Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes

PubMed Central

Tiwari, Sandhya P.; Reuter, Nathalie

2016-01-01

The conservation of the intrinsic dynamics of proteins emerges as we attempt to understand the relationship between sequence, structure and functional conservation. We characterise the conservation of such dynamics in a case where the structure is conserved but function differs greatly. The triosephosphate isomerase barrel fold (TBF), renowned for its 8 β-strand-α-helix repeats that close to form a barrel, is one of the most diverse and abundant folds found in known protein structures. Proteins with this fold have diverse enzymatic functions spanning five of six Enzyme Commission classes, and we have picked five different superfamily candidates for our analysis using elastic network models. We find that the overall shape is a large determinant in the similarity of the intrinsic dynamics, regardless of function. In particular, the β-barrel core is highly rigid, while the α-helices that flank the β-strands have greater relative mobility, allowing for the many possibilities for placement of catalytic residues. We find that these elements correlate with each other via the loops that link them, as opposed to being directly correlated. We are also able to analyse the types of motions encoded by the normal mode vectors of the α-helices. We suggest that the global conservation of the intrinsic dynamics in the TBF contributes greatly to its success as an enzymatic scaffold both through evolution and enzyme design. PMID:27015412

The shear response of copper bicrystals with Σ11 symmetric and asymmetric tilt grain boundaries by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Liang; Lu, Cheng; Tieu, Kiet; Zhao, Xing; Pei, Linqing

2015-04-01

Grain boundaries (GBs) are important microstructure features and can significantly affect the properties of nanocrystalline materials. Molecular dynamics simulation was carried out in this study to investigate the shear response and deformation mechanisms of symmetric and asymmetric Σ11<1 1 0> tilt GBs in copper bicrystals. Different deformation mechanisms were reported, depending on GB inclination angles and equilibrium GB structures, including GB migration coupled to shear deformation, GB sliding caused by local atomic shuffling, and dislocation nucleation from GB. The simulation showed that migrating Σ11(1 1 3) GB under shear can be regarded as sliding of GB dislocations and their combination along the boundary plane. A non-planar structure with dissociated intrinsic stacking faults was prevalent in Σ11 asymmetric GBs of Cu. This type of structure can significantly increase the ductility of bicrystal models under shear deformation. A grain boundary can be a source of dislocation and migrate itself at different stress levels. The intrinsic free volume involved in the grain boundary area was correlated with dislocation nucleation and GB sliding, while the dislocation nucleation mechanism can be different for a grain boundary due to its different equilibrium structures.Grain boundaries (GBs) are important microstructure features and can significantly affect the properties of nanocrystalline materials. Molecular dynamics simulation was carried out in this study to investigate the shear response and deformation mechanisms of symmetric and asymmetric Σ11<1 1 0> tilt GBs in copper bicrystals. Different deformation mechanisms were reported, depending on GB inclination angles and equilibrium GB structures, including GB migration coupled to shear deformation, GB sliding caused by local atomic shuffling, and dislocation nucleation from GB. The simulation showed that migrating Σ11(1 1 3) GB under shear can be regarded as sliding of GB dislocations and their combination along the boundary plane. A non-planar structure with dissociated intrinsic stacking faults was prevalent in Σ11 asymmetric GBs of Cu. This type of structure can significantly increase the ductility of bicrystal models under shear deformation. A grain boundary can be a source of dislocation and migrate itself at different stress levels. The intrinsic free volume involved in the grain boundary area was correlated with dislocation nucleation and GB sliding, while the dislocation nucleation mechanism can be different for a grain boundary due to its different equilibrium structures. Electronic supplementary information (ESI) available: Movies show the evolution of different grain boundaries under shear deformation: S-0, S-54.74, S-70.53-A, S-70.53-B, S-90. See DOI: 10.1039/c4nr07496c

Utilization of protein intrinsic disorder knowledge in structural proteomics

PubMed Central

Oldfield, Christopher J.; Xue, Bin; Van, Ya-Yue; Ulrich, Eldon L.; Markley, John L.; Dunker, A. Keith; Uversky, Vladimir N.

2014-01-01

Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed. PMID:23232152

Arginine Kinase. Joint Crystallographic & NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility

PubMed Central

Niu, Xiaogang; Brüschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.

2010-01-01

The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a “high energy” phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and –bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, “substrate-induced” motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection. PMID:21075117

Atomistic study on the FCC/BCC interface structure with {112}KS orientation

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

Kang, Keonwook; Beyerlein, Irene; Han, Weizhong

2011-09-23

In this study, atomistic simulation is used to explore the atomic interface structure, the intrinsic defect network, and mechanism of twin formation from the {112}KS Cu-Nb interface. The interface structure of different material systems AI-Fe and AI-Nb are also compared with Cu-Nb interface.

Sequence Determinants of Compaction in Intrinsically Disordered Proteins

PubMed Central

Marsh, Joseph A.; Forman-Kay, Julie D.

2010-01-01

Abstract Intrinsically disordered proteins (IDPs), which lack folded structure and are disordered under nondenaturing conditions, have been shown to perform important functions in a large number of cellular processes. These proteins have interesting structural properties that deviate from the random-coil-like behavior exhibited by chemically denatured proteins. In particular, IDPs are often observed to exhibit significant compaction. In this study, we have analyzed the hydrodynamic radii of a number of IDPs to investigate the sequence determinants of this compaction. Net charge and proline content are observed to be strongly correlated with increased hydrodynamic radii, suggesting that these are the dominant contributors to compaction. Hydrophobicity and secondary structure, on the other hand, appear to have negligible effects on compaction, which implies that the determinants of structure in folded and intrinsically disordered proteins are profoundly different. Finally, we observe that polyhistidine tags seem to increase IDP compaction, which suggests that these tags have significant perturbing effects and thus should be removed before any structural characterizations of IDPs. Using the relationships observed in this analysis, we have developed a sequence-based predictor of hydrodynamic radius for IDPs that shows substantial improvement over a simple model based upon chain length alone. PMID:20483348

Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases.

PubMed

Zubrienė, Asta; Smirnov, Alexey; Dudutienė, Virginija; Timm, David D; Matulienė, Jurgita; Michailovienė, Vilma; Zakšauskas, Audrius; Manakova, Elena; Gražulis, Saulius; Matulis, Daumantas

2017-01-20

The goal of rational drug design is to understand structure-thermodynamics correlations in order to predict the chemical structure of a drug that would exhibit excellent affinity and selectivity for a target protein. In this study we explored the contribution of added functionalities of benzenesulfonamide inhibitors to the intrinsic binding affinity, enthalpy, and entropy for recombinant human carbonic anhydrases (CA) CA I, CA II, CA VII, CA IX, CA XII, and CA XIII. The binding enthalpies of compounds possessing similar chemical structures and affinities were found to be very different, spanning a range from -90 to +10 kJ mol -1 , and are compensated by a similar opposing entropy contribution. The intrinsic parameters of binding were determined by subtracting the linked protonation reactions. The sulfonamide group pK a values of the compounds were measured spectrophotometrically, and the protonation enthalpies were measured by isothermal titration calorimetry (ITC). Herein we describe the development of meta- or ortho-substituted fluorinated benzenesulfonamides toward the highly potent compound 10 h, which exhibits an observed dissociation constant value of 43 pm and an intrinsic dissociation constant value of 1.1 pm toward CA IX, an anticancer target that is highly overexpressed in various tumors. Fluorescence thermal shift assays, ITC, and X-ray crystallography were all applied in this work. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hidden Structural Codes in Protein Intrinsic Disorder.

PubMed

Borkosky, Silvia S; Camporeale, Gabriela; Chemes, Lucía B; Risso, Marikena; Noval, María Gabriela; Sánchez, Ignacio E; Alonso, Leonardo G; de Prat Gay, Gonzalo

2017-10-17

Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and β-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.

Multiple structure-intrinsic disorder interactions regulate and coordinate Hox protein function

NASA Astrophysics Data System (ADS)

Bondos, Sarah

During animal development, Hox transcription factors determine fate of developing tissues to generate diverse organs and appendages. Hox proteins are famous for their bizarre mutant phenotypes, such as replacing antennae with legs. Clearly, the functions of individual Hox proteins must be distinct and reliable in vivo, or the organism risks malformation or death. However, within the Hox protein family, the DNA-binding homeodomains are highly conserved and the amino acids that contact DNA are nearly invariant. These observations raise the question: How do different Hox proteins correctly identify their distinct target genes using a common DNA binding domain? One possible means to modulate DNA binding is through the influence of the non-homeodomain protein regions, which differ significantly among Hox proteins. However genetic approaches never detected intra-protein interactions, and early biochemical attempts were hindered because the special features of ``intrinsically disordered'' sequences were not appreciated. We propose the first-ever structural model of a Hox protein to explain how specific contacts between distant, intrinsically disordered regions of the protein and the homeodomain regulate DNA binding and coordinate this activity with other Hox molecular functions.

Ensemble characterization of an intrinsically disordered FG-Nup peptide and its F>A mutant in DMSO-d6.

PubMed

Reid, Korey M; Sunanda, Punnepalli; Raghothama, S; Krishnan, V V

2017-11-01

Intrinsically disordered proteins (IDP) lack a well-defined 3D-structure under physiological conditions, yet, the inherent disorder represented by an ensemble of conformation plays a critical role in many cellular and regulatory processes. Nucleoporins, or Nups, are the proteins found in the nuclear pore complex (NPC). The central pore of the NPC is occupied by Nups, which have phenylalanine-glycine domain repeats and are intrinsically disordered, and therefore are termed FG-Nups. These FG-domain repeats exhibit differing cohesiveness character and differ from least (FG) to most (GLFG) cohesive. The designed FG-Nup is a 25 AA model peptide containing a noncohesive FG-motif flanked by two cohesive GLFG-motifs (WT peptide). Complete NMR-based ensemble characterization of this peptide along with a control peptide with an F>A substitution (MU peptide) are discussed. Ensemble characterization of the NMR-determined models suggests that both the peptides do not have consistent secondary structures and continue to be disordered. Nonetheless, the role of cohesive elements mediated by the GLFG motifs is evident in the WT ensemble of structures that are more compact than the MU peptide. The approach presented here allows an alternate way to investigate the specific roles of distinct amino acid motifs that translate into the long-range organization of the ensemble of structures and in general on the nature of IDPs. © 2017 Wiley Periodicals, Inc.

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

NASA Astrophysics Data System (ADS)

Knott, Michael; Best, Robert B.

2014-05-01

Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an "induced fit" or "conformational selection" mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.

Protein disorder in the human diseasome: unfoldomics of human genetic diseases

PubMed Central

Midic, Uros; Oldfield, Christopher J; Dunker, A Keith; Obradovic, Zoran; Uversky, Vladimir N

2009-01-01

Background Intrinsically disordered proteins lack stable structure under physiological conditions, yet carry out many crucial biological functions, especially functions associated with regulation, recognition, signaling and control. Recently, human genetic diseases and related genes were organized into a bipartite graph (Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685–8690). This diseasome network revealed several significant features such as the common genetic origin of many diseases. Methods and findings We analyzed the abundance of intrinsic disorder in these diseasome network proteins by means of several prediction algorithms, and we analyzed the functional repertoires of these proteins based on prior studies relating disorder to function. Our analyses revealed that (i) Intrinsic disorder is common in proteins associated with many human genetic diseases; (ii) Different disease classes vary in the IDP contents of their associated proteins; (iii) Molecular recognition features, which are relatively short loosely structured protein regions within mostly disordered sequences and which gain structure upon binding to partners, are common in the diseasome, and their abundance correlates with the intrinsic disorder level; (iv) Some disease classes have a significant fraction of genes affected by alternative splicing, and the alternatively spliced regions in the corresponding proteins are predicted to be highly disordered; and (v) Correlations were found among the various diseasome graph-related properties and intrinsic disorder. Conclusion These observations provide the basis for the construction of the human-genetic-disease-associated unfoldome. PMID:19594871

Theory of extrinsic and intrinsic heterojunctions in thermal equilibrium

NASA Technical Reports Server (NTRS)

Von Ross, O.

1980-01-01

A careful analysis of an abrupt heterojunction consisting of two distinct semiconductors either intrinsic or extrinsic is presented. The calculations apply to a one-dimensional, nondegenerate structure. Taking into account all appropriate boundary conditions, it is shown that the intrinsic Fermi level shows a discontinuity at the interface between the two materials which leads to a discontinuity of the valence band edge equal to the difference in the band gap energies of the two materials. The conduction band edge stays continuous however. This result is independent of possible charged interface states and in sharp contrast to the Anderson model. The reasons for this discrepancy are discussed.

