Facilitated diffusion in chromatin lattices: mechanistic diversity and regulatory potential.

PubMed

Kampmann, Martin

2005-08-01

The interaction between a protein and a specific DNA site is the molecular basis for vital processes in all organisms. Location of the DNA target site by the protein commonly involves facilitated diffusion. Mechanisms of facilitated diffusion vary among proteins; they include one- and two-dimensional sliding along DNA, direct transfer between uncorrelated sites, as well as combinations of these mechanisms. Facilitated diffusion has almost exclusively been studied in vitro. This review discusses facilitated diffusion in the context of the living cell and proposes a theoretical model for facilitated diffusion in chromatin lattices. Chromatin structure differentially affects proteins in different modes of diffusion. The interplay of facilitated diffusion and chromatin structure can determine the rate of protein association with the target site, the frequency of association-dissociation events at the target site, and, under particular conditions, the occupancy of the target site. Facilitated diffusion is required in vivo for efficient DNA repair and bacteriophage restriction and has potential roles in fine-tuning gene regulatory networks and kinetically compartmentalizing the eukaryotic nucleus.

Disturbance and density-dependent processes (competition and facilitation) influence the fine-scale genetic structure of a tree species' population.

PubMed

Fajardo, Alex; Torres-Díaz, Cristian; Till-Bottraud, Irène

2016-01-01

Disturbances, dispersal and biotic interactions are three major drivers of the spatial distribution of genotypes within populations, the last of which has been less studied than the other two. This study aimed to determine the role of competition and facilitation in the degree of conspecific genetic relatedness of nearby individuals of tree populations. It was expected that competition among conspecifics will lead to low relatedness, while facilitation will lead to high relatedness (selection for high relatedness within clusters). The stand structure and spatial genetic structure (SGS) of trees were examined within old-growth and second-growth forests (including multi-stemmed trees at the edge of forests) of Nothofagus pumilio following large-scale fires in Patagonia, Chile. Genetic spatial autocorrelations were computed on a spatially explicit sampling of the forests using five microsatellite loci. As biotic plant interactions occur among immediate neighbours, mean nearest neighbour distance (MNND) among trees was computed as a threshold for distinguishing the effects of disturbances and biotic interactions. All forests exhibited a significant SGS for distances greater than the MNND. The old-growth forest genetic and stand structure indicated gap recolonization from nearby trees (significantly related trees at distances between 4 and 10 m). At distances smaller than the MNND, trees of the second-growth interior forest showed significantly lower relatedness, suggesting a fading of the recolonization structure by competition, whereas the second-growth edge forest showed a positive and highly significant relatedness among trees (higher among stems of a cluster than among stems of different clusters), resulting from facilitation. Biotic interactions are shown to influence the genetic composition of a tree population. However, facilitation can only persist if individuals are related. Thus, the genetic composition in turn influences what type of biotic interactions

Woody structure facilitates invasion of woody plants by providing perches for birds.

PubMed

Prather, Chelse M; Huynh, Andrew; Pennings, Steven C

2017-10-01

Woody encroachment threatens prairie ecosystems globally, and thus understanding the mechanisms that facilitate woody encroachment is of critical importance. Coastal tallgrass prairies along the Gulf Coast of the US are currently threatened by the spread of several species of woody plants. We studied a coastal tallgrass prairie in Texas, USA, to determine if existing woody structure increased the supply of seeds from woody plants via dispersal by birds. Specifically, we determined if (i) more seedlings of an invasive tree ( Tridacia sebifera ) are present surrounding a native woody plant ( Myrica cerifera ); (ii) wooden perches increase the quantity of seeds dispersed to a grassland; and (iii) perches alter the composition of the seed rain seasonally in prairie habitats with differing amounts of native and invasive woody vegetation, both underneath and away from artificial wooden perches. More T. sebifera seedlings were found within M. cerifera patches than in graminoid-dominated areas. Although perches did not affect the total number of seeds, perches changed the composition of seed rain to be less dominated by grasses and forbs. Specifically, 20-30 times as many seeds of two invasive species of woody plants were found underneath perches independent of background vegetation, especially during months when seed rain was highest. These results suggest that existing woody structure in a grassland can promote further woody encroachment by enhancing seed dispersal by birds. This finding argues for management to reduce woody plant abundance before exotic plants set seeds and argues against the use of artificial perches as a restoration technique in grasslands threatened by woody species.

Germination phenology determines the propensity for facilitation and competition.

PubMed

Leverett, Lindsay D

2017-09-01

A single plant can interact both positively and negatively with its neighbors through the processes of facilitation and competition, respectively. Much of the variation in the balance of facilitation and competition that individuals experience can be explained by the degree of physical stress and the sizes or ages of plants during the interaction. Germination phenology partly controls both of these factors, but its role in defining the facilitation-competition balance has not been explicitly considered. I performed an experiment in a population of the winter annual Arabidopsis thaliana (Brassicaceae) to test whether germinating during physically stressful periods leads to facilitation while germinating during periods that promote growth and reproduction leads to competition. I manipulated germination and neighbor presence across two years in order to quantify the effects of the local plant community on survival, fecundity, and total fitness as a function of germination phenology. Neighbors increased survival when germination occurred under conditions that were unsuitable for survival, but they reduced fecundity in germinants that were otherwise the most fecund. Later germination was associated with facilitation in the first year but competition in the second year. These episodes of facilitation and competition opposed each other, leading to no net effect of neighbors when averaged over all cohorts. These results indicate that variation in germination timing can explain some of the variation in the facilitation-competition balance in plant communities. © 2017 by the Ecological Society of America.

How self-determined choice facilitates performance: a key role of the ventromedial prefrontal cortex.

PubMed

Murayama, Kou; Matsumoto, Madoka; Izuma, Keise; Sugiura, Ayaka; Ryan, Richard M; Deci, Edward L; Matsumoto, Kenji

2015-05-01

Recent studies have documented that self-determined choice does indeed enhance performance. However, the precise neural mechanisms underlying this effect are not well understood. We examined the neural correlates of the facilitative effects of self-determined choice using functional magnetic resonance imaging (fMRI). Participants played a game-like task involving a stopwatch with either a stopwatch they selected (self-determined-choice condition) or one they were assigned without choice (forced-choice condition). Our results showed that self-determined choice enhanced performance on the stopwatch task, despite the fact that the choices were clearly irrelevant to task difficulty. Neuroimaging results showed that failure feedback, compared with success feedback, elicited a drop in the vmPFC activation in the forced-choice condition, but not in the self-determined-choice condition, indicating that negative reward value associated with the failure feedback vanished in the self-determined-choice condition. Moreover, the vmPFC resilience to failure in the self-determined-choice condition was significantly correlated with the increased performance. Striatal responses to failure and success feedback were not modulated by the choice condition, indicating the dissociation between the vmPFC and striatal activation pattern. These findings suggest that the vmPFC plays a unique and critical role in the facilitative effects of self-determined choice on performance. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.

PubMed

Bailey, Lucas J; Sheehy, Kimberly M; Dominik, Pawel K; Liang, Wenguang G; Rui, Huan; Clark, Michael; Jaskolowski, Mateusz; Kim, Yejoon; Deneka, Dawid; Tang, Wei-Jen; Kossiakoff, Anthony A

2018-02-02

Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the "elbow" regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab-antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones. Copyright © 2017 Elsevier Ltd. All rights reserved.

Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations.

PubMed

Martins, Suzana Cláudia Silveira; Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

2016-01-01

There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation.

Direct Determination of Atomic Structure and Magnetic Coupling of Magnetite Twin Boundaries.

PubMed

Chen, Chunlin; Li, Hongping; Seki, Takehito; Yin, Deqiang; Sanchez-Santolino, Gabriel; Inoue, Kazutoshi; Shibata, Naoya; Ikuhara, Yuichi

2018-03-27

Clarifying how the atomic structure of interfaces/boundaries in materials affects the magnetic coupling nature across them is of significant academic value and will facilitate the development of state-of-the-art magnetic devices. Here, by combining atomic-resolution transmission electron microscopy, atomistic spin-polarized first-principles calculations, and differential phase contrast imaging, we conduct a systematic investigation of the atomic and electronic structures of individual Fe 3 O 4 twin boundaries (TBs) and determine their concomitant magnetic couplings. We demonstrate that the magnetic coupling across the Fe 3 O 4 TBs can be either antiferromagnetic or ferromagnetic, which directly depends on the TB atomic core structures and resultant electronic structures within a few atomic layers. Revealing the one-to-one correspondence between local atomic structures and magnetic properties of individual grain boundaries will shed light on in-depth understanding of many interesting magnetic behaviors of widely used polycrystalline magnetic materials, which will surely promote the development of advanced magnetic materials and devices.

Facilitating the openEHR approach - organizational structures for defining high-quality archetypes.

PubMed

Kohl, Christian Dominik; Garde, Sebastian; Knaup, Petra

2008-01-01

Using openEHR archetypes to establish an electronic patient record promises rapid development and system interoperability by using or adopting existing archetypes. However, internationally accepted, high quality archetypes which enable a comprehensive semantic interoperability require adequate development and maintenance processes. Therefore, structures have to be created involving different health professions. In the following we present a model which facilitates and governs distributed but cooperative development and adoption of archetypes by different professionals including peer reviews. Our model consists of a hierarchical structure of professional committees and descriptions of the archetype development process considering these different committees.

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations

PubMed Central

Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

2016-01-01

There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation. PMID:26904719

Structured Uncertainty Bound Determination From Data for Control and Performance Validation

NASA Technical Reports Server (NTRS)

Lim, Kyong B.

2003-01-01

This report attempts to document the broad scope of issues that must be satisfactorily resolved before one can expect to methodically obtain, with a reasonable confidence, a near-optimal robust closed loop performance in physical applications. These include elements of signal processing, noise identification, system identification, model validation, and uncertainty modeling. Based on a recently developed methodology involving a parameterization of all model validating uncertainty sets for a given linear fractional transformation (LFT) structure and noise allowance, a new software, Uncertainty Bound Identification (UBID) toolbox, which conveniently executes model validation tests and determine uncertainty bounds from data, has been designed and is currently available. This toolbox also serves to benchmark the current state-of-the-art in uncertainty bound determination and in turn facilitate benchmarking of robust control technology. To help clarify the methodology and use of the new software, two tutorial examples are provided. The first involves the uncertainty characterization of a flexible structure dynamics, and the second example involves a closed loop performance validation of a ducted fan based on an uncertainty bound from data. These examples, along with other simulation and experimental results, also help describe the many factors and assumptions that determine the degree of success in applying robust control theory to practical problems.

Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination.

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

Stols, L.; Sanville Millard, C.; Dementieva, I.

2004-03-01

A simplified approach developed recently for the production of heterologous proteins in Escherichia coli uses 2-liter polyethylene terephthalate beverage bottles as disposable culture vessels [Sanville Millard, C. et al. 2003. Protein Expr. Purif. 29, 311-320]. The method greatly reduces the time and effort needed to produce native proteins for structural or functional studies. We now demonstrate that the approach is also well suited for production of proteins in defined media with incorporation of selenomethionine to facilitate structure determination by multiwavelength anomalous diffraction. Induction of a random set of Bacillus stearothermophilus target genes under the new protocols generated soluble selenomethionyl proteinsmore » in good yield. Several selenomethionyl proteins were purified in good yields and three were subjected to amino acid analysis. Incorporation of selenomethionine was determined to be greater than 95% in one protein and greater than 98% in the other two. In the preceding paper [Zhao et al., this issue, pp. 87-93], the approach is further extended to production of [U-15N]- or [U-13C, U-15N]-labeled proteins. The approach thus appears suitable for high-throughput production of proteins for structure determination by X-ray crystallography or nuclear magnetic resonance spectroscopy.« less

Maintaining gender sensitivity in the family practice: facilitators and barriers.

PubMed

Celik, Halime; Lagro-Janssen, Toine; Klinge, Ineke; van der Weijden, Trudy; Widdershoven, Guy

2009-12-01

This study aims to identify the facilitators and barriers perceived by General Practitioners (GPs) to maintain a gender perspective in family practice. Nine semi-structured interviews were conducted among nine pairs of GPs. The data were analysed by means of deductive content analysis using theory-based methods to generate facilitators and barriers to gender sensitivity. Gender sensitivity in family practice can be influenced by several factors which ultimately determine the extent to which a gender sensitive approach is satisfactorily practiced by GPs in the doctor-patient relationship. Gender awareness, repetition and reminders, motivation triggers and professional guidelines were found to facilitate gender sensitivity. On the other hand, lacking skills and routines, scepticism, heavy workload and the timing of implementation were found to be barriers to gender sensitivity. While the potential effect of each factor affecting gender sensitivity in family practice has been elucidated, the effects of the interplay between these factors still need to be determined.

Velocity Structure Determination Through Seismic Waveform Modeling and Time Deviations

NASA Astrophysics Data System (ADS)

Savage, B.; Zhu, L.; Tan, Y.; Helmberger, D. V.

2001-12-01

Through the use of seismic waveforms recorded by TriNet, a dataset of earthquake focal mechanisms and deviations (time shifts) relative to a standard model facilitates the investigation of the crust and uppermost mantle of southern California. The CAP method of focal mechanism determination, in use by TriNet on a routine basis, provides time shifts for surface waves and Pnl arrivals independently relative to the reference model. These shifts serve as initial data for calibration of local and regional seismic paths. Time shifts from the CAP method are derived by splitting the Pnl section of the waveform, the first arriving Pn to just before the arrival of the S wave, from the much slower surface waves then cross-correlating the data with synthetic waveforms computed from a standard model. Surface waves interact with the entire crust, but the upper crust causes the greatest effect. Whereas, Pnl arrivals sample the deeper crust, upper mantle, and source region. This natural division separates the upper from lower crust for regional calibration and structural modeling and allows 3-D velocity maps to be created using the resulting time shifts. Further examination of Pnl and other arrivals which interact with the Moho illuminate the complex nature of this boundary. Initial attempts at using the first 10 seconds of the Pnl section to determine upper most mantle structure have proven insightful. Two large earthquakes north of southern California in Nevada and Mammoth Lakes, CA allow the creation of record sections from 200 to 600 km. As the paths swing from east to west across southern California, simple 1-D models turn into complex structure, dramatically changing the waveform character. Using finite difference models to explain the structure, we determine that a low velocity zone is present at the base of the crust and extends to 100 km in depth. Velocity variations of 5 percent of the mantle in combination with steeply sloping edges produces complex waveform variations

Proposed structure of putative glucose channel in GLUT1 facilitative glucose transporter.

PubMed Central

Zeng, H; Parthasarathy, R; Rampal, A L; Jung, C Y

1996-01-01

A family of structurally related intrinsic membrane proteins (facilitative glucose transporters) catalyzes the movement of glucose across the plasma membrane of animal cells. Evidence indicates that these proteins show a common structural motif where approximately 50% of the mass is embedded in lipid bilayer (transmembrane domain) in 12 alpha-helices (transmembrane helices; TMHs) and accommodates a water-filled channel for substrate passage (glucose channel) whose tertiary structure is currently unknown. Using recent advances in protein structure prediction algorithms we proposed here two three-dimensional structural models for the transmembrane glucose channel of GLUT1 glucose transporter. Our models emphasize the physical dimension and water accessibility of the channel, loop lengths between TMHs, the macrodipole orientation in four-helix bundle motif, and helix packing energy. Our models predict that five TMHs, either TMHs 3, 4, 7, 8, 11 (Model 1) or TMHs 2, 5, 11, 8, 7 (Model 2), line the channel, and the remaining TMHs surround these channel-lining TMHs. We discuss how our models are compatible with the experimental data obtained with this protein, and how they can be used in designing new biochemical and molecular biological experiments in elucidation of the structural basis of this important protein function. Images FIGURE 1 FIGURE 2 FIGURE 4 FIGURE 5 PMID:8770183

Competition and facilitation structure plant communities under nurse tree canopies in extremely stressful environments.

PubMed

Al-Namazi, Ali A; El-Bana, Magdy I; Bonser, Stephen P

2017-04-01

Nurse plant facilitation in stressful environments can produce an environment with relatively low stress under its canopy. These nurse plants may produce the conditions promoting intense competition between coexisting species under the canopy, and canopies may establish stress gradients, where stress increases toward the edge of the canopy. Competition and facilitation on these stress gradients may control species distributions in the communities under canopies. We tested the following predictions: (1) interactions between understory species shift from competition to facilitation in habitats experiencing increasing stress from the center to the edge of canopy of a nurse plant, and (2) species distributions in understory communities are controlled by competitive interactions at the center of canopy, and facilitation at the edge of the canopy. We tested these predictions using a neighbor removal experiment under nurse trees growing in arid environments. Established individuals of each of four of the most common herbaceous species in the understory were used in the experiment. Two species were more frequent in the center of the canopy, and two species were more frequent at the edge of the canopy. Established individuals of each species were subjected to neighbor removal or control treatments in both canopy center and edge habitats. We found a shift from competitive to facilitative interactions from the center to the edge of the canopy. The shift in the effect of neighbors on the target species can help to explain species distributions in these canopies. Canopy-dominant species only perform well in the presence of neighbors in the edge microhabitat. Competition from canopy-dominant species can also limit the performance of edge-dominant species in the canopy microhabitat. The shift from competition to facilitation under nurse plant canopies can structure the understory communities in extremely stressful environments.

Argument structure hierarchy system and method for facilitating analysis and decision-making processes

DOEpatents

Janssen, Terry

2000-01-01

A system and method for facilitating decision-making comprising a computer program causing linkage of data representing a plurality of argument structure units into a hierarchical argument structure. Each argument structure unit comprises data corresponding to a hypothesis and its corresponding counter-hypothesis, data corresponding to grounds that provide a basis for inference of the hypothesis or its corresponding counter-hypothesis, data corresponding to a warrant linking the grounds to the hypothesis or its corresponding counter-hypothesis, and data corresponding to backing that certifies the warrant. The hierarchical argument structure comprises a top level argument structure unit and a plurality of subordinate level argument structure units. Each of the plurality of subordinate argument structure units comprises at least a portion of the grounds of the argument structure unit to which it is subordinate. Program code located on each of a plurality of remote computers accepts input from one of a plurality of contributors. Each input comprises data corresponding to an argument structure unit in the hierarchical argument structure and supports the hypothesis or its corresponding counter-hypothesis. A second programming code is adapted to combine the inputs into a single hierarchical argument structure. A third computer program code is responsive to the second computer program code and is adapted to represent a degree of support for the hypothesis and its corresponding counter-hypothesis in the single hierarchical argument structure.

Structure of the TRPV1 ion channel determined by electron cryo-microscopy.

PubMed

Liao, Maofu; Cao, Erhu; Julius, David; Cheng, Yifan

2013-12-05

Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4 Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane segments 5-6 (S5-S6) and the intervening pore loop, which is flanked by S1-S4 voltage-sensor-like domains. TRPV1 has a wide extracellular 'mouth' with a short selectivity filter. The conserved 'TRP domain' interacts with the S4-S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including amino-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function.

Structure of the TRPV1 ion channel determined by electron cryo-microscopy

PubMed Central

Liao, Maofu; Cao, Erhu; Julius, David; Cheng, Yifan

2014-01-01

Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here, we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane helices S5–S6 and the intervening pore loop, which is flanked by S1–S4 voltage sensor-like domains. TRPV1 has a wide extracellular ‘mouth’ with short selectivity filter. The conserved ‘TRP domain’ interacts with the S4–S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including N-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function. PMID:24305160

Reduction of herbivorous fish pressure can facilitate focal algal species forestation on artificial structures.

PubMed

Gianni, Fabrizio; Bartolini, Fabrizio; Airoldi, Laura; Mangialajo, Luisa

2018-07-01

Coastal areas have been transformed worldwide by urbanization, so that artificial structures are now widespread. Current coastal development locally depletes many native marine species, while offering limited possibilities for their expansion. Eco-engineering interventions intend to identify ways to facilitate the presence of focal species and their associated functions on artificial habitats. An important but overlooked factor controlling restoration operations is overgrazing by herbivores. The aim of this study was to quantify the effects of different potential feeders on Cystoseira amentacea, a native canopy-forming alga of the Mediterranean infralittoral fringe, and test whether manipulation of grazing pressure can facilitate the human-guided installation of this focal species on coastal structures. Results of laboratory tests and field experiments revealed that Sarpa salpa, the only strictly native herbivorous fish in the Western Mediterranean Sea, can be a very effective grazer of C. amentacea in artificial habitats, up to as far as the infralittoral fringe, which is generally considered less accessible to fishes. S. salpa can limit the success of forestation operations in artificial novel habitats, causing up to 90% of Cystoseira loss after a few days. Other grazers, such as limpets and crabs, had only a moderate impact. Future engineering operations,intended to perform forestation of canopy-forming algae on artificial structures, should consider relevant biotic factors, such as fish overgrazing, identifying cost-effective techniques to limit their impact, as is the usual practice in restoration programmes on land. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structure of catalase determined by MicroED

PubMed Central

Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

2014-01-01

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

Computing approximate solutions of the protein structure determination problem using global constraints on discrete crystal lattices.

PubMed

Dal Palù, Alessandro; Dovier, Agostino; Pontelli, Enrico

2010-01-01

Crystal lattices are discrete models of the three-dimensional space that have been effectively employed to facilitate the task of determining proteins' natural conformation. This paper investigates alternative global constraints that can be introduced in a constraint solver over discrete crystal lattices. The objective is to enhance the efficiency of lattice solvers in dealing with the construction of approximate solutions of the protein structure determination problem. Some of them (e.g., self-avoiding-walk) have been explicitly or implicitly already used in previous approaches, while others (e.g., the density constraint) are new. The intrinsic complexities of all of them are studied and preliminary experimental results are discussed.

Structural barriers and facilitators in HIV prevention: a review of international research.

PubMed

Parker, R G; Easton, D; Klein, C H

2000-06-01

This article provides an overview of a growing body of international research focusing on the structural and environmental factors that shape the spread of the HIV/AIDS epidemic, and create barriers and facilitators in relation to HIV-prevention programs. OVERVIEW OF STRUCTURAL-FACTORS LITERATURE: Most of the research on structural and environmental factors can be grouped into a small number of analytically distinct but interconnected categories: economic (under)development and poverty; mobility, including migration, seasonal work, and social disruption due to war and political instability; and gender inequalities. An additional focus in research on structural and environmental factors has been on the effects of particular governmental and intergovernmental policies in increasing or diminishing HIV vulnerability and transmission. A smaller subset of the research on structural factors describes and/or evaluates specific interventions in detail. Approaches that have received significant attention include targeted interventions developed for heterosexual women, female commercial sex workers, male truck drivers, and men who have sex with men. The structural and environmental factors literature offers important insights and reveals a number of productive intervention strategies that might be explored in both resource-rich and -poor settings. However, new methodologies are required to document and evaluate the effects of the structural interventions, which by their very nature involve large-scale elements that cannot be easily controlled by experimental or quasi-experimental research designs. Innovative, interdisciplinary approaches are needed that can move beyond the limited successes of traditional behavioral interventions and explicitly attempt to achieve broader social and structural change.

Viewing Artworks: Contributions of Cognitive Control and Perceptual Facilitation to Aesthetic Experience

ERIC Educational Resources Information Center

Cupchik, Gerald C.; Vartanian, Oshin; Crawley, Adrian; Mikulis, David J.

2009-01-01

When we view visual images in everyday life, our perception is oriented toward object identification. In contrast, when viewing visual images "as artworks", we also tend to experience subjective reactions to their stylistic and structural properties. This experiment sought to determine how cognitive control and perceptual facilitation contribute…

Structural Determinants of Autoproteolysis of the Haemophilus influenzae Hap Autotransporter▿

PubMed Central

Kenjale, Roma; Meng, Guoyu; Fink, Doran L.; Juehne, Twyla; Ohashi, Tomoo; Erickson, Harold P.; Waksman, Gabriel; St. Geme, Joseph W.

2009-01-01

Haemophilus influenzae is a gram-negative bacterium that initiates infection by colonizing the upper respiratory tract. The H. influenzae Hap autotransporter protein mediates adherence, invasion, and microcolony formation in assays with respiratory epithelial cells and presumably facilitates colonization. The serine protease activity of Hap is associated with autoproteolytic cleavage and extracellular release of the HapS passenger domain, leaving the Hapβ C-terminal domain embedded in the outer membrane. Cleavage occurs most efficiently at the LN1036-37 peptide bond and to a lesser extent at three other sites. In this study, we utilized site-directed mutagenesis, homology modeling, and assays with a peptide library to characterize the structural determinants of Hap proteolytic activity and cleavage specificity. In addition, we used homology modeling to predict the S1, S2, and S4 subsite residues of the Hap substrate groove. Our results indicate that the P1 and P2 positions at the Hap cleavage sites are critical for cleavage, with leucine preferred over larger hydrophobic residues or other amino acids in these positions. The substrate groove is formed by L263 and N274 at the S1 subsite, R264 at the S2 subsite, and E265 at the S4 subsite. This information may facilitate design of approaches to block Hap activity and interfere with H. influenzae colonization. PMID:19687208

Student Perceptions of School Efforts to Facilitate Student Involvement, School Commitment, Self-Determination, and High School Graduation

ERIC Educational Resources Information Center

Cavendish, Wendy

2013-01-01

This study examined the relationship between student perceptions of school efforts to facilitate student involvement, school commitment, self-determination skills, and on track indicators for graduation in 10th grade and actual graduation outcomes two years later. The participants were 154 primarily minority students in a large, urban school…

NMR-based automated protein structure determination.

PubMed

Würz, Julia M; Kazemi, Sina; Schmidt, Elena; Bagaria, Anurag; Güntert, Peter

2017-08-15

NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures. Copyright © 2017 Elsevier Inc. All rights reserved.

Structured Play Therapy Groups for Preschoolers: facilitating the emergence of social competence.

PubMed

Stone, Susan; Stark, Martha

2013-01-01

Over the years, we have developed a working model of Structured Play Therapy Groups for Preschoolers, an innovative treatment approach designed to address the needs of young children ages 3 to 5 struggling to adjust to the social demands of their preschool classrooms. These short-term therapy groups facilitate development of the young child's social competence and capacity to participate effectively in a classroom environment. Although the literature on therapy groups for children suggests that preschoolers are not yet evolved enough developmentally to engage actively in a group process, our experience indicates otherwise. The model of treatment presented here will therefore challenge that contention with the claim that not only can preschoolers participate in a structured therapy group of peers but they can, by virtue of that very participation, benefit in ways that will prepare them (as they transition from preschool to kindergarten) for the ever-increasing demands of their ever-expanding social milieus.

Determiner Primes as Facilitators of Lexical Retrieval in English

ERIC Educational Resources Information Center

Gregory, Emma; Varley, Rosemary; Herbert, Ruth

2012-01-01

Gender priming studies have demonstrated facilitation of noun production following pre-activation of a target noun's grammatical gender. Findings provide support for models in which syntactic information relating to words is stored within the lexicon and activated during lexical retrieval. Priming effects are observed in the context of determiner…

The m6A pathway facilitates sex determination in Drosophila

PubMed Central

Kan, Lijuan; Grozhik, Anya V.; Vedanayagam, Jeffrey; Patil, Deepak P.; Pang, Nan; Lim, Kok-Seong; Huang, Yi-Chun; Joseph, Brian; Lin, Ching-Jung; Despic, Vladimir; Guo, Jian; Yan, Dong; Kondo, Shu; Deng, Wu-Min; Dedon, Peter C.; Jaffrey, Samie R.; Lai, Eric C.

2017-01-01

The conserved modification N6-methyladenosine (m6A) modulates mRNA processing and activity. Here, we establish the Drosophila system to study the m6A pathway. We first apply miCLIP to map m6A across embryogenesis, characterize its m6A ‘writer’ complex, validate its YTH ‘readers’ CG6422 and YT521-B, and generate mutants in five m6A factors. While m6A factors with additional roles in splicing are lethal, m6A-specific mutants are viable but present certain developmental and behavioural defects. Notably, m6A facilitates the master female determinant Sxl, since multiple m6A components enhance female lethality in Sxl sensitized backgrounds. The m6A pathway regulates Sxl processing directly, since miCLIP data reveal Sxl as a major intronic m6A target, and female-specific Sxl splicing is compromised in multiple m6A pathway mutants. YT521-B is a dominant m6A effector for Sxl regulation, and YT521-B overexpression can induce female-specific Sxl splicing. Overall, our transcriptomic and genetic toolkit reveals in vivo biologic function for the Drosophila m6A pathway. PMID:28675155

Automation of NMR structure determination of proteins.

PubMed

Altieri, Amanda S; Byrd, R Andrew

2004-10-01

The automation of protein structure determination using NMR is coming of age. The tedious processes of resonance assignment, followed by assignment of NOE (nuclear Overhauser enhancement) interactions (now intertwined with structure calculation), assembly of input files for structure calculation, intermediate analyses of incorrect assignments and bad input data, and finally structure validation are all being automated with sophisticated software tools. The robustness of the different approaches continues to deal with problems of completeness and uniqueness; nevertheless, the future is very bright for automation of NMR structure generation to approach the levels found in X-ray crystallography. Currently, near completely automated structure determination is possible for small proteins, and the prospect for medium-sized and large proteins is good. Copyright 2004 Elsevier Ltd.

STEP and STEPSPL: Computer programs for aerodynamic model structure determination and parameter estimation

NASA Technical Reports Server (NTRS)

Batterson, J. G.

1986-01-01

The successful parametric modeling of the aerodynamics for an airplane operating at high angles of attack or sideslip is performed in two phases. First the aerodynamic model structure must be determined and second the associated aerodynamic parameters (stability and control derivatives) must be estimated for that model. The purpose of this paper is to document two versions of a stepwise regression computer program which were developed for the determination of airplane aerodynamic model structure and to provide two examples of their use on computer generated data. References are provided for the application of the programs to real flight data. The two computer programs that are the subject of this report, STEP and STEPSPL, are written in FORTRAN IV (ANSI l966) compatible with a CDC FTN4 compiler. Both programs are adaptations of a standard forward stepwise regression algorithm. The purpose of the adaptation is to facilitate the selection of a adequate mathematical model of the aerodynamic force and moment coefficients of an airplane from flight test data. The major difference between STEP and STEPSPL is in the basis for the model. The basis for the model in STEP is the standard polynomial Taylor's series expansion of the aerodynamic function about some steady-state trim condition. Program STEPSPL utilizes a set of spline basis functions.

Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis

PubMed Central

Vilar, Santiago; Harpaz, Rave; Chase, Herbert S; Costanzi, Stefano; Rabadan, Raul

2011-01-01

Background Adverse drug events (ADE) cause considerable harm to patients, and consequently their detection is critical for patient safety. The US Food and Drug Administration maintains an adverse event reporting system (AERS) to facilitate the detection of ADE in drugs. Various data mining approaches have been developed that use AERS to detect signals identifying associations between drugs and ADE. The signals must then be monitored further by domain experts, which is a time-consuming task. Objective To develop a new methodology that combines existing data mining algorithms with chemical information by analysis of molecular fingerprints to enhance initial ADE signals generated from AERS, and to provide a decision support mechanism to facilitate the identification of novel adverse events. Results The method achieved a significant improvement in precision in identifying known ADE, and a more than twofold signal enhancement when applied to the ADE rhabdomyolysis. The simplicity of the method assists in highlighting the etiology of the ADE by identifying structurally similar drugs. A set of drugs with strong evidence from both AERS and molecular fingerprint-based modeling is constructed for further analysis. Conclusion The results demonstrate that the proposed methodology could be used as a pharmacovigilance decision support tool to facilitate ADE detection. PMID:21946238

Facilitating the Design of a Campus Leadership Team

ERIC Educational Resources Information Center

Meyers, Renee A.; Johnson, John R.

2008-01-01

This essay describes how we facilitated the design of a campus leadership team. What is particularly interesting about this consultative project is that both authors participated--one as facilitator and the other as participant. The facilitation included a needs assessment prior to the event, the use of structured controversy techniques,…

Facilitators in Ambivalence

ERIC Educational Resources Information Center

Karlsson, Mikael R.; Erlandson, Peter

2018-01-01

This is part of a larger ethnographical study concerning how school development in a local educational context sets cultural and social life in motion. The main data "in this article" consists of semi-structural interviews with teachers (facilitators) who have the responsibility of carrying out a project about formative assessment in…

Cross-Linking and Mass Spectrometry Methodologies to Facilitate Structural Biology: Finding a Path through the Maze

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

Merkley, Eric D.; Cort, John R.; Adkins, Joshua N.

2013-09-01

Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature.more » These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes.« less

Advances in RNA Structure Determination | Center for Cancer Research

Cancer.gov

The recent years have witnessed a revolution in the field of RNA structure and function. Until recently the main contribution of RNA in cellular and disease functions was considered to be a role defined by the central dogma, namely DNA codes for mRNAs, which in turn encode for proteins, a notion facilitated by non-coding ribosomal RNA and tRNA. It was also assumed at the time

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

PubMed Central

Schmitz, Christophe; Vernon, Robert; Otting, Gottfried; Baker, David; Huber, Thomas

2013-01-01

Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δχ-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δχ-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations. PMID:22285518

Automated crystallographic system for high-throughput protein structure determination.

PubMed

Brunzelle, Joseph S; Shafaee, Padram; Yang, Xiaojing; Weigand, Steve; Ren, Zhong; Anderson, Wayne F

2003-07-01

High-throughput structural genomic efforts require software that is highly automated, distributive and requires minimal user intervention to determine protein structures. Preliminary experiments were set up to test whether automated scripts could utilize a minimum set of input parameters and produce a set of initial protein coordinates. From this starting point, a highly distributive system was developed that could determine macromolecular structures at a high throughput rate, warehouse and harvest the associated data. The system uses a web interface to obtain input data and display results. It utilizes a relational database to store the initial data needed to start the structure-determination process as well as generated data. A distributive program interface administers the crystallographic programs which determine protein structures. Using a test set of 19 protein targets, 79% were determined automatically.

Facilitation and practice in verb acquisition.

PubMed

Keren-Portnoy, Tamar

2006-08-01

This paper presents a model of syntax acquisition, whose main points are as follows: Syntax is acquired in an item-based manner; early learning facilitates subsequent learning--as evidenced by the accelerating rate of new verbs entering a given structure; and mastery of syntactic knowledge is typically achieved through practice--as evidenced by intensive use and common word order errors--and this slows down learning during the early stages of acquiring a structure. The facilitation and practice hypotheses were tested on naturalistic production samples of six Hebrew-acquiring children ranging from ages 1;1 to 2;7 (average ages 1;6 to 2;4 months). Results show that most structures did in fact accelerate; the notion of 'practice' is supported by the inverse correlation found between number of verbs and number of errors in the earliest productions in a given structure; and the absence of acceleration in a minority of the structures is due to the fact that they involve relatively less practice.

Recent Methods for Purification and Structure Determination of Oligonucleotides.

PubMed

Zhang, Qiulong; Lv, Huanhuan; Wang, Lili; Chen, Man; Li, Fangfei; Liang, Chao; Yu, Yuanyuan; Jiang, Feng; Lu, Aiping; Zhang, Ge

2016-12-18

Aptamers are single-stranded DNA or RNA oligonucleotides that can interact with target molecules through specific three-dimensional structures. The excellent features, such as high specificity and affinity for target proteins, small size, chemical stability, low immunogenicity, facile chemical synthesis, versatility in structural design and engineering, and accessible for site-specific modifications with functional moieties, make aptamers attractive molecules in the fields of clinical diagnostics and biopharmaceutical therapeutics. However, difficulties in purification and structural identification of aptamers remain a major impediment to their broad clinical application. In this mini-review, we present the recently attractive developments regarding the purification and identification of aptamers. We also discuss the advantages, limitations, and prospects for the major methods applied in purifying and identifying aptamers, which could facilitate the application of aptamers.

Parent Involvement Facilitators: Unlocking Social Capital Wealth

ERIC Educational Resources Information Center

Ferrara, Margaret M.

2015-01-01

This case study provides an overview of a family outreach intervention that supports student retention in school through a school-home communication link. This intervention structure, which employs staff appropriately called parent involvement facilitators (PIFs), is one that school districts have employed to facilitate family engagement in…

Structural plasticity in hippocampal cells related to the facilitative effect of intracranial self-stimulation on a spatial memory task.

PubMed

Chamorro-López, Jacobo; Miguéns, Miguel; Morgado-Bernal, Ignacio; Kastanauskaite, Asta; Selvas, Abraham; Cabané-Cucurella, Alberto; Aldavert-Vera, Laura; DeFelipe, Javier; Segura-Torres, Pilar

2015-12-01

Posttraining intracranial self-stimulation (SS) in the lateral hypothalamus facilitates the acquisition and retention of several implicit and explicit memory tasks. Here, intracellular injections of Lucifer yellow were used to assess morphological changes in hippocampal neurons that might be specifically related to the facilitative posttraining SS effect upon the acquisition and retention of a distributed spatial task in the Morris water maze. We examined the structure, size and branching complexity of cornus ammonis 1 (CA1) cells, and the spine density of CA1 pyramidal neurons and granular cells of the dentate gyrus (DG). Animals that received SS after each acquisition session performed faster and better than Sham ones--an improvement that was also evident in a probe trial 3 days after the last training session. The neuromorphological analysis revealed an increment in the size and branching complexity in apical CA1 dendritic arborization in SS-treated subjects as compared with Sham animals. Furthermore, increased spine density was observed in the CA1 field in SS animals, whereas no effects were observed in DG cells. Our results support the hypothesis that the facilitating effect of SS on the acquisition and retention of a spatial memory task could be related to structural plasticity in CA1 hippocampal cells. (c) 2015 APA, all rights reserved).

The facilitators and impediment factors of structural empowerment in pregnancy and delivery care: achievement of power

PubMed Central

Janighorban, M; Yousefi, H; Yamani, N

2015-01-01

Background: The organizations essentially affect empowerment of personnel through the preparation of the needed grounds for them. Also, the students may acquire the required potentials and capabilities in the educational organizations when the possibility is provided to them to access power and opportunity in educational environments. Objective: The present study aimed to explain the facilitators and impediment factors of structural empowerment in pregnancy and delivery care. Methods: According to Kanter’s theory, this qualitative study was conducted with the participation of 15 superior midwifery students, ten academic teachers of midwifery, and two midwives employed in the educational hospitals. Data were collected by semi-structured interviews individually and in the group and analyzed by using a directed content analysis method. Results: To explain the facilitators and impediment factors of empowerment in pregnancy and delivery care in the power structure, the access was provided to a support formed by three broad categories of support from the instructors, support from personnel, and support from a classmate. The access to resources was created with three broad categories of access to the appropriate clinical environment, to the laboratory of clinical skills and to information sources, and to information, forming with two broad categories of awareness of the educational objectives as well as legal and legitimate issues. Conclusion: One could prepare the ground for the midwifery students to access this empowerment in pregnancy and delivery cares more than ever by providing equipped clinical environments and the presence of all-inclusive supportive climate in such environments. Along with the efficient training of students in the laboratory PMID:28316710

Structure of the periplasmic adaptor protein from a major facilitator superfamily (MFS) multidrug efflux pump.

PubMed

Hinchliffe, Philip; Greene, Nicholas P; Paterson, Neil G; Crow, Allister; Hughes, Colin; Koronakis, Vassilis

2014-08-25

Periplasmic adaptor proteins are key components of bacterial tripartite efflux pumps. The 2.85 Å resolution structure of an MFS (major facilitator superfamily) pump adaptor, Aquifex aeolicus EmrA, shows linearly arranged α-helical coiled-coil, lipoyl, and β-barrel domains, but lacks the fourth membrane-proximal domain shown in other pumps to interact with the inner membrane transporter. The adaptor α-hairpin, which binds outer membrane TolC, is exceptionally long at 127 Å, and the β-barrel contains a conserved disordered loop. The structure extends the view of adaptors as flexible, modular components that mediate diverse pump assembly, and suggests that in MFS tripartite pumps a hexamer of adaptors could provide a periplasmic seal. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Structural determination of intact proteins using mass spectrometry

DOEpatents

Kruppa, Gary [San Francisco, CA; Schoeniger, Joseph S [Oakland, CA; Young, Malin M [Livermore, CA

2008-05-06

The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

Oligonucleotide facilitators may inhibit or activate a hammerhead ribozyme.

PubMed Central

Jankowsky, E; Schwenzer, B

1996-01-01

Facilitators are oligonucleotides capable of affecting hammerhead ribozyme activity by interacting with the substrate at the termini of the ribozyme. Facilitator effects were determined in vitro using a system consisting of a ribozyme with 7 nucleotides in every stem sequence and two substrates with inverted facilitator binding sequences. The effects of 9mer and 12mer RNA as well as DNA facilitators which bind either adjacent to the 3'- or 5'-end of the ribozyme were investigated. A kinetic model was developed which allows determination of the apparent dissociation constant of the ribozyme-substrate complex from single turnover reactions. We observed a decreased dissociation constant of the ribozyme-substrate complex due to facilitator addition corresponding to an additional stabilization energy of delta delta G=-1.7 kcal/mol with 3'-end facilitators. The cleavage rate constant was increased by 3'-end facilitators and decreased by 5'-end facilitators. Values for Km were slightly lowered by all facilitators and kcat was increased by 3'-end facilitators and decreased by 5'-end facilitators in our system. Generally the facilitator effects increased with the length of the facilitators and RNA provided greater effects than DNA of the same sequence. Results suggest facilitator influences on several steps of the hammerhead reaction, substrate association, cleavage and dissociation of products. Moreover, these effects are dependent in different manners on ribozyme and substrate concentration. This leads to the conclusion that there is a concentration dependence whether activation or inhibition is caused by facilitators. Conclusions are drawn with regard to the design of hammerhead ribozyme facilitator systems. PMID:8602353

Experiences of practice facilitators working on the Improved Delivery of Cardiovascular Care project: Retrospective case study.

PubMed

Liddy, Clare; Rowan, Margo; Valiquette-Tessier, Sophie-Claire; Drosinis, Paul; Crowe, Lois; Hogg, William

2018-01-01

To examine the barriers to and facilitators of practice facilitation experienced by participants in the Improving Delivery of Cardiovascular Care (IDOCC) project. Case studies of practice facilitators' narrative reports. Eastern Ontario. Primary care practices that participated in the IDOCC project. Cases were identified by calculating sum scores in order to determine practices' performance relative to their peers. Two case exemplars were selected that scored within ± 1 SD of the total mean score, and a qualitative analysis of practice facilitators' narrative reports was conducted using a 5-factor implementation framework to identify barriers and facilitators. Narratives were divided into 3 phases: planning, implementation, and sustainability. Barriers and facilitators fluctuated over the intervention's 3 phases. Site A reported more barriers (n = 47) than facilitators (n = 38), while site B reported a roughly equal number of barriers (n = 144) and facilitators (n = 136). In both sites, the most common barriers involved organizational and provider factors and the most common facilitators were associated with innovation and structural factors. Both practices encountered various barriers and facilitators throughout the IDOCC's 3 phases. The case studies reveal the complex interactions of these factors over time, and provide insight into the implementation of practice facilitation programs. Copyright© the College of Family Physicians of Canada.

Structure Determination of Natural Products by Mass Spectrometry.

PubMed

Biemann, Klaus

2015-01-01

I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts.

Determination of interstitial oxygen atom position in U2N3+xOy by near edge structure study

NASA Astrophysics Data System (ADS)

Jiang, A. K.; Zhao, Y. W.; Long, Z.; Hu, Y.; Wang, X. F.; Yang, R. L.; Bao, H. L.; Zeng, R. G.; Liu, K. Z.

2018-06-01

The determination of interstitial oxygen atom site in U2N3+xOy film could facilitate the understanding of the oxidation mechanism of α-U2N3 and the effect of U2N3+xOy on anti-oxidation. By comparing the similarities and variances between N K edge and O K edge electron energy loss spectra (EELS) for oxidized α-U2N3 and UO2, the present work looks at the local structure of nitrogen and oxygen atoms in U2N3+xOy film, identifying the most possible position of interstitial O atom.

"Stepping Up": A Focus on Facilitator Development

ERIC Educational Resources Information Center

Kostouros, Patricia; Warthe, D. Gaye; Carter-Snell, Catherine; Burnett, Che

2016-01-01

This article examines the impact on peer facilitators in "Stepping Up," a dating violence prevention program at a Canadian university. A focus group held eight months following the delivery of the program determined the personal impact of involvement in the program. Results indicate that peer facilitators experienced personal growth as…

Self-determination theory and the facilitation of intrinsic motivation, social development, and well-being.

PubMed

Ryan, R M; Deci, E L

2000-01-01

Human beings can be proactive and engaged or, alternatively, passive and alienated, largely as a function of the social conditions in which they develop and function. Accordingly, research guided by self-determination theory has focused on the social-contextual conditions that facilitate versus forestall the natural processes of self-motivation and healthy psychological development. Specifically, factors have been examined that enhance versus undermine intrinsic motivation, self-regulation, and well-being. The findings have led to the postulate of three innate psychological needs--competence, autonomy, and relatedness--which when satisfied yield enhanced self-motivation and mental health and when thwarted lead to diminished motivation and well-being. Also considered is the significance of these psychological needs and processes within domains such as health care, education, work, sport, religion, and psychotherapy.

Constructal Law of Vascular Trees for Facilitation of Flow

PubMed Central

Razavi, Mohammad S.; Shirani, Ebrahim; Salimpour, Mohammad Reza; Kassab, Ghassan S.

2014-01-01

Diverse tree structures such as blood vessels, branches of a tree and river basins exist in nature. The constructal law states that the evolution of flow structures in nature has a tendency to facilitate flow. This study suggests a theoretical basis for evaluation of flow facilitation within vascular structure from the perspective of evolution. A novel evolution parameter (Ev) is proposed to quantify the flow capacity of vascular structures. Ev is defined as the ratio of the flow conductance of an evolving structure (configuration with imperfection) to the flow conductance of structure with least imperfection. Attaining higher Ev enables the structure to expedite flow circulation with less energy dissipation. For both Newtonian and non-Newtonian fluids, the evolution parameter was developed as a function of geometrical shape factors in laminar and turbulent fully developed flows. It was found that the non-Newtonian or Newtonian behavior of fluid as well as flow behavior such as laminar or turbulent behavior affects the evolution parameter. Using measured vascular morphometric data of various organs and species, the evolution parameter was calculated. The evolution parameter of the tree structures in biological systems was found to be in the range of 0.95 to 1. The conclusion is that various organs in various species have high capacity to facilitate flow within their respective vascular structures. PMID:25551617

Rapid and reliable protein structure determination via chemical shift threading.

