even when target-flanker distances far exceeded the typical crowding range. This phenomenon ("supercrowding") shares critical features with standard crowding: flankers similar to the target impair performance more than dissimilar flankers, and the characteristic anisotropic profile of crowding is preserved. Supercrowding may reflect a general interaction between crowding and other forms of masking.

  5. When crowding meets binocular rivalry: challenges for object perception.

    Science.gov (United States)

    Kim, Sangrae; Shin, Eunsam; Chong, Sang Chul

    2013-01-14

    Both crowding and binocular rivalry impair object perception, but their influence on object perception has so far only been investigated in separate fields. Three experiments investigated the joint influences of crowding and rivalry on object perception (orientation discrimination). Experiment 1 investigated how crowding and rivalry influence orientation discrimination together. Experiment 2 tested whether rivalry between flankers affects crowding using an orientation discrimination task. Experiment 3 tested whether crowding affects the temporal dynamics of the rivalry between a target and a rival stimulus. In Experiment 1, judgments of target orientation were more impaired when crowding and rivalry were simultaneously induced than when they were separately induced and their effects were combined. In Experiment 2, judgments of target orientation were impaired even when flankers were undergoing rivalry, thus highlighting the importance of the presence of flankers. Experiment 3 showed that flankers presented in the neighborhood of a target undergoing rivalry shortened target dominance and prolonged target suppression. The augmented impairments of object perception found in Experiments 1 and 3 suggest that crowding and rivalry interact, presumably through signal suppression. The adverse effect of flankers shown in Experiment 2 suggests that inappropriate feature integration may have additionally contributed to this interaction.

  6. Typical magnitude and spatial extent of crowding in autism.

    Science.gov (United States)

    Freyberg, Jan; Robertson, Caroline E; Baron-Cohen, Simon

    2016-01-01

    Enhanced spatial processing of local visual details has been reported in individuals with autism spectrum conditions (ASC), and crowding is postulated to be a mechanism that may produce this ability. However, evidence for atypical crowding in ASC is mixed, with some studies reporting a complete lack of crowding in autism and others reporting a typical magnitude of crowding between individuals with and without ASC. Here, we aim to disambiguate these conflicting results by testing both the magnitude and the spatial extent of crowding in individuals with ASC (N = 25) and age- and IQ-matched controls (N = 23) during an orientation discrimination task. We find a strong crowding effect in individuals with and without ASC, which falls off as the distance between target and flanker is increased. Both the magnitude and the spatial range of this effect were comparable between individuals with and without ASC. We also find typical (uncrowded) orientation discrimination thresholds in individuals with ASC. These findings suggest that the spatial extent of crowding is unremarkable in ASC, and is therefore unlikely to account for the visual symptoms reported in individuals with the diagnosis.

  7. Exits in order: How crowding affects particle lifetimes

    Science.gov (United States)

    Penington, Catherine J.; Baker, Ruth E.; Simpson, Matthew J.

    2016-06-01

    Diffusive processes are often represented using stochastic random walk frameworks. The amount of time taken for an individual in a random walk to intersect with an absorbing boundary is a fundamental property that is often referred to as the particle lifetime, or the first passage time. The mean lifetime of particles in a random walk model of diffusion is related to the amount of time required for the diffusive process to reach a steady state. Mathematical analysis describing the mean lifetime of particles in a standard model of diffusion without crowding is well known. However, the lifetime of agents in a random walk with crowding has received much less attention. Since many applications of diffusion in biology and biophysics include crowding effects, here we study a discrete model of diffusion that incorporates crowding. Using simulations, we show that crowding has a dramatic effect on agent lifetimes, and we derive an approximate expression for the mean agent lifetime that includes crowding effects. Our expression matches simulation results very well, and highlights the importance of crowding effects that are sometimes overlooked.

  8. iCrowd: agent-based behavior modeling and crowd simulator

    Science.gov (United States)

    Kountouriotis, Vassilios I.; Paterakis, Manolis; Thomopoulos, Stelios C. A.

    2016-05-01

    Initially designed in the context of the TASS (Total Airport Security System) FP-7 project, the Crowd Simulation platform developed by the Integrated Systems Lab of the Institute of Informatics and Telecommunications at N.C.S.R. Demokritos, has evolved into a complete domain-independent agent-based behavior simulator with an emphasis on crowd behavior and building evacuation simulation. Under continuous development, it reflects an effort to implement a modern, multithreaded, data-oriented simulation engine employing latest state-of-the-art programming technologies and paradigms. It is based on an extensible architecture that separates core services from the individual layers of agent behavior, offering a concrete simulation kernel designed for high-performance and stability. Its primary goal is to deliver an abstract platform to facilitate implementation of several Agent-Based Simulation solutions with applicability in several domains of knowledge, such as: (i) Crowd behavior simulation during [in/out] door evacuation. (ii) Non-Player Character AI for Game-oriented applications and Gamification activities. (iii) Vessel traffic modeling and simulation for Maritime Security and Surveillance applications. (iv) Urban and Highway Traffic and Transportation Simulations. (v) Social Behavior Simulation and Modeling.

  9. Probabilistic Catalogs for Crowded Stellar Fields

    CERN Document Server

    Brewer, Brendon J; Hogg, David W

    2012-01-01

    We introduce a probabilistic (Bayesian) method for producing catalogs from images of crowded stellar fields. The method is capable of inferring the number of sources (N) in the image and can also handle the challenges introduced by overlapping sources. The luminosity function of the stars can also be inferred even when the precise luminosity of each star is uncertain. This is in contrast with standard techniques which produce a single catalog, potentially underestimating the uncertainties in any study of the stellar population and discarding information about sources at or below the detection limit. The method is implemented using advanced Markov Chain Monte Carlo (MCMC) techniques including Reversible Jump and Nested Sampling. The computational feasibility of the method is demonstrated on simulated data where the luminosity function of the stars is a broken power-law. The parameters of the luminosity function can be recovered with moderate uncertainties. We compare the results obtained from our method with t...

  10. Crowding of molecular motors determines microtubule depolymerization

    CERN Document Server

    Reese, Louis; Frey, Erwin

    2011-01-01

    Assembly and disassembly dynamics of microtubules (MTs) is tightly controlled by MT associated proteins. Here, we investigate how plus-end-directed depolymerases of the kinesin-8 family regulate MT depolymerization dynamics. Employing an individual-based model, we reproduce experimental findings. Moreover, crowding is identified as the key regulatory mechanism of depolymerization dynamics. Our analysis gives two qualitatively distinct regimes. For motor densities above a particular threshold, a macroscopic traffic jam emerges at the plus-end and the MT dynamics become independent of the motor concentration. Below this threshold, microscopic traffic jams at the tip arise which cancel out the effect of the depolymerization kinetics such that the depolymerization speed is solely determined by the motor density. Because this density changes over the MT length, length-dependent regulation is possible. Remarkably, motor cooperativity does not affect the depolymerization speed but only the end-residence time of depo...

  11. Crowd-Sourced Global Earthquake Early Warning

    Science.gov (United States)

    Minson, S. E.; Brooks, B. A.; Glennie, C. L.; Murray, J. R.; Langbein, J. O.; Owen, S. E.; Iannucci, B. A.; Hauser, D. L.

    2014-12-01

    Although earthquake early warning (EEW) has shown great promise for reducing loss of life and property, it has only been implemented in a few regions due, in part, to the prohibitive cost of building the required dense seismic and geodetic networks. However, many cars and consumer smartphones, tablets, laptops, and similar devices contain low-cost versions of the same sensors used for earthquake monitoring. If a workable EEW system could be implemented based on either crowd-sourced observations from consumer devices or very inexpensive networks of instruments built from consumer-quality sensors, EEW coverage could potentially be expanded worldwide. Controlled tests of several accelerometers and global navigation satellite system (GNSS) receivers typically found in consumer devices show that, while they are significantly noisier than scientific-grade instruments, they are still accurate enough to capture displacements from moderate and large magnitude earthquakes. The accuracy of these sensors varies greatly depending on the type of data collected. Raw coarse acquisition (C/A) code GPS data are relatively noisy. These observations have a surface displacement detection threshold approaching ~1 m and would thus only be useful in large Mw 8+ earthquakes. However, incorporating either satellite-based differential corrections or using a Kalman filter to combine the raw GNSS data with low-cost acceleration data (such as from a smartphone) decreases the noise dramatically. These approaches allow detection thresholds as low as 5 cm, potentially enabling accurate warnings for earthquakes as small as Mw 6.5. Simulated performance tests show that, with data contributed from only a very small fraction of the population, a crowd-sourced EEW system would be capable of warning San Francisco and San Jose of a Mw 7 rupture on California's Hayward fault and could have accurately issued both earthquake and tsunami warnings for the 2011 Mw 9 Tohoku-oki, Japan earthquake.

  12. Gastronomia Molecular: Desconstruindo 20 anos de Uma Tendência

    Directory of Open Access Journals (Sweden)

    Joana Pellerano

    2013-06-01

    Full Text Available A gastronomia molecular gera interesse e controvérsia desde que foi criada, em 1992, nos workshops de Erice, na Itália. Da curiosidade dos cientistas Nicholas Kurti e Hervé This, que desenvolveram a disciplina, à aplicação prática encontrada por chefs de todo o mundo, a gastronomia molecular é perseguida por parecer ser mais complicada do que realmente é: o estudo meticuloso dos alimentos. O objetivo desse artigo é descrever o seu surgimento e o que trouxe ao cenário contemporâneo enquanto tendência gastronômica. Para tanto, foi realizada uma revisão bibliográfica em livros e citações na imprensa estrangeira, o que permitiu descrever os motivos para que essa forma de cozinhar cause tanta polêmica.

  13. Estrutura de mercado e tendências da atividade comercial

    Directory of Open Access Journals (Sweden)

    Jefferson Mariano

    2007-11-01

    Full Text Available O presente artigo busca realizar uma caracterização do setor comercial, com ênfase na RMSP, destacando o processo de concentração, evidenciado principalmente no segmento de hiper e supermercados. Na primeira seção, busca-se ilustrar o processo de concentração em alguns segmentos do comércio varejista, à luz das teorias de estrutura de mercado. Na segunda, apresenta se um painel com o perfil dessa atividade econômica, com informações agregadas para Brasil, Estado de São Paulo e Região Metropolitana de São Paulo. Na terceira, são apontadas as tendências e perspectivas do setor.

  14. Tendências atuais da pesquisa na escola

    Directory of Open Access Journals (Sweden)

    Marli Eliza Dalmazo Afonso de André

    Full Text Available O presente texto procura mostrar que o interesse dos pesquisadores pela etnografia, no final dos anos 70, está relacionado com o estudo das questões de integração na sala de aula e com os novos metodos de avaliação educacional. Em seguida o texto destaca alguns propósitos e contribuições do uso da etnografia em educação e aponta as principais críticas que vem sendo feitas aos estudos que focalizem a vida escolar cotidiana. Na última parte do texto são discutidos os principais dilemas trazidos pelo uso da abordagem etnográfica em educação e a novas tendências para tentar superar esses dilemas.

  15. Tend to Compare and Tend to Be Fair: The Relationship between Social Comparison Sensitivity and Justice Sensitivity.

    Directory of Open Access Journals (Sweden)

    Shanshan Zhen

    Full Text Available Social comparison is a prerequisite for processing fairness, although the two types of cognition may be associated with different emotions. Whereas social comparison may induce envy, the perception of unfairness may elicit anger. Yet, it remains unclear whether people who tend to have a strong sense of fairness also tend to compare themselves more with others. Here, Study 1 used a modified ultimatum game (UG and a social comparison game (SCG to examine the relationship between justice sensitivity and social comparison sensitivity in 51 young adults. Study 2 examined self-reported social comparison and justice sensitivity in 142 young adults. Both studies showed a positive correlation between social comparison sensitivity and justice sensitivity. We reason that social comparison and justice sensitivity have an important positive correlation in human decision-making. The rejection of self-disadvantageous inequality offers may be due to the social comparison effect, which suggests that the tendency to compare oneself with others may contribute to having a strong sense of justice. Our findings suggest that the predictions of game theory may vary depending on the social culture context and incorporating notions of fairness and social comparison tendency may be essential to better predict the actual behavior of players in social interactive situations.

  16. Tend to Compare and Tend to Be Fair: The Relationship between Social Comparison Sensitivity and Justice Sensitivity.

    Science.gov (United States)

    Zhen, Shanshan; Yu, Rongjun

    2016-01-01

    Social comparison is a prerequisite for processing fairness, although the two types of cognition may be associated with different emotions. Whereas social comparison may induce envy, the perception of unfairness may elicit anger. Yet, it remains unclear whether people who tend to have a strong sense of fairness also tend to compare themselves more with others. Here, Study 1 used a modified ultimatum game (UG) and a social comparison game (SCG) to examine the relationship between justice sensitivity and social comparison sensitivity in 51 young adults. Study 2 examined self-reported social comparison and justice sensitivity in 142 young adults. Both studies showed a positive correlation between social comparison sensitivity and justice sensitivity. We reason that social comparison and justice sensitivity have an important positive correlation in human decision-making. The rejection of self-disadvantageous inequality offers may be due to the social comparison effect, which suggests that the tendency to compare oneself with others may contribute to having a strong sense of justice. Our findings suggest that the predictions of game theory may vary depending on the social culture context and incorporating notions of fairness and social comparison tendency may be essential to better predict the actual behavior of players in social interactive situations.

  17. The wisdom of the crowd in funding: : Information heterogeneity and social networks of crowdfunder

    NARCIS (Netherlands)

    Polzin, F.H.J.; Toxopeus, H.S.; Stam, F.C.

    2016-01-01

    Crowdfunding has enabled large crowds to fund innovative projects. This type of funding might tap into the wisdom of crowds who were previously disconnected from the funding process. We distinguish between in-crowd and out-crowd funders (with and without ties to project creators) in order to test fo

  18. Crowding is unlike ordinary masking: distinguishing feature integration from detection.

    Science.gov (United States)

    Pelli, Denis G; Palomares, Melanie; Majaj, Najib J

    2004-12-30

    A letter in the peripheral visual field is much harder to identify in the presence of nearby letters. This is "crowding." Both crowding and ordinary masking are special cases of "masking," which, in general, refers to any effect of a "mask" pattern on the discriminability of a signal. Here we characterize crowding, and propose a diagnostic test to distinguish it from ordinary masking. In ordinary masking, the signal disappears. In crowding, it remains visible, but is ambiguous, jumbled with its neighbors. Masks are usually effective only if they overlap the signal, but the crowding effect extends over a large region. The width of that region is proportional to signal eccentricity from the fovea and independent of signal size, mask size, mask contrast, signal and mask font, and number of masks. At 4 deg eccentricity, the threshold contrast for identification of a 0.32 deg signal letter is elevated (up to six-fold) by mask letters anywhere in a 2.3 deg region, 7 times wider than the signal. In ordinary masking, threshold contrast rises as a power function of mask contrast, with a shallow log-log slope of 0.5 to 1, whereas, in crowding, threshold is a sigmoidal function of mask contrast, with a steep log-log slope of 2 at close spacing. Most remarkably, although the threshold elevation decreases exponentially with spacing, the threshold and saturation contrasts of crowding are independent of spacing. Finally, ordinary masking is similar for detection and identification, but crowding occurs only for identification, not detection. More precisely, crowding occurs only in tasks that cannot be done based on a single detection by coarsely coded feature detectors. These results (and observers' introspections) suggest that ordinary masking blocks feature detection, so the signal disappears, while crowding (like "illusory conjunction") is excessive feature integration - detected features are integrated over an inappropriately large area because there are no smaller integration

  19. Household crowding and psychosocial health among Inuit in Greenland

    DEFF Research Database (Denmark)

    Riva, Mylène; Larsen, Christina Viskum Lytken; Bjerregaard, Peter

    2014-01-01

    using logistic regression models, adjusting for individuals' characteristics. RESULTS: Household crowding was associated with poorer mental well-being. Binge drinking was more common among people living in households without children. These effects were more important for women than for men....... The association between household crowding and mental well-being was significantly mediated by social support. This suggests that having a strong social network may buffer the deleterious impacts of household crowding. CONCLUSIONS: Targeting housing conditions and fostering social support as part of population...

  20. CROWDING AND SHOPPING VALUE IN LOW-INCOME RETAIL CENTERS

    Directory of Open Access Journals (Sweden)

    Izabelle Quezado

    2014-07-01

    Full Text Available Considering the great potential of low-income consumption, this research is based on the scales developed by Babin, Darden and Griffin (1994 and by Machleit, Kellaris and Eroglu (1994, aiming to investigate hedonic and utilitarian consumer behavior and its relation with low-income perception of crowding. A research was performed with 404 consumers in real store environment and the results showed that consumers revealed being prone to utilitarian behavior in both centers. About crowding phenomenon, the consumers felt more uncomfortable by crowding at the commercial center with less infrastructure. There were indices that this discomfort was less intense in hedonic consumers.

  1. "Crowd-out": what it means for children's health insurance.

    Science.gov (United States)

    1998-06-01

    As states finalize proposals for the federal Title XXI Children's Health Insurance Program (CHIP), consumers, advocates, legislators, and policymakers across the country are facing the issue of "crowd-out." How can they prevent CHIP's new public funds from "crowding out"--or supplanting--private funds now used to insure children? This issue of States of Health looks at research on crowd-out and reviews what some states have learned as a result of previous Medicaid expansions. Their experiences shed light on the challenge of making sure that Title XXI health care dollars reach the intended consumers, children who lack adequate insurance.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-07-01

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

  3. Tendências em medicina laboratorial Trends in laboratory medicine

    Directory of Open Access Journals (Sweden)

    Gustavo Aguiar Campana

    2011-08-01

    Full Text Available A patologia clínica/medicina laboratorial é uma especialidade direcionada à realização de exames complementares no auxílio ao diagnóstico, com impacto nos diferentes estágios da cadeia de saúde: prevenção, diagnóstico, prognóstico e acompanhamento terapêutico. Diversos elementos apontam para maior utilização da medicina diagnóstica no futuro. Para discutirmos as principais tendências na medicina laboratorial, descrevemos os fatores que colaboram e são fundamentais para o crescimento desse mercado denominados, neste estudo, drivers de crescimento. As principais tendências que terão forte impacto na medicina laboratorial, e que serão descritas neste artigo, são: ferramentas de gestão, inserção de novos testes no mercado e rol de procedimentos, qualidade dos serviços em medicina diagnóstica, modelos de operação, automação, consolidação e integração, tecnologia da informação, medicina personalizada e genética. Sabemos que a medicina diagnóstica demonstra sua importância ao participar de 70% das decisões clínicas, absorvendo uma pequena parte dos custos em saúde (cerca de 10%. Todas as tendências analisadas neste trabalho apontam para um crescimento na utilização dos exames laboratoriais e também para sua importância na cadeia de saúde. Esse novo posicionamento, somado às novas expectativas de alta resolubilidade, pressiona o mercado e as companhias que o compõem a buscar mudanças e novas estratégias de atuação.Clinical pathology/laboratory medicine, a specialty focused on performing complementary tests to aid diagnosis, has impact upon several stages of health care: prevention, diagnosis, prognosis, and therapeutic management. There are several factors that will foster the use of laboratory medicine in the future. In order to discuss the main trends in laboratory medicine, this article describes the major factors that have promoted growth in this market, which herein are referred to as growth

  4. Contemporary understanding of riots: classical crowd psychology, ideology and the social identity approach

    OpenAIRE

    Stott, CJT

    2016-01-01

    This article explores the origins and ideology of classical crowd psychology, a body of theory reflected in contemporary popularised understandings such as of the 2011 English ‘riots’. This article argues that during the nineteenth century, the crowd came to symbolise a fear of ‘mass society’ and that ‘classical’ crowd psychology was a product of these fears. Classical crowd psychology pathologised, reified and decontextualised the crowd, offering the ruling elites a perceived opportunity to ...

  5. [The condition of crowding and spacing. Measuring or estimation?].

    Science.gov (United States)

    Reukers, H A; Kuijpers-Jagtman, A M; van 't Hof, M A

    1994-10-01

    Two methods for the assessment of the amount of crowding or spacing (measuring and assessment by eye) are compared. Both methods are well comparable and reproducible. Assessment by eye has the practical advantage that it takes considerable less time.

  6. Attention-dependent early cortical suppression contributes to crowding.

    Science.gov (United States)

    Chen, Juan; He, Yingchen; Zhu, Ziyun; Zhou, Tiangang; Peng, Yujia; Zhang, Xilin; Fang, Fang

    2014-08-01

    Crowding, the identification difficulty for a target in the presence of nearby flankers, is ubiquitous in spatial vision and is considered a bottleneck of object recognition and visual awareness. Despite its significance, the neural mechanisms of crowding are still unclear. Here, we performed event-related potential and fMRI experiments to measure the cortical interaction between the target and flankers in human subjects. We found that the magnitude of the crowding effect was closely associated with an early suppressive cortical interaction. The cortical suppression was reflected in the earliest event-related potential component (C1), which originated in V1, and in the BOLD signal in V1, but not other higher cortical areas. Intriguingly, spatial attention played a critical role in the manifestation of the suppression. These findings provide direct and converging evidence that attention-dependent V1 suppression contributes to crowding at a very early stage of visual processing.

  7. State Variability in Childrens Medicaid Crowd-Out Estimates

    Data.gov (United States)

    U.S. Department of Health & Human Services — Health insurance crowd-out occurs when individuals enrolled in a public health insurance plan would have enrolled in a private plan but for the public option. The...

  8. Robot-Assisted Crowd Evacuation under Emergency Situations: A Survey

    Directory of Open Access Journals (Sweden)

    Ibraheem Sakour

    2017-04-01

    Full Text Available In the case of emergency situations, robotic systems can play a key role and save human lives in recovery and evacuation operations. To realize such a potential, we have to address many scientific and technical challenges encountered during robotic search and rescue missions. This paper reviews current state-of-the-art robotic technologies that have been deployed in the simulation of crowd evacuation, including both macroscopic and microscopic models used in simulating a crowd. Existing work on crowd simulation is analyzed and the robots used in crowd evacuation are introduced. Finally, the paper demonstrates how autonomous robots could be effectively deployed in disaster evacuation, as well as search and rescue missions.

  9. Diffusion in crowded biological environments: applications of Brownian dynamics

    Directory of Open Access Journals (Sweden)

    Długosz Maciej

    2011-03-01

    Full Text Available Abstract Biochemical reactions in living systems occur in complex, heterogeneous media with total concentrations of macromolecules in the range of 50 - 400 mgml. Molecular species occupy a significant fraction of the immersing medium, up to 40% of volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between macromolecules may hinder diffusion - a major process determining metabolism, transport, and signaling. Also, the crowded media can alter, both qualitatively and quantitatively, the reactions in vivo in comparison with their in vitro counterparts. This review focuses on recent developments in particle-based Brownian dynamics algorithms, their applications to model diffusive transport in crowded systems, and their abilities to reproduce and predict the behavior of macromolecules under in vivo conditions.

