Efficient parallel implementations of QM/MM-REMD (quantum mechanical/molecular mechanics-replica-exchange MD) and umbrella sampling: isomerization of H2O2 in aqueous solution.

PubMed

Fedorov, Dmitri G; Sugita, Yuji; Choi, Cheol Ho

2013-07-03

An efficient parallel implementation of QM/MM-based replica-exchange molecular dynamics (REMD) as well as umbrella samplings techniques was proposed by adopting the generalized distributed data interface (GDDI). Parallelization speed-up of 40.5 on 48 cores was achieved, making our QM/MM-MD engine a robust tool for studying complex chemical dynamics in solution. They were comparatively used to study the torsional isomerization of hydrogen peroxide in aqueous solution. All results by QM/MM-REMD and QM/MM umbrella sampling techniques yielded nearly identical potentials of mean force (PMFs) regardless of the particular QM theories for solute, showing that the overall dynamics are mainly determined by solvation. Although the entropic penalty of solvent rearrangements exists in cisoid conformers, it was found that both strong intermolecular hydrogen bonding and dipole-dipole interactions preferentially stabilize them in solution, reducing the torsional free-energy barrier at 0° by about 3 kcal/mol as compared to that in gas phase.

[The interview as a research data collection method].

PubMed

Debout, Christophe

2016-04-01

The interview is a widely-used method for collecting research data, notably in qualitative and mixed protocols. However, it is an umbrella term which groups together numerous types of interviews adapted to the methodological diversity which characterises nursing science. Copyright © 2016. Published by Elsevier Masson SAS.

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review

PubMed Central

Miao, Yinglong; McCammon, J. Andrew

2016-01-01

Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations. PMID:27453631

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.

PubMed

Miao, Yinglong; McCammon, J Andrew

Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.

Adapting Unconventional Warfare Doctrine to Cyberspace Operations: An Examination of Hacktivist Based Insurgencies

DTIC Science & Technology

2015-06-12

Unconventional Warfare, Cyberspace Operations, Cyber Warfare , Hacktivism, China, Russia, Georgia, Estonia, Umbrella Revolution, UW, Cyber, Guerilla, Hacktivist...6 Cyber Warfare ............................................................................................................. 7...Internet, and cyber warfare , the nature of the human element in cyberspace exhibits only a scientific advancement in the evolution of warfare, not a

Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression.

PubMed

Meng, Yilin; Roux, Benoît

2015-08-11

The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost.

Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression

PubMed Central

2015-01-01

The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost. PMID:26574437

Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics.

PubMed

Awasthi, Shalini; Kapil, Venkat; Nair, Nisanth N

2016-06-15

Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad, and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary-Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad, and unbound free energy surfaces. This technique also allows for a distributed sampling of a high-dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high-dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Transcatheter umbrella closure of valvular and paravalvular leaks.

PubMed

Hourihan, M; Perry, S B; Mandell, V S; Keane, J F; Rome, J J; Bittl, J A; Lock, J E

1992-11-15

Our aim was to adapt the technique of transcatheter umbrella closure of intracardiac defects for closure of valvular and paravalvular defects. The double-umbrella device developed by Rashkind and Cuaso has been safely and effectively delivered across a host of intracardiac defects, but transcatheter closure of valvular and paravalvular leaks has not been reported. Between February 1987 and September 1990, eight patients who were believed to be poor operative candidates were taken to the catheterization laboratory for transcatheter double-umbrella closure of a valvular or a paravalvular leak. Four patients had a paravalvular leak around a prosthetic aortic valve. The other four patients had a valvular leak: one patient with a regurgitant native aortic valve after a Stansel procedure and three patients with a regurgitant porcine valve in a left ventricular apex to descending aorta conduit. Placement of a double-umbrella device was attempted in seven of the eight patients and was successful in all seven. Device placement was not attempted in one patient because of the crescentic shape of his defect. Two patients required two devices for each closure; the other five required only one device each. Angiography, performed on six patients after device closure, demonstrated that three patients had a completely occluded defect, two had trivial residual flow and one patient had mild residual flow through the device. All significant complications occurred in one patient who had hemolysis and oliguria that resolved when the initial umbrella was replaced by a larger device. In addition, two devices migrated to the patient's pulmonary arteries but were retrieved in the catheterization laboratory without difficulty. No other early or late complications occurred in 21 to 50 months of follow-up. Of the four patients with a paravalvular leak, the one who did not receive a device died at operation, one patient died at operation for an associated defect (in the operating room the umbrella was found securely in place across the paraaortic defect) and two patients are clinically well at home after 21 and 32 months, respectively. Of the four patients with closure of a valvular leak, one patient remains well at home 50 months later, one patient died at operation for associated defects and two patients had additional successful surgical treatment and remain well 29 months after device placement. Transcatheter umbrella closure appears to be a reasonable alternative for closure of a valvular or paravalvular leak in patients who are poor operative candidates.

Quantifying Density Fluctuations in Volumes of All Shapes and Sizes Using Indirect Umbrella Sampling

NASA Astrophysics Data System (ADS)

Patel, Amish J.; Varilly, Patrick; Chandler, David; Garde, Shekhar

2011-10-01

Water density fluctuations are an important statistical mechanical observable and are related to many-body correlations, as well as hydrophobic hydration and interactions. Local water density fluctuations at a solid-water surface have also been proposed as a measure of its hydrophobicity. These fluctuations can be quantified by calculating the probability, P v ( N), of observing N waters in a probe volume of interest v. When v is large, calculating P v ( N) using molecular dynamics simulations is challenging, as the probability of observing very few waters is exponentially small, and the standard procedure for overcoming this problem (umbrella sampling in N) leads to undesirable impulsive forces. Patel et al. (J. Phys. Chem. B 114:1632, 2010) have recently developed an indirect umbrella sampling (INDUS) method, that samples a coarse-grained particle number to obtain P v ( N) in cuboidal volumes. Here, we present and demonstrate an extension of that approach to volumes of other basic shapes, like spheres and cylinders, as well as to collections of such volumes. We further describe the implementation of INDUS in the NPT ensemble and calculate P v ( N) distributions over a broad range of pressures. Our method may be of particular interest in characterizing the hydrophobicity of interfaces of proteins, nanotubes and related systems.

Free Energies of Quantum Particles: The Coupled-Perturbed Quantum Umbrella Sampling Method.

PubMed

Glover, William J; Casey, Jennifer R; Schwartz, Benjamin J

2014-10-14

We introduce a new simulation method called Coupled-Perturbed Quantum Umbrella Sampling that extends the classical umbrella sampling approach to reaction coordinates involving quantum mechanical degrees of freedom. The central idea in our method is to solve coupled-perturbed equations to find the response of the quantum system's wave function along a reaction coordinate of interest. This allows for propagation of the system's dynamics under the influence of a quantum biasing umbrella potential and provides a method to rigorously undo the effects of the bias to compute equilibrium ensemble averages. In this way, one can drag electrons into regions of high free energy where they would otherwise not go, thus enabling chemistry by fiat. We demonstrate the applicability of our method for two condensed-phase systems of interest. First, we consider the interaction of a hydrated electron with an aqueous sodium cation, and we calculate a potential of mean force that shows that an e(-):Na(+) contact pair is the thermodynamically favored product starting from either a neutral sodium atom or the separate cation and electron species. Second, we present the first determination of a hydrated electron's free-energy profile relative to an air/water interface. For the particular model parameters used, we find that the hydrated electron is more thermodynamically stable in the bulk rather than at the interface. Our analysis suggests that the primary driving force keeping the electron away from the interface is the long-range electron-solvent polarization interaction rather than the short-range details of the chosen pseudopotential.

Umbrella sampling of proton transfer in a creatine-water system

NASA Astrophysics Data System (ADS)

Ivchenko, Olga; Bachert, Peter; Imhof, Petra

2014-04-01

Proton transfer reactions are among the most common processes in chemistry and biology. Proton transfer between creatine and surrounding solvent water is underlying the chemical exchange saturation transfer used as a contrast in magnetic resonance imaging. The free energy barrier, determined by first-principles umbrella sampling simulations (EaDFT 3 kcal/mol) is in the same order of magnitude as the experimentally obtained activation energy. The underlying mechanism is a first proton transfer from the guanidinium group to the water pool, followed by a second transition where a proton is "transferred back" from the nearest water molecule to the deprotonated nitrogen atom of creatine.

Conformational free energies of methyl-α-L-iduronic and methyl-β-D-glucuronic acids in water

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Sagui, Celeste

2010-03-01

We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a nonequilibrium umbrella sampling method, in this case, the recently developed adaptively biased molecular dynamics method, to compute an approximate free energy for the slow modes of the solute in explicit solvent. This approximate free energy is then used to set up a Hamiltonian replica exchange scheme that samples both from biased and unbiased distributions. The final accurate free energy is recovered via the weighted histogram analysis technique applied to all the replicas, and equilibrium properties of the solute are computed from the unbiased trajectory. We illustrate the approach by applying it to the study of the puckering landscapes of the methyl glycosides of α-L-iduronic acid and its C5 epimer β-D-glucuronic acid in water. Big savings in computational resources are gained in comparison to the standard parallel tempering method.

Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water.

PubMed

Babin, Volodymyr; Sagui, Celeste

2010-03-14

We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a nonequilibrium umbrella sampling method, in this case, the recently developed adaptively biased molecular dynamics method, to compute an approximate free energy for the slow modes of the solute in explicit solvent. This approximate free energy is then used to set up a Hamiltonian replica exchange scheme that samples both from biased and unbiased distributions. The final accurate free energy is recovered via the weighted histogram analysis technique applied to all the replicas, and equilibrium properties of the solute are computed from the unbiased trajectory. We illustrate the approach by applying it to the study of the puckering landscapes of the methyl glycosides of alpha-L-iduronic acid and its C5 epimer beta-D-glucuronic acid in water. Big savings in computational resources are gained in comparison to the standard parallel tempering method.

Rare behavior of growth processes via umbrella sampling of trajectories

NASA Astrophysics Data System (ADS)

Klymko, Katherine; Geissler, Phillip L.; Garrahan, Juan P.; Whitelam, Stephen

2018-03-01

We compute probability distributions of trajectory observables for reversible and irreversible growth processes. These results reveal a correspondence between reversible and irreversible processes, at particular points in parameter space, in terms of their typical and atypical trajectories. Thus key features of growth processes can be insensitive to the precise form of the rate constants used to generate them, recalling the insensitivity to microscopic details of certain equilibrium behavior. We obtained these results using a sampling method, inspired by the "s -ensemble" large-deviation formalism, that amounts to umbrella sampling in trajectory space. The method is a simple variant of existing approaches, and applies to ensembles of trajectories controlled by the total number of events. It can be used to determine large-deviation rate functions for trajectory observables in or out of equilibrium.

Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling.

PubMed

Hansen, Halvor S; Daura, Xavier; Hünenberger, Philippe H

2010-09-14

A new method, fragment-based local elevation umbrella sampling (FB-LEUS), is proposed to enhance the conformational sampling in explicit-solvent molecular dynamics (MD) simulations of solvated polymers. The method is derived from the local elevation umbrella sampling (LEUS) method [ Hansen and Hünenberger , J. Comput. Chem. 2010 , 31 , 1 - 23 ], which combines the local elevation (LE) conformational searching and the umbrella sampling (US) conformational sampling approaches into a single scheme. In LEUS, an initial (relatively short) LE build-up (searching) phase is used to construct an optimized (grid-based) biasing potential within a subspace of conformationally relevant degrees of freedom, which is then frozen and used in a (comparatively longer) US sampling phase. This combination dramatically enhances the sampling power of MD simulations but, due to computational and memory costs, is only applicable to relevant subspaces of low dimensionalities. As an attempt to expand the scope of the LEUS approach to solvated polymers with more than a few relevant degrees of freedom, the FB-LEUS scheme involves an US sampling phase that relies on a superposition of low-dimensionality biasing potentials optimized using LEUS at the fragment level. The feasibility of this approach is tested using polyalanine (poly-Ala) and polyvaline (poly-Val) oligopeptides. Two-dimensional biasing potentials are preoptimized at the monopeptide level, and subsequently applied to all dihedral-angle pairs within oligopeptides of 4,  6,  8, or 10 residues. Two types of fragment-based biasing potentials are distinguished: (i) the basin-filling (BF) potentials act so as to "fill" free-energy basins up to a prescribed free-energy level above the global minimum; (ii) the valley-digging (VD) potentials act so as to "dig" valleys between the (four) free-energy minima of the two-dimensional maps, preserving barriers (relative to linearly interpolated free-energy changes) of a prescribed magnitude. The application of these biasing potentials may lead to an impressive enhancement of the searching power (volume of conformational space visited in a given amount of simulation time). However, this increase is largely offset by a deterioration of the statistical efficiency (representativeness of the biased ensemble in terms of the conformational distribution appropriate for the physical ensemble). As a result, it appears difficult to engineer FB-LEUS schemes representing a significant improvement over plain MD, at least for the systems considered here.

Two-dimensional replica exchange approach for peptide-peptide interactions

NASA Astrophysics Data System (ADS)

Gee, Jason; Shell, M. Scott

2011-02-01

The replica exchange molecular dynamics (REMD) method has emerged as a standard approach for simulating proteins and peptides with rugged underlying free energy landscapes. We describe an extension to the original methodology—here termed umbrella-sampling REMD (UREMD)—that offers specific advantages in simulating peptide-peptide interactions. This method is based on the use of two dimensions in the replica cascade, one in temperature as in conventional REMD, and one in an umbrella sampling coordinate between the center of mass of the two peptides that aids explicit exploration of the complete association-dissociation reaction coordinate. To mitigate the increased number of replicas required, we pursue an approach in which the temperature and umbrella dimensions are linked at only fully associated and dissociated states. Coupled with the reweighting equations, the UREMD method aids accurate calculations of normalized free energy profiles and structural or energetic measures as a function of interpeptide separation distance. We test the approach on two families of peptides: a series of designed tetrapeptides that serve as minimal models for amyloid fibril formation, and a fragment of a classic leucine zipper peptide and its mutant. The results for these systems are compared to those from conventional REMD simulations, and demonstrate good convergence properties, low statistical errors, and, for the leucine zippers, an ability to sample near-native structures.

Greater sage-grouse as an umbrella species for shrubland passerine birds: a multiscale assessment

USGS Publications Warehouse

Hanser, Steven E.; Knick, Steven T.; Knick, Steven T.; Connelly, John W.

2011-01-01

Working groups and government agen-cies are planning and conducting land actions in sagebrush (Artemisia spp.) habitats to benefit Greater Sage-Grouse (Centrocercus urophasianus) populations. Managers have adopted an umbrella concept, creating habitat characteristics specific to sage-grouse requirements, in the belief that other wildlife species dependent on sagebrush will benefit. We tested the efficacy of this approach by first identifying the primary environmental gradients underlying sagebrush steppe bird com-munities (including Greater Sage-Grouse). We integrated field sampling for birds and vegetation with geographic information system (GIS) data to characterize 305 sites sampled throughout the current range of Greater Sage-Grouse in the Intermountain West, United States. The primary environmental axis defining the bird community represented a gradient from local-scale Wyoming/basin big sagebrush (A. t. ssp. wyomingensis/A. t. ssp. tridentata), and bare ground cover to local and regional grassland cover; the second axis repre-sented a transition from low-elevation Wyoming/basin big sagebrush and bare ground to mountain big sagebrush (A. t. ssp. vaseyana) and habitat edge. We identified the relative overlap of sage-grouse with 13 species of passerine birds along the multiscale gradients and estimated the width of the umbrella when applying management guidelines specific to sage-grouse. Passerine birds associated with sagebrush steppe habitats had high levels of overlap with Greater Sage-Grouse along the multiscale environmental gradients. However, the overlap of the umbrella was prima-rily a function of the broad range of sagebrush habitats used by sage-grouse. Management that focuses on creating a narrow set of plot-scale con-ditions will likely be less effective than restoration efforts that recognize landscape scale heterogene-ity and multiscale organization of habitats. These multiscale efforts may improve some sage-grouse habitats and strengthen the management umb-rella for shrub steppe passerine birds.

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation

NASA Astrophysics Data System (ADS)

Autieri, E.; Sega, M.; Pederiva, F.; Guella, G.

2010-09-01

We present the results of a combined metadynamics-umbrella sampling investigation of the puckered conformers of pyranoses described using the GROMOS 45a4 force field. The free energy landscape of Cremer-Pople puckering coordinates has been calculated for the whole series of α and β aldohexoses, showing that the current force field parameters fail in reproducing proper puckering free energy differences between chair conformers. We suggest a modification to the GROMOS 45a4 parameter set which improves considerably the agreement of simulation results with theoretical and experimental estimates of puckering free energies. We also report on the experimental measurement of altrose conformer populations by means of NMR spectroscopy, which show good agreement with the predictions of current theoretical models.

Looking beyond rare species as umbrella species: Northern Bobwhites (Colinus virginianus) and conservation of grassland and shrubland birds

USGS Publications Warehouse

Crosby, Andrew D.; Elmore, R.D.; Leslie,, David M.; Will, Rodney E.

2015-01-01

Changes in land use and land cover throughout the eastern half of North America have caused substantial declines in populations of birds that rely on grassland and shrubland vegetation types, including socially and economically important game birds such as the Northern Bobwhite (Colinus virginianus; hereafter bobwhites). As much attention is focused on habitat management and restoration for bobwhites, they may act as an umbrella species for other bird species with similar habitat requirements. We quantified the relationship of bobwhites to the overall bird community and evaluated the potential for bobwhites to act as an umbrella species for grassland and shrubland birds. We monitored bobwhite presence and bird community composition within 31 sample units on selected private lands in the south-central United States from 2009 to 2011. Bobwhites were strongly associated with other grassland and shrubland birds and were a significant positive predictor for 9 species. Seven of these, including Bell's Vireo (Vireo bell), Dicksissel (Spiza americana), and Grasshopper Sparrow (Ammodramus savannarum), are listed as species of conservation concern. Species richness and occupancy probability of grassland and shrubland birds were higher relative to the overall bird community in sample units occupied by bobwhites. Our results show that bobwhites can act as an umbrella species for grassland and shrubland birds, although the specific species in any given situation will depend on region and management objectives. These results suggest that efficiency in conservation funding can be increased by using public interest in popular game species to leverage resources to meet multiple conservation objectives.

Protein side chain rotational isomerization: A minimum perturbation mapping study

NASA Astrophysics Data System (ADS)

Haydock, Christopher

1993-05-01

A theory of the rotational isomerization of the indole side chain of tryptophan-47 of variant-3 scorpion neurotoxin is presented. The isomerization potential energy, entropic part of the isomerization free energy, isomer probabilities, transition state theory reaction rates, and indole order parameters are calculated from a minimum perturbation mapping over tryptophan-47 χ1×χ2 torsion space. A new method for calculating the fluorescence anisotropy from molecular dynamics simulations is proposed. The method is based on an expansion that separates transition dipole orientation from chromophore dynamics. The minimum perturbation potential energy map is inverted and applied as a bias potential for a 100 ns umbrella sampling simulation. The entropic part of the isomerization free energy as calculated by minimum perturbation mapping and umbrella sampling are in fairly close agreement. Throughout, the approximation is made that two glutamine and three tyrosine side chains neighboring tryptophan-47 are truncated at the Cβ atom. Comparison with the previous combination thermodynamic perturbation and umbrella sampling study suggests that this truncated neighbor side chain approximation leads to at least a qualitatively correct theory of tryptophan-47 rotational isomerization in the wild type variant-3 scorpion neurotoxin. Analysis of van der Waals interactions in a transition state region indicates that for the simulation of barrier crossing trajectories a linear combination of three specially defined dihedral angles will be superior to a simple side chain dihedral reaction coordinate.

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.

PubMed

Di Palma, Francesco; Bottaro, Sandro; Bussi, Giovanni

2015-01-01

Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be elucidated. In this open framework it has been suggested that the ligand stabilizes the interaction of the distal "kissing loop" complex. Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts. In this work, we used umbrella sampling simulations to study the thermodynamics of the kissing loop complex in the presence and in the absence of the cognate ligand. We enforced the breaking/formation of the loop-loop interaction restraining the distance between the two loops. We also assessed the convergence of the results by using two alternative initialization protocols. A structural analysis was performed using a novel approach to analyze base contacts. Contacts between the two loops were progressively lost when larger inter-loop distances were enforced. Inter-loop Watson-Crick contacts survived at larger separation when compared with non-canonical pairing and stacking interactions. Intra-loop stacking contacts remained formed upon loop undocking. Our simulations qualitatively indicated that the ligand could stabilize the kissing loop complex. We also compared with previously published simulation studies. Kissing complex stabilization given by the ligand was compatible with available experimental data. However, the dependence of its value on the initialization protocol of the umbrella sampling simulations posed some questions on the quantitative interpretation of the results and called for better converged enhanced sampling simulations.

Standardized methods for Grand Canyon fisheries research 2015

USGS Publications Warehouse

Persons, William R.; Ward, David L.; Avery, Luke A.

2013-01-01

This document presents protocols and guidelines to persons sampling fishes in the Grand Canyon, to help ensure consistency in fish handling, fish tagging, and data collection among different projects and organizations. Most such research and monitoring projects are conducted under the general umbrella of the Glen Canyon Dam Adaptive Management Program and include studies by the U.S. Geological Survey (USGS), U.S. Fish and Wildlife Service (FWS), National Park Service (NPS), the Arizona Game and Fish Department (AGFD), various universities, and private contractors. This document is intended to provide guidance to fieldworkers regarding protocols that may vary from year to year depending on specific projects and objectives. We also provide herein documentation of standard methods used in the Grand Canyon that can be cited in scientific publications, as well as a summary of changes in protocols since the document was first created in 2002.

CAST: a new program package for the accurate characterization of large and flexible molecular systems.

PubMed

Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

2014-09-15

The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

Information Behavior and Information Practice: Reviewing the "Umbrella Concepts" of Information-Seeking Studies

ERIC Educational Resources Information Center

Savolainen, Reijo

2007-01-01

Information behavior and information practice, two major concepts denoting the general ways in which people deal with information, are analyzed. Because of their general nature, they may be conceived of as umbrella concepts drawing on "umbrella discourses" with similar names. Information behavior is currently the dominating umbrella concept, while…

Ecological neighborhoods as a framework for umbrella species selection

USGS Publications Warehouse

Stuber, Erica F.; Fontaine, Joseph J.

2018-01-01

Umbrella species are typically chosen because they are expected to confer protection for other species assumed to have similar ecological requirements. Despite its popularity and substantial history, the value of the umbrella species concept has come into question because umbrella species chosen using heuristic methods, such as body or home range size, are not acting as adequate proxies for the metrics of interest: species richness or population abundance in a multi-species community for which protection is sought. How species associate with habitat across ecological scales has important implications for understanding population size and species richness, and therefore may be a better proxy for choosing an umbrella species. We determined the spatial scales of ecological neighborhoods important for predicting abundance of 8 potential umbrella species breeding in Nebraska using Bayesian latent indicator scale selection in N-mixture models accounting for imperfect detection. We compare the conservation value measured as collective avian abundance under different umbrella species selected following commonly used criteria and selected based on identifying spatial land cover characteristics within ecological neighborhoods that maximize collective abundance. Using traditional criteria to select an umbrella species resulted in sub-maximal expected collective abundance in 86% of cases compared to selecting an umbrella species based on land cover characteristics that maximized collective abundance directly. We conclude that directly assessing the expected quantitative outcomes, rather than ecological proxies, is likely the most efficient method to maximize the potential for conservation success under the umbrella species concept.

Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

PubMed

Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

2014-04-01

Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.

Free energy landscapes of short peptide chains using adaptively biased molecular dynamics

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2009-03-01

We present the results of a computational study of the free energy landscapes of short polypeptide chains, as a function of several reaction coordinates meant to distinguish between several known types of helices. The free energy landscapes were calculated using the recently developed adaptively biased molecular dynamics method followed up with equilibrium ``umbrella correction'' runs. Specific polypeptides investigated include small chains of pure and mixed alanine, glutamate, leucine, lysine and methionine (all amino acids with strong helix-forming propensities), as well as glycine, proline(having a low helix forming propensities), tyrosine, serine and arginine. Our results are consistent with the existing experimental and other theoretical evidence.

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

PubMed Central

Babin, Volodymyr; Roland, Christopher; Darden, Thomas A.; Sagui, Celeste

2007-01-01

There is considerable interest in developing methodologies for the accurate evaluation of free energies, especially in the context of biomolecular simulations. Here, we report on a reexamination of the recently developed metadynamics method, which is explicitly designed to probe “rare events” and areas of phase space that are typically difficult to access with a molecular dynamics simulation. Specifically, we show that the accuracy of the free energy landscape calculated with the metadynamics method may be considerably improved when combined with umbrella sampling techniques. As test cases, we have studied the folding free energy landscape of two prototypical peptides: Ace-(Gly)2-Pro-(Gly)3-Nme in vacuo and trialanine solvated by both implicit and explicit water. The method has been implemented in the classical biomolecular code AMBER and is to be distributed in the next scheduled release of the code. © 2006 American Institute of Physics. PMID:17144742

Ames Infusion Stories for NASA Annual Technology Report: Nano Entry System for CubeSat-Class Payloads

NASA Technical Reports Server (NTRS)

Smith, Brandon; Jan, Darrell Leslie; Venkatapathy, Etiraj

2015-01-01

The Nano Entry System for CubeSat-Class Payloads led to the development of the Nano-Adaptable Deployable Entry and Placement Technology ("Nano-ADEPT"). Nano-ADEPT is a mechanically deployed entry, descent, and landing (EDL) system that stows during launch and cruise (like an umbrella) and serves as both heat shield and primary structure during EDL. It is especially designed for small spacecraft where volume is a limiting constraint.

Recipes for free energy calculations in biomolecular systems.

PubMed

Moradi, Mahmoud; Babin, Volodymyr; Sagui, Celeste; Roland, Christopher

2013-01-01

During the last decade, several methods for sampling phase space and calculating various free energies in biomolecular systems have been devised or refined for molecular dynamics (MD) simulations. Thus, state-of-the-art methodology and the ever increasing computer power allow calculations that were forbidden a decade ago. These calculations, however, are not trivial as they require knowledge of the methods, insight into the system under study, and, quite often, an artful combination of different methodologies in order to avoid the various traps inherent in an unknown free energy landscape. In this chapter, we illustrate some of these concepts with two relatively simple systems, a sugar ring and proline oligopeptides, whose free energy landscapes still offer considerable challenges. In order to explore the configurational space of these systems, and to surmount the various free energy barriers, we combine three complementary methods: a nonequilibrium umbrella sampling method (adaptively biased MD, or ABMD), replica-exchange molecular dynamics (REMD), and steered molecular dynamics (SMD). In particular, ABMD is used to compute the free energy surface of a set of collective variables; REMD is used to improve the performance of ABMD, to carry out sampling in space complementary to the collective variables, and to sample equilibrium configurations directly; and SMD is used to study different transition mechanisms.

Building a Persian Gulf Ballistic Missile Defense Umbrella: A Comparative Case Study Analysis of Regional Phased Adaptive Approaches

DTIC Science & Technology

2013-06-01

following literature is in addition to the literature already cited that focuses on threat capability and strategic balance, Tom Sauer, Eliminating Nuclear...Missile Defenses (Claremont: Regina Books, 2003 ), 15. 16 have constituted something of a sibling rivalry with the offense gaining favor and eventually...Freedman, The Evolution of Nuclear Strategy, 3rd ed. (New York: Palgrave Macmillan, 2003 ), 242. 30 Ibid., 232–242; Burns and Brune, The Quest for Missile

Perforation of the right aortic valve cusp: complication of ventricular septal defect closure with a modified Rashkind umbrella.

PubMed

Vogel, M; Rigby, M L; Shore, D

1996-01-01

An 18-month-old boy with a perimembranous ventricular septal defect (VSD) had undergone transcatheter closure of the defect with a modified 17 mm Rashkind umbrella device at age 4 months (weight 3.8 kg). The clinical signs of a VSD persisted, and he developed aortic incompetence, first detected 5 months after the procedure, which progressed from mild to moderate. A three-dimensional echocardiographic study demonstrated that one of the four arms holding the umbrella was protruding into the aortic valve and had perforated the right aortic valve cusp. This diagnosis was confirmed at subsequent surgery. Surgical repair of the perforated right aortic valve leaflet was necessary. The umbrella was adherent to the tricuspid valve and could not be removed. Instead it was left in situ, but three of the stainless steel arms were cut off. When umbrella closure of a perimembranous VSD is undertaken, the close proximity of part of the distal umbrella to the aortic valve can lead to aortic regurgitation.

Mechanistic insights into Pin1 peptidyl-prolyl cis-trans isomerization from umbrella sampling simulations.

PubMed

Di Martino, Giovanni Paolo; Masetti, Matteo; Cavalli, Andrea; Recanatini, Maurizio

2014-11-01

The peptidyl-proyl isomerase Pin1 plays a key role in the regulation of phospho(p)-Ser/Thr-Pro proteins, acting as a molecular timer of the cell cycle. After recognition of these motifs, Pin1 catalyzes the rapid cis-trans isomerization of proline amide bonds of substrates, contributing to maintain the equilibrium between the two conformations. Although a great interest has arisen on this enzyme, its catalytic mechanism has long been debated. Here, the cis-trans isomerization of a model peptide system was investigated by means of umbrella sampling simulations in the Pin1-bound and unbound states. We obtained free energy barriers consistent with experimental data, and identified several enzymatic features directly linked to the acceleration of the prolyl bond isomerization. In particular, an enhanced autocatalysis, the stabilization of perturbed ground state conformations, and the substrate binding in a procatalytic conformation were found as main contributions to explain the lowering of the isomerization free energy barrier. © 2014 Wiley Periodicals, Inc.

78 FR 9066 - Endangered and Threatened Wildlife and Plants; Enhancement of Survival Permit Application; Draft...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-07

... impacts to the human environment from the proposed Umbrella CCAA and alternatives to the action. DATES..., State, and local governments: Draft Greater Sage-grouse Umbrella Candidate Conservation Agreement with Assurances for Wyoming Ranch Management (Umbrella CCAA), and Draft Environment Assessment of the Greater Sage...

Improving Clinical Trial Efficiency: Thinking outside the Box.

PubMed

Mandrekar, Sumithra J; Dahlberg, Suzanne E; Simon, Richard

2015-01-01

Clinical trial design strategies have evolved over the past few years as a means to accelerate the drug development process so that the right therapies can be delivered to the right patients. Basket, umbrella, and adaptive enrichment strategies represent a class of novel designs for testing targeted therapeutics in oncology. Umbrella trials include a central infrastructure for screening and identification of patients, and focus on a single tumor type or histology with multiple subtrials, each testing a targeted therapy within a molecularly defined subset. Basket trial designs offer the possibility to include multiple molecularly defined subpopulations, often across histology or tumor types, but included in one cohesive design to evaluate the targeted therapy in question. Adaptive enrichment designs offer the potential to enrich for patients with a particular molecular feature that is predictive of benefit for the test treatment based on accumulating evidence from the trial. This review will aim to discuss the fundamentals of these design strategies, the underlying statistical framework, the logistical barriers of implementation, and, ultimately, the interpretation of the trial results. New statistical approaches, extensive multidisciplinary collaboration, and state of the art data capture technologies are needed to implement these strategies in practice. Logistical challenges to implementation arising from centralized assay testing, requirement of multiple specimens, multidisciplinary collaboration, and infrastructure requirements will also be discussed. This review will present these concepts in the context of the National Cancer Institute's precision medicine initiative trials: MATCH, ALCHEMIST, Lung MAP, as well as other trials such as FOCUS4.

A dynamic structural model of expanded RNA CAG repeats: A refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations

PubMed Central

Yildirim, Ilyas; Park, Hajeung; Disney, Matthew D.; Schatz, George C.

2013-01-01

One class of functionally important RNA is repeating transcripts that cause disease through various mechanisms. For example, expanded r(CAG) repeats can cause Huntington’s and other disease through translation of toxic proteins. Herein, crystal structure of r[5ʹUUGGGC(CAG)3GUCC]2, a model of CAG expanded transcripts, refined to 1.65 Å resolution is disclosed that show both anti-anti and syn-anti orientations for 1×1 nucleotide AA internal loops. Molecular dynamics (MD) simulations using Amber force field in explicit solvent were run for over 500 ns on model systems r(5ʹGCGCAGCGC)2 (MS1) and r(5ʹCCGCAGCGG)2 (MS2). In these MD simulations, both anti-anti and syn-anti AA base pairs appear to be stable. While anti-anti AA base pairs were dynamic and sampled multiple anti-anti conformations, no syn-anti↔anti-anti transformations were observed. Umbrella sampling simulations were run on MS2, and a 2D free energy surface was created to extract transformation pathways. In addition, over 800 ns explicit solvent MD simulation was run on r[5ʹGGGC(CAG)3GUCC]2, which closely represents the refined crystal structure. One of the terminal AA base pairs (syn-anti conformation), transformed to anti-anti conformation. The pathway followed in this transformation was the one predicted by umbrella sampling simulations. Further analysis showed a binding pocket near AA base pairs in syn-anti conformations. Computational results combined with the refined crystal structure show that global minimum conformation of 1×1 nucleotide AA internal loops in r(CAG) repeats is anti-anti but can adopt syn-anti depending on the environment. These results are important to understand RNA dynamic-function relationships and develop small molecules that target RNA dynamic ensembles. PMID:23441937

When BVD doesn't look like BVD

USDA-ARS?s Scientific Manuscript database

Due to the sheer number of different clinical presentations existing under the BVD umbrella, diagnosing BVD based on clinical signs is not advisable. Thus diagnosis relies upon testing of samples in diagnostic laboratories. In the US, most of the diagnostic effort has been focused on identifying a...

Radioactivity in three species of eastern Mediterranean jellyfish.

PubMed

Mamish, S; Al-Masri, M S; Durgham, H

2015-11-01

Activity concentrations of (137)Cs, (40)K, (210)Po, (210)Pb, (234)U and (238)U were determined in umbrella and oral arms of three widely distributed jellyfish species; namely Rhopilema nomadica Galil, 1990, Aurelia aurita Linne, 1758 and Aequorea forskalea Péron & Lesueur, 1810 collected from February 2011 to January 2012 in four sampling locations along the Syrian coast (Eastern Mediterranean Sea). The results have shown significant variations in radionuclides activity concentrations amongst the species. The average activity concentrations of (40)K, (210)Po, (210)Pb, (234)U and (238)U in the umbrella of R. nomadica species were higher than the average activity concentrations in the umbrella of A. aurita species by about 3.2, 1.4, 1.8, 3.2 and 3.2 folds, and A. forskalea species by about 45.5, 15.4, 19, 7.4 and 7.6 folds, respectively. The average activity concentrations of (40)K, (210)Po, (210)Pb, (234)U and (238)U in oral arms of R. nomadica species were higher than the average activity concentrations in oral arms of A. aurita species by about 3.8, 1.7, 1.9, 2.8 and 2.9 folds, respectively. (137)Cs activity concentrations were below the detection limit in all measured samples. In addition, activity concentrations of (137)Cs, (40)K, (210)Po, (210)Pb, (234)U and (238)U were also determined in 44 surface seawater samples and the activity concentrations ranged between 10.6 and 11.9 Bq l(-1) for (40)K, 1.1 and 1.4 mBq l(-1) for (210)Po, 0.5 and 0.7 mBq l(-1) for (210)Pb, 40.8 and 44.5 mBq l(-1) for (234)U, and 36.9 and 38.4 mBq l(-1) for (238)U, while (137)Cs activity concentrations were below the detection limit in all measured samples. Moreover, the umbrella and oral arms readily accumulated (40)K, (210)Po, (210)Pb, (234)U and (238)U above ambient seawater levels in the sequence of (210)Po > (210)Pb > (4) K > (234)U and (238)U. Concentration ratio (CR) values were relatively high for (210)Po and (210)Pb and reached 10(3) and 10(2), respectively for the jellyfish R. nomadica species compared to A. aurita and A. forskalea species. Therefore, R. nomadica can be used as biomonitor for these two radionuclides in the Eastern Mediterranean Sea. However, the obtained data can be considered the first reported baseline values for radioactivity in jellyfish. Copyright © 2015 Elsevier Ltd. All rights reserved.

Summarizing systematic reviews: methodological development, conduct and reporting of an umbrella review approach.

PubMed

Aromataris, Edoardo; Fernandez, Ritin; Godfrey, Christina M; Holly, Cheryl; Khalil, Hanan; Tungpunkom, Patraporn

2015-09-01

With the increase in the number of systematic reviews available, a logical next step to provide decision makers in healthcare with the evidence they require has been the conduct of reviews of existing systematic reviews. Syntheses of existing systematic reviews are referred to by many different names, one of which is an umbrella review. An umbrella review allows the findings of reviews relevant to a review question to be compared and contrasted. An umbrella review's most characteristic feature is that this type of evidence synthesis only considers for inclusion the highest level of evidence, namely other systematic reviews and meta-analyses. A methodology working group was formed by the Joanna Briggs Institute to develop methodological guidance for the conduct of an umbrella review, including diverse types of evidence, both quantitative and qualitative. The aim of this study is to describe the development and guidance for the conduct of an umbrella review. Discussion and testing of the elements of methods for the conduct of an umbrella review were held over a 6-month period by members of a methodology working group. The working group comprised six participants who corresponded via teleconference, e-mail and face-to-face meeting during this development period. In October 2013, the methodology was presented in a workshop at the Joanna Briggs Institute Convention. Workshop participants, review authors and methodologists provided further testing, critique and feedback on the proposed methodology. This study describes the methodology and methods developed for the conduct of an umbrella review that includes published systematic reviews and meta-analyses as the analytical unit of the review. Details are provided regarding the essential elements of an umbrella review, including presentation of the review question in a Population, Intervention, Comparator, Outcome format, nuances of the inclusion criteria and search strategy. A critical appraisal tool with 10 questions to help assess risk of bias in systematic reviews and meta-analyses was also developed and tested. Relevant details to extract from included reviews and how to best present the findings of both quantitative and qualitative systematic reviews in a reader friendly format are provided. Umbrella reviews provide a ready means for decision makers in healthcare to gain a clear understanding of a broad topic area. The umbrella review methodology described here is the first to consider reviews that report other than quantitative evidence derived from randomized controlled trials. The methodology includes an easy to use and informative summary of evidence table to readily provide decision makers with the available, highest level of evidence relevant to the question posed.

Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy

NASA Astrophysics Data System (ADS)

Zheng, Lianqing; Yang, Wei

2008-07-01

Recently, accelerated molecular dynamics (AMD) technique was generalized to realize essential energy space random walks so that further sampling enhancement and effective localized enhanced sampling could be achieved. This method is especially meaningful when essential coordinates of the target events are not priori known; moreover, the energy space metadynamics method was also introduced so that biasing free energy functions can be robustly generated. Despite the promising features of this method, due to the nonequilibrium nature of the metadynamics recursion, it is challenging to rigorously use the data obtained at the recursion stage to perform equilibrium analysis, such as free energy surface mapping; therefore, a large amount of data ought to be wasted. To resolve such problem so as to further improve simulation convergence, as promised in our original paper, we are reporting an alternate approach: the adaptive-length self-healing (ALSH) strategy for AMD simulations; this development is based on a recent self-healing umbrella sampling method. Here, the unit simulation length for each self-healing recursion is increasingly updated based on the Wang-Landau flattening judgment. When the unit simulation length for each update is long enough, all the following unit simulations naturally run into the equilibrium regime. Thereafter, these unit simulations can serve for the dual purposes of recursion and equilibrium analysis. As demonstrated in our model studies, by applying ALSH, both fast recursion and short nonequilibrium data waste can be compromised. As a result, combining all the data obtained from all the unit simulations that are in the equilibrium regime via the weighted histogram analysis method, efficient convergence can be robustly ensured, especially for the purpose of free energy surface mapping.

Position paper: Rationale for the treatment of Wilms tumour in the UMBRELLA SIOP-RTSG 2016 protocol.

PubMed

van den Heuvel-Eibrink, Marry M; Hol, Janna A; Pritchard-Jones, Kathy; van Tinteren, Harm; Furtwängler, Rhoikos; Verschuur, Arnauld C; Vujanic, Gordan M; Leuschner, Ivo; Brok, Jesper; Rübe, Christian; Smets, Anne M; Janssens, Geert O; Godzinski, Jan; Ramírez-Villar, Gema L; de Camargo, Beatriz; Segers, Heidi; Collini, Paola; Gessler, Manfred; Bergeron, Christophe; Spreafico, Filippo; Graf, Norbert

2017-12-01

The Renal Tumour Study Group of the International Society of Paediatric Oncology (SIOP-RTSG) has developed a new protocol for the diagnosis and treatment of childhood renal tumours, the UMBRELLA SIOP-RTSG 2016 (the UMBRELLA protocol), to continue international collaboration in the treatment of childhood renal tumours. This protocol will support integrated biomarker and imaging research, focussing on assessing the independent prognostic value of genomic changes within the tumour and the volume of the blastemal component that survives preoperative chemotherapy. Treatment guidelines for Wilms tumours in the UMBRELLA protocol include recommendations for localized, metastatic, and bilateral disease, for all age groups, and for relapsed disease. These recommendations have been established by a multidisciplinary panel of leading experts on renal tumours within the SIOP-RTSG. The UMBRELLA protocol should promote international collaboration and research and serve as the SIOP-RTSG best available treatment standard.

Pickett angles and Cremer-Pople coordinates as collective variables for the enhanced sampling of six-membered ring conformations

NASA Astrophysics Data System (ADS)

Sega, M.; Autieri, E.; Pederiva, F.

2011-01-01

Although completely equivalent for the description of puckered ring conformers, the two popular coordinates sets of Strauss-Pickett dihedral angles and Cremer-Pople spherical coordinates are shown to have contrasting features when employed as collective variables in free-energy calculations with accelerated sampling techniques. Results from a 100 ns molecular dynamics simulation at conformational equilibrium and from combined metadynamics/umbrella sampling calculations of glucose are exploited to elucidate these differences.

Sun Protection by Beach Umbrella vs Sunscreen With a High Sun Protection Factor: A Randomized Clinical Trial.

PubMed

Ou-Yang, Hao; Jiang, Lily I; Meyer, Karen; Wang, Steve Q; Farberg, Aaron S; Rigel, Darrell S

2017-03-01

Sun-protective behavior affects skin cancer prevention. Shade works by physically shielding skin from direct harmful UV rays; however, skin may still remain exposed to reflected and indirect UV rays. There is no current standard metric to evaluate shade for its effectiveness in sun protection, and there is insufficient clinical evidence that a beach umbrella alone can provide adequate sun protection. To directly measure sunburn protection offered by a standard beach umbrella compared with that provided by sunscreen with a high sun protection factor under actual use conditions. A single-center, evaluator-blinded, randomized clinical study was conducted from August 13 to 15, 2014, in Lake Lewisville, Texas (elevation, 159 m above sea level), among 81 participants with Fitzpatrick skin types I (n = 1), II (n = 42), and III (n = 38). Participants were randomly assigned to 2 groups: 1 using only a beach umbrella, and the other using only sunscreen with a sun protection factor of 100. All participants remained at a sunny beach for 3½ hours at midday. Clinical sunburn evaluation of each individual for all exposed body sites was conducted 22 to 24 hours after sun exposure. The shade provided by a beach umbrella or protection provided by sunscreen with a sun protection factor of 100. Sunburn on all exposed body sites 22 to 24 hours after sun exposure. Among the 81 participants (25 male and 56 female; mean [SD] age, 41 [16] years) for all body sites evaluated (face, back of neck, upper chest, arms, and legs), the umbrella group showed a statistically significant increase in clinical sunburn scores compared with baseline and had higher postexposure global scores than the sunscreen group (0.75 vs 0.05; P < .001). There was a total of 142 sunburn incidences in the umbrella group vs 17 in the sunscreen group. Thirty-two of the 41 participants (78%) in the umbrella group showed erythema in 1 or more sites vs 10 of the 40 participants (25%) in the sunscreen group (P < .001). Neither umbrella nor sunscreen alone completely prevented sunburn. A beach umbrella alone may not provide sufficient protection for extended UV exposure. It is important to educate the public that combining multiple sun protection measures may be needed to achieve optimal protection. isrctn.org Identifier: ISRCTN19177299.

Free energy calculations of short peptide chains using Adaptively Biased Molecular Dynamics

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2008-10-01

We performed a computational study of monomer peptides composed of methionine, alanine, leucine, glutamate, lysine (all amino acids with a helix-forming propensities); and proline, glycine tyrosine, serine, arginine (which all have poor helix-forming propensities). The free energy landscapes as a function of the handedness and radius of gyration have been calculated using the recently introduced Adaptively Biased Molecular Dynamics (ABMD) method, combined with replica exchange, multiple walkers, and post-processing Umbrella Correction (UC). Minima that correspond to some of the left- and right-handed 310-, α- and π-helixes were identified by secondary structure assignment methods (DSSP, Stride). The resulting free energy surface (FES) and the subsequent steered molecular dynamics (SMD) simulation results are in agreement with the empirical evidence of preferred secondary structures for the peptide chains considered.

Gregg T. Beckham | NREL

Science.gov Websites

Molecular Dynamics, and a suite of free energy methods such as MD Umbrella Sampling, Equilibrium Path chain on the crystal surface, and the degree of crystallinity in the substrate. We have used free energy shows the free energy results for edge, middle, and corner chains for all four types of cellulose. All

Peace umbrella, a vague policy and checkered past. Research report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Biszak, G.A.

1997-03-01

With the break-up of the former Soviet Union, the United Nations Security Council enjoyed a greater consensus among its members in confronting aggression and participation in humanitarian and peace operations. Deploying significant military forces under the peace umbrella at the beginning of this decade was highly unlikely. However, since 1990, 25 deployments have been conducted with the majority falling under the peace umbrella. This paper analyzes current national and military strategy in regards to the peace umbrella, specifically peace enforcement, military doctrine, and the case of Somalia. In addition, this paper looks at doctrine and directives that currently guide deploymentmore » of forces and the potential for future peace operations.« less

Specificity and timescales of cortical adaptation as inferences about natural movie statistics.

PubMed

Snow, Michoel; Coen-Cagli, Ruben; Schwartz, Odelia

2016-10-01

Adaptation is a phenomenological umbrella term under which a variety of temporal contextual effects are grouped. Previous models have shown that some aspects of visual adaptation reflect optimal processing of dynamic visual inputs, suggesting that adaptation should be tuned to the properties of natural visual inputs. However, the link between natural dynamic inputs and adaptation is poorly understood. Here, we extend a previously developed Bayesian modeling framework for spatial contextual effects to the temporal domain. The model learns temporal statistical regularities of natural movies and links these statistics to adaptation in primary visual cortex via divisive normalization, a ubiquitous neural computation. In particular, the model divisively normalizes the present visual input by the past visual inputs only to the degree that these are inferred to be statistically dependent. We show that this flexible form of normalization reproduces classical findings on how brief adaptation affects neuronal selectivity. Furthermore, prior knowledge acquired by the Bayesian model from natural movies can be modified by prolonged exposure to novel visual stimuli. We show that this updating can explain classical results on contrast adaptation. We also simulate the recent finding that adaptation maintains population homeostasis, namely, a balanced level of activity across a population of neurons with different orientation preferences. Consistent with previous disparate observations, our work further clarifies the influence of stimulus-specific and neuronal-specific normalization signals in adaptation.

Specificity and timescales of cortical adaptation as inferences about natural movie statistics

PubMed Central

Snow, Michoel; Coen-Cagli, Ruben; Schwartz, Odelia

2016-01-01

Adaptation is a phenomenological umbrella term under which a variety of temporal contextual effects are grouped. Previous models have shown that some aspects of visual adaptation reflect optimal processing of dynamic visual inputs, suggesting that adaptation should be tuned to the properties of natural visual inputs. However, the link between natural dynamic inputs and adaptation is poorly understood. Here, we extend a previously developed Bayesian modeling framework for spatial contextual effects to the temporal domain. The model learns temporal statistical regularities of natural movies and links these statistics to adaptation in primary visual cortex via divisive normalization, a ubiquitous neural computation. In particular, the model divisively normalizes the present visual input by the past visual inputs only to the degree that these are inferred to be statistically dependent. We show that this flexible form of normalization reproduces classical findings on how brief adaptation affects neuronal selectivity. Furthermore, prior knowledge acquired by the Bayesian model from natural movies can be modified by prolonged exposure to novel visual stimuli. We show that this updating can explain classical results on contrast adaptation. We also simulate the recent finding that adaptation maintains population homeostasis, namely, a balanced level of activity across a population of neurons with different orientation preferences. Consistent with previous disparate observations, our work further clarifies the influence of stimulus-specific and neuronal-specific normalization signals in adaptation. PMID:27699416

A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes.

PubMed

Ovchinnikov, Victor; Nam, Kwangho; Karplus, Martin

2016-08-25

A method is developed to obtain simultaneously free energy profiles and diffusion constants from restrained molecular simulations in diffusive systems. The method is based on low-order expansions of the free energy and diffusivity as functions of the reaction coordinate. These expansions lead to simple analytical relationships between simulation statistics and model parameters. The method is tested on 1D and 2D model systems; its accuracy is found to be comparable to or better than that of the existing alternatives, which are briefly discussed. An important aspect of the method is that the free energy is constructed by integrating its derivatives, which can be computed without need for overlapping sampling windows. The implementation of the method in any molecular simulation program that supports external umbrella potentials (e.g., CHARMM) requires modification of only a few lines of code. As a demonstration of its applicability to realistic biomolecular systems, the method is applied to model the α-helix ↔ β-sheet transition in a 16-residue peptide in implicit solvent, with the reaction coordinate provided by the string method. Possible modifications of the method are briefly discussed; they include generalization to multidimensional reaction coordinates [in the spirit of the model of Ermak and McCammon (Ermak, D. L.; McCammon, J. A. J. Chem. Phys. 1978, 69, 1352-1360)], a higher-order expansion of the free energy surface, applicability in nonequilibrium systems, and a simple test for Markovianity. In view of the small overhead of the method relative to standard umbrella sampling, we suggest its routine application in the cases where umbrella potential simulations are appropriate.

Numerical simulation of flow field in umbrella wind turbine

NASA Astrophysics Data System (ADS)

Daorina, Bao; Xiaoxue, Wang; Wei, Shang; Yadong, Liu; Daorina, Bao; Xiaoxue, Wang; Wei, Shang; Yadong, Liu

2018-05-01

Umbrella wind turbine can control the swept area by adjusting the shrinking angle of the rotor so as to ensure that output power is near the rated value. This is very helpful for the utilization of wind energy in sandstorms and typhoon-prone areas of our country. In this paper, Fluent software is used to simulate the velocity field and pressure field of 5kW Umbrella Wind Turbine at 0° 45°and 60°angle of contraction. The results provide a theoretical basis for further improving the power adjustment mechanism of Umbrella Wind Turbines, At the same time, it also provide a reference for our country to perfect the wind energy utilization system about the typhoon environment in the coastal areas.

Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality.

PubMed

Wei, Qichao; Zhao, Weilong; Yang, Yang; Cui, Beiliang; Xu, Zhijun; Yang, Xiaoning

2018-03-19

Considerable interest in characterizing protein/peptide-surface interactions has prompted extensive computational studies on calculations of adsorption free energy. However, in many cases, each individual study has focused on the application of free energy calculations to a specific system; therefore, it is difficult to combine the results into a general picture for choosing an appropriate strategy for the system of interest. Herein, three well-established computational algorithms are systemically compared and evaluated to compute the adsorption free energy of small molecules on two representative surfaces. The results clearly demonstrate that the characteristics of studied interfacial systems have crucial effects on the accuracy and efficiency of the adsorption free energy calculations. For the hydrophobic surface, steered molecular dynamics exhibits the highest efficiency, which appears to be a favorable method of choice for enhanced sampling simulations. However, for the charged surface, only the umbrella sampling method has the ability to accurately explore the adsorption free energy surface. The affinity of the water layer to the surface significantly affects the performance of free energy calculation methods, especially at the region close to the surface. Therefore, a general principle of how to discriminate between methodological and sampling issues based on the interfacial characteristics of the system under investigation is proposed. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient Construction of Free Energy Profiles of Breathing Metal–Organic Frameworks Using Advanced Molecular Dynamics Simulations

PubMed Central

2017-01-01

In order to reliably predict and understand the breathing behavior of highly flexible metal–organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials. PMID:29131647

Efficient Construction of Free Energy Profiles of Breathing Metal-Organic Frameworks Using Advanced Molecular Dynamics Simulations.