PubMed

Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

2018-01-01

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

Integrated Structural Biology for α-Helical Membrane Protein Structure Determination.

PubMed

Xia, Yan; Fischer, Axel W; Teixeira, Pedro; Weiner, Brian; Meiler, Jens

2018-04-03

While great progress has been made, only 10% of the nearly 1,000 integral, α-helical, multi-span membrane protein families are represented by at least one experimentally determined structure in the PDB. Previously, we developed the algorithm BCL::MP-Fold, which samples the large conformational space of membrane proteins de novo by assembling predicted secondary structure elements guided by knowledge-based potentials. Here, we present a case study of rhodopsin fold determination by integrating sparse and/or low-resolution restraints from multiple experimental techniques including electron microscopy, electron paramagnetic resonance spectroscopy, and nuclear magnetic resonance spectroscopy. Simultaneous incorporation of orthogonal experimental restraints not only significantly improved the sampling accuracy but also allowed identification of the correct fold, which is demonstrated by a protein size-normalized transmembrane root-mean-square deviation as low as 1.2 Å. The protocol developed in this case study can be used for the determination of unknown membrane protein folds when limited experimental restraints are available. Copyright © 2018 Elsevier Ltd. All rights reserved.

Algorithms for Determining Physical Responses of Structures Under Load

NASA Technical Reports Server (NTRS)

Richards, W. Lance; Ko, William L.

2012-01-01

Ultra-efficient real-time structural monitoring algorithms have been developed to provide extensive information about the physical response of structures under load. These algorithms are driven by actual strain data to measure accurately local strains at multiple locations on the surface of a structure. Through a single point load calibration test, these structural strains are then used to calculate key physical properties of the structure at each measurement location. Such properties include the structure s flexural rigidity (the product of the structure's modulus of elasticity, and its moment of inertia) and the section modulus (the moment of inertia divided by the structure s half-depth). The resulting structural properties at each location can be used to determine the structure s bending moment, shear, and structural loads in real time while the structure is in service. The amount of structural information can be maximized through the use of highly multiplexed fiber Bragg grating technology using optical time domain reflectometry and optical frequency domain reflectometry, which can provide a local strain measurement every 10 mm on a single hair-sized optical fiber. Since local strain is used as input to the algorithms, this system serves multiple purposes of measuring strains and displacements, as well as determining structural bending moment, shear, and loads for assessing real-time structural health. The first step is to install a series of strain sensors on the structure s surface in such a way as to measure bending strains at desired locations. The next step is to perform a simple ground test calibration. For a beam of length l (see example), discretized into n sections and subjected to a tip load of P that places the beam in bending, the flexural rigidity of the beam can be experimentally determined at each measurement location x. The bending moment at each station can then be determined for any general set of loads applied during operation.

Development of XAFS Into a Structure Determination Technique

NASA Astrophysics Data System (ADS)

Stern, E. A.

After the detection of diffraction of x-rays by M. Laue in 1912, the technique was soon applied to structure determination by Bragg within a year. On the other hand, although the edge steps in X-Ray absorption were discovered even earlier by Barkla and both the near edge (XANES) and extended X-Ray fine structure (EXAFS) past the edge were detected by 1929, it still took over 40 years to realize the structure information contained in this X-Ray absorption fine structure (XAFS). To understand this delay a brief historical review of the development of the scientific ideas that transformed XAFS into the premiere technique for local structure determination is given. The development includes both advances in theoretical understanding and calculational capabilities, and in experimental facilities, especially synchrotron radiation sources. The present state of the XAFS technique and its capabilities are summarized.

Species-specific defence responses facilitate conspecifics and inhibit heterospecifics in above–belowground herbivore interactions

PubMed Central

Huang, Wei; Siemann, Evan; Xiao, Li; Yang, Xuefang; Ding, Jianqing

2014-01-01

Conspecific and heterospecific aboveground and belowground herbivores often occur together in nature and their interactions may determine community structure. Here we show how aboveground adults and belowground larvae of the tallow tree specialist beetle Bikasha collaris and multiple heterospecific aboveground species interact to determine herbivore performance. Conspecific aboveground adults facilitate belowground larvae, but other aboveground damage inhibits larvae or has no effect. Belowground larvae increase conspecific adult feeding, but decrease heterospecific aboveground insect feeding and abundance. Chemical analyses and experiments with plant populations varying in phenolics show that all these positive and negative effects on insects are closely related to root and shoot tannin concentrations. Our results show that specific plant herbivore responses allow herbivore facilitation and inhibition to co-occur, likely shaping diverse aboveground and belowground communities. Considering species-specific responses of plants is critical for teasing apart inter- and intraspecific interactions in aboveground and belowground compartments. PMID:25241651

An exploration of tutors' experiences of facilitating problem-based learning. Part 2--implications for the facilitation of problem based learning.

PubMed

Haith-Cooper, Melanie

2003-01-01

This paper is the second of two parts exploring a study that was undertaken to investigate the role of the tutor in facilitating problem-based learning (PBL). The first part focussed on the methodological underpinnings of the study. This paper aims to focus on the findings of the study and their implications for the facilitation of PBL. Six essential themes emerged from the findings that described the facilitation role. The tutors believed that their facilitation role was essentially structured around the decision of when to intervene and how to intervene in the PBL process. Modelling and non-verbal communication were seen as essential strategies for the facilitator. Underpinning these decisions was the need to trust in the philosophy of PBL. However, within many of the themes, there was a divergence of opinion as to how the role should actually be undertaken. Despite this, these findings have implications for the future role of PBL facilitators in Health Professional Education.

Student Veteran perceptions of facilitators and barriers to achieving academic goals.

PubMed

Norman, Sonya B; Rosen, Jay; Himmerich, Sara; Myers, Ursula S; Davis, Brittany; Browne, Kendall C; Piland, Neill

2015-01-01

According to recent estimates, over 1 million Operation Iraqi Freedom/Operation Enduring Freedom (OIF/OEF) Veterans are utilizing the post-9/11 GI Bill to pursue higher education. Data collected by the Department of Defense suggests that greater than 17% of returning Veterans may suffer from mental and physical health disorders, which can negatively affect school performance. The current study explored student Veterans' perceived facilitators and barriers to achieving academic goals. Thirty-one student Veterans completed self-report measures and interviews. Results suggested that Veterans that were reporting problems or symptoms in one mental or physical health domain were likely to be reporting symptoms or problems in others as well. The interview data were coded, and three overarching themes related to barriers and facilitators emerged: person features (e.g., discipline and determination, symptoms and stressors), institutional structure (i.e., what schools and the Department of Veterans Affairs do that was perceived to help or hinder student Veteran success), and policy concerns (i.e., how the structure of the GI Bill affects student Veteran school experience). Results from this research indicate the need for larger studies and program development efforts aimed at enhancing academic outcomes for Veterans.

Structural Determinants of Arrestin Functions

PubMed Central

Gurevich, Vsevolod V.; Gurevich, Eugenia V.

2015-01-01

Arrestins are a small protein family with only four members in mammals. Arrestins demonstrate an amazing versatility, interacting with hundreds of different G protein-coupled receptor (GPCR) subtypes, numerous nonreceptor signaling proteins, and components of the internalization machinery, as well as cytoskeletal elements, including regular microtubules and centrosomes. Here, we focus on the structural determinants that mediate various arrestin functions. The receptor-binding elements in arrestins were mapped fairly comprehensively, which set the stage for the construction of mutants targeting particular GPCRs. The elements engaged by other binding partners are only now being elucidated and in most cases we have more questions than answers. Interestingly, even very limited and imprecise identification of structural requirements for the interaction with very few other proteins has enabled the development of signaling-biased arrestin mutants. More comprehensive understanding of the structural underpinning of different arrestin functions will pave the way for the construction of arrestins that can link the receptor we want to the signaling pathway of our choosing. PMID:23764050

Method of fan sound mode structure determination

NASA Technical Reports Server (NTRS)

Pickett, G. F.; Sofrin, T. G.; Wells, R. W.

1977-01-01

A method for the determination of fan sound mode structure in the Inlet of turbofan engines using in-duct acoustic pressure measurements is presented. The method is based on the simultaneous solution of a set of equations whose unknowns are modal amplitude and phase. A computer program for the solution of the equation set was developed. An additional computer program was developed which calculates microphone locations the use of which results in an equation set that does not give rise to numerical instabilities. In addition to the development of a method for determination of coherent modal structure, experimental and analytical approaches are developed for the determination of the amplitude frequency spectrum of randomly generated sound models for use in narrow annulus ducts. Two approaches are defined: one based on the use of cross-spectral techniques and the other based on the use of an array of microphones.

The smoker's health project: a self-determination theory intervention to facilitate maintenance of tobacco abstinence.

PubMed

Williams, Geoffrey C; Patrick, Heather; Niemiec, Christopher P; Ryan, Richard M; Deci, Edward L; Lavigne, Holly McGregor

2011-07-01

A previous randomized clinical trial based on self-determination theory (SDT) and consistent with the Public Health Service (PHS) Guideline for Treating Tobacco Use and Dependence demonstrated that an intensive intervention could change autonomous self-regulation and perceived competence, which in part facilitated long-term tobacco abstinence. The current article describes a pragmatic comparative effectiveness trial of three SDT-based intensive tobacco-dependence interventions. Eligible participants are randomized to one of the three treatment conditions designed to facilitate long-term maintenance of tobacco abstinence, namely, Community Care (CC), which includes the 6 month SDT-based intervention previously shown to promote autonomous self-regulation, perceived competence, medication use, and tobacco abstinence; Extended Need Support (ENS), which extends the 6 month SDT-based intervention to 12 months and trains an important other to provide support for smokers' basic psychological needs; and Harm Reduction (HR), which provides extended need support and recommends medication use for participants who do not want to stop smoking completely within 30 days but who are willing to reduce their cigarette use by half. The primary outcome is 12 month prolonged abstinence from tobacco, which is assessed one year following termination of treatment (two years post-randomization). Secondary outcomes include 7- and 30 day point prevalence tobacco abstinence, number of days using smoking-cessation medication, change in autonomous self-regulation and perceived competence, and perceived need support from important others. Copyright © 2011 Elsevier Inc. All rights reserved.

Structural determinants of the interaction between the Haemophilus influenzae Hap autotransporter and fibronectin.

PubMed

Spahich, Nicole A; Kenjale, Roma; McCann, Jessica; Meng, Guoyu; Ohashi, Tomoo; Erickson, Harold P; St Geme, Joseph W

2014-06-01

Haemophilus influenzae is a Gram-negative cocco-bacillus that initiates infection by colonizing the upper respiratory tract. Hap is an H. influenzae serine protease autotransporter protein that mediates adherence, invasion and microcolony formation in assays with human epithelial cells and is presumed to facilitate the process of colonization. Additionally, Hap mediates adherence to fibronectin, laminin and collagen IV, extracellular matrix (ECM) proteins that are present in the respiratory tract and are probably important targets for H. influenzae colonization. The region of Hap responsible for adherence to ECM proteins has been localized to the C-terminal 511 aa of the Hap passenger domain (HapS). In this study, we characterized the structural determinants of the interaction between HapS and fibronectin. Using defined fibronectin fragments, we established that Hap interacts with the fibronectin repeat fragment called FNIII(1-2). Using site-directed mutagenesis, we found a series of motifs in the C-terminal region of HapS that contribute to the interaction with fibronectin. Most of these motifs are located on the F1 and F3 faces of the HapS structure, suggesting that the F1 and F3 faces may be responsible for the HapS-fibronectin interaction. © 2014 The Authors.

Structural determinants of the interaction between the Haemophilus influenzae Hap autotransporter and fibronectin

PubMed Central

Spahich, Nicole A.; Kenjale, Roma; McCann, Jessica; Meng, Guoyu; Ohashi, Tomoo; Erickson, Harold P.

2014-01-01

Haemophilus influenzae is a Gram-negative cocco-bacillus that initiates infection by colonizing the upper respiratory tract. Hap is an H. influenzae serine protease autotransporter protein that mediates adherence, invasion and microcolony formation in assays with human epithelial cells and is presumed to facilitate the process of colonization. Additionally, Hap mediates adherence to fibronectin, laminin and collagen IV, extracellular matrix (ECM) proteins that are present in the respiratory tract and are probably important targets for H. influenzae colonization. The region of Hap responsible for adherence to ECM proteins has been localized to the C-terminal 511 aa of the Hap passenger domain (HapS). In this study, we characterized the structural determinants of the interaction between HapS and fibronectin. Using defined fibronectin fragments, we established that Hap interacts with the fibronectin repeat fragment called FNIII(1–2). Using site-directed mutagenesis, we found a series of motifs in the C-terminal region of HapS that contribute to the interaction with fibronectin. Most of these motifs are located on the F1 and F3 faces of the HapS structure, suggesting that the F1 and F3 faces may be responsible for the HapS–fibronectin interaction. PMID:24687948

Automated protein NMR structure determination using wavelet de-noised NOESY spectra.

PubMed

Dancea, Felician; Günther, Ulrich

2005-11-01

A major time-consuming step of protein NMR structure determination is the generation of reliable NOESY cross peak lists which usually requires a significant amount of manual interaction. Here we present a new algorithm for automated peak picking involving wavelet de-noised NOESY spectra in a process where the identification of peaks is coupled to automated structure determination. The core of this method is the generation of incremental peak lists by applying different wavelet de-noising procedures which yield peak lists of a different noise content. In combination with additional filters which probe the consistency of the peak lists, good convergence of the NOESY-based automated structure determination could be achieved. These algorithms were implemented in the context of the ARIA software for automated NOE assignment and structure determination and were validated for a polysulfide-sulfur transferase protein of known structure. The procedures presented here should be commonly applicable for efficient protein NMR structure determination and automated NMR peak picking.

Sequence and structure determinants of Drosophila Hsp70 mRNA translation: 5'UTR secondary structure specifically inhibits heat shock protein mRNA translation.

PubMed Central

Hess, M A; Duncan, R F

1996-01-01

Preferential translation of Drosophila heat shock protein 70 (Hsp70) mRNA requires only the 5'-untranslated region (5'-UTR). The sequence of this region suggests that it has relatively little secondary structure, which may facilitate efficient protein synthesis initiation. To determine whether minimal 5'-UTR secondary structure is required for preferential translation during heat shock, the effect of introducing stem-loops into the Hsp70 mRNA 5'-UTR was measured. Stem-loops of -11 kcal/mol abolished translation during heat shock, but did not reduce translation in non-heat shocked cells. A -22 kcal/mol stem-loop was required to comparably inhibit translation during growth at normal temperatures. To investigate whether specific sequence elements are also required for efficient preferential translation, deletion and mutation analyses were conducted in a truncated Hsp70 5'-UTR containing only the cap-proximal and AUG-proximal segments. Linker-scanner mutations in the cap-proximal segment (+1 to +37) did not impair translation. Re-ordering the segments reduced mRNA translational efficiency by 50%. Deleting the AUG-proximal segment severely inhibited translation. A 5-extension of the full-length leader specifically impaired heat shock translation. These results indicate that heat shock reduces the capacity to unwind 5-UTR secondary structure, allowing only mRNAs with minimal 5'-UTR secondary structure to be efficiently translated. A function for specific sequences is also suggested. PMID:8710519

Structure-Guided Combinatorial Engineering Facilitates Affinity and Specificity Optimization of Anti-CD81 Antibodies.

PubMed

Nelson, Bryce; Adams, Jarrett; Kuglstatter, Andreas; Li, Zhijian; Harris, Seth F; Liu, Yang; Bohini, Sandya; Ma, Han; Klumpp, Klaus; Gao, Junjun; Sidhu, Sachdev S

2018-07-06

Hepatitis C viral infection is the major cause of chronic hepatitis that affects as many as 71 million people worldwide. Rather than target the rapidly shifting viruses and their numerous serotypes, four independent antibodies were made to target the host antigen CD81 and were shown to block hepatitis C viral entry. The single-chain variable fragment of each antibody was crystallized in complex with the CD81 large extracellular loop in order to guide affinity maturation of two distinct antibodies by phage display. Affinity maturation of antibodies using phage display has proven to be critical to therapeutic antibody development and typically involves modification of the paratope for increased affinity, improved specificity, enhanced stability or a combination of these traits. One antibody was engineered for increased affinity for human CD81 large extracellular loop that equated to increased efficacy, while the second antibody was engineered for cross-reactivity with cynomolgus CD81 to facilitate animal model testing. The use of structures to guide affinity maturation library design demonstrates the utility of combining structural analysis with phage display technologies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Can we infer plant facilitation from remote sensing? A test across global drylands

PubMed Central

Xu, Chi; Holmgren, Milena; Van Nes, Egbert H.; Maestre, Fernando T.; Soliveres, Santiago; Berdugo, Miguel; Kéfi, Sonia; Marquet, Pablo A.; Abades, Sebastian; Scheffer, Marten

2016-01-01

Facilitation is a major force shaping the structure and diversity of plant communities in terrestrial ecosystems. Detecting positive plant-plant interactions relies on the combination of field experimentation and the demonstration of spatial association between neighboring plants. This has often restricted the study of facilitation to particular sites, limiting the development of systematic assessments of facilitation over regional and global scales. Here we explore whether the frequency of plant spatial associations detected from high-resolution remotely-sensed images can be used to infer plant facilitation at the community level in drylands around the globe. We correlated the information from remotely-sensed images freely available through Google Earth™ with detailed field assessments, and used a simple individual-based model to generate patch-size distributions using different assumptions about the type and strength of plant-plant interactions. Most of the patterns found from the remotely-sensed images were more right-skewed than the patterns from the null model simulating a random distribution. This suggests that the plants in the studied drylands show stronger spatial clustering than expected by chance. We found that positive plant co-occurrence, as measured in the field, was significantly related to the skewness of vegetation patch-size distribution measured using Google Earth™ images. Our findings suggest that the relative frequency of facilitation may be inferred from spatial pattern signals measured from remotely-sensed images, since facilitation often determines positive co-occurrence among neighboring plants. They pave the road for a systematic global assessment of the role of facilitation in terrestrial ecosystems. PMID:26552256

Facilitating Developmental Guidance through Behavioral Management.

ERIC Educational Resources Information Center

Davis, Donna H.

1980-01-01

The counselor, facilitating classroom development guidance lessons, may experience conflict and difficulty. The management system presented here allows for flexibility and provides sufficient behavioral structure, while encouraging individual expression from students. This behavioral management approach is supportive of, but secondary to,…

Structural determinants of arrestin functions.

PubMed

Gurevich, Vsevolod V; Gurevich, Eugenia V

2013-01-01

Arrestins are a small protein family with only four members in mammals. Arrestins demonstrate an amazing versatility, interacting with hundreds of different G protein-coupled receptor (GPCR) subtypes, numerous nonreceptor signaling proteins, and components of the internalization machinery, as well as cytoskeletal elements, including regular microtubules and centrosomes. Here, we focus on the structural determinants that mediate various arrestin functions. The receptor-binding elements in arrestins were mapped fairly comprehensively, which set the stage for the construction of mutants targeting particular GPCRs. The elements engaged by other binding partners are only now being elucidated and in most cases we have more questions than answers. Interestingly, even very limited and imprecise identification of structural requirements for the interaction with very few other proteins has enabled the development of signaling-biased arrestin mutants. More comprehensive understanding of the structural underpinning of different arrestin functions will pave the way for the construction of arrestins that can link the receptor we want to the signaling pathway of our choosing. Copyright © 2013 Elsevier Inc. All rights reserved.

Modelling the social and structural determinants of tuberculosis: opportunities and challenges

PubMed Central

Boccia, D.; Dodd, P. J.; Lönnroth, K.; Dowdy, D. W.; Siroka, A.; Kimerling, M. E.; White, R. G.; Houben, R. M. G. J.

2017-01-01

INTRODUCTION: Despite the close link between tuberculosis (TB) and poverty, most mathematical models of TB have not addressed underlying social and structural determinants. OBJECTIVE: To review studies employing mathematical modelling to evaluate the epidemiological impact of the structural determinants of TB. METHODS: We systematically searched PubMed and personal libraries to identify eligible articles. We extracted data on the modelling techniques employed, research question, types of structural determinants modelled and setting. RESULTS: From 232 records identified, we included eight articles published between 2008 and 2015; six employed population-based dynamic TB transmission models and two non-dynamic analytic models. Seven studies focused on proximal TB determinants (four on nutritional status, one on wealth, one on indoor air pollution, and one examined overcrowding, socioeconomic and nutritional status), and one focused on macro-economic influences. CONCLUSIONS: Few modelling studies have attempted to evaluate structural determinants of TB, resulting in key knowledge gaps. Despite the challenges of modelling such a complex system, models must broaden their scope to remain useful for policy making. Given the intersectoral nature of the interrelations between structural determinants and TB outcomes, this work will require multidisciplinary collaborations. A useful starting point would be to focus on developing relatively simple models that can strengthen our knowledge regarding the potential effect of the structural determinants on TB outcomes. PMID:28826444

Representing Personal Determinants in Causal Structures.

ERIC Educational Resources Information Center

Bandura, Albert

1984-01-01

Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

Organizational Structure as a Determinant of Job Burnout.

PubMed

Bilal, Atif; Ahmed, Hafiz Mushtaq

2017-03-01

This exploratory study determined the impact of organizational structure, particularly participation in decision making, instrumental communication, formalization, integration, and promotional opportunity, on burnout among Pakistani pediatric nurses. Data were collected from pediatric nurses working for Punjab's largest state-run hospital. The findings revealed that participation in decision making, instrumental communication, and promotional opportunity prevented burnout. Formalization contributed to burnout but integration was not related to burnout. Quite interestingly, except for supervisory status, most control variables for this study were not significantly related to emotional burnout. Hence, the hypothesis that organizational structure is a determinant of job burnout was accepted.

Facilitating classroom based interprofessional learning: a grounded theory study of university educators' perceptions of their role adequacy as facilitators.

PubMed

Derbyshire, Julie A; Machin, Alison I; Crozier, Suzanne

2015-01-01

The provision of inter professional learning (IPL) within undergraduate programmes is now well established within many Higher Education Institutions (HEIs). IPL aims to better equip nurses and other health professionals with effective collaborative working skills and knowledge to improve the quality of patient care. Although there is still ambiguity in relation to the optimum timing and method for delivering IPL, effective facilitation is seen as essential. This paper reports on a grounded theory study of university educators' perceptions of the knowledge and skills needed for their role adequacy as IPL facilitators. Data was collected using semi structured interviews with nine participants who were theoretically sampled from a range of professional backgrounds, with varied experiences of education and involvement in facilitating IPL. Constant comparative analysis was used to generate four data categories: creating and sustaining an IPL group culture through transformational IPL leadership (core category), readiness for IPL facilitation, drawing on past interprofessional learning and working experiences and role modelling an interprofessional approach. The grounded theory generated from this study, although propositional, suggests that role adequacy for IPL facilitation is dependent on facilitator engagement in a process of 'transformational interprofessional learning leadership' to create and sustain a group culture. Copyright © 2014 Elsevier Ltd. All rights reserved.

Do intraspecific or interspecific interactions determine responses to predators feeding on a shared size-structured prey community?

PubMed

ten Brink, Hanna; Mazumdar, Abul Kalam Azad; Huddart, Joseph; Persson, Lennart; Cameron, Tom C

2015-03-01

Coexistence of predators that share the same prey is common. This is still the case in size-structured predator communities where predators consume prey species of different sizes (interspecific prey responses) or consume different size classes of the same species of prey (intraspecific prey responses). A mechanism has recently been proposed to explain coexistence between predators that differ in size but share the same prey species, emergent facilitation, which is dependent on strong intraspecific responses from one or more prey species. Under emergent facilitation, predators can depend on each other for invasion, persistence or success in a size-structured prey community. Experimental evidence for intraspecific size-structured responses in prey populations remains rare, and further questions remain about direct interactions between predators that could prevent or limit any positive effects between predators [e.g. intraguild predation (IGP)]. Here, we provide a community-wide experiment on emergent facilitation including natural predators. We investigate both the direct interactions between two predators that differ in body size (fish vs. invertebrate predator), and the indirect interaction between them via their shared prey community (zooplankton). Our evidence supports the most likely expectation of interactions between differently sized predators that IGP rates are high, and interspecific interactions in the shared prey community dominate the response to predation (i.e. predator-mediated competition). The question of whether emergent facilitation occurs frequently in nature requires more empirical and theoretical attention, specifically to address the likelihood that its pre-conditions may co-occur with high rates of IGP. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Synthesis and Crystal Structure Study of 2’-Se-Adenosine-Derivatized DNA

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

Sheng, J.; Salon, J; Gan, J

2010-01-01

The selenium derivatization of nucleic acids is a novel and promising strategy for 3D structure determination of nucleic acids. Selenium can serve as an excellent anomalous scattering center to solve the phase problem, which is one of the two major bottlenecks in macromolecule X-ray crystallography. The other major bottleneck is crystallization. It has been demonstrated that the incorporated selenium functionality at the 2'-positions of the nucleosides and nucleotides is stable and does not cause significant structure perturbation. Furthermore, it was observed that the 2'-Se-derivatization could facilitate crystallization of oligonucleotides with fast crystal growth and high diffraction quality. Herein, we describemore » a convenient synthesis of the 2'-Se-adenosine phosphoramidite, and report the first synthesis and X-ray crystal structure determination of the DNA containing the 2'-Se-A derivatization. The 3D structure of 2'-Se-A-DNA decamer [5'-GTACGCGT(2'-Se-A)C-3']{sub 2} was determined at 1.75 {angstrom} resolution, the 2'-Se-functionality points to the minor groove, and the Se-modified and native structures are virtually identical. Moreover, we have observed that the 2'-Se-A modification can greatly facilitate the crystal growth with high diffraction quality. In conjunction with the crystallization facilitation by the 2'-Se-U and 2'-Se-T, this novel observation on the 2'-Se-A functionality suggests that the 2'-Se moiety is sole responsible for the crystallization facilitation and the identity of nucleobases does not influence the crystal growth significantly.« less

Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9)

PubMed Central

Fu, Qinqin; Yuan, Y. Adam

2013-01-01

Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA. PMID:23361462

Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9).

PubMed

Fu, Qinqin; Yuan, Y Adam

2013-03-01

Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA.

Perceived facilitators of and barriers to healthful eating among university students.

PubMed

Garcia, Alicia C; Sykes, Lesley; Matthews, June; Martin, Noelle; Leipert, Beverly

2010-01-01

Photovoice, an innovative qualitative research method in health care, has not been used to its full potential in nutrition/dietetics. We explored the use of Photovoice to determine perceived facilitators of and barriers to healthful eating among university students. The study included 28 students enrolled in a 2008 introductory nutrition class. The students participated in a camera orientation session to review ethics and privacy issues. They took photographs and selected two for discussion in a focus group moderated by a graduate student who used a semi-structured facilitation guide. Researchers coded the transcripts, analyzed the pictures and students' written comments about the project, and ensured data trustworthiness through credibility, dependability, confirmability, and transferability of data and methods. Six major themes emerged as facilitators and/or barriers: environment, nutrition knowledge, convenience foods, time, media influence, and food cost. More than one-third of the students thought the study "stimulated their critical thinking." They felt more empowered in sharing their perceptions and "getting their voices heard." Photovoice was a useful, "motivating," and "engaging" method for research on nutrition knowledge and dietary patterns of university students. Registered dietitians and other health professionals may benefit from the use of the Photovoice method when they are working with students.

Using the stepladder technique to facilitate the performance of audioconferencing groups.

PubMed

Rogelberg, Steven G; O'Connor, Matthew S; Sederburg, Matthew

2002-10-01

Organizational workforces are becoming increasingly dispersed. To facilitate communications among individuals or groups of people located in a number of different locations, teleconferencing technologies, such as audioconferencing, have been developed. The authors examined whether a structural group intervention, the stepladder technique, can facilitate the task performance of 4-person groups (n = 52) when using audioconferencing. Consistent with research conducted on face-to-face groups, the stepladder technique was found to facilitate the decision-making performance of groups interacting via audioconference. The authors postulated that certain structural elements of the stepladder technique compensate for obstacles inherent in nonvisual communications. Supplementary analyses examined best member influence and the existence of order of entry effects into the stepladder process.

The Smoker’s Health Project: A self-determination theory intervention to facilitate maintenance of tobacco abstinence

PubMed Central

Williams, Geoffrey C.; Patrick, Heather; Niemiec, Christopher P.; Ryan, Richard M.; Deci, Edward L.; Lavigne, Holly McGregor

2011-01-01

A previous randomized clinical trial based on self-determination theory (SDT) and consistent with the Public Health Service (PHS) Guideline for Treating Tobacco Use and Dependence demonstrated that an intensive intervention could change autonomous self-regulation and perceived competence which in part facilitated long-term tobacco abstinence. The current article describes a pragmatic comparative effectiveness trial of three SDT-based intensive tobacco-dependence interventions. Eligible participants are randomized to one of three treatment conditions designed to facilitate long-term maintenance of tobacco abstinence, namely, Community Care (CC), which includes the 6-month SDT-based intervention previously shown to promote autonomous self-regulation, perceived competence, medication use, and tobacco abstinence; Extended Need Support (ENS), which extends the 6-month SDT-based intervention to 12 months and trains an important other to provide support for smokers’ basic psychological needs; and Harm Reduction (HR), which provides extended need support and recommends medication use for participants who do not want to stop smoking completely within 30 days but who are willing to reduce their cigarette use by half. The primary outcome is 12-month prolonged abstinence from tobacco, which is assessed one year following termination of treatment (two years post-randomization). Secondary outcomes include 7- and 30-day point prevalence tobacco abstinence, number of days using smoking-cessation medication, change in autonomous self-regulation and perceived competence, and perceived need support from important others. PMID:21382516

Barriers and facilitators to establishing a national public health observatory.

PubMed

Pooransingh, Shalini; Misir, Akenath; Ramdath, Dan; Ramsewak, Samuel; Jaglal, Susan; Cameron, Cathy; Goel, Vivek

2015-11-01

To determine what stakeholders perceive as barriers and facilitators to creating a national public health observatory (PHO) in Trinidad and Tobago. A descriptive study was conducted based on 15 key informant interviews carried out from April to September 2013. The key informants worked within the health care sector in Trinidad and Tobago. Using a semi-structured interview guide, information was collected on knowledge, attitudes, and beliefs about creating a PHO; barriers and facilitators to creating and sustaining a PHO; legal considerations; and human resource and information technology requirements. Common themes of the responses were identified. The majority of participants supported the development of a national PHO, recognized its value in informing their work, and indicated that a national PHO could 1) provide information to support evidence-informed decision-making for health policy and strategic planning; 2) facilitate data management by establishing data policies, procedures, and standards; 3) increase the use of data by synthesizing and disseminating information; and 4) provide data for benchmarking. However, a number of barriers were identified, including 1) the perception that data collection is not valued; 2) untimely availability of data; 3) limited data synthesis, dissemination, and utilization to inform decision-making; and 4) challenges related to the allocation of human resources and existing information technology. Key informants support the development of a national PHO in Trinidad and Tobago. The findings align well within the components of the conceptual framework for establishing national health observatories. A stepwise approach to establishing a national PHO in Trinidad and Tobago, beginning with structural components and followed by functional components, is recommended. A national PHO in Trinidad and Tobago could serve as a model for other countries in the Caribbean.

Method and apparatus for determining material structural integrity

DOEpatents

Pechersky, M.J.

1994-01-01

Disclosed are a nondestructive method and apparatus for determining the structural integrity of materials by combining laser vibrometry with damping analysis to determine the damping loss factor. The method comprises the steps of vibrating the area being tested over a known frequency range and measuring vibrational force and velocity vs time over the known frequency range. Vibrational velocity is preferably measured by a laser vibrometer. Measurement of the vibrational force depends on the vibration method: if an electromagnetic coil is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by the coil current. If a reciprocating transducer is used, the vibrational force is determined by a force gauge in the transducer. Using vibrational analysis, a plot of the drive point mobility of the material over the preselected frequency range is generated from the vibrational force and velocity data. Damping loss factor is derived from a plot of the drive point mobility over the preselected frequency range using the resonance dwell method and compared with a reference damping loss factor for structural integrity evaluation.

Facilitation and Practice in Verb Acquisition

ERIC Educational Resources Information Center

Keren-Portnoy, Tamar

2006-01-01

This paper presents a model of syntax acquisition, whose main points are as follows: Syntax is acquired in an item-based manner; early learning facilitates subsequent learning--as evidenced by the accelerating rate of new verbs entering a given structure; and mastery of syntactic knowledge is typically achieved through practice--as evidenced by…

Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction.

PubMed

Masica, David L; Ash, Jason T; Ndao, Moise; Drobny, Gary P; Gray, Jeffrey J

2010-12-08

Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized. Copyright © 2010 Elsevier Ltd. All rights reserved.

Project SELF: Preparing Professionals to Facilitate Self-Determination

ERIC Educational Resources Information Center

Blasco, P. M.; Falco, R. A.; Munson, L. J.

2006-01-01

Only recently have professionals recognized the importance of self-determination for young children and their families. Project SELF used the philosophy of self-determination in an interdisciplinary model to prepare graduate students to serve young children with disabilities and their families. Through Participatory Action Research (PAR) projects,…

Fine structure of heliumlike ions and determination of the fine structure constant.

PubMed

Pachucki, Krzysztof; Yerokhin, Vladimir A

2010-02-19

We report a calculation of the fine-structure splitting in light heliumlike atoms, which accounts for all quantum electrodynamical effects up to order alpha{5} Ry. For the helium atom, we resolve the previously reported disagreement between theory and experiment and determine the fine-structure constant with an accuracy of 31 ppb. The calculational results are extensively checked by comparison with the experimental data for different nuclear charges and by evaluation of the hydrogenic limit of individual corrections.

Qualitative evaluation of the implementation of the Interdisciplinary Management Tool: a reflective tool to enhance interdisciplinary teamwork using Structured, Facilitated Action Research for Implementation.

PubMed

Nancarrow, Susan A; Smith, Tony; Ariss, Steven; Enderby, Pamela M

2015-07-01

Reflective practice is used increasingly to enhance team functioning and service effectiveness; however, there is little evidence of its use in interdisciplinary teams. This paper presents the qualitative evaluation of the Interdisciplinary Management Tool (IMT), an evidence-based change tool designed to enhance interdisciplinary teamwork through structured team reflection. The IMT incorporates three components: an evidence-based resource guide; a reflective implementation framework based on Structured, Facilitated Action Research for Implementation methodology; and formative and summative evaluation components. The IMT was implemented with intermediate care teams supported by independent facilitators in England. Each intervention lasted 6 months and was evaluated over a 12-month period. Data sources include interviews, a focus group with facilitators, questionnaires completed by team members and documentary feedback from structured team reports. Data were analysed qualitatively using the Framework approach. The IMT was implemented with 10 teams, including 253 staff from more than 10 different disciplines. Team challenges included lack of clear vision; communication issues; limited career progression opportunities; inefficient resource use; need for role clarity and service development. The IMT successfully engaged staff in the change process, and resulted in teams developing creative strategies to address the issues identified. Participants valued dedicated time to focus on the processes of team functioning; however, some were uncomfortable with a focus on teamwork at the expense of delivering direct patient care. The IMT is a relatively low-cost, structured, reflective way to enhance team function. It empowers individuals to understand and value their own, and others' roles and responsibilities within the team; identify barriers to effective teamwork, and develop and implement appropriate solutions to these. To be successful, teams need protected time to take

Evolution of local facilitation in arid ecosystems.

PubMed

Kéfi, Sonia; van Baalen, Minus; Rietkerk, Max; Loreau, Michel

2008-07-01

In harsh environments, sessile organisms can make their habitat more hospitable by buffering environmental stress or increasing resource availability. Although the ecological significance of such local facilitation is widely established, the evolutionary aspects have been seldom investigated. Yet addressing the evolutionary aspects of local facilitation is important because theoretical studies show that systems with such positive interactions can exhibit alternative stable states and that such systems may suddenly become extinct when they evolve (evolutionary suicide). Arid ecosystems currently experience strong changes in climate and human pressures, but little is known about the effects of these changes on the selective pressures exerted on the vegetation. Here, we focus on the evolution of local facilitation in arid ecosystems, using a lattice-structured model explicitly considering local interactions among plants. We found that the evolution of local facilitation depends on the seed dispersal strategy. In systems characterized by short-distance seed dispersal, adaptation to a more stressful environment leads to high local facilitation, allowing the population to escape extinction. In contrast, systems characterized by long-distance seed dispersal become extinct under increased stress even when allowed to adapt. In this case, adaptation in response to climate change and human pressures could give the final push to the desertification of arid ecosystems.

Global search in photoelectron diffraction structure determination using genetic algorithms

NASA Astrophysics Data System (ADS)

Viana, M. L.; Díez Muiño, R.; Soares, E. A.; Van Hove, M. A.; de Carvalho, V. E.

2007-11-01

Photoelectron diffraction (PED) is an experimental technique widely used to perform structural determinations of solid surfaces. Similarly to low-energy electron diffraction (LEED), structural determination by PED requires a fitting procedure between the experimental intensities and theoretical results obtained through simulations. Multiple scattering has been shown to be an effective approach for making such simulations. The quality of the fit can be quantified through the so-called R-factor. Therefore, the fitting procedure is, indeed, an R-factor minimization problem. However, the topography of the R-factor as a function of the structural and non-structural surface parameters to be determined is complex, and the task of finding the global minimum becomes tough, particularly for complex structures in which many parameters have to be adjusted. In this work we investigate the applicability of the genetic algorithm (GA) global optimization method to this problem. The GA is based on the evolution of species, and makes use of concepts such as crossover, elitism and mutation to perform the search. We show results of its application in the structural determination of three different systems: the Cu(111) surface through the use of energy-scanned experimental curves; the Ag(110)-c(2 × 2)-Sb system, in which a theory-theory fit was performed; and the Ag(111) surface for which angle-scanned experimental curves were used. We conclude that the GA is a highly efficient method to search for global minima in the optimization of the parameters that best fit the experimental photoelectron diffraction intensities to the theoretical ones.

MOTIVATION INTERNALIZATION AND SIMPLEX STRUCTURE IN SELF-DETERMINATION THEORY.

PubMed

Ünlü, Ali; Dettweiler, Ulrich

2015-12-01

Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure.

Determinants of Market Structure and the Airline Industry

NASA Technical Reports Server (NTRS)

Raduchel, W.

1972-01-01

The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints

NASA Astrophysics Data System (ADS)

Alber, Frank; Chait, Brian T.; Rout, Michael P.; Sali, Andrej

To understand the cell, we need to determine the structures of macromolecular assemblies, many of which consist of tens to hundreds of components. A great variety of experimental data can be used to characterize the assemblies at several levels of resolution, from atomic structures to component configurations. To maximize completeness, resolution, accuracy, precision and efficiency of the structure determination, a computational approach is needed that can use spatial information from a variety of experimental methods. We propose such an approach, defined by its three main components: a hierarchical representation of the assembly, a scoring function consisting of spatial restraints derived from experimental data, and an optimization method that generates structures consistent with the data. We illustrate the approach by determining the configuration of the 456 proteins in the nuclear pore complex from Baker's yeast.

Determining Barriers and Facilitators Associated With Willingness to Use a Personal Health Information Management System to Support Worksite Wellness Programs.

PubMed

Neyens, David M; Childers, Ashley Kay

2017-07-01

To determine the barriers and facilitators associated with willingness to use personal health information management (PHIM) systems to support an existing worksite wellness program (WWP). The study design involved a Web-based survey. The study setting was a regional hospital. Hospital employees comprised the study subjects. Willingness, barriers, and facilitators associated with PHIM were measured. Bivariate logit models were used to model two binary dependent variables. One model predicted the likelihood of believing PHIM systems would positively affect overall health and willingness to use. Another predicted the likelihood of worrying about online security and not believing PHIM systems would benefit health goals. Based on 333 responses, believing PHIM systems would positively affect health was highly associated with willingness to use PHIM systems (p < .01). Those comfortable online were 7.22 times more willing to use PHIM systems. Participants in exercise-based components of WWPs were 3.03 times more likely to be willing to use PHIM systems. Those who worried about online security were 5.03 times more likely to believe PHIM systems would not help obtain health goals. Comfort with personal health information online and exercise-based WWP experience was associated with willingness to use PHIM systems. However, nutrition-based WWPs did not have similar effects. Implementation barriers relate to technology anxiety and trust in security, as well as experience with specific WWP activities. Identifying differences between WWP components and addressing technology concerns before implementation of PHIM systems into WWPs may facilitate improved adoption and usage.

Protein structure determination by exhaustive search of Protein Data Bank derived databases.

PubMed

Stokes-Rees, Ian; Sliz, Piotr

2010-12-14

Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.

Functional and structural cerebral changes in key brain regions after a facilitation programme for episodic future thought in relapsing-remitting multiple sclerosis patients.

PubMed

Ernst, Alexandra; Sourty, Marion; Roquet, Daniel; Noblet, Vincent; Gounot, Daniel; Blanc, Frédéric; De Seze, Jérôme; Manning, Liliann

2016-06-01

Increasingly studied, episodic future thought (EFT) impairment negatively affects patients' daily life. Along these lines, working with relapsing-remitting multiple sclerosis (RR-MS) patients, we documented the clinical effectiveness of a mental visual imagery (MVI)-based facilitation programme on EFT impairment related to executive function difficulties. We aimed at improving the characterisation of the cognitive and neural underpinnings of RR-MS patients' EFT amelioration, by exploring the structural and functional brain changes following the MVI programme. Seventeen non-depressed RR-MS patients were recruited and randomly assigned in the (i) experimental group (n=10), who followed the MVI programme or in the control group (n=7), who followed a verbal control programme. Using an adapted version of the Autobiographical Interview to assess EFT, after facilitation, significant improvement was observed in the experimental group only. This was accompanied by increased activation in the prefrontal region during the generation of future events and was positively correlated with grey matter volume increase in this same brain area. Increased activations in the parahippocampal and the middle temporal gyri were also observed in the experimental group in post-facilitation. Likewise, functional connectivity changes were observed in the posterior brain regions after facilitation. Only minor cerebral changes were observed in the control group, likely reflecting practice effects. Our study showed that EFT improvement following the MVI programme led to functional and structural changes in brain regions sustaining contextual processing, visual imagery, the integration and maintenance of multimodal information. Taken together, these findings suggest that a cognitive intervention focusing on scene construction can be efficient to alleviate EFT impairment related to executive dysfunction. As such, this study opens the way to the development of tailor-made rehabilitation programmes

Facilitators for practice change in Spanish community pharmacy.

PubMed

Gastelurrutia, Miguel A; Benrimoj, S I Charlie; Castrillon, Carla C; de Amezua, María J Casado; Fernandez-Llimos, Fernando; Faus, Maria J

2009-02-01

To identify and prioritise facilitators for practice change in Spanish community pharmacy. Spanish community pharmacies. Qualitative study. Thirty-three semi-structured interviews were conducted with community pharmacists (n = 15) and pharmacy strategists (n = 18), and the results were examined using the content analysis method. In addition, two nominal groups (seven community pharmacists and seven strategists) were formed to identify and prioritise facilitators. Results of both techniques were then triangulated. Facilitators for practice change. Twelve facilitators were identified and grouped into four domains (D1: Pharmacist; D2: Pharmacy as an organisation; D3: Pharmaceutical profession; D4: Miscellaneous). Facilitators identified in D1 include: the need for more clinical education at both pre- and post-graduate levels; the need for clearer and unequivocal messages from professional leaders about the future of the professional practice; and the need for a change in pharmacists' attitudes. Facilitators in D2 are: the need to change the reimbursement system to accommodate cognitive service delivery as well as dispensing; and the need to change the front office of pharmacies. Facilitators identified in D3 are: the need for the Spanish National Professional Association to take a leadership role in the implementation of cognitive services; the need to reduce administrative workload; and the need for universities to reduce the gap between education and research. Other facilitators identified in this study include: the need to increase patients' demand for cognitive services at pharmacies; the need to improve pharmacist-physician relationships; the need for support from health care authorities; and the need for improved marketing of cognitive services and their benefits to society, including physicians and health care authorities. Twelve facilitators were identified. Strategists considered clinical education and pharmacists' attitude as the most important, and

Structure determination of helical filaments by solid-state NMR spectroscopy

PubMed Central

Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

2016-01-01

The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

Orientation determination of interfacial beta-sheet structures in situ.

PubMed

Nguyen, Khoi Tan; King, John Thomas; Chen, Zhan

2010-07-01

Structural information such as orientations of interfacial proteins and peptides is important for understanding properties and functions of such biological molecules, which play crucial roles in biological applications and processes such as antimicrobial selectivity, membrane protein activity, biocompatibility, and biosensing performance. The alpha-helical and beta-sheet structures are the most widely encountered secondary structures in peptides and proteins. In this paper, for the first time, a method to quantify the orientation of the interfacial beta-sheet structure using a combined attenuated total reflectance Fourier transformation infrared spectroscopic (ATR-FTIR) and sum frequency generation (SFG) vibrational spectroscopic study was developed. As an illustration of the methodology, the orientation of tachyplesin I, a 17 amino acid peptide with an antiparallel beta-sheet, adsorbed to polymer surfaces as well as associated with a lipid bilayer was determined using the regular and chiral SFG spectra, together with polarized ATR-FTIR amide I signals. Both the tilt angle (theta) and the twist angle (psi) of the beta-sheet at interfaces are determined. The developed method in this paper can be used to obtain in situ structural information of beta-sheet components in complex molecules. The combination of this method and the existing methodology that is currently used to investigate alpha-helical structures will greatly broaden the application of optical spectroscopy in physical chemistry, biochemistry, biophysics, and structural biology.

