Generating structured light with phase helix and intensity helix using reflection-enhanced plasmonic metasurface at 2 μm

Science.gov (United States)

Zhao, Yifan; Du, Jing; Zhang, Jinrun; Shen, Li; Wang, Jian

2018-04-01

Mid-infrared (2-20 μm) light has been attracting great attention in many areas of science and technology. Beyond the extended wavelength range from visible and near-infrared to mid-infrared, shaping spatial structures may add opportunities to grooming applications of mid-infrared photonics. Here, we design and fabricate a reflection-enhanced plasmonic metasurface and demonstrate efficient generation of structured light with the phase helix and intensity helix at 2 μm. This work includes two distinct aspects. First, structured light (phase helix, intensity helix) generation at 2 μm, which is far beyond the ability of conventional spatial light modulators, is enabled by the metasurface with sub-wavelength engineered structures. Second, the self-referenced intensity helix against environmental noise is generated without using a spatially separated light. The demonstrations may open up advanced perspectives to structured light applications at 2 μm, such as phase helix for communications and non-communications (imaging, sensing) and intensity helix for enhanced microscopy and advanced metrology.

A Classification of Basic Helix-Loop-Helix Transcription Factors of Soybean

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Karen A. Hudson

2015-01-01

Full Text Available The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281 of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

OpenAIRE

Pires, Nuno; Dolan, Liam

2009-01-01

Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use wh...

Recognition and Binding of a Helix-Loop-Helix Peptide to Carbonic Anhydrase Occurs via Partly Folded Intermediate Structures

Science.gov (United States)

Lignell, Martin; Becker, Hans-Christian

2010-01-01

Abstract We have studied the association of a helix-loop-helix peptide scaffold carrying a benzenesulfonamide ligand to carbonic anhydrase using steady-state and time-resolved fluorescence spectroscopy. The helix-loop-helix peptide, developed for biosensing applications, is labeled with the fluorescent probe dansyl, which serves as a polarity-sensitive reporter of the binding event. Using maximum entropy analysis of the fluorescence lifetime of dansyl at 1:1 stoichiometry reveals three characteristic fluorescence lifetime groups, interpreted as differently interacting peptide/protein structures. We characterize these peptide/protein complexes as mostly bound but unfolded, bound and partly folded, and strongly bound and folded. Furthermore, analysis of the fluorescence anisotropy decay resulted in three different dansyl rotational correlation times, namely 0.18, 1.2, and 23 ns. Using the amplitudes of these times, we can correlate the lifetime groups with the corresponding fluorescence anisotropy component. The 23-ns rotational correlation time, which appears with the same amplitude as a 17-ns fluorescence lifetime, shows that the dansyl fluorophore follows the rotational diffusion of carbonic anhydrase when it is a part of the folded peptide/protein complex. A partly folded and partly hydrated interfacial structure is manifested in an 8-ns dansyl fluorescence lifetime and a 1.2-ns rotational correlation time. This structure, we believe, is similar to a molten-globule-like interfacial structure, which allows segmental movement and has a higher degree of solvent exposure of dansyl. Indirect excitation of dansyl on the helix-loop-helix peptide through Förster energy transfer from one or several tryptophans in the carbonic anhydrase shows that the helix-loop-helix scaffold binds to a tryptophan-rich domain of the carbonic anhydrase. We conclude that binding of the peptide to carbonic anhydrase involves a transition from a disordered to an ordered structure of the

Chirality-specific lift forces of helix under shear flows: Helix perpendicular to shear plane.

Science.gov (United States)

Zhang, Qi-Yi

2017-02-01

Chiral objects in shear flow experience a chirality-specific lift force. Shear flows past helices in a low Reynolds number regime were studied using slender-body theory. The chirality-specific lift forces in the vorticity direction experienced by helices are dominated by a set of helix geometry parameters: helix radius, pitch length, number of turns, and helix phase angle. Its analytical formula is given. The chirality-specific forces are the physical reasons for the chiral separation of helices in shear flow. Our results are well supported by the latest experimental observations. © 2016 Wiley Periodicals, Inc.

Stretched versus compressed exponential kinetics in α-helix folding

International Nuclear Information System (INIS)

Hamm, Peter; Helbing, Jan; Bredenbeck, Jens

2006-01-01

In a recent paper (J. Bredenbeck, J. Helbing, J.R. Kumita, G.A. Woolley, P. Hamm, α-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time resolved IR spectroscopy, Proc. Natl. Acad. Sci USA 102 (2005) 2379), we have investigated the folding of a photo-switchable α-helix with a kinetics that could be fit by a stretched exponential function exp(-(t/τ) β ). The stretching factor β became smaller as the temperature was lowered, a result which has been interpreted in terms of activated diffusion on a rugged energy surface. In the present paper, we discuss under which conditions diffusion problems occur with stretched exponential kinetics (β 1). We show that diffusion problems do have a strong tendency to yield stretched exponential kinetics, yet, that there are conditions (strong perturbation from equilibrium, performing the experiment in the folding direction) under which compressed exponential kinetics would be expected instead. We discuss the kinetics on free energy surfaces predicted by simple initiation-propagation models (zipper models) of α-helix folding, as well as by folding funnel models. We show that our recent experiment has been performed under condition for which models with strong downhill driving force, such as the zipper model, would predict compressed, rather than stretched exponential kinetics, in disagreement with the experimental observation. We therefore propose that the free energy surface along a reaction coordinate that governs the folding kinetics must be relatively flat and has a shape similar to a 1D golf course. We discuss how this conclusion can be unified with the thermodynamically well established zipper model by introducing an additional kinetic reaction coordinate

Structural Analysis and Aggregation Propensity of Pyroglutamate Aβ(3-40 in Aqueous Trifluoroethanol.

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Christina Dammers

Full Text Available A hallmark of Alzheimer's disease (AD is the accumulation of extracellular amyloid-β (Aβ plaques in the brains of patients. N-terminally truncated pyroglutamate-modified Aβ (pEAβ has been described as a major compound of Aβ species in senile plaques. pEAβ is more resistant to degradation, shows higher toxicity and has increased aggregation propensity and β-sheet stabilization compared to non-modified Aβ. Here we characterized recombinant pEAβ(3-40 in aqueous trifluoroethanol (TFE solution regarding its aggregation propensity and structural changes in comparison to its non-pyroglutamate-modified variant Aβ(1-40. Secondary structure analysis by circular dichroism spectroscopy suggests that pEAβ(3-40 shows an increased tendency to form β-sheet-rich structures in 20% TFE containing solutions where Aβ(1-40 forms α-helices. Aggregation kinetics of pEAβ(3-40 in the presence of 20% TFE monitored by thioflavin-T (ThT assay showed a typical sigmoidal aggregation in contrast to Aβ(1-40, which lacks ThT positive structures under the same conditions. Transmission electron microscopy confirms that pEAβ(3-40 aggregated to large fibrils and high molecular weight aggregates in spite of the presence of the helix stabilizing co-solvent TFE. High resolution NMR spectroscopy of recombinantly produced and uniformly isotope labeled [U-15N]-pEAβ(3-40 in TFE containing solutions indicates that the pyroglutamate formation affects significantly the N-terminal region, which in turn leads to decreased monomer stability and increased aggregation propensity.

Wave Propagation of Coupled Modes in the DNA Double Helix

International Nuclear Information System (INIS)

Tabi, Conrad B.; Mohamadou, Alidou; Kofane, Timoleon C.

2010-06-01

The dynamics of waves propagating along the DNA molecule is described by the coupled nonlinear Schroedinger equations. We consider both the single and the coupled nonlinear excitation modes, and we discuss their biological implications. Furthermore, the characteristics of the coupled mode solution are discussed and we show that such a solution can describe the local opening observed within the transcription and the replication phenomena. (author)

Helix-Hopes on Finite Hyperfields

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Thomas Vougiouklis

2016-12-01

Full Text Available Hyperstructure theory can overcome restrictions which ordinary algebraic structures have. A hyperproduct on non-square ordinary matrices can be defined by using the so called helix-hyperoperations. We study the helix-hyperstructures on the representations using ordinary fields. The related theory can be faced by defining the hyperproduct on the set of non square matrices. The main tools of the Hyperstructure Theory are the fundamental relations which connect the largest class of hyperstructures, the Hv-structures, with the corresponding classical ones. We focus on finite dimensional helix-hyperstructures and on small Hv-fields, as well.

Gibberellin-regulated gene in the basal region of rice leaf sheath encodes basic helix-loop-helix transcription factor.

Science.gov (United States)

Komatsu, Setsuko; Takasaki, Hironori

2009-07-01

Genes regulated by gibberellin (GA) during leaf sheath elongation in rice seedlings were identified using the transcriptome approach. mRNA from the basal regions of leaf sheaths treated with GA3 was analyzed by high-coverage gene expression profiling. 33,004 peaks were detected, and 30 transcripts showed significant changes in the presence of GA3. Among these, basic helix-loop-helix transcription factor (AK073385) was significantly upregulated. Quantitative PCR analysis confirmed that expression of AK073385 was controlled by GA3 in a time- and dose-dependent manner. Basic helix-loop-helix transcription factor (AK073385) is therefore involved in the regulation of gene expression by GA3.

Double-helix stellarator

International Nuclear Information System (INIS)

Moroz, P.E.

1997-09-01

A new stellarator configuration, the Double-Helix Stellarator (DHS), is introduced. This novel configuration features a double-helix center post as the only helical element of the stellarator coil system. The DHS configuration has many unique characteristics. One of them is the extreme low plasma aspect ratio, A ∼ 1--1.2. Other advantages include a high enclosed volume, appreciable rotational transform, and a possibility of extreme-high-β MHD equilibria. Moreover, the DHS features improved transport characteristics caused by the absence of the magnetic field ripple on the outboard of the torus. Compactness, simplicity and modularity of the coil system add to the DHS advantages for fusion applications

Track propagation methods for the correlation of charged tracks with clusters in the calorimeter of the bar PANDA experiment

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Nasawasd, T.; Simantathammakul, T.; Herold, C.; Stockmanns, T.; Ritman, J.; Kobdaj, C.

2018-02-01

To classify clusters of hits in the electromagnetic calorimeter (EMC) of bar PANDA (antiProton ANnihilation at DArmstadt), one has to match these EMC clusters with tracks of charged particles reconstructed from hits in the tracking system. Therefore the tracks are propagated to the surface of the EMC and associated with EMC clusters which are nearby and below a cut parameter. In this work, we propose a helix propagator to extrapolate the track from the Straw Tube Tracker (STT) to the inner surface of the EMC instead of the GEANE propagator which is already embedded within the PandaRoot computational framework. The results for both propagation methods show a similar quality, with a 30% gain in CPU time when using the helix propagator. We use Monte-Carlo truth information to compare the particle ID of the EMC clusters with the ID of the extrapolated points, thus deciding upon the correctness of the matches. By varying the cut parameter as a function of transverse momentum and particle type, our simulations show that the purity can be increased by 3-5% compared to the default value which is a constant cut in the bar PANDA simulation framework PandaRoot.

Designing cooperatively folded abiotic uni- and multimolecular helix bundles

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de, Soumen; Chi, Bo; Granier, Thierry; Qi, Ting; Maurizot, Victor; Huc, Ivan

2018-01-01

Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.

Propensity, Probability, and Quantum Theory

Science.gov (United States)

Ballentine, Leslie E.

2016-08-01

Quantum mechanics and probability theory share one peculiarity. Both have well established mathematical formalisms, yet both are subject to controversy about the meaning and interpretation of their basic concepts. Since probability plays a fundamental role in QM, the conceptual problems of one theory can affect the other. We first classify the interpretations of probability into three major classes: (a) inferential probability, (b) ensemble probability, and (c) propensity. Class (a) is the basis of inductive logic; (b) deals with the frequencies of events in repeatable experiments; (c) describes a form of causality that is weaker than determinism. An important, but neglected, paper by P. Humphreys demonstrated that propensity must differ mathematically, as well as conceptually, from probability, but he did not develop a theory of propensity. Such a theory is developed in this paper. Propensity theory shares many, but not all, of the axioms of probability theory. As a consequence, propensity supports the Law of Large Numbers from probability theory, but does not support Bayes theorem. Although there are particular problems within QM to which any of the classes of probability may be applied, it is argued that the intrinsic quantum probabilities (calculated from a state vector or density matrix) are most naturally interpreted as quantum propensities. This does not alter the familiar statistical interpretation of QM. But the interpretation of quantum states as representing knowledge is untenable. Examples show that a density matrix fails to represent knowledge.

Helix probe areas for the utilization of geothermal power. A practical example; Helix-Sondenfelder zur Nutzung von Erdwaerme. Ein Praxisbeispiel

Energy Technology Data Exchange (ETDEWEB)

Kuebert, Markus; Walker-Hertkorn, Simone [tewag Technologie - Erdwaermeanlagen - Umweltschutz GmbH, Starzach (Germany); Tietz, Jan [REHAU AG und Co., Erlangen-Eltersdorf (Germany); Riepold, Markus; Gloeckl, Andreas [MR Tiefbau GmbH, Brunnen (Germany)

2013-02-01

Thanks to their spiral shape so-called helix probes with a tube length of 40 meter have a height of only three meter: A lot of heat exchange area in a small space. Thus, helix probes are an ideal solution for the utilization of geothermal energy at places at which one cannot drill deeply due to geothermal reasons. Under this aspect, the contribution under consideration reports on the planning of a helix probe area being sustainably adapted to the user requirements for the new construction of a production facility.

A magnetic torsional wave near the Galactic Centre traced by a 'double helix' nebula.

Science.gov (United States)

Morris, Mark; Uchida, Keven; Do, Tuan

2006-03-16

The magnetic field in the central few hundred parsecs of the Milky Way has a dipolar geometry and is substantially stronger than elsewhere in the Galaxy, with estimates ranging up to a milligauss (refs 1-6). Characterization of the magnetic field at the Galactic Centre is important because it can affect the orbits of molecular clouds by exerting a drag on them, inhibit star formation, and could guide a wind of hot gas or cosmic rays away from the central region. Here we report observations of an infrared nebula having the morphology of an intertwined double helix about 100 parsecs from the Galaxy's dynamical centre, with its axis oriented perpendicular to the Galactic plane. The observed segment is about 25 parsecs in length, and contains about 1.25 full turns of each of the two continuous, helically wound strands. We interpret this feature as a torsional Alfvén wave propagating vertically away from the Galactic disk, driven by rotation of the magnetized circumnuclear gas disk. The direct connection between the circumnuclear disk and the double helix is ambiguous, but the images show a possible meandering channel that warrants further investigation.

[Propensity score matching in SPSS].

Science.gov (United States)

Huang, Fuqiang; DU, Chunlin; Sun, Menghui; Ning, Bing; Luo, Ying; An, Shengli

2015-11-01

To realize propensity score matching in PS Matching module of SPSS and interpret the analysis results. The R software and plug-in that could link with the corresponding versions of SPSS and propensity score matching package were installed. A PS matching module was added in the SPSS interface, and its use was demonstrated with test data. Score estimation and nearest neighbor matching was achieved with the PS matching module, and the results of qualitative and quantitative statistical description and evaluation were presented in the form of a graph matching. Propensity score matching can be accomplished conveniently using SPSS software.

Interactions between the mixotrophic dinoflagellate Takayama helix and common heterotrophic protists.

Science.gov (United States)

Ok, Jin Hee; Jeong, Hae Jin; Lim, An Suk; Lee, Kyung Ha

2017-09-01

The phototrophic dinoflagellate Takayama helix that is known to be harmful to abalone larvae has recently been revealed to be mixotrophic. Although mixotrophy elevates the growth rate of T. helix by 79%-185%, its absolute growth rate is still as low as 0.3d -1 . Thus, if the mortality rate of T. helix due to predation is high, this dinoflagellate may not easily prevail. To investigate potential effective protistan grazers on T. helix, feeding by diverse heterotrophic dinoflagellates such as engulfment-feeding Oxyrrhis marina, Gyrodinium dominans, Gyrodinium moestrupii, Polykrikos kofoidii, and Noctiluca scintillans, peduncle-feeding Aduncodinium glandula, Gyrodiniellum shiwhaense, Luciella masanensis, and Pfiesteria piscicida, pallium-feeding Oblea rotunda and Protoperidinium pellucidum, and the naked ciliates Pelagostrobilidium sp. (ca. 40μm in cell length) and Strombidinopsis sp. (ca. 150μm in cell length) on T. helix was explored. Among the tested heterotrophic protists, O. marina, G. dominans, G. moestrupii, A. glandula, L. masanensis, P. kofoidii, P. piscicida, and Strombidinopsis sp. were able to feed on T. helix. The growth rates of all these predators except Strombidinopsis sp. with T. helix prey were lower than those without the prey. The growth rate of Strombidinopsis sp. on T. helix was almost zero although the growth rate of Strombidinopsis sp. with T. helix prey was higher than those without the prey. Moreover, T. helix fed on O. marina and P. pellucidum and lysed the cells of P. kofoidii and G. shiwhaense. With increasing the concentrations of T. helix, the growth rates of O. marina and P. kofoidii decreased, but those of G. dominans and L. masanensis largely did not change. Therefore, reciprocal predation, lysis, no feeding, and the low ingestion rates of the common protists preying on T. helix may result in a low mortality rate due to predation, thereby compensating for this species' low growth rate. Copyright © 2017 Elsevier B.V. All rights

Comparative Study on the Adaptation and Growth Dynamics of the Helix pomatia and Helix aspersa Muller Terrestrial Snails Under Different Feeding Regimes

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Adrian Toader-Williams

2010-05-01

Full Text Available We used Helix pomatia and Helix aspersa species and measure their growth as the snails were approaching the hibernation season. Helix pomatia 2yo shown a decrease in weight while being raised in enclosed parcels of 4sqm the younger Helix pomatia 1yo as well as Helix aspersa Muller demonstrated the ability to adapt relatively fast to the same conditions. We established 5 experimental lots in a Helix pomatia farm, GPS coordinates N46.606040 E23.599950. Control lot contained Taraxacum officinales, Sonchus oleraceus, Equisetum arvense and Atriplex hortensis, wild flora found within the farm. The other lots contained the same plants as the control lot plus different combinations of imported plants from other areals. The H. pomatia 2yo weight decreased in the control lot by a mean of -3.86% while H. aspersa 1yo marked an increase of +16.89% in the same lot during the same period. The lot containing lupinus polyphyllus delivered snails with weight gain of +24.66% for H. pomatia 2yo and an increase of only +1.98% for H. aspersa 1yo. As a contrast, H. pomatia 2yo gained only +7.72% while H. aspersa 1yo gained +28.89%, in the lot containing Lavanda officinalis, Foeniculum vulgare and Hyssopus officinalis among the other plants.

Prion disease susceptibility is affected by β-structure folding propensity and local side-chain interactions in PrP

Science.gov (United States)

Khan, M. Qasim; Sweeting, Braden; Mulligan, Vikram Khipple; Arslan, Pharhad Eli; Cashman, Neil R.; Pai, Emil F.; Chakrabartty, Avijit

2010-01-01

Prion diseases occur when the normally α-helical prion protein (PrP) converts to a pathological β-structured state with prion infectivity (PrPSc). Exposure to PrPSc from other mammals can catalyze this conversion. Evidence from experimental and accidental transmission of prions suggests that mammals vary in their prion disease susceptibility: Hamsters and mice show relatively high susceptibility, whereas rabbits, horses, and dogs show low susceptibility. Using a novel approach to quantify conformational states of PrP by circular dichroism (CD), we find that prion susceptibility tracks with the intrinsic propensity of mammalian PrP to convert from the native, α-helical state to a cytotoxic β-structured state, which exists in a monomer–octamer equilibrium. It has been controversial whether β-structured monomers exist at acidic pH; sedimentation equilibrium and dual-wavelength CD evidence is presented for an equilibrium between a β-structured monomer and octamer in some acidic pH conditions. Our X-ray crystallographic structure of rabbit PrP has identified a key helix-capping motif implicated in the low prion disease susceptibility of rabbits. Removal of this capping motif increases the β-structure folding propensity of rabbit PrP to match that of PrP from mouse, a species more susceptible to prion disease. PMID:21041683

Prion disease susceptibility is affected by beta-structure folding propensity and local side-chain interactions in PrP.

Science.gov (United States)

Khan, M Qasim; Sweeting, Braden; Mulligan, Vikram Khipple; Arslan, Pharhad Eli; Cashman, Neil R; Pai, Emil F; Chakrabartty, Avijit

2010-11-16

Prion diseases occur when the normally α-helical prion protein (PrP) converts to a pathological β-structured state with prion infectivity (PrP(Sc)). Exposure to PrP(Sc) from other mammals can catalyze this conversion. Evidence from experimental and accidental transmission of prions suggests that mammals vary in their prion disease susceptibility: Hamsters and mice show relatively high susceptibility, whereas rabbits, horses, and dogs show low susceptibility. Using a novel approach to quantify conformational states of PrP by circular dichroism (CD), we find that prion susceptibility tracks with the intrinsic propensity of mammalian PrP to convert from the native, α-helical state to a cytotoxic β-structured state, which exists in a monomer-octamer equilibrium. It has been controversial whether β-structured monomers exist at acidic pH; sedimentation equilibrium and dual-wavelength CD evidence is presented for an equilibrium between a β-structured monomer and octamer in some acidic pH conditions. Our X-ray crystallographic structure of rabbit PrP has identified a key helix-capping motif implicated in the low prion disease susceptibility of rabbits. Removal of this capping motif increases the β-structure folding propensity of rabbit PrP to match that of PrP from mouse, a species more susceptible to prion disease.

Government and Governance of Regional Triple Helix Interactions

Science.gov (United States)

Danson, Mike; Todeva, Emanuela

2016-01-01

This conceptual paper contributes to the discussion of the role of regional government and regional Triple Helix constellations driving economic development and growth within regional boundaries. The impact of regionalism and subsidiarity on regional Triple Helix constellations, and the questions of governmentality, governance and institutional…

A basic helix-loop-helix transcription factor, PhFBH4, regulates flower senescence by modulating ethylene biosynthesis pathway in petunia

Science.gov (United States)

The basic helix-loop-helix (bHLH) transcription factors (TFs) play important roles in regulating multiple biological processes in plants. However, there are few reports about the function of bHLHs in flower senescence. In this study, a bHLH TF, PhFBH4, was found to be dramatically upregulated during...

Double helix vortex breakdown in a turbulent swirling annular jet flow

Science.gov (United States)

Vanierschot, M.; Percin, M.; van Oudheusden, B. W.

2018-03-01

In this paper, we report on the structure and dynamics of double helix vortex breakdown in a turbulent annular swirling jet. Double helix breakdown has been reported previously for the laminar flow regime, but this structure has rarely been observed in turbulent flow. The flow field is investigated experimentally by means of time-resolved tomographic particle image velocimetry. Notwithstanding the axisymmetric nature of the time-averaged flow, analysis of the instantaneous three-dimensional (3D) vortical structures shows the existence of a vortex core along the central axis which breaks up into a double helix downstream. The winding sense of this double helix is opposite to the swirl direction (m =-2 ) and it is wrapped around a central vortex breakdown bubble. This structure is quite different from double helix breakdown found in laminar flows where the helix is formed in the wake of the bubble and not upstream. The double helix precesses around the central axis of the jet with a precessing frequency corresponding to a Strouhal number of 0.27.

An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions.

Science.gov (United States)

Grison, Claire M; Miles, Jennifer A; Robin, Sylvie; Wilson, Andrew J; Aitken, David J

2016-09-05

A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein-protein interactions (PPIs). In this work, trans-2-aminocyclobutanecarboxylic acid (tACBC) was used as the key β-amino acid component in the design of α/β/γ-peptides to structurally mimic a native α-helix. Suitably functionalized α/β/γ-peptides assume an α-helix-mimicking 12,13-helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild-type α-peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

IFITM3 requires an amphipathic helix for antiviral activity.

Science.gov (United States)

Chesarino, Nicholas M; Compton, Alex A; McMichael, Temet M; Kenney, Adam D; Zhang, Lizhi; Soewarna, Victoria; Davis, Matthew; Schwartz, Olivier; Yount, Jacob S

2017-10-01

Interferon-induced transmembrane protein 3 (IFITM3) is a cellular factor that blocks virus fusion with cell membranes. IFITM3 has been suggested to alter membrane curvature and fluidity, though its exact mechanism of action is unclear. Using a bioinformatic approach, we predict IFITM3 secondary structures and identify a highly conserved, short amphipathic helix within a hydrophobic region of IFITM3 previously thought to be a transmembrane domain. Consistent with the known ability of amphipathic helices to alter membrane properties, we show that this helix and its amphipathicity are required for the IFITM3-dependent inhibition of influenza virus, Zika virus, vesicular stomatitis virus, Ebola virus, and human immunodeficiency virus infections. The homologous amphipathic helix within IFITM1 is also required for the inhibition of infection, indicating that IFITM proteins possess a conserved mechanism of antiviral action. We further demonstrate that the amphipathic helix of IFITM3 is required to block influenza virus hemagglutinin-mediated membrane fusion. Overall, our results provide evidence that IFITM proteins utilize an amphipathic helix for inhibiting virus fusion. © 2017 The Authors.

Effect of Hedera helix on lung histopathology in chronic asthma.

Science.gov (United States)

Hocaoglu, Arzu Babayigit; Karaman, Ozkan; Erge, Duygu Olmez; Erbil, Guven; Yilmaz, Osman; Kivcak, Bijen; Bagriyanik, H Alper; Uzuner, Nevin

2012-12-01

Hedera helix is widely used to treat bronchial asthma for many years. However, effects of this herb on lung histopathology is still far from clear. We aimed to determine the effect of oral administration of Hedera helix on lung histopathology in a murine model of chronic asthma.BALB/c mice were divided into four groups; I (Placebo), II (Hedera helix), III (Dexamethasone) and IV (Control). All mice except controls were sensitized and challenged with ovalbumin. Then, mice in group I received saline, group II 100 mg/kg Hedera helix and group III 1 mg/kg dexamethasone via orogastic gavage once daily for one week. Airway histopathology was evaluated by using light and electron microscopy in all groups.Goblet cell numbers and thicknesses of basement membrane were found significantly lower in group II, but there was no statistically significant difference in terms of number of mast cells, thicknesses of epithelium and subepithelial smooth muscle layers between group I and II. When Hedera helix and dexamethasone groups were compared with each other, thickness of epithelium, subepithelial muscle layers, number of mast cells and goblet cells of group III were significantly ameliorated when compared with the group II. Although Hedera helix administration reduced only goblet cell counts and the thicknesses of basement membrane in the asthmatic airways, dexamethasone ameliorated all histopathologic parameters except thickness of basement membrane better than Hedera helix.

Dimerization of the docking/adaptor protein HEF1 via a carboxy-terminal helix-loop-helix domain.

Science.gov (United States)

Law, S F; Zhang, Y Z; Fashena, S J; Toby, G; Estojak, J; Golemis, E A

1999-10-10

HEF1, p130(Cas), and Efs define a family of multidomain docking proteins which plays a central coordinating role for tyrosine-kinase-based signaling related to cell adhesion. HEF1 function has been specifically implicated in signaling pathways important for cell adhesion and differentiation in lymphoid and epithelial cells. While the SH3 domains and SH2-binding site domains (substrate domains) of HEF1 family proteins are well characterized and binding partners known, to date the highly conserved carboxy-terminal domains of the three proteins have lacked functional definition. In this study, we have determined that the carboxy-terminal domain of HEF1 contains a divergent helix-loop-helix (HLH) motif. This motif mediates HEF1 homodimerization and HEF1 heterodimerization with a recognition specificity similar to that of the transcriptional regulatory HLH proteins Id2, E12, and E47. We had previously demonstrated that the HEF1 carboxy-terminus expressed as a separate domain in yeast reprograms cell division patterns, inducing constitutive pseudohyphal growth. Here we show that pseudohyphal induction by HEF1 requires an intact HLH, further supporting the idea that this motif has an effector activity for HEF1, and implying that HEF1 pseudohyphal activity derives in part from interactions with yeast helix-loop-helix proteins. These combined results provide initial insight into the mode of function of the HEF1 carboxy-terminal domain and suggest that the HEF1 protein may interact with cellular proteins which control differentiation. Copyright 1999 Academic Press.

The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA

NARCIS (Netherlands)

Popovic, Matija; Wienk, Hans; Coglievina, Maristella; Boelens, Rolf; Pongor, Sándor; Pintar, Alessandro

2014-01-01

Hairy and enhancer of split 1, one of the main downstream effectors in Notch signaling, is a transcriptional repressor of the basic helix-loop-helix (bHLH) family. Using nuclear magnetic resonance methods, we have determined the structure and dynamics of a recombinant protein, H1H, which includes an

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin.

Directory of Open Access Journals (Sweden)

Vasyl V Mykuliak

2018-04-01

Full Text Available Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.

DNA-like double helix formed by peptide nucleic acid

DEFF Research Database (Denmark)

Wittung, P; Nielsen, Peter E.; Buchardt, O

1994-01-01

Although the importance of the nucleobases in the DNA double helix is well understood, the evolutionary significance of the deoxyribose phosphate backbone and the contribution of this chemical entity to the overall helical structure and stability of the double helix is not so clear. Peptide nucleic...

An analytical approach for the Propagation Saw Test

Science.gov (United States)

Benedetti, Lorenzo; Fischer, Jan-Thomas; Gaume, Johan

2016-04-01

The Propagation Saw Test (PST) [1, 2] is an experimental in-situ technique that has been introduced to assess crack propagation propensity in weak snowpack layers buried below cohesive snow slabs. This test attracted the interest of a large number of practitioners, being relatively easy to perform and providing useful insights for the evaluation of snow instability. The PST procedure requires isolating a snow column of 30 centimeters of width and -at least-1 meter in the downslope direction. Then, once the stratigraphy is known (e.g. from a manual snow profile), a saw is used to cut a weak layer which could fail, potentially leading to the release of a slab avalanche. If the length of the saw cut reaches the so-called critical crack length, the onset of crack propagation occurs. Furthermore, depending on snow properties, the crack in the weak layer can initiate the fracture and detachment of the overlying slab. Statistical studies over a large set of field data confirmed the relevance of the PST, highlighting the positive correlation between test results and the likelihood of avalanche release [3]. Recent works provided key information on the conditions for the onset of crack propagation [4] and on the evolution of slab displacement during the test [5]. In addition, experimental studies [6] and simplified models [7] focused on the qualitative description of snowpack properties leading to different failure types, namely full propagation or fracture arrest (with or without slab fracture). However, beside current numerical studies utilizing discrete elements methods [8], only little attention has been devoted to a detailed analytical description of the PST able to give a comprehensive mechanical framework of the sequence of processes involved in the test. Consequently, this work aims to give a quantitative tool for an exhaustive interpretation of the PST, stressing the attention on important parameters that influence the test outcomes. First, starting from a pure

"Special Issue": Regional Dimensions of the Triple Helix Model

Science.gov (United States)

Todeva, Emanuela; Danson, Mike

2016-01-01

This paper introduces the rationale for the special issue and its contributions, which bridge the literature on regional development and the Triple Helix model. The concept of the Triple Helix at the sub-national, and specifically regional, level is established and examined, with special regard to regional economic development founded on…

A smallest 6 kda metalloprotease, mini-matrilysin, in living world: a revolutionary conserved zinc-dependent proteolytic domain- helix-loop-helix catalytic zinc binding domain (ZBD

Directory of Open Access Journals (Sweden)

Yu Wei-Hsuan

2012-05-01

Full Text Available Abstract Background The Aim of this study is to study the minimum zinc dependent metalloprotease catalytic folding motif, helix B Met loop-helix C, with proteolytic catalytic activities in metzincin super family. The metzincin super family share a catalytic domain consisting of a twisted five-stranded β sheet and three long α helices (A, B and C. The catalytic zinc is at the bottom of the cleft and is ligated by three His residues in the consensus sequence motif, HEXXHXXGXXH, which is located in helix B and part of the adjacent Met turn region. An interesting question is - what is the minimum portion of the enzyme that still possesses catalytic and inhibitor recognition?” Methods We have expressed a 60-residue truncated form of matrilysin which retains only the helix B-Met turn-helix C region and deletes helix A and the five-stranded β sheet which form the upper portion of the active cleft. This is only 1/4 of the full catalytic domain. The E. coli derived 6 kDa MMP-7 ZBD fragments were purified and refolded. The proteolytic activities were analyzed by Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay and CM-transferrin zymography analysis. SC44463, BB94 and Phosphoramidon were computationally docked into the 3day structure of the human MMP7 ZBD and TAD and thermolysin using the docking program GOLD. Results This minimal 6 kDa matrilysin has been refolded and shown to have proteolytic activity in the Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 peptide assay. Triton X-100 and heparin are important factors in the refolding environment for this mini-enzyme matrilysin. This minienzyme has the proteolytic activity towards peptide substrate, but the hexamer and octamer of the mini MMP-7 complex demonstrates the CM-transferrin proteolytic activities in zymographic analysis. Peptide digestion is inhibited by SC44463, specific MMP7 inhibitors, but not phosphorimadon. Interestingly, the mini MMP-7 can be processed by autolysis and producing ~ 6�

Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C.

Science.gov (United States)

Brown, Nathan J; Wu, Cindy W; Seurynck-Servoss, Shannon L; Barron, Annelise E

2008-02-12

The hydrophobic proteins of lung surfactant (LS), SP-B and SP-C, are critical constituents of an effective surfactant replacement therapy for the treatment of respiratory distress syndrome. Because of concerns and difficulties associated with animal-derived surfactants, recent investigations have focused on the creation of synthetic analogues of the LS proteins. However, creating an accurate mimic of SP-C that retains its biophysical surface activity is extraordinarily challenging given the lipopeptide's extreme hydrophobicity and propensity to misfold and aggregate. One successful approach that overcomes these difficulties is the use of poly-N-substituted glycines, or peptoids, to mimic SP-C. To develop a non-natural, bioactive mimic of SP-C and to investigate the effects of side chain chemistry and length of the helical hydrophobic region, we synthesized, purified, and performed in vitro testing of two classes of peptoid SP-C mimics: those having a rigid alpha-chiral aromatic helix and those having a biomimetic alpha-chiral aliphatic helix. The length of the two classes of mimics was also systematically altered. Circular dichroism spectroscopy gave evidence that all of the peptoid-based mimics studied here emulated SP-C's secondary structure, forming stable helical structures in solution. Langmuir-Wilhelmy surface balance, fluorescence microscopy, and pulsating bubble surfactometry experiments provide evidence that the aromatic-based SP-C peptoid mimics, in conjunction with a synthetic lipid mixture, have superior surface activity and biomimetic film morphology in comparison to the aliphatic-based mimics and that there is an increase in surface activity corresponding to increasing helical length.

The C-Terminal RpoN Domain of sigma54 Forms an unpredictedHelix-Turn-Helix Motif Similar to domains of sigma70

Energy Technology Data Exchange (ETDEWEB)

Doucleff, Michaeleen; Malak, Lawrence T.; Pelton, Jeffrey G.; Wemmer, David E.

2005-11-01

The ''{delta}'' subunit of prokaryotic RNA-polymerase allows gene-specific transcription initiation. Two {sigma} families have been identified, {sigma}{sup 70} and {sigma}{sup 54}, which use distinct mechanisms to initiate transcription and share no detectable sequence homology. Although the {sigma}{sup 70}-type factors have been well characterized structurally by x-ray crystallography, no high-resolution structural information is available for the {sigma}{sup 54}-type factors. Here we present the NMR derived structure of the C-terminal domain of {sigma}{sup 54} from Aquifex aeolicus. This domain (Thr323 to Gly389), which contains the highly conserved RpoN box sequence, consists of a poorly structured N-terminal tail followed by a three-helix bundle, which is surprisingly similar to domains of the {sigma}{sup 70}-type proteins. Residues of the RpoN box, which have previously been shown to be critical for DNA binding, form the second helix of an unpredicted helix-turn-helix motif. This structure's homology with other DNA binding proteins, combined with previous biochemical data, suggest how the C-terminal domain of {sigma}{sup 54} binds to DNA.

Identification of basic/helix-loop-helix transcription factors reveals candidate genes involved in anthocyanin biosynthesis from the strawberry white-flesh mutant

OpenAIRE

Zhao, Fengli; Li, Gang; Hu, Panpan; Zhao, Xia; Li, Liangjie; Wei, Wei; Feng, Jiayue; Zhou, Houcheng

2018-01-01

As the second largest transcription factor family in plant, the basic helix-loop-helix (bHLH) transcription factor family, characterized by the conserved bHLH domain, plays a central regulatory role in many biological process. However, the bHLH transcription factor family of strawberry has not been systematically identified, especially for the anthocyanin biosynthesis. Here, we identified a total of 113 bHLH transcription factors and described their chromosomal distribution and bioinformatics...

Hope, Perceived Financial Risk and Propensity for Indebtedness

Directory of Open Access Journals (Sweden)

Lucia Barros

2012-10-01

Full Text Available Hope is an important construct in marketing, since it is an antecedent of important marketing variables, such as trust, expectation and satisfaction (MacInnis & Mello, 2005. Specifically, literature suggests that hope plays an important influence in risk perception (MacInnis & Mello, 2005 and propensity for indebtedness (Fleming, 2008. Thus, we aim to investigate the relationships among hope, risk perception related to purchasing and consumption and propensity for indebtedness by conducting two empirical studies. The first is a laboratory experiment, which accessed hope and risk perception of getting a mortgage loan. The second is a survey, investigating university students’ propensity to get indebted to pay for their university tuition, analyzed through the Structural Equations Modeling method. These studies found that higher levels of hope predicted an increase in the propensity to accept the mortgage loan, independent of actual risks, and an increase in the propensity of college students to get indebted to pay for their studies. In addition, the first study suggests that hope may lead to a decrease in risk perception, which, however, wasn’t confirmed by the second study. Finally, this research offers some methodological contributions, using an experimental approach to understand hope and its relationship with perceived financial risk and propensity for indebtedness.

TOWARDS UNDERSTANDING OF HELIX B BASED CONFORMATIONAL DISEASES IN SERPIN

Directory of Open Access Journals (Sweden)

Mohamad Aman Jairajpuri

2012-12-01

Full Text Available Serine protease inhibitors (serpins are a unique family of protease inhibitors that are prone to polymer formation due to their metastable nature and a complex inhibition mechanism that involves large scale conformational change. Helix B is in the shutter region near the strand 2A and strand 3A of �-sheet A, where reactive centre loop inserts during the serpin inhibition mechanism. Helix B region in serpins is a mutation hotspot for naturally occurring variants that result in pathological conditions due to polymerization. Helix B residues are completely buried in the native state and loop inserted latent state but not in the inhibitory loop inserted cleaved conformation. Native to cleaved transition during inhibition forms a large cavity in the shutter region, which invariably is the largest cavity in most serpins in native state. In a recent paper we had for the first time hypothesized that exposure of helix B at the N-terminal end is important for smooth insertion of the reactive center loop during serpin inhibition mechanism. It is therefore possible that natural variant that induces conformational deformation of helix B probably alter the cavity size which increases the rate of loop-sheet interaction between the monomers resulting in increased polymerization.

The role of risk propensity in predicting self-employment.

Science.gov (United States)

Nieß, Christiane; Biemann, Torsten

2014-09-01

This study aims to untangle the role of risk propensity as a predictor of self-employment entry and self-employment survival. More specifically, it examines whether the potentially positive effect of risk propensity on the decision to become self-employed turns curvilinear when it comes to the survival of the business. Building on a longitudinal sample of 4,973 individuals from the German Socio-Economic Panel, we used event history analyses to evaluate the influence of risk propensity on self-employment over a 7-year time period. Results indicated that whereas high levels of risk propensity positively predicted the decision to become self-employed, the relationship between risk propensity and self-employment survival followed an inverted U-shaped curve. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Nucleic acid helix structure determination from NMR proton chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

2013-06-15

We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

Genome-wide identification of basic helix-loop-helix and NF-1 motifs underlying GR binding sites in male rat hippocampus

DEFF Research Database (Denmark)

Pooley, John R.; Flynn, Ben P.; Grøntved, Lars

2017-01-01

linked to structural and organizational roles, an absence of major tethering partners for GRs, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix motif closely resembling a NeuroD1 or Olig2 binding site was found underlying a subset of GR binding......Glucocorticoids regulate hippocampal function in part by modulating gene expression through the glucocorticoid receptor (GR). GR binding is highly cell type specific, directed to accessible chromatin regions established during tissue differentiation. Distinct classes of GR binding sites...

Regional Dimensions of the Triple Helix Model: Setting the Context

Science.gov (United States)

Todeva, Emanuela; Danson, Mike

2016-01-01

This paper introduces the rationale for the special issue and its contributions, which bridge the literature on regional development and the Triple Helix model. The concept of the Triple Helix at the sub-national, and specifically regional, level is established and examined, with special regard to regional economic development founded on…

FMRFamide receptors of Helix aspersa

International Nuclear Information System (INIS)

Payza, K.

1988-01-01

A receptor binding assay and an isolated heart bioassay were used to identify and characterize the FMRFamide receptors in Helix. In the heart bioassay, FMRFamide increased myocardial contraction force. A potent FMRFamide analog, desaminoTyr-Phe-norLeu-arg-Phe-amide (daYFnLRFamide), was used as a radioiodinated receptor ligand. The high affinity binding of 125 I-daYFnLRFamide at 0 degree C to Helix brain membranes was reversible, saturable, pH-dependent and specific, with a K D of 13-14 nM. A lower affinity (245 nM) site was also observed. Radioligand binding sites were also identified in the heart, male reproductive organs and digestive organs. The structure-activity relations (SAR) of cardiostimulation correlated with the specificity of 125 I-daYFnLRFamide binding to brain and heart receptors. The SAR were similar to those of other molluscan FMRFamide bioassays, except that they showed a marked preference for some analogs with blocked amino-terminals

Elevated temperature triggers human respiratory syncytial virus F protein six-helix bundle formation

International Nuclear Information System (INIS)

Yunus, Abdul S.; Jackson, Trent P.; Crisafi, Katherine; Burimski, Irina; Kilgore, Nicole R.; Zoumplis, Dorian; Allaway, Graham P.; Wild, Carl T.; Salzwedel, Karl

2010-01-01

Human respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infection in infants, immunocompromised patients, and the elderly. The RSV fusion (F) protein mediates fusion of the viral envelope with the target cell membrane during virus entry and is a primary target for antiviral drug and vaccine development. The F protein contains two heptad repeat regions, HR1 and HR2. Peptides corresponding to these regions form a six-helix bundle structure that is thought to play a critical role in membrane fusion. However, characterization of six-helix bundle formation in native RSV F protein has been hindered by the fact that a trigger for F protein conformational change has yet to be identified. Here we demonstrate that RSV F protein on the surface of infected cells undergoes a conformational change following exposure to elevated temperature, resulting in the formation of the six-helix bundle structure. We first generated and characterized six-helix bundle-specific antibodies raised against recombinant peptides modeling the RSV F protein six-helix bundle structure. We then used these antibodies as probes to monitor RSV F protein six-helix bundle formation in response to a diverse array of potential triggers of conformational changes. We found that exposure of 'membrane-anchored' RSV F protein to elevated temperature (45-55 deg. C) was sufficient to trigger six-helix bundle formation. Antibody binding to the six-helix bundle conformation was detected by both flow cytometry and cell-surface immunoprecipitation of the RSV F protein. None of the other treatments, including interaction with a number of potential receptors, resulted in significant binding by six-helix bundle-specific antibodies. We conclude that native, untriggered RSV F protein exists in a metastable state that can be converted in vitro to the more stable, fusogenic six-helix bundle conformation by an increase in thermal energy. These findings help to better define the mechanism of

Crosslinked Aspartic Acids as Helix-Nucleating Templates.

Science.gov (United States)

Zhao, Hui; Liu, Qi-Song; Geng, Hao; Tian, Yuan; Cheng, Min; Jiang, Yan-Hong; Xie, Ming-Sheng; Niu, Xiao-Gang; Jiang, Fan; Zhang, Ya-Ou; Lao, Yuan-Zhi; Wu, Yun-Dong; Xu, Nai-Han; Li, Zi-Gang

2016-09-19

Described is a facile helix-nucleating template based on a tethered aspartic acid at the N-terminus [terminal aspartic acid (TD)]. The nucleating effect of the template is subtly influenced by the substituent at the end of the side-chain-end tether as indicated by circular dichroism, nuclear magnetic resonance, and molecular dynamics simulations. Unlike most nucleating strategies, the N-terminal amine is preserved, thus enabling further modification. Peptidomimetic estrogen receptor modulators (PERMs) constructed using this strategy show improved therapeutic properties. The current strategy can be regarded as a good complement to existing helix-stabilizing methods. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Is the propensity to complain increasing over time?

DEFF Research Database (Denmark)

Juhl, Hans Jørn; Thøgersen, John; Poulsen, Carsten Stig

2006-01-01

The purpose of this paper is twofold. First we present some of the measurement problems involved in interpreting consumer complaint data. Second we provide some unique longitudinal results on complaint propensity documenting that, in spite of a doubling of the number of cases submitted...... to the Danish National Complaints Board, the propensity to complain in Denmark has not increased in the past 25 years. We conclude by discussing how the analysis could be extended from merely describing to explaining the variation in propensity to complain across consumers....

On the helix equation

Directory of Open Access Journals (Sweden)

Taouil Hajer

2012-08-01

Full Text Available This paper is devoted to the helices processes, i.e. the solutions H : ℝ × Ω → ℝd, (t, ω ↦ H(t, ω of the helix equation egin{eqnarray} H(0,o=0; quad H(s+t,o= H(s,Phi(t,o +H(t,oonumber end{eqnarray} H ( 0 ,ω = 0 ;   H ( s + t,ω = H ( s, Φ ( t,ω + H ( t,ω where Φ : ℝ × Ω → Ω, (t, ω ↦ Φ(t, ω is a dynamical system on a measurable space (Ω, ℱ. More precisely, we investigate dominated solutions and non differentiable solutions of the helix equation. For the last case, the Wiener helix plays a fundamental role. Moreover, some relations with the cocycle equation defined by Φ, are investigated. Ce papier est consacré aux hélices, c’est-à-dire les solutions H : ℝ × Ω → ℝd, (t, ω ↦ H(t, ω de l’équation fonctionnelle egin{eqnarray} H(0,o=0; quad H(s+t,o= H(s,Phi(t,o +H(t,o onumber end{eqnarray} H ( 0 ,ω = 0 ;   H ( s + t,ω = H ( s, Φ ( t,ω + H ( t,ω où Φ : ℝ × Ω → Ω, (t, ω ↦ Φ(t, ω est un système dynamique défini sur un espace mesurable (Ω, ℱ. Plus présisément, nous déterminons d’abord les hélices dominées puis nous caractérisons les hélices non différentiables. Dans ce dernier cas, l’hélice de Wiener joue un rôle important. Nous précisons aussi quelques relations des hélices avec les cocycles définis par Φ.

Genome-wide identification and analysis of the chicken basic helix-loop-helix factors.

Science.gov (United States)

Liu, Wu-Yi; Zhao, Chun-Jiang

2010-01-01

Members of the basic helix-loop-helix (bHLH) family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus) genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ''orphans". A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO) enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

A genome-wide survey on basic helix-loop-helix transcription factors in giant panda.

Directory of Open Access Journals (Sweden)

Chunwang Dang

Full Text Available The giant panda (Ailuropoda melanoleuca is a critically endangered mammalian species. Studies on functions of regulatory proteins involved in developmental processes would facilitate understanding of specific behavior in giant panda. The basic helix-loop-helix (bHLH proteins play essential roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, mouse and human. Our present study identified 107 bHLH family members being encoded in giant panda genome. Phylogenetic analyses revealed that they belong to 44 bHLH families with 46, 25, 15, 4, 11 and 3 members in group A, B, C, D, E and F, respectively, while the remaining 3 members were assigned into "orphan". Compared to mouse, the giant panda does not encode seven bHLH proteins namely Beta3a, Mesp2, Sclerax, S-Myc, Hes5 (or Hes6, EBF4 and Orphan 1. These results provide useful background information for future studies on structure and function of bHLH proteins in the regulation of giant panda development.

Organizing product innovation: hierarchy, market or triple-helix networks?

Science.gov (United States)

Fitjar, Rune Dahl; Gjelsvik, Martin; Rodríguez-Pose, Andrés

This paper assesses the extent to which the organization of the innovation effort in firms, as well as the geographical scale at which this effort is pursued, affects the capacity to benefit from product innovations. Three alternative modes of organization are studied: hierarchy, market and triple-helix-type networks. Furthermore, we consider triple-helix networks at three geographical scales: local, national and international. These relationships are tested on a random sample of 763 firms located in five urban regions of Norway which reported having introduced new products or services during the preceding 3 years. The analysis shows that firms exploiting internal hierarchy or triple-helix networks with a wide range of partners managed to derive a significantly higher share of their income from new products, compared to those that mainly relied on outsourcing within the market. In addition, the analysis shows that the geographical scale of cooperation in networks, as well as the type of partner used, matters for the capacity of firms to benefit from product innovation. In particular, firms that collaborate in international triple-helix-type networks involving suppliers, customers and R&D institutions extract a higher share of their income from product innovations, regardless of whether they organize the processes internally or through the network.

Broadband and high-efficiency vortex beam generator based on a hybrid helix array.

Science.gov (United States)

Fang, Chaoqun; Wu, Chao; Gong, Zhijie; Zhao, Song; Sun, Anqi; Wei, Zeyong; Li, Hongqiang

2018-04-01

The vortex beam which carries the orbital angular momentum has versatile applications, such as high-resolution imaging, optical communications, and particle manipulation. Generating vortex beams with the Pancharatnam-Berry (PB) phase has drawn considerable attention for its unique spin-to-orbital conversion features. Despite the PB phase being frequency independent, an optical element with broadband high-efficiency circular polarization conversion feature is still needed for the broadband high-efficiency vortex beam generation. In this work, a broadband and high-efficiency vortex beam generator based on the PB phase is built with a hybrid helix array. Such devices can generate vortex beams with arbitrary topological charge. Moreover, vortex beams with opposite topological charge can be generated with an opposite handedness incident beam that propagates backward. The measured efficiency of our device is above 65% for a wide frequency range, with the relative bandwidth of 46.5%.

Double helix vortex breakdown in a turbulent swirling annular jet flow

NARCIS (Netherlands)

Vanierschot, M.; Perçin, M.; van Oudheusden, B.W.

2018-01-01

In this paper, we report on the structure and dynamics of double helix vortex breakdown in a turbulent annular swirling jet. Double helix breakdown has been reported previously for the laminar flow regime, but this structure has rarely been observed in turbulent flow. The flow field is

Enlistment Propensities of University Students

National Research Council Canada - National Science Library

Moskos, Charles

2004-01-01

Enlistment propensities of undergraduates were assessed through surveys conducted at Northwestern University, University of Arizona, University of California-Los Angeles, and University of Illinois-Chicago...

Unraveling the Role of the C-terminal Helix Turn Helix of the Coat-binding Domain of Bacteriophage P22 Scaffolding Protein*

Science.gov (United States)

Padilla-Meier, G. Pauline; Gilcrease, Eddie B.; Weigele, Peter R.; Cortines, Juliana R.; Siegel, Molly; Leavitt, Justin C.; Teschke, Carolyn M.; Casjens, Sherwood R.

2012-01-01

Many viruses encode scaffolding and coat proteins that co-assemble to form procapsids, which are transient precursor structures leading to progeny virions. In bacteriophage P22, the association of scaffolding and coat proteins is mediated mainly by ionic interactions. The coat protein-binding domain of scaffolding protein is a helix turn helix structure near the C terminus with a high number of charged surface residues. Residues Arg-293 and Lys-296 are particularly important for coat protein binding. The two helices contact each other through hydrophobic side chains. In this study, substitution of the residues of the interface between the helices, and the residues in the β-turn, by aspartic acid was used examine the importance of the conformation of the domain in coat binding. These replacements strongly affected the ability of the scaffolding protein to interact with coat protein. The severity of the defect in the association of scaffolding protein to coat protein was dependent on location, with substitutions at residues in the turn and helix 2 causing the most significant effects. Substituting aspartic acid for hydrophobic interface residues dramatically perturbs the stability of the structure, but similar substitutions in the turn had much less effect on the integrity of this domain, as determined by circular dichroism. We propose that the binding of scaffolding protein to coat protein is dependent on angle of the β-turn and the orientation of the charged surface on helix 2. Surprisingly, formation of the highly complex procapsid structure depends on a relatively simple interaction. PMID:22879595

Genome-Wide Identification and Analysis of the Chicken Basic Helix-Loop-Helix Factors

Directory of Open Access Journals (Sweden)

Wu-yi Liu

2010-01-01

Full Text Available Members of the basic helix-loop-helix (bHLH family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ‘‘orphans’’. A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

Youth Attitude Tracking Study: 1999 Propensity and Advertising Report

National Research Council Canada - National Science Library

Wilson, Miahael

2000-01-01

... such as their future plans, current events, military recruiting advertising, and media habits. The primary focus of YATS has been to measure enlistment propensity-active duty, Reserve/National Guard, composite, and Service- specific propensity...

Propensity to Search: Common, Leisure, and Labor Models of Consumer Behavior

Directory of Open Access Journals (Sweden)

Sergey MALAKHOV

2015-05-01

Full Text Available The analysis of the propensity to search specifies the “common” or the ordinary model of consumer behavior based on the synthesis of the neoclassical approach with satisficing concept, and “leisure” and “labor” models of behavior that represent different combinations of conspicuous consumption, leisure, and labor. While the “common model” of behavior demonstrates a moderate propensity to search, “leisure” and “labor” models of consumer behavior exhibit vigorous propensities to search that results in purchase of unnecessary items and therefore in overconsumption. This trend is also presented in home production where vigorous propensity to search takes the form of the vigorous propensity to produce at home. The analysis of trends in allocation of time provides grounds for the assumption that men have more accentuated propensity to search and to produce at home than women that results in overconsumption of unnecessary items.

The Discovery of the Double Helix

CERN Multimedia

CERN. Geneva

2011-01-01

Professor James D. Watson has kindly agreed to make a presentation on the 1953 finding of the Double Helix at the Cavendish Laboratory by Francis Crick and himself. Being one of the greatest scientific discoveries in human history, little else needs to be added.

Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

Science.gov (United States)

Ng, Derek P; Deber, Charles M

2016-08-09

Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid bilayer when the pH decreases. We have previously shown that the α-helicity and helix-helix interactions of the TM2 α-helix of the proteolipid protein (PLP) are sensitive to the local hydrophobicity at its C-terminus. Given that there is an ionizable residue (Glu-88) at the C-terminus of this transmembrane (TM) segment, we hypothesized that changing the ionization state of this residue through pH may alter the local hydrophobicity of the peptide enough to affect both its secondary structure and helix-helix interactions. To examine this phenomenon, we synthesized peptide analogues of the PLP TM2 α-helix (wild-type sequence (66)AFQYVIYGTASFFFLYGALLLAEGF(90)). Using circular dichroism and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate, we found that a decrease in pH increases both peptide α-helicity and the extent of self-association. This pH-dependent effect is due specifically to the presence of Glu-88 at the C-terminus. Additional experiments in which Phe-90 was mutated to residues of varying hydrophobicities indicated that the strength of this effect is dependent on the local hydrophobicity near Glu-88. Our results have implications for the design of TM peptide switches and improve our understanding of how membrane protein structure and activity can be regulated through local molecular environmental changes.

Exploring the membrane fusion mechanism through force-induced disassembly of HIV-1 six-helix bundle

Energy Technology Data Exchange (ETDEWEB)

Gao, Kai [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhang, Yong [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Lou, Jizhong, E-mail: jlou@ibp.ac.cn [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

2016-05-13

Enveloped virus, such as HIV-1, employs membrane fusion mechanism to invade into host cell. HIV-1 gp41 ectodomain uses six-helix bundle configuration to accomplish this process. Using molecular dynamic simulations, we confirmed the stability of this six-helix bundle by showing high occupancy of hydrogen bonds and hydrophobic interactions. Key residues and interactions important for the bundle integration were characterized by force-induced unfolding simulations of six-helix bundle, exhibiting the collapse order of these groups of interactions. Moreover, our results in some way concerted with a previous theory that the formation of coiled-coil choose a route which involved cooperative interactions between the N-terminal and C-terminal helix. -- Highlights: •Unfolding of HIV-1 gp41 six-helix bundle is studied by molecular dynamics simulations. •Specific interactions responsible for the stability of HIV-1 envelope post-fusion conformation were identified. •The gp41 six-helix bundle transition inducing membrane fusion might be a cooperative process of the three subunits.

FPGA helix tracking algorithm for PANDA

Energy Technology Data Exchange (ETDEWEB)

Liang, Yutie; Galuska, Martin; Gessler, Thomas; Kuehn, Wolfgang; Lange, Jens Soeren; Muenchow, David; Spruck, Bjoern [II. Physikalisches Institut, Giessen University (Germany); Ye, Hua [Institute of High Energy Physics, Beijing (China); Collaboration: PANDA-Collaboration

2015-07-01

The PANDA detector is a general-purpose detector for physics with high luminosity cooled antiproton beams, planed to operate at the FAIR facility in Darmstadt, Germany. The central detector includes a silicon Micro Vertex Detector (MVD) and a Straw Tube Tracker (STT). Without any hardware trigger, large amounts of raw data are streaming into the data acquisition system. The data reduction task is performed in the online system by reconstruction algorithms programmed on FPGAs (Field Programmable Gate Arrays) as first level and on a farm of GPUs or PCs as a second level. One important part in the system is the online track reconstruction. In this presentation, an online tracking algorithm for helix tracking reconstruction in the solenoidal field is shown. The tracking algorithm is composed by two parts, a road finding module followed by an iterative helix parameter calculation module. A performance study using C++ and the status of the VHDL implementation are presented.

Intersegment interactions and helix-coil transition within the generalized model of polypeptide chains approach

Science.gov (United States)

Badasyan, A. V.; Hayrapetyan, G. N.; Tonoyan, Sh. A.; Mamasakhlisov, Y. Sh.; Benight, A. S.; Morozov, V. F.

2009-09-01

The generalized model of polypeptide chains is extended to describe the helix-coil transition in a system comprised of two chains interacting side-by-side. The Hamiltonian of the model takes into account four possible types of interactions between repeated units of the two chains, i.e., helix-helix, helix-coil, coil-helix, and coil-coil. Analysis reveals when the energy Ihh+Icc of (h-h, c-c) interactions overwhelms the energy Ihc+Ich of mixed (h-c, c-h) interactions, the correlation length rises substantially, resulting in narrowing of the transition interval. In the opposite case, when Ihh+Icchelix formation and disfavored intersegment interactions from the same theoretical perspective.