  10. Crowding-induced Cooperativity in DNA Surface Hybridization

    Science.gov (United States)

    Lei, Qun-li; Ren, Chun-lai; Su, Xiao-hang; Ma, Yu-qiang

    2015-01-01

    High density DNA brush is not only used to model cellular crowding, but also has a wide application in DNA-functionalized materials. Experiments have shown complicated cooperative hybridization/melting phenomena in these systems, raising the question that how molecular crowding influences DNA hybridization. In this work, a theoretical modeling including all possible inter and intramolecular interactions, as well as molecular details for different species, is proposed. We find that molecular crowding can lead to two distinct cooperative behaviours: negatively cooperative hybridization marked by a broader transition width, and positively cooperative hybridization with a sharper transition, well reconciling the experimental findings. Moreover, a phase transition as a result of positive cooperativity is also found. Our study provides new insights in crowding and compartmentation in cell, and has the potential value in controlling surface morphologies of DNA functionalized nano-particles. PMID:25875056

  11. Designing interactive technology for crowd experiences - beyond sanitization

    DEFF Research Database (Denmark)

    Veerasawmy, Rune

    2014-01-01

    experience within interaction design. This dissertation introduces an understanding of crowd experience as a distinct type of social experiences driven by non-rational behavior. This conceptual understanding is established in the intersection between sociological crowd theory and a pragmatist perspective...... sanitization. The domain of my experimental design inquiries is at sporting events. From extensive theoretical studies and my empirical explorations I present a perspective on modern and professionalized sporting events as sanitized, where the spectator experiences and technology are being produced, controlled......This dissertation concerns the topic on designing interactive technology for crowd expe- riences. It takes the outset in the experience-oriented design approach within interaction design, exploring the research question how can we conceptually understand and design interactive technology for crowd...

  12. A Survey of Crowd Sensing Opportunistic Signals for Indoor Localization

    Directory of Open Access Journals (Sweden)

    Ling Pei

    2016-01-01

    Full Text Available Sensor-rich smartphone enables a novel approach to training the fingerprint database for mobile indoor localization via crowd sensing. In this survey, we discuss the crowd sensing based mobile indoor localization in terms of foundational knowledge, signals of fingerprints, trajectory of obtaining fingerprints, indoor maps, evolution of a fingerprint database, positioning algorithms, state-of-the-art solutions, and challenges. The survey concludes that the crowd sensing is a low cost solution of generating and updating an organic fingerprint database. Although the crowd sensing concept is widely accepted by the academic community in these years, there are a lot of unsolved problems which hinder the concept of transferring into a practical system. We address the challenges and predict future trends in the end.

  13. The simulation and analysis of pedestrian crowd and behavior

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Pedestrian crowd in public buildings is usually a hidden trouble.The more serious the crowd,the higher the accident risk,and the heavier the casualties and loss may be.Based on the social force model,this paper puts forward an improved model which takes into account the anisotropic charac-teristic of pedestrian movement and the avoidance of dynamic congested areas.Furthermore,the al-gorithm has been optimized with the help of static force grid,so the simulation becomes more veritable and computational speed is also greatly accelerated.The improved model is also applied to research on the characters of pedestrian crowd,and the conclusion can provide a basis for the risk assessment of pedestrian crowd and the design of public buildings.

  14. The simulation and analysis of pedestrian crowd and behavior

    Institute of Scientific and Technical Information of China (English)

    HU QingMei; FANG WeiNing; JIA YuQuan; DENG Ye

    2009-01-01

    Pedestrian crowd in public buildings is usually a hidden trouble. The more serious the crowd, the higher the accident risk, and the heavier the casualties and loss may be. Based on the social force model, this paper puts forward an improved model which takes into account the anisotropic charac-teristic of pedestrian movement and the avoidance of dynamic congested areas. Furthermore, the al-gorithm has been optimized with the help of static force grid, so the simulation becomes more veritable and computational speed is also greatly accelerated. The improved model is also applied to research on the characters of pedestrian crowd, and the conclusion can provide a basis for the risk assessment of pedestrian crowd and the design of public buildings.

  15. Mingo National Wildlife Refuge : Station Crowd Control Plan

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This Crowd Control Plan for Mingo NWR outlines operational procedures in the event of a civil disorder on the Refuge. An inventory of resources is provided, along...

  16. Evaluation of working conditions of workers engaged in tending horses

    Directory of Open Access Journals (Sweden)

    Bożena Nowakowicz-Dębek

    2014-11-01

    Full Text Available [b]introduction[/b]. A growing interest in the horse business has resulted in the increased engagement of many people in this area, and the health problems occurring among workers create the need to search for prophylactic measures. [b]objective[/b]. The objective of the study was evaluation of the level of exposure to air pollution in a stable, and estimation of the degree of work load among workers engaged in tending horses. [b]material and methods[/b]. The study was conducted twice, during the winter season, in a stable maintaining race horses, and in a social room. In order to evaluate workers’ exposure, air samples were collected by the aspiration method. After the incubation of material, the total number of bacteria and fungi in the air was determined, as well as the number of aerobic mesophilic and thermophilic bacteria, expressed as the number of colony forming units per cubic meter of air (CFU/m[sup]3[/sup]. The measurement of total dust concentration in the air was also performed, simultaneously with the measurement of microclimatic parameters. The study of work load also covered the measurement of energy expenditure, evaluation of static physical load, and monotony of movements performed. [b]conclusions[/b]. The stable may be considered as a workplace with considerable risk of the occurrence of unfavourable health effects.

  17. Funding Agencies Rarely Tend to Risk Their Money

    Science.gov (United States)

    Rapisarda, Andrea

    Complexity science is for sure a challenging interdisciplinary field of research which will provide new useful perspectives and novel tools for a more efficient participatory society in the next years. Groundbreaking discoveries and innovation are the results of the interplay of many different factors which emerge in a nonlinear and often unpredictable complex way from the fruitful bottom-up mixing of different disciplines. This fact, however, although advocated by many, is unfortunately very rarely fostered and put in practice. Nowadays, funding agencies, often forgetting that research means working at the edge of human knowledge and can be also unsuccessful, rarely tend to risk their money in unconventional proposals regarding complexity. They are more inclined to support scientists, projects, and ideas that have a well settled successful past and operate within well established and more conventional fields of research. This is certainly not a good policy for promoting innovative results. As stigmatized in a recent editorial by Nature (Take more risk, 528, 8/2015), such policies stimulate a conservative and not very efficient behavior, which discourage young scientists and force them to a scientific conformism. The same happens for careers. Today it is not easy for a scientist in complex systems to get a permanent job...

  18. Characterizing Crowd Participation and Productivity of Foldit Through Web Scraping

    Science.gov (United States)

    2016-03-01

    primarily with statically generated goals, items, puzzles, quests, and other game-related material. Interaction with other players is at a minimum...CROWD PARTICIPATION AND PRODUCTIVITY OF FOLDIT THROUGH WEB SCRAPING by Jonathan A. Yee March 2016 Thesis Advisor: Geoffrey Xie Second...AND DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE CHARACTERIZING CROWD PARTICIPATION AND PRODUCTIVITY OF FOLDIT THROUGH WEB SCRAPING 5

  19. Bringing macromolecular machinery to life using 3D animation.

    Science.gov (United States)

    Iwasa, Janet H

    2015-04-01

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

  20. BLOOD FLOW AND MACROMOLECULAR TRANSPORT IN CURVED BLOOD VESSELS

    Institute of Scientific and Technical Information of China (English)

    WEI Lan; WEN Gong-bi; TAN Wen-chang

    2006-01-01

    A numerical analysis of the steady/pulsatile flow and macromolecular (such as LDL and Albumin) transport in curved blood vessels was carried out. The computational results predict that the vortex of the secondary flow is time-dependent in the aortic arch.The concentration of macromolecule concentrates at the region of sharp curve, and the wall concentration at the outer part is higher than that at the inner part. Atherosclerosis and thrombosis are prone to develop in such regions with sharp flow.

  1. Country-level entrepreneurship: Crowding out the population’s need for autonomy

    Directory of Open Access Journals (Sweden)

    Colin D. Reddy

    2015-02-01

    Full Text Available Purpose and problem: Governments through their policy support of new and growing enterprises continue to emphasise economic incentives as if most members of the population prioritise material gain. This article argues that high levels of government policy support for new and growing enterprises crowd out the population’s need for autonomy when potential entrepreneurs perceive government to be controlling.Methodology: The researchers constructed a country-level panel data set based on the Global Entrepreneurship Monitor, World Bank Group Entrepreneurship Survey, the World Economic Forum competitiveness reports and the International Monetary Fund data base for 44 countries over the period 2000 to 2007. Since we relied on eight years of secondary data, we applied panel analysis to the regressions. We used multiple regression to model the moderating effects of government policy support on the autonomy-entrepreneurship relationship.Findings: The findings show that government policy support tends to buffer the effect of autonomy on entrepreneurship, lending support to the article’s argument.Implications: This research has tested one of the most important anomalies in economics on entrepreneurship data: that ‘crowding out’ might reverse the most fundamental economic law, namely that raising economic incentives increases the supply of entrepreneurship.

  2. Does Temporal Integration Occur for Unrecognizable Words in Visual Crowding?

    Science.gov (United States)

    Zhou, Jifan; Lee, Chia-Lin; Li, Kuei-An; Tien, Yung-Hsuan; Yeh, Su-Ling

    2016-01-01

    Visual crowding-the inability to see an object when it is surrounded by flankers in the periphery-does not block semantic activation: unrecognizable words due to visual crowding still generated robust semantic priming in subsequent lexical decision tasks. Based on the previous finding, the current study further explored whether unrecognizable crowded words can be temporally integrated into a phrase. By showing one word at a time, we presented Chinese four-word idioms with either a congruent or incongruent ending word in order to examine whether the three preceding crowded words can be temporally integrated to form a semantic context so as to affect the processing of the ending word. Results from both behavioral (Experiment 1) and Event-Related Potential (Experiment 2 and 3) measures showed congruency effect in only the non-crowded condition, which does not support the existence of unconscious multi-word integration. Aside from four-word idioms, we also found that two-word (modifier + adjective combination) integration-the simplest kind of temporal semantic integration-did not occur in visual crowding (Experiment 4). Our findings suggest that integration of temporally separated words might require conscious awareness, at least under the timing conditions tested in the current study.

  3. The effect of motion on crowding: zooming text.

    Science.gov (United States)

    Husk, Jesse S; Yu, Deyue

    2015-01-14

    Crowding is the major sensory factor responsible for the slow reading speeds exhibited in peripheral vision. Past attempts to improve peripheral reading via crowding reduction have generally focused on applying spatial changes to the stimulus and have been largely ineffective. Recent evidence indicates that dynamic approaches have good potential for reducing crowding in peripheral reading. We tested this hypothesis by introducing "zooming" motion (smooth letter resizing across the presentation duration) to trigram stimuli (groups of three randomly selected letters) presented at 10° in the lower visual field and evaluating recognition of the middle letter. Crowding was alleviated in the presence of this motion, both when dynamic cues were introduced to all letters in the trigram simultaneously and when they were applied to individual letters alone. The magnitude and direction of crowding reduction depended on the amplitude and direction of motion. These results suggest that dynamic presentation may be a useful tool for improving peripheral reading through reducing letter crowding. Zooming motion, in particular, has the additional advantage of conserving text layout, making it a good candidate for such an application.

  4. L0 Regularized Stationary-time Estimation for Crowd Analysis.

    Science.gov (United States)

    Yi, Shuai; Wang, Xiaogang; Lu, Cewu; Jia, Jiaya; Li, Hongsheng

    2016-04-29

    In this paper, we tackle the problem of stationary crowd analysis which is as important as modeling mobile groups in crowd scenes and finds many important applications in crowd surveillance. Our key contribution is to propose a robust algorithm for estimating how long a foreground pixel becomes stationary. It is much more challenging than only subtracting background because failure at a single frame due to local movement of objects, lighting variation, and occlusion could lead to large errors on stationary-time estimation. To achieve robust and accurate estimation, sparse constraints along spatial and temporal dimensions are jointly added by mixed partials (which are second-order gradients) to shape a 3D stationary-time map. It is formulated as an L0 optimization problem. Besides background subtraction, it distinguishes among different foreground objects, which are close or overlapped in the spatio-temporal space by using a locally shared foreground codebook. The proposed technologies are further demonstrated through three applications. 1) Based on the results of stationary-time estimation, twelve descriptors are proposed to detect four types of stationary crowd activities. 2) The averaged stationary-time map is estimated to analyze crowd scene structures. 3) The result of stationary-time estimation is also used to study the influence of stationary crowd groups to traffic patterns.

  5. A comparison of 15 year old children with excellent occlusion and with crowding of the teeth, Angle Class I malocclusion, in respect of face size and shape and tooth size.

    Science.gov (United States)

    Adams, C P

    1982-01-01

    The biological conflict that manifests itself in crowding of the teeth in man has fascinated orthodontists for generations. Correlations between tooth size and tooth arrangement can be shown, but such correlations tend to leave much unexplained in practical terms. The present report presents data from a preliminary examination of face size and shape and tooth size in boys and girls of 15-16 years, of which 47 had excellently arranged teeth and 91 showed crowding. Measurements were taken from lateral and posteroanterior cephalometric X-ray films and from dental casts. The statistical test used was the standard student t-test. Girls' faces were found to be on average significantly smaller than boys' whether the teeth were well arranged or were crowded. The comparisons of face size and shape of boys and girls with well arranged teeth with the faces of those with crowded teeth was less definite in its outcome. Girls' total tooth substance was on average significantly smaller than boys' whether the teeth were well arranged or crowded. Boys and girls with crowded teeth had a larger mean total tooth size than boys and girls with well arranged teeth.

  6. Crowded letter and crowded picture logMAR acuity in children with amblyopia: a quantitative comparison.

    Science.gov (United States)

    O'Boyle, Cathy; Chen, Sean I; Little, Julie-Anne

    2017-04-01

    Clinically, picture acuity tests are thought to overestimate visual acuity (VA) compared with letter tests, but this has not been systematically investigated in children with amblyopia. This study compared VA measurements with the LogMAR Crowded Kay Picture test to the LogMAR Crowded Keeler Letter acuity test in a group of young children with amblyopia. 58 children (34 male) with amblyopia (22 anisometropic, 18 strabismic and 18 with both strabismic/anisometropic amblyopia) aged 4-6 years (mean=68.7, range=48-83 months) underwent VA measurements. VA chart testing order was randomised, but the amblyopic eye was tested before the fellow eye. All participants wore up-to-date refractive correction. The Kay Picture test significantly overestimated VA by 0.098 logMAR (95% limits of agreement (LOA), 0.13) in the amblyopic eye and 0.088 logMAR (95% LOA, 0.13) in the fellow eye, respectively (pamblyopia on VA results (p>0.23). For both the amblyopic and fellow eyes, Bland-Altman plots demonstrated a systematic and predictable difference between Kay Picture and Keeler Letter charts across the range of acuities tested (Keeler acuity: amblyopic eye 0.75 to -0.05 logMAR; fellow eye 0.45 to -0.15 logMAR). Linear regression analysis (pamblyopia. Due to the predictable difference found between both crowded logMAR acuity tests, it is reasonable to adjust Kay Picture acuity thresholds by +0.10 logMAR to compute expected Keeler Letter acuity scores. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  7. CrowdMag - Crowdsourcing magnetic data

    Science.gov (United States)

    Nair, M. C.; Boneh, N.; Chulliat, A.

    2014-12-01

    In the CrowdMag project, we explore whether digital magnetometers built in modern mobile phones can be used as scientific instruments to measure Earth's magnetic field. Most modern mobile phones have digital magnetometers to orient themselves. A phone's magnetometer measures three components of the local magnetic field with a typical sensitivity of about 150 to 600 nanotesla (nT). By combining data from vector magnetometers and accelerometers, phone's orientation is determined. Using phone's Internet connection, magnetic data and location are sent to a central server. At the server, we check quality of the magnetic data from all users and make the data available to the public as aggregate maps. We have two long-term goals. 1) Develop near-real-time models of Earth's time changing magnetic field by reducing man-made noise from crowdsourced data and combining it with geomagnetic data from other sources. 2) Improving accuracy of magnetic navigation by mapping magnetic noise sources (for e.g. power transformer and iron pipes). Key challenges to this endeavor are the low sensitivity of the phone's magnetometer and the noisy environment within and surrounding the phone. URL : http://www.ngdc.noaa.gov/geomag/crowdmag.shtml

  8. Crowding: a cortical constraint on object recognition.

    Science.gov (United States)

    Pelli, Denis G

    2008-08-01

    The external world is mapped retinotopically onto the primary visual cortex (V1). We show here that objects in the world, unless they are very dissimilar, can be recognized only if they are sufficiently separated in visual cortex: specifically, in V1, at least 6mm apart in the radial direction (increasing eccentricity) or 1mm apart in the circumferential direction (equal eccentricity). Objects closer together than this critical spacing are perceived as an unidentifiable jumble. This is called 'crowding'. It severely limits visual processing, including speed of reading and searching. The conclusion about visual cortex rests on three findings. First, psychophysically, the necessary 'critical' spacing, in the visual field, is proportional to (roughly half) the eccentricity of the objects. Second, the critical spacing is independent of the size and kind of object. Third, anatomically, the representation of the visual field on the cortical surface is such that the position in V1 (and several other areas) is the logarithm of eccentricity in the visual field. Furthermore, we show that much of this can be accounted for by supposing that each 'combining field', defined by the critical spacing measurements, is implemented by a fixed number of cortical neurons.

  9. Bottleneck effects on the bidirectional crowd dynamics

    Science.gov (United States)

    Yang, Xiao-Xia; Dong, Hai-Rong; Yao, Xiu-Ming; Sun, Xu-Bin

    2016-12-01

    The bottleneck effect on bidirectional crowd dynamics is of great theoretical and practical significance, especially for the designing of corridors in public places, such as subway stations or airports. Based on the famous social force model, this paper investigates the bottleneck effects on the free flow dynamics and breakdown phenomenon under different scenarios, in which different corridor shapes and inflow ratios are considered simultaneously. Numerical simulation finds an interesting self-organization phenomenon in the bidirectional flow, a typical characteristic of such a phenomenon is called lane formation, and the existence of which is independent of the corridor’s shape and inflow rate. However, the pattern of the lane formed by pedestrian flow is related to the corridor’s shape, and the free flow efficiency has close relationship with the inflow rate. Specifically, breakdown phenomenon occurs when inflows from both sides of the corridor are large enough, which mostly originates from the bottleneck and then gradually spreads to the other regions. Simulation results further indicate that the leaving efficiency becomes low as breakdown occurs, and the degree of congestion is proportional to the magnitude of inflow. The findings presented in this paper match well with some of our daily observations, hence it is possible to use them to provide us with theoretical suggestions in design of infrastructures. Project supported jointly by the National Natural Science Foundation of China (Grant Nos. 61322307 and 2016YJS023).

  10. Active Particles in Complex and Crowded Environments

    Science.gov (United States)

    Bechinger, Clemens; Di Leonardo, Roberto; Löwen, Hartmut; Reichhardt, Charles; Volpe, Giorgio; Volpe, Giovanni

    2016-10-01

    Differently from passive Brownian particles, active particles, also known as self-propelled Brownian particles or microswimmers and nanoswimmers, are capable of taking up energy from their environment and converting it into directed motion. Because of this constant flow of energy, their behavior can be explained and understood only within the framework of nonequilibrium physics. In the biological realm, many cells perform directed motion, for example, as a way to browse for nutrients or to avoid toxins. Inspired by these motile microorganisms, researchers have been developing artificial particles that feature similar swimming behaviors based on different mechanisms. These man-made micromachines and nanomachines hold a great potential as autonomous agents for health care, sustainability, and security applications. With a focus on the basic physical features of the interactions of self-propelled Brownian particles with a crowded and complex environment, this comprehensive review will provide a guided tour through its basic principles, the development of artificial self-propelling microparticles and nanoparticles, and their application to the study of nonequilibrium phenomena, as well as the open challenges that the field is currently facing.

  11. Identifying and visualizing macromolecular flexibility in structural biology

    Directory of Open Access Journals (Sweden)

    Martina Palamini

    2016-09-01

    Full Text Available Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes.

  12. Enzymes as Green Catalysts for Precision Macromolecular Synthesis.

    Science.gov (United States)

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

    2016-02-24

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

  13. Critical review and perspective of macromolecularly imprinted polymers.

    Science.gov (United States)

    Kryscio, David R; Peppas, Nicholas A

    2012-02-01

    Molecular recognition is a fundamental and ubiquitous process that is the driving force behind life. Natural recognition elements - including antibodies, enzymes, nucleic acids, and cells - exploit non-covalent interactions to bind to their targets with exceptionally strong affinities. Due to this unparalleled proficiency, scientists have long sought to mimic natural recognition pathways. One promising approach is molecularly imprinted polymers (MIPs), which are fully synthetic systems formed via the crosslinking of organic polymers in the presence of a template molecule, which results in stereo-specific binding sites for this analyte of interest. Macromolecularly imprinted polymers, those synthesized in the presence of macromolecule templates (>1500 Da), are of particular importance because they open up the field for a whole new set of robust diagnostic tools. Although the specific recognition of small-molecular-weight analytes is now considered routine, extension of these efficacious procedures to the protein regime has, thus far, proved challenging. This paper reviews the main approaches employed, highlights studies of interest with an emphasis on recent work, and offers suggestions for future success in the field of macromolecularly imprinted polymers.

  14. The macromolecular crystallography facility at the advanced light source

    Science.gov (United States)

    Earnest, Thomas; Padmore, Howard; Cork, Carl; Behrsing, Rolf; Kim, Sung-Hou

    1996-10-01

    Synchrotron radiation offers several advantages over the use of rotating anode sources for biological crystallography, which allow for the collection of higher-resolution data, substantially more rapid data collection, phasing by multiwavelength anomalous diffraction (MAD) techniques, and time-resolved experiments using polychromatic radiation (Laue diffraction). The use of synchrotron radiation is often necessary to record useful data from crystals which diffract weakly or have very large unit cells. The high brightness and stability characteristics of the advanced light source (ALS) at Lawrence Berkeley National Laboratory, along with the low emittance and long straight sections to accommodate insertion devices present in third generation synchrotrons like the ALS, lead to several advantages in the field of macromolecular crystallography. We are presently constructing a macromolecular crystallography facility at the ALS which is optimized for user-friendliness and high-throughput data collection, with advanced capabilities for MAD and Laue experiments. The X-rays will be directed to three branchlines. A well-equipped support lab will be available for biochemistry, crystal mounting and sample storage, as well as computer hardware and software available, along with staff support, allowing for the complete processing of data on site.

  15. MMDB and VAST+: tracking structural similarities between macromolecular complexes.

    Science.gov (United States)

    Madej, Thomas; Lanczycki, Christopher J; Zhang, Dachuan; Thiessen, Paul A; Geer, Renata C; Marchler-Bauer, Aron; Bryant, Stephen H

    2014-01-01

    The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI's Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI's Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi.nlm.nih.gov/Structure.

  16. PRIGo: a new multi-axis goniometer for macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-09

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

  17. Enhancing Endosomal Escape for Intracellular Delivery of Macromolecular Biologic Therapeutics.

    Science.gov (United States)

    Lönn, Peter; Kacsinta, Apollo D; Cui, Xian-Shu; Hamil, Alexander S; Kaulich, Manuel; Gogoi, Khirud; Dowdy, Steven F

    2016-09-08

    Bioactive macromolecular peptides and oligonucleotides have significant therapeutic potential. However, due to their size, they have no ability to enter the cytoplasm of cells. Peptide/Protein transduction domains (PTDs), also called cell-penetrating peptides (CPPs), can promote uptake of macromolecules via endocytosis. However, overcoming the rate-limiting step of endosomal escape into the cytoplasm remains a major challenge. Hydrophobic amino acid R groups are known to play a vital role in viral escape from endosomes. Here we utilize a real-time, quantitative live cell split-GFP fluorescence complementation phenotypic assay to systematically analyze and optimize a series of synthetic endosomal escape domains (EEDs). By conjugating EEDs to a TAT-PTD/CPP spilt-GFP peptide complementation assay, we were able to quantitatively measure endosomal escape into the cytoplasm of live cells via restoration of GFP fluorescence by intracellular molecular complementation. We found that EEDs containing two aromatic indole rings or one indole ring and two aromatic phenyl groups at a fixed distance of six polyethylene glycol (PEG) units from the TAT-PTD-cargo significantly enhanced cytoplasmic delivery in the absence of cytotoxicity. EEDs address the critical rate-limiting step of endosomal escape in delivery of macromolecular biologic peptide, protein and siRNA therapeutics into cells.