Importance and challenges of measuring intrinsic foot muscle strength

PubMed Central

2012-01-01

Background Intrinsic foot muscle weakness has been implicated in a range of foot deformities and disorders. However, to establish a relationship between intrinsic muscle weakness and foot pathology, an objective measure of intrinsic muscle strength is needed. The aim of this review was to provide an overview of the anatomy and role of intrinsic foot muscles, implications of intrinsic weakness and evaluate the different methods used to measure intrinsic foot muscle strength. Method Literature was sourced from database searches of MEDLINE, PubMed, SCOPUS, Cochrane Library, PEDro and CINAHL up to June 2012. Results There is no widely accepted method of measuring intrinsic foot muscle strength. Methods to estimate toe flexor muscle strength include the paper grip test, plantar pressure, toe dynamometry, and the intrinsic positive test. Hand-held dynamometry has excellent interrater and intrarater reliability and limits toe curling, which is an action hypothesised to activate extrinsic toe flexor muscles. However, it is unclear whether any method can actually isolate intrinsic muscle strength. Also most methods measure only toe flexor strength and other actions such as toe extension and abduction have not been adequately assessed. Indirect methods to investigate intrinsic muscle structure and performance include CT, ultrasonography, MRI, EMG, and muscle biopsy. Indirect methods often discriminate between intrinsic and extrinsic muscles, but lack the ability to measure muscle force. Conclusions There are many challenges to accurately measure intrinsic muscle strength in isolation. Most studies have measured toe flexor strength as a surrogate measure of intrinsic muscle strength. Hand-held dynamometry appears to be a promising method of estimating intrinsic muscle strength. However, the contribution of extrinsic muscles cannot be excluded from toe flexor strength measurement. Future research should clarify the relative contribution of intrinsic and extrinsic muscles during intrinsic foot muscle strength testing. PMID:23181771

Fine Structure in Quasar Flows Revealed by Lens-Aided Multi-Angle Spectroscopy (LAMAS)

NASA Astrophysics Data System (ADS)

Green, Paul J.

2006-09-01

Spectral differences between lensed quasar image components are common. Since lensing is intrinsically achromatic, these differences are typically explained as the effect of either microlensing, or as light path time delays sampling intrinsic quasar spectral variability. In some cases, neither explanation seems sufficient. Here we advance a novel third hypothesis: some spectral differences are due to small line-of- sight differences through quasar disk wind outflows, taking the widest separation lens SDSSJ1004+4112 as a key example. We show that small changes in sightline may traverse streams with significantly differing columns. The implications are many. Fine structure in these outflows may change the observed spectra on arcsec scales. Though difficult to detect observationally, high ionization, high velocity-width streams may sculpt the optical and X-ray spectra of most quasars. We discuss existing multi-epoch optical/UV spectroscopy and results from X-ray observations both by Chandra and XMM in this context, and sketch further possible tests. The author gratefully acknowledges support through NASA contract NAS8-03060 (CXC).

No Association between Cortical Gyrification or Intrinsic Curvature and Attention-deficit/Hyperactivity Disorder in Adolescents and Young Adults.

PubMed

Forde, Natalie J; Ronan, Lisa; Zwiers, Marcel P; Alexander-Bloch, Aaron F; Faraone, Stephen V; Oosterlaan, Jaap; Heslenfeld, Dirk J; Hartman, Catharina A; Buitelaar, Jan K; Hoekstra, Pieter J

2017-01-01

Magnetic resonance imaging (MRI) studies have highlighted subcortical, cortical, and structural connectivity abnormalities associated with attention-deficit/hyperactivity disorder (ADHD). Gyrification investigations of the cortex have been inconsistent and largely negative, potentially due to a lack of sensitivity of the previously used morphological parameters. The innovative approach of applying intrinsic curvature analysis, which is predictive of gyrification pattern, to the cortical surface applied herein allowed us greater sensitivity to determine whether the structural connectivity abnormalities thus far identified at a centimeter scale also occur at a millimeter scale within the cortical surface. This could help identify neurodevelopmental processes that contribute to ADHD. Structural MRI datasets from the NeuroIMAGE project were used [ n = 306 ADHD, n = 164 controls, and n = 148 healthy siblings of individuals with ADHD (age in years, mean(sd); 17.2 (3.4), 16.8 (3.2), and 17.7 (3.8), respectively)]. Reconstructions of the cortical surfaces were computed with FreeSurfer. Intrinsic curvature (taken as a marker of millimeter-scale surface connectivity) and local gyrification index were calculated for each point on the surface (vertex) with Caret and FreeSurfer, respectively. Intrinsic curvature skew and mean local gyrification index were extracted per region; frontal, parietal, temporal, occipital, cingulate, and insula. A generalized additive model was used to compare the trajectory of these measures between groups over age, with sex, scanner site, total surface area of hemisphere, and familiality accounted for. After correcting for sex, scanner site, and total surface area no group differences were found in the developmental trajectory of intrinsic curvature or local gyrification index. Despite the increased sensitivity of intrinsic curvature, compared to gyrification measures, to subtle morphological abnormalities of the cortical surface we found no milimeter-scale connectivity abnormalities associated with ADHD.

Intrinsic rewards experienced by a group of dentists working with underserved populations.

PubMed

Gardner, S P; Roberts-Thomson, K F; Winning, T A; Peterson, R

2014-09-01

The aim of this study was to explore, using qualitative methods, the intrinsic reasons why dentists work with underserved groups. Minority and marginalized groups of Australians suffer a greater burden of dental disease than the general population due to disparities in accessing care. Recruitment and retention of dentists to care for underserved groups is problematic due to personal, professional and structural reasons. What drives dentists to work with underserved groups is not widely known. Sixteen dentists were recruited using 'snowball' purposeful sampling. Semi-structured in-depth interviews were conducted. Thematic analysis was conducted on the transcriptions to identify themes. Five key themes emerged: (1) 'tapped on the shoulder', being personally approached or invited; (2) 'dental school experience', the challenges faced as a student; (3) 'empathic concern', the non-judgemental expressions of care toward others; (4) 'resilience', the ability to bounce back after setbacks; (5) 'intrinsic reward', the personal gain and satisfaction received. This study focuses on the intrinsic rewards which were found to be simple, unexpected, and associated with relieving pain, community engagement and making a difference. Emphasizing personal fulfilment and intrinsic reward could be useful when promoting dentistry as a career and when encouraging graduates to consider working with disadvantaged groups. © 2014 Australian Dental Association.

Global Dynamics of Proteins: Bridging Between Structure and Function

PubMed Central

Bahar, Ivet; Lezon, Timothy R.; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold. PMID:20192781

Global dynamics of proteins: bridging between structure and function.

PubMed

Bahar, Ivet; Lezon, Timothy R; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold.

Planetary magnetospheres

NASA Technical Reports Server (NTRS)

Hill, T. W.; Michel, F. C.

1975-01-01

Space-probe observations of planetary magnetospheres are discussed. Three different categories of planetary magnetospheres are identified (intrinsic slowly rotating, intrinsic rapidly rotating, and induced), and the characteristics of each type are outlined. The structure and physical processes of the magnetospheres of Mercury, Mars, and Jupiter are described, and possible configurations are presented for the Martian and Jovian ones. Expected magnetic moments are derived for Saturn, Uranus, and Neptune. Models are constructed for possible induced magnetospheres of the moon, Mercury, Venus, Mars, and Io.

Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling

NASA Astrophysics Data System (ADS)

D'Urzo, Annalisa; Konijnenberg, Albert; Rossetti, Giulia; Habchi, Johnny; Li, Jinyu; Carloni, Paolo; Sobott, Frank; Longhi, Sonia; Grandori, Rita

2015-03-01

Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered NTAIL domain and the phosphoprotein X domain (PXD) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire NTAIL domain bound to PXD at atomic resolution.

Intrinsically Disordered Energy Landscapes

PubMed Central

Chebaro, Yassmine; Ballard, Andrew J.; Chakraborty, Debayan; Wales, David J.

2015-01-01

Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such ‘intrinsically disordered’ landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an -helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium. PMID:25999294

Intellectual development is positively related to intrinsic motivation and course grades for female but not male students.

PubMed

Cortright, Ronald N; Lujan, Heidi L; Cox, Julie H; Cortright, Maria A; Langworthy, Brandon M; Petta, Lorene M; Tanner, Charles J; DiCarlo, Stephen E

2015-09-01

We hypothesized that the intellectual development of students, i.e., their beliefs about the nature of knowledge and learning, affects their intrinsic motivation and class performance. Specifically, we hypothesized that students with low intellectual development (i.e., the naive beliefs that knowledge is simple, absolute, and certain) have low intrinsic motivation and low class performance, whereas students with high intellectual development (i.e., more sophisticated beliefs that knowledge is complex, tentative, and evolving) have high intrinsic motivation and class performance. To test this hypothesis, we administered the Learning Context Questionnaire to measure intellectual development. In addition, we administered the Intrinsic Motivation Inventory to assess our students' intrinsic motivation. Furthermore, we performed regression analyses between intellectual development with both intrinsic motivation and class performance. The results document a positive relationship among intellectual development, intrinsic motivation, and class performance for female students only. In sharp contrast, there was a negative relationship between intellectual development, intrinsic motivation, and class performance for male students. The slope comparisons documented significant differences in the slopes relating intellectual development, intrinsic motivation, and class performance between female and male students. Thus, female students with more sophisticated beliefs that knowledge is personally constructed, complex, and evolving had higher intrinsic motivation and class performance. In contrast, male students with the naive beliefs that the structure of knowledge is simple, absolute, and certain had higher levels of intrinsic motivation and class performance. The results suggest that sex influences intellectual development, which has an effect on intrinsic motivation for learning a specific topic. Copyright © 2015 The American Physiological Society.

Electronic and optical properties of antiferromagnetic iron doped NiO - A first principles study

NASA Astrophysics Data System (ADS)

Petersen, John E.; Twagirayezu, Fidele; Scolfaro, Luisa M.; Borges, Pablo D.; Geerts, Wilhelmus J.

2017-05-01

Antiferromagnetic NiO is a candidate for next generation high-speed and scaled RRAM devices. Here, electronic and optical properties of antiferromagnetic NiO: Fe 25% in the rock salt structure are studied and compared to intrinsic NiO. From density of states and complex dielectric function analysis, the first optical transition is found to be at lower frequency than intrinsic NiO due to an Fe impurity level being the valence band maximum. The resulting effects on refractive index, reflectivity, absorption, optical conductivity and loss function for Fe-doped NiO are compared to those of intrinsic NiO, and notable differences are analyzed. The electronic component of the static dielectric constant of NiO: Fe 25% is calculated to be about 2% less than that of intrinsic NiO.

RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae.

PubMed

Ivanyi-Nagy, Roland; Lavergne, Jean-Pierre; Gabus, Caroline; Ficheux, Damien; Darlix, Jean-Luc

2008-02-01

RNA chaperone proteins are essential partners of RNA in living organisms and viruses. They are thought to assist in the correct folding and structural rearrangements of RNA molecules by resolving misfolded RNA species in an ATP-independent manner. RNA chaperoning is probably an entropy-driven process, mediated by the coupled binding and folding of intrinsically disordered protein regions and the kinetically trapped RNA. Previously, we have shown that the core protein of hepatitis C virus (HCV) is a potent RNA chaperone that can drive profound structural modifications of HCV RNA in vitro. We now examined the RNA chaperone activity and the disordered nature of core proteins from different Flaviviridae genera, namely that of HCV, GBV-B (GB virus B), WNV (West Nile virus) and BVDV (bovine viral diarrhoea virus). Despite low-sequence similarities, all four proteins demonstrated general nucleic acid annealing and RNA chaperone activities. Furthermore, heat resistance of core proteins, as well as far-UV circular dichroism spectroscopy suggested that a well-defined 3D protein structure is not necessary for core-induced RNA structural rearrangements. These data provide evidence that RNA chaperoning-possibly mediated by intrinsically disordered protein segments-is conserved in Flaviviridae core proteins. Thus, besides nucleocapsid formation, core proteins may function in RNA structural rearrangements taking place during virus replication.

RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae

PubMed Central

Ivanyi-Nagy, Roland; Lavergne, Jean-Pierre; Gabus, Caroline; Ficheux, Damien; Darlix, Jean-Luc

2008-01-01

RNA chaperone proteins are essential partners of RNA in living organisms and viruses. They are thought to assist in the correct folding and structural rearrangements of RNA molecules by resolving misfolded RNA species in an ATP-independent manner. RNA chaperoning is probably an entropy-driven process, mediated by the coupled binding and folding of intrinsically disordered protein regions and the kinetically trapped RNA. Previously, we have shown that the core protein of hepatitis C virus (HCV) is a potent RNA chaperone that can drive profound structural modifications of HCV RNA in vitro. We now examined the RNA chaperone activity and the disordered nature of core proteins from different Flaviviridae genera, namely that of HCV, GBV-B (GB virus B), WNV (West Nile virus) and BVDV (bovine viral diarrhoea virus). Despite low-sequence similarities, all four proteins demonstrated general nucleic acid annealing and RNA chaperone activities. Furthermore, heat resistance of core proteins, as well as far-UV circular dichroism spectroscopy suggested that a well-defined 3D protein structure is not necessary for core-induced RNA structural rearrangements. These data provide evidence that RNA chaperoning—possibly mediated by intrinsically disordered protein segments—is conserved in Flaviviridae core proteins. Thus, besides nucleocapsid formation, core proteins may function in RNA structural rearrangements taking place during virus replication. PMID:18033802

Characterization of Lateral Structure of the p-i-n Diode for Thin-Film Silicon Solar Cell.

PubMed

Kiaee, Zohreh; Joo, Seung Ki

2018-03-01

The lateral structure of the p-i-n diode was characterized for thin-film silicon solar cell application. The structure can benefit from a wide intrinsic layer, which can improve efficiency without increasing cell thickness. Compared with conventional thin-film p-i-n cells, the p-i-n diode lateral structure exploited direct light irradiation on the absorber layer, one-side contact, and bifacial irradiation. Considering the effect of different carrier lifetimes and recombinations, we calculated efficiency parameters by using a commercially available simulation program as a function of intrinsic layer width, as well as the distance between p/i or n/i junctions to contacts. We then obtained excellent parameter values of 706.52 mV open-circuit voltage, 24.16 mA/Cm2 short-circuit current, 82.66% fill factor, and 14.11% efficiency from a lateral cell (thickness = 3 μm; intrinsic layer width = 53 μm) in monofacial irradiation mode (i.e., only sunlight from the front side was considered). Simulation results of the cell without using rear-side reflector in bifacial irradiation mode showed 11.26% front and 9.72% rear efficiencies. Our findings confirmed that the laterally structured p-i-n cell can be a potentially powerful means for producing highly efficient, thin-film silicon solar cells.

Dynamic analysis of suspension cable based on vector form intrinsic finite element method

NASA Astrophysics Data System (ADS)

Qin, Jian; Qiao, Liang; Wan, Jiancheng; Jiang, Ming; Xia, Yongjun

2017-10-01

A vector finite element method is presented for the dynamic analysis of cable structures based on the vector form intrinsic finite element (VFIFE) and mechanical properties of suspension cable. Firstly, the suspension cable is discretized into different elements by space points, the mass and external forces of suspension cable are transformed into space points. The structural form of cable is described by the space points at different time. The equations of motion for the space points are established according to the Newton’s second law. Then, the element internal forces between the space points are derived from the flexible truss structure. Finally, the motion equations of space points are solved by the central difference method with reasonable time integration step. The tangential tension of the bearing rope in a test ropeway with the moving concentrated loads is calculated and compared with the experimental data. The results show that the tangential tension of suspension cable with moving loads is consistent with the experimental data. This method has high calculated precision and meets the requirements of engineering application.

Galaxy Alignments: Theory, Modelling & Simulations

NASA Astrophysics Data System (ADS)

Kiessling, Alina; Cacciato, Marcello; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L.; Rassat, Anais

2015-11-01

The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both N-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the field, providing a solid basis for future work.

Predominance of Intrinsic Mechanism of Resting Heart Rate Control and Preserved Baroreflex Sensitivity in Professional Cyclists after Competitive Training.

PubMed

Azevedo, Luciene Ferreira; Perlingeiro, Patricia; Hachul, Denise Tessariol; Gomes-Santos, Igor Lucas; Tsutsui, Jeane Mike; Negrao, Carlos Eduardo; De Matos, Luciana D N J

2016-01-01

Different season trainings may influence autonomic and non-autonomic cardiac control of heart rate and provokes specific adaptations on heart's structure in athletes. We investigated the influence of transition training (TT) and competitive training (CT) on resting heart rate, its mechanisms of control, spontaneous baroreflex sensitivity (BRS) and relationships between heart rate mechanisms and cardiac structure in professional cyclists (N = 10). Heart rate (ECG) and arterial blood pressure (Pulse Tonometry) were recorded continuously. Autonomic blockade was performed (atropine-0.04 mg.kg-1; esmolol-500 μg.kg-1 = 0.5 mg). Vagal effect, intrinsic heart rate, parasympathetic (n) and sympathetic (m) modulations, autonomic influence, autonomic balance and BRS were calculated. Plasma norepinephrine (high-pressure liquid chromatography) and cardiac structure (echocardiography) were evaluated. Resting heart rate was similar in TT and CT. However, vagal effect, intrinsic heart rate, autonomic influence and parasympathetic modulation (higher n value) decreased in CT (P≤0.05). Sympathetic modulation was similar in both trainings. The autonomic balance increased in CT but still showed parasympathetic predominance. Cardiac diameter, septum and posterior wall thickness and left ventricular mass also increased in CT (P<0.05) as well as diastolic function. We observed an inverse correlation between left ventricular diastolic diameter, septum and posterior wall thickness and left ventricular mass with intrinsic heart rate. Blood pressure and BRS were similar in both trainings. Intrinsic heart rate mechanism is predominant over vagal effect during CT, despite similar resting heart rate. Preserved blood pressure levels and BRS during CT are probably due to similar sympathetic modulation in both trainings.

How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA.

PubMed

Hur, Sun; Stroud, Robert M

2007-04-27

Translational accuracy and efficiency depend upon modification of uridines in the tRNA anticodon stem loop (ASL) by a highly conserved pseudouridine synthase TruA. TruA specifically modifies uridines at positions 38, 39, and/or 40 of tRNAs with highly divergent sequences and structures through a poorly characterized mechanism that differs from previously studied RNA-modifying enzymes. The molecular basis for the site and substrate "promiscuity" was studied by determining the crystal structures of E. coli TruA in complex with two different leucyl tRNAs in conjunction with functional assays and computer simulation. The structures capture three stages of the TruA*tRNA reaction, revealing the mechanism by which TruA selects the target site. We propose that TruA utilizes the intrinsic flexibility of the ASL for site promiscuity and also to select against intrinsically stable tRNAs to avoid their overstabilization through pseudouridylation, thereby maintaining the balance between the flexibility and stability required for its biological function.

The relationship between motivational structure, sense of control, intrinsic motivation and university students' alcohol consumption.

PubMed

Shamloo, Zohreh Sepehri; Cox, W Miles

2010-02-01

The aim of this study was to determine how sense of control and intrinsic motivation are related to university students' motivational structure and alcohol consumption. Participants were 94 university students who completed the Personal Concerns Inventory, Shapiro Control Inventory, Helplessness Questionnaire, Intrinsic-Extrinsic Aspirations Scale, and Alcohol Use Questionnaire. Results showed that sense of control and intrinsic motivation were positively correlated with adaptive motivation and negatively correlated with alcohol consumption. Mediational analyses indicated that adaptive motivation fully mediated the relationship between sense of control/intrinsic motivation and alcohol consumption.

The alphabet of intrinsic disorder

PubMed Central

Uversky, Vladimir N

2013-01-01

The ability of a protein to fold into unique functional state or to stay intrinsically disordered is encoded in its amino acid sequence. Both ordered and intrinsically disordered proteins (IDPs) are natural polypeptides that use the same arsenal of 20 proteinogenic amino acid residues as their major building blocks. The exceptional structural plasticity of IDPs, their capability to exist as heterogeneous structural ensembles and their wide array of important disorder-based biological functions that complements functional repertoire of ordered proteins are all rooted within the peculiar differential usage of these building blocks by ordered proteins and IDPs. In fact, some residues (so-called disorder-promoting residues) are noticeably more common in IDPs than in sequences of ordered proteins, which, in their turn, are enriched in several order-promoting residues. Furthermore, residues can be arranged according to their “disorder promoting potencies,” which are evaluated based on the relative abundances of various amino acids in ordered and disordered proteins. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and concerns glutamic acid, which is the second most disorder-promoting residue. PMID:28516010

Intrinsic spin-orbit torque in a single-domain nanomagnet

NASA Astrophysics Data System (ADS)

Kalitsov, A.; Nikolaev, S. A.; Velev, J.; Chshiev, M.; Mryasov, O.

2017-12-01

We present theoretical studies of the intrinsic spin-orbit torque (SOT) in a single-domain ferromagnetic layer with Rashba spin-orbit coupling (SOC) using the nonequilibrium Green's function formalism for a tight-binding Hamiltonian. We find that, in the case of a small electric field, the intrinsic SOT to first order in SOC has only the field-like torque symmetry and can be interpreted as the longitudinal spin current induced by the charge current and Rashba field. We analyze the results in terms of the material-related parameters of the electronic structure, such as the band filling, bandwidth, exchange splitting, and the Rashba SOC strength. On the basis of these numerical and analytical results, we discuss the magnitude and sign of SOT. Our results suggest that the different sign of SOT in identical ferromagnets with different supporting layers, e.g., Co/Pt and Co/Ta, can be attributed to electrostatic doping of the ferromagnetic layer by the support.

Comment on 'Observation of intrinsic bistability in resonant-tunneling structures'

NASA Technical Reports Server (NTRS)

Sollner, T. C. L. G.

1987-01-01

It is suggested that the intrinsic bistability observed by Goldman et al. (1987) occurred not because of charging of the well, as is claimed, but because of oscillations in the negative-resistance region. A typical I-V curve for a double-barrier resonant-tunneling (DBRT) diode which is known to be oscillating is presented. In a reply to this comment, Goldman et al. show that the series resistance (of about 100 ohms) in Sollner's sample leads to extrinsic, rather than intrinsic, bistability. It is furthermore suggested that the mere presence of an oscillation does not in itself exclude intrinsic bistability in a DBRT structure. It is also noted that the intrinsic bistability and buildup of negative charge-space in a DBRT structure well has been demonstrated experimentally by Payling et al. (1987).

Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings.

PubMed

Sanchez-Martinez, M; Crehuet, R

2014-12-21

We present a method based on the maximum entropy principle that can re-weight an ensemble of protein structures based on data from residual dipolar couplings (RDCs). The RDCs of intrinsically disordered proteins (IDPs) provide information on the secondary structure elements present in an ensemble; however even two sets of RDCs are not enough to fully determine the distribution of conformations, and the force field used to generate the structures has a pervasive influence on the refined ensemble. Two physics-based coarse-grained force fields, Profasi and Campari, are able to predict the secondary structure elements present in an IDP, but even after including the RDC data, the re-weighted ensembles differ between both force fields. Thus the spread of IDP ensembles highlights the need for better force fields. We distribute our algorithm in an open-source Python code.

Two-state protein model with water interactions: Influence of temperature on the intrinsic viscosity of myoglobin

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

Bakk, Audun

2001-06-01

We describe a single-domain protein as a two-state system with water interactions. Around the unfolded apolar parts of the protein we incorporate the hydration effect by introducing hydrogen bonds between the water molecules in order to mimic the {open_quotes}icelike{close_quotes} shell structure. Intrinsic viscosity, proportional to the effective hydrodynamic volume, for sperm whale metmyoglobin is assigned from experimental data in the folded and in the denaturated state. By weighing statistically the two states against the degree of folding, we express the total intrinsic viscosity. The temperature dependence of the intrinsic viscosity, for different chemical potentials, is in good correspondence with experimentalmore » data [P. L. Privalov , J. Mol. Biol. >190, 487 (1986)]. Cold and warm unfolding, common to small globular proteins, is also a result of the model.« less

Job Orientation of Black and White College Graduates in Business.

ERIC Educational Resources Information Center

Brenner, O. C.; Tomkiewicz, Joseph

1982-01-01

Examined differences in job orientation between Black and White male and female business college graduates. Significant race differences were found. Factor analysis indicates that Blacks value long-range career objectives and structure considerably more than do Whites, while their preference for intrinsic and extrinsic factors was less pronounced.…

Intrinsic Differences in the Inner Jets of High and Low Optically Polarized Radio Quasars

NASA Technical Reports Server (NTRS)

Lister, M.; Smith, P.

2000-01-01

We have conducted a high-resolution polarization study with the VLBA at 22 and 43 GHz to look for differences in the parsec-scale magnetic field structures of 18 high- and low-optically polarized, compact radio-loud quasars (HPQs and LPRQs, respectively).