PubMed

Demuynck, Ruben; Rogge, Sven M J; Vanduyfhuys, Louis; Wieme, Jelle; Waroquier, Michel; Van Speybroeck, Veronique

2017-12-12

In order to reliably predict and understand the breathing behavior of highly flexible metal-organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials.

Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures

NASA Astrophysics Data System (ADS)

Bishop, Kevin P.; Roy, Pierre-Nicholas

2018-03-01

Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures.

PubMed

Bishop, Kevin P; Roy, Pierre-Nicholas

2018-03-14

Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

Evidence-Based Practice Guidelines for Fetal Alcohol Spectrum Disorder and Literacy and Learning

ERIC Educational Resources Information Center

Mitten, H. Rae

2013-01-01

Evidence-based Practice Guidelines for Fetal Alcohol Spectrum Disorder (FASD) and Literacy and Learning are derived from an inductive analysis of qualitative data collected in field research. FASD is the umbrella term for a spectrum of neurocognitive and physical disabilities caused by prenatal exposure to alcohol. Data from a sample of N=150 was…

Evidence-Based Practice Guidelines for Fetal Alcohol Spectrum Disorder and Literacy and Learning

ERIC Educational Resources Information Center

Mitten, H. Rae

2013-01-01

Evidence-based Practice Guidelines for Fetal Alcohol Spectrum Disorder (FASD) and Literacy and Learning are derived from an inductive analysis of qualitative data collected in field research. FASD is the umbrella term for a spectrum of neurocognitive and physical disabilities caused by prenatal exposure to alcohol. Data from a sample of N =150 was…

Deploying swarm intelligence in medical imaging identifying metastasis, micro-calcifications and brain image segmentation.

PubMed

al-Rifaie, Mohammad Majid; Aber, Ahmed; Hemanth, Duraiswamy Jude

2015-12-01

This study proposes an umbrella deployment of swarm intelligence algorithm, such as stochastic diffusion search for medical imaging applications. After summarising the results of some previous works which shows how the algorithm assists in the identification of metastasis in bone scans and microcalcifications on mammographs, for the first time, the use of the algorithm in assessing the CT images of the aorta is demonstrated along with its performance in detecting the nasogastric tube in chest X-ray. The swarm intelligence algorithm presented in this study is adapted to address these particular tasks and its functionality is investigated by running the swarms on sample CT images and X-rays whose status have been determined by senior radiologists. In addition, a hybrid swarm intelligence-learning vector quantisation (LVQ) approach is proposed in the context of magnetic resonance (MR) brain image segmentation. The particle swarm optimisation is used to train the LVQ which eliminates the iteration-dependent nature of LVQ. The proposed methodology is used to detect the tumour regions in the abnormal MR brain images.

Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association

PubMed Central

2016-01-01

Potential of mean force (PMF) calculations are used to characterize the free energy landscape of protein–lipid and protein–protein association within membranes. Coarse-grained simulations allow binding free energies to be determined with reasonable statistical error. This accuracy relies on defining a good collective variable to describe the binding and unbinding transitions, and upon criteria for assessing the convergence of the simulation toward representative equilibrium sampling. As examples, we calculate protein–lipid binding PMFs for ANT/cardiolipin and Kir2.2/PIP2, using umbrella sampling on a distance coordinate. These highlight the importance of replica exchange between windows for convergence. The use of two independent sets of simulations, initiated from bound and unbound states, provide strong evidence for simulation convergence. For a model protein–protein interaction within a membrane, center-of-mass distance is shown to be a poor collective variable for describing transmembrane helix–helix dimerization. Instead, we employ an alternative intermolecular distance matrix RMS (DRMS) coordinate to obtain converged PMFs for the association of the glycophorin transmembrane domain. While the coarse-grained force field gives a reasonable Kd for dimerization, the majority of the bound population is revealed to be in a near-native conformation. Thus, the combination of a refined reaction coordinate with improved sampling reveals previously unnoticed complexities of the dimerization free energy landscape. We propose the use of replica-exchange umbrella sampling starting from different initial conditions as a robust approach for calculation of the binding energies in membrane simulations. PMID:27807980

Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bieler, Noah S.; Hünenberger, Philippe H., E-mail: phil@igc.phys.chem.ethz.ch

2014-11-28

In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006–3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires “filling up”more » all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.« less

Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association.

PubMed

Domański, Jan; Hedger, George; Best, Robert B; Stansfeld, Phillip J; Sansom, Mark S P

2017-04-20

Potential of mean force (PMF) calculations are used to characterize the free energy landscape of protein-lipid and protein-protein association within membranes. Coarse-grained simulations allow binding free energies to be determined with reasonable statistical error. This accuracy relies on defining a good collective variable to describe the binding and unbinding transitions, and upon criteria for assessing the convergence of the simulation toward representative equilibrium sampling. As examples, we calculate protein-lipid binding PMFs for ANT/cardiolipin and Kir2.2/PIP 2 , using umbrella sampling on a distance coordinate. These highlight the importance of replica exchange between windows for convergence. The use of two independent sets of simulations, initiated from bound and unbound states, provide strong evidence for simulation convergence. For a model protein-protein interaction within a membrane, center-of-mass distance is shown to be a poor collective variable for describing transmembrane helix-helix dimerization. Instead, we employ an alternative intermolecular distance matrix RMS (D RMS ) coordinate to obtain converged PMFs for the association of the glycophorin transmembrane domain. While the coarse-grained force field gives a reasonable K d for dimerization, the majority of the bound population is revealed to be in a near-native conformation. Thus, the combination of a refined reaction coordinate with improved sampling reveals previously unnoticed complexities of the dimerization free energy landscape. We propose the use of replica-exchange umbrella sampling starting from different initial conditions as a robust approach for calculation of the binding energies in membrane simulations.

Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

NASA Astrophysics Data System (ADS)

Bieler, Noah S.; Hünenberger, Philippe H.

2014-11-01

In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006-3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires "filling up" all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.

The relationship between childhood body weight and dental caries experience: an umbrella systematic review protocol.

PubMed

Carson, Susan J; Abuhaloob, Lamis; Richards, Derek; Hector, Mark P; Freeman, Ruth

2017-10-25

Obesity and dental caries are global public health problems which can impact in childhood and throughout the life course. In simple terms, childhood dental caries and body weight are linked via the common risk factor of diet. An association between dental caries and obesity has been described in a number of studies and reviews. However, similarly, a relationship has also been noted between low body weight and caries experience in children. This protocol will provide the framework for an umbrella review to address the following question: Does the available evidence support a relationship between dental caries experience and body weight in the child population? This review protocol outlines the process to carry out an umbrella systematic review which will synthesise previous reviews of childhood dental caries experience and body weight. An umbrella review methodology will be used to examine the methodological and reporting quality of existing reviews. The final umbrella review aims to aggregate the available evidence in order to provide a summary for policymakers and to inform healthcare interventions. PROSPERO CRD42016047304.

High-Grade Urothelial Carcinoma on Urine Cytology Resembling Umbrella Cells.

PubMed

Renshaw, Andrew A; Gould, Edwin W

2018-01-01

High-grade urothelial carcinoma (UC) cells have many appearances on urine cytology, but according to The Paris System, they can be easily distinguished from umbrella cells. We aimed to define the incidence and appearance of high-grade UC cells that resemble umbrella cells in Cytospin preparations on urine cytology. Cytospin preparations from 331 cases with biopsy follow-up (230 benign/low-grade and 101 malignant [22 carcinoma in situ, 52 papillary, 19 invasive UC, 8 other] cases) were reviewed. A total of 18 cases with malignant cells resembling umbrella cells were identified (17.8% of the malignant cases) and were the only type of malignant cell in 3% of the cases. Two patterns were identified. Tumor cells were either identifiable by at least 20 abnormal cells which were large, had abundant cytoplasm but an elevated nuclear-to-cytoplasmic ratio, and markedly enlarged, round-to-elongated nucleoli, or else rare cells with abundant cytoplasm but obviously malignant nuclei. Cells without nucleoli or obviously malignant nuclei were not specific. Malignant cells resembling umbrella cells can be seen in up to 17% of urine cytology specimens. © 2017 S. Karger AG, Basel.

Transcatheter Closure of Bilateral Multiple Huge Pulmonary Arteriovenous Malformations with Homemade Double-Umbrella Occluders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhong Hongshan, E-mail: zhonghongshan@hotmail.com; Xu Ke; Shao Haibo

2008-07-15

A 28-year-old man underwent successful transcatheter occlusion of three huge pulmonary arteriovenous malformations (PAVMs) using homemade double-umbrella occluders and stainless steel coils. Thoracic CT with three-dimensional reconstruction and pulmonary angiography were used for treatment planning and follow-up. The diameters of the feeding vessels were 11 mm, 13 mm, and 14 mm, respectively. This report demonstrates the novel design and utility of the double-umbrella occluder, an alternative tool for treatment of large PAVMs.

Arcjet Testing of Woven Carbon Cloth for Use on Adaptive Deployable Entry Placement Technology

NASA Technical Reports Server (NTRS)

Arnold, James O.; laub, Bernard; Chen, Yih-Kang; Prabhu, Dinesh K.; Bittner, M. E.; Venkatapathy, Ethiraj

2013-01-01

This paper describes arcjet testing and analysis that has successfully demonstrated the viability of three dimensional woven carbon cloth for dual use in the Adaptive Deployable Entry Placement Technology (ADEPT). ADEPT is an umbrella-like entry system that is folded for stowage in the launch vehicle s shroud and deployed in space prior to reaching the atmospheric interface. A key feature of the ADEPT concept is its lower ballistic coefficient for delivery of a given payload than those for conventional, rigid body entry systems. The benefits that accrue from the lower ballistic coefficient include factor of ten reductions of deceleration forces and entry heating. The former enables consideration of new classes of scientific instruments for solar system exploration while the latter enables the design of a more efficient thermal protection system. The carbon cloth now base lined for ADEPT has a dual use in that it serves as ADEPT s thermal protection system and as the "skin" that transfers aerodynamic deceleration loads to its umbrella-like substructure. The arcjet testing described in this paper was conducted for some of the higher heating conditions for a future Venus mission using the ADEPT concept, thereby showing that the carbon cloth can perform in a relevant entry environment. The ADEPT project considered the carbon cloth to be mission enabling and was carrying it as a major risk during Fiscal Year 2012. The testing and analysis reported here played a major role in retiring that risk and is highly significant to the success and possible adoption of ADEPT for future NASA missions. Finally, this paper also describes a preliminary engineering level code, based on the arcjet data, that can be used to estimate cloth thickness for future missions using ADEPT and to predict carbon cloth performance in future arcjet tests.

Viability of 3 D Woven Carbon Cloth and Advanced Carbon-Carbon Ribs for Adaptive Deployable Entry Placement Technology (ADEPT) for Future NASA Missions

NASA Technical Reports Server (NTRS)

Venkatapathy, Ethiraj; Arnold, James O.; Peterson, K. H.; Blosser, M. L.

2013-01-01

This paper describes aerothermodynamic and thermal structural testing that demonstrate the viability of three dimensional woven carbon cloth and advanced carbon-carbon (ACC) ribs for use in the Adaptive Deployable Entry Placement Technology (ADEPT). ADEPT is an umbrella-like entry system that is folded for stowage in the launch vehicle's shroud and deployed prior to reaching the atmeopheric interface. A key feature of the ADEPT concept is a lower ballistic coefficient for delivery of a given payload than seen with conventional, rigid body entry systems. The benefits that accrue from the lower ballistic coefficient incllude factor-of-ten reductions of deceleration forces and entry heating. The former enables consideration of new classes of scientific instruments for solar system exploration while the latter enables the design of a more efficient thermal protection system. The carbon cloth base lined for ADEPT has a dual use in that it serves as the thermal protection system and as the "skin" that transfers aerdynamic deceleration loads to its umbrella-like substructure. Arcjet testing described in this paper was conducted for some of the higher heating conditions for a future Venus mission using the ADEPT concept, thereby showing that the carbon cloth can perform in a relevant entry environment. Recently completed the thermal structural testing of the cloth attached to a representative ACC rib design is also described. Finally, this paper describes a preliminary engineering level code, based on the arcjet data, that can be used to estimate cloth thickness for future ADEPT missions and to predict carbon cloth performance in future arcjet tests.

How maltose influences structural changes to bind to maltose-binding protein: results from umbrella sampling simulation.

PubMed

Mascarenhas, Nahren Manuel; Kästner, Johannes

2013-02-01

A well-studied periplasmic-binding protein involved in the abstraction of maltose is maltose-binding protein (MBP), which undergoes a ligand-induced conformational transition from an open (ligand-free) to a closed (ligand-bound) state. Umbrella sampling simulations have been us to estimate the free energy of binding of maltose to MBP and to trace the potential of mean force of the unbinding event using the center-of-mass distance between the protein and ligand as the reaction coordinate. The free energy thus obtained compares nicely with the experimentally measured value justifying our theoretical basis. Measurement of the domain angle (N-terminal-domain - hinge - C-terminal-domain) along the unbinding pathway established the existence of three different states. Starting from a closed state, the protein shifts to an open conformation during the initial unbinding event of the ligand then resides in a semi-open conformation and later resides predominantly in an open-state. These transitions along the ligand unbinding pathway have been captured in greater depth using principal component analysis. It is proposed that in mixed-model, both conformational selection and an induced-fit mechanism combine to the ligand recognition process in MBP. Copyright © 2012 Wiley Periodicals, Inc.

29. Umbrella sheds behind South Station. Boston, Suffolk Co., MA. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

29. Umbrella sheds behind South Station. Boston, Suffolk Co., MA. Sec. 4116, MP 229.50. - Northeast Railroad Corridor, Amtrak Route between RI/MA State Line & South Station, Boston, Suffolk County, MA

Defining and evaluating the umbrella species concept for conserving and restoring landscape connectivity.

PubMed

Breckheimer, Ian; Haddad, Nick M; Morris, William F; Trainor, Anne M; Fields, William R; Jobe, R Todd; Hudgens, Brian R; Moody, Aaron; Walters, Jeffrey R

2014-12-01

Conserving or restoring landscape connectivity between patches of breeding habitat is a common strategy to protect threatened species from habitat fragmentation. By managing connectivity for some species, usually charismatic vertebrates, it is often assumed that these species will serve as conservation umbrellas for other species. We tested this assumption by developing a quantitative method to measure overlap in dispersal habitat of 3 threatened species-a bird (the umbrella), a butterfly, and a frog-inhabiting the same fragmented landscape. Dispersal habitat was determined with Circuitscape, which was parameterized with movement data collected for each species. Despite differences in natural history and breeding habitat, we found substantial overlap in the spatial distributions of areas important for dispersal of this suite of taxa. However, the intuitive umbrella species (the bird) did not have the highest overlap with other species in terms of the areas that supported connectivity. Nevertheless, we contend that when there are no irreconcilable differences between the dispersal habitats of species that cohabitate on the landscape, managing for umbrella species can help conserve or restore connectivity simultaneously for multiple threatened species with different habitat requirements. © 2014 Society for Conservation Biology.

Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space.

PubMed

Kim, Ilsoo; Allen, Toby W

2012-04-28

Free energy perturbation, a method for computing the free energy difference between two states, is often combined with non-Boltzmann biased sampling techniques in order to accelerate the convergence of free energy calculations. Here we present a new extension of the Bennett acceptance ratio (BAR) method by combining it with umbrella sampling (US) along a reaction coordinate in configurational space. In this approach, which we call Bennett acceptance ratio with umbrella sampling (BAR-US), the conditional histogram of energy difference (a mapping of the 3N-dimensional configurational space via a reaction coordinate onto 1D energy difference space) is weighted for marginalization with the associated population density along a reaction coordinate computed by US. This procedure produces marginal histograms of energy difference, from forward and backward simulations, with higher overlap in energy difference space, rendering free energy difference estimations using BAR statistically more reliable. In addition to BAR-US, two histogram analysis methods, termed Bennett overlapping histograms with US (BOH-US) and Bennett-Hummer (linear) least square with US (BHLS-US), are employed as consistency and convergence checks for free energy difference estimation by BAR-US. The proposed methods (BAR-US, BOH-US, and BHLS-US) are applied to a 1-dimensional asymmetric model potential, as has been used previously to test free energy calculations from non-equilibrium processes. We then consider the more stringent test of a 1-dimensional strongly (but linearly) shifted harmonic oscillator, which exhibits no overlap between two states when sampled using unbiased Brownian dynamics. We find that the efficiency of the proposed methods is enhanced over the original Bennett's methods (BAR, BOH, and BHLS) through fast uniform sampling of energy difference space via US in configurational space. We apply the proposed methods to the calculation of the electrostatic contribution to the absolute solvation free energy (excess chemical potential) of water. We then address the controversial issue of ion selectivity in the K(+) ion channel, KcsA. We have calculated the relative binding affinity of K(+) over Na(+) within a binding site of the KcsA channel for which different, though adjacent, K(+) and Na(+) configurations exist, ideally suited to these US-enhanced methods. Our studies demonstrate that the significant improvements in free energy calculations obtained using the proposed methods can have serious consequences for elucidating biological mechanisms and for the interpretation of experimental data.

Free-Energy Profiles of Membrane Insertion of the M2 Transmembrane Peptide from Influenza A Virus

DTIC Science & Technology

2008-12-01

ABSTRACT The insertion of the M2 transmembrane peptide from influenza A virus into a membrane has been studied with molecular - dynamics simulations ...performed replica-exchange molecular - dynamics simulations with umbrella-sampling techniques to characterize the probability distribution and conformation...atomic- detailed molecular dynamics (MD) simulation techniques represent a valuable complementary methodology to inves- tigate membrane-insertion of

Chloride Ion Transport by the E. coli CLC Cl-/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study.

PubMed

Wang, Chun-Hung; Duster, Adam W; Aydintug, Baris O; Zarecki, MacKenzie G; Lin, Hai

2018-01-01

We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl - ion migration through the transmembrane domain of a prototypical E. coli CLC Cl - /H + antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl - . Moving the anion into the external binding site (S ext ) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl - traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl - exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl - along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl - changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl - and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl - ion due to electron delocalization. The results suggested that it is important to explore these quantum effects for accurate descriptions of the Cl - transport.

Chloride Ion Transport by the E. coli CLC Cl−/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study

PubMed Central

Wang, Chun-Hung; Duster, Adam W.; Aydintug, Baris O.; Zarecki, MacKenzie G.; Lin, Hai

2018-01-01

We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl− ion migration through the transmembrane domain of a prototypical E. coli CLC Cl−/H+ antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl−. Moving the anion into the external binding site (Sext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl− traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl− exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl− along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl− changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl− and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl− ion due to electron delocalization. The results suggested that it is important to explore these quantum effects for accurate descriptions of the Cl− transport. PMID:29594103

Chloride Ion Transport by the E. coli CLC Cl–/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study

NASA Astrophysics Data System (ADS)

Wang, Chun-Hung; Duster, Adam W.; Aydintug, Baris O.; Zarecki, MacKenzie G.; Lin, Hai

2018-03-01

We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl– ion migration through the transmembrane domain of a prototypical E. coli CLC Cl–/H+ antiporter employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found critical to full access of the channel entrance by Cl–. Moving the anion into the external binding site (Sext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl– travelled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl– exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl– along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing pi bonds (e.g. the Tyr445 side chain), while the charges of the H atoms coordinating Cl– changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers ( 10 kcal/mol) than the MM PMF ( 2 kcal/mol). Binding energy calculations indicated that the interactions between Cl– and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing pi bonds, missing the stabilizations of the Cl– ion due to electron delocalization. The results suggested that it is important to explore these quantum effects for accurate descriptions of the Cl– transport.

Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

NASA Astrophysics Data System (ADS)

Awasthi, Shalini; Nair, Nisanth N.

2017-03-01

Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective variables, which severely limits the predictive power of the enhanced sampling approaches. Here we propose a method called Temperature Accelerated Sliced Sampling (TASS) that combines temperature accelerated molecular dynamics with umbrella sampling and metadynamics to sample the collective variable space in an efficient manner. The presented method can sample a large number of collective variables and is advantageous for controlled exploration of broad and unbound free energy basins. TASS is also shown to achieve quick free energy convergence and is practically usable with ab initio molecular dynamics techniques.

The Flatstent versus the conventional umbrella devices in the percutaneous closure of patent foramen ovale.

PubMed

Aral, Mert; Mullen, Michael

2015-05-01

Patent foramen ovale (PFO) has been associated with paradoxical embolism leading to stroke/transient ischemic attack, migraine, and neurological decompression sickness. In search for the optimal device that would achieve effective clinical closure with minimal complications, a better device selection based on PFO anatomy and improvements in device design is needed. The Flatstent is a new device designed to treat the highly prevalent long-tunnel PFOs from within, minimizing the amount of material left behind in an attempt to reduce device-related complications. The objective is to compare the safety and efficacy of the novel Flatstent versus the conventional umbrella devices in the transcatheter closure of PFO in a nonrandomized, retrospective, single-center study. Between March 2010 and March 2013, 88 patients underwent PFO closure at The Heart Hospital, London with either the novel Flatstent or one of the four conventionally used umbrella devices (GORE Helex Septal Occluder, Occlutech Figulla Flex, Biostar Septal Occluder, and Amplatzer PFO Occluder) depending on their PFO anatomy. Patients were then evaluated with contrast transthoracic echocardiography (TTE) and/or transoesophageal echocardiography (TOE) at 6 weeks and 1 year after the procedure. The residual shunt and complication rates between the Flatstent and umbrella devices were compared. The Flatstent was used in 27 patients (30.7%), whereas 61 patients (69.3%) received one of the four umbrella devices. Primary efficacy point of clinical closure defined as grade 0 or grade 1; residual shunt was achieved in 81.3% in the Flatstent cohort and 80.3% in the umbrella device group at 6 weeks follow-up. At 1 year, the clinical closure rates reached 92.6 and 91.8%. There were two device embolizations, one in each cohort during the immediate postoperative period (<24 hrs), with successful retrieval. One patient in the umbrella device group developed transient atrial fibrillation, which was controlled medically. Event recurrence rate was 0% at 1 year. No difference was found in closure or complication rates between the Flatstent and the umbrella devices. With appropriate preassessment of the PFO anatomy, the Flatstent works as a safe and effective method of treating the PFO from within the tunnel, especially in those with long-tunnel PFOs. Longer follow-up is needed to establish superiority. © 2014 Wiley Periodicals, Inc.

Umbrella occlusion of persistent arterial duct in children under two years.

PubMed Central

Gatzoulis, M A; Rigby, M L; Redington, A N

1994-01-01

OBJECTIVE--To assess the use of trans-catheter occlusion of a persistent arterial duct in symptomatic children < 2 years of age. DESIGN--Descriptive study of selected, non-randomised infants with persistent arterial duct who underwent attempted umbrella occlusion. SETTING--Tertiary referral centre. PATIENTS--Between June 1990 and April 1993, 29 young children with a symptomatic persistent arterial duct underwent attempted transcatheter occlusion. Their age ranged from 1.5 to 23 months, with the youngest infant weighing 2.9 kg. The diagnosis was established before operation in all patients by cross sectional echocardiography. INTERVENTION--Transcatheter occlusion of a haemodynamically important persistent arterial duct was performed with the Rashkind ductal umbrella. In the past year the front loading technique has been used to place the 12 mm umbrella through a 6 F (French) sheath and the 17 mm device through a 8 F sheath so extending the indications for their use. RESULTS--Umbrellas were successfully placed in 25 (86.2%) infants and there was symptomatic improvement in all. There were no deaths or severe complications. The four failures occurred early in the series. They were caused by kinking of the 11 F sheath in two cases and embolisation into the left pulmonary artery in one case. The procedure was abandoned in the fourth case because of a large duct. Only three of the 25 patients had small residual shunts at one year follow up (all with 17 mm devices) but no stenosis or turbulence was noted in any of the patients. CONCLUSION--The transcatheter occlusion of persistent arterial duct in young children with symptoms is a safe alternative to surgery. The new front loading umbrella technique enables successful ductal closure in even smaller infants than earlier devices. Images PMID:7833196

Non-target effects on songbirds from habitat manipulation for Greater Sage-Grouse: Implications for the umbrella species concept

USGS Publications Warehouse

Carlisle, Jason D.; Chalfoun, Anna D.; Smith, Kurt T.; Beck, Jeffery L.

2018-01-01

The “umbrella species” concept is a conservation strategy in which creating and managing reserve areas to meet the needs of one species is thought to benefit other species indirectly. Broad-scale habitat protections on behalf of an umbrella species are assumed to benefit co-occurring taxa, but targeted management actions to improve local habitat suitability for the umbrella species may produce unintended effects on other species. Our objective was to quantify the effects of a common habitat treatment (mowing of big sagebrush [Artemisia tridentata]) intended to benefit a high-profile umbrella species (Greater Sage-Grouse [Centrocercus urophasianus]) on 3 sympatric songbird species of concern. We used a before–after control-impact experimental design spanning 3 yr in Wyoming, USA, to quantify the effect of mowing on the abundance, nest-site selection, nestling condition, and nest survival of 2 sagebrush-obligate songbirds (Brewer's Sparrow [Spizella breweri] and Sage Thrasher [Oreoscoptes montanus]) and one open-habitat generalist songbird (Vesper Sparrow [Pooecetes gramineus]). Mowing was associated with lower abundance of Brewer's Sparrows and Sage Thrashers but higher abundance of Vesper Sparrows. We found no Brewer's Sparrows or Sage Thrashers nesting in the mowed footprint posttreatment, which suggests complete loss of nesting habitat for these species. Mowing was associated with higher nestling condition and nest survival for Vesper Sparrows but not for the sagebrush-obligate species. Management prescriptions that remove woody biomass within a mosaic of intact habitat may be tolerated by sagebrush-obligate songbirds but are likely more beneficial for open-habitat generalist species. By definition, umbrella species conservation entails habitat protections at broad spatial scales. We caution that habitat manipulations to benefit Greater Sage-Grouse could negatively affect nontarget species of conservation concern if implemented across large spatial extents.

Mechanism and Energetics of Charybdotoxin Unbinding from a Potassium Channel from Molecular Dynamics Simulations

PubMed Central

Chen, Po-chia; Kuyucak, Serdar

2009-01-01

Ion channel-toxin complexes are ideal systems for computational studies of protein-ligand interactions, because, in most cases, the channel axis provides a natural reaction coordinate for unbinding of a ligand and a wealth of physiological data is available to check the computational results. We use a recently determined structure of a potassium channel-charybdotoxin complex in molecular dynamics simulations to investigate the mechanism and energetics of unbinding. Pairs of residues on the channel protein and charybdotoxin that are involved in the binding are identified, and their behavior is traced during umbrella-sampling simulations as charybdotoxin is moved away from the binding site. The potential of mean force for the unbinding of charybdotoxin is constructed from the umbrella sampling simulations using the weighted histogram analysis method, and barriers observed are correlated with specific breaking of interactions and influx of water molecules into the binding site. Charybdotoxin is found to undergo conformational changes as a result of the reaction coordinate choice—a nontrivial decision for larger ligands—which we explore in detail, and for which we propose solutions. Agreement between the calculated and the experimental binding energies is obtained once the energetic consequences of these conformational changes are included in the calculations. PMID:19348743

The liquid-liquid transition in supercooled ST2 water: a comparison between umbrella sampling and well-tempered metadynamics.

PubMed

Palmer, Jeremy C; Car, Roberto; Debenedetti, Pablo G

2013-01-01

We investigate the metastable phase behaviour of the ST2 water model under deeply supercooled conditions. The phase behaviour is examined using umbrella sampling (US) and well-tempered metadynamics (WT-MetaD) simulations to compute the reversible free energy surface parameterized by density and bond-orientation order. We find that free energy surfaces computed with both techniques clearly show two liquid phases in coexistence, in agreement with our earlier US and grand canonical Monte Carlo calculations [Y. Liu, J. C. Palmer, A. Z. Panagiotopoulos and P. G. Debenedetti, J Chem Phys, 2012, 137, 214505; Y. Liu, A. Z. Panagiotopoulos and P. G. Debenedetti, J Chem Phys, 2009, 131, 104508]. While we demonstrate that US and WT-MetaD produce consistent results, the latter technique is estimated to be more computationally efficient by an order of magnitude. As a result, we show that WT-MetaD can be used to study the finite-size scaling behaviour of the free energy barrier separating the two liquids for systems containing 192, 300 and 400 ST2 molecules. Although our results are consistent with the expected N(2/3) scaling law, we conclude that larger systems must be examined to provide conclusive evidence of a first-order phase transition and associated second critical point.

Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Tsukamoto, Shuichiro; Sakae, Yoshitake; Itoh, Yukihiro; Suzuki, Takayoshi; Okamoto, Yuko

2018-03-01

We performed protein-ligand docking simulations with a ligand T247, which has been reported as a selective inhibitor of a histone deacetylase HDAC3, by the replica-exchange umbrella sampling method in order to estimate the free energy profiles along ligand docking pathways of HDAC3-T247 and HDAC2-T247 systems. The simulation results showed that the docked state of the HDAC3-T247 system is more stable than that of the HDAC2-T247 system although the amino-acid sequences and structures of HDAC3 and HDAC2 are very similar. By comparing structures obtained from the simulations of both systems, we found the difference between structures of hydrophobic residues at the entrance of the catalytic site. Moreover, we performed conventional molecular dynamics simulations of HDAC3 and HDAC2 systems without T247, and the results also showed the same difference of the hydrophobic structures. Therefore, we consider that this hydrophobic structure contributes to the stabilization of the docked state of the HDAC3-T247 system. Furthermore, we show that Tyr209, which is one of the hydrophobic residues in HDAC2, plays a key role in the instability from the simulation results of a mutated-HDAC2 system.

Optimization of antioxidant activity by response surface methodology in hydrolysates of jellyfish (Rhopilema esculentum) umbrella collagen.

PubMed

Zhuang, Yong-liang; Zhao, Xue; Li, Ba-fang

2009-08-01

To optimize the hydrolysis conditions to prepare hydrolysates of jellyfish umbrella collagen with the highest hydroxyl radical scavenging activity, collagen extracted from jellyfish umbrella was hydrolyzed with trypsin, and response surface methodology (RSM) was applied. The optimum conditions obtained from experiments were pH 7.75, temperature (T) 48.77 degrees C, and enzyme-to-substrate ratio ([E]/[S]) 3.50%. The analysis of variance in RSM showed that pH and [E]/[S] were important factors that significantly affected the process (P<0.05 and P<0.01, respectively). The hydrolysates of jellyfish umbrella collagen were fractionated by high performance liquid chromatography (HPLC), and three fractions (HF-1>3000 Da, 1000 Da

Optimization of antioxidant activity by response surface methodology in hydrolysates of jellyfish (Rhopilema esculentum) umbrella collagen*

PubMed Central

Zhuang, Yong-liang; Zhao, Xue; Li, Ba-fang

2009-01-01

To optimize the hydrolysis conditions to prepare hydrolysates of jellyfish umbrella collagen with the highest hydroxyl radical scavenging activity, collagen extracted from jellyfish umbrella was hydrolyzed with trypsin, and response surface methodology (RSM) was applied. The optimum conditions obtained from experiments were pH 7.75, temperature (T) 48.77 °C, and enzyme-to-substrate ratio ([E]/[S]) 3.50%. The analysis of variance in RSM showed that pH and [E]/[S] were important factors that significantly affected the process (P<0.05 and P<0.01, respectively). The hydrolysates of jellyfish umbrella collagen were fractionated by high performance liquid chromatography (HPLC), and three fractions (HF-1>3000 Da, 1000 Da

Improvement of fluorescence intensity of nitrogen vacancy centers in self-formed diamond microstructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Furuyama, S.; Yaita, J.; Kondo, M.

2015-10-19

We present umbrella-shaped diamond microstructures with metal mirrors at the bottom in order to improve the amount of collected photons from nitrogen vacancy centers. The metal mirrors at the bottom are self-aligned to the umbrella-shaped diamond microstructures which are selectively grown through holes created on a metal mask. By the finite-difference time-domain simulations, we found that the umbrella-shaped microstructures, which have an effect similar to solid immersion lens, could collect photons more efficiently than bulk or pillar-shaped microstructures. Improvement of the fluorescence intensity by factors of from 3 to 5 is shown experimentally.

Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer.

PubMed

Jiang, Wei; Luo, Yun; Maragliano, Luca; Roux, Benoît

2012-11-13

An extremely scalable computational strategy is described for calculations of the potential of mean force (PMF) in multidimensions on massively distributed supercomputers. The approach involves coupling thousands of umbrella sampling (US) simulation windows distributed to cover the space of order parameters with a Hamiltonian molecular dynamics replica-exchange (H-REMD) algorithm to enhance the sampling of each simulation. In the present application, US/H-REMD is carried out in a two-dimensional (2D) space and exchanges are attempted alternatively along the two axes corresponding to the two order parameters. The US/H-REMD strategy is implemented on the basis of parallel/parallel multiple copy protocol at the MPI level, and therefore can fully exploit computing power of large-scale supercomputers. Here the novel technique is illustrated using the leadership supercomputer IBM Blue Gene/P with an application to a typical biomolecular calculation of general interest, namely the binding of calcium ions to the small protein Calbindin D9k. The free energy landscape associated with two order parameters, the distance between the ion and its binding pocket and the root-mean-square deviation (rmsd) of the binding pocket relative the crystal structure, was calculated using the US/H-REMD method. The results are then used to estimate the absolute binding free energy of calcium ion to Calbindin D9k. The tests demonstrate that the 2D US/H-REMD scheme greatly accelerates the configurational sampling of the binding pocket, thereby improving the convergence of the potential of mean force calculation.

Finite Element Simulation of NiTi Umbrella-Shaped Implant Used on Femoral Head under Different Loadings.

PubMed

Mehrabi, Reza; Dorri, Milad; Elahinia, Mohammad

2017-03-12

In this study, an umbrella-shaped device that is used for osteonecrosis treatment is simulated. The femoral head is subjected to various complex loadings as a result of a person's daily movements. Implant devices used in the body are made of shape memory alloy materials because of their remarkable resistance to wear and corrosion, good biocompatibility, and variable mechanical properties. Since this NiTi umbrella-shaped implant is simultaneously under several loadings, a 3-D model of shape memory alloy is utilized to investigate the behavior of the implant under different conditions. Shape memory and pseudo-elasticity behavior of NiTi is analyzed using a numerical model. The simulation is performed within different temperatures and in an isothermal condition with varied and complex loadings. The objective of this study is to evaluate the performance of the device under thermal and multi-axial forces via numerically study. Under tensile loading, the most critical points are on the top part of the implant. It is also shown that changes in temperature have a minor effect on the Von Mises stress. Applied forces and torques have significant influence on the femoral head. Simulations results indicate that the top portion of the umbrella is under the most stress when embedded in the body. Consequently, the middle, curved portion of the umbrella is under the least amount of stress.

Finite Element Simulation of NiTi Umbrella-Shaped Implant Used on Femoral Head under Different Loadings

PubMed Central

Mehrabi, Reza; Dorri, Milad; Elahinia, Mohammad

2017-01-01

In this study, an umbrella-shaped device that is used for osteonecrosis treatment is simulated. The femoral head is subjected to various complex loadings as a result of a person’s daily movements. Implant devices used in the body are made of shape memory alloy materials because of their remarkable resistance to wear and corrosion, good biocompatibility, and variable mechanical properties. Since this NiTi umbrella-shaped implant is simultaneously under several loadings, a 3-D model of shape memory alloy is utilized to investigate the behavior of the implant under different conditions. Shape memory and pseudo-elasticity behavior of NiTi is analyzed using a numerical model. The simulation is performed within different temperatures and in an isothermal condition with varied and complex loadings. The objective of this study is to evaluate the performance of the device under thermal and multi-axial forces via numerically study. Under tensile loading, the most critical points are on the top part of the implant. It is also shown that changes in temperature have a minor effect on the Von Mises stress. Applied forces and torques have significant influence on the femoral head. Simulations results indicate that the top portion of the umbrella is under the most stress when embedded in the body. Consequently, the middle, curved portion of the umbrella is under the least amount of stress. PMID:28952502

Reflective Practice in Healthcare Education: An Umbrella Review

ERIC Educational Resources Information Center

Fragkos, Konstantinos C.

2016-01-01

Reflection in healthcare education is an emerging topic with many recently published studies and reviews. This current systematic review of reviews (umbrella review) of this field explores the following aspects: which definitions and models are currently in use; how reflection impacts design, evaluation, and assessment; and what future challenges…

Under the Whole Language Umbrella: Many Cultures, Many Voices.

ERIC Educational Resources Information Center

Flurkey, Alan D., Ed.; Meyer, Richard J., Ed.

Originally presented at the second annual Whole Language Umbrella Conference, the 18 essays in this book address the three related themes of identity, responsibility, and practice. The essays in the book discuss how whole language is defined, and how its practitioners come to define themselves; how whole language teachers act upon their identities…

Identification of Regime Transitions in Umbrella Cloud Growth for Short- and Long-Lived Eruptions

NASA Astrophysics Data System (ADS)

Pouget, S.; Bursik, M. I.; Johnson, C. G.; Hogg, A. J.; Sparks, R. S. J.; Phillips, J.

2014-12-01

The ability to characterize the transition between fluid dynamic regimes in an umbrella cloud as it spreads as a gravity current is important for volcanologists and atmospheric scientists. It would allow a better understanding of how ash behaves and spreads in the atmosphere and therefore better estimate the location and propagation of the ash during an eruption. We tested a new gravity current model that allows us to study the transition from one flow regime to another in data plume growth data from several eruptions. It was found that previous asymptotic models of umbrella cloud growth only treat one part of the evolution of the cloud. The new model allows for the study of the duration of different regimes and the timing of transitions during growth of the umbrella cloud. It was found, by testing the effect of the different input parameters of the model, that the duration of release from the volcanic source has a larger impact than the drag force and the initial radius of the intrusion on the initial and downwind spreading.

Le Chatelier's Principle in Sensation and Perception: Fractal-Like Enfolding at Different Scales

PubMed Central

Norwich, Kenneth H.

2010-01-01

Le Chatelier's principle asserts that a disturbance, when applied to a resting system may drive the system away from its equilibrium state, but will invoke a countervailing influence that will counteract the effect of the disturbance. When applied to the field of sensation and perception, a generalized stimulus will displace the system from equilibrium, and a generalized adaptation process will serve as the countervailing influence tending to reduce the impact of the stimulus. The principle applies at all levels, from the behavioral to the neural, the larger enfolding the smaller in fractal-like form. Le Chatelier's principle, so applied, leads to the unification of many concepts in sensory science. Ideas as diverse as sensory adaptation, reflex arcs, and simple deductive logic can be brought under the umbrella of a single orienting principle. Beyond unification, this principle allows us to approach many questions in pathophysiology from a different perspective. For example, we find new direction toward the reduction of phantom-limb pain and possibly of vertigo. PMID:21423359

Higher emotional intelligence is related to lower test anxiety among students

PubMed Central

Ahmadpanah, Mohammad; Keshavarz, Mohammadreza; Haghighi, Mohammad; Jahangard, Leila; Bajoghli, Hafez; Sadeghi Bahmani, Dena; Holsboer-Trachsler, Edith; Brand, Serge

2016-01-01

Background For students attending university courses, experiencing test anxiety (TA) dramatically impairs cognitive performance and success at exams. Whereas TA is a specific case of social phobia, emotional intelligence (EI) is an umbrella term covering interpersonal and intrapersonal skills, along with positive stress management, adaptability, and mood. In the present study, we tested the hypothesis that higher EI and lower TA are associated. Further, sex differences were explored. Method During an exam week, a total of 200 university students completed questionnaires covering sociodemographic information, TA, and EI. Results Higher scores on EI traits were associated with lower TA scores. Relative to male participants, female participants reported higher TA scores, but not EI scores. Intrapersonal and interpersonal skills and mood predicted low TA, while sex, stress management, and adaptability were excluded from the equation. Conclusion The pattern of results suggests that efforts to improve intrapersonal and interpersonal skills, and mood might benefit students with high TA. Specifically, social commitment might counteract TA. PMID:26834474

The Psychological Challenge of Late-Life Vision Impairment: Concepts, Findings, and Practical Implications

PubMed Central

Wahl, Hans-Werner

2013-01-01

The intention is to summarize the body of evidence speaking to the psychological challenges faced by visually impaired older adults, as well as their coping efforts. This evidence is substantiated by a rich set of concepts, theories, and empirical findings that have accumulated under the umbrella of age-related psychoophthalmology (APO). I introduce the field of APO and continue with a discussion of important concepts and theories for a better understanding of adaptational processes in visually impaired older adults. I then summarize the most relevant and most recent data from four areas: (1) everyday competence, (2) cognitive functioning, (3) social functioning, and (4) subjective well-being-related outcomes, depression, and adaptational processes. Thereafter, major insights related to the current state-of-the art psychosocial interventions with visuallyimpaired older adults are reviewed. I close with the need that the public health community should become more aware of and address the psychosocial needs of visually impaired older adults. PMID:23691277

Of mice and men: Dissecting the interaction between Listeria monocytogenes Internalin A and E-cadherin

PubMed Central

Genheden, Samuel; Eriksson, Leif A

2013-01-01

We report a study of the interaction between internalin A (inlA) and human or murine E-cadherin (Ecad). inlA is used by Listeria monocytogenes to internalize itself into host cell, but the bacterium is unable to invade murine cells, which has been attributed to the difference in sequence between hEcad and mEcad. Using molecular dynamics simulations, MM/GBSA free energy calculations, hydrogen bond analysis, water characterization and umbrella sampling, we provide a complete atomistic picture of the binding between inlA and Ecad. We dissect key residues in the protein–protein interface and analyze the energetics using MM/GBSA. From this analysis it is clear that the binding of inlA–mEcad is weaker than inlA–hEcad, on par with the experimentally observed inability of inlA to bind to mEcad. However, extended MD simulations of 200 ns in length show no destabilization of the inlA–mEcad complex and the estimation of the potential of mean force (PMF) using umbrella sampling corroborates this conclusion. The binding strength computed from the PMFs show no significant difference between the two protein complexes. Hence, our study suggests that the inability of L. monocytogenes to invade murine cells cannot be explained by processes at the nanosecond to sub-microsecond time scale probed by the simulations performed here. PMID:24688730

Of mice and men: Dissecting the interaction between Listeria monocytogenes Internalin A and E-cadherin.

PubMed

Genheden, Samuel; Eriksson, Leif A

2013-01-01

We report a study of the interaction between internalin A (inlA) and human or murine E-cadherin (Ecad). inlA is used by Listeria monocytogenes to internalize itself into host cell, but the bacterium is unable to invade murine cells, which has been attributed to the difference in sequence between hEcad and mEcad. Using molecular dynamics simulations, MM/GBSA free energy calculations, hydrogen bond analysis, water characterization and umbrella sampling, we provide a complete atomistic picture of the binding between inlA and Ecad. We dissect key residues in the protein-protein interface and analyze the energetics using MM/GBSA. From this analysis it is clear that the binding of inlA-mEcad is weaker than inlA-hEcad, on par with the experimentally observed inability of inlA to bind to mEcad. However, extended MD simulations of 200 ns in length show no destabilization of the inlA-mEcad complex and the estimation of the potential of mean force (PMF) using umbrella sampling corroborates this conclusion. The binding strength computed from the PMFs show no significant difference between the two protein complexes. Hence, our study suggests that the inability of L. monocytogenes to invade murine cells cannot be explained by processes at the nanosecond to sub-microsecond time scale probed by the simulations performed here.

Umbrella Sampling and X-ray Crystallographic Analysis Unveil an Arg-Asp Gate Facilitating Inhibitor Binding Inside Phosphopantetheine Adenylyltransferase Allosteric Cleft.

PubMed

Mondal, A; Chatterjee, R; Datta, S

2018-02-08

Phosphopantetheine adenylyltransferase (PPAT) is a rate-limiting enzyme essential for biosynthesis of coenzyme A (CoA), which in turn is responsible to regulate the secretion of exotoxins via type III secretion system in Pseudomonas aeruginosa, causing severe health concerns ranging from nosocomial infections to respiratory failure. Acetyl coenzyme A (AcCoA) is a newly reported inhibitor of PPAT, believed to regulate the cellular levels of CoA and thereby the pathogenesis. Very little is known so far regarding the mechanistic details of AcCoA binding inside PPAT-binding cleft. Herein, we have used extensive umbrella sampling simulations to decipher mechanistic insight into the inhibitor accommodation inside the binding cavity. We found that R90 and D94 residues act like a gate near the binding cavity to accommodate and stabilize the incoming ligand. Mutational models concerning these residues also show considerable difference in AcCoA-binding thermodynamics. To substantiate our findings, we have solved the first crystal structure of apo-PPAT from P. aeruginosa, which also found to agree with the simulation results. Collectively, these results describe the mechanistic details of accommodation of inhibitor molecule inside PPAT-binding cavity and also offer valuable insight into regulating cellular levels of CoA/AcCoA and thus controlling the pathogenicity.

Evaluation of Selected New York City Umbrella Programs, 1974-1975 School Year.

ERIC Educational Resources Information Center

Fordham Univ., Bronx, NY. Inst. for Research and Evaluation.

An evaluation of twelve different New York City Umbrella Programs coordinated in New York City public schools during the 1974-1975 school year is contained in this document. This report presents a description and evaluation of these programs, together with the major findings. The programs were implemented in the following areas: (1) tutoring in…

Greater sage-grouse as an umbrella species for sagebrush-associated vertebrates.

Treesearch

Mary M. Rowland; Michael J. Wisdom; Lowell Suring; Cara W. Meinke

2006-01-01

Widespread degradation of the sagebrush ecosystem in the western United States, including the invasion of cheatgrass, has prompted resource managers to consider a variety of approaches to restore and conserve habitats for sagebrush-associated species. One such approach involves the use of greater sage-grouse, a species of prominent conservation interest, as an umbrella...

Urothelial cells in smears from cervix uteri

PubMed Central

Palaoro, Luis Alberto; Guerra, Fernando; Angeleri, Anabela; Palamas, Marta; Melba, Sardi-Segovia; Rocher, Adriana Esther

2012-01-01

Objectives: To establish the cytological criteria to identify the urothelial cells in cervical smears in order to avoid mistakes in the cytological diagnosis. Materials and Methods: Cervical smears from 34 post menopausal women with vesicovaginal fistulas, advanced bladder prolapse and genital erosive lichen planes (vulvar kraurosis) (Group 1) and transitional cell metaplasia of the cervix (TCM, Group 2) were stained with Papanicolaou technique. The cervical samples were taken during the routine annual examination for prevention of the uterine cancer. Results: The smears of cervix from Group 1 showed urothelial cells from the three layers of the transitional epithelium. The umbrella cells are the bigger ones with relatively large nuclei. Frequently, they are multinucleated with single or multiple nucleoli and a typical “frothy” cytoplasm (cytoplasmic vacuoles). The cells of the Group 2 showed nuclei with oval to spindled shapes, some tapered ends, less cytoplasm than squamous metaplastic cells, powdery chromatin, small nucleoli and nuclear grooves. Conclusions: The umbrella cells may be mistaken for dysplastic cells originating in low grade squamous intraepithelial lesions lesions (LSILs) due to their nuclear and cytoplasm sizes. Therefore, it is important to know the possibility of their appearance in the cervical smears, especially in post menopausal patients in order to avoid a false diagnosis of an intraepithelial lesion. It is unlikely that deeper cells of urothelium would be confused with high grade squamous intraepithelial lesion (HSIL) cells. However, their presence might be a reason of mistake in the diagnosis. TCM is an under-recognized metaplastic phenomenon of the cervix and vagina, which is a mimicker of high-grade squamous intraepithelial lesion. The differential characteristic between umbrella cells, cells from TCM and the deeper urothelial cells, and LSIL and HSIL are detailed in the present paper. PMID:22438615

Quality Assurance and Evaluation through Brazilian Lenses: An Exploration into the Validity of Umbrella Concepts

ERIC Educational Resources Information Center

Centeno, Vera G.; Kauko, Jaakko; Candido, Helena H. D.

2018-01-01

In our present research we address the question of whether it is valid to apply the Quality Assurance and Evaluation (QAE) umbrella concept, which was formulated to explain new phenomena in European educational governance, to similar developments in Brazilian basic education. This led us to reflect on the possible pitfalls and potential strengths…

Minimally Invasive Surgical Device for Precise Application of Bioadhesives to Prevent iPPROM.

PubMed

Devaud, Yannick Robert; Züger, Silvia; Zimmermann, Roland; Ehrbar, Martin; Ochsenbein-Kölble, Nicole

2018-06-19

The benefits of endoscopic fetal surgery are deteriorated by the high risk of iatrogenic preterm prelabor rupture of fetal membranes (iPPROM). While previous studies have reported good sealing candidates to prevent membrane rupture, the delivery of these materials to the location of membrane puncture remains unsolved. We describe an approach to apply sealing materials onto the amnion through the fetoscopy port. We developed a device composed of an umbrella-shaped polyester coated nitinol mesh and an applicator. The spontaneously unfolding umbrella is pushed through the port, pulled against the amnion, and glued onto the amnion defect site. We tested the adhesion strength of multiple glues and tested the feasibility and reproducibility of this fetal membrane sealing approach in an ex vivo model. The umbrella unfolded and was well positioned in all tests (n = 18). When applied via the fetoscopy port, umbrellas were successfully glued onto the fetal membrane, and all of them completely covered the defect (n = 5). The mean time needed for the whole procedure was 3 min. This study is a proof of concept presenting a potential future solution for the precise local application of bioadhesives for the prevention of iPPROM. © 2018 S. Karger AG, Basel.

Geological support for the Umbrella Effect as a link between geomagnetic field and climate

PubMed Central

Kitaba, Ikuko; Hyodo, Masayuki; Nakagawa, Takeshi; Katoh, Shigehiro; Dettman, David L.; Sato, Hiroshi

2017-01-01

The weakening of the geomagnetic field causes an increase in galactic cosmic ray (GCR) flux. Some researchers argue that enhanced GCR flux might lead to a climatic cooling by increasing low cloud formation, which enhances albedo (umbrella effect). Recent studies have reported geological evidence for a link between weakened geomagnetic field and climatic cooling. However, more work is needed on the mechanism of this link, including whether the umbrella effect is playing a central role. In this research, we present new geological evidence that GCR flux change had a greater impact on continental climate than on oceanic climate. According to pollen data from Osaka Bay, Japan, the decrease in temperature of the Siberian air mass was greater than that of the Pacific air mass during geomagnetic reversals in marine isotope stages (MIS) 19 and 31. Consequently, the summer land-ocean temperature gradient was smaller, and the summer monsoon was weaker. Greater terrestrial cooling indicates that a reduction of insolation is playing a key role in the link between the weakening of the geomagnetic field and climatic cooling. The most likely candidate for the mechanism seems to be the increased albedo of the umbrella effect. PMID:28091595

Geological support for the Umbrella Effect as a link between geomagnetic field and climate.

PubMed

Kitaba, Ikuko; Hyodo, Masayuki; Nakagawa, Takeshi; Katoh, Shigehiro; Dettman, David L; Sato, Hiroshi

2017-01-16

The weakening of the geomagnetic field causes an increase in galactic cosmic ray (GCR) flux. Some researchers argue that enhanced GCR flux might lead to a climatic cooling by increasing low cloud formation, which enhances albedo (umbrella effect). Recent studies have reported geological evidence for a link between weakened geomagnetic field and climatic cooling. However, more work is needed on the mechanism of this link, including whether the umbrella effect is playing a central role. In this research, we present new geological evidence that GCR flux change had a greater impact on continental climate than on oceanic climate. According to pollen data from Osaka Bay, Japan, the decrease in temperature of the Siberian air mass was greater than that of the Pacific air mass during geomagnetic reversals in marine isotope stages (MIS) 19 and 31. Consequently, the summer land-ocean temperature gradient was smaller, and the summer monsoon was weaker. Greater terrestrial cooling indicates that a reduction of insolation is playing a key role in the link between the weakening of the geomagnetic field and climatic cooling. The most likely candidate for the mechanism seems to be the increased albedo of the umbrella effect.