Facilitation of Retention by White Noise

ERIC Educational Resources Information Center

Baumeister, Alfred A.; Kistler, Doris

1975-01-01

This study attempted to determine if white noise (an arousing stimulus), when presented at the time of recall, facilitates performance of second and fifth grade students, and if this effect generalizes across different kinds of learning tasks. Findings indicate that white noise produces improvements in performance in both age groups. (GO)

Facilitating Discussion Among Expectant Fathers: Is Anyone Interested?

PubMed Central

Friedewald, Mark

2007-01-01

Within childbirth education circles, catering effectively to the needs of expectant fathers who attend antenatal education programs has become an issue of concern. This article reviews the literature on all-male discussion groups for expectant fathers as a strategy to address identified deficits in relation to the inclusion of men within existing program structures. An exploration of the attributes considered appropriate for those who facilitate such groups is undertaken, and the article concludes with a report on the recruitment of male facilitators at a health service in New South Wales, Australia. PMID:18311334

A Fast Surrogate-facilitated Data-driven Bayesian Approach to Uncertainty Quantification of a Regional Groundwater Flow Model with Structural Error

NASA Astrophysics Data System (ADS)

Xu, T.; Valocchi, A. J.; Ye, M.; Liang, F.

2016-12-01

Due to simplification and/or misrepresentation of the real aquifer system, numerical groundwater flow and solute transport models are usually subject to model structural error. During model calibration, the hydrogeological parameters may be overly adjusted to compensate for unknown structural error. This may result in biased predictions when models are used to forecast aquifer response to new forcing. In this study, we extend a fully Bayesian method [Xu and Valocchi, 2015] to calibrate a real-world, regional groundwater flow model. The method uses a data-driven error model to describe model structural error and jointly infers model parameters and structural error. In this study, Bayesian inference is facilitated using high performance computing and fast surrogate models. The surrogate models are constructed using machine learning techniques to emulate the response simulated by the computationally expensive groundwater model. We demonstrate in the real-world case study that explicitly accounting for model structural error yields parameter posterior distributions that are substantially different from those derived by the classical Bayesian calibration that does not account for model structural error. In addition, the Bayesian with error model method gives significantly more accurate prediction along with reasonable credible intervals.

Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

PubMed

Potrzebowski, Wojciech; André, Ingemar

2015-07-01

For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints.

Practice Facilitators' and Leaders' Perspectives on a Facilitated Quality Improvement Program.

PubMed

McHugh, Megan; Brown, Tiffany; Liss, David T; Walunas, Theresa L; Persell, Stephen D

2018-04-01

Practice facilitation is a promising approach to helping practices implement quality improvements. Our purpose was to describe practice facilitators' and practice leaders' perspectives on implementation of a practice facilitator-supported quality improvement program and describe where their perspectives aligned and diverged. We conducted interviews with practice leaders and practice facilitators who participated in a program that included 35 improvement strategies aimed at the ABCS of heart health (aspirin use in high-risk individuals, blood pressure control, cholesterol management, and smoking cessation). Rapid qualitative analysis was used to collect, organize, and analyze the data. We interviewed 17 of the 33 eligible practice leaders, and the 10 practice facilitators assigned to those practices. Practice leaders and practice facilitators both reported value in the program's ability to bring needed, high-quality resources to practices. Practice leaders appreciated being able to set the schedule for facilitation and select among the 35 interventions. According to practice facilitators, however, relying on practice leaders to set the pace of the intervention resulted in a lower level of program intensity than intended. Practice leaders preferred targeted assistance, particularly electronic health record documentation guidance and linkages to state smoking cessation programs. Practice facilitators reported that the easiest interventions were those that did not alter care practices. The dual perspectives of practice leaders and practice facilitators provide a more holistic picture of enablers and barriers to program implementation. There may be greater opportunities to assist small practices through simple, targeted practice facilitator-supported efforts rather than larger, comprehensive quality improvement projects. © 2018 Annals of Family Medicine, Inc.

Structural Determinants and Children's Oral Health: A Cross-National Study.

PubMed

Baker, S R; Foster Page, L; Thomson, W M; Broomhead, T; Bekes, K; Benson, P E; Aguilar-Diaz, F; Do, L; Hirsch, C; Marshman, Z; McGrath, C; Mohamed, A; Robinson, P G; Traebert, J; Turton, B; Gibson, B J

2018-03-01

Much research on children's oral health has focused on proximal determinants at the expense of distal (upstream) factors. Yet, such upstream factors-the so-called structural determinants of health-play a crucial role. Children's lives, and in turn their health, are shaped by politics, economic forces, and social and public policies. The aim of this study was to examine the relationship between children's clinical (number of decayed, missing, and filled teeth) and self-reported oral health (oral health-related quality of life) and 4 key structural determinants (governance, macroeconomic policy, public policy, and social policy) as outlined in the World Health Organization's Commission for Social Determinants of Health framework. Secondary data analyses were carried out using subnational epidemiological samples of 8- to 15-y-olds in 11 countries ( N = 6,648): Australia (372), New Zealand (three samples; 352, 202, 429), Brunei (423), Cambodia (423), Hong Kong (542), Malaysia (439), Thailand (261, 506), United Kingdom (88, 374), Germany (1498), Mexico (335), and Brazil (404). The results indicated that the type of political regime, amount of governance (e.g., rule of law, accountability), gross domestic product per capita, employment ratio, income inequality, type of welfare regime, human development index, government expenditure on health, and out-of-pocket (private) health expenditure by citizens were all associated with children's oral health. The structural determinants accounted for between 5% and 21% of the variance in children's oral health quality-of-life scores. These findings bring attention to the upstream or structural determinants as an understudied area but one that could reap huge rewards for public health dentistry research and the oral health inequalities policy agenda.

X-ray structure determination at low resolution

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

Brunger, Axel T., E-mail: brunger@stanford.edu; Department of Molecular and Cellular Physiology, Stanford University; Department of Neurology and Neurological Sciences, Stanford University

2009-02-01

Refinement is meaningful even at 4 Å or lower, but with present methodologies it should start from high-resolution crystal structures whenever possible. As an example of structure determination in the 3.5–4.5 Å resolution range, crystal structures of the ATPase p97/VCP, consisting of an N-terminal domain followed by a tandem pair of ATPase domains (D1 and D2), are discussed. The structures were originally solved by molecular replacement with the high-resolution structure of the N-D1 fragment of p97/VCP, whereas the D2 domain was manually built using its homology to the D1 domain as a guide. The structure of the D2 domain alonemore » was subsequently solved at 3 Å resolution. The refined model of D2 and the high-resolution structure of the N-D1 fragment were then used as starting models for re-refinement against the low-resolution diffraction data for full-length p97. The re-refined full-length models showed significant improvement in both secondary structure and R values. The free R values dropped by as much as 5% compared with the original structure refinements, indicating that refinement is meaningful at low resolution and that there is information in the diffraction data even at ∼4 Å resolution that objectively assesses the quality of the model. It is concluded that de novo model building is problematic at low resolution and refinement should start from high-resolution crystal structures whenever possible.« less

Method and apparatus for determining material structural integrity

DOEpatents

Pechersky, Martin

1996-01-01

A non-destructive method and apparatus for determining the structural integrity of materials by combining laser vibrometry with damping analysis techniques to determine the damping loss factor of a material. The method comprises the steps of vibrating the area being tested over a known frequency range and measuring vibrational force and velocity as a function of time over the known frequency range. Vibrational velocity is preferably measured by a laser vibrometer. Measurement of the vibrational force depends on the vibration method. If an electromagnetic coil is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by the amount of coil current used in vibrating the magnet. If a reciprocating transducer is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by a force gauge in the reciprocating transducer. Using known vibrational analysis methods, a plot of the drive point mobility of the material over the preselected frequency range is generated from the vibrational force and velocity measurements. The damping loss factor is derived from a plot of the drive point mobility over the preselected frequency range using the resonance dwell method and compared with a reference damping loss factor for structural integrity evaluation.

Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo

PubMed Central

Ritchey, Laura E.; Su, Zhao; Tang, Yin; Tack, David C.

2017-01-01

Abstract RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. We also present a variation of Structure-seq2 in which a biotinylated nucleotide is incorporated during reverse transcription, which greatly facilitates the protocol by eliminating two PAGE purification steps. We benchmark Structure-seq2 on both mRNA and rRNA structure in rice (Oryza sativa). We demonstrate that Structure-seq2 can lead to new biological insights. Our Structure-seq2 datasets uncover hidden breaks in chloroplast rRNA and identify a previously unreported N1-methyladenosine (m1A) in a nuclear-encoded Oryza sativa rRNA. Overall, Structure-seq2 is a rapid, sensitive, and unbiased method to probe RNA in vivo and genome-wide that facilitates new insights into RNA biology. PMID:28637286

Improved in-cell structure determination of proteins at near-physiological concentration

PubMed Central

Ikeya, Teppei; Hanashima, Tomomi; Hosoya, Saori; Shimazaki, Manato; Ikeda, Shiro; Mishima, Masaki; Güntert, Peter; Ito, Yutaka

2016-01-01

Investigating three-dimensional (3D) structures of proteins in living cells by in-cell nuclear magnetic resonance (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. In-cell NMR provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be determined based on data derived only from in-cell NMR. Here we introduce methods that enable in-cell NMR protein structure determination for a larger number of proteins at concentrations that approach physiological ones. The new methods comprise (1) advances in the processing of non-uniformly sampled NMR data, which reduces the measurement time for the intrinsically short-lived in-cell NMR samples, (2) automatic chemical shift assignment for obtaining an optimal resonance assignment, and (3) structure refinement with Bayesian inference, which makes it possible to calculate accurate 3D protein structures from sparse data sets of conformational restraints. As an example application we determined the structure of the B1 domain of protein G at about 250 μM concentration in living E. coli cells. PMID:27910948

The importance of supporting autonomy and perceived competence in facilitating long-term tobacco abstinence

PubMed Central

Williams, Geoffrey C.; Niemiec, Christopher P.; Patrick, Heather; Ryan, Richard M.; Deci, Edward L.

2010-01-01

Background The Public Health Service (PHS) Guideline for Treating Tobacco Use and Dependence (1) recommends supporting autonomy and perceived competence to facilitate tobacco abstinence. Purpose To evaluate the effectiveness of an intensive tobacco-dependence intervention based on self-determination theory (SDT) and intended to support autonomy and perceived competence in facilitating long-term tobacco abstinence. Methods One thousand and six adult smokers were recruited into a randomized cessation-induction trial. Community care participants received cessation pamphlets and information on local treatment programs. Intervention participants received the same materials and were asked to meet four times with counselors over six months to discuss their health in a manner intended to support autonomy and perceived competence. The primary outcome was 24-month prolonged abstinence from tobacco. The secondary outcome was 7-day point prevalence tobacco abstinence at 24 months post-intervention. Results Smokers in the intervention were more likely to attain both tobacco abstinence outcomes and these effects were partially mediated by change in both autonomous self-regulation and perceived competence from baseline to six months. Structural equation modeling confirmed the SDT model of health-behavior change in facilitating long-term tobacco abstinence. Conclusions An intervention based on SDT and consistent with the PHS Guideline, which was intended to support autonomy and perceived competence, facilitated long-term tobacco abstinence. PMID:19373517

The importance of supporting autonomy and perceived competence in facilitating long-term tobacco abstinence.

PubMed

Williams, Geoffrey C; Niemiec, Christopher P; Patrick, Heather; Ryan, Richard M; Deci, Edward L

2009-06-01

The Public Health Service (PHS) Guideline for Treating Tobacco Use and Dependence (Fiore et al. 2000) recommends supporting autonomy and perceived competence to facilitate tobacco abstinence. The aim of the study was to evaluate the effectiveness of an intensive tobacco-dependence intervention based on self-determination theory (SDT) and intended to support autonomy and perceived competence in facilitating long-term tobacco abstinence. One thousand and six adult smokers were recruited into a randomized cessation-induction trial. Community care participants received cessation pamphlets and information on local treatment programs. Intervention participants received the same materials and were asked to meet four times with counselors over 6 months to discuss their health in a manner intended to support autonomy and perceived competence. The primary outcome was 24-month prolonged abstinence from tobacco. The secondary outcome was 7-day point prevalence tobacco abstinence at 24 months postintervention. Smokers in the intervention were more likely to attain both tobacco abstinence outcomes and these effects were partially mediated by change in both autonomous self-regulation and perceived competence from baseline to 6 months. Structural equation modeling confirmed the SDT model of health-behavior change in facilitating long-term tobacco abstinence. An intervention based on SDT and consistent with the PHS Guideline, which was intended to support autonomy and perceived competence, facilitated long-term tobacco abstinence.

Deducing chemical structure from crystallographically determined atomic coordinates

PubMed Central

Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

2011-01-01

An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

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

Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani

2009-10-21

One major obstacle to membrane protein structure determination is the selection of a detergent micelle that mimics the native lipid bilayer. Currently, detergents are selected by exhaustive screening because the effects of protein-detergent interactions on protein structure are poorly understood. In this study, the structure and dynamics of an integral membrane protein in different detergents is investigated by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS). The results suggest that matching of the micelle dimensions to the protein's hydrophobic surface avoids exchange processes that reduce the completeness of the NMR observations. Based onmore » these dimensions, several mixed micelles were designed that improved the completeness of NMR observations. These findings provide a basis for the rational design of mixed micelles that may advance membrane protein structure determination by NMR.« less

Task Integration Facilitates Multitasking.

PubMed

de Oliveira, Rita F; Raab, Markus; Hegele, Mathias; Schorer, Jörg

2017-01-01

The aim of this study was to investigate multi-task integration in a continuous tracking task. We were particularly interested in how manipulating task structure in a dual-task situation affects learning of a constant segment embedded in a pursuit-tracking task. Importantly, we examined if dual-task effects could be attributed to task integration by varying the structural similarity and difficulty of the primary and secondary tasks. In Experiment 1 participants performed a pursuit tracking task while counting high-pitched tones and ignoring low-pitched tones. The tones were either presented randomly or structurally 250 ms before each tracking turn. Experiment 2 increased the motor load of the secondary tasks by asking participants to tap their feet to the tones. Experiment 3 further increased motor load of the primary task by increasing its speed and having participants tracking with their non-dominant hand. The results show that dual-task interference can be moderated by secondary task conditions that match the structure of the primary task. Therefore our results support proposals of task integration in continuous tracking paradigms. We conclude that multi-tasking is not always detrimental for motor learning but can be facilitated through task-integration.

Facilitating Conceptual Change in Students' Understanding of Electrochemistry.

ERIC Educational Resources Information Center

Niaz, Mansoor

2002-01-01

Constructs a teaching strategy to facilitate conceptual change in freshman students' understanding of electrochemistry. Provides students with the correct response along with alternative responses (teaching experiments), producing a conflicting situation that is conducive to an equilibration of their cognitive structures. Concludes that the…

The Influence of Facilitator and Facilitation Characteristics on Participants' Ratings of Stepfamily Education

ERIC Educational Resources Information Center

Higginbotham, Brian J.; Myler, Cory

2010-01-01

We examine the relative importance of facilitator and facilitation characteristics on participant ratings of a stepfamily education program. Data from 48 facilitators and 598 participants suggest that quality facilitation is more meaningful to participants than whether facilitators have comparable demographic characteristics or life experiences.…

Coping with employee, family, and student roles: evidence of dispositional conflict and facilitation tendencies.

PubMed

Hecht, Tracy D; McCarthy, Julie M

2010-07-01

Balancing multiple roles is a challenge for individuals in many sectors of the population. The purpose of this study was to test the hypothesis that individuals have dispositional tendencies to experience interrole conflict and facilitation. We also aimed to show that coping styles and life satisfaction are correlates of dispositional conflict and facilitation tendencies. Two survey studies were conducted with individuals involved in 3 life roles (i.e., employee, student, and family member; Study 1: N = 193; Study 2: N = 284). The hierarchical structure of conflict and facilitation was examined in both studies. Support for the dispositional model was found in both cases through the use of hierarchical confirmatory factor analyses. In Study 2, a longitudinal assessment of the nomological network surrounding conflict and facilitation tendencies was conducted with structural equation modeling analyses; we found that coping styles had synchronous relations with dispositional conflict and facilitation; dispositional conflict had a lagged and negative relation with life satisfaction.

Accurate protein structure modeling using sparse NMR data and homologous structure information.

PubMed

Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

2012-06-19

While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

Rotational characterization of methyl methacrylate: Internal dynamics and structure determination

NASA Astrophysics Data System (ADS)

Herbers, Sven; Wachsmuth, Dennis; Obenchain, Daniel A.; Grabow, Jens-Uwe

2018-01-01

Rotational constants, Watson's S centrifugal distortion coefficients, and internal rotation parameters of the two most stable conformers of methyl methacrylate were retrieved from the microwave spectrum. Splittings of rotational energy levels were caused by two non equivalent methyl tops. Constraining the centrifugal distortion coefficients and internal rotation parameters to the values of the main isotopologues, the rotational constants of all single substituted 13C and 18O isotopologues were determined. From these rotational constants the substitution structures and semi-empirical zero point structures of both conformers were precisely determined.

Cell-free protein synthesis for structure determination by X-ray crystallography.

PubMed

Watanabe, Miki; Miyazono, Ken-ichi; Tanokura, Masaru; Sawasaki, Tatsuya; Endo, Yaeta; Kobayashi, Ichizo

2010-01-01

Structure determination has been difficult for those proteins that are toxic to the cells and cannot be prepared in a large amount in vivo. These proteins, even when biologically very interesting, tend to be left uncharacterized in the structural genomics projects. Their cell-free synthesis can bypass the toxicity problem. Among the various cell-free systems, the wheat-germ-based system is of special interest due to the following points: (1) Because the gene is placed under a plant translational signal, its toxic expression in a bacterial host is reduced. (2) It has only little codon preference and, especially, little discrimination between methionine and selenomethionine (SeMet), which allows easy preparation of selenomethionylated proteins for crystal structure determination by SAD and MAD methods. (3) Translation is uncoupled from transcription, so that the toxicity of the translation product on DNA and its transcription, if any, can be bypassed. We have shown that the wheat-germ-based cell-free protein synthesis is useful for X-ray crystallography of one of the 4-bp cutter restriction enzymes, which are expected to be very toxic to all forms of cells retaining the genome. Our report on its structure represents the first report of structure determination by X-ray crystallography using protein overexpressed with the wheat-germ-based cell-free protein expression system. This will be a method of choice for cytotoxic proteins when its cost is not a problem. Its use will become popular when the crystal structure determination technology has evolved to require only a tiny amount of protein.

Using learning theory, interprofessional facilitation competencies, and behavioral indicators to evaluate facilitator training.

PubMed

LeGros, Theresa A; Amerongen, Helen M; Cooley, Janet H; Schloss, Ernest P

2015-01-01

Despite the increasing need for faculty and preceptors skilled in interprofessional facilitation (IPF), the relative novelty of the field poses a challenge to the development and evaluation of IPF programs. We use learning theory and IPF competencies with associated behavioral indicators to develop and evaluate six key messages in IPF training and experience. Our mixed methods approach included two phases: quantitative data collection with embedded qualitative data, followed by qualitative data collection in explanatory sequential fashion. This enabled triangulated analyses of both data types and of facilitation behaviors from facilitator and student perspectives. Results indicate the competency-based training was effective. Facilitators felt comfortable performing behaviors associated with IPF competencies; student observations of those behaviors supported facilitator self-reported performance. Overall, students perceived more facilitation opportunities than facilitators. Findings corroborate the importance of recruiting seasoned facilitators and establishing IPF guidelines that acknowledge variable team dynamics and help facilitators recognize teachable moments.

The Determination of Molecular Structure from Rotational Spectra

DOE R&D Accomplishments Database

Laurie, V. W.; Herschbach, D. R.

1962-07-01

An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

PubMed Central

Boutet, Sébastien; Lomb, Lukas; Williams, Garth J.; Barends, Thomas R. M.; Aquila, Andrew; Doak, R. Bruce; Weierstall, Uwe; DePonte, Daniel P.; Steinbrener, Jan; Shoeman, Robert L.; Messerschmidt, Marc; Barty, Anton; White, Thomas A.; Kassemeyer, Stephan; Kirian, Richard A.; Seibert, M. Marvin; Montanez, Paul A.; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M.; Philipp, Hugh T.; Tate, Mark W.; Hromalik, Marianne; Koerner, Lucas J.; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J.; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y.; Hunter, Mark S.; Johansson, Linda C.; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V.; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A.; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C. H.; Chapman, Henry N.; Schlichting, Ilme

2013-01-01

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

Impact of Student vs Faculty Facilitators on Motivational Interviewing Student Outcomes

PubMed Central

Widder-Prewett, Rebecca; Cameron, Ginger; Anderson, Douglas; Pinkerton, Mark; Chen, Aleda M. H.

2017-01-01

Objective. To determine the impact of student or faculty facilitation on student self-assessed attitudes, confidence, and competence in motivational interviewing (MI) skills; actual competence; and evaluation of facilitator performance. Methods. Second-year pharmacy (P2) students were randomly assigned to a student or faculty facilitator for a four-hour, small-group practice of MI skills. MI skills were assessed in a simulated patient encounter with the mMITI (modified Motivational Interviewing Treatment Integrity) tool. Students completed a pre-post, 6-point, Likert-type assessment addressing the research objectives. Differences were assessed using a Mann-Whitney U test. Results. Student (N=44) post-test attitudes, confidence, perceived or actual competence, and evaluations of facilitator performance were not different for faculty- and student-facilitated groups. Conclusion. Using pharmacy students as small-group facilitators did not affect student performance and were viewed as equally favorable. Using pharmacy students as facilitators can lessen faculty workload and provide an outlet for students to develop communication and facilitation skills that will be needed in future practice. PMID:28970608

Impact of Student vs Faculty Facilitators on Motivational Interviewing Student Outcomes.

PubMed

Widder-Prewett, Rebecca; Draime, Juanita A; Cameron, Ginger; Anderson, Douglas; Pinkerton, Mark; Chen, Aleda M H

2017-08-01

Objective. To determine the impact of student or faculty facilitation on student self-assessed attitudes, confidence, and competence in motivational interviewing (MI) skills; actual competence; and evaluation of facilitator performance. Methods. Second-year pharmacy (P2) students were randomly assigned to a student or faculty facilitator for a four-hour, small-group practice of MI skills. MI skills were assessed in a simulated patient encounter with the mMITI (modified Motivational Interviewing Treatment Integrity) tool. Students completed a pre-post, 6-point, Likert-type assessment addressing the research objectives. Differences were assessed using a Mann-Whitney U test. Results. Student (N=44) post-test attitudes, confidence, perceived or actual competence, and evaluations of facilitator performance were not different for faculty- and student-facilitated groups. Conclusion. Using pharmacy students as small-group facilitators did not affect student performance and were viewed as equally favorable. Using pharmacy students as facilitators can lessen faculty workload and provide an outlet for students to develop communication and facilitation skills that will be needed in future practice.

DNA Nanotubes for NMR Structure Determination of Membrane Proteins

PubMed Central

Bellot, Gaëtan; McClintock, Mark A.; Chou, James J; Shih, William M.

2013-01-01

Structure determination of integral membrane proteins by solution NMR represents one of the most important challenges of structural biology. A Residual-Dipolar-Coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size, however, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for weak alignment of membrane proteins was severely limited. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400nm-long six-helix bundles each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, towards collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes via counter ions and small DNA binding molecules. This detergent-resistant liquid-crystal media offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility, and structural programmability. Production of sufficient nanotubes for 4–5 NMR experiments can be completed in one week by a single individual. PMID:23518667

Self-Optimized Biological Channels in Facilitating the Transmembrane Movement of Charged Molecules

PubMed Central

Huyen, V. T. N.; Lap, Vu Cong; Nguyen, V. Lien

2016-01-01

We consider an anisotropically two-dimensional diffusion of a charged molecule (particle) through a large biological channel under an external voltage. The channel is modeled as a cylinder of three structure parameters: radius, length, and surface density of negative charges located at the channel interior-lining. These charges induce inside the channel a potential that plays a key role in controlling the particle current through the channel. It was shown that to facilitate the transmembrane particle movement the channel should be reasonably self-optimized so that its potential coincides with the resonant one, resulting in a large particle current across the channel. Observed facilitation appears to be an intrinsic property of biological channels, regardless of the external voltage or the particle concentration gradient. This facilitation is very selective in the sense that a channel of definite structure parameters can facilitate the transmembrane movement of only particles of proper valence at corresponding temperatures. Calculations also show that the modeled channel is nonohmic with the ion conductance which exhibits a resonance at the same channel potential as that identified in the current. PMID:27022394

X-ray structure determination and deuteration of nattokinase.

PubMed

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

2013-11-01

Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

X-ray structure determination and deuteration of nattokinase

PubMed Central

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

2013-01-01

Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis. PMID:24121331

Protein secondary structure determination by constrained single-particle cryo-electron tomography.

PubMed

Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram

2012-12-05

Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series. Copyright © 2012 Elsevier Ltd. All rights reserved.

High-throughput determination of RNA structure by proximity ligation.

PubMed

Ramani, Vijay; Qiu, Ruolan; Shendure, Jay

2015-09-01

We present an unbiased method to globally resolve RNA structures through pairwise contact measurements between interacting regions. RNA proximity ligation (RPL) uses proximity ligation of native RNA followed by deep sequencing to yield chimeric reads with ligation junctions in the vicinity of structurally proximate bases. We apply RPL in both baker's yeast (Saccharomyces cerevisiae) and human cells and generate contact probability maps for ribosomal and other abundant RNAs, including yeast snoRNAs, the RNA subunit of the signal recognition particle and the yeast U2 spliceosomal RNA homolog. RPL measurements correlate with established secondary structures for these RNA molecules, including stem-loop structures and long-range pseudoknots. We anticipate that RPL will complement the current repertoire of computational and experimental approaches in enabling the high-throughput determination of secondary and tertiary RNA structures.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

NASA Astrophysics Data System (ADS)

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-04-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

PubMed

Zhou, X Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Suino-Powell, Kelly M; Boutet, Sébastien; Williams, Garth J; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2016-04-12

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

PubMed Central

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C.H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-01-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes. PMID:27070998

New Form Discovery for the Analgesics Flurbiprofen and Sulindac Facilitated by Polymer-Induced Heteronucleation

PubMed Central

GRZESIAK, ADAM L.; MATZGER, ADAM J.

2008-01-01

The selection and discovery of new crystalline forms is a longstanding issue in solid-state chemistry of critical importance because of the effect molecular packing arrangement exerts on materials properties. Polymer-induced heteronucleation has recently been developed as a powerful approach to discover and control the production of crystal modifications based on the insoluble polymer heteronucleant added to the crystallization solution. The selective nucleation and discovery of new crystal forms of the well-studied pharmaceuticals flurbiprofen (FBP) and sulindac (SUL) has been achieved utilizing this approach. For the first time, FBP form III was produced in bulk quantities and its crystal structure was also determined. Furthermore, a novel 3:2 FBP:H2O phase was discovered that nucleates selectively from only a few polymers. Crystallization of SUL in the presence of insoluble polymers facilitated the growth of form I single crystals suitable for structure determination. Additionally, a new SUL polymorph (form IV) was discovered by this method. The crystal forms of FBP and SUL are characterized by Raman and FTIR spectroscopies, X-ray diffraction, and differential scanning calorimetry. PMID:17567888

Labor Market Structure and Salary Determination among Professional Basketball Players.

ERIC Educational Resources Information Center

Wallace, Michael

1988-01-01

The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)

Determinants of community structure of zooplankton in heavily polluted river ecosystems

NASA Astrophysics Data System (ADS)

Xiong, Wei; Li, Jie; Chen, Yiyong; Shan, Baoqing; Wang, Weimin; Zhan, Aibin

2016-02-01

River ecosystems are among the most affected habitats globally by human activities, such as the release of chemical pollutants. However, it remains largely unknown how and to what extent many communities such as zooplankton are affected by these environmental stressors in river ecosystems. Here, we aim to determine major factors responsible for shaping community structure of zooplankton in heavily polluted river ecosystems. Specially, we use rotifers in the Haihe River Basin (HRB) in North China as a case study to test the hypothesis that species sorting (i.e. species are “filtered” by environmental factors and occur at environmental suitable sites) plays a key role in determining community structure at the basin level. Based on an analysis of 94 sites across the plain region of HRB, we found evidence that both local and regional factors could affect rotifer community structure. Interestingly, further analyses indicated that local factors played a more important role in determining community structure. Thus, our results support the species sorting hypothesis in highly polluted rivers, suggesting that local environmental constraints, such as environmental pollution caused by human activities, can be stronger than dispersal limitation caused by regional factors to shape local community structure of zooplankton at the basin level.

Determining modulus of elasticity of ancient structural timber

Treesearch

Houjiang Zhang; Lei Zhu; Yanliang Sun; Xiping Wang; Haicheng Yan

2011-01-01

During maintenance of ancient timber architectures, it is important to determine mechanical properties of the wood component materials non-destructively and effectively, so that degraded members may be replaced or repaired to avoid structural failure. Experimental materials are four larch (Larix principis-rupprechtii Mayr.) components, which were taken down from the...

Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.

PubMed

Didenko, Tatiana; Proudfoot, Andrew; Dutta, Samit Kumar; Serrano, Pedro; Wüthrich, Kurt

2015-08-24

High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Children's active play: self-reported motivators, barriers and facilitators

PubMed Central

2011-01-01

Background Physical activity has important benefits for children's physical health and mental wellbeing, but many children do not meet recommended levels. Research suggests that active play has the potential to make a valuable contribution to children's overall physical activity, whilst providing additional cognitive, social and emotional benefits. However, relatively little is known about the determinants of UK children's active play. Understanding these factors provides the critical first step in developing interventions to increase children's active play, and therefore overall physical activity. Methods Eleven focus groups were conducted with 77, 10-11 year old children from four primary schools in Bristol, UK. Focus groups examined: (i) factors which motivate children to take part in active play; (ii) factors which limit children's active play and (iii) factors which facilitate children's active play. All focus groups were audio-taped and transcribed verbatim. Data were analysed using a thematic approach. Results Children were motivated to engage in active play because they perceived it to be enjoyable, to prevent boredom, to have physical and mental health benefits and to provide freedom from adult control, rules and structure. However, children's active play was constrained by a number of factors, including rainy weather and fear of groups of teenagers in their play spaces. Some features of the physical environment facilitated children's active play, including the presence of green spaces and cul-de-sacs in the neighbourhood. Additionally, children's use of mobile phones when playing away from home was reported to help to alleviate parents' safety fears, and therefore assist children's active play. Conclusions Children express a range of motivational and environmental factors that constrain and facilitate their active play. Consideration of these factors should improve effectiveness of interventions designed to increase active play. PMID:21663605

Children's active play: self-reported motivators, barriers and facilitators.

PubMed

Brockman, Rowan; Jago, Russell; Fox, Kenneth R

2011-06-10

Physical activity has important benefits for children's physical health and mental wellbeing, but many children do not meet recommended levels. Research suggests that active play has the potential to make a valuable contribution to children's overall physical activity, whilst providing additional cognitive, social and emotional benefits. However, relatively little is known about the determinants of UK children's active play. Understanding these factors provides the critical first step in developing interventions to increase children's active play, and therefore overall physical activity. Eleven focus groups were conducted with 77, 10-11 year old children from four primary schools in Bristol, UK. Focus groups examined: (i) factors which motivate children to take part in active play; (ii) factors which limit children's active play and (iii) factors which facilitate children's active play. All focus groups were audio-taped and transcribed verbatim. Data were analysed using a thematic approach. Children were motivated to engage in active play because they perceived it to be enjoyable, to prevent boredom, to have physical and mental health benefits and to provide freedom from adult control, rules and structure. However, children's active play was constrained by a number of factors, including rainy weather and fear of groups of teenagers in their play spaces. Some features of the physical environment facilitated children's active play, including the presence of green spaces and cul-de-sacs in the neighbourhood. Additionally, children's use of mobile phones when playing away from home was reported to help to alleviate parents' safety fears, and therefore assist children's active play. Children express a range of motivational and environmental factors that constrain and facilitate their active play. Consideration of these factors should improve effectiveness of interventions designed to increase active play.

Synthesis/literature review for determining structural layer coefficients (SLC) of bases.

DOT National Transportation Integrated Search

2014-12-01

FDOTs current method of determining a base material structural layer coefficient (SLC) is detailed in the : Materials Manual, Chapter 2.1, Structural Layer Coefficients for Flexible Pavement Base Materials. : Currently, any new base material not a...

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

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

Zhou, X. Edward; Gao, Xiang; Barty, Anton

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

DOE PAGES

Zhou, X. Edward; Gao, Xiang; Barty, Anton; ...

2016-04-12

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

Advancing knowledge on practice change: linking facilitation to the senses framework.

PubMed

Cooper, Julie; Meyer, Julienne; Holman, Cheryl

2013-06-01

To explore the facilitating factors that enabled staff on a rehabilitation ward for older people engage in change activities. The importance of facilitation in practice change is widely acknowledged; however, little nursing research has taken place in relation to its nature. Following identification in the early phases of an action research study that learned helplessness states and the use of socially structured defence techniques were preventing staff on a rehabilitation ward for older people from engaging in practice development, some change was achieved. What facilitated this to take place needed to be explored. An action research approach was used. Data gained from 13 in-depth interviews with staff and managers together with three years of researcher field notes were analysed using thematic analysis. The continuous presence and neutrality of the researcher who worked together with staff on their issues of concern using a flexible ward-based approach, combined with giving staff the opportunity to explore what it was like for them working in this area, were considered key in helping staff to engage with change. Analysis of findings suggests that the senses framework presents a theoretical approach to facilitation that can help staff move out of learned helplessness states and reduce the need for the use of socially structured defence techniques. This study identifies a facilitation approach that enabled staff to engage with practice change. Although carried out in the UK, its findings have wider relevance through the application of a theoretical perspective for practice change facilitation that has not before been considered in this literature, and which is likely to be of interest to those involved in practice change internationally. © 2013 Blackwell Publishing Ltd.

A Distance Education Classroom Designed to Facilitate Synchronous Learner and Instructor Interactions

ERIC Educational Resources Information Center

Bernstein, Stuart P.

2013-01-01

The purpose of this study was to determine whether a live, synchronous distance delivery technology would facilitate interaction, immediacy, and presence between an instructor and his contiguous and remote classrooms, and whether it would facilitate interaction between the two groups of students. This study researched the opinions of students on…

Barriers and facilitators to mobile phone use for people with aphasia.

PubMed

Greig, Carole-Ann; Harper, Renée; Hirst, Tanya; Howe, Tami; Davidson, Bronwyn

2008-01-01

Mobile phone use increases social participation. People with the communication disorder of aphasia are disadvantaged in the use of information and communication technology such as mobile phones and are reported to be more socially isolated than their peers. The World Health Organization's International Classification of Functioning, Disability and Health provides a framework to address the impact of environmental factors on individual participation. The aim of this preliminary study was to identify the barriers and facilitators to mobile phone use for people with aphasia. A qualitative descriptive study involving two phases was conducted: (1) semi-structured interviews with 6 individuals with aphasia who owned or expressed a desire to own a mobile phone; (2) structured observations of key scenarios identified in the interviews of 3 participants who were sampled from the interview study. Results identified 18 barriers and 9 facilitators to mobile phone use. Key barriers and facilitators were identified in the areas of design and features, written support and training, and communicative partners. Mobile phone use can be problematic for people with aphasia. Intervention needs to address the barriers and utilise the facilitators to mobile phone use for this population. Further research is required to inform policy and intervention programs to ensure that people with aphasia have access to this technology.

Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

PubMed Central

Levin, Igor; Vanderah, Terrell

2008-01-01

The functional responses (e.g., dielectric, magnetic, catalytic, etc.) of many industrially-relevant materials are controlled by their local structure—a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer) to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale—the so-called “nanostructure problem”—at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem—an ultimate frontier in materials characterization—necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed “institute” would provide an intellectual infrastructure for local structure determination by (1) developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2), (2) connecting industrial and academic users with experts in measurement techniques, (3

A case study: the evolution of a "facilitator model" liaison program in an academic medical library.

PubMed

Crossno, Jon E; DeShay, Claudia H; Huslig, Mary Ann; Mayo, Helen G; Patridge, Emily F

2012-07-01

What type of liaison program would best utilize both librarians and other library staff to effectively promote library services and resources to campus departments? The case is an academic medical center library serving a large, diverse campus. The library implemented a "facilitator model" program to provide personalized service to targeted clients that allowed for maximum staff participation with limited subject familiarity. To determine success, details of liaison-contact interactions and results of liaison and department surveys were reviewed. Liaisons successfully recorded 595 interactions during the program's first 10 months of existence. A significant majority of departmental contact persons (82.5%) indicated they were aware of the liaison program, and 75% indicated they preferred email communication. The "facilitator model" provides a well-defined structure for assigning liaisons to departments or groups; however, training is essential to ensure that liaisons are able to communicate effectively with their clients.

Document boundary determination using structural and lexical analysis

NASA Astrophysics Data System (ADS)

Taghva, Kazem; Cartright, Marc-Allen

2009-01-01

The document boundary determination problem is the process of identifying individual documents in a stack of papers. In this paper, we report on a classification system for automation of this process. The system employs features based on document structure and lexical content. We also report on experimental results to support the effectiveness of this system.

Facilitators of Survivorship Care Among Underserved Breast Cancer Survivors: a Qualitative Study.

PubMed

Ustjanauskas, Amy E; Quinn, Gwendolyn P; Pan, Tonya M; Rivera, Maria; Vázquez-Otero, Coralia; Ung, Danielle; Roetzheim, Richard G; Laronga, Christine; Johnson, Kenneth; Norton, Marilyn; Carrizosa, Claudia; Muñoz, Dariana; Goldenstein, Marissa; Nuhaily, Sumayah; Wells, Kristen J

2017-12-01

Research investigating facilitators of survivorship care among underserved breast cancer survivors (BCS) is sparse. This study aimed to explore facilitators of survivorship care among underserved BCS within the first 5 years following chemotherapy, radiation, or surgery for breast cancer. In-depth interviews were conducted, using a semi-structured interview guide, with underserved BCS exploring survivorship care experiences. Content analysis of the verbatim transcripts was applied, and results were summarized according to themes related to facilitators of breast cancer survivorship care. Interviews were conducted with 25 BCS. Eight main themes were identified: coordination of care; positive perceptions of health care providers; communication between patient and health care providers; financial and insurance facilitators; information, classes, and programs provided; assistance provided by organizations and health care professionals; transportation facilitators; and job flexibility. This study provides a comprehensive look at facilitators of survivorship care among underserved BCS. BCS endorsed several facilitators of their survivorship care, mainly at the interpersonal, organizational, and societal level. This study adds to the research literature on catalysts of care among underserved BCS. Results from this study are currently being used to inform a patient navigation intervention to facilitate care among this population.

Educational differences in the diet of Finnish adults and the associations between education and the determinants and facilitators of dietary fat quality.

PubMed

Ovaskainen, Marja-Leena; Paturi, Merja; Tapanainen, Heli; Harald, Kennet

2010-06-01

The aim of the study is to elucidate differences in adults' diet by education, and to analyse the associations between dietary facilitators, education and dietary fat quality. In all, one-third of subjects from the national FINRISK health survey were invited to participate in the FINDIET 2007 Survey. A 48 h dietary interview was used for dietary data and personal background data were collected by the health survey questionnaire. Representative sample from five regions in Finland in spring 2007. A total of 1576 adults, participation rate 60 %. Oil used in cooking differed by education. Instead perception of cardiovascular risk, or the following of a cholesterol-lowering diet, were equal across all educational categories. The diet of men with low education contained less protein and carbohydrates, more fat and more SFA and MUFA than that of highly educated men. The diet of women with low education contained less PUFA, vitamin C and vitamin E than in the highly educated category. High education remained a significant determinant for the lower intake of SFA in men, and for the higher intake of PUFA in women, after adjusting for the determinants and facilitators of dietary behaviour and age. The lower intake of SFA was also associated with following a cholesterol-lowering diet in both genders. In addition to education, the intake of unsaturated fatty acids was determined by the oil used in cooking by women, and by frequent lunches served by caterers for men. In dietary behaviour, awareness and reporting of cholesterol-lowering diet seem to indicate a tendency to control the intake of saturated fat. Health messages are likely to enhance tools for increasing the intake of PUFA, in addition to reducing the intake of SFA.

Quantification of the impact of PSI:Biology according to the annotations of the determined structures.

PubMed

DePietro, Paul J; Julfayev, Elchin S; McLaughlin, William A

2013-10-21

Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third phase entailed the formation of PSI:Biology Partnerships which are composed of structural genomics centers and biomedical science laboratories. We present a method to examine the impact of protein structures determined under the auspices of PSI:Biology by measuring their rates of annotations. The mean numbers of annotations per structure and per residue are examined. These are designed to provide measures of the amount of structure to function connections that can be leveraged from each structure. One result is that PSI:Biology structures are found to have a higher rate of annotations than structures determined during the first two phases of PSI. A second result is that the subset of PSI:Biology structures determined through PSI:Biology Partnerships have a higher rate of annotations than those determined exclusive of those partnerships. Both results hold when the annotation rates are examined either at the level of the entire protein or for annotations that are known to fall at specific residues within the portion of the protein that has a determined structure. We conclude that PSI:Biology determines structures that are estimated to have a higher degree of biomedical interest than those determined during the first two phases of PSI based on a broad array of biomedical annotations. For the PSI:Biology Partnerships, we see that there is an associated added value that represents part of the progress toward the goals of PSI:Biology. We interpret the added value to mean that team-based structural biology projects that utilize the expertise and technologies of structural genomics centers together with biological laboratories in the community are conducted in a synergistic manner. We show that the annotation rates can be used in conjunction with established metrics, i

Quantification of the impact of PSI:Biology according to the annotations of the determined structures

PubMed Central

2013-01-01

Background Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third phase entailed the formation of PSI:Biology Partnerships which are composed of structural genomics centers and biomedical science laboratories. We present a method to examine the impact of protein structures determined under the auspices of PSI:Biology by measuring their rates of annotations. The mean numbers of annotations per structure and per residue are examined. These are designed to provide measures of the amount of structure to function connections that can be leveraged from each structure. Results One result is that PSI:Biology structures are found to have a higher rate of annotations than structures determined during the first two phases of PSI. A second result is that the subset of PSI:Biology structures determined through PSI:Biology Partnerships have a higher rate of annotations than those determined exclusive of those partnerships. Both results hold when the annotation rates are examined either at the level of the entire protein or for annotations that are known to fall at specific residues within the portion of the protein that has a determined structure. Conclusions We conclude that PSI:Biology determines structures that are estimated to have a higher degree of biomedical interest than those determined during the first two phases of PSI based on a broad array of biomedical annotations. For the PSI:Biology Partnerships, we see that there is an associated added value that represents part of the progress toward the goals of PSI:Biology. We interpret the added value to mean that team-based structural biology projects that utilize the expertise and technologies of structural genomics centers together with biological laboratories in the community are conducted in a synergistic manner. We show that the annotation rates can be used in

Role of electrostatic interactions in determining the G-quadruplex structures

NASA Astrophysics Data System (ADS)

Lee, Jinkeong; Im, Haeri; Chong, Song-Ho; Ham, Sihyun

2018-02-01

We investigate the energetics of the antiparallel, hybrid and parallel type G-quadruplex structures of the human telomere DNA sequence. We find that both the conformational energy and solvation free energy of these structures are roughly inversely proportional to their radii of gyration. We rationalize this finding in terms of the dominance of the electrostatic contributions. We also show that the solvation free energy is more significant than the conformational energy in determining the G-quadruplex structures, which is in contrast to the canonical B-DNA structures. Our work will contribute to an understanding of the molecular mechanisms dictating various G-quadruplex topologies.

Teaching Note--Constructing Critical Conversations: A Model for Facilitating Classroom Dialogue for Critical Learning

ERIC Educational Resources Information Center

Kang, Hye-Kyung; O'Neill, Peggy

2018-01-01

Discussions of power and privilege, oppression, and structural inequities in classrooms can produce complex understanding and critical analysis when facilitated effectively. In this article we present the critical conversations model for facilitating conversations that open up space for discussing such issues and encourage the development of…

Using Ground Radar Interferometry for Precise Determining of Deformation and Vertical Deflection of Structures

NASA Astrophysics Data System (ADS)

Talich, Milan

2017-12-01

The paper describes possibilities of the relatively new technics - ground based radar interferometry for precise determining of deformation of structures. Special focus on the vertical deflection of bridge structures and on the horizontal movements of high-rise buildings and structural objects is presented. The technology of ground based radar interferometry can be used in practice to the contactless determination of deformations of structures with accuracy up to 0.01 mm in real time. It is also possible in real time to capture oscillations of the object with a frequency up to 50 Hz. Deformations can be determined simultaneously in multiple places of the object, for example a bridge structure at points distributed on the bridge deck at intervals of one or more meters. This allows to obtain both overall and detailed information about the properties of the structure during the dynamic load and monitoring the impact of movements either individual vehicles or groups. In the case of high-rise buildings, it is possible to monitor the horizontal vibration of the whole object at its different height levels. It is possible to detect and determine the compound oscillations that occur in some types of buildings. Then prevent any damage or even disasters in these objects. In addition to the necessary theory basic principles of using radar interferometry for determining of deformation of structures are given. Practical examples of determining deformation of bridge structures, water towers reservoirs, factory chimneys and wind power plants are also given. The IBIS-S interferometric radar of the Italian IDS manufacturer was used for the measurements.

Facilitating the Development of School-Based Learning Networks

ERIC Educational Resources Information Center

Kubiak, Chris; Bertram, Joan

2010-01-01

Purpose: This paper aims to contribute to the knowledge base on leading and facilitating the growth of school improvement networks by describing the activities and challenges faced by network leaders. Design/methodology/approach: A total of 19 co-leaders from 12 networks were interviewed using a semi-structured schedule about the growth of their…

One-to-One Encounters: Facilitators, Participants, and Friendship

ERIC Educational Resources Information Center

Higgins, Lee

2012-01-01

In this article, I explore the claim that one-to-one encounters between community music facilitators and music participants can be described as friendships. By exploring the relational structure through the call and the welcome, I make some general comments on friendship before finally tackling the question lying at the heart of this article: How…

Speech rhythm facilitates syntactic ambiguity resolution: ERP evidence.