  18. Eyes on crowding: crowding is preserved when responding by eye and similarly affects identity and position accuracy.

    Science.gov (United States)

    Yildirim, Funda; Meyer, Vincent; Cornelissen, Frans W

    2015-02-16

    Peripheral vision guides recognition and selection of targets for eye movements. Crowding—a decline in recognition performance that occurs when a potential target is surrounded by other, similar, objects—influences peripheral object recognition. A recent model study suggests that crowding may be due to increased uncertainty about both the identity and the location of peripheral target objects, but very few studies have assessed these properties in tandem. Eye tracking can integrally provide information on both the perceived identity and the position of a target and therefore could become an important approach in crowding studies. However, recent reports suggest that around the moment of saccade preparation crowding may be significantly modified. If these effects were to generalize to regular crowding tasks, it would complicate the interpretation of results obtained with eye tracking and the comparison to results obtained using manual responses. For this reason, we first assessed whether the manner by which participants responded—manually or by eye—affected their performance. We found that neither recognition performance nor response time was affected by the response type. Hence, we conclude that crowding magnitude was preserved when observers responded by eye. In our main experiment, observers made eye movements to the location of a tilted Gabor target while we varied flanker tilt to manipulate target-flanker similarity. The results indicate that this similarly affected the accuracy of peripheral recognition and saccadic target localization. Our results inform about the importance of both location and identity uncertainty in crowding.

  19. Aprendizagem e tecnologias: Tendências e desafios

    Directory of Open Access Journals (Sweden)

    Isolina Oliveira

    2015-11-01

    Full Text Available Digital technologies are designed to lead to learning and, in this sense, are increasingly adopted; however, its incorporation into daily practice and teaching-learning processes does not follow as quickly as one would expect. In turn, there seems to be a growing movement for investing more in the use of technologies than in encouraging change practices of teachers. This article intends to contribute to debate about challenges related to the use of digital technologies in people's lives and their relationship to new ways of learning. Analyzes trends in education, based on empirical evidence, emphasizing the use of digital technologies and seeks to situate them in the field of dialogical perspectives. These assume the dialogue as central concept in learning and research on practices and interactions in the new learning scenarios. As tecnologias digitais são projetadas como propiciadoras de aprendizagem e, neste sentido, são cada vez mais adotadas; no entanto, a sua incorporação nas práticas diárias e nos processos de ensino-aprendizagem não decorre tão rapidamente como se esperaria. Por sua vez, parece haver um movimento crescente no sentido de perspectivar o futuro para a aprendizagem investindo mais no uso das tecnologias do que no incentivo à mudança de práticas dos professores. Este artigo pretende contribuir para o debate em torno dos desafios suscitados com a naturalização das tecnologias digitais na vida das pessoas e sua relação com novos modos de aprender. Analisa tendências em educação, baseadas em evidências empíricas, enfatizando o uso das tecnologias digitais e procura situá-las no campo das perspectivas dialógicas que assumem o conceito de diálogo como central na aprendizagem e na investigação sobre práticas e interações nos novos cenários de aprendizagem.

  20. From Mindless Masses to Small Groups: Conceptualizing Collective Behavior in Crowd Modeling.

    Science.gov (United States)

    Templeton, Anne; Drury, John; Philippides, Andrew

    2015-09-01

    Computer simulations are increasingly used to monitor and predict behavior at large crowd events, such as mass gatherings, festivals and evacuations. We critically examine the crowd modeling literature and call for future simulations of crowd behavior to be based more closely on findings from current social psychological research. A systematic review was conducted on the crowd modeling literature (N = 140 articles) to identify the assumptions about crowd behavior that modelers use in their simulations. Articles were coded according to the way in which crowd structure was modeled. It was found that 2 broad types are used: mass approaches and small group approaches. However, neither the mass nor the small group approaches can accurately simulate the large collective behavior that has been found in extensive empirical research on crowd events. We argue that to model crowd behavior realistically, simulations must use methods which allow crowd members to identify with each other, as suggested by self-categorization theory.

  1. The allocation of attention and working memory in visual crowding.

    Science.gov (United States)

    Bacigalupo, Felix; Luck, Steven J

    2015-06-01

    When the distance between a visual target and nearby flankers falls below a critical distance, target discrimination declines precipitously. This is called "crowding." Many researchers have proposed that selective attention plays a role in crowding. However, although some research has examined the effects of directing attention toward versus away from the targets, no previous research has assessed how attentional allocation varies as a function of target-flanker distance in crowding. Here, we used ERPs to assess the operation of attention during crowding, focusing on the attention-related N2pc component. We used a typical crowding task in which participants were asked to report the category (vowel/consonant) of a lateralized target letter flanked by distractor letters at different distances. We tested the hypothesis that attention fails when the target-flanker distance becomes too small for attention to operate effectively. Consistent with this hypothesis, we found that N2pc amplitude was maximal at intermediate target-flanker distances and decreased substantially when crowding became severe. In addition, we examined the sustained posterior contralateral negativity (SPCN), which reflects the amount of information being maintained in working memory. Unlike the N2pc component, the SPCN increased in amplitude at small target-flanker distances, suggesting that observers stored information about the target and flankers in working memory when attention failed to select the target. Together, the N2pc and SPCN results suggest that attention and working memory play distinctive roles in crowding: Attention operates to minimize interference from the flankers at intermediate target-flanker distances, whereas working memory may be recruited when attention fails to select the target at small target-flanker distances.

  2. Crowd Funding: the New Frontier of Sports Sponsorship?

    Directory of Open Access Journals (Sweden)

    Yann Abdourazakou

    2016-04-01

    Full Text Available Background: At a time when the economy becomes increasingly unstable, some large companies put an end to their partnerships. Sports sponsorship must therefore be reinvented with a more collaborative vision. Individuals but also corporations can now actively help their favorite teams or athletes and be rewarded for their success. Objective: The present study aims at studying these two concepts by analyzing their potential substitution as financing models. Our research offers an insight into the implementation of those two concepts. Our goal is to assess the potential substitution or co-existence of sponsorship and crowd funding in communication strategies. Method: This study is based on two qualitative analyses. The first was made with crowd funding platform professionals considered as equity financing experts. Five interviews were conducted, with an interview guide articulated around two axes: corporate motivations supporting crowd funding projects and perception of substitution between sponsorship and crowd funding. Second, based on the business objectives identified among sponsors, a grid of thematic analysis was built. A qualitative study was then conducted with project leaders (people looking for financing. The information was gathered via mail. Following those two steps, an analysis of the career financing modes chronology for the athletes prior to filing a project was studied. Results: The results of our qualitative analysis articulate points of views from platform leaders and elite athletes, i.e. users of these platforms. It appears that specialists see these two sport funding modes as complement, particularly in the communication strategy of large corporations. But results show that there is no systematic permanence between getting a project funded and having access to corporate financing. The study shows the existence of a hybrid model between sponsorship and crowd funding: participatory sponsorship. Conclusion: Sponsorship targets long

  3. Crowding effects on word identification in developmental dyslexia.

    Science.gov (United States)

    Spinelli-, Donatella; De Luca, Maria; Judica, Anna; Zoccolotti, Pierluigi

    2002-04-01

    The effect of crowding on the identification of words was examined in normal readers and subjects with developmental dyslexia. In Experiment 1, a matching task was used. Words were presented either alone or embedded in other words. Vocal reaction times (RT) of dyslexics were slower and more sensitive to the presence of the surrounding stimuli than those of control subjects. Similar results were obtained in a control experiment using the same task for strings of symbols (isolated or crowded) instead of words. These data indicate that differences in crowding in control and dyslexic subjects arise at a pre-linguistic level. In Experiment 2, vocal RTs to word reading were measured. Two conditions putatively reducing the effect of crowding were tested: increasing inter-letter spacing and blurring. A moderate increase of inter-letter spacing produced faster vocal RTs in dyslexics, while no effect was present in normal controls. Moderate blurring of stimuli did not change dyslexics' RTs, while normal readers became slower. Group and individual results are discussed to evaluate the extent to which crowding contributes to the genesis of developmental dyslexia.

  4. Pooling of continuous features provides a unifying account of crowding.

    Science.gov (United States)

    Keshvari, Shaiyan; Rosenholtz, Ruth

    2016-01-01

    Visual crowding refers to phenomena in which the perception of a peripheral target is strongly affected by nearby flankers. Observers often report seeing the stimuli as "jumbled up," or otherwise confuse the target with the flankers. Theories of visual crowding contend over which aspect of the stimulus gets confused in peripheral vision. Attempts to test these theories have led to seemingly conflicting results, with some experiments suggesting that the mechanism underlying crowding operates on unbound features like color or orientation (Parkes, Lund, Angelucci, Solomon, & Morgan, 2001), while others suggest it "jumbles up" more complex features, or even objects like letters (Korte, 1923). Many of these theories operate on discrete features of the display items, such as the orientation of each line or the identity of each item. By contrast, here we examine the predictions of the Texture Tiling Model, which operates on continuous feature measurements (Balas, Nakano, & Rosenholtz, 2009). We show that the main effects of three studies from the crowding literature are consistent with the predictions of Texture Tiling Model. This suggests that many of the stimulus-specific curiosities surrounding crowding are the inherent result of the informativeness of a rich set of image statistics for the particular tasks.

  5. Discrete Element Crowd Model for Pedestrian Evacuation Through an Exit

    CERN Document Server

    Lin, Peng; Lo, Siuming

    2016-01-01

    A series of accidents caused by crowd within the last decades evoked a lot of scientific interest in modeling the movement of pedestrian crowds. Based on discrete element method, a granular dynamic model, in which human body is simplified as self-driven sphere, is proposed to simulate the characteristics of crowd flow through an exit. In this model, the repulsive force among people is considered to have an anisotropic feature, and the physical contact force due to body deformation is quantified by the Hertz contact model. The movement of human body is simulated by applying the second Newton's law. The crowd flow through an exit at different desired velocities is studied and simulation results indicated that crowd flow exhibits three distinct states, i.e., smooth state, transition state and phase separation state. In the simulation, clogging phenomenon occurs more easily when the velocity of desired is high and the exit may as a result be totally blocked at a desired velocity of 1.6m/s or above, leading to fas...

  6. Modelling Crowd Dynamics: a Multiscale, Measure-theoretical Approach

    CERN Document Server

    Evers, Joep

    2011-01-01

    We present a strategy capable of describing basic features of the dynamics of crowds. The behaviour of the crowd is considered from a twofold perspective. We examine both the large scale behaviour of the crowd, and phenomena happening at the individual pedestrian's level. We unify micro and macro in a single model, by working with general mass measures and their transport. We improve existing modelling by coupling a measure-theoretical framework with basic ideas of mixture theory formulated in terms of measures. This strategy allows us to define several constituents of the crowd, each having its own partial velocity. We can thus examine the interaction between subpopulations that have distinct characteristics. We give special features to those pedestrians that are represented by the microscopic (discrete) part. In real life they would play the role of leaders, predators etc. Since we are interested in the global behaviour of the rest of the crowd, we model this part as a continuum. By identifying a suitable c...

  7. Is Malnutrition Associated with Crowding in Permanent Dentition?

    Directory of Open Access Journals (Sweden)

    Erika B. A. F. Thomaz

    2010-09-01

    Full Text Available Evidence suggests that energy-protein malnutrition is associated with impaired growth and development of facial bones. The objective of this study was to investigate the association between nutritional status and reduced space for dental eruption (crowding in permanent dentition. A cross-sectional study with probabilistic sampling design was used. We evaluated 2,060 students aged 12 to 15 years enrolled in schools in the northeast of Brazil. Crowding was defined according to World Health Organization (WHO as misalignment of teeth due to lack of space for them to erupt in the correct position. Nutritional status was evaluated by means of body mass index and height-for-age, using the WHO’s reference curves. Parents and adolescents responded to a questionnaire about demographic, socioeconomic, biological and behavioral characteristics. The associations were estimated by odds ratio (OR in multivariate logistic regression analysis (alpha = 0.05. Confounding and effect-modification were taken into account. An association between low height-for-age (z-score < –1SD and crowding was only observed in adolescents with a prolonged history of mouth breathing (OR = 3.1. No association was observed between underweight and crowding. Malnutrition is related to crowding in permanent dentition among mouth-breathing adolescents. Policy actions aimed at reducing low height-for-age and unhealthy oral habits are strongly recommended. However, further studies are needed to increase the consistency of these findings and improve understanding of the subject.

  8. Crowding on DNA in Protein Search for Targets.

    Science.gov (United States)

    Shvets, Alexey A; Kolomeisky, Anatoly B

    2016-07-07

    Proteins searching and recognizing specific sites on DNA is required for initiating all major biological processes. While the details of the protein search for targets on DNA in purified in vitro systems are reasonably well understood, the situation in real cells is much less clear. The presence of other types of molecules on DNA should prevent reaching the targets, but experiments show that, surprisingly, the molecular crowding on DNA influences the search dynamics much less than expected. We develop a theoretical method that allowed us to clarify the mechanisms of the protein search on DNA in the presence of crowding. It is found that the dimensionality of the search trajectories specifies whether the crowding will affect the target finding. For 3D search pathways it is minimal, while the strongest effect is for 1D search pathways when the crowding particle can block the search. In addition, for 1D search we determined that the critical parameter is a mobility of crowding agents: highly mobile molecules do not affect the search dynamics, while the slow particles can significantly slow down the process. Physical-chemical explanations of the observed phenomena are presented. Our theoretical predictions thus explain the experimental observations, and they are also supported by extensive numerical simulations.

  9. Visual crowding cannot be wholly explained by feature pooling.

    Science.gov (United States)

    Ester, Edward F; Klee, Daniel; Awh, Edward

    2014-06-01

    Visual perception is dramatically impaired when a peripheral target is embedded within clutter, a phenomenon known as visual crowding. Despite decades of study, the mechanisms underlying crowding remain a matter of debate. Feature pooling models assert that crowding results from a compulsory pooling (e.g., averaging) of target and distractor features. This view has been extraordinarily influential in recent years, so much so that crowding is typically regarded as synonymous with pooling. However, many demonstrations of feature pooling can also be accommodated by a probabilistic substitution model where observers occasionally report a distractor as the target. Here, we directly compared pooling and substitution using an analytical approach sensitive to both alternatives. In four experiments, we asked observers to report the precise orientation of a target stimulus flanked by two irrelevant distractors. In all cases, the observed data were well described by a quantitative model that assumes probabilistic substitution, and poorly described by a quantitative model that assumes that targets and distractors are averaged. These results challenge the widely held assumption that crowding can be wholly explained by compulsory pooling. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  10. Discrete element crowd model for pedestrian evacuation through an exit

    Science.gov (United States)

    Peng, Lin; Jian, Ma; Siuming, Lo

    2016-03-01

    A series of accidents caused by crowds within the last decades evoked a lot of scientific interest in modeling the movement of pedestrian crowds. Based on the discrete element method, a granular dynamic model, in which the human body is simplified as a self-driven sphere, is proposed to simulate the characteristics of crowd flow through an exit. In this model, the repulsive force among people is considered to have an anisotropic feature, and the physical contact force due to body deformation is quantified by the Hertz contact model. The movement of the human body is simulated by applying the second Newton’s law. The crowd flow through an exit at different desired velocities is studied and simulation results indicated that crowd flow exhibits three distinct states, i.e., smooth state, transition state and phase separation state. In the simulation, the clogging phenomenon occurs more easily when the desired velocity is high and the exit may as a result be totally blocked at a desired velocity of 1.6 m/s or above, leading to faster-to-frozen effect. Project supported by the National Natural Science Foundation of China (Grant Nos. 71473207, 51178445, and 71103148), the Research Grant Council, Government of Hong Kong, China (Grant No. CityU119011), and the Fundamental Research Funds for the Central Universities, China (Grant Nos. 2682014CX103 and 2682014RC05).

  11. PROFESSOR TEJ PAL SINGH: THE LEGEND OF INDIAN MACROMOLECULAR CRYSTALLOGRAPHY

    Directory of Open Access Journals (Sweden)

    Md. Imtaiyaz Hassan

    2013-12-01

    Full Text Available Professor Tej Pal Singh, an internationally recognized Indian scientist par excellence, is one of the pioneers of Indian macromolecular crystallography. He is a person of significant and enduring accomplishments as a teacher, scientist, administrator and family man. He has developed various methods to crystallize wide varieties of proteins. He has successfully determined crystal structures of lactoferrin, phospholipase A2, lactoperoxidase, peptidoglycan recognition proteins, disintegrin, zinc-α2-glycoprotein and several others including various protein-ligand and protein-protein complexes. He has a remarkably high number of structural entries in protein data bank. He received most of the prestigious awards and honors by Indian Government. This article covers most of his research and other achievements which will be a source of inspiration for young scientific community, motivation for peers and joy for his fellow colleagues and friends.

  12. Detecting stoichiometry of macromolecular complexes in live cells using FRET

    Science.gov (United States)

    Ben-Johny, Manu; Yue, Daniel N.; Yue, David T.

    2016-01-01

    The stoichiometry of macromolecular interactions is fundamental to cellular signalling yet challenging to detect from living cells. Fluorescence resonance energy transfer (FRET) is a powerful phenomenon for characterizing close-range interactions whereby a donor fluorophore transfers energy to a closely juxtaposed acceptor. Recognizing that FRET measured from the acceptor's perspective reports a related but distinct quantity versus the donor, we utilize the ratiometric comparison of the two to obtain the stoichiometry of a complex. Applying this principle to the long-standing controversy of calmodulin binding to ion channels, we find a surprising Ca2+-induced switch in calmodulin stoichiometry with Ca2+ channels—one calmodulin binds at basal cytosolic Ca2+ levels while two calmodulins interact following Ca2+ elevation. This feature is curiously absent for the related Na channels, also potently regulated by calmodulin. Overall, our assay adds to a burgeoning toolkit to pursue quantitative biochemistry of dynamic signalling complexes in living cells. PMID:27922011

  13. An analysis of fractal geometry of macromolecular gelation

    Institute of Scientific and Technical Information of China (English)

    左榘; 陈天红; 冉少峰; 何炳林; 董宝中; 生文君; 杨恒林

    1996-01-01

    With fractal geometry theory and based on experiments, an analysis of fractal geometry behavior of gelation of macromolecules was carried out. Using the cross-linking copolymerization of styrene-divinylbenzene (DVB) as an example, through the determinations of the evolution of the molecular weight, size and the dependence of scattering intensity on the angle of macromolecules by employing laser and synchrotron small angle X-ray scattering, respectively, this chemical reaction was described quantitatively, its fractal behavior was analyzed and the fractal dimension was also measured. By avoiding the complex theories on gelation, this approach is based on modern physical techniques and theories to perform the analysis of the behavior of fractal geometry of macromolecular gelation and thus is able to reveal the rules of this kind of complicated gelation more essentially and profoundly.

  14. Revealing the macromolecular targets of complex natural products

    Science.gov (United States)

    Reker, Daniel; Perna, Anna M.; Rodrigues, Tiago; Schneider, Petra; Reutlinger, Michael; Mönch, Bettina; Koeberle, Andreas; Lamers, Christina; Gabler, Matthias; Steinmetz, Heinrich; Müller, Rolf; Schubert-Zsilavecz, Manfred; Werz, Oliver; Schneider, Gisbert

    2014-12-01

    Natural products have long been a source of useful biological activity for the development of new drugs. Their macromolecular targets are, however, largely unknown, which hampers rational drug design and optimization. Here we present the development and experimental validation of a computational method for the discovery of such targets. The technique does not require three-dimensional target models and may be applied to structurally complex natural products. The algorithm dissects the natural products into fragments and infers potential pharmacological targets by comparing the fragments to synthetic reference drugs with known targets. We demonstrate that this approach results in confident predictions. In a prospective validation, we show that fragments of the potent antitumour agent archazolid A, a macrolide from the myxobacterium Archangium gephyra, contain relevant information regarding its polypharmacology. Biochemical and biophysical evaluation confirmed the predictions. The results obtained corroborate the practical applicability of the computational approach to natural product ‘de-orphaning’.

  15. Macromolecularly "Caged" Carbon Nanoparticles for Intracellular Trafficking via Switchable Photoluminescence.

    Science.gov (United States)

    Misra, Santosh K; Srivastava, Indrajit; Tripathi, Indu; Daza, Enrique; Ostadhossein, Fatemeh; Pan, Dipanjan

    2017-02-08

    Reversible switching of photoluminescence (PL) of carbon nanoparticles (CNP) can be achieved with counterionic macromolecular caging and decaging at the nanoscale. A negatively charged uncoated, "bare" CNP with high luminescence loses its PL when positively charged macromolecules are wrapped around its surface. Prepared caged carbons could regain their emission only through interaction with anionic surfactant molecules, representing anionic amphiphiles of endocytic membranes. This process could be verified by gel electrophoresis, spectroscopically and in vitro confocal imaging studies. Results indicated for the first time that luminescence switchable CNPs can be synthesized for efficient intracellular tracking. This study further supports the origin of photoluminescence in CNP as a surface phenomenon correlated a function of characteristic charged macromolecules.

  16. On macromolecular refinement at subatomic resolution withinteratomic scatterers

    Energy Technology Data Exchange (ETDEWEB)

    Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.; Lunin, Vladimir Y.; Urzhumtsev, Alexandre

    2007-11-09

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

  17. [Progress in researches on synthetic antimicrobial macromolecular polymers].

    Science.gov (United States)

    Wei, Gang; Yang, Lihua; Chu, Liangyin

    2010-08-01

    Broad-spectrum antimicrobial peptides provide a new way to address the urgent growing problem of bacterial resistance. However, the limited natural resources and the high cost of extraction and purification of natural antimicrobial peptides can not meet the requirements of clinical application. In order to solve this problem, researchers have utilized two basic common structural features (amphiphilic and cationic) for designing and preparing synthetic antimicrobial macromolecular polymers. During the last decade, several kinds of amphiphilic polymers, including arylamide oligomers, phenylene ethynylenes, polymethacrylates, polynorbornenes as well as nylon-3 polymers have been synthesized. In this paper, the structures, antibacterial activities and selectivities of these polymers are reviewed, and the effects of molecular size, polarity and ratio of hydrophobic groups, positive charge density on antibacterial activity and selectivity are also summarized.

  18. Macromolecular Crystallization with Microfluidic Free-Interface Diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Segelke, B

    2005-02-24

    Fluidigm released the Topaz 1.96 and 4.96 crystallization chips in the fall of 2004. Topaz 1.96 and 4.96 are the latest evolution of Fluidigm's microfluidics crystallization technologies that enable ultra low volume rapid screening for macromolecular crystallization. Topaz 1.96 and 4.96 are similar to each other but represent a major redesign of the Topaz system and have of substantially improved ease of automation and ease of use, improved efficiency and even further reduced amount of material needed. With the release of the new Topaz system, Fluidigm continues to set the standard in low volume crystallization screening which is having an increasing impact in the field of structural genomics, and structural biology more generally. In to the future we are likely to see further optimization and increased utility of the Topaz crystallization system, but we are also likely to see further innovation and the emergence of competing technologies.

  19. In-vacuum long-wavelength macromolecular crystallography.

    Science.gov (United States)

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

    2016-03-01

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

  20. Extracting trends from two decades of microgravity macromolecular crystallization history

    Science.gov (United States)

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

    2005-01-01

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

  1. Large-volume protein crystal growth for neutron macromolecular crystallography.

    Science.gov (United States)

    Ng, Joseph D; Baird, James K; Coates, Leighton; Garcia-Ruiz, Juan M; Hodge, Teresa A; Huang, Sijay

    2015-04-01

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.