Towards the Better: Intrinsic Property Amelioration in Bulk Metallic Glasses

NASA Astrophysics Data System (ADS)

Sarac, Baran; Zhang, Long; Kosiba, Konrad; Pauly, Simon; Stoica, Mihai; Eckert, Jürgen

2016-06-01

Tailoring the intrinsic length-scale effects in bulk metallic glasses (BMGs) via post-heat treatment necessitates a systematic analyzing strategy. Although various achievements were made in the past years to structurally enhance the properties of different BMG alloys, the influence of short-term sub-glass transition annealing on the relaxation kinetics is still not fully covered. Here, we aim for unraveling the connection between the physical, (thermo)mechanical and structural changes as a function of selected pre-annealing temperatures and time scales with an in-house developed Cu46Zr44Al8Hf2 based BMG alloy. The controlled formation of nanocrystals below 50 nm with homogenous distribution inside the matrix phase via thermal treatment increase the material’s resistance to strain softening by almost an order of magnitude. The present work determines the design aspects of metallic glasses with enhanced mechanical properties via nanostructural modifications, while postulating a counter-argument to the intrinsic property degradation accounted for long-term annealing.

The effects of intrinsic properties and defect structures on the indentation size effect in metals

NASA Astrophysics Data System (ADS)

Maughan, Michael R.; Leonard, Ariel A.; Stauffer, Douglas D.; Bahr, David F.

2017-08-01

The indentation size effect has been linked to the generation of geometrically necessary dislocations that may be impacted by intrinsic materials properties, such as stacking fault energy, and extrinsic defects, such as statistically stored dislocations. Nanoindentation was carried out at room temperature and elevated temperatures on four different metals in a variety of microstructural conditions. A size effect parameter was determined for each material set combining the effects of temperature and existing dislocation structure. Extrinsic defects, particularly dislocation density, dominate the size effect parameter over those due to intrinsic properties such as stacking fault energy. A multi-mechanism description using a series of mechanisms, rather than a single mechanism, is presented as a phenomenological explanation for the observed size effect in these materials. In this description, the size effect begins with a volume scale dominated by sparse sources, next is controlled by the ability of dislocations to cross-slip and multiply, and then finally at larger length scales work hardening and recovery dominate the effect.

S. pombe Uba1-Ubc15 Structure Reveals a Novel Regulatory Mechanism of Ubiquitin E2 Activity.

PubMed

Lv, Zongyang; Rickman, Kimberly A; Yuan, Lingmin; Williams, Katelyn; Selvam, Shanmugam Panneer; Woosley, Alec N; Howe, Philip H; Ogretmen, Besim; Smogorzewska, Agata; Olsen, Shaun K

2017-02-16

Ubiquitin (Ub) E1 initiates the Ub conjugation cascade by activating and transferring Ub to tens of different E2s. How Ub E1 cooperates with E2s that differ substantially in their predicted E1-interacting residues is unknown. Here, we report the structure of S. pombe Uba1 in complex with Ubc15, a Ub E2 with intrinsically low E1-E2 Ub thioester transfer activity. The structure reveals a distinct Ubc15 binding mode that substantially alters the network of interactions at the E1-E2 interface compared to the only other available Ub E1-E2 structure. Structure-function analysis reveals that the intrinsically low activity of Ubc15 largely results from the presence of an acidic residue at its N-terminal region. Notably, Ub E2 N termini are serine/threonine rich in many other Ub E2s, leading us to hypothesize that phosphorylation of these sites may serve as a novel negative regulatory mechanism of Ub E2 activity, which we demonstrate biochemically and in cell-based assays. Copyright © 2017 Elsevier Inc. All rights reserved.

Nonlinear spectral imaging of biological tissues

NASA Astrophysics Data System (ADS)

Palero, J. A.

2007-07-01

The work presented in this thesis demonstrates live high resolution 3D imaging of tissue in its native state and environment. The nonlinear interaction between focussed femtosecond light pulses and the biological tissue results in the emission of natural autofluorescence and second-harmonic signal. Because biological intrinsic emission is generally very weak and extends from the ultraviolet to the visible spectral range, a broad-spectral range and high sensitivity 3D spectral imaging system is developed. Imaging the spectral characteristics of the biological intrinsic emission reveals the structure and biochemistry of the cells and extra-cellular components. By using different methods in visualizing the spectral images, discrimination between different tissue structures is achieved without the use of any stain or fluorescent label. For instance, RGB real color spectral images of the intrinsic emission of mouse skin tissues show blue cells, green hair follicles, and purple collagen fibers. The color signature of each tissue component is directly related to its characteristic emission spectrum. The results of this study show that skin tissue nonlinear intrinsic emission is mainly due to the autofluorescence of reduced nicotinamide adenine dinucleotide (phosphate), flavins, keratin, melanin, phospholipids, elastin and collagen and nonlinear Raman scattering and second-harmonic generation in Type I collagen. In vivo time-lapse spectral imaging is implemented to study metabolic changes in epidermal cells in tissues. Optical scattering in tissues, a key factor in determining the maximum achievable imaging depth, is also investigated in this work.

Meta-structure correlation in protein space unveils different selection rules for folded and intrinsically disordered proteins.

PubMed

Naranjo, Yandi; Pons, Miquel; Konrat, Robert

2012-01-01

The number of existing protein sequences spans a very small fraction of sequence space. Natural proteins have overcome a strong negative selective pressure to avoid the formation of insoluble aggregates. Stably folded globular proteins and intrinsically disordered proteins (IDPs) use alternative solutions to the aggregation problem. While in globular proteins folding minimizes the access to aggregation prone regions, IDPs on average display large exposed contact areas. Here, we introduce the concept of average meta-structure correlation maps to analyze sequence space. Using this novel conceptual view we show that representative ensembles of folded and ID proteins show distinct characteristics and respond differently to sequence randomization. By studying the way evolutionary constraints act on IDPs to disable a negative function (aggregation) we might gain insight into the mechanisms by which function-enabling information is encoded in IDPs.

Unfoldomics of human diseases: linking protein intrinsic disorder with diseases

PubMed Central

Uversky, Vladimir N; Oldfield, Christopher J; Midic, Uros; Xie, Hongbo; Xue, Bin; Vucetic, Slobodan; Iakoucheva, Lilia M; Obradovic, Zoran; Dunker, A Keith

2009-01-01

Background Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack stable tertiary and/or secondary structure yet fulfills key biological functions. The recent recognition of IDPs and IDRs is leading to an entire field aimed at their systematic structural characterization and at determination of their mechanisms of action. Bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. These activities complement the functions of structured proteins. IDPs and IDRs were shown to participate in both one-to-many and many-to-one signaling. Alternative splicing and posttranslational modifications are frequently used to tune the IDP functionality. Several individual IDPs were shown to be associated with human diseases, such as cancer, cardiovascular disease, amyloidoses, diabetes, neurodegenerative diseases, and others. This raises questions regarding the involvement of IDPs and IDRs in various diseases. Results IDPs and IDRs were shown to be highly abundant in proteins associated with various human maladies. As the number of IDPs related to various diseases was found to be very large, the concepts of the disease-related unfoldome and unfoldomics were introduced. Novel bioinformatics tools were proposed to populate and characterize the disease-associated unfoldome. Structural characterization of the members of the disease-related unfoldome requires specialized experimental approaches. IDPs possess a number of unique structural and functional features that determine their broad involvement into the pathogenesis of various diseases. Conclusion Proteins associated with various human diseases are enriched in intrinsic disorder. These disease-associated IDPs and IDRs are real, abundant, diversified, vital, and dynamic. These proteins and regions comprise the disease-related unfoldome, which covers a significant part of the human proteome. Profound association between intrinsic disorder and various human diseases is determined by a set of unique structural and functional characteristics of IDPs and IDRs. Unfoldomics of human diseases utilizes unrivaled bioinformatics and experimental techniques, paves the road for better understanding of human diseases, their pathogenesis and molecular mechanisms, and helps develop new strategies for the analysis of disease-related proteins. PMID:19594884

The Work Preference Inventory: assessing intrinsic and extrinsic motivational orientations.

PubMed

Amabile, T M; Hill, K G; Hennessey, B A; Tighe, E M

1994-05-01

The Work Preference Inventory (WPI) is designed to assess individual differences in intrinsic and extrinsic motivational orientations. Both the college student and the working adult versions aim to capture the major elements of intrinsic motivation (self-determination, competence, task involvement, curiosity, enjoyment, and interest) and extrinsic motivation (concerns with competition, evaluation, recognition, money or other tangible incentives, and constraint by others). The instrument is scored on two primary scales, each subdivided into 2 secondary scales. The WPI has meaningful factor structures, adequate internal consistency, good short-term test-retest reliability, and good longer term stability. Moreover, WPI scores are related in meaningful ways to other questionnaire and behavioral measures of motivation, as well as personality characteristics, attitudes, and behaviors.

The intrinsic cephalosporin resistome of Listeria monocytogenes in the context of stress response, gene regulation, pathogenesis and therapeutics.

PubMed

Krawczyk-Balska, A; Markiewicz, Z

2016-02-01

Intrinsic resistance to antibiotics is a serious therapeutic problem in the case of many bacterial species. The Gram-positive human pathogen Listeria monocytogenes is intrinsically resistant to broad spectrum cephalosporin antibiotics, which are commonly used in therapy of bacterial infections. Besides three penicillin-binding proteins the intrinsic cephalosporin resistome of L. monocytogenes includes multidrug resistance transporter transporters, proteins involved in peptidoglycan biosynthesis and modification, cell envelope proteins with structural or general detoxification function, cytoplasmic proteins with unknown function and regulatory proteins. Analysis of the regulation of the expression of genes involved in the intrinsic resistance of L. monocytogenes to cephalosporins highlights the high complexity of control of the intrinsic resistance phenotype. The regulation of the transcription of the intrinsic resistome determinants involves the activity of eight regulators, namely LisR, CesR, LiaR, VirR, σ(B) , σ(H) , σ(L) and PrfA, of which the most prominent role play LisR, CesR and σ(B) . Furthermore, the vast majority of the intrinsic resistome determinants contribute to the tolerance of different stress conditions and virulence. A study indicates that O-acetyltransferase OatA is the most promising candidate for co-drug development since an agent targeting OatA should sensitize L. monocytogenes to certain antibiotics, therefore improving the efficacy of listeriosis treatment as well as food preservation measures. © 2015 The Society for Applied Microbiology.

pH-Manipulated Underwater-Oil Adhesion Wettability Behavior on the Micro/Nanoscale Semicircular Structure and Related Thermodynamic Analysis.

PubMed

Tie, Lu; Guo, Zhiguang; Liu, Weimin

2015-05-20

Controlling oil of wettability behavior in response to the underwater out stimulation has shown promising applications in understanding and designing novel micro- or nanofluidic devices. In this article, the pH-manipulated underwater-oil adhesion wetting phenomenon and superoleophobicity on the micro- and nanotexture copper mesh films (CMF) were investigated. It should be noted that the surface exhibits underwater superoleophobicity under different pH values of the solution; however, the underwater-oil adhesion behavior on the surface is dramatically influenced by the pH value of the solution. On the basis of the thermodynamic analysis, a plausible mechanism to explain the pH-controllable underwater-oil adhesion and superoleophobic wetting behavior observed on a micro- and nanoscale semicircular structure has been revealed. Furthermore, variation of chemistry (intrinsic oil contact angle (OCA)) of the responsive surface that due to the carboxylic acid groups is protonated or deprotonated by the acidic or basic solution on free energy (FE) with its barrier (FEB) and equilibrium oil contact angle (EOCA) with it hysteresis (OCAH) are discussed. The result shows that a critical intrinsic OCA on the micro- and nano- semicircular texture is necessary for conversion from the oil Cassie impregnating to oil Cassie wetting state. In a water/oil/solid system, the mechanism reveals that the differences between the underwater OCA and oil adhesive force of the responsive copper mesh film under different pH values of solution are ascribed to the different oil wetting state that results from combining the changing intrinsic OCA and micro-/nanosemicircular structures. These results are well in agreement with the experiment.

Implications of Self-Deception for Self-Reported Intrinsic and Extrinsic Motivational Dispositions and Actual Learning Performance: A Higher Order Structural Model

ERIC Educational Resources Information Center

Hirschfeld, Robert R.; Thomas, Christopher H.; McNatt, D. Brian

2008-01-01

The authors explored implications of individuals' self-deception (a trait) for their self-reported intrinsic and extrinsic motivational dispositions and their actual learning performance. In doing so, a higher order structural model was developed and tested in which intrinsic and extrinsic motivational dispositions were underlying factors that…

Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota.