PubMed

Roncaglia-Denissen, Maria Paula; Schmidt-Kassow, Maren; Kotz, Sonja A

2013-01-01

In the current event-related potential (ERP) study, we investigated how speech rhythm impacts speech segmentation and facilitates the resolution of syntactic ambiguities in auditory sentence processing. Participants listened to syntactically ambiguous German subject- and object-first sentences that were spoken with either regular or irregular speech rhythm. Rhythmicity was established by a constant metric pattern of three unstressed syllables between two stressed ones that created rhythmic groups of constant size. Accuracy rates in a comprehension task revealed that participants understood rhythmically regular sentences better than rhythmically irregular ones. Furthermore, the mean amplitude of the P600 component was reduced in response to object-first sentences only when embedded in rhythmically regular but not rhythmically irregular context. This P600 reduction indicates facilitated processing of sentence structure possibly due to a decrease in processing costs for the less-preferred structure (object-first). Our data suggest an early and continuous use of rhythm by the syntactic parser and support language processing models assuming an interactive and incremental use of linguistic information during language processing.

Speech Rhythm Facilitates Syntactic Ambiguity Resolution: ERP Evidence

PubMed Central

Roncaglia-Denissen, Maria Paula; Schmidt-Kassow, Maren; Kotz, Sonja A.

2013-01-01

In the current event-related potential (ERP) study, we investigated how speech rhythm impacts speech segmentation and facilitates the resolution of syntactic ambiguities in auditory sentence processing. Participants listened to syntactically ambiguous German subject- and object-first sentences that were spoken with either regular or irregular speech rhythm. Rhythmicity was established by a constant metric pattern of three unstressed syllables between two stressed ones that created rhythmic groups of constant size. Accuracy rates in a comprehension task revealed that participants understood rhythmically regular sentences better than rhythmically irregular ones. Furthermore, the mean amplitude of the P600 component was reduced in response to object-first sentences only when embedded in rhythmically regular but not rhythmically irregular context. This P600 reduction indicates facilitated processing of sentence structure possibly due to a decrease in processing costs for the less-preferred structure (object-first). Our data suggest an early and continuous use of rhythm by the syntactic parser and support language processing models assuming an interactive and incremental use of linguistic information during language processing. PMID:23409109

Determination of the Basin Structure Beneath European Side of Istanbul

NASA Astrophysics Data System (ADS)

Karabulut, Savas; Cengiz Cinku, Mulla; Thomas, Michael; Lamontagne, Maurice

2016-04-01

Istanbul (near North Anatolian Fault Zone:NAFZ, Turkey) is located in northern part of Sea of Marmara, an area that has been influenced by possible Marmara Earthquakes. The general geology of Istanbul divided into two stratigraphic unit such as sedimentary (from Oligocene to Quaternary Deposits) and bedrock (Paleozoic and Eocene). The bedrock units consists of sand stone, clay stone to Paleozoic age and limestone to Eocene age and sedimentary unit consist of sand, clay, mil and gravel from Oligocene to Quaternary age. Earthquake disaster mitigation studies divided into two important phases, too. Firstly, earthquake, soil and engineering structure problems identify for investigation area, later on strategic emergency plan can prepare for these problems. Soil amplification play important role the disaster mitigation and the site effect analysis and basin structure is also a key parameter for determining of site effect. Some geophysical, geological and geotechnical measurements are requeired to defined this relationship. Istanbul Megacity has been waiting possible Marmara Earthquake and their related results. In order to defined to possible damage potential related to site effect, gravity measurements carried out for determining to geological structure, basin geometry and faults in Istanbul. Gravity data were collected at 640 sites by using a Scientrex CG-5 Autogravity meter Standard corrections applied to the gravity data include those for instrumental drift, Earth tides and latitude, and the free-air and Bouguer corrections. The corrected gravity data were imported into a Geosoft database to create a grid and map of the Bouguer gravity anomaly (grid cell size of 200 m). As a previously results, we determined some lineminants, faults and basins beneath Istanbul City. Especially, orientation of faults were NW-SE direction and some basin structures determined on between Buyukcekmece and Kucukcekmece Lake.

Team assembly mechanisms determine collaboration network structure and team performance.

PubMed

Guimerà, Roger; Uzzi, Brian; Spiro, Jarrett; Amaral, Luís A Nunes

2005-04-29

Agents in creative enterprises are embedded in networks that inspire, support, and evaluate their work. Here, we investigate how the mechanisms by which creative teams self-assemble determine the structure of these collaboration networks. We propose a model for the self-assembly of creative teams that has its basis in three parameters: team size, the fraction of newcomers in new productions, and the tendency of incumbents to repeat previous collaborations. The model suggests that the emergence of a large connected community of practitioners can be described as a phase transition. We find that team assembly mechanisms determine both the structure of the collaboration network and team performance for teams derived from both artistic and scientific fields.

Phospholipid component volumes: determination and application to bilayer structure calculations.

PubMed

Armen, R S; Uitto, O D; Feller, S E

1998-08-01

We present a new method for the determination of bilayer structure based on a combination of computational studies and laboratory experiments. From molecular dynamics simulations, the volumes of submolecular fragments of saturated and unsaturated phosphatidylcholines in the liquid crystalline state have been extracted with a precision not available experimentally. Constancy of component volumes, both among different lipids and as a function of membrane position for a given lipid, have been examined. The component volumes were then incorporated into the liquid crystallographic method described by Wiener and White (1992. Biophys. J. 61:434-447, and references therein) for determining the structure of a fluid-phase dioleoylphosphatidylcholine bilayer from x-ray and neutron diffraction experiments.

Phospholipid component volumes: determination and application to bilayer structure calculations.

PubMed Central

Armen, R S; Uitto, O D; Feller, S E

1998-01-01

We present a new method for the determination of bilayer structure based on a combination of computational studies and laboratory experiments. From molecular dynamics simulations, the volumes of submolecular fragments of saturated and unsaturated phosphatidylcholines in the liquid crystalline state have been extracted with a precision not available experimentally. Constancy of component volumes, both among different lipids and as a function of membrane position for a given lipid, have been examined. The component volumes were then incorporated into the liquid crystallographic method described by Wiener and White (1992. Biophys. J. 61:434-447, and references therein) for determining the structure of a fluid-phase dioleoylphosphatidylcholine bilayer from x-ray and neutron diffraction experiments. PMID:9675175

Understanding Facilitation: Theory and Principles.

ERIC Educational Resources Information Center

Hogan, Christine

This book introduces newcomers to the concept of facilitation, and it presents a critical analysis of established and current theory on facilitation for existing practitioners. The following are among the topics discussed: (1) emergence of the field of facilitation; (2) development of facilitation in management; (3) development of facilitation in…

Metacommunity and phylogenetic structure determine wildlife and zoonotic infectious disease patterns in time and space.

PubMed

Suzán, Gerardo; García-Peña, Gabriel E; Castro-Arellano, Ivan; Rico, Oscar; Rubio, André V; Tolsá, María J; Roche, Benjamin; Hosseini, Parviez R; Rizzoli, Annapaola; Murray, Kris A; Zambrana-Torrelio, Carlos; Vittecoq, Marion; Bailly, Xavier; Aguirre, A Alonso; Daszak, Peter; Prieur-Richard, Anne-Helene; Mills, James N; Guégan, Jean-Francois

2015-02-01

The potential for disease transmission at the interface of wildlife, domestic animals and humans has become a major concern for public health and conservation biology. Research in this subject is commonly conducted at local scales while the regional context is neglected. We argue that prevalence of infection at local and regional levels is influenced by three mechanisms occurring at the landscape level in a metacommunity context. First, (1) dispersal, colonization, and extinction of pathogens, reservoir or vector hosts, and nonreservoir hosts, may be due to stochastic and niche-based processes, thus determining distribution of all species, and then their potential interactions, across local communities (metacommunity structure). Second, (2) anthropogenic processes may drive environmental filtering of hosts, nonhosts, and pathogens. Finally, (3) phylogenetic diversity relative to reservoir or vector host(s), within and between local communities may facilitate pathogen persistence and circulation. Using a metacommunity approach, public heath scientists may better evaluate the factors that predispose certain times and places for the origin and emergence of infectious diseases. The multidisciplinary approach we describe fits within a comprehensive One Health and Ecohealth framework addressing zoonotic infectious disease outbreaks and their relationship to their hosts, other animals, humans, and the environment.

Studying and Facilitating Dialogue in Select Online Management Courses

ERIC Educational Resources Information Center

Ivancevich, John M.; Gilbert, Jacqueline A.; Konopaske, Robert

2009-01-01

Dialogue is arguably one of the most significant elements of learning in higher education. The premise of this article is that online instructors can creatively facilitate dialogue for effectively teaching online management courses. This article presents a dialogue-focused framework for addressing significant behavioral, structural, and…

Thermodynamic Origins of Monovalent Facilitated RNA Folding

PubMed Central

Holmstrom, Erik D.; Fiore, Julie L.; Nesbitt, David J.

2012-01-01

Cations have long been associated with formation of native RNA structure and are commonly thought to stabilize the formation of tertiary contacts by favorably interacting with the electrostatic potential of the RNA, giving rise to an “ion atmosphere”. A significant amount of information regarding the thermodynamics of structural transitions in the presence of an ion atmosphere has accumulated and suggests stabilization is dominated by entropic terms. This work provides an analysis of how RNA–cation interactions affect the entropy and enthalpy associated with an RNA tertiary transition. Specifically, temperature-dependent single-molecule fluorescence resonance energy transfer studies have been exploited to determine the free energy (ΔG°), enthalpy (ΔH°), and entropy (ΔS°) of folding for an isolated tetraloop–receptor tertiary interaction as a function of Na+ concentration. Somewhat unexpectedly, increasing the Na+ concentration changes the folding enthalpy from a strongly exothermic process [e.g., ΔH° = −26(2) kcal/mol at 180 mM] to a weakly exothermic process [e.g., ΔH° = −4(1) kcal/mol at 630 mM]. As a direct corollary, it is the strong increase in folding entropy [Δ(ΔS°) > 0] that compensates for this loss of exothermicity for the achievement of more favorable folding [Δ(ΔG°) < 0] at higher Na+ concentrations. In conjunction with corresponding measurements of the thermodynamics of the transition state barrier, these data provide a detailed description of the folding pathway associated with the GAAA tetraloop–receptor interaction as a function of Na+ concentration. The results support a potentially universal mechanism for monovalent facilitated RNA folding, whereby an increasing monovalent concentration stabilizes tertiary structure by reducing the entropic penalty for folding. PMID:22448852

System for determining the angle of impact of an object on a structure

NASA Technical Reports Server (NTRS)

Prosser, William H. (Inventor); Gorman, Michael R. (Inventor)

1993-01-01

A method for determining the angle of impact of an object on a thin-walled structure which determines the angle of impact through analysis of the acoustic waves which result when an object impacts a structure is presented. Transducers are placed on and in the surface of the structure which sense the wave caused in the structure by impact. The waves are recorded and saved for analysis. For source motion normal to the surface, the antisymmetric mode has a large amplitude while that of the symmetric mode is very small. As the source angle increases with respect to the surface normal, the symmetric mode amplitude increases while the antisymmetric mode amplitude decreases. Thus, the angle of impact is determined by measuring the relative amplitudes of these two lowest order modes.

Evaluations of children who have disclosed sexual abuse via facilitated communication.

PubMed

Botash, A S; Babuts, D; Mitchell, N; O'Hara, M; Lynch, L; Manuel, J

1994-12-01

To review the findings of interdisciplinary team evaluations of children who disclosed sexual abuse via facilitated communication. Case series. Tertiary care hospital outpatient child sexual abuse program in central New York. Between January 1990 and March 1993, 13 children who disclosed sexual abuse via facilitated communication and were referred to a university hospital child abuse referral and evaluation center. The range of previously determined developmental diagnosis included mental retardation, speech delay, and autism. None. Medical records were reviewed for (1) disclosure, (2) physical evidence, (3) child's behavioral and medical history, (4) disclosures by siblings, (5) perpetrator's confession, (6) child protective services determinations, and (7) court findings. Four children had evidence of sexual abuse: two had physical findings consistent with sexual abuse, one also disclosed the allegation verbally, and one perpetrator confessed. These results neither support nor refute validation of facilitated communication. However, many children had other evidence of sexual abuse, suggesting that each child's case should be evaluated without bias.

A Laboratory Exercise in the Determination of Carbohydrate Structures.

ERIC Educational Resources Information Center

White, Bernard J.; Robyt, John F.

1988-01-01

Describes an experiment in which students are given a naturally occurring oligosaccharide as an unknown and are asked to determine both its monosaccharide composition and its structure. Discusses methods and experimental techniques including thin layer chromatography and the use of enzymes. (CW)

Determining the size dependence of structural properties of clusters

NASA Astrophysics Data System (ADS)

Dong, Yi; Springborg, Michael

2012-12-01

Problems related to the determination of the structure of the global total-energy minimum for clusters are discussed through three examples. For isolated gold clusters it is shown that low-symmetry structures result due to covalent bonding. Subsequently, SiNGeN and (HAlO)N clusters are treated for which the occurrence of so called homotops leads to additional computational complexity. For the former it is found that the structures are not directly related to those of the pure monatomic clusters, and for the latter the results are shown to be in agreement with available experimental information on nanostructured HAlO. In order to illustrate and analyze the results, various descriptors are introduced and applied.

What determines the spectrum of protein native state structures?

PubMed

Lezon, Timothy R; Banavar, Jayanth R; Lesk, Arthur M; Maritan, Amos

2006-05-01

We present a brief summary of the key factors underlying protein structure, as developed in the investigations of Pauling, Ramachandran, and Rose. We then outline a simplified physical model of proteins that focuses on geometry and symmetry. Although this model superficially appears unrelated to the detailed chemical descriptions commonly applied to proteins, we show that it captures the essential elements of the chemistry and provides a unified framework for understanding the common characteristics of folded proteins. We suggest that the spectrum of protein native state structures is determined by geometry and symmetry and the role of the sequence is to choose its native state structure from this predetermined menu. 2006 Wiley-Liss, Inc.

Requirements on paramagnetic relaxation enhancement data for membrane protein structure determination by NMR.

PubMed

Gottstein, Daniel; Reckel, Sina; Dötsch, Volker; Güntert, Peter

2012-06-06

Nuclear magnetic resonance (NMR) structure calculations of the α-helical integral membrane proteins DsbB, GlpG, and halorhodopsin show that distance restraints from paramagnetic relaxation enhancement (PRE) can provide sufficient structural information to determine their structure with an accuracy of about 1.5 Å in the absence of other long-range conformational restraints. Our systematic study with simulated NMR data shows that about one spin label per transmembrane helix is necessary for obtaining enough PRE distance restraints to exclude wrong topologies, such as pseudo mirror images, if only limited other NMR restraints are available. Consequently, an experimentally realistic amount of PRE data enables α-helical membrane protein structure determinations that would not be feasible with the very limited amount of conventional NOESY data normally available for these systems. These findings are in line with our recent first de novo NMR structure determination of a heptahelical integral membrane protein, proteorhodopsin, that relied extensively on PRE data. Copyright © 2012 Elsevier Ltd. All rights reserved.

Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems.

PubMed

Prischi, Filippo; Pastore, Annalisa

2016-01-01

The current main challenge of Structural Biology is to undertake the structure determination of increasingly complex systems in the attempt to better understand their biological function. As systems become more challenging, however, there is an increasing demand for the parallel use of more than one independent technique to allow pushing the frontiers of structure determination and, at the same time, obtaining independent structural validation. The combination of different Structural Biology methods has been named hybrid approaches. The aim of this review is to critically discuss the most recent examples and new developments that have allowed structure determination or experimentally-based modelling of various molecular complexes selecting them among those that combine the use of nuclear magnetic resonance and small angle scattering techniques. We provide a selective but focused account of some of the most exciting recent approaches and discuss their possible further developments.

Structure determination of an integral membrane protein at room temperature from crystals in situ

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

Axford, Danny; Foadi, James; Imperial College London, London SW7 2AZ

2015-05-14

The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated. The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samplesmore » and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination of Haemophilus influenza TehA at 2.3 Å resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines.« less

Analysis of phases in the structure determination of an icosahedral virus

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

Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G.

2012-03-15

The constraints imposed on structure-factor phases by noncrystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to themore » correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or {pi}. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed.« less

Analysis of phases in the structure determination of an icosahedral virus

PubMed Central

Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G.

2011-01-01

The constraints imposed on structure-factor phases by non­crystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to the correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or π. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed. PMID:21636897

DNA nanotubes for NMR structure determination of membrane proteins.

PubMed

Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

2013-04-01

Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

Regional mechanics determine collagen fiber structure in healing myocardial infarcts.

PubMed

Fomovsky, Gregory M; Rouillard, Andrew D; Holmes, Jeffrey W

2012-05-01

Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shape, and/or location produce different patterns of mechanical stretch that guide evolving collagen fiber structure. We tested the effects of infarct shape and location using a combined experimental and computational approach. We studied mechanics and collagen fiber structure in cryoinfarcts in 53 Sprague-Dawley rats and found that regardless of shape or orientation, cryoinfarcts near the equator of the left ventricle stretched primarily in the circumferential direction and developed circumferentially aligned collagen, while infarcts at the apex stretched similarly in the circumferential and longitudinal directions and developed randomly oriented collagen. In a computational model of infarct healing, an effect of mechanical stretch on fibroblast and collagen alignment was required to reproduce the experimental results. We conclude that mechanical environment determines collagen fiber structure in healing myocardial infarcts. Our results suggest that emerging post-infarction therapies that alter regional mechanics will also alter infarct collagen structure, offering both potential risks and novel therapeutic opportunities. Copyright © 2012 Elsevier Ltd. All rights reserved.

Regional Mechanics Determine Collagen Fiber Structure in Healing Myocardial Infarcts

PubMed Central

Fomovsky, Gregory M.; Rouillard, Andrew D.; Holmes, Jeffrey W.

2012-01-01

Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shape, and/or location produce different patterns of mechanical stretch that guide evolving collagen fiber structure. We tested the effects of infarct shape and location using a combined experimental and computational approach. We studied mechanics and collagen fiber structure in cryoinfarcts in 53 Sprague-Dawley rats and found that regardless of shape or orientation, cryoinfarcts near the equator of the left ventricle stretched primarily in the circumferential direction and developed circumferentially aligned collagen, while infarcts at the apex stretched similarly in the circumferential and longitudinal direction and developed randomly oriented collagen. In a computational model of infarct healing, an effect of mechanical stretch on fibroblast and collagen alignment was required to reproduce the experimental results. We conclude that mechanical environment determines collagen fiber structure in healing myocardial infarcts. Our results suggest that emerging post-infarction therapies that alter regional mechanics will also alter infarct collagen structure, offering both potential risks and novel therapeutic opportunities. PMID:22418281

Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts.

PubMed

Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

2017-03-07

Computational and nuclear magnetic resonance hybrid approaches provide efficient tools for 3D structure determination of small proteins, but currently available algorithms struggle to perform with larger proteins. Here we demonstrate a new computational algorithm that assembles the 3D structure of a protein from its constituent super-secondary structural motifs (Smotifs) with the help of pseudocontact shift (PCS) restraints for backbone amide protons, where the PCSs are produced from different metal centers. The algorithm, DINGO-PCS (3D assembly of Individual Smotifs to Near-native Geometry as Orchestrated by PCSs), employs the PCSs to recognize, orient, and assemble the constituent Smotifs of the target protein without any other experimental data or computational force fields. Using a universal Smotif database, the DINGO-PCS algorithm exhaustively enumerates any given Smotif. We benchmarked the program against ten different protein targets ranging from 100 to 220 residues with different topologies. For nine of these targets, the method was able to identify near-native Smotifs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Protein Flexibility Facilitates Quaternary Structure Assembly and Evolution

PubMed Central

Marsh, Joseph A.; Teichmann, Sarah A.

2014-01-01

The intrinsic flexibility of proteins allows them to undergo large conformational fluctuations in solution or upon interaction with other molecules. Proteins also commonly assemble into complexes with diverse quaternary structure arrangements. Here we investigate how the flexibility of individual protein chains influences the assembly and evolution of protein complexes. We find that flexibility appears to be particularly conducive to the formation of heterologous (i.e., asymmetric) intersubunit interfaces. This leads to a strong association between subunit flexibility and homomeric complexes with cyclic and asymmetric quaternary structure topologies. Similarly, we also observe that the more nonhomologous subunits that assemble together within a complex, the more flexible those subunits tend to be. Importantly, these findings suggest that subunit flexibility should be closely related to the evolutionary history of a complex. We confirm this by showing that evolutionarily more recent subunits are generally more flexible than evolutionarily older subunits. Finally, we investigate the very different explorations of quaternary structure space that have occurred in different evolutionary lineages. In particular, the increased flexibility of eukaryotic proteins appears to enable the assembly of heteromeric complexes with more unique components. PMID:24866000

Facilitated family presence at resuscitation: effectiveness of a nursing student toolkit.

PubMed

Kantrowitz-Gordon, Ira; Bennett, Deborah; Wise Stauffer, Debra; Champ-Gibson, Erla; Fitzgerald, Cynthia; Corbett, Cynthia

2013-10-01

Facilitated family presence at resuscitation is endorsed by multiple nursing and specialty practice organizations. Implementation of this practice is not universal so there is a need to increase familiarity and competence with facilitated family presence at resuscitation during this significant life event. One strategy to promote this practice is to use a nursing student toolkit for pre-licensure and graduate nursing students. The toolkit includes short video simulations of facilitated family presence at resuscitation, a PowerPoint presentation of evidence-based practice, and questions to facilitate guided discussion. This study tested the effectiveness of this toolkit in increasing nursing students' knowledge, perceptions, and confidence in facilitated family presence at resuscitation. Nursing students from five universities in the United States completed the Family Presence Risk-Benefit Scale, Family Presence Self-Confidence Scale, and a knowledge test before and after the intervention. Implementing the facilitated family presence at resuscitation toolkit significantly increased nursing students' knowledge, perceptions, and confidence related to facilitated family presence at resuscitation (p<.001). The effect size was large for knowledge (d=.90) and perceptions (d=1.04) and moderate for confidence (d=.51). The facilitated family presence at resuscitation toolkit used in this study had a positive impact on students' knowledge, perception of benefits and risks, and self-confidence in facilitated family presence at resuscitation. The toolkit provides students a structured opportunity to consider the presence of family members at resuscitation prior to encountering this situation in clinical practice. Copyright © 2012 Elsevier Ltd. All rights reserved.

Membrane protein structure determination — The next generation☆☆☆

PubMed Central

Moraes, Isabel; Evans, Gwyndaf; Sanchez-Weatherby, Juan; Newstead, Simon; Stewart, Patrick D. Shaw

2014-01-01

The field of Membrane Protein Structural Biology has grown significantly since its first landmark in 1985 with the first three-dimensional atomic resolution structure of a membrane protein. Nearly twenty-six years later, the crystal structure of the beta2 adrenergic receptor in complex with G protein has contributed to another landmark in the field leading to the 2012 Nobel Prize in Chemistry. At present, more than 350 unique membrane protein structures solved by X-ray crystallography (http://blanco.biomol.uci.edu/mpstruc/exp/list, Stephen White Lab at UC Irvine) are available in the Protein Data Bank. The advent of genomics and proteomics initiatives combined with high-throughput technologies, such as automation, miniaturization, integration and third-generation synchrotrons, has enhanced membrane protein structure determination rate. X-ray crystallography is still the only method capable of providing detailed information on how ligands, cofactors, and ions interact with proteins, and is therefore a powerful tool in biochemistry and drug discovery. Yet the growth of membrane protein crystals suitable for X-ray diffraction studies amazingly remains a fine art and a major bottleneck in the field. It is often necessary to apply as many innovative approaches as possible. In this review we draw attention to the latest methods and strategies for the production of suitable crystals for membrane protein structure determination. In addition we also highlight the impact that third-generation synchrotron radiation has made in the field, summarizing the latest strategies used at synchrotron beamlines for screening and data collection from such demanding crystals. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding. PMID:23860256

Anticipatory coarticulation facilitates word recognition in toddlers.

PubMed

Mahr, Tristan; McMillan, Brianna T M; Saffran, Jenny R; Ellis Weismer, Susan; Edwards, Jan

2015-09-01

Children learn from their environments and their caregivers. To capitalize on learning opportunities, young children have to recognize familiar words efficiently by integrating contextual cues across word boundaries. Previous research has shown that adults can use phonetic cues from anticipatory coarticulation during word recognition. We asked whether 18-24 month-olds (n=29) used coarticulatory cues on the word "the" when recognizing the following noun. We performed a looking-while-listening eyetracking experiment to examine word recognition in neutral vs. facilitating coarticulatory conditions. Participants looked to the target image significantly sooner when the determiner contained facilitating coarticulatory cues. These results provide the first evidence that novice word-learners can take advantage of anticipatory sub-phonemic cues during word recognition. Copyright © 2015 Elsevier B.V. All rights reserved.

Life history determines genetic structure and evolutionary potential of host-parasite interactions.

PubMed

Barrett, Luke G; Thrall, Peter H; Burdon, Jeremy J; Linde, Celeste C

2008-12-01

Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns.

Facilitated versus Non-Facilitated Online Case Discussions: Comparing Differences in Problem Space Coverage

ERIC Educational Resources Information Center

Ertmer, Peggy A.; Koehler, Adrie A.

2015-01-01

The facilitator plays a key role in guiding students' efforts during case discussions. However, few studies have compared differences in learning outcomes for students participating in facilitated versus non-facilitated discussions. In this research, we used "problem space coverage" as a learning measure to compare outcomes between…

[Health care access barriers and facilitators: a qualitative systematic review].

PubMed

Hirmas Adauy, Macarena; Poffald Angulo, Lucy; Jasmen Sepúlveda, Anita María; Aguilera Sanhueza, Ximena; Delgado Becerra, Iris; Vega Morales, Jeanette

2013-03-01

To determine whether health care access barriers and facilitators cut across different populations, countries, and pathologies, and if so, at which stages of health care access they occur most frequently. A qualitative systematic review of literature published between 2000 and 2010 was undertaken drawing on six international sources: Fuente Académica, MEDLINE (full-text), Academic Search Complete (a full-text multidisciplinary academic database), PubMed, SciELO, and LILACS. Scientific appraisal guidelines from the Critical Appraisal Skills Programme Español (CASPe) and Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) were applied. Gray literature was also reviewed. From the review of scientific literature, 19 of 1 160 articles and 8 of 12 gray literature documents were selected. A total of 230 barriers and 35 facilitators were identified in countries with different contexts and degrees of development. The 230 barriers were classified according to the Tanahashi framework: 25 corresponded to availability, 67 to access, 87 to acceptability, and 51 to contact. Most of the barriers were related to acceptability and access. The facilitating elements that were identified had to do with personal factors, the provider-client relationship, social support, knowledge about diseases, and adaptation of the services to patients. The barriers and facilitators were seen mostly in people who initiated contact with the health systems, and they occurred at all stages of health care access. Only a few of the studies looked at people who did not initiate contact with the health services. The barriers and facilitators identified were socially determined and largely a reflection of existing social inequities in the countries. To reduce or eliminate them, joint action with other non-health sectors will be necessary.

Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE

PubMed Central

Wisedchaisri, Goragot; Park, Min-Sun; Iadanza, Matthew G.; Zheng, Hongjin; Gonen, Tamir

2014-01-01

The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins. PMID:25088546

SFG analysis of surface bound proteins: a route towards structure determination.

PubMed

Weidner, Tobias; Castner, David G

2013-08-14

The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge X-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface.

SFG analysis of surface bound proteins: A route towards structure determination

PubMed Central

Weidner, Tobias; Castner, David G.

2013-01-01

The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge x-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface. PMID:23727992

Thermostabilisation of membrane proteins for structural studies

PubMed Central

Magnani, Francesca; Serrano-Vega, Maria J.; Shibata, Yoko; Abdul-Hussein, Saba; Lebon, Guillaume; Miller-Gallacher, Jennifer; Singhal, Ankita; Strege, Annette; Thomas, Jennifer A.; Tate, Christopher G.

2017-01-01

The thermostability of an integral membrane protein in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals suitable for structure determination. However, many mammalian membrane proteins are too unstable for crystallisation. We developed a thermostabilisation strategy based on systematic mutagenesis coupled to a radioligand-binding thermostability assay that can be applied to receptors, ion channels and transporters. It takes approximately 6-12 months to thermostabilise a G protein-coupled receptor (GPCR) containing 300 amino acid residues. The resulting thermostabilised membrane proteins are more easily crystallised and result in high-quality structures. This methodology has facilitated structure-based drug design applied to GPCRs, because it is possible to determine multiple structures of the thermostabilised receptors bound to low affinity ligands. Protocols and advice are given on how to develop thermostability assays for membrane proteins and how to combine mutations to make an optimally stable mutant suitable for structural studies. PMID:27466713

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129Xe NMR Spectroscopy

PubMed Central

Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

2017-01-01

Abstract An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o‐ and m‐fluorophenol, whose previously unknown clathrate structures have been studied by 129Xe NMR spectroscopy. The high sensitivity of the 129Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures. PMID:28111848

A mathematical modeling method for determination of local vibroacoustic characteristics of structures

NASA Technical Reports Server (NTRS)

Tartakovskiy, B. D.; Dubner, A. B.

1973-01-01

A method is proposed for determining vibroacoustic characteristics from the results of measurements of the distribution of vibrational energy in a structure. The method is based on an energy model of a structure studied earlier. Equations are written to describe the distribution of vibrational energy in a hypothetical diffuse energy state in structural elements.

Direct demodulation method for heavy atom position determination in protein crystallography

NASA Astrophysics Data System (ADS)

Zhou, Liang; Liu, Zhong-Chuan; Liu, Peng; Dong, Yu-Hui

2013-01-01

The first step of phasing in any de novo protein structure determination using isomorphous replacement (IR) or anomalous scattering (AD) experiments is to find heavy atom positions. Traditionally, heavy atom positions can be solved by inspecting the difference Patterson maps. Due to the weak signals in isomorphous or anomalous differences and the noisy background in the Patterson map, the search for heavy atoms may become difficult. Here, the direct demodulation (DD) method is applied to the difference Patterson maps to reduce the noisy backgrounds and sharpen the signal peaks. The real space Patterson search by using these optimized maps can locate the heavy atom positions more accurately. It is anticipated that the direct demodulation method can assist in heavy atom position determination and facilitate the de novo structure determination of proteins.

Neophyte facilitator experiences of interprofessional education: implications for faculty development.

PubMed

Egan-Lee, Eileen; Baker, Lindsay; Tobin, Stasey; Hollenberg, Elisa; Dematteo, Dale; Reeves, Scott

2011-09-01

The facilitation of learners from different professional groups requires a range of interprofessional knowledge and skills (e.g. an understanding of possible sources of tension between professions) in addition to those that are more generic, such as how to manage a small group of learners. The development and delivery of interprofessional education (IPE) programs tends to rely on a small cohort of facilitators who have typically gained expertise through 'hands-on' involvement in facilitating IPE and through mentorship from more experienced colleagues. To avoid burn-out and to meet a growing demand for IPE, a larger number of facilitators are needed. However, empirical evidence regarding effective approaches to prepare for this type of work is limited. This article draws on data from a multiple case study of four IPE programs based in an urban setting in North America with a sample of neophyte facilitators and provides insight into their perceptions and experiences in preparing for and delivering IPE. Forty-one semi-structured interviews were conducted before (n = 20) and after (n = 21) program delivery with 21 facilitators. Findings indicated that despite participating in a three-fold faculty development strategy designed to support them in their IPE facilitation work, many felt unprepared and continued to have a poor conceptual understanding of core IPE and interprofessional collaboration principles, resulting in problematic implications (e.g. 'missed teachable moments') within their IPE programs. Findings from this study are discussed in relation to the IPE, faculty development and wider educational literature before implications are offered for the future delivery of interprofessional faculty development activities.

δ-Conotoxins synthesized using an acid-cleavable solubility tag approach reveal key structural determinants for NaV subtype selectivity.

PubMed

Peigneur, Steve; Paolini-Bertrand, Marianne; Gaertner, Hubert; Biass, Daniel; Violette, Aude; Stöcklin, Reto; Favreau, Philippe; Tytgat, Jan; Hartley, Oliver

2014-12-19

Conotoxins are venom peptides from cone snails with multiple disulfide bridges that provide a rigid structural scaffold. Typically acting on ion channels implicated in neurotransmission, conotoxins are of interest both as tools for pharmacological studies and as potential new medicines. δ-Conotoxins act by inhibiting inactivation of voltage-gated sodium channels (Nav). Their pharmacology has not been extensively studied because their highly hydrophobic character makes them difficult targets for chemical synthesis. Here we adopted an acid-cleavable solubility tag strategy that facilitated synthesis, purification, and directed disulfide bridge formation. Using this approach we readily produced three native δ-conotoxins from Conus consors plus two rationally designed hybrid peptides. We observed striking differences in Nav subtype selectivity across this group of compounds, which differ in primary structure at only three positions: 12, 23, and 25. Our results provide new insights into the structure-activity relationships underlying the Nav subtype selectivity of δ-conotoxins. Use of the acid-cleavable solubility tag strategy should facilitate synthesis of other hydrophobic peptides with complex disulfide bridge patterns. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Facilitation of Ferroelectric Switching via Mechanical Manipulation of Hierarchical Nanoscale Domain Structures.

PubMed

Chen, Zibin; Hong, Liang; Wang, Feifei; Ringer, Simon P; Chen, Long-Qing; Luo, Haosu; Liao, Xiaozhou

2017-01-06

Heterogeneous ferroelastic transition that produces hierarchical 90° tetragonal nanodomains via mechanical loading and its effect on facilitating ferroelectric domain switching in relaxor-based ferroelectrics were explored. Combining in situ electron microscopy characterization and phase-field modeling, we reveal the nature of the transition process and discover that the transition lowers by 40% the electrical loading threshold needed for ferroelectric domain switching. Our results advance the fundamental understanding of ferroelectric domain switching behavior.

Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory

ERIC Educational Resources Information Center

Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.

2012-01-01

This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

Analysis of phases in the structure determination of an icosahedral virus.

PubMed

Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G

2011-06-01

The constraints imposed on structure-factor phases by noncrystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to the correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or π. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed. © 2011 International Union of Crystallography

Antenatal group consultations: Facilitating patient-patient education.

PubMed

Nisbeth Jensen, Matilde; Fage-Butler, Antoinette Mary

2016-12-01

This article investigates the perspectives of pregnant women attending antenatal group consultations to gain their understandings of whether and how peer learning is facilitated in this setting. We conducted semi-structured individual interviews with 16 women who had participated in group consultations at Aarhus University Hospital, Denmark, and analysed the data using qualitative content analysis. Our research design also included observations and patient guest book data. Women who were pregnant for the first time greatly appreciated the experiential knowledge of multiparous women in the group. Group consultations provided new learning opportunities, as individuals' questions prompted learning within the groups, as well as questions and answers. There was more time for reflection in group consultations than in dyadic communication. Midwives played a key role in facilitating peer learning. Some topics were not deemed appropriate for discussion. Antenatal group consultations can support learning, as individuals participate positively both in their own knowledge acquisition and that of others. We call such peer learning patient-patient education. Our study indicates the strengths of group consultations for learning from the perspective of the group members. It highlights how learning may be facilitated in group consultations, and thus has broad practical relevance. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Barriers to, and facilitators of post-operative pain management in Iranian nursing: a qualitative research study.

PubMed

Rejeh, N; Ahmadi, F; Mohammadi, E; Anoosheh, M; Kazemnejad, A

2008-12-01

Unrelieved post-operative pain continues to be a major clinical challenge, despite advances in management. Although nurses have embraced a crucial role in pain management, its extent is often limited in Iranian nursing practice. To determine Iranian nurses' perceptions of the barriers and facilitators influencing their management of post-operative pain. This study was qualitative with 26 participant nurses. Data were obtained through semi-structured serial interviews and analysed using the content analysis method. Several themes emerged to describe the factors that hindered or facilitated post-operative pain management. These were grouped into two main themes: (1) barriers to pain management after surgery with subgroups such as powerlessness, policies and rules of organization, physicians leading practice, time constraints, limited communication, interruption of activities relating to pain, and (2) factors that facilitated post-operative pain management that included the nurse-patient relationship, nurses' responsibility, the physician as a colleague, and nurses' knowledge and skills. Postoperative pain management in Iran is contextually complex, and may be controversial. Participants believed that in this context accurate pain management is difficult for nurses due to the barriers mentioned. Therefore, nurses make decisions and act as a patient comforter for pain after surgery because of the barriers to effective pain management.

Aquaporin-facilitated transmembrane diffusion of hydrogen peroxide.

PubMed

Bienert, Gerd P; Chaumont, François

2014-05-01

Hydrogen peroxide (H2O2) is an important signaling compound that has recently been identified as a new substrate for several members of the aquaporin superfamily in various organisms. Evidence is emerging about the physiological significance of aquaporin-facilitated H2O2 diffusion. This review summarizes current knowledge about aquaporin-facilitated H2O2 diffusion across cellular membranes. It focuses on physicochemical and experimental evidence demonstrating the involvement of aquaporins in the transport of this redox signaling compound and discusses the regulation and structural prerequisites of these channels to transmit this signal. It also provides perspectives about the potential importance of aquaporin-facilitated H2O2 diffusion processes and places this knowledge in the context of the current understanding of transmembrane redox signaling processes. Specific aquaporin isoforms facilitate the passive diffusion of H2O2 across biological membranes and control H2O2 membrane permeability and signaling in living organisms. Redox signaling is a very important process regulating the physiology of cells and organisms in a similar way to the well-characterized hormonal and calcium signaling pathways. Efficient transmembrane diffusion of H2O2, a key molecule in the redox signaling network, requires aquaporins and makes these channels important players in this signaling process. Channel-mediated membrane transport allows the fine adjustment of H2O2 levels in the cytoplasm, intracellular organelles, the apoplast, and the extracellular space, which are essential for it to function as a signal molecule. This article is part of a Special Issue entitled Aquaporins. © 2013.

Organizational determinants of evaluation practice in Australian prevention agencies.

PubMed

Schwarzman, J; Bauman, A; Gabbe, B; Rissel, C; Shilton, T; Smith, B J

2018-06-01

Program evaluation is essential to inform decision making, contribute to the evidence base for strategies, and facilitate learning in health promotion and disease prevention organizations. Theoretical frameworks of organizational learning, and studies of evaluation capacity building describe the organization as central to evaluation capacity. Australian prevention organizations recognize limitations to current evaluation effectiveness and are seeking guidance to build evaluation capacity. This qualitative study identifies organizational facilitators and barriers to evaluation practice, and explores their interactions in Australian prevention organizations. We conducted semi-structured interviews with 40 experienced practitioners from government and non-government organizations. Using thematic analysis, we identified seven key themes that influence evaluation practice: leadership, organizational culture, organizational systems and structures, partnerships, resources, workforce development and training and recruitment and skills mix. We found organizational determinants of evaluation to have multi-level interactions. Leadership and organizational culture influenced organizational systems, resource allocation and support of staff. Partnerships were important to overcome resource deficits, and systems were critical to embed evaluation within the organization. Organizational factors also influenced the opportunities for staff to develop skills and confidence. We argue that investment to improve these factors would allow organizations to address evaluation capacity at multiple levels, and ultimately facilitate effective evaluation practice.

Life history determines genetic structure and evolutionary potential of host–parasite interactions

PubMed Central

Barrett, Luke G.; Thrall, Peter H.; Burdon, Jeremy J.; Linde, Celeste C.

2009-01-01

Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns. PMID:18947899

Meeting Report: Structural Determination of Environmentally Responsive Proteins

PubMed Central

Reinlib, Leslie

2005-01-01

The three-dimensional structure of gene products continues to be a missing lynchpin between linear genome sequences and our understanding of the normal and abnormal function of proteins and pathways. Enhanced activity in this area is likely to lead to better understanding of how discrete changes in molecular patterns and conformation underlie functional changes in protein complexes and, with it, sensitivity of an individual to an exposure. The National Institute of Environmental Health Sciences convened a workshop of experts in structural determination and environmental health to solicit advice for future research in structural resolution relative to environmentally responsive proteins and pathways. The highest priorities recommended by the workshop were to support studies of structure, analysis, control, and design of conformational and functional states at molecular resolution for environmentally responsive molecules and complexes; promote understanding of dynamics, kinetics, and ligand responses; investigate the mechanisms and steps in posttranslational modifications, protein partnering, impact of genetic polymorphisms on structure/function, and ligand interactions; and encourage integrated experimental and computational approaches. The workshop participants also saw value in improving the throughput and purity of protein samples and macromolecular assemblies; developing optimal processes for design, production, and assembly of macromolecular complexes; encouraging studies on protein–protein and macromolecular interactions; and examining assemblies of individual proteins and their functions in pathways of interest for environmental health. PMID:16263521

A glimpse of structural biology through X-ray crystallography.

PubMed

Shi, Yigong

2014-11-20

Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.

Facilitators on networks reveal optimal interplay between information exchange and reciprocity.

PubMed

Szolnoki, Attila; Perc, Matjaž; Mobilia, Mauro

2014-04-01

Reciprocity is firmly established as an important mechanism that promotes cooperation. An efficient information exchange is likewise important, especially on structured populations, where interactions between players are limited. Motivated by these two facts, we explore the role of facilitators in social dilemmas on networks. Facilitators are here mirrors to their neighbors-they cooperate with cooperators and defect with defectors-but they do not participate in the exchange of strategies. As such, in addition to introducing direct reciprocity, they also obstruct information exchange. In well-mixed populations, facilitators favor the replacement and invasion of defection by cooperation as long as their number exceeds a critical value. In structured populations, on the other hand, there exists a delicate balance between the benefits of reciprocity and the deterioration of information exchange. Extensive Monte Carlo simulations of social dilemmas on various interaction networks reveal that there exists an optimal interplay between reciprocity and information exchange, which sets in only when a small number of facilitators occupy the main hubs of the scale-free network. The drawbacks of missing cooperative hubs are more than compensated for by reciprocity and, at the same time, the compromised information exchange is routed via the auxiliary hubs with only marginal losses in effectivity. These results indicate that it is not always optimal for the main hubs to become leaders of the masses, but rather to exploit their highly connected state to promote tit-for-tat-like behavior.

Facilitators on networks reveal optimal interplay between information exchange and reciprocity

NASA Astrophysics Data System (ADS)

Szolnoki, Attila; Perc, Matjaž; Mobilia, Mauro

2014-04-01

Reciprocity is firmly established as an important mechanism that promotes cooperation. An efficient information exchange is likewise important, especially on structured populations, where interactions between players are limited. Motivated by these two facts, we explore the role of facilitators in social dilemmas on networks. Facilitators are here mirrors to their neighbors—they cooperate with cooperators and defect with defectors—but they do not participate in the exchange of strategies. As such, in addition to introducing direct reciprocity, they also obstruct information exchange. In well-mixed populations, facilitators favor the replacement and invasion of defection by cooperation as long as their number exceeds a critical value. In structured populations, on the other hand, there exists a delicate balance between the benefits of reciprocity and the deterioration of information exchange. Extensive Monte Carlo simulations of social dilemmas on various interaction networks reveal that there exists an optimal interplay between reciprocity and information exchange, which sets in only when a small number of facilitators occupy the main hubs of the scale-free network. The drawbacks of missing cooperative hubs are more than compensated for by reciprocity and, at the same time, the compromised information exchange is routed via the auxiliary hubs with only marginal losses in effectivity. These results indicate that it is not always optimal for the main hubs to become leaders of the masses, but rather to exploit their highly connected state to promote tit-for-tat-like behavior.

Facilitating HIV Disclosure Across Diverse Settings: A Review

PubMed Central

Baijal, Parijat; Pegurri, Elisabetta

2011-01-01

HIV status disclosure is central to debates about HIV because of its potential for HIV prevention and its links to privacy and confidentiality as human-rights issues. Our review of the HIV-disclosure literature found that few people keep their status completely secret; disclosure tends to be iterative and to be higher in high-income countries; gender shapes disclosure motivations and reactions; involuntary disclosure and low levels of partner disclosure highlight the difficulties faced by health workers; the meaning and process of disclosure differ across settings; stigmatization increases fears of disclosure; and the ethical dilemmas resulting from competing values concerning confidentiality influence the extent to which disclosure can be facilitated. Our results suggest that structural changes, including making more services available, could facilitate HIV disclosure as much as individual approaches and counseling do. PMID:21493947

Embellishing Problem-Solving Examples with Deep Structure Information Facilitates Transfer

ERIC Educational Resources Information Center

Lee, Hee Seung; Betts, Shawn; Anderson, John R.

2017-01-01

Appreciation of problem structure is critical to successful learning. Two experiments investigated effective ways of communicating problem structure in a computer-based learning environment and tested whether verbal instruction is necessary to specify solution steps, when deep structure is already embellished by instructional examples.…

How do we facilitate international clinical placements for nursing students: A cross-sectional exploration of the structure, aims and objectives of placements.

PubMed

Browne, Caroline A; Fetherston, Catherine M

2018-07-01

International clinical placements provide undergraduate students with a unique and complex clinical learning environment, to explore cultural awareness, experience different health care settings and achieve clinical competencies. Higher education institutions need to consider how to structure these placements to ensure appropriate and achievable aims and learning outcomes. In this study we described the structure, aims and learning outcomes associated with international clinical placement opportunities currently undertaken by Australian undergraduate nursing students in the Asia region. Forty eight percent (n = 18) of the institutions invited responded. Eight institutions met the inclusion criteria, one of which offered three placements in the region, resulting in 10 international placements for which data were provided. An online survey tool was used to collect data during August and September 2015 on international clinical placements conducted by the participating universities. Descriptive data on type and numbers of placements is presented, along with results from the content analysis conducted to explore data from open ended questions on learning aims and outcomes. One hundred students undertook 10 International Clinical Placements offered in the Asian region by eight universities. Variations across placements were found in the length of placement, the number of students participating, facilitator to student ratios and assessment techniques used. Five categories related to the aims of the programs were identified: 'becoming culturally aware through immersion', 'working with the community to promote health', 'understanding the role of nursing within the health care setting', 'translating theory into professional clinical practice', and 'developing relationships in international learning environments'. Four categories related to learning outcomes were identified: 'understanding healthcare and determinants of health', 'managing challenges', 'understanding the

A case study: the evolution of a “facilitator model” liaison program in an academic medical library*

PubMed Central

DeShay, Claudia H.; Huslig, Mary Ann; Mayo, Helen G.; Patridge, Emily F.