Fluoropyrimidine and platinum toxicity pharmacogenetics: an umbrella review of systematic reviews and meta-analyses.

PubMed

Campbell, Jared M; Bateman, Emma; Peters, Micah Dj; Bowen, Joanne M; Keefe, Dorothy M; Stephenson, Matthew D

2016-03-01

Fluoropyrimidine (FU) and platinum-based chemotherapies are greatly complicated by their associated toxicities. This umbrella systematic review synthesized all systematic reviews that investigated associations between germline variations and toxicity, with the aim of informing personalized medicine. Systematic reviews are important in pharmacogenetics where false positives are common. Four systematic reviews were identified for FU-induced toxicity and three for platinum. Polymorphisms of DPYD and TYMS, but not MTHFR, were statistically significantly associated with FU-induced toxicity (although only DPYD had clinical significance). For platinum, GSTP1 was found to not be associated with toxicity. This umbrella systematic review has synthesized the best available evidence on the pharmacogenetics of FU and platinum toxicity. It provides a useful reference for clinicians and identifies important research gaps.

Is Liberal Studies a Political Instrument in the Secondary School Curriculum? Lessons from the Umbrella Movement in Post-Colonial Hong Kong

ERIC Educational Resources Information Center

Fung, Dennis Chun-Lok; Lui, Wai-Mei

2017-01-01

This paper examines whether Hong Kong teachers and students perceived Liberal Studies and its ongoing curriculum review as politically driven during and after the Umbrella Movement, a large-scale civil disobedience campaign that took place in September 2014. The findings presented herein show that both groups disagreed with the claim that Liberal…

Umbrellas can work under water: Using threatened species as indicator and management surrogates can improve coastal conservation

NASA Astrophysics Data System (ADS)

Gilby, Ben L.; Olds, Andrew D.; Connolly, Rod M.; Yabsley, Nicholas A.; Maxwell, Paul S.; Tibbetts, Ian R.; Schoeman, David S.; Schlacher, Thomas A.

2017-12-01

Species surrogates, the use of particular species to index habitat condition or to represent ecological assemblages are commonly identified in many ecosystems, but are less tested, and therefore less employed in estuaries. Estuaries provide important ecosystem goods (e.g. harvestable species) and services (e.g. carbon processing, coastal armouring), but require protection from multiple human activities, meaning that finding surrogates for estuarine condition or faunal assemblages is a significant knowledge gap. In this study, we test the efficacy of the threatened estuary ray Hemitrygon fluviorum, as a suitable indicator of ecosystem condition and management umbrella surrogate species for conservation prioritisation and monitoring purposes within estuaries. We surveyed fish assemblages and ray presence at ten sites within each of 22 estuaries in southeast Queensland, Australia, using one hour deployments of baited video arrays. We then tested for correlations between ray presence, a series of environmental variables considered important to ecosystem management within estuaries (i.e. testing rays as indicator species), and the co-occurring fish species (i.e. testing rays as umbrella species). Estuary rays function as both umbrella species and ecological indicators of habitat status in subtropical Australian estuaries. As umbrellas, ray occurrence concords with elevated species richness. As ecological indicators, ray distribution concords with habitats of good water quality (especially low turbidity) and more natural vegetation remaining in the catchment. These results highlight the potential for other threatened aquatic vertebrates that are both readily detectable and that are reliable proxies for ecosystems status to be become useful management tools in estuaries. The protection of such large, threatened species in coastal seascapes allows managers to address multiple targets for conservation, especially; (1) protecting species of conservation concern; (2) maintaining diversity; and (3) protecting optimal habitats by better placing reserves.

Experimental Investigation of the Performance of Image Registration and De-aliasing Algorithms

DTIC Science & Technology

2009-09-01

spread function In the literature these types of algorithms are sometimes hcluded under the broad umbrella of superresolution . However, in the current...We use one of these patterns to visually demonstrate successful de-aliasing 15. SUBJECT TERMS Image de-aliasing Superresolution Microscanning Image...undersampled point spread function. In the literature these types of algorithms are sometimes included under the broad umbrella of superresolution . However, in

Reaction mechanism of Ru(II) piano-stool complexes: umbrella sampling QM/MM MD study.

PubMed

Futera, Zdeněk; Burda, Jaroslav V

2014-07-15

Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied in this article by hybrid quantum mechanics-molecular mechanics (QM/MM) computational technique. The whole reaction mechanism is divided into three phases: (i) hydration of the [Ru(II) (η(6) -benzene)(en)Cl](+) complex, (ii) monoadduct formation between the resulting aqua-Ru(II) complex and N7 position of one of the guanines in the ds-DNA oligomer, and (iii) formation of the intrastrand Ru(II) bridge (cross-link) between two adjacent guanines. Free energy profiles of all the reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex and two guanines represent a quantum core, which is described by density functional theory methods. The combined QM/MM scheme is realized by our own software, which was developed to couple several quantum chemical programs (in this study Gaussian 09) and Amber 11 package. Calculated free energy barriers of the both ruthenium hydration and Ru(II)-N7(G) DNA binding process are in good agreement with experimentally measured rate constants. Then, this method was used to study the possibility of cross-link formation. One feasible pathway leading to Ru(II) guanine-guanine cross-link with synchronous releasing of the benzene ligand is predicted. The cross-linking is an exergonic process with the energy barrier lower than for the monoadduct reaction of Ru(II) complex with ds-DNA. Copyright © 2014 Wiley Periodicals, Inc.

Longitudinal Patterns and Predictors of Depression Trajectories Related to the 2014 Occupy Central/Umbrella Movement in Hong Kong

PubMed Central

Li, Tom K.; Pang, Herbert; Chan, Brandford H. Y.; Kawachi, Ichiro; Viswanath, Kasisomayajula; Schooling, Catherine Mary; Leung, Gabriel Matthew

2017-01-01

Objectives. To examine the longitudinal patterns and predictors of depression trajectories before, during, and after Hong Kong’s 2014 Occupy Central/Umbrella Movement. Methods. In a prospective study, between March 2009 and November 2015, we interviewed 1170 adults randomly sampled from the population-representative FAMILY Cohort. We used the Patient Health Questionnaire-9 to assess depressive symptoms and probable major depression. We investigated pre-event and time-varying predictors of depressive symptoms. Results. We identified 4 trajectories: resistant (22.6% of sample), resilient (37.0%), mild depressive symptoms (32.5%), and persistent moderate depression (8.0%). Baseline predictors that appeared to protect against persistent moderate depression included higher household income (odds ratio [OR] = 0.18; 95% confidence interval [CI] = 0.06, 0.56), greater psychological resilience (OR = 0.63; 95% CI = 0.48, 0.82), more family harmony (OR = 0.68; 95% CI = 0.56, 0.83), higher family support (OR = 0.80; 95% CI = 0.69, 0.92), better self-rated health (OR = 0.28; 95% CI = 0.16, 0.49), and fewer depressive symptoms (OR = 0.59; 95% CI = 0.43, 0.81). Conclusions. Depression trajectories after a major protest are comparable to those after major population events. Health care professionals should be aware of the mental health consequences during and after social movements, particularly among individuals lacking social support. PMID:28207329

Making structural sense of dimerization interfaces of delta opioid receptor homodimers.

PubMed

Johnston, Jennifer M; Aburi, Mahalaxmi; Provasi, Davide; Bortolato, Andrea; Urizar, Eneko; Lambert, Nevin A; Javitch, Jonathan A; Filizola, Marta

2011-03-15

Opioid receptors, like other members of the G protein-coupled receptor (GPCR) family, have been shown to associate to form dimers and/or oligomers at the plasma membrane. Whether this association is stable or transient is not known. Recent compelling evidence suggests that at least some GPCRs rapidly associate and dissociate. We have recently calculated binding affinities from free energy estimates to predict transient association between mouse delta opioid receptor (DOR) protomers at a symmetric interface involving the fourth transmembrane (TM4) helix (herein termed "4" dimer). Here we present disulfide cross-linking experiments with DOR constructs with cysteines substituted at the extracellular ends of TM4 or TM5 that confirm the formation of DOR complexes involving these helices. Our results are consistent with the involvement of TM4 and/or TM5 at the DOR homodimer interface, but possibly with differing association propensities. Coarse-grained (CG) well-tempered metadynamics simulations of two different dimeric arrangements of DOR involving TM4 alone or with TM5 (herein termed "4/5" dimer) in an explicit lipid-water environment confirmed the presence of two structurally and energetically similar configurations of the 4 dimer, as previously assessed by umbrella sampling calculations, and revealed a single energetic minimum of the 4/5 dimer. Additional CG umbrella sampling simulations of the 4/5 dimer indicated that the strength of association between DOR protomers varies depending on the protein region at the interface, with the 4 dimer being more stable than the 4/5 dimer.

Reinvention/reengineering of business and technical processes

NASA Technical Reports Server (NTRS)

Olsen, Eugene A.

1996-01-01

The changing marketplace as evidenced by global competition is requiring American organizations to rethink, regroup, and redesign their processes. The umbrella of total quality management (TQM) includes many quality methods, techniques, tools, and approaches. There is no right way for every situation or circumstance. Adaptability and experimentation of several tools is necessary. Process management when properly applied can lead to continuous quality improvements. But some processes simply need to be discarded and new ones developed. This reengineering often results in vertical compression and job redesign and restructuring. Work activities must be designed around processes, not processes around work activities. Reengineering and process management do not stand alone--they support each other. Senior executive leadership and empowerment of workers at all organizational levels is vital for both short-term and long-term success.

Multistate λ-local-elevation umbrella-sampling (MS-λ-LEUS): method and application to the complexation of cations by crown ethers.

PubMed

Bieler, Noah S; Tschopp, Jan P; Hünenberger, Philippe H

2015-06-09

An extension of the λ-local-elevation umbrella-sampling (λ-LEUS) scheme [ Bieler et al. J. Chem. Theory Comput. 2014 , 10 , 3006 ] is proposed to handle the multistate (MS) situation, i.e. the calculation of the relative free energies of multiple physical states based on a single simulation. The key element of the MS-λ-LEUS approach is to use a single coupling variable Λ controlling successive pairwise mutations between the states of interest in a cyclic fashion. The Λ variable is propagated dynamically as an extended-system variable, using a coordinate transformation with plateaus and a memory-based biasing potential as in λ-LEUS. Compared to other available MS schemes (one-step perturbation, enveloping distribution sampling and conventional λ-dynamics) the proposed method presents a number of important advantages, namely: (i) the physical states are visited explicitly and over finite time periods; (ii) the extent of unphysical space required to ensure transitions is kept minimal and, in particular, one-dimensional; (iii) the setup protocol solely requires the topologies of the physical states; and (iv) the method only requires limited modifications in a simulation code capable of handling two-state mutations. As an initial application, the absolute binding free energies of five alkali cations to three crown ethers in three different solvents are calculated. The results are found to reproduce qualitatively the main experimental trends and, in particular, the experimental selectivity of 18C6 for K(+) in water and methanol, which is interpreted in terms of opposing trends along the cation series between the solvation free energy of the cation and the direct electrostatic interactions within the complex.

Kinetics and thermodynamics of gas diffusion in a NiFe hydrogenase.

PubMed

Topin, Jérémie; Rousset, Marc; Antonczak, Serge; Golebiowski, Jérôme

2012-03-01

We have investigated O₂ and H₂ transport across a NiFe hydrogenase at the atomic scale by means of computational methods. The Wild Type protein has been compared with the V74Q mutant. Two distinct methodologies have been applied to study the gas access to the active site. Temperature locally enhanced sampling simulations have emphasized the importance of protein dynamics on gas diffusion. The O₂ diffusion free energy profiles, obtained by umbrella sampling, are in agreement with the known kinetic data and show that in the V74Q mutant, the inhibition process is lowered from both a kinetic and a thermodynamic point of view. Copyright © 2011 Wiley Periodicals, Inc.

Neyman-Pearson classification algorithms and NP receiver operating characteristics

PubMed Central

Tong, Xin; Feng, Yang; Li, Jingyi Jessica

2018-01-01

In many binary classification applications, such as disease diagnosis and spam detection, practitioners commonly face the need to limit type I error (that is, the conditional probability of misclassifying a class 0 observation as class 1) so that it remains below a desired threshold. To address this need, the Neyman-Pearson (NP) classification paradigm is a natural choice; it minimizes type II error (that is, the conditional probability of misclassifying a class 1 observation as class 0) while enforcing an upper bound, α, on the type I error. Despite its century-long history in hypothesis testing, the NP paradigm has not been well recognized and implemented in classification schemes. Common practices that directly limit the empirical type I error to no more than α do not satisfy the type I error control objective because the resulting classifiers are likely to have type I errors much larger than α, and the NP paradigm has not been properly implemented in practice. We develop the first umbrella algorithm that implements the NP paradigm for all scoring-type classification methods, such as logistic regression, support vector machines, and random forests. Powered by this algorithm, we propose a novel graphical tool for NP classification methods: NP receiver operating characteristic (NP-ROC) bands motivated by the popular ROC curves. NP-ROC bands will help choose α in a data-adaptive way and compare different NP classifiers. We demonstrate the use and properties of the NP umbrella algorithm and NP-ROC bands, available in the R package nproc, through simulation and real data studies. PMID:29423442

Neyman-Pearson classification algorithms and NP receiver operating characteristics.

PubMed

Tong, Xin; Feng, Yang; Li, Jingyi Jessica

2018-02-01

In many binary classification applications, such as disease diagnosis and spam detection, practitioners commonly face the need to limit type I error (that is, the conditional probability of misclassifying a class 0 observation as class 1) so that it remains below a desired threshold. To address this need, the Neyman-Pearson (NP) classification paradigm is a natural choice; it minimizes type II error (that is, the conditional probability of misclassifying a class 1 observation as class 0) while enforcing an upper bound, α, on the type I error. Despite its century-long history in hypothesis testing, the NP paradigm has not been well recognized and implemented in classification schemes. Common practices that directly limit the empirical type I error to no more than α do not satisfy the type I error control objective because the resulting classifiers are likely to have type I errors much larger than α, and the NP paradigm has not been properly implemented in practice. We develop the first umbrella algorithm that implements the NP paradigm for all scoring-type classification methods, such as logistic regression, support vector machines, and random forests. Powered by this algorithm, we propose a novel graphical tool for NP classification methods: NP receiver operating characteristic (NP-ROC) bands motivated by the popular ROC curves. NP-ROC bands will help choose α in a data-adaptive way and compare different NP classifiers. We demonstrate the use and properties of the NP umbrella algorithm and NP-ROC bands, available in the R package nproc, through simulation and real data studies.

287(g): Cross-Delegating State and Local Law Enforcement Officers with Federal Immigration Authority - Homeland Security Remedy or Rue?

DTIC Science & Technology

2008-12-01

ICE Office of Investigations uses its legal authority to investigate issues such as immigration crime , human rights violations, and human smuggling...communities. Crimes committed by foreign nationals — many exploited by terrorists — pose ideological, legal and resource challenges to state and local...umbrella of the Special Agent In Charge (SAC) in Denver , Colorado . Utah ICE OI falls under the supervisory umbrella of the Assistant Special Agent In

Security Force Assistance Logistics: The Key to Self-Reliance?

DTIC Science & Technology

2011-05-19

internal defense – the umbrella term that SFA falls under – and directly linked to assisting the foreign security force (FSF) “with the procurement...ideology.6 To some extent or another logistics figures prominently under the umbrella of military advising, so there is understandably a certain degree...billion” under the Mutual Defense Assistance Program (MDAP), which “included more than 1,100 medium-gun M47 and M48 Patton tanks, 152 light-gun tanks

Threat to democracy: Physical and mental health impact of democracy movement in Hong Kong.

PubMed

Hou, Wai Kai; Hall, Brian J; Canetti, Daphna; Lau, Kam Man; Ng, Sin Man; Hobfoll, Stevan E

2015-11-01

This study examined the prevalence and critical predictors of anxiety and depressive symptoms and self-rated health, following the Umbrella Movement in Hong Kong. Random digit dialing recruited a population-representative sample of 1208 Chinese Hong Kong citizens (mean age=46.89 years; 63% female) in the first two weeks of February 2015. Respondents gave their informed consent and reported personal, social, and economic resource loss since the Umbrella Movement (Conservation of Resources-Evaluation), current anxiety symptoms (State-Trait Anxiety Inventory) and depressive symptoms (Patient Health Questionnaire-9), and self-rated health (1=very good, 4=very bad). A total of 47.35% (95% CI=44.55, 50.17) respondents reported moderate/severe anxiety symptoms and 14.4% (95% CI=12.54, 16.50) reported moderate/severe depressive symptoms; 9.11% (95% CI=7.61, 10.86) reported "poor" or "very poor" health. Multivariable regressions revealed that personal and social resource loss was associated with higher anxiety and depressive symptoms and greater odds of "very poor" health (adjusted odds ratios/incidence rate ratios=5-102%), independent of lower education level and income and being unmarried. This study was cross-sectional in nature and thus could not determine causality from the associations between resource loss and outcome variables. Second, the telephone survey relied on self-reports; response bias and social desirability could influence respondents' answers and discount data validity. Third, potential confounders such as preexisting mental and physical health issues and concurrent predictors like exposure to the Umbrella Movement were not assessed. This is one of the first studies following any recent political movement (e.g., The Arab Spring) to quantify distress and the associated correlates of distress among affected citizens. Perceived psychosocial resource losses were critical predictors of poor outcomes. Copyright © 2015 Elsevier B.V. All rights reserved.

Maintaining animal assemblages through single-species management: the case of threatened caribou in boreal forest.

PubMed

Bichet, Orphé; Dupuch, Angélique; Hébert, Christian; Le Borgne, Hélène Le; Fortin, Daniel

2016-03-01

With the intensification of human activities, preserving animal populations is a contemporary challenge of critical importance. In this context, the umbrella species concept is appealing because preserving a single species should result in the protection of multiple co-occurring species. Practitioners, though, face the task of having to find suitable umbrellas to develop single-species management guidelines. In North America, boreal forests must be managed to facilitate the recovery of the threatened boreal caribou (Rangifer tarandus). Yet, the effect of caribou conservation on co-occurring animal species remains poorly documented. We tested if boreal caribou can constitute an effective umbrella for boreal fauna. Birds, small mammals, and insects were sampled along gradients of post-harvest and post-fire forest succession. Predictive models of occupancy were developed from the responses of 95 species to characteristics of forest stands and their surroundings. We then assessed the similarity of species occupancy expected between simulated harvested landscapes and a 90 000-km2 uncut landscape. Managed landscapes were simulated based on three levels of disturbance, two timber-harvest rotation cycles, and dispersed or aggregated cut-blocks. We found that management guidelines that were more likely to maintain caribou populations should also better preserve animal assemblages. Relative to fragmentation or harvest cycle, we detected a stronger effect of habitat loss on species assemblages. Disturbing 22%, 35%, and 45% of the landscape should result, respectively, in 80%, 60%, and 40% probability for caribou populations to be sustainable; in turn, this should result in regional species assemblages with Jaccard similarity indices of 0.86, 0.79, and 0.74, respectively, relative to the uncut landscape. Our study thus demonstrates the value of single-species management for animal conservation. Our quantitative approach allows for the evaluation of management guidelines prior to implementation, thereby providing a tool for establishing suitable compromises between economic and environmental sustainability of human activities.

An intertebrate ecosystem engineer likely covered under the umbrella of sage-grouse conservation

USGS Publications Warehouse

Carlisle, Jason D.; Stewart, David R.; Chalfoun, Anna D.

2017-01-01

Conservation practitioners often rely on areas designed to protect species of greatest conservation priority to also conserve co-occurring species (i.e., the umbrella species concept). The extent to which vertebrate species may serve as suitable umbrellas for invertebrate species, however, has rarely been explored. Sage-grouse (Centrocercus spp.) have high conservation priority throughout much of the rangelands of western North America and are considered an umbrella species through which the conservation of entire rangeland ecosystems can be accomplished. Harvester ants are ecosystem engineers and play important roles in the maintenance and function of rangeland ecosystems. We compared indices of the abundance of western harvester ants (Pogonomyrmex occidentalis) and Greater Sage-Grouse (Centrocercus urophasianus) at 72 sites in central Wyoming, USA, in 2012. The abundance of harvester ant mounds was best predicted by a regression model that included a combination of local habitat characteristics and the abundance of sage-grouse. When controlling for habitat-related factors, areas with higher abundances of sage-grouse pellets (an index of sage-grouse abundance and/or habitat use) had higher abundances of ant mounds than areas with lower abundances of sage-grouse pellets. The causal mechanism underlying this positive relationship between sage-grouse and ant mound abundance at the fine scale could be indirect (e.g., both species prefer similar environmental conditions) or direct (e.g., sage-grouse prefer areas with a high abundance of ant mounds because ants are an important prey item during certain life stages). We observed no relationship between a broad-scale index of breeding sage-grouse density and the abundance of ant mounds. We suspect that consideration of the nonbreeding habitat of sage-grouse and finer-scale measures of sagegrouse abundance are critical to the utility of sage-grouse as an umbrella species for the conservation of harvester ants and their important role in rangeland ecosystems.

Intense pumping and time- and frequency-resolved CARS for driving and tracking structural deformation and recovery of liquid nitromethane molecules

NASA Astrophysics Data System (ADS)

Wang, Chang; Wu, Hong-lin; Song, Yun-fei; He, Xing; Yang, Yan-qiang; Tan, Duo-wang

2015-11-01

A modified CARS technique with an intense nonresonant femtosecond laser is presented to drive the structural deformation of liquid nitromethane molecules and track their structural relaxation process. The CARS spectra reveal that the internal rotation of the molecule can couple with the CN symmetric stretching vibration and the molecules undergo ultrafast structural deformation of the CH3 groups from 'opened umbrella' to 'closed umbrella' shape, and then experience a structural recovery process within 720 fs.

Fetal Alcohol Spectrum Disorders (FASD) and competency to stand trial (CST): Suggestions for a 'best practices' approach to forensic evaluation.

PubMed

Brown, Jerrod M; Haun, Jeffrey; Zapf, Patricia A; Brown, Natalie Novick

Fetal Alcohol Spectrum Disorders (FASD), an umbrella term for neurodevelopmental conditions caused by prenatal alcohol exposure, is overrepresented in the U.S. juvenile and adult criminal justice systems. The brain damage in FASD manifests in a combination of cognitive and adaptive impairments that potentially reduce ability to function adequately during the criminal justice process, including capacity to stand trial (CST). Despite the high risk of arrest and conviction in this population, relatively little research guides CST assessment for defendants who have or may have FASD. Therefore, the purpose of this article is to describe how FASD may affect CST and suggest ways forensic professionals might modify assessment protocols to address possible effects of FASD-associated impairments on adjudicative capacity. Copyright © 2017 Elsevier Ltd. All rights reserved.

The intrapsychics of gender: a model of self-socialization.

PubMed

Tobin, Desiree D; Menon, Meenakshi; Menon, Madhavi; Spatta, Brooke C; Hodges, Ernest V E; Perry, David G

2010-04-01

This article outlines a model of the structure and the dynamics of gender cognition in childhood. The model incorporates 3 hypotheses featured in different contemporary theories of childhood gender cognition and unites them under a single theoretical framework. Adapted from Greenwald et al. (2002), the model distinguishes three constructs: gender identity, gender stereotypes, and attribute self-perceptions. The model specifies 3 causal processes among the constructs: Gender identity and stereotypes interactively influence attribute self-perceptions (stereotype emulation hypothesis); gender identity and attribute self-perceptions interactively influence gender stereotypes (stereotype construction hypothesis); and gender stereotypes and attribute self-perceptions interactively influence identity (identity construction hypothesis). The model resolves nagging ambiguities in terminology, organizes diverse hypotheses and empirical findings under a unifying conceptual umbrella, and stimulates many new research directions. PsycINFO Database Record (c) 2010 APA, all rights reserved.

STS-42 MS Hilmers and Payload Specialist Merbold use IML-1 visual stimulator

NASA Image and Video Library

1992-01-30

STS042-203-024 (22-30 Jan. 1992) --- Astronaut David C. Hilmers (right), STS-42 mission specialist, assists European Space Agency (ESA) payload specialist Ulf Merbold with the visual stimulator experiment on the Space Shuttle Discovery's middeck. This particular test is part of an ongoing study of the Space Adaptation Syndrome (SAS). Seated in a stationary mini-sled, Merbold (or any other subject for this test) stares at an umbrella-shaped rotating dome with a pattern of colored dots on its interior. While observing the rotating dome, the subject turns a knob to indicate his perception of body rotation. The strength of circular vection is calculated by comparing the signals from the dome and the knob. The greater the false sense of circular vection, the more the subject is relying on visual information instead of otolith information.

Making Structural Sense of Dimerization Interfaces of Delta Opioid Receptor Homodimers†

PubMed Central

2011-01-01

Opioid receptors, like other members of the G protein-coupled receptor (GPCR) family, have been shown to associate to form dimers and/or oligomers at the plasma membrane. Whether this association is stable or transient is not known. Recent compelling evidence suggests that at least some GPCRs rapidly associate and dissociate. We have recently calculated binding affinities from free energy estimates to predict transient association between mouse delta opioid receptor (DOR) protomers at a symmetric interface involving the fourth transmembrane (TM4) helix (herein termed “4” dimer). Here we present disulfide cross-linking experiments with DOR constructs with cysteines substituted at the extracellular ends of TM4 or TM5 that confirm the formation of DOR complexes involving these helices. Our results are consistent with the involvement of TM4 and/or TM5 at the DOR homodimer interface, but possibly with differing association propensities. Coarse-grained (CG) well-tempered metadynamics simulations of two different dimeric arrangements of DOR involving TM4 alone or with TM5 (herein termed “4/5” dimer) in an explicit lipid−water environment confirmed the presence of two structurally and energetically similar configurations of the 4 dimer, as previously assessed by umbrella sampling calculations, and revealed a single energetic minimum of the 4/5 dimer. Additional CG umbrella sampling simulations of the 4/5 dimer indicated that the strength of association between DOR protomers varies depending on the protein region at the interface, with the 4 dimer being more stable than the 4/5 dimer. PMID:21261298

Some Surprising Implications of NMR-directed Simulations of Substrate Recognition and Binding by Cytochrome P450cam (CYP101A1).

PubMed

Asciutto, Eliana K; Pochapsky, Thomas C

2018-04-27

Cytochrome P450 cam (CYP101A1) catalyzes the stereospecific 5-exo hydroxylation of d-camphor by molecular oxygen. Previously, residual dipolar couplings measured for backbone amide 1 H- 15 N correlations in both substrate-free and bound forms of CYP101A1 were used as restraints in soft annealing molecular dynamic simulations in order to identify average conformations of the enzyme with and without substrate bound. Multiple substrate-dependent conformational changes remote from the enzyme active site were identified, and site-directed mutagenesis and activity assays confirmed the importance of these changes in substrate recognition. The current work makes use of perturbation response scanning (PRS) and umbrella sampling molecular dynamic of the residual dipolar coupling-derived CYP101A1 structures to probe the roles of remote structural features in enforcing the regio- and stereospecific nature of the hydroxylation reaction catalyzed by CYP101A1. An improper dihedral angle Ψ was defined and used to maintain substrate orientation in the CYP101A1 active site, and it was observed that different values of Ψ result in different PRS response maps. Umbrella sampling methods show that the free energy of the system is sensitive to Ψ, and bound substrate forms an important mechanical link in the transmission of mechanical coupling through the enzyme structure. Finally, a qualitative approach to interpreting PRS maps in terms of the roles of secondary structural features is proposed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer

PubMed Central

2012-01-01

Atomistic molecular dynamics (MD) simulations of druglike molecules embedded in lipid bilayers are of considerable interest as models for drug penetration and positioning in biological membranes. Here we analyze partitioning of coumarin in dioleoylphosphatidylcholine (DOPC) bilayer, based on both multiple, unbiased 3 μs MD simulations (total length) and free energy profiles along the bilayer normal calculated by biased MD simulations (∼7 μs in total). The convergences in time of free energy profiles calculated by both umbrella sampling and z-constraint techniques are thoroughly analyzed. Two sets of starting structures are also considered, one from unbiased MD simulation and the other from “pulling” coumarin along the bilayer normal. The structures obtained by pulling simulation contain water defects on the lipid bilayer surface, while those acquired from unbiased simulation have no membrane defects. The free energy profiles converge more rapidly when starting frames from unbiased simulations are used. In addition, z-constraint simulation leads to more rapid convergence than umbrella sampling, due to quicker relaxation of membrane defects. Furthermore, we show that the choice of RESP, PRODRG, or Mulliken charges considerably affects the resulting free energy profile of our model drug along the bilayer normal. We recommend using z-constraint biased MD simulations based on starting geometries acquired from unbiased MD simulations for efficient calculation of convergent free energy profiles of druglike molecules along bilayer normals. The calculation of free energy profile should start with an unbiased simulation, though the polar molecules might need a slow pulling afterward. Results obtained with the recommended simulation protocol agree well with available experimental data for two coumarin derivatives. PMID:22545027

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer.

PubMed

Paloncýová, Markéta; Berka, Karel; Otyepka, Michal

2012-04-10

Atomistic molecular dynamics (MD) simulations of druglike molecules embedded in lipid bilayers are of considerable interest as models for drug penetration and positioning in biological membranes. Here we analyze partitioning of coumarin in dioleoylphosphatidylcholine (DOPC) bilayer, based on both multiple, unbiased 3 μs MD simulations (total length) and free energy profiles along the bilayer normal calculated by biased MD simulations (∼7 μs in total). The convergences in time of free energy profiles calculated by both umbrella sampling and z-constraint techniques are thoroughly analyzed. Two sets of starting structures are also considered, one from unbiased MD simulation and the other from "pulling" coumarin along the bilayer normal. The structures obtained by pulling simulation contain water defects on the lipid bilayer surface, while those acquired from unbiased simulation have no membrane defects. The free energy profiles converge more rapidly when starting frames from unbiased simulations are used. In addition, z-constraint simulation leads to more rapid convergence than umbrella sampling, due to quicker relaxation of membrane defects. Furthermore, we show that the choice of RESP, PRODRG, or Mulliken charges considerably affects the resulting free energy profile of our model drug along the bilayer normal. We recommend using z-constraint biased MD simulations based on starting geometries acquired from unbiased MD simulations for efficient calculation of convergent free energy profiles of druglike molecules along bilayer normals. The calculation of free energy profile should start with an unbiased simulation, though the polar molecules might need a slow pulling afterward. Results obtained with the recommended simulation protocol agree well with available experimental data for two coumarin derivatives.

Enhanced sampling simulations of DNA step parameters.

PubMed

Karolak, Aleksandra; van der Vaart, Arjan

2014-12-15

A novel approach for the selection of step parameters as reaction coordinates in enhanced sampling simulations of DNA is presented. The method uses three atoms per base and does not require coordinate overlays or idealized base pairs. This allowed for a highly efficient implementation of the calculation of all step parameters and their Cartesian derivatives in molecular dynamics simulations. Good correlation between the calculated and actual twist, roll, tilt, shift, and slide parameters is obtained, while the correlation with rise is modest. The method is illustrated by its application to the methylated and unmethylated 5'-CATGTGACGTCACATG-3' double stranded DNA sequence. One-dimensional umbrella simulations indicate that the flexibility of the central CG step is only marginally affected by methylation. © 2014 Wiley Periodicals, Inc.

An umbrella review of meta-analyses of interventions to improve maternal outcomes for teen mothers.

PubMed

SmithBattle, Lee; Loman, Deborah G; Chantamit-O-Pas, Chutima; Schneider, Joanne Kraenzle

2017-08-01

The purpose of this study was to perform an umbrella review of meta-analyses of intervention studies designed to improve outcomes of pregnant or parenting teenagers. An extensive search retrieved nine reports which provided 21 meta-analyses analyses. Data were extracted by two reviewers. Methodological quality was assessed using the AMSTAR Instrument. Most effect sizes were small but high quality studies showed significant outcomes for reduced low birth weight (RR = 0.60), repeat pregnancies/births (OR = 0.47-0.62), maternal education (OR = 1.21-1.83), and maternal employment (OR = 1.26). Several parenting outcomes (parent-child teaching interaction post-intervention [SMD = -0.91] and at follow-up [SMD = -1.07], and parent-child relationship post-intervention [SMD = -0.71] and at follow-up [SMD = -0.90]) were significant, but sample sizes were very small. Many reports did not include moderator analyses. Behavioral interventions offer limited resources and occur too late to mitigate the educational and social disparities that precede teen pregnancy. Future intervention research and policies that redress the social determinants of early childbearing are recommended. Copyright © 2017 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Psychometric properties of the Brand Personality Scale: evidence from a business school.

PubMed

Caruana, Albert; Pitt, Leyland F; Berthon, Pierre; Berthon, J-P

2007-06-01

The Brand Personality Scale has received considerable attention and has been frequently used and cited in the branding literature. This paper describes an investigation of the psychometric characteristics of the Brand Personality Scale in a business school context where umbrella branding is used. A sample (N=262) of students attending the MBA program of a major business school in eastern USA completed the scale. Results indicate problems with the scale's dimensionality, poor reliability, convergent and nomological validity of the Ruggedness dimension, and lack of support for discriminant validity. Managerial and research implications and limitations are noted.

Adaptable Deployable Entry & Placement Technology (ADEPT) for Cubesat Delivery to Mars Surface

NASA Technical Reports Server (NTRS)

Wercinski, Paul

2014-01-01

The Adaptable, Deployable Entry and Placement Technology (ADEPT), uses a mechanical skeleton to deploy a revolutionary carbon fabric system that serves as both heat shield and primary structure during atmospheric entry. The NASA ADEPT project, currently funded by the Game Changing Development Program in STMD is currently focused on 1m class hypersonic decelerators for the delivery of very small payloads ( 5 kg) to locations of interest in an effort to leverage low-cost platforms to rapidly mature the technology while simultaneously delivering high-value science. Preliminary mission design and aerothermal performance testing in arcjets have shown the ADEPT system is quite capable of safe delivery of cubesats to Mars surface. The ability of the ADEPT to transit to Mars in a stowed configuration (similar to an umbrella) provides options for integration with the Mars 2020 cruise stage, even to consider multiple ADEPTs. System-level test campaigns are underway for FY15 execution or planning for FY16. These include deployment testing, wind tunnel testing, system-level arc jet testing, and a sounding rocket flight test. The goal is system level maturation (TRL 6) at a 1m class Mars design reference mission configuration.

A Fast Technology Infusion Model for Aerospace Organizations

NASA Technical Reports Server (NTRS)

Shapiro, Andrew A.; Schone, Harald; Brinza, David E.; Garrett, Henry B.; Feather, Martin S.

2006-01-01

A multi-year Fast Technology Infusion initiative proposes a model for aerospace organizations to improve the cost-effectiveness by which they mature new, in-house developed software and hardware technologies for space mission use. The first year task under the umbrella of this initiative will provide the framework to demonstrate and document the fast infusion process. The viability of this approach will be demonstrated on two technologies developed in prior years with internal Jet Propulsion Laboratory (JPL) funding. One hardware technology and one software technology were selected for maturation within one calendar year or less. The overall objective is to achieve cost and time savings in the qualification of technologies. At the end of the recommended three-year effort, we will have demonstrated for six or more in-house developed technologies a clear path to insertion using a documented process that permits adaptation to a broad range of hardware and software projects.

Comparison of clinical outcomes of multi-point umbrella suturing and single purse suturing with two-point traction after procedure for prolapse and hemorrhoids (PPH) surgery.

PubMed

Jiang, Huiyong; Hao, Xiuyan; Xin, Ying; Pan, Youzhen

2017-11-01

To compare the clinical outcomes of multipoint umbrella suture and single-purse suture with two-point traction after procedure for prolapse and hemorrhoids surgery (PPH) for the treatment of mixed hemorrhoids. Ninety patients were randomly divided into a PPH plus single-purse suture group (Group A) and a PPH plus multipoint umbrella suture (Group B). All operations were performed by an experienced surgeon. Operation time, width of the specimen, hemorrhoids retraction extent, postoperative pain, postoperative bleeding, and length of hospitalization were recorded and compared. Statistical analysis was conducted by t-test and χ2 test. There were no significant differences in sex, age, course of disease, and degree of prolapse of hemorrhoids between the two groups. The operative time in Group A was significantly shorter than that in Group B (P < 0.05). However, the incidence rates of submucosal hematoma and incomplete hemorrhoid core retraction were significantly lower in Group B (P < 0.05), whereas the width of the specimens in Group B was greater than that in Group A (P < 0.05). There were fewer redundant skin tags in Group B at three months follow-up. No significant difference in postoperative pain, postoperative bleeding, and time of hospital stay (P > 0.05 for all comparisons) was observed. The multipoint umbrella suture showed better clinical outcomes because of its targeted suture according to the extent of hemorrhoid prolapse. Copyright © 2017. Published by Elsevier Ltd.

Thermodynamic free energy methods to investigate shape transitions in bilayer membranes.

PubMed

Ramakrishnan, N; Tourdot, Richard W; Radhakrishnan, Ravi

2016-06-01

The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While computational methods to delineate the free energy landscape are routinely used to analyze the relative stability of conformational states, to determine phase boundaries, and to compute ligand-receptor binding energies its use in problems involving the cell membrane is limited. Here, we present an overview of four different free energy methods to study morphological transitions in bilayer membranes, induced either by the action of curvature remodeling proteins or due to the application of external forces. Using a triangulated surface as a model for the cell membrane and using the framework of dynamical triangulation Monte Carlo, we have focused on the methods of Widom insertion, thermodynamic integration, Bennett acceptance scheme, and umbrella sampling and weighted histogram analysis. We have demonstrated how these methods can be employed in a variety of problems involving the cell membrane. Specifically, we have shown that the chemical potential, computed using Widom insertion, and the relative free energies, computed using thermodynamic integration and Bennett acceptance method, are excellent measures to study the transition from curvature sensing to curvature inducing behavior of membrane associated proteins. The umbrella sampling and WHAM analysis has been used to study the thermodynamics of tether formation in cell membranes and the quantitative predictions of the computational model are in excellent agreement with experimental measurements. Furthermore, we also present a method based on WHAM and thermodynamic integration to handle problems related to end-point-catastrophe that are common in most free energy methods.

Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.

PubMed

Wang, Jinan; Shao, Qiang; Xu, Zhijian; Liu, Yingtao; Yang, Zhuo; Cossins, Benjamin P; Jiang, Hualiang; Chen, Kaixian; Shi, Jiye; Zhu, Weiliang

2014-01-09

Large-scale conformational changes of proteins are usually associated with the binding of ligands. Because the conformational changes are often related to the biological functions of proteins, understanding the molecular mechanisms of these motions and the effects of ligand binding becomes very necessary. In the present study, we use the combination of normal-mode analysis and umbrella sampling molecular dynamics simulation to delineate the atomically detailed conformational transition pathways and the associated free-energy landscapes for three well-known protein systems, viz., adenylate kinase (AdK), calmodulin (CaM), and p38α kinase in the absence and presence of respective ligands. For each protein under study, the transient conformations along the conformational transition pathway and thermodynamic observables are in agreement with experimentally and computationally determined ones. The calculated free-energy profiles reveal that AdK and CaM are intrinsically flexible in structures without obvious energy barrier, and their ligand binding shifts the equilibrium from the ligand-free to ligand-bound conformation (population shift mechanism). In contrast, the ligand binding to p38α leads to a large change in free-energy barrier (ΔΔG ≈ 7 kcal/mol), promoting the transition from DFG-in to DFG-out conformation (induced fit mechanism). Moreover, the effect of the protonation of D168 on the conformational change of p38α is also studied, which reduces the free-energy difference between the two functional states of p38α and thus further facilitates the conformational interconversion. Therefore, the present study suggests that the detailed mechanism of ligand binding and the associated conformational transition is not uniform for all kinds of proteins but correlated to their respective biological functions.

Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling.

PubMed

Lonsdale, Richard; Hoyle, Simon; Grey, Daniel T; Ridder, Lars; Mulholland, Adrian J

2012-02-28

Soluble epoxide hydrolase (sEH) is an enzyme involved in drug metabolism that catalyzes the hydrolysis of epoxides to form their corresponding diols. sEH has a broad substrate range and shows high regio- and enantioselectivity for nucleophilic ring opening by Asp333. Epoxide hydrolases therefore have potential synthetic applications. We have used combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations (at the AM1/CHARMM22 level) and high-level ab initio (SCS-MP2) QM/MM calculations to analyze the reactions, and determinants of selectivity, for two substrates: trans-stilbene oxide (t-SO) and trans-diphenylpropene oxide (t-DPPO). The calculated free energy barriers from the QM/MM (AM1/CHARMM22) umbrella sampling MD simulations show a lower barrier for phenyl attack in t-DPPO, compared with that for benzylic attack, in agreement with experiment. Activation barriers in agreement with experimental rate constants are obtained only with the highest level of QM theory (SCS-MP2) used. Our results show that the selectivity of the ring-opening reaction is influenced by several factors, including proximity to the nucleophile, electronic stabilization of the transition state, and hydrogen bonding to two active site tyrosine residues. The protonation state of His523 during nucleophilic attack has also been investigated, and our results show that the protonated form is most consistent with experimental findings. The work presented here illustrates how determinants of selectivity can be identified from QM/MM simulations. These insights may also provide useful information for the design of novel catalysts for use in the synthesis of enantiopure compounds.

Excited state free energy calculations of Cy3 in different environments

NASA Astrophysics Data System (ADS)

Sawangsang, Pilailuk; Buranachai, Chittanon; Punwong, Chutintorn

2015-05-01

Cy3, a cyanine dye, is one of the most widely used dyes in investigating the structure and dynamics of biomolecules by means of fluorescence methods. However, Cy3 fluorescence emission is strongly competed by trans-cis isomerization, whose efficiency is dictated by the isomerization energy barrier and the environment of Cy3. The fluorescence quantum yield of Cy3 is very low when the dye is free in homogeneous solution but it is considerably enhanced in an environment that rigidifies the structure, e.g. when it is attached to a DNA strand. In this work, the barriers for isomerization on the excited state of free Cy3, and Cy3 attached to single- and double-stranded DNA in methanol, are presented. The free energy and subsequently the isomerization barrier calculations are performed using the umbrella sampling technique with the weighted histogram analysis method. The hybrid quantum mechanics/molecular mechanics (QM/MM) approach is employed to provide the potential energy surfaces for the excited state dynamics simulations in umbrella sampling. The semiempirical floating occupation molecular orbital configuration interaction method is used for electronic excited state calculations of the QM region (Cy3). From the free energy calculations, the barrier of Cy3 attached to the single-stranded DNA is highest, in agreement with previously reported experimental results. This is likely due to the stacking interaction between Cy3 and DNA. Such a stacking interaction is likely associated with steric hindrance that prevents the rotation around the conjugated bonds of Cy3. If Cy3 experiences high steric hindrance, it has a higher isomerization barrier and thus the efficiency of fluorescence emission increases.

Modeling ash fall distribution from a Yellowstone supereruption

USGS Publications Warehouse

Mastin, Larry G.; Van Eaton, Alexa R.; Lowenstern, Jacob B.

2014-01-01

We used the volcanic ash transport and dispersion model Ash3d to estimate the distribution of ashfall that would result from a modern-day Plinian supereruption at Yellowstone volcano. The simulations required modifying Ash3d to consider growth of a continent-scale umbrella cloud and its interaction with ambient wind fields. We simulated eruptions lasting 3 days, 1 week, and 1 month, each producing 330 km3 of volcanic ash, dense-rock equivalent (DRE). Results demonstrate that radial expansion of the umbrella cloud is capable of driving ash upwind (westward) and crosswind (N-S) in excess of 1500 km, producing more-or-less radially symmetric isopachs that are only secondarily modified by ambient wind. Deposit thicknesses are decimeters to meters in the northern Rocky Mountains, centimeters to decimeters in the northern Midwest, and millimeters to centimeters on the East, West, and Gulf Coasts. Umbrella cloud growth may explain the extremely widespread dispersal of the ∼640 ka and 2.1 Ma Yellowstone tephra deposits in the eastern Pacific, northeastern California, southern California, and South Texas.

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Hao; Mey, Antonia S. J. S.; Noé, Frank

2014-12-07

We propose a discrete transition-based reweighting analysis method (dTRAM) for analyzing configuration-space-discretized simulation trajectories produced at different thermodynamic states (temperatures, Hamiltonians, etc.) dTRAM provides maximum-likelihood estimates of stationary quantities (probabilities, free energies, expectation values) at any thermodynamic state. In contrast to the weighted histogram analysis method (WHAM), dTRAM does not require data to be sampled from global equilibrium, and can thus produce superior estimates for enhanced sampling data such as parallel/simulated tempering, replica exchange, umbrella sampling, or metadynamics. In addition, dTRAM provides optimal estimates of Markov state models (MSMs) from the discretized state-space trajectories at all thermodynamic states. Under suitablemore » conditions, these MSMs can be used to calculate kinetic quantities (e.g., rates, timescales). In the limit of a single thermodynamic state, dTRAM estimates a maximum likelihood reversible MSM, while in the limit of uncorrelated sampling data, dTRAM is identical to WHAM. dTRAM is thus a generalization to both estimators.« less

Exercise for adults with fibromyalgia: an umbrella systematic review with synthesis of best evidence.

PubMed

Bidonde, Julia; Busch, Angela Jean; Bath, Brenna; Milosavljevic, Stephan

2014-01-01

The objective of this umbrella systematic review was to identify, evaluate, and synthesize systematic reviews of physical activity interventions for adults with fibromyalgia (FM) focussing on four outcomes: pain, multidimensional function (wellness or quality of life), physical function (self-reported physical function or measured physical fitness) and adverse effects. A further objective was to link these outcomes with details of the interventions so as to guide and shape future practice and research. Electronic databases including Medline, EMBASE, CINAHL, AMED, the Cochrane Library, and DARE, were searched for the January 1(st) 2007 to March 31(st) 2013 period. Nine systematic reviews (60 RCTs with 3816 participants) were included. Meta-analysis was not conducted due to the heterogeneity of the sample. We found positive results of diverse exercise interventions on pain, multidimensional function, and self-reported physical function, and no supporting evidence for new (to FM) interventions (i.e., qigong, tai chi). There were no serious adverse effects reported. The variability of the interventions in the reviews prevented us from answering important clinical questions to guide practical decisions about optimal modes or dosages (i.e., frequency, intensity, duration). Finally, the number of review articles is proliferating, leading researchers and reviewers to consider the rigor and quality of the information being reviewed. As well, consumers of these reviews (i.e., clinicians, individuals with FM) should not rely on them without careful consideration.

Health education for patients with acute coronary syndrome and type 2 diabetes mellitus: an umbrella review of systematic reviews and meta-analyses.

PubMed

Liu, Xian-Liang; Shi, Yan; Willis, Karen; Wu, Chiung-Jung Jo; Johnson, Maree

2017-10-16

This umbrella review aimed to identify the current evidence on health education-related interventions for patients with acute coronary syndrome (ACS) or type two diabetes mellitus (T2DM); identify the educational content, delivery methods, intensity, duration and setting required. The purpose was to provide recommendations for educational interventions for high-risk patients with both ACS and T2DM. Umbrella review of systematic reviews and meta-analyses. Inpatient and postdischarge settings. Patients with ACS and T2DM. CINAHL, Cochrane Library, Joanna Briggs Institute, Journals@Ovid, EMBase, Medline, PubMed and Web of Science databases from January 2000 through May 2016. Clinical outcomes (such as glycated haemoglobin), behavioural outcomes (such as smoking), psychosocial outcomes (such as anxiety) and medical service use. Fifty-one eligible reviews (15 for ACS and 36 for T2DM) consisting of 1324 relevant studies involving 2 88 057 patients (15 papers did not provide the total sample); 30 (58.8%) reviews were rated as high quality. Nurses only and multidisciplinary teams were the most frequent professionals to provide education, and most educational interventions were delivered postdischarge. Face-to-face sessions were the most common delivery formats, and many education sessions were also delivered by telephone or via web contact. The frequency of educational sessions was weekly or monthly, and an average of 3.7 topics was covered per education session. Psychoeducational interventions were generally effective at reducing smoking and admissions for patients with ACS. Culturally appropriate health education, self-management educational interventions, group medical visits and psychoeducational interventions were generally effective for patients with T2DM. Results indicate that there is a body of current evidence about the efficacy of health education, its content and delivery methods for patients with ACS or T2DM. These results provide recommendations about the content for, and approach to, health education intervention for these high-risk patients. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Health education for patients with acute coronary syndrome and type 2 diabetes mellitus: an umbrella review of systematic reviews and meta-analyses

PubMed Central

Liu, Xian-liang; Shi, Yan; Willis, Karen; Wu, Chiung-Jung (Jo); Johnson, Maree

2017-01-01

Objectives This umbrella review aimed to identify the current evidence on health education-related interventions for patients with acute coronary syndrome (ACS) or type two diabetes mellitus (T2DM); identify the educational content, delivery methods, intensity, duration and setting required. The purpose was to provide recommendations for educational interventions for high-risk patients with both ACS and T2DM. Design Umbrella review of systematic reviews and meta-analyses. Setting Inpatient and postdischarge settings. Participants Patients with ACS and T2DM. Data sources CINAHL, Cochrane Library, Joanna Briggs Institute, Journals@Ovid, EMBase, Medline, PubMed and Web of Science databases from January 2000 through May 2016. Outcomes measures Clinical outcomes (such as glycated haemoglobin), behavioural outcomes (such as smoking), psychosocial outcomes (such as anxiety) and medical service use. Results Fifty-one eligible reviews (15 for ACS and 36 for T2DM) consisting of 1324 relevant studies involving 2 88 057 patients (15 papers did not provide the total sample); 30 (58.8%) reviews were rated as high quality. Nurses only and multidisciplinary teams were the most frequent professionals to provide education, and most educational interventions were delivered postdischarge. Face-to-face sessions were the most common delivery formats, and many education sessions were also delivered by telephone or via web contact. The frequency of educational sessions was weekly or monthly, and an average of 3.7 topics was covered per education session. Psychoeducational interventions were generally effective at reducing smoking and admissions for patients with ACS. Culturally appropriate health education, self-management educational interventions, group medical visits and psychoeducational interventions were generally effective for patients with T2DM. Conclusions Results indicate that there is a body of current evidence about the efficacy of health education, its content and delivery methods for patients with ACS or T2DM. These results provide recommendations about the content for, and approach to, health education intervention for these high-risk patients. PMID:29042383

The Cholangiocyte Glycocalyx Stabilizes the 'Biliary HCO3 Umbrella': An Integrated Line of Defense against Toxic Bile Acids.

PubMed

Maillette de Buy Wenniger, Lucas J; Hohenester, Simon; Maroni, Luca; van Vliet, Sandra J; Oude Elferink, Ronald P; Beuers, Ulrich

2015-01-01

Destruction of cholangiocytes is the hallmark of chronic cholangiopathies such as primary biliary cirrhosis. Under physiologic conditions, cholangiocytes display a striking resistance to the high, millimolar concentrations of toxic bile salts present in bile. We recently showed that a 'biliary HCO3(-) umbrella', i.e. apical cholangiocellular HCO3(-) secretion, prevents cholangiotoxicity of bile acids, and speculated on a role for extracellular membrane-bound glycans in the stabilization of this protective layer. This paper summarizes published and thus far unpublished evidence supporting the role of the glycocalyx in stabilizing the 'biliary HCO3(-) umbrella' and thus preventing cholangiotoxicity of bile acids. The apical glycocalyx of a human cholangiocyte cell line and mouse liver sections were visualized by electron microscopy. FACS analysis was used to characterize the surface glycan profile of cultured human cholangiocytes. Using enzymatic digestion with neuraminidase the cholangiocyte glycocalyx was desialylated to test its protective function. Using lectin assays, we demonstrated that the main N-glycans in human and mouse cholangiocytes were sialylated biantennary structures, accompanied by high expression of the H-antigen (α1-2 fucose). Apical neuraminidase treatment induced desialylation without affecting cell viability, but lowered cholangiocellular resistance to bile acid-induced toxicity: both glycochenodeoxycholate and chenodeoxycholate (pKa ≥4), but not taurochenodeoxycholate (pKa <2), displayed cholangiotoxic effects after desialylation. A 24-hour reconstitution period allowed cholangiocytes to recover to a pretreatment bile salt susceptibility pattern. Experimental evidence indicates that an apical cholangiocyte glycocalyx with glycosylated mucins and other glycan-bearing membrane glycoproteins stabilizes the 'biliary HCO3(-) umbrella', thus aiding in the protection of human cholangiocytes against bile acid toxicity. 2015 S. Karger AG, Basel.