PubMed

Leiva, Diego; Clavero-León, Claudia; Carú, Margarita; Orlando, Julieta

2016-11-01

Definition of lichens has evolved from bi(tri)partite associations to multi-species symbioses, where bacteria would play essential roles. Besides, although soil bacterial communities are known to be affected by edaphic factors, when lichens grow upon them these could become less preponderant. We hypothesized that the structure of both the lichen microbiota and the microbiota in the soil underneath lichens is shaped by lichen intrinsic and extrinsic factors. In this work, intrinsic factors corresponded to mycobiont and cyanobiont identities of Peltigera lichens, metabolite diversity and phenoloxidase activity and extrinsic factors involved the site of the forest where lichens grow. Likewise, the genetic and metabolic structure of the lichen and soil bacterial communities were analyzed by fingerprinting. Among the results, metabolite diversity was inversely related to the genetic structure of bacterial communities of lichens and soils, highlighting the far-reaching effect of these substances; while phenoloxidase activity was inversely related to the metabolic structure only of the lichen bacterial microbiota, presuming a more limited effect of the products of these enzymes. Soil bacterial microbiota was different depending on the site and, strikingly, according to the cyanobiont present in the lichen over them, which could indicate an influence of the photobiont metabolism on the availability of soil nutrients. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A new subfamily LIP of the major intrinsic proteins.

PubMed

Khabudaev, Kirill Vladimirovich; Petrova, Darya Petrovna; Grachev, Mikhail Aleksandrovich; Likhoshway, Yelena Valentinovna

2014-03-04

Proteins of the major intrinsic protein (MIP) family, or aquaporins, have been detected in almost all organisms. These proteins are important in cells and organisms because they allow for passive transmembrane transport of water and other small, uncharged polar molecules. We compared the predicted amino acid sequences of 20 MIPs from several algae species of the phylum Heterokontophyta (Kingdom Chromista) with the sequences of MIPs from other organisms. Multiple sequence alignments revealed motifs that were homologous to functionally important NPA motifs and the so-called ar/R-selective filter of glyceroporins and aquaporins. The MIP sequences of the studied chromists fell into several clusters that belonged to different groups of MIPs from a wide variety of organisms from different Kingdoms. Two of these proteins belong to Plasma membrane intrinsic proteins (PIPs), four of them belong to GlpF-like intrinsic proteins (GIPs), and one of them belongs to a specific MIPE subfamily from green algae. Three proteins belong to the unclassified MIPs, two of which are of bacterial origin. Eight of the studied MIPs contain an NPM-motif in place of the second conserved NPA-motif typical of the majority of MIPs. The MIPs of heterokonts within all detected clusters can differ from other MIPs in the same cluster regarding the structure of the ar/R-selective filter and other generally conserved motifs. We proposed placing nine MIPs from heterokonts into a new group, which we have named the LIPs (large intrinsic proteins). The possible substrate specificities of the studied MIPs are discussed.

[Spatial scale effect of urban land use landscape pattern in Shanghai City].

PubMed

Xu, Li-Hua; Yue, Wen Ze; Cao, Yu

2007-12-01

Based on geographic information system (GIS) and remote sensing (RS) techniques, the landscape classes of urban land use in Shanghai City were extracted from SPOT images with 5 m spatial resolution in 2002, and then, the classified data were applied to quantitatively explore the change patterns of several basic landscape metrics at different scales. The results indicated that landscape metrics were sensitive to grain- and extent variance. Urban landscape pattern was spatially dependent. In other words, different landscape metrics showed different responses to scale. The resolution of 40 m was an intrinsic observing scale for urban landscape in Shanghai City since landscape metrics showed random characteristics while the grain was less than 40 m. The extent of 24 km was a symbol scale in a series of extents, which was consistent with the boundary between urban built-up area and suburban area in Shanghai City. As a result, the extent of 12 km away from urban center would be an intrinsic handle scale for urban landscape in Shanghai City. However, due to the complexity of urban structure and asymmetry of urban spatial expansion, the intrinsic handle scale was not regular extent, and the square with size of 24 km was just an approximate intrinsic extent for Shanghai City.

Efficiency Improvement of HIT Solar Cells on p-Type Si Wafers.

PubMed

Wei, Chun-You; Lin, Chu-Hsuan; Hsiao, Hao-Tse; Yang, Po-Chuan; Wang, Chih-Ming; Pan, Yen-Chih

2013-11-22

Single crystal silicon solar cells are still predominant in the market due to the abundance of silicon on earth and their acceptable efficiency. Different solar-cell structures of single crystalline Si have been investigated to boost efficiency; the heterojunction with intrinsic thin layer (HIT) structure is currently the leading technology. The record efficiency values of state-of-the art HIT solar cells have always been based on n-type single-crystalline Si wafers. Improving the efficiency of cells based on p-type single-crystalline Si wafers could provide broader options for the development of HIT solar cells. In this study, we varied the thickness of intrinsic hydrogenated amorphous Si layer to improve the efficiency of HIT solar cells on p-type Si wafers.

Lens-Aided Multi-Angle Spectroscopy (LAMAS) Reveals Small-Scale Outflow Structure in Quasars

NASA Astrophysics Data System (ADS)

Green, Paul J.

2006-06-01

Spectral differences between lensed quasar image components are common. Since lensing is intrinsically achromatic, these differences are typically explained as the effect of either microlensing, or as light path time delays sampling intrinsic quasar spectral variability. Here we advance a novel third hypothesis: some spectral differences are due to small line-of-sight differences through quasar disk wind outflows. In particular, we propose that variable spectral differences seen only in component A of the widest separation lens SDSS J1004+4112 are due to differential absorption along the sight lines. The absorber properties required by this hypothesis are akin to known broad absorption line (BAL) outflows but must have a broader, smoother velocity profile. We interpret the observed C IV emission-line variability as further evidence for spatial fine structure transverse to the line of sight. Since outflows are likely to be rotating, such absorber fine structure can consistently explain some of the UV and X-ray variability seen in AGNs. The implications are many: (1) Spectroscopic differences in other lensed objects may be due to this ``lens-aided multi-angle spectroscopy'' (LAMAS). (2) Outflows have fine structure on size scales of arcseconds, as seen from the nucleus. (3) Assuming either broad absorption line region sizes proposed in recent wind models, or typically assumed continuum emission region sizes, LAMAS and/or variability provide broadly consistent absorber size scale estimates of ~1015 cm. (4) Very broad smooth absorption may be ubiquitous in quasar spectra, even when no obvious troughs are seen.

Ontic structural realism and quantum field theory: Are there intrinsic properties at the most fundamental level of reality?

NASA Astrophysics Data System (ADS)

Berghofer, Philipp

2018-05-01

Ontic structural realism refers to the novel, exciting, and widely discussed basic idea that the structure of physical reality is genuinely relational. In its radical form, the doctrine claims that there are, in fact, no objects but only structure, i.e., relations. More moderate approaches state that objects have only relational but no intrinsic properties. In its most moderate and most tenable form, ontic structural realism assumes that at the most fundamental level of physical reality there are only relational properties. This means that the most fundamental objects only possess relational but no non-reducible intrinsic properties. The present paper will argue that our currently best physics refutes even this most moderate form of ontic structural realism. More precisely, I will claim that 1) according to quantum field theory, the most fundamental objects of matter are quantum fields and not particles, and show that 2) according to the Standard Model, quantum fields have intrinsic non-relational properties.

A metrics for soil hydrological processes and their intrinsic dimensionality in heterogeneous systems

NASA Astrophysics Data System (ADS)

Lischeid, G.; Hohenbrink, T.; Schindler, U.

2012-04-01

Hydrology is based on the observation that catchments process input signals, e.g., precipitation, in a highly deterministic way. Thus, the Darcy or the Richards equation can be applied to model water fluxes in the saturated or vadose zone, respectively. Soils and aquifers usually exhibit substantial spatial heterogeneities at different scales that can, in principle, be represented by corresponding parameterisations of the models. In practice, however, data are hardly available at the required spatial resolution, and accounting for observed heterogeneities of soil and aquifer structure renders models very time and CPU consuming. We hypothesize that the intrinsic dimensionality of soil hydrological processes, which is induced by spatial heterogeneities, actually is very low and that soil hydrological processes in heterogeneous soils follow approximately the same trajectory. That means, the way how the soil transforms any hydrological input signals is the same for different soil textures and structures. Different soils differ only with respect to the extent of transformation of input signals. In a first step, we analysed the output of a soil hydrological model, based on the Richards equation, for homogeneous soils down to 5 m depth for different soil textures. A matrix of time series of soil matrix potential and soil water content at 10 cm depth intervals was set up. The intrinsic dimensionality of that matrix was assessed using the Correlation Dimension and a non-linear principal component approach. The latter provided a metrics for the extent of transformation ("damping") of the input signal. In a second step, model outputs for heterogeneous soils were analysed. In a last step, the same approaches were applied to 55 time series of observed soil water content from 15 sites and different depths. In all cases, the intrinsic dimensionality in fact was very close to unity, confirming our hypothesis. The metrics provided a very efficient tool to quantify the observed behaviour, depending on depth and soil heterogeneity: Different soils differed primarily with respect to the extent of damping per depth interval rather than to the kind of damping. We will show how that metrics can be used in a very efficient way for representing soil heterogeneities in simulation models.

The genetic basis of developmental abnormalities in interpopulation hybrids of the moss Ceratodon purpureus.

PubMed

McDaniel, Stuart F; Willis, John H; Shaw, A Jonathan

2008-07-01

Divergent populations are intrinsically reproductively isolated when hybrids between them either fail to develop properly or do not produce viable offspring. Intrinsic isolation may result from Dobzhansky-Muller (DM) incompatibilities, in which deleterious interactions among genes or gene products lead to developmental problems or underdominant chromosome structure differences between the parents. These mechanisms can be tested by studying marker segregation patterns in a hybrid mapping population. Here we examine the genetic basis of abnormal development in hybrids between two geographically distant populations of the moss Ceratodon purpureus. Approximately half of the hybrid progeny exhibited a severely reduced growth rate in early gametophyte development. We identified four unlinked quantitative trait loci (QTL) that interacted asymmetrically to cause the abnormal development phenotype. This pattern is consistent with DM interactions. We also found an excess of recombination between three marker pairs in the abnormally developing progeny, relative to that estimated in the normal progeny. This suggests that structural differences in these regions contribute to hybrid breakdown. Two QTL coincided with inferred structural differences, consistent with recent theory suggesting that rearrangements may harbor population divergence alleles. These observations suggest that multiple complex genetic factors contribute to divergence among populations of C. purpureus.

Modelling and analysis of the stress distribution in a multi-thin film system Pt/USG/Si

NASA Astrophysics Data System (ADS)

Yao, W. Z.; Roqueta, F.; Craveur, J. C.; Belhenini, S.; Gardes, P.; Tougui, A.

2018-04-01

Residual stress analysis is commonly achieved through curvature measurement with the help of Stoney’s formula. However, this conventional approach is inadequate for multi-layer thin film systems, which are widely used in today’s microelectronics. Also, for the thin film case, the residual stress is composed of thermal stress and intrinsic stress. Measuring the wafer curvature at room temperature provides a value for the average stresses in the layer, the two components cannot be distinguished by the existing methodologies of curvature measurement. To alleviate these problems, a modified curvature method combining finite element (FE) modelling is proposed to study the stress distribution in a Pt/USG/Si structure. A 2D FE model is firstly built in order to calculate the thermal stress in the multilayer structure, the obtained thermal stresses in respective films are verified by an analytical model. Then, we calculate the warpage of the multilayer structure by considering the intrinsic stress in the respective films. The residual stresses in the films are determined by minimizing the difference between the simulated warpage and that of experimental measurement. The proposed approach can be used to calculate not only the average residual stress but also thermal and intrinsic stress components in the USG and Platinum films. The obtained residual and intrinsic stresses from a numerical model are compared with the values of other studies. There is no limitation for the application of our methodologies regarding the number of the layers in the stack.

Ankle Joint Intrinsic Dynamics is More Complex than a Mass-Spring-Damper Model.

PubMed

Sobhani Tehrani, Ehsan; Jalaleddini, Kian; Kearney, Robert E

2017-09-01

This paper describes a new small signal parametric model of ankle joint intrinsic mechanics in normal subjects. We found that intrinsic ankle mechanics is a third-order system and the second-order mass-spring-damper model, referred to as IBK, used by many researchers in the literature cannot adequately represent ankle dynamics at all frequencies in a number of important tasks. This was demonstrated using experimental data from five healthy subjects with no voluntary muscle contraction and at seven ankle positions covering the range of motion. We showed that the difference between the new third-order model and the conventional IBK model increased from dorsi to plantarflexed position. The new model was obtained using a multi-step identification procedure applied to experimental input/output data of the ankle joint. The procedure first identifies a non-parametric model of intrinsic joint stiffness where ankle position is the input and torque is the output. Then, in several steps, the model is converted into a continuous-time transfer function of ankle compliance, which is the inverse of stiffness. Finally, we showed that the third-order model is indeed structurally consistent with agonist-antagonist musculoskeletal structure of human ankle, which is not the case for the IBK model.