  2. NATO Advanced Study Institute on Evolving Methods for Macromolecular Gystallography

    CERN Document Server

    Read, Randy J

    2007-01-01

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

  3. Macromolecular and dendrimer-based magnetic resonance contrast agents

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-15

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

  4. Radiation damage to nucleoprotein complexes in macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Bury, Charles; Garman, Elspeth F.; Ginn, Helen Mary [University of Oxford, South Parks Road, Oxford OX1 3QU (United Kingdom); Ravelli, Raimond B. G. [Maastricht University, PO Box 616, Maastricht 6200 MD (Netherlands); Carmichael, Ian [University of Notre Dame, Notre Dame, IN 46556 (United States); Kneale, Geoff; McGeehan, John E., E-mail: john.mcgeehan@port.ac.uk [University of Portsmouth, King Henry 1st Street, Portsmouth PO1 2DY (United Kingdom)

    2015-01-30

    Quantitative X-ray induced radiation damage studies employing a model protein–DNA complex revealed a striking partition of damage sites. The DNA component was observed to be far more resistant to specific damage compared with the protein. Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein–DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07–44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N{sub 1}—C and sugar-phosphate C—O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses.

  5. Spatial attention alleviates temporal crowding, but neither temporal nor spatial uncertainty are necessary for the emergence of temporal crowding.

    Science.gov (United States)

    Tkacz-Domb, Shira; Yeshurun, Yaffa

    2017-03-01

    Recently, we demonstrated temporal crowding with normal observers: Target identification was impaired when it was surrounded by other stimuli in time, even when the interstimuli intervals (ISIs) were relatively long. Here, we examined whether temporal and spatial uncertainties play a critical role in the emergence of temporal crowding. We presented a sequence of three letters to the same peripheral location, right or left of fixation, separated by varying ISI (106-459 ms). One of these letters was the target, and the observers indicated its orientation. To eliminate temporal uncertainty, the position of the target within the sequence was fixed for an entire block (Experiment 1). To eliminate spatial uncertainty, we employed spatial attentional precues that indicated the letters' location. The precue was either auditory (Experiment 2) or visual (Experiment 3). We found temporal crowding to result in worse performance with shorter ISIs, even when there was no temporal or spatial uncertainty. Unlike the auditory cue, the visual cue affected performance. Specifically, when there was uncertainty regarding the target location (i.e., when the target appeared in the first display), precueing the target location improved overall performance and reduced the ISI effect, although it was not completely eliminated. These results suggest that temporal and spatial uncertainties are not necessary for the emergence of temporal crowding and that spatial attention can reduce temporal crowding.

  6. Hierarchical Self-Similarity in Group and Crowd Behaviors

    Science.gov (United States)

    Ivancevic, Vladimir G.; Reid, Darryn J.

    2015-11-01

    In this Chapter, a nonlinear, complex, Hamiltonian description of socio-cognio-physical dynamics at the oscopic, classical, inter-personal crowd level and microscopic, quantum, intra-personal agent level, is presented, uniquely, in the form of the open Liouville equation. At the microscopic level, this can be considered to be a nonlinear extension of the linear correlation and factor dynamics. This implies the arrow of time in both microscopic and oscopic processes and shows the existence of the formal crowd-agent space-time self-similarity. This in itself shows the existence of a unique control law, which acts on different scales of agent functioning. This self-similar socio-cognio-physical control law enables us to use the crowd dynamics simulator (previously developed at Defence Science & Technology Organisation, Australia), for recursive simulation of individual agents' representation spaces on a cluster of computers.

  7. What crowding can tell us about object representations.

    Science.gov (United States)

    Manassi, Mauro; Lonchampt, Sophie; Clarke, Aaron; Herzog, Michael H

    2016-01-01

    In crowding, perception of a target usually deteriorates when flanking elements are presented next to the target. Surprisingly, adding further flankers can lead to a release from crowding. In previous work we showed that, for example, vernier offset discrimination at 9° of eccentricity deteriorated when a vernier was embedded in a square. Adding further squares improved performance. The more squares presented, the better the performance, extending across 20° of the visual field. Here, we show that very similar results hold true for shapes other than squares, including unfamiliar, irregular shapes. Hence, uncrowding is not restricted to simple and familiar shapes. Our results provoke the question of whether any type of shape is represented at any location in the visual field. Moreover, small changes in the orientation of the flanking shapes led to strong increases in crowding strength. Hence, highly specific shape-specific interactions across large parts of the visual field determine vernier acuity.

  8. The Crowding out Effect on the Labor Market in Romania

    Directory of Open Access Journals (Sweden)

    Mihaela Hrisanta DOBRE

    2011-01-01

    Full Text Available Discrimination expresses any distinction, exclusion, restriction, preference or different treatment that disadvantages a person or group, in comparison with others in similar situations. The crowding out effect was first formulated by Bergmann (1974 and explains that an individual can obtain lower returns if he belongs to a branch dominated by the members of another group. The difference in pay between women and men is also reinforced by the segregation in the labor market, which may explain the crowding out effect. In this article we analyzed the level of segregation in the Romanian labor market starting from the workers professional status and their distribution by branch from 2003 to 2008. Crowding out effect was analyzed based on the gain function of the two groups (women and men.

  9. Motivating crowding theory - opening the black box of intrinsic motivation

    DEFF Research Database (Denmark)

    Jacobsen, Christian Bøtcher

    2010-01-01

    employees. Motivation crowding theory claims that this may be at the expense of intrinsic motivation, if the extrinsic motivation factor is perceived to be controlling. On the other hand, intrinsic motivation will be enhanced (crowded in), if the extrinsic motivation factor is perceived to be supportive......Public employees work for many other reasons than because they are paid for it. In other words, intrinsic motivation is an important determinant for their performance. Nonetheless, public sector organizations increasingly rely on extrinsic motivation factors such as monetary incentives to motivate....... Studies have found support for the motivation crowding claim, but have neglected intrinsic motivation. This study opens the black box of intrinsic motivation and finds a meaningful distinction between task motivation and public service motivation. Among 2,772 physiotherapists in the Danish public sector...

  10. Stellar Crowding and the Science Case for Extremely Large Telescopes

    CERN Document Server

    Olsen, K A G; Rigaut, F; Olsen, Knut A.G.; Blum, Robert D.; Rigaut, Francois

    2003-01-01

    We present a study of the effect of crowding on stellar photometry. We develop an analytical model through which we are able to predict the error in magnitude and color for a given star for any combination of telescope resolution, stellar luminosity function, background surface brightness, and distance. We test our predictions with Monte Carlo simulations of the LMC globular cluster NGC 1835, for resolutions corresponding to a seeing-limited telescope, the $HST$, and an AO-corrected 30-m (near diffraction limited) telescope. Our analytically predicted magnitude errors agree with the simulation results to within $\\sim$20%. The analytical model also predicts that errors in color are strongly affected by the correlation of crowding--induced photometric errors between bands as is seen in the simulations. Using additional Monte Carlo simulations and our analytical crowding model, we investigate the photometric accuracy which 30-m and 100-m Extremely Large Telescopes (ELTs) will be able to achieve at distances exte...

  11. Abnormal events detection in crowded scenes by trajectory cluster

    Science.gov (United States)

    Zhou, Shifu; Zhang, Zhijiang; Zeng, Dan; Shen, Wei

    2015-02-01

    Abnormal events detection in crowded scenes has been a challenge due to volatility of the definitions for both normality and abnormality, the small number of pixels on the target, appearance ambiguity resulting from the dense packing, and severe inter-object occlusions. A novel framework was proposed for the detection of unusual events in crowded scenes using trajectories produced by moving pedestrians based on an intuition that the motion patterns of usual behaviors are similar to these of group activity, whereas unusual behaviors are not. First, spectral clustering is used to group trajectories with similar spatial patterns. Different trajectory clusters represent different activities. Then, unusual trajectories can be detected using these patterns. Furthermore, behavior of a mobile pedestrian can be defined by comparing its direction with these patterns, such as moving in the opposite direction of the group or traversing the group. Experimental results indicated that the proposed algorithm could be used to reliably locate the abnormal events in crowded scenes.

  12. Agent-Based Crowd Simulation of Daily Goods Traditional Markets

    Directory of Open Access Journals (Sweden)

    Purba D. Kusuma

    2016-10-01

    Full Text Available In traditional market, buyers are not only moving from one place to another, but also interacting with traders to purchase their products. When a buyer interacts with a trader, he blocks some space in the corridor. Besides, while buyers are walking, they may be attracted by non-preferred traders, though they may have preferred traders. These situations have not been covered in most existing crowd simulation models. Hence, these existing models cannot be directly implemented in traditional market environments since they mainly focus on crowd members’ movement. This research emphasizes on a crowd model that includes simplified movement and unplanned purchasing models. This model has been developed based on intelligent agent concept, where each agent represents a buyer. Two traditional markets are used for simulation in this research, namely Gedongkuning and Ngasem, in Yogyakarta, Indonesia. The simulation shows that some places are visited more frequently than others. Overall, the simulation result matches the situation found in the real world.

  13. Saccade-confounded image statistics explain visual crowding.

    Science.gov (United States)

    Nandy, Anirvan S; Tjan, Bosco S

    2012-01-08

    Processing of shape information in human peripheral visual fields is impeded beyond what can be expected by poor spatial resolution. Visual crowding, the inability to identify objects in clutter, has been shown to be the primary factor limiting shape perception in peripheral vision. Despite the well-documented effects of crowding, its underlying causes remain poorly understood. Given that spatial attention both facilitates learning of image statistics and directs saccadic eye movements, we propose that the acquisition of image statistics in peripheral visual fields is confounded by eye-movement artifacts. Specifically, the image statistics acquired under a peripherally deployed spotlight of attention are systematically biased by saccade-induced image displacements. These erroneously represented image statistics lead to inappropriate contextual interactions in the periphery and cause crowding.

  14. Guided crowd dynamics via modified social force model

    Science.gov (United States)

    Yang, Xiaoxia; Dong, Hairong; Wang, Qianling; Chen, Yao; Hu, Xiaoming

    2014-10-01

    Pedestrian dynamics is of great theoretical significance for strategy design of emergency evacuation. Modification of pedestrian dynamics based on the social force model is presented to better reflect pedestrians' behavioral characteristics in emergency. Specifically, the modified model can be used for guided crowd dynamics in large-scale public places such as subway stations and stadiums. This guided crowd model is validated by explicitly comparing its density-speed and density-flow diagrams with fundamental diagrams. Some social phenomena such as gathering, balance and conflicts are clearly observed in simulation, which further illustrate the effectiveness of the proposed modeling method. Also, time delay for pedestrians with time-dependent desired velocities is observed and explained using the established model in this paper. Furthermore, this guided crowd model is applied to the simulation system of Beijing South Railway Station for predictive evacuation experiments.

  15. Motivating crowding theory - opening the black box of intrinsic motivation

    DEFF Research Database (Denmark)

    Jacobsen, Christian Bøtcher

    2010-01-01

    Public employees work for many other reasons than because they are paid for it. In other words, intrinsic motivation is an important determinant for their performance. Nonetheless, public sector organizations increasingly rely on extrinsic motivation factors such as monetary incentives to motivate...... employees. Motivation crowding theory claims that this may be at the expense of intrinsic motivation, if the extrinsic motivation factor is perceived to be controlling. On the other hand, intrinsic motivation will be enhanced (crowded in), if the extrinsic motivation factor is perceived to be supportive....... Studies have found support for the motivation crowding claim, but have neglected intrinsic motivation. This study opens the black box of intrinsic motivation and finds a meaningful distinction between task motivation and public service motivation. Among 2,772 physiotherapists in the Danish public sector...

  16. Contemporary understanding of riots: Classical crowd psychology, ideology and the social identity approach.

    Science.gov (United States)

    Stott, Clifford; Drury, John

    2016-04-01

    This article explores the origins and ideology of classical crowd psychology, a body of theory reflected in contemporary popularised understandings such as of the 2011 English 'riots'. This article argues that during the nineteenth century, the crowd came to symbolise a fear of 'mass society' and that 'classical' crowd psychology was a product of these fears. Classical crowd psychology pathologised, reified and decontextualised the crowd, offering the ruling elites a perceived opportunity to control it. We contend that classical theory misrepresents crowd psychology and survives in contemporary understanding because it is ideological. We conclude by discussing how classical theory has been supplanted in academic contexts by an identity-based crowd psychology that restores the meaning to crowd action, replaces it in its social context and in so doing transforms theoretical understanding of 'riots' and the nature of the self.

  17. Rapid and long-lasting reduction of crowding through training.

    Science.gov (United States)

    Yashar, Amit; Chen, Jiageng; Carrasco, Marisa

    2015-01-01

    Crowding is the failure to identify an object in the peripheral visual field in the presence of nearby objects. Recent studies have shown that crowding can be alleviated after several days of training, but the processes underlying this improvement are still unclear. Here we tested whether a few hundred trials within a short period of training can alleviate crowding, whether the learning is location specific, and whether the improvement reflects facilitation by target enhancement or flankers suppression. Observers were asked to identify the orientation of a letter in the periphery surrounded by two flanker letters. Observers were tested before (pretest) and after (posttest) training (600 trials). In Experiment 1 we tested whether learning is location specific or can transfer to a different location; the training and test occurred at the same or different hemifields. In a control experiment, we ruled out alternative explanations for the learning effect in Experiment 1. In Experiment 2, we assessed different components of feature selection by training with either the same flanker polarity as the pre/posttest but opposite polarity group (flanker polarity group) or the same target polarity as the pre/posttest but opposite flanker polarity (target polarity group). Following training, overall performance increased in all four conditions, but only the same-location group (Experiment 1) and the same flanker polarity (Experiment 2) showed a significant reduction in crowding as assessed by the distance at which the flankers no longer interfere with target identification, that is, the critical spacing. These results show that training can rapidly reduce crowding and that improvement primarily reflects learning to ignore the irrelevant flankers. Remarkably, in the two conditions in which training significantly reduced crowding, the benefit of short training persisted for up to a year.

  18. Characterizing the role of disparity information in alleviating visual crowding.

    Science.gov (United States)

    Astle, Andrew T; McGovern, David P; McGraw, Paul V

    2014-11-25

    The ability to identify a target is reduced by the presence of nearby objects, a phenomenon known as visual crowding. The extent to which crowding impairs our perception is generally governed by the degree of similarity between a target stimulus and its surrounding flankers. Here we investigated the influence of disparity differences between target and flankers on crowding. Orientation discrimination thresholds for a parafoveal target were first measured when the target and flankers were presented at the same depth to establish a flanker separation that induced a significant elevation in threshold for each individual. Flankers were subsequently fixed at this spatial separation while the disparity of the flankers relative to the target was altered. For all participants, thresholds showed a systematic decrease as flanker-target disparity increased. The resulting tuning function was asymmetric: Crowding was lower when the target was perceived to be in front of the flankers rather than behind. A series of control experiments confirmed that these effects were driven by disparity, as opposed to other factors such as flanker-target separation in three-dimensional (3-D) space or monocular positional offsets used to create disparity. When flankers were distributed over a range of crossed and uncrossed disparities, such that the mean was in the plane of the target, there was an equivalent or greater release of crowding compared to when all flankers were presented at the maximum disparity of that range. Overall, our results suggest that depth cues can reduce the effects of visual crowding, and that this reduction is unlikely to be caused by grouping of flankers or positional shifts in the monocular image.

  19. Crowd-sourced Archaeological Research: The MicroPasts Project

    Directory of Open Access Journals (Sweden)

    Chiara Bonacchi

    2014-10-01

    Full Text Available This paper offers a brief introduction to MicroPasts, a web-enabled crowd-sourcing and crowd-funding project whose overall goal is to promote the collection and use of high quality research data via institutional and community collaborations, both on- and off-line. In addition to introducing this initiative, the discussion below is a reflection of its lead author’s core contribution to the project and will dwell in more detail on one particular aspect of MicroPasts: its relevance to research and practice in public archaeology, cultural policy and heritage studies.

  20. Modeling, simulation and visual analysis of crowds a multidisciplinary perspective

    CERN Document Server

    Ali, Saad; Manocha, Dinesh; Shah, Mubarak

    2013-01-01

    Over the last several years there has been a growing interest in developing computational methodologies for modeling and analyzing movements and behaviors of 'crowds' of people. This interest spans several scientific areas that includes Computer Vision, Computer Graphics, and Pedestrian Evacuation Dynamics. Despite the fact that these different scientific fields are trying to model the same physical entity (i.e. a crowd of people), research ideas have evolved independently. As a result each discipline has developed techniques and perspectives that are characteristically their own.

  1. Moving in a crowd: human perception as a multiscale process

    CERN Document Server

    Colombi, Annachiara; Tosin, Andrea

    2015-01-01

    The strategic behavior of pedestrians is largely determined by how they perceive and consequently react to neighboring people. Such interpersonal interactions may be dictated by the emotional state of the individuals, the purpose of their trip, the local crowding, the quality of the environment to mention but a few common examples. This issue is addressed in this paper by a mathematical model which combines, in an evolutionary time- and space-dependent way, discrete and continuous effects of pedestrian interactions. Numerical simulations and qualitative analysis suggest that human perception, and its impact on crowd dynamics, can be effectively modeled as a multiscale process based on such a dual representation of groups of agents.

  2. Theoretical mechanics: Crowd synchrony on the Millennium Bridge

    Science.gov (United States)

    Strogatz, Steven H.; Abrams, Daniel M.; McRobie, Allan; Eckhardt, Bruno; Ott, Edward

    2005-11-01

    Soon after the crowd streamed on to London's Millennium Bridge on the day it opened, the bridge started to sway from side to side: many pedestrians fell spontaneously into step with the bridge's vibrations, inadvertently amplifying them. Here we model this unexpected and now notorious phenomenon - which was not due to the bridge's innovative design as was first thought - by adapting ideas originally developed to describe the collective synchronization of biological oscillators such as neurons and fireflies. Our approach should help engineers to estimate the damping needed to stabilize other exceptionally crowded footbridges against synchronous lateral excitation by pedestrians.

  3. A Neurophysiologically Plausible Population Code Model for Feature Integration Explains Visual Crowding

    NARCIS (Netherlands)

    Berg, Ronald van den; Roerdink, Jos B.T.M.; Cornelissen, Frans W.

    2010-01-01

    An object in the peripheral visual field is more difficult to recognize when surrounded by other objects. This phenomenon is called "crowding". Crowding places a fundamental constraint on human vision that limits performance on numerous tasks. It has been suggested that crowding results from spatial

  4. Developmental Changes during Childhood in Single-Letter Acuity and Its Crowding by Surrounding Contours

    Science.gov (United States)

    Jeon, Seong Taek; Hamid, Joshua; Maurer, Daphne; Lewis, Terri L.

    2010-01-01

    Crowding refers to impaired target recognition caused by surrounding contours. We investigated the development of crowding in central vision by comparing single-letter and crowding thresholds in groups of 5-year-olds, 8-year-olds, 11-year-olds, and adults. The task was to discriminate the orientation of a Sloan letter E. Single-letter thresholds,…

  5. Comparing State- Versus Facility-Level Effects on Crowding in U.S. Correctional Facilities

    Science.gov (United States)

    Steiner, Benjamin; Wooldredge, John

    2008-01-01

    The literature on prison crowding underscores the potential importance of both state- and facility-level effects on crowding, although empirical research has not assessed these relative effects because of the sole focus on states as units of analysis. This article describes findings from bi-level analyses of crowding across 459 state-operated…

  6. Saccadic selection and crowding in visual search : stronger lateral masking leads to shorter search times

    NARCIS (Netherlands)

    de Vries, Jelmer P.; Hooge, Ignace T. C.; Wiering, Marco A.; Verstraten, Frans A. J.

    2011-01-01

    We investigated the role of crowding in saccadic selection during visual search. To guide eye movements, often information from the visual periphery is used. Crowding is known to deteriorate the quality of peripheral information. In four search experiments, we studied the role of crowding, by accomp

  7. Prospects for simulating macromolecular surfactant chemistry at the ocean-atmosphere boundary

    Science.gov (United States)

    Elliott, S.; Burrows, S. M.; Deal, C.; Liu, X.; Long, M.; Ogunro, O.; Russell, L. M.; Wingenter, O.

    2014-05-01

    Biogenic lipids and polymers are surveyed for their ability to adsorb at the water-air interfaces associated with bubbles, marine microlayers and particles in the overlying boundary layer. Representative ocean biogeochemical regimes are defined in order to estimate local concentrations for the major macromolecular classes. Surfactant equilibria and maximum excess are then derived based on a network of model compounds. Relative local coverage and upward mass transport follow directly, and specific chemical structures can be placed into regional rank order. Lipids and denatured protein-like polymers dominate at the selected locations. The assigned monolayer phase states are variable, whether assessed along bubbles or at the atmospheric spray droplet perimeter. Since oceanic film compositions prove to be irregular, effects on gas and organic transfer are expected to exhibit geographic dependence as well. Moreover, the core arguments extend across the sea-air interface into aerosol-cloud systems. Fundamental nascent chemical properties including mass to carbon ratio and density depend strongly on the geochemical state of source waters. High surface pressures may suppress the Kelvin effect, and marine organic hygroscopicities are almost entirely unconstrained. While bubble adsorption provides a well-known means for transporting lipidic or proteinaceous material into sea spray, the same cannot be said of polysaccharides. Carbohydrates tend to be strongly hydrophilic so that their excess carbon mass is low despite stacked polymeric geometries. Since sugars are abundant in the marine aerosol, gel-based mechanisms may be required to achieve uplift. Uncertainties distill to a global scale dearth of information regarding two dimensional kinetics and equilibria. Nonetheless simulations are recommended, to initiate the process of systems level quantification.

  8. Prospects for Simulating Macromolecular Surfactant Chemistry at the Ocean-Atmosphere Boundary

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, S.; Burrows, Susannah M.; Deal, C.; Liu, Xiaohong; Long, M.; Ogunro, O.; Russell, Lynn M.; Wingenter, O.

    2014-05-01

    Biogenic lipids and polymers are surveyed for their ability to adsorb at the water-air interfaces associated with bubbles, marine microlayers and particles in the overlying boundary layer. Representative ocean biogeochemical regimes are defined in order to estimate local concentrations for the major macromolecular classes. Surfactant equilibria and maximum excess are then derived based on a network of model compounds. Relative local coverage and upward mass transport follow directly, and specific chemical structures can be placed into regional rank order. Lipids and denatured protein-like polymers dominate at the selected locations. The assigned monolayer phase states are variable, whether assessed along bubbles or at the atmospheric spray droplet perimeter. Since oceanic film compositions prove to be irregular, effects on gas and organic transfer are expected to exhibit geographic dependence as well. Moreover, the core arguments extend across the sea-air interface into aerosol-cloud systems. Fundamental nascent chemical properties including mass to carbon ratio and density depend strongly on the geochemical state of source waters. High surface pressures may suppress the Kelvin effect, and marine organic hygroscopicities are almost entirely unconstrained. While bubble adsorption provides a well-known means for transporting lipidic or proteinaceous material into sea spray, the same cannot be said of polysaccharides. Carbohydrates tend to be strongly hydrophilic so that their excess carbon mass is low despite stacked polymeric geometries. Since sugars are abundant in the marine aerosol, gel-based mechanisms may be required to achieve uplift. Uncertainties in the surfactant logic distill to a global scale dearth of information regarding two dimensional kinetics and equilibria. Nonetheless simulations are recommended, to initiate the process of systems level quantification.

  9. An analytical method for disentangling the roles of adhesion and crowding for random walk models on a crowded lattice

    Science.gov (United States)

    Ellery, Adam J.; Baker, Ruth E.; Simpson, Matthew J.

    2016-10-01

    Migration of cells and molecules in vivo is affected by interactions with obstacles. These interactions can include crowding effects, as well as adhesion/repulsion between the motile cell/molecule and the obstacles. Here we present an analytical framework that can be used to separately quantify the roles of crowding and adhesion/repulsion using a lattice-based random walk model. Our method leads to an exact calculation of the long time Fickian diffusivity, and avoids the need for computationally expensive stochastic simulations.