Imaging of oxygen gradients in giant umbrella cells: an ex vivo PLIM study.

PubMed

Zhdanov, A V; Golubeva, A V; Okkelman, I A; Cryan, J F; Papkovsky, D B

2015-10-01

O2 plays a pivotal role in aerobic metabolism and regulation of cell and tissue function. Local differences and fluctuations in tissue O2 levels are well documented; however, the physiological significance of O2 microgradients, particularly at the subcellular level, remains poorly understood. Using the cell-penetrating phosphorescent O2 probe Pt-Glc and confocal fluorescence microscopy, we visualized O2 distribution in individual giant (>100-μm) umbrella cells located superficially in the urinary bladder epithelium. We optimized conditions for in vivo phosphorescent staining of the inner surface of the mouse bladder and subsequent ex vivo analysis of excised live tissue. Imaging experiments revealed significant (≤85 μM) and heterogeneous deoxygenation within respiring umbrella cells, with radial O2 gradients of up to 40 μM across the cell, or ∼0.6 μM/μm. Deeply deoxygenated (5-15 μM O2) regions were seen to correspond to the areas enriched with polarized mitochondria. Pharmacological activation of mitochondrial respiration decreased oxygenation and O2 gradients in umbrella cells, while inhibition with antimycin A dissipated the gradients and caused gradual reoxygenation of the tissue to ambient levels. Detailed three-dimensional maps of O2 distribution potentially can be used for the modeling of intracellular O2-dependent enzymatic reactions and downstream processes, such as hypoxia-inducible factor signaling. Further ex vivo and in vivo studies on intracellular and tissue O2 gradients using confocal imaging can shed light on the molecular mechanisms regulating O2-dependent (patho)physiological processes in the bladder and other tissues. Copyright © 2015 the American Physiological Society.

An Umbrella Review of Nuts Intake and Risk of Cardiovascular Disease.

PubMed

Schwingshackl, Lukas; Hoffmann, Georg; Missbach, Benjamin; Stelmach-Mardas, Marta; Boeing, Heiner

2017-01-01

Nuts have been an indispensable component of the human diet for hundreds because of their unique nutrient composition and are thought to play a beneficial part in the prevention of cardiovascular diseases. To evaluate the extent, validity and presence of evidence for studies investigating the impact of nuts intake on biomarkers of cardiovascular disease and cardiovascular events, we performed an umbrella review of all published meta-analyses synthesizing data from both observational studies and randomized controlled trials. PubMed (between 1966 and April 2016) was searched for systematic reviews and meta-analyses. Methodological quality was assessed by applying the AMSTAR score (0-11 points), and the meta-evidence by applying NutriGrade, our recently developed scoring system (0-10 points). In total, 14 meta-analyses were included in the umbrella review. Only 4 out of 14 reported an AMSTAR score ≥8 (high methodological quality), whereas NutriGrade meta-evidence score varied between 2 (very low meta-evidence) and 7.9 (moderate meta-evidence). There is consistent evidence from intervention trials, reporting significant reductions for total cholesterol, and from observational studies that higher intakes of nuts were associated with reduced risk of cardiovascular disease and hypertension. On the other side no effect could be observed for stroke, HDL-cholesterol, and blood pressure in the normal range. In summary, the present umbrella review showed that nuts intake was associated with reduced risk of cardiovascular disease and hypertension, and lower levels of total cholesterol. The observed evidence is limited by the moderate methodological quality and very low to moderate quality of evidence. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

In situ characterization of glycans in the urothelium of donkey bladder: evidence of secretion of sialomucins.

PubMed

Desantis, Salvatore; Accogli, Gianluca; Zizza, Sara; Arrighi, Silvana

2013-09-01

The glycoprotein pattern was investigated by lectin histochemistry in the urothelium lining the urinary bladder of the donkey Equus asinus. Tissue sections were stained with a panel of twelve lectins, in combination with saponification and sialidase digestion (K-s). The urinary bladder urothelium has three distinct layers from the basal zone to the lumen consisting of basal, intermediate and superficial cells (umbrella cells). Cytoplasm of basal cells reacted with SNA, PNA, K-s-PNA, GSA I-B4 and Con A showing glycans ending with Neu5Acα2,6Gal/GalNAc, Neu5AcGalβ1,3GalNAc, αGal and with terminal/internal αMan. The cytoplasm of umbrella cells displayed an increase of Neu5AcGalβ1,3GalNAc and the appearance of Neu5AcGalβ1,3GalNAc, Neu5acα2,3Galβ1,4GlcNAc and Neu5AcGalNAc residues (MAL II, K-s-SBA and K-s-HPA staining). Scattered umbrella cells were characterized by glycans terminating with GalNAc binding DBA, SBA and HPA. The mucosa forms folds with a crypt-like appearance where the urothelium shows a different pattern of glycans. The bladder luminal surface stained with K-s-PNA, K-s-DBA, KOH-s-SBA, and K-s-HPA displaying a coating of sialoglycoproteins belonging to O-linked glycans (typical secretory moieties). These findings show that different glycosylation patterns exist along the donkey bladder urothelium, and different sub-populations of umbrella cells are present secreting the sialoglycans which constitute the protective gel layer lining the bladder. Copyright © 2013 Elsevier GmbH. All rights reserved.

Policy determinants of physical activity across the life course: a 'DEDIPAC' umbrella systematic literature review.

PubMed

Puggina, Anna; Aleksovska, Katina; Buck, Christoph; Burns, Con; Cardon, Greet; Carlin, Angela; Chantal, Simon; Ciarapica, Donatella; Condello, Giancarlo; Coppinger, Tara; Cortis, Cristina; D'Haese, Sara; De Craemer, Marieke; Di Blasio, Andrea; Hansen, Sylvia; Iacoviello, Licia; Issartel, Johann; Izzicupo, Pascal; Jaeschke, Lina; Kanning, Martina; Kennedy, Aileen; Chun Man Ling, Fiona; Luzak, Agnes; Napolitano, Giorgio; Nazare, Julie-Anne; Perchoux, Camille; Pischon, Tobias; Polito, Angela; Sannella, Alessandra; Schulz, Holger; Sohun, Rhoda; Steinbrecher, Astrid; Schlicht, Wolfgang; Ricciardi, Walter; MacDonncha, Ciaran; Capranica, Laura; Boccia, Stefania

2018-02-01

Despite the large number of studies and reviews available, the evidence regarding the policy determinants of physical activity (PA) is inconclusive. This umbrella systematic literature review (SLR) summarizes the current evidence on the policy determinants of PA across the life course, by pooling the results of the available SLRs and meta-analyses (MAs). A systematic online search was conducted on MEDLINE, ISI Web of Science, Scopus and SPORTDiscus databases up to April 2016. SLRs and MAs of observational studies investigating the association between policy determinants of PA and having PA as outcome were considered eligible. The extracted data were assessed based on the importance of the determinants, the strength of evidence and the methodological quality. Fourteen reviews on 27 policy determinants of PA were eligible for this umbrella SLR. The majority of the reviews were of moderate quality. Among children, a clear association between time spent outdoors and PA emerged. Among adults, working hours were negatively associated with PA, though evidence was limited. At the population level, community- and street-scale urban design and land use policies were found to positively support PA levels, but levels of evidences were low. With this umbrella SLR the policy determinants of PA at individual-level and population-level have been summarized and assessed. None of the investigated policy determinants had a convincing level of evidence, and very few had a probable level of evidence. Further research is needed, preferably by using prospective study designs, standardized definitions of PA and objective measurement of PA. © The Author 2017. Published by Oxford University Press on behalf of the European Public Health Association.

Evidence for curricular and instructional design approaches in undergraduate medical education: An umbrella review.

PubMed

Onyura, Betty; Baker, Lindsay; Cameron, Blair; Friesen, Farah; Leslie, Karen

2016-01-01

An umbrella review compiles evidence from multiple reviews into a single accessible document. This umbrella review synthesizes evidence from systematic reviews on curricular and instructional design approaches in undergraduate medical education, focusing on learning outcomes. We conducted bibliographic database searches in Medline, EMBASE and ERIC from database inception to May 2013 inclusive, and digital keyword searches of leading medical education journals. We identified 18,470 abstracts; 467 underwent duplicate full-text scrutiny. Thirty-six articles met all eligibility criteria. Articles were abstracted independently by three authors, using a modified Kirkpatrick model for evaluating learning outcomes. Evidence for the effectiveness of diverse educational approaches is reported. This review maps out empirical knowledge on the efficacy of a broad range of educational approaches in medical education. Critical knowledge gaps, and lapses in methodological rigour, are discussed, providing valuable insight for future research. The findings call attention to the need for adopting evaluative strategies that explore how contextual variabilities and individual (teacher/learner) differences influence efficacy of educational interventions. Additionally, the results underscore that extant empirical evidence does not always provide unequivocal answers about what approaches are most effective. Educators should incorporate best available empirical knowledge with experiential and contextual knowledge.

Understanding and protecting the world's biodiversity: the role and legacy of the SCAR programme "Evolution and Biodiversity in the Antarctic".

PubMed

di Prisco, Guido; Convey, Peter; Gutt, Julian; Cowan, Don; Conlan, Kathleen; Verde, Cinzia

2012-12-01

Current global changes are prompting scientists and governments to consider the risk of extinction of species inhabiting environments influenced by ice. Concerted, multidisciplinary, international programmes aimed at understanding life processes, evolution and adaptations in the Polar Regions will help to counteract such an event by protecting polar life and ecosystems. There is a long tradition of international scientific cooperation in Antarctica that provides a strong foundation for such approaches. While basic understanding is emerging, we still largely lack predictive biological models, and need to achieve further integration amongst biological and non-biological disciplines. The ongoing SCAR Science Research Programme, "Evolution and Biodiversity in the Antarctic (EBA)" has successfully carried out its crucial role of providing an overarching umbrella for SCAR research in Life Sciences. Now is the time for aiming to progress beyond this important role, and the Antarctic biology community is proposing two programmes, focussed on distinct but complementary aspects of polar biology and working across marine, freshwater and terrestrial environments: "State of the Antarctic Ecosystem (AntEco)", and "Antarctic Thresholds--Ecosystem Resilience and Adaptation (AnT-ERA)". These programmes are the legacy of EBA, and they are key to understanding and protect Antarctic biodiversity. Copyright © 2012 Elsevier B.V. All rights reserved.

On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, α-, and π-Helices.

PubMed

Lin, Zhixiong; Liu, Haiyan; Riniker, Sereina; van Gunsteren, Wilfred F

2011-12-13

Enveloping distribution sampling (EDS) is a powerful method to compute relative free energies from simulation. So far, the EDS method has only been applied to alchemical free energy differences, i.e., between different Hamiltonians defining different systems, and not yet to obtain free energy differences between different conformations or conformational states of a system. In this article, we extend the EDS formalism such that it can be applied to compute free energy differences of different conformations and apply it to compute the relative free enthalpy ΔG of 310-, α-, and π-helices of an alanine deca-peptide in explicit water solvent. The resulting ΔG values are compared to those obtained by standard thermodynamic integration (TI) and from so-called end-state simulations. A TI simulation requires the definition of a λ-dependent pathway which in the present case is based on hydrogen bonds of the different helical conformations. The values of ⟨(∂VTI)/(∂λ)⟩λ show a sharp change for a particular range of λ values, which is indicative of an energy barrier along the pathway, which lowers the accuracy of the resulting ΔG value. In contrast, in a two-state EDS simulation, an unphysical reference-state Hamiltonian which connects the parts of conformational space that are relevant to the different end states is constructed automatically; that is, no pathway needs to be defined. In the simulation using this reference state, both helices were sampled, and many transitions between them occurred, thus ensuring the accuracy of the resulting free enthalpy difference. According to the EDS simulations, the free enthalpy differences of the π-helix and the 310-helix versus the α-helix are 5 kJ mol(-1) and 47 kJ mol(-1), respectively, for an alanine deca-peptide in explicit SPC water solvent using the GROMOS 53A6 force field. The EDS method, which is a particular form of umbrella sampling, is thus applicable to compute free energy differences between conformational states as well as between systems and has definite advantages over the traditional TI and umbrella sampling methods to compute relative free energies.

Exploiting Lipid Permutation Symmetry to Compute Membrane Remodeling Free Energies.

PubMed

Bubnis, Greg; Risselada, Herre Jelger; Grubmüller, Helmut

2016-10-28

A complete physical description of membrane remodeling processes, such as fusion or fission, requires knowledge of the underlying free energy landscapes, particularly in barrier regions involving collective shape changes, topological transitions, and high curvature, where Canham-Helfrich (CH) continuum descriptions may fail. To calculate these free energies using atomistic simulations, one must address not only the sampling problem due to high free energy barriers, but also an orthogonal sampling problem of combinatorial complexity stemming from the permutation symmetry of identical lipids. Here, we solve the combinatorial problem with a permutation reduction scheme to map a structural ensemble into a compact, nondegenerate subregion of configuration space, thereby permitting straightforward free energy calculations via umbrella sampling. We applied this approach, using a coarse-grained lipid model, to test the CH description of bending and found sharp increases in the bending modulus for curvature radii below 10 nm. These deviations suggest that an anharmonic bending term may be required for CH models to give quantitative energetics of highly curved states.

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

PubMed

Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro; Mori, Takaharu; Ando, Tadashi; Tamura, Koichi; Kamiya, Motoshi; Sugita, Yuji

2017-09-30

GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Selectivity trend of gas separation through nanoporous graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Hongjun; Chen, Zhongfang; Dai, Sheng

2014-01-29

We demonstrate that porous graphene can efficiently separate gases according to their molecular sizes using molecular dynamic (MD) simulations,. The flux sequence from the classical MD simulation is H 2>CO 2>>N 2>Ar>CH 4, which generally follows the trend in the kinetic diameters. Moreover, this trend is also confirmed from the fluxes based on the computed free energy barriers for gas permeation using the umbrella sampling method and kinetic theory of gases. Both brute-force MD simulations and free-energy calcualtions lead to the flux trend consistent with experiments. Case studies of two compositions of CO 2/N 2 mixtures further demonstrate the separationmore » capability of nanoporous graphene.« less

Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water

NASA Astrophysics Data System (ADS)

Reinhardt, Aleks; Doye, Jonathan P. K.; Noya, Eva G.; Vega, Carlos

2012-11-01

We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Lu; Hanson, David E

Here we present the results on the study of surface properties of {beta}-HMX crystal utilizing molecular simulations. The surface polarity of three principal crystal surfaces are investigated by measuring the water contact angles. The calculated contact angles agree excellently with the values measured by experiment and show that the surface polarity of three crystal surfaces are different. The free energies and forces of detaching an Estane chain with and without nitroplasticizer from the three principal crystal surfaces were calculated using umbrella sampling technique. We find that the detaching free energy/force increases with the increasing HMX surface polarity. In addition, ourmore » results also show that nitroplasticizer plays an important role in the adhesion forces between Estane and HMX surfaces.« less

Vection is modulated by the semantic meaning of stimuli and experimental instructions.

PubMed

Ogawa, Masaki; Seno, Takeharu

2014-01-01

Vection strength is modulated by the semantic meanings of stimuli. In experiment 1--even though vection stimuli were of uniform size, color, and luminance--when they also had semantic meaning as falling objects, vection was inhibited. Specifically, stimuli perceived as feathers, petals, and leaves did not effectively induce vection. In experiment 2 we used the downward motion of identical dots to induce vection. Participants observed stimuli while holding either an umbrella or a wooden sword. Results showed that vection was inhibited when participants held the umbrella and the stimuli was perceived as rain or snow falling. The two experiments suggest that vection is modulated by the semantic meaning of stimuli.

Encephalitis, proventricular and ventricular myositis, and myenteric ganglioneuritis in an umbrella cockatoo.

PubMed

Joyner, K L; Kock, N; Styles, D

1989-01-01

Myenteric ganglioneuritis and encephalomyelitis were diagnosed in an umbrella cockatoo. The cockatoo exhibited clinical signs that were milder than those associated with this syndrome, such as anorexia, muscle wasting, regurgitation, depression, and changes in fecal consistency. The gross lesions also differed from earlier reports in that only the duodenum and proximal jejunum were grossly dilated. Normally the proventriculus and ventriculus are dilated without visible intestinal changes. The histopathological lesions, however, such as perivascular cuffs in the brain stem and muscular mass of the ventriculus and proventriculus, were similar to earlier reports. A virus was suspected, although transmission and isolation of a virus has not occurred in other reports and was not attempted in this case.

Dissociative electron attachment and vibrational excitation of CF{sub 3}Cl: Effect of two vibrational modes revisited

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tarana, Michal; JILA, University of Colorado and NIST, Boulder, Colorado 80309-0440; Houfek, Karel

We present a study of dissociative electron attachment and vibrational excitation processes in electron collisions with the CF{sub 3}Cl molecule. The calculations are based on the two-dimensional nuclear dynamics including the C-Cl symmetric stretch coordinate and the CF{sub 3} symmetric deformation (umbrella) coordinate. The complex potential energy surfaces are calculated using the ab initio R-matrix method. The results for dissociative attachment and vibrational excitation of the umbrella mode agree quite well with experiment whereas the cross section for excitation of the C-Cl symmetric stretch vibrations is about a factor-of-three too low in comparison with experimental data.

On the use of transition matrix methods with extended ensembles.

PubMed

Escobedo, Fernando A; Abreu, Charlles R A

2006-03-14

Different extended ensemble schemes for non-Boltzmann sampling (NBS) of a selected reaction coordinate lambda were formulated so that they employ (i) "variable" sampling window schemes (that include the "successive umbrella sampling" method) to comprehensibly explore the lambda domain and (ii) transition matrix methods to iteratively obtain the underlying free-energy eta landscape (or "importance" weights) associated with lambda. The connection between "acceptance ratio" and transition matrix methods was first established to form the basis of the approach for estimating eta(lambda). The validity and performance of the different NBS schemes were then assessed using as lambda coordinate the configurational energy of the Lennard-Jones fluid. For the cases studied, it was found that the convergence rate in the estimation of eta is little affected by the use of data from high-order transitions, while it is noticeably improved by the use of a broader window of sampling in the variable window methods. Finally, it is shown how an "elastic" window of sampling can be used to effectively enact (nonuniform) preferential sampling over the lambda domain, and how to stitch the weights from separate one-dimensional NBS runs to produce a eta surface over a two-dimensional domain.

ADVANCING SITE CHARACTERIZATION AND MONITORING ...

EPA Pesticide Factsheets

There is no astract available for htis product. If further information is requested, please refer to the bibliogaphic citation and contact the person listed under Contract field. The overall objective of this task is to provide the Agency with improved state-of-the-science guidance, strategies, and techniques to more accurately and effectively collect environmental samples. Under this umbrella objective, research is being conducted to: (a) reduce/minimize the loss of VOCs during sample collection, handling, and preservation, (b) collect undisturbed surface sediments so that the effects of recent depositional events (e.g., flooding or dredging) can clearly be delineated as to their influence on the contamination concentrations present downstream (or where the sediments are deposited), and (c) to determine an effective method to effectively and efficiently separate asbestos in soils from the rest of the soil matrix while maintaining the integrity (i.e, no fiber size reduction) of the asbestos fibers.

Perspective on the reactions between F- and CH3CH2F: the free energy landscape of the E2 and SN2 reaction channels.

PubMed

Ensing, Bernd; Klein, Michael L

2005-05-10

Recently, we computed the 3D free energy surface of the base-induced elimination reaction between F(-) and CH(3)CH(2)F by using a powerful technique within Car-Parrinello molecular dynamics simulation. Here, the set of three order parameters is expanded to six, which allows the study of the competing elimination and substitution reactions simultaneously. The power of the method is exemplified by the exploration of the six-dimensional free energy landscape, sampling, and mapping out the eight stable states as well as the connecting bottlenecks. The free energy profile and barrier along the E2 and S(N)2 reaction channels are refined by using umbrella sampling. The two mechanisms do not share a common "E2C-like" transition state. Comparison with the zero temperature profiles shows a particularly significant entropy contribution to the S(N)2 channel.

Spontaneous Thought and Vulnerability to Mood Disorders: The Dark Side of the Wandering Mind.

PubMed

Marchetti, Igor; Koster, Ernst H W; Klinger, Eric; Alloy, Lauren B

2016-09-01

There is increasing interest in spontaneous thought, namely task-unrelated or rest-related mental activity. Spontaneous thought is an umbrella term for processes like mindwandering, involuntary autobiographical memory, and daydreaming, with evidence elucidating adaptive and maladaptive consequences. In this theoretical framework, we propose that, apart from its positive functions, spontaneous thought is a precursor for cognitive vulnerability in individuals who are at-risk for mood disorders. Importantly, spontaneous thought mostly focuses on unattained goals and evaluates the discrepancy between current and desired status (Klinger, 1971, 2013a). In individuals who stably (i.e., trait negative affectivity) or transitorily (i.e., stress) experience negative emotions in reaction to goal-discrepancy, spontaneous thought fosters major cognitive vulnerabilities (e.g., rumination, hopelessness, low self-esteem, and cognitive reactivity) which, in turn, enhance depression. Furthermore, we also highlight preliminary links between spontaneous thought and bipolar disorder. The evidence for this framework is reviewed and we discuss theoretical and clinical implications of our proposal.

The strength of a loosely defined movement: eugenics and medicine in imperial Russia.

PubMed

Krementsov, Nikolai

2015-01-01

This essay examines the 'infiltration' of eugenics into Russian medical discourse during the formation of the eugenics movement in western Europe and North America in 1900-17. It describes the efforts of two Russian physicians, the bacteriologist and hygienist Nikolai Gamaleia (1859-1949) and the psychiatrist Tikhon Iudin (1879-1949), to introduce eugenics to the Russian medical community, analysing in detail what attracted these representatives of two different medical specialties to eugenic ideas, ideals, and policies advocated by their western colleagues. On the basis of a close examination of the similarities and differences in Gamaleia's and Iudin's attitudes to eugenics, the essay argues that lack of cohesiveness gave the early eugenics movement a unique strength. The loose mix of widely varying ideas, ideals, methods, policies, activities and proposals covered by the umbrella of eugenics offered to a variety of educated professionals in Russia and elsewhere the possibility of choosing, adopting and adapting particular elements to their own national, professional, institutional and disciplinary contexts, interests and agendas.

Spontaneous Thought and Vulnerability to Mood Disorders: The Dark Side of the Wandering Mind

PubMed Central

Marchetti, Igor; Koster, Ernst H.W.; Klinger, Eric; Alloy, Lauren B.

2017-01-01

There is increasing interest in spontaneous thought, namely task-unrelated or rest-related mental activity. Spontaneous thought is an umbrella term for processes like mindwandering, involuntary autobiographical memory, and daydreaming, with evidence elucidating adaptive and maladaptive consequences. In this theoretical framework, we propose that, apart from its positive functions, spontaneous thought is a precursor for cognitive vulnerability in individuals who are at-risk for mood disorders. Importantly, spontaneous thought mostly focuses on unattained goals and evaluates the discrepancy between current and desired status (Klinger, 1971, 2013a). In individuals who stably (i.e., trait negative affectivity) or transitorily (i.e., stress) experience negative emotions in reaction to goal-discrepancy, spontaneous thought fosters major cognitive vulnerabilities (e.g., rumination, hopelessness, low self-esteem, and cognitive reactivity) which, in turn, enhance depression. Furthermore, we also highlight preliminary links between spontaneous thought and bipolar disorder. The evidence for this framework is reviewed and we discuss theoretical and clinical implications of our proposal. PMID:28785510

Application of a Multimedia Service and Resource Management Architecture for Fault Diagnosis

PubMed Central

Castro, Alfonso; Sedano, Andrés A.; García, Fco. Javier; Villoslada, Eduardo

2017-01-01

Nowadays, the complexity of global video products has substantially increased. They are composed of several associated services whose functionalities need to adapt across heterogeneous networks with different technologies and administrative domains. Each of these domains has different operational procedures; therefore, the comprehensive management of multi-domain services presents serious challenges. This paper discusses an approach to service management linking fault diagnosis system and Business Processes for Telefónica’s global video service. The main contribution of this paper is the proposal of an extended service management architecture based on Multi Agent Systems able to integrate the fault diagnosis with other different service management functionalities. This architecture includes a distributed set of agents able to coordinate their actions under the umbrella of a Shared Knowledge Plane, inferring and sharing their knowledge with semantic techniques and three types of automatic reasoning: heterogeneous, ontology-based and Bayesian reasoning. This proposal has been deployed and validated in a real scenario in the video service offered by Telefónica Latam. PMID:29283398

Application of a Multimedia Service and Resource Management Architecture for Fault Diagnosis.

PubMed

Castro, Alfonso; Sedano, Andrés A; García, Fco Javier; Villoslada, Eduardo; Villagrá, Víctor A

2017-12-28

Nowadays, the complexity of global video products has substantially increased. They are composed of several associated services whose functionalities need to adapt across heterogeneous networks with different technologies and administrative domains. Each of these domains has different operational procedures; therefore, the comprehensive management of multi-domain services presents serious challenges. This paper discusses an approach to service management linking fault diagnosis system and Business Processes for Telefónica's global video service. The main contribution of this paper is the proposal of an extended service management architecture based on Multi Agent Systems able to integrate the fault diagnosis with other different service management functionalities. This architecture includes a distributed set of agents able to coordinate their actions under the umbrella of a Shared Knowledge Plane, inferring and sharing their knowledge with semantic techniques and three types of automatic reasoning: heterogeneous, ontology-based and Bayesian reasoning. This proposal has been deployed and validated in a real scenario in the video service offered by Telefónica Latam.

Implementing a Spinosad-Based Local Bait Station to Control Bactrocera cucurbitae (Diptera: Tephritidae) in High Rainfall Areas of Reunion Island

PubMed Central

Delpoux, Camille; Deguine, Jean-Philippe

2015-01-01

Three species of fruit flies cause serious damage to cucurbit crops on Reunion Island: Bactrocera cucurbitae (Diptera: Tephritidae) (Coquillett 1899), Dacus ciliatus (Loew 1901), and Dacus demmerezi (Bezzi 1917). To control them, a program of agroecological management of cucurbit flies has been implemented based on the application of Synéis-appât, especially spot sprays on corn borders. However, the high rainfall on Reunion Island limits the long-term efficiency of the bait; in addition, this method cannot be used for large chayote trellises, because corn borders cannot be planted around them. The aim of this study was to design a bait station adapted to prevailing conditions on Reunion Island. An ‘umbrella trap’ tested in Taiwan was used as a reference to compare its efficacy with our local bait station. Experiments were conducted in field cages on B. cucurbitae to test different characteristics of bait stations and to construct one using local materials. Results were validated in the field. The attractiveness of the bait station was related mainly to the color of the external surface, yellow being the most attractive color. The efficacy of the bait station with respect to fly mortality was found to be linked to the accessibility of the bait, and direct application of Synéis-appât on the bait station was found to be the most efficient. In the field, B. cucurbitae were more attracted to the local bait station than to the umbrella trap, while the two other fly species displayed equal attraction to both trap types. Our local bait station is a useful alternative to spot sprays of Synéis-appât and is now included in a local pest management program and is well accepted by farmers. PMID:25688089

Implementing a spinosad-based local bait station to control Bactrocera cucurbitae (Diptera: Tephritidae) in high rainfall areas of Reunion Island.

PubMed

Delpoux, Camille; Deguine, Jean-Philippe

2015-01-01

Three species of fruit flies cause serious damage to cucurbit crops on Reunion Island: Bactrocera cucurbitae (Diptera: Tephritidae) (Coquillett 1899), Dacus ciliatus (Loew 1901), and Dacus demmerezi (Bezzi 1917). To control them, a program of agroecological management of cucurbit flies has been implemented based on the application of Synéis-appât, especially spot sprays on corn borders. However, the high rainfall on Reunion Island limits the long-term efficiency of the bait; in addition, this method cannot be used for large chayote trellises, because corn borders cannot be planted around them. The aim of this study was to design a bait station adapted to prevailing conditions on Reunion Island. An 'umbrella trap' tested in Taiwan was used as a reference to compare its efficacy with our local bait station. Experiments were conducted in field cages on B. cucurbitae to test different characteristics of bait stations and to construct one using local materials. Results were validated in the field. The attractiveness of the bait station was related mainly to the color of the external surface, yellow being the most attractive color. The efficacy of the bait station with respect to fly mortality was found to be linked to the accessibility of the bait, and direct application of Synéis-appât on the bait station was found to be the most efficient. In the field, B. cucurbitae were more attracted to the local bait station than to the umbrella trap, while the two other fly species displayed equal attraction to both trap types. Our local bait station is a useful alternative to spot sprays of Synéis-appât and is now included in a local pest management program and is well accepted by farmers. © The Author 2015. Published by Oxford University Press on behalf of the Entomological Society of America.

The changing face of Hanford security 1990--1994

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thielman, J.

The meltdown of the Cold War was a shock to the systems built to cope with it. At the DOE`s Hanford Site in Washington State, a world-class safeguards and security system was suddenly out of step with the times. The level of protection for nuclear and classified materials was exceptional. But the cost was high and the defense facilities that funded security were closing down. The defense mission had created an umbrella of security over the sprawling Hanford Site. Helicopters designed to ferry special response teams to any trouble spot on the 1,456 square-kilometer site made the umbrella analogy almostmore » literally true. Facilities were grouped into areas, fenced off like a military base, and entrance required a badge check for everyone. Within the fence, additional rings of protection were set up around security interests or targets. The security was effective, but costly to operate and inconvenient for employees and visitors alike. Moreover, the umbrella meant that virtually all employees needed a security clearance just to get to work, whether they worked on classified or unclassified projects. Clearly, some fundamental rethinking of safeguards and security was needed. The effort to meet that challenge is the story of transition at Hanford and documented here.« less

The most popular terms for medically unexplained symptoms: the views of CFS patients.

PubMed

Picariello, Federica; Ali, Sheila; Moss-Morris, Rona; Chalder, Trudie

2015-05-01

Medically unexplained symptoms/syndromes are common, highly distressing and are often associated with profound disability. One of the controversies surrounding this area relates to which umbrella term should be used to group such symptoms. The purpose of this research was to establish the preferences of patients with chronic fatigue syndrome (CFS) for an umbrella term for medically unexplained symptoms. A cross-sectional mixed methods survey design was used. Participants were asked to indicate their three most preferred terms out of a list of commonly used terms and to provide any extra comments. Frequency analysis was employed to look at the preferences of terms for each rank. Comments were analysed using principles of inductive thematic analysis. Eighty-seven patients with CFS completed a self-report survey. The term "Persistent Physical Symptoms" was the most popular first choice term chosen by 20.7% of patients. Terms containing the word "physical" were consistently more likely to be chosen. Three main themes emerged from the thematic analysis: 1) Physical nature of the illness, 2) Stigma, and 3) Evaluation of the terms, giving a more in-depth understanding of the findings. According to CFS patients, an umbrella term has to reflect the physical experience of MUS. Copyright © 2015 Elsevier Inc. All rights reserved.

Behavioral determinants of physical activity across the life course: a "DEterminants of DIet and Physical ACtivity" (DEDIPAC) umbrella systematic literature review.

PubMed

Condello, Giancarlo; Puggina, Anna; Aleksovska, Katina; Buck, Christoph; Burns, Con; Cardon, Greet; Carlin, Angela; Simon, Chantal; Ciarapica, Donatella; Coppinger, Tara; Cortis, Cristina; D'Haese, Sara; De Craemer, Marieke; Di Blasio, Andrea; Hansen, Sylvia; Iacoviello, Licia; Issartel, Johann; Izzicupo, Pascal; Jaeschke, Lina; Kanning, Martina; Kennedy, Aileen; Ling, Fiona Chun Man; Luzak, Agnes; Napolitano, Giorgio; Nazare, Julie-Anne; Perchoux, Camille; Pesce, Caterina; Pischon, Tobias; Polito, Angela; Sannella, Alessandra; Schulz, Holger; Sohun, Rhoda; Steinbrecher, Astrid; Schlicht, Wolfgang; Ricciardi, Walter; MacDonncha, Ciaran; Capranica, Laura; Boccia, Stefania

2017-05-02

Low levels of physical activity (PA) are a global concern and increasing PA engagement is becoming a priority in current public health policies. Despite the large number of studies and reviews available, the evidence regarding the behavioral determinants of PA is still inconclusive. Thus, the aim of this umbrella systematic literature review (SLR) was to summarize the evidence on the behavioral determinants of PA across the life course. A systematic online search was conducted on MEDLINE, ISI Web of Science, Scopus, and SPORTDiscus databases. The search was limited to studies published in English from January, 2004 to April, 2016. SLRs and meta-analyses (MAs) of observational studies that investigated the behavioral determinants of PA were considered eligible. The extracted data were assessed based on the importance of the determinants, the strength of evidence, and the methodological quality. The full protocol is available from PROSPERO (PROSPERO 2014:CRD42015010616). Seventeen reviews on 35 behavioral determinants of PA were eligible for this umbrella SLR. Regardless of age, the most investigated determinants were those related with 'screen use' and 'smoking'. For youth, probable positive evidence emerged for 'previous PA' and 'independent mobility and active transport' among children and adolescents. For the adult population, 'transition to university' and 'pregnancy/having a child' showed probable negative associations. Although the majority of the evidence was limited and most of the determinants were not associated with PA, this umbrella SLR provided a comprehensive overview of the associations between behavioral determinants and PA. Youth should be physically active in the early years and increase active transportation to/from school, independent mobility, and 'free-range activities' without adult supervision, whilst adult PA behaviors are mostly influenced by the life events. Finally, more research is needed that incorporates prospective study designs, standardized definitions of PA, objective measurement methods of PA assessment, and the use of interactionist and mediational approaches for the evaluation of different behavioral determinants influencing PA behaviors.

The macro-economic determinants of health and health inequalities-umbrella review protocol.

PubMed

Naik, Yannish; Baker, Peter; Walker, Ian; Tillmann, Taavi; Bash, Kristin; Quantz, Darryl; Hillier-Brown, Frances; Bambra, Clare

2017-11-03

The economic determinants of health have been widely recognised as crucial factors affecting health; however, to date, no comprehensive review has been undertaken to summarise these factors and the ways in which they can influence health. We conceptualise the economy as a complex system made up of underlying approaches, regulation from institutions, markets, finance, labour, the public-private balance as well as production and distributional effects, which collectively impact on health through the effect of moderators. This protocol details the methods for an umbrella review to explore the macro-economic factors, strategies, policies and interventions that affect health outcomes and health inequalities. We will identify relevant systematic reviews using search terms derived from the Journal of Economic Literature classification. Reviews will be included if they meet the Database of Abstracts and Reviews of Effects criteria for systematic reviews. Reviews of studies with and without controls will be included; both association and intervention studies will be included. Primary outcomes will include but are not limited to morbidity, mortality, prevalence and incidence of conditions and life expectancy. Secondary outcomes will include health inequalities by gender, ethnicity or socio-economic status. Six databases will be searched using tailored versions of our piloted search strategy to locate relevant reviews. Data will be extracted using a standardized pro forma, and the findings will be synthesized into a conceptual framework to address our review aim. Our umbrella review protocol provides a robust method to systematically appraise the evidence in this field, using new conceptual models derived specifically to address the study question. This will yield important information for policymakers, practitioners and researchers at the local, national and international level. It will also help set the future research agenda in this field and guide the development of interventions. This umbrella review protocol has been registered with PROSPERO CRD42017068357 .

Selecting a Conservation Surrogate Species for Small Fragmented Habitats Using Ecological Niche Modelling

PubMed Central

Nekaris, K. Anne-Isola; Arnell, Andrew P.; Svensson, Magdalena S.

2015-01-01

Simple Summary Large “charismatic” animals (with widespread popular appeal) are often used as flagship species to raise awareness for conservation. Deforestation and forest fragmentation are among the main threats to biodiversity, and in many places such species are disappearing. In this paper we aim to find a suitable species among the less charismatic animal species left in the fragmented forests of South-western Sri Lanka. We selected ten candidates, using a questionnaire survey along with computer modelling of their distributions. The red slender loris and the fishing cat came out as finalists as they were both appealing to local people, and fulfilled selected ecological criteria. Abstract Flagship species are traditionally large, charismatic animals used to rally conservation efforts. Accepted flagship definitions suggest they need only fulfil a strategic role, unlike umbrella species that are used to shelter cohabitant taxa. The criteria used to select both flagship and umbrella species may not stand up in the face of dramatic forest loss, where remaining fragments may only contain species that do not suit either set of criteria. The Cinderella species concept covers aesthetically pleasing and overlooked species that fulfil the criteria of flagships or umbrellas. Such species are also more likely to occur in fragmented habitats. We tested Cinderella criteria on mammals in the fragmented forests of the Sri Lankan Wet Zone. We selected taxa that fulfilled both strategic and ecological roles. We created a shortlist of ten species, and from a survey of local perceptions highlighted two finalists. We tested these for umbrella characteristics against the original shortlist, utilizing Maximum Entropy (MaxEnt) modelling, and analysed distribution overlap using ArcGIS. The criteria highlighted Loris tardigradus tardigradus and Prionailurus viverrinus as finalists, with the former having highest flagship potential. We suggest Cinderella species can be effective conservation surrogates especially in habitats where traditional flagship species have been extirpated. PMID:26479135

Use of simulation-based learning in undergraduate nurse education: An umbrella systematic review.

PubMed

Cant, Robyn P; Cooper, Simon J

2017-02-01

To conduct a systematic review to appraise and review evidence on the impact of simulation-based education for undergraduate/pre-licensure nursing students, using existing reviews of literature. An umbrella review (review of reviews). Cumulative Index of Nursing and Allied Health Literature (CINAHLPlus), PubMed, and Google Scholar. Reviews of literature conducted between 2010 and 2015 regarding simulation-based education for pre-licensure nursing students. The Joanna Briggs Institute methodology for conduct of an umbrella review was used to inform the review process. Twenty-five systematic reviews of literature were included, of which 14 were recent (2013-2015). Most described the level of evidence of component studies as a mix of experimental and quasi-experimental designs. The reviews measured around 14 different main outcome variables, thus limiting the number of primary studies that each individual review could pool to appraise. Many reviews agreed on the key learning outcome of knowledge acquisition, although no overall quantitative effect was derived. Three of four high-quality reviews found that simulation supported psychomotor development; a fourth found too few high quality studies to make a statistical comparison. Simulation statistically improved self-efficacy in pretest-posttest studies, and in experimental designs self-efficacy was superior to that of other teaching methods; lower level research designs limiting further comparison. The reviews commonly reported strong student satisfaction with simulation education and some reported improved confidence and/or critical thinking. This umbrella review took a global view of 25 reviews of simulation research in nursing education, comprising over 700 primary studies. To discern overall outcomes across reviews, statistical comparison of quantitative results (effect size) must be the key comparator. Simulation-based education contributes to students' learning in a number of ways when integrated into pre-licensure nursing curricula. Overall, use of a constellation of instruments and a lack of high quality study designs mean that there are still some gaps in evidence of effects that need to be addressed. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Dynamics of Volcanic Umbrella Clouds

NASA Astrophysics Data System (ADS)

Tait, S.; Kaminski, E. C.; Carazzo, G.; Limare, A.

2017-12-01

Atmospheric injection of volcanic ash during explosive eruptions is controlled by the dynamics of a volcanic column and associated umbrella cloud, which are subject to a wind field, and are connected by a turbulent fountain which initiates horizontal spreading at the neutral buoyancy level. We present a new theoretical and experimental study of an axisymmetric turbulent umbrella cloud intruding horizontally at its neutral buoyancy level into a static environment linearly stratified in density. The intrusion is fed by a constant horizontal volume flux (Q0) at a finite radius (R0), where it has a constant thickness (2H0). The characteristics of the fountain (R0, H0, Q0) derive from a vertical forced plume (source momentum and buoyancy fluxes Mi , Fi) and environmental stratification N. Buoyancy drives horizontal flow but, despite high Reynolds number, impedes entrainment of ambient fluid into the umbrella cloud. Turbulent stresses are nevertheless crucial in the momentum balance. Our theory highlights the vertical profiles of density and velocity within the current of which we present experimental measurements. Initially, current buoyancy is opposed by the inertia of the ambient fluid, and current radius (RN(t)) grows linearly in time. Subsequently, turbulent drag opposes buoyancy, and the current breaks down into two parts: i) between the source and a transition radius (R0T(t)), a steady region where current thickness (2H) and mean velocity (U) are time-independent and decreasing functions of r ; ii), a contiguous unsteady « frontal » region, between the transition radius and the front (RTN), in which the current thickens. The theory predicts current shape and an asymptotic spreading behaviour (RN t^5/9) which agree well with experimental data. Our analysis of satellite observations of several sustained plinian events including the Pinatubo 1991 climactic eruption shows that both the initial and asymptotic spreading regimes predicted by the model are present.

The 1815 Tambora ash fall: implications for transport and deposition of distal ash on land and in the deep sea

NASA Astrophysics Data System (ADS)

Kandlbauer, Jessica; Carey, Steven N.; Sparks, R. Stephen J.

2013-04-01

Tambora volcano lies on the Sanggar Peninsula of Sumbawa Island in the Indonesian archipelago. During the great 1815 explosive eruption, the majority of the erupted pyroclastic material was dispersed and subsequently deposited into the Indian Ocean and Java Sea. This study focuses on the grain size distribution of distal 1815 Tambora ash deposited in the deep sea compared to ash fallen on land. Grain size distribution is an important factor in assessing potential risks to aviation and human health, and provides additional information about the ash transport mechanisms within volcanic umbrella clouds. Grain size analysis was performed using high precision laser diffraction for a particle range of 0.2 μm-2 mm diameter. The results indicate that the deep-sea samples provide a smooth transition to the land samples in terms of grain size distributions despite the different depositional environments. Even the very fine ash fraction (<10 μm) is deposited in the deep sea, suggesting vertical density currents as a fast and effective means of transport to the seafloor. The measured grain size distribution is consistent with an improved atmospheric gravity current sedimentation model that takes into account the finite duration of an eruption. In this model, the eruption time and particle fall velocity are the critical parameters for assessing the ash component depositing while the cloud advances versus the ash component depositing once the eruption terminates. With the historical data on eruption duration (maximum 24 h) and volumetric flow rate of the umbrella cloud (˜1.5-2.5 × 1011 m3/s) as input to the improved model, and assuming a combination of 3 h Plinian phase and 21 h co-ignimbrite phase, it reduces the mean deviation of the predicted versus observed grain size distribution by more than half (˜9.4 % to ˜3.7 %) if both ash components are considered.

Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Li, Hongzhi; Min, Donghong; Liu, Yusong; Yang, Wei

2007-09-01

To overcome the possible pseudoergodicity problem, molecular dynamic simulation can be accelerated via the realization of an energy space random walk. To achieve this, a biased free energy function (BFEF) needs to be priori obtained. Although the quality of BFEF is essential for sampling efficiency, its generation is usually tedious and nontrivial. In this work, we present an energy space metadynamics algorithm to efficiently and robustly obtain BFEFs. Moreover, in order to deal with the associated diffusion sampling problem caused by the random walk in the total energy space, the idea in the original umbrella sampling method is generalized to be the random walk in the essential energy space, which only includes the energy terms determining the conformation of a region of interest. This essential energy space generalization allows the realization of efficient localized enhanced sampling and also offers the possibility of further sampling efficiency improvement when high frequency energy terms irrelevant to the target events are free of activation. The energy space metadynamics method and its generalization in the essential energy space for the molecular dynamics acceleration are demonstrated in the simulation of a pentanelike system, the blocked alanine dipeptide model, and the leucine model.

Effects of Rolling and Cooling Conditions on Microstructure of Umbrella-Bone Steel

NASA Astrophysics Data System (ADS)

Wu, Yan-Xin; Fu, Jian-Xun; Zhang, Hua; Xu, Jie; Zhai, Qi-Jie

2017-10-01

The effects of deformation temperature and cooling rate on the micro-structure evolution of umbrella-bone steel was investigated using a Gleeble thermal-mechanical testing machine and dynamic continuous cooling transformation (CCT) curves. The results show that fast cooling which lowers the starting temperature of ferrite transformation leads to finer ferrite grains and more pearlite. Low temperature deformation enhances the hardening effect of austenite and reduces hardenability, allowing a wider range of cooling rates and thus avoiding martensite transformation after deformation. According to the phase transformation rules, the ultimate tensile strength and reduction in area of the wire rod formed in the optimized industrial trial are 636 MPa and 73.6 %, respectively, showing excellent strength and plasticity.

Investigations of belukha whales in coastal waters of western and northern Alaska, 1982-1983: marking and tracking of whales in Bristol Bay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frost, K.J.; Lowry, L.F.; Nelson, R.R.

1983-12-01

A 2-year study was conducted in Bristol Bay, Alaska, to develop and test techniques for marking belukha whales with visual and radio tags. Information was also gathered on belukha distribution and abundance, foods and feeding, and rates and causes of mortality. Two types of radio packages were developed: an OAR backpack designed to be bolted through the dorsal ridge, and a Telonics barnacle tag with an umbrella-stake attachment. Testing of tags and attachments revealed that the more-powerful OAR radio could be received at longer distances and lower antenna heights, and the the umbrella-stake attachment penetrated too deeply for reliable usemore » on belukhas.« less

Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.

PubMed

Chodera, John D; Shirts, Michael R

2011-11-21

The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in discovering new ways to enhance the phase space mixing of these protocols in order to improve sampling of uncorrelated configurations. Here, we demonstrate how both of these classes of algorithms can be considered as special cases of Gibbs sampling within a Markov chain Monte Carlo framework. Gibbs sampling is a well-studied scheme in the field of statistical inference in which different random variables are alternately updated from conditional distributions. While the update of the conformational degrees of freedom by Metropolis Monte Carlo or molecular dynamics unavoidably generates correlated samples, we show how judicious updating of the thermodynamic state indices--corresponding to thermodynamic parameters such as temperature or alchemical coupling variables--can substantially increase mixing while still sampling from the desired distributions. We show how state update methods in common use can lead to suboptimal mixing, and present some simple, inexpensive alternatives that can increase mixing of the overall Markov chain, reducing simulation times necessary to obtain estimates of the desired precision. These improved schemes are demonstrated for several common applications, including an alchemical expanded ensemble simulation, parallel tempering, and multidimensional replica exchange umbrella sampling.

The Clawpack Community of Codes

NASA Astrophysics Data System (ADS)

Mandli, K. T.; LeVeque, R. J.; Ketcheson, D.; Ahmadia, A. J.

2014-12-01

Clawpack, the Conservation Laws Package, has long been one of the standards for solving hyperbolic conservation laws but over the years has extended well beyond this role. Today a community of open-source codes have been developed that address a multitude of different needs including non-conservative balance laws, high-order accurate methods, and parallelism while remaining extensible and easy to use, largely by the judicious use of Python and the original Fortran codes that it wraps. This talk will present some of the recent developments in projects under the Clawpack umbrella, notably the GeoClaw and PyClaw projects. GeoClaw was originally developed as a tool for simulating tsunamis using adaptive mesh refinement but has since encompassed a large number of other geophysically relevant flows including storm surge and debris-flows. PyClaw originated as a Python version of the original Clawpack algorithms but has since been both a testing ground for new algorithmic advances in the Clawpack framework but also an easily extensible framework for solving hyperbolic balance laws. Some of these extensions include the addition of WENO high-order methods, massively parallel capabilities, and adaptive mesh refinement technologies, made possible largely by the flexibility of the Python language and community libraries such as NumPy and PETSc. Because of the tight integration with Python tecnologies, both packages have benefited also from the focus on reproducibility in the Python community, notably IPython notebooks.

Understanding informal carers' experiences of caring for older people with a hip fracture: a systematic review of qualitative studies.

PubMed

Saletti-Cuesta, Lorena; Tutton, Elizabeth; Langstaff, Debbie; Willett, Keith

2018-04-01

This systematic review aimed to reconceptualize experiences from a variety of papers to provide direction for research, policy and practice. Meta-ethnography was used to inform the review, and 21 studies were included. The analysis identified a core theme of "engaging in care: struggling through", as carers, who wanted to be involved in caring, learnt to live with the intense and stressful impact of caring and changes to their life. The core theme is represented through three themes (1) Helping another to live, (2) Adapting ways of living and (3) Negotiating the unknown. The discussion identified a focus on carers of people suffering from a hip fracture, the willingness of informal carers to engage in caring and the intense experience of adapting to changes in relationships and dependency alongside a steep experiential learning curve. Tensions exist in negotiations with complex health care systems as carers do not feel their expertise is valued and struggle to find and understand information. Implications for Rehabilitation Including relatives/carers in the umbrella of care within a family-centred approach. Involving relatives/carers within shared decision-making about care requirements and rehabilitation goals. Utilizing forms of experiential learning to help the development of relatives/carers skills in relation to their role as carer. Providing opportunities for carers to explore ways of sustaining their own health through self-compassion.

Geometric and energetic considerations of surface fluctuations during ion transfer across the water-immiscible organic liquid interface

NASA Astrophysics Data System (ADS)

Karnes, John J.; Benjamin, Ilan

2016-07-01

Molecular dynamics simulations and umbrella sampling free energy calculations are used to examine the thermodynamics, energetics, and structural fluctuations that accompany the transfer of a small hydrophilic ion (Cl-) across the water/nitrobenzene interface. By examining several constrained interface structures, we isolate the energetic costs of interfacial deformation and co-transfer of hydration waters during the ion transfer. The process is monitored using both energy-based solvation coordinates and a geometric coordinate recently introduced by Morita and co-workers to describe surface fluctuations. Our simulations show that these coordinates provide a complimentary description of the water surface fluctuations during the transfer and are necessary for elucidating the mechanism of the ion transfer.

Replica Exchange Molecular Dynamics in the Age of Heterogeneous Architectures

NASA Astrophysics Data System (ADS)

Roitberg, Adrian

2014-03-01

The rise of GPU-based codes has allowed MD to reach timescales only dreamed of only 5 years ago. Even within this new paradigm there is still need for advanced sampling techniques. Modern supercomputers (e.g. Blue Waters, Titan, Keeneland) have made available to users a significant number of GPUS and CPUS, which in turn translate into amazing opportunities for dream calculations. Replica-exchange based methods can optimally use tis combination of codes and architectures to explore conformational variabilities in large systems. I will show our recent work in porting the program Amber to GPUS, and the support for replica exchange methods, where the replicated dimension could be Temperature, pH, Hamiltonian, Umbrella windows and combinations of those schemes.

Adaptive sampling in research on risk-related behaviors.

PubMed

Thompson, Steven K; Collins, Linda M

2002-11-01

This article introduces adaptive sampling designs to substance use researchers. Adaptive sampling is particularly useful when the population of interest is rare, unevenly distributed, hidden, or hard to reach. Examples of such populations are injection drug users, individuals at high risk for HIV/AIDS, and young adolescents who are nicotine dependent. In conventional sampling, the sampling design is based entirely on a priori information, and is fixed before the study begins. By contrast, in adaptive sampling, the sampling design adapts based on observations made during the survey; for example, drug users may be asked to refer other drug users to the researcher. In the present article several adaptive sampling designs are discussed. Link-tracing designs such as snowball sampling, random walk methods, and network sampling are described, along with adaptive allocation and adaptive cluster sampling. It is stressed that special estimation procedures taking the sampling design into account are needed when adaptive sampling has been used. These procedures yield estimates that are considerably better than conventional estimates. For rare and clustered populations adaptive designs can give substantial gains in efficiency over conventional designs, and for hidden populations link-tracing and other adaptive procedures may provide the only practical way to obtain a sample large enough for the study objectives.