Different Ligands of the TRPV3 Cation Channel Cause Distinct Conformational Changes as Revealed by Intrinsic Tryptophan Fluorescence Quenching*

PubMed Central

Billen, Bert; Brams, Marijke; Debaveye, Sarah; Remeeva, Alina; Alpizar, Yeranddy A.; Waelkens, Etienne; Kreir, Mohamed; Brüggemann, Andrea; Talavera, Karel; Nilius, Bernd; Voets, Thomas; Ulens, Chris

2015-01-01

TRPV3 is a thermosensitive ion channel primarily expressed in epithelial tissues of the skin, nose, and tongue. The channel has been implicated in environmental thermosensation, hyperalgesia in inflamed tissues, skin sensitization, and hair growth. Although transient receptor potential (TRP) channel research has vastly increased our understanding of the physiological mechanisms of nociception and thermosensation, the molecular mechanics of these ion channels are still largely elusive. In order to better comprehend the functional properties and the mechanism of action in TRP channels, high-resolution three-dimensional structures are indispensable, because they will yield the necessary insights into architectural intimacies at the atomic level. However, structural studies of membrane proteins are currently hampered by difficulties in protein purification and in establishing suitable crystallization conditions. In this report, we present a novel protocol for the purification of membrane proteins, which takes advantage of a C-terminal GFP fusion. Using this protocol, we purified human TRPV3. We show that the purified protein is a fully functional ion channel with properties akin to the native channel using planar patch clamp on reconstituted channels and intrinsic tryptophan fluorescence spectroscopy. Using intrinsic tryptophan fluorescence spectroscopy, we reveal clear distinctions in the molecular interaction of different ligands with the channel. Altogether, this study provides powerful tools to broaden our understanding of ligand interaction with TRPV channels, and the availability of purified human TRPV3 opens up perspectives for further structural and functional studies. PMID:25829496

Intrinsic magnetic properties of bimetallic nanoparticles elaborated by cluster beam deposition.

PubMed

Dupuis, V; Khadra, G; Hillion, A; Tamion, A; Tuaillon-Combes, J; Bardotti, L; Tournus, F

2015-11-14

In this paper, we present some specific chemical and magnetic order obtained very recently on characteristic bimetallic nanoalloys prepared by mass-selected Low Energy Cluster Beam Deposition (LECBD). We study how the competition between d-atom hybridization, complex structure, morphology and chemical affinity affects their intrinsic magnetic properties at the nanoscale. The structural and magnetic properties of these nanoalloys were investigated using various experimental techniques that include High Resolution Transmission Electron Microscopy (HRTEM), Superconducting Quantum Interference Device (SQUID) magnetometry, as well as synchrotron techniques such as Extended X-ray Absorption Fine Structure (EXAFS) and X-ray Magnetic Circular Dichroism (XMCD). Depending on the chemical nature of the nanoalloys we observe different magnetic responses compared to their bulk counterparts. In particular, we show how specific relaxation in nanoalloys impacts their magnetic anisotropy; and how finite size effects (size reduction) inversely enhance their magnetic moment.

Optical spectra and band structure of Ag(x)Ga(x)Ge(1-x)Se2 (x = 0.333, 0.250, 0.200, 0.167) single crystals: experiment and theory.

PubMed

Reshak, A H; Parasyuk, O V; Fedorchuk, A O; Kamarudin, H; Auluck, S; Chyský, J

2013-12-05

Theoretical and experimental studies of the Ag(x)Ga(x)Ge(1-x)Se2 (x = 0.333, 0.250, 0.200, 0.167) single crystals are performed. These crystals possess a lot of intrinsic defects which are responsible for their optoelectronic features. The theoretical investigations were performed by means of DFT calculations using different exchange-correlation potentials. The experimental studies were carried out using the modulated VUV ellipsometry for dielectric constants and birefringence studies. The comparison of the structure obtained from X-ray with the theoretically optimized structure is presented. The crucial role of the intrinsic defect states is manifested in the choice of the exchange correlation potential used. The data may be applicable for a large number of the ternary chalcogenides which are sensitive to the presence of the local disordered states near the band edges.

What We Know About the Brain Structure-Function Relationship.

PubMed

Batista-García-Ramó, Karla; Fernández-Verdecia, Caridad Ivette

2018-04-18

How the human brain works is still a question, as is its implication with brain architecture: the non-trivial structure–function relationship. The main hypothesis is that the anatomic architecture conditions, but does not determine, the neural network dynamic. The functional connectivity cannot be explained only considering the anatomical substrate. This involves complex and controversial aspects of the neuroscience field and that the methods and methodologies to obtain structural and functional connectivity are not always rigorously applied. The goal of the present article is to discuss about the progress made to elucidate the structure–function relationship of the Central Nervous System, particularly at the brain level, based on results from human and animal studies. The current novel systems and neuroimaging techniques with high resolutive physio-structural capacity have brought about the development of an integral framework of different structural and morphometric tools such as image processing, computational modeling and graph theory. Different laboratories have contributed with in vivo, in vitro and computational/mathematical models to study the intrinsic neural activity patterns based on anatomical connections. We conclude that multi-modal techniques of neuroimaging are required such as an improvement on methodologies for obtaining structural and functional connectivity. Even though simulations of the intrinsic neural activity based on anatomical connectivity can reproduce much of the observed patterns of empirical functional connectivity, future models should be multifactorial to elucidate multi-scale relationships and to infer disorder mechanisms.

Genome-Wide Prediction of Intrinsic Disorder; Sequence Alignment of Intrinsically Disordered Proteins

ERIC Educational Resources Information Center

Midic, Uros

2012-01-01

Intrinsic disorder (ID) is defined as a lack of stable tertiary and/or secondary structure under physiological conditions in vitro. Intrinsically disordered proteins (IDPs) are highly abundant in nature. IDPs possess a number of crucial biological functions, being involved in regulation, recognition, signaling and control, e.g. their functional…

Reward Structures in the Public High School

ERIC Educational Resources Information Center

Spuck, Dennis W.

1974-01-01

Examines the relationship between eight categories of rewards available to teachers in high schools and teacher behaviors of absenteeism, recruitment, and retention. Findings emphasize the importance of intrinsic motivators in professional organizations and suggest basic differences in motivational patterns between professional and production…

Large epidemic thresholds emerge in heterogeneous networks of heterogeneous nodes

NASA Astrophysics Data System (ADS)

Yang, Hui; Tang, Ming; Gross, Thilo

2015-08-01

One of the famous results of network science states that networks with heterogeneous connectivity are more susceptible to epidemic spreading than their more homogeneous counterparts. In particular, in networks of identical nodes it has been shown that network heterogeneity, i.e. a broad degree distribution, can lower the epidemic threshold at which epidemics can invade the system. Network heterogeneity can thus allow diseases with lower transmission probabilities to persist and spread. However, it has been pointed out that networks in which the properties of nodes are intrinsically heterogeneous can be very resilient to disease spreading. Heterogeneity in structure can enhance or diminish the resilience of networks with heterogeneous nodes, depending on the correlations between the topological and intrinsic properties. Here, we consider a plausible scenario where people have intrinsic differences in susceptibility and adapt their social network structure to the presence of the disease. We show that the resilience of networks with heterogeneous connectivity can surpass those of networks with homogeneous connectivity. For epidemiology, this implies that network heterogeneity should not be studied in isolation, it is instead the heterogeneity of infection risk that determines the likelihood of outbreaks.

Large epidemic thresholds emerge in heterogeneous networks of heterogeneous nodes.

PubMed

Yang, Hui; Tang, Ming; Gross, Thilo

2015-08-21

One of the famous results of network science states that networks with heterogeneous connectivity are more susceptible to epidemic spreading than their more homogeneous counterparts. In particular, in networks of identical nodes it has been shown that network heterogeneity, i.e. a broad degree distribution, can lower the epidemic threshold at which epidemics can invade the system. Network heterogeneity can thus allow diseases with lower transmission probabilities to persist and spread. However, it has been pointed out that networks in which the properties of nodes are intrinsically heterogeneous can be very resilient to disease spreading. Heterogeneity in structure can enhance or diminish the resilience of networks with heterogeneous nodes, depending on the correlations between the topological and intrinsic properties. Here, we consider a plausible scenario where people have intrinsic differences in susceptibility and adapt their social network structure to the presence of the disease. We show that the resilience of networks with heterogeneous connectivity can surpass those of networks with homogeneous connectivity. For epidemiology, this implies that network heterogeneity should not be studied in isolation, it is instead the heterogeneity of infection risk that determines the likelihood of outbreaks.

Organizational commitment and intrinsic motivation of regular and contractual primary health care providers.

PubMed

Kumar, Pawan; Mehra, Anu; Inder, Deep; Sharma, Nandini

2016-01-01

Motivated and committed employees deliver better health care, which results in better outcomes and higher patient satisfaction. To assess the Organizational Commitment and Intrinsic Motivation of Primary Health Care Providers (HCPs) in New Delhi, India. Study was conducted in 2013 on a sample of 333 HCPs who were selected using multistage stage random sampling technique. The sample includes medical officers, auxiliary nurses and midwives, and pharmacists and laboratory technicians/assistants among regular and contractual staff. Data were collected using the pretested structured questionnaire for organization commitment (OC), job satisfiers, and intrinsic job motivation. Analysis was done by using SPSS version 18 and appropriate statistical tests were applied. The mean score for OC for entire regular staff is 1.6 ± 0.39 and contractual staff is 1.3 ± 0.45 which has statistically significant difference (t = 5.57; P = 0.00). In both regular and contractual staff, none of them show high emotional attachment with the organization and does not feel part of the family in the organization. Contractual staff does not feel proud to work in a present organization for rest of their career. Intrinsic motivation is high in both regular and contractual groups but intergroup difference is significant (t = 2.38; P < 0.05). Contractual staff has more dissatisfier than regular, and the difference is significant (P < 0.01). Organizational commitment and intrinsic motivation of contractual staff are lesser than the permanent staff. Appropriate changes are required in the predictors of organizational commitment and factors responsible for satisfaction in the organization to keep the contractual human resource motivated and committed to the organization.

Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter.

PubMed

Roux-Rouquie, M; Marilley, M

2000-09-15

We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends split the IGS into domains of common but different helical features. Local parameters at inter-domain junctions exhibit a high variability with respect to intrinsic curvature, bendability and thermal stability. Secondly, the repeated sequence blocks of the IGS exhibit right-handed supercoiled structures which could be related to their enhancer properties. Thirdly, the gene promoter presents both inherent curvature and minor groove narrowing which may be viewed as motifs of a structural code for protein recognition and binding. Such pre-existing deformations could simply be remodeled during the binding of the transcription complex. Alternatively, these deformations could pre-shape the promoter in such a way that further remodeling is facilitated. Mutations shown to abolish promoter curvature as well as intrinsic minor groove narrowing, in a variant which maintained full transcriptional activity, bring circumstantial evidence for structurally-preorganized motifs in relation to transcription regulation and promotion. Using well documented X. laevis rDNA regulatory sequences we showed that computer modeling may be of invaluable assistance in assessing encrypted architectural motifs. The evidence of these DNA topological motifs with respect to the concept of structural code is discussed.

Effect of intrinsic zinc oxide coating on the properties of Al-doped zinc oxide nanorod arrays

NASA Astrophysics Data System (ADS)

Saidi, S. A.; Mamat, M. H.; Ismail, A. S.; Malek, M. F.; Yusoff, M. M.; Sin, N. D. Md.; Zoolfakar, A. S.; Khusaimi, Z.; Rusop, M.

2018-05-01

The aim of this study was to explore the influence of intrinsic zinc oxide (ZnO) coating fabricated by a simple immersion method. X-ray powder diffraction (XRD) analysis indicated that the Al-doped ZnO nanorod arrays films had a hexagonal wurtzite structure, similar to that of an intrinsic ZnO coating. Structural properties of the samples were characterised using field emission scanning electron microscopy (FESEM; JEOL JSM-7600F) and optical properties using X-ray diffraction (XRD). The XRD results showed that all films were crystallized under hexagonal wurtzite structure and presented a preferential orientation along the c-axis (002) was obtained. The XRD results showed that the intrinsic ZnO coating material had a strong orientation, whereas the ZnO was randomly oriented. Overall these results indicate that intrinsic ZnO coating are pontetial for the creation of functional materials such as barrier protection, optoelectronic devices, humidity sensor and ultraviolet photoconductive sensor.

Unusual biophysics of intrinsically disordered proteins.

PubMed

Uversky, Vladimir N

2013-05-01

Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the "turned-out" response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the "edge of chaos" systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly. Copyright © 2012 Elsevier B.V. All rights reserved.