Regulation of TCF ETS-domain transcription factors by helix-loop-helix motifs.

Science.gov (United States)

Stinson, Julie; Inoue, Toshiaki; Yates, Paula; Clancy, Anne; Norton, John D; Sharrocks, Andrew D

2003-08-15

DNA binding by the ternary complex factor (TCF) subfamily of ETS-domain transcription factors is tightly regulated by intramolecular and intermolecular interactions. The helix-loop-helix (HLH)-containing Id proteins are trans-acting negative regulators of DNA binding by the TCFs. In the TCF, SAP-2/Net/ERP, intramolecular inhibition of DNA binding is promoted by the cis-acting NID region that also contains an HLH-like motif. The NID also acts as a transcriptional repression domain. Here, we have studied the role of HLH motifs in regulating DNA binding and transcription by the TCF protein SAP-1 and how Cdk-mediated phosphorylation affects the inhibitory activity of the Id proteins towards the TCFs. We demonstrate that the NID region of SAP-1 is an autoinhibitory motif that acts to inhibit DNA binding and also functions as a transcription repression domain. This region can be functionally replaced by fusion of Id proteins to SAP-1, whereby the Id moiety then acts to repress DNA binding in cis. Phosphorylation of the Ids by cyclin-Cdk complexes results in reduction in protein-protein interactions between the Ids and TCFs and relief of their DNA-binding inhibitory activity. In revealing distinct mechanisms through which HLH motifs modulate the activity of TCFs, our results therefore provide further insight into the role of HLH motifs in regulating TCF function and how the inhibitory properties of the trans-acting Id HLH proteins are themselves regulated by phosphorylation.

Selective intercalation of six ligands molecules in a self-assembled triple helix

NARCIS (Netherlands)

Mateos timoneda, Miguel; Kerckhoffs, J.M.C.A.; Reinhoudt, David; Crego Calama, Mercedes

2007-01-01

The addition of a ligand molecule to an artificial self-assembled triple helix leads to the selective intercalation of two hydrogen-bonded trimers in specific binding pockets. Furthermore, the triple helix suffers large conformational rearrangements in order to accommodate the ligand molecules in a

Thermal helix-coil transition in UV irradiated collagen from rat tail tendon.

Science.gov (United States)

Sionkowska, A; Kamińska, A

1999-05-01

The thermal helix-coil transition in UV irradiated collagen solution, collagen film and pieces of rat tail tendon (RTT) were compared. Their thermal stability's were determined by differential scanning calorimeter (DSC) and by viscometric measurements. The denaturation temperatures of collagen solution, film and pieces of RTT were different. The helix-coil transition occur near 40 degrees C in collagen solution, near 112 degrees C in collagen film, and near 101 degrees C in pieces of RTT. After UV irradiation the thermal helix-coil transition of collagen samples were changed. These changes depend on the degree of hydratation.

Triple helix interactions for eco-innovation

DEFF Research Database (Denmark)

Hermann, Roberto Rivas; Riisgaard, Henrik; Remmen, Arne

the role of science parks in promoting eco-innovation. This study uses qualitative data gathered in two units of analysis: Panama Canal Authority and City of Knowledge Science Park. The study examines how Triple Helix interactions have built the regional system of eco-innovation at the Panama Canal...

Solitons in an isolated helix chain

DEFF Research Database (Denmark)

Christiansen, Peter Leth; Zolotaryuk, Alexander; Savin, A.V.

1997-01-01

as a generalization of the well-known one-dimensional Fermi-Pasta-Ulam model to include transverse degrees of freedom of the chain molecules. In the particular case of the alpha-helix molecular chain, the intermolecular interactions involved into the model are the point-point bonds connecting the first-, second...

Democracy and environment as references for quadruple and quintuple helix innovation systems

Science.gov (United States)

Carayannis, Elias G.; Campbell, David F. J.; Orr, Barron J.

2015-04-01

The perspective of democracy and the ecological context define key references for knowledge production and innovation in innovation systems. Particularly under conditions of environmental change where enhancing the potential for adaptation is critical, this requires a closer look at ecological responsibility and sensitivity in the different innovation models and governance regimes. The "Quintuple Helix" innovation model is an approach that stresses the necessary socio-ecological transition of society and economy by adding an environment helix to an innovation system already made up of three (university-industry-government) or four (civil society relations) helices in a way that supports adaptation by incorporating global warming as both a challenge to and a driver of innovation. There is the proposition that knowledge production and innovation co-evolve with democracy (Carayannis and Campbell, 2014). In the Triple Helix model (Etzkowitz and Leydesdorff, 2000) the existence of a democracy does not appear to be necessary for knowledge production and innovation. However, the Quadruple Helix (Carayannis and Campbell, 2009, 2010 and 2014) is defined and represented by additional key attributes and components: "media-based and culture-based public", "civil society" and "arts, artistic research and arts-based innovation" (Bast, Carayannis and Campbell, 2015). Implications of this are that the fourth helix in the Quadruple Helix innovation systems brings in and represents the perspective of "dimension of democracy" or the "context of democracy" for knowledge in general and knowledge production and innovation in more particular. Within theories of democracy there is a competition between narrow and broader concepts of democracy (Campbell, 2013). This is particularly true when democracy is to be understood to transcend more substantially the narrow understanding of being primarily based on or being primarily rooted in government institutions (within a Triple Helix

Structure of bacteriophage [phi]29 head fibers has a supercoiled triple repeating helix-turn-helix motif

Energy Technology Data Exchange (ETDEWEB)

Xiang, Ye; Rossmann, Michael G. (Purdue)

2011-12-22

The tailed bacteriophage {phi}29 capsid is decorated with 55 fibers attached to quasi-3-fold symmetry positions. Each fiber is a homotrimer of gene product 8.5 (gp8.5) and consists of two major structural parts, a pseudohexagonal base and a protruding fibrous portion that is about 110 {angstrom} in length. The crystal structure of the C-terminal fibrous portion (residues 112-280) has been determined to a resolution of 1.6 {angstrom}. The structure is about 150 {angstrom} long and shows three distinct structural domains designated as head, neck, and stem. The stem region is a unique three-stranded helix-turn-helix supercoil that has not previously been described. When fitted into a cryoelectron microscope reconstruction of the virus, the head structure corresponded to a disconnected density at the distal end of the fiber and the neck structure was located in weak density connecting it to the fiber. Thin section studies of Bacillus subtilis cells infected with fibered or fiberless {phi}29 suggest that the fibers might enhance the attachment of the virions onto the host cell wall.

Structural and functional aspects of winged-helix domains at the core of transcription initiation complexes.

Science.gov (United States)

Teichmann, Martin; Dumay-Odelot, Hélène; Fribourg, Sébastien

2012-01-01

The winged helix (WH) domain is found in core components of transcription systems in eukaryotes and prokaryotes. It represents a sub-class of the helix-turn-helix motif. The WH domain participates in establishing protein-DNA and protein-protein-interactions. Here, we discuss possible explanations for the enrichment of this motif in transcription systems.

A Review of Propensity-Score Methods and Their Use in Cardiovascular Research.

Science.gov (United States)

Deb, Saswata; Austin, Peter C; Tu, Jack V; Ko, Dennis T; Mazer, C David; Kiss, Alex; Fremes, Stephen E

2016-02-01

Observational studies using propensity-score methods have been increasing in the cardiovascular literature because randomized controlled trials are not always feasible or ethical. However, propensity-score methods can be confusing, and the general audience may not fully understand the importance of this technique. The objectives of this review are to describe (1) the fundamentals of propensity score methods, (2) the techniques to assess for propensity-score model adequacy, (3) the 4 major methods for using the propensity score (matching, stratification, covariate adjustment, and inverse probability of treatment weighting [IPTW]) using examples from previously published cardiovascular studies, and (4) the strengths and weaknesses of these 4 techniques. Our review suggests that matching or IPTW using the propensity score have shown to be most effective in reducing bias of the treatment effect. Copyright © 2016 Canadian Cardiovascular Society. Published by Elsevier Inc. All rights reserved.

Inactivation of colicin Y by intramembrane helix–helix interaction with its immunity protein

Czech Academy of Sciences Publication Activity Database

Šmajs, D.; Doležalová, M.; Macek, Pavel; Žídek, L.

2008-01-01

Roč. 275, č. 21 (2008), s. 5325-5331 ISSN 1742-464X Institutional research plan: CEZ:AV0Z50200510 Keywords : colicin immunity * colicin y * helix-helix interaction Subject RIV: CE - Biochemistry Impact factor: 3.139, year: 2008

PH4 of petunia is an R2R3-MYB protein that activates vacuolar acidification through interactions with Basic-Helix-Loop-Helix transcription factors of the anthocyanin pathway.

NARCIS (Netherlands)

Quattrocchio, F.M.; Verweij, C.W.; Spelt, C.E.; Mol, J.N.M.; Koes, R.E.

2007-01-01

The Petunia hybrids genes ANTHOCYANIN1 (AN1) and AN2 encode transcription factors with a basic-helix-loop-helix (BHLH) and a MYB domain, respectively, that are required for anthocyanin synthesis and acidification of the vacuole in petal cells. Mutation of PH4 results in a bluer flower color,

Lysine as helix C-capping residue in a synthetic peptide.

Science.gov (United States)

Esposito, G; Dhanapal, B; Dumy, P; Varma, V; Mutter, M; Bodenhausen, G

1997-01-01

The structure of the synthetic peptide CH3CO(Leu-Ser-Leu-Leu-Leu-Ser-Leu)3Lys-NH2 in trifluoroethanol/water 60/40 (volume ratio) was characterized by two-dimensional nmr spectroscopy. The peptide, closely related to the amphiphilic helix models designed by W. F. De-Grado and co-workers to mimic protein ion channels [(1988) Science, Vol. 240, p. 1177-1181], folds into a regular helix spanning residues 1-20. Evidence for a helix C-terminal capping conformation, involving the terminal lysine residue, was observed from Overhauser effects and checked for consistency by restrained molecular dynamics simulations. The side-chain amino group of Lys22 forms a hydrogen bond with the carbonyl of Leu18, and the distorted helical geometry of the terminal dipeptide allows the inclusion of a water bridge between the backbone NH of the Lys22 residue and the carbonyls of Leu19 and Ser20.

Thermodynamic Effects of Replacements of Pro Residues in Helix Interiors of Maltose-Binding Protein

OpenAIRE

Prajapati, RS; Lingaraju, GM; Bacchawat, Kiran; Surolia, Avadhesha; Varadarajan, Raghavan

2003-01-01

Introduction of Pro residues into helix interiors results in protein destabilization. It is currently unclear if the converse substitution (i.e., replacement of Pro residues that naturally occur in helix interiors would be stabilizing). Maltose-binding protein is a large 370-amino acid protein that contains 21 Pro residues. Of these, three nonconserved residues (P48, P133, and P159) occur at helix interiors. Each of the residues was replaced with Ala and Ser. Stabilities were characterized by...

Conformational Diffusion and Helix Formation Kinetics

International Nuclear Information System (INIS)

Hummer, Gerhard; Garcia, Angel E.; Garde, Shekhar

2000-01-01

The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society

Conformational Diffusion and Helix Formation Kinetics

Energy Technology Data Exchange (ETDEWEB)

Hummer, Gerhard [Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States); Garcia, Angel E. [Theoretical Biology and Biophysics Group T-10, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Garde, Shekhar [Department of Chemical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180 (United States)

2000-09-18

The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. (c) 2000 The American Physical Society.

Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity.

Science.gov (United States)

Harper, Shannon M; Christie, John M; Gardner, Kevin H

2004-12-28

Light plays a crucial role in activating phototropins, a class of plant photoreceptors that are sensitive to blue and UV-A wavelengths. Previous studies indicated that phototropin uses a bound flavin mononucleotide (FMN) within its light-oxygen-voltage (LOV) domain to generate a protein-flavin covalent bond under illumination. In the C-terminal LOV2 domain of Avena sativa phototropin 1, formation of this bond triggers a conformational change that results in unfolding of a helix external to this domain called Jalpha [Harper, S. M., et al. (2003) Science 301, 1541-1545]. Though the structural effects of illumination were characterized, it was unknown how these changes are coupled to kinase activation. To examine this, we made a series of point mutations along the Jalpha helix to disrupt its interaction with the LOV domain in a manner analogous to light activation. Using NMR spectroscopy and limited proteolysis, we demonstrate that several of these mutations displace the Jalpha helix from the LOV domain independently of illumination. When placed into the full-length phototropin protein, these point mutations display constitutive kinase activation, without illumination of the sample. These results indicate that unfolding of the Jalpha helix is the critical event in regulation of kinase signaling for the phototropin proteins.

13-Helix folding of a β/γ-peptide manifold designed from a "minimal-constraint" blueprint.

Science.gov (United States)

Grison, Claire M; Robin, Sylvie; Aitken, David J

2016-06-14

A bottom-up design rationale was adopted to devise β/γ-peptide foldamer manifolds which would adopt preferred 13-helix conformations, relying on minimal steric imposition brought by the constituent amino acid residues. In this way, a well-defined 13-helix conformer was revealed for short oligomers of trans-2-aminocyclobutanecarboxylic acid and γ(4)-amino acids in alternation, which gave good topological superposition upon an α-helix motif.

An evaluation of bias in propensity score-adjusted non-linear regression models.

Science.gov (United States)

Wan, Fei; Mitra, Nandita

2018-03-01

Propensity score methods are commonly used to adjust for observed confounding when estimating the conditional treatment effect in observational studies. One popular method, covariate adjustment of the propensity score in a regression model, has been empirically shown to be biased in non-linear models. However, no compelling underlying theoretical reason has been presented. We propose a new framework to investigate bias and consistency of propensity score-adjusted treatment effects in non-linear models that uses a simple geometric approach to forge a link between the consistency of the propensity score estimator and the collapsibility of non-linear models. Under this framework, we demonstrate that adjustment of the propensity score in an outcome model results in the decomposition of observed covariates into the propensity score and a remainder term. Omission of this remainder term from a non-collapsible regression model leads to biased estimates of the conditional odds ratio and conditional hazard ratio, but not for the conditional rate ratio. We further show, via simulation studies, that the bias in these propensity score-adjusted estimators increases with larger treatment effect size, larger covariate effects, and increasing dissimilarity between the coefficients of the covariates in the treatment model versus the outcome model.

Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor.

Directory of Open Access Journals (Sweden)

Jolene Read

2015-06-01

Full Text Available Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation.

The Disgust Propensity and Sensitivity Scale - Revised : Its predictive value for avoidance behavior

NARCIS (Netherlands)

van Overveld, Mark; de Jong, Peter J.; Peters, Madelon L.

Disgust propensity appears involved in psychopathology. However, current disgust propensity indices display inflated correlations with psychopathology indices due to conceptual overlap. The recently developed Disgust Propensity and Sensitivity Scale - Revised (DPSS-R) is unique in that it measures

Adding propensity scores to pure prediction models fails to improve predictive performance

Directory of Open Access Journals (Sweden)

Amy S. Nowacki

2013-08-01

Full Text Available Background. Propensity score usage seems to be growing in popularity leading researchers to question the possible role of propensity scores in prediction modeling, despite the lack of a theoretical rationale. It is suspected that such requests are due to the lack of differentiation regarding the goals of predictive modeling versus causal inference modeling. Therefore, the purpose of this study is to formally examine the effect of propensity scores on predictive performance. Our hypothesis is that a multivariable regression model that adjusts for all covariates will perform as well as or better than those models utilizing propensity scores with respect to model discrimination and calibration.Methods. The most commonly encountered statistical scenarios for medical prediction (logistic and proportional hazards regression were used to investigate this research question. Random cross-validation was performed 500 times to correct for optimism. The multivariable regression models adjusting for all covariates were compared with models that included adjustment for or weighting with the propensity scores. The methods were compared based on three predictive performance measures: (1 concordance indices; (2 Brier scores; and (3 calibration curves.Results. Multivariable models adjusting for all covariates had the highest average concordance index, the lowest average Brier score, and the best calibration. Propensity score adjustment and inverse probability weighting models without adjustment for all covariates performed worse than full models and failed to improve predictive performance with full covariate adjustment.Conclusion. Propensity score techniques did not improve prediction performance measures beyond multivariable adjustment. Propensity scores are not recommended if the analytical goal is pure prediction modeling.

Geometry of the toroidal N-helix: optimal-packing and zero-twist

DEFF Research Database (Denmark)

Olsen, Kasper; Bohr, Jakob

2012-01-01

Two important geometrical properties of N-helix structures are influenced by bending. One is maximizing the volume fraction, which is called optimal-packing, and the other is having a vanishing strain-twist coupling, which is called zero-twist. Zero-twist helices rotate neither in one nor...... helix. General N-helices are discussed, as well as zero-twist helices for N > 1. The derived geometrical restrictions are gradually modified by changing the aspect ratio of the torus....

Alternative reproductive tactics and the propensity of hybridization.

Science.gov (United States)

Tynkkynen, K; Raatikainen, K J; Häkkilä, M; Haukilehto, E; Kotiaho, J S

2009-12-01

One explanation for hybridization between species is the fitness benefits it occasionally confers to the hybridizing individuals. This explanation is possible in species that have evolved alternative male reproductive tactics: individuals with inferior tactics might be more prone to hybridization provided it increases their reproductive success and fitness. Here we experimentally tested whether the propensity of hybridization in the wild depends on male reproductive tactic in Calopteryx splendens damselflies. Counter to our expectation, it was males adopting the superior reproductive tactic (territoriality) that had greatest propensity to hybridize than males adopting the inferior tactics (sneakers and floaters). Moreover, among the territorial males, the most ornamented males had greatest propensity to hybridize whereas the pattern was reversed in the sneaker males. Our results suggest that there is fluctuating selection on male mate discrimination against heterospecific females depending on both ornament size and the male's reproductive tactic.

Gender differences in entrepreneurial propensity

NARCIS (Netherlands)

Koellinger, P.; Minniti, M.; Schade, C.

2013-01-01

Using data from representative population surveys in 17 countries, we find that the lower rate of female business ownership is primarily due to women's lower propensity to start businesses rather than to differences in survival rates across genders. We show that women are less confident in their

Gender Differences in Entrepreneurial Propensity

NARCIS (Netherlands)

Ph.D. Koellinger (Philipp); M. Minniti (Maria); C. Schade (Christian)

2013-01-01

textabstractUsing data from representative population surveys in 17 countries, we find that the lower rate of female business ownership is primarily due to women's lower propensity to start businesses rather than to differences in survival rates across genders. We show that women are less confident

Progesterone modulation of transmembrane helix-helix interactions between the α-subunit of Na/K-ATPase and phospholipid N-methyltransferase in the oocyte plasma membrane

Directory of Open Access Journals (Sweden)

Askari Amir

2010-05-01

Full Text Available Abstract Background Progesterone binding to the surface of the amphibian oocyte initiates the meiotic divisions. Our previous studies with Rana pipiens oocytes indicate that progesterone binds to a plasma membrane site within the external loop between the M1 and M2 helices of the α-subunit of Na/K-ATPase, triggering a cascade of lipid second messengers and the release of the block at meiotic prophase. We have characterized this site, using a low affinity ouabain binding isoform of the α1-subunit. Results Preparations of isolated plasma membranes from Rana oocytes demonstrate that physiological levels of progesterone (or the non-metabolizable progestin R5020 successively activate phosphatidylethanolamine-N-methyltransferase (PE-NMT and sphingomyelin synthase within seconds. Inhibition of PE-NMT blocks the progesterone induction of meiosis in intact oocytes, whereas its initial product, phosphatidylmonomethylethanolamine (PME, can itself initiate meiosis in the presence of the inhibitor. Published X-ray crystallographic data on Na/K-ATPase, computer-generated 3D projections, heptad repeat analysis and hydrophobic cluster analysis of the transmembrane helices predict that hydrophobic residues L, V, V, I, F and Y of helix M2 of the α1-subunit interact with F, L, G, L, L and F, respectively, of helix M3 of PE-NMT. Conclusion We propose that progesterone binding to the first external loop of the α1-subunit facilitates specific helix-helix interactions between integral membrane proteins to up-regulate PE-NMT, and, that successive interactions between two or more integral plasma membrane proteins induce the signaling cascades which result in completion of the meiotic divisions.

Genome-wide identification and analysis of basic helix-loop-helix domains in dog, Canis lupus familiaris.

Science.gov (United States)

Wang, Xu-Hua; Wang, Yong; Liu, A-Ke; Liu, Xiao-Ting; Zhou, Yang; Yao, Qin; Chen, Ke-Ping

2015-04-01

The basic helix-loop-helix (bHLH) domain is a highly conserved amino acid motif that defines a group of DNA-binding transcription factors. bHLH proteins play essential regulatory roles in a variety of biological processes in animal, plant, and fungus. The domestic dog, Canis lupus familiaris, is a good model organism for genetic, physiological, and behavioral studies. In this study, we identified 115 putative bHLH genes in the dog genome. Based on a phylogenetic analysis, 51, 26, 14, 4, 12, and 4 dog bHLH genes were assigned to six separate groups (A-F); four bHLH genes were categorized as ''orphans''. Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with positional conservation, other conserved domains flanking the bHLH motif, and highly conserved intron/exon patterns in other vertebrates. Our analytical results confirmed the GenBank annotations of 89 dog bHLH proteins and provided information that could be used to update the annotations of the remaining 26 dog bHLH proteins. These data will provide good references for further studies on the structures and regulatory functions of bHLH proteins in the growth and development of dogs, which may help in understanding the mechanisms that underlie the physical and behavioral differences between dogs and wolves.

DNA binding specificity of the basic-helix-loop-helix protein MASH-1.

Science.gov (United States)

Meierhan, D; el-Ariss, C; Neuenschwander, M; Sieber, M; Stackhouse, J F; Allemann, R K

1995-09-05

Despite the high degree of sequence similarity in their basic-helix-loop-helix (BHLH) domains, MASH-1 and MyoD are involved in different biological processes. In order to define possible differences between the DNA binding specificities of these two proteins, we investigated the DNA binding properties of MASH-1 by circular dichroism spectroscopy and by electrophoretic mobility shift assays (EMSA). Upon binding to DNA, the BHLH domain of MASH-1 underwent a conformational change from a mainly unfolded to a largely alpha-helical form, and surprisingly, this change was independent of the specific DNA sequence. The same conformational transition could be induced by the addition of 20% 2,2,2-trifluoroethanol. The apparent dissociation constants (KD) of the complexes of full-length MASH-1 with various oligonucleotides were determined from half-saturation points in EMSAs. MASH-1 bound as a dimer to DNA sequences containing an E-box with high affinity KD = 1.4-4.1 x 10(-14) M2). However, the specificity of DNA binding was low. The dissociation constant for the complex between MASH-1 and the highest affinity E-box sequence (KD = 1.4 x 10(-14) M2) was only a factor of 10 smaller than for completely unrelated DNA sequences (KD = approximately 1 x 10(-13) M2). The DNA binding specificity of MASH-1 was not significantly increased by the formation of an heterodimer with the ubiquitous E12 protein. MASH-1 and MyoD displayed similar binding site preferences, suggesting that their different target gene specificities cannot be explained solely by differential DNA binding. An explanation for these findings is provided on the basis of the known crystal structure of the BHLH domain of MyoD.

Hispanic Youth and Military Enlistment Propensity

National Research Council Canada - National Science Library

O'Connor

1999-01-01

The purpose of this report is to explore the issue of Hispanic propensity in more depth than has previously been available, and to identify possible causes of Hispanic youths' declining interest in military service...

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

International Nuclear Information System (INIS)

Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H.; Prodromou, Chrisostomos

2015-01-01

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90) 2 –Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

Energy Technology Data Exchange (ETDEWEB)

Morgan, Rhodri M. L.; Pal, Mohinder; Roe, S. Mark; Pearl, Laurence H., E-mail: laurence.pearl@sussex.ac.uk; Prodromou, Chrisostomos, E-mail: laurence.pearl@sussex.ac.uk [University of Sussex, Falmer, Brighton BN1 9RQ (United Kingdom)

2015-05-01

A helix swap involving the fifth helix between two adjacently bound Tah1 molecules restores the normal binding environment of the conserved MEEVD peptide of Hsp90. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes with Hsp90 and Tah1. Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6–(Hsp90){sub 2}–Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes.

α-helix to β-hairpin transition of human amylin monomer

Science.gov (United States)

Singh, Sadanand; Chiu, Chi-cheng; Reddy, Allam S.; de Pablo, Juan J.

2013-04-01

The human islet amylin polypeptide is produced along with insulin by pancreatic islets. Under some circumstances, amylin can aggregate to form amyloid fibrils, whose presence in pancreatic cells is a common pathological feature of Type II diabetes. A growing body of evidence indicates that small, early stage aggregates of amylin are cytotoxic. A better understanding of the early stages of the amylin aggregation process and, in particular, of the nucleation events leading to fibril growth could help identify therapeutic strategies. Recent studies have shown that, in dilute solution, human amylin can adopt an α-helical conformation, a β-hairpin conformation, or an unstructured coil conformation. While such states have comparable free energies, the β-hairpin state exhibits a large propensity towards aggregation. In this work, we present a detailed computational analysis of the folding pathways that arise between the various conformational states of human amylin in water. A free energy surface for amylin in explicit water is first constructed by resorting to advanced sampling techniques. Extensive transition path sampling simulations are then employed to identify the preferred folding mechanisms between distinct minima on that surface. Our results reveal that the α-helical conformer of amylin undergoes a transformation into the β-hairpin monomer through one of two mechanisms. In the first, misfolding begins through formation of specific contacts near the turn region, and proceeds via a zipping mechanism. In the second, misfolding occurs through an unstructured coil intermediate. The transition states for these processes are identified. Taken together, the findings presented in this work suggest that the inter-conversion of amylin between an α-helix and a β-hairpin is an activated process and could constitute the nucleation event for fibril growth.

Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET.

Science.gov (United States)

Khadria, Ambalika S; Senes, Alessandro

2015-07-01

Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations. © 2015 Wiley Periodicals, Inc.

Interactions between an alpha-helix and a beta-sheet. Energetics of alpha/beta packing in proteins.

Science.gov (United States)

Chou, K C; Némethy, G; Rumsey, S; Tuttle, R W; Scheraga, H A

1985-12-05

Conformational energy computations have been carried out to determine the favorable ways of packing a right-handed alpha-helix on a right-twisted antiparallel or parallel beta-sheet. Co-ordinate transformations have been developed to relate the position and orientation of the alpha-helix to the beta-sheet. The packing was investigated for a CH3CO-(L-Ala)16-NHCH3 alpha-helix interacting with five-stranded beta-sheets composed of CH3CO-(L-Val)6-NHCH3 chains. All internal and external variables for both the alpha-helix and the beta-sheet were allowed to change during energy minimization. Four distinct classes of low-energy packing arrangements were found for the alpha-helix interacting with both the parallel and the anti-parallel beta-sheet. The classes differ in the orientation of the axis of the alpha-helix relative to the direction of the strands of the right-twisted beta-sheet. In the class with the most favorable arrangement, the alpha-helix is oriented along the strands of the beta-sheet, as a result of attractive non-bonded side-chain-side-chain interactions along the entire length of the alpha-helix. A class with nearly perpendicular orientation of the helix axis to the strands is also of low energy, because it allows similarly extensive attractive interactions. In the other two classes, the helix is oriented diagonally relative to the strands of the beta-sheet. In one of them, it interacts with the convex surface near the middle of the saddle-shaped twisted beta-sheet. In the other, it is oriented along the concave diagonal of the beta-sheet and, therefore, it interacts only with the corner regions of the sheet, so that this packing is energetically less favorable. The packing arrangements involving an antiparallel and a parallel beta-sheet are generally similar, although the antiparallel beta-sheet has been found to be more flexible. The major features of 163 observed alpha/beta packing arrangements in 37 proteins are accounted for in terms of the computed

Effects of spring conditions on breeding propensity of Greater Snow Goose females

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Reed, E. T.

2004-06-01

Full Text Available Breeding propensity, defined as the probability that a sexually mature adult will breed in a given year, is an important determinant of annual productivity. It is also one of the least known demographic parameters in vertebrates. We studied the relationship between breeding propensity and conditions on spring staging areas (a spring conservation hunt and the breeding grounds (spring snow cover in Greater Snow Geese (Chen caerulescens atlantica, a long distance migrant that breeds in the High Arctic. We combined information from mark–recapture, telemetry, and nest survey data to estimate breeding propensity over a 7– year period. True temporal variation in breeding propensity was considerable (mean: 0.574 [95% CI considering only process variation: 0.13 to 1.0]. Spring snow cover was negatively related to breeding propensity (bsnow=-2,05 ± 0,96 SE and tended to be reduced in years with a spring hunt (b = -0,78 ± 0,35. Nest densities on the breeding colony and fall ratios of young:adults were good indices of annual variation in breeding propensity, with nest densities being slightly more precise. These results suggest that conditions encountered during the pre-breeding period can have a significant impact on productivity of Arctic-nesting birds

Gate-controlled switching between persistent and inverse persistent spin helix states

International Nuclear Information System (INIS)

Yoshizumi, K.; Sasaki, A.; Kohda, M.; Nitta, J.

2016-01-01

We demonstrate gate-controlled switching between persistent spin helix (PSH) state and inverse PSH state, which are detected by quantum interference effect on magneto-conductance. These special symmetric spin states showing weak localization effect give rise to a long spin coherence when the strength of Rashba spin-orbit interaction (SOI) is close to that of Dresselhaus SOI. Furthermore, in the middle of two persistent spin helix states, where the Rashba SOI can be negligible, the bulk Dresselhaus SOI parameter in a modulation doped InGaAs/InAlAs quantum well is determined.

Gate-controlled switching between persistent and inverse persistent spin helix states

Energy Technology Data Exchange (ETDEWEB)

Yoshizumi, K.; Sasaki, A.; Kohda, M.; Nitta, J. [Department of Materials Science, Tohoku University, Sendai 980-8579 (Japan)

2016-03-28

We demonstrate gate-controlled switching between persistent spin helix (PSH) state and inverse PSH state, which are detected by quantum interference effect on magneto-conductance. These special symmetric spin states showing weak localization effect give rise to a long spin coherence when the strength of Rashba spin-orbit interaction (SOI) is close to that of Dresselhaus SOI. Furthermore, in the middle of two persistent spin helix states, where the Rashba SOI can be negligible, the bulk Dresselhaus SOI parameter in a modulation doped InGaAs/InAlAs quantum well is determined.

The Quadruple Helix Model Enhancing Innovative Performance Of Indonesian Creative Industry

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Sri Wahyu Lelly Hana Setyanti

2017-11-01

Full Text Available The creative industry in Indonesia has contributed positively to the national economic growth. Creative industry grows from the creativity and innovation performance of the business actors. The challenge of creative industry is how to completely understand the creative and innovative processes in business management. Therefore it requires an approach that combines the synergy between academicians entrepreneurs government and society in a quadruple helix model. The objective of this research is to develop a creativity model through a quadruple helix model in improving innovation performance of the creative industry.

Design and synthesis of DNA four-helix bundles

Energy Technology Data Exchange (ETDEWEB)

Rangnekar, Abhijit; Gothelf, Kurt V [Department of Chemistry, Centre for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C (Denmark); LaBean, Thomas H, E-mail: kvg@chem.au.dk, E-mail: thl@cs.duke.edu [Department of Chemistry, Duke University, Durham, NC 27708 (United States)

2011-06-10

The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

Design and synthesis of DNA four-helix bundles

International Nuclear Information System (INIS)

Rangnekar, Abhijit; Gothelf, Kurt V; LaBean, Thomas H

2011-01-01

The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

Lane-changing model with dynamic consideration of driver's propensity

Science.gov (United States)

Wang, Xiaoyuan; Wang, Jianqiang; Zhang, Jinglei; Ban, Xuegang Jeff

2015-07-01

Lane-changing is the driver's selection result of the satisfaction degree in different lane driving conditions. There are many different factors influencing lane-changing behavior, such as diversity, randomicity and difficulty of measurement. So it is hard to accurately reflect the uncertainty of drivers' lane-changing behavior. As a result, the research of lane-changing models is behind that of car-following models. Driver's propensity is her/his emotion state or the corresponding preference of a decision or action toward the real objective traffic situations under the influence of various dynamic factors. It represents the psychological characteristics of the driver in the process of vehicle operation and movement. It is an important factor to influence lane-changing. In this paper, dynamic recognition of driver's propensity is considered during simulation based on its time-varying discipline and the analysis of the driver's psycho-physic characteristics. The Analytic Hierarchy Process (AHP) method is used to quantify the hierarchy of driver's dynamic lane-changing decision-making process, especially the influence of the propensity. The model is validated using real data. Test results show that the developed lane-changing model with the dynamic consideration of a driver's time-varying propensity and the AHP method are feasible and with improved accuracy.

Design, synthesis, and evaluation of an alpha-helix mimetic library targeting protein-protein interactions.

Science.gov (United States)

Shaginian, Alex; Whitby, Landon R; Hong, Sukwon; Hwang, Inkyu; Farooqi, Bilal; Searcey, Mark; Chen, Jiandong; Vogt, Peter K; Boger, Dale L

2009-04-22

The design and solution-phase synthesis of an alpha-helix mimetic library as an integral component of a small-molecule library targeting protein-protein interactions are described. The iterative design, synthesis, and evaluation of the candidate alpha-helix mimetic was initiated from a precedented triaryl template and refined by screening the designs for inhibition of MDM2/p53 binding. Upon identifying a chemically and biologically satisfactory design and consistent with the screening capabilities of academic collaborators, the corresponding complete library was assembled as 400 mixtures of 20 compounds (20 x 20 x 20-mix), where the added subunits are designed to mimic all possible permutations of the naturally occurring i, i + 4, i + 7 amino acid side chains of an alpha-helix. The library (8000 compounds) was prepared using a solution-phase synthetic protocol enlisting acid/base liquid-liquid extractions for purification on a scale that insures its long-term availability for screening campaigns. Screening of the library for inhibition of MDM2/p53 binding not only identified the lead alpha-helix mimetic upon which the library was based, but also suggests that a digestion of the initial screening results that accompany the use of such a comprehensive library can provide insights into the nature of the interaction (e.g., an alpha-helix mediated protein-protein interaction) and define the key residues and their characteristics responsible for recognition.

Mechanism of death at high temperatures in Helix and Patella

Energy Technology Data Exchange (ETDEWEB)

Grainger, J N.R.

1975-10-01

In Patella vulgata and Helix aspersa which had been killed by exposure to high temperatures, the rates of oxygen consumption of gill, foot muscle and hepatopancreas are remarkably steady when measured at lower temperatures, although the absolute levels are in some cases different from normal animals. These tissues are thus substantially metabolically intact in heat dead individuals. In Helix there is a fall in blood sodium and a rise in blood potassium during heat death. In Patella there is a marked rise in blood Na/sup +/ and a consequent disturbance of the Na/sup +//K/sup +/ ratio. These ionic disturbances are thought to be a prime cause of heat death. The significance of the results is discussed.

Modeling the flocking propensity of passerine birds in two Neotropical habitats.

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Pomara, Lars Y; Cooper, Robert J; Petit, Lisa J

2007-08-01

We examined the importance of mixed-species flock abundance, individual bird home range size, foraging height, and foraging patch characteristics in predicting the propensity for five Neotropical passerine bird species (Slaty Antwren, Myrmotherula schisticolor; Golden-crowned Warbler, Basileuterus culicivorus; Slate-throated Redstart, Myioborus miniatus; Wilson's Warbler, Wilsonia pusilla; and Black-and-white Warbler, Mniotilta varia) to forage within flocks, rather than solitarily. We used study plots in primary mid-elevation forest and in shade coffee fields in western Panama. We expected that all species would spend as much time as possible flocking, but that the social and environmental factors listed above would limit compatibility between flock movements and individual bird movements, explaining variability in flocking propensity both within and among species. Flocking propensity was well predicted by home range size and flock abundance together, for four of the five species. While flock abundance was uniform across plots, home range sizes varied among species and plots, so that home range size appeared to be the principle factor limiting flocking propensity. Estimates of flock abundance were still required, however, for calculating flocking propensity values. Foraging height and patch characteristics slightly improved predictive ability for the remaining species, M. miniatus. In general, individual birds tended to join flocks whenever one was available inside their home range, regardless of a flock's specific location within the home range. Flocking propensities of individual species were lower in shade coffee fields than in forests, and probably vary across landscapes with variations in habitat. This variability affects the stability and species composition of flocks, and may affect survival rates of individual species.

Stability and Change in Risk-Taking Propensity Across the Adult Lifespan

Science.gov (United States)

Josef, Anika K.; Richter, David; Samanez-Larkin, Gregory R.; Wagner, Gert G.; Hertwig, Ralph; Mata, Rui

2016-01-01

Can risk-taking propensity be thought of as a trait that captures individual differences across domains, measures, and time? Studying stability in risk-taking propensities across the lifespan can help to answer such questions by uncovering parallel, or divergent, trajectories across domains and measures. We contribute to this effort by using data from respondents aged 18 to 85 in the German Socio-Economic Panel Study (SOEP) and by examining (1) differential stability, (2) mean-level differences, and (3) individual-level changes in self-reported general (N = 44,076) and domain-specific (N =11,903) risk-taking propensities across adulthood. In addition, we investigate (4) the correspondence between cross-sectional trajectories of self-report and behavioral measures of social (trust game; N = 646) and nonsocial (monetary gamble; N = 433) risk taking. The results suggest that risk-taking propensity can be understood as a trait with moderate stability. Results show reliable mean-level differences across the lifespan, with risk-taking propensities typically decreasing with age, although significant variation emerges across domains and individuals. Interestingly, the mean-level trajectory for behavioral measures of social and nonsocial risk taking was similar to those obtained from self-reported risk, despite small correlations between task behavior and self-reports. Individual-level analyses suggest a link between changes in risk-taking propensities both across domains and in relation to changes in some of the Big Five personality traits. Overall, these results raise important questions concerning the role of common processes or events that shape the lifespan development of risk-taking across domains as well as other major personality facets. PMID:26820061

Ab initio theory of helix <-> coil phase transition

DEFF Research Database (Denmark)

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

2008-01-01

In this paper, we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix <-> random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely ...

Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms.

Science.gov (United States)

Murrugarra, David; Miller, Jacob; Mueller, Alex N

2016-01-01

Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS) are a modeling framework that considers two propensity parameters for updating each node and uses one when the update has a positive impact on the variable, that is, when the update causes the variable to increase its value, and uses the other when the update has a negative impact, that is, when the update causes it to decrease its value. This framework offers additional features for simulations but also adds a complexity in parameter estimation of the propensities. This paper presents a method for estimating the propensity parameters for SDDS. The method is based on adding noise to the system using the Google PageRank approach to make the system ergodic and thus guaranteeing the existence of a stationary distribution. Then with the use of a genetic algorithm, the propensity parameters are estimated. Approximation techniques that make the search algorithms efficient are also presented and Matlab/Octave code to test the algorithms are available at http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html.

Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics

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Haruki Nakamura

2012-02-01

Full Text Available The phosphorylated kinase-inducible activation domain (pKID adopts a helix–loop–helix structure upon binding to its partner KIX, although it is unstructured in the unbound state. The N-terminal and C-terminal regions of pKID, which adopt helices in the complex, are called, respectively, αA and αB. We performed all-atom multicanonical molecular dynamics simulations of pKID with and without KIX in explicit solvents to generate conformational ensembles. Although the unbound pKID was disordered overall, αA and αB exhibited a nascent helix propensity; the propensity of αA was stronger than that of αB, which agrees with experimental results. In the bound state, the free-energy landscape of αB involved two low free-energy fractions: native-like and non-native fractions. This result suggests that αB folds according to the induced-fit mechanism. The αB-helix direction was well aligned as in the NMR complex structure, although the αA helix exhibited high flexibility. These results also agree quantitatively with experimental observations. We have detected that the αB helix can bind to another site of KIX, to which another protein MLL also binds with the adopting helix. Consequently, MLL can facilitate pKID binding to the pKID-binding site by blocking the MLL-binding site. This also supports experimentally obtained results.

Propensity score methodology for confounding control in health care utilization databases

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Elisabetta Patorno

2013-06-01

Full Text Available Propensity score (PS methodology is a common approach to control for confounding in nonexperimental studies of treatment effects using health care utilization databases. This methodology offers researchers many advantages compared with conventional multivariate models: it directly focuses on the determinants of treatment choice, facilitating the understanding of the clinical decision-making process by the researcher; it allows for graphical comparisons of the distribution of propensity scores and truncation of subjects without overlapping PS indicating a lack of equipoise; it allows transparent assessment of the confounder balance achieved by the PS at baseline; and it offers a straightforward approach to reduce the dimensionality of sometimes large arrays of potential confounders in utilization databases, directly addressing the “curse of dimensionality” in the context of rare events. This article provides an overview of the use of propensity score methodology for pharmacoepidemiologic research with large health care utilization databases, covering recent discussions on covariate selection, the role of automated techniques for addressing unmeasurable confounding via proxies, strategies to maximize clinical equipoise at baseline, and the potential of machine-learning algorithms for optimized propensity score estimation. The appendix discusses the available software packages for PS methodology. Propensity scores are a frequently used and versatile tool for transparent and comprehensive adjustment of confounding in pharmacoepidemiology with large health care databases.

Controlling chirality with helix inversion in cholesteric liquid crystals

NARCIS (Netherlands)

Katsonis, Nathalie Hélène; Lacaze, E.; Ferrarini, A.

2012-01-01

The helical organization of cholesteric liquid crystals is omnipresent in living matter. Achieving control over the structure of the cholesteric helix consequently holds great potential for developing stimuli-responsive materials matching the level of sophistication of biological systems. In

Equilibrium shift in solution: molecular shape recognition and precipitation of a synthetic double helix using helicene-grafted silica nanoparticles.

Science.gov (United States)

Miyagawa, Masamichi; Ichinose, Wataru; Yamaguchi, Masahiko

2014-01-27

Chiral silica nanoparticles (70 nm) grafted with (P)-helicene recognized the molecular shape of double helix and random coil (P)-ethynylhelicene oligomers in solution. A mixture of the (P)-nanoparticles and double helix precipitated much faster than a mixture of the (P)-nanoparticles and random coil, and the precipitate contained only the double helix. The mixture of the (P)-nanoparticles and (P)-ethynylhelicene pentamer reversibly dispersed in trifluoromethylbenzene upon heating at 70 °C and precipitated upon cooling at 25 °C. When a 10:90 equilibrium mixture of the double helix and random coil in solution was treated with the (P)-nanoparticles, the double helix was precipitated in 53% yield and was accompanied by equilibrium shift. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis.

Science.gov (United States)

Liu, Ake; Wang, Yong; Zhang, Debao; Wang, Xuhua; Song, Huifang; Dang, Chunwang; Yao, Qin; Chen, Keping

2013-08-01

Helix-loop-helix (bHLH) proteins play essential regulatory roles in a variety of biological processes. These highly conserved proteins form a large transcription factor superfamily, and are commonly identified in large numbers within animal, plant, and fungal genomes. The bHLH domain has been well studied in many animal species, but has not yet been characterized in non-avian reptiles. In this study, we identified 102 putative bHLH genes in the genome of the green anole lizard, Anolis carolinensis. Based on phylogenetic analysis, these genes were classified into 43 families, with 43, 24, 16, 3, 10, and 3 members assigned into groups A, B, C, D, E, and F, respectively, and 3 members categorized as "orphans". Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with highly conserved patterns observed for introns and additional domains. Results from phylogenetic analysis of the H/E(spl) family suggest that genome and tandem gene duplications have contributed to this family's expansion. Our classification and evolutionary analysis has provided insights into the evolutionary diversification of animal bHLH genes, and should aid future studies on bHLH protein regulation of key growth and developmental processes.

Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors

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Wuyi Liu

2013-01-01

Full Text Available The previous survey identified 70 basic helix-loop-helix (bHLH proteins, but it was proved to be incomplete, and the functional information and regulatory networks of frog bHLH transcription factors were not fully known. Therefore, we conducted an updated genome-wide survey in the Xenopus tropicalis genome project databases and identified 105 bHLH sequences. Among the retrieved 105 sequences, phylogenetic analyses revealed that 103 bHLH proteins belonged to 43 families or subfamilies with 46, 26, 11, 3, 15, and 4 members in the corresponding supergroups. Next, gene ontology (GO enrichment analyses showed 65 significant GO annotations of biological processes and molecular functions and KEGG pathways counted in frequency. To explore the functional pathways, regulatory gene networks, and/or related gene groups coding for Xenopus tropicalis bHLH proteins, the identified bHLH genes were put into the databases KOBAS and STRING to get the signaling information of pathways and protein interaction networks according to available public databases and known protein interactions. From the genome annotation and pathway analysis using KOBAS, we identified 16 pathways in the Xenopus tropicalis genome. From the STRING interaction analysis, 68 hub proteins were identified, and many hub proteins created a tight network or a functional module within the protein families.

Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin

Science.gov (United States)

Urano, Ryo; Okamoto, Yuko

2015-12-01

We applied a newly proposed prediction method for membrane protein structures to bacteriorhodopsin that has distorted transmembrane helices in the native structure. This method uses an implicit membrane model, which restricts sampling space during folding in a membrane region, and includes helix bending. Replica-exchange simulations were performed with seven transmembrane helices only without a retinal molecule. Obtained structures were classified into clusters of similar structures, which correspond to local-minimum free energy states. The two lowest free energy states corresponded to a native-like structure with the correct empty space for retinal and a structure with this empty space filled with a helix. Previous experiments of bacteriorhodopsin suggested that association of transmembrane helices enables them to make a room for insertion of a retinal. Our results are consistent with these results. Moreover, distortions of helices in the native-like structures were successfully reproduced. In the distortions, whereas the locations of kinks for all helices were similar to those of Protein Data Bank's data, the amount of bends was more similar for helices away from the retinal than for those close to the retinal in the native structure. This suggests a hypothesis that the amino-acid sequence specifies the location of kinks in transmembrane helices and that the amount of distortions depends on the interactions with the surrounding molecules such as neighboring helices, lipids, and retinal.

Estimating Propensity Parameters using Google PageRank and Genetic Algorithms

Directory of Open Access Journals (Sweden)

David Murrugarra

2016-11-01

Full Text Available Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS are a modeling framework that considers two propensity parameters for updating each node and uses one when the update has a positive impact on the variable, that is, when the update causes the variable to increase its value, and uses the other when the update has a negative impact, that is, when the update causes it to decrease its value. This framework offers additional features for simulations but also adds a complexity in parameter estimation of the propensities. This paper presents a method for estimating the propensity parameters for SDDS. The method is based on adding noise to the system using the Google PageRank approach to make the system ergodic and thus guaranteeing the existence of a stationary distribution. Then with the use of a genetic algorithm, the propensity parameters are estimated. Approximation techniques that make the search algorithms efficient are also presented and Matlab/Octave code to test the algorithms are available at~href{http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html}{http://www.ms.uky.edu/$sim$dmu228GeneticAlgCode.html}.

Self-assembled RNA-triple-helix hydrogel scaffold for microRNA modulation in the tumour microenvironment

Science.gov (United States)

Conde, João; Oliva, Nuria; Atilano, Mariana; Song, Hyun Seok; Artzi, Natalie

2016-03-01

The therapeutic potential of miRNA (miR) in cancer is limited by the lack of efficient delivery vehicles. Here, we show that a self-assembled dual-colour RNA-triple-helix structure comprising two miRNAs--a miR mimic (tumour suppressor miRNA) and an antagomiR (oncomiR inhibitor)--provides outstanding capability to synergistically abrogate tumours. Conjugation of RNA triple helices to dendrimers allows the formation of stable triplex nanoparticles, which form an RNA-triple-helix adhesive scaffold upon interaction with dextran aldehyde, the latter able to chemically interact and adhere to natural tissue amines in the tumour. We also show that the self-assembled RNA-triple-helix conjugates remain functional in vitro and in vivo, and that they lead to nearly 90% levels of tumour shrinkage two weeks post-gel implantation in a triple-negative breast cancer mouse model. Our findings suggest that the RNA-triple-helix hydrogels can be used as an efficient anticancer platform to locally modulate the expression of endogenous miRs in cancer.

Strong contributions from vertical triads to helix-partner preferences in parallel coiled coils.

Science.gov (United States)

Steinkruger, Jay D; Bartlett, Gail J; Woolfson, Derek N; Gellman, Samuel H

2012-09-26

Pairing preferences in heterodimeric coiled coils are determined by complementarities among side chains that pack against one another at the helix-helix interface. However, relationships between dimer stability and interfacial residue identity are not fully understood. In the context of the "knobs-into-holes" (KIH) packing pattern, one can identify two classes of interactions between side chains from different helices: "lateral", in which a line connecting the adjacent side chains is perpendicular to the helix axes, and "vertical", in which the connecting line is parallel to the helix axes. We have previously analyzed vertical interactions in antiparallel coiled coils and found that one type of triad constellation (a'-a-a') exerts a strong effect on pairing preferences, while the other type of triad (d'-d-d') has relatively little impact on pairing tendencies. Here, we ask whether vertical interactions (d'-a-d') influence pairing in parallel coiled-coil dimers. Our results indicate that vertical interactions can exert a substantial impact on pairing specificity, and that the influence of the d'-a-d' triad depends on the lateral a' contact within the local KIH motif. Structure-informed bioinformatic analyses of protein sequences reveal trends consistent with the thermodynamic data derived from our experimental model system in suggesting that heterotriads involving Leu and Ile are preferred over homotriads involving Leu and Ile.

What can triple helix frameworks offer to the analysis of eco-innovation dynamics? Theoretical and methodological considerations

DEFF Research Database (Denmark)

Yang, Yan; Holgaard, Jette Egelund; Remmen, Arne

2012-01-01

stakeholder groups are interacting in this connection. Taking the triple helix as the theoretical departure point, this paper discusses the opportunities offered by these triple helix frameworks for analyzing eco-innovation dynamics from both theoretical and practical perspectives. It adds to the debate about......Bringing environmental concerns into focus of innovation processes will in several cases also expand the numbers of actors involved. Eco-innovation and triple helix are often frameworks applied to analyse how environmental concerns are integrated in the innovation processes and how different...

Living Labs as boundary-spanners between Triple Helix actors

NARCIS (Netherlands)

van Geenhuizen, M.S.

2016-01-01

Living labs are an increasingly popular methodology to enhance innovation. Living labs aim to span boundaries between different organizations, among others Triple helix actors, by acting as a network organization typically in a real-life environment to foster co-creation by user-groups. This paper

The Triple Helix Model and the Knowledge-Based Economy

NARCIS (Netherlands)

Leydesdorff, L.; Meyer, M.

2010-01-01

The Triple Helix model of university-industry-government relations can be generalized from a neo-institutional model of networks of relations to a neo-evolutionary model of how three selection environments operate upon one another. Two selection mechanisms operating upon each other can mutually

Role of amphipathic helix of a herpesviral protein in membrane deformation and T cell receptor downregulation.

Directory of Open Access Journals (Sweden)

Chan-Ki Min

2008-11-01

Full Text Available Lipid rafts are membrane microdomains that function as platforms for signal transduction and membrane trafficking. Tyrosine kinase interacting protein (Tip of T lymphotropic Herpesvirus saimiri (HVS is targeted to lipid rafts in T cells and downregulates TCR and CD4 surface expression. Here, we report that the membrane-proximal amphipathic helix preceding Tip's transmembrane (TM domain mediates lipid raft localization and membrane deformation. In turn, this motif directs Tip's lysosomal trafficking and selective TCR downregulation. The amphipathic helix binds to the negatively charged lipids and induces liposome tubulation, the TM domain mediates oligomerization, and cooperation of the membrane-proximal helix with the TM domain is sufficient for localization to lipid rafts and lysosomal compartments, especially the mutivesicular bodies. These findings suggest that the membrane-proximal amphipathic helix and TM domain provide HVS Tip with the unique ability to deform the cellular membranes in lipid rafts and to downregulate TCRs potentially through MVB formation.

A rare polyglycine type II-like helix motif in naturally occurring proteins.

Science.gov (United States)

Warkentin, Eberhard; Weidenweber, Sina; Schühle, Karola; Demmer, Ulrike; Heider, Johann; Ermler, Ulrich

2017-11-01

Common structural elements in proteins such as α-helices or β-sheets are characterized by uniformly repeating, energetically favorable main chain conformations which additionally exhibit a completely saturated hydrogen-bonding network of the main chain NH and CO groups. Although polyproline or polyglycine type II helices (PP II or PG II ) are frequently found in proteins, they are not considered as equivalent secondary structure elements because they do not form a similar self-contained hydrogen-bonding network of the main chain atoms. In this context our finding of an unusual motif of glycine-rich PG II -like helices in the structure of the acetophenone carboxylase core complex is of relevance. These PG II -like helices form hexagonal bundles which appear to fulfill the criterion of a (largely) saturated hydrogen-bonding network of the main-chain groups and therefore may be regarded in this sense as a new secondary structure element. It consists of a central PG II -like helix surrounded by six nearly parallel PG II -like helices in a hexagonal array, plus an additional PG II -like helix extending the array outwards. Very related structural elements have previously been found in synthetic polyglycine fibers. In both cases, all main chain NH and CO groups of the central PG II -helix are saturated by either intra- or intermolecular hydrogen-bonds, resulting in a self-contained hydrogen-bonding network. Similar, but incomplete PG II -helix patterns were also previously identified in a GTP-binding protein and an antifreeze protein. © 2017 Wiley Periodicals, Inc.

Propensity for Bistability of Bursting and Silence in the Leech Heart Interneuron

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Tatiana Dashevskiy

2018-02-01

Full Text Available The coexistence of neuronal activity regimes has been reported under normal and pathological conditions. Such multistability could enhance the flexibility of the nervous system and has many implications for motor control, memory, and decision making. Multistability is commonly promoted by neuromodulation targeting specific membrane ionic currents. Here, we investigated how modulation of different ionic currents could affect the neuronal propensity for bistability. We considered a leech heart interneuron model. It exhibits bistability of bursting and silence in a narrow range of the leak current parameters, conductance (gleak and reversal potential (Eleak. We assessed the propensity for bistability of the model by using bifurcation diagrams. On the diagram (gleak, Eleak, we mapped bursting and silent regimes. For the canonical value of Eleak we determined the range of gleak which supported the bistability. We use this range as an index of propensity for bistability. We investigated how this index was affected by alterations of ionic currents. We systematically changed their conductances, one at a time, and built corresponding bifurcation diagrams in parameter planes of the maximal conductance of a given current and the leak conductance. We found that conductance of only one current substantially affected the index of propensity; the increase of the maximal conductance of the hyperpolarization-activated cationic current increased the propensity index. The second conductance with the strongest effect was the conductance of the low-threshold fast Ca2+ current; its reduction increased the propensity index although the effect was about two times smaller in magnitude. Analyzing the model with both changes applied simultaneously, we found that the diagram (gleak, Eleak showed a progressively expanded area of bistability of bursting and silence.

Efficient Fatigue Analysis of Helix Elements in Umbilicals and Flexible Risers: Theory and Applications

Directory of Open Access Journals (Sweden)

Geir Skeie

2012-01-01

Full Text Available Fatigue analysis of structural components such as helix tensile armors and steel tubes is a critical design issue for dynamic umbilicals and flexible pipes. The basis for assessment of fatigue damage of such elements is the long-term stress cycle distribution at critical locations on the helix elements caused by long-term environmental loading on the system. The long-term stress cycle distribution will hence require global dynamic time domain analysis followed by a detailed cross-sectional analysis in a large number of irregular sea states. An overall computational consistent and efficient fatigue analysis scheme is outlined with due regard of the cross-sectional analysis technique required for fatigue stress calculation with particular attention to the helix elements. The global cross-section is exposed to pure bending, tensile, torsion, and pressure loading. The state of the different cross-section elements is based on the global response. Special emphasis is placed on assessment of friction stresses caused by the stick-slip behavior of helix elements in bending that are of special importance for fatigue life assessments. The described cross-sectional analysis techniques are based on an extensive literature survey and are hence considered to represent industry consensus. The performance of the described calculation scheme is illustrated by case studies.

Identification of a basic helix-loop-helix-type transcription regulator gene in Aspergillus oryzae by systematically deleting large chromosomal segments.

Science.gov (United States)

Jin, Feng Jie; Takahashi, Tadashi; Machida, Masayuki; Koyama, Yasuji

2009-09-01

We previously developed two methods (loop-out and replacement-type recombination) for generating large-scale chromosomal deletions that can be applied to more effective chromosomal engineering in Aspergillus oryzae. In this study, the replacement-type method is used to systematically delete large chromosomal DNA segments to identify essential and nonessential regions in chromosome 7 (2.93 Mb), which is the smallest A. oryzae chromosome and contains a large number of nonsyntenic blocks. We constructed 12 mutants harboring deletions that spanned 16- to 150-kb segments of chromosome 7 and scored phenotypic changes in the resulting mutants. Among the deletion mutants, strains designated Delta5 and Delta7 displayed clear phenotypic changes involving growth and conidiation. In particular, the Delta5 mutant exhibited vigorous growth and conidiation, potentially beneficial characteristics for certain industrial applications. Further deletion analysis allowed identification of the AO090011000215 gene as the gene responsible for the Delta5 mutant phenotype. The AO090011000215 gene was predicted to encode a helix-loop-helix binding protein belonging to the bHLH family of transcription factors. These results illustrate the potential of the approach for identifying novel functional genes.

Nonlinear time-dependent simulation of helix traveling wave tubes

International Nuclear Information System (INIS)

Peng Wei-Feng; Yang Zhong-Hai; Hu Yu-Lu; Li Jian-Qing; Lu Qi-Ru; Li Bin

2011-01-01

A one-dimensional nonlinear time-dependent theory for helix traveling wave tubes is studied. A generalized electromagnetic field is applied to the expression of the radio frequency field. To simulate the variations of the high frequency structure, such as the pitch taper and the effect of harmonics, the spatial average over a wavelength is substituted by a time average over a wave period in the equation of the radio frequency field. Under this assumption, the space charge field of the electron beam can be treated by a space charge wave model along with the space charge coefficient. The effects of the radio frequency and the space charge fields on the electrons are presented by the equations of the electron energy and the electron phase. The time-dependent simulation is compared with the frequency-domain simulation for a helix TWT, which validates the availability of this theory. (interdisciplinary physics and related areas of science and technology)

Analysis of eco-innovation with triple helix approach: case-study of biofloc catfish farming in Yogyakarta

Science.gov (United States)

Purwadi, D.; Nurlaily, I.