From field to database : a user-oriented approche to promote cyber-curating of scientific drilling cores

NASA Astrophysics Data System (ADS)

Pignol, C.; Arnaud, F.; Godinho, E.; Galabertier, B.; Caillo, A.; Billy, I.; Augustin, L.; Calzas, M.; Rousseau, D. D.; Crosta, X.

2016-12-01

Managing scientific data is probably one the most challenging issues in modern science. In plaeosciences the question is made even more sensitive with the need of preserving and managing high value fragile geological samples: cores. Large international scientific programs, such as IODP or ICDP led intense effort to solve this problem and proposed detailed high standard work- and dataflows thorough core handling and curating. However many paleoscience results derived from small-scale research programs in which data and sample management is too often managed only locally - when it is… In this paper we present a national effort leads in France to develop an integrated system to curate ice and sediment cores. Under the umbrella of the national excellence equipment program CLIMCOR, we launched a reflexion about core curating and the management of associated fieldwork data. Our aim was then to conserve all data from fieldwork in an integrated cyber-environment which will evolve toward laboratory-acquired data storage in a near future. To do so, our demarche was conducted through an intimate relationship with field operators as well laboratory core curators in order to propose user-oriented solutions. The national core curating initiative proposes a single web portal in which all teams can store their fieldwork data. This portal is used as a national hub to attribute IGSNs. For legacy samples, this requires the establishment of a dedicated core list with associated metadata. However, for forthcoming core data, we developed a mobile application to capture technical and scientific data directly on the field. This application is linked with a unique coring-tools library and is adapted to most coring devices (gravity, drilling, percussion etc.) including multiple sections and holes coring operations. Those field data can be uploaded automatically to the national portal, but also referenced through international standards (IGSN and INSPIRE) and displayed in international portals (currently, NOAA's IMLGS). In this paper, we present the architecture of the integrated system, future perspectives and the approach we adopted to reach our goals. We will also present our mobile application through didactic examples.

Nonpharmacologic, nonherbal management of menopause-associated vasomotor symptoms: an umbrella systematic review (protocol).

PubMed

Goldstein, Karen M; McDuffie, Jennifer R; Shepherd-Banigan, Megan; Befus, Deanna; Coeytaux, Remy R; Van Noord, Megan G; Goode, Adam P; Masilamani, Varsha; Adam, Soheir; Nagi, Avishek; Williams, John W

2016-04-07

Vasomotor symptoms such as hot flashes and night sweats are a common concern of perimenopausal and postmenopausal women and are associated with a decreased quality of life. These symptoms can be effectively managed with hormone therapy, but safety concerns limit its use. Thus, understanding the effectiveness of nonpharmacologic therapies such as acupuncture or yoga is critical to managing these common symptoms in older women. Our review seeks to address the following question: In women with menopause-associated vasomotor symptoms, what are the effects on health-related quality of life, vasomotor symptoms, and adverse events of the following nonpharmacologic, nonherbal interventions as compared with any inactive control or active comparator: (a) acupuncture, (b) yoga, tai chi, and qigong, (c) structured exercise, and (d) meditation, mindfulness-based practices, and relaxation? We describe a protocol for an umbrella review approach, supplemented by evaluating randomized controlled trials (RCTs) published after the most recent good-quality systematic review for each of the eligible interventions. Specific interventions were chosen based on current literature and with input from a technical expert panel and organizational stakeholders. We will conduct a thorough literature search and perform a quality assessment of potentially included systematic reviews and RCTs. Our umbrella review, supplemented by an additional search for eligible RCTs, aims to synthesize existing evidence on the use of nonpharmacologic, nonherbal interventions to manage bothersome vasomotor symptoms in perimenopausal and postmenopausal women. PROSPERO CRD42016029335.

Uroplakins, specific membrane proteins of urothelial umbrella cells, as histological markers of metastatic transitional cell carcinomas.

PubMed Central

Moll, R.; Wu, X. R.; Lin, J. H.; Sun, T. T.

1995-01-01

Uroplakins (UPs) Ia, Ib, II, and III, transmembrane proteins constituting the asymmetrical unit membrane of urothelial umbrella cells, are the first specific urothelial differentiation markers described. We investigated the presence and localization patterns of UPs in various human carcinomas by applying immunohistochemistry (avidin-biotin-peroxidase complex method), using rabbit antibodies against UPs II and III, to paraffin sections. Positive reactions for UP III (sometimes very focal) were noted in 14 of the 16 papillary noninvasive transitional cell carcinomas (TCCs) (88%), 29 of the 55 invasive TCCs (53%), and 23 of the 35 TCC metastases (66%). Different localization patterns of UPs could be distinguished, including superficial membrane staining like that found in normal umbrella cells (in papillary carcinoma), luminal (microluminal) membrane staining (in papillary and invasive carcinoma), and, against expectations, peripheral membrane staining (in invasive carcinoma). Non-TCC carcinomas of various origins (n = 177) were consistently negative for UPs. The presence of UPs in metastatic TCCs represents a prime example of even advanced tumor progression being compatible with the (focal) expression of highly specialized differentiation repertoires. Although of only medium-grade sensitivity, UPs do seem to be highly specific urothelial lineage markers, thus operating up interesting histodiagnostic possibilities in cases of carcinoma metastases of uncertain origin. Images Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 PMID:7485401

Theoretical study of the vibrational relaxation of the methyl radical in collisions with helium

NASA Astrophysics Data System (ADS)

Ma, Qianli; Dagdigian, Paul J.; Alexander, Millard H.

2013-03-01

We report a theoretical investigation of the relaxation of the umbrella vibrational mode (the ν2 mode) of the CH3 molecule in its ground tilde{X}^2A_2^' ' } electronic state in collisions with helium. We have calculated a four-dimensional potential energy surface (PES) for the interaction between CH3 with different umbrella displacements and a helium atom, using a restricted open-shell coupled-cluster method with inclusion of all single, double, and (perturbatively) triple excitations [RCCSD(T)]. With this PES we carried out full close-coupling scattering calculations including all CH3 umbrella-rotational levels with v2 ⩽ 3. To our knowledge, this work represents the first fully quantum calculations of ro-vibrational relaxation of a polyatomic. In more detail, we investigate propensities in the calculated ro-vibrational cross sections and the dependence on initial rotational excitation, as well as determining thermal rate constants. Overall, ro-vibrational relaxation is nearly two orders of magnitude less efficient than pure-rotational relaxation, with a noticeable dependence on the initial rotational level. We predict the room temperature v2 = 1 vibrational relaxation rate constant to be 5.4 × 10-12 cm3 molecule-1 s-1, compared to the rate constants for pure-rotational relaxation of the lower rotational levels (˜2.0 × 10-10 cm3 molecule-1 s-1).

A new minimally invasive heart surgery instrument for atrial fibrillation treatment: first in vitro and animal tests.

PubMed

Abadie, J; Faure, A; Chaillet, N; Rougeot, P; Beaufort, D; Goldstein, J P; Finlay, P A; Bogaerts, G

2006-06-01

The paper presents a new robotic system for beating heart surgery. The final goal of this project is to develop a tele-operated system for the thoracoscopic treatment of patients with atrial fibrillation. The system consists of a robot that moves an innovative end-effector used to perform lines as in the Cox-Maze technique. The device is an electrode mesh that is introduced in the thorax through a trocar and is deployed inside the left atrium, where it can create selective ablation lines at any atrial region, using radio frequency. The current version of the umbrella has 22 electrodes. Using visual feedback from an ultrasound based navigation system, the surgeon can choose which electrodes on the mesh to activate. Once the umbrella is in contact with the endocardium of the left atrium, at the expected position, the surgeon activates the chosen electrodes sequentially. The umbrella can then be moved to another position. In vitro and in vivo animal tests have been carried out in order to test and improve the instrument, the robotic system and the operative procedure. The performed trials proved the ability of the system to treat atrial fibrillation. More in vivo tests are currently being performed to make the robot and its device ready for clinical use. Copyright 2006 John Wiley & Sons, Ltd.

Solvation structures of water in trihexyltetradecylphosphonium-orthoborate ionic liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yong-Lei, E-mail: wangyonl@gmail.com; System and Component Design, Department of Machine Design, KTH Royal Institute of Technology, SE-100 44 Stockholm; Sarman, Sten

2016-08-14

Atomistic molecular dynamics simulations have been performed to investigate effective interactions of isolated water molecules dispersed in trihexyltetradecylphosphonium-orthoborate ionic liquids (ILs). The intrinsic free energy changes in solvating one water molecule from gas phase into bulk IL matrices were estimated as a function of temperature, and thereafter, the calculations of potential of mean force between two dispersed water molecules within different IL matrices were performed using umbrella sampling simulations. The systematic analyses of local ionic microstructures, orientational preferences, probability and spatial distributions of dispersed water molecules around neighboring ionic species indicate their preferential coordinations to central polar segments in orthoboratemore » anions. The effective interactions between two dispersed water molecules are partially or totally screened as their separation distance increases due to interference of ionic species in between. These computational results connect microscopic anionic structures with macroscopically and experimentally observed difficulty in completely removing water from synthesized IL samples and suggest that the introduction of hydrophobic groups to central polar segments and the formation of conjugated ionic structures in orthoborate anions can effectively reduce residual water content in the corresponding IL samples.« less

Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.

PubMed

Gao, J

2016-01-01

Path-integral free energy perturbation (PI-FEP) theory is presented to directly determine the ratio of quantum mechanical partition functions of different isotopologs in a single simulation. Furthermore, a double averaging strategy is used to carry out the practical simulation, separating the quantum mechanical path integral exactly into two separate calculations, one corresponding to a classical molecular dynamics simulation of the centroid coordinates, and another involving free-particle path-integral sampling over the classical, centroid positions. An integrated centroid path-integral free energy perturbation and umbrella sampling (PI-FEP/UM, or simply, PI-FEP) method along with bisection sampling was summarized, which provides an accurate and fast convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. The PI-FEP method is illustrated by a number of applications, to highlight the computational precision and accuracy, the rule of geometrical mean in kinetic isotope effects, enhanced nuclear quantum effects in enzyme catalysis, and protein dynamics on temperature dependence of kinetic isotope effects. © 2016 Elsevier Inc. All rights reserved.

Umbrella project for Bangladesh: strengthening NGO capacity and linkages to improve reproductive health service and information. RAS/98/P55.

PubMed

1999-06-01

In Bangladesh, the UN Population Fund is working to strengthen nongovernmental organization (NGO) capacity and linkages to improve reproductive health services and information. Specifically, the aim is to strengthen the technical and human resource capacity of participating NGOs and the functional linkages between national NGOs and relevant government agencies to help harmonize and standardize the delivery of reproductive health information and services. This umbrella project collaborates with RHI-participating NGOs in a policy paper on adolescent reproductive health, and will maintain contact with the regional dimension project to collaborate its activities. Programs implemented by partner NGOs are being reviewed and monitored, and linkages among national NGOs and government agencies are being developed. The main activities of the project are enumerated.

Biotechnology Process Engineering Center at MIT Home

Science.gov Websites

BPEC Definition 77 Massachusetts Avenue, Building 16 Room 429, Cambridge, MA 02139 Telephone (617 Leadership Council Facilities | Umbrella Programs | Events | News | Links | MIT | National Science Foundation

Spectral gap optimization of order parameters for sampling complex molecular systems

PubMed Central

Tiwary, Pratyush; Berne, B. J.

2016-01-01

In modern-day simulations of many-body systems, much of the computational complexity is shifted to the identification of slowly changing molecular order parameters called collective variables (CVs) or reaction coordinates. A vast array of enhanced-sampling methods are based on the identification and biasing of these low-dimensional order parameters, whose fluctuations are important in driving rare events of interest. Here, we describe a new algorithm for finding optimal low-dimensional CVs for use in enhanced-sampling biasing methods like umbrella sampling, metadynamics, and related methods, when limited prior static and dynamic information is known about the system, and a much larger set of candidate CVs is specified. The algorithm involves estimating the best combination of these candidate CVs, as quantified by a maximum path entropy estimate of the spectral gap for dynamics viewed as a function of that CV. The algorithm is called spectral gap optimization of order parameters (SGOOP). Through multiple practical examples, we show how this postprocessing procedure can lead to optimization of CV and several orders of magnitude improvement in the convergence of the free energy calculated through metadynamics, essentially giving the ability to extract useful information even from unsuccessful metadynamics runs. PMID:26929365

Dose-response relationship between cigarette smoking and site-specific cancer risk: protocol for a systematic review with an original design combining umbrella and traditional reviews.

PubMed

Lugo, Alessandra; Bosetti, Cristina; Peveri, Giulia; Rota, Matteo; Bagnardi, Vincenzo; Gallus, Silvano

2017-11-01

Only a limited number of meta-analyses providing risk curve functions of dose-response relationships between various smoking-related variables and cancer-specific risk are available. To identify all relevant original publications on the issue, we will conduct a series of comprehensive systematic reviews based on three subsequent literature searches: (1) an umbrella review, to identify meta-analyses, pooled analyses and systematic reviews published before 28 April 2017 on the association between cigarette smoking and the risk of 28 (namely all) malignant neoplasms; (2) for each cancer site, an updated review of original publications on the association between cigarette smoking and cancer risk, starting from the last available comprehensive review identified through the umbrella review; and (3) a review of all original articles on the association between cigarette smoking and site-specific cancer risk included in the publications identified through the umbrella review and the updated reviews. The primary outcomes of interest will be (1) the excess incidence/mortality of various cancers for smokers compared with never smokers; and (2) the dose-response curves describing the association between smoking intensity, duration and time since stopping and incidence/mortality for various cancers. For each cancer site, we will perform a meta-analysis by pooling study-specific estimates for smoking status. We will also estimate the dose-response curves for other smoking-related variables through random-effects meta-regression models based on a non-linear dose-response relationship framework. Ethics approval is not required for this study. Main results will be published in peer-reviewed journals and will also be included in a publicly available website. We will provide therefore the most complete and updated estimates on the association between various measures of cigarette smoking and site-specific cancer risk. This will allow us to obtain precise estimates on the cancer burden attributable to cigarette smoking. This protocol was registered in the International Prospective Register of Systematic Reviews (CRD42017063991). © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The solar ultraviolet B radiation protection provided by shading devices with regard to its diffuse component.

PubMed

Kudish, Avraham I; Harari, Marco; Evseev, Efim G

2011-10-01

The composition of the incident solar global ultraviolet B (UVB) radiation with regard to its beam and diffuse radiation fractions is highly relevant with regard to outdoor sun protection. This is especially true with respect to sun protection during leisure-time outdoor sun exposure at the shore and pools, where people tend to escape the sun under shade trees or different types of shading devices, e.g., umbrellas, overhangs, etc., believing they offer protection from the erythemal solar radiation. The degree of sun protection offered by such devices is directly related to the composition of the solar global UVB radiation, i.e., its beam and diffuse fractions. The composition of the incident solar global UVB radiation can be determined by measuring the global UVB (using Solar Light Co. Inc., Model 501A UV-Biometer) and either of its components. The beam component of the UVB radiation was determined by measuring the normal incidence beam radiation using a prototype, tracking instrument consisting of a Solar Light Co. Inc. Model 501A UV-Biometer mounted on an Eppley Solar Tracker Model St-1. The horizontal beam component of the global UVB radiation was calculated from the measured normal incidence using a simple geometric correlation and the diffuse component is determined as the difference between global and horizontal beam radiations. Horizontal and vertical surfaces positioned under a horizontal overhang/sunshade or an umbrella are not fully protected from exposure to solar global UVB radiation. They can receive a significant fraction of the UVB radiation, depending on their location beneath the shading device, the umbrella radius and the albedo (reflectance) of the surrounding ground surface in the case of a vertical surface. Shading devices such as an umbrella or horizontal overhang/shade provide relief from the solar global radiation and do block the solar global UVB radiation to some extent; nevertheless, a significant fraction of the solar global UVB radiation does penetrate this supposedly 'protective or comfort zone'. As a result, it is imperative to either apply sunscreen or cover up the exposed body surfaces even when under such shading devices. © 2011 John Wiley & Sons A/S.

Comparing solvophobic and multivalent induced collapse in polyelectrolyte brushes

DOE PAGES

Jackson, Nicholas E.; Brettmann, Blair K.; Vishwanath, Venkatram; ...

2017-02-03

Here, coarse-grained molecular dynamics enhanced by free-energy sampling methods is used to examine the roles of solvophobicity and multivalent salts on polyelectrolyte brush collapse. Specifically, we demonstrate that while ostensibly similar, solvophobic collapsed brushes and multivalent-ion collapsed brushes exhibit distinct mechanistic and structural features. Notably, multivalent-induced heterogeneous brush collapse is observed under good solvent polymer backbone conditions, demonstrating that the mechanism of multivalent collapse is not contingent upon a solvophobic backbone. Umbrella sampling of the potential of mean-force (PMF) between two individual brush strands confirms this analysis, revealing starkly different PMFs under solvophobic and multivalent conditions, suggesting the role ofmore » multivalent “bridging” as the discriminating feature in trivalent collapse. Structurally, multivalent ions show a propensity for nucleating order within collapsed brushes, whereas poor-solvent collapsed brushes are more disordered; this difference is traced to the existence of a metastable PMF minimum for poor solvent conditions, and a global PMF minimum for trivalent systems, under experimentally relevant conditions.« less

Comparing solvophobic and multivalent induced collapse in polyelectrolyte brushes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, Nicholas E.; Brettmann, Blair K.; Vishwanath, Venkatram

Here, coarse-grained molecular dynamics enhanced by free-energy sampling methods is used to examine the roles of solvophobicity and multivalent salts on polyelectrolyte brush collapse. Specifically, we demonstrate that while ostensibly similar, solvophobic collapsed brushes and multivalent-ion collapsed brushes exhibit distinct mechanistic and structural features. Notably, multivalent-induced heterogeneous brush collapse is observed under good solvent polymer backbone conditions, demonstrating that the mechanism of multivalent collapse is not contingent upon a solvophobic backbone. Umbrella sampling of the potential of mean-force (PMF) between two individual brush strands confirms this analysis, revealing starkly different PMFs under solvophobic and multivalent conditions, suggesting the role ofmore » multivalent “bridging” as the discriminating feature in trivalent collapse. Structurally, multivalent ions show a propensity for nucleating order within collapsed brushes, whereas poor-solvent collapsed brushes are more disordered; this difference is traced to the existence of a metastable PMF minimum for poor solvent conditions, and a global PMF minimum for trivalent systems, under experimentally relevant conditions.« less

Perspective on the reactions between F– and CH3CH2F: The free energy landscape of the E2 and SN2 reaction channels

PubMed Central

Ensing, Bernd; Klein, Michael L.

2005-01-01

Recently, we computed the 3D free energy surface of the base-induced elimination reaction between F– and CH3CH2F by using a powerful technique within Car–Parrinello molecular dynamics simulation. Here, the set of three order parameters is expanded to six, which allows the study of the competing elimination and substitution reactions simultaneously. The power of the method is exemplified by the exploration of the six-dimensional free energy landscape, sampling, and mapping out the eight stable states as well as the connecting bottlenecks. The free energy profile and barrier along the E2 and SN2 reaction channels are refined by using umbrella sampling. The two mechanisms do not share a common “E2C-like” transition state. Comparison with the zero temperature profiles shows a particularly significant entropy contribution to the SN2 channel. PMID:15863622

Clinical Laboratory Science: Applied Biology with Great Potential.

ERIC Educational Resources Information Center

Stanley, Melissa

1990-01-01

Described are a variety of careers under the umbrella of medical technology. The status of medical technology and medical technology education are discussed. Different curricula for medical technology are compared. (CW)

Biotechnology Process Engineering Center at MIT Home

Science.gov Websites

is speaking at the 2004 Congressional Biomedical Research Caucus Briefings on July 14th. Her briefing | Education & Outreach | Research | Industrial Programs | Student Leadership Council Facilities | Umbrella

Autism Spectrum Disorder: Primary Care Principles.

PubMed

Sanchack, Kristian E; Thomas, Craig A

2016-12-15

Autism spectrum disorder is characterized by difficulty with social communication and restricted, repetitive patterns of behavior, interest, or activities. The Diagnostic and Statistical Manual of Mental Disorders, 5th ed., created an umbrella diagnosis that includes several previously separate conditions: autistic disorder, Asperger syndrome, childhood disintegrative disorder, and pervasive developmental disorder not otherwise specified. There is insufficient evidence to recommend screening for autism spectrum disorder in children 18 to 30 months of age in whom the disorder is not suspected; however, there is a growing body of evidence that early intensive behavioral intervention based on applied behavior analysis improves cognitive ability, language, and adaptive skills. Therefore, early identification of autism spectrum disorder is important, and experts recommend the use of a validated screening tool at 18- and 24-month well-child visits. Medications can be used as adjunctive treatment for maladaptive behaviors and comorbid psychiatric conditions, but there is no single medical therapy that is effective for all symptoms of autism spectrum disorder. Prognosis is heavily affected by the severity of diagnosis and the presence of intellectual disability. Children with optimal outcomes receive earlier, more intensive behavioral interventions and less pharmacologic treatment.

2014 Summer Series - Ethiraj Venkatapathy - Mary Poppins Approach to Human Mars Mission Entry, Descent and Landing

NASA Image and Video Library

2014-06-17

NASA is investing in a number of technologies to extend Entry, Descent and Landing (EDL) capabilities to enable Human Missions to Mars. These technologies will also enable robotic Science missions. Human missions will require landing payloads of 10?s of metric tons, not possible with today's technology. Decelerating from entry speeds around 15,000 miles per hour to landing in a matter of minutes will require very large drag or deceleration. The one way to achieve required deceleration is to deploy a large surface that can be stowed during launch and deployed prior to entry. This talk will highlight a simple concept similar to an umbrella. Though the concept is simple, the size required for human Mars missions and the heating encountered during entry are significant challenges. The mechanically deployable system can also enable robotic science missions to Venus and is also equally applicable for bringing back cube-satellites and other small payloads. The scalable concept called Adaptive Deployable Entry and Placement Technology (ADEPT) is under development and is the focus of this talk.

The Strength of a Loosely Defined Movement: Eugenics and Medicine in Imperial Russia

PubMed Central

Krementsov, Nikolai

2015-01-01

This essay examines the ‘infiltration’ of eugenics into Russian medical discourse during the formation of the eugenics movement in western Europe and North America in 1900–17. It describes the efforts of two Russian physicians, the bacteriologist and hygienist Nikolai Gamaleia (1859–1949) and the psychiatrist Tikhon Iudin (1879–1949), to introduce eugenics to the Russian medical community, analysing in detail what attracted these representatives of two different medical specialties to eugenic ideas, ideals, and policies advocated by their western colleagues. On the basis of a close examination of the similarities and differences in Gamaleia’s and Iudin’s attitudes to eugenics, the essay argues that lack of cohesiveness gave the early eugenics movement a unique strength. The loose mix of widely varying ideas, ideals, methods, policies, activities and proposals covered by the umbrella of eugenics offered to a variety of educated professionals in Russia and elsewhere the possibility of choosing, adopting and adapting particular elements to their own national, professional, institutional and disciplinary contexts, interests and agendas. PMID:25498435

Harmonic Fourier beads method for studying rare events on rugged energy surfaces.

PubMed

Khavrutskii, Ilja V; Arora, Karunesh; Brooks, Charles L

2006-11-07

We present a robust, distributable method for computing minimum free energy paths of large molecular systems with rugged energy landscapes. The method, which we call harmonic Fourier beads (HFB), exploits the Fourier representation of a path in an appropriate coordinate space and proceeds iteratively by evolving a discrete set of harmonically restrained path points-beads-to generate positions for the next path. The HFB method does not require explicit knowledge of the free energy to locate the path. To compute the free energy profile along the final path we employ an umbrella sampling method in two generalized dimensions. The proposed HFB method is anticipated to aid the study of rare events in biomolecular systems. Its utility is demonstrated with an application to conformational isomerization of the alanine dipeptide in gas phase.

Application of adaptive cluster sampling to low-density populations of freshwater mussels

USGS Publications Warehouse

Smith, D.R.; Villella, R.F.; Lemarie, D.P.

2003-01-01

Freshwater mussels appear to be promising candidates for adaptive cluster sampling because they are benthic macroinvertebrates that cluster spatially and are frequently found at low densities. We applied adaptive cluster sampling to estimate density of freshwater mussels at 24 sites along the Cacapon River, WV, where a preliminary timed search indicated that mussels were present at low density. Adaptive cluster sampling increased yield of individual mussels and detection of uncommon species; however, it did not improve precision of density estimates. Because finding uncommon species, collecting individuals of those species, and estimating their densities are important conservation activities, additional research is warranted on application of adaptive cluster sampling to freshwater mussels. However, at this time we do not recommend routine application of adaptive cluster sampling to freshwater mussel populations. The ultimate, and currently unanswered, question is how to tell when adaptive cluster sampling should be used, i.e., when is a population sufficiently rare and clustered for adaptive cluster sampling to be efficient and practical? A cost-effective procedure needs to be developed to identify biological populations for which adaptive cluster sampling is appropriate.

Effects of collagen and collagen hydrolysate from jellyfish umbrella on histological and immunity changes of mice photoaging.

PubMed

Fan, Jian; Zhuang, Yongliang; Li, Bafang

2013-01-17

Jellyfish collagen (JC) was extracted from jellyfish umbrella and hydrolyzed to prepare jellyfish collagen hydrolysate (JCH). The effects of JC and JCH on UV-induced skin damage of mice were evaluated by the skin moisture, microscopic analyses of skin and immunity indexes. The skin moisture analyses showed that moisture retention ability of UV-induced mice skin was increased by JC and JCH. Further histological analysis showed that JC and JCH could repair the endogenous collagen and elastin protein fibers, and could maintain the natural ratio of type I to type III collagen. The immunity indexes showed that JC and JCH play a role in enhancing immunity of photoaging mice in vivo. JCH showed much higher protective ability than JC. These results suggest that JCH as a potential novel antiphotoaging agent from natural resources.

Health Benefits of Dietary Whole Grains: An Umbrella Review of Meta-analyses.

PubMed

McRae, Marc P

2017-03-01

The purpose of this study is to review the effectiveness of the role of whole grain as a therapeutic agent in type 2 diabetes, cardiovascular disease, cancer, and obesity. An umbrella review of all published meta-analyses was performed. A PubMed search from January 1, 1980, to May 31, 2016, was conducted using the following search strategy: (whole grain OR whole grains) AND (meta-analysis OR systematic review). Only English language publications that provided quantitative statistical analysis on type 2 diabetes, cardiovascular disease, cancer, and weight loss were retrieved. Twenty-one meta-analyses were retrieved for inclusion in this umbrella review, and all the meta-analyses reported statistically significant positive benefits for reducing the incidence of type 2 diabetes (relative risk [RR] = 0.68-0.80), cardiovascular disease (RR = 0.63-0.79), and colorectal, pancreatic, and gastric cancers (RR = 0.57-0.94) and a modest effect on body weight, waist circumference, and body fat mass. Significant reductions in cardiovascular and cancer mortality were also observed (RR = 0.82 and 0.89, respectively). Some problems of heterogeneity, publication bias, and quality assessment were found among the studies. This review suggests that there is some evidence for dietary whole grain intake to be beneficial in the prevention of type 2 diabetes, cardiovascular disease, and colorectal, pancreatic, and gastric cancers. The potential benefits of these findings suggest that the consumption of 2 to 3 servings per day (~45 g) of whole grains may be a justifiable public health goal.

[Comparative experiments of stripping sheep maxillary sinus mucosal with new-type stripper and umbrella detacher].

PubMed

Jiadong, Fan; Yanfeng, Li; Le, Liu; Yishi, Han; Pin, Hu; Yue, Zhang; Wenya, Bao

2016-10-01

To compare the stripping length obtained through the model of 0.012 and 0.014 of the nickel-titanium dual-stage maxillary sinus mucosa stripper, and the umbrella detacher. Twenty-four goats (1.5-2 years old) were chosen, randomly divided into A, B, C groups, each group of eight. Group A was 0.012 model group, group B was 0.014 model group, group C was umbrella detacher group. Animal model was established, and maxillary sinus mucosa was stripped to the left and right sides of the bottom of the sinus in three groups. The data was measured when stripping to the limit or being perforated. The average length of group A was 12.41 mm±4.35 mm, two cases perforated. The average length of group B was 23.38 mm±4.84 mm, one case perforated. The average length of group C was 2.61 mm±0.30 mm. The population mean of stripping length in three groups was not all the same calculated by analysis of variance (P<0.01). There were significant differences in the stripping length of the three groups by the SNK test (P<0.05). The nickel-titanium dual-stage maxillary sinus mucosa stripper can achieve a larger mucosal stripping range. The stripper with a model of 0.014 has a moderate flexibility and safety, and it can strip a large area of sinus mucosa.
.

Adaptive sampling in behavioral surveys.

PubMed

Thompson, S K

1997-01-01

Studies of populations such as drug users encounter difficulties because the members of the populations are rare, hidden, or hard to reach. Conventionally designed large-scale surveys detect relatively few members of the populations so that estimates of population characteristics have high uncertainty. Ethnographic studies, on the other hand, reach suitable numbers of individuals only through the use of link-tracing, chain referral, or snowball sampling procedures that often leave the investigators unable to make inferences from their sample to the hidden population as a whole. In adaptive sampling, the procedure for selecting people or other units to be in the sample depends on variables of interest observed during the survey, so the design adapts to the population as encountered. For example, when self-reported drug use is found among members of the sample, sampling effort may be increased in nearby areas. Types of adaptive sampling designs include ordinary sequential sampling, adaptive allocation in stratified sampling, adaptive cluster sampling, and optimal model-based designs. Graph sampling refers to situations with nodes (for example, people) connected by edges (such as social links or geographic proximity). An initial sample of nodes or edges is selected and edges are subsequently followed to bring other nodes into the sample. Graph sampling designs include network sampling, snowball sampling, link-tracing, chain referral, and adaptive cluster sampling. A graph sampling design is adaptive if the decision to include linked nodes depends on variables of interest observed on nodes already in the sample. Adjustment methods for nonsampling errors such as imperfect detection of drug users in the sample apply to adaptive as well as conventional designs.

Promoting physical activity for children and adolescents in low- and middle-income countries: An umbrella systematic review: A review on promoting physical activity in LMIC.

PubMed

Barbosa Filho, Valter Cordeiro; Minatto, Giseli; Mota, Jorge; Silva, Kelly Samara; de Campos, Wagner; Lopes, Adair da Silva

2016-07-01

It is unknown how much previous reviews on promoting physical activity (PA) for children and adolescents (aged 6-18years) take into account studies from low- and middle-income countries (LMIC, based on the World Bank definition) and the level of evidence of the effect of PA interventions in this population. This study aims to answer such questions using an umbrella systematic review approach. We searched for peer-reviewed systematic reviews and original studies in eight electronic databases, screening of reference lists and expert contacts. Information in systematic reviews on PA interventions for children and adolescents from LMIC was discussed. Original studies on PA interventions (randomized-controlled trials [RCT], cluster-RCT and non-RCT) with children and adolescents from LMIC were eligible. We assessed the methodological quality in all studies, and the evidence level of effect on PA in intervention studies. Fifty systematic reviews (nine meta-analyses) and 25 original studies (20 different interventions) met eligibility criteria. Only 3.1% of mentioned studies in previous reviews were from LMIC. Strong and LMIC-specific evidence was found that school-based, multicomponent, and short-term (up to six months) interventions, focused on adolescents primarily (aged 13-18years), can promote PA in children and adolescents from LMIC. Other intervention characteristics had inconclusive evidence due to the low number of studies, low methodological quality, and/or small sample size. A minimal part of PA interventions mentioned in previous reviews are from LMIC. Our LMIC-specific analyses showed priorities of implementation and practical implication that can be used in public policies for PA promotion in LMIC. Copyright © 2016 Elsevier Inc. All rights reserved.

ENCOURAGING INNOVATION THROUGH UMBRELLA PERMITTING

EPA Science Inventory

The purpose of this project is to assess the behavioral, technical, economic, and environmental effects of removing disincentives to innovation in production and pollution management through more flexible environmental permitting. The study will examine the characteristics of tra...

Fermilab | LBNF | Home

Science.gov Websites

million to LBNF/DUNE in first-ever umbrella science agreement with U.S. Jo Johnson (UK Minister of State Minister of State for Universities, Science, Research and Innovation Jo Johnson signed the U.S.-UK Science

Surface sampling techniques for 3D object inspection

NASA Astrophysics Data System (ADS)

Shih, Chihhsiong S.; Gerhardt, Lester A.

1995-03-01

While the uniform sampling method is quite popular for pointwise measurement of manufactured parts, this paper proposes three novel sampling strategies which emphasize 3D non-uniform inspection capability. They are: (a) the adaptive sampling, (b) the local adjustment sampling, and (c) the finite element centroid sampling techniques. The adaptive sampling strategy is based on a recursive surface subdivision process. Two different approaches are described for this adaptive sampling strategy. One uses triangle patches while the other uses rectangle patches. Several real world objects were tested using these two algorithms. Preliminary results show that sample points are distributed more closely around edges, corners, and vertices as desired for many classes of objects. Adaptive sampling using triangle patches is shown to generally perform better than both uniform and adaptive sampling using rectangle patches. The local adjustment sampling strategy uses a set of predefined starting points and then finds the local optimum position of each nodal point. This method approximates the object by moving the points toward object edges and corners. In a hybrid approach, uniform points sets and non-uniform points sets, first preprocessed by the adaptive sampling algorithm on a real world object were then tested using the local adjustment sampling method. The results show that the initial point sets when preprocessed by adaptive sampling using triangle patches, are moved the least amount of distance by the subsequently applied local adjustment method, again showing the superiority of this method. The finite element sampling technique samples the centroids of the surface triangle meshes produced from the finite element method. The performance of this algorithm was compared to that of the adaptive sampling using triangular patches. The adaptive sampling with triangular patches was once again shown to be better on different classes of objects.

Morphological keys in the differential diagnosis of bladder inverted papilloma. Study of two types, trabecular and glandular.

PubMed

Sabater Marco, Vicente; Navalón Verdejo, Pedro; Morera Faet, Arturo

2012-09-01

Inverted papilloma of the urinary bladder is an uncommon urothelial neoplasm that may be specially difficult to distinguish from urothelial carcinoma. Two patients with obstructive symptoms and hematuria have been studied. In the transurethral resection, accidentally, one showed a papillary lesion in the context of nodular hyperplasia of the prostate, where as the other showed a polypoid tumor of the urinary bladder Histologically, in both cases, a bladder inverted papilloma was demonstrated, originating from the surface transitional epithelium. Basal cells exhibited peripheral palisading pattern in the trabecular form. In the glandular type, Dogiel or umbrella cells into the gland-like structures, were recognized. Immunohistochemical stains for p53 and Ki-67 were negative. Umbrella cells were positive for cytokeratin 20. Two cases of bladder inverted papilloma with relevant morphological aspects are presented, which we consider useful for the differential diagnosis with urothelial carcinoma.

Communication: Reactivity borrowing in the mode selective chemistry of H + CHD3 → H2 + CD3

NASA Astrophysics Data System (ADS)

Ellerbrock, Roman; Manthe, Uwe

2017-12-01

Quantum state-resolved reaction probabilities for the H + CHD3 → H2 + CD3 reaction are calculated by accurate full-dimensional quantum dynamics calculations using the multi-layer multi-configurational time-dependent Hartree approach and the quantum transition state concept. Reaction probabilities of various ro-vibrational states of the CHD3 reactant are investigated for vanishing total angular momentum. While the reactivity of the different vibrational states of CHD3 mostly follows intuitive patterns, an unusually large reaction probability is found for CHD3 molecules triply excited in the CD3 umbrella-bending vibration. This surprising reactivity can be explained by a Fermi resonance-type mixing of the single CH-stretch excited and the triple CD3 umbrella-bend excited vibrational states of CHD3. These findings show that resonant energy transfer can significantly affect the mode-selective chemistry of CHD3 and result in counter-intuitive reactivity patterns.

Effects of Collagen and Collagen Hydrolysate from Jellyfish Umbrella on Histological and Immunity Changes of Mice Photoaging

PubMed Central

Fan, Jian; Zhuang, Yongliang; Li, Bafang

2013-01-01

Jellyfish collagen (JC) was extracted from jellyfish umbrella and hydrolyzed to prepare jellyfish collagen hydrolysate (JCH). The effects of JC and JCH on UV-induced skin damage of mice were evaluated by the skin moisture, microscopic analyses of skin and immunity indexes. The skin moisture analyses showed that moisture retention ability of UV-induced mice skin was increased by JC and JCH. Further histological analysis showed that JC and JCH could repair the endogenous collagen and elastin protein fibers, and could maintain the natural ratio of type I to type III collagen. The immunity indexes showed that JC and JCH play a role in enhancing immunity of photoaging mice in vivo. JCH showed much higher protective ability than JC. These results suggest that JCH as a potential novel antiphotoaging agent from natural resources. PMID:23344251

Oral healthcare challenges for older Punjabi-speaking immigrants.

PubMed

MacEntee, Michael I; Wong, Sabrina T; Smith, André; Beattie, B Lynn; Brondani, Mario; Bryant, S Ross; Graf, Peter; Soheilipour, Shimae

2014-06-01

This study explored how older Punjabi-speaking South-Asian immigrants (four focus groups; 33 participants) in Surrey, British Columbia, perceive oral health and related problems. Content analysis revealed two umbrella themes: (a) interpretations of mouth conditions and (b) challenges to oral health. The umbrella themes had four sub-themes: damage caused by heat (wai), disturbances caused by caries, coping with dentures, and quality of life. Three challenges were considered: home remedies, Western dentistry, and difficulties accessing dentists. Participants explained oral diseases in terms of a systemic infection (resha), and preferred to decrease imbalances of wai in the mouth with home remedies from India. We conclude that older Punjabi-speaking immigrants interpret oral health and disease in the context of both Western and Ayurvedic traditions, and that they manage dental problems with a mix of traditional remedies supplemented, if possible, by elective oral health care in India, and by emergency dental care in Canada.

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations.

PubMed

Sun, Huiyong; Tian, Sheng; Zhou, Shunye; Li, Youyong; Li, Dan; Xu, Lei; Shen, Mingyun; Pan, Peichen; Hou, Tingjun

2015-02-13

How does a type II inhibitor bind to/unbind from a kinase target is still a confusing question because the small molecule occupies both the ATP pocket and the allosteric pocket of the kinase binding site. Here, by using enhanced sampling simulations (umbrella sampling, US) and two-end-state free energy calculations (MM/GSBA), we systemically studied the dissociation processes of two distinct small molecules escaping from the binding pocket of p38 MAP kinase through the allosteric channel and the ATP channel. The results show that the unbinding pathways along the allosteric channel have much lower PMF depths than those along the ATP channel, suggesting that the allosteric channel is more favorable for the dissociations of the two inhibitors and thereby supporting the general understanding that the largest channel of a target is usually the entry/exit pathway for the binding/dissociation of small molecules. Interestingly, the MM/GBSA approach yielded similar PMF profiles compared with those based on US, a much time consuming approach, indicating that for a general study, such as detecting the important transition state of a ligand binding/unbinding process, MM/GBSA may be a feasible choice.

Rapid exploration of configuration space with diffusion-map-directed molecular dynamics.

PubMed

Zheng, Wenwei; Rohrdanz, Mary A; Clementi, Cecilia

2013-10-24

The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named diffusion-map-directed MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses a diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here, we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems, we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300 K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.

Rapid Exploration of Configuration Space with Diffusion Map-directed-Molecular Dynamics

PubMed Central

Zheng, Wenwei; Rohrdanz, Mary A.; Clementi, Cecilia

2013-01-01

The gap between the timescale of interesting behavior in macromolecular systems and that which our computational resources can afford oftentimes limits Molecular Dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named Diffusion Map-directed-MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD. PMID:23865517

The urothelium of a hibernator: the American black bear

PubMed Central

Spector, David A; Deng, Jie; Coleman, Richard; Wade, James B

2015-01-01

The American black bear undergoes a 3–5 month winter hibernation during which time bears do not eat, drink, defecate, or urinate. During hibernation renal function (GFR) is 16–50% of normal but urine is reabsorbed across the urinary bladder (UB) urothelium thus enabling metabolic recycling of all urinary constituents. To elucidate the mechanism(s) whereby urine is reabsorbed, we examined the UBs of five nonhibernating wild bears using light, electron (EM), and confocal immunofluorescent (IF) microscopy–concentrating on two components of the urothelial permeability barrier – the umbrella cell apical membranes and tight junctions (TJ). Bear UB has the same tissue layers (serosa, muscularis, lamina propria, urothelia) and its urothelia has the same cell layers (basal, intermediate, umbrella cells) as other mammalians. By EM, the bear apical membrane demonstrated a typical mammalian scalloped appearance with hinge and plaque regions – the latter containing an asymmetric trilaminar membrane and, on IF, uroplakins Ia, IIIa, and IIIb. The umbrella cell TJs appeared similar to those in other mammals and also contained TJ proteins occludin and claudin - 4, and not claudin –2. Thus, we were unable to demonstrate urothelial apical membrane or TJ differences between active black bears and other mammals. Expression and localization of UT-B, AQP-1 and -3, and Na+, K+-ATPase on bear urothelial membranes was similar to that of other mammals. Similar studies of urothelia of hibernating bears, including evaluation of the apical membrane lipid bilayer and GAGs layer are warranted to elucidate the mechanism(s) whereby hibernating bears reabsorb their daily urine output and thus ensure successful hibernation. PMID:26109187

Greater sage-grouse as an umbrella species for sagebrush-associated vertebrates

USGS Publications Warehouse

Rowland, M.M.; Wisdom, M.J.; Suring, L.H.; Meinke, C.W.

2006-01-01

Widespread degradation of the sagebrush ecosystem in the western United States, including the invasion of cheatgrass, has prompted resource managers to consider a variety of approaches to restore and conserve habitats for sagebrush-associated species. One such approach involves the use of greater sage-grouse, a species of prominent conservation interest, as an umbrella species. This shortcut approach assumes that managing habitats to conserve sage-grouse will simultaneously benefit other species of conservation concern. The efficacy of using sage-grouse as an umbrella species for conservation management, however, has not been fully evaluated. We tested that concept by comparing: (1) commonality in land-cover associations, and (2) spatial overlap in habitats between sage-grouse and 39 other sagebrush-associated vertebrate species of conservation concern in the Great Basin ecoregion. Overlap in species' land-cover associations with those of sage-grouse, based on the ?? (phi) correlation coefficient, was substantially greater for sagebrush obligates (x??=0.40) than non-obligates (x??=0.21). Spatial overlap between habitats of target species and those associated with sage-grouse was low (mean ?? = 0.23), but somewhat greater for habitats at high risk of displacement by cheatgrass (mean ?? = 0.33). Based on our criteria, management of sage-grouse habitats likely would offer relatively high conservation coverage for sagebrush obligates such as pygmy rabbit (mean ?? = 0.84), but far less for other species we addressed, such as lark sparrow (mean ?? = 0.09), largely due to lack of commonality in land-cover affinity and geographic ranges of these species and sage-grouse.

Methotrexate-induced toxicity pharmacogenetics: an umbrella review of systematic reviews and meta-analyses.

PubMed

Campbell, Jared M; Bateman, Emma; Stephenson, Matthew D; Bowen, Joanne M; Keefe, Dorothy M; Peters, Micah D J

2016-07-01

Methotrexate chemotherapy is associated with various toxicities which can result in the interruption or discontinuation of treatment and a subsequently raised risk of relapse. This umbrella systematic review was conducted to synthesize the results of all existing systematic reviews that investigate the pharmacogenetics of methotrexate-induced toxicity, with the aim of developing a comprehensive reference for personalized medicine. Databases searched were PubMed, Embase, JBI Database of Systematic Reviews and Implementation Reports, DARE, and ProQuest. Papers were critically appraised by two reviewers, and data were extracted using a standardized tool. Three systematic reviews on methotrexate-induced toxicity were included in the review. Meta-analyses were reported across Asian, Caucasian, pediatric and adult patients for the MTHFR C677T and A1298C polymorphisms. Toxicity outcomes included different forms of hematologic, ectodermal and hepatic toxicities. Results varied considerably depending on the patient groups and subgroups investigated in the different systematic reviews, as well as the genetic models utilized. However, significant associations were found between the MTHFR C677T allele and; hepatic toxicity, myelosuppression, oral mucositis, gastrointestinal toxicity, and skin toxicity. Additionally, limited evidence suggests that the MTHFR A1298C polymorphism may be associated with decreased risk of skin toxicity and leukopenia. This umbrella systematic review has synthesized the best available evidence on the pharmacogenetics of methotrexate toxicity. The next step in making personalized medicine for methotrexate therapy a clinical reality is research on the effectiveness and cost-effectiveness of MTHFR genotype testing to enable the close monitoring of at-risk patients for the timely initiation of rescue therapies.

New silicate-germanate Cs2Pb2[(Si0.6Ge0.4)2O7] from the series A2Pb2[B2O7], A = K, Cs, B = Si, Ge with the umbrella-like [PbO3]4- group

NASA Astrophysics Data System (ADS)

Belokoneva, Elena L.; Morozov, Ivan A.; Volkov, Anatoly S.; Dimitrova, Olga V.; Stefanovich, Sergey Yu.

2018-04-01

New silicate-germanate Cs2Pb2[(Si0.6Ge0.4)2O7] was synthesized in multi-components hydrothermal solution with 20 w.% concentration of Cs2CO3 mineralizer, pH = 10. Novel mixed compound belongs to the structure type A2Pb2[B2O7] previously indicated for powders with A = K, B=Si or Ge. Singe crystal structure determination of Cs2Pb2[(Si0.6Ge0.4)2O7] revealed the need for the correction of the space group of the earlier suggested structural model from P-3 to P-3m1, as well as for the splitting of the Pb-atom position. Umbrella-like groups [PbO3]4- are located between [(Si,Ge)O4]4- tetrahedra in mica-like honeycomb layers and play the role of tetrahedra with the Pb-lone-pair as the forth apex. Crystal chemical comparison revealed similarities and differences with the classical structure type of α-celsian Ba[Al2Si2O8] with the tetrahedral double layer. Recently investigated nonlinear optical acentric borates Pb2(BO3)(NO3) and Pb2(BO3)Cl are both related to this structural type, possessing umbrella-like groups [PbO3]4- and honeycomb layers [Pb2(BO3)]+ with the BO3-triangles on the tetrahedral positions.

STORMWATER BEST MANAGEMENT PRACTICE MONITORING

EPA Science Inventory

Implementation of an effective BMP monitoring program is not a straight-forward task. BMPs by definition are devices, practices, or methods used to manage stormwater runoff. This umbrella term lumps widely varying techniques into a single category. Also, with the existence of ...

New York hospital group striving for brand recognition. HealthStar Network.

PubMed

Herreria, J

1998-01-01

HealthStar Network established a new concept in its eastern market--a group of hospitals forming one association. Marketers of HealthStar are conducting a branding campaign to distinguish individual expertise under one umbrella company.

78 FR 25260 - Combined Notice of Filings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-30

...: Boardwalk Storage Company, LLC. Description: Revise Hub Services and Umbrella Pro Forma Agmts to be... Pipeline Company of America. Description: Negotiated Rate--EDF Trading to be effective 5/1/2013. Filed Date...: Kern River Gas Transmission Company. [[Page 25261

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sehgal, Ray M.; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu, E-mail: ford@ecs.umass.edu; Ford, David M., E-mail: maroudas@ecs.umass.edu, E-mail: ford@ecs.umass.edu

We have developed a coarse-grained description of the phase behavior of the isolated 38-atom Lennard-Jones cluster (LJ{sub 38}). The model captures both the solid-solid polymorphic transitions at low temperatures and the complex cluster breakup and melting transitions at higher temperatures. For this coarse model development, we employ the manifold learning technique of diffusion mapping. The outcome of the diffusion mapping analysis over a broad temperature range indicates that two order parameters are sufficient to describe the cluster's phase behavior; we have chosen two such appropriate order parameters that are metrics of condensation and overall crystallinity. In this well-justified coarse-variable space,more » we calculate the cluster's free energy landscape (FEL) as a function of temperature, employing Monte Carlo umbrella sampling. These FELs are used to quantify the phase behavior and onsets of phase transitions of the LJ{sub 38} cluster.« less

Crystal nucleation of colloidal hard dumbbells

NASA Astrophysics Data System (ADS)

Ni, Ran; Dijkstra, Marjolein

2011-01-01

Using computer simulations, we investigate the homogeneous crystal nucleation in suspensions of colloidal hard dumbbells. The free energy barriers are determined by Monte Carlo simulations using the umbrella sampling technique. We calculate the nucleation rates for the plastic crystal and the aperiodic crystal phase using the kinetic prefactor as determined from event driven molecular dynamics simulations. We find good agreement with the nucleation rates determined from spontaneous nucleation events observed in event driven molecular dynamics simulations within error bars of one order of magnitude. We study the effect of aspect ratio of the dumbbells on the nucleation of plastic and aperiodic crystal phases, and we also determine the structure of the critical nuclei. Moreover, we find that the nucleation of the aligned close-packed crystal structure is strongly suppressed by a high free energy barrier at low supersaturations and slow dynamics at high supersaturations.

Molecular dynamics simulation of the structure and dynamics of 5-HT3 serotonin receptor

NASA Astrophysics Data System (ADS)

Antonov, M. Yu.; Popinako, A. V.; Prokopiev, G. A.

2016-10-01

In this work, we investigated structure, dynamics and ion transportation in transmembrane domain of the 5-HT3 serotonin receptor. High-resolution (0.35 nm) structure of the 5-HT3 receptor in complex with stabilizing nanobodies was determined by protein crystallography in 2014 (Protein data bank (PDB) code 4PIR). Transmembrane domain of the structure was prepared in complex with explicit membrane environment (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)) and solvent (TIP3P water model). Molecular dynamics protocols for simulation and stabilization of the transmembrane domain of the 5-HT3 receptor model were developed and 60 ns simulation of the structure was conducted in order to explore structural parameters of the system. We estimated the mean force profile for Na+ ions using umbrella sampling method.

Surface polarity of beta-HMX crystal and the related adhesive forces with Estane binder.

PubMed

Yang, Lu

2008-12-02

Here I present the results on the study of surface properties of beta-HMX crystal utilizing molecular dynamics simulations. The surface polarity of three principal crystal surfaces, (011), (010), and (110), is investigated by measuring the water contact angles. The calculated contact angles are in excellent agreement with the values measured by experiment and show that the surface polarity of three crystal surfaces are different. The free energies and forces of detaching an Estane chain (with and without surrounding nitroplasticizer molecules) from the three principal crystal surfaces are also calculated using the umbrella sampling method. I find that the force for Estane detachment increases with the increasing HMX surface polarity. In addition, my results show that the nitroplasticizer also plays an important role in the adhesion between Estane and HMX surfaces.