  10. Stability of maxillary anterior crowding treatment Estabilidade do tratamento de apinhamento anterossuperior

    Directory of Open Access Journals (Sweden)

    Camila Leite Quaglio

    2012-08-01

    Full Text Available OBJECTIVE: To evaluate the stability and the relapse of maxillary anterior crowding treatment on cases with premolar extraction and evaluate the tendency of the teeth to return to their pretreatment position. METHODS: The experimental sample consisted of 70 patients of both sex with an initial Class I and Class II maloclusion and treated with first premolar extractions. The initial mean age was 13,08 years. Dental casts' measurements were obtained at three stages (pretreatment, posttreatment and posttreatment of 9 years on average and the variables assessed were Little Irregularity Index, maxillary arch length and intercanine. Pearson correlation coefficient was used to know if some studied variable would have influence on the crowding in the three stages (LII1, LII2, LII3 and in each linear displacement of the Little irregularity index (A, B, C, D, E in the initial and post-retention phases. RESULTS: The maxillary crowding relapse ( LII3-2 is influenced by the initial ( LII1, and the teeth tend to return to their pretreatment position. CONCLUSION: The results underline the attention that the orthodontist should be given to the maxillary anterior relapse, primarily on those teeth that are crowded before the treatment.OBJETIVO: avaliar a estabilidade e recidiva do tratamento de apinhamento dos dentes anterossuperiores em casos com extrações de pré-molares e avaliar a tendência dos dentes apinhados, no início do tratamento, a retornar à sua posição original. MÉTODOS: a amostra consistiu de 70 pacientes de ambos os sexos, com má oclusão inicial de Classe I e Classe II de Angle, tratados com extrações dos primeiros pré-molares. A idade média inicial foi de 13,08 anos. Foram avaliados os modelos de estudo nas fases inicial (T1, final (T2 e, em média, 9 anos pós-tratamento (T3 de cada paciente. As variáveis da arcada superior avaliadas e comparadas estatisticamente pela Análise de Variância (ANOVA foram: índice de irregularidade

  11. Spacing and crowding among African and Caucasian children.

    NARCIS (Netherlands)

    Mugonzibwa, E.A.; Eskeli, R.; Laine-Alava, M.T.; Kuijpers-Jagtman, A.M.; Katsaros, C.

    2008-01-01

    OBJECTIVE: To determine spacing and crowding according to ethnic group, gender and dental emergence stage among Tanzanian African and Caucasian children. DESIGN: Cross-sectional epidemiological clinical study. SETTING: A total of 869 African (428 boys, 441 girls) and 706 Caucasian (319 boys, 387 gir

  12. Nonlinear Effects in Examples of Crowd Evacuation Scenarios

    DEFF Research Database (Denmark)

    Starke, Jens; Berg Thomsen, Kristian; Sørensen, Asger;

    2014-01-01

    Severe accidents with many fatalities have occurred when too many pedestrians had to maneuver in too tight surroundings, as during evacuations of mass events. This demonstrates the importance of a better general understanding of pedestrians and emergent complex behavior in crowds. To this end, we...

  13. Hardy' s Pessimism in Far from the Madding Crowd

    Institute of Scientific and Technical Information of China (English)

    乌楠

    2011-01-01

    Thomas Hardy, noted as a pessimistic writer, depicts his pessimistic veins in many of his books. In this paper, the author argues that in his famous Far from the Madding Crowd, Hardy' s pessimism is shown in the main characters' conflicts with nature and

  14. Public Service Motivation and Monetary Incentives: Substitutes or Motivation Crowding?

    DEFF Research Database (Denmark)

    Jacobsen, Christian Bøtcher

    2011-01-01

    motivation is the most important type of motivation in the delivery of public service, because it substitutes for egoistic motivation. Organizations whose members have high levels of PSM are therefore expected to be less dependent on utilitarian motivators such as monetary incentives. Motivation crowding...

  15. Chenang Beach and its Crowding Capacity: A Malaysian Perspective

    Directory of Open Access Journals (Sweden)

    Mohamad Diana

    2014-01-01

    Full Text Available This working paper focuses in enjoyment factors, specifically: number of beach users, perceived maximum number of beach users accepted, perceived maximum number of beach users that affects the tourism experience and perceived maximum number of beach users that affects the beach quality. At a deeper extent, the evaluation is categorized by number of visitation, visitation motivations, and Chenang Island’s push and pull factors. Relationships between variables were assessed using a two-phase evaluation framework where interestingly, only one demographic factor works with all the studied independent variables. It is also learned that the density of an area number of people seen is considered as a n accepted crowding factor, as opposed to this working paper scope experienced crowding . A unique relationship was observed for crowding level, and visitation satisfaction level and overall evaluation of Chenang beach quality. This working paper further supports the previous literature on the significance of beach carrying capacity management and it is learned that the idea of crowding standard is interlinks with ‘gender, ‘time spend’ and ‘number of boaters’. From findings, this working paper envisages the preferences polar exchange where this should be of interest to tourism-related personnel. It is within this working paper interest to highlight the pressing need in brandishing the image of Chenang Beach. This is to ensure that Chenang Beach, as a field, is maintaining its importance and popularity.

  16. Editorial Bias in Crowd-Sourced Political Information.

    Science.gov (United States)

    Kalla, Joshua L; Aronow, Peter M

    2015-01-01

    The Internet has dramatically expanded citizens' access to and ability to engage with political information. On many websites, any user can contribute and edit "crowd-sourced" information about important political figures. One of the most prominent examples of crowd-sourced information on the Internet is Wikipedia, a free and open encyclopedia created and edited entirely by users, and one of the world's most accessed websites. While previous studies of crowd-sourced information platforms have found them to be accurate, few have considered biases in what kinds of information are included. We report the results of four randomized field experiments that sought to explore what biases exist in the political articles of this collaborative website. By randomly assigning factually true but either positive or negative and cited or uncited information to the Wikipedia pages of U.S. senators, we uncover substantial evidence of an editorial bias toward positivity on Wikipedia: Negative facts are 36% more likely to be removed by Wikipedia editors than positive facts within 12 hours and 29% more likely within 3 days. Although citations substantially increase an edit's survival time, the editorial bias toward positivity is not eliminated by inclusion of a citation. We replicate this study on the Wikipedia pages of deceased as well as recently retired but living senators and find no evidence of an editorial bias in either. Our results demonstrate that crowd-sourced information is subject to an editorial bias that favors the politically active.

  17. Crowd Analysis by Using Optical Flow and Density Based Clustering

    DEFF Research Database (Denmark)

    Santoro, Francesco; Pedro, Sergio; Tan, Zheng-Hua

    2010-01-01

    In this paper, we present a system to detect and track crowds in a video sequence captured by a camera. In a first step, we compute optical flows by means of pyramidal Lucas-Kanade feature tracking. Afterwards, a density based clustering is used to group similar vectors. In the last step...

  18. DNA strand exchange catalyzed by molecular crowding in PEG solutions

    KAUST Repository

    Feng, Bobo

    2010-01-01

    DNA strand exchange is catalyzed by molecular crowding and hydrophobic interactions in concentrated aqueous solutions of polyethylene glycol, a discovery of relevance for understanding the function of recombination enzymes and with potential applications to DNA nanotechnology. © 2010 The Royal Society of Chemistry.

  19. Esthetic rehabilitation of crowded and protruded anterior dentition

    Directory of Open Access Journals (Sweden)

    Cecilia G. J. lunardhi

    2009-03-01

    Full Text Available Background: Recent trends put estheticrehabilitationas a demandingtreatmentin order to correct malpositionedanteriordentition. This is enhanced by the patient’s background, especially careers that require prime appearance for the public. Purpose: To describe that even though there are many treatment alternatives and procedures, esthetic rehabilitation on crowded and protruded anterior dentition using endodontic treatment, cast posts and all ceramic crowns, can improve patient’s appearance. Case: This article presents a case report on esthetic rehabilitation of crowded and protruded anterior dentition. Treatment was done due to patient’s refusal in receiving orthodontic treatment. The patient requested esthetic rehabilitation as an expectation for faster and instant esthetic result. Case management: Endodontic treatment was done to the involved dentition prior to the final restoration. Cast posts and all ceramic crowns were used as final restoration to correct the crowded and protruded anterior teeth. Conclusion: Esthetic rehabilitation can be done successfully on crowded and protruded anterior dentition. Instant result could be achieved by this treatment. This is supported by the fact that dentists should be aware of not only choosing the right treatment and materials but also patient’s expectations and conditions.

  20. Track-based event recognition in a realistic crowded environment

    NARCIS (Netherlands)

    Huis, J.R. van; Bouma, H.; Baan, J.; Burghouts, G.J.; Eendebak, P.T.; Hollander, R.J.M.; Dijk, J.; Rest, J.H.C. van

    2014-01-01

    Automatic detection of abnormal behavior in CCTV cameras is important to improve the security in crowded environments, such as shopping malls, airports and railway stations. This behavior can be characterized at different time scales, e.g., by small-scale subtle and obvious actions or by large-scale

  1. Estimating the crowding level with a neuro-fuzzy classifier

    Science.gov (United States)

    Boninsegna, Massimo; Coianiz, Tarcisio; Trentin, Edmondo

    1997-07-01

    This paper introduces a neuro-fuzzy system for the estimation of the crowding level in a scene. Monitoring the number of people present in a given indoor environment is a requirement in a variety of surveillance applications. In the present work, crowding has to be estimated from the image processing of visual scenes collected via a TV camera. A suitable preprocessing of the images, along with an ad hoc feature extraction process, is discussed. Estimation of the crowding level in the feature space is described in terms of a fuzzy decision rule, which relies on the membership of input patterns to a set of partially overlapping crowding classes, comprehensive of doubt classifications and outliers. A society of neural networks, either multilayer perceptrons or hyper radial basis functions, is trained to model individual class-membership functions. Integration of the neural nets within the fuzzy decision rule results in an overall neuro-fuzzy classifier. Important topics concerning the generalization ability, the robustness, the adaptivity and the performance evaluation of the system are explored. Experiments with real-world data were accomplished, comparing the present approach with statistical pattern recognition techniques, namely linear discriminant analysis and nearest neighbor. Experimental results validate the neuro-fuzzy approach to a large extent. The system is currently working successfully as a part of a monitoring system in the Dinegro underground station in Genoa, Italy.

  2. Will the swine strain crowd out the seasonal influenza strain?

    CERN Document Server

    Schinazi, Rinaldo B

    2010-01-01

    We use spatial and non spatial models to argue that competition alone may explain why two influenza strains do not usually coexist. The more virulent strain is likely to crowd out the less virulent one. This can be seen as a consequence of the Exclusion Principle of Ecology. We exhibit, however, a spatial model for which coexistence is possible.

  3. NMR RELAXIVITY AND IMAGING OF NEUTRAL MACROMOLECULAR POLYESTER GADOLINIUM (Ⅲ) COMPLEXES

    Institute of Scientific and Technical Information of China (English)

    Kai-chao Yu; Hong-bing Hu; Mai-li Liu; Han-zhen Yuan; Chao-hui Ye; Ren-xi Zhuo

    1999-01-01

    Five neutral macromolecular polyester gadolinium (Ⅲ) complexes with pendant hydrophobic alkyl and aromatic functional groups were prepared. The longitudinal relaxation rates of these complexes were measured. One of these Gd (Ⅲ) complexes was chosen for the acute toxicity test and T1-weighted imaging measurement. Preliminary results showed that. compared with Gd-DTPA, the neutral macromolecular gadolinium (Ⅲ) complexes provide higher T1 relaxivity enhancement and longer function duration.

  4. Effect of Joule heating and current crowding on electromigration in mobile technology

    Science.gov (United States)

    Tu, K. N.; Liu, Yingxia; Li, Menglu

    2017-03-01

    In the present era of big data and internet of things, the use of microelectronic products in all aspects of our life is manifested by the ubiquitous presence of mobile devices as i-phones and wearable i-products. These devices are facing the need for higher power and greater functionality applications such as in i-health, yet they are limited by physical size. At the moment, software (Apps) is much ahead of hardware in mobile technology. To advance hardware, the end of Moore's law in two-dimensional integrated circuits can be extended by three-dimensional integrated circuits (3D ICs). The concept of 3D ICs has been with us for more than ten years. The challenge in 3D IC technology is dense packing by using both vertical and horizontal interconnections. Mass production of 3D IC devices is behind schedule due to cost because of low yield and uncertain reliability. Joule heating is serious in a dense structure because of heat generation and dissipation. A change of reliability paradigm has advanced from failure at a specific circuit component to failure at a system level weak-link. Currently, the electronic industry is introducing 3D IC devices in mainframe computers, where cost is not an issue, for the purpose of collecting field data of failure, especially the effect of Joule heating and current crowding on electromigration. This review will concentrate on the positive feedback between Joule heating and electromigration, resulting in an accelerated system level weak-link failure. A new driving force of electromigration, the electric potential gradient force due to current crowding, will be reviewed critically. The induced failure tends to occur in the low current density region.

  5. Dynamics of Crowd Behaviors: From Complex Plane to Quantum Random Fields

    Science.gov (United States)

    Ivancevic, Vladimir G.; Reid, Darryn J.

    2015-11-01

    The following sections are included: * Complex Plane Dynamics of Crowds and Groups * Introduction * Complex-Valued Dynamics of Crowd and Group Behaviors * Kähler Geometry of Crowd and Group Dynamics * Computer Simulations of Crowds and Croups Dynamics * Braids of Agents' Behaviors in the Complex Plane * Hilbert-Space Control of Crowds and Groups Dynamics * Quantum Random Fields: A Unique Framework for Simulation, Optimization, Control and Learning * Introduction * Adaptive Quantum Oscillator * Optimization and Learning on Banach and Hilbert Spaces * Appendix * Complex-Valued Image Processing * Linear Integral Equations * Riemann-Liouville Fractional Calculus * Rigorous Geometric Quantization * Supervised Machine-Learning Methods * First-Order Logic and Quantum Random Fields

  6. Global and local magnetic mapping using CrowdMag data

    Science.gov (United States)

    Saltus, R.; Nair, M. C.

    2016-12-01

    NOAA's National Centers for Environmental Information (NCEI), in partnership with the University of Colorado's CIRES develop magnetic field models to aid navigation, resource exploration and scientific research. We use observatories, satellites and ship/airborne surveys to map and model the Earth's magnetic field. However, the available measurements leave gaps in coverage, particularly for short-wavelength anomalies associated with man-made infrastructure ("urban noise"). In 2014, we started a project to address these gaps through the collection of vector magnetic data from digital magnetometers in smartphones. In October 2014, we released the "CrowdMag" Android and iOS apps for harvesting data from phones. Currently, the CrowdMag project has more than 10,000 enthusiastic users contributing more than 12 million magnetic data measurements from around the world. We present the first analysis results from the crowdsourced magnetic data. A global magnetic model derived solely from CrowdMag data is consistent to degree and order 4 with satellite-derived models such as World Magnetic Model. A unique contribution of CrowdMag project is the collection of ground level magnetic data in densely populated regions with an unprecedented spatial resolution. To demonstrate, we generated a magnetic map (by binning the data collected in 200x200m cells) of central Boulder, Colorado using 170,000 data points collected by about 60 devices over the duration October 2014- January 2016. The median value is consistent with the expected magnitude of the Earth's background magnetic field. The standard deviation of the CrowdMag total field (F) values is much higher than the expected natural (i.e., diurnal and geologic) magnetic field variation. However, the phone's magnetometer is sensitive enough to capture the larger magnitude magnetic signature from the urban magnetic sources. We discuss the potential reliability of crowdsourced magnetic maps and their applications to navigation and other

  7. The effects of crowding on eye movement patterns in reading.

    Science.gov (United States)

    Bricolo, Emanuela; Salvi, Carola; Martelli, Marialuisa; Arduino, Lisa S; Daini, Roberta

    2015-09-01

    Crowding is a phenomenon that characterizes normal periphery limiting letter identification when other letters surround the signal. We investigated the nature of the reading limitation of crowding by analyzing eye-movement patterns. The stimuli consisted of two items varying across trials for letter spacing (spaced, unspaced and increased size), lexicality (words or pseudowords), number of letters (4, 6, 8), and reading modality (oral and silent). In Experiments 1 and 2 (oral and silent reading, respectively) the results show that an increase in letter spacing induced an increase in the number of fixations and in gaze duration, but a reduction in the first fixation duration. More importantly, increasing letter size (Experiment 3) produced the same first fixation duration advantage as empty spacing, indicating that, as predicted by crowding, only center-to-center letter distance, and not spacing per se, matters. Moreover, when the letter size was enlarged the number of fixations did not increase as much as in the previous experiments, suggesting that this measure depends on visual acuity rather than on crowding. Finally, gaze duration, a measure of word recognition, did not change with the letter size enlargement. No qualitative differences were found between oral and silent reading experiments (1 and 2), indicating that the articulatory process did not influence the outcome. Finally, a facilitatory effect of lexicality was found in all conditions, indicating an interaction between perceptual and lexical processing. Overall, our results indicate that crowding influences normal word reading by means of an increase in first fixation duration, a measure of word encoding, which we interpret as a modulatory effect of attention on critical spacing.

  8. 基于心理调查和空间干预的人群心理仿真%Crowd Psychology Simulation Incorporating Psychometrics and Intervention of Relationship Spaces

    Institute of Scientific and Technical Information of China (English)

    廖东升; 侯波南; 王兵; 郭勤; 郭静

    2011-01-01

    Computer simulation is a promising approach to better understand the crowd psychological dynamics. The lack of real data in crowd simulations, however, usually results in heavy dependence on assumptions, and thus hampers the confidence. This research presents the simulation of crowds under confrontation of psychological stimuli, which focuses on the psychological aspect of the crowd and introduces the intervention between two different relationship spaces in the crowd. Firstly, with the agent-based approach, psychometrics is employed in the construction of the individual model to improve the trustworthiness. Secondly, the research describe, by means of the model, the phenomenon that individuals tend to get involved in various relationship spaces, which plays an important role in the procedure of psychological propagation. Finally, a scenario of a crowd in large-scale public activity under terrorist threat is studied, in which the workflow for psychometrics based crowd simulation is demonstrated, and the preliminary results are also discussed.%突发危机事件中人群心理评估是当前危机管理急需解决的难点问题.由于突发危机事件群体心理数据采集的困难性和人群心理变化的复杂性等原因,传统方法很难准确评估群体心理效果.随着计算机科学的发展,建模仿真成为解决这类问题的有效手段.以复杂适应系统理论为指导,采用基于Agent的建模与仿真方法,研究外部事件刺激下群体的心理行为,构建群体心理评估模型,开发人群心理评估系统.根据心理调查结果,将个体建立为自主的Agent模型,个体之间按照心理驱动行为方式进行交互,完成心理传播过程.将影响个体心理的外部刺激事件采用五元组量化表示.将群体中的正式组织和非正式组织建立平行组织模型.以实际案例进行仿真实验,验证了模型的科学性和有效性.

  9. A versatile microparticle-based immunoaggregation assay for macromolecular biomarker detection and quantification.

    Directory of Open Access Journals (Sweden)

    Haiyan Wu

    Full Text Available The rapid, sensitive and low-cost detection of macromolecular biomarkers is critical in clinical diagnostics, environmental monitoring, research, etc. Conventional assay methods usually require bulky, expensive and designated instruments and relative long assay time. For hospitals and laboratories that lack immediate access to analytical instruments, fast and low-cost assay methods for the detection of macromolecular biomarkers are urgently needed. In this work, we developed a versatile microparticle (MP-based immunoaggregation method for the detection and quantification of macromolecular biomarkers. Antibodies (Abs were firstly conjugated to MP through streptavidin-biotin interaction; the addition of macromolecular biomarkers caused the aggregation of Ab-MPs, which were subsequently detected by an optical microscope or optical particle sizer. The invisible nanometer-scale macromolecular biomarkers caused detectable change of micrometer-scale particle size distributions. Goat anti-rabbit immunoglobulin and human ferritin were used as model biomarkers to demonstrate MP-based immunoaggregation assay in PBS and 10% FBS to mimic real biomarker assay in the complex medium. It was found that both the number ratio and the volume ratio of Ab-MP aggregates caused by biomarker to all particles were directly correlated to the biomarker concentration. In addition, we found that the detection range could be tuned by adjusting the Ab-MP concentration. We envision that this novel MP-based immunoaggregation assay can be combined with multiple detection methods to detect and quantify macromolecular biomarkers at the nanogram per milliliter level.

  10. 外商直接投资对国内投资挤入挤出效应的重新检验%Retesting the Crowd out and Crowd in Effects of Foreign Direct Investments on Domestic Investments

    Institute of Scientific and Technical Information of China (English)

    王志鹏; 李子奈

    2004-01-01

    By reconstructing the absolute crowding in or out relationship between FDI and domestic investment, we correct the flaws of the existed relative crowding in or out model. Using larger sample of Panel data and comparing the different estimates from "absolute" and "relative" models, we find no significant crowding in or out effects in China from the country level. However, further study reveals that the crowding in or out effects show a fine regional characteristic:crowding out effects dominate in eastern China, crowding in effects lead in mid China, and crowding out effects are insignificant in west China.

  11. JBluIce-EPICS control system for macromolecular crystallography.

    Energy Technology Data Exchange (ETDEWEB)

    Stepanov, S.; Makarov, O.; Hilgart, M.; Pothineni, S.; Urakhchin, A.; Devarapalli, S.; Yoder, D.; Becker, M.; Ogata, C.; Sanishvili, R.; Nagarajan, V.; Smith, J. L.; Fischetti, R. F. (Biosciences Division); (Univ. of Michigan)

    2011-01-01

    The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline component. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallographic experiments, especially in the field of microcrystallography.

  12. Patch-clamp detection of macromolecular translocation along nuclear pores

    Directory of Open Access Journals (Sweden)

    Bustamante J.O.

    1998-01-01

    Full Text Available The present paper reviews the application of patch-clamp principles to the detection and measurement of macromolecular translocation along the nuclear pores. We demonstrate that the tight-seal 'gigaseal' between the pipette tip and the nuclear membrane is possible in the presence of fully operational nuclear pores. We show that the ability to form a gigaseal in nucleus-attached configurations does not mean that only the activity of channels from the outer membrane of the nuclear envelope can be detected. Instead, we show that, in the presence of fully operational nuclear pores, it is likely that the large-conductance ion channel activity recorded derives from the nuclear pores. We conclude the technical section with the suggestion that the best way to demonstrate that the nuclear pores are responsible for ion channel activity is by showing with fluorescence microscopy the nuclear translocation of ions and small molecules and the exclusion of the same from the cisterna enclosed by the two membranes of the envelope. Since transcription factors and mRNAs, two major groups of nuclear macromolecules, use nuclear pores to enter and exit the nucleus and play essential roles in the control of gene activity and expression, this review should be useful to cell and molecular biologists interested in understanding how patch-clamp can be used to quantitate the translocation of such macromolecules into and out of the nucleus

  13. Timely deposition of macromolecular structures is necessary for peer review

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-12-01

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

  14. Synchrotron radiation macromolecular crystallography: science and spin-offs

    Directory of Open Access Journals (Sweden)

    John R. Helliwell

    2015-03-01

    Full Text Available A current overview of synchrotron radiation (SR in macromolecular crystallography (MX instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development.