2018-03-01

Concerning environmental into focus of innovation process will expand the number of actor involved. Eco-innovation and triple helix are often frameworks applied to analyse how environmental concern are integrated in innovation process and how different stakeholder groups are having inter relation. Case study from biofloc catfish farming in Yogyakarta is presented to demonstrate a possible approach for researching the success of triple helix frameworks. This case is considered on basic of the result of a survey among farmers, academician and government. The paper concludes the creating of full triple helix encounters problem in practice. It also includes suggestion for further research on fisheries development.

Tunable single photonic defect-mode in cholesteric liquid crystals with laser-induced local modifications of helix

International Nuclear Information System (INIS)

Yoshida, Hiroyuki; Lee, Chee Heng; Fujii, Akihiko; Ozaki, Masanori

2006-01-01

The authors demonstrate a tunable single photonic defect-mode in a single cholesteric liquid crystal material based on a structural defect introduced by local modification of the helix. An unpolymerized region of cholesteric liquid crystal acting as the defect was left between two polymerized regions via a two-photon excitation laser-lithography process. Upon polymerization, the cholesteric liquid crystal helix elongated and became thermally stable, and a single photonic defect mode was exhibited due to the contrast in the helix pitch at the defect. The defect mode showed tunability upon heating, and a 36 nm redshift was seen over a temperature range of 30 deg. C

Kevlar: Transitioning Helix for Research to Practice

Science.gov (United States)

2016-03-01

x86 binaries, although it can be targeted to any platform that is targeted by IDA Pro. Currently, IDA Pro targets more than 40 processors and...effects its own transformations. Helix/Kevlar then automatically generates SPRI rules for any program variants by essentially performing a “ smart diff...execute permission on the pages of memory it uses, leaving only execute (but not write) permission on the code cache. Strata also watches for attempts

Nanotech: propensity in foods and bioactives.

Science.gov (United States)

Kuan, Chiu-Yin; Yee-Fung, Wai; Yuen, Kah-Hay; Liong, Min-Tze

2012-01-01

Nanotechnology is seeing higher propensity in various industries, including food and bioactives. New nanomaterials are constantly being developed from both natural biodegradable polymers of plant and animal origins such as polysaccharides and derivatives, peptides and proteins, lipids and fats, and biocompatible synthetic biopolyester polymers such as polylactic acid (PLA), polyhydroxyalkonoates (PHA), and polycaprolactone (PCL). Applications in food industries include molecular synthesis of new functional food compounds, innovative food packaging, food safety, and security monitoring. The relevance of bioactives includes targeted delivery systems with improved bioavailability using nanostructure vehicles such as association colloids, lipid based nanoencapsulator, nanoemulsions, biopolymeric nanoparticles, nanolaminates, and nanofibers. The extensive use of nanotechnology has led to the need for parallel safety assessment and regulations to protect public health and adverse effects to the environment. This review covers the use of biopolymers in the production of nanomaterials and the propensity of nanotechnology in food and bioactives. The exposure routes of nanoparticles, safety challenges, and measures undertaken to ensure optimal benefits that outweigh detriments are also discussed.

RISKS MANAGEMENT. A PROPENSITY SCORE APPLICATION

Directory of Open Access Journals (Sweden)

Constangioara Alexandru

2008-05-01

Full Text Available Risk management is relatively unexplored in Romania. Although Romanian specialists dwell on theoretical aspects such as the risks classification and the important distinction between risks and uncertainty the practical relevance of the matter is outside existing studies. Present paper uses a dataset of consumer data to build a propensity scorecard based on relevant quantitative modeling.

Rotational symmetry and the transformation of innovation systems in a Triple Helix of university-industry-government relations

NARCIS (Netherlands)

Ivanova, I.A.; Leydesdorff, L.

2014-01-01

Using a mathematical model, we show that a Triple Helix (TH) system contains self-interaction, and therefore self-organization of innovations can be expected in waves, whereas a Double Helix (DH) remains determined by its linear constituents. (The mathematical model is fully elaborated in the

n examination of risk propensities in an orginizational context: differences by discipline and position

Directory of Open Access Journals (Sweden)

M.R. Walls

2003-12-01

Full Text Available Previous studies of risk-taking suggest there are significant variations across individuals' willingness to take financial risk within the organisational context. For example, a decision maker's propensity to take risk may be more aligned with his unique planning horizon. Previous research also suggests that division and lower level managers are typically more risk averse than top managers in the organisation. In this case study we investigate differences in risk propensity across managerial and functional designations in a major oil company, BP Exploration, Inc. We present a model for measuring risk propensity, examine the results of a survey of 39 staff and supervisory personnel, and explore the implications of a divergence between individual risk propensities and the firm's corporate risk policy.

Drawing causal inferences using propensity scores: a practical guide for community psychologists.

Science.gov (United States)

Lanza, Stephanie T; Moore, Julia E; Butera, Nicole M

2013-12-01

Confounding present in observational data impede community psychologists' ability to draw causal inferences. This paper describes propensity score methods as a conceptually straightforward approach to drawing causal inferences from observational data. A step-by-step demonstration of three propensity score methods-weighting, matching, and subclassification-is presented in the context of an empirical examination of the causal effect of preschool experiences (Head Start vs. parental care) on reading development in kindergarten. Although the unadjusted population estimate indicated that children with parental care had substantially higher reading scores than children who attended Head Start, all propensity score adjustments reduce the size of this overall causal effect by more than half. The causal effect was also defined and estimated among children who attended Head Start. Results provide no evidence for improved reading if those children had instead received parental care. We carefully define different causal effects and discuss their respective policy implications, summarize advantages and limitations of each propensity score method, and provide SAS and R syntax so that community psychologists may conduct causal inference in their own research.

The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution.

Science.gov (United States)

Fidler, Aaron L; Boudko, Sergei P; Rokas, Antonis; Hudson, Billy G

2018-04-09

The cellular microenvironment, characterized by an extracellular matrix (ECM), played an essential role in the transition from unicellularity to multicellularity in animals (metazoans), and in the subsequent evolution of diverse animal tissues and organs. A major ECM component are members of the collagen superfamily -comprising 28 types in vertebrates - that exist in diverse supramolecular assemblies ranging from networks to fibrils. Each assembly is characterized by a hallmark feature, a protein structure called a triple helix. A current gap in knowledge is understanding the mechanisms of how the triple helix encodes and utilizes information in building scaffolds on the outside of cells. Type IV collagen, recently revealed as the evolutionarily most ancient member of the collagen superfamily, serves as an archetype for a fresh view of fundamental structural features of a triple helix that underlie the diversity of biological activities of collagens. In this Opinion, we argue that the triple helix is a protein structure of fundamental importance in building the extracellular matrix, which enabled animal multicellularity and tissue evolution. © 2018. Published by The Company of Biologists Ltd.

Educational Research with Real-World Data: Reducing Selection Bias with Propensity Scores

Directory of Open Access Journals (Sweden)

Jill L. Adelson

2013-12-01

Full Text Available Often it is infeasible or unethical to use random assignment in educational settings to study important constructs and questions. Hence, educational research often uses observational data, such as large-scale secondary data sets and state and school district data, and quasi-experimental designs. One method of reducing selection bias in estimations of treatment effects is propensity score analysis. This method reduces a large number of pretreatment covariates to a single scalar function and allows researchers to compare subjects with similar probability to receive the treatment. This article provides an introduction to propensity score analysis and stratification, an example illustrating its use, and suggestions for using propensity score analysis in educational research.

Functional Traits, Flocking Propensity, and Perceived Predation Risk in an Amazonian Understory Bird Community.

Science.gov (United States)

Martínez, Ari E; Gomez, Juan P; Ponciano, José Miguel; Robinson, Scott K

2016-05-01

Within a community, different species might share similar predation risks, and, thus, the ability of species to signal and interpret heterospecific threat information may determine species' associations. We combined observational, experimental, and phylogenetic approaches to determine the extent to which evolutionary history and functional traits determined flocking propensity and perceived predation risk (response to heterospecific alarm calls) in a lowland Amazonian bird community. We predicted that small birds that feed myopically and out in the open would have higher flocking propensities and account for a higher proportion of positive responses to alarms. Using generalized linear models and the incorporation of phylogeny on data from 56 species, our results suggest that phylogenetic relationships alongside body size, foraging height, vegetation density, and response to alarm calls influence flocking propensity. Conversely, phylogenetic relationships did not influence response to heterospecific alarm calls. Among functional traits, however, foraging strategy, foraging density, and flocking propensity partially explained responses to alarm calls. Our results suggest that flocking propensity and perceived predation risk are positively related and that functional ecological traits and evolutionary history may explain certain species' associations.

Hydrated and Dehydrated Tertiary Interactions–Opening and Closing–of a Four-Helix Bundle Peptide

Science.gov (United States)

Lignell, Martin; Tegler, Lotta T.; Becker, Hans-Christian

2009-01-01

Abstract The structural heterogeneity and thermal denaturation of a dansyl-labeled four-helix bundle homodimeric peptide was studied with steady-state and time-resolved fluorescence spectroscopy and with circular dichroism (CD). At room temperature the fluorescence decay of the polarity-sensitive dansyl, located in the hydrophobic core region, can be described by a broad distribution of fluorescence lifetimes, reflecting the heterogeneous microenvironment. However, the lifetime distribution is nearly bimodal, which we ascribe to the presence of two major conformational subgroups. Since the fluorescence lifetime reflects the water content of the four-helix bundle conformations, we can use the lifetime analysis to monitor the change in hydration state of the hydrophobic core of the four-helix bundle. Increasing the temperature from 9°C to 23°C leads to an increased population of molten-globule-like conformations with a less ordered helical backbone structure. The fluorescence emission maximum remains constant in this temperature interval, and the hydrophobic core is not strongly affected. Above 30°C the structural dynamics involve transient openings of the four-helix bundle structure, as evidenced by the emergence of a water-quenched component and less negative CD. Above 60°C the homodimer starts to dissociate, as shown by the increasing loss of CD and narrow, short-lived fluorescence lifetime distributions. PMID:19619472

Increased helix and protein stability through the introduction of a new tertiary hydrogen bond.

Science.gov (United States)

Peterson, R W; Nicholson, E M; Thapar, R; Klevit, R E; Scholtz, J M

1999-03-12

In an effort to quantify the importance of hydrogen bonding and alpha-helix formation to protein stability, a capping box motif was introduced into the small phosphocarrier protein HPr. Previous studies had confirmed that Ser46, at the N-cap position of the short helix-B in HPr, serves as an N-cap in solution. Thus, only a single-site mutation was required to produce a canonical S-X-X-E capping box: Lys49 at the N3 position was substituted with a glutamic acid residue. Thermal and chemical denaturation studies on the resulting K49E HPr show that the designed variant is approximately 2 kcal mol-1 more stable than the wild-type protein. However, NMR studies indicate that the side-chain of Glu49 does not participate in the expected capping H-bond interaction, but instead forms a new tertiary H-bond that links helix-B to the four-stranded beta-sheet of HPr. Here, we demonstrate that a strategy in which new non-native H-bonds are introduced can generate proteins with increased stability. We discuss why the original capping box design failed, and compare the energetic consequences of the new tertiary side-chain to main-chain H-bond with a local (helix-capping) side-chain to main-chain H-bond on the protein's global stability. Copyright 1999 Academic Press.

Helix Nebula Science Cloud pilot phase open session

CERN Multimedia

CERN. Geneva

2018-01-01

This Helix Nebula Science Cloud (HNSciCloud) public session is open to everyone and will be webcast. The session will provide the audience with an overview of the HNSciCloud pre-commercial procurement project and the innovative cloud platforms that have been developed. A number of practical use-cases from the physics community will be presented as well as the next steps to be undertaken.

Balancing Treatment and Control Groups in Quasi-Experiments: An Introduction to Propensity Scoring

Science.gov (United States)

Connelly, Brian S.; Sackett, Paul R.; Waters, Shonna D.

2013-01-01

Organizational and applied sciences have long struggled with improving causal inference in quasi-experiments. We introduce organizational researchers to propensity scoring, a statistical technique that has become popular in other applied sciences as a means for improving internal validity. Propensity scoring statistically models how individuals in…

Executive Risk Propensity and Accounting Conservatism Through the Lens of Life History Theory

DEFF Research Database (Denmark)

Holm, Morten; Schneider, Melanie L.

First, we intend to investigate the impact of CFO risk propensity on accounting conservatism. Second, we will examine the role of CEOs in this context. By drawing on life history theory, we propose variables reflecting executive risk propensity. Based on this, we hypothesize that CFO risk...

Studying the propensity of compounds to supersaturate

DEFF Research Database (Denmark)

Palmelund, Henrik; Madsen, Cecilie Maria; Christensen, Jakob Plum

2016-01-01

Supersaturating drug delivery systems can enhance the oral bioavailability of poorly soluble drug compounds. Supersaturation of such compounds has been studied in many different ways; however, a more standardized method is required. The rationale of choosing suitable concentrations of supersatura......Supersaturating drug delivery systems can enhance the oral bioavailability of poorly soluble drug compounds. Supersaturation of such compounds has been studied in many different ways; however, a more standardized method is required. The rationale of choosing suitable concentrations...... of supersaturation to study has previously been very inconsistent. This makes comparisons between studies and compounds difficult, as the propensity of compounds to supersaturate varies greatly. This study presents a standardized method to study the supersaturation of drug compounds. The method allows, both......, for a ranking of compounds according to their supersaturation propensity and the effectiveness of precipitation inhibitors. The time-concentration profile of supersaturation and precipitation was studied in situ for 4 different concentrations for 6 model compounds (albendazole, aprepitant, danazol, felodipine...

RelB and RelE of Escherichia coli Form a Tight Complex That Represses Transcription via The Ribbon-Helix-Helix Motif in RelB

DEFF Research Database (Denmark)

Overgaard, Martin; Borch, Jonas; Gerdes, Kenn

2009-01-01

RelB, the Ribbon-Helix-Helix (RHH) repressor encoded by the relBE toxin-antitoxin locus of Escherichia coli, forms a tight complex with RelE and thereby counteracts the mRNA cleavage activity of RelE. In addition, RelB dimers repress the strong relBE promoter and this repression by RelB is enhanced...... by RelE - that is - RelE functions as a transcriptional co-repressor. RelB is a Lon protease substrate and Lon is required both for activation of relBE transcription and for activation of the mRNA cleavage activity of RelE. Here we characterize the molecular interactions important for transcriptional...... motif recognizes four 6 bp repeats within the bipartite binding site. The spacing between each half-site was found to be essential for cooperative interactions between adjacently bound RelB dimers stabilized by the co-repressor RelE. Kinetic and stoichiometric measurements of the interaction between Rel...

Improving causal inference with a doubly robust estimator that combines propensity score stratification and weighting.

Science.gov (United States)

Linden, Ariel

2017-08-01

When a randomized controlled trial is not feasible, health researchers typically use observational data and rely on statistical methods to adjust for confounding when estimating treatment effects. These methods generally fall into 3 categories: (1) estimators based on a model for the outcome using conventional regression adjustment; (2) weighted estimators based on the propensity score (ie, a model for the treatment assignment); and (3) "doubly robust" (DR) estimators that model both the outcome and propensity score within the same framework. In this paper, we introduce a new DR estimator that utilizes marginal mean weighting through stratification (MMWS) as the basis for weighted adjustment. This estimator may prove more accurate than treatment effect estimators because MMWS has been shown to be more accurate than other models when the propensity score is misspecified. We therefore compare the performance of this new estimator to other commonly used treatment effects estimators. Monte Carlo simulation is used to compare the DR-MMWS estimator to regression adjustment, 2 weighted estimators based on the propensity score and 2 other DR methods. To assess performance under varied conditions, we vary the level of misspecification of the propensity score model as well as misspecify the outcome model. Overall, DR estimators generally outperform methods that model one or the other components (eg, propensity score or outcome). The DR-MMWS estimator outperforms all other estimators when both the propensity score and outcome models are misspecified and performs equally as well as other DR estimators when only the propensity score is misspecified. Health researchers should consider using DR-MMWS as the principal evaluation strategy in observational studies, as this estimator appears to outperform other estimators in its class. © 2017 John Wiley & Sons, Ltd.

From Family Based to Industrial Based Production: Local Economic Development Initiatives and the HELIX Model

Directory of Open Access Journals (Sweden)

Bartjan W Pennink

2013-01-01

Full Text Available To build a strong local economy, good practice tells us that each community should undertake a collaborative, strategically planned process to understand and then act upon its own strengths, weaknesses, opportunities and threats. From this perspective we start with the local communities but how is this related to the perspective from the Helix model in which three actors are explicitly introduced: the Government, the Industry and the Universities? The purpose of local economic development (LED is to build up the economic capacity of a local area to improve its economic future and the quality of life for all. To support  the Local Economic Development in remote areas,   a program  has been developed based on the LED frame work of the world bank. This approach and  the experiences over  the past years with this program are  described in the first part.  In the second part of the paper, We analyse work done with that program with the help of the social capital concept and the triple helix model.  In all cases it is important to pay attention to who is taken the initiative after the first move (and it is not always the governance as actor and for the triple helix we suggest  that the concepts of (national Government, Industry and University need a translation to Local Governance Agency, Cooperation or other ways of cooperation of local communities and Local Universities. Although a push from outside might help  a local region in development the endogenous factors are  also needed. Keywords: Triple Helix model, Local Economic Development, Local Actors, Double Triangle within the Helix Model

Propensity scores as a basis for equating groups: basic principles and application in clinical treatment outcome research.

Science.gov (United States)

West, Stephen G; Cham, Heining; Thoemmes, Felix; Renneberg, Babette; Schulze, Julian; Weiler, Matthias

2014-10-01

A propensity score is the probability that a participant is assigned to the treatment group based on a set of baseline covariates. Propensity scores provide an excellent basis for equating treatment groups on a large set of covariates when randomization is not possible. This article provides a nontechnical introduction to propensity scores for clinical researchers. If all important covariates are measured, then methods that equate on propensity scores can achieve balance on a large set of covariates that mimics that achieved by a randomized experiment. We present an illustration of the steps in the construction and checking of propensity scores in a study of the effectiveness of a health coach versus treatment as usual on the well-being of seriously ill individuals. We then consider alternative methods of equating groups on propensity scores and estimating treatment effects including matching, stratification, weighting, and analysis of covariance. We illustrate a sensitivity analysis that can probe for the potential effects of omitted covariates on the estimate of the causal effect. Finally, we briefly consider several practical and theoretical issues in the use of propensity scores in applied settings. Propensity score methods have advantages over alternative approaches to equating groups particularly when the treatment and control groups do not fully overlap, and there are nonlinear relationships between covariates and the outcome. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity

Energy Technology Data Exchange (ETDEWEB)

Manjasetty, Babu A.; Halavaty, Andrei S.; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F.; Joachimiak, Andrzej

2016-04-01

Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56 Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices a4 and a7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix a4 is stabilized by the hydrogen bond between Glu67 (helix a4) and Gln130 (helix a7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix a4. This local conformational switch of helix a4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution smallmolecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol.

Statin use and kidney cancer outcomes: A propensity score analysis.

Science.gov (United States)

Nayan, Madhur; Finelli, Antonio; Jewett, Michael A S; Juurlink, David N; Austin, Peter C; Kulkarni, Girish S; Hamilton, Robert J

2016-11-01

Studies evaluating the association between statin use and survival outcomes in renal cell carcinoma have demonstrated conflicting results. Our objective was to evaluate this association in a large clinical cohort by using propensity score methods to reduce confounding from measured covariates. We performed a retrospective review of 893 patients undergoing nephrectomy for unilateral, M0 renal cell carcinoma between 2000 and 2014 at a tertiary academic center. Inverse probability of treatment weights were derived from a propensity score model based on clinical, surgical, and pathological characteristics. We used Cox proportional hazard models to evaluate the association between statin use and disease-free survival, cancer-specific survival, and overall survival in the sample weighted by the inverse probability of treatment weights. A secondary analysis was performed matching statin users 1:1 to statin nonusers on the propensity score. Of the 893 patients, 259 (29%) were on statins at the time of surgery. Median follow-up was 47 months (interquartile range: 20-80). Statin use was not significantly associated with disease-free survival (hazard ratio [HR] = 1.09, 95% CI: 0.65-1.81), cancer-specific survival (HR = 0.90, 95% CI: 0.40-2.01), or overall survival (HR = 0.89, 95% CI: 0.55-1.44). Similar results were observed when using propensity score matching. The present study found no significant association between statin use and kidney cancer outcomes. Population-based studies are needed to further evaluate the role of statins in kidney cancer therapy. Copyright © 2016 Elsevier Inc. All rights reserved.

Distinct Prion Domain Sequences Ensure Efficient Amyloid Propagation by Promoting Chaperone Binding or Processing In Vivo.

Directory of Open Access Journals (Sweden)

Christine R Langlois

2016-11-01

Full Text Available Prions are a group of proteins that can adopt a spectrum of metastable conformations in vivo. These alternative states change protein function and are self-replicating and transmissible, creating protein-based elements of inheritance and infectivity. Prion conformational flexibility is encoded in the amino acid composition and sequence of the protein, which dictate its ability not only to form an ordered aggregate known as amyloid but also to maintain and transmit this structure in vivo. But, while we can effectively predict amyloid propensity in vitro, the mechanism by which sequence elements promote prion propagation in vivo remains unclear. In yeast, propagation of the [PSI+] prion, the amyloid form of the Sup35 protein, has been linked to an oligopeptide repeat region of the protein. Here, we demonstrate that this region is composed of separable functional elements, the repeats themselves and a repeat proximal region, which are both required for efficient prion propagation. Changes in the numbers of these elements do not alter the physical properties of Sup35 amyloid, but their presence promotes amyloid fragmentation, and therefore maintenance, by molecular chaperones. Rather than acting redundantly, our observations suggest that these sequence elements make complementary contributions to prion propagation, with the repeat proximal region promoting chaperone binding to and the repeats promoting chaperone processing of Sup35 amyloid.

Youth Attitude Tracking Study 1997: Propensity and Advertising Report

National Research Council Canada - National Science Library

Wilson, Michael

1998-01-01

.... Findings cover results from questions on enlistment propensity, advertising awareness, recruiter contact, slogan recognition, media habits, and Internet usage among 16- to 24- year-old American youth...

Youth Attitude Tracking Study: 1998 Propensity and Advertising Report

National Research Council Canada - National Science Library

Wilson, Michael

2000-01-01

.... Findings cover results from questions on enlistment propensity, advertising awareness, recruiter contact, slogan recognition, media habits, and Internet usage among 16- to 24- year-old American youth...

Authoritarian Parenting, Power Distance, and Bullying Propensity

Science.gov (United States)

Georgiou, Stelios N.; Stavrinides, Panayiotis; Fousiani, Kyriaki

2013-01-01

This study aimed at examining the existing relation among parenting, cultural value orientation, and bullying propensity at school. The participants (N = 231) were early adolescents randomly selected from 11 different schools in urban and rural areas of Cyprus. The results showed that a statistically significant relation exists between parental…

Disgust propensity and disgust sensitivity : Separate constructs that are differentially related to specific fears

NARCIS (Netherlands)

van Overveld, W. J. M.; de Jong, P. J.; Peters, M. L.; Cavanagh, K.; Davey, G. C. L.

Studies concentrating on interindividual differences in experiencing disgust have indicated that disgust propensity is associated with certain disorders, such as fear of blood and fear of spiders (de Jong & Merckelbach, 1998). However, current indices of disgust propensity suffer from conceptual

Extreme bendability of DNA double helix due to bending asymmetry

NARCIS (Netherlands)

Salari, H.; Eslami-Mossallam, B.; Nederi, S.; Ejtehadi, M.R.

2015-01-01

Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for

An Amphipathic Helix Directs Cellular Membrane Curvature Sensing and Function of the BAR Domain Protein PICK1.

Science.gov (United States)

Herlo, Rasmus; Lund, Viktor K; Lycas, Matthew D; Jansen, Anna M; Khelashvili, George; Andersen, Rita C; Bhatia, Vikram; Pedersen, Thomas S; Albornoz, Pedro B C; Johner, Niklaus; Ammendrup-Johnsen, Ina; Christensen, Nikolaj R; Erlendsson, Simon; Stoklund, Mikkel; Larsen, Jannik B; Weinstein, Harel; Kjærulff, Ole; Stamou, Dimitrios; Gether, Ulrik; Madsen, Kenneth L

2018-05-15

BAR domains are dimeric protein modules that sense, induce, and stabilize lipid membrane curvature. Here, we show that membrane curvature sensing (MCS) directs cellular localization and function of the BAR domain protein PICK1. In PICK1, and the homologous proteins ICA69 and arfaptin2, we identify an amphipathic helix N-terminal to the BAR domain that mediates MCS. Mutational disruption of the helix in PICK1 impaired MCS without affecting membrane binding per se. In insulin-producing INS-1E cells, super-resolution microscopy revealed that disruption of the helix selectively compromised PICK1 density on insulin granules of high curvature during their maturation. This was accompanied by reduced hormone storage in the INS-1E cells. In Drosophila, disruption of the helix compromised growth regulation. By demonstrating size-dependent binding on insulin granules, our finding highlights the function of MCS for BAR domain proteins in a biological context distinct from their function, e.g., at the plasma membrane during endocytosis. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

One-dimensional nonlinear theory for rectangular helix traveling-wave tube

Energy Technology Data Exchange (ETDEWEB)

Fu, Chengfang, E-mail: fchffchf@126.com; Zhao, Bo; Yang, Yudong; Ju, Yongfeng [Faculty of Electronic Information Engineering, Huaiyin Institute of Technology, Huai' an 223003 (China); Wei, Yanyu [School of Physical Electronics, University of Electronic and Technology of China, Chengdu 610054 (China)

2016-08-15

A 1-D nonlinear theory of a rectangular helix traveling-wave tube (TWT) interacting with a ribbon beam is presented in this paper. The RF field is modeled by a transmission line equivalent circuit, the ribbon beam is divided into a sequence of thin rectangular electron discs with the same cross section as the beam, and the charges are assumed to be uniformly distributed over these discs. Then a method of computing the space-charge field by solving Green's Function in the Cartesian Coordinate-system is fully described. Nonlinear partial differential equations for field amplitudes and Lorentz force equations for particles are solved numerically using the fourth-order Runge-Kutta technique. The tube's gain, output power, and efficiency of the above TWT are computed. The results show that increasing the cross section of the ribbon beam will improve a rectangular helix TWT's efficiency and reduce the saturated length.

Gender and propensity to risk in advanced countries: Comparison between entrepreneurs and non-entrepreneurs

Directory of Open Access Journals (Sweden)

Maria Lago

2018-03-01

Full Text Available Purpose – The purpose of this paper is to compare the way in which gender and propensity to risk are associated in two samples, one of entrepreneurs and the other of non-entrepreneurs, while controlling for other factors, namely, national cultures. Design/methodology/approach – On the basis of data from 19 advanced countries, and by using two different samples, one of entrepreneurs and the other of non-entrepreneurs, the authors have used logistical regression analysis to analyse the relation between gender and propensity to risk has been used. Findings – Findings suggest that gender and culture are much stronger in influencing risk propensity among non-entrepreneurs than among entrepreneurs. Originality/value – Instead of analysing the effects of propensity to risk in entrepreneurship, as is usually done, the authors study some of its determinants, highlighting the differences between men and women.

Clear cell hidradenocarcinoma of the ear helix: report of primary ear helix adnexal carcinoma with regional lymph node metastasis.

Science.gov (United States)

Bae, Tae Hui; Kang, Shin Hyuk; Kim, Han Koo; Kim, Woo Seob; Kim, Mi Kyung

2014-07-01

Clear cell hidradenocarcinoma is a rare tumor of eccrine sweat gland origin that has a predilection for the head and neck. It has an indolent growth pattern and a higher incidence of regional and distant metastases. Metastasizing adnexal carcinomas are rare; thus, currently there is no uniform treatment guideline. We report a case of an 89-year-old female patient with clear cell hidradenocarcinoma manifesting in the right ear helix that metastasized to the right parotid gland who was treated by wide local excision and radiation therapy.

The Effect of a Helix-Coil Transition on the Extension Elasticity

Science.gov (United States)

Buhot, Arnaud; Halperin, Avi

2000-03-01

The secondary structure of a polymer affects its deformation behavior in accordance with the Le Chatelier principle. An important example of such secondary structure is the alpha helix encountered in polypeptides. Similar structure was recently proposed for PEO in aqueous media. Our discussion concerns the coupling of the cooperative helix-coil transition and the extension elasticity. In particular, we analyze the extension of a long single chain by use of optical tweezers or AFM. We consider chains that exist in the coil-state when unperturbed. The transition nevertheless occurs because the extension favors the low entropy helical state. As a result, the corresponding force law exhibits a plateau. The analysis of this situation involves two ingredients: (I) the stretching free energy penalty for a rod-coil mutiblock copolymer (II) the entropy associated with the possible placements of the rod and coil blocks.

Chiral transformation: From single nanowire to double helix

KAUST Repository

Wang, Yong

2011-12-21

We report a new type of water-soluble ultrathin Au-Ag alloy nanowire (NW), which exhibits unprecedented behavior in a colloidal solution. Upon growth of a thin metal (Pd, Pt, or Au) layer, the NW winds around itself to give a metallic double helix. We propose that the winding originates from the chirality within the as-synthesized Au-Ag NWs, which were induced to untwist upon metal deposition. © 2011 American Chemical Society.

A Helix-Stabilizing Linker Improves Subcutaneous Bioavailability of a Helical Peptide Independent of Linker Lipophilicity

Science.gov (United States)

Zhang, Liang; Navaratna, Tejas; Thurber, Greg M.

2016-01-01

Stabilized peptides address several limitations to peptide-based imaging agents and therapeutics such as poor stability and low affinity due to conformational flexibility. There is also active research in developing these compounds for intracellular drug targeting, and significant efforts have been invested to determine the effects of helix stabilization on intracellular delivery. However, much less is known about the impact on other pharmacokinetic parameters such as plasma clearance and bioavailability. We investigated the effect of different fluorescent helix-stabilizing linkers with varying lipophilicity on subcutaneous (SC) bioavailability using the glucagon-like peptide-1 (GLP-1) receptor ligand exendin as a model system. The stabilized peptides showed significantly higher protease resistance and increased bioavailability independent of linker hydrophilicity, and all subcutaneously delivered conjugates were able to successfully target the islets of Langerhans with high specificity. The lipophilic peptide variants had slower absorption and plasma clearance than their respective hydrophilic conjugates, and the absolute bioavailability was also lower likely due to the longer residence times in the skin. The ease and efficiency of double-click helix stabilization chemistries is a useful tool for increasing the bioavailability of peptide therapeutics, many of which suffer from rapid in vivo protease degradation. Helix stabilization using linkers of varying lipophilicity can further control SC absorption and clearance rates to customize plasma pharmacokinetics. PMID:27327034

The human early-life exposome (HELIX): project rationale and design.

Science.gov (United States)

Vrijheid, Martine; Slama, Rémy; Robinson, Oliver; Chatzi, Leda; Coen, Muireann; van den Hazel, Peter; Thomsen, Cathrine; Wright, John; Athersuch, Toby J; Avellana, Narcis; Basagaña, Xavier; Brochot, Celine; Bucchini, Luca; Bustamante, Mariona; Carracedo, Angel; Casas, Maribel; Estivill, Xavier; Fairley, Lesley; van Gent, Diana; Gonzalez, Juan R; Granum, Berit; Gražulevičienė, Regina; Gutzkow, Kristine B; Julvez, Jordi; Keun, Hector C; Kogevinas, Manolis; McEachan, Rosemary R C; Meltzer, Helle Margrete; Sabidó, Eduard; Schwarze, Per E; Siroux, Valérie; Sunyer, Jordi; Want, Elizabeth J; Zeman, Florence; Nieuwenhuijsen, Mark J

2014-06-01

Developmental periods in early life may be particularly vulnerable to impacts of environmental exposures. Human research on this topic has generally focused on single exposure-health effect relationships. The "exposome" concept encompasses the totality of exposures from conception onward, complementing the genome. The Human Early-Life Exposome (HELIX) project is a new collaborative research project that aims to implement novel exposure assessment and biomarker methods to characterize early-life exposure to multiple environmental factors and associate these with omics biomarkers and child health outcomes, thus characterizing the "early-life exposome." Here we describe the general design of the project. In six existing birth cohort studies in Europe, HELIX will estimate prenatal and postnatal exposure to a broad range of chemical and physical exposures. Exposure models will be developed for the full cohorts totaling 32,000 mother-child pairs, and biomarkers will be measured in a subset of 1,200 mother-child pairs. Nested repeat-sampling panel studies (n = 150) will collect data on biomarker variability, use smartphones to assess mobility and physical activity, and perform personal exposure monitoring. Omics techniques will determine molecular profiles (metabolome, proteome, transcriptome, epigenome) associated with exposures. Statistical methods for multiple exposures will provide exposure-response estimates for fetal and child growth, obesity, neurodevelopment, and respiratory outcomes. A health impact assessment exercise will evaluate risks and benefits of combined exposures. HELIX is one of the first attempts to describe the early-life exposome of European populations and unravel its relation to omics markers and health in childhood. As proof of concept, it will form an important first step toward the life-course exposome.

Propensity of farmers to conserve forest within REDD+ projects in areas affected by armed-conflict

DEFF Research Database (Denmark)

Nunez, Augusto Carlos Castro; Mertz, Ole; Quintero, Marcela

2016-01-01

design and application of forest conservation and climate change mitigation approaches such as the mechanism for Reducing Emissions from Deforestation and Forest Degradation (REDD. +) in such contexts remain little studied. Unanswered questions relate to the propensity of farmers in conflict affected...... Colombian government REDD. + activities. A household survey (n = 90) showed that four explanatory variables are significantly related to the 'propensity to conserve forest'. 'Harvest of non-timber forest products' (specifically bush meat) positively influences a farmer's propensity to conserve forest...

Right- and left-handed three-helix proteins. I. Experimental and simulation analysis of differences in folding and structure.

Science.gov (United States)

Glyakina, Anna V; Pereyaslavets, Leonid B; Galzitskaya, Oxana V

2013-09-01

Despite the large number of publications on three-helix protein folding, there is no study devoted to the influence of handedness on the rate of three-helix protein folding. From the experimental studies, we make a conclusion that the left-handed three-helix proteins fold faster than the right-handed ones. What may explain this difference? An important question arising in this paper is whether the modeling of protein folding can catch the difference between the protein folding rates of proteins with similar structures but with different folding mechanisms. To answer this question, the folding of eight three-helix proteins (four right-handed and four left-handed), which are similar in size, was modeled using the Monte Carlo and dynamic programming methods. The studies allowed us to determine the orders of folding of the secondary-structure elements in these domains and amino acid residues which are important for the folding. The obtained data are in good correlation with each other and with the experimental data. Structural analysis of these proteins demonstrated that the left-handed domains have a lesser number of contacts per residue and a smaller radius of cross section than the right-handed domains. This may be one of the explanations of the observed fact. The same tendency is observed for the large dataset consisting of 332 three-helix proteins (238 right- and 94 left-handed). From our analysis, we found that the left-handed three-helix proteins have some less-dense packing that should result in faster folding for some proteins as compared to the case of right-handed proteins. Copyright © 2013 Wiley Periodicals, Inc.

Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity.

Science.gov (United States)

Manjasetty, Babu A; Halavaty, Andrei S; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F; Joachimiak, Andrzej

2016-04-01

Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices α4 and α7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix α4 is stabilized by the hydrogen bond between Glu67 (helix α4) and Gln130 (helix α7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix α4. This local conformational switch of helix α4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution small-molecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol. Copyright © 2016. Published by Elsevier Inc.

An unusual helix-turn-helix protease inhibitory motif in a novel trypsin inhibitor from seeds of Veronica (Veronica hederifolia L.).

Science.gov (United States)

Conners, Rebecca; Konarev, Alexander V; Forsyth, Jane; Lovegrove, Alison; Marsh, Justin; Joseph-Horne, Timothy; Shewry, Peter; Brady, R Leo

2007-09-21

The storage tissues of many plants contain protease inhibitors that are believed to play an important role in defending the plant from invasion by pests and pathogens. These proteinaceous inhibitor molecules belong to a number of structurally distinct families. We describe here the isolation, purification, initial inhibitory properties, and three-dimensional structure of a novel trypsin inhibitor from seeds of Veronica hederifolia (VhTI). The VhTI peptide inhibits trypsin with a submicromolar apparent K(i) and is expected to be specific for trypsin-like serine proteases. VhTI differs dramatically in structure from all previously described families of trypsin inhibitors, consisting of a helix-turn-helix motif, with the two alpha helices tightly associated by two disulfide bonds. Unusually, the crystallized complex is in the form of a stabilized acyl-enzyme intermediate with the scissile bond of the VhTI inhibitor cleaved and the resulting N-terminal portion of the inhibitor remaining attached to the trypsin catalytic serine 195 by an ester bond. A synthetic, truncated version of the VhTI peptide has also been produced and co-crystallized with trypsin but, surprisingly, is seen to be uncleaved and consequently forms a noncovalent complex with trypsin. The VhTI peptide shows that effective enzyme inhibitors can be constructed from simple helical motifs and provides a new scaffold on which to base the design of novel serine protease inhibitors.

Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development.

Directory of Open Access Journals (Sweden)

Chao Gao

Full Text Available The basic/helix-loop-helix (bHLH proteins constitute a superfamily of transcription factors that are known to play a range of regulatory roles in eukaryotes. Over the past few decades, many bHLH family genes have been well-characterized in model plants, such as Arabidopsis, rice and tomato. However, the bHLH protein family in peanuts has not yet been systematically identified and characterized. Here, 132 and 129 bHLH proteins were identified from two wild ancestral diploid subgenomes of cultivated tetraploid peanuts, Arachis duranensis (AA and Arachis ipaensis (BB, respectively. Phylogenetic analysis indicated that these bHLHs could be classified into 19 subfamilies. Distribution mapping results showed that peanut bHLH genes were randomly and unevenly distributed within the 10 AA chromosomes and 10 BB chromosomes. In addition, 120 bHLH gene pairs between the AA-subgenome and BB-subgenome were found to be orthologous and 101 of these pairs were highly syntenic in AA and BB chromosomes. Furthermore, we confirmed that 184 bHLH genes expressed in different tissues, 22 of which exhibited tissue-specific expression. Meanwhile, we identified 61 bHLH genes that may be potentially involved in peanut-specific subterranean. Our comprehensive genomic analysis provides a foundation for future functional dissection and understanding of the regulatory mechanisms of bHLH transcription factors in peanuts.

Salt- and pH-Triggered Helix-Coil Transition of Ionic Polypeptides under Physiology Conditions.

Science.gov (United States)

Yuan, Jingsong; Zhang, Yi; Sun, Yue; Cai, Zhicheng; Yang, Lijiang; Lu, Hua

2018-06-11

Controlling the helix-coil transition of polypeptides under physiological conditions is an attractive way toward smart functional materials. Here, we report the synthesis of a series of tertiary amine-functionalized ethylene glycol (EG x )-linked polypeptide electrolytes with their secondary structures tunable under physiological conditions. The resultant polymers, denoted as P(EG x DMA-Glu) ( x = 1, 2, and 3), show excellent aqueous solubility (>20 mg/mL) regardless of their charge states. Unlike poly-l-lysine that can form a helix only at pH above 10, P(EG x DMA-Glu) undergo a pH-dependent helix-coil switch with their transition points within the physiological range (pH ∼5.3-6.5). Meanwhile, P(EG x DMA-Glu) exhibit an unusual salt-induced helical conformation presumably owing to the unique properties of EG x linkers. Together, the current work highlights the importance of fine-tuning the linker chemistry in achieving conformation-switchable polypeptides and represents a facile approach toward stimuli-responsive biopolymers for advanced biological applications.

Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language.

Science.gov (United States)

Metlagel, Zoltan; Kikkawa, Yayoi S; Kikkawa, Masahide

2007-01-01

Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.

Structure of the Membrane Anchor of Pestivirus Glycoprotein Erns, a Long Tilted Amphipathic Helix

Science.gov (United States)

Aberle, Daniel; Muhle-Goll, Claudia; Bürck, Jochen; Wolf, Moritz; Reißer, Sabine; Luy, Burkhard; Wenzel, Wolfgang; Ulrich, Anne S.; Meyers, Gregor

2014-01-01

Erns is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the Erns membrane contact, processing and secretion. PMID:24586172

SclR, a basic helix-loop-helix transcription factor, regulates hyphal morphology and promotes sclerotial formation in Aspergillus oryzae.

Science.gov (United States)

Jin, Feng Jie; Takahashi, Tadashi; Matsushima, Ken-ichiro; Hara, Seiichi; Shinohara, Yasutomo; Maruyama, Jun-ichi; Kitamoto, Katsuhiko; Koyama, Yasuji

2011-07-01

Most known basic-region helix-loop-helix (bHLH) proteins belong to a superfamily of transcription factors often involved in the control of growth and differentiation. Therefore, inappropriate expression of genes encoding bHLH proteins is frequently associated with developmental dysfunction. In our previously reported study, a novel bHLH protein-encoding gene (AO090011000215) of Aspergillus oryzae was identified. The gene-disrupted strain was found to produce dense conidia, but sparse sclerotia, relative to the parent strain. Here, to further analyze its function, we generated an overexpressing strain using the A. oryzae amyB gene promoter. Genetic overexpression led to a large number of initial hyphal aggregations and then the formation of mature sclerotia; it was therefore designated sclR (sclerotium regulator). At the same time, the sclR-overexpressing strain also displayed both delayed and decreased conidiation. Scanning electron microscopy indicated that the aerial hyphae of the sclR-overexpressing strain were extremely branched and intertwined with each other. In the generation of the SclR-enhanced green fluorescent protein (EGFP) expression strain, the SclR-EGFP protein fusion was conditionally detected in the nuclei. In addition, the loss of sclR function led to rapid protein degradation and cell lysis in dextrin-polypeptone-yeast extract liquid medium. Taken together, these observations indicate that SclR plays an important role in hyphal morphology, asexual conidiospore formation, and the promotion of sclerotial production, even retaining normal cell function, at least in submerged liquid culture.

Unified description of inelastic propensity rules for electron transport through nanoscale junctions

DEFF Research Database (Denmark)

Paulsson, Magnus; Frederiksen, Thomas; Ueba, Hiromu

2008-01-01

We present a method to analyze the results of first-principles based calculations of electronic currents including inelastic electron-phonon effects. This method allows us to determine the electronic and vibrational symmetries in play, and hence to obtain the so-called propensity rules for the st......We present a method to analyze the results of first-principles based calculations of electronic currents including inelastic electron-phonon effects. This method allows us to determine the electronic and vibrational symmetries in play, and hence to obtain the so-called propensity rules...... for the studied systems. We show that only a few scattering states-namely those belonging to the most transmitting eigenchannels-need to be considered for a complete description of the electron transport. We apply the method on first-principles calculations of four different systems and obtain the propensity...

Health and Environment Linked for Information Exchange in Atlanta (HELIX-Atlanta): A Pilot Tracking System

Science.gov (United States)

Rickman, Doug; Shire, J.; Qualters, J.; Mitchell, K.; Pollard, S.; Rao, R.; Kajumba, N.; Quattrochi, D.; Estes, M., Jr.; Meyer, P.;

Workplace mavericks: how personality and risk-taking propensity predicts maverickism.

Science.gov (United States)

Gardiner, Elliroma; Jackson, Chris J

2012-11-01

We examine the relationship between lateral preference, the Five-Factor Model of personality, risk-taking propensity, and maverickism. We take an original approach by narrowing our research focus to only functional aspects of maverickism. Results with 458 full-time workers identify lateral preference as a moderator of the neuroticism-maverickism relationship. Extraversion, openness to experience, and low agreeableness were also each found to predict maverickism. The propensity of individuals high in maverickism to take risks was also found to be unaffected by task feedback. Our results highlight the multifaceted nature of maverickism, identifying both personality and task conditions as determinants of this construct. ©2011 The British Psychological Society.

Defining the structural requirements for a helix in 23 S ribosomal RNA that confers erythromycin resistance

DEFF Research Database (Denmark)

Douthwaite, S; Powers, T; Lee, J Y

1989-01-01

The helix spanning nucleotides 1198 to 1247 (helix 1200-1250) in Escherichia coli 23 S ribosomal RNA (rRNA) is functionally important in protein synthesis, and deletions in this region confer erythromycin resistance. In order to define the structural requirements for resistance, we have dissected...... deletion mutants show a sensitive phenotype. Deletions that extend into the base-pairing between GCC1208 and GGU1240 result in non-functional 23 S RNAs, which consequently do not confer resistance. A number of phylogenetically conserved nucleotides have been shown to be non-essential for 23 S RNA function....... However, removal of either these or non-conserved nucleotides from helix 1200-1250 measurably reduces the efficiency of 23 S RNA in forming functional ribosomes. We have used chemical probing and a modified primer extension method to investigate erythromycin binding to wild-type and resistant ribosomes...

Facilitating Quintuple helix innovation with urban living labs

OpenAIRE

Baccarne, Bastiaan; Schuurman, Dimitri; De Marez, Lieven

2015-01-01

This paper discusses the Urban Living Lab approach as a way to put the Quintuple Helix model for innovation into practice. In this analysis we focus on the concepts innovation democracy, ‘mode 3’ knowledge production, the innovation ecosystem as a system of societal subsystems and socioecological transition. The empirical analysis is performed by means of a multidimensional case study design, applied on a project-based ad hoc collaborative innovation development process in an ecological doma...

The type II collagen fragments Helix-II and CTX-II reveal different enzymatic pathways of human cartilage collagen degradation

DEFF Research Database (Denmark)

Charni-Ben Tabassi, N; Desmarais, S; Jensen, Anne-Christine Bay

2008-01-01

human recombinant cathepsins (Cats) and matrix-metalloproteases (MMPs). Next, we analyzed the spontaneous release of Helix-II and CTX-II from cartilage sections of patients with knee OA who were immediately deep frozen after joint replacement to preserve endogenous enzyme activity until assay. Cartilage....... Cat D was unable to digest intact cartilage. MMPs-1, -3, -7, -9, and -13 efficiently released CTX-II, but only small amount of Helix-II. Neither CTX-II nor Helix-II alone was able to reflect accurately the collagenolytic activity of Cats and MMPs as reflected by the release of hydroxyproline. In OA...

Helix Nebula and CERN: A Symbiotic approach to exploiting commercial clouds

CERN Document Server

Barreiro Megino, Fernando Harald; Kucharczyk, Katarzyna; Medrano Llamas, Ramón; van der Ster, Daniel

2014-01-01

The recent paradigm shift toward cloud computing in IT, and general interest in "Big Data" in particular, have demonstrated that the computing requirements of HEP are no longer globally unique. Indeed, the CERN IT department and LHC experiments have already made significant R&D investments in delivering and exploiting cloud computing resources. While a number of technical evaluations of interesting commercial offerings from global IT enterprises have been performed by various physics labs, further technical, security, sociological, and legal issues need to be address before their large-scale adoption by the research community can be envisaged. Helix Nebula - the Science Cloud is an initiative that explores these questions by joining the forces of three European research institutes (CERN, ESA and EMBL) with leading European commercial IT enterprises. The goals of Helix Nebula are to establish a cloud platform federating multiple commercial cloud providers, along with new business models, which can sustain ...

Helix Nebula and CERN: A Symbiotic approach to exploiting commercial clouds

CERN Multimedia

Barreiro Megino, Fernando Harald; Kucharczyk, Katarzyna; Medrano Llamas, Ramón; van der Ster, Daniel

2013-01-01

The recent paradigm shift toward cloud computing in IT, and general interest in "Big Data" in particular, have demonstrated that the computing requirements of HEP are no longer globally unique. Indeed, the CERN IT department and LHC experiments have already made significant R&D; investments in delivering and exploiting cloud computing resources. While a number of technical evaluations of interesting commercial offerings from global IT enterprises have been performed by various physics labs, further technical, security, sociological, and legal issues need to be address before their large-scale adoption by the research community can be envisaged. Helix Nebula - the Science Cloud is an initiative that explores these questions by joining the forces of three European research institutes (CERN, ESA and EMBL) with leading European commercial IT enterprises. The goals of Helix Nebula are to establish a cloud platform federating multiple commercial cloud providers, along with new business models, which can sustain...

Elevated endogenous expression of the dominant negative basic helix-loop-helix protein ID1 correlates with significant centrosome abnormalities in human tumor cells

Directory of Open Access Journals (Sweden)

Gutmann Anja

2010-01-01

Full Text Available Abstract Background ID proteins are dominant negative inhibitors of basic helix-loop-helix transcription factors that have multiple functions during development and cellular differentiation. Ectopic (over-expression of ID1 extends the lifespan of primary human epithelial cells. High expression levels of ID1 have been detected in multiple human malignancies, and in some have been correlated with unfavorable clinical prognosis. ID1 protein is localized at the centrosomes and forced (over-expression of ID1 results in errors during centrosome duplication. Results Here we analyzed the steady state expression levels of the four ID-proteins in 18 tumor cell lines and assessed the number of centrosome abnormalities. While expression of ID1, ID2, and ID3 was detected, we failed to detect protein expression of ID4. Expression of ID1 correlated with increased supernumerary centrosomes in most cell lines analyzed. Conclusions This is the first report that shows that not only ectopic expression in tissue culture but endogenous levels of ID1 modulate centrosome numbers. Thus, our findings support the hypothesis that ID1 interferes with centrosome homeostasis, most likely contributing to genomic instability and associated tumor aggressiveness.

Helix Nebula and CERN: A Symbiotic approach to exploiting commercial clouds

Science.gov (United States)

Barreiro Megino, Fernando H.; Jones, Robert; Kucharczyk, Katarzyna; Medrano Llamas, Ramón; van der Ster, Daniel

2014-06-01

The recent paradigm shift toward cloud computing in IT, and general interest in "Big Data" in particular, have demonstrated that the computing requirements of HEP are no longer globally unique. Indeed, the CERN IT department and LHC experiments have already made significant R&D investments in delivering and exploiting cloud computing resources. While a number of technical evaluations of interesting commercial offerings from global IT enterprises have been performed by various physics labs, further technical, security, sociological, and legal issues need to be address before their large-scale adoption by the research community can be envisaged. Helix Nebula - the Science Cloud is an initiative that explores these questions by joining the forces of three European research institutes (CERN, ESA and EMBL) with leading European commercial IT enterprises. The goals of Helix Nebula are to establish a cloud platform federating multiple commercial cloud providers, along with new business models, which can sustain the cloud marketplace for years to come. This contribution will summarize the participation of CERN in Helix Nebula. We will explain CERN's flagship use-case and the model used to integrate several cloud providers with an LHC experiment's workload management system. During the first proof of concept, this project contributed over 40.000 CPU-days of Monte Carlo production throughput to the ATLAS experiment with marginal manpower required. CERN's experience, together with that of ESA and EMBL, is providing a great insight into the cloud computing industry and highlighted several challenges that are being tackled in order to ease the export of the scientific workloads to the cloud environments.

Psychological Factors Predicting Risk-Taking Propensity of Poultry ...

African Journals Online (AJOL)

Using a correlational design, the following measures were used: Performance Failure Appraisal Inventory (PFAI), Need for achievement scale, Locus of Control Behaviour and Risk-taking propensity. Results indicate a significant joint influence of perceived of fear of failure, achievement motivation, locus of control, age and ...

Dimensionality of trust: An analysis of the relations between propensity, trustworthiness and trust

Directory of Open Access Journals (Sweden)

Marita Heyns

2015-05-01

Research purpose: This study examined the dynamic interplay between trust propensity, trustworthiness beliefs and the decision to trust, as perceived within dyadic workplace relationships. Motivation for the study: No studies, as far as the authors are aware, have ever attempted to use a combination of Mayer and Davis’s well-known assessment of trustworthiness and Gillespie’s measure of behavioural trust within the same study. By including measures of main antecedents and the actual decision to trust in the same study, the multidimensionality of trust can be established more concretely. Research approach, design and method: A cross-sectional survey design with a convenience sample (N = 539 was used. The Behavioural Trust Inventory and the Organisational Trust Instrument were administered. Main findings: Results confirmed the distinctness of propensity, trustworthiness and trust as separate main constructs. Trust was strongly associated with trustworthiness beliefs. Trustworthiness beliefs fully mediated the relationship between propensity and trust. The observed relations between propensity and trustworthiness suggest that individuals with a natural predisposition to trust others will be more inclined to perceive a specific trust referent as trustworthy. Practical/managerial implications: Leaders should realise that their attitudes and behaviour have a decisive impact on trust formation processes: if they are being perceived as trustworthy, followers will be likely to respond by engaging in trusting behaviours towards them. Tools to assess followers’ perceptions of the trustworthiness of the leader may provide useful feedback that can guide leaders. Contribution/value-add: This study contributes to scientific knowledge regarding the influence of propensity to trust and trustworthiness on trust of leaders.

The Impact of the ‘Austrian’ Mutation of the Amyloid Precursor Protein Transmembrane Helix is Communicated to the Hinge Region

DEFF Research Database (Denmark)

Stelzer, Walter; Scharnagl, Christina; Leurs, Ulrike

2016-01-01

The transmembrane helix of the amyloid precursor protein is subject to proteolytic cleavages by γ-secretase at different sites resulting in Aβ peptides of different length and toxicity. A number of point mutations within this transmembrane helix alter the cleavage pattern thus enhancing production...... destabilizes amide hydrogen bonds in the hinge which connects dimerization and cleavage regions. Weaker intrahelical hydrogen bonds at the hinge may enhance helix bending and thereby affect recognition of the transmembrane substrate by the enzyme and/or presentation of its cleavage sites to the catalytic cleft....

Escaping peril: perceived predation risk affects migratory propensity

DEFF Research Database (Denmark)

Hulthén, Kaj; Chapman, Ben B.; Nilsson, P. Anders

2015-01-01

Although migratory plasticity is increasingly documented, the ecological drivers of plasticity are not well understood. Predation risk can influence migratory dynamics, but whether seasonal migrants can adjust their migratory behaviour according to perceived risk is unknown. We used electronic ta......) affected timing but not propensity showing that elevated risk carried over to alter migratory behaviour in the wild. Our key finding demonstrates predator-driven migratory plasticity, highlighting the powerful role of predation risk for migratory decision-making and dynamics.......Although migratory plasticity is increasingly documented, the ecological drivers of plasticity are not well understood. Predation risk can influence migratory dynamics, but whether seasonal migrants can adjust their migratory behaviour according to perceived risk is unknown. We used electronic tags...... in their lake summer habitat and monitored individual migration to connected streams over an entire season. Individuals exposed to increased perceived direct predation risk (i.e. a live predator) showed a higher migratory propensity but no change in migratory timing, while indirect risk (i.e. roach density...

Rendezvous of the "Third Kind": Triple Helix Origins and Future Possibilities

Science.gov (United States)

Etzkowitz, Henry

2015-01-01

The Triple Helix, representing university-industry-government interactions, was rooted in a 1993 International Workshop on University-Industry Relations at UNAM's Centro Para la Innovacion Technologica in Mexico City. Impelled by Mexican reality, where university-industry interactions and the institutions themselves operated within a governmental…

Unpredictable responses of garden snail (Helix aspersa) populations to climate change

NARCIS (Netherlands)

Bezemer, T.M.; Knight, K.J.

2001-01-01

We studied the impact of climate change on the population dynamics of the garden snail (Helix aspersa) in the Ecotron controlled environment facility. The experimental series ran for three plant generations, allowing the snails to reproduce. We investigated the isolated and combined effects of

Self-esteem, propensity for sensation seeking, and risk behaviour among adults with tattoos and piercings.

Science.gov (United States)

Hong, Bo-Kyung; Lee, Hyo Young

2017-12-13

Background: In recent years, increasing numbers of adults and adolescents have opted to undergo tattoo and piercing procedures. Studies among adolescents with tattoo and piercing have usually explored the relationship between one factor and the decision to have tattoos and/or piercings. The aim of this study was to determine relationships between body cosmetic procedures and selfesteem, propensity for sensation seeking, and risk behaviours among adults. Materials and Methods: The subjects were divided into two groups, i.e. , those with (n=429) and those without tattoos/piercings (n=237), and self-esteem, propensity for sensation seeking, and risk behaviour were compared between the two groups using self-report questionnaires. To analyse differences in self-esteem and the propensity for sensation seeking, general characteristics were statistically adjusted. In addition, general characteristics, self-esteem, and propensity for sensation seeking were statistically adjusted to determine differences in the propensity for risk behaviour between the two groups. Results: Significant differences were observed in age, marital status, income level, occupation, values or sensitivity to fashion, and educational level between the group with and that without tattoos/ piercings. There was no significant difference in self-esteem, whereas there were significant differences in the propensity for sensation seeking and risk behaviour between the two groups. Conclusions: Continuous attention to, and interest in, the increased incidence of tattooing and piercing are necessary, especially in terms of public interventions for health education and health promotion, as these forms of self-adornment are associated with behaviours that pose a risk to health.

Get the most from your data: a propensity score model comparison on real-life data.

Science.gov (United States)

Ferdinand, Dennis; Otto, Mirko; Weiss, Christel

2016-01-01

In the past, the propensity score has been in the middle of several discussions in terms of its abilities and limitations. With a comprehensive review and a practical example, this study examines the effect of propensity score analysis of real-life data and introduces a simple and effective clinical approach. After the authors reviewed current publications, they applied their insights to the data of a nonrandomized clinical trial in bariatric surgery. This study examined weight loss in 173 patients where 127 patients received Roux-en-Y gastric bypass surgery and 46 patients sleeve gastrectomy. Both groups underwent analysis in terms of their covariate distribution using Mann-Whitney U and χ (2) testing. Mean differences within excess weight loss in native data were examined with Student's t-test. Three propensity score models were defined and matching was performed. Covariate distribution and mean differences in excess weight loss were checked with Mann-Whitney U and χ (2) testing. Native data implied a significant difference in excess weight loss. The propensity score models did not confirm this difference. All models proved that both surgical procedures were equal, due to their weight-loss induction. Covariate distribution improved after the matching procedure in terms of an equal distribution. It seemed that a practical clinical approach with outcome-related covariates as a propensity score base is the ideal midpoint between an equal distribution in covariates and an acceptable loss of data. Nevertheless, propensity score models designed with clinical intent seemed to be absolutely suitable for overcoming heterogeneity in covariate distribution.