What causes psychosis? An umbrella review of risk and protective factors

PubMed Central

Radua, Joaquim; Ramella‐Cravaro, Valentina; Ioannidis, John P.A.; Reichenberg, Abraham; Phiphopthatsanee, Nacharin; Amir, Taha; Yenn Thoo, Hyi; Oliver, Dominic; Davies, Cathy; Morgan, Craig; McGuire, Philip; Murray, Robin M.; Fusar‐Poli, Paolo

2018-01-01

Psychosis is a heterogeneous psychiatric condition for which a multitude of risk and protective factors have been suggested. This umbrella review aimed to classify the strength of evidence for the associations between each factor and psychotic disorders whilst controlling for several biases. The Web of Knowledge database was searched to identify systematic reviews and meta‐analyses of observational studies which examined associations between socio‐demographic, parental, perinatal, later factors or antecedents and psychotic disorders, and which included a comparison group of healthy controls, published from 1965 to January 31, 2017. The literature search and data extraction followed PRISMA and MOOSE guidelines. The association between each factor and ICD or DSM diagnoses of non‐organic psychotic disorders was graded into convincing, highly suggestive, suggestive, weak, or non‐significant according to a standardized classification based on: number of psychotic cases, random‐effects p value, largest study 95% confidence interval, heterogeneity between studies, 95% prediction interval, small study effect, and excess significance bias. In order to assess evidence for temporality of association, we also conducted sensitivity analyses restricted to data from prospective studies. Fifty‐five meta‐analyses or systematic reviews were included in the umbrella review, corresponding to 683 individual studies and 170 putative risk or protective factors for psychotic disorders. Only the ultra‐high‐risk state for psychosis (odds ratio, OR=9.32, 95% CI: 4.91‐17.72) and Black‐Caribbean ethnicity in England (OR=4.87, 95% CI: 3.96‐6.00) showed convincing evidence of association. Six factors were highly suggestive (ethnic minority in low ethnic density area, second generation immigrants, trait anhedonia, premorbid IQ, minor physical anomalies, and olfactory identification ability), and nine were suggestive (urbanicity, ethnic minority in high ethnic density area, first generation immigrants, North‐African immigrants in Europe, winter/spring season of birth in Northern hemisphere, childhood social withdrawal, childhood trauma, Toxoplasma gondii IgG, and non‐right handedness). When only prospective studies were considered, the evidence was convincing for ultra‐high‐risk state and suggestive for urbanicity only. In summary, this umbrella review found several factors to be associated with psychotic disorders with different levels of evidence. These risk or protective factors represent a starting point for further etiopathological research and for the improvement of the prediction of psychosis. PMID:29352556

Exhaustively sampling peptide adsorption with metadynamics.

PubMed

Deighan, Michael; Pfaendtner, Jim

2013-06-25

Simulating the adsorption of a peptide or protein and obtaining quantitative estimates of thermodynamic observables remains challenging for many reasons. One reason is the dearth of molecular scale experimental data available for validating such computational models. We also lack simulation methodologies that effectively address the dual challenges of simulating protein adsorption: overcoming strong surface binding and sampling conformational changes. Unbiased classical simulations do not address either of these challenges. Previous attempts that apply enhanced sampling generally focus on only one of the two issues, leaving the other to chance or brute force computing. To improve our ability to accurately resolve adsorbed protein orientation and conformational states, we have applied the Parallel Tempering Metadynamics in the Well-Tempered Ensemble (PTMetaD-WTE) method to several explicitly solvated protein/surface systems. We simulated the adsorption behavior of two peptides, LKα14 and LKβ15, onto two self-assembled monolayer (SAM) surfaces with carboxyl and methyl terminal functionalities. PTMetaD-WTE proved effective at achieving rapid convergence of the simulations, whose results elucidated different aspects of peptide adsorption including: binding free energies, side chain orientations, and preferred conformations. We investigated how specific molecular features of the surface/protein interface change the shape of the multidimensional peptide binding free energy landscape. Additionally, we compared our enhanced sampling technique with umbrella sampling and also evaluated three commonly used molecular dynamics force fields.

From early days of elitism to earning a wider respect.

PubMed

Stammer, T

1979-07-20

Gone are those early elitist days in the life of the Association of NHS Supplies Officers. It has widened its umbrella and its ambitions. Author traces the association's origins and ruminates on what lies in store for it.

Identifying the local and regional travel effects of activity centers in the Austin, Texas area.

DOT National Transportation Integrated Search

2015-02-01

Metropolitan planning organizations (MPOs) have become increasingly interested in : incorporating innovated land use planning and design into transportation plan-making. Many : design ideas are recommended under the umbrella of the New Urbanism; yet ...

Study shows women fail to land top grants

NASA Astrophysics Data System (ADS)

Jenner, Nicola

2014-05-01

Women in the UK are less successful than men at securing research council funding at almost every stage of their careers, according to an analysis published by Research Councils UK (RCUK) - the umbrella organization for the country's seven research councils.

Evaluation of the cooperative multi-carrier delivery initiatives.

DOT National Transportation Integrated Search

2013-12-01

In the last several years there has been a surge of interest in fostering more sustainable logistical operations in : urban areas. Under the umbrella of the generic term City Logistics, these initiatives try to take advantage of : the coordinating po...

Acid Rain: Resource Materials for Schools.

ERIC Educational Resources Information Center

American Biology Teacher, 1983

1983-01-01

Provides listings of acid rain resource material groups under: (1) printed materials (pamphlets, books, articles); (2) audiovisuals (slide/tape presentations, tape, video-cassette); (3) miscellaneous (buttons, pocket lab, umbrella); (4) transparencies; (5) bibliographies; and (6) curriculum materials. Sources and prices (when applicable) are…

Offshore energy boom providing opportunities outside Medicare's umbrella.

PubMed

Robb, N

1998-09-08

Physicians upset by limits imposed by the medicare system are getting a chance to spread their entrepreneurial wings on the East Coast. A boom in offshore exploration, led by Newfoundland's massive Hibernia project, has led to numerous business opportunities for physicians.

36 CFR 504.12 - Items to be checked.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Section 504.12 Parks, Forests, and Public Property SMITHSONIAN INSTITUTION RULES AND REGULATIONS GOVERNING SMITHSONIAN INSTITUTION BUILDINGS AND GROUNDS § 504.12 Items to be checked. Umbrellas, canes (not needed to... to be checked in buildings where checking facilities are provided. ...

Can Whole-Grain Foods Lower Blood Pressure?

MedlinePlus

... Flint AJ, et al. Whole grains and incident hypertension in men. American Journal of Clinical Nutrition. 2009;90:493. Dietary guidelines ... whole grains: An umbrella review of meta-analyses. Journal of Chiropractic Medicine. 2017;16:10. Feb. 22, 2018 Original ... . Mayo ...

Voluntary Organisation

ERIC Educational Resources Information Center

Williams, Shirley; Spiret, Claire; Dimitriadi, Yota; McCrindle, Rachel

2013-01-01

The World Association of Girl Guides and Girl Scouts (WAGGGS) is the umbrella organisation for Member Organisations from 145 countries, with a total membership of 10 million. While Member Organisations offer training and development within their own countries, WAGGGS offers international opportunities, such as leadership development at…

Metadynamics convergence law in a multidimensional system

NASA Astrophysics Data System (ADS)

Crespo, Yanier; Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro

2010-05-01

Metadynamics is a powerful sampling technique that uses a nonequilibrium history-dependent process to reconstruct the free-energy surface as a function of the relevant collective variables s . In Bussi [Phys. Rev. Lett. 96, 090601 (2006)] it is proved that, in a Langevin process, metadynamics provides an unbiased estimate of the free energy F(s) . We here study the convergence properties of this approach in a multidimensional system, with a Hamiltonian depending on several variables. Specifically, we show that in a Monte Carlo metadynamics simulation of an Ising model the time average of the history-dependent potential converge to F(s) with the same law of an umbrella sampling performed in optimal conditions (i.e., with a bias exactly equal to the negative of the free energy). Remarkably, after a short transient, the error becomes approximately independent on the filling speed, showing that even in out-of-equilibrium conditions metadynamics allows recovering an accurate estimate of F(s) . These results have been obtained introducing a functional form of the history-dependent potential that avoids the onset of systematic errors near the boundaries of the free-energy landscape.

Metadynamics convergence law in a multidimensional system.

PubMed

Crespo, Yanier; Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro

2010-05-01

Metadynamics is a powerful sampling technique that uses a nonequilibrium history-dependent process to reconstruct the free-energy surface as a function of the relevant collective variables s . In Bussi [Phys. Rev. Lett. 96, 090601 (2006)] it is proved that, in a Langevin process, metadynamics provides an unbiased estimate of the free energy F(s) . We here study the convergence properties of this approach in a multidimensional system, with a Hamiltonian depending on several variables. Specifically, we show that in a Monte Carlo metadynamics simulation of an Ising model the time average of the history-dependent potential converge to F(s) with the same law of an umbrella sampling performed in optimal conditions (i.e., with a bias exactly equal to the negative of the free energy). Remarkably, after a short transient, the error becomes approximately independent on the filling speed, showing that even in out-of-equilibrium conditions metadynamics allows recovering an accurate estimate of F(s) . These results have been obtained introducing a functional form of the history-dependent potential that avoids the onset of systematic errors near the boundaries of the free-energy landscape.

Multiensemble Markov models of molecular thermodynamics and kinetics.

PubMed

Wu, Hao; Paul, Fabian; Wehmeyer, Christoph; Noé, Frank

2016-06-07

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models-clustering of high-dimensional spaces and modeling of complex many-state systems-with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein-ligand binding model.

Multiensemble Markov models of molecular thermodynamics and kinetics

PubMed Central

Wu, Hao; Paul, Fabian; Noé, Frank

2016-01-01

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models—clustering of high-dimensional spaces and modeling of complex many-state systems—with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein–ligand binding model. PMID:27226302

Self-expansion and flow in couples' momentary experiences: an experience sampling study.

PubMed

Graham, James M

2008-09-01

The self-expansion model of close relationships posits that when couples engage in exciting and activating conjoint activities, they feel connected with their partners and more satisfied with their relationships. In the present study, the experience sampling method was used to examine the predictions of the self-expansion model in couples' momentary experiences. In addition, the author generated several new hypotheses by integrating the self-expansion model with existing research on flow. Over the course of 1 week, 20 couples were signaled at quasi-random intervals to provide data on 1,265 unique experiences. The results suggest that the level of activation experienced during an activity was positively related to experience-level relationship quality. This relationship was consistent across free-time and nonfree-time contexts and was mediated by positive affect. Activation was not found to predict later affect unless the level of activation exceeded what was typical for the individual. Also examined was the influence of interpersonal context and activity type on self-expansion. The results support the self-expansion model and suggest that it could be considered under the broader umbrella of flow.

An adaptive two-stage sequential design for sampling rare and clustered populations

USGS Publications Warehouse

Brown, J.A.; Salehi, M.M.; Moradi, M.; Bell, G.; Smith, D.R.

2008-01-01

How to design an efficient large-area survey continues to be an interesting question for ecologists. In sampling large areas, as is common in environmental studies, adaptive sampling can be efficient because it ensures survey effort is targeted to subareas of high interest. In two-stage sampling, higher density primary sample units are usually of more interest than lower density primary units when populations are rare and clustered. Two-stage sequential sampling has been suggested as a method for allocating second stage sample effort among primary units. Here, we suggest a modification: adaptive two-stage sequential sampling. In this method, the adaptive part of the allocation process means the design is more flexible in how much extra effort can be directed to higher-abundance primary units. We discuss how best to design an adaptive two-stage sequential sample. ?? 2008 The Society of Population Ecology and Springer.

Development of a Decision Model for Selection of Appropriate Timely Delivery Techniques for Highway Projects

DOT National Transportation Integrated Search

2009-04-01

"The primary umbrella method used by the Oregon Department of Transportation (ODOT) to ensure on-time performance in standard construction contracting is liquidated damages. The assessment value is usually a matter of some judgment. In practice...

Virtual Beach Manager Toolset

EPA Science Inventory

The Virtual Beach Manager Toolset (VB) is a set of decision support software tools developed to help local beach managers make decisions as to when beaches should be closed due to predicted high levels of water borne pathogens. The tools are being developed under the umbrella of...

Lovelace simplifies, saves big with single-source imaging equipment service contract.

PubMed

1997-11-01

Lovelace Health System traded in its disorganized mess of service contracts for imaging and cardiology equipment for one umbrella contract--and is now saving more than $200,000 a year as a result. Find out how to achieve similar savings.

Offshore energy boom providing opportunities outside medicare's umbrella

PubMed Central

Robb, N

1998-01-01

Physicians upset by limits imposed by the medicare system are getting a chance to spread their entrepreneurial wings on the East Coast. A boom in offshore exploration, led by Newfoundland's massive Hibernia project, has led to numerous business opportunities for physicians. PMID:9757185

Extreme Events and Disaster Risk Reduction - a Future Earth KAN initiative

NASA Astrophysics Data System (ADS)

Frank, Dorothea; Reichstein, Markus

2017-04-01

The topic of Extreme Events in the context of global environmental change is both a scientifically challenging and exciting topic, and of very high societal relevance. The Future Earth Cluster initiative E3S organized in 2016 a cross-community/co-design workshop on Extreme Events and Environments from Climate to Society (http://www.e3s-future-earth.eu/index.php/ConferencesEvents/ConferencesAmpEvents). Based on the results, co-design research strategies and established network of the workshop, and previous activities, E3S is thriving to establish the basis for a longer-term research effort under the umbrella of Future Earth. These led to an initiative for a Future Earth Knowledge Action Network on Extreme Events and Disaster Risk Reduction. Example initial key question in this context include: What are meaningful indices to describe and quantify impact-relevant (e.g. climate) extremes? Which system properties yield resistance and resilience to extreme conditions? What are the key interactions between global urbanization processes, extreme events, and social and infrastructure vulnerability and resilience? The long-term goal of this KAN is to contribute to enhancing the resistance, resilience, and adaptive capacity of socio-ecological systems across spatial, temporal and institutional scales, in particular in the light of hazards affected by ongoing environmental change (e.g. climate change, global urbanization and land use/land cover change). This can be achieved by enhanced understanding, prediction, improved and open data and knowledge bases for detection and early warning decision making, and by new insights on natural and societal conditions and governance for resilience and adaptive capacity.

Exploration of molecular interactions in cholesterol superlattices: effect of multibody interactions.

PubMed

Huang, Juyang

2002-08-01

Experimental evidences have indicated that cholesterol may adapt highly regular lateral distributions (i.e., superlattices) in a phospholipid bilayer. We investigated the formations of superlattices at cholesterol mole fraction of 0.154, 0.25, 0.40, and 0.5 using Monte Carlo simulation. We found that in general, conventional pairwise-additive interactions cannot produce superlattices. Instead, a multibody (nonpairwise) interaction is required. Cholesterol superlattice formation reveals that although the overall interaction between cholesterol and phospholipids is favorable, it contains two large opposing components: an interaction favoring cholesterol-phospholipid mixing and an unfavorable acyl chain multibody interaction that increases nonlinearly with the number of cholesterol contacts. The magnitudes of interactions are in the order of kT. The physical origins of these interactions can be explained by our umbrella model. They most likely come from the requirement for polar phospholipid headgroups to cover the nonpolar cholesterol to avoid the exposure of cholesterol to water and from the sharp decreasing of acyl chain conformation entropy due to cholesterol contact. This study together with our previous work demonstrate that the driving force of cholesterol-phospholipid mixing is a hydrophobic interaction, and multibody interactions dominate others over a wide range of cholesterol concentration.

A Quantitative Evaluation of the Conservation Umbrella of Spotted Owl Management Areas in the Sierra Nevada

PubMed Central

Burnett, Ryan D.; Roberts, L. Jay

2015-01-01

Whether by design or default, single species management often serves as an umbrella for species with similar habitat requirements. In recent decades the focus of National Forest management in the Sierra Nevada of California has shifted towards increasing closed canopy mature forest conditions through the protection of areas occupied by the California Spotted Owl (Strix occidentalis occidentalis). To evaluate the implications of these habitat changes and the potential umbrella resulting from a system of owl reserves on the broader avian community, we estimated occupancy of birds inside and outside of Spotted Owl Home Range Core Areas in northeastern California. We used point count data in a multi-species hierarchical Bayesian model incorporating the detection history of 81 species over a two-year time period (2005-2006). A small set of vegetation cover and topography covariates were included in the model to account for broad differences in habitat conditions, as well as a term identifying whether or not a site was within a Core Area. Seventeen species had a negative Core Area effect, seven had a positive effect, and the rest were not significant. Estimated species richness was significantly different with 23.1 species per 100 m radius circle outside Core Areas and 21.7 inside Core Areas. The majority of the species negatively associated with Core Areas are tied to early successional and other disturbance-dependent habitats. Conservation and climate vulnerability rankings were mixed. On average we found higher scores (greater risk) for the species positively associated with Core Areas, but a larger number of species with the highest scores were negatively associated with Core Areas. We discuss the implications for managing the Sierra Nevada ecosystem and illustrate the role of monitoring broader suites of species in guiding management of large complex ecosystems. PMID:25905920

Gradient-free MCMC methods for dynamic causal modelling

DOE PAGES

Sengupta, Biswa; Friston, Karl J.; Penny, Will D.

2015-03-14

Here, we compare the performance of four gradient-free MCMC samplers (random walk Metropolis sampling, slice-sampling, adaptive MCMC sampling and population-based MCMC sampling with tempering) in terms of the number of independent samples they can produce per unit computational time. For the Bayesian inversion of a single-node neural mass model, both adaptive and population-based samplers are more efficient compared with random walk Metropolis sampler or slice-sampling; yet adaptive MCMC sampling is more promising in terms of compute time. Slice-sampling yields the highest number of independent samples from the target density -- albeit at almost 1000% increase in computational time, in comparisonmore » to the most efficient algorithm (i.e., the adaptive MCMC sampler).« less

Cultural Proficiency. Research Brief

ERIC Educational Resources Information Center

Walker, Karen

2007-01-01

Cultural proficiency and diversity are often used interchangeably, yet there are some distinct differences between them. Cultural proficiency is the umbrella under which diversity falls. According to one source, "Cultural proficiency is a way of being that allows individuals and organizations to interact effectively with people who differ from…

Status Report on Speech Research, 1 January-31 March 1982.

DTIC Science & Technology

1982-03-01

PUMPKIN RHYTHM Nonwords SUBMARINE CONKZMER SURGERY ENGKSTERN THIRD FTERNAPS TOMATO HSPERACH UMBRELLA PGANTERLH VEHICLE PIOTLANING VIDEO PUANT VINEGAR ...and productionI (TABLE 6) data for Catalan subjects with special reference to ferment transions.Ordlnate: F2 ranges (in Hz)abaolsea: PS ranges (in

Statistical controversies in clinical research: basket trials, umbrella trials, and other master protocols: a review and examples

PubMed Central

Renfro, L. A.; Sargent, D. J.

2017-01-01

Abstract In recent years, cancers once viewed as relatively homogeneous in terms of organ location and treatment strategy are now better understood to be increasingly heterogeneous across biomarker and genetically defined patient subgroups. This has produced a shift toward development of biomarker-targeted agents during a time when funding for cancer research has been limited; as a result, the need for improved operational efficiency in studying many agent-and-target combinations in parallel has emerged. Platform trials, basket trials, and umbrella trials are new approaches to clinical research driven by this need for enhanced efficiency in the modern era of increasingly specific cancer subpopulations and decreased resources to study treatments for individual cancer subtypes in a traditional way. In this review, we provide an overview of these new types of clinical trial designs, including discussions of motivation for their use, recommended terminology, examples, and challenges encountered in their application. PMID:28177494

The Continuing Umbrella of Research Experiences (CURE): a model for training underserved scientists in cancer research.

PubMed

Franco, Idalid; Bailey, LeeAnn O; Bakos, Alexis D; Springfield, Sanya A

2011-03-01

Mentoring is a critical aspect of research and training; and the adoption of a successful mentoring model for guiding researchers through the educational pipeline is lacking. The Continuing Umbrella of Research Experiences (CURE) program was established in the Comprehensive Minority Biomedical Branch; which is part of the National Cancer Institute. This program offers unique training and career development opportunities to enhance diversity in cancer research. The CURE initiative focuses on broadening the cadre of underserved investigators engaging in cancer research. CURE begins with high school students and fosters scientific, academic and research excellence throughout the trainee's educational progression. The program supports students throughout the entirety of their training career. During this period, the trainee matures into a competitive early stage investigator; capable of securing advanced research project funding in academic and industry workforces. Thus, the CURE program provides a comprehensive vehicle for training and reinforces the critical mass of underserved investigators conducting cancer research.

Miscibility at the immiscible liquid/liquid interface: A molecular dynamics study of thermodynamics and mechanism

NASA Astrophysics Data System (ADS)

Karnes, John J.; Benjamin, Ilan

2018-01-01

Molecular dynamics simulations are used to study the dissolution of water into an adjacent, immiscible organic liquid phase. Equilibrium thermodynamic and structural properties are calculated during the transfer of water molecule(s) across the interface using umbrella sampling. The net free energy of transfer agrees reasonably well with experimental solubility values. We find that water molecules "prefer" to transfer into the adjacent phase one-at-a-time, without co-transfer of the hydration shell, as in the case of evaporation. To study the dynamics and mechanism of transfer of water to liquid nitrobenzene, we collected over 400 independent dissolution events. Analysis of these trajectories suggests that the transfer of water is facilitated by interfacial protrusions of the water phase into the organic phase, where one water molecule at the tip of the protrusion enters the organic phase by the breakup of a single hydrogen bond.

Early-Aggregation Studies of Polyglutamine in Solution

NASA Astrophysics Data System (ADS)

Fluitt, Aaron; de Pablo, Juan

2012-02-01

Several neurodegenerative diseases, notably Huntington's disease, are associated with certain proteins containing extended polyglutamine tracts. In all polyglutamine diseases, the age of onset is inversely correlated with the length of the polyglutamine domain beyond some pathological threshold. Diseased cells are characterized by intranuclear inclusions rich in aggregated polyglutamine. Experimental evidence suggests that oligomeric aggregate species, not mature amyloid fibrils, are the species most toxic to the cell. Little is known about the structures and aggregation dynamics of polyglutamine oligomers due to their short lifetimes. A better understanding of the pathway through which polyglutamine peptides form oligomeric aggregates will aid the design of therapies to inhibit their toxic activity. In this work, we report structural characterization of polyglutamine monomers and dimers from atomistic molecular dynamics simulations in explicit water. Umbrella sampling simulations reveal that the stability of the dimer species with respect to the disassociated monomers is an increasing function of the chain length.

Removing systematic errors in interionic potentials of mean force computed in molecular simulations using reaction-field-based electrostatics

PubMed Central

Baumketner, Andrij

2009-01-01

The performance of reaction-field methods to treat electrostatic interactions is tested in simulations of ions solvated in water. The potential of mean force between sodium chloride pair of ions and between side chains of lysine and aspartate are computed using umbrella sampling and molecular dynamics simulations. It is found that in comparison with lattice sum calculations, the charge-group-based approaches to reaction-field treatments produce a large error in the association energy of the ions that exhibits strong systematic dependence on the size of the simulation box. The atom-based implementation of the reaction field is seen to (i) improve the overall quality of the potential of mean force and (ii) remove the dependence on the size of the simulation box. It is suggested that the atom-based truncation be used in reaction-field simulations of mixed media. PMID:19292522

Insight into the Mechanism of Hydrolysis of Meropenem by OXA-23 Serine-β-lactamase Gained by Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Sgrignani, Jacopo; Grazioso, Giovanni; De Amici, Marco

2016-09-13

The fast and constant development of drug resistant bacteria represents a serious medical emergency. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this work, we investigated, at the atomistic level, the mechanisms of hydrolysis of Meropenem by OXA-23, a class D β-lactamase, combining unbiased classical molecular dynamics and umbrella sampling simulations with classical force field-based and quantum mechanics/molecular mechanics potentials. Our calculations provide a detailed structural and dynamic picture of the molecular steps leading to the formation of the Meropenem-OXA-23 covalent adduct, the subsequent hydrolysis, and the final release of the inactive antibiotic. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements, validating the expected reaction path.

Accurate rates of the complex mechanisms for growth and dissolu-tion of minerals using a combination of rare event theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stack, Andrew G; Raiten, Paolo; Gale, Julian D.

2012-01-01

Mineral growth and dissolution are often treated as occurring via a single, reversible process that governs the rate of reaction. We show that multiple, distinct intermediate states can occur during both growth and dissolution. Specifically, we have used metadynamics, a method to efficiently explore the free energy landscape of a system, coupled to umbrella sampling and reactive flux calculations, to examine the mechanism and rates of attachment and detachment of a barium ion onto a stepped, barite (BaSO4) surface. The activation energies calculated for the rate limiting reactions, which are different for attachment and detachment, precisely match those measured experimentallymore » during both growth and dissolution. These results can potentially explain anomalous, non-steady state mineral reaction rates observed experimentally, and will enable the design of more efficient growth inhibitors and facilitate an understanding of the effect of impurities.« less

Effect of tension and curvature on the chemical potential of lipids in lipid aggregates.

PubMed

Grafmüller, Andrea; Lipowsky, Reinhard; Knecht, Volker

2013-01-21

Understanding the factors that influence the free energy of lipids in bilayer membranes is an essential step toward understanding exchange processes of lipids between membranes. In general, both lipid composition and membrane geometry can affect lipid exchange rates between bilayer membranes. Here, the free energy change ΔG(des) for the desorption of dipalmitoyl-phosphatidylcholine (DPPC) lipids from different lipid aggregates has been computed using molecular dynamics simulations and umbrella sampling. The value of ΔG(des) is found to depend strongly on the local properties of the aggregate, in that both tension and curvature lead to an increase in ΔG(des). A detailed analysis shows that the increased desorption free energy for tense bilayers arises from the increased conformational entropy of the lipid tails, which reduces the favorable component -TΔS(L) of the desorption free energy.

Gradient-free MCMC methods for dynamic causal modelling.

PubMed

Sengupta, Biswa; Friston, Karl J; Penny, Will D

2015-05-15

In this technical note we compare the performance of four gradient-free MCMC samplers (random walk Metropolis sampling, slice-sampling, adaptive MCMC sampling and population-based MCMC sampling with tempering) in terms of the number of independent samples they can produce per unit computational time. For the Bayesian inversion of a single-node neural mass model, both adaptive and population-based samplers are more efficient compared with random walk Metropolis sampler or slice-sampling; yet adaptive MCMC sampling is more promising in terms of compute time. Slice-sampling yields the highest number of independent samples from the target density - albeit at almost 1000% increase in computational time, in comparison to the most efficient algorithm (i.e., the adaptive MCMC sampler). Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations

NASA Astrophysics Data System (ADS)

Jo, Sunhwan; Jiang, Wei

2015-12-01

Replica Exchange with Solute Tempering (REST2) is a powerful sampling enhancement algorithm of molecular dynamics (MD) in that it needs significantly smaller number of replicas but achieves higher sampling efficiency relative to standard temperature exchange algorithm. In this paper, we extend the applicability of REST2 for quantitative biophysical simulations through a robust and generic implementation in greatly scalable MD software NAMD. The rescaling procedure of force field parameters controlling REST2 "hot region" is implemented into NAMD at the source code level. A user can conveniently select hot region through VMD and write the selection information into a PDB file. The rescaling keyword/parameter is written in NAMD Tcl script interface that enables an on-the-fly simulation parameter change. Our implementation of REST2 is within communication-enabled Tcl script built on top of Charm++, thus communication overhead of an exchange attempt is vanishingly small. Such a generic implementation facilitates seamless cooperation between REST2 and other modules of NAMD to provide enhanced sampling for complex biomolecular simulations. Three challenging applications including native REST2 simulation for peptide folding-unfolding transition, free energy perturbation/REST2 for absolute binding affinity of protein-ligand complex and umbrella sampling/REST2 Hamiltonian exchange for free energy landscape calculation were carried out on IBM Blue Gene/Q supercomputer to demonstrate efficacy of REST2 based on the present implementation.

Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics.

PubMed

Alibay, Irfan; Burusco, Kepa K; Bruce, Neil J; Bryce, Richard A

2018-03-08

Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free-energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling, and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 μs trajectories; these simulations find a predominance of closed conformer and a range of low-occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the 4 C 1 form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 μs unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.

Mission of PROCINORTE'S Tropical and Subtropical Fruit Task Force

USDA-ARS?s Scientific Manuscript database

Canada, Mexico and United States are countries that share many interests in agricultural affairs. The three countries have been commercial partners for many years, and most recently they have been working under the North American Free Trade Agreement (NAFTA) umbrella. The three countries are natura...

Critiquing Whole Language and Classroom Inquiry. WLU Series.

ERIC Educational Resources Information Center

Boran, Sibel, Ed.; Comber, Barbara, Ed.

This book, part of the Whole Language Umbrella Series, offers a critical reexamination of "inquiry" and "whole language" as tools for rethinking literacy, schooling, and humanistic citizenship in the complexities of today's multicultural world. The essays in the book explore the political implications of literacy theories and…

Development of a decision model for selection of appropriate timely delivery techniques for highway projects : final report, April 2009.

DOT National Transportation Integrated Search

2009-04-01

The primary umbrella method used by the Oregon Department of Transportation (ODOT) to ensure on-time performance in standard construction contracting is liquidated damages. The assessment value is usually a matter of some judgment. In practice,...

Under the Nuclear Umbrella.

ERIC Educational Resources Information Center

Williams, Leon F.

1987-01-01

Entertains the thesis that social work has a stake in the technological-humanistic debate and should greet the recent and spectacular technological failures with protest and alarm. Discusses relationship of nuclear issue and social work, effects of nuclear issue on children, and Chernobyl. Advocates pacifism, activism, and a coherent conception of…

"Supra-Institutional Research": A Cost-Effective Contribution towards Enhancement

ERIC Educational Resources Information Center

Yorke, Mantz

2010-01-01

Relatively inexpensive studies that go beyond the boundaries of individual institutions have considerable attraction, particularly at a time when resources are under significant constraint. These studies can be viewed as existing under the rather larger umbrella of "supra-institutional research". Three examples illustrate the argument…

A 10-year ecosystem restoration community of practice tracks large-scale restoration trends

EPA Science Inventory

In 2004, a group of large-scale ecosystem restoration practitioners across the United States convened to start the process of sharing restoration science, management, and best practices under the auspices of a traditional conference umbrella. This forum allowed scientists and dec...

Try This: Umbrella--Materials Testing

ERIC Educational Resources Information Center

Preston, Christine

2016-01-01

This article is the second in "Teaching Science's" "Try This" series. These hands-on activities are designed especially for early childhood students to encourage their natural curiosity and promote development of scientific thinking. In this activity, the problem-based learning approach means that the children are engaged in a…

Mission of PROCINORTE’s Tropical and Subtropical Fruit Taskforce

USDA-ARS?s Scientific Manuscript database

Canada, Mexico and United States are countries that share many interests in agricultural affairs. The three countries have been commercial partners for many years, and most recently they have been working under the North American Free Trade Agreement (NAFTA) umbrella. The three countries are natural...

Counseling in Brazil: Past, Present, and Future

ERIC Educational Resources Information Center

Hutz-Midgett, Aida; Hutz, Claudio Simon

2012-01-01

This article describes counseling in Brazil, which is rooted in career and vocational guidance. Although considered a distinct discipline, counseling falls under the umbrella of psychology. The multicultural movement is gaining momentum in Brazil, and counselors are pioneers working with socioracial minority college students. This is an emerging…

78 FR 14554 - Agency Forms Undergoing Paperwork Reduction Act Review

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-06

... Project Formative Research for the Development of CDC's Act Against AIDS Social Marketing Campaigns... period to develop various social marketing campaigns aimed at increasing HIV testing rates, increasing... social marketing campaigns under the umbrella of the larger Act Against AIDS campaign. The campaigns will...

Structure, Agency, Complexity Theory and Interdisciplinary Research in Education Studies

ERIC Educational Resources Information Center

Smith, John A.

2013-01-01

This article argues that Education Studies needs to develop its existing interdisciplinarity understanding of structures and agencies by giving greater attention to the modern process theories of self-organisation in the physical, biological, psychological and social sciences, sometimes given the umbrella term "complexity theory". The…

An Umbrella for Acid Rain.

ERIC Educational Resources Information Center

Randal, Judith

1979-01-01

The Environmental Protection Agency has awarded several grants to study effects of and possible solutions to the problem of "acid rain"; pollution from atmospheric nitric and sulfuric acids. The research program is administered through North Carolina State University at Raleigh and will focus on biological effects of acid rain. (JMF)

Transgender Youth

ERIC Educational Resources Information Center

Ludeke, Micah

2009-01-01

"Transgender" is an umbrella term for people who self-identify as other than their birth sex (male or female). The exploration of gender nonconformance occurs among people across all ethnic, racial, and socioeconomic groups. Transgender or questioning students may have unique challenges and stressors in their daily lives, including school. Often,…

Virtual Beach: Decision Support Tools for Beach Pathogen Prediction

EPA Science Inventory

The Virtual Beach Managers Tool (VB) is decision-making software developed to help local beach managers make decisions as to when beaches should be closed due to predicted high levels of water borne pathogens. The tool is being developed under the umbrella of EPA's Advanced Monit...

Connect Computer Education to Policies.

ERIC Educational Resources Information Center

Kimmelman, Paul

1985-01-01

The computer phenomenon has made rapid inroads into school curricula, often without proper board guidance or approval. Accordingly, this pamphlet discusses why and how computer education should be provided in schools and sets forth guidelines for school board policy regarding computers. An umbrella policy is proposed, defining "computer literacy"…

Program Spotlight: CRCHD Mock Grant Review

Cancer.gov

The NCI Center to Reduce Cancer Health Disparities (CRCHD) held a Professional Development Workshop for its Continuing Umbrella of Research Experience (CURE) scholars on June 23-24, 2014, in Rockville, Maryland. As part of the workshop, attendees had an opportunity to observe and participate in a Mock Grant Review.

BVDV: Detection, Risk Management and Control

USDA-ARS?s Scientific Manuscript database

The terms bovine viral diarrhea (BVD) and bovine viral diarrhea viruses (BVDV) are difficult to define in simple straightforward statements because both are umbrella terms covering a wide range of observations and entities. While diarrhea is in the name, BVD, it is used in reference to a number of ...

Career Adapt-Abilities Scale in a French-Speaking Swiss Sample: Psychometric Properties and Relationships to Personality and Work Engagement

ERIC Educational Resources Information Center

Rossier, Jerome; Zecca, Gregory; Stauffer, Sarah D.; Maggiori, Christian; Dauwalder, Jean-Pierre

2012-01-01

The aim of this study was to analyze the psychometric properties of the Career Adapt-Abilities Scale (CAAS) in a French-speaking Swiss sample and its relationship with personality dimensions and work engagement. The heterogeneous sample of 391 participants (M[subscript age] = 39.59, SD = 12.30) completed the CAAS-International and a short version…

Adaptive web sampling.

PubMed

Thompson, Steven K

2006-12-01

A flexible class of adaptive sampling designs is introduced for sampling in network and spatial settings. In the designs, selections are made sequentially with a mixture distribution based on an active set that changes as the sampling progresses, using network or spatial relationships as well as sample values. The new designs have certain advantages compared with previously existing adaptive and link-tracing designs, including control over sample sizes and of the proportion of effort allocated to adaptive selections. Efficient inference involves averaging over sample paths consistent with the minimal sufficient statistic. A Markov chain resampling method makes the inference computationally feasible. The designs are evaluated in network and spatial settings using two empirical populations: a hidden human population at high risk for HIV/AIDS and an unevenly distributed bird population.

Developmental Coordination Disorder, An Umbrella Term for Motor Impairments in Children: Nature and Co-Morbid Disorders

PubMed Central

Vaivre-Douret, Laurence; Lalanne, Christophe; Golse, Bernard

2016-01-01

Background: Developmental Coordination Disorder (DCD) defines a heterogeneous class of children exhibiting marked impairment in motor coordination as a general group of deficits in fine and gross motricity (subtype mixed group) common to all research studies, and with a variety of other motor disorders that have been little investigated. No consensus about symptoms and etiology has been established. Methods: Data from 58 children aged 6 to 13 years with DCD were collected on DSM-IV criteria, similar to DSM-5 criteria. They had no other medical condition and inclusion criteria were strict (born full-term, no medication, no occupational/physical therapy). Multivariate statistical methods were used to evidence relevant interactions between discriminant features in a general DCD subtype group and to highlight specific co-morbidities. The study examined age-calibrated standardized scores from completed assessments of psychological, neuropsychological, and neuropsychomotor functions, and more specifically the presence of minor neurological dysfunctions (MND) including neurological soft signs (NSS), without evidence of focal neurological brain involvement. These were not considered in most previous studies. Results: Findings show the salient DCD markers for the mixed subtype (imitation of gestures, digital perception, digital praxia, manual dexterity, upper, and lower limb coordination), vs. surprising co-morbidities, with 33% of MND with mild spasticity from phasic stretch reflex (PSR), not associated with the above impairments but rather with sitting tone (p = 0.004) and dysdiadochokinesia (p = 0.011). PSR was not specific to a DCD subtype but was related to increased impairment of coordination between upper and lower limbs and manual dexterity. Our results highlight the major contribution of an extensive neuro-developmental assessment (mental and physical). Discussion: The present study provides important new evidence in favor of a complete physical neuropsychomotor assessment, including neuromuscular tone examination, using appropriate standardized neurodevelopmental tools (common tasks across ages with age-related normative data) in order to distinguish motor impairments gathered under the umbrella term of developmental coordination disorders (subcortical vs. cortical). Mild spasticity in the gastrocnemius muscles, such as phasic stretch reflex (PSR), suggests disturbances of the motor pathway, increasing impairment of gross and fine motricity. These findings contribute to understanding the nature of motor disorders in DCD by taking account of possible co-morbidities (corticospinal tract disturbances) to improve diagnosis and adapt treatment programmes in clinical practice. PMID:27148114

Adaptive Oceanographic Sampling in a Coastal Environment Using Autonomous Gliding Vehicles

DTIC Science & Technology

2003-08-01

cost autonomous vehicles with near-global range and modular sensor payload. Particular emphasis is placed on the development of adaptive sampling...environment. Secondary objectives include continued development of adaptive sampling strategies suitable for large fleets of slow-moving autonomous ... vehicles , and development and implementation of new oceanographic sensors and sampling methodologies. The main task completed was a complete redesign of

Digital Video and Writing with Priority Learners

ERIC Educational Resources Information Center

Diglin, Peter

2016-01-01

Digital technology has become more ubiquitous in classrooms across the western world. Literacy learning is topical in New Zealand education under the umbrella of the current National Standards policy, a policy introduced on the basis of rhetoric around improving achievement for priority learners. The study presented in this paper would then appear…

Endowment Investing: Time for a Sustainability Play?

ERIC Educational Resources Information Center

Pelletier, Stephen G.

2010-01-01

Managers of university endowment funds are paying closer attention to investing in "green" industries, commonly bundled under the umbrella "cleantech." Cleantech offers the possibility of buying in while prices are low "and" making a "green" investment play, but it also harbors the risks inherent in any emerging industry. Cleantech has varying…

Perspectives Regarding Classroom Management Style: Differences between Elementary and Secondary Level Teachers.

ERIC Educational Resources Information Center

Martin, Nancy K.; Baldwin, Beatrice

This study represents a continuation of research efforts to further refine the Inventory of Classroom Management Style, an instrument designed to measure teachers' perceptions of their classroom management beliefs and practices. "Classroom management" is an umbrella term describing teacher efforts to oversee a multitude of activities in…

The Changing Atmosphere: UNEP Environment Brief No. 1.

ERIC Educational Resources Information Center

United Nations Environment Programme, Nairobi (Kenya).

Discussed are the following topics: (1) the greenhouse problem, including the processes involved and some possible resulting scenarios; (2) ozone, the "umbrella" protecting the earth from lethal concentrations of ultraviolet rays and the problem of decreasing ozone levels; (3) what could happen as the earth gets warmer (including…

CLIL Implementation: From Policy-Makers to Individual Initiatives

ERIC Educational Resources Information Center

de Zarobe, Yolanda Ruiz

2013-01-01

Since Do Coyle and Hugo Baetens Beardsmore published their Special Issue on "Research on Content and Language Integrated Learning (CLIL)" in the "International Journal of Bilingual Education and Bilingualism" in 2007, there has been a great deal of interest and debate about the approach, which under the umbrella term of Content…

The Reactivation of the Western European Union

DTIC Science & Technology

1989-06-02

position under the US nuclear umbrella. Meanwhile, it seeks to conserve its 14 David Kramer and Glenn Yago , ŕ West Germany Contends with the Alliance...Kramer and Glenn Yago , "West Germany Contends with the Alliance Crisis": p. 133. 64 RELEVANT ACTORS ECONOMY. Figure 4 compares the GDPs of the WEU

A Collaborative Group Method of Inclusive Research

ERIC Educational Resources Information Center

Bigby, Christine; Frawley, Patsie; Ramcharan, Paul

2014-01-01

Background: Funding bodies in Australia and the United Kingdom require research on issues that affect the lives of people with intellectual disability to be inclusive. Debate continues about the nature and benefits of inclusive research, which has become an umbrella term encompassing a broad spectrum of approaches. Method: This study proposes one…

Service, Sex Work, and the Profession

ERIC Educational Resources Information Center

Potts, Donna L.

2012-01-01

The author serves as the chair of the American Association of University Professors' (AAUP) Assembly of State Conferences, the umbrella organization for individual state AAUP conferences; a moderator for Pandora's Project, a website for survivors of sexual abuse and assault; a volunteer for Veronica's Voice, a support program for women and girls…

Current uses of 2.0 applications in transportation : case studies of select state departments of transportation.

DOT National Transportation Integrated Search

2010-03-01

Web 2.0 is an umbrella term for websites or online applications that are user-driven and emphasize collaboration and user interactivity. The trend away from static web pages to a more user-driven Internet model has also occurred in the public s...

Students' Development of Representational Competence through the Sense of Touch

ERIC Educational Resources Information Center

Magana, Alejandra J.; Balachandran, Sadhana

2017-01-01

Electromagnetism is an umbrella encapsulating several different concepts like electric current, electric fields and forces, and magnetic fields and forces, among other topics. However, a number of studies in the past have highlighted the poor conceptual understanding of electromagnetism concepts by students even after instruction. This study aims…

30 CFR Appendix to Part 553 - List of U.S. Geological Survey Topographic Maps

Code of Federal Regulations, 2013 CFR

2013-07-01

...; Three Mile Bay; Tigre Lagoon; Timbalier Island; Triumph; Venice; Weeks; West of Johnson Bayou; Western... Islands; Tivoli SE; Turtle Bay; Umbrella Point; Virginia Point; West of Johnson Bayou; Whites Ranch...; Hollingers Island; Isle Aux Herbes; Kreole; Lillian; Little Dauphin Island; Little Point Clear; Magnolia...

30 CFR Appendix to Part 553 - List of U.S. Geological Survey Topographic Maps

Code of Federal Regulations, 2012 CFR

2012-07-01

...; Three Mile Bay; Tigre Lagoon; Timbalier Island; Triumph; Venice; Weeks; West of Johnson Bayou; Western... Islands; Tivoli SE; Turtle Bay; Umbrella Point; Virginia Point; West of Johnson Bayou; Whites Ranch...; Hollingers Island; Isle Aux Herbes; Kreole; Lillian; Little Dauphin Island; Little Point Clear; Magnolia...

30 CFR Appendix to Part 553 - List of U.S. Geological Survey Topographic Maps

Code of Federal Regulations, 2014 CFR

2014-07-01

...; Three Mile Bay; Tigre Lagoon; Timbalier Island; Triumph; Venice; Weeks; West of Johnson Bayou; Western... Islands; Tivoli SE; Turtle Bay; Umbrella Point; Virginia Point; West of Johnson Bayou; Whites Ranch...; Hollingers Island; Isle Aux Herbes; Kreole; Lillian; Little Dauphin Island; Little Point Clear; Magnolia...

The New School Collaborates: Organization and Communication in Immersive International Field Programs with Artisan Communities

ERIC Educational Resources Information Center

Lawson, Cynthia

2010-01-01

Under the umbrella terms of "humanitarian design," "social design" and "social responsibility," educational institutions and specifically design programs are more and more searching for opportunities to engage their students in critical and hands-on learning via collaborations between students, faculty, communities in…

Systematic Thinking on Dialogical Education

ERIC Educational Resources Information Center

Sarid, Ariel

2012-01-01

Dialogic or dialogical education is an umbrella term that encompasses a myriad of different and at times conflicting approaches. As there is no agreed-upon definition of "dialogue" (not that there is or should be one unified definition), and even fewer clear and systematic guidelines for application, researchers and practitioners in the DE field…

Everything Is Connected: Giftedness within a Broad Framework for Cognition

ERIC Educational Resources Information Center

Woolcott, Geoff

2012-01-01

Ziegler and Phillipson (Z&P) have provided a valuable discussion of the identification and development of giftedness under a systemic umbrella, including issues of differing theoretical approaches and efficacy. This commentary considers their discussion within a novel systemic framework that links also individuals and environment, but in terms of…

Understanding Horizontal Governance. Research Brief

ERIC Educational Resources Information Center

Ferguson, Daniel

2009-01-01

Horizontal governance is an umbrella term that covers a range of approaches to policy development, service delivery issues, and management practices. A horizontal initiative may take place across levels of government, across boundaries between units of a single department or agency or among multiple departments or agencies, or across public,…

A Ghetto Land Pedagogy: An Antidote for Settler Environmentalism

ERIC Educational Resources Information Center

Paperson, La

2014-01-01

A ghetto land pedagogy begins with two axioms that align it with land education more broadly, and that distinguish it from the general umbrella of environmental education. First, ghetto colonialism is a specialization of settler colonialism. Second, land justice requires decolonization, not just environmental justice. A ghetto land pedagogy thus…

Urban Education: A Model for Leadership and Policy

ERIC Educational Resources Information Center

Gallagher, Karen Symms, Ed.; Goodyear, Rodney, Ed.; Brewer, Dominic, Ed.; Rueda, Robert, Ed.

2011-01-01

Many factors complicate the education of urban students. Among them have been issues related to population density; racial, ethnic, cultural, and linguistic diversity; poverty; racism (individual and institutional); and funding levels. Although urban educators have been addressing these issues for decades, placing them under the umbrella of "urban…

Improving Girls' Education in Guatemala. Impact Evaluation.

ERIC Educational Resources Information Center

Agency for International Development (IDCA), Washington, DC. Center for Development Information and Evaluation.

In Guatemala, many girls attend no school. A project by the United States Agency for International Development (USAID), Basic Education Strengthening (BEST), demonstrated that improving educational quality is the best approach to enhancing girls' participation. BEST included a Girls Education Program (GEP) activity. Under the BEST/GEP umbrella,…

A Multidimensional Needs Assessment of Social Emotional Learning Skill Areas

ERIC Educational Resources Information Center

Yopp, Ashley; McKim, Billy R.; Moore, Lori L.; Odom, Summer F.; Hanagriff, Roger

2017-01-01

Social and Emotional Learning (SEL) has often been an umbrella term for a wide range of competencies, including emotional processes, social and interpersonal skills, and cognitive regulation (Jones, Bouffard, & Weissbourd, 2013). We used the Borich (1980) needs assessment model to assess the professional development needs of Texas agricultural…

Analyzing Sustainability Themes in State Science Standards: Two Case Studies

ERIC Educational Resources Information Center

Miller, Hannah K.; Jones, Linda Cronin

2014-01-01

Due to the interdisciplinary nature of environmental education, addressing the range of socioscientific issues included under the umbrella of sustainability can be challenging for educators working within the context of mandated state subject area standards. Two states (Washington and Vermont) have been recognized as leaders in incorporating…

Developing Psychological Literacy: Is There a Role for Reflective Practice?

ERIC Educational Resources Information Center

Coulson, Debra; Homewood, Judi

2016-01-01

Psychological literacy is an umbrella term that is widely used to describe the attributes or capabilities of psychology graduate (Cranney & Dunn 2011). This article explores some of the complexities inherent in the learning and teaching of psychological literacy by exploring challenges to the development of self-awareness and cultural…

LIFE CYCLE IMPACT ASSESSMENT WORKSHOP SUMMARY - MIDPOINTS VERSUS ENDPOINTS: THE SACRIFICES AND BENEFITS

EPA Science Inventory

On 5/25-26/2000 in Brighton, England, the third international workshop was held under the umbrella of UNEP addressing issues in Life Cycle Impact Assessment (LCIA). The workshop provided a forum for experts to discuss midpoint vs. endpoint modeling. Midpoints are considered to be...

Distance Education for Technology Teachers

ERIC Educational Resources Information Center

Williams, P. John

2004-01-01

A typical definition of distance education is the delivery of instruction in a format that separates the teacher and learner, often both in time and space. It tends to be an umbrella term that may encompass more specific forms of education such as distributed learning, independent study, correspondence education, satellite education, etc. This…

BRIDGES: Connecting with Families to Facilitate and Enhance Involvement

ERIC Educational Resources Information Center

Sawyer, Mary

2015-01-01

"Parent involvement" is an umbrella term for activities characterized by varying levels of frequency, response effort, and types of settings in which they occur. Parent involvement in a child's education can occur in a variety of school-related contexts, including helping with homework and supporting academic development at home. It…

Enhancement of gold recovery using bioleaching from gold concentrate

NASA Astrophysics Data System (ADS)

Choi, S. H.; Cho, K. H.; Kim, B. J.; Choi, N. C.; Park, C. Y.

2012-04-01

The gold in refractory ores is encapsulated as fine particles (sometimes at a molecular level) in the crystal structure of the sulfide (typically pyrite with or without arsenopyrite) matrix. This makes it impossible to extract a significant amount of refractory gold by cyanidation since the cyanide solution cannot penetrate the pyrite/arsenopyrite crystals and dissolve gold particles, even after fine grinding. To effectively extract gold from these ores, an oxidative pretreatment is necessary to break down the sulfide matrix. The most popular methods of pretreatment include nitric acid oxidation, roasting, pressure oxidation and biological oxidation by microorganisms. This study investigated the bioleaching efficiency of Au concentrate under batch experimental conditions (adaptation cycles and chemical composition adaptation) using the indigenous acidophilic bacteria collected from gold mine leachate in Sunsin gold mine, Korea. We conducted the batch experiments at two different chemical composition (CuSO4 and ZnSO4), two different adaptation cycles 1'st (3 weeks) and 2'nd (6 weeks). The results showed that the pH in the bacteria inoculating sample decreased than initial condition and Eh increased. In the chemical composition adaptation case, the leached accumulation content of Fe and Pb was exhibited in CuSO4 adaptation bacteria sample more than in ZnSO4 adaptation bacteria samples, possibly due to pre-adaptation effect on chalcopyrite (CuFeS2) in gold concentrate. And after 21 days on the CuSO4 adaptation cycles case, content of Fe and Pb was appeared at 1'st adaptation bacteria sample(Fe - 1.82 and Pb - 25.81 times per control sample) lower than at 2'nd adaptation bacteria sample(Fe - 2.87 and Pb - 62.05 times per control sample). This study indicates that adaptation chemical composition and adaptation cycles can play an important role in bioleaching of gold concentrate in eco-/economic metallurgy process.

Adaptive Learning and Risk Taking

ERIC Educational Resources Information Center

Denrell, Jerker

2007-01-01

Humans and animals learn from experience by reducing the probability of sampling alternatives with poor past outcomes. Using simulations, J. G. March (1996) illustrated how such adaptive sampling could lead to risk-averse as well as risk-seeking behavior. In this article, the author develops a formal theory of how adaptive sampling influences risk…

A Structure-Adaptive Hybrid RBF-BP Classifier with an Optimized Learning Strategy

PubMed Central

Wen, Hui; Xie, Weixin; Pei, Jihong

2016-01-01

This paper presents a structure-adaptive hybrid RBF-BP (SAHRBF-BP) classifier with an optimized learning strategy. SAHRBF-BP is composed of a structure-adaptive RBF network and a BP network of cascade, where the number of RBF hidden nodes is adjusted adaptively according to the distribution of sample space, the adaptive RBF network is used for nonlinear kernel mapping and the BP network is used for nonlinear classification. The optimized learning strategy is as follows: firstly, a potential function is introduced into training sample space to adaptively determine the number of initial RBF hidden nodes and node parameters, and a form of heterogeneous samples repulsive force is designed to further optimize each generated RBF hidden node parameters, the optimized structure-adaptive RBF network is used for adaptively nonlinear mapping the sample space; then, according to the number of adaptively generated RBF hidden nodes, the number of subsequent BP input nodes can be determined, and the overall SAHRBF-BP classifier is built up; finally, different training sample sets are used to train the BP network parameters in SAHRBF-BP. Compared with other algorithms applied to different data sets, experiments show the superiority of SAHRBF-BP. Especially on most low dimensional and large number of data sets, the classification performance of SAHRBF-BP outperforms other training SLFNs algorithms. PMID:27792737

Evaluating sampling designs by computer simulation: A case study with the Missouri bladderpod

USGS Publications Warehouse

Morrison, L.W.; Smith, D.R.; Young, C.; Nichols, D.W.