  15. New concepts and applications in the macromolecular chemistry of fullerenes.

    Science.gov (United States)

    Giacalone, Francesco; Martín, Nazario

    2010-10-08

    A new classification on the different types of fullerene-containing polymers is presented according to their different properties and applications they exhibit in a variety of fields. Because of their interest and novelty, water-soluble and biodegradable C(60)-polymers are discussed first, followed by polyfullerene-based membranes where unprecedented supramolecular structures are presented. Next are compounds that involve hybrid materials formed from fullerenes and other components such as silica, DNA, and carbon nanotubes (CNTs) where the most recent advances have been achieved. A most relevant topic is still that of C(60)-based donor-acceptor (D-A) polymers. Since their application in photovoltaics D-A polymers are among the most realistic applications of fullerenes in the so-called molecular electronics. The most relevant aspects in these covalently connected fullerene/polymer hybrids as well as new concepts to improve energy conversion efficiencies are presented.The last topics disccused relate to supramolecular aspects that are in involved in C(60)-polymer systems and in the self-assembly of C(60)-macromolecular structures, which open a new scenario for organizing, by means of non-covalent interactions, new supramolecular structures at the nano- and micrometric scale, in which the combination of the hydrofobicity of fullerenes with the versatility of the noncovalent chemistry afford new and spectacular superstructures.

  16. Macromolecular metallurgy of binary mesocrystals via designed multiblock terpolymers.

    Science.gov (United States)

    Xie, Nan; Liu, Meijiao; Deng, Hanlin; Li, Weihua; Qiu, Feng; Shi, An-Chang

    2014-02-26

    Self-assembling block copolymers provide access to the fabrication of various ordered phases. In particular, the ordered spherical phases can be used to engineer soft mesocrystals with domain size at the 5-100 nm scales. Simple block copolymers, such as diblock copolymers, form a limited number of mesocrystals. However multiblock copolymers are capable to form more complex mesocrystals. We demonstrate that designed B1AB2CB3 multiblock terpolymers, in which the A- and C-blocks form spherical domains and the packing of these spheres can be controlled by changing the lengths of the middle and terminal B-blocks, self-assemble into various binary mesocrystals with space group symmetries of a large number of binary ionic crystals, including NaCl, CsCl, ZnS, α-BN, AlB2, CaF2, TiO2, ReO3, Li3Bi, Nb3Sn(A15), and α-Al2O3. This approach can be generalized to other terpolymers as well as to tetrapolymers to obtain ternary mesocrystals. Our study provides a new concept of macromolecular metallurgy for producing crystal phases in a mesoscale and thus makes multiblock copolymers a robust platform for the engineering of functional materials.

  17. Macromolecular Powder Diffraction: Ready for genuine biological problems.

    Science.gov (United States)

    Karavassili, Fotini; Margiolaki, Irene

    2016-01-01

    Knowledge of 3D structures of biological molecules plays a major role in both understanding important processes of life and developing pharmaceuticals. Among several methods available for structure determination, macromolecular X-ray powder diffraction (XRPD) has transformed over the past decade from an impossible dream to a respectable method. XRPD can be employed in biosciences for various purposes such as observing phase transitions, characterizing bulk pharmaceuticals, determining structures via the molecular replacement method, detecting ligands in protein-ligand complexes, as well as combining micro-sized single crystal crystallographic data and powder diffraction data. Studies using synchrotron and laboratory sources in some standard configuration setups are reported in this review, including their respective advantages and disadvantages. Methods presented here provide an alternative, complementary set of tools to resolve structural problems. A variety of already existing software packages for powder diffraction data processing and analysis, some of which have been adapted to large unit cell studies, are briefly described. This review aims to provide necessary elements of theory and current methods, along with practical explanations, available software packages and highlighted case studies.

  18. Canadian macromolecular crystallography facility: a suite of fully automated beamlines.

    Science.gov (United States)

    Grochulski, Pawel; Fodje, Michel; Labiuk, Shaunivan; Gorin, James; Janzen, Kathryn; Berg, Russ

    2012-06-01

    The Canadian light source is a 2.9 GeV national synchrotron radiation facility located on the University of Saskatchewan campus in Saskatoon. The small-gap in-vacuum undulator illuminated beamline, 08ID-1, together with the bending magnet beamline, 08B1-1, constitute the Canadian Macromolecular Crystallography Facility (CMCF). The CMCF provides service to more than 50 Principal Investigators in Canada and the United States. Up to 25% of the beam time is devoted to commercial users and the general user program is guaranteed up to 55% of the useful beam time through a peer-review process. CMCF staff provides "Mail-In" crystallography service to users with the highest scored proposals. Both beamlines are equipped with very robust end-stations including on-axis visualization systems, Rayonix 300 CCD series detectors and Stanford-type robotic sample auto-mounters. MxDC, an in-house developed beamline control system, is integrated with a data processing module, AutoProcess, allowing full automation of data collection and data processing with minimal human intervention. Sample management and remote monitoring of experiments is enabled through interaction with a Laboratory Information Management System developed at the facility.

  19. Crowd Behaviour during High-Stress Evacuations in an Immersive Virtual Environment

    CERN Document Server

    Moussaïd, Mehdi; Thrash, Tyler; Sumner, Robert W; Gross, Markus; Helbing, Dirk; Hölscher, Christoph

    2016-01-01

    Understanding the collective dynamics of crowd movements during stressful emergency situations is central to reducing the risk of deadly crowd disasters. Yet, their systematic experimental study remains a challenging open problem due to ethical and methodological constraints. In this paper, we demonstrate the viability of shared 3D virtual environments as an experimental platform for conducting crowd experiments with real people. In particular, we show that crowds of real human subjects moving and interacting in an immersive 3D virtual environment exhibit typical patterns of real crowds as observed in real-life crowded situations. These include the manifestation of social conventions and the emergence of self-organized patterns during egress scenarios. High-stress evacuation experiments conducted in this virtual environment reveal movements characterized by mass herding and dangerous overcrowding as they occur in crowd disasters. We describe the behavioral mechanisms at play under such extreme conditions and ...

  20. Factors Influencing Perceived Crowding of Tourists and Sustainable Tourism Destination Management

    Directory of Open Access Journals (Sweden)

    Qian Jin

    2016-09-01

    Full Text Available Studies on tourists crowding are developed to explore the perception of crowding, and these studies indicate crowding influence on sustainable development of tourist destinations. This study aims to reveal the influential factors of tourists’ perceived crowding. We obtained data from interviewing over 400 tourists and five senior tourism officials in Xi’an, China. This study firstly applies factor analysis to identify the constructed variables of tourists’ motivations from the principle component analysis. It then examines the correlation between nationality and perceived crowding. Consequently, a multiple regression is used to identify the connection between motivations and perceived crowding. The results of the study indicate nationality and motivation as two significant influential factors to perceived crowding management. This study also shows that management in tourist destinations would benefit from provision of the authentic travel experience integrated with zoning the travel destination.

  1. DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions.

    Science.gov (United States)

    Kuang, Xingyan; Dhroso, Andi; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

    2016-01-01

    Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction's mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein-protein interactions or protein-DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1,040,000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43,000 RNA-mediated interactions, and ∼12,000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network

  2. Non-contact luminescence lifetime cryothermometry for macromolecular crystallography.

    Science.gov (United States)

    Mykhaylyk, V B; Wagner, A; Kraus, H

    2017-05-01

    Temperature is a very important parameter when aiming to minimize radiation damage to biological samples during experiments that utilize intense ionizing radiation. A novel technique for remote, non-contact, in situ monitoring of the protein crystal temperature has been developed for the new I23 beamline at the Diamond Light Source, a facility dedicated to macromolecular crystallography (MX) with long-wavelength X-rays. The temperature is derived from the temperature-dependent decay time constant of luminescence from a minuscule scintillation sensor (luminescence lifetime thermometry is presented, the features of the detection method and the choice of temperature sensor are discussed, and it is demonstrated how the temperature monitoring system was integrated within the viewing system of the endstation used for the visualization of protein crystals. The thermometry system was characterized using a Bi4Ge3O12 crystal scintillator that exhibits good responsivity of the decay time constant as a function of temperature over a wide range (8-270 K). The scintillation sensor was calibrated and the uncertainty of the temperature measurements over the primary operation temperature range of the beamline (30-150 K) was assessed to be ±1.6 K. It has been shown that the temperature of the sample holder, measured using the luminescence sensor, agrees well with the expected value. The technique was applied to characterize the thermal performance of different sample mounts that have been used in MX experiments at the I23 beamline. The thickness of the mount is shown to have the greatest impact upon the temperature distribution across the sample mount. Altogether, these tests and findings demonstrate the usefulness of the thermometry system in highlighting the challenges that remain to be addressed for the in-vacuum MX experiment to become a reliable and indispensable tool for structural biology.

  3. A Compact X-Ray System for Macromolecular Crystallography. 5

    Science.gov (United States)

    Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Joy, Marshall

    2000-01-01

    We describe the design and performance of a high flux x-ray system for macromolecular crystallography that combines a microfocus x-ray generator (40 gm FWHM spot size at a power level of 46.5Watts) and a 5.5 mm focal distance polycapillary optic. The Cu K(sub alpha) X-ray flux produced by this optimized system is 7.0 times above the X-ray flux previously reported. The X-ray flux from the microfocus system is also 3.2 times higher than that produced by the rotating anode generator equipped with a long focal distance graded multilayer monochromator (Green optic; CMF24-48-Cu6) and 30% less than that produced by the rotating anode generator with the newest design of graded multilayer monochromator (Blue optic; CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 Watts, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42,540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym) 5.0% for the data extending to 1.7A, and 4.8% for the complete set of data to 1.85A. The amplitudes of the reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

  4. A Compact X-Ray System for Macromolecular Crystallography

    Science.gov (United States)

    Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Gibson, Walter; Joy, Marshall

    2000-01-01

    We describe the design and performance of a high flux x-ray system for a macromolecular crystallography that combines a microfocus x-ray generator (40 micrometer full width at half maximum spot size at a power level of 46.5 W) and a collimating polycapillary optic. The Cu Ka lpha x-ray flux produced by this optimized system through a 500,um diam orifice is 7.0 times greater than the x-ray flux previously reported by Gubarev et al. [M. Gubarev et al., J. Appl. Crystallogr. 33, 882 (2000)]. The x-ray flux from the microfocus system is also 2.6 times higher than that produced by a rotating anode generator equipped with a graded multilayer monochromator (green optic, Osmic Inc. CMF24-48-Cu6) and 40% less than that produced by a rotating anode generator with the newest design of graded multilayer monochromator (blue optic, Osmic, Inc. CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 W, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42 540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym)=5.0% for data extending to 1.70 A, and 4.8% for the complete set of data to 1.85 A. The amplitudes of the observed reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

  5. The Effect of Aging on Crowded Letter Recognition in the Peripheral Visual Field

    Science.gov (United States)

    Astle, Andrew T.; Blighe, Alan J.; Webb, Ben S.; McGraw, Paul V.

    2014-01-01

    Purpose. Crowding describes the increased difficulty in identifying a target object when it is surrounded by nearby objects (flankers). A recent study investigated the effect of age on visual crowding and found equivocal results: Although crowded visual acuity was worse in older participants, crowding expressed as a ratio did not change with age. However, the spatial extent of crowding is a better index of crowding effects and remains unknown. In the present study, we used established psychophysical methods to characterize the effect of age on visual crowding (magnitude and extent) in a letter recognition task. Methods. Letter recognition thresholds were determined for three different flanker separations in 54 adults (aged 18–76 years) with normal vision. Additionally, the spatial extent of crowding was established by measuring spacing thresholds: the flanker-to-target separation required to produce a given reduction in performance. Uncrowded visual acuity, crowded visual acuity, and spacing thresholds were expressed as a function of age, avoiding arbitrary categorization of young and old participants. Results. Our results showed that uncrowded and crowded visual acuities do not change significantly as a function of age. Furthermore, spacing thresholds did not change with age and approximated Bouma's law (half eccentricity). Conclusions. These data show that crowding in adults is unaffected by senescence and provide additional evidence for distinct neural mechanisms mediating surround suppression and visual crowding, since the former shows a significant age effect. Finally, our data suggest that the well-documented age-related decline in peripheral reading ability is not due to age-related changes in visual crowding. PMID:24985476

  6. Saliency-based abnormal event detection in crowded scenes

    Science.gov (United States)

    Shi, Yanjiao; Liu, Yunxiang; Zhang, Qing; Yi, Yugen; Li, Wenju

    2016-11-01

    Abnormal event detection plays a critical role for intelligent video surveillance, and detection in crowded scenes is a challenging but more practical task. We present an abnormal event detection method for crowded video. Region-wise modeling is proposed to address the inconsistent detected motion of the same object due to different depths of field. Comparing to traditional block-wise modeling, the region-wise method not only can reduce heavily the number of models to be built but also can enrich the samples for training the normal events model. In order to reduce the computational burden and make the region-based anomaly detection feasible, a saliency detection technique is adopted in this paper. By identifying the salient parts of the image sequences, the irrelevant blocks are ignored, which removes the disturbance and improves the detection performance further. Experiments on the benchmark dataset and comparisons with the state-of-the-art algorithms validate the advantages of the proposed method.

  7. Foot force models of crowd dynamics on a wobbly bridge

    CERN Document Server

    Belykh, Igor; Belykh, Vladamir

    2016-01-01

    Modern pedestrian and suspension bridges are designed using industry-standard packages, yet disastrous resonant vibrations are observed, necessitating multi-million dollar repairs. Recent examples include pedestrian induced vibrations during the openings of the Solf\\'erino Bridge in Paris in 1999 and the increased bouncing of the Squibb Park Bridge in Brooklyn in 2014. The most prominent example of an unstable lively bridge is the London Millennium Bridge which started wobbling as a result of pedestrian-bridge interactions. Pedestrian phase-locking due to footstep phase adjustment, is suspected to be the main cause of its large lateral vibrations; however, its role in the initiation of wobbling was debated. In this paper, we develop foot force models of pedestrians' response to bridge motion and detailed, yet analytically tractable models of crowd phase-locking. We use bio-mechanically inspired models of crowd lateral movement to investigate to what degree pedestrian synchrony must be present for a bridge to ...

  8. Crowding effect on helix-coil transition: Beyond entropic stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Koutsioubas, A.; Lairez, D.; Combet, S.; Longeville, S. [Laboratoire Leon Brillouin, CEA/CNRS UMR 12, CEA-Saclay, 91191 Gif-sur-Yvette Cedex (France); Fadda, G. C. [Laboratoire Leon Brillouin, CEA/CNRS UMR 12, CEA-Saclay, 91191 Gif-sur-Yvette Cedex (France); Universite Paris 13, UFR SMBH, 93017 Bobigny (France); Zalczer, G. [Service de Physique de l' Etat Condense, CEA-Saclay, 91191 Gif-sur-Yvette Cedex (France)

    2012-06-07

    We report circular dichroism measurements on the helix-coil transition of poly(L-glutamic acid) in solution with polyethylene glycol (PEG) as a crowding agent. The PEG solutions have been characterized by small angle neutron scattering and are well described by the picture of a network of mesh size {xi}, usual for semi-dilute chains in good solvent. We show that the increase of PEG concentration stabilizes the helices and increases the transition temperature. But more unexpectedly, we also notice that the increase of concentration of crowding agent reduces the mean helix extent at the transition, or in other words reduces its cooperativity. This result cannot be taken into account for by an entropic stabilization mechanism. Comparing the mean length of helices at the transition and the mesh size of the PEG network, our results strongly suggest two regimes: helices shorter or longer than the mesh size.

  9. WORLD POLITICS NETWORK: FROM CONCEPTUALIZATION PROBLEM TO THE CROWD GLOBALIZATION

    Directory of Open Access Journals (Sweden)

    Dmitry Feldman

    2014-01-01

    Full Text Available The article deals with theoretical problems associated with understanding of world politics as a network object. The author assumes that the transformation of world politics in a global, global network actualizes the study of the individual as its most ancient and constant actor, acting according to the «rules of the network». He sets out his understanding of the network approach to world politics and analysis of the subject-object relations arising in the course of development of the world political processes. A significant attention is paid to crowd facing the global arena and opportunities of manipulating them. Mastered means of access to global communication networks crowd gets the opportunity of «governance without government». This, according to the author, can’t turn him into a trendsetter in world politics. 

  10. SPITZER IRAC PHOTOMETRY FOR TIME SERIES IN CROWDED FIELDS

    Energy Technology Data Exchange (ETDEWEB)

    Novati, S. Calchi; Beichman, C. [NASA Exoplanet Science Institute, MS 100-22, California Institute of Technology, Pasadena, CA 91125 (United States); Gould, A.; Fausnaugh, M.; Gaudi, B. S.; Pogge, R. W.; Wibking, B.; Zhu, W.; Poleski, R. [Department of Astronomy, Ohio State University, 140 W. 18th Ave., Columbus, OH 43210 (United States); Yee, J. C. [Harvard-Smithsonian Center for Astrophysics, 60 Garden St., Cambridge, MA 02138 (United States); Bryden, G.; Henderson, C. B.; Shvartzvald, Y. [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Carey, S. [Spitzer, Science Center, MS 220-6, California Institute of Technology, Pasadena, CA (United States); Udalski, A.; Pawlak, M.; Szymański, M. K.; Skowron, J.; Mróz, P.; Kozłowski, S. [Warsaw University Observatory, Al. Ujazdowskie 4, 00-478 Warszawa (Poland); Collaboration: Spitzer team; OGLE group; and others

    2015-12-01

    We develop a new photometry algorithm that is optimized for the Infrared Array Camera (IRAC) Spitzer time series in crowded fields and that is particularly adapted to faint or heavily blended targets. We apply this to the 170 targets from the 2015 Spitzer microlensing campaign and present the results of three variants of this algorithm in an online catalog. We present detailed accounts of the application of this algorithm to two difficult cases, one very faint and the other very crowded. Several of Spitzer's instrumental characteristics that drive the specific features of this algorithm are shared by Kepler and WFIRST, implying that these features may prove to be a useful starting point for algorithms designed for microlensing campaigns by these other missions.

  11. Spitzer IRAC Photometry for Time Series in Crowded Fields

    CERN Document Server

    Novati, S Calchi; Yee, J C; Beichman, C; Bryden, G; Carey, S; Fausnaugh, M; Gaudi, B S; Henderson, C B; Pogge, R W; Shvartzvald, Y; Wibking, B; Zhu, W; Udalski, A; Poleski, R; Pawlak, M; Szymański, M K; Skowron, J; Mróz, P; Kozłowski, S; Wyrzykowski, Ł; Pietrukowicz, P; Pietrzyński, G; Soszyński, I; Ulaczyk, K

    2015-01-01

    We develop a new photometry algorithm that is optimized for $Spitzer$ time series in crowded fields and that is particularly adapted to faint and/or heavily blended targets. We apply this to the 170 targets from the 2015 $Spitzer$ microlensing campaign and present the results of three variants of this algorithm in an online catalog. We present detailed accounts of the application of this algorithm to two difficult cases, one very faint and the other very crowded. Several of $Spitzer$'s instrumental characteristics that drive the specific features of this algorithm are shared by $Kepler$ and $WFIRST$, implying that these features may prove to be a useful starting point for algorithms designed for microlensing campaigns by these other missions.

  12. Emergence of collective intonation in the musical performance of crowds

    Science.gov (United States)

    Lacasa, Lucas

    2016-09-01

    The average individual is typically a mediocre singer, with a rather restricted capacity to sing a melody in tune. Yet when many singers are assembled to perform collectively, the resulting melody of the crowd is suddenly perceived by an external listener as perfectly tuned —as if it was actually a choral performance— even if each individual singer is out of tune. This collective phenomenon is an example of a wisdom of crowds effect that can be routinely observed in music concerts or other social events, when a group of people spontaneously sings at unison. In this paper we rely on the psychoacoustic properties of pitch and provide a simple mechanistic explanation for the onset of this emergent behavior.

  13. Crowd-Sourcing the Aesthetics of Platform Games

    DEFF Research Database (Denmark)

    Shaker, Noor; Yannakakis, Georgios N.; Togelius, Julian

    2014-01-01

    What are the aesthetics of platform games and what makes a platform level engaging, challenging and/or frustrating? We attempt to answer such questions through mining a large-set of crowd-sourced gameplay data of a clone of the classic platform game Super Mario Bros. The data consists of 40 short...... game levels that differ along six key level design parameters. Collectively, these levels are played 1560 times over the Internet and the perceived experience is annotated by experiment participants via self-reported ranking (pairwise preferences). Given the wealth of this crowd-sourced data, as all...... details about players’ in-game behaviour are logged, the problem becomes one of extracting meaningful numerical features at the appropriate level of abstraction for the construction of generic computational models of player experience and, thereby, game aesthetics. We explore dissimilar types of features...

  14. A physically-based particle model of emergent crowd behaviors

    CERN Document Server

    Heïgeas, Laure; Thollot, Joëlle; Castagné, Nicolas

    2010-01-01

    This paper presents a modeling process in order to produce a realistic simulation of crowds in the ancient Greek agora of Argos. This place was a social theater in which two kinds of collective phenomena took place: interpersonal interactions (small group discussion and negotiation, etc.) and global collective phenomena, such as flowing and jamming. In this paper, we focus on the second type of collective human phenomena, called non-deliberative emergent crowd phenomena. This is a typical case of collective emergent self-organization. When a great number of individuals move within a confined environment and under a common fate, collective structures appear spontaneously: jamming with inner collapses, organized flowing with queues, curls, and vortices, propagation effects, etc. These are particularly relevant features to enhance the realism - more precisely the "truthfulness" - of models of this kind of collective phenomena. We assume that this truthfulness is strongly associated with the concept of emergence:...

  15. CrowdFounder:众筹需有法可依

    Institute of Scientific and Technical Information of China (English)

    柯实

    2014-01-01

    CrowdFounder创办不到一年,但在它的平台上,已有25家初创公司完成了天使轮和A轮融资,有超过1万家初创公司和超过6万个VC和受信投资人在该平台上进行投融资交流。作为股权众筹平台,CrowdFounder与其他众筹平台如Indiegogo、KickStarter等的不同之处在于,投资人在该平台募款后,可以得到被投资公司的股权,而不只是商品或服务。

  16. Structures and functions in the crowded nucleus: new biophysical insights

    Directory of Open Access Journals (Sweden)

    Ronald eHancock

    2014-09-01

    Full Text Available Concepts and methods from the physical sciences have catalysed remarkable progress in understanding the cell nucleus in recent years. To share this excitement with physicists and encourage their interest in this field, this review offers an overview of how the physics which underlies structures and functions in the nucleus is becoming more clear thanks to methods which have been developed to simulate and study macromolecules, polymers, and colloids. The environment in the nucleus is very crowded with macromolecules, making entropic (depletion forces major determinants of interactions. Simulation and experiments are consistent with their key role in forming membraneless compartments such as nucleoli, PML and Cajal bodies, and discrete territories for chromosomes. The chromosomes, giant linear polyelectrolyte polymers, exist in vivo in a state like a polymer melt. Looped conformations are predicted in crowded conditions, and have been confirmed experimentally and are central to the regulation of gene expression. Polymer theory has revealed how the chromosomes are so highly compacted in the nucleus, forming a crumpled globule with fractal properties which avoids knots and entanglements in DNA while allowing facile accessibility for its replication and transcription. Entropic repulsion between looped polymers can explain the confinement of each chromosome to a discrete region of the nucleus. Crowding and looping are predicted to facilitate finding the specific targets of factors which modulate activities of DNA. Simulation shows that entropic effects contribute to finding and repairing potentially lethal double-strand breaks in DNA by increasing the mobility of the broken ends, favouring their juxtaposition for repair. Signaling pathways are strongly influenced by crowding, which favours a processive mode of response (consecutive reactions without releasing substrates. This new information contributes to understanding the sometimes counter

  17. Task-based crowd simulation for heterogeneous architectures

    OpenAIRE

    Perez, Hugo; Hernandez, Benjamin; Rudomin, Isaac; Ayguadé Parra, Eduard

    2016-01-01

    Industry trends in the coming years imply the availability of cluster computing with hundreds to thousands of cores per chip, as well as the use of accelerators. Programming presents a challenge due to this heterogeneous architecture; thus, using novel programming models that facilitate this process is necessary. In this chapter, the case of simulation and visualization of crowds is presented. The authors analyze and compare the use of two programming models: OmpSs and CUDA. OmpSs allows to t...