Self-esteem, propensity for sensation seeking, and risk behaviour among adults with tattoos and piercings

Directory of Open Access Journals (Sweden)

Bo-Kyung Hong

2017-12-01

Full Text Available Background: In recent years, increasing numbers of adults and adolescents have opted to undergo tattoo and piercing procedures. Studies among adolescents with tattoo and piercing have usually explored the relationship between one factor and the decision to have tattoos and/or piercings. The aim of this study was to determine relationships between body cosmetic procedures and selfesteem, propensity for sensation seeking, and risk behaviours among adults. Materials and Methods: The subjects were divided into two groups, i.e., those with (n=429 and those without tattoos/piercings (n=237, and self-esteem, propensity for sensation seeking, and risk behaviour were compared between the two groups using self-report questionnaires. To analyse differences in self-esteem and the propensity for sensation seeking, general characteristics were statistically adjusted. In addition, general characteristics, self-esteem, and propensity for sensation seeking were statistically adjusted to determine differences in the propensity for risk behaviour between the two groups. Results: Significant differences were observed in age, marital status, income level, occupation, values or sensitivity to fashion, and educational level between the group with and that without tattoos/ piercings. There was no significant difference in self-esteem, whereas there were significant differences in the propensity for sensation seeking and risk behaviour between the two groups. Conclusions: Continuous attention to, and interest in, the increased incidence of tattooing and piercing are necessary, especially in terms of public interventions for health education and health promotion, as these forms of self-adornment are associated with behaviours that pose a risk to health.

Genome-wide identification, classification, and functional analysis of the basic helix-loop-helix transcription factors in the cattle, Bos Taurus.

Science.gov (United States)

Li, Fengmei; Liu, Wuyi

2017-06-01

The basic helix-loop-helix (bHLH) transcription factors (TFs) form a huge superfamily and play crucial roles in many essential developmental, genetic, and physiological-biochemical processes of eukaryotes. In total, 109 putative bHLH TFs were identified and categorized successfully in the genomic databases of cattle, Bos Taurus, after removing redundant sequences and merging genetic isoforms. Through phylogenetic analyses, 105 proteins among these bHLH TFs were classified into 44 families with 46, 25, 14, 3, 13, and 4 members in the high-order groups A, B, C, D, E, and F, respectively. The remaining 4 bHLH proteins were sorted out as 'orphans.' Next, these 109 putative bHLH proteins identified were further characterized as significantly enriched in 524 significant Gene Ontology (GO) annotations (corrected P value ≤ 0.05) and 21 significantly enriched pathways (corrected P value ≤ 0.05) that had been mapped by the web server KOBAS 2.0. Furthermore, 95 bHLH proteins were further screened and analyzed together with two uncharacterized proteins in the STRING online database to reconstruct the protein-protein interaction network of cattle bHLH TFs. Ultimately, 89 bHLH proteins were fully mapped in a network with 67 biological process, 13 molecular functions, 5 KEGG pathways, 12 PFAM protein domains, and 25 INTERPRO classified protein domains and features. These results provide much useful information and a good reference for further functional investigations and updated researches on cattle bHLH TFs.

The N-terminal tail of hERG contains an amphipathic α-helix that regulates channel deactivation.

Directory of Open Access Journals (Sweden)

Chai Ann Ng

Full Text Available The cytoplasmic N-terminal domain of the human ether-a-go-go related gene (hERG K+ channel is critical for the slow deactivation kinetics of the channel. However, the mechanism(s by which the N-terminal domain regulates deactivation remains to be determined. Here we show that the solution NMR structure of the N-terminal 135 residues of hERG contains a previously described Per-Arnt-Sim (PAS domain (residues 26-135 as well as an amphipathic α-helix (residues 13-23 and an initial unstructured segment (residues 2-9. Deletion of residues 2-25, only the unstructured segment (residues 2-9 or replacement of the α-helix with a flexible linker all result in enhanced rates of deactivation. Thus, both the initial flexible segment and the α-helix are required but neither is sufficient to confer slow deactivation kinetics. Alanine scanning mutagenesis identified R5 and G6 in the initial flexible segment as critical for slow deactivation. Alanine mutants in the helical region had less dramatic phenotypes. We propose that the PAS domain is bound close to the central core of the channel and that the N-terminal α-helix ensures that the flexible tail is correctly orientated for interaction with the activation gating machinery to stabilize the open state of the channel.

Circadian Rhythms in Socializing Propensity

Science.gov (United States)

Zhang, Cheng; Phang, Chee Wei; Zeng, Xiaohua; Wang, Ximeng; Xu, Yunjie; Huang, Yun; Contractor, Noshir

2015-01-01

Using large-scale interaction data from a virtual world, we show that people’s propensity to socialize (forming new social connections) varies by hour of the day. We arrive at our results by longitudinally tracking people’s friend-adding activities in a virtual world. Specifically, we find that people are most likely to socialize during the evening, at approximately 8 p.m. and 12 a.m., and are least likely to do so in the morning, at approximately 8 a.m. Such patterns prevail on weekdays and weekends and are robust to variations in individual characteristics and geographical conditions. PMID:26353080

Circadian Rhythms in Socializing Propensity.

Science.gov (United States)

Zhang, Cheng; Phang, Chee Wei; Zeng, Xiaohua; Wang, Ximeng; Xu, Yunjie; Huang, Yun; Contractor, Noshir

2015-01-01

Using large-scale interaction data from a virtual world, we show that people's propensity to socialize (forming new social connections) varies by hour of the day. We arrive at our results by longitudinally tracking people's friend-adding activities in a virtual world. Specifically, we find that people are most likely to socialize during the evening, at approximately 8 p.m. and 12 a.m., and are least likely to do so in the morning, at approximately 8 a.m. Such patterns prevail on weekdays and weekends and are robust to variations in individual characteristics and geographical conditions.

Restrictions on TWT Helix Voltage Ripple for Acceptable Notch Filter Performance

Energy Technology Data Exchange (ETDEWEB)

Hyslop, B.

1984-12-01

An ac ripple on the helix voltage of the 1-2 GHz TWT's creates FM sidebands that cause amplitude and phase modulation of the microwave TWT output signal. A limit of 16 volts peak-to-peak is required for acceptable superconducting notch filter performance.

Using propensity scores to estimate the effects of insecticides on stream invertebrates from observational data

Science.gov (United States)

Lester L. Yuan,; Amina I. Pollard,; Carlisle, Daren M.

2009-01-01

Analyses of observational data can provide insights into relationships between environmental conditions and biological responses across a broader range of natural conditions than experimental studies, potentially complementing insights gained from experiments. However, observational data must be analyzed carefully to minimize the likelihood that confounding variables bias observed relationships. Propensity scores provide a robust approach for controlling for the effects of measured confounding variables when analyzing observational data. Here, we use propensity scores to estimate changes in mean invertebrate taxon richness in streams that have experienced insecticide concentrations that exceed aquatic life use benchmark concentrations. A simple comparison of richness in sites exposed to elevated insecticides with those that were not exposed suggests that exposed sites had on average 6.8 fewer taxa compared to unexposed sites. The presence of potential confounding variables makes it difficult to assert a causal relationship from this simple comparison. After controlling for confounding factors using propensity scores, the difference in richness between exposed and unexposed sites was reduced to 4.1 taxa, a difference that was still statistically significant. Because the propensity score analysis controlled for the effects of a wide variety of possible confounding variables, we infer that the change in richness observed in the propensity score analysis was likely caused by insecticide exposure.

Usefulness of a Short Dietary Propensity Questionnaire in Japan.

Science.gov (United States)

Okuda, Nagako; Itai, Kazuyoshi; Okayama, Akira

2018-05-01

There is a growing need for nutritional education for prevention and non-pharmacological treatment of risk factors for cardiovascular diseases (CVD). We compared the results of a short dietary propensity questionnaire (SDPQ) with those from the food frequency and quantity survey (FF Quantity), which had been previously quantitatively assessed by comparison with the 24-hr dietary recall (24hr-DR), to examine the usefulness of the SDPQ. The SDPQ was designed to assess dietary propensities of 12 food/nutrients relevant to CVD risk factors. We conducted a dietary survey using the SDPQ on Japanese men and women. After 2-3 weeks, we conducted the FF Quantity survey with the same participants. For each of the 12 food/nutrient categories, the relationships between quintiles of results from the SDPQ and FF Quantity were examined. Results from 79 participants who completed both surveys were used. Spearman's correlation coefficients (r) were significant for all food/nutrient categories. Good correlations were found with alcohol (r=0.792), starchy foods (r=0.566), and milk and dairy products (r=0.687), for which good correlations between the FF Quantity and 24hr-DR had been observed previously. Moderate correlations were found for vegetables (r=0.386) and high-salt foods (r=0.505), although the FF Quantity survey poorly correlated with the 24hr-DR. The SDPQ may be useful for assessment of dietary propensities for alcohol, starchy foods, and milk and dairy products in Japan.

Community demographics and the propensity to report animal cruelty.

Science.gov (United States)

Taylor, Nicola; Signal, Tania D

2006-01-01

The last decade has seen an increased awareness concerning links between violence to nonhuman animals and violence to humans. This has resulted in a number of cross-reporting initiatives between family service providers and animal welfare organizations. The success of these initiatives rests on individuals being willing to report such violence. Thus, there is a need to determine which variables influence an individual's willingness to report deliberate animal cruelty and abuse. The aim of this study was to examine demographic and attitudinal variables to ascertain their impact on propensity to report deliberate animal harm. A telephone questionnaire resulted in 1,208 valid responses from members of the general community. Results showed a number of variables that affected the propensity to report: gender, occupation, and acknowledgment of the link between family violence and deliberate animal harm. This article discusses these variables and their implications.

Glass-like dynamics of the strain-induced coil/helix transition on a permanent polymer network.

Science.gov (United States)

Ronsin, O; Caroli, C; Baumberger, T

2016-02-14

We study the stress response to a step strain of covalently bonded gelatin gels in the temperature range where triple helix reversible crosslink formation is prohibited. We observe slow stress relaxation towards a T-dependent finite asymptotic level. We show that this is assignable to the strain-induced coil → helix transition, previously evidenced by Courty et al. [Proc. Natl. Acad. Sci. U. S. A. 102, 13457 (2005)], of a fraction of the polymer strands. Relaxation proceeds, in a first stage, according to a stretched exponential dynamics, then crosses over to a terminal simple exponential decay. The respective characteristic times τK and τf exhibit an Arrhenius-like T-dependence with an associated energy E incompatibly larger than the activation barrier height for the isomerisation process which sets the clock for an elementary coil → helix transformation event. We tentatively assign this glass-like slowing down of the dynamics to the long-range couplings due to the mechanical noise generated by the local elementary events in this random elastic medium.

Structure of the membrane anchor of pestivirus glycoprotein E(rns, a long tilted amphipathic helix.

Directory of Open Access Journals (Sweden)

Daniel Aberle

2014-02-01

Full Text Available E(rns is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the E(rns membrane contact, processing and secretion.

Structure of the membrane anchor of pestivirus glycoprotein E(rns), a long tilted amphipathic helix.

Science.gov (United States)

Aberle, Daniel; Muhle-Goll, Claudia; Bürck, Jochen; Wolf, Moritz; Reißer, Sabine; Luy, Burkhard; Wenzel, Wolfgang; Ulrich, Anne S; Meyers, Gregor

2014-02-01

E(rns) is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the E(rns) membrane contact, processing and secretion.

Unfolding four-helix bundles

Science.gov (United States)

Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2011-03-01

A geometrical model has been developed to describe the early stages of unfolding of cytochromes c‧ and c-b562 . Calculations are based on a step-wise extension of the polypeptide chain subject to the constraint that the spatial relationship among the residues of each triplet is fixed by the native-state crystallographic data. The response of each protein to these structural perturbations allows the evolution of each of the four helices in these two proteins to be differentiated. It is found that the two external helices in c‧ unfold before its two internal helices, whereas exactly the opposite behaviour is demonstrated by c-b562 . Each of these cytochromes has an extended, internal, non-helical ('turning') region that initially lags behind the most labile helix but then, at a certain stage (identified for each cytochrome), unravels before any of the four helices present in the native structure. It is believed that these predictions will be useful in guiding future experimental studies on the unfolding of these two cytochromes.

Immigrants' Propensity to Self-Employment: Evidence from Canada.

Science.gov (United States)

Li, Peter S.

2001-01-01

Uses Canada's Longitudinal Immigration Data Base to highlight patterns of self-employment in various entry cohorts of immigrants between 1980-95 and develop a model to predict immigrants' propensity to self-employment. Overall, arrival in better economic years, longer residence in Canada, higher educational levels, older age, and being selected…

The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization.

Directory of Open Access Journals (Sweden)

Qian Yan

Full Text Available Basic/helix-loop-helix (bHLH proteins comprise one of the largest transcription factor families and play important roles in diverse cellular and molecular processes. Comprehensive analyses of the composition and evolution of the bHLH family in cotton are essential to elucidate their functions and the molecular basis of cotton development. By searching bHLH homologous genes in sequenced diploid cotton genomes (Gossypium raimondii and G. arboreum, a set of cotton bHLH reference genes containing 289 paralogs were identified and named as GobHLH001-289. Based on their phylogenetic relationships, these cotton bHLH proteins were clustered into 27 subfamilies. Compared to those in Arabidopsis and cacao, cotton bHLH proteins generally increased in number, but unevenly in different subfamilies. To further uncover evolutionary changes of bHLH genes during tetraploidization of cotton, all genes of S5a and S5b subfamilies in upland cotton and its diploid progenitors were cloned and compared, and their transcript profiles were determined in upland cotton. A total of 10 genes of S5a and S5b subfamilies (doubled from A- and D-genome progenitors maintained in tetraploid cottons. The major sequence changes in upland cotton included a 15-bp in-frame deletion in GhbHLH130D and a long terminal repeat retrotransposon inserted in GhbHLH062A, which eliminated GhbHLH062A expression in various tissues. The S5a and S5b bHLH genes of A and D genomes (except GobHLH062 showed similar transcription patterns in various tissues including roots, stems, leaves, petals, ovules, and fibers, while the A- and D-genome genes of GobHLH110 and GobHLH130 displayed clearly different transcript profiles during fiber development. In total, this study represented a genome-wide analysis of cotton bHLH family, and revealed significant changes in sequence and expression of these genes in tetraploid cottons, which paved the way for further functional analyses of bHLH genes in the cotton genus.

Helix Nebula and CERN: A Symbiotic approach to exploiting commercial clouds

International Nuclear Information System (INIS)

Megino, Fernando H Barreiro; Jones, Robert; Llamas, Ramón Medrano; Ster, Daniel van der; Kucharczyk, Katarzyna

2014-01-01

The recent paradigm shift toward cloud computing in IT, and general interest in 'Big Data' in particular, have demonstrated that the computing requirements of HEP are no longer globally unique. Indeed, the CERN IT department and LHC experiments have already made significant R and D investments in delivering and exploiting cloud computing resources. While a number of technical evaluations of interesting commercial offerings from global IT enterprises have been performed by various physics labs, further technical, security, sociological, and legal issues need to be address before their large-scale adoption by the research community can be envisaged. Helix Nebula – the Science Cloud is an initiative that explores these questions by joining the forces of three European research institutes (CERN, ESA and EMBL) with leading European commercial IT enterprises. The goals of Helix Nebula are to establish a cloud platform federating multiple commercial cloud providers, along with new business models, which can sustain the cloud marketplace for years to come. This contribution will summarize the participation of CERN in Helix Nebula. We will explain CERN's flagship use-case and the model used to integrate several cloud providers with an LHC experiment's workload management system. During the first proof of concept, this project contributed over 40.000 CPU-days of Monte Carlo production throughput to the ATLAS experiment with marginal manpower required. CERN's experience, together with that of ESA and EMBL, is providing a great insight into the cloud computing industry and highlighted several challenges that are being tackled in order to ease the export of the scientific workloads to the cloud environments.

CFD analysis and flow model reduction for surfactant production in helix reactor

NARCIS (Netherlands)

Nikačević, N.M.; Thielen, L.; Twerda, A.; Hof, P.M.J. van den

2014-01-01

Flow pattern analysis in a spiral Helix reactor is conducted, for the application in the commercial surfactant production. Step change response curves (SCR) were obtained from numerical tracer experiments by three-dimensional computational fluid dynamics (CFD) simulations. Non-reactive flow is

Surface expression and subunit specific control of steady protein levels by the Kv7.2 helix A-B linker.

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Paloma Aivar

Full Text Available Kv7.2 and Kv7.3 are the main components of the neuronal voltage-dependent M-current, which is a subthreshold potassium conductance that exerts an important control on neuronal excitability. Despite their predominantly intracellular distribution, these channels must reach the plasma membrane in order to control neuronal activity. Thus, we analyzed the amino acid sequence of Kv7.2 to identify intrinsic signals that may control its surface expression. Removal of the interlinker connecting helix A and helix B of the intracellular C-terminus produces a large increase in the number of functional channels at the plasma membrane. Moreover, elimination of this linker increased the steady-state amount of protein, which was not associated with a decrease of protein degradation. The magnitude of this increase was inversely correlated with the number of helix A - helix B linkers present in the tetrameric channel assemblies. In contrast to the remarkable effect on the amount of Kv7.2 protein, removal of the Kv7.2 linker had no detectable impact on the steady-state levels of Kv7.3 protein.

Helix-helix inversion of an optically-inactive π-conjugated foldamer triggered by concentration changes of a single enantiomeric guest leading to a change in the helical stability.

Science.gov (United States)

Liu, Lijia; Ousaka, Naoki; Horie, Miki; Mamiya, Fumihiko; Yashima, Eiji

2016-09-27

A preferred-handed helicity induced in an optically-inactive poly(phenyleneethynylene)-based foldamer bearing carboxylic acid pendants upon complexation with a single enantiomeric diamine was subsequently inverted into the opposite helix upon further addition of the diamine, accompanied by a remarkable change in the stability of the helices.

Cesium-134 assimilation and retention in the landsnail Helix aspersa Muller 1974. Its potential usefulness as bioindicator for radioactive contamination

International Nuclear Information System (INIS)

Alfonso, L.A.; Carvalho, F.P.

1986-01-01

Cesium-134 retention was experimentally studied on two groups (n=20 in each) of the land-snail Helix aspersa, labelled either through ingestion of labelled food or the radionuclide injection into the foot muscle. Cesium elimination was found to be not dependent from the labelling technique used. The mean biological half-life for Cs retention in both Helix groups was 53.6+- 0.8 d for the largest retention component, accounting for 0.88 of the initally absorbed Cs. Another experiment runned on a similar size Helix group allowed the gravimetric determination of food ingestion rate (8.8 mg/ g/day) and food assimilation efficiency (0.70+-0.20). Predictive modelling of Cs accumulation by Helix indicates a relatively high bioaccumulation potential in this species. This fact, together with the long biological half-life found for Cs retention, indicate that land snails could be used as suitable bioindicators for radioactive pollution in restrict terrestrial areas. (author)

Contact Stress Analysis for Gears of Different Helix Angle Using Finite Element Method

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Patil Santosh

2014-07-01

Full Text Available The gear contact stress problem has been a great point of interest for many years, but still an extensive research is required to understand the various parameters affecting this stress. Among such parameters, helix angle is one which has played a crucial role in variation of contact stress. Numerous studies have been carried out on spur gear for contact stress variation. Hence, the present work is an attempt to study the contact stresses among the helical gear pairs, under static conditions, by using a 3D finite element method. The helical gear pairs on which the analysis is carried are 0, 5, 15, 25 degree helical gear sets. The Lagrange multiplier algorithm has been used between the contacting pairs to determine the stresses. The helical gear contact stress is evaluated using FE model and results have also been found at different coefficient of friction, varying from 0.0 to 0.3. The FE results have been further compared with the analytical calculations. The analytical calculations are based upon Hertz and AGMA equations, which are modified to include helix angle. The commercial finite element software was used in the study and it was shown that this approach can be applied to gear design efficiently. The contact stress results have shown a decreasing trend, with increase in helix angle.

Emergence of the persistent spin helix in semiconductor quantum wells

International Nuclear Information System (INIS)

Koralek, Jake; Weber, Chris; Orenstein, Joe; Bernevig, Andrei; Zhang, Shoucheng; Mack, Shawn; Awschalom, David

2008-01-01

According to Noether's theorem, for every symmetry in nature there is a corresponding conservation law. For example, invariance with respect to spatial translation corresponds to conservation of momentum. In another well-known example, invariance with respect to rotation of the electron's spin, or SU(2) symmetry, leads to conservation of spin polarization. For electrons in a solid, this symmetry is ordinarily broken by spin-orbit (SO) coupling, allowing spin angular momentum to flow to orbital angular momentum. However, it has recently been predicted that SU(2) can be recovered in a two-dimensional electron gas (2DEG), despite the presence of SO coupling. The corresponding conserved quantities include the amplitude and phase of a helical spin density wave termed the 'persistent spin helix' (PSH) .2 SU(2) is restored, in principle, when the strength of two dominant SO interactions, the Rashba (alpha) and linear Dresselhaus (beta 1), are equal. This symmetry is predicted to be robust against all forms of spin-independent scattering, including electron-electron interactions, but is broken by the cubic Dresselhaus term (beta 3) and spin-dependent scattering. When these terms are negligible, the distance over which spin information can propagate is predicted to diverge as alpha approaches beta 1. Here we observe experimentally the emergence of the PSH in GaAs quantum wells (QW's) by independently tuning alpha and beta 1. Using transient spin-grating spectroscopy (TSG), we find a spin-lifetime enhancement of two orders of magnitude near the symmetry point. Excellent quantitative agreement with theory across a wide range of sample parameters allows us to obtain an absolute measure of all relevant SO terms, identifying beta 3 as the main SU(2) violating term in our samples. The tunable suppression of spin-relaxation demonstrated in this work is well-suited for application to spintronics

Emergence of the Persistent Spin Helix in Semiconductor Quantum Wells

International Nuclear Information System (INIS)

Koralek, Jake

2011-01-01

According to Noether's theorem, for every symmetry in nature there is a corresponding conservation law. For example, invariance with respect to spatial translation corresponds to conservation of momentum. In another well-known example, invariance with respect to rotation of the electron's spin, or SU(2) symmetry, leads to conservation of spin polarization. For electrons in a solid, this symmetry is ordinarily broken by spin-orbit (SO) coupling, allowing spin angular momentum to flow to orbital angular momentum. However, it has recently been predicted that SU(2) can be recovered in a two-dimensional electron gas (2DEG), despite the presence of SO coupling. The corresponding conserved quantities include the amplitude and phase of a helical spin density wave termed the 'persistent spin helix' (PSH). SU(2) is restored, in principle, when the strength of two dominant SO interactions, the Rashba (α) and linear Dresselhaus (β 1 ), are equal. This symmetry is predicted to be robust against all forms of spin-independent scattering, including electron-electron interactions, but is broken by the cubic Dresselhaus term (β 3 ) and spin-dependent scattering. When these terms are negligible, the distance over which spin information can propagate is predicted to diverge as α → β 1 . Here we observe experimentally the emergence of the PSH in GaAs quantum wells (QW's) by independently tuning α and β 1 . Using transient spin-grating spectroscopy (TSG), we find a spin-lifetime enhancement of two orders of magnitude near the symmetry point. Excellent quantitative agreement with theory across a wide range of sample parameters allows us to obtain an absolute measure of all relevant SO terms, identifying β 3 as the main SU(2) violating term in our samples. The tunable suppression of spin-relaxation demonstrated in this work is well-suited for application to spintronics.

Bacterial morphogenesis and the enigmatic MreB helix.

Science.gov (United States)

Errington, Jeff

2015-04-01

Work over the past decade has highlighted the pivotal role of the actin-like MreB family of proteins in the determination and maintenance of rod cell shape in bacteria. Early images of MreB localization revealed long helical filaments, which were suggestive of a direct role in governing cell wall architecture. However, several more recent, higher-resolution studies have questioned the existence or importance of the helical structures. In this Opinion article, I navigate a path through these conflicting reports, revive the helix model and summarize the key questions that remain to be answered.

Multicenter comparative study of laparoscopic and open distal pancreatectomy using propensity score-matching.

Science.gov (United States)

Nakamura, Masafumi; Wakabayashi, Go; Miyasaka, Yoshihiro; Tanaka, Masao; Morikawa, Takanori; Unno, Michiaki; Tajima, Hiroshi; Kumamoto, Yusuke; Satoi, Sohei; Kwon, Masanori; Toyama, Hirochika; Ku, Yonson; Yoshitomi, Hideyuki; Nara, Satoshi; Shimada, Kazuaki; Yokoyama, Takahide; Miyagawa, Shinichi; Toyama, Yoichi; Yanaga, Katsuhiko; Fujii, Tsutomu; Kodera, Yasuhiro; Tomiyama, Yasuyuki; Miyata, Hiroaki; Takahara, Takeshi; Beppu, Toru; Yamaue, Hiroki; Miyazaki, Masaru; Takada, Tadahiro

2015-10-01

Laparoscopic distal pancreatectomy has been shown to be associated with favorable postoperative outcomes using meta-analysis. However, there have been no randomized controlled studies yet. This study aimed to compare laparoscopic and open distal pancreatectomy using propensity score-matching. We retrospectively collected perioperative data of 2,266 patients who underwent distal pancreatectomy in 69 institutes from 2006-2013 in Japan. Among them, 2,010 patients were enrolled in this study and divided into two groups, laparoscopic distal pancreatectomy and open distal pancreatectomy. Perioperative outcomes were compared between the groups using unmatched and propensity matched analysis. After propensity score-matching, laparoscopic distal pancreatectomy was associated with favorable perioperative outcomes compared with open distal pancreatectomy, including higher rate of preservation of spleen and splenic vessels (P pancreatectomy was associated with more favorable perioperative outcomes than open distal pancreatectomy. © 2015 Japanese Society of Hepato-Biliary-Pancreatic Surgery.

Mechanical evaluation of quad-helix appliance made of low-nickel stainless steel wire.

Science.gov (United States)

dos Santos, Rogério Lacerda; Pithon, Matheus Melo

2013-01-01

The objective of this study was to test the hypothesis that there is no difference between stainless steel and low-nickel stainless steel wires as regards mechanical behavior. Force, resilience, and elastic modulus produced by Quad-helix appliances made of 0.032-inch and 0.036-inch wires were evaluated. Sixty Quad-helix appliances were made, thirty for each type of alloy, being fifteen for each wire thickness, 0.032-in and 0.036-in. All the archwires were submitted to mechanical compression test using an EMIC DL-10000 machine simulating activations of 4, 6, 9, and 12 mm. Analysis of variance (ANOVA) with multiple comparisons and Tukey's test were used (p nickel stainless steel alloy had force, resilience, and elastic modulus similar to those made of stainless steel alloy.

Get the most from your data: a propensity score model comparison on real-life data

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Ferdin

2016-05-01

Full Text Available Dennis Ferdinand,1 Mirko Otto,2 Christel Weiss1 1Department of Biomathematics and Medical Statistics, 2Department of Surgery, University Medical Center Mannheim (UMM, University of Heidelberg, Mannheim, Germany Purpose: In the past, the propensity score has been in the middle of several discussions in terms of its abilities and limitations. With a comprehensive review and a practical example, this study examines the effect of propensity score analysis of real-life data and introduces a simple and effective clinical approach. Materials and methods: After the authors reviewed current publications, they applied their insights to the data of a nonrandomized clinical trial in bariatric surgery. This study examined weight loss in 173 patients where 127 patients received Roux-en-Y gastric bypass surgery and 46 patients sleeve gastrectomy. Both groups underwent analysis in terms of their covariate distribution using Mann–Whitney U and χ2 testing. Mean differences within excess weight loss in native data were examined with Student’s t-test. Three propensity score models were defined and matching was performed. Covariate distribution and mean differences in excess weight loss were checked with Mann–Whitney U and χ2 testing. Results: Native data implied a significant difference in excess weight loss. The propensity score models did not confirm this difference. All models proved that both surgical procedures were equal, due to their weight-loss induction. Covariate distribution improved after the matching procedure in terms of an equal distribution. Conclusion: It seemed that a practical clinical approach with outcome-related covariates as a propensity score base is the ideal midpoint between an equal distribution in covariates and an acceptable loss of data. Nevertheless, propensity score models designed with clinical intent seemed to be absolutely suitable for overcoming heterogeneity in covariate distribution. Keywords: nonrandomized clinical

The Penta Helix Model of Innovation in Oman: An HEI Perspective

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Alrence S Halibas

2017-05-01

Full Text Available Aim/Purpose: Countries today strategically pursue regional development and economic diversification to compete in the world market. Higher Education Institutions (HEIs are at the crux of this political strategy. The paper reviews how HEIs can propel regional socio-economic growth and development by way of research innovation and entrepreneurship. Background: Offering an academic perspective about the role of HEIs using the Penta Helix innovation network for business and social innovation, the paper discusses opportunities and challenges in gestating an innovation culture. It likewise seeks, identifies and details strategies and workable programs. Methodology: Best-practice innovation campaigns initiated by Omani HEIs in collaboration with capstone programs organized by the government were parsed from selected local and international literature. The study includes a causal analysis of innovation information contained in 40 out of 44 published OAAA Quality Audit reports about HEIs from 2009 to 2016. The best-practice programs serve as success indicators and will be used as a field metric effect a Penta Helix blueprint for innovation. Contribution: The paper discusses how HEIs can engender, nurture, drive, and sustain innovation and entrepreneurial activity by using an innovation strategic blueprint like the Penta Helix model. It gathers together the recent historical attempts at promoting innovation by HEIs. It likewise suggests the creation of a network channel to allow key players in the innovation network to share innovation information and to collaborate with each other. Furthermore, it contributes to the development of innovation culture in HEIs. Findings: Expectations run high in academia. For one, universities believe that all innovations embryonically begin within their halls. Universities–too–believe it is naturally incumbent on them to stimulate and advance innovation despite that most innovation programs are initiated by the

Lead reduces shell mass in juvenile garden snails (Helix aspersa)

International Nuclear Information System (INIS)

Beeby, Alan; Richmond, Larry; Herpe, Florian

2002-01-01

A high Pb diet causes differential depression of juvenile shell mass in populations of Helix. - In an earlier paper examining inherited tolerance to Pb, the shell growth of laboratory-bred offspring of Helix aspersa from contaminated sites was compared with that of juveniles from naieve populations on dosed and undosed diets. Eight-week-old snails were fed either 500 μg g -1 Pb or a control food in competitive trials between two populations. In the first series of trials, a parental history of exposure to Pb did not confer any advantage to either of two populations (BI and MI) competing with a naieve population (LE), whether Pb was present in the diet or not. However, in the analysis of their metal concentrations reported here, LE are found to retain higher levels of Pb in the soft tissues than either BI or MI. Compared to their siblings on the unleaded diet, dosed LE and BI juveniles had lower soft tissue concentrations of Ca and Mg. Although the growth in shell height is unaffected by diet, LE and BI juveniles build lighter shells on the Pb-dosed diet, achieving around 75% of the shell mass of their controls. In contrast, the shell weights of dosed MI juveniles are depressed by only 15% and show no change in the essential metal concentrations of their soft tissues. A second experiment using five populations fed only the dosed food show that the shell weight/soft tissue weight ratios are comparable to the dosed snails of the previous experiment. Building a lighter shell thus appears to be the common response of all Helix populations to a high Pb diet, at least amongst juveniles. The reduction in its mass means that less Ca and Mg is added to the shell and, along with the lowered soft tissue concentrations observed in some populations, may be a consequence of an increased effort to excrete Pb. The possibility that the MI population shows a genotypic adaptation, perhaps as some form of modification of its Ca metabolism, is briefly discussed

High-Flux Hemodialysis and High-Volume Hemodiafiltration Improve Serum Calcification Propensity.

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Marijke Dekker

Full Text Available Calciprotein particles (CPPs may play an important role in the calcification process. The calcification propensity of serum (T50 is highly predictive of all-cause mortality in chronic kidney disease patients. Whether T50 is therapeutically improvable, by high-flux hemodialysis (HD or hemodiafiltration (HDF, has not been studied yet.We designed a cross-sectional single center study, and included stable prevalent in-center dialysis patients on HD or HDF. Patients were divided into two groups based on dialysis modality, were on a thrice-weekly schedule, had a dialysis vintage of > 3 months and vascular access providing a blood flow rate > 300 ml/min. Calcification propensity of serum was measured by the time of transformation from primary to secondary CPP (T50 test, by time-resolved nephelometry.We included 64 patients, mean convective volume was 21.7L (SD 3.3L. In the pooled analysis, T50 levels increased in both the HD and HDF group with pre- and post-dialysis (mean (SD of 244(64 - 301(57 and 253(55 - 304(61 min respectively (P = 0.43(HD vs. HDF. The mean increase in T50 was 26.29% for HD and 21.97% for HDF patients (P = 0.61 (HD vs. HDF. The delta values (Δ of calcium, phosphate and serum albumin were equal in both groups. Baseline T50 was negatively correlated with phosphate, and positively correlated with serum magnesium and fetuin-A. The ΔT50 was mostly influenced by Δ phosphate (r = -0.342; P = 0.002 HD and r = -0.396; P<0.001 HDF in both groups.HD and HDF patients present with same baseline T50 calcification propensity values pre-dialysis. Calcification propensity is significantly improved during both HD and HDF sessions without significant differences between both modalities.

Antimicrobial Effects of Helix D-derived Peptides of Human Antithrombin III*

Science.gov (United States)

Papareddy, Praveen; Kalle, Martina; Bhongir, Ravi K. V.; Mörgelin, Matthias; Malmsten, Martin; Schmidtchen, Artur

2014-01-01

Antithrombin III (ATIII) is a key antiproteinase involved in blood coagulation. Previous investigations have shown that ATIII is degraded by Staphylococcus aureus V8 protease, leading to release of heparin binding fragments derived from its D helix. As heparin binding and antimicrobial activity of peptides frequently overlap, we here set out to explore possible antibacterial effects of intact and degraded ATIII. In contrast to intact ATIII, the results showed that extensive degradation of the molecule yielded fragments with antimicrobial activity. Correspondingly, the heparin-binding, helix d-derived, peptide FFFAKLNCRLYRKANKSSKLV (FFF21) of human ATIII, was found to be antimicrobial against particularly the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa. Fluorescence microscopy and electron microscopy studies demonstrated that FFF21 binds to and permeabilizes bacterial membranes. Analogously, FFF21 was found to induce membrane leakage of model anionic liposomes. In vivo, FFF21 significantly reduced P. aeruginosa infection in mice. Additionally, FFF21 displayed anti-endotoxic effects in vitro. Taken together, our results suggest novel roles for ATIII-derived peptide fragments in host defense. PMID:25202017

Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils.

Science.gov (United States)

Honda, Ryo; Kuwata, Kazuo

2018-02-01

Amyloid fibrils are filamentous protein aggregates associated with the pathogenesis of a wide variety of human diseases. The formation of such aggregates typically follows nucleation-dependent kinetics, wherein the assembly and structural conversion of amyloidogenic proteins into oligomeric aggregates (nuclei) is the rate-limiting step of the overall reaction. In this study, we sought to gain structural insights into the oligomeric nuclei of the human prion protein (PrP) by preparing a series of deletion mutants lacking 14-44 of the C-terminal 107 residues of PrP and examined the kinetics and thermodynamics of these mutants in amyloid formation. An analysis of the experimental data using the concepts of the Φ-value analysis indicated that the helix 2 region (residues 168-196) acquires an amyloid-like β-sheet during nucleation, whereas the other regions preserves a relatively disordered structure in the nuclei. This finding suggests that the helix 2 region serves as the nucleation site for the assembly of amyloid fibrils.-Honda, R., Kuwata, K. Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils.

Human telomeric DNA: G-quadruplex, i-motif and Watson–Crick double helix

Science.gov (United States)

Phan, Anh Tuân; Mergny, Jean-Louis

2002-01-01

Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson–Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C·C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding. PMID:12409451

Academic Spin-off as Triple Helix Element: Case-Study of Russian Regions

Directory of Open Access Journals (Sweden)

Konstantin Ivanovich Grasmik

2016-10-01

Full Text Available The innovation process is becoming more open. According to the concept of the Triple Helix, this requires the creation of institutions capable of mediating the interaction of agents, primarily related to the different elements of the innovation system. The academic spin-off is not only a form of technology transfer, set up at the university but also the institution that provides the interaction of scientists and entrepreneurs. This article gives an analysis of the implementation of the program of creating academic spin-offs in Russia. The main focus of the study is to analyze the affiliation of university spin-off with other companies, including personal links of founders. Research reveals that linkages are substantially personal: University staff member at the same time could be an entrepreneur. This finding allows not only clarifying the concept of the Triple Helix but also increasing the effectiveness of innovation policy, focusing on employees who can combine science and entrepreneurship.

Salt bridge interactions within the β2 integrin α7 helix mediate force-induced binding and shear resistance ability.

Science.gov (United States)

Zhang, Xiao; Li, Linda; Li, Ning; Shu, Xinyu; Zhou, Lüwen; Lü, Shouqin; Chen, Shenbao; Mao, Debin; Long, Mian

2018-01-01

The functional performance of the αI domain α 7 helix in β 2 integrin activation depends on the allostery of the α 7 helix, which axially slides down; therefore, it is critical to elucidate what factors regulate the allostery. In this study, we determined that there were two conservative salt bridge interaction pairs that constrain both the upper and bottom ends of the α 7 helix. Molecular dynamics (MD) simulations for three β 2 integrin members, lymphocyte function-associated antigen-1 (LFA-1; α L β 2 ), macrophage-1 antigen (Mac-1; α M β 2 ) and α x β 2 , indicated that the magnitude of the salt bridge interaction is related to the stability of the αI domain and the strength of the corresponding force-induced allostery. The disruption of the salt bridge interaction, especially with double mutations in both salt bridges, significantly reduced the force-induced allostery time for all three members. The effects of salt bridge interactions of the αI domain α 7 helix on β 2 integrin conformational stability and allostery were experimentally validated using Mac-1 constructs. The results demonstrated that salt bridge mutations did not alter the conformational state of Mac-1, but they did increase the force-induced ligand binding and shear resistance ability, which was consistent with MD simulations. This study offers new insight into the importance of salt bridge interaction constraints of the αI domain α 7 helix and external force for β 2 integrin function. © 2017 Federation of European Biochemical Societies.

The Helix Nebula Viewed in HCO+: Large-scale Mapping of the J = 1 → 0 Transition

Science.gov (United States)

Zeigler, N. R.; Zack, L. N.; Woolf, N. J.; Ziurys, L. M.

2013-11-01

The J = 1 → 0 transition of HCO+ at 89 GHz has been mapped across the Helix Nebula (NGC 7293) with 70'' spatial resolution (1.68 km s-1 velocity resolution) using the Arizona Radio Observatory 12 m telescope. This work is the first large-scale mapping project of a dense gas tracer (n(H2) ~ 105 cm-3) in old planetary nebulae. Observations of over 200 positions encompassing the classical optical image were conducted with a 3σ noise level of ~20 mK. HCO+ was detected at most positions, often exhibiting multiple velocity components indicative of complex kinematic structures in dense gas. The HCO+ spectra suggest that the Helix is composed of a bipolar, barrel-like structure with red- and blue-shifted halves, symmetric with respect to the central star and oriented ~10° east from the line of sight. A second bipolar, higher velocity outflow exists as well, situated along the direction of the Helix "plumes." The column density of HCO+ across the Helix is N tot ~ 1.5 × 1010-5.0 × 1011 cm-2, with an average value N ave ~ 1 × 1011 cm-2, corresponding to an abundance, relative to H2, of f ~ 1.4 × 10-8. This value is similar to that observed in young PN, and contradicts chemical models, which predict that the abundance of HCO+ decreases with nebular age. This study indicates that polyatomic molecules readily survive the ultraviolet field of the central white dwarf, and can be useful in tracing nebular morphology in the very late stages of stellar evolution.

Abrupt transition to heightened poliomyelitis epidemicity in England and Wales, 1947-1957, associated with a pronounced increase in the geographical rate of disease propagation.

Science.gov (United States)

Smallman-Raynor, M R; Cliff, A D

2014-03-01

The abrupt transition to heightened poliomyelitis epidemicity in England and Wales, 1947-1957, was associated with a profound change in the spatial dynamics of the disease. Drawing on the complete record of poliomyelitis notifications in England and Wales, we use a robust method of spatial epidemiological analysis (swash-backwash model) to evaluate the geographical rate of disease propagation in successive poliomyelitis seasons, 1940-1964. Comparisons with earlier and later time periods show that the period of heightened poliomyelitis epidemicity corresponded with a sudden and pronounced increase in the spatial rate of disease propagation. This change was observed for both urban and rural areas and points to an abrupt enhancement in the propensity for the geographical spread of polioviruses. Competing theories of the epidemic emergence of poliomyelitis in England and Wales should be assessed in the light of this evidence.

A conserved phenylalanine as a relay between the α5 helix and the GDP binding region of heterotrimeric Gi protein α subunit.

Science.gov (United States)

Kaya, Ali I; Lokits, Alyssa D; Gilbert, James A; Iverson, Tina M; Meiler, Jens; Hamm, Heidi E

2014-08-29

G protein activation by G protein-coupled receptors is one of the critical steps for many cellular signal transduction pathways. Previously, we and other groups reported that the α5 helix in the G protein α subunit plays a major role during this activation process. However, the precise signaling pathway between the α5 helix and the guanosine diphosphate (GDP) binding pocket remains elusive. Here, using structural, biochemical, and computational techniques, we probed different residues around the α5 helix for their role in signaling. Our data showed that perturbing the Phe-336 residue disturbs hydrophobic interactions with the β2-β3 strands and α1 helix, leading to high basal nucleotide exchange. However, mutations in β strands β5 and β6 do not perturb G protein activation. We have highlighted critical residues that leverage Phe-336 as a relay. Conformational changes are transmitted starting from Phe-336 via β2-β3/α1 to Switch I and the phosphate binding loop, decreasing the stability of the GDP binding pocket and triggering nucleotide release. When the α1 and α5 helices were cross-linked, inhibiting the receptor-mediated displacement of the C-terminal α5 helix, mutation of Phe-336 still leads to high basal exchange rates. This suggests that unlike receptor-mediated activation, helix 5 rotation and translocation are not necessary for GDP release from the α subunit. Rather, destabilization of the backdoor region of the Gα subunit is sufficient for triggering the activation process. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Involvement of Na,K-pump in SEPYLRFamide-mediated reduction of cholinosensitivity in Helix neurons.

Science.gov (United States)

Pivovarov, Arkady S; Foreman, Richard C; Walker, Robert J

2007-02-01

SEPYLRFamide acts as an inhibitory modulator of acetylcholine (ACh) receptors in Helix lucorum neurones. Ouabain, a specific inhibitor of Na,K-pump, (0.1 mM, bath application) decreased the ACh-induced inward current (ACh-current) and increased the leak current. Ouabain decreased the modulatory SEPYLRFamide effect on the ACh-current. There was a correlation between the effects of ouabain on the amplitude of the ACh-current and on the modulatory peptide effect. Ouabain and SEPYLRFamide inhibited the activity of Helix aspersa brain Na,K-ATPase. Activation of Na,K-pump by intracellular injection of 3 M Na acetate or 3 M NaCl reduced the modulatory peptide effect on the ACh-current. An inhibitor of Na/Ca-exchange, benzamil (25 muM, bath application), and an inhibitor of Ca(2+)-pump in the endoplasmic reticulum, thapsigargin (TG, applied intracellularly), both prevented the effect of ouabain on SEPYLRFamide-mediated modulatory effect. Another inhibitor of Ca(2+)-pump in the endoplasmic reticulum, cyclopiazonic acid (applied intracellularly), did not prevent the effect of ouabain on SEPYLRFamide-mediated modulatory effect. These results indicate that Na,K-pump is responsible for the SEPYLRFamide-mediated inhibition of ACh receptors in Helix neurons. Na/Ca-exchange and intracellular Ca(2+) released from internal pools containing TG-sensitive Ca(2+)-pump are involved in the Na,K-pump pathway for the SEPYLRFamide-mediated inhibition of ACh receptors.

Thermodynamic effects of replacements of Pro residues in helix interiors of maltose-binding protein.

Science.gov (United States)

Prajapati, R S; Lingaraju, G M; Bacchawat, Kiran; Surolia, Avadhesha; Varadarajan, Raghavan

2003-12-01

Introduction of Pro residues into helix interiors results in protein destabilization. It is currently unclear if the converse substitution (i.e., replacement of Pro residues that naturally occur in helix interiors would be stabilizing). Maltose-binding protein is a large 370-amino acid protein that contains 21 Pro residues. Of these, three nonconserved residues (P48, P133, and P159) occur at helix interiors. Each of the residues was replaced with Ala and Ser. Stabilities were characterized by differential scanning calorimetry (DSC) as a function of pH and by isothermal urea denaturation studies as a function of temperature. The P48S and P48A mutants were found to be marginally more stable than the wild-type protein. In the pH range of 5-9, there is an average increase in T(m) values of P48A and P48S of 0.4 degrees C and 0.2 degrees C, respectively, relative to the wild-type protein. The other mutants are less stable than the wild type. Analysis of the effects of such Pro substitutions in MBP and in three other proteins studied to date suggests that substitutions are more likely to be stabilizing if the carbonyl group i-3 or i-4 to the mutation site is not hydrogen bonded in the wild-type protein. Copyright 2003 Wiley-Liss, Inc.

Dynamic Recognition of Driver’s Propensity Based on GPS Mobile Sensing Data and Privacy Protection

Directory of Open Access Journals (Sweden)

Xiaoyuan Wang

2016-01-01

Full Text Available Driver’s propensity is a dynamic measurement of driver’s emotional preference characteristics in driving process. It is a core parameter to compute driver’s intention and consciousness in safety driving assist system, especially in vehicle collision warning system. It is also an important influence factor to achieve the Driver-Vehicle-Environment Collaborative Wisdom and Control macroscopically. In this paper, dynamic recognition model of driver’s propensity based on support vector machine is established taking the vehicle safety controlled technology and respecting and protecting the driver’s privacy as precondition. The experiment roads travel time obtained through GPS is taken as the characteristic parameter. The sensing information of Driver-Vehicle-Environment was obtained through psychological questionnaire tests, real vehicle experiments, and virtual driving experiments, and the information is used for parameter calibration and validation of the model. Results show that the established recognition model of driver’s propensity is reasonable and feasible, which can achieve the dynamic recognition of driver’s propensity to some extent. The recognition model provides reference and theoretical basis for personalized vehicle active safety systems taking people as center especially for the vehicle safety technology based on the networking.

Praevalensen afhud- og slimhindesymptomer blandt gartnere der omgås Ficus benjamina (stuebirk) og Hedera helix (vedbend). Et tvaersnitsstudie

DEFF Research Database (Denmark)

Jørs, Erik

2003-01-01

Allergic and toxic initiative symptoms from skin, eyes and respiratory tract are well known among gardeners This study reports the prevalence of these symptoms among gardeners working with Ficus Benjamina (Fb) and Hedera helix (Hh).......Allergic and toxic initiative symptoms from skin, eyes and respiratory tract are well known among gardeners This study reports the prevalence of these symptoms among gardeners working with Ficus Benjamina (Fb) and Hedera helix (Hh)....

High-resolution orientation and depth of insertion of the voltage-sensing S4 helix of a potassium channel in lipid bilayers.

Science.gov (United States)

Doherty, Tim; Su, Yongchao; Hong, Mei

2010-08-27

The opening and closing of voltage-gated potassium (Kv) channels are controlled by several conserved Arg residues in the S4 helix of the voltage-sensing domain. The interaction of these positively charged Arg residues with the lipid membrane has been of intense interest for understanding how membrane proteins fold to allow charged residues to insert into lipid bilayers against free-energy barriers. Using solid-state NMR, we have now determined the orientation and insertion depth of the S4 peptide of the KvAP channel in lipid bilayers. Two-dimensional (15)N correlation experiments of macroscopically oriented S4 peptide in phospholipid bilayers revealed a tilt angle of 40 degrees and two possible rotation angles differing by 180 degrees around the helix axis. Remarkably, the tilt angle and one of the two rotation angles are identical to those of the S4 helix in the intact voltage-sensing domain, suggesting that interactions between the S4 segment and other helices of the voltage-sensing domain are not essential for the membrane topology of the S4 helix. (13)C-(31)P distances between the S4 backbone and the lipid (31)P indicate a approximately 9 A local thinning and 2 A average thinning of the DMPC (1,2-dimyristoyl-sn-glycero-3-phosphochloline)/DMPG (1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol) bilayer, consistent with neutron diffraction data. Moreover, a short distance of 4.6 A from the guanidinium C(zeta) of the second Arg to (31)P indicates the existence of guanidinium phosphate hydrogen bonding and salt bridges. These data suggest that the structure of the Kv gating helix is mainly determined by protein-lipid interactions instead of interhelical protein-protein interactions, and the S4 amino acid sequence encodes sufficient information for the membrane topology of this crucial gating helix. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Adverse Childhood Experiences and Criminal Propensity Among Intimate Partner Violence Offenders.

Science.gov (United States)

Hilton, N Zoe; Ham, Elke; Green, Michelle M

2016-10-01

Adverse childhood experiences (ACEs), defined as exposure to abuse and adverse household events, are prevalent among certain offenders including those who commit intimate partner violence (IPV). However, it is not clear how ACEs relate to criminal propensity among IPV offenders, who have been shown to exhibit less antisociality and institutional violence than other offenders. We compared 99 male offenders with a current or previous offense of IPV with 233 non-IPV violent offenders and 103 nonviolent offenders undergoing institutional forensic assessment. This convenience sample allowed for use of extensive psychosocial records as well as study of institutional violence. IPV offenders had the highest mean ACE score and more extensive criminal propensity on some measures (violent and nonviolent criminal history and psychopathy) than both other groups. ACEs were associated with most measures of criminal propensity in the whole sample but with only one (actuarial risk of violent recidivism) in the subsample of IPV offenders. Finding that ACEs are prevalent among IPV offenders even in this sample with extensive mental illness demonstrates the robustness of this phenomenon. IPV offenders, though, are similar to other violent offenders in this respect, and there is insufficient evidence that ACEs represent a criminogenic need among IPV offenders specifically. Further research could draw from the batterer typology literature and attend to IPV offenders' broader criminal careers.

Forced evolution of a regulatory RNA helix in the HIV-1 genome

NARCIS (Netherlands)

Berkhout, B.; Klaver, B.; Das, A. T.

1997-01-01

The 5'and 3'end of the HIV-1 RNA genome forms a repeat (R) element that encodes a double stem-loop structure (the TAR and polyA hairpins). Phylogenetic analysis of the polyA hairpin in different human and simian immunodeficiency viruses suggests that the thermodynamic stability of the helix is

Propensity rules for orientation in singly-charged ion-atom collisions

International Nuclear Information System (INIS)

Nielsen, S.E.; Dubois, A.; Hansen, J.P.

1990-01-01

Orientation effects for electron capture and excitation in singly-charged ion-atom collisions are analysed using the atomic basis impact parameter method with full inclusion of electron translational factors. We find that the orientation preferences previously predicted for excitation in terms of propensity rules may still be observed when capture is present in ion-atom collisions. Furthermore, in spite of intricate behaviour of the direct capture couplings during the collision, we draw some parallel conclusions for the orientation of the capture states. We illustrate these perturbative predictions by close-coupling calculations for H + -Na(3s) collisions where clear propensity for orientation of the H(2p) capture state is demonstrated in impact parameter and velocity dependences. Finally we predict pronounced orientation effects for H(2s) and H(2p) capture in collisions of H + with initially oriented Na(3p) states. (author)

Antimicrobial effects of helix D-derived peptides of human antithrombin III.

Science.gov (United States)

Papareddy, Praveen; Kalle, Martina; Bhongir, Ravi K V; Mörgelin, Matthias; Malmsten, Martin; Schmidtchen, Artur

2014-10-24

Antithrombin III (ATIII) is a key antiproteinase involved in blood coagulation. Previous investigations have shown that ATIII is degraded by Staphylococcus aureus V8 protease, leading to release of heparin binding fragments derived from its D helix. As heparin binding and antimicrobial activity of peptides frequently overlap, we here set out to explore possible antibacterial effects of intact and degraded ATIII. In contrast to intact ATIII, the results showed that extensive degradation of the molecule yielded fragments with antimicrobial activity. Correspondingly, the heparin-binding, helix D-derived, peptide FFFAKLNCRLYRKANKSSKLV (FFF21) of human ATIII, was found to be antimicrobial against particularly the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa. Fluorescence microscopy and electron microscopy studies demonstrated that FFF21 binds to and permeabilizes bacterial membranes. Analogously, FFF21 was found to induce membrane leakage of model anionic liposomes. In vivo, FFF21 significantly reduced P. aeruginosa infection in mice. Additionally, FFF21 displayed anti-endotoxic effects in vitro. Taken together, our results suggest novel roles for ATIII-derived peptide fragments in host defense. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Spin Propensities of Octahedral Complexes From Density Functional Theory

DEFF Research Database (Denmark)

Mortensen, Sara R.; Kepp, Kasper Planeta

2015-01-01

assessment of spin state propensities versus ligand and metal type and reveal, e.g., that CN- is consistently weaker than CO for M(II) but stronger than CO for M(III) and SCN- and NCS- change order in M(II) versus M(III) complexes. Contrary to expectation based on the spectrochemical series, Cl- and Br...

The close-packed triple helix as a possible new structural motif for collagen

DEFF Research Database (Denmark)

Bohr, Jakob; Olsen, Kasper

2010-01-01

that close packing form the underlying principle behind the structure of collagen, and the implications of this suggestion are considered. Further, it is shown that the unique zero-twist structure with no strain-twist coupling is practically identical to the close-packed triple helix. Some...

Helix Nebula - the Science Cloud: a public-private partnership to build a multidisciplinary cloud platform for data intensive science

Science.gov (United States)

Jones, Bob; Casu, Francesco

2013-04-01

The feasibility of using commercial cloud services for scientific research is of great interest to research organisations such as CERN, ESA and EMBL, to the suppliers of cloud-based services and to the national and European funding agencies. Through the Helix Nebula - the Science Cloud [1] initiative and with the support of the European Commission, these stakeholders are driving a two year pilot-phase during which procurement processes and governance issues for a framework of public/private partnership will be appraised. Three initial flagship use cases from high energy physics, molecular biology and earth-observation are being used to validate the approach, enable a cost-benefit analysis to be undertaken and prepare the next stage of the Science Cloud Strategic Plan [2] to be developed and approved. The power of Helix Nebula lies in a shared set of services for initially 3 very different sciences each supporting a global community and thus building a common e-Science platform. Of particular relevance is the ESA sponsored flagship application SuperSites Exploitation Platform (SSEP [3]) that offers the global geo-hazard community a common platform for the correlation and processing of observation data for supersites monitoring. The US-NSF Earth Cube [4] and Ocean Observatory Initiative [5] (OOI) are taking a similar approach for data intensive science. The work of Helix Nebula and its recent architecture model [6] has shown that is it technically feasible to allow publicly funded infrastructures, such as EGI [7] and GEANT [8], to interoperate with commercial cloud services. Such hybrid systems are in the interest of the existing users of publicly funded infrastructures and funding agencies because they will provide "freedom of choice" over the type of computing resources to be consumed and the manner in which they can be obtained. But to offer such freedom-of choice across a spectrum of suppliers, various issues such as intellectual property, legal responsibility

An examination of the developmental propensity model of conduct problems.

Science.gov (United States)

Rhee, Soo Hyun; Friedman, Naomi P; Corley, Robin P; Hewitt, John K; Hink, Laura K; Johnson, Daniel P; Smith Watts, Ashley K; Young, Susan E; Robinson, JoAnn; Waldman, Irwin D; Zahn-Waxler, Carolyn

2016-05-01

The present study tested specific hypotheses advanced by the developmental propensity model of the etiology of conduct problems in the Colorado Longitudinal Twin Study, a prospective, longitudinal, genetically informative sample. High negative emotionality, low behavioral inhibition, low concern and high disregard for others, and low cognitive ability assessed during toddlerhood (age 14 to 36 months) were examined as predictors of conduct problems in later childhood and adolescence (age 4 to 17 years). Each hypothesized antisocial propensity dimension predicted conduct problems, but some predictions may be context specific or due to method covariance. The most robust predictors were observed disregard for others (i.e., responding to others' distress with active, negative responses such as anger and hostility), general cognitive ability, and language ability, which were associated with conduct problems reported by parents, teachers, and adolescents, and change in observed negative emotionality (i.e., frustration tolerance), which was associated with conduct problems reported by teachers and adolescents. Furthermore, associations between the most robust early predictors and later conduct problems were influenced by the shared environment rather than genes. We conclude that shared environmental influences that promote disregard for others and detract from cognitive and language development during toddlerhood also predispose individuals to conduct problems in later childhood and adolescence. The identification of those shared environmental influences common to early antisocial propensity and later conduct problems is an important future direction, and additional developmental behavior genetic studies examining the interaction between children's characteristics and socializing influences on conduct problems are needed. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Gender Differences in Teens' Digital Propensity and Perceptions and Preferences with Regard to Digital and Printed Text

Science.gov (United States)

Seok, Soonhwa; DaCosta, Boaventura

2017-01-01

Gender differences between the reading of digital and printed text were explored in this study. Predictors of digital propensity were investigated along with gender differences in the context of digital propensity and perceptions and preferences toward the reading of digital and printed text. Findings strengthened results reported in existing…

Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment.

Science.gov (United States)

Shelar, Ashish; Bansal, Manju

2014-12-01

α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. © 2014 Wiley Periodicals, Inc.

Representing environment-induced helix-coil transitions in a coarse grained peptide model

Science.gov (United States)

Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine

2016-10-01

Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that

Can We Train Machine Learning Methods to Outperform the High-dimensional Propensity Score Algorithm?

Science.gov (United States)

Karim, Mohammad Ehsanul; Pang, Menglan; Platt, Robert W

2018-03-01

The use of retrospective health care claims datasets is frequently criticized for the lack of complete information on potential confounders. Utilizing patient's health status-related information from claims datasets as surrogates or proxies for mismeasured and unobserved confounders, the high-dimensional propensity score algorithm enables us to reduce bias. Using a previously published cohort study of postmyocardial infarction statin use (1998-2012), we compare the performance of the algorithm with a number of popular machine learning approaches for confounder selection in high-dimensional covariate spaces: random forest, least absolute shrinkage and selection operator, and elastic net. Our results suggest that, when the data analysis is done with epidemiologic principles in mind, machine learning methods perform as well as the high-dimensional propensity score algorithm. Using a plasmode framework that mimicked the empirical data, we also showed that a hybrid of machine learning and high-dimensional propensity score algorithms generally perform slightly better than both in terms of mean squared error, when a bias-based analysis is used.