2008-01-01

To effectively manage rare populations, accurate monitoring data are critical. Yet many monitoring programs are initiated without careful consideration of whether chosen sampling designs will provide accurate estimates of population parameters. Obtaining accurate estimates is especially difficult when natural variability is high, or limited budgets determine that only a small fraction of the population can be sampled. The Missouri bladderpod, Lesquerella filiformis Rollins, is a federally threatened winter annual that has an aggregated distribution pattern and exhibits dramatic interannual population fluctuations. Using the simulation program SAMPLE, we evaluated five candidate sampling designs appropriate for rare populations, based on 4 years of field data: (1) simple random sampling, (2) adaptive simple random sampling, (3) grid-based systematic sampling, (4) adaptive grid-based systematic sampling, and (5) GIS-based adaptive sampling. We compared the designs based on the precision of density estimates for fixed sample size, cost, and distance traveled. Sampling fraction and cost were the most important factors determining precision of density estimates, and relative design performance changed across the range of sampling fractions. Adaptive designs did not provide uniformly more precise estimates than conventional designs, in part because the spatial distribution of L. filiformis was relatively widespread within the study site. Adaptive designs tended to perform better as sampling fraction increased and when sampling costs, particularly distance traveled, were taken into account. The rate that units occupied by L. filiformis were encountered was higher for adaptive than for conventional designs. Overall, grid-based systematic designs were more efficient and practically implemented than the others. ?? 2008 The Society of Population Ecology and Springer.

Lateral Coherence and Mixing in the Coastal Ocean: Adaptive Sampling using Gliders

DTIC Science & Technology

2012-09-30

Adaptive Sampling using Gliders R. Kipp Shearman Jonathan D. Nash James N. Moum John A. Barth College of Oceanic & Atmospheric Sciences Oregon State...persistent on O (3 day) timescales, so are ideally suited to be adaptively sampled by autonomous gliders that actively report both turbulent and...plan to deploy 4 AUV gliders to perform intensive, adaptive surveys. Newly-enhanced to measure turbulent mixing, water-column currents and dye

Lateral Coherence and Mixing in the Coastal Ocean: Adaptive Sampling using Gliders

DTIC Science & Technology

2011-09-30

Coherence and Mixing in the Coastal Ocean: Adaptive Sampling using Gliders R. Kipp Shearman Jonathan D. Nash James N. Moum John A. Barth College of...These structures evolve yet are often persistent on O (3 day) timescales, so are ideally suited to be adaptively sampled by autonomous gliders that...processes driving lateral dispersion, we plan to deploy 4 AUV gliders to perform intensive, adaptive surveys. Newly-enhanced to measure turbulent mixing

Two-stage sequential sampling: A neighborhood-free adaptive sampling procedure

USGS Publications Warehouse

Salehi, M.; Smith, D.R.

2005-01-01

Designing an efficient sampling scheme for a rare and clustered population is a challenging area of research. Adaptive cluster sampling, which has been shown to be viable for such a population, is based on sampling a neighborhood of units around a unit that meets a specified condition. However, the edge units produced by sampling neighborhoods have proven to limit the efficiency and applicability of adaptive cluster sampling. We propose a sampling design that is adaptive in the sense that the final sample depends on observed values, but it avoids the use of neighborhoods and the sampling of edge units. Unbiased estimators of population total and its variance are derived using Murthy's estimator. The modified two-stage sampling design is easy to implement and can be applied to a wider range of populations than adaptive cluster sampling. We evaluate the proposed sampling design by simulating sampling of two real biological populations and an artificial population for which the variable of interest took the value either 0 or 1 (e.g., indicating presence and absence of a rare event). We show that the proposed sampling design is more efficient than conventional sampling in nearly all cases. The approach used to derive estimators (Murthy's estimator) opens the door for unbiased estimators to be found for similar sequential sampling designs. ?? 2005 American Statistical Association and the International Biometric Society.

Seafloor Science and Remotely Operated Vehicle (SSROV) Day Camp: A Week-Long, Hands-On STEM Summer Camp

NASA Astrophysics Data System (ADS)

Wheat, C. G.; Fournier, T.; Monahan, K.; Paul, C.

2015-12-01

RETINA (Robotic Exploration Technologies IN Astrobiology) has developed a program geared towards stimulating our youth with innovative and relevant hands-on learning modules under a STEM umbrella. Given the breadth of potential science and engineering topics that excite children, the RETINA Program focuses on interactive participation in the design and development of simple robotic and sensor systems, providing a range of challenges to engage students through project-based learning (PBL). Thus, young students experience scientific discovery through the use and understanding of technology. This groundwork serves as the foundation for SSROV Camp, a week-long, summer day camp for 6th-8th grade students. The camp is centered on the sensors and platforms that guide seafloor exploration and discovery and builds upon the notion that transformative discoveries in the deep sea result from either sampling new environments or making new measurements with sensors adapted to this extreme environment. These technical and scientific needs are folded into the curriculum. Each of the first four days of the camp includes four team-based, hands-on technical challenges, communication among peer groups, and competition. The fifth day includes additional activities, culminating in camper-led presentations to describe a planned mission based on a given geologic setting. Presentations include hypotheses, operational requirements and expected data products. SSROV Camp was initiated last summer for three sessions, two in Monterey, CA and one in Oxford, MS. Campers from both regions grasped key elements of the program, based on written responses to questions before and after the camp. On average, 32% of the pre-test questions were answered correctly compared with 80% of the post-test questions. Additional confirmation of gains in campers' knowledge, skills, and critical thinking on environmental issues and engineering problems were apparent during the "jeopardy" competition, nightly homework, and mission presentations. On the basis of this successful effort, we hope to expand to other towns.

Engineering antimicrobial peptides with improved antimicrobial and hemolytic activities.

PubMed

Zhao, Jun; Zhao, Chao; Liang, Guizhao; Zhang, Mingzhen; Zheng, Jie

2013-12-23

The rapid rise of antibiotic resistance in pathogens becomes a serious and growing threat to medicine and public health. Naturally occurring antimicrobial peptides (AMPs) are an important line of defense in the immune system against invading bacteria and microbial infection. In this work, we present a combined computational and experimental study of the biological activity and membrane interaction of the computationally designed Bac2A-based peptide library. We used the MARTINI coarse-grained molecular dynamics with adaptive biasing force method and the umbrella sampling technique to investigate the translocation of a total of 91 peptides with different amino acid substitutions through a mixed anionic POPE/POPG (3:1) bilayer and a neutral POPC bilayer, which mimic the bacterial inner membrane and the human red blood cell (hRBC) membrane, respectively. Potential of mean force (PMF, free energy profile) was obtained to measure the free energy barrier required to transfer the peptides from the bulk water phase to the water-membrane interface and to the bilayer interior. Different PMF profiles can indeed identify different membrane insertion scenarios by mapping out peptide-lipid energy landscapes, which are correlated with antimicrobial activity and hemolytic activity. Computationally designed peptides were further tested experimentally for their antimicrobial and hemolytic activities using bacteria growth inhibition assay and hemolysis assay. Comparison of PMF data with cell assay results reveals a good correlation of the peptides between predictive transmembrane activity and antimicrobial/hemolytic activity. Moreover, the most active mutants with the balanced substitutions of positively charged Arg and hydrophobic Trp residues at specific positions were discovered to achieve the improved antimicrobial activity while minimizing red blood cell lysis. Such substitutions provide more effective and cooperative interactions to distinguish the peptide interaction with different lipid bilayers. This work provides a useful computational tool to better understand the mechanism and energetics of membrane insertion of AMPs and to rationally design more effective AMPs.

Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation.

PubMed

Shore, Sabrina; Henderson, Jordana M; Lebedev, Alexandre; Salcedo, Michelle P; Zon, Gerald; McCaffrey, Anton P; Paul, Natasha; Hogrefe, Richard I

2016-01-01

For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.

Solvent, Temperature And Concentration Effects on the Optical Activity of Chiral FIVE-And-SIX Membered Ring Ketones Conformers

NASA Astrophysics Data System (ADS)

Al-Basheer, Watheq

2017-06-01

Chiral five-and-six membered ring ketones are important molecules that are found in many biological systems and can exist in many possible conformers. In this talk, experimental and computational investigation of solvent, temperature and concentration effects on the circular dichroism (CD) and optical rotation (OR) of (R)-3 -methylcyclohexanone (R3MCH), (R)-3-methylcyclopentanone (R3MCP) and carvone conformers will be discussed. CD and OR measurements of these ketones gaseous samples and in ten common solvents of wide polarity range for different concentrations and sample temperatures were recorded and related to molecular conformation. Density functional theoretical calculations were performed using Gaussian09 at B3LYP functions with aug-cc-pVDZ level of theory. Also, CD and OR spectra for the optimized geometries of the ketones dominant conformers were computed over the ultraviolet and visible region in the gas phase as well as in ten solvents of varying polarity range, and under the umbrella of the polarizable continuum model (PCM). By comparing theoretical and experimental results, few thermodynamic parameters were deduced for the individual equatorial and axial conformers of each molecule in gas phase and in solvation.

Free energy barriers to evaporation of water in hydrophobic confinement.

PubMed

Sharma, Sumit; Debenedetti, Pablo G

2012-11-08

We use umbrella sampling Monte Carlo and forward and reverse forward flux sampling (FFS) simulation techniques to compute the free energy barriers to evaporation of water confined between two hydrophobic surfaces separated by nanoscopic gaps, as a function of the gap width, at 1 bar and 298 K. The evaporation mechanism for small (1 × 1 nm(2)) surfaces is found to be fundamentally different from that for large (3 × 3 nm(2)) surfaces. In the latter case, the evaporation proceeds via the formation of a gap-spanning tubular cavity. The 1 × 1 nm(2) surfaces, in contrast, are too small to accommodate a stable vapor cavity. Accordingly, the associated free energy barriers correspond to the formation of a critical-sized cavity for sufficiently large confining surfaces, and to complete emptying of the gap region for small confining surfaces. The free energy barriers to evaporation were found to be of O(20kT) for 14 Å gaps, and to increase by approximately ~5kT with every 1 Å increase in the gap width. The entropy contribution to the free energy of evaporation was found to be independent of the gap width.

Systems and methods for self-synchronized digital sampling

NASA Technical Reports Server (NTRS)

Samson, Jr., John R. (Inventor)

2008-01-01

Systems and methods for self-synchronized data sampling are provided. In one embodiment, a system for capturing synchronous data samples is provided. The system includes an analog to digital converter adapted to capture signals from one or more sensors and convert the signals into a stream of digital data samples at a sampling frequency determined by a sampling control signal; and a synchronizer coupled to the analog to digital converter and adapted to receive a rotational frequency signal from a rotating machine, wherein the synchronizer is further adapted to generate the sampling control signal, and wherein the sampling control signal is based on the rotational frequency signal.

Educating Professional Musicians: Lessons Learned from School Music

ERIC Educational Resources Information Center

Carruthers, Glen

2008-01-01

Music in Canadian schools at one time focused on skills development. Building on talent, aptitude, prior learning and physical coordination, students would become better at singing or playing an instrument by studying it at school. Over time, new approaches to music teaching and learning opened the umbrella to a more comprehensive range of…

Identifying Risk and Promoting Resilience in Infants and Toddlers with Fetal Alcohol Spectrum Disorders

ERIC Educational Resources Information Center

Shah, Prachi; Milgrom, Tedi; Munzer, Tiffany; Hoyme, H. Eugene

2015-01-01

Fetal alcohol spectrum disorders (FASDs) is an umbrella term that describes a variety of conditions characterized by a pattern of atypical facial features, growth restriction, structural physical abnormalities, and brain dysfunction resulting from prenatal alcohol exposure. Studies suggest that the prevalence of FASDs ranges between 2-5% (of the…

Should I Pack My Umbrella? Clinical versus Statistical Prediction of Mental Health Decisions

ERIC Educational Resources Information Center

Aegisdottir, Stefania; Spengler, Paul M.; White, Michael J.

2006-01-01

In this rejoinder, the authors respond to the insightful commentary of Strohmer and Arm, Chwalisz, and Hilton, Harris, and Rice about the meta-analysis on statistical versus clinical prediction techniques for mental health judgments. The authors address issues including the availability of statistical prediction techniques for real-life psychology…

A strategic systems perspective of organizational learning theory: models for a case study at the Jet Propulsion Laboratory

NASA Technical Reports Server (NTRS)

Neece, O.

2000-01-01

Organizational learning is an umbrella term that covers a variety of topics including; learning curves, productivity, organizational memory, organizational forgetting, knowledge transfer, knowledge sharing and knowledge creation. This treatise will review some of these theories in concert with a model of how organizations learn.

Cyber Forensics and Security as an ABET-CAC Accreditable Program

ERIC Educational Resources Information Center

Wood, David F.; Kohun, Frederick G.; Ali, Azad; Paullet, Karen; Davis, Gary A.

2010-01-01

This paper frames the recent ABET accreditation model with respect to the balance between IS programs and innovation. With the current relaxation of the content of the information systems requirement by ABET, it is possible to include innovation into the accreditation umbrella. To this extent this paper provides a curricular model that provides…

Writing in the Workplace: Implications for Human Resource Development

ERIC Educational Resources Information Center

Akdere, Mesut; Azevedo, Ross E.

2005-01-01

Writing in the workplace is among the understudied business topics in the field of HRD. Yet, the impacts of writing in today's workplace are significant, and organizations making it a priority benefit from it. Furthermore, writing is related to the issue of workplace literacy which is the umbrella term for basic communication skills. This…

PROCSEE: Policy Challenges for Professional Higher Education in Central and South-Eastern Europe

ERIC Educational Resources Information Center

Policnik, Jasmina; Sauli Miklavcic, Alicia Leonor; Alupei-Durach, Flavia; Nožica, Žarko; Chrást, Ondrej; Voldánová, Iva; Karpíšek, Michal; Dinya, László; Medve, Anna; Wéber, György; Racsko, Réka; Perényi, Petra; Camilleri, Anthony F.

2016-01-01

PROCSEE is a policy-oriented project, aimed at strengthening the provision of professional higher education, by strengthening the policy-work conducted by umbrella organizations representing professional higher education institutions in Central and South-Eastern in Europe. Working together over three years, the project intends to: (1) identify the…

Education as a Spectral Technology: Corporate Culture at Work in Ontario's Schools

ERIC Educational Resources Information Center

Martin, Susan Marie

2012-01-01

This paper addresses the sweeping neoliberal reforms implemented in Ontario's schools in 2000, and conceptualises them within the terms of "millennial capitalism" (Comaroff & Comaroff, 2000). A close reading of secondary school curriculum documents and the umbrella policies that shape education from ages 5 to 18 years reveals how…

Emotional Disturbance. NICHCY Disability Fact Sheet #5

ERIC Educational Resources Information Center

National Dissemination Center for Children with Disabilities, 2010

2010-01-01

The mental health of our children is a natural and important concern for us all. The fact is, many mental disorders have their beginnings in childhood or adolescence, yet may go undiagnosed and untreated for years. "Umbrella" terms such as emotional disturbance, behavioral disorders, or mental illness are used to refer to mental…

Outcome Assessment of the Visiting Fulbright Scholar Program

ERIC Educational Resources Information Center

US Department of State, 2005

2005-01-01

The Office of Policy and Evaluation of the Bureau of Educational and Cultural Affairs of the U.S. Department of State contracted with SRI International to conduct a series of assessments of outcomes and impacts of various specialized exchange programs under the overall umbrella of the Fulbright Educational Exchange Program, the U.S. government's…

Multi-taxa population connectivity in the northern Rocky Mountains

Treesearch

Samuel A. Cushman; Erin L. Landguth

2012-01-01

Effective broad-spectrum biodiversity conservation requires that conservation strategies simultaneously meet the needs of multiple species. However, little is known about how maintaining habitat connectivity for one species or species group may also act as an umbrella for other species. We evaluated the degree to which predicted connected habitat for each of 144...

BDSM Disclosure and Stigma Management: Identifying Opportunities for Sex Education

ERIC Educational Resources Information Center

Bezreh, Tanya; Weinberg, Thomas S.; Edgar, Timothy

2012-01-01

While participation in the activities like bondage, domination, submission/sadism, masochism that fall under the umbrella term BDSM is widespread, stigma surrounding BDSM poses risks to practitioners who wish to disclose their interest. We examined risk factors involved with disclosure to posit how sex education might diffuse stigma and warn of…

Measuring the Test-Wiseness of Medical Students.

ERIC Educational Resources Information Center

Harvill, Leo M.

The objectives for this study were to: (1) develop a valid, reliable measure of test-wiseness with equivalent forms for use with students in the health sciences; and (2) determine the level of test-wiseness of entering medical students. The test-wiseness areas included in this study were: similar options, umbrella term, item give-away, convergence…

Unintended Revelations in History Textbooks: The Precarious Authenticity and Historical Continuity of the Slovak Nation

ERIC Educational Resources Information Center

Šulíková, Jana

2016-01-01

Purpose: This article proposes an analytical framework that helps to identify and challenge misconceptions of ethnocentrism found in pre-tertiary teaching resources for history and the social sciences in numerous countries. Design: Drawing on nationalism studies, the analytical framework employs ideas known under the umbrella terms of…

Making It Personal: The Importance of Student Experience in Creating Autonomy-Supportive Classrooms for Millennial Learners

ERIC Educational Resources Information Center

Conklin, Thomas A.

2013-01-01

This article reviews andragogy as the philosophy resident in the broad arena of experience-based learning. Beneath the umbrella of experience-based learning lie the specific classroom orientations of student-centered learning, problem-based learning, and classrooms as organizations. These orientations contribute to the creation of…

The Changing World of Higher Education: Where Do Language Centres Fit in?

ERIC Educational Resources Information Center

Dijk, Anje; Engelen, Christine; Korebrits, Liesbet

2014-01-01

This article assesses the current trends in language centre (LC) management in the Netherlands and Dutch-speaking Belgium. Twenty-five LCs are united under the umbrella of NUT, which offers its members the possibility to meet and discuss concrete professional subjects. Solutions, strategies and decisions emphasise the importance of national…

Current uses of Web 2.0 applications in transportation : case studies of select state departments of transportation

DOT National Transportation Integrated Search

2010-03-01

Web 2.0 is an umbrella term for websites or online applications that are user-driven and emphasize collaboration and user interactivity. The trend away from static web pages to a more user-driven Internet model has also occurred in the public s...

Divergence and Convergence within Greek Library Education: An Applied vs a Theoretical Approach

ERIC Educational Resources Information Center

Kyriaki-Manessi, Daphne

2008-01-01

This paper explores the differences and similarities of the three library schools educating librarians and information professionals in Greece. The structure of higher education in Greece has recently undergone major changes (2002) integrating technological institutions and universities under one umbrella that of higher education. As a result,…

Evaluating the Theory of Executive Dysfunction in Autism

ERIC Educational Resources Information Center

Hill, Elisabeth L.

2004-01-01

In this paper studies of executive function in autism spectrum disorder are reviewed. Executive function is an umbrella term for functions such as planning, working memory, impulse control, inhibition, and shifting set, as well as for the initiation and monitoring of action. In this review, the focus will be on planning, inhibition, shifting set,…

Parent Abuse: A Review

ERIC Educational Resources Information Center

Kennair, Nicola; Mellor, David

2007-01-01

A recent focus of research and clinical practice has been on the issue of abuse of parents by their children (parent abuse). This paper reviews the literature on this phenomenon. While parent abuse falls under the umbrella of family violence, it appears to be qualitatively different from other forms of intra-family abuse. Research has primarily…

Building a Blended Learning Program

ERIC Educational Resources Information Center

McLester, Susan

2011-01-01

"Online learning" often serves as an umbrella term that includes the subcategory of blended learning, which might also be referred to as hybrid learning, and comprises some combination of online and face-to-face time. Spurred in part by a 2009 U.S. Department of Education study, "Evaluation of Evidence-Based Practices in Online Learning," which…

Education in Action, School Year 1975-1976.

ERIC Educational Resources Information Center

Robin, Fay

This report is an evaluation of selected New York City Umbrella Programs funded under a special grant from the New York State Legislature. The 1975-76 Education in Action Program, a community health education program, served 427 elementary and junior high school students and 105 community parents in the Harlem and East Harlem communities. The…

Media Storytelling, Curriculum, and the Next 100 Years

ERIC Educational Resources Information Center

Lipschultz, Jeremy Harris

2012-01-01

Journalism as an academic field in the United States has frequently changed and grown through new professions and new industries coming under its umbrella (sometimes but not always driven by technological and/or economic changes) and academic developments such as cultural studies and media studies. But journalism is still rooted in good…

Investigation of the Relationship between Learning Process and Learning Outcomes in E-Learning Environments

ERIC Educational Resources Information Center

Yurdugül, Halil; Menzi Çetin, Nihal

2015-01-01

Problem Statement: Learners can access and participate in online learning environments regardless of time and geographical barriers. This brings up the umbrella concept of learner autonomy that contains self-directed learning, self-regulated learning and the studying process. Motivation and learning strategies are also part of this umbrella…

When Technology, Science and Culture Meet: Insights from Ancient Chinese Technology

ERIC Educational Resources Information Center

Lee, Yeung Chung

2018-01-01

This paper draws together two important agendas in science education. The first is making science education more inclusive such that students from non-Western or indigenous cultures can benefit from culturally relevant curricula. The second is integrating technology into the curriculum under the umbrella of Science-Technology-Society (STS)…

The Impact of Tougher Education Standards: Evidence from Florida

ERIC Educational Resources Information Center

Clark, Damon; See, Edward

2011-01-01

Many of the policies that fall under the school accountability umbrella are designed to incentivize students. Prominent among these are high school exit exams, standardized tests that, in some states, students must pass to earn a high school diploma. Proponents of these tests argue that by incentivizing students, they induce them to work harder…

Report from the European Prison Education Association

ERIC Educational Resources Information Center

Behan, Cormac

2008-01-01

Since the last edition of the Journal, the European Prison Education Association (EPEA) has been officially elected a member of the European Association for the Education of Adults (EAEA) at EAEA's General Assembly held at the University of Latvia in Riga. The EAEA is the largest umbrella organization in Europe advocating lifelong learning. It is…

APPA Promotes Leadership in Energy and Sustainability with New FPI Tool

ERIC Educational Resources Information Center

Boyce, Darryl K.

2012-01-01

Although sustainability best practices for buildings are generally well understood, campuses face unique challenges because they are developed to support a diverse community with a variety of facilities. From academic facilities and labs to residences and sports facilities, all operate under one organizational umbrella. This can make it difficult…

Understanding and Implementing the CLT (Communicative Language Teaching) Paradigm

ERIC Educational Resources Information Center

Jacobs, George M.; Farell, Thomas S. C.

2003-01-01

The call to change seems to be a constant in education. In second language education, a constellation of changes have been proposed and, to some extent, implemented. This constellation of interconnected changes can perhaps best be termed a paradigm shift, with this paradigm fitting under the general umbrella of Communicative Language Teaching…

Digital Media, Technologies and Scholarship: Some Shapes of eResearch in Educational Inquiry

ERIC Educational Resources Information Center

Markauskaite, Lina

2010-01-01

This paper discusses some recent developments in digital media, research technologies and scholarly practices that are known under the umbrella term of "eResearch". Drawing on conceptual ideas of digital materialism, epistemic artefacts and epistemic tools, this paper discusses how the digital inscription of knowledge and knowing could…

Socially Indigenous Help: The Community Cares for Itself.

ERIC Educational Resources Information Center

Curry, Ronald; Young, Richard D.

Recently, interest has increased in self-help groups, lay referral networks, social support networks, natural helpers, and others which may be placed under a single conceptual umbrella--socially indigenous help--because they all deal with the issue of how people use other people, social groups, and lay institutions to alleviate problems in living,…

Morbidity and Mortality: Building the Culture for Professional Growth and Innovation

ERIC Educational Resources Information Center

Howland, Jonathan

2011-01-01

Like their counterparts in law and medicine, teachers are professionals whose habits and techniques and strategies--whose "practices"--must be derived and customized and refined from a panoply of available prospects. So, while there are surely some pedagogies they might gather under the umbrella of "worst practices," one effective teacher's "best…

Technology-Supported Orchestration Matters: Outperforming Paper-Based Scripting in a Jigsaw Classroom

ERIC Educational Resources Information Center

Balestrini, Mara; Hernandez-Leo, Davinia; Nieves, Raul; Blat, Josep

2014-01-01

Under the umbrella of ubiquitous technologies, many computational artifacts have been designed to enhance the learning experience in physical settings such as classrooms or playgrounds, but few of them focus on aiding orchestration. This paper presents a systematic evaluation of the signal orchestration system (SOS) used by students for a jigsaw…

One for Autism: A Powerful Formula for Success

ERIC Educational Resources Information Center

Caroff, Maria

2007-01-01

One for Autism is a thriving and ever-growing facility for children with autism and other developmental delays. One for Autism, Inc., umbrellas One for Autism Academy, which offers a classroom setting, as well as One for Autism Center, which provides one-on-one comprehensive therapies, including behavioral therapy, occupational therapy and speech…

Multi-species attributes as the condition for adaptive sampling of rare species using two-stage sequential sampling with an auxiliary variable

USGS Publications Warehouse

Panahbehagh, B.; Smith, D.R.; Salehi, M.M.; Hornbach, D.J.; Brown, D.J.; Chan, F.; Marinova, D.; Anderssen, R.S.

2011-01-01

Assessing populations of rare species is challenging because of the large effort required to locate patches of occupied habitat and achieve precise estimates of density and abundance. The presence of a rare species has been shown to be correlated with presence or abundance of more common species. Thus, ecological community richness or abundance can be used to inform sampling of rare species. Adaptive sampling designs have been developed specifically for rare and clustered populations and have been applied to a wide range of rare species. However, adaptive sampling can be logistically challenging, in part, because variation in final sample size introduces uncertainty in survey planning. Two-stage sequential sampling (TSS), a recently developed design, allows for adaptive sampling, but avoids edge units and has an upper bound on final sample size. In this paper we present an extension of two-stage sequential sampling that incorporates an auxiliary variable (TSSAV), such as community attributes, as the condition for adaptive sampling. We develop a set of simulations to approximate sampling of endangered freshwater mussels to evaluate the performance of the TSSAV design. The performance measures that we are interested in are efficiency and probability of sampling a unit occupied by the rare species. Efficiency measures the precision of population estimate from the TSSAV design relative to a standard design, such as simple random sampling (SRS). The simulations indicate that the density and distribution of the auxiliary population is the most important determinant of the performance of the TSSAV design. Of the design factors, such as sample size, the fraction of the primary units sampled was most important. For the best scenarios, the odds of sampling the rare species was approximately 1.5 times higher for TSSAV compared to SRS and efficiency was as high as 2 (i.e., variance from TSSAV was half that of SRS). We have found that design performance, especially for adaptive designs, is often case-specific. Efficiency of adaptive designs is especially sensitive to spatial distribution. We recommend that simulations tailored to the application of interest are highly useful for evaluating designs in preparation for sampling rare and clustered populations.

The relieving effects of shelter modes on physiological stress of traffic police in summer

NASA Astrophysics Data System (ADS)

Zheng, G. Z.; Wang, Y. J.; Bu, W. T.; Lu, Y. Z.; Li, Ke; Li, Z. H.

2018-03-01

In summer, high temperature and strong sun radiation last for a long time. However, traffic police still stick to their positions to ensure normal traffic order. Therefore, the health and safety of traffic police are challenged by the high temperature weather. To protect the safety of the traffic police in the outdoor high temperature environment, some shelter modes, such as sun hat and sun umbrella are selected for duty traffic police. The relieving effects on the physiological stress of the shelter modes are analyzed by comparison of the physiological parameters in these shelter modes. The results show that sun umbrella has a good effect on relieving physiological stress. And sun hat has no effect on relieving physiological stress, although it avoids the direct sunlight on the face. However, it causes the increase of the thermal sensation. This study can provide important methods for health protecting of traffic police in the outdoor high temperature environment. It also provides a theoretical support for the revision of the outdoor high temperature labour protection standard.

Power attenuation characteristics as switch-over criterion in personal satellite mobile communications

NASA Technical Reports Server (NTRS)

Castro, Jonathan P.

1993-01-01

A third generation mobile system intends to support communications in all environments (i.e., outdoors, indoors at home or office and when moving). This system will integrate services that are now available in architectures such as cellular, cordless, mobile data networks, paging, including satellite services to rural areas. One way through which service integration will be made possible is by supporting a hierarchical cellular structure based on umbrella cells, macro cells, micro and pico cells. In this type of structure, satellites are part of the giant umbrella cells allowing continuous global coverage, the other cells belong to cities, neighborhoods, and buildings respectively. This does not necessarily imply that network operation of terrestrial and satellite segments interconnect to enable roaming and spectrum sharing. However, the cell concept does imply hand-off between different cell types, which may involve change of frequency. Within this propsective, the present work uses power attenuation characteristics to determine a dynamic criterion that allows smooth transition from space to terrestrial networks. The analysis includes a hybrid channel that combines Rician, Raleigh and Log Normal fading characteristics.

Coffee, Caffeine, and Health Outcomes: An Umbrella Review.

PubMed

Grosso, Giuseppe; Godos, Justyna; Galvano, Fabio; Giovannucci, Edward L

2017-08-21

To evaluate the associations between coffee and caffeine consumption and various health outcomes, we performed an umbrella review of the evidence from meta-analyses of observational studies and randomized controlled trials (RCTs). Of the 59 unique outcomes examined in the selected 112 meta-analyses of observational studies, coffee was associated with a probable decreased risk of breast, colorectal, colon, endometrial, and prostate cancers; cardiovascular disease and mortality; Parkinson's disease; and type-2 diabetes. Of the 14 unique outcomes examined in the 20 selected meta-analyses of observational studies, caffeine was associated with a probable decreased risk of Parkinson's disease and type-2 diabetes and an increased risk of pregnancy loss. Of the 12 unique acute outcomes examined in the selected 9 meta-analyses of RCTs, coffee was associated with a rise in serum lipids, but this result was affected by significant heterogeneity, and caffeine was associated with a rise in blood pressure. Given the spectrum of conditions studied and the robustness of many of the results, these findings indicate that coffee can be part of a healthful diet.

Effect of adaptation and pulp density on bioleaching of mine waste using indigenous acidophilic bacteria

NASA Astrophysics Data System (ADS)

Cho, K.; Kim, B.; Lee, D.; Choi, N.; Park, C.

2011-12-01

Adaptation to environment is a natural phenomena that takes place in many animals, plants and microorganisms. These adapted organisms achieve stronger applicability than unadapted organisms after habitation in a specific environment for a long time. In the biohydrometallurgical industry, adaptation to special environment conditions by selective culturing is the most popular method for improving bioleaching activity of strains-although that is time consuming. This study investigated the influence of the bioleaching efficiency of mine waste under batch experimental conditions (adaptation and pulp density) using the indigenous acidophilic bacteria collected from acid mine drainage in Go-seong and Yeon-hwa, Korea. We conducted the batch experiments at the influences of parameters, such as the adaptation of bacteria and pulp density of the mine waste. In the adaptation case, the value of pH in 1'st adaptation bacteria sample exhibited lower than in 2'nd adaptation bacteria sample. And the content of both Cu and Zn at 1'st adaptation bacteria sample appeared lower than at 2'nd adaptation bacteria sample. In the SEM analysis, the rod-shaped bacteria with 1μm in length were observed on the filter paper (pore size - 0.45μm). The results of pulp density experiments revealed that the content of both Cu and Zn increased with increasing pulp density, since the increment of pulp density resulted in the enhancement of bioleaching capacity.

How Big Is Big Enough? Sample Size Requirements for CAST Item Parameter Estimation

ERIC Educational Resources Information Center

Chuah, Siang Chee; Drasgow, Fritz; Luecht, Richard

2006-01-01

Adaptive tests offer the advantages of reduced test length and increased accuracy in ability estimation. However, adaptive tests require large pools of precalibrated items. This study looks at the development of an item pool for 1 type of adaptive administration: the computer-adaptive sequential test. An important issue is the sample size required…

An umbrella review of garlic intake and risk of cardiovascular disease.

PubMed

Schwingshackl, Lukas; Missbach, Benjamin; Hoffmann, Georg

2016-10-15

To gain further insight into the strength of evidence and extent of possible biases in the scope of studies investigating the impact of garlic and garlic supplement intake on biomarkers of cardiovascular disease, we performed an umbrella review of all published meta-analyses synthesizing data from both observational studies and randomized controlled trials. Electronic database PubMed (between 1966 and June 2015) was searched for systematic reviews and meta-analyses using following search terms: ("garlic" OR "allium sativum" OR "allicin" OR "organosulfur") AND ("cardiovascular" OR "coronary" OR "cholesterol" OR "triglyceride" OR "atherosclerosis" OR "blood pressure" OR "hypertension" OR "blood glucose") AND ("systematic review" OR "meta-analysis"), with no restriction to calendar data and language. Hand-search of reference lists and relevant clinical guidelines was performed as well. Nine systematic reviews investigated the effects of garlic on lipid parameters and eight systematic reviews analyzed the effects on blood pressure parameters were identified. Eight of nine meta-analyses synthesizing the effect of garlic on blood lipids reported significantly decreased total cholesterol levels. Inconsistent results could be detected for HDL-cholestrol, LDL-cholesterol, and triacylglycerols. The effect of garlic on systolic blood pressure showed consistent results across publications with 7 out of 8 meta-analyses demonstrating a substantial decrease in systolic blood pressure. Similar results could be reported regarding the effect of garlic on diastolic blood pressure, i.e. 6 out of 8 meta-analyses detected significant reductions in diastolic blood pressure levels following interventions with garlic. According to the data summarized in the present umbrella review, garlic preparations as well as garlic exerted some positive effects on indicators and biomarkers of cardiovascular disease, typically without causing any serious side effects. However, with regard to the substantial heterogeneities between the different trials enrolled in the various meta-analyses of this review, a conservative interpretation of the outcome seems to be appropriate. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cross-sector Service Provision in Health and Social Care: An Umbrella Review.

PubMed

Winters, Shannon; Magalhaes, Lilian; Anne Kinsella, Elizabeth; Kothari, Anita

2016-04-08

Meeting the complex health needs of people often requires interaction among numerous different sectors. No one service can adequately respond to the diverse care needs of consumers. Providers working more effectively together is frequently touted as the solution. Cross-sector service provision is defined as independent, yet interconnected sectors working together to better meet the needs of consumers and improve the quality and effectiveness of service provision. Cross-sector service provision is expected, yet much remains unknown about how it is conceptualised or its impact on health status. This umbrella review aims to clarify the critical attributes that shape cross-sector service provision by presenting the current state of the literature and building on the findings of the 2004 review by Sloper. Literature related to cross-sector service provision is immense, which poses a challenge for decision makers wishing to make evidence-informed decisions. An umbrella review was conducted to articulate the overall state of cross-sector service provision literature and examine the evidence to allow for the discovery of consistencies and discrepancies across the published knowledge base. Sixteen reviews met the inclusion criteria. Seven themes emerged: Focusing on the consumer, developing a shared vision of care, leadership involvement, service provision across the boundaries, adequately resourcing the arrangement, developing novel arrangements or aligning with existing relationships, and strengthening connections between sectors. Future research from a cross-organisational, rather than individual provider, perspective is needed to better understand what shapes cross-sector service provision at the boundaries. Findings aligned closely with the work done by Sloper and raise red flags related to reinventing what is already known. Future researchers should look to explore novel areas rather than looking into areas that have been explored at length. Evaluations of out-comes related to cross-sector service provision are still needed before any claims about effectiveness can be made.

Is chocolate consumption associated with health outcomes? An umbrella review of systematic reviews and meta-analyses.

PubMed

Veronese, Nicola; Demurtas, Jacopo; Celotto, Stefano; Caruso, Maria Gabriella; Maggi, Stefania; Bolzetta, Francesco; Firth, Joseph; Smith, Lee; Schofield, Patricia; Koyanagi, Ai; Yang, Lin; Solmi, Marco; Stubbs, Brendon

2018-06-01

The literature regarding the potential health benefits of chocolate consumption are unclear and the epidemiological credibility has not been systematically scrutinized, while the strength of the evidence is undetermined. We therefore aimed to map and grade the diverse health outcomes associated with chocolate consumption using an umbrella review of systematic reviews. Umbrella review of systematic reviews of observational and intervention studies (randomized placebo-controlled trials, RCTs). For each association, random-effects summary effect size, 95% confidence interval, and 95% prediction interval were estimated. We also assessed heterogeneity, evidence for small-study effect and evidence for excess significance bias. For significant outcomes of the RCTs, the GRADE assessment was furtherly used. From 240 articles returned, 10 systematic reviews were included (8 of which included a meta-analysis), including a total of 84 studies (36 prospective observational studies and 48 interventional). Nineteen different outcomes were included. Among observational studies, including a total of 1,061,637 participants, the best available evidence suggests that chocolate consumption is associated with reduced risk of cardiovascular disease (CVD) death (n = 4 studies), acute myocardial infarction (n = 6), stroke (n = 5) and diabetes (n = 6), although this was based on a weak evidence of credibility. Across meta-analyses of intervention studies, chocolate consumption was positively associated with flow-mediated dilatation at 90-150 min (n = 3) and at 2-18 weeks (n = 3), and insulin resistance markers (n = 2). However, using the GRADE assessment, the evidence for these outcomes was low or very low. Data from two systematic reviews, reported that chocolate consumption was not associated with better depressive mood or cognitive function. There is weak evidence to suggest that chocolate consumption may be associated with favorable health outcomes. Copyright © 2018 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

Cross-sector Service Provision in Health and Social Care: An Umbrella Review

PubMed Central

Magalhaes, Lilian; Anne Kinsella, Elizabeth; Kothari, Anita

2016-01-01

Introduction: Meeting the complex health needs of people often requires interaction among numerous different sectors. No one service can adequately respond to the diverse care needs of consumers. Providers working more effectively together is frequently touted as the solution. Cross-sector service provision is defined as independent, yet interconnected sectors working together to better meet the needs of consumers and improve the quality and effectiveness of service provision. Cross-sector service provision is expected, yet much remains unknown about how it is conceptualised or its impact on health status. This umbrella review aims to clarify the critical attributes that shape cross-sector service provision by presenting the current state of the literature and building on the findings of the 2004 review by Sloper. Methods: Literature related to cross-sector service provision is immense, which poses a challenge for decision makers wishing to make evidence-informed decisions. An umbrella review was conducted to articulate the overall state of cross-sector service provision literature and examine the evidence to allow for the discovery of consistencies and discrepancies across the published knowledge base. Findings: Sixteen reviews met the inclusion criteria. Seven themes emerged: Focusing on the consumer, developing a shared vision of care, leadership involvement, service provision across the boundaries, adequately resourcing the arrangement, developing novel arrangements or aligning with existing relationships, and strengthening connections between sectors. Future research from a cross-organisational, rather than individual provider, perspective is needed to better understand what shapes cross-sector service provision at the boundaries. Conclusion: Findings aligned closely with the work done by Sloper and raise red flags related to reinventing what is already known. Future researchers should look to explore novel areas rather than looking into areas that have been explored at length. Evaluations of out-comes related to cross-sector service provision are still needed before any claims about effectiveness can be made. PMID:27616954

Shallow velocity structure across the Mariana arc

NASA Astrophysics Data System (ADS)

Tait, S.; Kaminski, E. C.; Carazzo, G.; Limare, A.

2016-12-01

Atmospheric injection of volcanic ash during explosive eruptions is controlled by the dynamics of a volcanic column and associated umbrella cloud, which are subject to a wind field, and are connected by a turbulent fountain which initiates horizontal spreading at the neutral buoyancy level. We present a new theoretical and experimental study of an axisymmetric turbulent umbrella cloud intruding horizontally at its neutral buoyancy level into a static environment linearly stratified in density. The intrusion is fed by a constant horizontal volume flux (Q0) at a finite radius (R0), where it has a constant thickness (2H0). The characteristics of the fountain (R0, H0, Q0) derive from a vertical forced plume (source momentum and buoyancy fluxes Mi , Fi) and environmental stratification N. Buoyancy drives horizontal flow but, despite high Reynolds number, impedes entrainment of ambient fluid into the umbrella cloud. Turbulent stresses are nevertheless crucial in the momentum balance. Our theory highlights the vertical profiles of density and velocity within the current of which we present experimental measurements. Initially, current buoyancy is opposed by the inertia of the ambient fluid, and current radius (RN(t)) grows linearly in time. Subsequently, turbulent drag opposes buoyancy, and the current breaks down into two parts: i) between the source and a transition radius (R0T(t)), a steady region where current thickness (2H) and mean velocity (U) are time-independent and decreasing functions of r ; ii), a contiguous unsteady « frontal » region, between the transition radius and the front (RTN), in which the current thickens. The theory predicts current shape and an asymptotic spreading behaviour (RN t^5/9) which agree well with experimental data. Our analysis of satellite observations of several sustained plinian events including the Pinatubo 1991 climactic eruption shows that both the initial and asymptotic spreading regimes predicted by the model are present.

A mixed signal ECG processing platform with an adaptive sampling ADC for portable monitoring applications.

PubMed

Kim, Hyejung; Van Hoof, Chris; Yazicioglu, Refet Firat

2011-01-01

This paper describes a mixed-signal ECG processing platform with an 12-bit ADC architecture that can adapt its sampling rate according to the input signals rate of change. This enables the sampling of ECG signals with significantly reduced data rate without loss of information. The presented adaptive sampling scheme reduces the ADC power consumption, enables the processing of ECG signals with lower power consumption, and reduces the power consumption of the radio while streaming the ECG signals. The test results show that running a CWT-based R peak detection algorithm using the adaptively sampled ECG signals consumes only 45.6 μW and it leads to 36% less overall system power consumption.

Clinical Trials of Precision Medicine through Molecular Profiling: Focus on Breast Cancer.

PubMed

Zardavas, Dimitrios; Piccart-Gebhart, Martine

2015-01-01

High-throughput technologies of molecular profiling in cancer, such as gene-expression profiling and next-generation sequencing, are expanding our knowledge of the molecular landscapes of several cancer types. This increasing knowledge coupled with the development of several molecularly targeted agents hold the promise for personalized cancer medicine to be fully realized. Moreover, an expanding armamentarium of targeted agents has been approved for the treatment of specific molecular cancer subgroups in different diagnoses. According to this paradigm, treatment selection should be dictated by the specific molecular aberrations found in each patient's tumor. The classical clinical trials paradigm of patients' eligibility being based on clinicopathologic parameters is being abandoned, with current clinical trials enrolling patients on the basis of specific molecular aberrations. New, innovative trial designs have been generated to better tackle the multiple challenges induced by the increasing molecular fragmentation of cancer, namely: (1) longitudinal cohort studies with or without downstream trials, (2) studies assessing the clinical utility of molecular profiling, (3) master or umbrella trials, (4) basket trials, (5) N-of-1 trials, and (6) adaptive design trials. This article provides an overview of the challenges for clinical trials in the era of molecular profiling of cancer. Subsequently, innovative trial designs with respective examples and their potential to expedite efficient clinical development of targeted anticancer agents is discussed.

Positive psychology: an approach to supporting recovery in mental illness.

PubMed

Schrank, B; Brownell, T; Tylee, A; Slade, M

2014-09-01

This paper reviews the literature on positive psychology with a special focus on people with mental illness. It describes the characteristics, critiques, and roots of positive psychology and positive psychotherapy, and summarises the existing evidence on positive psychotherapy. Positive psychology aims to refocus psychological research and practice on the positive aspects of experience, strengths, and resources. Despite a number of conceptual and applied research challenges, the field has rapidly developed since its introduction at the turn of the century. Today positive psychology serves as an umbrella term to accommodate research investigating positive emotions and other positive aspects such as creativity, optimism, resilience, empathy, compassion, humour, and life satisfaction. Positive psychotherapy is a therapeutic intervention that evolved from this research. It shows promising results for reducing depression and increasing well-being in healthy people and those with depression. Positive psychology and positive psychotherapy are increasingly being applied in mental health settings, but research evidence involving people with severe mental illness is still scarce. The focus on strengths and resources in positive psychology and positive psychotherapy may be a promising way to support recovery in people with mental illness, such as depression, substance abuse disorders, and psychosis. More research is needed to adapt and establish these approaches and provide an evidence base for their application.

Behavioral Interventions for Enhancing Life Participation in behavioral variant Frontotemporal Dementia and Primary Progressive Aphasia

PubMed Central

Kortte, Kathleen B.; Rogalski, Emily J.

2013-01-01

Primary progressive aphasia (PPA) and behavioral-variant frontotemporal dementia (bvFTD) are clinical syndromes under the umbrella term “frontotemporal dementia (FTD)” and are caused by a neurodegenerative disease with an onset most typically in the productive years of adulthood. The cognitive and behavioral impairments associated with FTD interfere with the successful engagement in typical life roles, such as parenting, working, and maintenance of interpersonal relationships. There are currently no treatments to stop or slow the degenerative process and there are only very limited medication options for the management of the cognitive-behavioral symptoms. However, alternative, non-pharmacological interventions may offer significant benefit to the quality of life of the diagnosed individual. The goal of this paper is to provide an overview of the approaches available through neurorehabilitation and community-based services that facilitate successful engagement in life activities and promote optimal quality of life for the individuals and families living with FTD. It is hoped that as medical providers become more familiar with behavioral interventions, referrals for services will increase thereby allowing individuals with FTD and their caregivers to learn ways to adapt, adjust, and participate in life to the fullest despite the impairments from this progressive disease. PMID:23611353

Intervention for individuals with fetal alcohol spectrum disorders: treatment approaches and case management.

PubMed

Paley, Blair; O'Connor, Mary J

2009-01-01

Exposure to alcohol in utero is considered to be the leading cause of developmental disabilities of known etiology. The most severe consequence of such exposure, fetal alcohol syndrome (FAS), is characterized by a distinct constellation of characteristic facial anomalies, growth retardation, and central nervous system (CNS) dysfunction. Some individuals with prenatal alcohol exposure (PAE) do not meet the full criteria for FAS, but instead are diagnosed with partial FAS, alcohol related neurodevelopmental disorder (ARND), or alcohol related birth defects (ARBD). The entire continuum of effects from PAE is increasingly being referred to under the umbrella term of fetal alcohol spectrum disorders (FASDs). An extensive body of research has documented major cognitive, behavioral, adaptive, social, and emotional impairments among individuals with FASDs. Although FAS was identified in the U.S. over 35 years ago, the development, evaluation, and dissemination of evidence-based interventions for individuals with FASDs have lagged behind significantly. Encouragingly, however, in recent years there has been a marked increase in efforts to design and test interventions to remediate the impairments associated with prenatal alcohol exposure. This article will review treatment needs and considerations for individuals with FASDs and their families, current empirically tested treatment approaches, case management issues, and suggestions for future directions in research on the treatment of FASDs. (c) 2009 Wiley-Liss, Inc.

Apparatus and method for handheld sampling

DOEpatents

Staab, Torsten A.

2005-09-20

The present invention includes an apparatus, and corresponding method, for taking a sample. The apparatus is built around a frame designed to be held in at least one hand. A sample media is used to secure the sample. A sample media adapter for securing the sample media is operated by a trigger mechanism connectively attached within the frame to the sample media adapter.

Molecular principle of the cyclin-dependent kinase selectivity of 4-(thiazol-5-yl)-2-(phenylamino) pyrimidine-5-carbonitrile derivatives revealed by molecular modeling studies.

PubMed

Kong, Xiaotian; Sun, Huiyong; Pan, Peichen; Tian, Sheng; Li, Dan; Li, Youyong; Hou, Tingjun

2016-01-21

Due to the high sequence identity of the binding pockets of cyclin-dependent kinases (CDKs), designing highly selective inhibitors towards a specific CDK member remains a big challenge. 4-(thiazol-5-yl)-2-(phenylamino) pyrimidine derivatives are effective inhibitors of CDKs, among which the most promising inhibitor 12u demonstrates high binding affinity to CDK9 and attenuated binding affinity to other homologous kinases, such as CDK2. In this study, in order to rationalize the principle of the binding preference towards CDK9 over CDK2 and to explore crucial information that may aid the design of selective CDK9 inhibitors, MM/GBSA calculations based on conventional molecular dynamics (MD) simulations and enhanced sampling simulations (umbrella sampling and steered MD simulations) were carried out on two representative derivatives (12u and 4). The calculation results show that the binding specificity of 12u to CDK9 is primarily controlled by conformational change of the G-loop and variation of the van der Waals interactions. Furthermore, the enhanced sampling simulations revealed the different reaction coordinates and transient interactions of inhibitors 12u and 4 as they dissociate from the binding pockets of CDK9 and CDK2. The physical principles obtained from this study may facilitate the discovery and rational design of novel and specific inhibitors of CDK9.

Sampling procedures for inventory of commercial volume tree species in Amazon Forest.

PubMed

Netto, Sylvio P; Pelissari, Allan L; Cysneiros, Vinicius C; Bonazza, Marcelo; Sanquetta, Carlos R

2017-01-01

The spatial distribution of tropical tree species can affect the consistency of the estimators in commercial forest inventories, therefore, appropriate sampling procedures are required to survey species with different spatial patterns in the Amazon Forest. For this, the present study aims to evaluate the conventional sampling procedures and introduce the adaptive cluster sampling for volumetric inventories of Amazonian tree species, considering the hypotheses that the density, the spatial distribution and the zero-plots affect the consistency of the estimators, and that the adaptive cluster sampling allows to obtain more accurate volumetric estimation. We use data from a census carried out in Jamari National Forest, Brazil, where trees with diameters equal to or higher than 40 cm were measured in 1,355 plots. Species with different spatial patterns were selected and sampled with simple random sampling, systematic sampling, linear cluster sampling and adaptive cluster sampling, whereby the accuracy of the volumetric estimation and presence of zero-plots were evaluated. The sampling procedures applied to species were affected by the low density of trees and the large number of zero-plots, wherein the adaptive clusters allowed concentrating the sampling effort in plots with trees and, thus, agglutinating more representative samples to estimate the commercial volume.

Partnership, Efficiency, and Effectiveness--AUA Annual Lecture 2015

ERIC Educational Resources Information Center

Diamond, Ian

2016-01-01

Professor Sir Ian Diamond is Principal and Vice-Chancellor of the University of Aberdeen, an appointment he has held since 1 April 2010. He was previously Chief Executive of the Economic and Social Research Council. He was also Chair of the Research Councils UK Executive Group (2004-2009) the umbrella body that represents all seven UK Research…

Youth Work Training Package Review: More of the Same or Radical Rationalisation?

ERIC Educational Resources Information Center

Corney, Tim; Broadbent, Robyn

2007-01-01

The development of a national youth work training package in Australia began over 15 years ago. The current package sits under the umbrella of the general Community Services Industry Training Package. The first stage of a review of this package has been completed and the subsequent report not only confirms the recent trend towards the…

School Community Education Program in New York City 1985-86: Volume II. OEA Evaluation Report.

ERIC Educational Resources Information Center

New York City Board of Education, Brooklyn. Office of Educational Assessment.