2012-01-01

Question: What type of liaison program would best utilize both librarians and other library staff to effectively promote library services and resources to campus departments? Setting: The case is an academic medical center library serving a large, diverse campus. Methods: The library implemented a “facilitator model” program to provide personalized service to targeted clients that allowed for maximum staff participation with limited subject familiarity. To determine success, details of liaison-contact interactions and results of liaison and department surveys were reviewed. Results: Liaisons successfully recorded 595 interactions during the program's first 10 months of existence. A significant majority of departmental contact persons (82.5%) indicated they were aware of the liaison program, and 75% indicated they preferred email communication. Conclusion: The “facilitator model” provides a well-defined structure for assigning liaisons to departments or groups; however, training is essential to ensure that liaisons are able to communicate effectively with their clients. PMID:22879805

Sport Participation for Elite Athletes With Physical Disabilities: Motivations, Barriers, and Facilitators.

PubMed

McLoughlin, Gabriella; Weisman Fecske, Courtney; Castaneda, Yvette; Gwin, Candace; Graber, Kim

2017-10-01

There are many reasons why individuals are motivated to participate in sports. Less attention, however, is given for studying motivation and athlete development in adapted sport. The purpose of this study was to identify the motivations, facilitators, and barriers to sports participation of elite athletes with a physical disability. Participants (N = 23, 17 males, six females, mean age: 24.3 years) were recruited through online listservs, e-mails, and snowball sampling. A semistructured interview guide was employed. Analysis was conducted and grounded in self-determination theory and literature surrounding barriers and facilitators of sports participation. Through coding by multiple researchers, six themes emerged. Themes indicated that athletes attributed participation to constructs of self-determination theory as well as overcoming specific barriers such as cost, time constraints, and lack of opportunity. Among facilitators to their athletic development, there were empowerment and advocacy, increased health, college scholarships, and achieving performance-related goals.

TOPSAN: a dynamic web database for structural genomics.

PubMed

Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John

2011-01-01

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.

Integrating NOE and RDC using sum-of-squares relaxation for protein structure determination.

PubMed

Khoo, Y; Singer, A; Cowburn, D

2017-07-01

We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a convex semidefinite program (SDP). However, often the NOE distance restraints are too imprecise and sparse for accurate structure determination. Residual dipolar coupling (RDC) measurements provide additional geometric information on the angles between atom-pair directions and axes of the principal-axis-frame. The optimization problem involving RDC is highly non-convex and requires a good initialization even within the simulated annealing framework. In this paper, we model the protein backbone as an articulated structure composed of rigid units. Determining the rotation of each rigid unit gives the full protein structure. We propose solving the non-convex optimization problems using the sum-of-squares (SOS) hierarchy, a hierarchy of convex relaxations with increasing complexity and approximation power. Unlike classical global optimization approaches, SOS optimization returns a certificate of optimality if the global optimum is found. Based on the SOS method, we proposed two algorithms-RDC-SOS and RDC-NOE-SOS, that have polynomial time complexity in the number of amino-acid residues and run efficiently on a standard desktop. In many instances, the proposed methods exactly recover the solution to the original non-convex optimization problem. To the best of our knowledge this is the first time SOS relaxation is introduced to solve non-convex optimization problems in structural biology. We further introduce a statistical tool, the Cramér-Rao bound (CRB), to provide an information theoretic bound on the highest resolution one can hope to achieve when determining protein structure from noisy measurements using any unbiased estimator. Our simulation results show that when the RDC measurements are

Development of biology student worksheets to facilitate science process skills of student

NASA Astrophysics Data System (ADS)

Rahayu, Y. S.; Pratiwi, R.; Indana, S.

2018-01-01

This research aims to describe development of Biology student worksheets to facilitate science process skills of student, at the same time to facilitate thinking skills of students in senior high school are equipped with Assesment Sheets. The worksheets development refers to cycle which includes phase analysis (analysis), planning (planning), design (design), development (development), implementation (implementation), evaluation and revision (evaluation and revision). Phase evaluation and revision is an ongoing activity conducted in each phase of the development cycle. That is, after the evaluation of the results of these activities and make revisions at any phase, then continue to the next phase. Based on the test results for grade X, XI, and XII in St. Agnes Surabaya high school, obtained some important findings. The findings are as follows. (1) Developed biology student worksheets could be used to facilitate thinking ability of students in particular skills integrated process that includes components to formulate the problem, formulate hypotheses, determine the study variables, formulate an operational definition of variables, determine the steps in the research, planning data tables, organizing Data in the form of tables/charts, drawing conclusions, (2) Developed biology student worksheets could also facilitate the development of social interaction of students such as working together, listening/respect the opinions of others, assembling equipment and materials, discuss and share information and facilitate the upgrading of skills hands-on student activity. (3) Developed biology worksheets basically could be implemented with the guidance of the teacher step by step, especially for students who have never used a similar worksheet. Guidance at the beginning of this need, especially for worksheets that require special skills or understanding of specific concepts as a prerequisite, such as using a microscope, determine the heart rate, understand the mechanism of

Peers for Promotion: Achieving Academic Advancement through Facilitated Peer Mentoring

ERIC Educational Resources Information Center

Ockene, Judith K.; Milner, Robert J.; Thorndyke, Luanne E.; Congdon, John; Cain, Joanna M.

2017-01-01

The promotion process is challenging, particularly for non-tenure track faculty in academic medicine. To address this challenge, we implemented a facilitated peer mentoring program that included a structured curriculum with regular meetings, guided by two senior faculty mentors. Participants expressed satisfaction with the program, showed…

Barriers and Facilitators to Central Venous Catheter Insertion: A Qualitative Study.

PubMed

Cameron, Kenzie A; Cohen, Elaine R; Hertz, Joelle R; Wayne, Diane B; Mitra, Debi; Barsuk, Jeffrey H

2018-03-14

The aims of the study were to identify perceived barriers and facilitators to central venous catheter (CVC) insertion among healthcare providers and to understand the extent to which an existing Simulation-Based Mastery Learning (SBML) program may address barriers and leverage facilitators. Providers participating in a CVC insertion SBML train-the-trainer program, in addition to intensive care unit nurse managers, were purposively sampled from Veterans Administration Medical Centers located in geographically diverse areas. We conducted semistructured interviews to assess perceptions of barriers and facilitators to CVC insertion. Deidentified transcripts were analyzed using a grounded theory approach and the constant comparative method. We subsequently mapped identified barriers and facilitators to our SBML curriculum to determine whether or not the curriculum addresses these factors. We interviewed 28 providers at six Veterans Administration Medical Centers, identifying the following five overarching factors of perceived barriers to CVC insertion: (1) equipment, (2) personnel/staff, (3) setting or organizational context, (4) patient or provider, and (5) time-related barriers. Three overarching factors of facilitators emerged: (1) equipment, (2) personnel, and (3) setting or organizational context facilitators. The SBML curriculum seems to address most identified barriers, while leveraging many facilitators; building on the commonly identified facilitator of nursing staff contribution by expanding the curriculum to explicitly include nurse involvement could improve team efficiency and organizational culture of safety. Many identified facilitators (e.g., ability to use ultrasound, personnel confidence/competence) were also identified as barriers. Evidence-based SBML programs have the potential to amplify these facilitators while addressing the barriers by providing an opportunity to practice and master CVC insertion skills.

Simple Approach for De Novo Structural Identification of Mannose Trisaccharides

NASA Astrophysics Data System (ADS)

Hsu, Hsu Chen; Liew, Chia Yen; Huang, Shih-Pei; Tsai, Shang-Ting; Ni, Chi-Kung

2018-03-01

Oligosaccharides have diverse functions in biological systems. However, the structural determination of oligosaccharides remains difficult and has created a bottleneck in carbohydrate research. In this study, a new approach for the de novo structural determination of underivatized oligosaccharides is demonstrated. A low-energy collision-induced dissociation (CID) of sodium ion adducts was used to facilitate the cleavage of desired chemical bonds during the dissociation. The selection of fragments for the subsequent CID was guided using a procedure that we built from the understanding of the saccharide dissociation mechanism. The linkages, anomeric configurations, and branch locations of oligosaccharides were determined by comparing the CID spectra of oligosaccharide with the fragmentation patterns based on the dissociation mechanism and our specially prepared disaccharide CID spectrum database. The usefulness of this method was demonstrated to determine the structures of several mannose trisaccharides. This method can also be applied in the structural determination of oligosaccharides larger than trisaccharides and containing hexose other than mannose if authentic standards are available. [Figure not available: see fulltext.

Simple Approach for De Novo Structural Identification of Mannose Trisaccharides

NASA Astrophysics Data System (ADS)

Hsu, Hsu Chen; Liew, Chia Yen; Huang, Shih-Pei; Tsai, Shang-Ting; Ni, Chi-Kung

2017-12-01

Oligosaccharides have diverse functions in biological systems. However, the structural determination of oligosaccharides remains difficult and has created a bottleneck in carbohydrate research. In this study, a new approach for the de novo structural determination of underivatized oligosaccharides is demonstrated. A low-energy collision-induced dissociation (CID) of sodium ion adducts was used to facilitate the cleavage of desired chemical bonds during the dissociation. The selection of fragments for the subsequent CID was guided using a procedure that we built from the understanding of the saccharide dissociation mechanism. The linkages, anomeric configurations, and branch locations of oligosaccharides were determined by comparing the CID spectra of oligosaccharide with the fragmentation patterns based on the dissociation mechanism and our specially prepared disaccharide CID spectrum database. The usefulness of this method was demonstrated to determine the structures of several mannose trisaccharides. This method can also be applied in the structural determination of oligosaccharides larger than trisaccharides and containing hexose other than mannose if authentic standards are available. [Figure not available: see fulltext.

Defining an essence of structure determining residue contacts in proteins.

PubMed

Sathyapriya, R; Duarte, Jose M; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2009-12-01

The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this "structural essence" has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts-such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed "cone-peeling" that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 A Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This "structural essence" opens new avenues in the

Defining an Essence of Structure Determining Residue Contacts in Proteins

PubMed Central

Sathyapriya, R.; Duarte, Jose M.; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2009-01-01

The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this “structural essence” has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts—such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed “cone-peeling” that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 Å Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This “structural essence” opens new

Facilitating the implementation of clinical technology in healthcare: what role does a national agency play?

PubMed

Harvey, Gill; Llewellyn, Sue; Maniatopoulos, Greg; Boyd, Alan; Procter, Rob

2018-05-10

Accelerating the implementation of new technology in healthcare is typically complex and multi-faceted. One strategy is to charge a national agency with the responsibility for facilitating implementation. This study examines the role of such an agency in the English National Health Service. In particular, it compares two different facilitation strategies employed by the agency to support the implementation of insulin pump therapy. The research involved an empirical case study of four healthcare organisations receiving different levels of facilitation from the national agency: two received active hands-on facilitation; one was the intended recipient of a more passive, web-based facilitation strategy; the other implemented the technology without any external facilitation. The primary method of data collection was semi-structured qualitative interviews with key individuals involved in implementation. The integrated-PARIHS framework was applied as a conceptual lens to analyse the data. The two sites that received active facilitation from an Implementation Manager in the national agency made positive progress in implementing the technology. In both sites there was a high level of initial receptiveness to implementation. This was similar to a site that had successfully introduced insulin pump therapy without facilitation support from the national agency. By contrast, a site that did not have direct contact with the national agency made little progress with implementation, despite the availability of a web-based implementation resource. Clinicians expressed differences of opinion around the value and effectiveness of the technology and contextual barriers related to funding for implementation persisted. The national agency's intended roll out strategy using passive web-based facilitation appeared to have little impact. When favourable conditions exist, in terms of agreement around the value of the technology, clinician receptiveness and motivation to change, active

BLM helicase facilitates telomere replication during leading strand synthesis of telomeres

PubMed Central

Kosiyatrakul, Settapong T.

2015-01-01

Based on its in vitro unwinding activity on G-quadruplex (G4) DNA, the Bloom syndrome–associated helicase BLM is proposed to participate in telomere replication by aiding fork progression through G-rich telomeric DNA. Single molecule analysis of replicated DNA (SMARD) was used to determine the contribution of BLM helicase to telomere replication. In BLM-deficient cells, replication forks initiating from origins within the telomere, which copy the G-rich strand by leading strand synthesis, moved slower through the telomere compared with the adjacent subtelomere. Fork progression through the telomere was further slowed in the presence of a G4 stabilizer. Using a G4-specific antibody, we found that deficiency of BLM, or another G4-unwinding helicase, the Werner syndrome-associated helicase WRN, resulted in increased G4 structures in cells. Importantly, deficiency of either helicase led to greater increases in G4 DNA detected in the telomere compared with G4 seen genome-wide. Collectively, our findings are consistent with BLM helicase facilitating telomere replication by resolving G4 structures formed during copying of the G-rich strand by leading strand synthesis. PMID:26195664

Exploring behavioural determinants relating to health professional reporting of medication errors: a qualitative study using the Theoretical Domains Framework.

PubMed

Alqubaisi, Mai; Tonna, Antonella; Strath, Alison; Stewart, Derek

2016-07-01

Effective and efficient medication reporting processes are essential in promoting patient safety. Few qualitative studies have explored reporting of medication errors by health professionals, and none have made reference to behavioural theories. The objective was to describe and understand the behavioural determinants of health professional reporting of medication errors in the United Arab Emirates (UAE). This was a qualitative study comprising face-to-face, semi-structured interviews within three major medical/surgical hospitals of Abu Dhabi, the UAE. Health professionals were sampled purposively in strata of profession and years of experience. The semi-structured interview schedule focused on behavioural determinants around medication error reporting, facilitators, barriers and experiences. The Theoretical Domains Framework (TDF; a framework of theories of behaviour change) was used as a coding framework. Ethical approval was obtained from a UK university and all participating hospital ethics committees. Data saturation was achieved after interviewing ten nurses, ten pharmacists and nine physicians. Whilst it appeared that patient safety and organisational improvement goals and intentions were behavioural determinants which facilitated reporting, there were key determinants which deterred reporting. These included the beliefs of the consequences of reporting (lack of any feedback following reporting and impacting professional reputation, relationships and career progression), emotions (fear and worry) and issues related to the environmental context (time taken to report). These key behavioural determinants which negatively impact error reporting can facilitate the development of an intervention, centring on organisational safety and reporting culture, to enhance reporting effectiveness and efficiency.

Communication: Gas-phase structural isomer identification by Coulomb explosion of aligned molecules

NASA Astrophysics Data System (ADS)

Burt, Michael; Amini, Kasra; Lee, Jason W. L.; Christiansen, Lars; Johansen, Rasmus R.; Kobayashi, Yuki; Pickering, James D.; Vallance, Claire; Brouard, Mark; Stapelfeldt, Henrik

2018-03-01

The gas-phase structures of four difluoroiodobenzene and two dihydroxybromobenzene isomers were identified by correlating the emission angles of atomic fragment ions created, following femtosecond laser-induced Coulomb explosion. The structural determinations were facilitated by confining the most polarizable axis of each molecule to the detection plane prior to the Coulomb explosion event using one-dimensional laser-induced adiabatic alignment. For a molecular target consisting of two difluoroiodobenzene isomers, each constituent structure could additionally be singled out and distinguished.

Transmission electron diffraction determination of the Ge(001)-(2 × 1) surface structure

NASA Astrophysics Data System (ADS)

Collazo-Davila, C.; Grozea, D.; Landree, E.; Marks, L. D.

1997-04-01

The lateral displacements in the Ge(001)-(2 × 1) surface reconstruction have been determined using transmission electron diffraction (TED). The best-fit model includes displacements extending six layers into the bulk. The atomic positions found agree with X-ray studies to within a few hundredths of an ångström. With the positions determined so precisely, it is suggested that the Ge(001)-(2 × 1) surface can now serve as a standard for comparison with theoretical surface structure calculations. The results from the currently available theoretical studies on the surface are compared with the experimentally determined structure.

Feasibility of one-shot-per-crystal structure determination using Laue diffraction

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

Cornaby, Sterling; CHESS; Szebenyi, Doletha M. E.

Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Lauemore » technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.« less

Establishing Interorganizational Structures That Facilitate Successful School Partnerships.

ERIC Educational Resources Information Center

Intriligator, Barbara A.

An organizational framework for establishing effective partnerships between school systems, social service providers, universities, and/or the private sector is presented in this paper. The different types of interorganizational structures, described along a continuum of increasing interdependence, include cooperative, coordinative, or…

Crystal structure determination and analysis of 11S coconut allergen: Cocosin.

PubMed

Vajravijayan, S; Nandhagopal, N; Gunasekaran, K

2017-12-01

Allergy is an abnormal immune response against an innocuous target. Food allergy is an adverse reaction caused by common foods most well-known being those involving peanuts. Apart from mono sensitized food allergy, cross-reactivity with other food allergens is also commonly observed. To understand the phenomenon of cross-reactivity related to immune response, three dimensional structures of the allergens and their antigenic epitopes has to be analysed in detail. The X-ray crystal structure of Cocosin, a common 11S food allergen from coconut, has been determined at 2.2Å resolution using molecular replacement technique. The monomer of 52kDa is composed of two β-jelly roll domains, one with acidic and the other with basic character. The structure shows hexameric association with two trimers facing each other. Though the overall structure of Cocosin is similar to other 11S allergens, the occurrence of experimentally determined epitopes of the peanut allergen Ara h 3 at flexible as well as variable regions could be the reason for the clinically reported result of cross-reactivity that the peanut allergic patients are not sensitized with coconut allergen. Copyright © 2017 Elsevier Ltd. All rights reserved.

Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance

PubMed Central

Barber-Zucker, Shiran; Uebe, René; Davidov, Geula; Navon, Yotam; Sherf, Dror; Chill, Jordan H.; Kass, Itamar; Bitton, Ronit; Schüler, Dirk; Zarivach, Raz

2016-01-01

Cation diffusion facilitators (CDF) are highly conserved, metal ion efflux transporters that maintain divalent transition metal cation homeostasis. Most CDF proteins contain two domains, the cation transporting transmembrane domain and the regulatory cytoplasmic C-terminal domain (CTD). MamM is a magnetosome-associated CDF protein essential for the biomineralization of magnetic iron-oxide particles in magnetotactic bacteria. To investigate the structure-function relationship of CDF cytoplasmic domains, we characterized a MamM M250P mutation that is synonymous with the disease-related mutation L349P of the human CDF protein ZnT-10. Our results show that the M250P exchange in MamM causes severe structural changes in its CTD resulting in abnormal reduced function. Our in vivo, in vitro and in silico studies indicate that the CTD fold is critical for CDF proteins’ proper function and support the previously suggested role of the CDF cytoplasmic domain as a CDF regulatory element. Based on our results, we also suggest a mechanism for the effects of the ZnT-10 L349P mutation in human. PMID:27550551

3D Structure Determination of Native Mammalian Cells using Cryo-FIB and Cryo-electron Tomography

PubMed Central

Wang, Ke; Strunk, Korrinn; Zhao, Gongpu; Gray, Jennifer L.; Zhang, Peijun

2012-01-01

Cryo-electron tomography (cryo-ET) has enabled high resolution three-dimensional (3D) structural analysis of virus and host cell interactions and many cell signaling events; these studies, however, have largely been limited to very thin, peripheral regions of eukaryotic cells or to small prokaryotic cells. Recent efforts to make thin, vitreous sections using cryo-ultramicrotomy have been successful, however, this method is technically very challenging and with many artifacts. Here, we report a simple and robust method for creating in situ, frozen-hydrated cell lamellas using a focused ion beam at cryogenic temperature (cryo-FIB), allowing access to any interior cellular regions of interest. We demonstrate the utility of cryo-FIB with high resolution 3D cellular structures from both bacterial cells and large mammalian cells. The method will not only facilitate high-throughput 3D structural analysis of biological specimens, but is also broadly applicable to sample preparation of thin films and surface materials without the need for FIB “lift-out”. PMID:22796867

Method for facilitating the introduction of material into cells

DOEpatents

Holcomb, David E.; McKnight, Timothy E.

2000-01-01

The present invention is a method for creating a localized disruption within a boundary of a cell or structure by exposing a boundary of a cell or structure to a set of energetically charged particles while regulating the energy of the charged particles so that the charged particles have an amount of kinetic energy sufficient to create a localized disruption within an area of the boundary of the cell or structure, then upon creation of the localized disruption, the amount of kinetic energy decreases to an amount insufficient to create further damage within the cell or structure beyond the boundary. The present invention is also a method for facilitating the introduction of a material into a cell or structure using the same methodology then further exciting the area of the boundary of the cell or structure where the localized disruption was created so to create a localized temporary opening within the boundary then further introducing the material through the temporary opening into the cell or structure.

GLOBAL EPIDEMIOLOGY OF HIV AMONG FEMALE SEX WORKERS: INFLUENCE OF STRUCTURAL DETERMINANTS

PubMed Central

Shannon, K; Strathdee, SA; Goldenberg, SM; Duff, P; Mwangi, P; Rusakova, M; Reza-Paul, S; Lau, J; Deering, K; Pickles, M; Boily, M-C

2014-01-01

SUMMARY Female sex workers (FSWs) bear a disproportionately large burden of HIV infection worldwide. Despite decades of research and programme activity, the epidemiology of HIV and the role that structural determinants have in mitigating or potentiating HIV epidemics and access to care for FSWs is poorly understood. We reviewed available published data for HIV prevalence and incidence, condom use, and structural determinants among this group. Only 87 (43%) of 204 unique studies reviewed explicitly examined structural determinants of HIV. Most studies were from Asia, with few from areas with a heavy burden of HIV such as sub-Saharan Africa, Russia, and eastern Europe. To further explore the potential effect of structural determinants on the course of epidemics, we used a deterministic transmission model to simulate potential HIV infections averted through structural changes in regions with concentrated and generalised epidemics, and high HIV prevalence among FSWs. This modelling suggested that elimination of sexual violence alone could avert 17% of HIV infections in Kenya (95% uncertainty interval [UI] 1–31) and 20% in Canada (95% UI 3–39) through its immediate and sustained effect on non-condom use) among FSWs and their clients in the next decade. In Kenya, scaling up of access to antiretroviral therapy among FSWs and their clients to meet WHO eligibility of a CD4 cell count of less than 500 cells per μL could avert 34% (95% UI 25–42) of infections and even modest coverage of sex worker-led outreach could avert 20% (95% UI 8–36) of infections in the next decade. Decriminalisation of sex work would have the greatest effect on the course of HIV epidemics across all settings, averting 33–46% of HIV infections in the next decade. Multipronged structural and community-led interventions are crucial to increase access to prevention and treatment and to promote human rights for FSWs worldwide. PMID:25059947

Identifying the barriers and facilitators to participation in physical activity for children with Down syndrome.

PubMed

Barr, M; Shields, N

2011-11-01

Many children with Down syndrome do not undertake the recommended amount of daily physical activity. The aim of this study was to explore the barriers and facilitators to physical activity for this group. Eighteen in-depth interviews were conducted with 20 parents (16 mothers, 4 fathers) of children with Down syndrome aged between 2 and 17 years to examine what factors facilitate physical activity and what factors are barriers to activity for their children. The participants were recruited through a community disability organisation that advocates for people with Down syndrome and their families. Interviews were recorded, transcribed and independently coded and analysed by two researchers using thematic analysis. Four themes on facilitators of physical activity were identified: (1) the positive role of the family; (2) opportunity for social interaction with peers; (3) structured accessible programmes that make adaptations for children with Down syndrome; and (4) children who were determined to succeed and physically skilled. Four themes on the barriers to physical activity were also identified: (1) characteristics commonly associated with Down syndrome; (2) competing family responsibilities; (3) reduced physical or behavioural skills; and (4) a lack of accessible programmes. The results highlight the important role of families in determining how much physical activity children with Down syndrome undertake and the effect that common characteristics associated with Down syndrome can have on maintaining an active lifestyle. Future research needs to concentrate on successful methods of encouraging physical activity, such as ensuring social interaction is part of the activity, and eliminating barriers to physical activity such as the a lack of appropriate programmes for children with Down syndrome. Implementing these strategies may encourage children with Down syndrome to participate more frequently in a physically active lifestyle. © 2011 The Authors. Journal of

Accurate Structural Correlations from Maximum Likelihood Superpositions

PubMed Central

Theobald, Douglas L; Wuttke, Deborah S

2008-01-01

The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. PMID:18282091

Barriers and facilitators to exchanging health information: a systematic review.

PubMed

Eden, Karen B; Totten, Annette M; Kassakian, Steven Z; Gorman, Paul N; McDonagh, Marian S; Devine, Beth; Pappas, Miranda; Daeges, Monica; Woods, Susan; Hersh, William R

2016-04-01

We conducted a systematic review of studies assessing facilitators and barriers to use of health information exchange (HIE). We searched MEDLINE, PsycINFO, CINAHL, and the Cochrane Library databases between January 1990 and February 2015 using terms related to HIE. English-language studies that identified barriers and facilitators of actual HIE were included. Data on study design, risk of bias, setting, geographic location, characteristics of the HIE, perceived barriers and facilitators to use were extracted and confirmed. Ten cross-sectional, seven multiple-site case studies, and two before-after studies that included data from several sources (surveys, interviews, focus groups, and observations of users) evaluated perceived barriers and facilitators to HIE use. The most commonly cited barriers to HIE use were incomplete information, inefficient workflow, and reports that the exchanged information that did not meet the needs of users. The review identified several facilitators to use. Incomplete patient information was consistently mentioned in the studies conducted in the US but not mentioned in the few studies conducted outside of the US that take a collective approach toward healthcare. Individual patients and practices in the US may exercise the right to participate (or not) in HIE which effects the completeness of patient information available to be exchanged. Workflow structure and user roles are key but understudied. We identified several facilitators in the studies that showed promise in promoting electronic health data exchange: obtaining more complete patient information; thoughtful workflow that folds in HIE; and inclusion of users early in implementation. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The 'patient's physician one-step removed': the evolving roles of medical tourism facilitators.

PubMed

Snyder, Jeremy; Crooks, Valorie A; Adams, Krystyna; Kingsbury, Paul; Johnston, Rory

2011-09-01

Medical tourism involves patients travelling internationally to receive medical services. This practice raises a range of ethical issues, including potential harms to the patient's home and destination country and risks to the patient's own health. Medical tourists often engage the services of a facilitator who may book travel and accommodation and link the patient with a hospital abroad. Facilitators have the potential to exacerbate or mitigate the ethical concerns associated with medical tourism, but their roles are poorly understood. 12 facilitators were interviewed from 10 Canadian medical tourism companies. Three themes were identified: facilitators' roles towards the patient, health system and medical tourism industry. Facilitators' roles towards the patient were typically described in terms of advocacy and the provision of information, but limited by facilitators' legal liability. Facilitators felt they played a positive role in the lives of their patients and the Canadian health system and served as catalysts for reform, although they noted an adversarial relationship with some Canadian physicians. Many facilitators described personally visiting medical tourism sites and forming personal relationships with surgeons abroad, but noted the need for greater regulation of their industry. Facilitators play a substantial and evolving role in the practice of medical tourism and may be entering a period of professionalisation. Because of the key role of facilitators in determining the effects of medical tourism on patients and public health, this paper recommends a planned conversation between medical tourism stakeholders to define and shape facilitators' roles.

Facilitating Facilitators to Facilitate, in Problem or Enquiry Based Learning Sessions

ERIC Educational Resources Information Center

Coelho, Catherine

2014-01-01

Problem based learning (PBL) has been used in dental education over the past 20 years and uses a patient case scenario to stimulate learning in a small group setting, where a trained facilitator does not teach but guides the group to bring about deep contextualized learning, to be empathetic to each other and to encourage fair and equitable…

Structural Insights into the HIV-1 Minus-strand Strong-stop DNA*

PubMed Central

Chen, Yingying; Maskri, Ouerdia; Chaminade, Françoise; René, Brigitte; Benkaroun, Jessica; Godet, Julien; Mély, Yves; Mauffret, Olivier; Fossé, Philippe

2016-01-01

An essential step of human immunodeficiency virus type 1 (HIV-1) reverse transcription is the first strand transfer that requires base pairing of the R region at the 3′-end of the genomic RNA with the complementary r region at the 3′-end of minus-strand strong-stop DNA (ssDNA). HIV-1 nucleocapsid protein (NC) facilitates this annealing process. Determination of the ssDNA structure is needed to understand the molecular basis of NC-mediated genomic RNA-ssDNA annealing. For this purpose, we investigated ssDNA using structural probes (nucleases and potassium permanganate). This study is the first to determine the secondary structure of the full-length HIV-1 ssDNA in the absence or presence of NC. The probing data and phylogenetic analysis support the folding of ssDNA into three stem-loop structures and the presence of four high-affinity binding sites for NC. Our results support a model for the NC-mediated annealing process in which the preferential binding of NC to four sites triggers unfolding of the three-dimensional structure of ssDNA, thus facilitating interaction of the r sequence of ssDNA with the R sequence of the genomic RNA. In addition, using gel retardation assays and ssDNA mutants, we show that the NC-mediated annealing process does not rely on a single pathway (zipper intermediate or kissing complex). PMID:26668324

Structure-function relationship of reduced cytochrome c probed by complete solution structure determination in 30% acetonitrile/water solution.

PubMed

Sivakolundu, Sivashankar G; Mabrouk, Patricia Ann

2003-05-01

The complete solution structure of ferrocytochrome c in 30% acetonitrile/70% water has been determined using high-field 1D and 2D (1)H NMR methods and deposited in the Protein Data Bank with codes 1LC1 and 1LC2. This is the first time a complete solution protein structure has been determined for a protein in nonaqueous media. Ferrocyt c retains a native protein secondary structure (five alpha-helices and two omega loops) in 30% acetonitrile. H18 and M80 residues are the axial heme ligands, as in aqueous solution. Residues believed to be axial heme ligands in the alkaline-like conformers of ferricyt c, specifically H33 and K72, are positioned close to the heme iron. The orientations of both heme propionates are markedly different in 30% acetonitrile/70% water. Comparative structural analysis of reduced cyt c in 30% acetonitrile/70% water solution with cyt c in different environments has given new insight into the cyt c folding mechanism, the electron transfer pathway, and cell apoptosis.

Facilitators and Barriers to Preparedness Partnerships: A Veterans Affairs Medical Center Perspective.

PubMed

Schmitz, Susan; Wyte-Lake, Tamar; Dobalian, Aram

2017-09-13

This study sought to understand facilitators and barriers faced by local US Department of Veterans Affairs Medical Center (VAMC) emergency managers (EMs) when collaborating with non-VA entities. Twelve EMs participated in semi-structured interviews lasting 60 to 90 minutes discussing their collaboration with non-VAMC organizations. Sections of the interview transcripts concerning facilitators and barriers to collaboration were coded and analyzed. Common themes were organized into 2 categories: (1) internal (ie, factors affecting collaboration from within VAMCs or by VA policy) and (2) external (ie, interagency or interpersonal factors). Respondents reported a range of facilitators and barriers to collaboration with community-based agencies. Internal factors facilitating collaboration included items such as leadership support. An internal barrier example included lack of clarity surrounding the VAMC's role in community disaster response. External factors noted as facilitators included a shared goal across organizations while a noted barrier was a perception that potential partners viewed a VAMC partnership with skepticism. Federal institutions are important partners for the success of community disaster preparedness and response. Understanding the barriers that VAMCs confront, as well as potential facilitators to collaboration, should enhance the development of VAMC-community partnerships and improve community health resilience. (Disaster Med Public Health Preparedness. 2017; page 1 of 6).

Use of 13Cα Chemical-Shifts in Protein Structure Determination

PubMed Central

Vila, Jorge A.; Ripoll, Daniel R.; Scheraga, Harold A.

2008-01-01

A physics-based method, aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts, is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid all-α-helical protein, namely the B. Subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank. PMID:17516673

Facilitative Components of Collaborative Learning: A Review of Nine Health Research Networks.

PubMed

Leroy, Lisa; Rittner, Jessica Levin; Johnson, Karin E; Gerteis, Jessie; Miller, Therese

2017-02-01

Collaborative research networks are increasingly used as an effective mechanism for accelerating knowledge transfer into policy and practice. This paper explored the characteristics and collaborative learning approaches of nine health research networks. Semi-structured interviews with representatives from eight diverse US health services research networks conducted between November 2012 and January 2013 and program evaluation data from a ninth. The qualitative analysis assessed each network's purpose, duration, funding sources, governance structure, methods used to foster collaboration, and barriers and facilitators to collaborative learning. The authors reviewed detailed notes from the interviews to distill salient themes. Face-to-face meetings, intentional facilitation and communication, shared vision, trust among members and willingness to work together were key facilitators of collaborative learning. Competing priorities for members, limited funding and lack of long-term support and geographic dispersion were the main barriers to coordination and collaboration across research network members. The findings illustrate the importance of collaborative learning in research networks and the challenges to evaluating the success of research network functionality. Conducting readiness assessments and developing process and outcome evaluation metrics will advance the design and show the impact of collaborative research networks. Copyright © 2017 Longwoods Publishing.

Formulation design facilitates magnetic nanoparticle delivery to diseased cells and tissues

PubMed Central

Singh, Dhirender; McMillan, JoEllyn M; Liu, Xin-Ming; Vishwasrao, Hemant M; Kabanov, Alexander V; Sokolsky-Papkov, Marina; Gendelman, Howard E

2015-01-01

Magnetic nanoparticles (MNPs) accumulate at disease sites with the aid of magnetic fields; biodegradable MNPs can be designed to facilitate drug delivery, influence disease diagnostics, facilitate tissue regeneration and permit protein purification. Because of their limited toxicity, MNPs are widely used in theranostics, simultaneously facilitating diagnostics and therapeutics. To realize therapeutic end points, iron oxide nanoparticle cores (5–30 nm) are encapsulated in a biocompatible polymer shell with drug cargos. Although limited, the toxic potential of MNPs parallels magnetite composition, along with shape, size and surface chemistry. Clearance is hastened by the reticuloendothelial system. To surmount translational barriers, the crystal structure, particle surface and magnetic properties of MNPs need to be optimized. With this in mind, we provide a comprehensive evaluation of advancements in MNP synthesis, functionalization and design, with an eye towards bench-to-bedside translation. PMID:24646020

High-definition transcranial direct-current stimulation of the right M1 further facilitates left M1 excitability during crossed facilitation.

PubMed

Cabibel, Vincent; Muthalib, Makii; Teo, Wei-Peng; Perrey, Stephane

2018-04-01

The crossed-facilitation (CF) effect refers to when motor-evoked potentials (MEPs) evoked in the relaxed muscles of one arm are facilitated by contraction of the opposite arm. The aim of this study was to determine whether high-definition transcranial direct-current stimulation (HD-tDCS) applied to the right primary motor cortex (M1) controlling the left contracting arm [50% maximum voluntary isometric contraction (MVIC)] would further facilitate CF toward the relaxed right arm. Seventeen healthy right-handed subjects participated in an anodal and cathodal or sham HD-tDCS session of the right M1 (2 mA for 20 min) separated by at least 48 h. Single-pulse transcranial magnetic stimulation (TMS) was used to elicit MEPs and cortical silent periods (CSPs) from the left M1 at baseline and 10 min into and after right M1 HD-tDCS. At baseline, compared with resting, CF (i.e., right arm resting, left arm 50% MVIC) increased left M1 MEP amplitudes (+97%) and decreased CSPs (-11%). The main novel finding was that right M1 HD-tDCS further increased left M1 excitability (+28.3%) and inhibition (+21%) from baseline levels during CF of the left M1, with no difference between anodal and cathodal HD-tDCS sessions. No modulation of CSP or MEP was observed during sham HD-tDCS sessions. Our findings suggest that CF of the left M1 combined with right M1 anodal or cathodal HD-tDCS further facilitated interhemispheric interactions during CF from the right M1 (contracting left arm) toward the left M1 (relaxed right arm), with effects on both excitatory and inhibitory processing. NEW & NOTEWORTHY This study shows modulation of the nonstimulated left M1 by right M1 HD-tDCS combined with crossed facilitation, which was probably achieved through modulation of interhemispheric interactions.

Determination of conformation and orientation of immobilized peptides and proteins at buried interfaces

NASA Astrophysics Data System (ADS)

Shen, Lei; Ulrich, Nathan W.; Mello, Charlene M.; Chen, Zhan

2015-01-01

Surface immobilized peptides/proteins have important applications such as antimicrobial coating and biosensing. We report a study of such peptides/proteins using sum frequency generation vibrational spectroscopy and ATR-FTIR. Immobilization on surfaces via physical adsorption and chemical coupling revealed that structures of chemically immobilized peptides are determined by immobilization sites, chemical environments, and substrate surfaces. In addition, controlling enzyme orientation by engineering the surface immobilization site demonstrated that structures can be well-correlated to measured chemical activity. This research facilitates the development of immobilized peptides/proteins with improved activities by optimizing their surface orientation and structure.

Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches†.

PubMed

Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

2017-03-22

To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating

Patellar tendon vibration reduces the increased facilitation from quadriceps to soleus in post-stroke hemiparetic individuals.

PubMed

Maupas, Eric; Dyer, Joseph-Omer; Melo, Sibele de Andrade; Forget, Robert

2017-09-01

Stimulation of the femoral nerve in healthy people can facilitate soleus H-reflex and electromyography (EMG) activity. In stroke patients, such facilitation of transmission in spinal pathways linking the quadriceps and soleus muscles is enhanced and related to co-activation of knee and ankle extensors while sitting and walking. Soleus H-reflex facilitation can be depressed by vibration of the quadriceps in healthy people, but the effects of such vibration have never been studied on the abnormal soleus facilitation observed in people after stroke. To determine whether vibration of the quadriceps can modify the enhanced heteronymous facilitation of the soleus muscle observed in people with spastic stroke after femoral nerve stimulation and compare post-vibration effects on soleus facilitation in control and stroke individuals. Modulation of voluntary soleus EMG activity induced by femoral nerve stimulation (2×motor threshold) was assessed before, during and after vibration of the patellar tendon in 10 healthy controls and 17 stroke participants. Voluntary soleus EMG activity was facilitated by femoral nerve stimulation in 4/10 (40%) controls and 11/17 (65%) stroke participants. The level of facilitation was greater in the stroke than control group. Vibration significantly reduced early heteronymous facilitation in both groups (50% of pre-vibration values). However, the delay in recovery of soleus facilitation after vibration was shorter for the stroke than control group. The control condition with the vibrator turned off had no effect on the modulation. Patellar tendon vibration can reduce the facilitation between knee and ankle extensors, which suggests effective presynaptic inhibition but decreased post-activation depression in the lower limb of people after chronic hemiparetic stroke. Further studies are warranted to determine whether such vibration could be used to reduce the abnormal extension synergy of knee and ankle extensors in people after hemiparetic

Decision Facilitator for Launch Operations using Intelligent Agents

NASA Technical Reports Server (NTRS)

Thirumalainambi, Rajkumar; Bardina, Jorge

2005-01-01

Launch operations require millions of micro-decisions which contribute to the macro decision of 'Go/No-Go' for a launch. Knowledge workers"(such as managers and technical professionals) need information in a timely precise manner as it can greatly affect mission success. The intelligent agent (web search agent) uses the words of a hypertext markup language document which is connected through the internet. The intelligent agent's actions are to determine if its goal of seeking a website containing a specified target (e.g., keyword or phrase), has been met. There are few parameters that should be defined for the keyword search like "Go" and "No-Go". Instead of visiting launch and range decision making servers individually, the decision facilitator constantly connects to all servers, accumulating decisions so the final decision can be decided in a timely manner. The facilitator agent uses the singleton design pattern, which ensures that only a single instance of the facilitator agent exists at one time. Negotiations could proceed between many agents resulting in a final decision. This paper describes details of intelligent agents and their interaction to derive an unified decision support system.

Characterization of Glycan Structures of Chondroitin Sulfate-Glycopeptides Facilitated by Sodium Ion-Pairing and Positive Mode LC-MS/MS

NASA Astrophysics Data System (ADS)

Nilsson, Jonas; Noborn, Fredrik; Gomez Toledo, Alejandro; Nasir, Waqas; Sihlbom, Carina; Larson, Göran

2017-02-01

Purification and liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of glycopeptides, originating from protease digests of glycoproteins, enables site-specific analysis of protein N- and O-glycosylations. We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive mode LC-MS/MS. The CS-glycopeptides, originating from the Bikunin proteoglycan of human urine samples, had ΔHexAGalNAcGlcAGalGalXyl- O-Ser hexasaccharide structure and were further substituted with 0-3 sulfate and 0-1 phosphate groups. However, it was not possible to exactly pinpoint sulfate attachment residues, for protonated precursors, due to extensive fragmentation of sulfate groups using high-energy collision induced dissociation (HCD). To circumvent the well-recognized sulfate instability, we now introduced Na+ ions to form sodiated precursors, which protected sulfate groups from decomposition and facilitated the assignment of sulfate modifications. Sulfate groups were pinpointed to both Gal residues and to the GalNAc of the hexasaccharide structure. The intensities of protonated and sodiated saccharide oxonium ions were very prominent in the HCD-MS2 spectra, which provided complementary structural analysis of sulfate substituents of CS-glycopeptides. We have demonstrated a considerable heterogeneity of the bikunin CS linkage region. The realization of these structural variants should be beneficial in studies aimed at investigating the importance of the CS linkage region with regards to the biosynthesis of CS and potential interactions to CS binding proteins. Also, the combined use of protonated and sodiated precursors for positive mode HCD fragmentation analysis will likely become useful for additional classes of sulfated glycopeptides.

Structural and conformational determinants of macrocycle cell permeability.

PubMed

Over, Björn; Matsson, Pär; Tyrchan, Christian; Artursson, Per; Doak, Bradley C; Foley, Michael A; Hilgendorf, Constanze; Johnston, Stephen E; Lee, Maurice D; Lewis, Richard J; McCarren, Patrick; Muncipinto, Giovanni; Norinder, Ulf; Perry, Matthew W D; Duvall, Jeremy R; Kihlberg, Jan

2016-12-01

Macrocycles are of increasing interest as chemical probes and drugs for intractable targets like protein-protein interactions, but the determinants of their cell permeability and oral absorption are poorly understood. To enable rational design of cell-permeable macrocycles, we generated an extensive data set under consistent experimental conditions for more than 200 non-peptidic, de novo-designed macrocycles from the Broad Institute's diversity-oriented screening collection. This revealed how specific functional groups, substituents and molecular properties impact cell permeability. Analysis of energy-minimized structures for stereo- and regioisomeric sets provided fundamental insight into how dynamic, intramolecular interactions in the 3D conformations of macrocycles may be linked to physicochemical properties and permeability. Combined use of quantitative structure-permeability modeling and the procedure for conformational analysis now, for the first time, provides chemists with a rational approach to design cell-permeable non-peptidic macrocycles with potential for oral absorption.

Modeling, estimation and identification methods for static shape determination of flexible structures. [for large space structure design

NASA Technical Reports Server (NTRS)

Rodriguez, G.; Scheid, R. E., Jr.

1986-01-01

This paper outlines methods for modeling, identification and estimation for static determination of flexible structures. The shape estimation schemes are based on structural models specified by (possibly interconnected) elliptic partial differential equations. The identification techniques provide approximate knowledge of parameters in elliptic systems. The techniques are based on the method of maximum-likelihood that finds parameter values such that the likelihood functional associated with the system model is maximized. The estimation methods are obtained by means of a function-space approach that seeks to obtain the conditional mean of the state given the data and a white noise characterization of model errors. The solutions are obtained in a batch-processing mode in which all the data is processed simultaneously. After methods for computing the optimal estimates are developed, an analysis of the second-order statistics of the estimates and of the related estimation error is conducted. In addition to outlining the above theoretical results, the paper presents typical flexible structure simulations illustrating performance of the shape determination methods.

Use of a structured template to facilitate practice-based learning and improvement projects.

PubMed

McClain, Elizabeth K; Babbott, Stewart F; Tsue, Terance T; Girod, Douglas A; Clements, Debora; Gilmer, Lisa; Persons, Diane; Unruh, Greg

2012-06-01

The Accreditation Council for Graduate Medical Education (ACGME) requires residency programs to meet and demonstrate outcomes across 6 competencies. Measuring residents' competency in practice-based learning and improvement (PBLI) is particularly challenging. We developed an educational tool to meet ACGME requirements for PBLI. The PBLI template helped programs document quality improvement (QI) projects and supported increased scholarly activity surrounding PBLI learning. We reviewed program requirements for 43 residency and fellowship programs and identified specific PBLI requirements for QI activities. We also examined ACGME Program Information Form responses on PBLI core competency questions surrounding QI projects for program sites visited in 2008-2009. Data were integrated by a multidisciplinary committee to develop a peer-protected PBLI template guiding programs through process, documentation, and evaluation of QI projects. All steps were reviewed and approved through our GME Committee structure. An electronic template, companion checklist, and evaluation form were developed using identified project characteristics to guide programs through the PBLI process and facilitate documentation and evaluation of the process. During a 24 month period, 27 programs have completed PBLI projects, and 15 have reviewed the template with their education committees, but have not initiated projects using the template. The development of the tool generated program leaders' support because the tool enhanced the ability to meet program-specific objectives. The peer-protected status of this document for confidentiality and from discovery has been beneficial for program usage. The document aggregates data on PBLI and QI initiatives, offers opportunities to increase scholarship in QI, and meets the ACGME goal of linking measures to outcomes important to meeting accreditation requirements at the program and institutional level.