Individual Feedback Propensities and Their Effects on Motivation, Training Success, and Performance

National Research Council Canada - National Science Library

Herols, David

1997-01-01

.... These propensities, if identified and measured, would be related to skill acquisition, performance improvement, self regulatory processes, performance maintenance, as well as a variety of affective...

Effects of mood induction on consumers with vs. without compulsive buying propensity: an experimental study.

Science.gov (United States)

Vogt, Sinje; Hunger, Antje; Türpe, Tina; Pietrowsky, Reinhard; Gerlach, Alexander L

2014-12-15

Compulsive buying (CB) is excessive and leads to impairment and distress. Several studies aimed to explore the phenomenology and antecedents of CB, especially affective states. However, these studies mostly used retrospective self-report and mostly focused on compulsive buyers only. Therefore, this study aims to directly compare consumers with CB propensity and controls on experimental proxies of buying behavior and to investigate 1) effects of neutral vs. negative mood inductions and 2) whether mood effects on buying behavior are specific to CB. Forty female consumers with CB propensity and 40 female controls were randomly assigned to a neutral or negative mood induction. Buying related behavior (likelihood to expose oneself to a shopping situation, urge and probability to buy, willingness to pay) was assessed. Consumers with CB propensity differed from controls in all buying behavior aspects except for willingness to pay. Neither main effects of mood nor group×mood interaction effects on buying behavior were found. However, consumers with CB propensity were emotionally more strongly affected by a negative mood induction. Although negative affect has previously been reported to precede buying episodes in CB, our findings do not indicate specific negative mood effects on buying, neither in CB nor in controls. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

FPGA helix tracking algorithm for PANDA

Energy Technology Data Exchange (ETDEWEB)

Liang, Yutie; Galuska, Martin; Gessler, Thomas; Hu, Jifeng; Kuehn, Wolfgang; Lange, Jens Soeren; Muenchow, David; Spruck, Bjoern [II. Physikalisches, Giessen University (Germany); Ye, Hua [II. Physikalisches, Giessen University (Germany); Institute of High Energy Physics, Beijing (China); Collaboration: PANDA-Collaboration

2014-07-01

The PANDA detector is a general-purpose detector for physics with high luminosity cooled antiproton beams, planed to operate at the FAIR facility in Darmstadt, Germany. The central detector includes a silicon Micro Vertex Detector (MVD) and a Straw Tube Tracker (STT). Without any hardware trigger, large amounts of raw data are streaming into the data acquisition system. The data reduction task is performed in the online system by reconstruction algorithms programmed in VHDL (Very High Speed Integrated Circuit Hardware Description Language) on FPGAs (Field Programmable Gate Arrays) as first level and on a farm of GPUs or PCs as a second level. One important part in the system is the online track reconstruction. In this presentation, an online tracking finding algorithm for helix track reconstruction in the solenoidal field is shown. A performance study using C++ and the status of the VHDL implementation are presented.

Introduction of potential helix-capping residues into an engineered helical protein.

Science.gov (United States)

Parker, M H; Hefford, M A

1998-08-01

MB-1 is an engineered protein that was designed to incorporate high percentages of four amino acid residues and to fold into a four-alpha-helix bundle motif. Mutations were made in the putative loop I and III regions of this protein with the aim of increasing the stability of the helix ends. Four variants, MB-3, MB-5, MB-11 and MB-13, have replacements intended to promote formation of an 'N-capping box'. The loop I and III sequences of MB-3 (both GDLST) and MB-11 (GGDST) were designed to cause alphaL C-terminal 'capping' motifs to form in helices I and III. MB-5 has a sequence, GPDST, that places proline in a favourable position for forming beta-turns, whereas MB-13 (GLDST) has the potential to form Schellman C-capping motifs. Size-exclusion chromatography suggested that MB-1, MB-3, MB-5, MB-11 and MB-13 all form dimers, or possibly trimers. Free energies for the unfolding of each of these variants were determined by urea denaturation, with the loss of secondary structure followed by CD spectroscopy. Assuming an equilibrium between folded dimer and unfolded monomer, MB-13 had the highest apparent stability (40.5 kJ/mol, with +/-2.5 kJ/mol 95% confidence limits), followed by MB-11 (39.3+/-5.9 kJ/mol), MB-3 (36.4+/-1.7 kJ/mol), MB-5 (34.7+/-2.1 kJ/mol) and MB-1 (29.3+/-1.3 kJ/mol); the same relative stabilities of the variants were found when a folded trimer to unfolded monomer model was used to calculate stabilities. All of the variants were relatively unstable for dimeric proteins, but were significantly more stable than MB-1. These findings suggest that it might be possible to increase the stability of a protein for which the three-dimensional structure is unknown by placing amino acid residues in positions that have the potential to form helix- and turn-stabilizing motifs.

Demonstration of slow light propagation in an optical fiber under dual pump light with co-propagation and counter-propagation

Science.gov (United States)

Qiu, Wei; Liu, Jianjun; Wang, Yuda; Yang, Yujing; Gao, Yuan; Lv, Pin; Jiang, Qiuli

2018-04-01

In this paper, a general theory of coherent population oscillation effect in an Er3+ -doped fiber under the dual-frequency pumping laser with counter-propagation and co-propagation at room temperature is presented. Using the numerical simulation, in case of dual frequency light waves (1480 nm and 980 nm) with co-propagation and counter-propagation, we analyze the effect of the pump optical power ratio (M) on the group speed of light. The group velocity of light can be varied with the change of M. We research the time delay and fractional delay in an Er3+-doped fiber under the dual-frequency pumping laser with counter-propagation and co-propagation. Compared to the methods of the single pumping, the larger time delay can be got by using the technique of dual-frequency laser pumped fiber with co-propagation and counter-propagation.

Dynamic Recognition of Driver’s Propensity Based on GPS Mobile Sensing Data and Privacy Protection

OpenAIRE

Xiaoyuan Wang; Jianqiang Wang; Jinglei Zhang; Jingheng Wang

2016-01-01

Driver’s propensity is a dynamic measurement of driver’s emotional preference characteristics in driving process. It is a core parameter to compute driver’s intention and consciousness in safety driving assist system, especially in vehicle collision warning system. It is also an important influence factor to achieve the Driver-Vehicle-Environment Collaborative Wisdom and Control macroscopically. In this paper, dynamic recognition model of driver’s propensity based on support vector machine is...

Empirical Benchmarks of Hidden Bias in Educational Research: Implication for Assessing How well Propensity Score Methods Approximate Experiments and Conducting Sensitivity Analysis

Science.gov (United States)

Dong, Nianbo; Lipsey, Mark

2014-01-01

When randomized control trials (RCT) are not feasible, researchers seek other methods to make causal inference, e.g., propensity score methods. One of the underlined assumptions for the propensity score methods to obtain unbiased treatment effect estimates is the ignorability assumption, that is, conditional on the propensity score, treatment…

Basic Tilted Helix Bundle – A new protein fold in human FKBP25/FKBP3 and HectD1

International Nuclear Information System (INIS)

Helander, Sara; Montecchio, Meri; Lemak, Alexander; Farès, Christophe; Almlöf, Jonas; Li, Yanjun; Yee, Adelinda; Arrowsmith, Cheryl H.; Dhe-Paganon, Sirano; Sunnerhagen, Maria

2014-01-01

Highlights: • We describe the structure of a novel fold in FKBP25 and HectD. • The new fold is named the Basic Tilted Helix Bundle (BTHB) domain. • A conserved basic surface patch is presented, suggesting a functional role. - Abstract: In this paper, we describe the structure of a N-terminal domain motif in nuclear-localized FKBP25 1–73 , a member of the FKBP family, together with the structure of a sequence-related subdomain of the E3 ubiquitin ligase HectD1 that we show belongs to the same fold. This motif adopts a compact 5-helix bundle which we name the Basic Tilted Helix Bundle (BTHB) domain. A positively charged surface patch, structurally centered around the tilted helix H4, is present in both FKBP25 and HectD1 and is conserved in both proteins, suggesting a conserved functional role. We provide detailed comparative analysis of the structures of the two proteins and their sequence similarities, and analysis of the interaction of the proposed FKBP25 binding protein YY1. We suggest that the basic motif in BTHB is involved in the observed DNA binding of FKBP25, and that the function of this domain can be affected by regulatory YY1 binding and/or interactions with adjacent domains

Basic Tilted Helix Bundle – A new protein fold in human FKBP25/FKBP3 and HectD1

Energy Technology Data Exchange (ETDEWEB)

Helander, Sara; Montecchio, Meri [Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping (Sweden); Lemak, Alexander [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Northeast Structural Genomics Consortium, Toronto, Ontario (Canada); Farès, Christophe [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Almlöf, Jonas [Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping (Sweden); Li, Yanjun [Structural Genomics Consortium, University of Toronto, 101 College St, Toronto, Ontario M5G 1L7 (Canada); Yee, Adelinda [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Northeast Structural Genomics Consortium, Toronto, Ontario (Canada); Arrowsmith, Cheryl H. [Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7 (Canada); Northeast Structural Genomics Consortium, Toronto, Ontario (Canada); Structural Genomics Consortium, University of Toronto, 101 College St, Toronto, Ontario M5G 1L7 (Canada); Dhe-Paganon, Sirano [Structural Genomics Consortium, University of Toronto, 101 College St, Toronto, Ontario M5G 1L7 (Canada); Sunnerhagen, Maria, E-mail: maria.sunnerhagen@liu.se [Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping (Sweden)

2014-04-25

Highlights: • We describe the structure of a novel fold in FKBP25 and HectD. • The new fold is named the Basic Tilted Helix Bundle (BTHB) domain. • A conserved basic surface patch is presented, suggesting a functional role. - Abstract: In this paper, we describe the structure of a N-terminal domain motif in nuclear-localized FKBP25{sub 1–73}, a member of the FKBP family, together with the structure of a sequence-related subdomain of the E3 ubiquitin ligase HectD1 that we show belongs to the same fold. This motif adopts a compact 5-helix bundle which we name the Basic Tilted Helix Bundle (BTHB) domain. A positively charged surface patch, structurally centered around the tilted helix H4, is present in both FKBP25 and HectD1 and is conserved in both proteins, suggesting a conserved functional role. We provide detailed comparative analysis of the structures of the two proteins and their sequence similarities, and analysis of the interaction of the proposed FKBP25 binding protein YY1. We suggest that the basic motif in BTHB is involved in the observed DNA binding of FKBP25, and that the function of this domain can be affected by regulatory YY1 binding and/or interactions with adjacent domains.

Propensity for paying home visits among general practitioners and the associations with cancer patients' place of care and death

DEFF Research Database (Denmark)

Winthereik, Anna K; Hjertholm, Peter; Neergaard, Mette Asbjoern

2017-01-01

BACKGROUND: Previous studies of associations between home visits by general practitioners and end-of-life care for cancer patients have been subject to confounding. AIM: To analyse associations between general practitioners' propensity to pay home visits and the likelihood of hospitalisation...... and dying out of hospital among their cancer patients. DESIGN: A national register cohort study with an ecological exposure. Standardised incidence rates of general practitioner home visits were calculated as a measure for propensity. Practices were grouped into propensity quartiles. Associations between...... propensity groups and end-of-life outcomes for cancer patients aged 40 or above were calculated. SETTING/PARTICIPANTS: Danish general practitioners and citizens aged 40 or above were included from 2003 to 2012. RESULTS: We included 2670 practices with 2,518,091 listed patients (18,364,679 person...

Perceived fairness of pay among people with and without disabilities: a propensity score matched analysis of working Australians.

Science.gov (United States)

Milner, Allison; Aitken, Zoe; Krnjacki, Lauren; Bentley, Rebecca; Blakely, Tony; LaMontagne, Anthony D; Kavanagh, Anne M

2015-09-01

Equity and fairness at work are associated with a range of organizational and health outcomes. Past research suggests that workers with disabilities experience inequity in the workplace. It is difficult to conclude whether the presence of disability is the reason for perceived unfair treatment due to the possible confounding of effect estimates by other demographic or socioeconomic factors. The data source was the Household, Income, and Labor Dynamics in Australia (HILDA) survey (2001-2012). Propensity for disability was calculated from logistic models including gender, age, education, country of birth, and father's occupational skill level as predictors. We then used nearest neighbor (on propensity score) matched analysis to match workers with disabilities to workers without disability. Results suggest that disability is independently associated with lower fairness of pay after controlling for confounding factors in the propensity score matched analysis; although results do suggest less than half a standard deviation difference, indicating small effects. Similar results were apparent in standard multivariable regression models and alternative propensity score analyses (stratification, covariate adjustment using the propensity score, and inverse probability of treatment weighting). Whilst neither multivariable regression nor propensity scores adjust for unmeasured confounding, and there remains the potential for other biases, similar results for the two methodological approaches to confounder adjustment provide some confidence of an independent association of disability with perceived unfairness of pay. Based on this, we suggest that the disparity in the perceived fairness of pay between people with and without disabilities may be explained by worse treatment of people with disabilities in the workplace.

Propensity Score Analysis: An Alternative Statistical Approach for HRD Researchers

Science.gov (United States)

Keiffer, Greggory L.; Lane, Forrest C.

2016-01-01

Purpose: This paper aims to introduce matching in propensity score analysis (PSA) as an alternative statistical approach for researchers looking to make causal inferences using intact groups. Design/methodology/approach: An illustrative example demonstrated the varying results of analysis of variance, analysis of covariance and PSA on a heuristic…

Propensity of bond exchange as a window into the mechanical properties of metallic glasses

Energy Technology Data Exchange (ETDEWEB)

Jiao, W.; Wang, X. L., E-mail: xlwang@um.cityu.edu.hk; Lan, S. [Department of Physics and Materials Science, City University of Hong Kong, Hong Kong (China); Pan, S. P. [College of Materials Science and Engineering, Taiyuan University of Technology, Taiyuan 030024 (China); Lu, Z. P. [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China)

2015-02-09

We investigated the mechanical properties of Zr-Cu-Al bulk metallic glasses, by compression experiment and molecular dynamics simulations. From the simulation, we found that the large, solvent atom, Zr, has high propensity of bond exchange compared to those of the smaller solute atoms. The difference in bond exchange is consistent with the observed disparity in mechanical behaviors: Zr-rich metallic glass exhibits low elastic modulus and large plastic strain. X-ray photoelectron spectroscopy measurements suggest that the increased propensity in bond exchange is related to the softening of Zr bonds with increasing Zr content.

Effect of Chronic Diseases on Work Productivity: A Propensity Score Analysis.

Science.gov (United States)

Fouad, Ahmed Mahmoud; Waheed, Amani; Gamal, Amira; Amer, Shaimaa Ahmed; Abdellah, Rasha Farouk; Shebl, Fatma Mohamed

2017-05-01

The aim of this study was to evaluate the effect of chronic disease(s) on work productivity. Using the Health & Work Performance Questionnaire, information was collected from 516 workers on chronic disease status and work productivity. Propensity-score matching was performed to identify matched-pairs of workers. In the propensity-score matched sample, workers with chronic diseases were more likely to have increased absenteeism and presenteeism rates, 6.34 and 2.36 times the rates if no chronic diseases, respectively. In addition, they had greater odds for getting negative critical work incidents and less odds for positive incidents than none or balanced status. Multimorbidity showed more significant increase in absenteeism and presenteeism rates, as well as increased odds for excess negative critical work incidents. Chronic disease(s) can significantly reduce work productivity by increasing absenteeism, presenteeism, and net negative critical incidents.

FPGA helix tracking algorithm for PANDA

Energy Technology Data Exchange (ETDEWEB)

Liang, Yutie; Galuska, Martin; Gessler, Thomas; Kuehn, Wolfgang; Lange, Jens Soeren; Muenchow, David [II. Physikalisches Institut, University of Giessen (Germany); Ye, Hua [Institute of High Energy Physics, CAS (China); Collaboration: PANDA-Collaboration

2016-07-01

The PANDA detector is a general-purpose detector for physics with high luminosity cooled antiproton beams, planed to operate at the FAIR facility in Darmstadt, Germany. The central detector includes a silicon Micro Vertex Detector (MVD) and a Straw Tube Tracker (STT). Without any hardware trigger, large amounts of raw data are streaming into the data acquisition system. The data reduction task is performed in the online system by reconstruction algorithms programmed on FPGAs (Field Programmable Gate Arrays) as first level and on a farm of GPUs or PCs as a second level. One important part in the system is the online track reconstruction. In this presentation, an online tracking algorithm for helix tracking reconstruction in the solenoidal field is shown. The VHDL-based algorithm is tested with different types of events, at different event rate. Furthermore, a study of T0 extraction from the tracking algorithm is performed. A concept of simultaneous tracking and T0 determination is presented.

Triple helix networks matching knowledge demand and supply in seven Dutch horticulture Greenport regions

NARCIS (Netherlands)

Geerling-Eiff, Florentien A.; Hoes, Anne-Charlotte; Dijkshoorn-Dekker, Marijke

2017-01-01

This paper investigates the triple helix (industry, knowledge workers and governments) cooperation on knowledge co-production and valorisation for innovation, which took place in seven horticultural regions in the Netherlands. It thus provides more empirical insight into the functioning of this form

Networks of entrepreneurs driving the Triple Helix: two cases of the Dutch energy system

NARCIS (Netherlands)

Werker, C.; Ubacht, J.; Ligtvoet, A.

2017-01-01

Entrepreneurs are often envisioned as small private start-up firms operating against all odds. Here, we investigate how in the context of the Triple Helix various entrepreneurs form communities and drive institutional and technological change. To theoretically shape a socialized view of

Influence of season, temperature, and photoperiod on growth of the land snail Helix aperta

NARCIS (Netherlands)

Benbellil-Tafoughalt, S.; Koene, J.M.

2015-01-01

Growth strategies are often plastic and influenced by environmental conditions. Terrestrial gastropods are particularly affected by seasonal and climatic variables, and growth rate and size at maturity are key traits in their life history. Therefore, we investigated juvenile growth of Helix aperta

A Case Study About Why It Can Be Difficult To Test Whether Propensity Score Analysis Works in Field Experiments

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Thomas D. Cook

2012-01-01

Full Text Available Peikes, Moreno and Orzol (2008 sensibly caution researchers that propensity score analysis may not lead to valid causal inference in field applications. But at the same time, they made the far stronger claim to have performed an ideal test of whether propensity score matching in quasi-experimental data is capable of approximating the results of a randomized experiment in their dataset, and that this ideal test showed that such matching could not do so. In this article we show that their study does not support that conclusion because it failed to meet a number of basic criteria for an ideal test. By implication, many other purported tests of the effectiveness of propensity score analysis probably also fail to meet these criteria, and are therefore questionable contributions to the literature on the effects of propensity score analysis.

MANGO PROPAGATION

OpenAIRE

ALBERTO CARLOS DE QUEIROZ PINTO; VICTOR GALÁN SAÚCO; SISIR KUMAR MITRA; FRANCISCO RICARDO FERREIRA

2018-01-01

ABSTRACT This Chapter has the objectives to search, through the review of the available literature, important informations on the evolution of mango propagation regarding theoretical and practical aspects from cellular base of sexual propagation, nursery structures and organizations, substrate compositions and uses, importance of rootstock and scion selections, also it will be described the preparation and transport of the grafts (stem and bud) as well as the main asexual propagation methods...

Probabilities, causes and propensities in physics

CERN Document Server

Suárez, Mauricio

2010-01-01

This volume defends a novel approach to the philosophy of physics: it is the first book devoted to a comparative study of probability, causality, and propensity, and their various interrelations, within the context of contemporary physics - particularly quantum and statistical physics. The philosophical debates and distinctions are firmly grounded upon examples from actual physics, thus exemplifying a robustly empiricist approach. The essays, by both prominent scholars in the field and promising young researchers, constitute a pioneer effort in bringing out the connections between probabilistic, causal and dispositional aspects of the quantum domain. This book will appeal to specialists in philosophy and foundations of physics, philosophy of science in general, metaphysics, ontology of physics theories, and philosophy of probability.

The feasibility of matching on a propensity score for acupuncture in a prospective cohort study of patients with chronic pain

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Eric S. Johnson

2017-03-01

Full Text Available Abstract Background Propensity scores are typically applied in retrospective cohort studies. We describe the feasibility of matching on a propensity score derived from a retrospective cohort and subsequently applied in a prospective cohort study of patients with chronic musculoskeletal pain before the start of acupuncture or usual care treatment and enrollment in a comparative effectiveness study that required patient reported pain outcomes. Methods We assembled a retrospective cohort study using data from 2010 to develop a propensity score for acupuncture versus usual care based on electronic healthcare record and administrative data (e.g., pharmacy from an integrated health plan, Kaiser Permanente Northwest. The propensity score’s probabilities allowed us to match acupuncture-referred and non-referred patients prospectively in 2013-14 after a routine outpatient visit for pain. Among the matched patients, we collected patient-reported pain before treatment and during follow-up to assess the comparative effectiveness of acupuncture. We assessed balance in patient characteristics with the post-matching c-statistic and standardized differences. Results Based on the propensity score and other characteristics (e.g., patient-reported pain, we were able to match all 173 acupuncture-referred patients to 350 non-referred (usual care patients. We observed a residual imbalance (based on the standardized differences for some characteristics that contributed to the score; for example, age, -0.283, and the Charlson comorbidity score, -0.264, had the largest standardized differences. The overall balance of the propensity score appeared more favorable according to the post-matching c-statistic, 0.503. Conclusion The propensity score matching was feasible statistically and logistically and allowed approximate balance on patient characteristics, some of which will require adjustment in the comparative effectiveness regression model. By transporting propensity

A Case Study About Why It Can Be Difficult To Test Whether Propensity Score Analysis Works in Field Experiments

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William R. Shadish

2013-02-01

Full Text Available Peikes, Moreno and Orzol (2008 sensibly caution researchers that propensity score analysis may not lead to valid causal inference in field applications. But at the same time, they made the far stronger claim to have performed an ideal test of whether propensity score matching in quasi-experimental data is capable of approximating the results of a randomized experiment in their dataset, and that this ideal test showed that such matching could not do so. In this article we show that their study does not support that conclusion because it failed to meet a number of basic criteria for an ideal test. By implication, many other purported tests of the effectiveness of propensity score analysis probably also fail to meet these criteria, and are therefore questionable contributions to the literature on the effects of propensity score analysis. DOI: 10.2458/azu_jmmss.v3i2.16475

The generalized model of polypeptide chain describing the helix-coil transition in biopolymers

International Nuclear Information System (INIS)

Mamasakhlisov, E.S.; Badasyan, A.V.; Tsarukyan, A.V.; Grigoryan, A.V.; Morozov, V.F.

2005-07-01

In this paper we summarize some results of our theoretical investigations of helix-coil transition both in single-strand (polypeptides) and two-strand (polynucleotides) macromolecules. The Hamiltonian of the Generalized Model of Polypeptide Chain (GMPC) is introduced to describe the system in which the conformations are correlated over some dimensional range Δ (it equals 3 for polypeptide, because one H-bond fixes three pairs of rotation, for double strand DNA it equals to one chain rigidity because of impossibility of loop formation on the scale less than Δ). The Hamiltonian does not contain any parameter designed especially for helix-coil transition and uses pure molecular microscopic parameters (the energy of hydrogen bond formation, reduced partition function of repeated unit, the number of repeated units fixed by one hydrogen bond, the energies of interaction between the repeated units and the solvent molecules). To calculate averages we evaluate the partition function using the transfer-matrix approach. The GMPC allowed to describe the influence of a number of factors, affecting the transition, basing on a unified microscopic approach. Thus we obtained, that solvents change transition temperature and interval in different ways, depending on type of solvent and on energy of solvent- macromolecule interaction; stacking on the background of H-bonding increases stability and decreases cooperativity of melting. For heterogeneous DNA we could analytically derive well known formulae for transition temperature and interval. In the framework of GMPC we calculate and show the difference of two order parameters of helix-coil transition - the helicity degree, and the average fraction of repeated units in helical conformation. Given article has the aim to review the results obtained during twenty years in the context of GMPC. (author)

PRESSURE - WATER and Other Data from ALPHA HELIX from 19981002 to 19990513 (NODC Accession 9900149)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature and salinity profiles were collected from CTD casts from the Alpha Helix from 02 October 1998 to 13 May 1999. These 6 CTD data sets are from two...

Propensity-score matching in the cardiovascular surgery literature from 2004 to 2006: a systematic review and suggestions for improvement.

Science.gov (United States)

Austin, Peter C

2007-11-01

I conducted a systematic review of the use of propensity score matching in the cardiovascular surgery literature. I examined the adequacy of reporting and whether appropriate statistical methods were used. I examined 60 articles published in the Annals of Thoracic Surgery, European Journal of Cardio-thoracic Surgery, Journal of Cardiovascular Surgery, and the Journal of Thoracic and Cardiovascular Surgery between January 1, 2004, and December 31, 2006. Thirty-one of the 60 studies did not provide adequate information on how the propensity score-matched pairs were formed. Eleven (18%) of studies did not report on whether matching on the propensity score balanced baseline characteristics between treated and untreated subjects in the matched sample. No studies used appropriate methods to compare baseline characteristics between treated and untreated subjects in the propensity score-matched sample. Eight (13%) of the 60 studies explicitly used statistical methods appropriate for the analysis of matched data when estimating the effect of treatment on the outcomes. Two studies used appropriate methods for some outcomes, but not for all outcomes. Thirty-nine (65%) studies explicitly used statistical methods that were inappropriate for matched-pairs data when estimating the effect of treatment on outcomes. Eleven studies did not report the statistical tests that were used to assess the statistical significance of the treatment effect. Analysis of propensity score-matched samples tended to be poor in the cardiovascular surgery literature. Most statistical analyses ignored the matched nature of the sample. I provide suggestions for improving the reporting and analysis of studies that use propensity score matching.

Alternative generation of well-aligned uniform lying helix texture in a cholesteric liquid crystal cell

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Chia-Hua Yu

2017-10-01

Full Text Available This work demonstrates a simple approach for obtaining a well-aligned uniform lying helix (ULH texture and a tri-bistable feature at ambient temperature in a typical 90°-twisted cell filled with a short-pitch cholesteric liquid crystal. This ULH texture is obtained at room temperature from initially field-induced helix-free homeotropic state by gradually decreasing the applied voltage. Depending on the way and rate of reducing the voltage, three stable states (i.e., Grandjean planar, focal conic, and ULH are generated and switching between any two of them is realized. Moreover, the electrical operation of the cell in the ULH state enables the tunability in phase retardation via the deformation of the ULH. The observations made in this work may be useful for applications such as tunable phase modulators and energy-efficient photonic devices.

Corruption as a Propensity: Personality and Motivational Determinants Among Nigerians.

Science.gov (United States)

Agbo, Aaron Adibe; Iwundu, Emmanuel Ifeanyi

2016-01-01

Psychologically oriented studies on corruption are lacking despite the fact that psychology has contributed enormously to the understanding of criminal behaviors over the past decades. Part of this problem relates to the lack of psychological tone in the definition and measurement of corruption. Taking a clue from the extensive psychological discourse on crime, which provides strong evidence for the existence of criminal tendencies, we conceptualized corruption here in terms of propensity. Possible personality and motivation determinants of this propensity were then explored. Results revealed that extraversion and conscientiousness positively and inversely predicted corruption tendencies, respectively. Results further showed that extrinsic motivation positively potentiates corruption tendencies, whereas intrinsic motivation was inversely related to corruption tendencies. Analysis of demographic variables revealed that males were more likely to be corrupt than their female counterparts. In general, findings here are consistent with the criminal behavior literature, which strongly suggests that the study of corruption is indeed amenable to psychological theories and methods and that individual differences variables constitute important explanatory variables in this regard.

BAROMETRIC PRESSURE and Other Data from ALPHA HELIX from 19971010 to 19980514 (NODC Accession 9800119)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Hydrophysical, hydrochemical, and other data were collected from CTD casts in the Gulf of Alaska from the R/V Alpha Helix from 10 October 1997 to 14 May 1998. Data...

Previous success and current body condition determine breeding propensity in Lesser Scaup: evidence for the individual heterogeneity hypothesis

Science.gov (United States)

Warren, Jeffrey M.; Cutting, Kyle A.; Takekawa, John Y.; De La Cruz, Susan E. W.; Williams, Tony D.; Koons, David N.

2014-01-01

The decision to breed influences an individual's current and future reproduction, and the proportion of individuals that breed is an important determinant of population dynamics. Age, experience, individual quality, and environmental conditions have all been demonstrated to influence breeding propensity. To elucidate which of these factors exerts the greatest influence on breeding propensity in a temperate waterfowl, we studied female Lesser Scaup (Aythya affinis) breeding in southwestern Montana. Females were captured during the breeding seasons of 2007–2009, and breeding status was determined on the basis of (1) presence of an egg in the oviduct or (2) blood plasma vitellogenin (VTG) levels. Presence on the study site in the previous year, a proxy for adult female success, was determined with stable isotope signatures of a primary feather collected at capture. Overall, 57% of females had evidence of breeding at the time of capture; this increased to 86% for females captured on or after peak nest initiation. Capture date and size-adjusted body condition positively influenced breeding propensity, with a declining body-condition threshold through the breeding season. We did not detect an influence of age on breeding propensity. Drought conditions negatively affected breeding propensity, reducing the proportion of breeding females to 0.85 (SE = 0.05) from 0.94 (SE = 0.03) during normal-water years. A female that was present in the previous breeding season was 5% more likely to breed than a female that was not present then. The positive correlation between age and experience makes it difficult to differentiate the roles of age, experience, and individual quality in reproductive success in vertebrates. Our results indicate that individual quality, as expressed by previous success and current body condition, may be among the most important determinants of breeding propensity in female Lesser Scaup, providing further support for the individual heterogeneity hypothesis.

The relation of risk-taking propensity, professional preferences and the approach to the selection of future profession

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Rosić-Marković Olga

2014-01-01

Full Text Available Research has shown that risk-taking individuals choose professions that involve a high level of uncertainty, change or flexibility. The aim of this research was to study the relation between risk-taking propensity and professional preferences, as well as between different indicators of the approach to the selection of future profession and risk-taking propensity. The study was conducted on the sample of 583 students attending the final grade of secondary school. For the assessment of risk-taking propensity we used a modified version of the Evaluation of Risk scale (EVAR, while professional interests were investigated by the Test of Professional Orientation (TPO. In addition, we analysed certain indicators of the approach to the selection of profession that were interesting in the context of career counselling, namely: duration of the selection of profession, the number of professional preferences and readiness to make a professional choice. The results have shown that risk-taking propensity is significantly correlated with professional preferences where risk is an important job feature (such as professions in the field of security as well as with the professions where risk is an important part of success (such as sports. It has also been shown that risk-taking individuals assess themselves as more ready to make decisions on their own professional choice. Based on the obtained results, it can be concluded that risk-taking propensity is an important characteristic that should be taken into account when studying professional preferences and the approach to the selection of future profession in adolescents.

Evaluation of a Pilot Surveillance System: Health and Environment Linked for Information Exchange in Atlanta (HELIX-Atlanta)

Science.gov (United States)

Meyer, P.; Shire, J.; Qualters, Judy; Daley, Randolph; Fiero, Leslie Todorov; Autry, Andy; Avchen, Rachel; Stock, Allison; Correa, Adolofo; Siffel, Csaba;

Propensity score estimation to address calendar time-specific channeling in comparative effectiveness research of second generation antipsychotics.

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Stacie B Dusetzina

Full Text Available Channeling occurs when a medication and its potential comparators are selectively prescribed based on differences in underlying patient characteristics. Drug safety advisories can provide new information regarding the relative safety or effectiveness of a drug product which might increase selective prescribing. In particular, when reported adverse effects vary among drugs within a therapeutic class, clinicians may channel patients toward or away from a drug based on the patient's underlying risk for an adverse outcome. If channeling is not identified and appropriately managed it might lead to confounding in observational comparative effectiveness studies.To demonstrate channeling among new users of second generation antipsychotics following a Food and Drug Administration safety advisory and to evaluate the impact of channeling on cardiovascular risk estimates over time.Florida Medicaid data from 2001-2006.Retrospective cohort of adults initiating second generation antipsychotics. We used propensity scores to match olanzapine initiators with other second generation antipsychotic initiators. To evaluate channeling away from olanzapine following an FDA safety advisory, we estimated calendar time-specific propensity scores. We compare the performance of these calendar time-specific propensity scores with conventionally-estimated propensity scores on estimates of cardiovascular risk.Increased channeling away from olanzapine was evident for some, but not all, cardiovascular risk factors and corresponded with the timing of the FDA advisory. Covariate balance was optimized within period and across all periods when using the calendar time-specific propensity score. Hazard ratio estimates for cardiovascular outcomes did not differ across models (Conventional PS: 0.97, 95%CI: 0.81-3.18 versus calendar time-specific PS: 0.93, 95%CI: 0.77-3.04.Changes in channeling over time was evident for several covariates but had limited impact on cardiovascular risk

Propensity rules for orientation by atom impact. Pt. 2

International Nuclear Information System (INIS)

Nielsen, S.E.; Andersen, N.

1986-01-01

This paper contains a theoretical analysis of orientation and alignment created in direct, collision-induced transitions among atomic states with arbitrary angular momentum. Using the natural coordinate frame, general propensity rules are derived in the velocity region of maximum transition probability and their range of validity is investigated. The predictions are tested and illustrated by nine-state calculation for Li(n=2,3) transitions in Li-He collisions. (orig.)

Propensity-score matching in economic analyses: comparison with regression models, instrumental variables, residual inclusion, differences-in-differences, and decomposition methods.

Science.gov (United States)

Crown, William H

2014-02-01

This paper examines the use of propensity score matching in economic analyses of observational data. Several excellent papers have previously reviewed practical aspects of propensity score estimation and other aspects of the propensity score literature. The purpose of this paper is to compare the conceptual foundation of propensity score models with alternative estimators of treatment effects. References are provided to empirical comparisons among methods that have appeared in the literature. These comparisons are available for a subset of the methods considered in this paper. However, in some cases, no pairwise comparisons of particular methods are yet available, and there are no examples of comparisons across all of the methods surveyed here. Irrespective of the availability of empirical comparisons, the goal of this paper is to provide some intuition about the relative merits of alternative estimators in health economic evaluations where nonlinearity, sample size, availability of pre/post data, heterogeneity, and missing variables can have important implications for choice of methodology. Also considered is the potential combination of propensity score matching with alternative methods such as differences-in-differences and decomposition methods that have not yet appeared in the empirical literature.

Modulating immunogenic properties of HIV-1 gp41 membrane-proximal external region by destabilizing six-helix bundle structure

Energy Technology Data Exchange (ETDEWEB)

Banerjee, Saikat; Shi, Heliang; Habte, Habtom H.; Qin, Yali; Cho, Michael W., E-mail: mcho@iastate.edu

2016-03-15

The C-terminal alpha-helix of gp41 membrane-proximal external region (MPER; {sup 671}NWFDITNWLWYIK{sup 683}) encompassing 4E10/10E8 epitopes is an attractive target for HIV-1 vaccine development. We previously reported that gp41-HR1-54Q, a trimeric protein comprised of the MPER in the context of a stable six-helix bundle (6HB), induced strong immune responses against the helix, but antibodies were directed primarily against the non-neutralizing face of the helix. To better target 4E10/10E8 epitopes, we generated four putative fusion intermediates by introducing double point mutations or deletions in the heptad repeat region 1 (HR1) that destabilize 6HB in varying degrees. One variant, HR1-∆10-54K, elicited antibodies in rabbits that targeted W672, I675 and L679, which are critical for 4E10/10E8 recognition. Overall, the results demonstrated that altering structural parameters of 6HB can influence immunogenic properties of the MPER and antibody targeting. Further exploration of this strategy could allow development of immunogens that could lead to induction of 4E10/10E8-like antibodies. - Highlights: • Four gp41 MPER-based immunogens that resemble fusion intermediates were generated. • C-terminal region of MPER that contains 4E10/10E8 epitopes was highly immunogenic. • Altering 6HB structure can influence immunogenic properties of the MPER. • Induced antibodies targeted multiple residues critical for 4E10/10E8 binding. • Development of immunogens based on fusion intermediates is a promising strategy.

Enhancing the innovative capacity of small firms through triple helix interactions : challenges and opportunities

NARCIS (Netherlands)

Ranga, Liana Marina; Miedema, Joost; Jorna, Rene

2008-01-01

This paper presents the results of a recent exploratory study aiming to enhance the innovative capacity of small firms in the Northern Netherlands, a region lagging behind the rest of the country in terms of economic growth and innovative capacity. The triple helix perspective is adopted to examine

Microbiological and chemical evaluation of Helix spp. snails from local and non-EU markets, utilised as food in Sardinia

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Arianna Corda

2014-04-01

Full Text Available With this study, 28 pools of snails of the genus Helix, respectively Helix aspersa (n=24 and Helix vermiculata (n=4 were analysed. They were taken from snail farming and stores. The snails were from Sardinia, other regions of Italy, and from abroad. All the samples were examined as pool looking for these microbiological target: Salmonella spp., Listeria monocytogenes, Escherichia coli O157, Clostridium perfringens, Norovirus and Hepatitis A Virus (HAV. In the same pools, the concentration of cadmium and lead by inductively coupled plasma mass spectrometry was also determined. The levels of these heavy metals were quite high, especially for cadmium. Two samples were positive for Salmonella spp., while no sample was positive for Escherichia coli O157, HAV and Norovirus. Two samples were positive for Clostridium perfringens and 8 for Listeria monocytogenes. The microrganisms related to Listeria monocytogenes were identified using biochemical techniques, then serotyped and gene sequenced by multiple loci sequence typing technique. Furthermore, antimicrobial restistence was tested on the same samples.

The N-terminal amphipathic helix of the topological specificity factor MinE is associated with shaping membrane curvature.

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Yu-Ling Shih

Full Text Available Pole-to-pole oscillations of the Min proteins in Escherichia coli are required for the proper placement of the division septum. Direct interaction of MinE with the cell membrane is critical for the dynamic behavior of the Min system. In vitro, this MinE-membrane interaction led to membrane deformation; however, the underlying mechanism remained unclear. Here we report that MinE-induced membrane deformation involves the formation of an amphipathic helix of MinE(2-9, which, together with the adjacent basic residues, function as membrane anchors. Biochemical evidence suggested that the membrane association induces formation of the helix, with the helical face, consisting of A2, L3, and F6, inserted into the membrane. Insertion of this helix into the cell membrane can influence local membrane curvature and lead to drastic changes in membrane topology. Accordingly, MinE showed characteristic features of protein-induced membrane tubulation and lipid clustering in in vitro reconstituted systems. In conclusion, MinE shares common protein signatures with a group of membrane trafficking proteins in eukaryotic cells. These MinE signatures appear to affect membrane curvature.

High accuracy prediction of beta-turns and their types using propensities and multiple alignments.

Science.gov (United States)

Fuchs, Patrick F J; Alix, Alain J P

2005-06-01

We have developed a method that predicts both the presence and the type of beta-turns, using a straightforward approach based on propensities and multiple alignments. The propensities were calculated classically, but the way to use them for prediction was completely new: starting from a tetrapeptide sequence on which one wants to evaluate the presence of a beta-turn, the propensity for a given residue is modified by taking into account all the residues present in the multiple alignment at this position. The evaluation of a score is then done by weighting these propensities by the use of Position-specific score matrices generated by PSI-BLAST. The introduction of secondary structure information predicted by PSIPRED or SSPRO2 as well as taking into account the flanking residues around the tetrapeptide improved the accuracy greatly. This latter evaluated on a database of 426 reference proteins (previously used on other studies) by a sevenfold crossvalidation gave very good results with a Matthews Correlation Coefficient (MCC) of 0.42 and an overall prediction accuracy of 74.8%; this places our method among the best ones. A jackknife test was also done, which gave results within the same range. This shows that it is possible to reach neural networks accuracy with considerably less computional cost and complexity. Furthermore, propensities remain excellent descriptors of amino acid tendencies to belong to beta-turns, which can be useful for peptide or protein engineering and design. For beta-turn type prediction, we reached the best accuracy ever published in terms of MCC (except for the irregular type IV) in the range of 0.25-0.30 for types I, II, and I' and 0.13-0.15 for types VIII, II', and IV. To our knowledge, our method is the only one available on the Web that predicts types I' and II'. The accuracy evaluated on two larger databases of 547 and 823 proteins was not improved significantly. All of this was implemented into a Web server called COUDES (French acronym

Marital Dissolution and Major Depression in Midlife: A Propensity Score Analysis.

Science.gov (United States)

Sbarra, David A; Emery, Robert E; Beam, Christopher R; Ocker, Bailey L

2014-05-01

Marital dissolution is commonly assumed to cause increased depression among adults, but causality can be questioned based on directionality and third variable concerns. The present study improves upon past research by using a propensity score matching algorithm to identify a sub-sample of continuously married participants equivalent in divorce risk to participants who actually experienced separation/divorce between two waves of the nationally representative study, Midlife Development in the United States (MIDUS). After correcting for participants' propensity to separate/divorce, increased rates of depression at the second assessment were observed only among participants who were (a) depressed at the initial assessment, and (b) experienced a separation/divorce. Participants who were not depressed at the initial assessment but who experienced a separation/divorce were not at increased risk for a later major depressive disorder (MDE). Thus, both social selection and social causation contribute to the increased risk for a MDE found among separated/divorced adults.

Conservation of Three-Dimensional Helix-Loop-Helix Structure through the Vertebrate Lineage Reopens the Cold Case of Gonadotropin-Releasing Hormone-Associated Peptide.

Science.gov (United States)

Pérez Sirkin, Daniela I; Lafont, Anne-Gaëlle; Kamech, Nédia; Somoza, Gustavo M; Vissio, Paula G; Dufour, Sylvie

2017-01-01

GnRH-associated peptide (GAP) is the C-terminal portion of the gonadotropin-releasing hormone (GnRH) preprohormone. Although it was reported in mammals that GAP may act as a prolactin-inhibiting factor and can be co-secreted with GnRH into the hypophyseal portal blood, GAP has been practically out of the research circuit for about 20 years. Comparative studies highlighted the low conservation of GAP primary amino acid sequences among vertebrates, contributing to consider that this peptide only participates in the folding or carrying process of GnRH. Considering that the three-dimensional (3D) structure of a protein may define its function, the aim of this study was to evaluate if GAP sequences and 3D structures are conserved in the vertebrate lineage. GAP sequences from various vertebrates were retrieved from databases. Analysis of primary amino acid sequence identity and similarity, molecular phylogeny, and prediction of 3D structures were performed. Amino acid sequence comparison and phylogeny analyses confirmed the large variation of GAP sequences throughout vertebrate radiation. In contrast, prediction of the 3D structure revealed a striking conservation of the 3D structure of GAP1 (GAP associated with the hypophysiotropic type 1 GnRH), despite low amino acid sequence conservation. This GAP1 peptide presented a typical helix-loop-helix (HLH) structure in all the vertebrate species analyzed. This HLH structure could also be predicted for GAP2 in some but not all vertebrate species and in none of the GAP3 analyzed. These results allowed us to infer that selective pressures have maintained GAP1 HLH structure throughout the vertebrate lineage. The conservation of the HLH motif, known to confer biological activity to various proteins, suggests that GAP1 peptides may exert some hypophysiotropic biological functions across vertebrate radiation.

Conservation of Three-Dimensional Helix-Loop-Helix Structure through the Vertebrate Lineage Reopens the Cold Case of Gonadotropin-Releasing Hormone-Associated Peptide

Directory of Open Access Journals (Sweden)

Daniela I. Pérez Sirkin

2017-08-01

Full Text Available GnRH-associated peptide (GAP is the C-terminal portion of the gonadotropin-releasing hormone (GnRH preprohormone. Although it was reported in mammals that GAP may act as a prolactin-inhibiting factor and can be co-secreted with GnRH into the hypophyseal portal blood, GAP has been practically out of the research circuit for about 20 years. Comparative studies highlighted the low conservation of GAP primary amino acid sequences among vertebrates, contributing to consider that this peptide only participates in the folding or carrying process of GnRH. Considering that the three-dimensional (3D structure of a protein may define its function, the aim of this study was to evaluate if GAP sequences and 3D structures are conserved in the vertebrate lineage. GAP sequences from various vertebrates were retrieved from databases. Analysis of primary amino acid sequence identity and similarity, molecular phylogeny, and prediction of 3D structures were performed. Amino acid sequence comparison and phylogeny analyses confirmed the large variation of GAP sequences throughout vertebrate radiation. In contrast, prediction of the 3D structure revealed a striking conservation of the 3D structure of GAP1 (GAP associated with the hypophysiotropic type 1 GnRH, despite low amino acid sequence conservation. This GAP1 peptide presented a typical helix-loop-helix (HLH structure in all the vertebrate species analyzed. This HLH structure could also be predicted for GAP2 in some but not all vertebrate species and in none of the GAP3 analyzed. These results allowed us to infer that selective pressures have maintained GAP1 HLH structure throughout the vertebrate lineage. The conservation of the HLH motif, known to confer biological activity to various proteins, suggests that GAP1 peptides may exert some hypophysiotropic biological functions across vertebrate radiation.

The decision-making matrix of propensity to outsourcing hospital services in Bandar Abbas, Iran.

Science.gov (United States)

Hayati, Ramin; Setoodehzadeh, Fateme; Heydarvand, Sanaz; Khammarnia, Mohammad; Ravangard, Ramin; Sadeghi, Ahmad; Sobhani, Ghasem

2015-12-01

To determine the level of managers' propensity for outsourcing the services in hospitals using decision-making matrix. The applied, cross-sectional study was conducted at three hospitals affiliated to Bandar Abbas University of Medical Sciences, Iran, in 2013, and comprised managers and employees of four service units: radiology, laboratory, nursing, and nutrition services. Data was collected using two questionnaires and face-to-face interviews. Data was analysed using SPSS 16 and by using decision-making matrix. Of the 122 subjects in the study, 12(9.8%) were managers and 110(90.2%) were other employees. The highest and lowest propensities for outsourcing were related to nutrition (66.6%) and nursing services one (8.33%). The decision-making matrix showed low outsourcing of the nursing, radiology, and laboratory services based on the services' features. However, there were difference between the results obtained from laboratory service decision-making matrix and the propensity for laboratory service outsourcing. The difference between the results obtained from the matrix and managers' viewpoint can be due to the lack of managers' sufficient attention to the features of hospital services when making decisions on outsourcing them.

Novel Plasma Reactor with Rotary Helix Electrode Used in Coupling of CH4 at Atmospheric Pressure

International Nuclear Information System (INIS)

Wang Dawang; Ma Tengcai

2006-01-01

At the ambient temperature and pressure a glow discharge plasma was used as a new approach for the coupling of methane with the newly-developed rotary multidentate helix electrode. In the presence of hydrogen, the effects of the input peak voltages and gas flow rates on methane conversion, C 2 single pass yield and selectivity were investigated, and then the results were compared with those from the three-disc multidentate electrode. This demonstrated, on an experimental scale, that the rotary multidentate helix electrode was better than the multidentate three-disc electrode as there was little accumulation of coke, and the C 2 yield per pass was 69.85% and C 2 selectivity over 99.14% with 70.46% methane conversion at an input peak voltage of 2300 V and 60 ml/min gas flow rate

Trace metallic elements in Helix aspersa terrestrial snails of a semiarid ecosystem; Elementos metalicos traza en caracoles terrestres Helix aspersa de un ecosistema semiarido

Energy Technology Data Exchange (ETDEWEB)

Gaso P, M.I.; Segovia, N.; Zarazua, G.; Montes, F. [Instituto Nacional de Investigaciones Nucleares, A.P. 18-1027, 11801 Mexico D.F. (Mexico); Morton, O.; Armienta, M.A.; Hernandez, E. [IGF-UNAM, Ciudad Universitaria, 04510 Mexico D.F. (Mexico)

2001-07-01

The concentration of some major elements and traces in soil samples and of Helix aspersa eatable terrestrial snails were analysed at the Radioactive Wastes Storage Center (CADER) and in other reference sites. The methodology includes the use of an atomic absorption spectrophotometer, an X-ray fluorescence equipment and an Icp-mass spectroscope. The concentrations of some toxic elements (Ba, Cd, Cr, Ni, Pb and V) in the soft tissue of the snails were greater than the toxic levels reported in the literature for such trace elements. The snails compared with another wild eatable foods present transfer coefficients soil-snail high relatively. (Author)

Single Motherhood, Alcohol Dependence, and Smoking During Pregnancy: A Propensity Score Analysis.

Science.gov (United States)

Waldron, Mary; Bucholz, Kathleen K; Lian, Min; Lessov-Schlaggar, Christina N; Miller, Ruth Huang; Lynskey, Michael T; Knopik, Valerie S; Madden, Pamela A F; Heath, Andrew C

2017-09-01

Few studies linking single motherhood and maternal smoking during pregnancy consider correlated risk from problem substance use beyond history of smoking and concurrent use of alcohol. In the present study, we used propensity score methods to examine whether the risk of smoking during pregnancy associated with single motherhood is the result of potential confounders, including alcohol dependence. Data were drawn from mothers participating in a birth cohort study of their female like-sex twin offspring (n = 257 African ancestry; n = 1,711 European or other ancestry). We conducted standard logistic regression models predicting smoking during pregnancy from single motherhood at twins' birth, followed by propensity score analyses comparing single-mother and two-parent families stratified by predicted probability of single motherhood. In standard models, single motherhood predicted increased risk of smoking during pregnancy in European ancestry but not African ancestry families. In propensity score analyses, rates of smoking during pregnancy were elevated in single-mother relative to two-parent European ancestry families across much of the spectrum a priori risk of single motherhood. Among African ancestry families, within-strata comparisons of smoking during pregnancy by single-mother status were nonsignificant. These findings highlight single motherhood as a unique risk factor for smoking during pregnancy in European ancestry mothers, over and above alcohol dependence. Additional research is needed to identify risks, beyond single motherhood, associated with smoking during pregnancy in African ancestry mothers.

Aggregation propensity of critical regions of the protein Tau

Science.gov (United States)

Muthee, Micaiah; Ahmed, Azka; Larini, Luca

The Alzheimer's disease is an irreversible, progressive brain disorder that slowly destroys memory and thinking skills, which eventually leads to the ability to not able to carry out the simplest tasks. The Alzheimer's disease is characterized by the formation of protein aggregates both within and outside of the brain's cells, the neurons. Within the neurons, the aggregation of the protein tau leads to the destruction of the microtubules in the axon of the neuron. Tau belongs to a group of proteins referred to as Microtubule-Associated Proteins. It is extremely flexible and is classified as an intrinsically unstructured protein due to its low propensity to form secondary structure. Tau promotes tubulin assembly into microtubules thereby stabilizing the cytoskeleton of the axon of the neurons. The microtubule binding region of tau consists of 4 pseudo-repeats. In this study, we will focus on the aggregation propensity of two fragments. In this study we will focus on the PHF43 fragment that contains the third pseudo-repeat and has been shown experimentally to aggregate readily. Another fragment that contains the second pseudo-repeat will be considered as well. Mutations in this region are associated with various form of dementia and for this reason we will consider the mutant P301L.

Open Innovation, Triple Helix and Regional Innovation Systems: Exploring CATAPULT Centres in the UK

Science.gov (United States)

Kerry, Christopher; Danson, Michael

2016-01-01

Through the lens of UK CATAPULT Centres this conceptual paper presents an examination of the links between open innovation, the Triple Helix model and regional innovation systems. Highlighting the importance of boundary-spanning intermediaries, the combined role of these concepts is explored in detail. A conceptual model is then proposed which…

Direct excitation in heavy atom collisions: A propensity rule for charge cloud orientation

International Nuclear Information System (INIS)

Andersen, N.; Aarhus Univ.; Nielsen, S.E.; Royal Danish School of Pharmacy, Copenhagen)

1985-01-01

The Massey Criterion prescribes maximum electronic excitation of atoms in heavy particle collisions for collision velocities v where Δε a/ℎv ≅ π. Here Δε is the energy defect and a is the effective interaction length. Experiments with planar symmetry have revealed a preferred way of rotation of the excited charge cloud in this velocity region. We demonstrate by analysis of a simple, yet realistic model why excitation favors states with a specific orientation. A general propensity rule is derived and its validity evaluated for a specific case, the Na-He system. Implications for future experiments are pointed out. In particular, the propensity rule predicts very different collisions behaviors of oppositely oriented atoms, as prepared e.g. by circular polarized laser light. (orig.)

Health and Environment Linked for Information Exchange (HELIX)-Atlanta: A CDC-NASA Joint Environmental Public Health Tracking Collaborative Project

Science.gov (United States)

Al-Hamdan, Mohammad; Luvall, Jeff; Crosson, Bill; Estes, Maury; Limaye, Ashutosh; Quattrochi, Dale; Rickman, Doug

2008-01-01

HELIX-Atlanta was developed to support current and future state and local EPHT programs to implement data linking demonstration projects which could be part of the CDC EPHT Network. HELIX-Atlanta is a pilot linking project in Atlanta for CDC to learn about the challenges the states will encounter. NASA/MSFC and the CDC are partners in linking environmental and health data to enhance public health surveillance. The use of NASA technology creates value added geospatial products from existing environmental data sources to facilitate public health linkages. Proving the feasibility of the approach is the main objective

MANGO PROPAGATION

Directory of Open Access Journals (Sweden)

ALBERTO CARLOS DE QUEIROZ PINTO

2018-03-01

Full Text Available ABSTRACT This Chapter has the objectives to search, through the review of the available literature, important informations on the evolution of mango propagation regarding theoretical and practical aspects from cellular base of sexual propagation, nursery structures and organizations, substrate compositions and uses, importance of rootstock and scion selections, also it will be described the preparation and transport of the grafts (stem and bud as well as the main asexual propagation methods their uses and practices. Finally, pattern and quality of graft mangos and their commercialization aspects will be discussed in this Chapter.

Private Venture Capital’s Investment on University Spin-Offs: A Case Study of Tsinghua University Based on Triple Helix Model

DEFF Research Database (Denmark)

Gao, Yuchen; Hu, Yimei; Wang, Jingyi

2015-01-01

and transition economies where governments are transforming their roles. Thus the main purpose of this study is to investigate how private venture capitals’ investment willingness on university spin-offs are influenced by universities and governments under the Chinese context based on the triple helix model....... Through an in-depth case study on the interactions of triple helix actors of Tsinghua University’s spin-offs, it is found that government and university developing an environment of marketization exert positive influences on the investment willingness of private venture capitals. Whilst financial direct...

Identification of helix capping and {beta}-turn motifs from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2012-03-15

We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and {sup 13}C{sup {beta}} chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of {beta}-turns: I, II, I Prime , II Prime and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and {beta}-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7-0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

Identification of helix capping and β-turn motifs from NMR chemical shifts

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2012-01-01

We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13 C β chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I′, II′ and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7–0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

Understanding Foster Youth Outcomes: Is Propensity Scoring Better than Traditional Methods?

Science.gov (United States)

Berzin, Stephanie Cosner

2010-01-01

Objectives: This study seeks to examine the relationship between foster care and outcomes using multiple comparison methods to account for factors that put foster youth at risk independent of care. Methods: Using the National Longitudinal Survey of Youth 1997, matching, propensity scoring, and comparisons to the general population are used to…

Estimating the Effectiveness of Health-Risk Communications with Propensity-Score Matching: Application to Arsenic Groundwater Contamination in Four US Locations

Directory of Open Access Journals (Sweden)

Andrew J. Leidner

2014-01-01

Full Text Available This paper provides a demonstration of propensity-score matching estimation methods to evaluate the effectiveness of health-risk communication efforts. This study develops a two-stage regression model to investigate household and respondent characteristics as they contribute to aversion behavior to reduce exposure to arsenic-contaminated groundwater. The aversion activity under study is a household-level point-of-use filtration device. Since the acquisition of arsenic contamination information and the engagement in an aversion activity may be codetermined, a two-stage propensity-score model is developed. In the first stage, the propensity for households to acquire arsenic contamination information is estimated. Then, the propensity scores are used to weight observations in a probit regression on the decision to avert the arsenic-related health risk. Of four potential sources of information, utility, media, friend, or others, information received from a friend appears to be the source of information most associated with aversion behavior. Other statistically significant covariates in the household’s decision to avert contamination include reported household income, the presence of children in household, and region-level indicator variables. These findings are primarily illustrative and demonstrate the usefulness of propensity-score methods to estimate health-risk communication effectiveness. They may also be suggestive of areas for future research.

Estimating the Effectiveness of Health-Risk Communications with Propensity-Score Matching: Application to Arsenic Groundwater Contamination in Four US Locations

Science.gov (United States)

Leidner, Andrew J.

2014-01-01

This paper provides a demonstration of propensity-score matching estimation methods to evaluate the effectiveness of health-risk communication efforts. This study develops a two-stage regression model to investigate household and respondent characteristics as they contribute to aversion behavior to reduce exposure to arsenic-contaminated groundwater. The aversion activity under study is a household-level point-of-use filtration device. Since the acquisition of arsenic contamination information and the engagement in an aversion activity may be codetermined, a two-stage propensity-score model is developed. In the first stage, the propensity for households to acquire arsenic contamination information is estimated. Then, the propensity scores are used to weight observations in a probit regression on the decision to avert the arsenic-related health risk. Of four potential sources of information, utility, media, friend, or others, information received from a friend appears to be the source of information most associated with aversion behavior. Other statistically significant covariates in the household's decision to avert contamination include reported household income, the presence of children in household, and region-level indicator variables. These findings are primarily illustrative and demonstrate the usefulness of propensity-score methods to estimate health-risk communication effectiveness. They may also be suggestive of areas for future research. PMID:25349622

Quantifying individual variation in the propensity to attribute incentive salience to reward cues.

Science.gov (United States)

Meyer, Paul J; Lovic, Vedran; Saunders, Benjamin T; Yager, Lindsay M; Flagel, Shelly B; Morrow, Jonathan D; Robinson, Terry E

2012-01-01

If reward-associated cues acquire the properties of incentive stimuli they can come to powerfully control behavior, and potentially promote maladaptive behavior. Pavlovian incentive stimuli are defined as stimuli that have three fundamental properties: they are attractive, they are themselves desired, and they can spur instrumental actions. We have found, however, that there is considerable individual variation in the extent to which animals attribute Pavlovian incentive motivational properties ("incentive salience") to reward cues. The purpose of this paper was to develop criteria for identifying and classifying individuals based on their propensity to attribute incentive salience to reward cues. To do this, we conducted a meta-analysis of a large sample of rats (N = 1,878) subjected to a classic Pavlovian conditioning procedure. We then used the propensity of animals to approach a cue predictive of reward (one index of the extent to which the cue was attributed with incentive salience), to characterize two behavioral phenotypes in this population: animals that approached the cue ("sign-trackers") vs. others that approached the location of reward delivery ("goal-trackers"). This variation in Pavlovian approach behavior predicted other behavioral indices of the propensity to attribute incentive salience to reward cues. Thus, the procedures reported here should be useful for making comparisons across studies and for assessing individual variation in incentive salience attribution in small samples of the population, or even for classifying single animals.