During 1985-86 the School Community Education Program (also known as the Umbrella Program), funded by the New York State Legislature, provided a variety of educational and training experiences to some 25,871 participants, including pre-kindergarten children and their parents; and students, teachers and supervisors from kindergarten through grade…

Understory Density Characteristics in Several Midlatitude Temperature Forests

DTIC Science & Technology

2003-03-01

Vaccinium corymbosum ), black gum (Nyssa sylvatica), white oak (Q. alba), mockemut hickory (Carya tomentosa), American beech (Fagus grandifolia), and...Cedar Juniperis virginiana Red Juniper U Fraser Magnolia Magnolia fraseri Umbrella-tree U Highbush Blueberry Vaccinium corymbosum Unkn. U Loblolly Pine...plants and shrubs include ferns (many species), lowbush blueberry ( Vaccinium augustifolium), southern running-pine (Lycopodium digitatum), poison ivy

Who's Blogging Now?: Linguistic Features and Authorship Analysis in Sports Blogs

ERIC Educational Resources Information Center

Cox, Taylor

2017-01-01

The field of authorship determination, previously largely falling under the umbrella of literary analysis but recently becoming a large subfield of forensic linguistics, has grown substantially over the last two decades. As its body of research and its record of successful forensic application continue to grow, this growth is paralleled by the…

Professional Development on an International Scale: Council of Europe--Pestalozzi Programme Virtual Community of Practice

ERIC Educational Resources Information Center

Mompoint Gaillard, Pascale; Rajic, Višnja

2014-01-01

Communities of practice as organisations of learning have developed different forms as: task-based, practice-based or knowledge based communities (Barab et al., 2004). The paper presents a case study of a successful community of practice developed under the umbrella of Council of Europe Pestalozzi programme for teacher development. The programme…

Contemporary American Success Stories: Famous People of Hispanic Heritage. Volume VI. A Mitchell Lane Multicultral Biography Series.

ERIC Educational Resources Information Center

1997

The term "Hispanic" is an umbrella term that encompasses people from many nationalities, all races, and many social and cultural groups. Hispanics are also collectively called Latinos. The biographies in this series represent the diversity of Hispanic heritage in the United States. The people featured are contemporary figures of…

Bakavi: Change the World I Want to Stay On.

ERIC Educational Resources Information Center

Nickerson, Mike

The booklet describes the natural ecosystem of the earth, the ways humans have evolved and diverged from basic life-supporting processes, and the problems that divergence has created. It also offers guidelines for overcoming those problems. Bakavi, a Hopi Indian word, is an umbrella term for the following objectives: to develop a way of life in…

Teachers' Responses to Using a Small-Group Delivery Method during Reading Instruction: A Qualitative Approach

ERIC Educational Resources Information Center

Reynolds, Dorothy M. Valentine

2010-01-01

The purpose of this research was to examine teachers' perspectives on transitioning from a predominately whole to small-group delivery method during reading instruction. This study used a qualitative approach and nested itself in an epistemology of constructivism. The research operated under the umbrella of practice ethnography as it closely…

Getting to Grips with Education and Training for Industry. A Development of the Concept of Key Technologies.

ERIC Educational Resources Information Center

Clyde, Albert

"Key technologies" is an umbrella term for appropriate technologies applied to give maximum economic benefit in particular circumstances that may cross traditional disciplinary boundaries. Development of the concept is necessitated by the rate of change of technological development. Key technologies may be classified in three groups related to…

A Few Cautions at the Millennium on the Merging of Feminist Studies with American Indian Women's Studies.

ERIC Educational Resources Information Center

Mihesuah, Devon A.

2000-01-01

Discusses possible intersections between feminist studies and American Indian women's studies, noting the complexity of identity politics when most contemporary Indians have mixed blood. No single authoritative Native women's position or feminist theory of Native women exists. These labels are often umbrella terms that inadequately represent those…

School Community Education Program in New York City 1988-89. Volume II. OREA Evaluation Section Report.

ERIC Educational Resources Information Center

Guerrero, Frank; Abbott, Lori

This second volume of a four-volume evaluation of the 1988-89 New York City School Community Education Program (also known as the Umbrella Program) comprises reports evaluating nine innovative elementary school projects on social, ethnical, and environmental studies, four of which included staff development workshops. Evaluation sources included…

Groundwater Resources Assessment under the Pressures of Humanity and Climate Changes

Treesearch

Bret Bruce; Diana Allen; Henrique Chaves; Gordon Grant; Gualbert Oude Essink; Henk Kooi; Ian White; Jason Gurdak; Jay Famiglietti; Jose Luis Martin-Bordes; Kevin Hiscock; Matthew Rodell; Neno Kukuric; Peter B. McMahon; Richard Taylor; Timothy Green; Yoseph Yechieli

2008-01-01

Given the vision and mission statements for GRAPHIC above, this document provides an updated framework for the GRAPHIC program. The approach to addressing global issues under the GRAPHIC umbrella involves case studies designed to cover a broad range of the identified Subjects, Methods, and Regions. Interdependencies of factors and processes affecting subsurface water...

The next century of wood products utilization : a call for reflection and innovation

Treesearch

John A. Youngquist; Thomas E. Hamilton

1999-01-01

Sustainable development has become the umbrella objective for forest management in many countries of the world, and managers are increasingly faced with the challenges of balancing environmental and economic health in their forest management and resource utilization decisions. It can no longer be assumed that abundant raw materials are available simply for the taking....

Comparing Face-To-Face and Asynchronous Online Communication as Mechanisms for Critical Reflective Dialogue

ERIC Educational Resources Information Center

Salter, Susan; Douglas, Tracy; Kember, David

2017-01-01

Two mechanisms for engaging in critical reflective dialogue are discussed and compared: face-to-face meetings and asynchronous online discussion. The context is an umbrella action research project, with over 20 participants, which aimed to improve practices in online teaching and contribute to the development of graduate attributes. The article…

U.S. Virgin Islands Department of Education 1993 Annual Report.

ERIC Educational Resources Information Center

Virgin Islands of the United States Dept. of Education, St. Thomas.

The Virgin Islands Department of Education represents one of the largest consolidated school districts in America, with 34 public schools serving 23,000 students. This annual report is designed to illustrate the many programs under the umbrella of the Virgin Islands Department of Education. The theme for 1993 is "The Year of Assessment,"…

DAGAL: Detailed Anatomy of Galaxies

NASA Astrophysics Data System (ADS)

Knapen, Johan H.

2017-03-01

The current IAU Symposium is closely connected to the EU-funded network DAGAL (Detailed Anatomy of Galaxies), with the final annual network meeting of DAGAL being at the core of this international symposium. In this short paper, we give an overview of DAGAL, its training activities, and some of the scientific advances that have been made under its umbrella.

The M in Stem via the M in Epidemiology

ERIC Educational Resources Information Center

Griffiths, Martin

2011-01-01

It is the case that some activities claiming to reside under the STEM umbrella do not, in fact, give participants the opportunity to engage in anything other than routine mathematics. With this in mind, we explore here the potential for developing and then delivering STEM activities based on the discipline of mathematical epidemiology. We argue…

Investigation of Parental Involvement Tasks as Predictors of Primary Students' Turkish, Math, and Science & Technology Achievement

ERIC Educational Resources Information Center

Sad, Suleyman Nihat

2012-01-01

Problem statement: Parental involvement is used as an umbrella term to imply parents' efforts to take an active role in their children's education. In this sense it takes many forms ranging from parent-child communication to participating/volunteering in school activities. Although parental involvement is one condition for students' success, the…

Empowering Ourselves and Transforming Schools: Educators Making a Difference. Suny Series, Teacher Preparation and Development.

ERIC Educational Resources Information Center

Irwin, Judith W.

This text examines the forces that keep educators and students from feeling fully empowered, that is, gaining the power to self-actualize and to facilitate this process for others. A feminist perspective is used to consider directions for educational reform and innovation broadly under an umbrella philosophy of empowerment, suggesting a paradigm…

Contemporary American Success Stories: Famous People of Hispanic Heritage. Volume IV. A Mitchell Lane Multicultral Biography Series.

ERIC Educational Resources Information Center

Marvis, Barbara J.

The term "Hispanic" is an umbrella term that encompasses people from many nationalities, all races, and many social and cultural groups. Hispanics are also collectively called Latinos. The biographies in this series represent the diversity of Hispanic heritage in the United States. The people featured are contemporary figures of…

Applied group theory applications in the engineering (physical, chemical, and medical), biological, social, and behavioral sciences and in the fine arts

NASA Technical Reports Server (NTRS)

Borg, S. F.

1976-01-01

A generalized applied group theory is developed, and it is shown that phenomena from a number of diverse disciplines may be included under the umbrella of a single theoretical formulation based upon the concept of a group consistent with the usual definition of this term.

21st Century Workforce Initiatives: Implications for Information Literacy Instruction in Academic Libraries

ERIC Educational Resources Information Center

Leavitt, Laura L.

2011-01-01

This discussion is designed to expose the readers to a selection of educational reform initiatives that fall under the "21st Century Workforce" umbrella. The aims of these initiatives are quite harmonious with the overarching goals of librarianship and the opportunities for librarians to become involved and to demonstrate leadership in this arena…

The Foundation Handbook: A Private Foundation Approach to Fund Raising at State Colleges and Universities.

ERIC Educational Resources Information Center

Lemish, Donald L.

Guidelines for state colleges and universities who wish to use a foundation as an umbrella organization for receiving all private gifts, restricted and unrestricted, are presented. In examining the need for a foundation, attention should be directed to: establishing credibility, marshalling volunteers, providing for a mechanism for accepting life…

The Voice of Women Scientists in EU Research Policy (abstract)

NASA Astrophysics Data System (ADS)

Šatkovskienė, Dalia

2009-04-01

The European Platform of Women Scientists (www.epws.org) is an umbrella organization bringing together networks of women scientists and organisations committed to gender equality in research in all disciplines all over Europe and the countries associated to the European Union's Framework Programmes for Research and Technological Development. The goals of EPWS and its activities are presented.

Evidence-Based Assessment of Compulsive Skin Picking, Chronic Tic Disorders and Trichotillomania in Children

ERIC Educational Resources Information Center

McGuire, Joseph F.; Kugler, Brittany B.; Park, Jennifer M.; Horng, Betty; Lewin, Adam B.; Murphy, Tanya K.; Storch, Eric A.

2012-01-01

Body-focused repetitive behavior (BFRB) is an umbrella term for debilitating, repetitive behaviors that target one or more body regions. Despite regularly occurring in youth, there has been limited investigation of BFRBs in pediatric populations. One reason for this may be that there are few reliable and valid assessments available to evaluate the…

How Social Networks Influence Female Students' Choices to Major in Engineering

ERIC Educational Resources Information Center

Weinland, Kathryn Ann

2012-01-01

Scope and Method of Study: This study examined how social influence plays a part in female students' choices of college major, specifically engineering instead of science, technology, and math. Social influence may show itself through peers, family members, and teachers and may encompass resources under the umbrella of social capital. The…

Setting Up a Grid-CERT: Experiences of an Academic CSIRT

ERIC Educational Resources Information Center

Moller, Klaus

2007-01-01

Purpose: Grid computing has often been heralded as the next logical step after the worldwide web. Users of grids can access dynamic resources such as computer storage and use the computing resources of computers under the umbrella of a virtual organisation. Although grid computing is often compared to the worldwide web, it is vastly more complex…

E-Assessment: Institutional Development Strategies and the Assessment Life Cycle

ERIC Educational Resources Information Center

Tomas, Carmen; Borg, Michaela; McNeil, Jane

2015-01-01

E-assessment is an umbrella term that comprises a complex array of tools of varying capacities. This paper focuses on the topic of e-assessment from the perspective of its strategic institutional development in higher education. The paper argues that research on e-assessment has been dominated by a focus on investigating benefits of use and…

Hands-on Science. How Do Sea Critters Make Their Moves?

ERIC Educational Resources Information Center

VanCleave, Janice

1998-01-01

Three science experiments teach elementary school students about marine-life locomotion. One teaches primary students how octopi and jellyfish move, using balloons and umbrellas. Another teaches K-6 students the up and down movement of fish in water, using condiment packets. A third teaches 4-6 students about the effect of fish swim bladders,…

Building Bridges of Understanding through Continuing Education and Professional Development of Arabs and Israelis

ERIC Educational Resources Information Center

Noyek, Arnold M.; Skinner, Harvey; Davis, Dave; Clark, Ian; Sriharan, Abi; Chalin, Catherine G.

2005-01-01

In this article, we present an educational approach uniquely linked to humanitarian and peace-building goals in conflicted regions of the world. We examine the Canada International Scientific Exchange Program and its lead program, the Middle East Association for Managing Hearing Loss, as a case study. Under a Canadian umbrella, continuing medical…

Relocating Precarity and Resiliency within Montreal: The Artists' Bloc of the Immigrant Workers' Centre

ERIC Educational Resources Information Center

Hall, Koby Rogers; Salamanca, Manuel

2017-01-01

In this document we describe our experience relocating precarity and resiliency by way of arts activism, to denounce and make visible social injustices experienced by im/migrant communities in Montreal. Under the umbrella of the Immigrant Workers' Centre, and other allies from the im/migrant workers' movement, we combine knowledge building, action…

Argumentation as a Path to the Thinking Development of Young Adolescents

ERIC Educational Resources Information Center

Kuhn, Deanna; Crowell, Amanda

2011-01-01

Argument has been referred to as the umbrella under which all reasoning lies--"the more general human process of which more specific forms of reasoning are a part". In this paper, the authors present an evidence that argumentive reasoning skills can be assessed and developed in facilitative settings. They focus on middle school as an optimal…

Inclusive Music Teaching Strategies for Elementary-Age Children with Developmental Dyslexia

ERIC Educational Resources Information Center

Heikkila, Elizabeth; Knight, Andrew

2012-01-01

Developmental dyslexia (DD) is more prevalent as an "umbrella" disorder than many educators realize. The music educator can play a particularly useful role in helping children in the general or choral classroom cope with DD, given the temporal nature of cognitive issues inherent in the disorder. The purposes of this article are to…

Early Achievements in Service Integration: What We Can Learn from No Wrong Door Startups.

ERIC Educational Resources Information Center

Washington State Dept. of Social and Health Services, Olympia. Office of Research and Data Analysis.

The Washington State Department of Social and Health Services (DSHS) was created as an umbrella agency, to bring together state human service programs, so that people could get comprehensive assistance with many, often interrelated needs. Efforts were made to co-locate various service program offices to make access to various services easier.…

Mathematics and Science Teachers' Use of and Confidence in Empirical Reasoning: Implications for STEM Teacher Preparation

ERIC Educational Resources Information Center

Wasserman, Nicholas H.; Rossi, Dara

2015-01-01

The recent trend to unite mathematically related disciplines (science, technology, engineering, and mathematics) under the broader umbrella of STEM education has advantages. In this new educational context of integration, however, STEM teachers need to be able to distinguish between sufficient proof and reasoning across different disciplines,…

Stories of Practitioner Enquiry: Using Narrative Interviews to Explore Teachers' Perspectives of Learning to Learn

ERIC Educational Resources Information Center

Thomas, Ulrike; Tiplady, Lucy; Wall, Kate

2014-01-01

The Campaign for Learning's Learning to Learn Phase 4 was a research project in which teachers undertook practitioner enquiry to explore innovative pedagogies under the umbrella term of learning to learn. In 2008, to gain greater understanding of what this process meant to the participating teachers the research team at Newcastle University…

Geochemical Reaction Mechanism Discovery from Molecular Simulation

DOE PAGES

Stack, Andrew G.; Kent, Paul R. C.

2014-11-10

Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineralmore » surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.« less

Kirkwood-Buff integrals of finite systems: shape effects

NASA Astrophysics Data System (ADS)

Dawass, Noura; Krüger, Peter; Simon, Jean-Marc; Vlugt, Thijs J. H.

2018-06-01

The Kirkwood-Buff (KB) theory provides an important connection between microscopic density fluctuations in liquids and macroscopic properties. Recently, Krüger et al. derived equations for KB integrals for finite subvolumes embedded in a reservoir. Using molecular simulation of finite systems, KB integrals can be computed either from density fluctuations inside such subvolumes, or from integrals of radial distribution functions (RDFs). Here, based on the second approach, we establish a framework to compute KB integrals for subvolumes with arbitrary convex shapes. This requires a geometric function w(x) which depends on the shape of the subvolume, and the relative position inside the subvolume. We present a numerical method to compute w(x) based on Umbrella Sampling Monte Carlo (MC). We compute KB integrals of a liquid with a model RDF for subvolumes with different shapes. KB integrals approach the thermodynamic limit in the same way: for sufficiently large volumes, KB integrals are a linear function of area over volume, which is independent of the shape of the subvolume.

Research methods to change clinical practice for patients with rare cancers.

PubMed

Billingham, Lucinda; Malottki, Kinga; Steven, Neil

2016-02-01

Rare cancers are a growing group as a result of reclassification of common cancers by molecular markers. There is therefore an increasing need to identify methods to assess interventions that are sufficiently robust to potentially affect clinical practice in this setting. Methods advocated for clinical trials in rare diseases are not necessarily applicable in rare cancers. This Series paper describes research methods that are relevant for rare cancers in relation to the range of incidence levels. Strategies that maximise recruitment, minimise sample size, or maximise the usefulness of the evidence could enable the application of conventional clinical trial design to rare cancer populations. Alternative designs that address specific challenges for rare cancers with the aim of potentially changing clinical practice include Bayesian designs, uncontrolled n-of-1 trials, and umbrella and basket trials. Pragmatic solutions must be sought to enable some level of evidence-based health care for patients with rare cancers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Coupling of Fast and Slow Modes in the Reaction Pathway of the Minimal Hammerhead Ribozyme Cleavage

PubMed Central

Radhakrishnan, Ravi

2007-01-01

By employing classical molecular dynamics, correlation analysis of coupling between slow and fast dynamical modes, and free energy (umbrella) sampling using classical as well as mixed quantum mechanics molecular mechanics force fields, we uncover a possible pathway for phosphoryl transfer in the self-cleaving reaction of the minimal hammerhead ribozyme. The significance of this pathway is that it initiates from the minimal hammerhead crystal structure and describes the reaction landscape as a conformational rearrangement followed by a covalent transformation. The delineated mechanism is catalyzed by two metal (Mg2+) ions, proceeds via an in-line-attack by CYT 17 O2′ on the scissile phosphorous (ADE 1.1 P), and is therefore consistent with the experimentally observed inversion configuration. According to the delineated mechanism, the coupling between slow modes involving the hammerhead backbone with fast modes in the cleavage site appears to be crucial for setting up the in-line nucleophilic attack. PMID:17545240

Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop

PubMed Central

Meng, Yilin; Roux, Benoît

2013-01-01

Molecular dynamics umbrella sampling simulations are used to compare the relative stability of the active conformation of the catalytic domain of c-Src kinase while the tyrosine 416 in the activation loop (A-loop) is either unphosphorylated or phosphorylated. When the A-loop is unphosphorylated, there is considerable flexiblity of the kinase. While the active conformation of the kinase is not forbidden and can be visited transiently, it is not the predominant state. This is consistent with the view that c-Src displays some catalytic activity even when the A-loop is unphosphorylated. In contrast, phosphorylation of the A-loop contributes to stabilize several structural features that are critical for catalysis, such as the hydrophobic regulatory spine, the HRD motif, and the electrostatic switch. In summary, the free energy landscape calculations demonstrate that phosphorylation of tyrosine 416 in the A-loop essentially “locks” the kinase into its catalytically competent conformation. PMID:24103328

Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes

PubMed Central

2017-01-01

In spite of the abundance of glycoproteins in biological processes, relatively little three-dimensional structural data is available for glycan structures. Here, we study the structure and flexibility of the vast majority of mammalian oligosaccharides appearing in N- and O-glycosylated proteins using a bottom up approach. We report the conformational free-energy landscapes of all relevant glycosidic linkages as obtained from local elevation simulations and subsequent umbrella sampling. To the best of our knowledge, this represents the first complete conformational library for the construction of N- and O-glycan structures. Next, we systematically study the effect of neighboring residues, by extensively simulating all relevant trisaccharides and one tetrasaccharide. This allows for an unprecedented comparison of disaccharide linkages in large oligosaccharides. With a small number of exceptions, the conformational preferences in the larger structures are very similar as in the disaccharides. This, finally, allows us to suggest several efficient approaches to construct complete N- and O-glycans on glycoproteins, as exemplified on two relevant examples. PMID:28816453

Theoretical and Experimental Study of Inclusion Complexes of β-Cyclodextrins with Chalcone and 2',4'-Dihydroxychalcone.

PubMed

Sancho, Matias I; Andujar, Sebastian; Porasso, Rodolfo D; Enriz, Ricardo D

2016-03-31

The inclusion complexes formed by chalcone and 2',4'-dihydroxychalcone with β-cyclodextrin have been studied combining experimental (phase solubility diagrams, Fourier transform infrared spectroscopy) and molecular modeling (molecular dynamics, quantum mechanics/molecular mechanics calculations) techniques. The formation constants of the complexes were determined at different temperatures, and the thermodynamic parameters of the process were obtained. The inclusion of chalcone in β-cyclodextrin is an exothermic process, while the inclusion of 2',4'-dihydroxychalcone is endothermic. Free energy profiles, derived from umbrella sampling using molecular dynamics simulations, were constructed to analyze the binding affinity and the complexation reaction at a molecular level. Hybrid QM/MM calculations were also employed to obtain a better description of the energetic and structural aspects of the complexes. The intermolecular interactions that stabilize both inclusion complexes were characterized by means of quantum atoms in molecules theory and reduce density gradient method. The calculated interactions were experimentally observed using FTIR.

Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.

PubMed

Ziada, Sonia; Braka, Abdennour; Diharce, Julien; Aci-Sèche, Samia; Bonnet, Pascal

2018-01-01

Nobel Laureate Richard P. Feynman stated: "[…] everything that living things do can be understood in terms of jiggling and wiggling of atoms […]." The importance of computer simulations of macromolecules, which use classical mechanics principles to describe atom behavior, is widely acknowledged and nowadays, they are applied in many fields such as material sciences and drug discovery. With the increase of computing power, molecular dynamics simulations can be applied to understand biological mechanisms at realistic timescales. In this chapter, we share our computational experience providing a global view of two of the widely used enhanced molecular dynamics methods to study protein structure and dynamics through the description of their characteristics, limits and we provide some examples of their applications in drug design. We also discuss the appropriate choice of software and hardware. In a detailed practical procedure, we describe how to set up, run, and analyze two main molecular dynamics methods, the umbrella sampling (US) and the accelerated molecular dynamics (aMD) methods.

The dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study.

PubMed

Tobi, Dror; Elber, Ron; Thirumalai, Devarajan

2003-03-01

The conformational equilibrium of a blocked valine peptide in water and aqueous urea solution is studied using molecular dynamics simulations. Pair correlation functions indicate enhanced concentration of urea near the peptide. Stronger hydrogen bonding of urea-peptide compared to water-peptide is observed with preference for helical conformation. The potential of mean force, computed using umbrella sampling, shows only small differences between urea and water solvation that are difficult to quantify. The changes in solvent structure around the peptide are explained by favorable electrostatic interactions (hydrogen bonds) of urea with the peptide backbone. There is no evidence for significant changes in hydrophobic interactions in the two conformations of the peptide in urea solution. Our simulations suggest that urea denatures proteins by preferentially forming hydrogen bonds to the peptide backbone, reducing the barrier for exposing protein residues to the solvent, and reaching the unfolded state. Copyright 2003 Wiley Periodicals, Inc. Biopolymers: 359-369, 2003

Amino acids at water-vapor interfaces: surface activity and orientational ordering.

PubMed

Vöhringer-Martinez, Esteban; Toro-Labbé, Alejandro

2010-10-14

The surface activity and orientational ordering of amino acids at water-vapor interfaces were studied with molecular dynamics simulations in combination with thermodynamic integration and umbrella sampling. Asparagine, representing amino acids with polar side chains, displays no surface activity. Tryptophan, in contrast, with its hydrophobic indole ring as side chain unveils a free energy minimum at the water-vapor interface, which lies 6 kJ/mol under the hydration free energy. To study the orientational ordering of tryptophan along the interface, the order parameter was calculated. At the free energy minimum and at the Gibbs dividing surface, the order parameter reveals a parallel alignment of the indole ring with the water surface exposing the π-system to electrophiles in the hydrophobic phase and indicating polarization dependent spectroscopy. In the vicinity of this position a perpendicular orientation is obtained. The surface excess, calculated from the potential of mean force along the interface, is in excellent agreement with experimental measurements.

In Silico Measurements of Twist and Bend Moduli for β-Solenoid Protein Self-Assembly Units.

PubMed

Heinz, Leonard P; Ravikumar, Krishnakumar M; Cox, Daniel L

2015-05-13

We compute potentials of mean force for bend and twist deformations via force pulling and umbrella sampling experiments for four β-solenoid proteins (BSPs) that show promise in nanotechnology applications. In all cases, we find quasi-Hooke's law behavior until the point of rupture. Bending moduli show modest anisotropy for two-sided and three-sided BSPs, and little anisotropy for a four-sided BSP. There is a slight clockwise/counterclockwise asymmetry in the twist potential of mean force, showing greater stiffness when the applied twist follows the intrinsic twist. When we extrapolate to beam theory appropriate for amyloid fibrils of the BSPs, we find bend/twist moduli which are somewhat smaller than those in the literature for other amyloid fibrils. Twist persistence lengths are on the order of a micron, and bend persistence lengths are several microns. Provided the intrinsic twist can be reversed, these results support the usage of BSPs in biomaterials applications.

GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins

PubMed Central

Louet, Maxime; Martinez, Jean; Floquet, Nicolas

2012-01-01

After extra-cellular stimulation of G-Protein Coupled Receptors (GPCRs), GDP/GTP exchange appears as the key, rate limiting step of the intracellular activation cycle of heterotrimeric G-proteins. Despite the availability of a large number of X-ray structures, the mechanism of GDP release out of heterotrimeric G-proteins still remains unknown at the molecular level. Starting from the available X-ray structure, extensive unconstrained/constrained molecular dynamics simulations were performed on the complete membrane-anchored Gi heterotrimer complexed to GDP, for a total simulation time overcoming 500 ns. By combining Targeted Molecular Dynamics (TMD) and free energy profiles reconstruction by umbrella sampling, our data suggest that the release of GDP was much more favored on its phosphate side. Interestingly, upon the forced extraction of GDP on this side, the whole protein encountered large, collective motions in perfect agreement with those we described previously including a domain to domain motion between the two ras-like and helical sub-domains of Gα. PMID:22829757

Molecular conformation of linear alkane molecules: From gas phase to bulk water through the interface

NASA Astrophysics Data System (ADS)

Murina, Ezequiel L.; Fernández-Prini, Roberto; Pastorino, Claudio

2017-08-01

We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface. In bulk water, their conformations up to dodecane are mainly extended. However, larger alkanes like eicosane present a more stable collapsed conformation as they approach bulk water. We have characterized the more probable configurations in all interface and bulk regions. The results obtained are of interest for the study of biomatter processes requiring the transfer of hydrophobic matter, especially chain-like molecules like LCAs, from gas to bulk aqueous systems through the interface.

Free energy surfaces for the interaction of D-glucose with planar aromatic groups in aqueous solution

NASA Astrophysics Data System (ADS)

Wohlert, Jakob; Schnupf, Udo; Brady, John W.

2010-10-01

Multidimensional potentials of mean force for the interactions in aqueous solution of both anomers of D-glucopyranose with two planar aromatic molecules, indole and para-methyl-phenol, have been calculated using molecular dynamics simulations with umbrella sampling and were subsequently used to estimate binding free energies. Indole and para-methyl-phenol serve as models for the side chains of the amino acids tryptophan and tyrosine, respectively. In all cases, a weak affinity between the glucose molecules and the flat aromatic surfaces was found. The global minimum for these interactions was found to be for the case when the pseudoplanar face of β-D-glucopyranose is stacked against the planar surfaces of the aromatic residues. The calculated binding free energies are in good agreement with both experiment and previous simulations. The multidimensional free energy maps suggest a mechanism that could lend kinetic stability to the complexes formed by sugars bound to sugar-binding proteins.

Dynamic information for cardiotoxin protein desorption from a methyl-terminated self-assembled monolayer using steered molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Hung, Shih-Wei; Hsiao, Pai-Yi; Chieng, Ching-Chang

2011-05-01

Dynamic information, such as force, structural change, interaction energy, and potential of mean force (PMF), about the desorption of a single cardiotoxin (CTX) protein from a methyl-terminated self-assembled monolayer (SAM) surface was investigated by means of steered molecular dynamics (SMD) simulations. The simulation results indicated that Loop I is the first loop to depart from the SAM surface, which is in good agreement with the results of the nuclear magnetic resonance spectroscopy experiment. The free energy landscape and the thermodynamic force of the CTX desorption process was represented by the PMF and by the derivative of PMF with respect to distance, respectively. By applying Jarzynski's equality, the PMF can be reconstructed from the SMD simulation. The PMFs, calculated by different estimators based upon Jarzynski's equality, were compared with the conventional umbrella sampling method. The best estimation was obtained by using the fluctuation-dissipation estimator with a pulling velocity of v = 0.25 nm/ns for the present study.

Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces.

PubMed

Levine, Zachary A; Rapp, Michael V; Wei, Wei; Mullen, Ryan Gotchy; Wu, Chun; Zerze, Gül H; Mittal, Jeetain; Waite, J Herbert; Israelachvili, Jacob N; Shea, Joan-Emma

2016-04-19

Translating sticky biological molecules-such as mussel foot proteins (MFPs)-into synthetic, cost-effective underwater adhesives with adjustable nano- and macroscale characteristics requires an intimate understanding of the glue's molecular interactions. To help facilitate the next generation of aqueous adhesives, we performed a combination of surface forces apparatus (SFA) measurements and replica-exchange molecular dynamics (REMD) simulations on a synthetic, easy to prepare, Dopa-containing peptide (MFP-3s peptide), which adheres to organic surfaces just as effectively as its wild-type protein analog. Experiments and simulations both show significant differences in peptide adsorption on CH3-terminated (hydrophobic) and OH-terminated (hydrophilic) self-assembled monolayers (SAMs), where adsorption is strongest on hydrophobic SAMs because of orientationally specific interactions with Dopa. Additional umbrella-sampling simulations yield free-energy profiles that quantitatively agree with SFA measurements and are used to extract the adhesive properties of individual amino acids within the context of MFP-3s peptide adhesion, revealing a delicate balance between van der Waals, hydrophobic, and electrostatic forces.

Body proportions of circumpolar peoples as evidenced from skeletal data: Ipiutak and Tigara (Point Hope) versus Kodiak Island Inuit.

PubMed

Holliday, Trenton W; Hilton, Charles E

2010-06-01

Given the well-documented fact that human body proportions covary with climate (presumably due to the action of selection), one would expect that the Ipiutak and Tigara Inuit samples from Point Hope, Alaska, would be characterized by an extremely cold-adapted body shape. Comparison of the Point Hope Inuit samples to a large (n > 900) sample of European and European-derived, African and African-derived, and Native American skeletons (including Koniag Inuit from Kodiak Island, Alaska) confirms that the Point Hope Inuit evince a cold-adapted body form, but analyses also reveal some unexpected results. For example, one might suspect that the Point Hope samples would show a more cold-adapted body form than the Koniag, given their more extreme environment, but this is not the case. Additionally, univariate analyses seldom show the Inuit samples to be more cold-adapted in body shape than Europeans, and multivariate cluster analyses that include a myriad of body shape variables such as femoral head diameter, bi-iliac breadth, and limb segment lengths fail to effectively separate the Inuit samples from Europeans. In fact, in terms of body shape, the European and the Inuit samples tend to be cold-adapted and tend to be separated in multivariate space from the more tropically adapted Africans, especially those groups from south of the Sahara. Copyright 2009 Wiley-Liss, Inc.

Adaptive Sampling for Urban Air Quality through Participatory Sensing

PubMed Central

Zeng, Yuanyuan; Xiang, Kai

2017-01-01

Air pollution is one of the major problems of the modern world. The popularization and powerful functions of smartphone applications enable people to participate in urban sensing to better know about the air problems surrounding them. Data sampling is one of the most important problems that affect the sensing performance. In this paper, we propose an Adaptive Sampling Scheme for Urban Air Quality (AS-air) through participatory sensing. Firstly, we propose to find the pattern rules of air quality according to the historical data contributed by participants based on Apriori algorithm. Based on it, we predict the on-line air quality and use it to accelerate the learning process to choose and adapt the sampling parameter based on Q-learning. The evaluation results show that AS-air provides an energy-efficient sampling strategy, which is adaptive toward the varied outside air environment with good sampling efficiency. PMID:29099766

Evaluation of single and two-stage adaptive sampling designs for estimation of density and abundance of freshwater mussels in a large river

USGS Publications Warehouse

Smith, D.R.; Rogala, J.T.; Gray, B.R.; Zigler, S.J.; Newton, T.J.

2011-01-01

Reliable estimates of abundance are needed to assess consequences of proposed habitat restoration and enhancement projects on freshwater mussels in the Upper Mississippi River (UMR). Although there is general guidance on sampling techniques for population assessment of freshwater mussels, the actual performance of sampling designs can depend critically on the population density and spatial distribution at the project site. To evaluate various sampling designs, we simulated sampling of populations, which varied in density and degree of spatial clustering. Because of logistics and costs of large river sampling and spatial clustering of freshwater mussels, we focused on adaptive and non-adaptive versions of single and two-stage sampling. The candidate designs performed similarly in terms of precision (CV) and probability of species detection for fixed sample size. Both CV and species detection were determined largely by density, spatial distribution and sample size. However, designs did differ in the rate that occupied quadrats were encountered. Occupied units had a higher probability of selection using adaptive designs than conventional designs. We used two measures of cost: sample size (i.e. number of quadrats) and distance travelled between the quadrats. Adaptive and two-stage designs tended to reduce distance between sampling units, and thus performed better when distance travelled was considered. Based on the comparisons, we provide general recommendations on the sampling designs for the freshwater mussels in the UMR, and presumably other large rivers.

Sample rotating turntable kit for infrared spectrometers

DOEpatents

Eckels, Joel Del [Livermore, CA; Klunder, Gregory L [Oakland, CA

2008-03-04

An infrared spectrometer sample rotating turntable kit has a rotatable sample cup containing the sample. The infrared spectrometer has an infrared spectrometer probe for analyzing the sample and the rotatable sample cup is adapted to receive the infrared spectrometer probe. A reflectance standard is located in the rotatable sample cup. A sleeve is positioned proximate the sample cup and adapted to receive the probe. A rotator rotates the rotatable sample cup. A battery is connected to the rotator.

Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model.

PubMed

Plotnikov, Nikolay V

2014-08-12

Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower level of accuracy from coarse-physics sampling. The method is analytically derived in terms of the umbrella sampling and the free-energy perturbation methods which are combined with the thermodynamic cycle and the targeted sampling strategy of the paradynamics approach. The algorithm starts by computing low-accuracy fine-physics free-energy surfaces from the coarse-physics sampling in order to identify the reaction path and to select regions for targeted sampling. Thus, the algorithm does not rely on the coarse-physics minimum free-energy reaction path. Next, segments of high-accuracy free-energy surface are computed locally at selected regions from the targeted fine-physics sampling and are positioned relative to the coarse-physics free-energy shifts. The positioning is done by averaging the free-energy perturbations computed with multistep linear response approximation method. This method is analytically shown to provide results of the thermodynamic integration and the free-energy interpolation methods, while being extremely simple in implementation. Incorporating the metadynamics sampling to the algorithm is also briefly outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM free-energy barrier for an enzymatic reaction using a semiempirical PM6/MM reference potential. These modifications allow computing the activation free energies at a significantly reduced computational cost but at the same level of accuracy compared to computing full potential of mean force.

Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model

PubMed Central

2015-01-01

Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower level of accuracy from coarse-physics sampling. The method is analytically derived in terms of the umbrella sampling and the free-energy perturbation methods which are combined with the thermodynamic cycle and the targeted sampling strategy of the paradynamics approach. The algorithm starts by computing low-accuracy fine-physics free-energy surfaces from the coarse-physics sampling in order to identify the reaction path and to select regions for targeted sampling. Thus, the algorithm does not rely on the coarse-physics minimum free-energy reaction path. Next, segments of high-accuracy free-energy surface are computed locally at selected regions from the targeted fine-physics sampling and are positioned relative to the coarse-physics free-energy shifts. The positioning is done by averaging the free-energy perturbations computed with multistep linear response approximation method. This method is analytically shown to provide results of the thermodynamic integration and the free-energy interpolation methods, while being extremely simple in implementation. Incorporating the metadynamics sampling to the algorithm is also briefly outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM free-energy barrier for an enzymatic reaction using a semiempirical PM6/MM reference potential. These modifications allow computing the activation free energies at a significantly reduced computational cost but at the same level of accuracy compared to computing full potential of mean force. PMID:25136268

Do as We Do and Not as We Say: Teacher Educators Supporting Student Teachers to Learn on Teaching Practice

ERIC Educational Resources Information Center

Chambers, Fiona C.; Armour, Kathleen M.

2011-01-01

This paper reports data from a larger study into the ways in which Physical Education Teacher Education (PETE) students engaged in professional learning during teaching practice (TP) in Ireland. The study comprised one umbrella case study of Greendale University, schools and PETE students that consisted of five individual cases: tetrads of PETE…

Controlled Synthesis of Nanomaterials at the Undergraduate Laboratory: Cu(OH)[subscript 2] and CuO Nanowires

ERIC Educational Resources Information Center

da Silva, Anderson G. M.; Rodrigues, Thenner S.; Parussulo, Andre´ L. A.; Candido, Eduardo G.; Geonmonond, Rafael S.; Brito, Hermi F.; Toma, Henrique E.; Camargo, Pedro H. C.

2017-01-01

Undergraduate-level laboratory experiments that involve the synthesis of nanomaterials with well-defined/controlled shapes are very attractive under the umbrella of nanotechnology education. Herein we describe a low-cost and facile experiment for the synthesis of Cu(OH)[subscript 2] and CuO nanowires comprising three main parts: (i) synthesis of…

Cedar Middle School's Response to Intervention Journey: A Systematic, Multi-Tier, Problem-Solving Approach to Program Implementation

ERIC Educational Resources Information Center

Dulaney, Shannon Kay

2010-01-01

The purpose of the present study was to record Cedar Middle School's (CMS) response to intervention implementation journey. It is a qualitative case study that examines one school's efforts to bring school improvements under the response to inventory (RtI) umbrella in order to achieve a more systematic approach to providing high-quality…

Multi-scale data to assess and monitor sudden oak death

Treesearch

Lisa M. Levien; Chris S. Fischer; Lianne C. Mahon; Jeff A. Mai

2002-01-01

The USDA Forest Service (FS) and California Department of Forestry and Fire Protection (CDF) are monitoring Sudden Oak Death (SOD) under the umbrella of the larger California Land Cover Mapping and Monitoring Program (LCMMP). The LCMMP is a statewide cooperative effort among the FS and CDF focused on mapping and monitoring California’s vegetation and land cover.

"Boys Don't Cry," a Movie Review: Implications for Counseling Persons Who Are Transgendered

ERIC Educational Resources Information Center

Aguilar, Jinnelle Veronique

2010-01-01

People who fall under the umbrella of transgender belong to one of the most marginalized groups within society. Many who do not pass within the gender binary categories imposed by social norms experience discrimination and marginalization. In this article, the author discusses the film "Boys Don't Cry" and introduces the reader to the varieties of…

Environmental Education Guide, Volume 3: An Environmental/Energy Education Primer for Grades Seven through Nine, 1981-84.

ERIC Educational Resources Information Center

Sly, Carolie; Rose, Larry

As one of four volumes in a K-12 series, this teaching guide contains classroom and outdoor activities pertaining to the environment and energy for seventh through ninth grades. The guide was developed based upon the understanding that environmental education can serve as an instructional umbrella covering many topics (conservation, marine…

Environmental Education Guide, Volume 2: An Environmental/Energy Education Primer for Grades Four through Six, 1981-1984.

ERIC Educational Resources Information Center

Sly, Carolie; Rose, Larry

As one of four volumes in a K-12 series, this teaching guide contains classroom and outdoor activities pertaining to the environment and energy for fourth through sixth grades. The guide was developed based upon the understanding that environmental education can serve as an instructional umbrella covering many topics (conservation, marine…

Environmental Education Guide, Volume 4: An Environmental/Energy Education Primer for Grades Ten through Twelve, 1981-1984.

ERIC Educational Resources Information Center

Sly, Carolie; Rose, Larry

As one of four volumes in a K-12 series, this teaching guide contains classroom and outdoor activities pertaining to the environment and energy for tenth through twelfth grades. The guide was developed based upon the understanding that environmental education can serve as an instructional umbrella covering many topics (conservation, marine…

Environmental Education Guide, Volume 1: An Environmental/Energy Education Primer for Kindergarten through Grade Three, 1981-1984.

ERIC Educational Resources Information Center

Sly, Carolie; Rose, Larry

As one of four volumes in a K-12 series, this teaching guide contains classroom and outdoor activities pertaining to the environment and energy for kindergarten through third grades. The guide was developed based upon the understanding that environmental education can serve as an instructional umbrella covering many topics (conservation, marine…

Teaching Other People's Children, Elsewhere, for a While: The Rhetoric of a Travelling Educational Reform

ERIC Educational Resources Information Center

Ellis, Viv; Maguire, Meg; Trippestad, Tom Are; Liu, Yunqiu; Yang, Xiaowei; Zeichner, Kenneth

2016-01-01

Teach for All is a good example of a globally travelling educational reform policy. In this article, we examine the rhetoric of the reform through an analysis of its public discourse, specifically the websites for the umbrella organization, 3 of its 35 constituent projects (Teach for America, Teach First and Teach for China) and one associated…

Musicking in the City: Reconceptualizing Urban Music Education as Cultural Practice

ERIC Educational Resources Information Center

Gaztambide-Fernandez, Ruben A.

2011-01-01

Descriptions of the urban contemporary format remain strongly grounded on the assumption that it is based on musical styles associated with African Americans, such as R&B, soul, hip hop, rap, and reggae. Even for the most progressive educators, to speak of urban music is to refer to a narrow set of musical genres associated with the umbrella term…

The Teaching of Complementary and Alternative Medicine in U.S. Medical Schools: A Survey of Course Directors.

ERIC Educational Resources Information Center

Brokaw, James J.; Tunnicliff, Godfrey; Raess, Beat U.; Saxon, Dale W.

2002-01-01

Surveyed medical schools to gauge the current state of complementary and alternative medicine (CAM) instruction by gathering details about the specific topics being taught and the objectives behind the instruction. Found that a wide variety of topics are being taught under the umbrella of CAM; for the most part, the instruction appears to be…

Data from: An Analysis of Nearly One Billion Dollars of Aquaculture Grants

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Us Search  Log inRegister Home Home Datasets Data from: An Analysis of Nearly One Billion Dollars : An Analysis of Nearly One Billion Dollars of Aquaculture Grants made by the United States Federal , or other details for analysis. A limited number of umbrella grants were issued to one institution

Connected Code: Why Children Need to Learn Programming. MacArthur Foundation Series on Digital Media and Learning

ERIC Educational Resources Information Center

Kafai, Yasmin B.; Burke, Quinn

2014-01-01

Coding, once considered an arcane craft practiced by solitary techies, is now recognized by educators and theorists as a crucial skill, even a new literacy, for all children. Programming is often promoted in K-12 schools as a way to encourage "computational thinking"--which has now become the umbrella term for understanding what computer…

Suggestions for the Design of E-Learning Environments to Enhance Learner Self-Efficacy

ERIC Educational Resources Information Center

Hodges, Charles B.

2013-01-01

In this paper e-learning is used as an umbrella term for all types of learning involving technology. Graesser et al (2007) note that technologies for learning exist that allow for e-learning systems to be much more than information delivery systems, but "unfortunately, the learning strategies of most students are extremely limited, so the…

Title I/PSEN Individualized Reading and Math Services for the Handicapped, 1980-81. Final Evaluation Report.

ERIC Educational Resources Information Center

New York City Board of Education, Brooklyn, NY. Office of Educational Evaluation.

The Title I Umbrella Program provided compensatory instruction in reading, mathematics, and writing to 24,000 mildly or moderately handicapped students in New York City. The program was comprised of seven discrete components for the remediation of reading and writing skills, five after-school models, and two components for the remediation of math…

The Effect of Executive Function on Science Achievement among Normally Developing 10-Year Olds

ERIC Educational Resources Information Center

Lederman, Sheri G.

2012-01-01

Executive function (EF) is an umbrella term used to identify a set of discrete but interrelated cognitive abilities that enable individuals to engage in goal-directed, future-oriented action in response to a novel context. Developmental studies indicate that EF is predictive of reading and math achievement in middle childhood. The purpose of this…

Jean Vigo's "Zéro De Conduite" and the Spaces of Revolt

ERIC Educational Resources Information Center

Vanobbergen, Bruno; Grosvenor, Ian; Simon, Frank

2014-01-01

In this article we will contribute to the contemporary theoretical debate about film by considering, from a history-of-education perspective, the film "Zéro de conduite" by Jean Vigo (1905--1934). This film is classified under the umbrella of "poetic realism": a product of "cinéma de gauche" and an avant-gardist,…

Policy Dialogue and Target Setting: Do Current Indicators of Education for All Signify Progress?

ERIC Educational Resources Information Center

Lewin, Keith M.

2011-01-01

Governments and development agencies met at Jomtien in 1990 and Dakar in 2000 and committed themselves to achieve "Education for All" (EFA). Most aid to education is now the umbrella of EFA and its associated goals, targets and indicators. This paper selects some of the indicators used for EFA and analyses their strengths and weaknesses. Gross and…

"You Can Stand under My Umbrella": Immersion, Clil and Bilingual Education. a Response to Cenoz, Genesee & Gorter (2013)

ERIC Educational Resources Information Center

Dalton-Puffer, Christiane; Llinares, Ana; Lorenzo, Francisco; Nikula, Tarja

2014-01-01

Classrooms the world over are full of people who, for different reasons, are learning additional languages and/or are studying through languages that are not their first. Gaining insight into such contexts is complicated for researchers and practitioners alike by the myriad of contextual variables that come with different implementations and make…

IUPESM: the international umbrella organisation for biomedical engineering and medical physics.

PubMed

Nagel, Jh

2007-07-01

An account of the development, aims and activities of the International Union for Physical and Engineering Sciences in Medicine (IUPESM) is presented. Associations with the International Council of Science (ICSU) and the World Health Organization (WHO) are leading to exciting new projects towards improving global health, healthcare, quality of life and support of health technologies in developing countries.

Tinkering with Student Journalists: Protest as Prologue to a Free Press in the 21st Century.

ERIC Educational Resources Information Center

Eveslage, Thomas

Twenty-eight years ago three students in Des Moines, Iowa who wore black armbands to protest the war in Vietnam were suspended from school. When the 1969 landmark Supreme Court case of "Tinker v. Des Moines Independent School District" brought public school pupils under the First Amendment umbrella, many educators began to…

Developing a Culture of Respecting Difference in Early Childhood Centers in Northern Ireland

ERIC Educational Resources Information Center

Fitzpatrick, Siobhan

2007-01-01

The Northern Ireland Pre-School Playgroup Association, now known as NIPPA--the Early Years Organisation, was founded in 1965. The history of NIPPA has been strongly influenced by the sectarian conflict between the Republicans and the Loyalists. NIPPA is an umbrella organization that provides a range of support to its 1,200 member groups. This…

Lessons and Impressions of the Czech Capital Markets

DTIC Science & Technology

2012-02-13

violently broke up a peaceful pro- democracy demonstration and brutally beat many student participants. In the days that followed, political groups ...united to become the Civic Forum, an umbrella group championing bureaucratic reform and civil liberties. Faced with an overwhelming popular...banks. Belgian KBC Bank acquired ČSOB in 1999 and Erste Group , a leading Austrian financial institution, acquired Ceska Sporitelna in 2000

Components Needed for the Design of a Sustainable Career and Technical Education Program

ERIC Educational Resources Information Center

Lassiter, Vann Mizzelle

2012-01-01

As education has changed to meet the needs of society and has been shaped by the enactment of new laws, various aspects included under the massive umbrella of education have also changed to maintain momentum One such educational program is career and technical education (CTE). Changes to CTE have been made to continually meet the needs of all…

School Community Education Program in New York City, 1984-85. Volume IV: OEA Final Evaluation Report.

ERIC Educational Resources Information Center

New York City Board of Education, Brooklyn. Office of Educational Assessment.

In 1984-85, the New York City Public Schools received $2,374,686 from the state legislature to operate the School Community Education Program (also known as the Umbrella Program). The program consisted of 46 different projects designed to provide innovative solutions to local educational and school problems. Thirteen of these projects are…

Reasons to Be Cheerful: The Story of One Community School and the New Labour Government

ERIC Educational Resources Information Center

Simmons, Katy

2010-01-01

This article was originally presented at a seminar run by the Secondary Umbrella Group on the theme of "A Review of Labour's Achievement: Where next for secondary education?" It looks at the struggle of one secondary school and its local community to improve educational opportunities and life chances for its students. The author, a…

New Literacies and the Common Core

ERIC Educational Resources Information Center

Kist, William

2013-01-01

It makes sense that an emphasis on new ways of reading and writing fits easily within the Common Core umbrella. After all, a primary thrust of the new standards is college and career readiness. How can young people be prepared to thrive in today's society--in which people are connected 24 hours a day by media and coworkers may well live in…

A Case Study of Cooperative Learning in Bushenyi District in Uganda: Educational Leaders' and Teachers' Perceptions

ERIC Educational Resources Information Center

Mujuni, John Bosco

2015-01-01

In 2003-2007, the government of Uganda through the Ministry of Education and Sports (MoES), under the umbrella of UPHOLD and in Partnership with USAID, introduced cooperative learning as a "student-centered teaching approach" in some selected districts and schools in Uganda. This dissertation explored the current state and practice of…

A Measurement of Charter School Efficiency in North Carolina Utilizing Modified Quadriform Analysis

ERIC Educational Resources Information Center

Sturdevant, Daniel C.

2017-01-01

Charter schools exist under the umbrella of public education, but are not subject to the same level of public oversight or accountability measures as traditional public schools in North Carolina and many other states (BiFulco and Ladd, 2006, Bettinger, 2004). There is a lack of easily accessible efficiency data on charter schools. The primary aim…

The 4-H Club Meeting: An Essential Youth Development Strategy

ERIC Educational Resources Information Center

Cassels, Alicia; Post, Liz; Nestor, Patrick I.

2015-01-01

The club meeting has served as a key delivery method for 4-H programming across the United States throughout its history. A survey of WV 4-H community club members reinforces the body of evidence that the 4-H club meeting is an effective vehicle for delivering positive youth learning opportunities within the umbrella of the Essential Elements of…

Suil Eile: Another Way of Seeing Minority Language Broadcasting

ERIC Educational Resources Information Center

Kenny, Colum

2005-01-01

This paper examines, in their social context, the origins and history of TG4. It notes that TG4 broadcasts mainly but by no means exclusively in the Irish language, being one of the Republic of Ireland's four national terrestrial television services and one of three operated under the umbrella of the state-owned RTE. The paper focuses on the…

Linking Marxism, Globalization, and Citizenship Education: Toward a Comparative and Critical Pedagogy Post 9/11

ERIC Educational Resources Information Center

Ibrahim, Awad

2007-01-01

In a post-9/11 world, where the politics of "us" versus "them" has reemerged under the umbrella of terrorism, especially in the United States, can we still envision an "education sans frontires": a globalized and critical praxis of citizenship education in which there are no borders? If it is possible to conceive it,…

Computational Fluid Dynamics Simulation of Flows in an Oxidation Ditch Driven by a New Surface Aerator.

PubMed

Huang, Weidong; Li, Kun; Wang, Gan; Wang, Yingzhe

2013-11-01

In this article, we present a newly designed inverse umbrella surface aerator, and tested its performance in driving flow of an oxidation ditch. Results show that it has a better performance in driving the oxidation ditch than the original one with higher average velocity and more uniform flow field. We also present a computational fluid dynamics model for predicting the flow field in an oxidation ditch driven by a surface aerator. The improved momentum source term approach to simulate the flow field of the oxidation ditch driven by an inverse umbrella surface aerator was developed and validated through experiments. Four kinds of turbulent models were investigated with the approach, including the standard k - ɛ model, RNG k - ɛ model, realizable k - ɛ model, and Reynolds stress model, and the predicted data were compared with those calculated with the multiple rotating reference frame approach (MRF) and sliding mesh approach (SM). Results of the momentum source term approach are in good agreement with the experimental data, and its prediction accuracy is better than MRF, close to SM. It is also found that the momentum source term approach has lower computational expenses, is simpler to preprocess, and is easier to use.