  18. Crowds As Complex Adaptive Systems: Strategic Implications For Law Enforcement

    Science.gov (United States)

    2016-03-01

    through critical analysis . A number of recommendations regarding policy, training, and equipment are presented in this thesis. Regarding policy, police...sound methodological research and analysis presented in this thesis. At the strategic level, crowd control operations in emergent conditions must...Covington, and Marcia Zangrilli, “Sentiment & Discourse Analysis:Theory, Extraction and Application,” in Socio-Cultural Analysis with the RSI Paradigm, ed

  19. Crowded, Confined, and Frustrated: Dynamics of Molecules Tethered to Nanoparticles

    KAUST Repository

    Agarwal, Praveen

    2012-12-01

    Above a critical chemistry-dependent molecular weight, all polymer molecules entangle and, as a result, exhibit slow dynamics, enhanced viscosity, and elasticity. Herein we report on the dynamics of low molecular weight polymers tethered to nanoparticles and find that even conventionally unentangled chains manifest dynamical features similar to entangled, long-chain molecules. Our findings are shown to imply that crowding and confinement of polymers on particles produce topological constraints analogous to those in entangled systems. © 2012 American Physical Society.

  20. Crowded, confined, and frustrated: dynamics of molecules tethered to nanoparticles.

    Science.gov (United States)

    Agarwal, Praveen; Kim, Sung A; Archer, Lynden A

    2012-12-21

    Above a critical chemistry-dependent molecular weight, all polymer molecules entangle and, as a result, exhibit slow dynamics, enhanced viscosity, and elasticity. Herein we report on the dynamics of low molecular weight polymers tethered to nanoparticles and find that even conventionally unentangled chains manifest dynamical features similar to entangled, long-chain molecules. Our findings are shown to imply that crowding and confinement of polymers on particles produce topological constraints analogous to those in entangled systems.

  1. Structures and functions in the crowded nucleus: new biophysical insights

    Science.gov (United States)

    Hancock, Ronald

    2014-09-01

    Concepts and methods from the physical sciences have catalysed remarkable progress in understanding the cell nucleus in recent years. To share this excitement with physicists and encourage their interest in this field, this review offers an overview of how the physics which underlies structures and functions in the nucleus is becoming more clear thanks to methods which have been developed to simulate and study macromolecules, polymers, and colloids. The environment in the nucleus is very crowded with macromolecules, making entropic (depletion) forces major determinants of interactions. Simulation and experiments are consistent with their key role in forming membraneless compartments such as nucleoli, PML and Cajal bodies, and discrete "territories" for chromosomes. The chromosomes, giant linear polyelectrolyte polymers, exist in vivo in a state like a polymer melt. Looped conformations are predicted in crowded conditions, and have been confirmed experimentally and are central to the regulation of gene expression. Polymer theory has revealed how the chromosomes are so highly compacted in the nucleus, forming a "crumpled globule" with fractal properties which avoids knots and entanglements in DNA while allowing facile accessibility for its replication and transcription. Entropic repulsion between looped polymers can explain the confinement of each chromosome to a discrete region of the nucleus. Crowding and looping are predicted to facilitate finding the specific targets of factors which modulate activities of DNA. Simulation shows that entropic effects contribute to finding and repairing potentially lethal double-strand breaks in DNA by increasing the mobility of the broken ends, favouring their juxtaposition for repair. Signaling pathways are strongly influenced by crowding, which favours a processive mode of response (consecutive reactions without releasing substrates). This new information contributes to understanding the sometimes counter-intuitive consequences.

  2. The multi-niche crowding genetic algorithm: Analysis and applications

    Energy Technology Data Exchange (ETDEWEB)

    Cedeno, Walter [Univ. of California, Davis, CA (United States)

    1995-09-01

    The ability of organisms to evolve and adapt to the environment has provided mother nature with a rich and diverse set of species. Only organisms well adapted to their environment can survive from one generation to the next, transferring on the traits, that made them successful, to their offspring. Competition for resources and the ever changing environment drives some species to extinction and at the same time others evolve to maintain the delicate balance in nature. In this disertation we present the multi-niche crowding genetic algorithm, a computational metaphor to the survival of species in ecological niches in the face of competition. The multi-niche crowding genetic algorithm maintains stable subpopulations of solutions in multiple niches in multimodal landscapes. The algorithm introduces the concept of crowding selection to promote mating among members with qirnilar traits while allowing many members of the population to participate in mating. The algorithm uses worst among most similar replacement policy to promote competition among members with similar traits while allowing competition among members of different niches as well. We present empirical and theoretical results for the success of the multiniche crowding genetic algorithm for multimodal function optimization. The properties of the algorithm using different parameters are examined. We test the performance of the algorithm on problems of DNA Mapping, Aquifer Management, and the File Design Problem. Applications that combine the use of heuristics and special operators to solve problems in the areas of combinatorial optimization, grouping, and multi-objective optimization. We conclude by presenting the advantages and disadvantages of the algorithm and describing avenues for future investigation to answer other questions raised by this study.

  3. Traffic instabilities in self-organized pedestrian crowds.

    Directory of Open Access Journals (Sweden)

    Mehdi Moussaïd

    Full Text Available In human crowds as well as in many animal societies, local interactions among individuals often give rise to self-organized collective organizations that offer functional benefits to the group. For instance, flows of pedestrians moving in opposite directions spontaneously segregate into lanes of uniform walking directions. This phenomenon is often referred to as a smart collective pattern, as it increases the traffic efficiency with no need of external control. However, the functional benefits of this emergent organization have never been experimentally measured, and the underlying behavioral mechanisms are poorly understood. In this work, we have studied this phenomenon under controlled laboratory conditions. We found that the traffic segregation exhibits structural instabilities characterized by the alternation of organized and disorganized states, where the lifetime of well-organized clusters of pedestrians follow a stretched exponential relaxation process. Further analysis show that the inter-pedestrian variability of comfortable walking speeds is a key variable at the origin of the observed traffic perturbations. We show that the collective benefit of the emerging pattern is maximized when all pedestrians walk at the average speed of the group. In practice, however, local interactions between slow- and fast-walking pedestrians trigger global breakdowns of organization, which reduce the collective and the individual payoff provided by the traffic segregation. This work is a step ahead toward the understanding of traffic self-organization in crowds, which turns out to be modulated by complex behavioral mechanisms that do not always maximize the group's benefits. The quantitative understanding of crowd behaviors opens the way for designing bottom-up management strategies bound to promote the emergence of efficient collective behaviors in crowds.

  4. Crowding out intrinsic motivation in the public sector

    OpenAIRE

    Georgellis, Yannis; Iossa, Elisabetta; Tabvuma, Vurain

    2011-01-01

    Employing intrinsically motivated individuals has been proposed as a means of improving public sector performance. In this article, we investigate whether intrinsic motivation affects the sorting of employees between the private and the public sectors, paying particular attention to whether extrinsic rewards crowd out intrinsic motivation. Using British longitudinal data, we find that individuals are attracted to the public sector by the intrinsic rather than the extrinsic rewards that the se...

  5. Crowding out intrinsic motivation in the public sector

    OpenAIRE

    Georgellis, Yannis; Iossa, Elisabetta; Tabvuma, Vurain

    2011-01-01

    Employing intrinsically motivated individuals has been proposed as a means of improving public sector performance. In this article, we investigate whether intrinsic motivation affects the sorting of employees between the private and the public sectors, paying particular attention to whether extrinsic rewards crowd out intrinsic motivation. Using British longitudinal data, we find that individuals are attracted to the public sector by the intrinsic rather than the extrinsic rewards that the se...

  6. Large crowding zones in peripheral vision for briefly presented stimuli.

    Science.gov (United States)

    Tripathy, Srimant Prasad; Cavanagh, Patrick; Bedell, Harold E

    2014-12-30

    When a target is flanked by distractors, it becomes more difficult to identify. In the periphery, this crowding effect extends over a wide range of target-flanker separations, called the spatial extent of interaction (EoI). A recent study showed that the EoI dramatically increases in size for short presentation durations (Chung & Mansfield, 2009). Here we investigate this duration-EoI relation in greater detail and show that (a) it holds even when visibility of the unflanked target is equated for different durations, (b) the function saturates for durations shorter than 30 to 80 ms, and (c) the largest EoIs represent a critical spacing greater than 50% of eccentricity. We also investigated the effect of same or different polarity for targets and flankers across different presentation durations. We found that EoIs for target and flankers having opposite polarity (one white, the other black) show the same temporal pattern as for same polarity stimuli, but are smaller at all durations by 29% to 44%. The observed saturation of the EoI for short-duration stimuli suggests that crowding follows the locus of temporal integration. Overall, the results constrain theories that map crowding zones to fixed spatial extents or to lateral connections of fixed length in the cortex.

  7. Crowding deficits in the visual periphery of schizophrenia patients.

    Directory of Open Access Journals (Sweden)

    Rainer Kraehenmann

    Full Text Available Accumulating evidence suggests that basic visual information processing is impaired in schizophrenia. However, deficits in peripheral vision remain largely unexplored. Here we hypothesized that sensory processing of information in the visual periphery would be impaired in schizophrenia patients and, as a result, crowding - the breakdown in target recognition that occurs in cluttered visual environments - would be stronger. Therefore, we assessed visual crowding in the peripheral vision of schizophrenia patients and healthy controls. Subjects were asked to identify a target letter that was surrounded by distracter letters of similar appearance. Targets and distracters were displayed at 8° and 10° of visual angle from the fixation point (eccentricity, and target-distracter spacing was 2°, 3°, 4°, 5°, 6°, 7° or 8° of visual angle. Eccentricity and target-distracter spacing were randomly varied. Accuracy was defined as the proportion of correctly identified targets. Critical spacing was defined as the spacing at which target identification accuracy began to deteriorate, and was assessed at viewing eccentricities of 8° and 10°. Schizophrenia patients were less accurate and showed a larger critical spacing than healthy individuals. These results indicate that crowding is stronger and sensory processing of information in the visual periphery is impaired in schizophrenia. This is in line with previous reports of preferential magnocellular dysfunction in schizophrenia. Thus, deficits in peripheral vision may account for perceptual alterations and contribute to cognitive dysfunction in schizophrenia.

  8. Crowding deficits in the visual periphery of schizophrenia patients.

    Science.gov (United States)

    Kraehenmann, Rainer; Vollenweider, Franz X; Seifritz, Erich; Kometer, Michael

    2012-01-01

    Accumulating evidence suggests that basic visual information processing is impaired in schizophrenia. However, deficits in peripheral vision remain largely unexplored. Here we hypothesized that sensory processing of information in the visual periphery would be impaired in schizophrenia patients and, as a result, crowding - the breakdown in target recognition that occurs in cluttered visual environments - would be stronger. Therefore, we assessed visual crowding in the peripheral vision of schizophrenia patients and healthy controls. Subjects were asked to identify a target letter that was surrounded by distracter letters of similar appearance. Targets and distracters were displayed at 8° and 10° of visual angle from the fixation point (eccentricity), and target-distracter spacing was 2°, 3°, 4°, 5°, 6°, 7° or 8° of visual angle. Eccentricity and target-distracter spacing were randomly varied. Accuracy was defined as the proportion of correctly identified targets. Critical spacing was defined as the spacing at which target identification accuracy began to deteriorate, and was assessed at viewing eccentricities of 8° and 10°. Schizophrenia patients were less accurate and showed a larger critical spacing than healthy individuals. These results indicate that crowding is stronger and sensory processing of information in the visual periphery is impaired in schizophrenia. This is in line with previous reports of preferential magnocellular dysfunction in schizophrenia. Thus, deficits in peripheral vision may account for perceptual alterations and contribute to cognitive dysfunction in schizophrenia.

  9. Conservation of Energy for Crowd Self-Driven Motion

    CERN Document Server

    Wang, Peng; Marsh, Kerry L

    2013-01-01

    For centuries, how an object moves given external forces is characterized by physical laws. As for creatures like human, their movements are self-driven, and the driving forces are generated by intention of people in a psychological sense. How to capture this characteristic in consistency with known physics laws is meaningful to understand human behaviors. By investigating a Newtonian-like model of a pedestrian, this paper presents a fluid-like model of crowd, showing that the physical concept of energy is also suited for psychological study of human collective behaviors. An energy balance equation is derived to characterize how the energy is transformed between the psychological forms and physical forms: the psychological drive arises as a potential form of energy, which aims at either accelerating or compressing a crowd as transformed to energy in physical forms (e.g., kinetic energy or static energy). If such transformation cannot be realized, disorder of the crowd may appear as a possible result. Based on...

  10. Bayesian network model of crowd emotion and negative behavior

    Science.gov (United States)

    Ramli, Nurulhuda; Ghani, Noraida Abdul; Hatta, Zulkarnain Ahmad; Hashim, Intan Hashimah Mohd; Sulong, Jasni; Mahudin, Nor Diana Mohd; Rahman, Shukran Abd; Saad, Zarina Mat

    2014-12-01

    The effects of overcrowding have become a major concern for event organizers. One aspect of this concern has been the idea that overcrowding can enhance the occurrence of serious incidents during events. As one of the largest Muslim religious gathering attended by pilgrims from all over the world, Hajj has become extremely overcrowded with many incidents being reported. The purpose of this study is to analyze the nature of human emotion and negative behavior resulting from overcrowding during Hajj events from data gathered in Malaysian Hajj Experience Survey in 2013. The sample comprised of 147 Malaysian pilgrims (70 males and 77 females). Utilizing a probabilistic model called Bayesian network, this paper models the dependence structure between different emotions and negative behaviors of pilgrims in the crowd. The model included the following variables of emotion: negative, negative comfortable, positive, positive comfortable and positive spiritual and variables of negative behaviors; aggressive and hazardous acts. The study demonstrated that emotions of negative, negative comfortable, positive spiritual and positive emotion have a direct influence on aggressive behavior whereas emotion of negative comfortable, positive spiritual and positive have a direct influence on hazardous acts behavior. The sensitivity analysis showed that a low level of negative and negative comfortable emotions leads to a lower level of aggressive and hazardous behavior. Findings of the study can be further improved to identify the exact cause and risk factors of crowd-related incidents in preventing crowd disasters during the mass gathering events.

  11. Demotivating incentives and motivation crowding out in charitable giving.

    Science.gov (United States)

    Chao, Matthew

    2017-07-11

    Research has shown that extrinsic incentives can crowd out intrinsic motivation in many contexts. Despite this, many nonprofits offer conditional thank-you gifts, such as mugs or tote bags, in exchange for donations. In collaboration with a nonprofit, this study implements a direct mail field experiment and demonstrates that thank-you gifts reduced donation rates in a fundraising campaign. Attention-based multiattribute choice models suggest that this is because prospective donors shift attention to the salient gift offer, causing them to underweight less salient intrinsic motives. Attention to the gift may also cause individuals to adopt a more cost-benefit mindset, further de-emphasizing intrinsic motives. Consistent with these hypotheses, crowding out was driven by those who donated higher amounts in the previous year (i.e., those who likely had higher intrinsic motivation). In a complementary online experiment, thank-you gifts also reduced donation rates but only when the gift was visually salient. This corroborates the mediating role of attention in crowding out. Taken together, the laboratory and field results demonstrate that this fundraising technique can be demotivating in some contexts and that this may occur through an attention-based mechanism.

  12. Crowd Mobility Analysis using WiFi Sniffers

    Directory of Open Access Journals (Sweden)

    Anas Basalamah

    2016-12-01

    Full Text Available Wi-fi enabled devices such as today’s smart-phones are regularly in-search for connectivity. They continuously send management frames called Probe Requests searching for previ-ously accessed networks. These frames contain the sender’s MAC addresses in clear text, which can be used as an identifier for that sender. Being able to sniff that MAC address at several locations allows us to understand the mobility behavior of that device. In this paper, we present a solar-powered, beagle-bone based standalone system that continuously sniffs the air for probes and extract their MAC addresses. We deployed the system in the world’s largest gathering (The Hajj and tested it at scale. Our objective was to build an infrastructure for non-invasive mass crowd analysis. Our deployment had a total of 8 sniffers covering a population of 185,000 people. We detected 37.5% of the population, analysed their arrival and departure behaviours, identified their smartphone manufacturers and extracted their transition patterns from one sub-location to another. By pre-senting valuable insights on the mobility of our target crowd, we validated the potential of our platform for crowd mobility analysis.

  13. Anatomy of the Crowd4Discovery crowdfunding campaign.

    Science.gov (United States)

    Perlstein, Ethan O

    2013-01-01

    Crowdfunding allows the public to fund creative projects, including curiosity-driven scientific research. Last Fall, I was part of a team that raised $25,460 from an international coalition of "micropatrons" for an open, pharmacological research project called Crowd4Discovery. The goal of Crowd4Discovery is to determine the precise location of amphetamines inside mouse brain cells, and we are sharing the results of this project on the Internet as they trickle in. In this commentary, I will describe the genesis of Crowd4Discovery, our motivations for crowdfunding, an analysis of our fundraising data, and the nuts and bolts of running a crowdfunding campaign. Science crowdfunding is in its infancy but has already been successfully used by an array of scientists in academia and in the private sector as both a supplement and a substitute to grants. With traditional government sources of funding for basic scientific research contracting, an alternative model that couples fundraising and outreach - and in the process encourages more openness and accountability - may be increasingly attractive to researchers seeking to diversify their funding streams.

  14. A solution to the single-question crowd wisdom problem.

    Science.gov (United States)

    Prelec, Dražen; Seung, H Sebastian; McCoy, John

    2017-01-25

    Once considered provocative, the notion that the wisdom of the crowd is superior to any individual has become itself a piece of crowd wisdom, leading to speculation that online voting may soon put credentialed experts out of business. Recent applications include political and economic forecasting, evaluating nuclear safety, public policy, the quality of chemical probes, and possible responses to a restless volcano. Algorithms for extracting wisdom from the crowd are typically based on a democratic voting procedure. They are simple to apply and preserve the independence of personal judgment. However, democratic methods have serious limitations. They are biased for shallow, lowest common denominator information, at the expense of novel or specialized knowledge that is not widely shared. Adjustments based on measuring confidence do not solve this problem reliably. Here we propose the following alternative to a democratic vote: select the answer that is more popular than people predict. We show that this principle yields the best answer under reasonable assumptions about voter behaviour, while the standard 'most popular' or 'most confident' principles fail under exactly those same assumptions. Like traditional voting, the principle accepts unique problems, such as panel decisions about scientific or artistic merit, and legal or historical disputes. The potential application domain is thus broader than that covered by machine learning and psychometric methods, which require data across multiple questions.

  15. Effects of Macromolecular Emulsifiers on Double-emulsions Stability and Application%大分子乳化剂对复乳稳定性的影响及应用

    Institute of Scientific and Technical Information of China (English)

    徐成业; 陈亭亭; 陆伟根

    2011-01-01

    In this paper the mechanism of double-emulsions stability improved by macromolecular emulsifiers as well as the applications of macromolecular emulsifiers in the double-emulsions are reviewed. Double-emulsions are complex liquid dispersion systems, which are inherent thermodynamic unstable systems and tend to delaminate,flocculate and coalesce. Double-emulsions are usually stabilized by adding monomeric emulsifiers. In recently years,macromolecular emulsifiers such as biopolymers, block copolymers and polymeric emulsifies have obtained the widespread application in the double-emulsions, because these macromolecules can improve the stability of them.%综述了大分子乳化剂改善复乳稳定性的作用机制及其在复乳中的应用现状.复乳是复杂的液体分散体系,为热力学不稳定系统,易发生分层、絮凝和合并,通常加入单体乳化剂以提高其稳定性.近年来大分子乳化剂如生物聚合物、嵌段聚合物、高分子乳化剂因能较好地改善复乳稳定性,在复乳中得到广泛应用.

  16. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography

    Directory of Open Access Journals (Sweden)

    Julian C.-H. Chen

    2017-01-01

    Full Text Available The Protein Crystallography Station (PCS, located at the Los Alamos Neutron Scattering Center (LANSCE, was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER for 13 years (2002–2014. The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallography in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

  17. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography.

    Science.gov (United States)

    Chen, Julian C-H; Unkefer, Clifford J

    2017-01-01

    The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002-2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo-graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

  18. Detection of Macromolecular Fractions in HCN Polymers Using Electrophoretic and Ultrafiltration Techniques.

    Science.gov (United States)

    Marín-Yaseli, Margarita R; Cid, Cristina; Yagüe, Ana I; Ruiz-Bermejo, Marta

    2017-02-01

    Elucidating the origin of life involves synthetic as well as analytical challenges. Herein, for the first time, we describe the use of gel electrophoresis and ultrafiltration to fractionate HCN polymers. Since the first prebiotic synthesis of adenine by Oró, HCN polymers have gained much interest in studies on the origins of life due to the identification of biomonomers and related compounds within them. Here, we demonstrate that macromolecular fractions with electrophoretic mobility can also be detected within HCN polymers. The migration of polymers under the influence of an electric field depends not only on their sizes (one-dimensional electrophoresis) but also their different isoelectric points (two-dimensional electrophoresis, 2-DE). The same behaviour was observed for several macromolecular fractions detected in HCN polymers. Macromolecular fractions with apparent molecular weights as high as 250 kDa were detected by tricine-SDS gel electrophoresis. Cationic macromolecular fractions with apparent molecular weights as high as 140 kDa were also detected by 2-DE. The HCN polymers synthesized were fractionated by ultrafiltration. As a result, the molecular weight distributions of the macromolecular fractions detected in the HCN polymers directly depended on the synthetic conditions used to produce these polymers. The implications of these results for prebiotic chemistry will be discussed.

  19. A Study on the Effect of Exit Widths and Crowd Sizes in the Formation of Arch in Clogged Crowds

    CERN Document Server

    Castro, Francisco Enrique Vicente G

    2015-01-01

    The arching phenomenon is an emergent pattern formed by a $c$-sized crowd of intelligent, goal-oriented, autonomous, heterogeneous individuals moving towards a $w$-wide exit along a long $W$-wide corridor, where $W>w$. We collected empirical data from microsimulations to identify the combination effects of~$c$ and~$w$ to the time~$T$ of the onset of and the size~$S$ of the formation of the arch. The arch takes on the form of the perimeter of a half ellipse halved along the minor axis. We measured the~$S$ with respect to the lengths of the major~$M$ and minor~$m$ axes of the ellipse, respectively. The mathematical description of the formation of this phenomenon will be an important information in the design of walkways to control and easily direct the flow of large crowds, especially during panic egress conditions.