Use of a Structured Template to Facilitate Practice-Based Learning and Improvement Projects

PubMed Central

McClain, Elizabeth K.; Babbott, Stewart F.; Tsue, Terance T.; Girod, Douglas A.; Clements, Debora; Gilmer, Lisa; Persons, Diane; Unruh, Greg

2012-01-01

Background The Accreditation Council for Graduate Medical Education (ACGME) requires residency programs to meet and demonstrate outcomes across 6 competencies. Measuring residents' competency in practice-based learning and improvement (PBLI) is particularly challenging. Purpose We developed an educational tool to meet ACGME requirements for PBLI. The PBLI template helped programs document quality improvement (QI) projects and supported increased scholarly activity surrounding PBLI learning. Methods We reviewed program requirements for 43 residency and fellowship programs and identified specific PBLI requirements for QI activities. We also examined ACGME Program Information Form responses on PBLI core competency questions surrounding QI projects for program sites visited in 2008–2009. Data were integrated by a multidisciplinary committee to develop a peer-protected PBLI template guiding programs through process, documentation, and evaluation of QI projects. All steps were reviewed and approved through our GME Committee structure. Results An electronic template, companion checklist, and evaluation form were developed using identified project characteristics to guide programs through the PBLI process and facilitate documentation and evaluation of the process. During a 24 month period, 27 programs have completed PBLI projects, and 15 have reviewed the template with their education committees, but have not initiated projects using the template. Discussion The development of the tool generated program leaders' support because the tool enhanced the ability to meet program-specific objectives. The peer-protected status of this document for confidentiality and from discovery has been beneficial for program usage. The document aggregates data on PBLI and QI initiatives, offers opportunities to increase scholarship in QI, and meets the ACGME goal of linking measures to outcomes important to meeting accreditation requirements at the program and institutional level. PMID

Proton assisted recoupling and protein structure determination

NASA Astrophysics Data System (ADS)

de Paëpe, Gaël; Lewandowski, Józef R.; Loquet, Antoine; Böckmann, Anja; Griffin, Robert G.

2008-12-01

We introduce a homonuclear version of third spin assisted recoupling, a second-order mechanism that can be used for polarization transfer between 13C or 15N spins in magic angle spinning (MAS) NMR experiments, particularly at high spinning frequencies employed in contemporary high field MAS experiments. The resulting sequence, which we refer to as proton assisted recoupling (PAR), relies on a cross-term between 1H-13C (or 1H-15N) couplings to mediate zero quantum 13C-13C (or 15N-15N recoupling). In particular, using average Hamiltonian theory we derive an effective Hamiltonian for PAR and show that the transfer is mediated by trilinear terms of the form C1+/-C2-/+HZ for 13C-13C recoupling experiments (or N1+/-N2-/+HZ for 15N-15N). We use analytical and numerical simulations to explain the structure of the PAR optimization maps and to delineate the PAR matching conditions. We also detail the PAR polarization transfer dependence with respect to the local molecular geometry and explain the observed reduction in dipolar truncation. Finally, we demonstrate the utility of PAR in structural studies of proteins with 13C-13C spectra of uniformly 13C, 15N labeled microcrystalline Crh, a 85 amino acid model protein that forms a domain swapped dimer (MW=2×10.4 kDa). The spectra, which were acquired at high MAS frequencies (ωr2π>20 kHz) and magnetic fields (750-900 MHz 1H frequencies) using moderate rf fields, exhibit numerous cross peaks corresponding to long (up to 6-7 A˚) 13C-13C distances which are particularly useful in protein structure determination. Using results from PAR spectra we calculate the structure of the Crh protein.

Self-determination and empowerment: a feminist standpoint analysis of talk about disability.

PubMed

Sprague, J; Hayes, J

2000-10-01

In this paper we offer a feminist analysis of talk about self-determination and empowerment in the context of disability, focusing on the case of developmental disabilities. We find strains of the same patterns feminist epistemologists have argued shape the organization of formal knowledge from the standpoint of the privileged. At the extreme, people with developmental disabilities appear as objects without selves, outside of the context of interpersonal and social structural relationships that constrain who they can be by defining them as other, often in multiple and interacting ways. Empowerment, from the dominant standpoint, becomes an abstract attribute or condition; something a person has or does not have. Taking the standpoint of women and other marginalized people offers a view of self-determination as a person's development of his or her self. Empowerment becomes a potential characteristic of a social relationship, one that facilitates the development of someone's self. The most empowering relationships are mutual, recognizing and building on the diverse contributions and needs of participants in ways that seek to minimize inequalities over time. The reason some of us are self-determining is that we are in interpersonal and social structural relationships that empower us. To construct interpersonal and social structural relationships that empower people with developmental disabilities requires challenging the way dominant conceptualizations of independence and productivity also express the standpoint of the privileged. The standpoint of women allows all of us to talk more of how we connect with and facilitate one another's developing selves within communities.

Homeless youth: Barriers and facilitators for service referrals.

PubMed

Black, Emma B; Fedyszyn, Izabela E; Mildred, Helen; Perkin, Rhianna; Lough, Richard; Brann, Peter; Ritter, Cheryl

2018-06-01

Young people who are homeless and experiencing mental health issues are reluctant to use relevant services for numerous reasons. Youth are also at risk of disengaging from services at times of referral to additional or alternative services. This study aimed to identify barriers and facilitators for inter-service referrals for homeless youth with mental health issues who have already engaged with a service. Qualitative, semi-structured interviews were conducted with homeless youth (n = 10), homelessness support workers (n = 10), and mental health clinicians (n = 10). Barriers included: resource shortages; programs or services having inflexible entry criteria; complexity of service systems; homeless youth feeling devalued; and a lack of communication between services, for example, abrupt referrals with no follow up. Referral facilitators included: services providers offering friendly and client-centred support; supported referrals; awareness of other services; and collaboration between services. Relationships with service providers and inter-service collaboration appeared essential for successful referrals for homeless youth. These facilitating factors may be undermined by sector separation and siloing, as well as resource shortages in both the homelessness and mental health sectors. Service transitions may be conceptualised as a genuine service outcome for homeless youth, and as a basis for successful future service provision. Copyright © 2018 Elsevier Ltd. All rights reserved.

Developing standards for an integrated approach to workplace facilitation for interprofessional teams in health and social care contexts: a Delphi study.

PubMed

Martin, Anne; Manley, Kim

2018-01-01

Integration of health and social care forms part of health and social care policy in many countries worldwide in response to changing health and social care needs. The World Health Organization's appeal for systems to manage the global epidemiologic transition advocates for provision of care that crosses boundaries between primary, community, hospital, and social care. However, the focus on structural and process changes has not yielded the full benefit of expected advances in care delivery. Facilitating practice in the workplace is a widely recognised cornerstone for developments in the delivery of health and social care as collaborative and inclusive relationships enable frontline staff to develop effective workplace cultures that influence whether transformational change is achieved and maintained. Workplace facilitation embraces a number of different purposes which may not independently lead to better quality of care or improved patient outcomes. Holistic workplace facilitation of learning, development, and improvement supports the integration remit across health and social care systems and avoids duplication of effort and waste of valuable resources. To date, no standards to guide the quality and effectiveness of integrated facilitation have been published. This study aimed to identify key elements constitute standards for an integrated approach to facilitating work-based learning, development, improvement, inquiry, knowledge translation, and innovation in health and social care contexts using a three rounds Delphi survey of facilitation experts from 10 countries. Consensus about priority elements was determined in the final round, following an iteration process that involved modifications to validate content. The findings helped to identify key qualities and skills facilitators need to support interprofessional teams to flourish and optimise performance. Further research could evaluate the impact of skilled integrated facilitation on health and social care

Using the TPACK Framework to Facilitate Decision Making on Instructional Technologies

ERIC Educational Resources Information Center

Sobel, Karen; Grotti, Margaret G.

2013-01-01

Technological pedagogical content knowledge ("TPACK") is a theoretical framework used primarily in the field of education to facilitate the integration of technology into educational endeavors. This framework can be particularly valuable to librarians, who are heavy users of technology, and can provide a structure that can help…

The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii

PubMed Central

Kaushik, Sanket; Singh, Nagendra; Yamini, Shavait; Singh, Avinash; Sinha, Mau; Arora, Ashish; Kaur, Punit; Sharma, Sujata; Singh, Tej P.

2013-01-01

The incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth) is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design. PMID:23844024

The mode of inhibitor binding to peptidyl-tRNA hydrolase: binding studies and structure determination of unbound and bound peptidyl-tRNA hydrolase from Acinetobacter baumannii.

PubMed

Kaushik, Sanket; Singh, Nagendra; Yamini, Shavait; Singh, Avinash; Sinha, Mau; Arora, Ashish; Kaur, Punit; Sharma, Sujata; Singh, Tej P

2013-01-01

The incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth) is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design.

Purification and identification of corn peptides that facilitate alcohol metabolism by semi-preparative high-performance liquid chromatography and nano liquid chromatography with electrospray ionization tandem mass spectrometry.

PubMed

Ma, Zhi-Li; Hou, Tao; Shi, Wen; Liu, Wei-Wei; Ibrahim, Salam A; He, Hui

2016-11-01

In this study, peptides that facilitate alcohol metabolism were purified and identified from corn protein hydrolysates. The ultra-filtered fraction with a molecular weight < 3 kDa (F3) potential activity was separated into six fractions (F3-H1-F3-H6) by semi-preparative high-performance liquid chromatography. Among the resultant six fractions, F3-H4 and F3-H5 exhibited the highest ability to eliminate alcohol in vivo. A total of 16 peptides with strong signal values were identified from F3-H4 and F3-H5 fractions by nano liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Several identified peptides were then selected and synthesized to determine their potential to facilitate alcohol metabolism. We found that Leu-Leu and Pro-Phe were the key structure units in Gln-Leu-Leu-Pro-Phe responsible for this peptide's ability to facilitate alcohol metabolism. However, the role of Leu-Leu and Pro-Phe may be affected by peptide chain length and hydrophobic properties. Our results have thus provided some insight into the study of the structure-activity relationships of corn peptides. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Contextual Facilitators and Maintaining of Compassion-Based Care: An Ethnographic Study.

PubMed

Babaei, Sima; Taleghani, Fariba; Keyvanara, Mahmoud

2017-01-01

Compassion is an important part of nursing. It fosters better relationships between nurses and their patients. Moreover, it gives patients more confidence in the care they receive. Determining facilitators of compassion are essential to holistic care. The purpose of this study was to explore these facilitators. This ethnographic study was conducted in 2014-2015 with 20 nurses, 12 patients, and 4 family members in the medical and surgical wards. Data collection was done through observations and in-depth semi-structured interviews with purposive sampling. The study was carried out in 15 months. Data analysis was performed using constant comparison based on Strauss and Corbin. Data analysis defined three main themes and eight subthemes as the fundamentals of compassion-based care. Nurses' personal factors with subcategories of personality, attitudes, and values and holistic view; and socio-cultural factors with subcategories of kindness role model, religious, and cultural values are needed to elicit compassionate behaviors. Initiator factors, with subcategories of patient suffering, patient communication demands, and patient emotional and psychological necessity are also needed to start compassionate behaviors. The findings of this study showed that nurses' communication with patients is nurse's duty in order to understand and respect the needs of patients. Attention should be paid to issues relating to compassion in nursing and practice educational programs. Indeed, creating a care environment with compassion, regardless of any shortcomings in the work condition, would help in the development of effective nursing.

26 CFR 1.7872-16 - Loans to an exchange facilitator under § 1.468B-6.

Code of Federal Regulations, 2010 CFR

2010-04-01

... TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES General Actuarial Valuations § 1.7872-16 Loans to... of approximate method permitted. The taxpayer and exchange facilitator may use the approximate method to determine the amount of forgone interest on any exchange facilitator loan. (f) Exemption for...

Through the eyes of the student: Best practices in clinical facilitation.

PubMed

Muthathi, Immaculate S; Thurling, Catherine H; Armstrong, Susan J

2017-08-28

Clinical facilitation is an essential part of the undergraduate nursing curriculum. A number of studies address the issue of clinical facilitation in South Africa, but there remains a lack of knowledge and understanding regarding what students perceive as best practice in clinical facilitation of their learning. To determine what type of clinical facilitation undergraduate students believe should be offered by clinical facilitators (nurse educators, professional nurses and clinical preceptors) in the clinical area in order to best facilitate their learning. A qualitative, exploratory and descriptive study was conducted. Purposive sampling was performed to select nursing students from the second, third and fourth year of studies from a selected nursing education institution in Johannesburg. The sampling resulted in one focus group for each level of nursing, namely second, third and fourth year nursing students. Interviews were digitally recorded and transcribed verbatim, thematic data analysis was used and trustworthiness was ensured by applying credibility, dependability, confirmability and transferability. The data revealed that participants differentiated between best practices in clinical facilitation in the clinical skills laboratory and clinical learning environment. In the clinical skills laboratory, pre-contact preparation, demonstration technique and optimising group learning were identified as best practices. In the clinical learning environment, a need for standardisation of procedures in simulation and practice, the allocation and support for students also emerged. There is a need for all nurses involved in undergraduate nursing education to reflect on how they approach clinical facilitation, in both clinical skills laboratory and clinical learning environment. There is also a need to improve consistency in clinical practices between the nursing education institution and the clinical learning environment so as to support students' adaptation to clinical

Continuing Education Preferences, Facilitators, and Barriers for Nursing Home Nurses.

PubMed

Dyck, Mary J; Kim, Myoung Jin

2018-01-01

The purpose of the study was to determine the continuing education needs for nursing home nurses in rural central Illinois and to determine any potential facilitators or barriers to obtaining continuing education. Data were collected using the Educational Needs Assessment questionnaire. Descriptive statistics were computed to examine continuing education preferences, facilitators, and barriers among nursing home nurses. Independent samples t tests were used to compare preferences between administrative and staff nurses. The sample included 317 nurses from 34 facilities. The five top needs were related to clinical problems. Administrative nurses had greater needs for professional issues, managerial skills, and quality improvement than staff nurses. Barriers included rural settings, need for vacation time for programs, and inadequate staffing. Continuing education needs of nursing home nurses in Illinois are similar to previous studies conducted in Arizona and North Carolina. Continuing education barriers were mostly organizational, rather than personal. J Contin Nurs Educ. 2018;49(1):26-33. Copyright 2018, SLACK Incorporated.

Barriers and facilitators among health professionals in primary care to prevention of cardiometabolic diseases: A systematic review.

PubMed

Wändell, Per E; de Waard, Anne-Karien M; Holzmann, Martin J; Gornitzki, Carl; Lionis, Christos; de Wit, Niek; Søndergaard, Jens; Sønderlund, Anders L; Kral, Norbert; Seifert, Bohumil; Korevaar, Joke C; Schellevis, François G; Carlsson, Axel C

2018-01-29

The aim of this study is to identify potential facilitators and barriers for health care professionals to undertake selective prevention of cardiometabolic diseases (CMD) in primary health care. We developed a search string for Medline, Embase, Cinahl and PubMed. We also screened reference lists of relevant articles to retain barriers and facilitators for prevention of CMD. We found 19 qualitative studies, 7 quantitative studies and 2 mixed qualitative and quantitative studies. In terms of five overarching categories, the most frequently reported barriers and facilitators were as follows: Structural (barriers: time restraints, ineffective counselling and interventions, insufficient reimbursement and problems with guidelines; facilitators: feasible and effective counselling and interventions, sufficient assistance and support, adequate referral, and identification of obstacles), Organizational (barriers: general organizational problems, role of practice, insufficient IT support, communication problems within health teams and lack of support services, role of staff, lack of suitable appointment times; facilitators: structured practice, IT support, flexibility of counselling, sufficient logistic/practical support and cooperation with allied health staff/community resources, responsibility to offer and importance of prevention), Professional (barriers: insufficient counselling skills, lack of knowledge and of experience; facilitators: sufficient training, effective in motivating patients), Patient-related factors (barriers: low adherence, causes problems for patients; facilitators: strong GP-patient relationship, appreciation from patients), and Attitudinal (barriers: negative attitudes to prevention; facilitators: positive attitudes of importance of prevention). We identified several frequently reported barriers and facilitators for prevention of CMD, which may be used in designing future implementation and intervention studies. © The Author(s) 2018. Published by

Developing facilitation skills--a narrative.

PubMed

Newton, Jennifer M

2003-07-01

Effective facilitation has been identified in the literature as one of three elements, along with context and evidence, that have a dynamic and coexisting relationship to enable the successful uptake of evidence into practice. This paper presents an overview of the concept of facilitation within the context of practice development, ahead of a personal and professional reflective account of a 'developing facilitator'. In the summer of 2001, the author was instrumental in organising the first Practice Development School in Melbourne. Thrown in at the deep end, she found herself co-facilitating with an experienced practice developer from the United Kingdom. Having never facilitated in the arena of an action learning group, nor worked in the field of practice development, there was initially a sense of impending overload and drowning in the new knowledge and skills that needed to be acquired. Drawing upon the work of narrative inquiry the author shares her experiences in the anticipation that in telling her story it will assist others in their journey of becoming a facilitator.

Determination of the complete structure of natural lecithins.

PubMed

Kuksis, A; Marai, L

1967-05-01

A method is described for the separation, identification, and quantitative estimation of the individual molecular species occurring in natural lecithin mixtures. Purified lecithin preparations are converted into diglyceride acetates by enzymic dephosphorylation and acetylation. The diglyceride acetates are separated on the basis of the degree of unsaturation and the molecular geometry by means of chromatography on thin layers of silica gel which are impregnated with silver nitrate. The various acetates thus resolved are separately recovered from the plates and diluted with tridecanoin internal standard; the quantitative distribution of the molecular weights is determined by gas chromatography.Suitable aliquots of the saturated and unsaturated diglyceride acetates are further analyzed for over-all and for positional distribution of fatty acids. The identity and proportions of the various lecithins are deduced by integration and normalization of all the experimental data. Where doubt exists, specific diglyceride acetates are isolated by preparative gas chromatography, and their fatty acid composition is determined. The method is illustrated with data obtained for the mixed lecithins of egg yolk. The general approach is applicable to the determination of the structure of other phospholipids of comparable complexity.

Genetic diversity and population structure of South African smallholder farmer sheep breeds determined using the OvineSNP50 beadchip.

PubMed

Molotsi, Annelin H; Taylor, Jeremy F; Cloete, Schalk W P; Muchadeyi, Farai; Decker, Jared E; Whitacre, Lynsey K; Sandenbergh, Lise; Dzama, Kennedy

2017-12-01

A population structure study was performed in South African ovine populations using the OvineSNP50 beadchip. Blood samples were obtained from 295 sheep of which 172 had been identified as smallholder Dorpers, 4 smallholder White Dorpers, 46 purebred Dorpers, 26 purebred South African Mutton Merinos and 47 purebred Namaqua Afrikaners. Blood from the latter three breeds were obtained from a resource flock maintained on the Nortier research farm. Genetic diversity was estimated using allelic richness (A r ), observed heterozygosity (H o ), expected heterozygosity (H e ) and inbreeding coefficient (F). Population structure analysis was performed using fastSTRUCTURE to determine the breed composition of each genotyped individual. The Namaqua Afrikaner had the lowest H e of 0.280 ± 0.18 while the H e of smallholder Dorper, Dorper and South African Mutton Merino did not differ and were 0.364 ± 0.13, 0.332 ± 0.16 and 0.329 ± 0.17, respectively. The average inbreeding coefficient was highest for the pure breeds, Namaqua Afrikaner, Dorper and South African Mutton Merino compared to the average inbreeding coefficient for the smallholder Dorper population. The smallholder Dorper were introgressed with Namaqua Afrikaner, South African Mutton Merino and White Dorpers. Similarly, the smallholder Dorper population was more genetically diverse than the purebred Dorper, South African Mutton Merino and Namaqua Afrikaner from the research farm. The higher genetic diversity among the smallholder sheep may be advantageous for their fitness and can be used to facilitate selective breeding.

Get it together: Issues that facilitate collaboration in teams of learners in intensive care.

PubMed

Conte, Helen; Jirwe, Maria; Scheja, Max; Hjelmqvist, Hans

2016-05-01

The study describes issues that facilitate collaboration in teams of learners in an interprofessional education unit in intensive care. A descriptive qualitative study design was applied using semi-structured interviews based on the critical incident technique and qualitative content analysis. Nineteen participants, eight learners in their specialist training, nine supervisors and two head supervisors in Sweden identified 47 incidents. Teams of learners having control was the core issue. Motivation, time, experiences and reflection were central issues for facilitating collaboration. Efficiently training teams how to collaborate requires learners having control while acting on their common understanding and supervisors taking a facilitating role supporting teams to take control of their critical analysis.

Third Structure Determination by Powder Diffractometery Round Robin (SDPDRR-3)

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

Le Bail, A.; Cranswick, L; Adil, K

2009-01-01

The results from a third structure determination by powder diffractometry (SDPD) round robin are discussed. From the 175 potential participants having downloaded the powder data, nine sent a total of 12 solutions (8 and 4 for samples 1 and 2, respectively, a tetrahydrated calcium tartrate and a lanthanum tungstate). Participants used seven different computer programs for structure solution (ESPOIR, EXPO, FOX, PSSP, SHELXS, SUPERFLIP, and TOPAS), applying Patterson, direct methods, direct space methods, and charge flipping approach. It is concluded that solving a structure from powder data remains a challenge, at least one order of magnitude more difficult than solvingmore » a problem with similar complexity from single-crystal data. Nevertheless, a few more steps in the direction of increasing the SDPD rate of success were accomplished since the two previous round robins: this time, not only the computer program developers were successful but also some users. No result was obtained from crystal structure prediction experts.« less

Medical students' and facilitators' experiences of an Early Professional Contact course: active and motivated students, strained facilitators.

PubMed

von Below, Bernhard; Hellquist, Gunilla; Rödjer, Stig; Gunnarsson, Ronny; Björkelund, Cecilia; Wahlqvist, Mats

2008-12-02

Today, medical students are introduced to patient contact, communication skills, and clinical examination in the preclinical years of the curriculum with the purpose of gaining clinical experience. These courses are often evaluated from the student perspective. Reports with an additional emphasis on the facilitator perspective are scarce. According to constructive alignment, an influential concept from research in higher education, the learning climate between students and teachers is also of great importance. In this paper, we approach the learning climate by studying both students' and facilitators' course experiences.In 2001, a new "Early Professional Contact" longitudinal strand through term 1-4, was introduced at the Sahlgrenska Academy, University of Gothenburg, Sweden. General practitioners and hospital specialists were facilitators.The aim of this study was to assess and analyse students' and clinical facilitators' experiences of the Early Professional Contact course and to illuminate facilitators' working conditions. Inspired by a Swedish adaptation of the Course Experience Questionnaire, an Early Professional Contact Questionnaire was constructed. In 2003, on the completion of the first longitudinal strand, a student and facilitator version was distributed to 86 students and 21 facilitators. In the analysis, both Chi-square and the Mann-Whitney tests were used. Sixty students (70%) and 15 facilitators (71%) completed the questionnaire. Both students and facilitators were satisfied with the course. Students reported gaining iiration for their future work as doctors along with increased confidence in meeting patients. They also reported increased motivation for biomedical studies. Differences in attitudes between facilitators and students were found. Facilitators experienced a greater workload, less reasonable demands and less support, than students. In this project, a new Early Professional Contact course was analysed from both student and facilitator

A Constructivist Model of Mentoring, Coaching, and Facilitating Online Discussions

ERIC Educational Resources Information Center

Murphy, Karen L.; Mahoney, Sue E.; Chen, Chun-Ying; Mendoza-Diaz, Noemi V.; Yang, Xiaobing

2005-01-01

This case study of an online graduate course determines the message characteristics of the instructor, volunteer teaching assistants, and students in online discussions, and proposes a mentoring, coaching, and facilitating model for online discussions. The researchers developed a coding system based on the literature of mentoring, coaching, and…

Determination of the structural phase and octahedral rotation angle in halide perovskites

NASA Astrophysics Data System (ADS)

dos Reis, Roberto; Yang, Hao; Ophus, Colin; Ercius, Peter; Bizarri, Gregory; Perrodin, Didier; Shalapska, Tetiana; Bourret, Edith; Ciston, Jim; Dahmen, Ulrich

2018-02-01

A key to the unique combination of electronic and optical properties in halide perovskite materials lies in their rich structural complexity. However, their radiation sensitive nature limits nanoscale structural characterization requiring dose efficient microscopic techniques in order to determine their structures precisely. In this work, we determine the space-group and directly image the Br halide sites of CsPbBr3, a promising material for optoelectronic applications. Based on the symmetry of high-order Laue zone reflections of convergent-beam electron diffraction, we identify the tetragonal (I4/mcm) structural phase of CsPbBr3 at cryogenic temperature. Electron ptychography provides a highly sensitive phase contrast measurement of the halide positions under low electron-dose conditions, enabling imaging of the elongated Br sites originating from the out-of-phase octahedral rotation viewed along the [001] direction of I4/mcm persisting at room temperature. The measurement of these features and comparison with simulations yield an octahedral rotation angle of 6.5°(±1.5°). The approach demonstrated here opens up opportunities for understanding the atomic scale structural phenomena applying advanced characterization tools on a wide range of radiation sensitive halide-based all-inorganic and hybrid organic-inorganic perovskites.

Determination of the structural phase and octahedral rotation angle in halide perovskites

DOE PAGES

dos Reis, Roberto; Yang, Hao; Ophus, Colin; ...

2018-02-12

A key to the unique combination of electronic and optical properties in halide perovskite materials lies in their rich structural complexity. However, their radiation sensitive nature limits nanoscale structural characterization requiring dose efficient microscopic techniques in order to determine their structures precisely. In this work, we determine the space-group and directly image the Br halide sites of CsPbBr 3, a promising material for optoelectronic applications. Based on the symmetry of high-order Laue zone reflections of convergent-beam electron diffraction, we identify the tetragonal (I4/mcm) structural phase of CsPbBr 3 at cryogenic temperature. Electron ptychography provides a highly sensitive phase contrast measurementmore » of the halide positions under low electron-dose conditions, enabling imaging of the elongated Br sites originating from the out-of-phase octahedral rotation viewed along the [001] direction of I4/mcm persisting at room temperature. The measurement of these features and comparison with simulations yield an octahedral rotation angle of 6.5°(±1.5°). Finally, the approach demonstrated here opens up opportunities for understanding the atomic scale structural phenomena applying advanced characterization tools on a wide range of radiation sensitive halide-based all-inorganic and hybrid organic-inorganic perovskites.« less

Determining the Cognitive Structures of Geography Teacher Candidates on "Earthquake"

ERIC Educational Resources Information Center

Kaya, Bastürk; Aladag, Caner

2017-01-01

The objective of this study is to determine the cognitive structures of the students of geography teaching department by identifying their conceptual frameworks about the concept of earthquake. A case study design from qualitative research approaches was used in this research. Sample group of the study constitutes 155 students from the Department…

Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

ERIC Educational Resources Information Center

Mariana, Neni

2010-01-01

Few researches have been concerned about relation between children's spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was…

Facilitation may not be an adequate mechanism of community succession on carrion.

PubMed

Michaud, Jean-Philippe; Moreau, Gaétan

2017-04-01

The facilitation model of ecological succession was advanced by plant ecologists in the late 1970s and was then introduced to carrion ecology in the late 1980s, without empirical evidence of its applicability. Ecologists in both disciplines proposed removing early colonists, in this case fly eggs and larvae, from the substrate to determine whether other species could still colonize, which to our knowledge has never been attempted. Here, we tested the facilitation model in a carrion system by removing fly eggs and larvae from carcasses that were exposed in agricultural fields and assigned to one of the following treatment levels of removal intensity: 0, <5, 50, and 100%. Subsequent patterns of colonisation did not provide support for the applicability of the facilitation model in carrion systems. Although results showed, in part, that the removal of fly eggs and larvae decreased the decomposition rate of carcasses, the removal did not prevent colonization by secondary colonizers. Finally, we discuss future studies and make recommendations as to how the facilitation model could be improved, firstly by being more specific about the scale where facilitation is believed to be occurring, secondly by clearly stating what environmental modification is believed to be involved, and thirdly by disentangling facilitation from priority effects.

Structure and properties of microporous titanosilicate determined by first-principles calculations

NASA Astrophysics Data System (ADS)

Ching, W. Y.; Xu, Yong-Nian; Gu, Zong-Quan

1996-12-01

The structure of EST-10, a member of synthetic microporous titanosilicates, was recently determined by an ingenious combination of experimental and simulational techniques. However, the locations of the alkali atoms in the framework remain elusive and its electronic structure is totally unknown. Based on first-principles local density calculations, the possible locations of the alkali atoms are identified and its electronic structure and bonding fully elucidated. ETS-10 is a semiconductor with a direct band gap of 2.33 eV. The Na atoms are likely to locate inside the seven-member ring pore adjacent to the one-dimensional Ti-O-Ti-O- chain.

The economic, institutional, and political determinants of public health delivery system structures.

PubMed

Ingram, Richard C; Scutchfield, F Douglas; Mays, Glen P; Bhandari, Michelyn W

2012-01-01

A typology of local public health systems was recently introduced, and a large degree of structural transformation over time was discovered in the systems analyzed. We present a qualitative exploration of the factors that determine variation and change in the seven structural configurations that comprise the local public health delivery system typology. We applied a 10-item semistructured telephone interview protocol to representatives from the local health agency in two randomly selected systems from each configuration--one that had maintained configuration over time and one that had changed configuration over time. We assessed the interviews for patterns of variation between the configurations. Four key determinants of structural change emerged: availability of financial resources, interorganizational relationships, public health agency organization, and political relationships. Systems that had changed were more likely to experience strengthened partnerships between public health agencies and other community organizations and enjoy support from policy makers, while stable systems were more likely to be characterized by strong partnerships between public health agencies and other governmental bodies and less supportive relationships with policy makers. This research provides information regarding the determinants of system change, and may help public health leaders to better prepare for the impacts of change in the areas discussed. It may also help those who are seeking to implement change to determine the contextual factors that need to be in place before change can happen, or how best to implement change in the face of contextual factors that are beyond their control.

Membrane organization determines barrier properties of endothelial cells and short-chain sphingolipid-facilitated doxorubicin influx.

PubMed

van Hell, A J; Klymchenko, A; Gueth, D M; van Blitterswijk, W J; Koning, G A; Verheij, M

2014-09-01

The endothelial lining and its outer lipid membrane are the first major barriers drug molecules encounter upon intravenous administration. Our previous work identified lipid analogs that counteract plasma membrane barrier function for a series of amphiphilic drugs. For example, short-chain sphingolipids (SCS), like N-octanoyl-glucosylceramide, effectively elevated doxorubicin accumulation in tumor cells, both in vitro and in vivo, and in endothelial cells, whereas other (normal) cells remained unaffected. We hypothesize here that local membrane lipid composition and the degree of lipid ordering define SCS efficacy in individual cells. To this end, we study the differential effect of SCS on bovine aortic endothelial cells (BAEC) in its confluent versus proliferative state, as a model system. While their (plasma membrane) lipidome stays remarkably unaltered when BAECs reach confluency, their lipids segregate to form apical and basolateral domains. Using probe NR12S, we reveal that lipids in the apical membrane are more condensed/liquid-ordered. SCS preferentially attenuate the barrier posed by these condensed membranes and facilitate doxorubicin influx in these particular membrane regions. We confirm these findings in MDCK cells and artificial membranes. In conclusion, SCS-facilitated drug traversal acts on condensed membrane domains, elicited by confluency in resting endothelium. Copyright © 2014 Elsevier B.V. All rights reserved.

Structure determination of a key intermediate of the enantioselective Pd complex catalyzed allylic substitution reaction

PubMed

Junker; Reif; Steinhagen; Junker; Felli; Reggelin; Griesinger

2000-09-01

The structure of a catalytic intermediate with important implications for the interpretation of the stereochemical outcome of the palladium complex catalyzed allylic substitution with phosphino-oxazoline (PHOX) ligands is determined by liquid state NMR. The complex displays a novel structure that is highly distorted compared with other palladium eta2-olefin complexes known so far. The structure has been determined from nuclear overhauser data (NOE), scalar coupling constants, and long range projection angle restraints derived from dipole dipole cross-correlated relaxation of multiple quantum coherence. The latter restraints have been implemented into a distance geometry protocol. The projection angle restraints yield a higher precision in the determination of the relative orientation of the two molecular moieties and are essential to provide an exact structural definition of the olefinic part of the catalytic intermediate with respect to the ligand.

NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins.

PubMed

Zook, James; Mo, Gina; Sisco, Nicholas J; Craciunescu, Felicia M; Hansen, Debra T; Baravati, Bobby; Cherry, Brian R; Sykes, Kathryn; Wachter, Rebekka; Van Horn, Wade D; Fromme, Petra

2015-06-02

Tularemia is a potentially fatal bacterial infection caused by Francisella tularensis, and is endemic to North America and many parts of northern Europe and Asia. The outer membrane lipoprotein, Flpp3, has been identified as a virulence determinant as well as a potential subunit template for vaccine development. Here we present the first structure for the soluble domain of Flpp3 from the highly infectious Type A SCHU S4 strain, derived through high-resolution solution nuclear magnetic resonance (NMR) spectroscopy; the first structure of a lipoprotein from the genus Francisella. The Flpp3 structure demonstrates a globular protein with an electrostatically polarized surface containing an internal cavity-a putative binding site based on the structurally homologous Bet v1 protein family of allergens. NMR-based relaxation studies suggest loop regions that potentially modulate access to the internal cavity. The Flpp3 structure may add to the understanding of F. tularensis virulence and contribute to the development of effective vaccines. Copyright © 2015 Elsevier Ltd. All rights reserved.

Facilitative Components of Collaborative Learning: A Review of Nine Health Research Networks

PubMed Central

Rittner, Jessica Levin; Johnson, Karin E.; Gerteis, Jessie; Miller, Therese

2017-01-01

Objective: Collaborative research networks are increasingly used as an effective mechanism for accelerating knowledge transfer into policy and practice. This paper explored the characteristics and collaborative learning approaches of nine health research networks. Data sources/study setting: Semi-structured interviews with representatives from eight diverse US health services research networks conducted between November 2012 and January 2013 and program evaluation data from a ninth. Study design: The qualitative analysis assessed each network's purpose, duration, funding sources, governance structure, methods used to foster collaboration, and barriers and facilitators to collaborative learning. Data collection: The authors reviewed detailed notes from the interviews to distill salient themes. Principal findings: Face-to-face meetings, intentional facilitation and communication, shared vision, trust among members and willingness to work together were key facilitators of collaborative learning. Competing priorities for members, limited funding and lack of long-term support and geographic dispersion were the main barriers to coordination and collaboration across research network members. Conclusion: The findings illustrate the importance of collaborative learning in research networks and the challenges to evaluating the success of research network functionality. Conducting readiness assessments and developing process and outcome evaluation metrics will advance the design and show the impact of collaborative research networks. PMID:28277202

Beech cupules as keystone structures for soil fauna.

PubMed

Melguizo-Ruiz, Nereida; Jiménez-Navarro, Gerardo; Moya-Laraño, Jordi

2016-01-01

Facilitative or positive interactions are ubiquitous in nature and play a fundamental role in the configuration of ecological communities. In particular, habitat modification and niche construction, in which one organism locally modifies abiotic conditions and favours other organisms by buffering the effects of adverse environmental factors, are among the most relevant facilitative interactions. In line with this, 'keystone structures', which provide resources, refuge, or advantageous services decisive for other species, may allow the coexistence of various species and thus considerably contribute to diversity maintenance. Beech cupules are woody husks harbouring beech fruits that remain in the forest soil for relatively long periods of time. In this study, we explored the potential role of these cupules in the distribution and maintenance of the soil fauna inhabiting the leaf litter layer. We experimentally manipulated cupule availability and soil moisture in the field to determine if such structures are limiting and can provide moist shelter to soil animals during drought periods, contributing to minimize desiccation risks. We measured invertebrate abundances inside relative to outside the cupules, total abundances in the leaf litter and animal body sizes, in both dry and wet experimental plots. We found that these structures are preferentially used by the most abundant groups of smaller soil animals-springtails, mites and enchytraeids-during droughts. Moreover, beech cupules can be limiting, as an increase in use was found with higher cupule densities, and are important resources for many small soil invertebrates, driving the spatial structure of the soil community and promoting higher densities in the leaf litter, probably through an increase in habitat heterogeneity. We propose that fruit woody structures should be considered 'keystone structures' that contribute to soil community maintenance. Therefore, beech trees may indirectly facilitate soil fauna

DETERMINANTS OF NETWORK OUTCOMES: THE IMPACT OF MANAGEMENT STRATEGIES.

PubMed

Ysa, Tamyko; Sierra, Vicenta; Esteve, Marc

2014-09-01

The literature on network management is extensive. However, it generally explores network structures, neglecting the impact of management strategies. In this article we assess the effect of management strategies on network outcomes, providing empirical evidence from 119 urban revitalization networks. We go beyond current work by testing a path model for the determinants of network outcomes and considering the interactions between the constructs: management strategies, trust, complexity, and facilitative leadership. Our results suggest that management strategies have a strong effect on network outcomes and that they enhance the level of trust. We also found that facilitative leadership has a positive impact on network management as well as on trust in the network. Our findings also show that complexity has a negative impact on trust. A key finding of our research is that managers may wield more influence on network dynamics than previously theorized.

A qualitative theory guided analysis of stroke survivors' perceived barriers and facilitators to physical activity.

PubMed

Nicholson, Sarah L; Donaghy, Marie; Johnston, Marie; Sniehotta, Falko F; van Wijck, Frederike; Johnston, Derek; Greig, Carolyn; McMurdo, Marion E T; Mead, Gillian

2014-01-01

After stroke, physical activity and physical fitness levels are low, impacting on health, activity and participation. It is unclear how best to support stroke survivors to increase physical activity. Little is known about the barriers and facilitators to physical activity after stroke. Thus, our aim was to explore stroke survivors' perceived barriers and facilitators to physical activity. Semi-structured interviews with 13 ambulatory stroke survivors exploring perceived barriers and facilitators to physical activity post stroke were conducted in participants' homes, audio-recorded and transcribed verbatim. The Theoretical Domains Framework (TDF) informed content analysis of the interview transcripts. Data saturation was reached after interviews with 13 participants (median age of 76 years (inter-quartile range (IQR) = 69-83 years). The median time since stroke was 345 d (IQR = 316-366 d). The most commonly reported TDF domains were "beliefs about capabilities", "environmental context and resources" and "social influence". The most commonly reported perceived motivators were: social interaction, beliefs of benefits of exercise, high self-efficacy and the necessity of routine behaviours. The most commonly reported perceived barriers were: lack of professional support on discharge from hospital and follow-up, transport issues to structured classes/interventions, lack of control and negative affect. Stroke survivors perceive several different barriers and facilitators to physical activity. Stroke services need to address barriers to physical activity and to build on facilitators to promote physical activity after stroke. Physical activity post stroke can improve physical fitness and function, yet physical activity remains low among stroke survivors. Understanding stroke survivors' perceived barriers and facilitators to physical activity is essential to develop targeted interventions to increase physical activity. Beliefs about capabilities, environmental

Midwives' experiences of facilitating normal birth in an obstetric-led unit: a feminist perspective.

PubMed

Keating, Annette; Fleming, Valerie E M

2009-10-01

to explore midwives' experiences of facilitating normal birth in an obstetric-led unit. a feminist approach using semi-structured interviews focusing on midwives' perceptions of normal birth and their ability to facilitate this birth option in an obstetric-led unit. Ireland. a purposeful sample of 10 midwives with 6-30 years of midwifery experience. All participants had worked for a minimum of 6 years in a labour ward setting, and had been in their current setting for the previous 2 years. the midwives' narratives related to the following four concepts of patriarchy: 'hierarchical thinking', 'power and prestige', 'a logic of domination' and 'either/or thinking' (dualisms). Two themes, 'hierarchical thinking' and 'either/or thinking', (dualisms) along with their subthemes are presented in this paper. this study identified some of the reasons why midwives find it difficult to facilitate normal birth in an obstetric unit setting, and identified a need for further research in this area. Midwifery education and supportive management structures are required if midwives are to become confident practitioners of normal birth.

5 CFR 532.263 - Special wage schedules for production facilitating positions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Special wage schedules for production facilitating positions. 532.263 Section 532.263 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PREVAILING RATE SYSTEMS Prevailing Rate Determinations § 532.263 Special wage...

The Phenix Software for Automated Determination of Macromolecular Structures

PubMed Central

Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor; Chen, Vincent B.; Echols, Nathaniel; Headd, Jeffrey J.; Hung, Li-Wei; Jain, Swati; Kapral, Gary J.; Grosse Kunstleve, Ralf W.; McCoy, Airlie J.; Moriarty, Nigel W.; Oeffner, Robert D.; Read, Randy J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Zwart, Peter H.

2011-01-01

X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favour of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. PMID:21821126

Covering complete proteomes with X-ray structures: A current snapshot

DOE PAGES

Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; ...

2014-10-23

Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtainedmore » through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.« less

Structure, function, and engineering of enzymes in isoflavonoid biosynthesis.

PubMed

Wang, Xiaoqiang

2011-03-01

Isoflavonoids are a large group of plant natural products and play important roles in plant defense. They also possess valuable health-promoting activities with significant health benefits for animals and humans. The isoflavonoids are identified primarily in leguminous plants and are synthesized through the central phenylpropanoid pathway and the specific isoflavonoid branch pathways in legumes. Structural studies of some key enzymes in the central phenylpropanoid pathway shed light on the early stages of the (iso)flavonoid biosynthetic process. Significant impact has also been made on structural studies of enzymes in the isoflavonoid branch pathways. Structures of isoflavonoid-specific NADPH-dependent reductases revealed how the (iso)flavonoid backbones are modified by reduction reactions and how enzymes specifically recognize isoflavonoids and catalyze stereo-specific reductions. Structural studies of isoflavonoid methyltransferases and glycosyltransferases revealed how isoflavonoids are further decorated with methyl group and sugars in different methylation and glycosylation patterns that determine their bioactivities and functions. In combination with mutagenesis and biochemical studies, the detailed structural information of these enzymes provides a basis for understanding the complex biosynthetic process, enzyme catalytic mechanisms, and substrate specificities. Structure-based homology modeling facilitates the functional characterization of these large groups of biosynthetic enzymes and their homologs. Structure-based enzyme engineering is becoming a new strategy for synthesis of bioactive isoflavonoids and also facilitates plant metabolic engineering towards improvement of quality and production of crop plants.

Online interprofessional education facilitation: A scoping review.

PubMed

Evans, Sherryn Maree; Ward, Catherine; Reeves, Scott

2018-04-22

The use of online media to deliver interprofessional education (IPE) is becoming more prevalent across health professions education settings. Facilitation of IPE activities is known to be critical to the effective delivery of IPE, however, specifics about the nature of online IPE facilitation remains unclear. To explore the health professions education literature to understand the extent, range and nature of research on online IPE facilitation. Scoping review methodology was used to guide a search of four electronic databases for relevant papers. Of the 2095 abstracts initially identified, after screening of both abstracts and full-text papers, 10 studies were selected for inclusion in this review. Following abstraction of key information from each study, a thematic analysis was undertaken. Three key themes emerged to describe the nature of the IPE facilitation literature: (1) types of online IPE facilitation contributions, (2) the experience of online IPE facilitation and (3) personal outcomes of online IPE facilitation. These IPE facilitation themes were particularly focused on facilitation of interprofessional student teams on an asynchronous basis. While the included studies provide some insight into the nature of online IPE facilitation, future research is needed to better understand facilitator contributions, and the facilitation experience and associated outcomes, both relating to synchronous and asynchronous online environments.

Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate

NASA Astrophysics Data System (ADS)

Khoshouei, Maryam; Radjainia, Mazdak; Baumeister, Wolfgang; Danev, Radostin

2017-06-01

With the advent of direct electron detectors, the perspectives of cryo-electron microscopy (cryo-EM) have changed in a profound way. These cameras are superior to previous detectors in coping with the intrinsically low contrast and beam-induced motion of radiation-sensitive organic materials embedded in amorphous ice, and hence they have enabled the structure determination of many macromolecular assemblies to atomic or near-atomic resolution. Nevertheless, there are still limitations and one of them is the size of the target structure. Here, we report the use of a Volta phase plate in determining the structure of human haemoglobin (64 kDa) at 3.2 Å. Our results demonstrate that this method can be applied to complexes that are significantly smaller than those previously studied by conventional defocus-based approaches. Cryo-EM is now close to becoming a fast and cost-effective alternative to crystallography for high-resolution protein structure determination.

Barriers and facilitators of sports in Dutch Paralympic athletes: An explorative study.

PubMed

Jaarsma, E A; Geertzen, J H B; de Jong, R; Dijkstra, P U; Dekker, R

2014-10-01

The purpose of this study was to gain insight in barriers and facilitators of sports in paralympic athletes. An online questionnaire was distributed through the Netherlands Olympic Committee and National Sports Confederation to determine personal and environmental barriers and facilitators of sports participation. The International Classification of Functioning, Disability and Health model and theory of planned behavior were used to respectively categorize the results in environmental and personal factors, and attitude, subjective norm and perceived behavioral control. Seventy-six Dutch Paralympic athletes completed the questionnaire (51% response rate). Barriers and facilitators experienced by ambulant and wheelchair athletes were compared. Most frequently mentioned personal barrier was dependency of others (22%), while most frequently mentioned environmental barrier was lack of sports facilities (30%). Wheelchair athletes mentioned more barriers (median = 3, interquartile range: 0.5-6), than ambulant athletes (median = 1.0,interquartile range:0.0-3.0, P = 0.023). One-third of the athletes did not experience any barriers. Most frequently mentioned personal facilitators to initiate sports participation were fun (78%), health (61%), and competition (53%). Most frequently mentioned environmental facilitator was social support (40%). This study indicated that barriers of sport were mostly environmental, while facilitators were usually personal factors. Attitude and subjective norm were considered the most important components for intention to participation in sports. The facilitators outweighed the barriers and kept the athletes being active in sports. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

NASA Astrophysics Data System (ADS)

Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

2016-04-01

The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

Three dimensional electron microscopy and in silico tools for macromolecular structure determination

PubMed Central

Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

2013-01-01

Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

The relationship between facilitators' questions and the level of reflection in postsimulation debriefing.