Can Cell to Cell Thermal Runaway Propagation be Prevented in a Li-ion Battery Module?

Science.gov (United States)

Jeevarajan, Judith; Lopez, Carlos; Orieukwu, Josephat

2014-01-01

Increasing cell spacing decreased adjacent cell damage center dotElectrically connected adjacent cells drained more than physically adjacent cells center dotRadiant barrier prevents propagation when fully installed between BP cells center dotBP cells vent rapidly and expel contents at 100% SOC -Slower vent with flame/smoke at 50% -Thermal runaway event typically occurs at 160 degC center dotLG cells vent but do not expel contents -Thermal runaway event typically occurs at 200 degC center dotSKC LFP modules did not propagate; fuses on negative terminal of cell may provide a benefit in reducing cell to cell damage propagation. New requirement in NASA-Battery Safety Requirements document: JSC 20793 Rev C 5.1.5.1 Requirements - Thermal Runaway Propagation a. For battery designs greater than a 80-Wh energy employing high specific energy cells (greater than 80 watt-hours/kg, for example, lithium-ion chemistries) with catastrophic failure modes, the battery shall be evaluated to ascertain the severity of a worst-case single-cell thermal runaway event and the propensity of the design to demonstrate cell-to-cell propagation in the intended application and environment. NASA has traditionally addressed the threat of thermal runaway incidents in its battery deployments through comprehensive prevention protocols. This prevention-centered approach has included extensive screening for manufacturing defects, as well as robust battery management controls that prevent abuse-induced runaway even in the face of multiple system failures. This focused strategy has made the likelihood of occurrence of such an event highly improbable. b. The evaluation shall include all necessary analysis and test to quantify the severity (consequence) of the event in the intended application and environment as well as to identify design modifications to the battery or the system that could appreciably reduce that severity. In addition to prevention protocols, programs developing battery designs with

Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture

OpenAIRE

Lacroix-Labonté, Julie; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

2011-01-01

Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure–function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS riboz...

Expression of the helix-loop-helix protein inhibitor of DNA binding-1 (ID-1) is activated by all-trans retinoic acid in normal human keratinocytes

International Nuclear Information System (INIS)

Villano, C.M.; White, L.A.

2006-01-01

The ID (inhibitor of differentiation or DNA binding) helix-loop-helix proteins are important mediators of cellular differentiation and proliferation in a variety of cell types through regulation of gene expression. Overexpression of the ID proteins in normal human keratinocytes results in extension of culture lifespan, indicating that these proteins are important for epidermal differentiation. Our hypothesis is that the ID proteins are targets of the retinoic acid signaling pathway in keratinocytes. Retinoids, vitamin A analogues, are powerful regulators of cell growth and differentiation and are widely used in the prevention and treatment of a variety of cancers in humans. Furthermore, retinoic acid is necessary for the maintenance of epithelial differentiation and demonstrates an inhibitory action on skin carcinogenesis. We examined the effect of all-trans retinoic acid on expression of ID-1, -2, -3, and -4 in normal human keratinocytes and found that exposure of these cells to all-trans retinoic acid causes an increase in both ID-1 and ID-3 gene expression. Furthermore, our data show that this increase is mediated by increased transcription involving several cis-acting elements in the distal portion of the promoter, including a CREB-binding site, an Egr1 element, and an YY1 site. These data demonstrate that the ID proteins are direct targets of the retinoic acid signaling pathway. Given the importance of the ID proteins to epidermal differentiation, these results suggest that IDs may be mediating some of the effects of all-trans retinoic acid in normal human keratinocytes

Part two: Error propagation

International Nuclear Information System (INIS)

Picard, R.R.

1989-01-01

Topics covered in this chapter include a discussion of exact results as related to nuclear materials management and accounting in nuclear facilities; propagation of error for a single measured value; propagation of error for several measured values; error propagation for materials balances; and an application of error propagation to an example of uranium hexafluoride conversion process

Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins.

Science.gov (United States)

de Sousa, Miguel M; Munteanu, Cristian R; Pazos, Alejandro; Fonseca, Nuno A; Camacho, Rui; Magalhães, A L

2011-02-21

A statistical approach has been applied to analyse primary structure patterns at inner positions of α-helices in proteins. A systematic survey was carried out in a recent sample of non-redundant proteins selected from the Protein Data Bank, which were used to analyse α-helix structures for amino acid pairing patterns. Only residues more than three positions apart from both termini of the α-helix were considered as inner. Amino acid pairings i, i+k (k=1, 2, 3, 4, 5), were analysed and the corresponding 20×20 matrices of relative global propensities were constructed. An analysis of (i, i+4, i+8) and (i, i+3, i+4) triplet patterns was also performed. These analysis yielded information on a series of amino acid patterns (pairings and triplets) showing either high or low preference for α-helical motifs and suggested a novel approach to protein alphabet reduction. In addition, it has been shown that the individual amino acid propensities are not enough to define the statistical distribution of these patterns. Global pair propensities also depend on the type of pattern, its composition and orientation in the protein sequence. The data presented should prove useful to obtain and refine useful predictive rules which can further the development and fine-tuning of protein structure prediction algorithms and tools. Copyright © 2010 Elsevier Ltd. All rights reserved.

Propensity Score Estimation with Data Mining Techniques: Alternatives to Logistic Regression

Science.gov (United States)

Keller, Bryan S. B.; Kim, Jee-Seon; Steiner, Peter M.

2013-01-01

Propensity score analysis (PSA) is a methodological technique which may correct for selection bias in a quasi-experiment by modeling the selection process using observed covariates. Because logistic regression is well understood by researchers in a variety of fields and easy to implement in a number of popular software packages, it has…

Propensity for intimate partner abuse and workplace productivity: why employers should care.

Science.gov (United States)

Rothman, Emily F; Corso, Phaedra S

2008-09-01

It has been demonstrated that intimate partner violence (IPV) victimization is costly to employers, but little is known about the economic consequences associated with employing perpetrators. This study investigated propensity for partner abuse as a predictor of missed work time and on-the-job decreases in productivity among a small sample of male employees at a state agency (N=61). Results suggest that greater propensity for abusiveness is positively associated with missing work and experiencing worse productivity on the job, controlling for level of education, income, marital status, age, and part-time versus full-time employment status. Additional research could clarify whether IPV perpetration is a predictor of decreased productivity among larger samples and a wider variety of workplace settings. Employers and IPV advocates should consider responding to potential IPV perpetrators through the workplace in addition to developing victim-oriented policies and prevention initiatives.

Constitutive Overexpression of the Basic Helix-Loop-Helix Nex1/MATH-2 Transcription Factor Promotes Neuronal Differentiation of PC12 Cells and Neurite Regeneration

Science.gov (United States)

Uittenbogaard, Martine; Chiaramello, Anne

2009-01-01

Elucidation of the intricate transcriptional pathways leading to neural differentiation and the establishment of neuronal identity is critical to the understanding and design of therapeutic approaches. Among the important players, the basic helix-loop-helix (bHLH) transcription factors have been found to be pivotal regulators of neurogenesis. In this study, we investigate the role of the bHLH differentiation factor Nex1/MATH-2 in conjunction with the nerve growth factor (NGF) signaling pathway using the rat phenochromocytoma PC12 cell line. We report that the expression of Nex1 protein is induced after 5 hr of NGF treatment and reaches maximal levels at 24 hr, when very few PC12 cells have begun extending neurites and ceased cell division. Furthermore, our study demonstrates that Nex1 has the ability to trigger neuronal differentiation of PC12 cells in the absence of neurotrophic factor. We show that Nex1 plays an important role in neurite outgrowth and has the capacity to regenerate neurite outgrowth in the absence of NGF. These results are corroborated by the fact that Nex1 targets a repertoire of distinct types of genes associated with neuronal differentiation, such as GAP-43, βIII-tubulin, and NeuroD. In addition, our findings show that Nex1 up-regulates the expression of the mitotic inhibitor p21WAF1, thus linking neuronal differentiation to cell cycle withdrawal. Finally, our studies show that overexpression of a Nex1 mutant has the ability to block the execution of NGF-induced differentiation program, suggesting that Nex1 may be an important effector of the NGF signaling pathway. PMID:11782967

Net (ERP/SAP2) one of the Ras-inducible TCFs, has a novel inhibitory domain with resemblance to the helix-loop-helix motif.

Science.gov (United States)

Maira, S M; Wurtz, J M; Wasylyk, B

1996-11-01

The three ternary complex factors (TCFs), Net (ERP/ SAP-2), ELK-1 and SAP-1, are highly related ets oncogene family members that participate in the response of the cell to Ras and growth signals. Understanding the different roles of these factors will provide insights into how the signals result in coordinate regulation of the cell. We show that Net inhibits transcription under basal conditions, in which SAP-1a is inactive and ELK-1 stimulates. Repression is mediated by the NID, the Net Inhibitory Domain of about 50 amino acids, which autoregulates the Net protein and also inhibits when it is isolated in a heterologous fusion protein. Net is particularly sensitive to Ras activation. Ras activates Net through the C-domain, which is conserved between the three TCFs, and the NID is an efficient inhibitor of Ras activation. The NID, as well as more C-terminal sequences, inhibit DNA binding. Net is more refractory to DNA binding than the other TCFs, possibly due to the presence of multiple inhibitory elements. The NID may adopt a helix-loop-helix (HLH) structure, as evidenced by homology to other HLH motifs, structure predictions, model building and mutagenesis of critical residues. The sequence resemblance with myogenic factors suggested that Net may form complexes with the same partners. Indeed, we found that Net can interact in vivo with the basic HLH factor, E47. We propose that Net is regulated at the level of its latent DNA-binding activity by protein interactions and/or phosphorylation. Net may form complexes with HLH proteins as well as SRF on specific promotor sequences. The identification of the novel inhibitory domain provides a new inroad into exploring the different roles of the ternary complex factors in growth control and transformation.

Nuclear receptor ligand-binding domains: reduction of helix H12 dynamics to favour crystallization

Energy Technology Data Exchange (ETDEWEB)

Nahoum, Virginie; Lipski, Alexandra; Quillard, Fabien; Guichou, Jean-François [INSERM, U554, 34090 Montpellier (France); Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale (CBS), 34090 Montpellier (France); Boublik, Yvan [CNRS, UMR5237, Centre de Recherche de Biochimie Macromoléculaire (CRBM), 34293 Montpellier (France); Pérez, Efrèn [Universidade de Vigo, Departamento de Quimica Organica, Facultad de Química, 36310 Vigo (Spain); Germain, Pierre [Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), BP 10142, 67404 Illkirch CEDEX (France); Lera, Angel R. de [Universidade de Vigo, Departamento de Quimica Organica, Facultad de Química, 36310 Vigo (Spain); Bourguet, William, E-mail: bourguet@cbs.cnrs.fr [INSERM, U554, 34090 Montpellier (France); Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale (CBS), 34090 Montpellier (France)

2008-07-01

Attempts have been made to crystallize the ligand-binding domain of the human retinoid X receptor in complex with a variety of newly synthesized ligands. An inverse correlation was observed between the ‘crystallizability’ and the structural dynamics of the various receptor–ligand complexes. Crystallization trials of the human retinoid X receptor α ligand-binding domain (RXRα LBD) in complex with various ligands have been carried out. Using fluorescence anisotropy, it has been found that when compared with agonists these small-molecule effectors enhance the dynamics of the RXRα LBD C-terminal helix H12. In some cases, the mobility of this helix could be dramatically reduced by the addition of a 13-residue co-activator fragment (CoA). In keeping with these observations, crystals have been obtained of the corresponding ternary RXRα LBD–ligand–CoA complexes. In contrast, attempts to crystallize complexes with a highly mobile H12 remained unsuccessful. These experimental observations substantiate the previously recognized role of co-regulator fragments in facilitating the crystallization of nuclear receptor LBDs.

Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions.

Science.gov (United States)

Watts, Joel C; Giles, Kurt; Saltzberg, Daniel J; Dugger, Brittany N; Patel, Smita; Oehler, Abby; Bhardwaj, Sumita; Sali, Andrej; Prusiner, Stanley B

2016-11-01

The biochemical and neuropathological properties of bovine spongiform encephalopathy (BSE) and variant Creutzfeldt-Jakob disease (vCJD) prions are faithfully maintained upon transmission to guinea pigs. However, primary and secondary transmissions of BSE and vCJD in guinea pigs result in long incubation periods of ∼450 and ∼350 days, respectively. To determine if the incubation periods of BSE and vCJD prions could be shortened, we generated transgenic (Tg) mice expressing guinea pig prion protein (GPPrP). Inoculation of Tg(GPPrP) mice with BSE and vCJD prions resulted in mean incubation periods of 210 and 199 days, respectively, which shortened to 137 and 122 days upon serial transmission. In contrast, three different isolates of sporadic CJD prions failed to transmit disease to Tg(GPPrP) mice. Many of the strain-specified biochemical and neuropathological properties of BSE and vCJD prions, including the presence of type 2 protease-resistant PrP Sc , were preserved upon propagation in Tg(GPPrP) mice. Structural modeling revealed that two residues near the N-terminal region of α-helix 1 in GPPrP might mediate its susceptibility to BSE and vCJD prions. Our results demonstrate that expression of GPPrP in Tg mice supports the rapid propagation of BSE and vCJD prions and suggest that Tg(GPPrP) mice may serve as a useful paradigm for bioassaying these prion isolates. Variant Creutzfeldt-Jakob disease (vCJD) and bovine spongiform encephalopathy (BSE) prions are two of the prion strains most relevant to human health. However, propagating these strains in mice expressing human or bovine prion protein has been difficult because of prolonged incubation periods or inefficient transmission. Here, we show that transgenic mice expressing guinea pig prion protein are fully susceptible to vCJD and BSE prions but not to sporadic CJD prions. Our results suggest that the guinea pig prion protein is a better, more rapid substrate than either bovine or human prion protein for

Worsening calcification propensity precedes all-cause and cardiovascular mortality in haemodialyzed patients.

Science.gov (United States)

Lorenz, Georg; Steubl, Dominik; Kemmner, Stephan; Pasch, Andreas; Koch-Sembdner, Wilhelm; Pham, Dang; Haller, Bernhard; Bachmann, Quirin; Mayer, Christopher C; Wassertheurer, Siegfried; Angermann, Susanne; Lech, Maciej; Moog, Philipp; Bauer, Axel; Heemann, Uwe; Schmaderer, Christoph

2017-10-17

A novel in-vitro test (T 50 -test) assesses ex-vivo serum calcification propensity which predicts mortality in HD patients. The association of longitudinal changes of T 50 with all-cause and cardiovascular mortality has not been investigated. We assessed T 50 in paired sera collected at baseline and at 24 months in 188 prevalent European HD patients from the ISAR cohort, most of whom were Caucasians. Patients were followed for another 19 [interquartile range: 11-37] months. Serum T 50 exhibited a significant decline between baseline and 24 months (246 ± 64 to 190 ± 68 minutes; p < 0.001). With serum Δ-phosphate showing the strongest independent association with declining T 50 (r = -0.39; p < 0.001) in multivariable linear regression. The rate of decline of T 50 over 24 months was a significant predictor of all-cause (HR = 1.51 per 1SD decline, 95% CI: 1.04 to 2.2; p = 0.03) and cardiovascular mortality (HR = 2.15; 95% CI: 1.15 to 3.97; p = 0.02) in Kaplan Meier and multivariable Cox-regression analysis, while cross-sectional T 50 at inclusion and 24 months were not. Worsening serum calcification propensity was an independent predictor of mortality in this small cohort of prevalent HD patients. Prospective larger scaled studies are needed to assess the value of calcification propensity as a longitudinal parameter for risk stratification and monitoring of therapeutic interventions.

Fabrication experiments for large helix heat exchangers

International Nuclear Information System (INIS)

Burgsmueller, P.

1978-01-01

The helical tube has gained increasing attention as a heat transfer element for various kinds of heat exchangers over the last decade. Regardless of reactor type and heat transport medium, nuclear steam generators of the helix type are now in operation, installlation, fabrication or in the project phase. As a rule, projects are based on the extrapolation of existing technologies. In the particlular case of steam generators for HTGR power stations, however, existing experience is with steam generators of up to about 2 m diameter whereas several projects involve units more than twice as large. For this reason it was felt that a fabrication experiment was necessary in order to verify the feasibility of modern steam generator designs. A test rig was erected in the SULZER steam generator shops at Mantes, France, and skilled personnel and conventional production tools were employed in conducting experiments relating to the coiling, handling and threading of large helices. (Auth.)

Chain length dependence of the helix orientation in Langmuir-Blodgett monolayers of alpha-helical diblock copolypeptides

NARCIS (Netherlands)

Nguyen, Le-Thu T.; Ardana, Aditya; Vorenkamp, Eltjo J.; ten Brinke, Gerrit; Schouten, Arend J.

2010-01-01

The effect of chain length on the helix orientation of alpha-helical diblock copolypeptides in Langmuir and Langmuir-Blodgett monolayers is reported for the first time. Amphiphilic diblock copolypeptides (PLGA-b-PMLGSLGs) of poly(alpha-L-glutamic acid) (PLGA) and

"helix Nebula - the Science Cloud", a European Science Driven Cross-Domain Initiative Implemented in via AN Active Ppp Set-Up

Science.gov (United States)

Lengert, W.; Mondon, E.; Bégin, M. E.; Ferrer, M.; Vallois, F.; DelaMar, J.

2015-12-01

Helix Nebula, a European science cross-domain initiative building on an active PPP, is aiming to implement the concept of an open science commons[1] while using a cloud hybrid model[2] as the proposed implementation solution. This approach allows leveraging and merging of complementary data intensive Earth Science disciplines (e.g. instrumentation[3] and modeling), without introducing significant changes in the contributors' operational set-up. Considering the seamless integration with life-science (e.g. EMBL), scientific exploitation of meteorological, climate, and Earth Observation data and models open an enormous potential for new big data science. The work of Helix Nebula has shown that is it feasible to interoperate publicly funded infrastructures, such as EGI [5] and GEANT [6], with commercial cloud services. Such hybrid systems are in the interest of the existing users of publicly funded infrastructures and funding agencies because they will provide "freedom and choice" over the type of computing resources to be consumed and the manner in which they can be obtained. But to offer such freedom and choice across a spectrum of suppliers, various issues such as intellectual property, legal responsibility, service quality agreements and related issues need to be addressed. Finding solutions to these issues is one of the goals of the Helix Nebula initiative. [1] http://www.egi.eu/news-and-media/publications/OpenScienceCommons_v3.pdf [2] http://www.helix-nebula.eu/events/towards-the-european-open-science-cloud [3] e.g. https://sentinel.esa.int/web/sentinel/sentinel-data-access [5] http://www.egi.eu/ [6] http://www.geant.net/

Temporal scaling in information propagation

Science.gov (United States)

Huang, Junming; Li, Chao; Wang, Wen-Qiang; Shen, Hua-Wei; Li, Guojie; Cheng, Xue-Qi

2014-06-01

For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers.

Probing the mechanistic role of the long α-helix in subunit L of respiratory Complex I from Escherichia coli by site-directed mutagenesis

Science.gov (United States)

Belevich, Galina; Knuuti, Juho; Verkhovsky, Michael I; Wikström, Mårten; Verkhovskaya, Marina

2011-01-01

The C-terminus of the NuoL subunit of Complex I includes a long amphipathic α-helix positioned parallel to the membrane, which has been considered to function as a piston in the proton pumping machinery. Here, we have introduced three types of mutations into the nuoL gene to test the piston-like function. First, NuoL was truncated at its C- and N-termini, which resulted in low production of a fragile Complex I with negligible activity. Second, we mutated three partially conserved residues of the amphipathic α-helix: Asp and Lys residues and a Pro were substituted for acidic, basic or neutral residues. All these variants exhibited almost a wild-type phenotype. Third, several substitutions and insertions were made to reduce rigidity of the amphipathic α-helix, and/or to change its geometry. Most insertions/substitutions resulted in a normal growth phenotype, albeit often with reduced stability of Complex I. In contrast, insertion of six to seven amino acids at a site of the long α-helix between NuoL and M resulted in substantial loss of proton pumping efficiency. The implications of these results for the proton pumping mechanism of Complex I are discussed. PMID:22060017

Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization.

Science.gov (United States)

Vymětal, Jiří; Bednárová, Lucie; Vondrášek, Jiří

2016-02-18

Fluorinated alcohols such as 2,2,2-trifluoroethanol (TFE) are among the most frequently used cosolvents in experiment studies of peptides. They have significant effects on secondary structure and a particularly strong promotion of α-helix is induced by TFE. In this study we validated recently proposed force field parameters for TFE in molecular dynamics simulations with two model peptides-alanine-rich AK-17 and antimicrobial peptide halictine-1 (HAL-1). In the case of HAL-1, we characterized the effect of TFE on this peptide experimentally by ECD spectroscopy. Our TFE model in question reproduced the helix-promoting effect of TFE and provided insight into the mechanisms of TFE action on peptides. Our simulations confirmed the preferential interaction of TFE molecules with α-helices, although the TFE molecules accumulate in the vicinity of the peptides in various conformations. Moreover, we observed a significant effect of TFE on the thermodynamics of the helix-coil transition and a change in local conformational preferences in the unfolded (coil) state induced by TFE. In addition, our simulation-based analysis suggests that different mechanisms participate in helix stabilization in both model peptides in water and TFE solution. Our results thus support the picture of complex TFE action on peptides that is further diversified by the identity and intrinsic properties of the peptide.

Cable-type flexible lithium ion battery based on hollow multi-helix electrodes

Energy Technology Data Exchange (ETDEWEB)

Kwon, Yo Han; Woo, Sang-Wook; Jung, Hye-Ran; Yu, Hyung Kyun; Kim, Kitae; Oh, Byung Hun; Ahn, Soonho; Kim, Je Young [Battery R and D, LG Chem, Ltd., 104-1 Moonji-dong, Yuseong-gu, Daejeon (Korea, Republic of); Lee, Sang-Young [School of Chemical Engineering, Kangwon National University, Chuncheon, Kangwondo (Korea, Republic of); Song, Seung-Wan [Graduate School of Green Energy Technology, Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon (Korea, Republic of); Cho, Jaephil [School of Energy Engineering and Converging Research Center for Innovative Battery Technologies, Ulsan National Institute of Science and Technology (UNIST), Ulsan (Korea, Republic of); Shin, Heon-Cheol [School of Materials Science and Engineering, Pusan National University, Busan (Korea, Republic of)

2012-10-02

The mechanical flexibility of a cable-type battery reaches levels far beyond what is possible with conventional designs. The hollow-spiral (helical) multi-helix anode architecture is critical to the robustness under mechanical stress and facilitates electrolyte wetting of the battery components. This design enables the battery to reliably power an LED screen or an MP3 player even under severe mechanical twisting and bending. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.

Directory of Open Access Journals (Sweden)

Jonathan C Fuller

Full Text Available The design of novel α-helix mimetic inhibitors of protein-protein interactions is of interest to pharmaceuticals and chemical genetics researchers as these inhibitors provide a chemical scaffold presenting side chains in the same geometry as an α-helix. This conformational arrangement allows the design of high affinity inhibitors mimicking known peptide sequences binding specific protein substrates. We show that GAFF and AutoDock potentials do not properly capture the conformational preferences of α-helix mimetics based on arylamide oligomers and identify alternate parameters matching solution NMR data and suitable for molecular dynamics simulation of arylamide compounds. Results from both docking and molecular dynamics simulations are consistent with the arylamides binding in the p53 peptide binding pocket. Simulations of arylamides in the p53 binding pocket of hDM2 are consistent with binding, exhibiting similar structural dynamics in the pocket as simulations of known hDM2 binders Nutlin-2 and a benzodiazepinedione compound. Arylamide conformations converge towards the same region of the binding pocket on the 20 ns time scale, and most, though not all dihedrals in the binding pocket are well sampled on this timescale. We show that there are two putative classes of binding modes for arylamide compounds supported equally by the modeling evidence. In the first, the arylamide compound lies parallel to the observed p53 helix. In the second class, not previously identified or proposed, the arylamide compound lies anti-parallel to the p53 helix.

CAXIAS DO SUL TECHNOLOGY INCUBATOR: TECHNOLOGICAL INNOVATION THROUGH THE TRIPLE HELIX

Directory of Open Access Journals (Sweden)

Priscila Bresolin Tisott

2014-09-01

on investment in the form of registered patents, attracting new students and recognition as a technological, entrepreneurial and innovative university. The perceived benefits for the industrial sector are training and development for businesses and entrepreneurs, while the municipal government perceives the reduced number of businesses failing and the financial returns, in the form of taxes, as benefits. The findings show that the Triple Helix concept developed by Etzkowitz (2009 plays a cooperative and participatory role in the Technology Incubator, even though it could be applied to more segments of society.

Phason thermal transport of three-helix state in insulating chiral magnets

Science.gov (United States)

Tatara, Gen

2018-06-01

Thermal dynamics of the three-helix state in a chiral magnet is studied based on a phason representation. Although phason representation is convenient for intuitive description, it is not straightforwardly compatible with microscopic linear response calculation of transport phenomena, because it is a (semi)macroscopic picture obtained by a coarse graining. By separating the slow phason mode and fast magnon mode, we show that phason thermal dynamics is driven by thermal magnon flow via the spin-transfer effect. The magnon and phason velocities are calculated by use of thermal vector potential formalism.

When Triple Helix Unravels: A Multi-Case Analysis of Failures in Industry-University Cooperative Research Centres

Science.gov (United States)

Gray, Denis; Sundstrom, Eric; Tornatzky, Louis G.; McGowen, Lindsey

2011-01-01

Cooperative research centres (CRCs) increasingly foster Triple Helix (industry-university-government) collaboration and represent significant vehicles for cooperation across sectors, the promotion of knowledge and technology transfer and ultimately the acceleration of innovation. A growing social science literature on CRCs focuses on their…

Low breeding propensity and wide-ranging movements by marbled murrelets in Washington

Science.gov (United States)

Teresa J. Lorenz; Martin G. Raphael; Thomas D. Bloxton; Patrick G. Cunningham

2016-01-01

The marbled murrelet (Brachyramphus marmoratus) is a threatened seabird that forages in nearshore marine waters but nests inland, commonly in older coniferous forests. Information on ranging behavior and breeding propensity can be useful for informing management, especially when comparisons can be made between declining or threatened populations...

Mathematical modeling and design parameters of crushing machines with variable-pitch helix of the screw

Directory of Open Access Journals (Sweden)

Pelenko V. V.

2017-11-01

Full Text Available From the point of view of the effectiveness of the top cutting unit, the helix angle in the end portion of the screw is the most important and characteristic parameter, as it determines the pressure of the meat material in the zone of interaction of a knife and grate. The importance of solving the problem of mathematical modeling of geometry is due to the need to address the problem of minimizing the reverse flow of the food material when injecting into the cutting zone, as the specified effect of "locking" significantly reduces the performance of the transfer process, increases energy consumption of the equipment and entails the deterioration of the quality of the raw materials output. The problem of determining the length of the helix variable pitch for screw chopper food materials has been formulated and solved by methods of differential geometry. The task of correct description of the law of changing the angle of helix inclination along its length has been defined in this case as a key to provide the required dependence of this angle tangent on the angle of the radius-vector of the circle. It has been taken into account that the reduction in the pitch of the screw in the direction of the product delivery should occur at a decreasing rate. The parametric equation of the helix has been written in the form of three functional dependencies of the corresponding cylindrical coordinates. Based on the wide range analysis and significant number of models of tops from different manufacturers the boundaries of possible changes in the angles of inclination of the helical line of the first and last turns of the screw have been identified. The auger screw length is determined mathematically in the form of an analytical relationship and both as a function of the variable angle of its rise, and as a function of the rotation angle of the radius-vector of the circle generatrix, which makes it possible to expand the design possibilities of this node. Along

Information quality, homophily, and risk propensity: Consumer responses to online hotel reviews

Directory of Open Access Journals (Sweden)

Sony Kusumasondjaja

2015-08-01

Full Text Available Searching through online review sites becomes an alternative for consumers to obtain product information. The efficiency and effectiveness in finding quality information on the online review sites contributes to the popularity of online review sites among consumers at the moment. There are some previous studies discussing consumer trust on hotels being reviewed on online review sites, but the roles of information quality, homophily, and consumer risk propensity as antecedents of trust and online purchase intention are still questionable. The purpose of this study is to investigate how information quality, homophily, and consumer risk propensity affect consumer trust on hotels being reviewed on online review sites and on intention to make a reservation. A survey involving 430 young travelers from 16 countries was conducted in popular tourist destination. Results confirm that information quality influences consumers’ trust on hotel being reviewed and intention to make reservation. Moreover, consumer online trust is also found to affect intention to make reservation.

Quantifying individual variation in the propensity to attribute incentive salience to reward cues.

Directory of Open Access Journals (Sweden)

Paul J Meyer

Full Text Available If reward-associated cues acquire the properties of incentive stimuli they can come to powerfully control behavior, and potentially promote maladaptive behavior. Pavlovian incentive stimuli are defined as stimuli that have three fundamental properties: they are attractive, they are themselves desired, and they can spur instrumental actions. We have found, however, that there is considerable individual variation in the extent to which animals attribute Pavlovian incentive motivational properties ("incentive salience" to reward cues. The purpose of this paper was to develop criteria for identifying and classifying individuals based on their propensity to attribute incentive salience to reward cues. To do this, we conducted a meta-analysis of a large sample of rats (N = 1,878 subjected to a classic Pavlovian conditioning procedure. We then used the propensity of animals to approach a cue predictive of reward (one index of the extent to which the cue was attributed with incentive salience, to characterize two behavioral phenotypes in this population: animals that approached the cue ("sign-trackers" vs. others that approached the location of reward delivery ("goal-trackers". This variation in Pavlovian approach behavior predicted other behavioral indices of the propensity to attribute incentive salience to reward cues. Thus, the procedures reported here should be useful for making comparisons across studies and for assessing individual variation in incentive salience attribution in small samples of the population, or even for classifying single animals.

Fluctuations in the DNA double helix

Science.gov (United States)

Peyrard, M.; López, S. C.; Angelov, D.

2007-08-01

DNA is not the static entity suggested by the famous double helix structure. It shows large fluctuational openings, in which the bases, which contain the genetic code, are temporarily open. Therefore it is an interesting system to study the effect of nonlinearity on the physical properties of a system. A simple model for DNA, at a mesoscopic scale, can be investigated by computer simulation, in the same spirit as the original work of Fermi, Pasta and Ulam. These calculations raise fundamental questions in statistical physics because they show a temporary breaking of equipartition of energy, regions with large amplitude fluctuations being able to coexist with regions where the fluctuations are very small, even when the model is studied in the canonical ensemble. This phenomenon can be related to nonlinear excitations in the model. The ability of the model to describe the actual properties of DNA is discussed by comparing theoretical and experimental results for the probability that base pairs open an a given temperature in specific DNA sequences. These studies give us indications on the proper description of the effect of the sequence in the mesoscopic model.

Effect of secondary structure on the potential of mean force for poly-L-lysine in the alpha-Helix and beta-sheet conformations

Energy Technology Data Exchange (ETDEWEB)

Grigsby, J.J.; Blanch, H.W.; Prausnitz, J.M.

2001-10-30

Because poly-L-lysine (PLL) can exist in the {alpha}-helix or {beta}-sheet conformation depending on solution preparation and solution conditions, PLL is a suitable candidate to probe the dependence of protein interactions on secondary structure. The osmotic second virial coefficient and weight-average molecular weight are reported from low-angle laser-light scattering measurements for PLL as a function of NaCl concentration, pH, and {alpha}-helix or {beta}-sheet content. Interactions between PLL molecules become more attractive as salt concentration increases due to screening of PLL charge by salt ions and at low salt concentration become more attractive as pH increases due to decreased net charge on PLL. The experimental results show that interactions are stronger for the {beta}-sheet conformation than for the {alpha}-helix conformation. A spherically-symmetric model for the potential of mean force is used to account for specific interactions not described by DLVO theory and to show how differences in secondary structure affect PLL interactions.

Antibacterial Activity of Silver Nanoparticles Synthesized by Using Extracts of Hedera helix

Directory of Open Access Journals (Sweden)

Ahmadreza Abbasifar

2017-01-01

Full Text Available Background Silver nanoparticles (AgNPs are one of the most widely applicable particles whose application is increasing in Nano world daily. Silver nanoparticles have expressed significant advances owing to wide range of applications in the field of bio-medical, sensors, antimicrobials, catalysts, electronics, optical fibers, agricultural, bio-labeling and the other areas. Green synthesis is the safe and easiest method of producing silver nanoparticles. Because of the production of the silver ions, silver nanoparticles are found to have the antibacterial activity. Objectives The aim of this study was to investigate antibacterial activity of silver nanoparticles synthesized by using extracts of Hedera helix against Bacillus subtilis and Klebsiella pneumoniae. Methods In this experimental study AgNPs were prepared by the reaction of 1mM silver nitrate and extracts of Hedera helix. Antibacterial activity of AgNPs was assessed by using disc diffusion method against Bacillus subtilis and Klebsiella pneumoniae. The AgNPs were characterized by UV-visible (vis spectrophotometer, particle size analyzer by dynamic light scattering (DLS method, transmission electron microscopy (TEM. Results AgNPs obtained showed significantly higher antimicrobial activities against B. subtilis and K. pneumonia in comparison to both AgNO3 and raw plant extracts. Conclusions Biological methods are a good competent for the chemical procedures, which are environment friendly and convenient.

The use of different concentrations of ginger root oil to improve the mating propensity of the Medfly sterile males

International Nuclear Information System (INIS)

Fadhl, Salma; Msaad Guerfali, M.; Kahlani, A.; Hamden, Haithem; Chevrier, C.

2008-01-01

The sterile insect technique in an efficient technique used to control fruit flies such as Medfly Ceratitis Capitata (Wiedemann) (Diptera : Tephritidae). Unfortunately, this technique involves mass breeding of huge quantities of target insects in the factory and sterilizing the males by exposing them to low doses of radiation. this procedure reduces the mating propensity of the sterile males which are the active agent of the technique. It was reported that the exposition of the sterile males to ginger root oil (Zingiber official Roscoe (Zingiberaceae)) improves the mating propensity of the sterile males in comparison with the non exposed ones. In this study, we exposed irradiated males at two different doses (100 and 110 Gy) to different concentrations of the ginger oil (20μl; 50μl; 80μl; 0.25 ml;0.5 ml; 1 ml) the third day after emergence. This study shows that the irradiated males at 100 Gy are more competitive in comparison with those irradiated at 110 Gy with a mating propensity percentage respectively of 60 and 35 %. regarding the exposition dose of the ginger oil, 1 ml gave the best mating propensity ( 42%) in comparison with the other concentrations

Association between long work hours and depressive state: a pilot study of propensity score matched Japanese white-collar workers.

Science.gov (United States)

Uchida, Mitsuo; Morita, Hiroshi

2018-06-01

Although long work hours have been associated with various physical health problems, studies of their association with mental health have yielded inconsistent results, due to differences in study settings, study outcome and/or unmeasured background factors. In this study, we used a propensity score method to evaluate the association between work hours and depressive state. A total of 467 Japanese white-collar workers were surveyed and divided into long and regular work hour groups according to overtime work records. Propensity score matching was performed based on 32 individual background and workplace factors, yielding 74 pairs of propensity-matched subjects. CES-D score, an indicator of depressive state, did not differ significantly among the two groups (p=0.203). However, work motivation, work control, social support and emotional stability correlated with CES-D score. These findings suggest that work control and social support factors are more associated with depressive state than control of work hours. These results also suggest that it is possible to use propensity score matching to evaluate the association between work hours and mental health in occupational study settings. Further studies, in larger populations, are required to determine the association between work hours and mental health parameters.

The Bacillus subtilis Conjugative Plasmid pLS20 Encodes Two Ribbon-Helix-Helix Type Auxiliary Relaxosome Proteins That Are Essential for Conjugation

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Andrés Miguel-Arribas

2017-11-01

Full Text Available Bacterial conjugation is the process by which a conjugative element (CE is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer (oriT, where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host. The conjugative plasmid pLS20 replicates in the Gram-positive Firmicute bacterium Bacillus subtilis. We have recently identified the relaxase gene and the oriT of pLS20, which are separated by a region of almost 1 kb. Here we show that this region contains two auxiliary genes that we name aux1LS20 and aux2LS20, and which we show are essential for conjugation. Both Aux1LS20 and Aux2LS20 are predicted to contain a Ribbon-Helix-Helix DNA binding motif near their N-terminus. Analyses of the purified proteins show that Aux1LS20 and Aux2LS20 form tetramers and hexamers in solution, respectively, and that they both bind preferentially to oriTLS20, although with different characteristics and specificities. In silico analyses revealed that genes encoding homologs of Aux1LS20 and/or Aux2LS20 are located upstream of almost 400 relaxase genes of the RelLS20 family (MOBL of relaxases. Thus, Aux1LS20 and Aux2LS20 of pLS20 constitute the founding member of the first two families of auxiliary proteins described for CEs of Gram-positive origin.

The Bacillus subtilis Conjugative Plasmid pLS20 Encodes Two Ribbon-Helix-Helix Type Auxiliary Relaxosome Proteins That Are Essential for Conjugation.

Science.gov (United States)

Miguel-Arribas, Andrés; Hao, Jian-An; Luque-Ortega, Juan R; Ramachandran, Gayetri; Val-Calvo, Jorge; Gago-Córdoba, César; González-Álvarez, Daniel; Abia, David; Alfonso, Carlos; Wu, Ling J; Meijer, Wilfried J J

2017-01-01

Bacterial conjugation is the process by which a conjugative element (CE) is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer ( oriT ), where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host. The conjugative plasmid pLS20 replicates in the Gram-positive Firmicute bacterium Bacillus subtilis . We have recently identified the relaxase gene and the oriT of pLS20, which are separated by a region of almost 1 kb. Here we show that this region contains two auxiliary genes that we name aux1 LS20 and aux2 LS20 , and which we show are essential for conjugation. Both Aux1 LS20 and Aux2 LS20 are predicted to contain a Ribbon-Helix-Helix DNA binding motif near their N-terminus. Analyses of the purified proteins show that Aux1 LS20 and Aux2 LS20 form tetramers and hexamers in solution, respectively, and that they both bind preferentially to oriT LS20 , although with different characteristics and specificities. In silico analyses revealed that genes encoding homologs of Aux1 LS20 and/or Aux2 LS20 are located upstream of almost 400 relaxase genes of the Rel LS20 family (MOB L ) of relaxases. Thus, Aux1 LS20 and Aux2 LS20 of pLS20 constitute the founding member of the first two families of auxiliary proteins described for CEs of Gram-positive origin.

Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

DEFF Research Database (Denmark)

Lou, Chenguang; Martos-Maldonado, Manuel C.; Madsen, Charlotte Stahl

2016-01-01

Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain ...

MicroRNA-212 post-transcriptionally regulates oocyte-specific basic-helix-loop-helix transcription factor, factor in the germline alpha (FIGLA, during bovine early embryogenesis.

Directory of Open Access Journals (Sweden)

Swamy K Tripurani

Full Text Available Factor in the germline alpha (FIGLA is an oocyte-specific basic helix-loop-helix transcription factor essential for primordial follicle formation and expression of many genes required for folliculogenesis, fertilization and early embryonic survival. Here we report the characterization of bovine FIGLA gene and its regulation during early embryogenesis. Bovine FIGLA mRNA expression is restricted to gonads and is detected in fetal ovaries harvested as early as 90 days of gestation. FIGLA mRNA and protein are abundant in germinal vesicle and metaphase II stage oocytes, as well as in embryos from pronuclear to eight-cell stage but barely detectable at morula and blastocyst stages, suggesting that FIGLA might be a maternal effect gene. Recent studies in zebrafish and mice have highlighted the importance of non-coding small RNAs (microRNAs as key regulatory molecules targeting maternal mRNAs for degradation during embryonic development. We hypothesized that FIGLA, as a maternal transcript, is regulated by microRNAs during early embryogenesis. Computational predictions identified a potential microRNA recognition element (MRE for miR-212 in the 3' UTR of the bovine FIGLA mRNA. Bovine miR-212 is expressed in oocytes and tends to increase in four-cell and eight-cell stage embryos followed by a decline at morula and blastocyst stages. Transient transfection and reporter assays revealed that miR-212 represses the expression of FIGLA in a MRE dependent manner. In addition, ectopic expression of miR-212 mimic in bovine early embryos dramatically reduced the expression of FIGLA protein. Collectively, our results demonstrate that FIGLA is temporally regulated during bovine early embryogenesis and miR-212 is an important negative regulator of FIGLA during the maternal to zygotic transition in bovine embryos.

The poplar basic helix-loop-helix transcription factor BEE3 – Like gene affects biomass production by enhancing proliferation of xylem cells in poplar

Energy Technology Data Exchange (ETDEWEB)

Noh, Seol Ah, E-mail: s6022029@korea.ac.kr; Choi, Young-Im, E-mail: yichoi99@forest.go.kr; Cho, Jin-Seong, E-mail: jinsung3932@gmail.com; Lee, Hyoshin, E-mail: hslee@forest.go.kr

2015-06-19

Brassinosteroids (BRs) play important roles in many aspects of plant growth and development, including regulation of vascular cambium activities and cell elongation. BR-induced BEE3 (brassinosteroid enhanced expression 3) is required for a proper BR response. Here, we identified a poplar (Populus alba × Populus glandulosa) BEE3-like gene, PagBEE3L, encoding a putative basic helix-loop-helix (bHLH)-type transcription factor. Expression of PagBEE3L was induced by brassinolide (BL). Transcripts of PagBEE3L were mainly detected in stems, with the internode having a low level of transcription and the node having a relatively higher level. The function of the PagBEE3L gene was investigated through phenotypic analyses with PagBEE3L-overexpressing (ox) transgenic lines. This work particularly focused on a potential role of PagBEE3L in stem growth and development of polar. The PagBEE3L-ox poplar showed thicker and longer stems than wild-type plants. The xylem cells from the stems of PagBEE3L-ox plants revealed remarkably enhanced proliferation, resulting in an earlier thickening growth than wild-type plants. Therefore, this work suggests that xylem development of poplar is accelerated in PagBEE3L-ox plants and PagBEE3L plays a role in stem growth by increasing the proliferation of xylem cells to promote the initial thickening growth of poplar stems. - Highlights: • We identify the BEE3-like gene form hybrid poplar (Populus alba × Populus glandulosa). • We examine effects of overexpression of PagBEE3L on growth in poplar. • We found that 35S:BEE3L transgenic plants showed more rapid growth than wild-type plants. • BEE3L protein plays an important role in the development of plant stem.

The poplar basic helix-loop-helix transcription factor BEE3 – Like gene affects biomass production by enhancing proliferation of xylem cells in poplar

International Nuclear Information System (INIS)

Noh, Seol Ah; Choi, Young-Im; Cho, Jin-Seong; Lee, Hyoshin

2015-01-01

Brassinosteroids (BRs) play important roles in many aspects of plant growth and development, including regulation of vascular cambium activities and cell elongation. BR-induced BEE3 (brassinosteroid enhanced expression 3) is required for a proper BR response. Here, we identified a poplar (Populus alba × Populus glandulosa) BEE3-like gene, PagBEE3L, encoding a putative basic helix-loop-helix (bHLH)-type transcription factor. Expression of PagBEE3L was induced by brassinolide (BL). Transcripts of PagBEE3L were mainly detected in stems, with the internode having a low level of transcription and the node having a relatively higher level. The function of the PagBEE3L gene was investigated through phenotypic analyses with PagBEE3L-overexpressing (ox) transgenic lines. This work particularly focused on a potential role of PagBEE3L in stem growth and development of polar. The PagBEE3L-ox poplar showed thicker and longer stems than wild-type plants. The xylem cells from the stems of PagBEE3L-ox plants revealed remarkably enhanced proliferation, resulting in an earlier thickening growth than wild-type plants. Therefore, this work suggests that xylem development of poplar is accelerated in PagBEE3L-ox plants and PagBEE3L plays a role in stem growth by increasing the proliferation of xylem cells to promote the initial thickening growth of poplar stems. - Highlights: • We identify the BEE3-like gene form hybrid poplar (Populus alba × Populus glandulosa). • We examine effects of overexpression of PagBEE3L on growth in poplar. • We found that 35S:BEE3L transgenic plants showed more rapid growth than wild-type plants. • BEE3L protein plays an important role in the development of plant stem

Political Violence and the Mediating Role of Violent Extremist Propensities

Directory of Open Access Journals (Sweden)

Nele Schils

2016-06-01

Full Text Available Research into violent extremism is lacking integrated theoretical frameworks explaining individual involvement in politically or religiously motivated violence, resulting in a poor understanding of causal mechanisms. Building on situational action theory, the current study moves beyond the dominant risk factor approach and proposes an integrated model for the explanation of political/religious violence, distinguishing between direct mechanisms and “causes of the causes.” The model integrates mechanisms from different but complementary traditions. Following previous work, this study focusses on the causes of the causes influencing direct key mechanisms, violent extremist propensity, and exposure to violent extremist moral settings that explain political/religious violence. The theoretical model is tested using structural equation modelling. The analyses are based on a web survey (N = 6,020 among adolescents and young adults in Belgium. Results show that violent extremist propensity and exposure to violent extremist moral settings have direct effects on the likelihood of political/religious violence. These direct mechanisms are in turn determined by a series of exogenous factors: perceived injustice and poor social integration. The relationship between perceived injustice and poor social integration and political/religious violence is further mediated by perceived alienation, perceived procedural justice, and religious authoritarianism. The implications of these findings are discussed.

Analysis of α-helix unfolding in the pine nut peptide Lys-Cys-His-Lys-Pro induced by pulsed electric field.

Science.gov (United States)

Xing, Jie; Zhang, Sitian; Zhang, Mingdi; Lin, Songyi

2017-09-01

A variety of analytical techniques were applied to explore the effects of pulsed electric field (PEF) on α-helix structural changes in the novel antioxidant peptide Lys-Cys-His-Lys-Pro (KCHKP, 611.76 Da). The relative α-helix content of the KCHKP peptide was significantly altered from 100% to 89.91 ± 0.97% when the electric pulse frequency was 1800 Hz and the field intensity was 10 kV cm -1 . Moreover, the 1,1-diphenyl-2-pycryl-hydrazyl (DPPH) and 2,2-azinobis diammonium salt (ABTS) radical-scavenging activities of PEF-treated KCHKP were increased from 56.31% ± 0.74% to 84.33% ± 1.23% and from 40.56% ± 0.78% to 51.33% ± 0.27%, respectively. PEF treatment increased peptide linkage stretch vibration and altered hydrogen bonding of KCHKP. The stability of the α-helix structure was influenced by hydrogen bonds within the peptide linkage of KCHKP induced by PEF and was related to changes in antioxidant activity. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Applications of Small Area Estimation to Generalization with Subclassification by Propensity Scores

Science.gov (United States)

Chan, Wendy

2018-01-01

Policymakers have grown increasingly interested in how experimental results may generalize to a larger population. However, recently developed propensity score-based methods are limited by small sample sizes, where the experimental study is generalized to a population that is at least 20 times larger. This is particularly problematic for methods…

Control Modes in International Service Operations: The Propensity to Franchise

OpenAIRE

Karin Fladmoe-Lindquist; Laurent L. Jacque

1995-01-01

What determines a service firm's organizational choice between equity-based control and franchising? This question, which has elicited some theoretical answers and a few empirical tests in a domestic setting, has never been addressed in an international context before. This study explains the mode of control chosen in terms of a theoretical framework which borrows from agency theory and transaction cost analysis. The propensity to franchise internationally was found to be directly related to ...

Estudio del hepatopáncreas de Helix Aspersa en situación normal y tras ayuno

OpenAIRE

Almendros Gallego, Antonio Manuel

2013-01-01

Se hace un estudio a microscopia electrónica de los diversos tipos celulares que componen el hepatopancreas de Helix Aspersa atendiendo a los componentes celulares característicos de cada uno de ellos tanto en situación normal como a diversos periodos de ayuno

Performance of Process Damping in Machining Titanium Alloys at Low Cutting Speed with Different Helix Tools

International Nuclear Information System (INIS)

Shaharun, M A; Yusoff, A R; Reza, M S; Jalal, K A

2012-01-01

Titanium is a strong, lustrous, corrosion-resistant and transition metal with a silver color to produce strong lightweight alloys for industrial process, automotive, medical instruments and other applications. However, it is very difficult to machine the titanium due to its poor machinability. When machining titanium alloys with the conventional tools, the wear rate of the tool is rapidly accelerate and it is generally difficult to achieve at high cutting speed. In order to get better understanding of machining titanium alloy, the interaction between machining structural system and the cutting process which result in machining instability will be studied. Process damping is a useful phenomenon that can be exploited to improve the limited productivity of low speed machining. In this study, experiments are performed to evaluate the performance of process damping of milling under different tool helix geometries. The results showed that the helix of 42° angle is significantly increase process damping performance in machining titanium alloy.

Right- and left-handed three-helix proteins. II. Similarity and differences in mechanical unfolding of proteins.

Science.gov (United States)

Glyakina, Anna V; Likhachev, Ilya V; Balabaev, Nikolay K; Galzitskaya, Oxana V

2014-01-01

Here, we study mechanical properties of eight 3-helix proteins (four right-handed and four left-handed ones), which are similar in size under stretching at a constant speed and at a constant force on the atomic level using molecular dynamics simulations. The analysis of 256 trajectories from molecular dynamics simulations with explicit water showed that the right-handed three-helix domains are more mechanically resistant than the left-handed domains. Such results are observed at different extension velocities studied (192 trajectories obtained at the following conditions: v = 0.1, 0.05, and 0.01 Å ps(-1) , T = 300 K) and under constant stretching force (64 trajectories, F = 800 pN, T = 300 K). We can explain this by the fact, at least in part, that the right-handed domains have a larger number of contacts per residue and the radius of cross section than the left-handed domains. Copyright © 2013 Wiley Periodicals, Inc.

Conservation of a helix-stabilizing dipole moment in the PP-fold family of regulatory peptides

DEFF Research Database (Denmark)

Bjørnholm, B; Jørgensen, Flemming Steen; Schwartz, T W

1993-01-01

arrangement were performed in two ways: (1) by the use of a Poisson-Boltzmann approach which allows for an estimate of the screening effect, and (2) by the use of a uniform dielectric model (Coulomb's law). It is found that the alpha-helix is stabilized by approximately 5-10 kcal/mol due to electrostatic...

Screening diagnostics of antivital experiences and propensity toward impulsive, autoagressive behavior in adolescents (preliminary results

Directory of Open Access Journals (Sweden)

Bannikov G.S.,

2014-08-01

Full Text Available Development of methods for revealing antivital experiences and propensity to autoaggressive behavior in educational institutions is one of the key steps in developing strategies for the primary prevention of suicidal behavior in adolescents. The purpose of this study was to develop an effective screening diagnostic package aimed at identifying antivital experiences and propensity to autoaggressive behavior. The survey methods we used were: Beck Hopelessness Scale, Russell Loneliness Scale, A.G. Shmelev Suicide Risk Questionnaire, PDQ-IV Borderline disorder and Narcissism scales. At the first stage we examined 750 minors aged 12-18 and identified risk group (85 people – 11.4%, which included adolescents with high levels of both individual scales, and their combination. At the second stage we examined 10 adolescents at risk. In 7 of them (70% were identified antivital, suicidal thoughts of passive or compulsive nature, signs of subjective and objective socio- psychological maladjustment. Our preliminary conclusion is that high levels of hopelessness and loneliness in adolescents are stable predictors of mental and emotional distress and psychosocial maladjustment in the period of psychological crises and decompensation of character accentuation of borderline and narcissistic types. These scales can be recommended for primary screening of antivital (depressive experiences and propensity to autoaggressive behavior in adolescents.

The neural correlates of risk propensity in males and females using resting-state fMRI

Directory of Open Access Journals (Sweden)

Yuan eZhou

2014-01-01

Full Text Available Men are more risk prone than women, but the underlying basis remains unclear. To investigate this question, we developed a trait-like measure of risk propensity which we correlated with resting-state functional connectivity to identify sex differences. Specifically, we used short- and long-range functional connectivity densities to identify associated brain regions and examined their functional connectivities in resting-state functional magnetic resonance imaging (fMRI data collected from a large sample of healthy young volunteers. We found that men had a higher level of general risk propensity (GRP than women. At the neural level, although they shared a common neural correlate of GRP in a network centered at the right inferior frontal gyrus, men and women differed in a network centered at the right secondary somatosensory cortex, which included the bilateral dorsal anterior/middle insular cortices and the dorsal anterior cingulate cortex. In addition, men and women differed in a local network centered at the left inferior orbitofrontal cortex. Most of the regions identified by this resting-state fMRI study have been previously implicated in risk processing when people make risky decisions. This study provides a new perspective on the brain-behavioral relationships in risky decision making and contributes to our understanding of sex differences in risk propensity.

Assembly of Liposomes Controlled by Triple Helix Formation

DEFF Research Database (Denmark)

Vogel, Stefan; Jakobsen, Ulla

2013-01-01

Attachment of DNA to the surface of different solid nanoparticles (e.g. gold- and silica nanoparticles) is well established and a number of DNA-modified solid nanoparticle systems have been applied to thermal denaturation analysis of oligonucleotides. We report herein the non-covalent immobilizat...... analysis (NTA) and dynamic light scattering (DLS) show independently from ultraviolet spectroscopy experiments the formation of liposome aggregates.......-covalent immobilization of oligonucleotides on the surface of soft nanoparticles (e.g. liposomes) and the subsequent controlled assembly by DNA triple helix formation. The non-covalent approach avoids tedious surface chemistry and necessary purification procedures and can simplify and extend the available methodology...... sequences (G or C-rich) to explore the applicability of the method for different triple helical assembly modes. We demonstrate advantages and limitations of the approach and proof the reversible and reproducible formation of liposome aggregates during thermal denaturation cycles. Nanoparticle tracking...

Modified Quad Helix for Correction of Severely Rotated Incisors in Cleft Cases

Directory of Open Access Journals (Sweden)

Aneesha Ashok Shetty

2014-01-01

Full Text Available Clefts of the lip, alveolus and/or palate are often associated with several dental anomalies, the most common of which are severely rotated maxillary incisors. Patients with such congenital deformities seek orthodontic treatment as early as possible, for an esthetic as well as psychosocial benefit. Here, a new clinical technique is demonstrated for correction of a severely rotated maxillary central incisor which can be carried out in the mixed dentition phase itself, by modifying a commonly used palatal expansion appliance: the quad helix.

Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes

NARCIS (Netherlands)

Sengupta, Durba; Marrink, Siewert J.

2010-01-01

The specific and non-specific driving forces of helix association within membranes are still poorly understood. Here, we use coarse-grain molecular dynamics simulations to study the association behavior of glycophorin A and two disruptive mutants, T87F and a triple mutant of the GxxxG motif

Preparation and evaluation of appertized from snail Helix aspersa M

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Nelson Loyola López

2015-01-01

Full Text Available This study includes the development and evaluation of snails (Helix aspersa M. appertized, collected at a heliciculture breeding center, located in Los Niches sector, Curico, Maule region, South-central of Chile. The test was conducted at the Laboratory of Sciences of the Catholic University of Maule, Nuestra Señora del Carmen Campus, Curico. The main objective of this work was to study the influence of appertized on sensory attributes and commercial durability of snail Helix aspersa M. Additionally, some specific objectives were proposed as follow: to provide this mollusc with a commercial alternative for it consume, to evaluate its organoleptic characteristics and guarantee the product from both the microbiological and nutritional points of view. Three media cover were used (T0: water + NaCl 2%; T1: Water + NaCl 2% + citric acid 0.5% + kilol and T2: extra virgin olive oil + spices + tocopherol. The product was assessed at two different times, after 30 and 90 days of storage. Two sensory evaluations were conducted to measure various organoleptic attributes and acceptability of the appertized by 14 trained panelists. Amino acid, vitamins, cholesterol, acidity, heavy metals, phosphorus and organochlorines analysis were performed. The presence of both total and fecal contaminant microorganisms was determined. Attributes such as color, flavor, aroma, texture and overall acceptability were also measured. Preserves made by T0 and T1 treatments were equally accepted by the panelists. However, preserve from treatment T2 was rejected because of the detection in them of a very dark color, odor and mealy texture. Positive results regarding the content of amino acids, vitamin C and low cholesterol, as well as the absence of pathogenic microorganisms were obtained for the three treatments.

Primer on statistical interpretation or methods report card on propensity-score matching in the cardiology literature from 2004 to 2006: a systematic review.

Science.gov (United States)

Austin, Peter C

2008-09-01

Propensity-score matching is frequently used in the cardiology literature. Recent systematic reviews have found that this method is, in general, poorly implemented in the medical literature. The study objective was to examine the quality of the implementation of propensity-score matching in the general cardiology literature. A total of 44 articles published in the American Heart Journal, the American Journal of Cardiology, Circulation, the European Heart Journal, Heart, the International Journal of Cardiology, and the Journal of the American College of Cardiology between January 1, 2004, and December 31, 2006, were examined. Twenty of the 44 studies did not provide adequate information on how the propensity-score-matched pairs were formed. Fourteen studies did not report whether matching on the propensity score balanced baseline characteristics between treated and untreated subjects in the matched sample. Only 4 studies explicitly used statistical methods appropriate for matched studies to compare baseline characteristics between treated and untreated subjects. Only 11 (25%) of the 44 studies explicitly used statistical methods appropriate for the analysis of matched data when estimating the effect of treatment on the outcomes. Only 2 studies described the matching method used, assessed balance in baseline covariates by appropriate methods, and used appropriate statistical methods to estimate the treatment effect and its significance. Application of propensity-score matching was poor in the cardiology literature. Suggestions for improving the reporting and analysis of studies that use propensity-score matching are provided.

Synchronization propensity in networks of dynamical systems: A purely topological indicator

OpenAIRE

Fasani, S.; Rinaldi, S.

2012-01-01

Synchronization in networks of identical dynamical systems is enhanced by the number of manifolds in which synchrony of groups of systems is conserved or reinforced. Since the number of these invariant manifolds depends only on the coupling architecture of the network, it can be proposed as a purely topological indicator of synchronization propensity. The proposal is empirically validated through the detailed study of an ecological application.