An objective structured clinical exam to measure intrinsic CanMEDS roles.

PubMed

Kassam, Aliya; Cowan, Michèle; Donnon, Tyrone

2016-01-01

Background The CanMEDS roles provide a comprehensive framework to organize competency-based curricula; however, there is a challenge in finding feasible, valid, and reliable assessment methods to measure intrinsic roles such as Communicator and Collaborator. The objective structured clinical exam (OSCE) is more commonly used in postgraduate medical education for the assessment of clinical skills beyond medical expertise. Method We developed the CanMEDS In-Training Exam (CITE), a six-station OSCE designed to assess two different CanMEDS roles (one primary and one secondary) and general communication skills at each station. Correlation coefficients were computed for CanMEDS roles within and between stations, and for general communication, global rating, and total scores. One-way analysis of variance (ANOVA) was used to investigate differences between year of residency, sex, and the type of residency program. Results In total, 63 residents participated in the CITE; 40 residents (63%) were from internal medicine programs, whereas the remaining 23 (37%) were pursuing other specialties. There was satisfactory internal consistency for all stations, and the total scores of the stations were strongly correlated with the global scores r=0.86, p<0.05. Noninternal medicine residents scored higher in terms of the Professional competency overall, whereas internal medicine residents scored significantly higher in the Collaborator competency overall. Discussion The OSCE checklists developed for the assessment of intrinsic CanMEDS roles were functional, but the specific items within stations required more uniformity to be used between stations. More generic types of checklists may also improve correlations across stations. Conclusion An OSCE measuring intrinsic competence is feasible; however, further development of our cases and checklists is needed. We provide a model of how to develop an OSCE to measure intrinsic CanMEDS roles that educators may adopt as residency programs move into competency-based medical education.

Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy.

PubMed

Delaforge, Elise; Kragelj, Jaka; Tengo, Laura; Palencia, Andrés; Milles, Sigrid; Bouvignies, Guillaume; Salvi, Nicola; Blackledge, Martin; Jensen, Malene Ringkjøbing

2018-01-24

Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R 1ρ , Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions.

Nanostructured Quantum Dots or Dashes in Photovoltaic Devices and Methods Thereof

NASA Technical Reports Server (NTRS)

Raffaele, Ryne P. (Inventor); Wilt, David M. (Inventor)

2015-01-01

A photovoltaic device includes one or more structures, an array of at least one of quantum dots and quantum dashes, at least one groove, and at least one conductor. Each of the structures comprises an intrinsic layer on one of an n type layer and a p type layer and the other one of the n type layer and the p type layer on the intrinsic layer. The array of at least one of quantum dots and quantum dashes is located in the intrinsic layer in at least one of the structures. The groove extends into at least one of the structures and the conductor is located along at least a portion of the groove.

Hydrogen-Exchange Mass Spectrometry for the Study of Intrinsic Disorder in Proteins

PubMed Central

Balasubramaniam, Deepa; Komives, Elizabeth A.

2012-01-01

Amide hydrogen/deuterium exchange detected by mass spectrometry (HXMS) is seeing wider use for the identification of intrinsically disordered parts of proteins. In this review, we discuss examples of how discovery of intrinsically disordered regions and their removal can aid in structure determination, biopharmaceutical quality control, the characterization of how posttranslational modifications affect weak structuring of disordered regions, the study of coupled folding and binding, and the characterization of amyloid formation. PMID:23099262

Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains

PubMed Central

Williams, Robert W; Xue, Bin; Uversky, Vladimir N; Dunker, A Keith

2013-01-01

The Pfam database groups regions of proteins by how well hidden Markov models (HMMs) can be trained to recognize similarities among them. Conservation pressure is probably in play here. The Pfam seed training set includes sequence and structure information, being drawn largely from the PDB. A long standing hypothesis among intrinsically disordered protein (IDP) investigators has held that conservation pressures are also at play in the evolution of different kinds of intrinsic disorder, but we find that predicted intrinsic disorder (PID) is not always conserved across Pfam domains. Here we analyze distributions and clusters of PID regions in 193024 members of the version 23.0 Pfam seed database. To include the maximum information available for proteins that remain unfolded in solution, we employ the 10 linearly independent Kidera factors1–3 for the amino acids, combined with PONDR4 predictions of disorder tendency, to transform the sequences of these Pfam members into an 11 column matrix where the number of rows is the length of each Pfam region. Cluster analyses of the set of all regions, including those that are folded, show 6 groupings of domains. Cluster analyses of domains with mean VSL2b scores greater than 0.5 (half predicted disorder or more) show at least 3 separated groups. It is hypothesized that grouping sets into shorter sequences with more uniform length will reveal more information about intrinsic disorder and lead to more finely structured and perhaps more accurate predictions. HMMs could be trained to include this information. PMID:28516017

Understanding and predicting profile structure and parametric scaling of intrinsic rotation

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

Wang, W. X.; Grierson, B. A.; Ethier, S.

2017-08-10

This study reports on a recent advance in developing physical understanding and a first-principles-based model for predicting intrinsic rotation profiles in magnetic fusion experiments. It is shown for the first time that turbulent fluctuation-driven residual stress (a non-diffusive component of momentum flux) along with diffusive momentum flux can account for both the shape and magnitude of the observed intrinsic toroidal rotation profile. Both the turbulence intensity gradient and zonal flow E×B shear are identified as major contributors to the generation of the k ∥-asymmetry needed for the residual stress generation. The model predictions of core rotation based on global gyrokineticmore » simulations agree well with the experimental measurements of main ion toroidal rotation for a set of DIII-D ECH discharges. The validated model is further used to investigate the characteristic dependence of residual stress and intrinsic rotation profile structure on the multi-dimensional parametric space covering the turbulence type, q-profile structure, and up-down asymmetry in magnetic geometry with the goal of developing the physics understanding needed for rotation profile control and optimization. It is shown that in the flat-q profile regime, intrinsic rotations driven by ITG and TEM turbulence are in the opposite direction (i.e., intrinsic rotation reverses). The predictive model also produces reversed intrinsic rotation for plasmas with weak and normal shear q-profiles.« less

The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition.

PubMed

Autiero, Ida; Ruvo, Menotti; Improta, Roberto; Vitagliano, Luigi

2018-04-01

Aptamers are RNA/DNA biomolecules representing an emerging class of protein interactors and regulators. Despite the growing interest in these molecules, current understanding of chemical-physical basis of their target recognition is limited. Recently, the characterization of the aptamer targeting the protein-S8 has suggested that flexibility plays important functional roles. We investigated the structural versatility of the S8-aptamer by molecular dynamics simulations. Five different simulations have been conducted by varying starting structures and temperatures. The simulation of S8-aptamer complex provides a dynamic view of the contacts occurring at the complex interface. The simulation of the aptamer in ligand-free state indicates that its central region is intrinsically endowed with a remarkable flexibility. Nevertheless, none of the trajectory structures adopts the structure observed in the S8-aptamer complex. The aptamer ligand-bound is very rigid in the simulation carried out at 300 K. A structural transition of this state, providing insights into the aptamer-protein recognition process, is observed in a simulation carried out at 400 K. These data indicate that a key event in the binding is linked to the widening of the central region of the aptamer. Particularly relevant is switch of the A26 base from its ligand-free state to a location that allows the G13-C28 base-pairing. Intrinsic flexibility of the aptamer is essential for partner recognition. Present data indicate that S8 recognizes the aptamer through an induced-fit rather than a population-shift mechanism. The present study provides deeper understanding of the structural basis of the structural versatility of aptamers. Copyright © 2018 Elsevier B.V. All rights reserved.

Quantum chemical ab initio prediction of proton exchange barriers between CH{sub 4} and different H-zeolites

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

Tuma, Christian; Sauer, Joachim, E-mail: js@chemie.hu-berlin.de

2015-09-14

A hybrid MP2:DFT (second-order Møller–Plesset perturbation theory–density functional theory) method that combines MP2 calculations for cluster models with DFT calculations for the full periodic structure is used to localize minima and transition structures for proton jumps at different Brønsted sites in different frameworks (chabazite, faujasite, ferrierite, and ZSM-5) and at different crystallographic positions of a given framework. The MP2 limit for the periodic structures is obtained by extrapolating the results of a series of cluster models of increasing size. A coupled-cluster (CCSD(T)) correction to MP2 energies is calculated for cluster models consisting of three tetrahedra. For the adsorption energies, thismore » difference is small, between 0.1 and 0.9 kJ/mol, but for the intrinsic proton exchange barriers, this difference makes a significant (10.85 ± 0.25 kJ/mol) and almost constant contribution across different systems. The total values of the adsorption energies vary between 22 and 34 kJ/mol, whereas the total proton exchange energy barriers fall in the narrow range of 152–156 kJ/mol. After adding nuclear motion contributions (harmonic approximation, 298 K), intrinsic enthalpy barriers between 134 and 141 kJ/mol and apparent energy barriers between 105 and 118 kJ/mol are predicted for the different sites examined for the different frameworks. These predictions are consistent with experimental results available for faujasite, ferrierite, and ZSM-5.« less

Photogrammetric Modeling and Image-Based Rendering for Rapid Virtual Environment Creation

DTIC Science & Technology

2004-12-01

area and different methods have been proposed. Pertinent methods include: Camera Calibration , Structure from Motion, Stereo Correspondence, and Image...Based Rendering 1.1.1 Camera Calibration Determining the 3D structure of a model from multiple views becomes simpler if the intrinsic (or internal...can introduce significant nonlinearities into the image. We have found that camera calibration is a straightforward process which can simplify the

Topologically Diverse Human Membrane Proteins Partition to Liquid-Disordered Domains in Phase-Separated Lipid Vesicles.

PubMed

Schlebach, Jonathan P; Barrett, Paul J; Day, Charles A; Kim, Ji Hun; Kenworthy, Anne K; Sanders, Charles R

2016-02-23

The integration of membrane proteins into "lipid raft" membrane domains influences many biochemical processes. The intrinsic structural properties of membrane proteins are thought to mediate their partitioning between membrane domains. However, whether membrane topology influences the targeting of proteins to rafts remains unclear. To address this question, we examined the domain preference of three putative raft-associated membrane proteins with widely different topologies: human caveolin-3, C99 (the 99 residue C-terminal domain of the amyloid precursor protein), and peripheral myelin protein 22. We find that each of these proteins are excluded from the ordered domains of giant unilamellar vesicles containing coexisting liquid-ordered and liquid-disordered phases. Thus, the intrinsic structural properties of these three topologically distinct disease-linked proteins are insufficient to confer affinity for synthetic raft-like domains.

Structure of gamma-ray burst jets: intrinsic versus apparent properties

NASA Astrophysics Data System (ADS)

Salafia, O. S.; Ghisellini, G.; Pescalli, A.; Ghirlanda, G.; Nappo, F.

2015-07-01

With this paper we introduce the concept of apparent structure of a gamma-ray burst (GRB) jet, as opposed to its intrinsic structure. The latter is customarily defined specifying the functions ɛ(θ) (the energy emitted per jet unit solid angle) and Γ(θ) (the Lorentz factor of the emitting material); the apparent structure is instead defined by us as the isotropic equivalent energy Eiso(θv) as a function of the viewing angle θv. We show how to predict the apparent structure of a jet given its intrinsic structure. We find that a Gaussian intrinsic structure yields a power-law apparent structure: this opens a new viewpoint on the Gaussian (which can be understood as a proxy for a realistic narrow, well-collimated jet structure) as a possible candidate for a quasi-universal GRB jet structure. We show that such a model (a) is consistent with recent constraints on the observed luminosity function of GRBs; (b) implies fewer orphan afterglows with respect to the standard uniform model; (c) can break out the progenitor star (in the collapsar scenario) without wasting an unreasonable amount of energy; (d) is compatible with the explanation of the Amati correlation as a viewing angle effect; (e) can be very standard in energy content, and still yield a very wide range of observed isotropic equivalent energies.

Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins.