PubMed

Husebø, Sissel Eikeland; Dieckmann, Peter; Rystedt, Hans; Søreide, Eldar; Friberg, Febe

2013-06-01

Simulation-based education is a learner-active method that may enhance teamwork skills such as leadership and communication. The importance of postsimulation debriefing to promote reflection is well accepted, but many questions concerning whether and how faculty promote reflection remain largely unanswered in the research literature. The aim of this study was therefore to explore the depth of reflection expressed in questions by facilitators and responses from nursing students during postsimulation debriefings. Eighty-one nursing students and 4 facilitators participated. The data were collected in February and March 2008, the analysis being conducted on 24 video-recorded debriefings from simulated resuscitation teamwork involving nursing students only. Using Gibbs' reflective cycle, we graded the facilitators' questions and nursing students' responses into stages of reflection and then correlated these. Facilitators asked most evaluative and fewest emotional questions, whereas nursing students answered most evaluative and analytic responses and fewest emotional responses. The greatest difference between facilitators and nursing students was in the analytic stage. Only 23 (20%) of 117 questions asked by the facilitators were analytic, whereas 45 (35%) of 130 students' responses were rated as analytic. Nevertheless, the facilitators' descriptive questions also elicited student responses in other stages such as evaluative and analytic responses. We found that postsimulation debriefings provide students with the opportunity to reflect on their simulation experience. Still, if the debriefing is going to pave the way for student reflection, it is necessary to work further on structuring the debriefing to facilitate deeper reflection. Furthermore, it is important that facilitators consider what kind of questions they ask to promote reflection. We think future research on debriefing should focus on developing an analytical framework for grading reflective questions. Such

COLLOID-FACILITATED TRANSPORT OF RADIONUCLIDES THROUGH THE VADOSE ZONE

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

Flury, Markus

2003-09-14

Contaminants have leaked into the vadose zone at the USDOE Hanford reservation. It is important to understand the fate and transport of these contaminants to design remediation strategies and long-term waste management plans at the Hanford reservation. Colloids may play an important role in fate and transport of strongly sorbing contaminants, such as Cs or Pu. This project seeks to improve the basic understanding of colloid and colloid-facilitated transport of contaminants in the vadose zone. The specific objectives addressed are: (1) Determine the structure, composition, and surface charge characteristics of colloidal particles formed under conditions similar to those occurring duringmore » leakage of waste typical of Hanford tank supernatants into soils and sediments surrounding the tanks. (2) Characterize the mutual interactions between colloids, contaminant, and soil matrix in batch experiments under various ionic strength and pH conditions. We will investigate the nature of the solid-liquid interactions and the kinetics of the reactions. (3) Evaluate mobility of colloids through soil under different degrees of water saturation and solution chemistry (ionic strength and pH). (4) Determine the potential of colloids to act as carriers to transport the contaminant through the vadose zone and verify the results through comparison with field samples collected under leaking tanks. (5) Improve conceptual characterization of colloid-contaminant-soil interactions and colloid-facilitated transport for implementation into reactive chemical transport models. This project was in part supported by an NSF-IGERT grant to Washington State University. The IGERT grant provided funding for graduate student research and education, and two graduate students were involved in the EMSP project. The IGERT program also supported undergraduate internships. The project is part of a larger EMSP program to study fate and transport of contaminants under leaking Hanford waste tanks. The

Self-determination, smoking, diet and health.

PubMed

Williams, Geoffrey C; Minicucci, Daryl S; Kouides, Ruth W; Levesque, Chantal S; Chirkov, Valery I; Ryan, Richard M; Deci, Edward L

2002-10-01

A Clinical Trial will test (1) a Self-Determination Theory (SDT) model of maintained smoking cessation and diet improvement, and (2) an SDT intervention, relative to usual care, for facilitating maintained behavior change and decreasing depressive symptoms for those who quit smoking. SDT is the only empirically derived theory which emphasizes patient autonomy and has a validated measure for each of its constructs, and this is the first trial to evaluate an SDT intervention. Adult smokers will be stratified for whether they are at National Cholesterol Education Program (1996) recommended goal for low-density lipoprotein cholesterol (LDL-C). Those with elevated LDL-C will be studied for diet improvement as well as smoking cessation. Six-month interventions involve a behavior-change counselor using principles of SDT to facilitate autonomous motivation and perceived competence for healthier behaving. Cotinine-validated smoking cessation and LDL-C-validated dietary recall of reduced fat intake, as well as depressive symptoms, will be assessed at 6 and 18 months. Structural equation modeling will test the model for both behaviors within the intervention and usual-care conditions.

Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

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

Abdur, Rob; Gerlits, Oksana O.; Gan, Jianhua

2014-02-01

Selenium-derivatized oligonucleotides may facilitate phase determination and high-resolution structure determination for protein–nucleic acid crystallography. The Se atom-specific mutagenesis (SAM) strategy may also enhance the study of nuclease catalysis. The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissilemore » phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.« less

Strippable grid facilitates removal of grid-surfaced conical workpiece from die

NASA Technical Reports Server (NTRS)

Ruppe, E. P.

1966-01-01

Female die facilitates the removal of a sheet metal structure from a die used for explosive forming of the metal. The female die consists of a smooth conical frustum made of fiber glass with a cured epoxy-resin surface on which a molded grid pattern made of a polyurethane resin is overlaid.

Chinese nurses' perceived barriers and facilitators of ethical sensitivity.

PubMed

Huang, Fei Fei; Yang, Qing; Zhang, Jie; Khoshnood, Kaveh; Zhang, Jing Ping

2016-08-01

An overview of ethical sensitivity among Chinese registered nurses is needed to develop and optimize the education programs and interventions to cultivate and improve ethical sensitivity. The study was conducted to explore the barriers to and facilitators of ethical sensitivity among Chinese registered nurses working in hospital settings. A convergent parallel mixed-methods research design was adopted. In the cross-sectional quantitative study, the Chinese Moral Sensitivity Questionnaire-revised version was used to assess the levels of ethical sensitivity among registered nurses, and the scores were correlated with key demographics, training experiences in ethics, and workplace cultural environments (n = 306). In the qualitative study, semi-structured interviews were used to elicit the nurses' perceptions of the barriers and facilitators in nurturing ethical sensitivity (n = 15). The data were collected from February to June 2014. This study was approved by the Institutional Review Boards of Yale University and Central South University. Despite moderately high overall Chinese Moral Sensitivity Questionnaire-revised version scores, the ethical sensitivity among Chinese nurses lags in practice. Barriers to ethical sensitivity include the lack of knowledge related to ethics, lack of working experience as a nurse, the hierarchical organizational climate, and the conformist working attitude. The positive workplace cultural environments and application of ethical knowledge in practice were considered potential facilitators of ethical sensitivity. The findings of this study were compared with studies from other countries to examine the barriers and facilitators of ethical sensitivity in Chinese nurses. This mixed-methods study showed that even though the Chinese nurses have moderately high sensitivity to the ethical issues encountered in hospitals, there is still room for improvement. The barriers to and facilitators of ethical sensitivity identified here offer new and

Databases of Conformations and NMR Structures of Glycan Determinants.

PubMed

Sarkar, Anita; Drouillard, Sophie; Rivet, Alain; Perez, Serge

2015-12-01

The present study reports a comprehensive nuclear magnetic resonance (NMR) characterization and a systematic conformational sampling of the conformational preferences of 170 glycan moieties of glycosphingolipids as produced in large-scale quantities by bacterial fermentation. These glycans span across a variety of families including the blood group antigens (A, B and O), core structures (Types 1, 2 and 4), fucosylated oligosaccharides (core and lacto-series), sialylated oligosaccharides (Types 1 and 2), Lewis antigens, GPI-anchors and globosides. A complementary set of about 100 glycan determinants occurring in glycoproteins and glycosaminoglycans has also been structurally characterized using molecular mechanics-based computation. The experimental and computational data generated are organized in two relational databases that can be queried by the user through a user-friendly search engine. The NMR ((1)H and (13)C, COSY, TOCSY, HMQC, HMBC correlation) spectra and 3D structures are available for visualization and download in commonly used structure formats. Emphasis has been given to the use of a common nomenclature for the structural encoding of the carbohydrates and each glycan molecule is described by four different types of representations in order to cope with the different usages in chemistry and biology. These web-based databases were developed with non-proprietary software and are open access for the scientific community available at http://glyco3d.cermav.cnrs.fr. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Moving forward on facilitation research: response to changing environments and effects on the diversity, functioning and evolution of plant communities

PubMed Central

Soliveres, Santiago; Smit, Christian; Maestre, Fernando T.

2015-01-01

Once seen as anomalous, facilitative interactions among plants and their importance for community structure and functioning are now widely recognized. The growing body of modelling, descriptive and experimental studies on facilitation covers a wide variety of terrestrial and aquatic systems throughout the globe. However, the lack of a general body of theory linking facilitation among different types of organisms and biomes and their responses to environmental changes prevents further advances in our knowledge regarding the evolutionary and ecological implications of facilitation in plant communities. Moreover, insights gathered from alternative lines of inquiry may substantially improve our understanding of facilitation, but these have been largely neglected thus far. Despite over 15 years of research and debate on this topic, there is no consensus on the degree to which plant–plant interactions change predictably along environmental gradients (i.e. the stress-gradient hypothesis), and this hinders our ability to predict how plant–plant interactions may affect the response of plant communities to ongoing global environmental change. The existing controversies regarding the response of plant–plant interactions across environmental gradients can be reconciled when clearly considering and determining the species-specificity of the response, the functional or individual stress type, and the scale of interest (pairwise interactions or community-level response). Here, we introduce a theoretical framework to do this, supported by multiple lines of empirical evidence. We also discuss current gaps in our knowledge regarding how plant–plant interactions change along environmental gradients. These include the existence of thresholds in the amount of species-specific stress that a benefactor can alleviate, the linearity or non-linearity of the response of pairwise interactions across distance from the ecological optimum of the beneficiary, and the need to explore

Moving forward on facilitation research: response to changing environments and effects on the diversity, functioning and evolution of plant communities.

PubMed

Soliveres, Santiago; Smit, Christian; Maestre, Fernando T

2015-02-01

Once seen as anomalous, facilitative interactions among plants and their importance for community structure and functioning are now widely recognized. The growing body of modelling, descriptive and experimental studies on facilitation covers a wide variety of terrestrial and aquatic systems throughout the globe. However, the lack of a general body of theory linking facilitation among different types of organisms and biomes and their responses to environmental changes prevents further advances in our knowledge regarding the evolutionary and ecological implications of facilitation in plant communities. Moreover, insights gathered from alternative lines of inquiry may substantially improve our understanding of facilitation, but these have been largely neglected thus far. Despite over 15 years of research and debate on this topic, there is no consensus on the degree to which plant-plant interactions change predictably along environmental gradients (i.e. the stress-gradient hypothesis), and this hinders our ability to predict how plant-plant interactions may affect the response of plant communities to ongoing global environmental change. The existing controversies regarding the response of plant-plant interactions across environmental gradients can be reconciled when clearly considering and determining the species-specificity of the response, the functional or individual stress type, and the scale of interest (pairwise interactions or community-level response). Here, we introduce a theoretical framework to do this, supported by multiple lines of empirical evidence. We also discuss current gaps in our knowledge regarding how plant-plant interactions change along environmental gradients. These include the existence of thresholds in the amount of species-specific stress that a benefactor can alleviate, the linearity or non-linearity of the response of pairwise interactions across distance from the ecological optimum of the beneficiary, and the need to explore further how

Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches †

PubMed Central

Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

2017-01-01

To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating

Structure and properties of microporous titanosilicate determined by first-principles calculations

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

Ching, W.Y.; Xu, Y.; Gu, Z.

1996-12-01

The structure of EST-10, a member of synthetic microporous titanosilicates, was recently determined by an ingenious combination of experimental and simulational techniques. However, the locations of the alkali atoms in the framework remain elusive and its electronic structure is totally unknown. Based on first-principles local density calculations, the possible locations of the alkali atoms are identified and its electronic structure and bonding fully elucidated. ETS-10 is a semiconductor with a direct band gap of 2.33 eV. The Na atoms are likely to locate inside the seven-member ring pore adjacent to the one-dimensional Ti-O-Ti-O- chain. {copyright} {ital 1996 The American Physicalmore » Society.}« less

New insights into structural determinants of prion protein folding and stability.

PubMed

Benetti, Federico; Legname, Giuseppe

2015-01-01

Prions are the etiological agent of fatal neurodegenerative diseases called prion diseases or transmissible spongiform encephalopathies. These maladies can be sporadic, genetic or infectious disorders. Prions are due to post-translational modifications of the cellular prion protein leading to the formation of a β-sheet enriched conformer with altered biochemical properties. The molecular events causing prion formation in sporadic prion diseases are still elusive. Recently, we published a research elucidating the contribution of major structural determinants and environmental factors in prion protein folding and stability. Our study highlighted the crucial role of octarepeats in stabilizing prion protein; the presence of a highly enthalpically stable intermediate state in prion-susceptible species; and the role of disulfide bridge in preserving native fold thus avoiding the misfolding to a β-sheet enriched isoform. Taking advantage from these findings, in this work we present new insights into structural determinants of prion protein folding and stability.

Evidence of Facilitation Cascade Processes as Drivers of Successional Patterns of Ecosystem Engineers at the Upper Altitudinal Limit of the Dry Puna.

PubMed

Malatesta, Luca; Tardella, Federico Maria; Piermarteri, Karina; Catorci, Andrea

2016-01-01

Facilitation processes constitute basic elements of vegetation dynamics in harsh systems. Recent studies in tropical alpine environments demonstrated how pioneer plant species defined as "ecosystem engineers" are capable of enhancing landscape-level richness by adding new species to the community through the modification of microhabitats, and also provided hints about the alternation of different ecosystem engineers over time. Nevertheless, most of the existing works analysed different ecosystem engineers separately, without considering the interaction of different ecosystem engineers. Focusing on the altitudinal limit of Peruvian Dry Puna vegetation, we hypothesized that positive interactions structure plant communities by facilitation cascades involving different ecosystem engineers, determining the evolution of the microhabitat patches in terms of abiotic resources and beneficiary species hosted. To analyze successional mechanisms, we used a "space-for-time" substitution to account for changes over time, and analyzed data on soil texture, composition, and temperature, facilitated species and their interaction with nurse species, and surface area of engineered patches by means of chemical analyses, indicator species analysis, and rarefaction curves. A successional process, resulting from the dynamic interaction of different ecosystem engineers, which determined a progressive amelioration of soil conditions (e.g. nitrogen and organic matter content, and temperature), was the main driver of species assemblage at the community scale, enhancing species richness. Cushion plants act as pioneers, by starting the successional processes that continue with shrubs and tussocks. Tussock grasses have sometimes been found to be capable of creating microhabitat patches independently. The dynamics of species assemblage seem to follow the nested assemblage mechanism, in which the first foundation species to colonize a habitat provides a novel substrate for colonization by other

Automated structure determination of proteins with the SAIL-FLYA NMR method.

PubMed

Takeda, Mitsuhiro; Ikeya, Teppei; Güntert, Peter; Kainosho, Masatsune

2007-01-01

The labeling of proteins with stable isotopes enhances the NMR method for the determination of 3D protein structures in solution. Stereo-array isotope labeling (SAIL) provides an optimal stereospecific and regiospecific pattern of stable isotopes that yields sharpened lines, spectral simplification without loss of information, and the ability to collect rapidly and evaluate fully automatically the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as those that can be analyzed using conventional methods. Here, we describe a protocol for the preparation of SAIL proteins by cell-free methods, including the preparation of S30 extract and their automated structure analysis using the FLYA algorithm and the program CYANA. Once efficient cell-free expression of the unlabeled or uniformly labeled target protein has been achieved, the NMR sample preparation of a SAIL protein can be accomplished in 3 d. A fully automated FLYA structure calculation can be completed in 1 d on a powerful computer system.

The Resourceful Facilitator: Teacher Leaders Constructing Identities as Facilitators of Teacher Peer Groups

ERIC Educational Resources Information Center

Allen, David

2016-01-01

The use of teacher peer groups is a prevalent strategy for school-based professional development and instructional improvement. Facilitation of such groups is an increasingly vital dimension of teacher leadership as a component of school improvement efforts. Drawing on a qualitative study of facilitation of teacher peer groups, the article…

Determining Science Student Teachers' Cognitive Structure on the Concept of "Food Chain"

ERIC Educational Resources Information Center

Çinar, Derya

2015-01-01

The current study aims to determine science student teachers' cognitive structure on the concept of food chain. Qualitative research method was applied in this study. Fallacies detected in the pre-service teachers' conceptual structures are believed to result in students' developing misconceptions in their future classes and will adversely affect…

Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination

PubMed Central

Kazmier, Kelli; Alexander, Nathan S.; Meiler, Jens; Mchaourab, Hassane S.

2010-01-01

A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al., 2008). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure elements yielded vastly improved models by Rosetta folding. 50% of all these models have the correct fold compared to only 21% and 8% correctly folded models when randomly placed restraints or no restraints are used, respectively. Moreover, the improvements in model quality require a limited number of optimized restraints, the number of which is determined by the pairwise connectivities of T4L α-helices. The predicted improvement in Rosetta model quality was verified by experimental determination of distances between spin labels pairs selected by the algorithm. Overall, our results reinforce the rationale for the combined use of sparse EPR distance restraints and de novo folding. By alleviating the experimental bottleneck associated with restraint selection, this algorithm sets the stage for extending computational structure determination to larger, traditionally elusive protein topologies of critical structural and biochemical importance. PMID:21074624

Facilitating normative judgments of conditional probability: frequency or nested sets?

PubMed

Yamagishi, Kimihiko

2003-01-01

Recent probability judgment research contrasts two opposing views. Some theorists have emphasized the role of frequency representations in facilitating probabilistic correctness; opponents have noted that visualizing the probabilistic structure of the task sufficiently facilitates normative reasoning. In the current experiment, the following conditional probability task, an isomorph of the "Problem of Three Prisoners" was tested. "A factory manufactures artificial gemstones. Each gemstone has a 1/3 chance of being blurred, a 1/3 chance of being cracked, and a 1/3 chance of being clear. An inspection machine removes all cracked gemstones, and retains all clear gemstones. However, the machine removes 1/2 of the blurred gemstones. What is the chance that a gemstone is blurred after the inspection?" A 2 x 2 design was administered. The first variable was the use of frequency instruction. The second manipulation was the use of a roulette-wheel diagram that illustrated a "nested-sets" relationship between the prior and the posterior probabilities. Results from two experiments showed that frequency alone had modest effects, while the nested-sets instruction achieved a superior facilitation of normative reasoning. The third experiment compared the roulette-wheel diagram to tree diagrams that also showed the nested-sets relationship. The roulette-wheel diagram outperformed the tree diagrams in facilitation of probabilistic reasoning. Implications for understanding the nature of intuitive probability judgments are discussed.

Beyond needs and expectations: identifying the barriers and facilitators to written medicine information provision and use in Australia

PubMed Central

Hamrosi, Kim K.; Aslani, Parisa; Raynor, David K.

2012-01-01

Abstract Purpose  This study aimed to explore peoples’ needs and expectations of written medicines information (WMI), and to determine the barriers and facilitators experienced or perceived in the context of WMI provision and use. Methods  We conducted eight focus groups with 62 participants over 6 weeks in late 2008 in New South Wales, Australia. Using a semi‐structured topic schedule and examples of WMI from Australia and other English‐speaking countries as a guide, we explored themes relevant to WMI, including participant experiences, attitudes, beliefs and expectations. Findings  Our findings suggest less than half had previously received WMI, with many unaware of its availability. Many, but not all, wanted WMI to supplement the spoken information they received but not to replace it, and it was predominantly used to facilitate informed choice, ascertain medicine suitability and review instructions. The current leaflets were considered technical and long, and a summary leaflet in addition to comprehensive information was favoured. Accurate side‐effect information was the most important element that participants desired. The most common barriers to effective WMI use were time constraints and patient confidence, with participants citing empowerment, time and health‐care professional (HCP)–patient relationships as important facilitators. Conclusion  The findings provide insight and understanding of peoples needs and expectations, and clarify issues associated with use and non‐use of WMI. Challenges include addressing the barriers, especially of time and HCP attitudes to drive changes to workplace practices, and learning from the facilitating factors to encourage awareness and accessibility to WMI as a tool to empower patients. PMID:22390211

Structural Analysis of Chemokine Receptor–Ligand Interactions

PubMed Central

2017-01-01

This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741

Event-related potentials dissociate facilitation and interference effects in the numerical Stroop paradigm.

PubMed

Szucs, Dénes; Soltész, Fruzsina

2007-11-05

In the numerical Stroop paradigm (NSP) participants compare simultaneously presented Arabic digits based on either their numerical or on their physical size dimension. Responses are faster when the numerical and size dimensions are congruent with each other (facilitation), and responses are slower when the numerical and size dimensions are incongruent with each other (interference). We aimed to find out whether facilitation and interference appears during the course of perceptual or response processing. To this end, facilitation and interference effects in the amplitude of event-related brain potentials (ERPs) were examined. The onset of motor preparation was determined by monitoring the lateralized readiness potential. In numerical comparison one facilitation effect was related to perceptual processing at the level of the magnitude representation. A second facilitation effect and interference effects appeared during response processing. In size comparison facilitation and interference appeared exclusively during response processing. In both tasks, ERP interference effects were probably related to contextual analysis and to the conflict monitoring and selection for action activity of the anterior cingulate cortex. The results demonstrate that facilitation and interference effects in the NSP appear during multiple stages of processing, and that they are related to different cognitive processes. Therefore these effects should be clearly separated in studies of the NSP. A model of the processes involved in the NSP is provided and implications for studies of the NSP are drawn.

Prolonged rote learning produces delayed memory facilitation and metabolic changes in the hippocampus of the ageing human brain.

PubMed

Roche, Richard Ap; Mullally, Sinéad L; McNulty, Jonathan P; Hayden, Judy; Brennan, Paul; Doherty, Colin P; Fitzsimons, Mary; McMackin, Deirdre; Prendergast, Julie; Sukumaran, Sunita; Mangaoang, Maeve A; Robertson, Ian H; O'Mara, Shane M

2009-11-20

Repeated rehearsal is one method by which verbal material may be transferred from short- to long-term memory. We hypothesised that extended engagement of memory structures through prolonged rehearsal would result in enhanced efficacy of recall and also of brain structures implicated in new learning. Twenty-four normal participants aged 55-70 (mean = 60.1) engaged in six weeks of rote learning, during which they learned 500 words per week every week (prose, poetry etc.). An extensive battery of memory tests was administered on three occasions, each six weeks apart. In addition, proton magnetic resonance spectroscopy (1H-MRS) was used to measure metabolite levels in seven voxels of interest (VOIs) (including hippocampus) before and after learning. Results indicate a facilitation of new learning that was evident six weeks after rote learning ceased. This facilitation occurred for verbal/episodic material only, and was mirrored by a metabolic change in left posterior hippocampus, specifically an increase in NAA/(Cr+Cho) ratio. Results suggest that repeated activation of memory structures facilitates anamnesis and may promote neuronal plasticity in the ageing brain, and that compliance is a key factor in such facilitation as the effect was confined to those who engaged fully with the training.

Exploring the Use of a Social Network to Facilitate and Integrate Long-Term Interprofessional Educational Experiences

ERIC Educational Resources Information Center

Pittenger, Amy L.

2011-01-01

The purpose of this study was to evaluate the feasibility and effectiveness of implementing interprofessional education to students from six health professional programs through use of an online social networking platform. Specifically, three pedagogical models (Minimally Structured, Facilitated, Highly Structured) were evaluated for impact on…

Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation.

PubMed

Wasserman, Michael R; Alejo, Jose L; Altman, Roger B; Blanchard, Scott C

2016-04-01

Directional translocation of the ribosome through the mRNA open reading frame is a critical determinant of translational fidelity. This process entails a complex interplay of large-scale conformational changes within the actively translating particle, which together coordinate the movement of tRNA and mRNA substrates with respect to the large and small ribosomal subunits. Using pre-steady state, single-molecule fluorescence resonance energy transfer imaging, we tracked the nature and timing of these conformational events within the Escherichia coli ribosome from five structural perspectives. Our investigations revealed direct evidence of structurally and kinetically distinct late intermediates during substrate movement, whose resolution determines the rate of translocation. These steps involve intramolecular events within the EF-G-GDP-bound ribosome, including exaggerated, reversible fluctuations of the small-subunit head domain, which ultimately facilitate peptidyl-tRNA's movement into its final post-translocation position.

Structural analysis of the starfish SALMFamide neuropeptides S1 and S2: the N-terminal region of S2 facilitates self-association.

PubMed

Otara, Claire B; Jones, Christopher E; Younan, Nadine D; Viles, John H; Elphick, Maurice R

2014-02-01

The neuropeptides S1 (GFNSALMFamide) and S2 (SGPYSFNSGLTFamide), which share sequence similarity, were discovered in the starfish Asterias rubens and are prototypical members of the SALMFamide family of neuropeptides in echinoderms. SALMFamide neuropeptides act as muscle relaxants and both S1 and S2 cause relaxation of cardiac stomach and tube foot preparations in vitro but S2 is an order of magnitude more potent than S1. Here we investigated a structural basis for this difference in potency using spectroscopic techniques. Circular dichroism spectroscopy showed that S1 does not have a defined structure in aqueous solution and this was supported by 2D nuclear magnetic resonance experiments. In contrast, we found that S2 has a well-defined conformation in aqueous solution. However, the conformation of S2 was concentration dependent, with increasing concentration inducing a transition from an unstructured to a structured conformation. Interestingly, this property of S2 was not observed in an N-terminally truncated analogue of S2 (short S2 or SS2; SFNSGLTFamide). Collectively, the data obtained indicate that the N-terminal region of S2 facilitates peptide self-association at high concentrations, which may have relevance to the biosynthesis and/or bioactivity of S2 in vivo. © 2013.

Crystal Structure of an Ammonia-Permeable Aquaporin

PubMed Central

Kirscht, Andreas; Kaptan, Shreyas S.; Bienert, Gerd Patrick; Chaumont, François; Nissen, Poul; de Groot, Bert L.; Kjellbom, Per; Gourdon, Pontus; Johanson, Urban

2016-01-01

Aquaporins of the TIP subfamily (Tonoplast Intrinsic Proteins) have been suggested to facilitate permeation of water and ammonia across the vacuolar membrane of plants, allowing the vacuole to efficiently sequester ammonium ions and counteract cytosolic fluctuations of ammonia. Here, we report the structure determined at 1.18 Å resolution from twinned crystals of Arabidopsis thaliana aquaporin AtTIP2;1 and confirm water and ammonia permeability of the purified protein reconstituted in proteoliposomes as further substantiated by molecular dynamics simulations. The structure of AtTIP2;1 reveals an extended selectivity filter with the conserved arginine of the filter adopting a unique unpredicted position. The relatively wide pore and the polar nature of the selectivity filter clarify the ammonia permeability. By mutational studies, we show that the identified determinants in the extended selectivity filter region are sufficient to convert a strictly water-specific human aquaporin into an AtTIP2;1-like ammonia channel. A flexible histidine and a novel water-filled side pore are speculated to deprotonate ammonium ions, thereby possibly increasing permeation of ammonia. The molecular understanding of how aquaporins facilitate ammonia flux across membranes could potentially be used to modulate ammonia losses over the plasma membrane to the atmosphere, e.g., during photorespiration, and thereby to modify the nitrogen use efficiency of plants. PMID:27028365

A Rational Approach to Determine Minimum Strength Thresholds in Novel Structural Materials

NASA Technical Reports Server (NTRS)

Schur, Willi W.; Bilen, Canan; Sterling, Jerry

2003-01-01

Design of safe and survivable structures requires the availability of guaranteed minimum strength thresholds for structural materials to enable a meaningful comparison of strength requirement and available strength. This paper develops a procedure for determining such a threshold with a desired degree of confidence, for structural materials with none or minimal industrial experience. The problem arose in attempting to use a new, highly weight-efficient structural load tendon material to achieve a lightweight super-pressure balloon. The developed procedure applies to lineal (one dimensional) structural elements. One important aspect of the formulation is that it extrapolates to expected probability distributions for long length specimen samples from some hypothesized probability distribution that has been obtained from a shorter length specimen sample. The use of the developed procedure is illustrated using both real and simulated data.

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

DOE PAGES

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; ...

2016-09-19

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstaclemore » is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined.We showwith four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.« less

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

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

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstaclemore » is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined.We showwith four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods.« less

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

PubMed Central

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; Collazo, Michael J.; Shi, Dan; Reyes, Francis E.; Gonen, Tamir; Eisenberg, David S.

2016-01-01

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods. PMID:27647903

A model of how targeted and universal welfare entitlements impact on material, psycho-social and structural determinants of health in older adults.

PubMed

Green, Judith; Buckner, Stefanie; Milton, Sarah; Powell, Katie; Salway, Sarah; Moffatt, Suzanne

2017-08-01

A growing body of research attests to the impact of welfare regimes on health and health equity. However, the mechanisms that link different kinds of welfare entitlement to health outcomes are less well understood. This study analysed the accounts of 29 older adults in England to delineate how the form of entitlement to welfare and other resources (specifically, whether this was understood as a universal entitlement or as targeted to those in need) impacts on the determinants of health. Mechanisms directly affecting access to material resources (through deterring uptake of benefits) have been well documented, but those that operate through psychosocial and more structural pathways less so, in part because they are more challenging to identify. Entitlement that was understood collectively, or as arising from financial or other contributions to a social body, had positive impacts on wellbeing beyond material gains, including facilitating access to important health determinants: social contact, recognition and integration. Entitlement understood as targeted in terms of individualised concepts of need or vulnerability deterred access to material resources, but also fostered debate about legitimacy, thus contributing to negative impacts on individual wellbeing and the public health through the erosion of social integration. This has important implications for both policy and evaluation. Calls to target welfare benefits at those in most need emphasise direct material pathways to health impact. We suggest a model for considering policy change and evaluation which also takes into account how psychosocial and structural pathways are affected by the nature of entitlement. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structure of UreG/UreF/UreH Complex Reveals How Urease Accessory Proteins Facilitate Maturation of Helicobacter pylori Urease

PubMed Central

Fong, Yu Hang; Wong, Ho Chun; Yuen, Man Hon; Lau, Pak Ho; Chen, Yu Wai; Wong, Kam-Bo

2013-01-01

Urease is a metalloenzyme essential for the survival of Helicobacter pylori in acidic gastric environment. Maturation of urease involves carbamylation of Lys219 and insertion of two nickel ions at its active site. This process requires GTP hydrolysis and the formation of a preactivation complex consisting of apo-urease and urease accessory proteins UreF, UreH, and UreG. UreF and UreH form a complex to recruit UreG, which is a SIMIBI class GTPase, to the preactivation complex. We report here the crystal structure of the UreG/UreF/UreH complex, which illustrates how UreF and UreH facilitate dimerization of UreG, and assembles its metal binding site by juxtaposing two invariant Cys66-Pro67-His68 metal binding motif at the interface to form the (UreG/UreF/UreH)2 complex. Interaction studies revealed that addition of nickel and GTP to the UreG/UreF/UreH complex releases a UreG dimer that binds a nickel ion at the dimeric interface. Substitution of Cys66 and His68 with alanine abolishes the formation of the nickel-charged UreG dimer. This nickel-charged UreG dimer can activate urease in vitro in the presence of the UreF/UreH complex. Static light scattering and atomic absorption spectroscopy measurements demonstrated that the nickel-charged UreG dimer, upon GTP hydrolysis, reverts to its monomeric form and releases nickel to urease. Based on our results, we propose a mechanism on how urease accessory proteins facilitate maturation of urease. PMID:24115911

A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein.

PubMed

Liu, Wei; Zhang, Jingfeng; Fan, Jing-Song; Tria, Giancarlo; Grüber, Gerhard; Yang, Daiwen

2016-05-10

Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Comparative Protein Structure Modeling Using MODELLER.

PubMed

Webb, Benjamin; Sali, Andrej

2014-09-08

Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. Copyright © 2014 John Wiley & Sons, Inc.

Self-recognition in corals facilitates deep-sea habitat engineering

USGS Publications Warehouse

Hennige, Sebastian J; Morrison, Cheryl L.; Form, Armin U.; Buscher, Janina; Kamenos, Nicholas A.; Roberts, J. Murray

2014-01-01

The ability of coral reefs to engineer complex three-dimensional habitats is central to their success and the rich biodiversity they support. In tropical reefs, encrusting coralline algae bind together substrates and dead coral framework to make continuous reef structures, but beyond the photic zone, the cold-water coral Lophelia pertusa also forms large biogenic reefs, facilitated by skeletal fusion. Skeletal fusion in tropical corals can occur in closely related or juvenile individuals as a result of non-aggressive skeletal overgrowth or allogeneic tissue fusion, but contact reactions in many species result in mortality if there is no ‘self-recognition’ on a broad species level. This study reveals areas of ‘flawless’ skeletal fusion in Lophelia pertusa, potentially facilitated by allogeneic tissue fusion, are identified as having small aragonitic crystals or low levels of crystal organisation, and strong molecular bonding. Regardless of the mechanism, the recognition of ‘self’ between adjacent L. pertusa colonies leads to no observable mortality, facilitates ecosystem engineering and reduces aggression-related energetic expenditure in an environment where energy conservation is crucial. The potential for self-recognition at a species level, and subsequent skeletal fusion in framework-forming cold-water corals is an important first step in understanding their significance as ecological engineers in deep-seas worldwide.

[Facilitators and barriers to implementation of intercultural health policy in Chile].

PubMed

Pérez, Camila; Nazar, Gabriela; Cova, Félix

2016-02-01

Objective To identify elements that either facilitate or hinder implementation of Chile's intercultural health policy. Methods A descriptive study was conducted with the participation of health services users from the Mapuche ethnic group, biomedical health professionals, intercultural facilitators, and key informants in two health facilities serving towns with a high density of Mapuche population. The information was obtained through semi-structured interviews that were analyzed thematically. Results Factors identified as facilitating the implementation of this policy include laws and regulations pertaining to the rights of indigenous peoples, the empowerment of users around their rights, the formation of implementation teams, the presence of professionals of Mapuche origin in health facilities, and the existence of processes for systematization of the work carried out. The asymmetric relationship between the Mapuche people and the state, and between the Mapuche health system and the biomedical model, constitutes a fundamental barrier. Other obstacles include the lack of theoretical and practical clarity around the concept of intercultural health and a lack of resources. Conclusions Despite the facilitators identified and the achievements to date, meaningful progress in implementation of an intercultural health policy is limited by barriers that are hard to change. These include the usual forms of government planning and the hegemony of the biomedical model.

C-glucosidic ellagitannins from Lythri herba (European Pharmacopoeia): chromatographic profile and structure determination.

PubMed

Piwowarski, Jakub P; Kiss, Anna K

2013-01-01

Lythri herba, a pharmacopoeial plant material (European Pharmacopoea), is obtained from flowering parts of purple loosestrife (Lythrum salicaria L.). Although extracts from this plant material have been proven to possess some interesting biological activities and its pharmacopoeial standardisation is based on total tannin content determination, the phytochemical characterisation of this main group of compounds has not yet been fully conducted. To isolate ellagitannins from Lythri herba, determine their structures and develop chromatographic methods for their qualitative analysis. Five C-glucosidic ellagitannins - monomeric- vescalagin and castalagin together with new dimeric structures - salicarinins A-C, composed of vescalagin and stachyurin, vescalagin and casuarinin, castalagin and casuarinin units connected via formation of valoneoyl group, were isolated using column chromatography and preparative HPLC. Structures were determined according to (1) H and (13) C-NMR (one- and two-dimensional), electrospray ionisation-time of flight (ESI-TOF), electrospray ionisation-ion trap (ESI-MS(n) ) and circular dichroism (CD) spectra, together with acidic hydrolysis products analysis. HPTLC on RP-18 modified plates and HPLC-DAD-MS(n) on RP-18 column methods were developed for separation of the five main ellagitannins. Copyright © 2012 John Wiley & Sons, Ltd.

Density functional theory determination of structural and electronic properties of struvite.

PubMed

Romanowski, Zbigniew; Kempisty, Paweł; Prywer, Jolanta; Krukowski, Stanisław; Torzewska, Agnieszka

2010-07-29

Crystallographic structure, total energy, electronic structure, and the most important elastic properties of struvite, NH(4)MgPO(4).6H(2)O, the main component of infectious urinary stones, are presented. The calculations were performed using ab initio full-electron calculations within the density functional theory-generalized gradient approximation (DFT-GGA) framework. The obtained crystallographic symmetry and the calculated lattice parameters and also the elastic constants are in good agreement with the experimental data. The elastic properties are essential for establishing an optimal response of urinary stones during shock-wave lithotripsy. The calculated electronic charge distribution confirms the layered structure of the struvite crystals. The polar character of the crystal, well-known from crystal growth experiments, was also confirmed by the magnitude of spontaneous polarization which was obtained from direct determination of the electrical dipole density. The calculated value of spontaneous polarization is equal to -8.8 microC cm(-2). This feature may play a key role in struvite crystallization, electrically binding the charged active impurities and other active species, and consequently determining urinary stone formation. We also present the results of our own experiment of the mineralization of struvite induced to growth by Proteus bacteria which are mainly isolated from infectious urinary stones.

Rare variation facilitates inferences of fine-scale population structure in humans.

PubMed

O'Connor, Timothy D; Fu, Wenqing; Mychaleckyj, Josyf C; Logsdon, Benjamin; Auer, Paul; Carlson, Christopher S; Leal, Suzanne M; Smith, Joshua D; Rieder, Mark J; Bamshad, Michael J; Nickerson, Deborah A; Akey, Joshua M

2015-03-01

Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale resequencing studies have shown an abundance of rare variation in humans, which may be particularly useful for making inferences of fine-scale population structure. To this end, we used an information theory framework and extensive coalescent simulations to rigorously quantify the informativeness of rare and common variation to detect signatures of fine-scale population structure. We show that rare variation affords unique insights into patterns of recent population structure. Furthermore, to empirically assess our theoretical findings, we analyzed high-coverage exome sequences in 6,515 European and African American individuals. As predicted, rare variants are more informative than common polymorphisms in revealing a distinct cluster of European-American individuals, and subsequent analyses demonstrate that these individuals are likely of Ashkenazi Jewish ancestry. Our results provide new insights into the population structure using rare variation, which will be an important factor to account for in rare variant association studies. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Hospital networks: how to make them work in Belgium? Facilitators and barriers of different governance models.

PubMed

De Pourcq, Kaat; De Regge, Melissa; Van den Heede, Koen; Van de Voorde, Carine; Gemmel, Paul; Eeckloo, Kristof

2018-03-29

Objectives This study aims to identify the facilitators and barriers to governance models of hospital collaborations. The country-specific characteristics of the Belgian healthcare system and legislation are taken into account. Methods A case study was carried out in six Belgian hospital collaborations. Different types of governance models were selected: two health systems, two participant-governed networks, and two lead-organization-governed networks. Within these collaborations, 43 people were interviewed. Results All structures have both advantages and disadvantages. It is important that the governance model fits the network. However, structural, procedural, and especially contextual factors also affect the collaborations, such as alignment of hospitals' and professionals' goals, competition, distance, level of integrated care, time needed for decision-making, and legal and financial incentives. Conclusion The fit between the governance model and the collaboration can facilitate the functioning of a collaboration. The main barriers we identified are contextual factors. The Belgian government needs to play a major role in facilitating collaboration.

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.

PubMed

Lee, Woonghee; Kim, Jin Hae; Westler, William M; Markley, John L

2011-06-15

PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY ((13)C-edited and/or (15)N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/.

A student-initiated and student-facilitated international health elective for preclinical medical students.

PubMed

Vora, Nirali; Chang, Mina; Pandya, Hemang; Hasham, Aliya; Lazarus, Cathy

2010-02-15

Global health education is becoming more important for developing well-rounded physicians and may encourage students toward a career in primary care. Many medical schools, however, lack adequate and structured opportunities for students beginning the curriculum. Second-year medical students initiated, designed, and facilitated a pass-fail international health elective, providing a curricular framework for preclinical medical students wishing to gain exposure to the clinical and cultural practices of a developing country. All course participants (N=30) completed a post-travel questionnaire within one week of sharing their experiences. Screening reflection essays for common themes that fulfill university core competencies yielded specific global health learning outcomes, including analysis of health care determinants. Medical students successfully implemented a sustainable global health curriculum for preclinical student peers. Financial constraints, language, and organizational burdens limit student participation. In future, long-term studies should analyze career impact and benefits to the host country.

Evaluation of the Facilitated Communication Pilot

ERIC Educational Resources Information Center

Cooper-Martin, Elizabeth

2014-01-01

The Office of Special Education and Student Services asked the Office of Shared Accountability to evaluate the "Facilitated Communication Pilot." In facilitated communication (FC), people with communication impairments express themselves by typing with the aid of a communication partner, called a facilitator, who provides physical (and…

DETERMINANTS OF NETWORK OUTCOMES: THE IMPACT OF MANAGEMENT STRATEGIES

PubMed Central

YSA, TAMYKO; SIERRA, VICENTA; ESTEVE, MARC

2014-01-01

The literature on network management is extensive. However, it generally explores network structures, neglecting the impact of management strategies. In this article we assess the effect of management strategies on network outcomes, providing empirical evidence from 119 urban revitalization networks. We go beyond current work by testing a path model for the determinants of network outcomes and considering the interactions between the constructs: management strategies, trust, complexity, and facilitative leadership. Our results suggest that management strategies have a strong effect on network outcomes and that they enhance the level of trust. We also found that facilitative leadership has a positive impact on network management as well as on trust in the network. Our findings also show that complexity has a negative impact on trust. A key finding of our research is that managers may wield more influence on network dynamics than previously theorized. PMID:25520529

Learning From Tests: Facilitation of Delayed Recall by Initial Recognition Alternatives.

ERIC Educational Resources Information Center

Whitten, William B., II; Leonard, Janet Mauriello

1980-01-01

Two experiments were designed to determine the effects of multiple-choice recognition test alternatives on subsequent memory for the correct answers. Results of both experiments are interpreted as demonstrations of the principle that long-term retention is facilitated such that memory evaluation occurs during initial recognition tests. (Author/RD)

From service quality in organisations to self-determination at home.

PubMed

Martínez-Tur, V; Moliner, C; Peñarroja, V; Gracia, E; Peiró, J M

2015-10-01

In our proposed model, family members' perceptions of service quality in organisations improve communication about self-determination. In turn, family perceptions of communication openness have a positive relationship with self-determination attitudes of family members. Finally, these attitudes predict self-determination behaviours of individuals with intellectual disability, as reported by family members. We tested this model with a sample of 625 family members (196 using 'day care services' and 429 using 'occupational services'). Multi-sample structural equation modelling (SEM) supported the model. Communication and attitudes fully mediated the link from service quality to self-determination behaviours. Improving family members' perceptions of service quality and opening channels of communication between professionals and family members are useful strategies to facilitate parents' positive attitudes and increase the frequency of self-determination behaviours at home. © 2015 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

PubMed Central

Khafizov, Kamil; Madrid-Aliste, Carlos; Almo, Steven C.; Fiser, Andras

2014-01-01

The exponential growth of protein sequence data provides an ever-expanding body of unannotated and misannotated proteins. The National Institutes of Health-supported Protein Structure Initiative and related worldwide structural genomics efforts facilitate functional annotation of proteins through structural characterization. Recently there have been profound changes in the taxonomic composition of sequence databases, which are effectively redefining the scope and contribution of these large-scale structure-based efforts. The faster-growing bacterial genomic entries have overtaken the eukaryotic entries over the last 5 y, but also have become more redundant. Despite the enormous increase in the number of sequences, the overall structural coverage of proteins—including proteins for which reliable homology models can be generated—on the residue level has increased from 30% to 40% over the last 10 y. Structural genomics efforts contributed ∼50% of this new structural coverage, despite determining only ∼10% of all new structures. Based on current trends, it is expected that ∼55% structural coverage (the level required for significant functional insight) will be achieved within 15 y, whereas without structural genomics efforts, realizing this goal will take approximately twice as long. PMID:24567391

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative.

PubMed

Khafizov, Kamil; Madrid-Aliste, Carlos; Almo, Steven C; Fiser, Andras

2014-03-11

The exponential growth of protein sequence data provides an ever-expanding body of unannotated and misannotated proteins. The National Institutes of Health-supported Protein Structure Initiative and related worldwide structural genomics efforts facilitate functional annotation of proteins through structural characterization. Recently there have been profound changes in the taxonomic composition of sequence databases, which are effectively redefining the scope and contribution of these large-scale structure-based efforts. The faster-growing bacterial genomic entries have overtaken the eukaryotic entries over the last 5 y, but also have become more redundant. Despite the enormous increase in the number of sequences, the overall structural coverage of proteins--including proteins for which reliable homology models can be generated--on the residue level has increased from 30% to 40% over the last 10 y. Structural genomics efforts contributed ∼50% of this new structural coverage, despite determining only ∼10% of all new structures. Based on current trends, it is expected that ∼55% structural coverage (the level required for significant functional insight) will be achieved within 15 y, whereas without structural genomics efforts, realizing this goal will take approximately twice as long.

Support Structures for Facilitators of Student Personal Development Planning: Lessons from Two Departmental Case Studies

ERIC Educational Resources Information Center

Hulme, Claire; Lisewski, Bernard

2010-01-01

In the UK, following guidelines set out by the Quality Assurance Agency, personal development planning (PDP) is now operational across all higher education (HE) awards. Like many policy initiatives, PDP requires change, and vital to its implementation are those who facilitate PDP at the grassroots level. Staff given the task of implementing PDP…

Hollow fibre liquid phase micro-extraction by facilitated anionic exchange for the determination of flavonoids in faba beans (Vicia faba L.).