Coherent helix vacancy phonon and its ultrafast dynamics waning in topological Dirac semimetal C d3A s2

Science.gov (United States)

Sun, Fei; Wu, Q.; Wu, Y. L.; Zhao, H.; Yi, C. J.; Tian, Y. C.; Liu, H. W.; Shi, Y. G.; Ding, H.; Dai, X.; Richard, P.; Zhao, Jimin

2017-06-01

We report an ultrafast lattice dynamics investigation of the topological Dirac semimetal C d3A s2 . A coherent phonon beating among three evenly spaced A1 g optical phonon modes (of frequencies 1.80, 1.96, and 2.11 THz, respectively) is unambiguously observed. The two side modes originate from the counter helixes composing Cd vacancies. Significantly, such helix vacancy-induced phonon (HVP) modes experience prominent extra waning in their ultrafast dynamics as temperature increases, which is immune to the central mode. Above 200 K, the HVP becomes inactive, which may potentially affect the topological properties. Our results in the lattice degree of freedom suggest the indispensable role of temperature in considering topological properties of such quantum materials.

Propensity Score Analysis Comparing Videothoracoscopic Lobectomy With Thoracotomy: A French Nationwide Study.

Science.gov (United States)

Pagès, Pierre-Benoit; Delpy, Jean-Philippe; Orsini, Bastien; Gossot, Dominique; Baste, Jean-Marc; Thomas, Pascal; Dahan, Marcel; Bernard, Alain

2016-04-01

Video-assisted thoracoscopic surgery (VATS) lobectomy has recently become the recommended approach for stage I non-small cell lung cancer. However, these guidelines are not based on any large randomized control trial. Our study used propensity scores and a sensitivity analysis to compare VATS lobectomy with open thoracotomy. From 2005 to 2012, 24,811 patients (95.1%) were operated on by open thoracotomy and 1,278 (4.9%) by VATS. The end points were 30-day postoperative death, postoperative complications, hospital stay, overall survival, and disease-free survival. Two propensity scores analyses were performed: matching and inverse probability of treatment weighting, and one sensitivity analysis to unmask potential hidden bias. A subgroup analysis was performed to compare "high-risk" with "low-risk" patients. Results are reported by odds ratios or hazard ratios and their 95% confidence intervals. Postoperative death was not significantly reduced by VATS whatever the analysis. Concerning postoperative complications, VATS significantly decreased the occurrence of atelectasis and pneumopathy with both analysis methods, but there were no differences in the occurrence of other postoperative complications. VATS did not provide a benefit for high-risk patients. The VATS approach decreased the hospital length of stay from 2.4 days (95% confidence interval, -1.7 to -3 days) to -4.68 days (95% confidence interval, -8.5 to 0.9 days). Overall survival and disease-free survival were not influenced by the surgical approach. The sensitivity analysis showed potential biases. The results must be interpreted carefully because of the differences observed according to the propensity scores method used. A multicenter randomized controlled trial is necessary to limit the biases. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

PH4 of petunia is an R2R3-MYB protein that activates vacuolar acidification through interactions with Basic-Helix-Loop transcription factors of the anthocyanin pathway.

NARCIS (Netherlands)

Quattrocchio, F.M.; Verweij, C.W.; Kroon, A.R.; Spelt, C.E.; Mol, J.N.M.; Koes, R.E.

2006-01-01

The Petunia hybrids genes ANTHOCYANIN1 (AN1) and AN2 encode transcription factors with a basic-helix-loop-helix (BHLH) and a MYB domain, respectively, that are required for anthocyanin synthesis and acidification of the vacuole in petal cells. Mutation of PH4 results in a bluer flower color,

Thrombocytopenia after aortic valve replacement with freedom solo bioprosthesis: a propensity study.

Science.gov (United States)

Piccardo, Alessandro; Rusinaru, Dan; Petitprez, Benoit; Marticho, Paul; Vaida, Ioana; Tribouilloy, Christophe; Caus, Thierry

2010-05-01

The incidence of postoperative thrombocytopenia after aortic valve replacement with the Freedom Solo bioprosthesis remains unclear. This propensity-matched study was carried out to evaluate the incidence and clinical impact of thrombocytopenia in patients receiving the Freedom Solo bioprosthesis. Patients who underwent aortic valve replacement with a Freedom Solo or Carpentier-Edwards Perimount pericardial prosthesis at our institution between 2006 and 2008 were screened retrospectively. Exclusion criteria included double valve replacement, redo surgery, and active endocarditis. Two hundred six patients were considered eligible for this analysis. Using propensity scores 36 matched pairs of patients with a Freedom Solo or Perimount bioprosthesis were obtained. The primary end point was the occurrence of postoperative thrombocytopenia. Secondary end points were postoperative thromboembolic or hemorrhagic events and 30-day mortality. Before matching, severe thrombocytopenia (Solo bioprosthesis and 1% with a Perimount bioprosthesis (p Solo (p Solo and Perimount bioprostheses, respectively (p Solo implantation. However, this complication was not related to any deleterious events in our study population. Copyright (c) 2010 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Wave propagation in elastic solids

CERN Document Server

Achenbach, Jan

1984-01-01

The propagation of mechanical disturbances in solids is of interest in many branches of the physical scienses and engineering. This book aims to present an account of the theory of wave propagation in elastic solids. The material is arranged to present an exposition of the basic concepts of mechanical wave propagation within a one-dimensional setting and a discussion of formal aspects of elastodynamic theory in three dimensions, followed by chapters expounding on typical wave propagation phenomena, such as radiation, reflection, refraction, propagation in waveguides, and diffraction. The treat

Career College Governance: A Study of the Faculty's Propensity to Participate

Science.gov (United States)

King, Stephen H.

2012-01-01

This study investigated faculty perceptions of and propensity to participate in shared governance activities in proprietary, post-secondary educational institutions. The sample population for this study (n = 22) included adjunct and full-time faculty members and administrators selected through a snowball sampling method and initially inclusive of…

Ceftriaxone pretreatment reduces the propensity of postpartum depression following stroke during pregnancy in rats.

Science.gov (United States)

Guan, Yonghong; Liu, Xianying; Su, Yuetian

2016-10-06

Ischemic stroke increases the propensity to develop depression in humans and laboratory animals, and we hypothesized that such an incidence during pregnancy may increase the risk for the development of postpartum depression (PPD). To test this hypothesis, we used bilateral common carotid arteries occlusion (BCCAO) to induce transient cerebral ischemia in pregnant rats, and evaluated its effects on subsequent development of PPD in dams. Additionally, we investigated whether ceftriaxone pretreatments before the induction of brain ischemia could alter the propensity of PPD. We found that 15min BCCAO during pregnancy enhanced immobility time and reduced the frequency of swimming or climbing behaviors in the forced swim test, and decreased the sucrose preference in dams at postpartum day 21. Such behavioral alterations were associated with lower level of GLT-1 expression in the medial prefrontal cortical regions (mPFC) of PPD dams. Specifically, mPFC GLT-1 expression levels in dams with ischemia history were correlated with sucrose preference levels at postpartum day 21. Finally, ceftriaxone pretreatment (200mg/kg/day, 5days) before the 15min BCCAO prevented the development of PPD, and prevented the reduction of GLT-1 expression in the mPFC. Taken together, our results suggested that ceftriaxone pretreatment before brain ischemia during pregnancy may reduce the propensity for the development of PPD by preventing the loss of GLT-1 expression in the mPFC. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Behavioural modification of the optic tentacle of Helix pom atia; effect of puromycin, activity of S-100

DEFF Research Database (Denmark)

Christoffersen, Gert Rene Juul; Frederiksen, K; Johansen, Jørgen

1981-01-01

1. 1. A long-term learning phenomenon in the tentacle of Helix pomatia has been observed.   2. 2. Repeated mechanical stimulation of the optic tentacle led to habituation of the associated withdrawal-extension action pattern whereas repeated combined mechanical and electrical stimulation potentia...

Circularly Polarized Planar Helix Phased Antenna Array for 5G Mobile Terminals

DEFF Research Database (Denmark)

Syrytsin, Igor A.; Zhang, Shuai; Pedersen, Gert F.

2017-01-01

In this paper, a planar helix mobile phased antenna array is proposed for 5th generation communication systems with operating frequency of 28GHz. The proposed array displays circular polarization in the endfire direction. Over 65 degrees of axial ratio beamwidth and 7GHz of axial ratio bandwidth...... has been achieved in the proposed design. The coverage performance of the proposed phased antenna array has also been studied by using the coverage efficiency metric. Coverage efficiency of 50 % at 5 dBi gain is achieved by the proposed phased mobile antenna array....

Insights into Unfolded Proteins from the Intrinsic phi/psi Propensities of the AAXAA Host-Guest Series

Czech Academy of Sciences Publication Activity Database

Towse, C. L.; Vymětal, Jiří; Vondrášek, Jiří; Daggett, V.

2016-01-01

Roč. 110, č. 2 (2016), s. 348-361 ISSN 0006-3495 R&D Projects: GA MŠk(CZ) LH11020 Institutional support: RVO:61388963 Keywords : polyproline-II helix * beta-sheet protein * random-coil behavior Subject RIV: BO - Biophysics Impact factor: 3.656, year: 2016

Database for propagation models

Science.gov (United States)

Kantak, Anil V.

1991-07-01

A propagation researcher or a systems engineer who intends to use the results of a propagation experiment is generally faced with various database tasks such as the selection of the computer software, the hardware, and the writing of the programs to pass the data through the models of interest. This task is repeated every time a new experiment is conducted or the same experiment is carried out at a different location generating different data. Thus the users of this data have to spend a considerable portion of their time learning how to implement the computer hardware and the software towards the desired end. This situation may be facilitated considerably if an easily accessible propagation database is created that has all the accepted (standardized) propagation phenomena models approved by the propagation research community. Also, the handling of data will become easier for the user. Such a database construction can only stimulate the growth of the propagation research it if is available to all the researchers, so that the results of the experiment conducted by one researcher can be examined independently by another, without different hardware and software being used. The database may be made flexible so that the researchers need not be confined only to the contents of the database. Another way in which the database may help the researchers is by the fact that they will not have to document the software and hardware tools used in their research since the propagation research community will know the database already. The following sections show a possible database construction, as well as properties of the database for the propagation research.

Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination

DEFF Research Database (Denmark)

Ejby, Morten; Sørensen, Michael A; Pedersen, Steen

2007-01-01

Escherichia coli strains with inactivated rluD genes were previously found to lack the conserved pseudouridines in helix 69 of 23S ribosomal RNA and to grow slowly. A suppressor mutant was isolated with a near normal growth rate that had changed the conserved Glu-172 codon to a Lys codon in prf...

A Grounded Theory for Regional Development through the IT Offshoring Industry with the Triple-Helix Involvment

Science.gov (United States)

Villarreal de la Garza, Sonia

2011-01-01

The purpose of this qualitative grounded study was to explore the thoughts, experiences, and needs of potential clients and of the triple-helix members with the intention to establish a framework to support the development of the regional economy through the information technology (IT) and business processing outsourcing (BPO) offshoring industry.…

Antecedents for Entrepreneurial Propensity: Findings from Singapore, Hong Kong and Taiwan

OpenAIRE

Lee, Lena; Wong, Poh Kam; Chua, Bee Leng; Chen, Jennifer

2005-01-01

The existing literature identifies a number of antecedent factors that positively influence the propensity of individuals to become entrepreneurs. Key among these are self-efficacy, prior knowledge of other entrepreneurs and perception of opportunities. At the same time, policy makers commonly identify fear of failure as a major deterrent factor for entrepreneurs taking the entrepreneurial plunge. This paper examines the relative impacts of these antecedents and deterrent factor on entre...

Temporary work and depressive symptoms: a propensity score analysis.

Science.gov (United States)

Quesnel-Vallée, Amélie; DeHaney, Suzanne; Ciampi, Antonio

2010-06-01

Recent decades have seen a tremendous increase in the complexity of work arrangements, through job sharing, flexible hours, career breaks, compressed work weeks, shift work, reduced job security, and part-time, contract and temporary work. In this study, we focus on one specific group of workers that arguably most embodies non-standard employment, namely temporary workers, and estimate the effect of this type of employment on depressive symptom severity. Accounting for the possibility of mental health selection into temporary work through propensity score analysis, we isolate the direct effects of temporary work on depressive symptoms with varying lags of time since exposure. We use prospective data from the U.S. National Longitudinal Survey of Youth 1979 (NLSY79), which has followed, longitudinally, from 1979 to the present, a nationally representative cohort of American men and women between 14 and 22 years of age in 1979. Three propensity score models were estimated, to capture the effect of different time lags (immediately following exposure, and 2 and 4 years post exposure) between the period of exposure to the outcome. The only significant effects were found among those who had been exposed to temporary work in the two years preceding the outcome measurement. These workers report 1.803 additional depressive symptoms from having experienced this work status (than if they had not been exposed). Moreover, this difference is both statistically and substantively significant, as it represents a 50% increase from the average level of depressive symptoms in this population. Copyright 2010 Elsevier Ltd. All rights reserved.

An evolutionary triple helix to strengthen energy regulation: Implications for management

Energy Technology Data Exchange (ETDEWEB)

Rizzi, Francesco; Borzoni, Matteo

2010-09-15

Regulation is the basic tool to implement energy policy. The evolution of the regulation is influenced by its impacts on the industrial activities. Consequently, entrepreneurs acts in a continuously adapting-by-interacting environment. Both from a systemic and an atomistic perspective, this paper provides a theoretical framework for energy regulation development in order to support management implications. This work builds on the triple helix model and extends it to energy regulation development processes. It concludes that the analysis of intangible resources and their related services at inter-organizational level is fundamental to guide companies in designing win-win corporate strategies and in their operazionalization.

A double-helix and cross-patterned solenoid used as a wirelessly powered receiver for medical implants

Science.gov (United States)

Mao, Shitong; Wang, Hao; Mao, Zhi-Hong; Sun, Mingui

2018-05-01

Many medical implants need to be designed in the shape of a cylinder (rod), a cuboid or a capsule in order to adapt to a specific site within the human body or facilitate the implantation procedure. In order to wirelessly power these types of implants, a pair of coils, one is located inside the human body and one is outside, is often used. Since most organs such as major muscles, blood vessels, and nerve bundles are anatomically parallel to the body surface, the most desired wireless power transfer (WPT) direction is from the external power transmission pad (a planar coil) to the lateral surface of the implant. However, to obtain optimal coupling, the currently used solenoid coil requires being positioned perpendicular to the body surface, which is often medically or anatomically unacceptable. In this research, a concentric double-helix (DH) coil with an air core is presented for use in implantable devices. Two helical coils are tilted at opposite angles (±45 degrees) to form a cross pattern. The WPT system is designed using the magnetic resonance concept for wireless power transfer (MR-WPT). The power transfer efficiency (PTE) relies on the near-field magnetic coupling which is closely related to the location and orientation of the DH coil. We explain how the novel structure of the DH solenoid magnifies the mutual inductance with the widely adopted circular planner coil and how the PTE is improved in comparison to the case of the conventional solenoid coil. We also study an important case where the double-helix power reception coil is laterally and angularly misaligned with the transmitter. Finally, our computational study using the finite element method and experimental study with actually constructed prototypes are presented which have proven our new double-helix coil design.

A double-helix and cross-patterned solenoid used as a wirelessly powered receiver for medical implants

Directory of Open Access Journals (Sweden)

Shitong Mao

2018-05-01

Full Text Available Many medical implants need to be designed in the shape of a cylinder (rod, a cuboid or a capsule in order to adapt to a specific site within the human body or facilitate the implantation procedure. In order to wirelessly power these types of implants, a pair of coils, one is located inside the human body and one is outside, is often used. Since most organs such as major muscles, blood vessels, and nerve bundles are anatomically parallel to the body surface, the most desired wireless power transfer (WPT direction is from the external power transmission pad (a planar coil to the lateral surface of the implant. However, to obtain optimal coupling, the currently used solenoid coil requires being positioned perpendicular to the body surface, which is often medically or anatomically unacceptable. In this research, a concentric double-helix (DH coil with an air core is presented for use in implantable devices. Two helical coils are tilted at opposite angles (±45 degrees to form a cross pattern. The WPT system is designed using the magnetic resonance concept for wireless power transfer (MR-WPT. The power transfer efficiency (PTE relies on the near-field magnetic coupling which is closely related to the location and orientation of the DH coil. We explain how the novel structure of the DH solenoid magnifies the mutual inductance with the widely adopted circular planner coil and how the PTE is improved in comparison to the case of the conventional solenoid coil. We also study an important case where the double-helix power reception coil is laterally and angularly misaligned with the transmitter. Finally, our computational study using the finite element method and experimental study with actually constructed prototypes are presented which have proven our new double-helix coil design.

Emphasis on Autonomy and Propensity for Suicidal Behavior in Younger and Older Adults

Science.gov (United States)

O'Riley, Alisa A.; Fiske, Amy

2012-01-01

A cognitive style marked by emphasis on autonomy has been linked to negative outcomes throughout the life span. Two preliminary studies are presented that examined factors on a measure of autonomy (Personal Style Inventory-Revised) in relation to propensity for suicidal behavior (Suicidal Behaviors Questionnaire-14; SBQ-14). Perfectionism, B =…

Evaluation of prognostic differences in elderly patients with pneumonia treated by between pulmonologists and non-pulmonologists: a propensity score analysis.

Science.gov (United States)

Komiya, Kosaku; Oka, Hiroaki; Ohama, Minoru; Uchida, Masahiro; Miyajima, Hajime; Iwashita, Tomohiko; Okabe, Eiji; Shuto, Osamu; Matsumoto, Taisuke; Ishii, Hiroshi; Kadota, Jun-Ichi

2016-07-01

The incidence of pneumonia among elderly people is increasing in aged countries, and both pulmonologists and non-pulmonologists treat such patients. The aim of this study was to assess prognostic differences between elderly patients treated by pulmonologists and those treated by non-pulmonologists. This study was a retrospective cohort using a propensity score analysis. Patients 65 years of age or over with pneumonia were consecutively included. The propensity score was estimated based on the patient's background and severity of pneumonia. The difference in 30-day and 90-day mortality depending on the attending physician's specialty was analyzed after adjusting for other variables, including the propensity score. We assessed 68 and 182 patients treated by pulmonologists and non-pulmonologists, respectively. The pulmonologists tended to be in charge of patients with hypoxemia, chronic obstructive pulmonary disease or dementia without aspiration pneumonia or renal dysfunction (area under receiver operating characteristic curve to predict treatment by a pulmonologist according to the propensity score = 0.737, P bedridden status (3.000, P = 0.013) and the serum albumin level (0.382, P elderly patients may not necessarily improve, irrespective of treatment by pulmonologists, and host factors seemed to be associated with mortality. © 2014 John Wiley & Sons Ltd.

Individual variation in the propensity to attribute incentive salience to a food cue: influence of sex.

Science.gov (United States)

Pitchers, Kyle K; Flagel, Shelly B; O'Donnell, Elizabeth G; Woods, Leah C Solberg; Sarter, Martin; Robinson, Terry E

2015-02-01

There is considerable individual variation in the propensity of animals to attribute incentive salience to discrete reward cues, but to date most of this research has been conducted in male rats. The purpose of this study was to determine whether sex influences the propensity to attribute incentive salience to a food cue, using rats from two different outbred strains (Sprague-Dawley [SD] and Heterogeneous Stock [HS]). The motivational value of a food cue was assessed in two ways: (i) by the ability of the cue to elicit approach toward it and (ii) by its ability to act as a conditioned reinforcer. We found that female SD rats acquired Pavlovian conditioned approach behavior slightly faster than males, but no sex difference was detected in HS rats, and neither strain showed a sex difference in asymptotic performance of approach behavior. Moreover, female approach behavior did not differ across estrous cycle. Compared to males, females made more active responses during the test for conditioned reinforcement, although they made more inactive responses as well. We conclude that although there are small sex differences in performance on these tasks, these are probably not due to a notable sex difference in the propensity to attribute incentive salience to a food cue. Copyright © 2014 Elsevier B.V. All rights reserved.

Primary tumor resection in metastatic breast cancer: A propensity-matched analysis, 1988-2011 SEER data base.

Science.gov (United States)

Vohra, Nasreen A; Brinkley, Jason; Kachare, Swapnil; Muzaffar, Mahvish

2018-03-02

Primary tumor resection (PTR) in metastatic breast cancer is not a standard treatment modality, and its impact on survival is conflicting. The primary objective of this study was to analyze impact of PTR on survival in metastatic patients with breast cancer. A retrospective study of metastatic patients with breast cancer was conducted using the 1988-2011 Surveillance, Epidemiology, and End Results (SEER) data base. Cox proportional hazards regression models were used to evaluate the relationship between PTR and survival and to adjust for the heterogeneity between the groups, and a propensity score-matched analysis was also performed. A total of 29 916 patients with metastatic breast cancer were included in the study, and 15 129 (51%) of patients underwent primary tumor resection, and 14 787 (49%) patients did not undergo surgery. Overall, decreasing trend in PTR for metastatic breast cancer in last decades was noted. Primary tumor resection was associated with a longer median OS (34 vs 18 months). In a propensity score-matched analysis, prognosis was also more favorable in the resected group (P = .0017). Primary tumor resection in metastatic breast cancer was associated with survival improvement, and the improvement persisted in propensity-matched analysis. © 2018 Wiley Periodicals, Inc.

Role of the future creative universities in the triple helix of science and technology corridors

Directory of Open Access Journals (Sweden)

Iraj nabipour

2015-01-01

Full Text Available The science and technology corridor is a complex cluster containing universities, science parks, research centers, high-tech companies, venture capital, institutional and physical infrastructures, and human capital in a defined geography with its unique management and legal structure in association with the business space and knowledge-based products. In fact, the science and technology corridor reflects the concept of development based on the knowledge region (the especial region for science and technology. The knowledge region is clearly a triple helix phenomenon par excellence: universities, governments and businesses combine their efforts to construct a common advantage which they would not be able to offer on their own. The future creative universities in connection with the knowledge city-regions not only will deal with innovation and entrepreneurial training but also produce a competitive, vibrant environment with high indices for quality of life and full of green technologies. In this article, we will present functional interactions of the creative universities in the triple helix, particularly the missions for the Iranian universities of medical sciences. As a theoretical model, the complex interactions of Bushehr University of Medical Sciences and Health Services with Bushehr Science and Technology Corridor will be discussed.

Assessment of balance in propensity score analysis in the medical literature: A systematic review

NARCIS (Netherlands)

Ali, M. Sanni|info:eu-repo/dai/nl/345709497; Groenwold, Rolf H.H.; Belitser, Svetlana V.; Pestman, Wiebe R.; Hoes, Arno W.; Roes, Kit C.B.; Boer, Ade; Klungel, Olaf H.|info:eu-repo/dai/nl/181447649

2013-01-01

Background: Assessing balance on co-variate distributions between treatment groups with a given propensity score (PS) is a crucial step in PS analysis. Several methodological papers comparing different balance measures have been published in the last decade. However, the current practice on

A hypothesis regarding the molecular mechanism underlying dietary soy-induced effects on seizure propensity.

Directory of Open Access Journals (Sweden)

Cara Jean Westmark

2014-09-01

Full Text Available Numerous neurological disorders including fragile X syndrome, Down syndrome, autism and Alzheimer’s disease are comorbid with epilepsy. We have observed elevated seizure propensity in mouse models of these disorders dependent on diet. Specifically, soy-based diets exacerbate audiogenic-induced seizures in juvenile mice. We have also found potential associations between the consumption of soy-based infant formula and seizure incidence, epilepsy comorbidity and autism diagnostic scores in autistic children by retrospective analyses of medical record data. In total, these data suggest that consumption of high levels of soy protein during postnatal development may affect neuronal excitability. Herein, we present our theory regarding the molecular mechanism underlying soy-induced effects on seizure propensity. We hypothesize that soy phytoestrogens interfere with metabotropic glutamate receptor signaling through an estrogen receptor-dependent mechanism, which results in elevated production of key synaptic proteins and decreased seizure threshold.

Patients with type 2 diabetes benefit from primary care-based disease management: a propensity score matched survival time analysis.

Science.gov (United States)

Drabik, Anna; Büscher, Guido; Thomas, Karsten; Graf, Christian; Müller, Dirk; Stock, Stephanie

2012-08-01

This study aimed to assess the impact of a nationwide German diabetes mellitus disease management program (DMP) on survival time and costs in comparison to routine care. The authors conducted a retrospective observational cohort study using routine administration data from Germany's largest sickness fund to identify insured suffering from diabetes in 2002. A total of 95,443 insured with type 2 diabetes mellitus who were born before January 1, 1962 met the defined inclusion criteria, resulting in 19,888 pairs of DMP participants and nonparticipants matched for socioeconomic and health status using propensity score matching methods. This is the first time propensity score matching has been used to evaluate a survival benefit of DMPs. In the time frame analyzed (3 years), mean survival time for the DMP group was 1045 days vs. 985 days for the routine care group (Ptime. They also incurred lower costs compared to propensity score matched insured in routine care.

Change in the fouling propensity of sludge in membrane bioreactors (MBR) in relation to the accumulation of biopolymer clusters.

Science.gov (United States)

Sun, Fei-yun; Wang, Xiao-mao; Li, Xiao-yan

2011-04-01

A membrane bioreactor (MBR) and an activated sludge process (ASP) were operated side by side to evaluate the change of sludge supernatant characteristics and the evolution of the sludge fouling propensity. The MBR sludge had a higher organic concentration and more biopolymer clusters (BPC) in the supernatant compared with ASP. BPC increased in both concentration and size in the MBR. The results show that the change in the liquid-phase property had a profound effect on the sludge fouling propensity. MBR operation transformed typical activated sludge to MBR sludge with a higher fouling propensity. Distinct from the ASP, membrane filtration retained soluble microbial products (SMP) within the MBR, and the vast membrane surface provided a unique environment for the transformation of SMP to large size BPC, leading to further sludge deposition on the membrane surface. Thus, membrane filtration is the crucial cause of the inevitable fouling problem in submerged MBRs. Copyright © 2011 Elsevier Ltd. All rights reserved.

A propensity scoring approach to characterizing the effects of maternal smoking during pregnancy on offspring's initial responses to cigarettes and alcohol

Science.gov (United States)

Bidwell, L. Cinnamon; Palmer, Rohan H.C.; Brick, Leslie; Madden, Pamela A.F.; Heath, Andrew C.; Knopik, Valerie S.

2016-01-01

When examining the effects of prenatal exposure to maternal smoking during pregnancy (MSDP) on later offspring substance use, it is critical to consider familial environments confounded with MSDP. The purpose of this study was to examine the effect of MSDP on offspring's initial reactions to cigarettes and alcohol, which are indicators of future substance-use related problems. We tested these effects using two propensity score approaches (1) by controlling for confounding using the MSDP propensity score and 2) examining effects of MSDP across the MSDP risk distribution by grouping individuals into quantiles based on their MSDP propensity score. This study used data from 829 unrelated mothers with a reported lifetime history of smoking to determine the propensity for smoking only during their first trimester (MSDP-E) or throughout their entire pregnancy (MSDP-T). Propensity score analyses focused on the offspring (N=1616 female twins) of a large subset of these mothers. We examined the effects of levels of MSDP-E/T on offspring initial reactions to their first experiences with alcohol and cigarettes, across the distribution of liability for MSDP-E/T. MSDP-E/T emerged as significant predictors of offspring reactions to alcohol and cigarettes, but the effects were confounded by the familial liability for MSDP. Further, the unique MSDP effects that emerged were not uniform across the MSDP familial risk distribution. Our findings underscore the importance of properly accounting for correlated familial risk factors when examining the effects of MSDP on substance related outcomes. PMID:27098899

An examination of the effects of mountaintop removal coal mining on respiratory symptoms and COPD using propensity scores.

Science.gov (United States)

Hendryx, Michael; Luo, Juhua

2015-01-01

Previous research on public health consequences of mountaintop removal (MTR) coal mining has been limited by the observational nature of the data. The current study used propensity scores, a method designed to overcome this limitation, to draw more confident causal inferences about mining effects on respiratory health using non-experimental data. These data come from a health survey of 682 adults residing in two rural areas of Virginia, USA characterized by the presence or absence of MTR mining. Persons with a history of occupational exposure as coal miners were excluded. Nine covariates including age, sex, current and former smoking, overweight, obesity, high school education, college education, and exposure to coal as a home-heating source were selected to estimate propensity scores. Propensity scores were tested for balance and then used as weights to create quasi-experimental exposed and unexposed groups. Results indicated that persons in the mountaintop mining group had significantly (p < 0.0001) elevated prevalence of respiratory symptoms and chronic obstructive pulmonary disease. The results suggest that impaired respiratory health results from exposure to MTR environments and not from other risks.

Propensity score matching of the gymnastics for diabetes mellitus using logistic regression

Science.gov (United States)

Otok, Bambang Widjanarko; Aisyah, Amalia; Purhadi, Andari, Shofi

2017-12-01

Diabetes Mellitus (DM) is a group of metabolic diseases with characteristics shows an abnormal blood glucose level occurring due to pancreatic insulin deficiency, decreased insulin effectiveness or both. The report from the ministry of health shows that DMs prevalence data of East Java province is 2.1%, while the DMs prevalence of Indonesia is only 1,5%. Given the high cases of DM in East Java, it needs the preventive action to control factors causing the complication of DM. This study aims to determine the combination factors causing the complication of DM to reduce the bias by confounding variables using Propensity Score Matching (PSM) with the method of propensity score estimation is binary logistic regression. The data used in this study is the medical record from As-Shafa clinic consisting of 6 covariates and health complication as response variable. The result of PSM analysis showed that there are 22 of 126 DMs patients attending gymnastics paired with patients who didnt attend to diabetes gymnastics. The Average Treatment of Treated (ATT) estimation results showed that the more patients who didnt attend to gymnastics, the more likely the risk for the patients having DMs complications.

Changes in the reproductive system of the snail Helix aspersa caused by mucus from the love dart

NARCIS (Netherlands)

Koene, J M; Chase, R.

The function of the love dart in certain species of terrestrial snails is unknown. In Helix aspersa, the dart is a sharp calcareous structure that is used to pierce the partner's skin during courtship. When expelled, the dart is covered with a thick mucus. The hypothesis tested here is that the

Trace metallic elements in Helix aspersa terrestrial snails of a semiarid ecosystem

International Nuclear Information System (INIS)

Gaso P, M.I.; Segovia, N.; Zarazua, G.; Montes, F.; Morton, O.; Armienta, M.A.; Hernandez, E.

2001-01-01

The concentration of some major elements and traces in soil samples and of Helix aspersa eatable terrestrial snails were analysed at the Radioactive Wastes Storage Center (CADER) and in other reference sites. The methodology includes the use of an atomic absorption spectrophotometer, an X-ray fluorescence equipment and an Icp-mass spectroscope. The concentrations of some toxic elements (Ba, Cd, Cr, Ni, Pb and V) in the soft tissue of the snails were greater than the toxic levels reported in the literature for such trace elements. The snails compared with another wild eatable foods present transfer coefficients soil-snail high relatively. (Author)

The effect of k-cubic Dresselhaus spin—orbit coupling on the decay time of persistent spin helix states in semiconductor two-dimensional electron gases

International Nuclear Information System (INIS)

Chai Zheng; Hu Mao-Jin; Wang Rui-Qiang; Hu Liang-Bin

2014-01-01

We study the theoretical effect of k-cubic (i.e. cubic-in-momentum) Dresselhaus spin—orbit coupling on the decay time of persistent spin helix states in semiconductor two-dimensional electron gases. We show that the decay time of persistent spin helix states may be suppressed substantially by k-cubic Dresselhaus spin—orbit coupling, and after taking the effect of k-cubic Dresselhaus spin—orbit interaction into account, the theoretical results obtained accord both qualitatively and quantitatively with other recent experimental results. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

Space confinement and rotation stress induced self-organization of double-helix nanostructure: a nanotube twist with a moving catalyst head.

Science.gov (United States)

Zhao, Meng-Qiang; Zhang, Qiang; Tian, Gui-Li; Huang, Jia-Qi; Wei, Fei

2012-05-22

Inorganic materials with double-helix structure have attracted intensive attention due to not only their elegant morphology but also their amazing morphology-related potential applications. The investigation on the formation mechanism of the inorganic double-helix nanostructure is the first step for the fundamental studies of their materials or physical properties. Herein, we demonstrated the space confinement and rotation stress induced self-organization mechanism of the carbon nanotube (CNT)-array double helices under scanning electron microscopy by directly observing their formation process from individual layered double hydroxide flakes, which is a kind of hydrotalcite-like material composed of positively charged layers and charge-balancing interlayer anions. Space confinement is considered to be the most important extrinsic factor for the formation of CNT-array double helices. Synchronous growth of the CNT arrays oppositely from LDH flakes with space confinement on both sides at the same time is essential for the growth of CNT-array double helices. Coiling of the as-grown CNT arrays into double helices will proceed by self-organization, tending to the most stable morphology in order to release their internal rotation stress. Based on the demonstrated mechanism, effective routes were carried out to improve the selectivity for CNT-array double helices. The work provides a promising method for the fabrication of double-helix nanostructures with their two helices connected at the end by self-assembly.

Propensity of University Students in the Region of Antofagasta, Chile to Create Enterprise

Science.gov (United States)

Romani, Gianni; Didonet, Simone; Contuliano, Sue-Hellen; Portilla, Rodrigo

2013-01-01

The authors aim to discuss the propensity or intention to create enterprise among university students in the region of Antofagasta, Chile, and to analyze the factors that influence the step from desire to intention. 681 students were surveyed. The data were analyzed by binary logistical regression. The results show that curriculum is among the…

Triple-resonance multidimensional NMR study of calmodulin complexed with the binding domain of skeletal muscle myosin light-chain kinase: Indication of a conformational change in the central helix

International Nuclear Information System (INIS)

Ikura, Mitsuhiko; Kay, L.E.; Bax, A.; Krinks, M.

1991-01-01

Heteronuclear 3D and 4D NMR experiments have been used to obtain 1 H, 13 C, and 15 N backbone chemical shift assignments in Ca 2+ -loaded clamodulin complexed with a 26-residue synthetic peptide (M13) corresponding to the calmodulin-bionding domain (residues 577-602) of rabbit skeletal muscle muosin light-chain kinase. Comparison of the chemical shift values with those observed in peptide-free calmodulin shows that binding of M13 peptide induces substantial chemical shift changes that are not localized in one particular region of the protein. The largest changes are found in the first helix of the Ca 2+ -binding site 1 (E11-E14), the N-terminal portion of the central helix (M72-D78), and the second helix of the Ca 2+ -binding site 4 (F141-M145). Analysis of backbone NOE connectivities indicates a change from α-helical to an extended conformation for residues 75-77 upon complexation with M13. Upon complexation with M13, a significant decrease in the amide exchange rate is observed for residues T110, L112, G113, and E114 at the end of the second helix of site 3

Peer Influence, Genetic Propensity, and Binge Drinking: A Natural Experiment and a Replication.

Science.gov (United States)

Guo, Guang; Li, Yi; Wang, Hongyu; Cai, Tianji; Duncan, Greg J

2015-11-01

The authors draw data from the College Roommate Study (ROOM) and the National Longitudinal Study of Adolescent Health to investigate gene-environment interaction effects on youth binge drinking. In ROOM, the environmental influence was measured by the precollege drinking behavior of randomly assigned roommates. Random assignment safeguards against friend selection and removes the threat of gene-environment correlation that makes gene-environment interaction effects difficult to interpret. On average, being randomly assigned a drinking peer as opposed to a nondrinking peer increased college binge drinking by 0.5-1.0 episodes per month, or 20%-40% the average amount of binge drinking. However, this peer influence was found only among youths with a medium level of genetic propensity for alcohol use; those with either a low or high genetic propensity were not influenced by peer drinking. A replication of the findings is provided in data drawn from Add Health. The study shows that gene-environment interaction analysis can uncover social-contextual effects likely to be missed by traditional sociological approaches.

Apex Dips of Experimental Flux Ropes: Helix or Cusp?

Energy Technology Data Exchange (ETDEWEB)

Wongwaitayakornkul, Pakorn; Haw, Magnus A.; Bellan, Paul M. [Applied Physics, California Institute of Technology, Pasadena, CA 91125 (United States); Li, Hui [Theoretical Division, Los Alamos National Laboratory, Mail Stop B227, Los Alamos, NM 87545 (United States); Li, Shengtai, E-mail: pwongwai@caltech.edu, E-mail: mhaw@caltech.edu [Mathematical Modeling and Analysis, Los Alamos National Laboratory, Mail Stop B284, Los Alamos, NM 87545 (United States)

2017-10-20

We present a new theory for the presence of apex dips in certain experimental flux ropes. Previously such dips were thought to be projections of a helical loop axis generated by the kink instability. However, new evidence from experiments and simulations suggest that the feature is a 2D cusp rather than a 3D helix. The proposed mechanism for cusp formation is a density pileup region generated by nonlinear interaction of neutral gas cones emitted from fast-gas nozzles. The results indicate that density perturbations can result in large distortions of an erupting flux rope, even in the absence of significant pressure or gravitational forces. The density pileup at the apex also suppresses the m = 1 kink mode by acting as a stationary node. Consequently, more accurate density profiles should be considered when attempting to model the stability and shape of solar and astrophysical flux ropes.

Attitudes towards insurance: the role of propensity to hold liquid asset

OpenAIRE

Antonino Iero; Giorgio Tassinari

2011-01-01

There’s a lack of research on the relationship between families’ attitudes toward insurance and their financial behavior. The Italian insurance market appears weak with regard to non life and non motor insurance: Italy ranks only 18th in Europe in terms of the ratio between non life and non motor premiums and GDP. The propensity to subscribe to an insurance contract appears largely to depend on geographical area, qualification and job activity. Regardless of their wealth, families subscribing...

Membrane-Dependent Effects of a Cytoplasmic Helix on the Structure and Drug Binding of the Influenza Virus M2 Protein

Science.gov (United States)

Cady, Sarah; Wang, Tuo; Hong, Mei

2011-01-01

The influenza A M2 protein forms a proton channel for virus infection and also mediates virus assembly and budding. The minimum protein length that encodes both functions contains the transmembrane (TM) domain (roughly residues 22 to 46) for the amantadine-sensitive proton-channel activity and an amphipathic cytoplasmic helix (roughly residues 45 to 62) for curvature induction and virus budding. However, structural studies involving the TM domain with or without the amphipathic helix differed on the drug-binding site. Here we use solid-state NMR spectroscopy to determine the amantadine binding site in the cytoplasmic-helix-containing M2(21–61). 13C-2H distance measurements of 13C-labeled protein and 2H-labeled amantadine showed that in DMPC bilayers, the first equivalent of drug bound S31 inside the M2(21–61) pore, similar to the behavior of M2TM in DMPC bilayers. The non-specific surface site of D44 observed in M2TM is disfavored in the longer peptide. Thus, the pharmacologically relevant drug-binding site in the fully functional M2(21–61) is S31 in the TM pore. Interestingly, when M2(21–61) was reconstituted into a virus-mimetic membrane containing 30% cholesterol, no chemical shift perturbation was observed for pore-lining residues, while M2TM in the same membrane exhibited drug-induced chemical shift changes. Reduction of the cholesterol level and the use of unsaturated phospholipids shifted the conformational equilibrium of M2TM fully to the bound state, but did not rescue drug binding to M2(21–61). These results suggest that the amphipathic helix, together with cholesterol, modulates the ability of the TM helices to bind amantadine. Thus, the M2 protein interacts with the lipid membrane and small-molecule inhibitors in a complex fashion, and a careful examination of the environmental dependence of the protein conformation is required to fully understand the structure-function relation of this protein. PMID:21661724

Variables affecting the propensity to buy branded beef among groups of Australian beef buyers.

Science.gov (United States)

Morales, L Emilio; Griffith, Garry; Wright, Victor; Fleming, Euan; Umberger, Wendy; Hoang, Nam

2013-06-01

Australian beef consumers have different preferences given their characteristics and the effect on expected quality of cues related to health, production process and eating experience. Beef brands using Meat Standards Australia (MSA) grades can help to signal quality and reduce consumers' uncertainty when shopping. The objective of this study is to identify the characteristics of beef buyers and their perceptions about product attributes that affect the propensity to buy branded beef. Binary logistic models were applied identifying differences between all respondents and the potential target market, including buyers in medium to high income segments, and between buyers in the target market who would buy branded beef for taste and health reasons. Variables increasing the propensity to buy branded beef include previous experience, appreciation for branded cuts and concern about quality more than size. Finally, variations in preferences for marbling and cut were found between buyers who would buy branded beef for taste and health reasons. Copyright © 2013 Elsevier Ltd. All rights reserved.

BAROMETRIC PRESSURE and Other Data from ALPHA HELIX From Chukchi Sea and Others from 19930709 to 19930807 (NODC Accession 9400062)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) and other data were collected in Bering Sea, Chukchi Sea. Data was collected from Ship ALPHA HELIX cruise Aleutian...

Proceedings of the Twentieth NASA Propagation Experimenters Meeting (NAPEX XX) and the Advanced Communications Technology Satellite (ACTS) Propagation Studies Miniworkshop

Science.gov (United States)

Golshan, Nassar (Editor)

1996-01-01

The NASA Propagation Experimenters (NAPEX) Meeting and associated Advanced Communications Technology Satellite (ACTS) Propagation Studies Miniworkshop convene yearly to discuss studies supported by the NASA Propagation Program. Representatives from the satellite communications (satcom)industry, academia, and government with an interest in space-ground radio wave propagation have peer discussion of work in progress, disseminate propagation results, and interact with the satcom industry. NAPEX XX, in Fairbanks, Alaska, June 4-5, 1996, had three sessions: (1) "ACTS Propagation Study: Background, Objectives, and Outcomes," covered results from thirteen station-years of Ka-band experiments; (2) "Propagation Studies for Mobile and Personal Satellite Applications," provided the latest developments in measurement, modeling, and dissemination of propagation phenomena of interest to the mobile, personal, and aeronautical satcom industry; and (3)"Propagation Research Topics," covered a range of topics including space/ground optical propagation experiments, propagation databases, the NASA Propagation Web Site, and revision plans for the NASA propagation effects handbooks. The ACTS Miniworkshop, June 6, 1996, covered ACTS status, engineering support for ACTS propagation terminals, and the ACTS Propagation Data Center. A plenary session made specific recommendations for the future direction of the program.

Temperature, salinity and transmissivity data from the Alpha Helix in the Arctic Ocean, 2000 - 2004 (NODC Accession 0059005)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This is calibrated CTD downcast data from five Alpha Helix cruises: HX235, 8/1/2000 - 9/30/2000 HX250, 9/1/2001 - 9/30/2001 HX260, 6/1/2002 - 6/30/2002 HX274,...

Use of Propensity Score Matching to Evaluate a National Smoking Cessation Media Campaign

Science.gov (United States)

Villanti, Andrea C.; Cullen, Jennifer; Vallone, Donna M.; Stuart, Elizabeth A.

2011-01-01

Sustained mass media campaigns have been recommended to stem the tobacco epidemic in the United States. Propensity score matching (PSM) was used to estimate the effect of awareness of a national smoking cessation media campaign (EX[R]) on quit attempts and cessation-related cognition. Participants were 4,067 smokers and recent quitters aged 18-49…

Dual catalytic purpose of the tungsten filament during the synthesis of single-helix carbon microcoils by hot-wire CVD

CSIR Research Space (South Africa)

Oliphant, CJ

2009-10-01

Full Text Available This paper reports on the deposition of crystalline single-helix carbon microcoils, in the as-deposited state, by the hot-wire chemical vapor deposition process without any special preparation of nano-sized transition metal catalysts and subsequent...

Propensity Customer the Proposition of Lawsuits: Development and test of Predictive Model for the Electricity Sector

Directory of Open Access Journals (Sweden)

Victor Manoel Cunha de Almeida

2014-11-01

Full Text Available The study aimed to propose and test a model to predict the propensity of lawsuits of Power sector utility customers. The effects of customer profile, motives of complaints, and the history of administrative actions, on the propensity to lawsuits, were investigated. The paradigm of disconfirmation of expectations was used as a theoretical framework for this study. We adopted a substantive approach to the development and testing of the predictive model. The technique of Classification Tree was chosen to operationalize the model. The method specified in this study for the creation of the decision tree was the CHAID (Chi Square Interaction Detector. Data analysis shows that the propensity to the proposition of a lawsuit does not solely depend on the nature of the problem faced by the client, but the profile and trajectory relationship with the utility provider. The results of this study offer empirical support to the theoretical paradigm of disconfirmation of expectations, more specifically, with regard to the Satisfaction Theory, Attribution Theory and the Theory of Justice and Equity. The main managerial contribution of the study lies in propose a predictive model that allows utility providers to assign each customer a probability to propose a lawsuit, which enables the proactive adoption of practices by the managers, aiming to better serve the public.

Spinal cord injury and Parkinson's disease: a population-based, propensity score-matched, longitudinal follow-up study.

Science.gov (United States)

Yeh, T-S; Huang, Y-P; Wang, H-I; Pan, S-L

2016-12-01

To investigate whether patients with spinal cord injury (SCI) are at an increased risk of developing Parkinson's disease (PD). A population-based, propensity score-matched, longitudinal follow-up cohort study. The study was conducted using the National Health Insurance (NHI) Research Database. A total of 10 125 patients with at least 2 ambulatory visits with a diagnosis of SCI in 2001 were enrolled in the SCI group. The non-SCI group comprised 10 125 propensity score-matched patients without SCI. The propensity scores were computed using a logistic regression model that included age, sex, comorbidities and socioeconomic status. The PD-free survival rates of the two groups were estimated using the Kaplan-Meier method. Stratified Cox proportional hazard regression was used to estimate the effect of SCI on subsequent occurrence of PD. During the 3-year follow-up period, 99 subjects in the SCI group and 59 in the non-SCI group developed PD. The hazard ratio of PD for the SCI group compared with the non-SCI group was 1.65 (95% confidence interval 1.16-2.33, P=0.0049). The PD-free survival rate for the SCI group was lower than that for the non-SCI group (P=0.0017). This study shows that SCI is associated with a subsequent increased risk of PD. Further studies are needed to elucidate the mechanism underlying this association.

Psychocultural Mechanisms of the Propensity toward Criminal Homicide: A Multidimensional View of the Culture of Honor

Directory of Open Access Journals (Sweden)

Monica G. T. C. Souza

2017-11-01

Full Text Available Introduction: Theory of the Culture of Honor is one of the few models in criminology specifically geared toward homicide. It proposes that, in certain societies, men must never show weakness and are required to react violently to any perceived threats to their reputation, thereby increasing their probability of committing a homicide. This has been suggested as the main explanation for the high rates of this type of crime in Brazil, particularly in the Northeast. Underlying this explanation there are complex mechanisms and processes that have yet to be clarified.Objectives: The present research aimed to investigate the workings of the possible psychocultural mechanisms underlying the culture of honor and the process through which they might affect the individual propensity toward homicide.Methods: A total of 336 Brazilian adults were assessed regarding a broad range of sociodemographic, psychological, and sociocultural variables, including their attitudes toward homicide. The resulting dataset was analyzed using Smallest Space Analysis and Facet Theory.Results: It seems that certain cultural elements associated to traditional masculinity and enhanced anger tend to promote negative personality traits and increase one’s propensity toward committing homicide.Conclusion: The findings obtained not only confirm the Theory of the Culture of Honor for the propensity toward homicide, but also explicit and clarify some of the psychocultural processes and mechanisms involved, suggesting a new scientific framework.

Tropospheric radiowave propagation beyond the horizon

CERN Document Server

Du Castel, François

1966-01-01

Tropospheric Radiowave Propagation Beyond the Horizon deals with developments concerning the tropospheric propagation of ultra-short radio waves beyond the horizon, with emphasis on the relationship between the theoretical and the experimental. Topics covered include the general conditions of propagation in the troposphere; general characteristics of propagation beyond the horizon; and attenuation in propagation. This volume is comprised of six chapters and begins with a brief historical look at the various stages that have brought the technique of transhorizon links to its state of developmen

Light propagation in linear optical media

CERN Document Server

Gillen, Glen D; Guha, Shekhar

2013-01-01

Light Propagation in Linear Optical Media describes light propagation in linear media by expanding on diffraction theories beyond what is available in classic optics books. In one volume, this book combines the treatment of light propagation through various media, interfaces, and apertures using scalar and vector diffraction theories. After covering the fundamentals of light and physical optics, the authors discuss light traveling within an anisotropic crystal and present mathematical models for light propagation across planar boundaries between different media. They describe the propagation o

PROPAGATOR: a synchronous stochastic wildfire propagation model with distributed computation engine

Science.gov (United States)

D´Andrea, M.; Fiorucci, P.; Biondi, G.; Negro, D.

2012-04-01

PROPAGATOR is a stochastic model of forest fire spread, useful as a rapid method for fire risk assessment. The model is based on a 2D stochastic cellular automaton. The domain of simulation is discretized using a square regular grid with cell size of 20x20 meters. The model uses high-resolution information such as elevation and type of vegetation on the ground. Input parameters are wind direction, speed and the ignition point of fire. The simulation of fire propagation is done via a stochastic mechanism of propagation between a burning cell and a non-burning cell belonging to its neighbourhood, i.e. the 8 adjacent cells in the rectangular grid. The fire spreads from one cell to its neighbours with a certain base probability, defined using vegetation types of two adjacent cells, and modified by taking into account the slope between them, wind direction and speed. The simulation is synchronous, and takes into account the time needed by the burning fire to cross each cell. Vegetation cover, slope, wind speed and direction affect the fire-propagation speed from cell to cell. The model simulates several mutually independent realizations of the same stochastic fire propagation process. Each of them provides a map of the area burned at each simulation time step. Propagator simulates self-extinction of the fire, and the propagation process continues until at least one cell of the domain is burning in each realization. The output of the model is a series of maps representing the probability of each cell of the domain to be affected by the fire at each time-step: these probabilities are obtained by evaluating the relative frequency of ignition of each cell with respect to the complete set of simulations. Propagator is available as a module in the OWIS (Opera Web Interfaces) system. The model simulation runs on a dedicated server and it is remote controlled from the client program, NAZCA. Ignition points of the simulation can be selected directly in a high-resolution, three

Organizational Cultures and Employees' Propensity to File Claims and/or Engage in Litigious Conduct

Science.gov (United States)

Abracosa, Gerilynn P.

2013-01-01

Purpose: The purposes of this study were to (a) investigate the connections between aspects of organizational cultures and employees' propensity to file claims and/or engage in litigious conduct against their organization, (b) ascertain behaviors of managers and supervisors implicitly sanctioned by the organization's culture that trigger employees…

Semiclassical propagation of Wigner functions.

Science.gov (United States)

Dittrich, T; Gómez, E A; Pachón, L A

2010-06-07

We present a comprehensive study of semiclassical phase-space propagation in the Wigner representation, emphasizing numerical applications, in particular as an initial-value representation. Two semiclassical approximation schemes are discussed. The propagator of the Wigner function based on van Vleck's approximation replaces the Liouville propagator by a quantum spot with an oscillatory pattern reflecting the interference between pairs of classical trajectories. Employing phase-space path integration instead, caustics in the quantum spot are resolved in terms of Airy functions. We apply both to two benchmark models of nonlinear molecular potentials, the Morse oscillator and the quartic double well, to test them in standard tasks such as computing autocorrelation functions and propagating coherent states. The performance of semiclassical Wigner propagation is very good even in the presence of marked quantum effects, e.g., in coherent tunneling and in propagating Schrodinger cat states, and of classical chaos in four-dimensional phase space. We suggest options for an effective numerical implementation of our method and for integrating it in Monte-Carlo-Metropolis algorithms suitable for high-dimensional systems.

Propagation phenomena in real world networks

CERN Document Server

Fay, Damien; Gabryś, Bogdan

2015-01-01

“Propagation, which looks at spreading in complex networks, can be seen from many viewpoints; it is undesirable, or desirable, controllable, the mechanisms generating that propagation can be the topic of interest, but in the end all depends on the setting. This book covers leading research on a wide spectrum of propagation phenomenon and the techniques currently used in its modelling, prediction, analysis and control. Fourteen papers range over topics including epidemic models, models for trust inference, coverage strategies for networks, vehicle flow propagation, bio-inspired routing algorithms, P2P botnet attacks and defences, fault propagation in gene-cellular networks, malware propagation for mobile networks, information propagation in crisis situations, financial contagion in interbank networks, and finally how to maximize the spread of influence in social networks. The compendium will be of interest to researchers, those working in social networking, communications and finance and is aimed at providin...

The Impact of Cooperation on Firms’ Innovation Propensity in Emerging Economies

Directory of Open Access Journals (Sweden)

Serdal Temel

2013-01-01

Full Text Available The importance of collaboration has been one of the main issues in innovation studies. Despite many different findings on collaboration and its impact on innovation performance, the impact of different types of collaboration on different types of innovation is still inconclusive. The purpose of this research is to investigate the effects of openness on the performance of the innovation process in a leading emerging economy. Based on Turkish CIS data, the findings reveal that doing R&D either continuously or occasionally affects the probability to introduce novelties. Conducting simultaneously marketing, organisational and process innovations also increases the likelihood to innovate. Furthermore, cooperation with partners and their effects on innovation propensity unveil that process, marketing and organisational innovations are determinants of product and service innovation, thus confirming that the various innovation types are intertwined and mutually supporting each other. From a geographical perspective, cooperating with external parties from the same country plays a dominant role in determining the innovation outcome. Cooperating with consultants and private labs on the other hand seems to negatively affect innovation performance. Surprisingly, the role of foreign cooperation remains ambiguous as results were not statistically significant. Another very interesting finding is the negative impact of firms’ size on innovation propensity. This paper, apart from its contribution to collaboration research, provides concise recommendations for policy makers and managers.

Validating the Italian Version of the Disgust and Propensity Scale-Revised

Directory of Open Access Journals (Sweden)

Riccardo M. Martoni

2017-05-01

Full Text Available The aim of this work is to evaluate the factor structure and psychometric properties of the Italian version of the Disgust Propensity and Sensitivity Scale-Revised (DPSS-R, 16 items in two samples taken from the general population. In the first study, 285 participants completed the DPSS-R questionnaire through a web-based survey. Exploratory factor analysis for ordinal Likert-type data supported the existence of four underlying factors, reflecting self-focused disgust, disgust propensity, somatic anxiety and disgust sensitivity. In the second study, an independent sample of 293 participants was enrolled as a test set to validate the factor structure obtained in the exploratory phase. The factor solution was confirmed, but showed quite highly correlated latent factors. We fitted the model and tested whether or not the bifactor structure was better than the previous one (four correlated factors. Actually, we had evidence supporting the presence of a general factor, providing a measure of disgust susceptibility, along with the four specific factors previously defined. This result could be useful also from the clinical perspective since the DPSS-R questionnaire will be used in clinical context, where underlying factors may be related to different and specific psychopathological profiles. Finally, we examined and visualized the interrelationships among the four DPSS-R factors and the external scales (Anxiety Sensitivity, Disgust Scale and Padua using a graphical model approach.

Propagation of dynamic measurement uncertainty

International Nuclear Information System (INIS)

Hessling, J P

2011-01-01

The time-dependent measurement uncertainty has been evaluated in a number of recent publications, starting from a known uncertain dynamic model. This could be defined as the 'downward' propagation of uncertainty from the model to the targeted measurement. The propagation of uncertainty 'upward' from the calibration experiment to a dynamic model traditionally belongs to system identification. The use of different representations (time, frequency, etc) is ubiquitous in dynamic measurement analyses. An expression of uncertainty in dynamic measurements is formulated for the first time in this paper independent of representation, joining upward as well as downward propagation. For applications in metrology, the high quality of the characterization may be prohibitive for any reasonably large and robust model to pass the whiteness test. This test is therefore relaxed by not directly requiring small systematic model errors in comparison to the randomness of the characterization. Instead, the systematic error of the dynamic model is propagated to the uncertainty of the measurand, analogously but differently to how stochastic contributions are propagated. The pass criterion of the model is thereby transferred from the identification to acceptance of the total accumulated uncertainty of the measurand. This increases the relevance of the test of the model as it relates to its final use rather than the quality of the calibration. The propagation of uncertainty hence includes the propagation of systematic model errors. For illustration, the 'upward' propagation of uncertainty is applied to determine if an appliance box is damaged in an earthquake experiment. In this case, relaxation of the whiteness test was required to reach a conclusive result

Identification of the roles of individual amino acid residues of the helix E of the major antenna of photosystem II (LHCII) by alanine scanning mutagenesis.

Science.gov (United States)

Liu, Cheng; Rao, Yan; Zhang, Lei; Yang, Chunhong

2014-10-01

The functions of the helix E (W97-F105), an amphiphilic lumenal 310 helix of the major antenna of photosystem II (LHCII), are still unidentified. To elucidate the roles of individual amino acid residue of the helix E, alanine scanning mutagenesis has been performed to mutate every residue of this domain to alanine. The influence of every alanine substitution on the structure and function of LHCII has been investigated biochemically and spectroscopically. The results show that all mutations have little impact on the pigment binding and configuration. However, many mutants presented decreased thermo- or photo-stability compared with the wild type, highlighting the significance of this helix to the stability of LHCII. The most critical residue for stability is W97. The mutant W97A yielded very fragile trimeric pigment protein complexes. The structural analysis revealed that the hydrogen bonding and aromatic interactions between W97, F195, F194 and a water molecule contributed greatly to the stability of LHCII. Moreover, Q103A and F105A have been identified to be able to reinforce the tendency of aggregation in vitro. The structural analysis suggested that the enhancement in aggregation formation for Q103A and F105A might be attributed to the changing hydrophobicity of the region. © The Authors 2014. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Dynamic compression plate (DCP) fixation of propagating medial condylar fractures of the third metacarpal/metatarsal bone in 30 racehorses: retrospective analysis (1990-2005).