  20. Ladder contours are undetectable in the periphery: a crowding effect?

    Science.gov (United States)

    May, Keith A; Hess, Robert F

    2007-10-29

    We studied the perceptual integration of contours consisting of Gabor elements positioned along a smooth path, embedded among distractor elements. Contour elements either formed tangents to the path ("snakes") or were perpendicular to it ("ladders"). Perfectly straight snakes and ladders were easily detected in the fovea but, at an eccentricity of 6 degrees , only the snakes were detectable. The disproportionate impairment of peripheral ladder detection remained when we brought foveal performance away from ceiling by jittering the orientations of the elements. We propose that the failure to detect peripheral ladders is a form of crowding, the phenomenon observed when identification of peripherally located letters is disrupted by flanking letters. D. G. Pelli, M. Palomares, and N. J. Majaj (2004) outlined a model in which simple feature detectors are followed by integration fields, which are involved in tasks, such as letter identification, that require the outputs of several detectors. They proposed that crowding occurs because small integration fields are absent from the periphery, leading to inappropriate feature integration by large peripheral integration fields. We argue that the "association field," which has been proposed to mediate contour integration (D. J. Field, A. Hayes, & R. F. Hess, 1993), is a type of integration field. Our data are explained by an elaboration of Pelli et al.'s model, in which weak ladder integration competes with strong snake integration. In the fovea, the association fields were small, and the model integrated snakes and ladders with little interference. In the periphery, the association fields were large, and integration of ladders was severely disrupted by interference from spurious snake contours. In contrast, the model easily detected snake contours in the periphery. In a further demonstration of the possible link between contour integration and crowding, we ran our contour integration model on groups of three-letter stimuli

  1. Crowd Sourcing for Challenging Technical Problems and Business Model

    Science.gov (United States)

    Davis, Jeffrey R.; Richard, Elizabeth

    2011-01-01

    Crowd sourcing may be defined as the act of outsourcing tasks that are traditionally performed by an employee or contractor to an undefined, generally large group of people or community (a crowd) in the form of an open call. The open call may be issued by an organization wishing to find a solution to a particular problem or complete a task, or by an open innovation service provider on behalf of that organization. In 2008, the Space Life Sciences Directorate (SLSD), with the support of Wyle Integrated Science and Engineering, established and implemented pilot projects in open innovation (crowd sourcing) to determine if these new internet-based platforms could indeed find solutions to difficult technical challenges. These unsolved technical problems were converted to problem statements, also called "Challenges" or "Technical Needs" by the various open innovation service providers, and were then posted externally to seek solutions. In addition, an open call was issued internally to NASA employees Agency wide (10 Field Centers and NASA HQ) using an open innovation service provider crowd sourcing platform to post NASA challenges from each Center for the others to propose solutions). From 2008 to 2010, the SLSD issued 34 challenges, 14 externally and 20 internally. The 14 external problems or challenges were posted through three different vendors: InnoCentive, Yet2.com and TopCoder. The 20 internal challenges were conducted using the InnoCentive crowd sourcing platform designed for internal use by an organization. This platform was customized for NASA use and promoted as NASA@Work. The results were significant. Of the seven InnoCentive external challenges, two full and five partial awards were made in complex technical areas such as predicting solar flares and long-duration food packaging. Similarly, the TopCoder challenge yielded an optimization algorithm for designing a lunar medical kit. The Yet2.com challenges yielded many new industry and academic contacts in bone

  2. Further characterization of the influence of crowding on medication errors

    Directory of Open Access Journals (Sweden)

    Hannah Watts

    2013-01-01

    Full Text Available Study Objectives: Our prior analysis suggested that error frequency increases disproportionately with Emergency department (ED crowding. To further characterize, we measured this association while controlling for the number of charts reviewed and the presence of ambulance diversion status. We hypothesized that errors would occur significantly more frequently as crowding increased, even after controlling for higher patient volumes. Materials and Methods: We performed a prospective, observational study in a large, community hospital ED from May to October of 2009. Our ED has full-time pharmacists who review orders of patients to help identify errors prior to their causing harm. Research volunteers shadowed our ED pharmacists over discrete 4- hour time periods during their reviews of orders on patients in the ED. The total numbers of charts reviewed and errors identified were documented along with details for each error type, severity, and category. We then measured the correlation between error rate (number of errors divided by total number of charts reviewed and ED occupancy rate while controlling for diversion status during the observational period. We estimated a sample size requirement of at least 45 errors identified to allow detection of an effect size of 0.6 based on our historical data. Results: During 324 hours of surveillance, 1171 charts were reviewed and 87 errors were identified. Median error rate per 4-hour block was 5.8% of charts reviewed (IQR 0-13. No significant change was seen with ED occupancy rate (Spearman′s rho = -.08, P = .49. Median error rate during times on ambulance diversion was almost twice as large (11%, IQR 0-17, but this rate did not reach statistical significance in univariate or multivariate analysis. Conclusions: Error frequency appears to remain relatively constant across the range of crowding in our ED when controlling for patient volume via the quantity of orders reviewed. Error quantity therefore increases

  3. Pushing the Boundaries of Crowd-enabled Databases with Query-driven Schema Expansion

    CERN Document Server

    Selke, Joachim; Balke, Wolf-Tilo

    2012-01-01

    By incorporating human workers into the query execution process crowd-enabled databases facilitate intelligent, social capabilities like completing missing data at query time or performing cognitive operators. But despite all their flexibility, crowd-enabled databases still maintain rigid schemas. In this paper, we extend crowd-enabled databases by flexible query-driven schema expansion, allowing the addition of new attributes to the database at query time. However, the number of crowd-sourced mini-tasks to fill in missing values may often be prohibitively large and the resulting data quality is doubtful. Instead of simple crowd-sourcing to obtain all values individually, we leverage the user-generated data found in the Social Web: By exploiting user ratings we build perceptual spaces, i.e., highly-compressed representations of opinions, impressions, and perceptions of large numbers of users. Using few training samples obtained by expert crowd sourcing, we then can extract all missing data automatically from ...

  4. Crowd noise as a cue in referee decisions contributes to the home advantage.

    Science.gov (United States)

    Unkelbach, Christian; Memmert, Daniel

    2010-08-01

    The home advantage is one of the best established phenomena in sports (Courneya & Carron, 1992), and crowd noise has been suggested as one of its determinants (Nevill & Holder, 1999). However, the psychological processes that mediate crowd noise influence and its contribution to the home advantage are still unclear. We propose that crowd noise correlates with the criteria referees have to judge. As crowd noise is a valid cue, referee decisions are strongly influenced by crowd noise. Yet, when audiences are not impartial, a home advantage arises. Using soccer as an exemplar, we show the relevance of this influence in predicting outcomes of real games via a database analysis. Then we experimentally demonstrate the influence of crowd noise on referees' yellow cards decisions in soccer. Finally, we discuss why the focus on referee decisions is useful, and how more experimental research could benefit investigations of the home advantage.

  5. Effects of face feature and contour crowding in facial expression adaptation.

    Science.gov (United States)

    Liu, Pan; Montaser-Kouhsari, Leila; Xu, Hong

    2014-12-01

    Prolonged exposure to a visual stimulus, such as a happy face, biases the perception of subsequently presented neutral face toward sad perception, the known face adaptation. Face adaptation is affected by visibility or awareness of the adapting face. However, whether it is affected by discriminability of the adapting face is largely unknown. In the current study, we used crowding to manipulate discriminability of the adapting face and test its effect on face adaptation. Instead of presenting flanking faces near the target face, we shortened the distance between facial features (internal feature crowding), and reduced the size of face contour (external contour crowding), to introduce crowding. We are interested in whether internal feature crowding or external contour crowding is more effective in inducing crowding effect in our first experiment. We found that combining internal feature and external contour crowding, but not either of them alone, induced significant crowding effect. In Experiment 2, we went on further to investigate its effect on adaptation. We found that both internal feature crowding and external contour crowding reduced its facial expression aftereffect (FEA) significantly. However, we did not find a significant correlation between discriminability of the adapting face and its FEA. Interestingly, we found a significant correlation between discriminabilities of the adapting and test faces. Experiment 3 found that the reduced adaptation aftereffect in combined crowding by the external face contour and the internal facial features cannot be decomposed into the effects from the face contour and facial features linearly. It thus suggested a nonlinear integration between facial features and face contour in face adaptation.

  6. Real Time Crowding Information (RTCI) Provision : Impacts and Proposed Technical Solution

    OpenAIRE

    Zhang, Yizhou

    2015-01-01

    The increasing population leads to higher passenger travel demand in Stockholm. The public transport becomes more and more crowded in rush hours. However, passengers carry out decisions usually based on limited traffic information and their travel experience. Passengers cannot take the initiative to avoid crowding based on existing SL traffic information. Real time crowding information (RTCI) research aims to help passenger to have more initiative to plan their travel in metro system, and ass...

  7. Empirical investigation on safety constraints of merging pedestrian crowd through macroscopic and microscopic analysis.

    Science.gov (United States)

    Shi, Xiaomeng; Ye, Zhirui; Shiwakoti, Nirajan; Tang, Dounan; Wang, Chao; Wang, Wei

    2016-10-01

    A recent crowd stampede during a New Year's Eve celebration in Shanghai, China resulted in 36 fatalities and over 49 serious injuries. Many of such tragic crowd accidents around the world resulted from complex multi-direction crowd movement such as merging behavior. Although there are a few studies on merging crowd behavior, none of them have conducted a systematic analysis considering the impact of both merging angle and flow direction towards the safety of pedestrian crowd movement. In this study, a series of controlled laboratory experiments were conducted to examine the safety constraints of merging pedestrian crowd movements considering merging angle (60°, 90° and 180°) and flow direction under slow running and blocked vision condition. Then, macroscopic and microscopic properties of crowd dynamics are obtained and visualized through the analysis of pedestrian crowd trajectory data derived from video footage. It was found that merging angle had a significant influence on the fluctuations of pedestrian flows, which is important in a critical situation such as emergency evacuation. As the merging angle increased, mean velocity and mean flow at the measuring region in the exit corridors decreased, while mean density increased. A similar trend was observed for the number of weaving and overtaking conflicts, which resulted in the increase of mean headway. Further, flow direction had a significant impact on the outflow of the individuals while blocked vision had an influence on pedestrian crowd interactions and merging process. Finally, this paper discusses safety assessments on crowd merging behaviors along with some recommendations for future research. Findings from this study can assist in the development and validation of pedestrian crowd simulation models as well as organization and control of crowd events.

  8. Effectiveness Testing and Evaluation of Non-Lethal Weapons for Crowd Management

    Science.gov (United States)

    2014-06-01

    Weapons”) • Participants were recruited from the general population to participate in an investigation on “ Crowd Movement ” • Fifty-two healthy men...U.S. Army Armament Research, Development, and Engineering Center EFFECTIVENESS TESTING AND EVALUATION OF NON-LETHAL WEAPONS FOR CROWD MANAGEMENT...SUBTITLE EFFECTIVENESS TESTING AND EVALUATION OF NON-LETHAL WEAPONS FOR CROWD MANAGEMENT Presented at the Virtual 82nd Military Operations Research

  9. Synthesis and characterization of miktoarm star copolymer of styrene and butadiene using multifunctional macromolecular initiator

    Institute of Scientific and Technical Information of China (English)

    Hai Yan Zhang; Xing Ying Zhang

    2009-01-01

    A new kind of multifunctional macromolecular initiator with Sn-C bonds and polydiene arms was synthesized by living anionic polymerization.At first,polydiene-stannum chloride(PD-SnCl3)was prepared by the reaction of n-butyl-Li(n-BuLi),stannic chloride(SnCl4)and diene.Then PD-SnCl3 was used to react with the dilithium initiator to prepare the multifunctional organic macromolecular initiators.The result suggested that the initiators had a remarkable yield by GPC,nearly 90%.By using these multifunctional macromolecular initiators,styrene and butadiene were effectively polymerized via anionic polymerization,which gave birth to novel miktoarm star copolymers.The relative molecular weight and polydispersity index,microstructure contents,copolymerization components,glass transition temperature(Tg)and morphology of the miktoarm star copolymers were investigated by GPC-UV,1H NMR,DSC and TEM,respectively.

  10. Use of Site-Specifically Tethered Chemical Nucleases to Study Macromolecular Reactions

    Directory of Open Access Journals (Sweden)

    Mukherjee Srabani

    2003-01-01

    Full Text Available During a complex macromolecular reaction multiple changes in molecular conformation and interactions with ligands may occur. X-ray crystallography may provide only a limited set of snapshots of these changes. Solution methods can augment such structural information to provide a more complete picture of a macromolecular reaction. We analyzed the changes in protein conformation and protein:nucleic acid interactions which occur during transcription initiation by using a chemical nuclease tethered to cysteines introduced site-specifically into the RNA polymerase of bacteriophage T7 (T7 RNAP. Changes in cleavage patterns as the polymerase steps through transcription reveal a series of structural transitions which mediate transcription initiation. Cleavage by tethered chemical nucleases is seen to be a powerful method for revealing the conformational dynamics of macromolecular reactions, and has certain advantages over cross-linking or energy transfer approaches.

  11. Stare in the crowd: frontal face guides overt attention independently of its gaze direction.

    Science.gov (United States)

    Aya, Shirama

    2012-01-01

    Whether or not a stare in the midst of many faces can guide visual attention is a controversial issue. Two experiments are reported that investigate the hypothesis that visual attention is guided toward a frontal face in the search for a stare among faces with varied head angles. The participants were required to search for a face with a direct gaze in a context where the target could be at any of various head angles and the target's head angle was unpredictable in one trial. The search performance was better for a frontal-face target than for deviated-face targets. Furthermore, eye-movement analyses revealed that a frontal-face stimulus tended to be initially fixated prior to deviated-face stimuli, and many of the initially fixated frontal-face stimuli had an averted gaze. The findings suggest that a frontal face guides overt attention independently of its gaze direction in the search for a stare in a crowd. The validity of prioritising a frontal face in order to find a direct gaze among faces and the characteristics of a human-face detection system are discussed.

  12. Macromolecular Hydrogen Sulfide Donors Trigger Spatiotemporally Confined Changes in Cell Signaling.

    Science.gov (United States)

    Ercole, Francesca; Mansfeld, Friederike M; Kavallaris, Maria; Whittaker, Michael R; Quinn, John F; Halls, Michelle L; Davis, Thomas P

    2016-01-11

    Hydrogen sulfide (H2S) is involved in a myriad of cell signaling processes that trigger physiological events ranging from vasodilation to cell proliferation. Moreover, disturbances to H2S signaling have been associated with numerous pathologies. As such, the ability to release H2S in a cellular environment and stimulate signaling events is of considerable interest. Herein we report the synthesis of macromolecular H2S donors capable of stimulating cell signaling pathways in both the cytosol and at the cell membrane. Specifically, copolymers having pendent oligo(ethylene glycol) and benzonitrile groups were synthesized, and the benzonitrile groups were subsequently transformed into primary aryl thioamide groups via thionation using sodium hydrosulfide. These thioamide moieties could be incorporated into a hydrophilic copolymer or a block copolymer (i.e., into either the hydrophilic or hydrophobic domain). An electrochemical sensor was used to demonstrate release of H2S under simulated physiological conditions. Subsequent treatment of HEK293 cells with a macromolecular H2S donor elicited a slow and sustained increase in cytosolic ERK signaling, as monitored using a FRET-based biosensor. The macromolecular donor was also shown to induce a small, fast and sustained increase in plasma membrane-localized PKC activity immediately following addition to cells. Studies using an H2S-selective fluorescent probe in live cells confirmed release of H2S from the macromolecular donor over physiologically relevant time scales consistent with the signaling observations. Taken together, these results demonstrate that by using macromolecular H2S donors it is possible to trigger spatiotemporally confined cell signaling events. Moreover, the localized nature of the observed signaling suggests that macromolecular donor design may provide an approach for selectively stimulating certain cellular biochemical pathways.

  13. Perceptual learning reduces crowding in amblyopia and in the normal periphery.

    Science.gov (United States)

    Hussain, Zahra; Webb, Ben S; Astle, Andrew T; McGraw, Paul V

    2012-01-11

    Amblyopia is a developmental visual disorder of cortical origin, characterized by crowding and poor acuity in central vision of the affected eye. Crowding refers to the adverse effects of surrounding items on object identification, common only in normal peripheral but not central vision. We trained a group of adult human amblyopes on a crowded letter identification task to assess whether the crowding problem can be ameliorated. Letter size was fixed well above the acuity limit, and letter spacing was varied to obtain spacing thresholds for central target identification. Normally sighted observers practiced the same task in their lower peripheral visual field. Independent measures of acuity were taken in flanked and unflanked conditions before and after training to measure crowding ratios at three fixed letter separations. Practice improved the letter spacing thresholds of both groups on the training task, and crowding ratios were reduced after posttest. The reductions in crowding in amblyopes were associated with improvements in standard measures of visual acuity. Thus, perceptual learning reduced the deleterious effects of crowding in amblyopia and in the normal periphery. The results support the effectiveness of plasticity-based approaches for improving vision in adult amblyopes and suggest experience-dependent effects on the cortical substrates of crowding.

  14. Crowding and visual acuity measured in adults using paediatric test letters, pictures and symbols.

    Science.gov (United States)

    Lalor, Sarah J H; Formankiewicz, Monika A; Waugh, Sarah J

    2016-04-01

    Crowding refers to the degradation of visual acuity for target optotypes with, versus without, surrounding features. Crowding is important clinically, however the effect of target-flanker spacing on acuity for symbols and pictures, compared to letters, has not been investigated. Five adults with corrected-to-normal vision had visual acuity measured for modified single target versions of Kay Pictures, Lea Symbols, HOTV and Cambridge Crowding Cards, tests. Single optotypes were presented in isolation and with surrounding features placed 0-5 stroke-widths away. Visual acuity measured with Kay Picture optotypes is 0.13-0.19logMAR better than for other test optotypes and varies significantly across picture. The magnitude of crowding is strongest when the surrounding features abut, or are placed 1 stroke-width away from the target optotype. The slope of the psychometric function is steeper in the region just beyond maximum crowding. Crowding is strongest and the psychometric function steepest, with the Cambridge Crowding Cards arrangement, than when any single optotype is surrounded by a box. Estimates of crowding extent are less variable across test when expressed in units of stroke-width, than optotype-width. Crowding for single target presentations of letters, symbols and pictures used in paediatric visual acuity tests can be maximised and made more sensitive to change in visual acuity, by careful selection of optotype, by surrounding the target with similar flankers, and by using a closer target-flanker separation than half an optotype-width.

  15. Crowding increases salivary cortisol but not self-directed behavior in captive baboons.

    Science.gov (United States)

    Pearson, Brandon L; Reeder, DeeAnn M; Judge, Peter G

    2015-04-01

    Reduced space can lead to crowding in social animals. Crowding increases the risk of agonistic interactions that, in turn, may require additional physiological defensive coping mechanisms affecting health. To determine the stress induced from increased social density in a group of nineteen baboons living in an indoor/outdoor enclosure, saliva cortisol levels and rates of anxiety-related behavior were analyzed across two unique crowding episodes. Initially, mean salivary cortisol levels when animals were restricted to their indoor quarters were compared to those when they also had access to their larger outdoor enclosure. Then, mean cortisol levels were compared before, during, and after two distinct crowding periods of long and short duration. Crowding resulted in significantly elevated cortisol during crowding periods compared to non-crowded periods. Cortisol levels returned to baseline following two crowding episodes contrasting in their length and ambient climate conditions. These cortisol elevations indicate greater metabolic costs of maintaining homeostasis under social stress resulting from reduced space. Self-directed behavior, conversely, was not reliably elevated during crowding. Results suggest that the potential for negative social interactions, and/or the uncertainty associated with social threat can cause physiological stress responses detected by salivary cortisol. Self-directed behavioral measures of stress may constitute inadequate indicators of social stress in colony-housed monkeys or represent subjective emotional arousal unrelated to hypothalamic-pituitary adrenal axis activation.

  16. Cyber-Physical Modeling and Control of Crowd of Pedestrians: A Review and New Framework

    CERN Document Server

    Cao, Ke-cai; Stuart, Dan; Yue, Dong

    2015-01-01

    Recent advances in modeling and control of crowds of pedestrians are briefly surveyed in this paper. Possibilities of applying fractional calculus in the modeling of crowd of pedestrians have been shortly reviewed and discussed from different aspects such as descriptions of motion, interactions of long range and effects of memory. Control of the crowd of pedestrians have also been formulated using the framework of Cyber-Physical Systems and been realized using networked Segways with onboard emergency response personnels to regulate the velocity and flux of the crowd. Platform for verification of the theoretical results are also provided in this paper.

  17. A clinical study of the relationship between crowding of teeth, plaque and gingival condition.

    Science.gov (United States)

    Ingervall, B; Jacobsson, U; Nyman, S

    1977-08-01

    A clinical trial was undertaken to assess whether crowded teeth were more likely to accumulate plaque and develop gingivitis than non-crowded teeth. A tooth was considered crowded if it was displaced by 2 mm and/or rotated 15 degrees or more from the normal position in the arch. The material consisted of 50 dental students aged 21 to 32 years. An initial examination comprised assessment of Plaque Index, Gingival Index and pocket depths. After this examination the subjects refrained from using interdental cleaning aids but continued with their normal toothbrushing for 40 days. After re-examination they were instructed in the effective use of dental floss. A final examination was carried out after 140 days. At the start of the trial no difference was found in regard to the Plaque Index between crowded and non-crowded teeth. The Gingival Index for growded front teeth, but not for crowded premolars, was somewhat higher than for the corresponding controls. The cessation of interdental cleaning resulted in a similar increase in plaque accumulation and gingival inflammation in both non-crowded and crowded teeth. The use of dental floss for approximal tooth cleaning resulted in a similar decrease in the Plaque- and Gingival Indices for both types of teeth. The results demonstrate that in a group of young adults, crowding of teeth (1) did not favour plaque accumulation on approximal tooth surfaces and (2) influenced the degree of gingival inflammation only to a minor extent.

  18. Social crowding stress diminishes the pituitary-adrenocortical and hypothalamic histamine response to adrenergic stimulation.

    Science.gov (United States)

    Bugajski, J; Gadek-Michalska, A; Borycz, J

    1993-12-01

    Social stress of crowding almost totally reduced the rise in serum corticosterone elicited by intracerebroventricular administration of isoprenaline, a beta-adrenergic receptor agonist, after 3 and 7 day of crowding and substantially diminished that response after 14 and 21 days. Crowding stress totally abolished the increase in hypothalamic histamine induced by isoprenaline in control rats. Crowding also significantly diminished the increase in serum corticosterone evoked by clonidine, an alpha 2-adrenergic agonist, and abolished the clonidine-induced elevation in hypothalamic histamine levels. The stimulatory effect of phenylephrine, an alpha 1-adrenergic agonist, on corticosterone secretion was only moderately diminished in crowded rats. Neither phenylephrine nor crowding stress changed significantly the hypothalamic histamine levels. These results indicate that social stress of crowding considerably impairs the hypothalamic-pituitary-adrenocortical responsiveness to central beta- and alpha 2-adrenergic receptor stimulation. Crowding also abolishes the rise in hypothalamic histamine induced by beta- and alpha 2-adrenergic agonist, suggesting a role of hypothalamic histamine in the HPA adaptation to the social stress of crowding.

  19. DDDAS-based Information-Aggregation for Crowd Dynamics Modeling with UAVs and UGVs

    Directory of Open Access Journals (Sweden)

    Yifei eYuan

    2015-04-01

    Full Text Available Unmanned aerial vehicles (UAVs and unmanned ground vehicles (UGVs collaboratively play important roles in crowd tracking for applications such as border patrol and crowd surveillance. Dynamic data-driven application systems (DDDAS paradigm has been developed for these applications to take advantage of real-time monitoring data. In the DDDAS paradigm, one crucial step in crowd surveillance is crowd dynamics modeling, which is based on multi-resolution crowd observation data collected from both UAVs and UGVs. Data collected from UAVs capture global crowd motion but have low resolution while those from UGVs have high resolution information of local crowd motion. This paper proposes an information-aggregation approach for crowd dynamics modeling by incorporating multi-resolution data, where a grid-based method is developed to model crowd motion with UAVs’ low-resolution global perception, and an autoregressive model is employed to model individuals’ motion based on UGVs’ detailed perception. A simulation experiment is provided to illustrate and demonstrate the effectiveness of the proposed approach.

  20. From individual behaviors to an evaluation of the collective evolution of crowds along footbridges

    CERN Document Server

    Corbetta, Alessandro; Bruno, Luca

    2012-01-01

    In the present work a mathematical model aimed at evaluating the dynamics of crowds is derived and discussed. In particular, on the basis of some phenomenological considerations focused on pedestrians' individual behavior, a model dealing with the collective evolution of the crowd, formalized in terms of a conservation law for a crowding measure, is obtained. To suit engineering needs, modeling efforts are made toward the simulation of real world crowd events specifically happening along pedestrian walkways. The response of the model as well as its tunability are studied in some computational domains inspired by existing footbridges.