PubMed

Chaieb, Nadia; López-Mesas, Montserrat; Luis González, Johannes; Mars, Messaoud; Valiente, Manuel

2015-01-01

Flavonoids are polyphenolic compounds found ubiquitously in foods of plant origin. They are commonly extracted from plant materials with ethanol, methanol, water, their combination or even with acidified extracting solutions. The disadvantages of these methods are the use of high quantity of organic solvent, the possible loss of analytes in the different steps and the laborious process of the techniques. In addition, the complexity of the phenolic mixtures present in plant materials requires a preliminary clean-up and fractionation of the crude extracts. To develop a hollow fibre liquid phase micro-extraction (HF-LPME) method for a one step clean-up and pre-concentration of flavonoids. Two flavonoids (catechin and rutin) has been extracted by HF-LPME and analysed by HPLC. The related driving force for the liquid membrane has been studied by means of facilitated and non-facilitated transport. Different ionic and non-ionic water insoluble compounds [trioctylamine (TOA), tributyl phosphate (TBP), trioctylphosphine oxide (TOPO) and methyltrioctylammonium chloride (aliquat 336)] were used as carriers. The liquid membrane was constituted by a solution of n-decanol in the presence or absence of carriers. Maximum enrichment factors were obtained with n-decanol/aliquat 336 (20%) as organic liquid membrane, sodium hydroxide (NaOH) (0.1 M) as donor solution, sodium chloride (NaCl) (2 M) as acceptor solution and 3 h as extraction time. Under these conditions, good results for validation parameters were obtained [for linearity, limit of detection (LOD), limit of quantitation (LOQ) and repeatability]. The developed method is simple, effective and has been successfully applied to determine catechin and rutin in ethanolic extracts of faba beans. Copyright © 2015 John Wiley & Sons, Ltd.

Combined NMR and EPR Spectroscopy to Determine Structures of Viral Fusion Domains in Membranes

PubMed Central

Tamm, Lukas K.; Lai, Alex L.; Li, Yinling

2008-01-01

Methods are described to determine the structures of viral membrane fusion domains in detergent micelles by NMR and in lipid bilayers by site-directed spin labeling and EPR spectroscopy. Since in favorable cases, the lower-resolution spin label data obtained in lipid bilayers fully support the higher-resolution structures obtained by solution NMR, it is possible to graft the NMR structural coordinates into membranes using the EPR-derived distance restraints to the lipid bilayer. Electron paramagnetic dynamics and distance measurements in bilayers support conclusions drawn from NMR in detergent micelles. When these methods are applied to a structure determination of the influenza virus fusion domain and four point mutations with different functional phenotypes, it is evident that a fixed-angle boomerang structure with a glycine edge on the outside of the N-terminal arm is both necessary and sufficient to support membrane fusion. The human immunodeficiency virus fusion domain forms a straight helix with a flexible C-terminus. While EPR data for this fusion domain are not yet available, it is tentatively speculated that, because of its higher hydrophobicity, a critically tilted insertion may occur even in the absence of a kinked boomerang structure in this case. PMID:17963720

Purification and Bicelle Crystallization for Structure Determination of the E. coli Outer Membrane Protein TamA.

PubMed

Gruss, Fabian; Hiller, Sebastian; Maier, Timm

2015-01-01

TamA is an Omp85 protein involved in autotransporter assembly in the outer membrane of Escherichia coli. It comprises a C-terminal 16-stranded transmembrane β-barrel as well as three periplasmic POTRA domains, and is a challenging target for structure determination. Here, we present a method for crystal structure determination of TamA, including recombinant expression in E. coli, detergent extraction, chromatographic purification, and bicelle crystallization in combination with seeding. As a result, crystals in space group P21212 are obtained, which diffract to 2.3 Å resolution. This protocol also serves as a template for structure determination of other outer membrane proteins, in particular of the Omp85 family.

Vitamin E Facilitates the Inactivation of the Kinase Akt by the Phosphatase PHLPP1

PubMed Central

Huang, Po-Hsien; Chuang, Hsiao-Ching; Chou, Chih-Chien; Wang, Huiling; Lee, Su-Lin; Yang, Hsiao-Ching; Chiu, Hao-Chieh; Kapuriya, Naval; Wang, Dasheng; Kulp, Samuel K.; Chen, Ching-Shih

2014-01-01

Vitamin E is a fat-soluble vitamin that includes isomers of tocopherols and tocotrienols which are known for their antioxidant properties. Tocopherols are the predominant form encountered in the diet and through supplementation, and have garnered interest for their potential cancer therapeutic and chemopreventive effects, which include the dephosphorylation of Akt, a serine/threonine kinase that plays a pivotal role in important cellular processes, such as cell growth, survival, metabolism and motility. Full catalytic activation of Akt requires phosphorylation at both Thr308 and Ser473. Dephosphorylation of Ser473 drastically reduces Akt catalytic activity and the number of downstream substrates it can regulate. The mechanism by which α- and γ-tocopherol facilitate the selective dephosphorylation of the kinase Akt at Ser473 was investigated. We showed that this site-specific Akt dephosphorylation was mediated through the pleckstrin homology (PH) domain-dependent recruitment to the plasma membrane of Akt and PHLPP1 (PH domain leucine-rich repeat protein phosphatase, isoform 1), a phosphatase that dephosphorylates Akt at Ser473. The ability of α- and γ-tocopherol to induce PHLPP-mediated Akt inhibition established PHLPP as a “druggable” target. We structurally optimized these tocopherols to obtain derivatives with greater in vitro potency and in vivo tumor-suppressive activity in two prostate xenograft tumor models. Binding affinities for the PH domains of Akt and PHLPP1 were greater than for other PH domain-containing proteins, which may underlie the preferential membrane recruitment of these proteins. Molecular modeling revealed the structural determinants of the interaction with the PH domain of Akt that may inform strategies for continued structural optimization. These findings describe a mechanism by which tocopherols facilitate the dephosphorylation of Akt at Ser473, thereby providing insights into the mode of antitumor action of tocopherols and a

Study of Factors Which Facilitate Increase of Effectiveness of University Education

ERIC Educational Resources Information Center

Albekov, Adam; Romanova, Tatyana; Vovchenko, Natalya; Epifanova, Tatyana

2017-01-01

Purpose: The purpose of this paper is to study the factors which facilitate the increase of effectiveness of university education and determination of perspectives of their management for provision of maximization of effectiveness of university education by the example of modern Russia. Design/methodology/approach: The authors define the notion…

Group Facilitation: Functions and Skills.

ERIC Educational Resources Information Center

Anderson, L. Frances; Robertson, Sharon E.

1985-01-01

Discusses a model based on a specific set of assumptions about causality and effectiveness in interactional groups. Discusses personal qualities of group facilitators and proposes five major functions and seven skill clusters central to effective group facilitation. (Author/BH)

Effects of Student-Facilitated Learning on Instructional Facilitators

ERIC Educational Resources Information Center

Bonner, Sarah M.; Somers, Jennifer A.; Rivera, Gwendelyn J.; Keiler, Leslie S.

2017-01-01

We investigated perceptions about learning strategy use and instructional roles among a sample of high needs adolescents (n = 230) who acted as near-peer instructional facilitators. The sample was drawn from science and mathematics classes in nonselective public secondary schools in New York City. Students participated in an inschool intervention…

Determination of the Effects of Magnesium on the Structural Order of Amorphous Calcium Phosphate

NASA Astrophysics Data System (ADS)

Hoeher, A.; Michel, F. M.; Rakovan, J. F.; Borkiewicz, O.; Klysubun, W.

2016-12-01

Determining the pathways and mechanisms of calcium phosphate formation is important for understanding bone mineralization and advancing potential biological applications such as coatings on internal prosthetics. Studies show that amorphous calcium phosphate (ACP) is a precursor phase in the low temperature crystallization of hydroxylapatite, the primary mineral component found in bone and teeth of most modern vertebrates. ACP has been shown to have a structural order out to about 1 nm. Our recent extended x-ray absorption fine structure (EXAFS) spectroscopy analysis of synthetic ACP showed that the local structure of calcium in ACP differed from that in hydroxylapatite. Phosphorus EXAFS, however, indicated that the local structure in ACP is similar to hydroxylapatite (i.e., tetrahedrally coordinated with oxygen). EXAFS results were limited to only the first and second nearest neighbors in these samples, so the intermediate range order in ACP is yet unexplored. Furthermore, it remains unclear how ACP structure varies as a function of initial solution chemistry, how common impurities such as Mg are incorporated, and what role they play in determining the structural and physical characteristics of the final crystalline solid. We are using synchrotron x-ray total scattering for pair distribution function (PDF) analysis to investigate the influence of initial solution chemistry and Mg content on the structure of ACP. Magnesium is commonly used to stabilize the amorphous nature of the material, preventing crystallization. Ex situ samples synthesized at pH 10, with Ca:Mg ratios of 2:1, and freeze-dried are structurally similar to hydroxylapatite. Samples synthesized in identical conditions without Mg are structurally similar to another calcium phosphate mineral, brushite. In situ PDF measurements done at similar conditions in a custom mixed-flow reactor reveal that the short range order of ACP after 10 minutes of reacting is structurally different from ACP formed ex situ

Evidence of Facilitation Cascade Processes as Drivers of Successional Patterns of Ecosystem Engineers at the Upper Altitudinal Limit of the Dry Puna

PubMed Central

2016-01-01

Facilitation processes constitute basic elements of vegetation dynamics in harsh systems. Recent studies in tropical alpine environments demonstrated how pioneer plant species defined as “ecosystem engineers” are capable of enhancing landscape-level richness by adding new species to the community through the modification of microhabitats, and also provided hints about the alternation of different ecosystem engineers over time. Nevertheless, most of the existing works analysed different ecosystem engineers separately, without considering the interaction of different ecosystem engineers. Focusing on the altitudinal limit of Peruvian Dry Puna vegetation, we hypothesized that positive interactions structure plant communities by facilitation cascades involving different ecosystem engineers, determining the evolution of the microhabitat patches in terms of abiotic resources and beneficiary species hosted. To analyze successional mechanisms, we used a “space-for-time” substitution to account for changes over time, and analyzed data on soil texture, composition, and temperature, facilitated species and their interaction with nurse species, and surface area of engineered patches by means of chemical analyses, indicator species analysis, and rarefaction curves. A successional process, resulting from the dynamic interaction of different ecosystem engineers, which determined a progressive amelioration of soil conditions (e.g. nitrogen and organic matter content, and temperature), was the main driver of species assemblage at the community scale, enhancing species richness. Cushion plants act as pioneers, by starting the successional processes that continue with shrubs and tussocks. Tussock grasses have sometimes been found to be capable of creating microhabitat patches independently. The dynamics of species assemblage seem to follow the nested assemblage mechanism, in which the first foundation species to colonize a habitat provides a novel substrate for colonization by

Determining the Structure of Oxalate Anion Using Infrared and Raman Spectroscopy Coupled with Gaussian Calculations

ERIC Educational Resources Information Center

Peterson, Karen I.; Pullman, David P.

2016-01-01

A laboratory project for the upper-division physical chemistry laboratory is described, and it combines IR and Raman spectroscopies with Gaussian electronic structure calculations to determine the structure of the oxalate anion in solid alkali oxalates and in aqueous solution. The oxalate anion has two limiting structures whose vibrational spectra…

Work-related barriers, facilitators, and strategies of breast cancer survivors working during curative treatment

PubMed Central

Sun, Wenjun; Chen, Karen; Terhaar, Abigail; Wiegmann, Douglas A.; Heidrich, Susan M.; Tevaarwerk, Amye J.; Sesto, Mary E.

2017-01-01

BACKGROUND Research has identified barriers and facilitators affecting cancer survivors’ return to work (RTW) following the end of active treatment (surgery, chemotherapy and/or radiation therapy). However, few studies have focused on barriers and facilitators that cancer survivors experience while working during active treatment. Strategies used by cancer survivors to solve work-related problems during active treatment are underexplored. OBJECTIVE The aim of this study was to describe factors that impact, either positively or negatively, breast cancer survivors’ work activities during active treatment. METHODS Semi-structured, recorded interviews were conducted with 35 breast cancer survivors who worked during active treatment. Transcripts of interviews were analyzed using inductive content analysis to identify themes regarding work-related barriers, facilitators and strategies. RESULTS Barriers identified included symptoms, emotional distress, appearance change, time constraints, work characteristics, unsupportive supervisors and coworkers, family issues and other illness. Facilitators included positive aspects of work, support outside of work, and coworker and supervisor support. Strategies included activities to improve health-related issues and changes to working conditions and tasks. CONCLUSIONS Breast cancer survivors encounter various barriers during active treatment. Several facilitators and strategies can help survivors maintain productive work activities. PMID:28059814

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.

PubMed

Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2013-11-01

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. © 2013 FEBS.

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

PubMed Central

Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2014-01-01

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. PMID:24034303

Détermination assistée par ordinateur de la structure des molécules organiques

NASA Astrophysics Data System (ADS)

Nuzillard, J.-M.

1998-02-01

Nuclear Magnetic Resonance spectroscopy offers the unique possibility of accessing proximity relationships between atoms by means of chemical shift correlation experiments. Structure determination of small molecules has become thus much simpler. Computer programs can use directly correlation information for structure analysis. The use and operation mechanism of such a program, LSD (Logic for Structure Determination) are presented. The example compound is gibberellic acid, a natural product. La spectroscopie de Résonance Magnétique Nucléaire offre un moyen unique de déterminer des relations de proximité entre atomes par le biais des expériences de corrélation. L'analyse structurale de petites molécules organiques s'en trouve extrêmement facilitée. Des programmes informatiques peuvent utiliser directement les informations de corrélation pour déduire des structures. Le fonctionnement et l'usage d'un tel programme, LSD (Logic for Structure Determination), sont détaillés sur un exemple, l'acide gibberellique.

Determination of scattering structures from spatial coherence measurements.

PubMed

Zarubin, A M

1996-03-01

A new method of structure determination and microscopic imaging with short-wavelength radiations (charged particles, X-rays, neutrons), based on measurements of the modulus and the phase of the degree of spatial coherence of the scattered radiation, is developed. The underlying principle of the method--transfer of structural information about the scattering potential via spatial coherence of the secondary (scattering) source of radiation formed by this potential--is expressed by the generalization of the van Cittert-Zernike theorem to wave and particle scattering [A.M. Zarubin, Opt. Commun. 100 (1993) 491; Opt. Commun. 102 (1993) 543]. Shearing interferometric techniques are proposed for implementing the above measurements; the limits of spatial resolution attainable by reconstruction of the absolute square of a 3D scattering potential and its 2D projections from the measurements are analyzed. It is shown theoretically that 3D imaging with atomic resolution can be realized in a "synthetic aperture" electron or ion microscope and that a 3D resolution of about 6 nm can be obtained with a "synthetic aperture" X-ray microscope. A proof-of-principle optical experiment is presented.

How can clinical practice guidelines be adapted to facilitate shared decision making? A qualitative key-informant study.

PubMed

van der Weijden, Trudy; Pieterse, Arwen H; Koelewijn-van Loon, Marije S; Knaapen, Loes; Légaré, France; Boivin, Antoine; Burgers, Jako S; Stiggelbout, Anne M; Faber, Marjan; Elwyn, Glyn

2013-10-01

To explore how clinical practice guidelines can be adapted to facilitate shared decision making. This was a qualitative key-informant study with group discussions and semi-structured interviews. First, 75 experts in guideline development or shared decision making participated in group discussions at two international conferences. Next, health professionals known as experts in depression or breast cancer, experts on clinical practice guidelines and/or shared decision making, and patient representatives were interviewed (N=20). Using illustrative treatment decisions on depression or breast cancer, we asked the interviewees to indicate as specifically as they could how guidelines could be used to facilitate shared decision making. Interviewees suggested some generic strategies, namely to include a separate chapter on the importance of shared decision making, to use language that encourages patient involvement, and to develop patient versions of guidelines. Recommendation-specific strategies, related to specific decision points in the guideline, were also suggested: These include structuring the presentation of healthcare options to increase professionals' option awareness; structuring the deliberation process between professionals and patients; and providing relevant patient support tools embedded at important decision points in the guideline. This study resulted in an overview of strategies to adapt clinical practice guidelines to facilitate shared decision making. Some strategies seemed more contentious than others. Future research should assess the feasibility and impact of these strategies to make clinical practice guidelines more conducive to facilitate shared decision making.

Structures of Ca(V) Ca**2+/CaM-IQ Domain Complexes Reveal Binding Modes That Underlie Calcium-Dependent Inactivation And Facilitation

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

Kim, E.Y.; Rumpf, C.H.; Fujiwara, Y.

2009-05-20

Calcium influx drives two opposing voltage-activated calcium channel (Ca{sub V}) self-modulatory processes: calcium-dependent inactivation (CDI) and calcium-dependent facilitation (CDF). Specific Ca{sup 2+}/calmodulin (Ca{sup 2+}/CaM) lobes produce CDI and CDF through interactions with the Ca{sub V}{alpha}{sub 1} subunit IQ domain. Curiously, Ca{sup 2+}/CaM lobe modulation polarity appears inverted between Ca{sub V}1s and Ca{sub V}2s. Here, we present crystal structures of Ca{sub V}2.1, Ca{sub V}2.2, and Ca{sub V}2.3 Ca{sup 2+}/CaM-IQ domain complexes. All display binding orientations opposite to Ca{sub V}1.2 with a physical reversal of the CaM lobe positions relative to the IQ {alpha}-helix. Titration calorimetry reveals lobe competition for a high-affinitymore » site common to Ca{sub V}1 and Ca{sub V}2 IQ domains that is occupied by the CDI lobe in the structures. Electrophysiological experiments demonstrate that the N-terminal Ca{sub V}2 Ca{sup 2+}/C-lobe anchors affect CDF. Together, the data unveil the remarkable structural plasticity at the heart of Ca{sub V} feedback modulation and indicate that Ca{sub V}1 and Ca{sub V}2 IQ domains bear a dedicated CDF site that exchanges Ca{sup 2+}/CaM lobe occupants.« less

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

DOE PAGES

Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; ...

2015-07-30

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

Shape determination and control for large space structures

NASA Technical Reports Server (NTRS)

Weeks, C. J.

1981-01-01

An integral operator approach is used to derive solutions to static shape determination and control problems associated with large space structures. Problem assumptions include a linear self-adjoint system model, observations and control forces at discrete points, and performance criteria for the comparison of estimates or control forms. Results are illustrated by simulations in the one dimensional case with a flexible beam model, and in the multidimensional case with a finite model of a large space antenna. Modal expansions for terms in the solution algorithms are presented, using modes from the static or associated dynamic mode. These expansions provide approximated solutions in the event that a used form analytical solution to the system boundary value problem is not available.

Strategies for healthcare professionals to facilitate patient illness understanding.

PubMed

Nunstedt, Håkan; Rudolfsson, Gudrun; Alsén, Pia; Pennbrant, Sandra

2017-12-01

To describe how healthcare professionals facilitate patient illness understanding. Healthcare professionals and patients differ in their illness understanding. If the information provided by healthcare professionals is not adapted to the patient's daily life, it may be unusable for the patient. Previous research has found that healthcare professionals should individualise the information to enable the patient to apply the knowledge to the personal situation and to develop illness understanding. However, little is known of how healthcare professionals can facilitate patient illness understanding. A qualitative descriptive study based on individual, semi-structured, open-ended and face-to-face interviews was conducted with healthcare professionals (n = 11) concerning how they facilitate patients illness understanding. Three health centres were involved during the period of March to November 2014. The interviews were analysed with qualitative content analysis. The result identified a continuous and collaborative process with three strategies used by healthcare professionals to facilitate the patient's illness understanding: (i) assess the patient's illness understanding, (ii) interact with the patient to develop illness understanding and (iii) support the patient's personal development for illness understanding. The steps in the process depend on each other. The results of our analysis indicate that healthcare professionals can use the continuous and collaborative process to enhance the patient's self-care ability and turn his or her knowledge into action for improving illness understanding. The three continuous and collaborative process strategies involving pedagogical approaches can create conditions for healthcare professionals to obtain a holistic view of the patient's life and to be a key resource for person-centred care. © 2017 John Wiley & Sons Ltd.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal.

PubMed

Clabbers, M T B; van Genderen, E; Wan, W; Wiegers, E L; Gruene, T; Abrahams, J P

2017-09-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm 3 , i.e. no more than 6 × 10 5 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

PubMed Central

Clabbers, M. T. B.; van Genderen, E.; Wiegers, E. L.; Gruene, T.; Abrahams, J. P.

2017-01-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm3, i.e. no more than 6 × 105 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures. PMID:28876237

The Internet Process Addiction Test: Screening for Addictions to Processes Facilitated by the Internet.

PubMed

Northrup, Jason C; Lapierre, Coady; Kirk, Jeffrey; Rae, Cosette

2015-07-28

The Internet Process Addiction Test (IPAT) was created to screen for potential addictive behaviors that could be facilitated by the internet. The IPAT was created with the mindset that the term "Internet addiction" is structurally problematic, as the Internet is simply the medium that one uses to access various addictive processes. The role of the internet in facilitating addictions, however, cannot be minimized. A new screening tool that effectively directed researchers and clinicians to the specific processes facilitated by the internet would therefore be useful. This study shows that the Internet Process Addiction Test (IPAT) demonstrates good validity and reliability. Four addictive processes were effectively screened for with the IPAT: Online video game playing, online social networking, online sexual activity, and web surfing. Implications for further research and limitations of the study are discussed.

Integrating pharmacists into primary care teams: barriers and facilitators.

PubMed

Jorgenson, Derek; Laubscher, Tessa; Lyons, Barry; Palmer, Rebecca

2014-08-01

This study evaluated the barriers and facilitators that were experienced as pharmacists were integrated into 23 existing primary care teams located in urban and rural communities in Saskatchewan, Canada. Qualitative design using data from one-on-one telephone interviews with pharmacists, physicians and nurse practitioners from the 23 teams that integrated a new pharmacist role. Four researchers from varied backgrounds used thematic analysis of the interview transcripts to determine key themes. The research team met on multiple occasions to agree on the key themes and received written feedback from an external auditor and two of the original interviewees. Seven key themes emerged describing the barriers and facilitators that the teams experienced during the pharmacist integration: (1) relationships, trust and respect; (2) pharmacist role definition; (3) orientation and support; (4) pharmacist personality and professional experience; (5) pharmacist presence and visibility; (6) resources and funding; and (7) value of the pharmacist role. Teams from urban and rural communities experienced some of these challenges in unique ways. Primary care teams that integrated a pharmacist experienced several common barriers and facilitators. The negative impact of these barriers can be mitigated with effective planning and support that is individualized for the type of community where the team is located. © 2013 Royal Pharmaceutical Society.

Inter-species competition-facilitation in stochastic riparian vegetation dynamics.

PubMed

Tealdi, Stefano; Camporeale, Carlo; Ridolfi, Luca

2013-02-07

Riparian vegetation is a highly dynamic community that lives on river banks and which depends to a great extent on the fluvial hydrology. The stochasticity of the discharge and erosion/deposition processes in fact play a key role in determining the distribution of vegetation along a riparian transect. These abiotic processes interact with biotic competition/facilitation mechanisms, such as plant competition for light, water, and nutrients. In this work, we focus on the dynamics of plants characterized by three components: (1) stochastic forcing due to river discharges, (2) competition for resources, and (3) inter-species facilitation due to the interplay between vegetation and fluid dynamics processes. A minimalist stochastic bio-hydrological model is proposed for the dynamics of the biomass of two vegetation species: one species is assumed dominant and slow-growing, the other is subdominant, but fast-growing. The stochastic model is solved analytically and the probability density function of the plant biomasses is obtained as a function of both the hydrologic and biologic parameters. The impact of the competition/facilitation processes on the distribution of vegetation species along the riparian transect is investigated and remarkable effects are observed. Finally, a good qualitative agreement is found between the model results and field data. Copyright © 2012 Elsevier Ltd. All rights reserved.

Biosynthetic multitasking facilitates thalassospiramide structural diversity in marine bacteria.

PubMed

Ross, Avena C; Xu, Ying; Lu, Liang; Kersten, Roland D; Shao, Zongze; Al-Suwailem, Abdulaziz M; Dorrestein, Pieter C; Qian, Pei-Yuan; Moore, Bradley S

2013-01-23

Thalassospiramides A and B are immunosuppressant cyclic lipopeptides first reported from the marine α-proteobacterium Thalassospira sp. CNJ-328. We describe here the discovery and characterization of an extended family of 14 new analogues from four Tistrella and Thalassospira isolates. These potent calpain 1 protease inhibitors belong to six structure classes in which the length and composition of the acylpeptide side chain varies extensively. Genomic sequence analysis of the thalassospiramide-producing microbes revealed related, genus-specific biosynthetic loci encoding hybrid nonribosomal peptide synthetase/polyketide synthases consistent with thalassospiramide assembly. The bioinformatics analysis of the gene clusters suggests that structural diversity, which ranges from the 803.4 Da thalassospiramide C to the 1291.7 Da thalassospiramide F, results from a complex sequence of reactions involving amino acid substrate channeling and enzymatic multimodule skipping and iteration. Preliminary biochemical analysis of the N-terminal nonribosomal peptide synthetase module from the Thalassospira TtcA megasynthase supports a biosynthetic model in which in cis amino acid activation competes with in trans activation to increase the range of amino acid substrates incorporated at the N terminus.

Biosynthetic Multitasking Facilitates Thalassospiramide Structural Diversity in Marine Bacteria

PubMed Central

Ross, Avena C.; Xu, Ying; Lu, Liang; Kersten, Roland D.; Shao, Zongze; Al-Suwailem, Abdulaziz M.; Dorrestein, Pieter C.; Qian, Pei-Yuan; Moore, Bradley S.

2013-01-01

Thalassospiramides A and B are immunosuppressant cyclic lipopeptides first reported from the marine α-proteobacterium Thalassospira sp. CNJ-328. We describe here the discovery and characterization of an extended family of 14 new analogues from four Tistrella and Thalassospira isolates. These potent calpain 1 protease inhibitors belong to six structure classes in which the length and composition of the acylpeptide side chain varies extensively. Genomic sequence analysis of the thalassospiramide-producing microbes revealed related, genus-specific biosynthetic loci encoding hybrid nonribosomal peptide synthetase/polyketide synthases consistent with thalassospiramide assembly. The bioinformatics analysis of the gene clusters suggests that structural diversity, which ranges from the 803.4 Da thalassospiramide C to the 1291.7 Da thalassospiramide F, results from a complex sequence of reactions involving amino acid substrate channeling and enzymatic multi-module skipping and iteration. Preliminary biochemical analysis of the N-terminal NRPS module from the Thalassospira TtcA megasynthase supports a biosynthetic model in which in cis amino acid activation competes with in trans activation to increase the range of amino acid substrates incorporated at the N-terminus. PMID:23270364

Exploiting the Synergy of Powder X-ray Diffraction and Solid-State NMR Spectroscopy in Structure Determination of Organic Molecular Solids

PubMed Central

2013-01-01

We report a strategy for structure determination of organic materials in which complete solid-state nuclear magnetic resonance (NMR) spectral data is utilized within the context of structure determination from powder X-ray diffraction (XRD) data. Following determination of the crystal structure from powder XRD data, first-principles density functional theory-based techniques within the GIPAW approach are exploited to calculate the solid-state NMR data for the structure, followed by careful scrutiny of the agreement with experimental solid-state NMR data. The successful application of this approach is demonstrated by structure determination of the 1:1 cocrystal of indomethacin and nicotinamide. The 1H and 13C chemical shifts calculated for the crystal structure determined from the powder XRD data are in excellent agreement with those measured experimentally, notably including the two-dimensional correlation of 1H and 13C chemical shifts for directly bonded 13C–1H moieties. The key feature of this combined approach is that the quality of the structure determined is assessed both against experimental powder XRD data and against experimental solid-state NMR data, thus providing a very robust validation of the veracity of the structure. PMID:24386493

Exploiting the Synergy of Powder X-ray Diffraction and Solid-State NMR Spectroscopy in Structure Determination of Organic Molecular Solids.

PubMed

Dudenko, Dmytro V; Williams, P Andrew; Hughes, Colan E; Antzutkin, Oleg N; Velaga, Sitaram P; Brown, Steven P; Harris, Kenneth D M

2013-06-13

We report a strategy for structure determination of organic materials in which complete solid-state nuclear magnetic resonance (NMR) spectral data is utilized within the context of structure determination from powder X-ray diffraction (XRD) data. Following determination of the crystal structure from powder XRD data, first-principles density functional theory-based techniques within the GIPAW approach are exploited to calculate the solid-state NMR data for the structure, followed by careful scrutiny of the agreement with experimental solid-state NMR data. The successful application of this approach is demonstrated by structure determination of the 1:1 cocrystal of indomethacin and nicotinamide. The 1 H and 13 C chemical shifts calculated for the crystal structure determined from the powder XRD data are in excellent agreement with those measured experimentally, notably including the two-dimensional correlation of 1 H and 13 C chemical shifts for directly bonded 13 C- 1 H moieties. The key feature of this combined approach is that the quality of the structure determined is assessed both against experimental powder XRD data and against experimental solid-state NMR data, thus providing a very robust validation of the veracity of the structure.

Facilitating Self-Determination in Adolescents with Intellectual Disabilities: A Curriculum

ERIC Educational Resources Information Center

Haelewyck, Marie-Claire; Bara, Melanie; Lachapelle, Yves

2005-01-01

Taking an active part and responsibilities in one's own life is not always easy, particularly at adolescence, which is a very important period in which people progressively find their identity and life project. This article describes the social validation analyses of a Belgian self-determination curriculum that was adapted from a French-Canadian…

Coaches' Perspectives on Their Roles in Facilitating the Personal Development of Student-Athletes

ERIC Educational Resources Information Center

Banwell, Jenessa; Kerr, Gretchen

2016-01-01

The purpose of this study was to investigate coaches' perspectives on the personal development student-athletes experience through interuniversity sport. Additionally, it explored the ways in which coaches understand, enable, and facilitate the personal development of student-athletes. Eight in-depth, semi-structured interviews were conducted with…

The History of Molecular Structure Determination Viewed through the Nobel Prizes

NASA Astrophysics Data System (ADS)

Jensen, William P.; Palenik, Gus J.; Suh, Il-Hwan

2003-07-01

For the past 100 years, with only a few exceptions during war times, Nobel Prizes have been awarded annually to men and women who have made exceptionally important discoveries in science. In thirteen of those years, prizes were awarded to individuals whose contributions helped explain the molecular world of matter through interactions of waves or particles with atoms. From William C. Röntgen, who received the very first Nobel Prize in Physics in 1901 for his work with X-rays, to von Laue and the father-and-son Bragg team in the second decade of the century, who used X-rays to understand atomic arrangements, much progress had been made revealing secrets at the molecular level of matter. In the 1930s Debye, Davisson, and Thomson revealed further information using, among other techniques, diffraction of electrons by matter. In the 1960s Crick, Watson, Wilkins, Perutz, Kendrew, and Hodgkin received Nobel Prizes for revealing structures of significantly more complex molecules including the DNA double helix, myoglobin, hemoglobin, and vitamin B12. In the 1970s and 1980s Lipscomb would be recognized for organizing our picture of boron hydrides, Klug would use electron diffraction to determine structures of important nucleic acid protein complexes, Hauptman and Karle would bring us a powerful new way to solve structures, and Deisenhofer, Huber, and Michel would determine the three-dimensional structure of a photosynthetic reaction center. Finally, in 1994 Brockhouse and Shull were recognized for their work with neutrons. Crystallography has been used to answer increasingly complex questions in the past, and will certainly remain an important tool in the future.

Facilitation of Endosomal Recycling by an IRG Protein Homolog Maintains Apical Tubule Structure in Caenorhabditis elegans

PubMed Central

Grussendorf, Kelly A.; Trezza, Christopher J.; Salem, Alexander T.; Al-Hashimi, Hikmat; Mattingly, Brendan C.; Kampmeyer, Drew E.; Khan, Liakot A.; Hall, David H.; Göbel, Verena; Ackley, Brian D.; Buechner, Matthew

2016-01-01

Determination of luminal diameter is critical to the function of small single-celled tubes. A series of EXC proteins, including EXC-1, prevent swelling of the tubular excretory canals in Caenorhabditis elegans. In this study, cloning of exc-1 reveals it to encode a homolog of mammalian IRG proteins, which play roles in immune response and autophagy and are associated with Crohn’s disease. Mutants in exc-1 accumulate early endosomes, lack recycling endosomes, and exhibit abnormal apical cytoskeletal structure in regions of enlarged tubules. EXC-1 interacts genetically with two other EXC proteins that also affect endosomal trafficking. In yeast two-hybrid assays, wild-type and putative constitutively active EXC-1 binds to the LIM-domain protein EXC-9, whose homolog, cysteine-rich intestinal protein, is enriched in mammalian intestine. These results suggest a model for IRG function in forming and maintaining apical tubule structure via regulation of endosomal recycling. PMID:27334269

Identifying Facilitators and Barriers to Physical Activity for Adults with Down Syndrome

ERIC Educational Resources Information Center

Mahy, J.; Shields, N.; Taylor, N. F.; Dodd, K. J.

2010-01-01

Background: Adults with Down syndrome are typically sedentary, and many do not participate in the recommended levels of physical activity per week. The aim of this study was to identify the facilitators and barriers to physical activity for this group. Method: Semi-structured interviews were conducted to elicit the views of adults with Down…

Facilitated Communication: An Experimental Evaluation.

ERIC Educational Resources Information Center

Regal, Robert A.; And Others

1994-01-01

Nineteen adults with developmental disabilities, judged competent in facilitated communication, participated in a validation study using an information passing design requiring short-term recall of stimulus cards with shapes, colors, and numbers. Results failed to validate facilitated communication for the group as a whole, any individual…

Virtual OD: Facilitating Groups Online

ERIC Educational Resources Information Center

Milton, Judy; Watkins, Karen E.; Daley, Barbara J.

2005-01-01

This study examined the role of facilitators in nine virtual action learning groups. A qualitative analysis of the facilitators' interventions across all groups resulted in a typology that included group management, group process, and support interventions. A model showing the relationship among these categories proposes that effective…

From the voices of women: facilitating survivor access to IPV services.

PubMed

Simmons, Catherine A; Farrar, Melissa; Frazer, Kitty; Thompson, Mary Jane

2011-10-01

This mixed-method study investigated perceptions women domestic violence survivors/victims have about why women do not seek help from formal support structures and actions domestic helping agencies can take to facilitate survivor access to services. Congruent with previous research, quantitative analysis identified 17 reasons women do not seek help from formal support structures. Expanding current knowledge, concept mapping revealed six ways family violence programs can better reach women in abusive relationships, including (1) remove barriers to services, (2) improve comfort with services, (3) "talk about it," (4) improve community awareness, (5) victim-targeted marketing, and (6) "I honestly don't know."

A student-initiated and student-facilitated international health elective for preclinical medical students

PubMed Central

Vora, Nirali; Chang, Mina; Pandya, Hemang; Hasham, Aliya; Lazarus, Cathy

2010-01-01

Introduction Global health education is becoming more important for developing well-rounded physicians and may encourage students toward a career in primary care. Many medical schools, however, lack adequate and structured opportunities for students beginning the curriculum. Methods Second-year medical students initiated, designed, and facilitated a pass–fail international health elective, providing a curricular framework for preclinical medical students wishing to gain exposure to the clinical and cultural practices of a developing country. Results All course participants (N=30) completed a post-travel questionnaire within one week of sharing their experiences. Screening reflection essays for common themes that fulfill university core competencies yielded specific global health learning outcomes, including analysis of health care determinants. Conclusion Medical students successfully implemented a sustainable global health curriculum for preclinical student peers. Financial constraints, language, and organizational burdens limit student participation. In future, long-term studies should analyze career impact and benefits to the host country. PMID:20186283

Ab initio structure determination and quantitative disorder analysis on nanoparticles by electron diffraction tomography.

PubMed

Krysiak, Yaşar; Barton, Bastian; Marler, Bernd; Neder, Reinhard B; Kolb, Ute

2018-03-01

Nanoscaled porous materials such as zeolites have attracted substantial attention in industry due to their catalytic activity, and their performance in sorption and separation processes. In order to understand the properties of such materials, current research focuses increasingly on the determination of structural features beyond the averaged crystal structure. Small particle sizes, various types of disorder and intergrown structures render the description of structures at atomic level by standard crystallographic methods difficult. This paper reports the characterization of a strongly disordered zeolite structure, using a combination of electron exit-wave reconstruction, automated diffraction tomography (ADT), crystal disorder modelling and electron diffraction simulations. Zeolite beta was chosen for a proof-of-principle study of the techniques, because it consists of two different intergrown polymorphs that are built from identical layer types but with different stacking sequences. Imaging of the projected inner Coulomb potential of zeolite beta crystals shows the intergrowth of the polymorphs BEA and BEB. The structures of BEA as well as BEB could be extracted from one single ADT data set using direct methods. A ratio for BEA/BEB = 48:52 was determined by comparison of the reconstructed reciprocal space based on ADT data with simulated electron diffraction data for virtual nanocrystals, built with different ratios of BEA/BEB. In this way, it is demonstrated that this smart interplay of the above-mentioned techniques allows the elaboration of the real structures of functional materials in detail - even if they possess a severely disordered structure.

Relative Ranking of Conditions that Facilitate Innovation Implementation in the USA

ERIC Educational Resources Information Center

Ensminger, David C.; Surry, Daniel W,

2008-01-01

This study compared how people working in three different types of organisations in the United States (K-12 schools, higher education, and business) rank the importance of eight conditions that have been shown to facilitate the implementation of innovations. The study also sought to determine if the nature of the innovation (i.e., technology or…

Common Perceived Barriers and Facilitators for Reducing Sedentary Behaviour among Office Workers

PubMed Central

Kallings, Lena V.; Blom, Victoria; Forsell, Yvonne; Ekblom, Maria M.

2018-01-01

Qualitative studies identified barriers and facilitators associated with work-related sedentary behaviour. The objective of this study was to determine common perceived barriers and facilitators among office workers, assess subgroup differences, and describe sedentary behaviour. From two Swedish companies, 547 office workers (41 years (IQR = 35–48), 65% women, 66% highly educated) completed questionnaires on perceived barriers and facilitators, for which subgroup differences in age, gender, education, and workplace sedentary behaviour were assessed. Sedentary behaviour was measured using inclinometers (n = 311). The most frequently reported barrier was sitting is a habit (67%), which was reported more among women than men (Χ2 = 5.14, p = 0.03) and more among highly sedentary office workers (Χ2 = 9.26, p < 0.01). The two other most reported barriers were that standing is uncomfortable (29%) and standing is tiring (24%). Facilitators with the most support were the introduction of either standing- or walking-meetings (respectively 33% and 29%) and more possibilities or reminders for breaks (31%). The proportion spent sedentary was 64% at the workplace, 61% on working days, and 57% on non-working days. This study provides a detailed understanding of office workers’ ideas about sitting and means to reduce sitting. We advise to include the supported facilitators and individualized support in interventions to work towards more effective strategies to reduce sedentary behaviour. PMID:29670047

Common Perceived Barriers and Facilitators for Reducing Sedentary Behaviour among Office Workers.

PubMed

Nooijen, Carla F J; Kallings, Lena V; Blom, Victoria; Ekblom, Örjan; Forsell, Yvonne; Ekblom, Maria M

2018-04-18

Qualitative studies identified barriers and facilitators associated with work-related sedentary behaviour. The objective of this study was to determine common perceived barriers and facilitators among office workers, assess subgroup differences, and describe sedentary behaviour. From two Swedish companies, 547 office workers (41 years (IQR = 35–48), 65% women, 66% highly educated) completed questionnaires on perceived barriers and facilitators, for which subgroup differences in age, gender, education, and workplace sedentary behaviour were assessed. Sedentary behaviour was measured using inclinometers ( n = 311). The most frequently reported barrier was sitting is a habit (67%), which was reported more among women than men (Χ² = 5.14, p = 0.03) and more among highly sedentary office workers (Χ² = 9.26, p < 0.01). The two other most reported barriers were that standing is uncomfortable (29%) and standing is tiring (24%). Facilitators with the most support were the introduction of either standing- or walking-meetings (respectively 33% and 29%) and more possibilities or reminders for breaks (31%). The proportion spent sedentary was 64% at the workplace, 61% on working days, and 57% on non-working days. This study provides a detailed understanding of office workers’ ideas about sitting and means to reduce sitting. We advise to include the supported facilitators and individualized support in interventions to work towards more effective strategies to reduce sedentary behaviour.

Use of an Objective Structured Clinical Examination in Clinical Nurse Specialist Education.

PubMed

Cuevas, Heather E; Timmerman, Gayle M

2016-01-01

Helping patients maximize their potential using expert coaching to facilitate lifestyle change is an important practice area for clinical nurse specialists (CNSs). The purpose is to determine the usefulness of objective structured clinical examinations (OSCEs) for evaluating CNS students' coaching competencies in the context of facilitating lifestyle change. Despite the use of OSCEs to assess competencies in clinical skills (eg, performance of procedures, decision making), its potential for evaluating coaching competencies for lifestyle change has not been demonstrated. We developed 4 OSCEs dealing with coaching patients in exercise, weight loss, stress reduction, or nonpharmacologic management of hyperlipidemia. Evaluation criteria included (1) approach to the patient, (2) information gathering, (3) motivational interviewing, and (4) management (medical and behavioral strategies). Student performance ranged from highly organized with proficient coaching skills to disorganized and focused solely on clinical management and prescriptive communication. Student responses were positive. Objective structured clinical examinations were highly useful for evaluating CNS students' coaching competencies for lifestyle change. Using OSCEs early in the semester to provide students feedback on their performance and again at the end to determine improvement optimizes use of this teaching strategy.

Facilitating Dialogues about Racial Realities

ERIC Educational Resources Information Center

Quaye, Stephen John

2014-01-01

Background/Context: Facilitating dialogues about racial issues in higher education classroom settings continues to be a vexing problem facing postsecondary educators. In order for students to discuss race with their peers, they need skilled facilitators who are knowledgeable about racial issues and able to support students in these difficult…

The Essential Elements of Facilitation.

ERIC Educational Resources Information Center

Priest, Simon; Gass, Michael; Gillis, Lee

Most organizations find it difficult to implement change, and only about 10 percent of learning from training and development experiences is actually applied in the workplace. This book advocates facilitation as a means of enhancing change and increasing productivity. Facilitation engages employees by enhancing the processes associated with their…

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases

PubMed Central

Mariani, Simona; Dell'Orco, Daniele; Felline, Angelo; Raimondi, Francesco; Fanelli, Francesca

2013-01-01

A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions. PMID:24009494

"Refreshed…reinforced…reflective": A qualitative exploration of interprofessional education facilitators' own interprofessional learning and collaborative practice.

PubMed

Evans, Sherryn; Shaw, Nicole; Ward, Catherine; Hayley, Alexa

2016-11-01

While there is extensive research examining the outcomes of interprofessional education (IPE) for students, minimal research has investigated how facilitating student learning influences the facilitators themselves. This exploratory case study aimed to explore whether and how facilitating IPE influences facilitators' own collaborative practice attitudes, knowledge, and workplace behaviours. Sixteen facilitators of an online pre-licensure IPE unit for an Australian university participated in semi-structured telephone interviews. Inductive thematic analysis revealed three emergent themes and associated subthemes characterising participants' reflexivity as IPE facilitators: interprofessional learning; professional behaviour change; and collaborative practice expertise. Participants experienced interprofessional learning in their role as facilitators, improving their understanding of other professionals' roles, theoretical and empirical knowledge underlying collaborative practice, and the use and value of online communication. Participants also reported having changed several professional behaviours, including improved interprofessional collaboration with colleagues, a change in care plan focus, a less didactic approach to supervising students and staff, and greater enthusiasm impressing the value of collaborative practice on placement students. Participants reported having acquired their prior interprofessional collaboration expertise via professional experience rather than formal learning opportunities and believed access to formal IPE as learners would aid their continuing professional development. Overall, the outcomes of the IPE experience extended past the intended audience of the student learners and positively impacted on the facilitators as well.

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination

PubMed Central

Lee, Woonghee; Kim, Jin Hae; Westler, William M.; Markley, John L.

2011-01-01

Summary: PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY (13C-edited and/or 15N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. Availability: The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/. Contact: whlee@nmrfam.wisc.edu; markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21511715

Implications of Mycobacterium Major Facilitator Superfamily for Novel Measures against Tuberculosis.

PubMed

Wang, Rui; Zhang, Zhen; Xie, Longxiang; Xie, Jianping

2015-01-01

Major facilitator superfamily (MFS) is an important secondary membrane transport protein superfamily conserved from prokaryotes to eukaryotes. The MFS proteins are widespread among bacteria and are responsible for the transfer of substrates. Pathogenic Mycobacterium MFS transporters, their distribution, function, phylogeny, and predicted crystal structures were studied to better understand the function of MFS and to discover specific inhibitors of MFS for better tuberculosis control.

Use of HIT for adverse event reporting in nursing homes: barriers and facilitators.

PubMed

Wagner, Laura M; Castle, Nicholas G; Handler, Steven M

2013-01-01

Approximately 8 million adverse events occur annually in nursing homes (NHs). The focus of this research is to determine barriers and health information technology (HIT)-related facilitators to adverse event reporting among U.S. NHs. Surveys were returned by 399 nursing home administrators using a mailed survey approach. Respondents were asked to report on their adverse event reporting processes focusing on barriers and role of HIT facilitators. About 15% of NHs had computerized entry by the nurse on the unit and almost 18% used no computer technology to track, monitor, or maintain adverse event data. One-third of nursing directors conducted data analysis "by-hand." NHs without HIT were more likely to not be accredited (p = 0.04) and not part of a chain/corporation (p = 0.03). Two of the top three barriers focused on fears of reporting as a barrier. This study found numerous barriers and few HIT-related facilitators to assist with adverse event reporting. Improvements in facilitating adverse event reporting through the use of HIT approaches may be warranted. Copyright © 2013 Mosby, Inc. All rights reserved.