Science.gov (United States)

Goodrich, L R; Nixon, A J; Conway, J D; Morley, P S; Bladon, B M; Hogan, P M

2014-11-01

An in-depth review of dynamic compression plate (DCP) fixation of propagating medial condyle fractures of the third metacarpus or metatarsus has not been previously reported. To describe the technique, evaluate short-term outcome and long-term race performance of racehorses that underwent DCP fixation for repair of propagating or spiralling medial condylar fractures of the third metacarpal (McIII) or metatarsal (MtIII) bone. Retrospective case series. The surgical case records of 30 horses with propagating fractures of the medial condyle of McIII or MtIII were reviewed. Medical information included: age, breed, sex, presentation, how injury occurred (racing or training), surgical treatment and post operative complications. Racing information included: starts, top 3 placing and career earnings. Long propagating fractures of the medial condyle of Mc/tIII were identified in 23 Thoroughbred (TB) and 7 Standardbred (STB) racehorses. The fracture spiralled proximally in 22 of 30 cases (73%). Standardbreds had a higher propensity for hindlimb involvement (71%), whereas TBs tended to have more front limb involvement (61%). Twelve of 30 (40%) horses raced post surgery. Career earnings were significantly lower for TB horses with medial condylar fractures; $34,916 when compared with the national average of $60,841 (P≤0.03). Overall, horses having DCP fixation for medial condylar fractures had less starts post surgery (3.1 TBs and 5.8 STBs) compared with the national average (7 TBs and 17.3 STBs) and decreased lifetime starts 13.4 (TBs) compared with 17.3 nationally. Propagating medial condyle fractures can be repaired with plate fixation to potentially lessen the risk of catastrophic fracture destabilisation and return to racing can be expected in 40% of horses. Further prospective studies are warranted comparing lag screw fixation with DCP fixation for repair of severe medial condylar fractures of the metacarpus/metatarsus. © 2013 The Authors. Equine Veterinary Journal

Single-photon absorption of isolated collagen mimetic peptides and triple-helix models in the VUV-X energy range

NARCIS (Netherlands)

Schwob, Lucas; Lalande, Mathieu; Rangama, Jimmy; Egorov, Dmitrii; Hoekstra, Ronnie; Pandey, Rahul; Eden, Samuel; Schlathölter, Thomas; Vizcaino, Violaine; Poully, Jean-Christophe

2017-01-01

Cartilage and tendons owe their special mechanical properties to the fibrous collagen structure. These strong fibrils are aggregates of a sub-unit consisting of three collagen proteins wound around each other in a triple helix. Even though collagen is the most abundant protein in the human body, the

Stakeholder engagement in quattro helix model for mobile phone reverse logistics in Indonesia: a conceptual framework

Science.gov (United States)

Maheswari, H.; Yudoko, G.; Adhiutama, A.

2017-12-01

The number of e-waste from mobile phone industry is still dominating until now. This is happened because there is no mutual commitment from all of parties i.e. businesses, government, and societies to reduce the use of mobile phone that has the shortest product life cycle. There are many researches study about firms’ motivation and government’s role, other discuss about actions of communities in supporting reverse logistics implementation. Unfortunately, research about engagement mechanism that involving all parties is still rare. Therefore, it is important to find the engagement model through this conceptual paper and it is expected useful to build the novel model. Through literature review, the results of this research are establishing the Quattro helix model as the appropriate structure to build the robust team by exploring stakeholder theories; mapping the engagement model either in form of collaboration or participation that consider stakeholders’ role and motivation and finding six types of engagement that consider their interest; and determining the novel model of engagement through Quattro helix model for implementing reverse logistics in handling e-waste by describing the linkage and the gaps among existing model.

An α‐Helix‐Mimicking 12,13‐Helix: Designed α/β/γ‐Foldamers as Selective Inhibitors of Protein–Protein Interactions

Science.gov (United States)

Grison, Claire M.; Miles, Jennifer A.; Robin, Sylvie

2016-01-01

Abstract A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein–protein interactions (PPIs). In this work, trans‐2‐aminocyclobutanecarboxylic acid (tACBC) was used as the key β‐amino acid component in the design of α/β/γ‐peptides to structurally mimic a native α‐helix. Suitably functionalized α/β/γ‐peptides assume an α‐helix‐mimicking 12,13‐helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild‐type α‐peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction. PMID:27467859

Propagation Engineering in Wireless Communications

CERN Document Server

Ghasemi, Abdollah; Ghasemi, Farshid

2012-01-01

Wireless communications has seen explosive growth in recent decades, in a realm that is both broad and rapidly expanding to include satellite services, navigational aids, remote sensing, telemetering, audio and video broadcasting, high-speed data communications, mobile radio systems and much more. Propagation Engineering in Wireless Communications deals with the basic principles of radiowaves propagation for frequency bands used in radio-communications, offering descriptions of new achievements and newly developed propagation models. The book bridges the gap between theoretical calculations and approaches, and applied procedures needed for advanced radio links design. The primary objective of this two-volume set is to demonstrate the fundamentals, and to introduce propagation phenomena and mechanisms that engineers are likely to encounter in the design and evaluation of radio links of a given type and operating frequency. Volume one covers basic principles, along with tropospheric and ionospheric propagation,...

Five Steps to Successfully Implement and Evaluate Propensity Score Matching in Clinical Research Studies.

Science.gov (United States)

Staffa, Steven J; Zurakowski, David

2018-01-09

In clinical research, the gold standard level of evidence is the randomized controlled trial (RCT). The availability of nonrandomized retrospective data is growing; however, a primary concern of analyzing such data is comparability of the treatment groups with respect to confounding variables. Propensity score matching (PSM) aims to equate treatment groups with respect to measured baseline covariates to achieve a comparison with reduced selection bias. It is a valuable statistical methodology that mimics the RCT, and it may create an "apples to apples" comparison while reducing bias due to confounding. PSM can improve the quality of anesthesia research and broaden the range of research opportunities. PSM is not necessarily a magic bullet for poor-quality data, but rather may allow the researcher to achieve balanced treatment groups similar to a RCT when high-quality observational data are available. PSM may be more appealing than the common approach of including confounders in a regression model because it allows for a more intuitive analysis of a treatment effect between 2 comparable groups.We present 5 steps that anesthesiologists can use to successfully implement PSM in their research with an example from the 2015 Pediatric National Surgical Quality Improvement Program: a validated, annually updated surgery and anesthesia pediatric database. The first step of PSM is to identify its feasibility with regard to the data at hand and ensure availability of data on any potential confounders. The second step is to obtain the set of propensity scores from a logistic regression model with treatment group as the outcome and the balancing factors as predictors. The third step is to match patients in the 2 treatment groups with similar propensity scores, balancing all factors. The fourth step is to assess the success of the matching with balance diagnostics, graphically or analytically. The fifth step is to apply appropriate statistical methodology using the propensity

The Digital Literacy Debate: An Investigation of Digital Propensity and Information and Communication Technology

Science.gov (United States)

Nasah, Angelique; DaCosta, Boaventura; Kinsell, Carolyn; Seok, Soonhwa

2010-01-01

Research suggests students' use of information and communication technology (ICT) may be more a matter of digital literacy and access rather than a generational trait. We sought to identify ICT preferences of post-secondary students (N = 580) through a Digital Propensity Index (DPI), investigating communication methods, Internet practices and the…

Comparing treatment effects after adjustment with multivariable Cox proportional hazards regression and propensity score methods

NARCIS (Netherlands)

Martens, Edwin P; de Boer, Anthonius; Pestman, Wiebe R; Belitser, Svetlana V; Stricker, Bruno H Ch; Klungel, Olaf H

PURPOSE: To compare adjusted effects of drug treatment for hypertension on the risk of stroke from propensity score (PS) methods with a multivariable Cox proportional hazards (Cox PH) regression in an observational study with censored data. METHODS: From two prospective population-based cohort

Income inequality and cooperative propensities in developing economies

DEFF Research Database (Denmark)

Rosenbaum, Stephen Mark; Billinger, Stephan; Twerefou, Daniel K.

2016-01-01

Purpose – The purpose of this paper is to examine the influence of income inequality on cooperative propensities, and thus the ability of individuals to resolve collective action dilemmas. Design/methodology/approach – The paper presents a meta-study of 32 developing country lab experiments...... income inequality. Findings – The meta-study findings of a significant negative relationship between income inequality and contribution levels in the PGG are corroborated by the own laboratory experimental findings that participants in more unequal Nigeria are significantly less altruistic and exhibit...... to elicit tacit cooperation in developing countries. Originality/value – The major contributions of this paper are the novel meta-analysis and the first attempt to examine the influence of personal income levels on cooperative behaviour in societies characterized by differential levels of income inequality....

Fatigue crack propagation behavior under creep conditions

International Nuclear Information System (INIS)

Ohji, Kiyotsugu; Kubo, Shiro

1991-01-01

The crack propagation behavior of the SUS 304 stainless steel under creep-fatigue conditions was reviewed. Cracks propagated either in purely time-dependent mode or in purely cycle-dependent mode, depending on loading conditions. The time-dependent crack propagation rate was correlated with modified J-integral J * and the cycle-dependent crack propagation rate was correlated with J-integral range ΔJ f . Threshold was observed in the cycle-dependent crack propagation, and below this threshold the time-dependent crack propagation appeared. The crack propagation rates were uniquely characterized by taking the effective values of J * and ΔJ f , when crack closure was observed. Change in crack propagation mode occurred reversibly and was predicted by the competitive damage model. The threshold disappeared and the cycle-dependent crack propagation continued in a subthreshold region under variable amplitude conditions, where the threshold was interposed between the maximum and minimum ΔJ f . (orig.)

The effects of breastfeeding on childhood BMI: a propensity score matching approach.

Science.gov (United States)

Gibson, Laura A; Hernández Alava, Mónica; Kelly, Michael P; Campbell, Michael J

2017-12-01

Many studies have found a statistical association between breastfeeding and childhood adiposity. This paper investigates whether breastfeeding has an effect on subsequent childhood body mass index (BMI) using propensity scores to account for confounding. We use data from the Millennium Cohort Study, a nationally representative UK cohort survey, which contains detailed information on infant feeding and childhood BMI. Propensity score matching is used to investigate the mean BMI in children breastfed exclusively and partially for different durations of time. We find statistically significant influences of breastfeeding on childhood BMI, particularly in older children, when breastfeeding is prolonged and exclusive. At 7 years, children who were exclusively breastfed for 16 weeks had a BMI 0.28 kg/m2 (95% confidence interval 0.07 to 0.49) lower than those who were never breastfed, a 2% reduction from the mean BMI of 16.6 kg/m2. For this young cohort, even small effects of breastfeeding on BMI could be important. In order to reduce BMI, breastfeeding should be encouraged as part of wider lifestyle intervention. This evidence could help to inform public health bodies when creating public health guidelines and recommendations. © The Author 2016. Published by Oxford University Press on behalf of Faculty of Public Health.

An Intramolecular Salt Bridge in Bacillus thuringiensis Cry4Ba Toxin Is Involved in the Stability of Helix α-3, Which Is Needed for Oligomerization and Insecticidal Activity.

Science.gov (United States)

Pacheco, Sabino; Gómez, Isabel; Sánchez, Jorge; García-Gómez, Blanca-Ines; Soberón, Mario; Bravo, Alejandra

2017-10-15

Bacillus thuringiensis three-domain Cry toxins kill insects by forming pores in the apical membrane of larval midgut cells. Oligomerization of the toxin is an important step for pore formation. Domain I helix α-3 participates in toxin oligomerization. Here we identify an intramolecular salt bridge within helix α-3 of Cry4Ba (D111-K115) that is conserved in many members of the family of three-domain Cry toxins. Single point mutations such as D111K or K115D resulted in proteins severely affected in toxicity. These mutants were also altered in oligomerization, and the mutant K115D was more sensitive to protease digestion. The double point mutant with reversed charges, D111K-K115D, recovered both oligomerization and toxicity, suggesting that this salt bridge is highly important for conservation of the structure of helix α-3 and necessary to promote the correct oligomerization of the toxin. IMPORTANCE Domain I has been shown to be involved in oligomerization through helix α-3 in different Cry toxins, and mutations affecting oligomerization also elicit changes in toxicity. The three-dimensional structure of the Cry4Ba toxin reveals an intramolecular salt bridge in helix α-3 of domain I. Mutations that disrupt this salt bridge resulted in changes in Cry4Ba oligomerization and toxicity, while a double point reciprocal mutation that restored the salt bridge resulted in recovery of toxin oligomerization and toxicity. These data highlight the role of oligomer formation as a key step in Cry4Ba toxicity. Copyright © 2017 American Society for Microbiology.

Critical significance of the region between Helix 1 and 2 for efficient dominant-negative inhibition by conversion-incompetent prion protein.

Directory of Open Access Journals (Sweden)

Yuzuru Taguchi

Full Text Available Prion diseases are fatal infectious neurodegenerative disorders in man and animals associated with the accumulation of the pathogenic isoform PrP(Sc of the host-encoded prion protein (PrP(c. A profound conformational change of PrP(c underlies formation of PrP(Sc and prion propagation involves conversion of PrP(c substrate by direct interaction with PrP(Sc template. Identifying the interfaces and modalities of inter-molecular interactions of PrPs will highly advance our understanding of prion propagation in particular and of prion-like mechanisms in general. To identify the region critical for inter-molecular interactions of PrP, we exploited here dominant-negative inhibition (DNI effects of conversion-incompetent, internally-deleted PrP (ΔPrP on co-expressed conversion-competent PrP. We created a series of ΔPrPs with different lengths of deletions in the region between first and second α-helix (H1∼H2 which was recently postulated to be of importance in prion species barrier and PrP fibril formation. As previously reported, ΔPrPs uniformly exhibited aberrant properties including detergent insolubility, limited protease digestion resistance, high-mannose type N-linked glycans, and intracellular localization. Although formerly controversial, we demonstrate here that ΔPrPs have a GPI anchor attached. Surprisingly, despite very similar biochemical and cell-biological properties, DNI efficiencies of ΔPrPs varied significantly, dependant on location and inversely correlated with the size of deletion. This data demonstrates that H1∼H2 and the region C-terminal to it are critically important for efficient DNI. It also suggests that this region is involved in PrP-PrP interaction and conversion of PrP(C into PrP(Sc. To reconcile the paradox of how an intracellular PrP can exert DNI, we demonstrate that ΔPrPs are subject to both proteasomal and lysosomal/autophagic degradation pathways. Using autophagy pathways ΔPrPs obtain access to the locale

Temperature, salinity, conductivity, pressure, transmissivity measurements collected using CTD from the Alpha Helix in the Chukchi Sea during 1996 (NODC Accession 0061042)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature, salinity, conductivity, pressure, and transmissivity data gathered by CTD from the Alpha Helix (cruise HX194), September 1996

The Association between the Availability of Sugar-Sweetened Beverage in School Vending Machines and Its Consumption among Adolescents in California: A Propensity Score Matching Approach

Directory of Open Access Journals (Sweden)

Lu Shi

2010-01-01

Full Text Available There is controversy over to what degree banning sugar-sweetened beverage (SSB sales at schools could decrease the SSB intake. This paper uses the adolescent sample of 2005 California Health Interview Survey to estimate the association between the availability of SSB from school vending machines and the amount of SSB consumption. Propensity score stratification and kernel-based propensity score matching are used to address the selection bias issue in cross-sectional data. Propensity score stratification shows that adolescents who had access to SSB through their school vending machines consumed 0.170 more drinks of SSB than those who did not (<.05. Kernel-based propensity score matching shows the SSB consumption difference to be 0.158 on the prior day (<.05. This paper strengthens the evidence for the association between SSB availability via school vending machines and the actual SSB consumption, while future studies are needed to explore changes in other beverages after SSB becomes less available.

Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer

NARCIS (Netherlands)

Forrest, LR; Tieleman, DP; Sansom, MSP

Integral membrane proteins containing at least one transmembrane (TM) alpha-helix are believed to account for between 20% and 30% of most genomes. There are several algorithms that accurately predict the number and position of TM helices within,a membrane protein sequence. However, these methods

Modelling the gluon propagator

Energy Technology Data Exchange (ETDEWEB)

Leinweber, D.B.; Parrinello, C.; Skullerud, J.I.; Williams, A.G

1999-03-01

Scaling of the Landau gauge gluon propagator calculated at {beta} = 6.0 and at {beta} = 6.2 is demonstrated. A variety of functional forms for the gluon propagator calculated on a large (32{sup 3} x 64) lattice at {beta} = 6.0 are investigated.

Vibrational autoionization in PF3: Doing violence to the propensity rule

International Nuclear Information System (INIS)

Berkowitz, J.; Greene, J.P.

1984-01-01

The photoionization spectrum of PF + 3 in its threshold region displays two prominent progressions of autoionization peaks. When these are analyzed, together with earlier photoabsorption studies and a photoelectron spectrum, they lead to the conclusion that vibrational autoionization is occurring, with Δν< or =-13. This conclusion stands in sharp contrast with the current theory of vibrational autoionization, which predicts a propensity rule Δν = -1. Other examples from the recent literature are summarized, to suggest that a more general theory of vibrational autoionization is required

Semiclassical propagator of the Wigner function.

Science.gov (United States)

Dittrich, Thomas; Viviescas, Carlos; Sandoval, Luis

2006-02-24

Propagation of the Wigner function is studied on two levels of semiclassical propagation: one based on the Van Vleck propagator, the other on phase-space path integration. Leading quantum corrections to the classical Liouville propagator take the form of a time-dependent quantum spot. Its oscillatory structure depends on whether the underlying classical flow is elliptic or hyperbolic. It can be interpreted as the result of interference of a pair of classical trajectories, indicating how quantum coherences are to be propagated semiclassically in phase space. The phase-space path-integral approach allows for a finer resolution of the quantum spot in terms of Airy functions.

Sound propagation in cities

NARCIS (Netherlands)

Salomons, E.; Polinder, H.; Lohman, W.; Zhou, H.; Borst, H.

2009-01-01

A new engineering model for sound propagation in cities is presented. The model is based on numerical and experimental studies of sound propagation between street canyons. Multiple reflections in the source canyon and the receiver canyon are taken into account in an efficient way, while weak

Unirradiated cladding rip-propagation tests

International Nuclear Information System (INIS)

Hu, W.L.; Hunter, C.W.

1981-04-01

The size of cladding rips which develop when a fuel pin fails can affect the subassembly cooling and determine how rapidly fuel escapes from the pin. The object of the Cladding Rip Propagation Test (CRPT) was to quantify the failure development of cladding so that a more realistic fuel pin failure modeling may be performed. The test results for unirradiated 20% CS 316 stainless steel cladding show significantly different rip propagation behavior at different temperatures. At room temperature, the rip growth is stable as the rip extension increases monotonically with the applied deformation. At 500 0 C, the rip propagation becomes unstable after a short period of stable rip propagation. The rapid propagation rate is approximately 200 m/s, and the critical rip length is 9 mm. At test temperatures above 850 0 C, the cladding exhibits very high failure resistances, and failure occurs by multiple cracking at high cladding deformation. 13 figures

A Triple Helix Strategy for Promoting SME Development: The Case of a Dried Banana Community Enterprise in Thailand

Science.gov (United States)

Yuwawutto, Sauwapa; Smitinont, Thitapha; Charoenanong, Numtip; Yokakul, Nattaka; Chatratana, Sonchai; Zawdie, Girma

2010-01-01

This paper examines the university-industry-government relationship as a mechanism for enhancing the efficiency and competitiveness of small and medium-sized enterprises (SMEs). The case of a community enterprise producing dried banana products in the north of Thailand is used to demonstrate the significance of the Triple Helix model for business…

Ulinastatin administration is associated with a lower incidence of acute kidney injury after cardiac surgery: a propensity score matched study.

Science.gov (United States)

Wan, Xin; Xie, Xiangcheng; Gendoo, Yasser; Chen, Xin; Ji, Xiaobing; Cao, Changchun

2016-02-17

Systemic inflammation is involved in the development of acute kidney injury (AKI) after cardiac surgery with cardiopulmonary bypass (CPB). Ulinastatin, a urinary trypsin inhibitor (UTI), possesses a variety of anti-inflammatory effects. Therefore, we hypothesized that the administration of ulinastatin would reduce the occurrence of AKI in patients undergoing cardiac surgery with CPB. A retrospective propensity score matched analysis was used to evaluate the effect of ulinastatin on the development of AKI in patients undergoing first documented cardiac surgery with CPB between January 2008 and December 2012 in our hospital. Multiple logistic regression models were also employed to identify the association between UTI administration and development of AKI. A total of 2072 patients who underwent cardiac surgery with CPB met the inclusion criteria. Before propensity score matching, variables such as age, baseline creatinine, CPB duration, red blood cells transfused, and hematocrit were statistically different between the ulinastatin (UTI) group and the control group. On the basis of propensity scores, 409 UTI patients were successfully matched to the 409 patients from among those 1663 patients without UTI administration. After propensity score matching, no statistically significant differences in the baseline characteristics were found between the UTI group and the control group. The propensity score matched cohort analysis revealed that AKI and the need for renal replacement therapy occurred more frequently in the control group than in the UTI group (40.83% vs. 30.32%, P = 0.002; 2.44% vs. 0.49%, P = 0.02, respectively). However, there were no significant differences in mortality, length of intensive care unit stay, and length of hospital stay between the UTI group and the control group. Using multivariate logistic regression analysis, we found ulinastatin played a protective role in the development of AKI after cardiac surgery (odds ratio 0.71, 95% confidence

Marginal Propensity to Consume in Hungary: The long-term versus Short-term Challenges to Policy Makers

Directory of Open Access Journals (Sweden)

Keith Write

2017-11-01

Full Text Available This study uses Hungarian quarterly data from the International Monetary Fund to estimate a distributed lag model whose coefficients allow derivation of the short-run and long-run marginal propensities to consume.  MPCs are main factors determining the consumption, investment, government spending, and export and import multipliers of the economy.  Hungary's economy has stagnated and its policy makers are exploring new ways to manage its economy.  Our model reveals that the numerical value of Hungarian short-run marginal propensity to consume (MPC is 0.4081181655 and the long-run MPC is 0.9458619.  These results are consistent with the corresponding figures in emerging and advanced economies.  These derived MPCs suggest that Hungarian economic policy makers should use fiscal instruments to bring these macroeconomic variables back to their long-term trend effectively

On the Importance of Reliable Covariate Measurement in Selection Bias Adjustments Using Propensity Scores

Science.gov (United States)

Steiner, Peter M.; Cook, Thomas D.; Shadish, William R.

2011-01-01

The effect of unreliability of measurement on propensity score (PS) adjusted treatment effects has not been previously studied. The authors report on a study simulating different degrees of unreliability in the multiple covariates that were used to estimate the PS. The simulation uses the same data as two prior studies. Shadish, Clark, and Steiner…

BAROMETRIC PRESSURE and Other Data from ALPHA HELIX From North Pacific Ocean and Others from 19931016 to 19931103 (NODC Accession 9400051)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Conductivity, Temperature and Depth (CTD) and other data were collected in Bering Sea and North Pacific Ocean. Data was collected from Ship ALPHA HELIX cruise...

Characterization of the biomechanical properties of T4 pili expressed by Streptococcus pneumoniae--a comparison between helix-like and open coil-like pili.

Science.gov (United States)

Castelain, Mickaël; Koutris, Efstratios; Andersson, Magnus; Wiklund, Krister; Björnham, Oscar; Schedin, Staffan; Axner, Ove

2009-07-13

Bacterial adhesion organelles, known as fimbria or pili, are expressed by gram-positive as well as gram-negative bacteria families. These appendages play a key role in the first steps of the invasion and infection processes, and they therefore provide bacteria with pathogenic abilities. To improve the knowledge of pili-mediated bacterial adhesion to host cells and how these pili behave under the presence of an external force, we first characterize, using force measuring optical tweezers, open coil-like T4 pili expressed by gram-positive Streptococcus pneumoniae with respect to their biomechanical properties. It is shown that their elongation behavior can be well described by the worm-like chain model and that they possess a large degree of flexibility. Their properties are then compared with those of helix-like pili expressed by gram-negative uropathogenic Escherichia coli (UPEC), which have different pili architecture. The differences suggest that these two types of pili have distinctly dissimilar mechanisms to adhere and sustain external forces. Helix-like pili expressed by UPEC bacteria adhere to host cells by single adhesins located at the distal end of the pili while their helix-like structures act as shock absorbers to dampen the irregularly shear forces induced by urine flow and to increase the cooperativity of the pili ensemble, whereas open coil-like pili expressed by S. pneumoniae adhere to cells by a multitude of adhesins distributed along the pili. It is hypothesized that these two types of pili represent different strategies of adhering to host cells in the presence of external forces. When exposed to significant forces, bacteria expressing helix-like pili remain attached by distributing the external force among a multitude of pili, whereas bacteria expressing open coil-like pili sustain large forces primarily by their multitude of binding adhesins which presumably detach sequentially.

A conserved degron containing an amphipathic helix regulates the cholesterol-mediated turnover of human squalene monooxygenase, a rate-limiting enzyme in cholesterol synthesis.

Science.gov (United States)

Chua, Ngee Kiat; Howe, Vicky; Jatana, Nidhi; Thukral, Lipi; Brown, Andrew J

2017-12-08

Cholesterol biosynthesis in the endoplasmic reticulum (ER) is tightly controlled by multiple mechanisms to regulate cellular cholesterol levels. Squalene monooxygenase (SM) is the second rate-limiting enzyme in cholesterol biosynthesis and is regulated both transcriptionally and post-translationally. SM undergoes cholesterol-dependent proteasomal degradation when cholesterol is in excess. The first 100 amino acids of SM (designated SM N100) are necessary for this degradative process and represent the shortest cholesterol-regulated degron identified to date. However, the fundamental intrinsic characteristics of this degron remain unknown. In this study, we performed a series of deletions, point mutations, and domain swaps to identify a 12-residue region (residues Gln-62-Leu-73), required for SM cholesterol-mediated turnover. Molecular dynamics and circular dichroism revealed an amphipathic helix within this 12-residue region. Moreover, 70% of the variation in cholesterol regulation was dependent on the hydrophobicity of this region. Of note, the earliest known Doa10 yeast degron, Deg1, also contains an amphipathic helix and exhibits 42% amino acid similarity with SM N100. Mutating SM residues Phe-35/Ser-37/Leu-65/Ile-69 into alanine, based on the key residues in Deg1, blunted SM cholesterol-mediated turnover. Taken together, our results support a model whereby the amphipathic helix in SM N100 attaches reversibly to the ER membrane depending on cholesterol levels; with excess, the helix is ejected and unravels, exposing a hydrophobic patch, which then serves as a degradation signal. Our findings shed new light on the regulation of a key cholesterol synthesis enzyme, highlighting the conservation of critical degron features from yeast to humans. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Propagation engineering in radio links design

CERN Document Server

Ghasemi, Abdollah; Ghasemi, Farshid

2013-01-01

Propagation Engineering in Radio Link Design covers the basic principles of radiowaves propagation in a practical manner.  This fundamental understanding enables the readers to design radio links efficiently. This book elaborates on new achievements as well as recently developed propagation models.  This is in addition to a comprehensive overview of fundamentals of propagation in various scenarios. It examines theoretical calculations, approaches and applied procedures needed for radio links design. The authors study and analysis of the main propagation phenomena and its mechanisms based on the recommendations of International Telecommunications Union, (ITU). The book has been organized in 9 chapters and examines the role of antennas and passive reflectors in radio services, propagation mechanisms related to radar, satellite, short distance, broadcasting and trans-horizon radio links, with two chapters devoted to radio noise and main  parameters of radio link design. The book presents some 278 illustration...

On the mechanism of irradiation effect on the function of Helix pomatia neuron Na+, K+-pump

International Nuclear Information System (INIS)

Ajrapetyan, S.N.; Egorova, E.G.; Sagiyan, A.A.; Dadalyan, S.S.; Dvoretskij, A.I.; Sulejmonyan, M.A.

1987-01-01

Mechanism of irradiation effect on passive permeability, Na + /Ca 2+ exchange, Na + , K + -pump function intensity, the number of membrane functionally active pump units (Na + , K + -ATP-ase molecules) was determined using Helix pomatia and nervous ganglions isolated from them and irradiated by 5.16 Kl/kg dose. The data obtained show that ionizing radiation leads to obvious destructions in the mechanisms of neuron Na + , K + -pump functioning

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome

Science.gov (United States)

2017-01-10

benchmarks of conformational sampling methods and their all-atom force fields plus solvent descriptions to accurately model structural transitions on a...mol·Å2). The utilities and programming libraries of the Multiscale Modeling Tools for Structural Biology (MMTSB) (Feig et al., 2004) were used to...extensively benchmarked with the CHARMM22 force field, this force field was applied with the CMAP backbone dihedral cross-term extension (Mackerell

Propensity scores-potential outcomes framework to incorporate severity probabilities in the highway safety manual crash prediction algorithm.

Science.gov (United States)

Sasidharan, Lekshmi; Donnell, Eric T

2014-10-01

Accurate estimation of the expected number of crashes at different severity levels for entities with and without countermeasures plays a vital role in selecting countermeasures in the framework of the safety management process. The current practice is to use the American Association of State Highway and Transportation Officials' Highway Safety Manual crash prediction algorithms, which combine safety performance functions and crash modification factors, to estimate the effects of safety countermeasures on different highway and street facility types. Many of these crash prediction algorithms are based solely on crash frequency, or assume that severity outcomes are unchanged when planning for, or implementing, safety countermeasures. Failing to account for the uncertainty associated with crash severity outcomes, and assuming crash severity distributions remain unchanged in safety performance evaluations, limits the utility of the Highway Safety Manual crash prediction algorithms in assessing the effect of safety countermeasures on crash severity. This study demonstrates the application of a propensity scores-potential outcomes framework to estimate the probability distribution for the occurrence of different crash severity levels by accounting for the uncertainties associated with them. The probability of fatal and severe injury crash occurrence at lighted and unlighted intersections is estimated in this paper using data from Minnesota. The results show that the expected probability of occurrence of fatal and severe injury crashes at a lighted intersection was 1 in 35 crashes and the estimated risk ratio indicates that the respective probabilities at an unlighted intersection was 1.14 times higher compared to lighted intersections. The results from the potential outcomes-propensity scores framework are compared to results obtained from traditional binary logit models, without application of propensity scores matching. Traditional binary logit analysis suggests that

A de novo designed monomeric, compact three helix bundle protein on a carbohydrate template

DEFF Research Database (Denmark)

Malik, Leila; Nygård, Jesper; Christensen, Niels Johan

2015-01-01

De novo design and chemical synthesis of proteins and of other artificial structures, which mimic them, is a central strategy for understanding protein folding and for accessing proteins with novel functions. We have previously described carbohydrates as templates for the assembly of artificial...... the template could facilitate protein folding. Here we report the design and synthesis of 3-helix bundle carboproteins on deoxy-hexopyranosides. The carboproteins were analyzed by CD, AUC, SAXS, and NMR, which revealed the formation of the first compact, and folded monomeric carboprotein distinctly different...

Triple Helix and European Union (EU Funding: The case of Latin America, especially Mexico and the Seventh European Framework Program

Directory of Open Access Journals (Sweden)

Jürgen Haberleithner

2010-05-01

Full Text Available The following analysis not only seeks to develop new potential intervention models; it also aims to create a detailed analysis of the existing problems with regards to communication among the active participants of Triple Helix (especially in Mexico. The special situation in Latin America with regards to existing corruption, the unequal distribution of power between the government and the private sector, dependence on other economies and other social issues will be analysed in accordance with the main focus of the investigation. The subsequent linking of potential partners to the development of an initiative for submitting a future Triple Helix/FP7 project represent an important contribution to a longer-term perspective on the preceding investigation. The potential partnerships between Europe and Latin America (in addition to other possible world regions, such as, for example, Pacific Asia will create an initial project draft within the scope of the conference.

Propagation engineering in wireless communications

CERN Document Server

Ghasemi, Abdollah; Ghasemi, Farshid

2016-01-01

This book covers the basic principles for understanding radio wave propagation for common frequency bands used in radio-communications. This includes achievements and developments in propagation models for wireless communication. This book is intended to bridge the gap between the theoretical calculations and approaches to the applied procedures needed for radio links design in a proper manner. The authors emphasize propagation engineering by giving fundamental information and explain the use of basic principles together with technical achievements. This new edition includes additional information on radio wave propagation in guided media and technical issues for fiber optics cable networks with several examples and problems. This book also includes a solution manual - with 90 solved examples distributed throughout the chapters - and 158 problems including practical values and assumptions.

Genotoxicity of Nicotiana tabacum leaves on Helix aspersa.

Science.gov (United States)

da Silva, Fernanda R; Erdtmann, Bernardo; Dalpiaz, Tiago; Nunes, Emilene; Ferraz, Alexandre; Martins, Tales L C; Dias, Johny F; da Rosa, Darlan P; Porawskie, Marilene; Bona, Silvia; da Silva, Juliana

2013-07-01

Tobacco farmers are routinely exposed to complex mixtures of inorganic and organic chemicals present in tobacco leaves. In this study, we examined the genotoxicity of tobacco leaves in the snail Helix aspersa as a measure of the risk to human health. DNA damage was evaluated using the micronucleus test and the Comet assay and the concentration of cytochrome P450 enzymes was estimated. Two groups of snails were studied: one fed on tobacco leaves and one fed on lettuce (Lactuca sativa L) leaves (control group). All of the snails received leaves (tobacco and lettuce leaves were the only food provided) and water ad libitum. Hemolymph cells were collected after 0, 24, 48 and 72 h. The Comet assay and micronucleus test showed that exposure to tobacco leaves for different periods of time caused significant DNA damage. Inhibition of cytochrome P450 enzymes occurred only in the tobacco group. Chemical analysis indicated the presence of the alkaloid nicotine, coumarins, saponins, flavonoids and various metals. These results show that tobacco leaves are genotoxic in H. aspersa and inhibit cytochrome P450 activity, probably through the action of the complex chemical mixture present in the plant.

Genotoxicity of Nicotiana tabacum leaves on Helix aspersa

Directory of Open Access Journals (Sweden)

Fernanda R. da Silva

2013-01-01

Full Text Available Tobacco farmers are routinely exposed to complex mixtures of inorganic and organic chemicals present in tobacco leaves. In this study, we examined the genotoxicity of tobacco leaves in the snail Helix aspersa as a measure of the risk to human health. DNA damage was evaluated using the micronucleus test and the Comet assay and the concentration of cytochrome P450 enzymes was estimated. Two groups of snails were studied: one fed on tobacco leaves and one fed on lettuce (Lactuca sativa L leaves (control group. All of the snails received leaves (tobacco and lettuce leaves were the only food provided and water ad libitum. Hemolymph cells were collected after 0, 24, 48 and 72 h. The Comet assay and micronucleus test showed that exposure to tobacco leaves for different periods of time caused significant DNA damage. Inhibition of cytochrome P450 enzymes occurred only in the tobacco group. Chemical analysis indicated the presence of the alkaloid nicotine, coumarins, saponins, flavonoids and various metals. These results show that tobacco leaves are genotoxic in H. aspersa and inhibit cytochrome P450 activity, probably through the action of the complex chemical mixture present in the plant.

Periodontitis and early mortality among adults treated with hemodialysis: a multinational propensity-matched cohort study.

Science.gov (United States)

Ruospo, Marinella; Palmer, Suetonia C; Wong, Germaine; Craig, Jonathan C; Petruzzi, Massimo; De Benedittis, Michele; Ford, Pauline; Johnson, David W; Tonelli, Marcello; Natale, Patrizia; Saglimbene, Valeria; Pellegrini, Fabio; Celia, Eduardo; Gelfman, Ruben; Leal, Miguel R; Torok, Marietta; Stroumza, Paul; Bednarek-Skublewska, Anna; Dulawa, Jan; Frantzen, Luc; Del Castillo, Domingo; Schon, Staffan; Bernat, Amparo G; Hegbrant, Jorgen; Wollheim, Charlotta; Gargano, Letizia; Bots, Casper P; Strippoli, Giovanni Fm

2017-05-22

Periodontitis is associated with cardiovascular mortality in the general population and adults with chronic diseases. However, it is unclear whether periodontitis predicts survival in the setting of kidney failure. ORAL-D was a propensity matched analysis in 3338 dentate adults with end-stage kidney disease treated in a hemodialysis network in Europe and South America designed to examine the association between periodontitis and all-cause and cardiovascular-related mortality in people on long-term hemodialysis. Participants were matched 1:1 on their propensity score for moderate to severe periodontitis assessed using the World Health Organization Community Periodontal Index. A random-effects Cox proportional hazards model was fitted with shared frailty to account for clustering of mortality risk within countries. Among the 3338 dentate participants, 1355 (40.6%) had moderate to severe periodontitis at baseline. After using propensity score methods to generate a matched cohort of participants with periodontitis similar to those with none or mild periodontal disease, moderate to severe periodontitis was associated with a lower risk of all-cause (9.1 versus 13.0 per 100 person years, hazard ratio 0.74, 95% confidence interval 0.61 to 0.90) and cardiovascular (4.3 versus 6.9 per 100 person years, hazard ratio 0.67, 0.51 to 0.88) mortality. These associations were not changed substantially when participants were limited to those with 12 or more natural teeth and when accounting for competing causes of cardiovascular death. In contrast to the general population, periodontitis does not appear to be associated with an increased risk of early death in adults treated with hemodialysis.

Observation Versus Embolization in Patients with Blunt Splenic Injury After Trauma: A Propensity Score Analysis.

Science.gov (United States)

Olthof, Dominique C; Joosse, Pieter; Bossuyt, Patrick M M; de Rooij, Philippe P; Leenen, Loek P H; Wendt, Klaus W; Bloemers, Frank W; Goslings, J Carel

2016-05-01

Non-operative management (NOM) is the standard of care in hemodynamically stable patients with blunt splenic injury after trauma. Splenic artery embolization (SAE) is reported to increase observation success rate. Studies demonstrating improved splenic salvage rates with SAE primarily compared SAE with historical controls. The aim of this study was to investigate whether SAE improves success rate compared to observation alone in contemporaneous patients with blunt splenic injury. We included adult patients with blunt splenic injury admitted to five Level 1 Trauma Centers between January 2009 and December 2012 and selected for NOM. Successful treatment was defined as splenic salvage and no splenic re-intervention. We calculated propensity scores, expressing the probability of undergoing SAE, using multivariable logistic regression and created five strata based on the quintiles of the propensity score distribution. A weighted relative risk (RR) was calculated across strata to express the chances of success with SAE. Two hundred and six patients were included in the study. Treatment was successful in 180 patients: 134/146 (92 %) patients treated with observation and 48/57 (84 %) patients treated with SAE. The weighted RR for success with SAE was 1.17 (0.94-1.45); for complications, the weighted RR was 0.71 (0.41-1.22). The mean number of transfused blood products was 4.4 (SD 9.9) in the observation group versus 9.1 (SD 17.2) in the SAE group. After correction for confounders with propensity score stratification technique, there was no significant difference between embolization and observation alone with regard to successful treatment in patients with blunt splenic injury after trauma.

Steady-state configurations and dynamics of the MreB helix within bacteria

Science.gov (United States)

Rutenberg, Andrew; Allard, Jun

2007-03-01

We present a quantitative model of the actin-like MreB cytoskeleton that is present in many prokaryotes. Individual MreB polymers are bundled into a supra-molecular array to make up helical cables. The cell wall imposes constraint forces through a global elasticity model. With variational techniques and stochastic simulations we obtain relationships between observable quantities such as the pitch of the helix, the total abundance of MreB molecules, and the thickness of the MreB cables. We address changes expected with slow cell growth, as well as turnover dynamics that are relevant to FRAP studies. We also address polarized macromolecular trafficking along the MreB cables without motor proteins.

Propagation into an unstable state

International Nuclear Information System (INIS)

Dee, G.

1985-01-01

We describe propagating front solutions of the equations of motion of pattern-forming systems. We make a number of conjectures concerning the properties of such fronts in connection with pattern selection in these systems. We describe a calculation which can be used to calculate the velocity and state selected by certain types of propagating fronts. We investigate the propagating front solutions of the amplitude equation which provides a valid dynamical description of many pattern-forming systems near onset

Studies on the Edible Terrestrial Snails Helix aspersa Muller Food Conversion Ratio in a Confined Microclimate System

Directory of Open Access Journals (Sweden)

Adrian Toader-Williams

2010-05-01

Full Text Available Terrestrial edible snail breeding is an agricultural activity that finds itself at pioneering stage in Romania. One of the species used in snail farming is Helix aspersa Muller. In order to accelerate their growth, farmers feed the snails with pumpkins as well as concentrated forage consisting of mix of flours to which calcium carbonate is added in order to supplement snails need for shell’s development. In a controlled microclimate environment we measured the average growth of six weeks old Helix aspersa Muller snails placed in four different plastic enclosures. The consumption of different type of foods within 24 hours period was measured. The wheat (60%, corn flour (20% and calcium carbonate (20% mix had a superior food conversion ratio (FCR of 4.80, whereas the second FCR registered 6.04 in the case of 53% pumpkin and 47% flour mix served in the same time followed by the pure fresh vegetable mix accounting for a FCR of 8.00 and by 19.02 when only the pumpkin has been administrated as meal. During the experiments the snails did not have access to soil, being known that soil is an integral part of their diet.

Radio wave propagation and parabolic equation modeling

CERN Document Server

Apaydin, Gokhan

2018-01-01

A thorough understanding of electromagnetic wave propagation is fundamental to the development of sophisticated communication and detection technologies. The powerful numerical methods described in this book represent a major step forward in our ability to accurately model electromagnetic wave propagation in order to establish and maintain reliable communication links, to detect targets in radar systems, and to maintain robust mobile phone and broadcasting networks. The first new book on guided wave propagation modeling and simulation to appear in nearly two decades, Radio Wave Propagation and Parabolic Equation Modeling addresses the fundamentals of electromagnetic wave propagation generally, with a specific focus on radio wave propagation through various media. The authors explore an array of new applications, and detail various v rtual electromagnetic tools for solving several frequent electromagnetic propagation problems. All of the methods described are presented within the context of real-world scenari...

Empirical prediction of ash deposition propensities in coal-fired utilities

Energy Technology Data Exchange (ETDEWEB)

Frandsen, F.

1997-01-01

This report contain an outline of some of the ash chemistry indices utilized in the EPREDEPO (Empirical PREdiction of DEPOsition) PC-program, version 1.0 (DEPO10), developed by Flemming Frandsen, The CHEC Research Programme, at the Department of Chemical Engineering, Technical University of Denmark. DEPO10 is a 1st generation FTN77 Fortran PC-programme designed to empirically predict ash deposition propensities in coal-fired utility boilers. Expectational data (empirical basis) from an EPRI-sponsored survey of ash deposition experiences at coal-fired utility boilers, performed by Battelle, have been tested for use on Danish coal chemistry - boiler operational conditions, in this study. (au) 31 refs.

PPII propensity of multiple-guest amino acids in a proline-rich environment.

Science.gov (United States)

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

2011-07-07

There has been considerable debate about the intrinsic PPII propensity of amino acid residues in denatured polypeptides. Experimentally, this scale is based on the behavior of guest amino acid residues placed in the middle of proline-based hosts. We have used classical molecular dynamics simulations combined with replica-exchange methods to carry out a comprehensive analysis of the conformational equilibria of proline-based host oligopeptides with multiple guest amino acids including alanine, glutamine, valine, and asparagine. The tracked structural characteristics include the secondary structural motifs based on the Ramachandran angles and the cis/trans isomerization of the prolyl bonds. In agreement with our recent study of single amino acid guests, we did not observe an intrinsic PPII propensity in any of the guest amino acids in a multiple-guest setting. Instead, the experimental results can be explained in terms of (i) the steric restrictions imposed on the C-terminal guest amino acid that is immediately followed by a proline residue and (ii) an increase in the trans content of the prolyl bonds due to the presence of guest residues. In terms of the latter, we found that the more guests added to the system, the larger the increase in the trans content of the prolyl bonds, which results in an effective increase in the PPII content of the peptide.

The propagator of quantum gravity in minisuperspace

International Nuclear Information System (INIS)

Louko, J.

1985-04-01

We study the quantum gravitational propagation amplitude between two spacelike three-surfaces in minisuperspaces where the supermomentum constraints are identically satisfied. We derive a well-defined path integral formula for the propagator and show that the propagator is an inverse of the canonical Hamiltonian operator. In an exactly solvable deSitter minisuperspace model the propagator is found to obey semi-classically correct boundary conditions. We discuss the implications for the full theory and suggest an approach to unravelling the physical meaning of the propagator. (orig.)

Neural network construction via back-propagation

International Nuclear Information System (INIS)

Burwick, T.T.

1994-06-01

A method is presented that combines back-propagation with multi-layer neural network construction. Back-propagation is used not only to adjust the weights but also the signal functions. Going from one network to an equivalent one that has additional linear units, the non-linearity of these units and thus their effective presence is then introduced via back-propagation (weight-splitting). The back-propagated error causes the network to include new units in order to minimize the error function. We also show how this formalism allows to escape local minima

Terrestrial propagation of long electromagnetic waves

CERN Document Server

Galejs, Janis; Fock, V A

2013-01-01

Terrestrial Propagation of Long Electromagnetic Waves deals with the propagation of long electromagnetic waves confined principally to the shell between the earth and the ionosphere, known as the terrestrial waveguide. The discussion is limited to steady-state solutions in a waveguide that is uniform in the direction of propagation. Wave propagation is characterized almost exclusively by mode theory. The mathematics are developed only for sources at the ground surface or within the waveguide, including artificial sources as well as lightning discharges. This volume is comprised of nine chapte

The accuracy of dynamic attitude propagation

Science.gov (United States)

Harvie, E.; Chu, D.; Woodard, M.

1990-01-01

Propagating attitude by integrating Euler's equation for rigid body motion has long been suggested for the Earth Radiation Budget Satellite (ERBS) but until now has not been implemented. Because of limited Sun visibility, propagation is necessary for yaw determination. With the deterioration of the gyros, dynamic propagation has become more attractive. Angular rates are derived from integrating Euler's equation with a stepsize of 1 second, using torques computed from telemetered control system data. The environmental torque model was quite basic. It included gravity gradient and unshadowed aerodynamic torques. Knowledge of control torques is critical to the accuracy of dynamic modeling. Due to their coarseness and sparsity, control actuator telemetry were smoothed before integration. The dynamic model was incorporated into existing ERBS attitude determination software. Modeled rates were then used for attitude propagation in the standard ERBS fine-attitude algorithm. In spite of the simplicity of the approach, the dynamically propagated attitude matched the attitude propagated with good gyros well for roll and yaw but diverged up to 3 degrees for pitch because of the very low resolution in pitch momentum wheel telemetry. When control anomalies significantly perturb the nominal attitude, the effect of telemetry granularity is reduced and the dynamically propagated attitudes are accurate on all three axes.

Innovative Development of Kazakhstan on The Basis of Triple Helix and Cluster Approach

Directory of Open Access Journals (Sweden)

Farkhat Musayevich Dnishev

2015-06-01

Full Text Available The aim of the research is to study the Triple Helix model feasibility in developing innovations and using cluster approach in Kazakhstan. There are possible points of the emergence of clusters in Kazakhstan. However, there are a lot of constraining factors. First of all, institutional and social factors: the culture of business, unfair competition, low trust of economic agents to each other and to power institutes, low psychological readiness for cooperation of the enterprises of various branches and regions, poor development of chambers of commerce, and industrial associations. For the time being, the majority of regions of Kazakhstan are characterized by a limited set of high technology industrial branches, and a sharp shortage of universities generating innovation and research institutes. The research results show that the open innovation model is realized in a limited scale that does not allow to export innovations into external markets, to participate in global technology chains and international research networks. At the same time, some interaction schemes and preconditions for the development of the Triple Helix model are emerging. However, in general, the innovation policy is not systemic; it does not unite actions in the sphere of science and technology, education, industry, and regional initiatives. As the result of the research, some policy implications are given. For the development of clusters in Kazakhstan, it is desirable to use such a way, as integration into global cluster networks. It is necessary to make use of foreign experience at which various specialized state agencies become participants of clusters. It is necessary to focus not only on science but also industry, which should play the central role in the innovation process.

Oxidation of Helix-3 methionines precedes the formation of PK resistant PrP.

Directory of Open Access Journals (Sweden)

Tamar Canello

2010-07-01

Full Text Available While elucidating the peculiar epitope of the alpha-PrP mAb IPC2, we found that PrPSc exhibits the sulfoxidation of residue M213 as a covalent signature. Subsequent computational analysis predicted that the presence of sulfoxide groups at both Met residues 206 and 213 destabilize the alpha-fold, suggesting oxidation may facilitate the conversion of PrPC into PrPSc. To further study the effect of oxidation on prion formation, we generated pAbs to linear PrP peptides encompassing the Helix-3 region, as opposed to the non-linear complexed epitope of IPC2. We now show that pAbs, whose epitopes comprise Met residues, readily detected PrPC, but could not recognize most PrPSc bands unless they were vigorously reduced. Next, we showed that the alpha-Met pAbs did not recognize newly formed PrPSc, as is the case for the PK resistant PrP present in lines of prion infected cells. In addition, these reagents did not detect intermediate forms such as PK sensitive and partially aggregated PrPs present in infected brains. Finally, we show that PrP molecules harboring the pathogenic mutation E200K, which is linked to the most common form of familial CJD, may be spontaneously oxidized. We conclude that the oxidation of methionine residues in Helix-3 represents an early and important event in the conversion of PrPC to PrPSc. We believe that further investigation into the mechanism and role of PrP oxidation will be central in finally elucidating the mechanism by which a normal cell protein converts into a pathogenic entity that causes fatal brain degeneration.

Propagation of SLF/ELF electromagnetic waves

CERN Document Server

Pan, Weiyan

2014-01-01

This book deals with the SLF/ELF wave propagation, an important branch of electromagnetic theory. The SLF/ELF wave propagation theory is well applied in earthquake electromagnetic radiation, submarine communication, thunderstorm detection, and geophysical prospecting and diagnostics. The propagation of SLF/ELF electromagnetic waves is introduced in various media like the earth-ionospheric waveguide, ionospheric plasma, sea water, earth, and the boundary between two different media or the stratified media. Applications in the earthquake electromagnetic radiation and the submarine communications are also addressed. This book is intended for scientists and engineers in the fields of radio propagation and EM theory and applications. Prof. Pan is a professor at China Research Institute of Radiowave Propagation in Qingdao (China). Dr. Li is a professor at Zhejiang University in Hangzhou (China).

Helix Nebula: Enabling federation of existing data infrastructures and data services to an overarching cross-domain e-infrastructure

Science.gov (United States)

Lengert, Wolfgang; Farres, Jordi; Lanari, Riccardo; Casu, Francesco; Manunta, Michele; Lassalle-Balier, Gerard

2014-05-01

Helix Nebula has established a growing public private partnership of more than 30 commercial cloud providers, SMEs, and publicly funded research organisations and e-infrastructures. The Helix Nebula strategy is to establish a federated cloud service across Europe. Three high-profile flagships, sponsored by CERN (high energy physics), EMBL (life sciences) and ESA/DLR/CNES/CNR (earth science), have been deployed and extensively tested within this federated environment. The commitments behind these initial flagships have created a critical mass that attracts suppliers and users to the initiative, to work together towards an "Information as a Service" market place. Significant progress in implementing the following 4 programmatic goals (as outlined in the strategic Plan Ref.1) has been achieved: × Goal #1 Establish a Cloud Computing Infrastructure for the European Research Area (ERA) serving as a platform for innovation and evolution of the overall infrastructure. × Goal #2 Identify and adopt suitable policies for trust, security and privacy on a European-level can be provided by the European Cloud Computing framework and infrastructure. × Goal #3 Create a light-weight governance structure for the future European Cloud Computing Infrastructure that involves all the stakeholders and can evolve over time as the infrastructure, services and user-base grows. × Goal #4 Define a funding scheme involving the three stake-holder groups (service suppliers, users, EC and national funding agencies) into a Public-Private-Partnership model to implement a Cloud Computing Infrastructure that delivers a sustainable business environment adhering to European level policies. Now in 2014 a first version of this generic cross-domain e-infrastructure is ready to go into operations building on federation of European industry and contributors (data, tools, knowledge, ...). This presentation describes how Helix Nebula is being used in the domain of earth science focusing on geohazards. The

Reporting of covariate selection and balance assessment in propensity score analysis is suboptimal: A systematic review

NARCIS (Netherlands)

Ali, M. Sanni|info:eu-repo/dai/nl/345709497; Groenwold, Rolf H.H.; Belitser, S.|info:eu-repo/dai/nl/304843865; Pestman, Wiebe R.; Hoes, Arno W.; Roes, Kit C.B.; Boer, Anthonius De|info:eu-repo/dai/nl/075097346; Klungel, Olaf H.|info:eu-repo/dai/nl/181447649

2015-01-01

Objectives To assess the current practice of propensity score (PS) analysis in the medical literature, particularly the assessment and reporting of balance on confounders. Study Design and Setting A PubMed search identified studies using PS methods from December 2011 through May 2012. For each

Proceedings of the Twenty-First NASA Propagation Experiments Meeting (NAPEX XXI) and the Advanced Communications Technology Satellite (ACTS) Propagation Studies Miniworkshop

Science.gov (United States)

Golshan, Nasser (Editor)

1997-01-01

The NASA Propagation Experimenters (NAPEX) meeting is convened each year to discuss studies supported by the NASA Propagation Program. Representatives from the satellite communications industry, academia and government who have an interest in space-ground radio wave propagation are invited to NAPEX meetings for discussions and exchange of information. The reports delivered at this meeting by program managers and investigators present recent activities and future plans. This forum provides an opportunity for peer discussion of work in progress, timely dissemination of propagation results, and close interaction with the satellite communications industry. NAPEX XXI took place in El Segundo, California on June 11-12, 1997 and consisted of three sessions. Session 1, entitled "ACTS Propagation Study Results & Outcome " covered the results of 20 station-years of Ka-band radio-wave propagation experiments. Session 11, 'Ka-band Propagation Studies and Models,' provided the latest developments in modeling, and analysis of experimental results about radio wave propagation phenomena for design of Ka-band satellite communications systems. Session 111, 'Propagation Research Topics,' covered a diverse range of propagation topics of interest to the space community, including overviews of handbooks and databases on radio wave propagation. The ACTS Propagation Studies miniworkshop was held on June 13, 1997 and consisted of a technical session in the morning and a plenary session in the afternoon. The morning session covered updates on the status of the ACTS Project & Propagation Program, engineering support for ACTS Propagation Terminals, and the Data Center. The plenary session made specific recommendations for the future direction of the program.

Triple-helix molecular switch-based aptasensors and DNA sensors.

Science.gov (United States)

Bagheri, Elnaz; Abnous, Khalil; Alibolandi, Mona; Ramezani, Mohammad; Taghdisi, Seyed Mohammad

2018-07-15

Utilization of traditional analytical techniques is limited because they are generally time-consuming and require high consumption of reagents, complicated sample preparation and expensive equipment. Therefore, it is of great interest to achieve sensitive, rapid and simple detection methods. It is believed that nucleic acids assays, especially aptamers, are very important in modern life sciences for target detection and biological analysis. Aptamers and DNA-based sensors have been widely used for the design of various sensors owing to their unique features. In recent years, triple-helix molecular switch (THMS)-based aptasensors and DNA sensors have been broadly utilized for the detection and analysis of different targets. The THMS relies on the formation of DNA triplex via Watson-Crick and Hoogsteen base pairings under optimal conditions. This review focuses on recent progresses in the development and applications of electrochemical, colorimetric, fluorescence and SERS aptasensors and DNA sensors, which are based on THMS. Also, the advantages and drawbacks of these methods are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

ACTS Propagation Measurements in Maryland and Virginia

Science.gov (United States)

Dissanayake, Asoka; Lin, Kuan-Ting

1996-01-01

Rapid growth in new satellite services incorporating very small aperture terminals (VSAT) and ultra small aperture terminals (USAT) is expected in the coming years. Small size terminals allow for widespread use of satellite services in small business and domestic applications. Due to congestion of lower frequency bands such as C and Ku, most of these services will use Ka-band (2/20 GHz) frequencies. Propagation impairments produced by the troposphere is a limiting factor for the effective use of the 20/30 GHz band and the use of smaller Earth terminals makes it difficult to provide sufficient link margins for propagation related outages. In this context, reliable prediction of propagation impairments for low margin systems becomes important. Due to the complexity of propagation phenomena propagation modeling is mainly attempted on an empirical basis. As such, the availability of reliable measured data that extend to probability levels well in excess of the traditional limit of 1 percent is of great importance in the development, validation, and refinement of propagation models. The beacon payload on the Advanced Communications Technology Satellite (ACTS) together with the propagation measurement terminals developed under the NASA ACTS propagation program provide an excellent opportunity to collect such data on a long-term basis. This paper presents the results of ACTS propagation measurements conducted in the Washington, DC metropolitan area by COMSAT Laboratories.

Propagation of waves

CERN Document Server

David, P

2013-01-01

Propagation of Waves focuses on the wave propagation around the earth, which is influenced by its curvature, surface irregularities, and by passage through atmospheric layers that may be refracting, absorbing, or ionized. This book begins by outlining the behavior of waves in the various media and at their interfaces, which simplifies the basic phenomena, such as absorption, refraction, reflection, and interference. Applications to the case of the terrestrial sphere are also discussed as a natural generalization. Following the deliberation on the diffraction of the "ground? wave around the ear

Group symmetries and information propagation

International Nuclear Information System (INIS)

Draayer, J.P.

1980-01-01

Spectroscopy concerns itself with the ways in which the Hamiltonian and other interesting operators defined in few-particle spaces are determined or determine properties of many-particle systems. But the action of the central limit theorem (CLT) filters the transmission of information between source and observed so whether propagating forward from a few-particle defining space, as is usual in theoretical studies, or projecting backward to it from measured things, each is only sensitive to averaged properties of the other. Our concern is with the propagation of spectroscopic information in the presence of good symmetries when filtering action of the CLT is effective. Specifically, we propose to address the question, What propagates and how. We begin with some examples, using both scalar and isospin geometries to illustrate simple propagation. Examples of matrix propagation are studied; contact with standard tensor algebra is established and an algorithm put forward for the expansion of any operator in terms of another set, complete or not; shell-model results for 20 Ne using a realistic interaction and two trace-equivalent forms are presented; and some further challenges are mentioned

The Association between the Availability of Sugar-Sweetened Beverage in School Vending Machines and Its Consumption among Adolescents in California: A Propensity Score Matching Approach

Science.gov (United States)

Shi, Lu

2010-01-01

There is controversy over to what degree banning sugar-sweetened beverage (SSB) sales at schools could decrease the SSB intake. This paper uses the adolescent sample of 2005 California Health Interview Survey to estimate the association between the availability of SSB from school vending machines and the amount of SSB consumption. Propensity score stratification and kernel-based propensity score matching are used to address the selection bias issue in cross-sectional data. Propensity score stratification shows that adolescents who had access to SSB through their school vending machines consumed 0.170 more drinks of SSB than those who did not (P vending machines and the actual SSB consumption, while future studies are needed to explore changes in other beverages after SSB becomes less available. PMID:20976298