PubMed

Uversky, Vladimir N

2015-03-01

Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins or regions that do not have unique 3D structures under functional conditions. Therefore, from the viewpoint of their lack of stable 3D structure, IDPs/IDPRs are inherently unstable. As much as structure and function of normal ordered globular proteins are determined by their amino acid sequences, the lack of unique 3D structure in IDPs/IDPRs and their disorder-based functionality are also encoded in the amino acid sequences. Because of their specific sequence features and distinctive conformational behavior, these intrinsically unstable proteins or regions have several applications in biotechnology. This review introduces some of the most characteristic features of IDPs/IDPRs (such as peculiarities of amino acid sequences of these proteins and regions, their major structural features, and peculiar responses to changes in their environment) and describes how these features can be used in the biotechnology, for example for the proteome-wide analysis of the abundance of extended IDPs, for recombinant protein isolation and purification, as polypeptide nanoparticles for drug delivery, as solubilization tools, and as thermally sensitive carriers of active peptides and proteins. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Organizational commitment and intrinsic motivation of regular and contractual primary health care providers

PubMed Central

Kumar, Pawan; Mehra, Anu; Inder, Deep; Sharma, Nandini

2016-01-01

Background: Motivated and committed employees deliver better health care, which results in better outcomes and higher patient satisfaction. Objective: To assess the Organizational Commitment and Intrinsic Motivation of Primary Health Care Providers (HCPs) in New Delhi, India. Materials and Methods: Study was conducted in 2013 on a sample of 333 HCPs who were selected using multistage stage random sampling technique. The sample includes medical officers, auxiliary nurses and midwives, and pharmacists and laboratory technicians/assistants among regular and contractual staff. Data were collected using the pretested structured questionnaire for organization commitment (OC), job satisfiers, and intrinsic job motivation. Analysis was done by using SPSS version 18 and appropriate statistical tests were applied. Results: The mean score for OC for entire regular staff is 1.6 ± 0.39 and contractual staff is 1.3 ± 0.45 which has statistically significant difference (t = 5.57; P = 0.00). In both regular and contractual staff, none of them show high emotional attachment with the organization and does not feel part of the family in the organization. Contractual staff does not feel proud to work in a present organization for rest of their career. Intrinsic motivation is high in both regular and contractual groups but intergroup difference is significant (t = 2.38; P < 0.05). Contractual staff has more dissatisfier than regular, and the difference is significant (P < 0.01). Conclusion: Organizational commitment and intrinsic motivation of contractual staff are lesser than the permanent staff. Appropriate changes are required in the predictors of organizational commitment and factors responsible for satisfaction in the organization to keep the contractual human resource motivated and committed to the organization. PMID:27453851

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Influence of the total gas flow rate on high rate growth microcrystalline silicon films and solar cells

NASA Astrophysics Data System (ADS)

Han, Xiao-Yan; Hou, Guo-Fu; Zhang, Xiao-Dan; Wei, Chang-Chun; Li, Gui-Jun; Zhang, De-Kun; Chen, Xin-Liang; Sun, Jian; Zhang, Jian-Jun; Zhao, Ying; Geng, Xin-Hua

2009-08-01

This paper reports that high-rate-deposition of microcrystalline silicon solar cells was performed by very-high-frequency plasma-enhanced chemical vapor deposition. These solar cells, whose intrinsic μc-Si:H layers were prepared by using a different total gas flow rate (Ftotal), behave much differently in performance, although their intrinsic layers have similar crystalline volume fraction, opto-electronic properties and a deposition rate of ~ 1.0 nm/s. The influence of Ftotal on the micro-structural properties was analyzed by Raman and Fourier transformed infrared measurements. The results showed that the vertical uniformity and the compact degree of μc-Si:H thin films were improved with increasing Ftotal. The variation of the microstructure was regarded as the main reason for the difference of the J-V parameters. Combined with optical emission spectroscopy, we found that the gas temperature plays an important role in determining the microstructure of thin films. With Ftotal of 300 sccm, a conversion efficiency of 8.11% has been obtained for the intrinsic layer deposited at 8.5 Å/s (1 Å = 0.1 nm).

Understanding and Addressing the Achievement Gap through Individualized Instruction and Formative Assessment

ERIC Educational Resources Information Center

Yeh, Stuart S.

2010-01-01

This article synthesizes findings regarding the development of competence and learned helplessness and factors influencing persistence and intrinsic motivation, suggests the process through which small differences in early achievement are magnified by the current structure of schools, and reviews evidence suggesting that the characteristics of a…

Silk protein aggregation kinetics revealed by Rheo-IR.

PubMed

Boulet-Audet, Maxime; Terry, Ann E; Vollrath, Fritz; Holland, Chris

2014-02-01

The remarkable mechanical properties of silk fibres stem from a multi-scale hierarchical structure created when an aqueous protein "melt" is converted to an insoluble solid via flow. To directly relate a silk protein's structure and function in response to flow, we present the first application of a Rheo-IR platform, which couples cone and plate rheology with attenuated total reflectance infrared spectroscopy. This technique provides a new window into silk processing by linking shear thinning to an increase in molecular alignment, with shear thickening affecting changes in the silk protein's secondary structure. Additionally, compared to other static characterization methods for silk, Rheo-IR proved particularly useful at revealing the intrinsic difference between natural (native) and reconstituted silk feedstocks. Hence Rheo-IR offers important novel insights into natural silk processing. This has intrinsic academic merit, but it might also be useful when designing reconstituted silk analogues alongside other polymeric systems, whether natural or synthetic. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter

PubMed Central

Roux-Rouquie, Magali; Marilley, Monique

2000-01-01

We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends split the IGS into domains of common but different helical features. Local parameters at inter-domain junctions exhibit a high variability with respect to intrinsic curvature, bendability and thermal stability. Secondly, the repeated sequence blocks of the IGS exhibit right-handed supercoiled structures which could be related to their enhancer properties. Thirdly, the gene promoter presents both inherent curvature and minor groove narrowing which may be viewed as motifs of a structural code for protein recognition and binding. Such pre-existing deformations could simply be remodeled during the binding of the transcription complex. Alternatively, these deformations could pre-shape the promoter in such a way that further remodeling is facilitated. Mutations shown to abolish promoter curvature as well as intrinsic minor groove narrowing, in a variant which maintained full transcriptional activity, bring circumstantial evidence for structurally-preorganized motifs in relation to transcription regulation and promotion. Using well documented X.laevis rDNA regulatory sequences we showed that computer modeling may be of invaluable assistance in assessing encrypted architectural motifs. The evidence of these DNA topological motifs with respect to the concept of structural code is discussed. PMID:10982860

Coarse-Grained Descriptions of Dynamics for Networks with Both Intrinsic and Structural Heterogeneities

PubMed Central

Bertalan, Tom; Wu, Yan; Laing, Carlo; Gear, C. William; Kevrekidis, Ioannis G.

2017-01-01

Finding accurate reduced descriptions for large, complex, dynamically evolving networks is a crucial enabler to their simulation, analysis, and ultimately design. Here, we propose and illustrate a systematic and powerful approach to obtaining good collective coarse-grained observables—variables successfully summarizing the detailed state of such networks. Finding such variables can naturally lead to successful reduced dynamic models for the networks. The main premise enabling our approach is the assumption that the behavior of a node in the network depends (after a short initial transient) on the node identity: a set of descriptors that quantify the node properties, whether intrinsic (e.g., parameters in the node evolution equations) or structural (imparted to the node by its connectivity in the particular network structure). The approach creates a natural link with modeling and “computational enabling technology” developed in the context of Uncertainty Quantification. In our case, however, we will not focus on ensembles of different realizations of a problem, each with parameters randomly selected from a distribution. We will instead study many coupled heterogeneous units, each characterized by randomly assigned (heterogeneous) parameter value(s). One could then coin the term Heterogeneity Quantification for this approach, which we illustrate through a model dynamic network consisting of coupled oscillators with one intrinsic heterogeneity (oscillator individual frequency) and one structural heterogeneity (oscillator degree in the undirected network). The computational implementation of the approach, its shortcomings and possible extensions are also discussed. PMID:28659781

Composition-related structural transition of random peptides: insight into the boundary between intrinsically disordered proteins and folded proteins.

PubMed

Kang, Wen-Bin; He, Chuan; Liu, Zhen-Xing; Wang, Jun; Wang, Wei

2018-05-16

Previous studies based on bioinformatics showed that there is a sharp distinction of structural features and residue composition between the intrinsically disordered proteins and the folded proteins. What induces such a composition-related structural transition? How do various kinds of interactions work in such processes? In this work, we investigate these problems based on a survey on peptides randomly composed of charged residues (including glutamic acids and lysines) and the residues with different hydrophobicity, such as alanines, glycines, or phenylalanines. Based on simulations using all-atom model and replica-exchange Monte Carlo method, a coil-globule transition is observed for each peptide. The corresponding transition temperature is found to be dependent on the contents of the hydrophobic and charged residues. For several cases, when the mean hydrophobicity is larger than a certain threshold, the transition temperature is higher than the room temperature, and vise versa. These thresholds of hydrophobicity and net charge are quantitatively consistent with the border line observed from the study of bioinformatics. These results outline the basic physical reasons for the compositional distinction between the intrinsically disordered proteins and the folded proteins. Furthermore, the contributions of various interactions to the structural variation of peptides are analyzed based on the contact statistics and the charge-pattern dependence of the gyration radii of the peptides. Our observations imply that the hydrophobicity contributes essentially to such composition-related transitions. Thus, we achieve a better understanding on composition-structure relation of the natural proteins and the underlying physics.

Structural vs. intrinsic carriers: contrasting effects of cation chemistry and disorder on ionic conductivity in pyrochlores

DOE PAGES

Perriot, Romain; Uberuaga, Blas P.

2015-04-21

We use molecular dynamics simulations to investigate the role of cation disorder on oxygen diffusion in Gd 2Zr 2O 7 (GZO) and Gd 2Ti 2O 7 (GTO) pyrochlores, a class of complex oxides which contain a structural vacancy relative to the basic fluorite structure. The introduction of disorder has distinct effects depending on the chemistry of the material, increasing the mobility of structural carriers by up to four orders of magnitude in GZO. In contrast, in GTO, there is no mobility at zero or low disorder on the ns timescale, but higher disorder liberates the otherwise immobile carriers, allowing diffusionmore » with rates comparable to GZO for the fully disordered material. Here, we show that the cation disorder enhances the diffusivity by both increasing the concentration of mobile structural carriers and their individual mobility. The disorder also influences the diffusion in materials containing intrinsic carriers, such as additional vacancies VO or oxygen interstitials OI. And while in ordered GZO and GTO the contribution of the intrinsic carriers dominates the overall diffusion of oxygen, OI in GZO contributes along with structural carriers, and the total diffusion rate can be calculated by assuming simple additive contributions from the two sources. Although the disorder in the materials with intrinsic defects usually enhances the diffusivity as in the defect-free case, in low concentrations, cation antisites AB or BA, where A = Gd and B = Zr or Ti, can act as traps for fast intrinsic defects. The trapping results in a lowering of the diffusivity, and causes a non-monotonic behavior of the diffusivity with disorder. Conversely, in the case of slow intrinsic defects, the main effect of the disorder is to liberate the structural carriers, resulting in an increase of the diffusivity regardless of the defect trapping.« less

Buried and accessible surface area control intrinsic protein flexibility.

PubMed

Marsh, Joseph A

2013-09-09

Proteins experience a wide variety of conformational dynamics that can be crucial for facilitating their diverse functions. How is the intrinsic flexibility required for these motions encoded in their three-dimensional structures? Here, the overall flexibility of a protein is demonstrated to be tightly coupled to the total amount of surface area buried within its fold. A simple proxy for this, the relative solvent-accessible surface area (Arel), therefore shows excellent agreement with independent measures of global protein flexibility derived from various experimental and computational methods. Application of Arel on a large scale demonstrates its utility by revealing unique sequence and structural properties associated with intrinsic flexibility. In particular, flexibility as measured by Arel shows little correspondence with intrinsic disorder, but instead tends to be associated with multiple domains and increased α-helical structure. Furthermore, the apparent flexibility of monomeric proteins is found to be useful for identifying quaternary-structure errors in published crystal structures. There is also a strong tendency for the crystal structures of more flexible proteins to be solved to lower resolutions. Finally, local solvent accessibility is shown to be a primary determinant of local residue flexibility. Overall, this work provides both fundamental mechanistic insight into the origin of protein flexibility and a simple, practical method for predicting flexibility from protein structures. © 2013 Elsevier Ltd. All rights reserved.

Intrinsic electronic defects and multiple-atom processes in the oxidic semiconductor Ga2O3

NASA Astrophysics Data System (ADS)

Schmeißer, Dieter; Henkel, Karsten

2018-04-01

We report on the electronic structure of gallium oxide (Ga2O3) single crystals as studied by resonant photoelectron spectroscopy (resPES). We identify intrinsic electronic defects that are formed by mixed-atomic valence states. We differentiate three coexisting defect states that differ in their electronic correlation energy and their spatial localization lengths. Their relative abundance is described by a fractional ionicity with covalent and ionic bonding contributions. For Ga2O3, our analyses of the resPES data enable us to derive two main aspects: first, experimental access is given to determine the ionicity based on the original concepts of Pauling and Phillips. Second, we report on multi-atomic energy loss processes in the Ga2p core level and X-ray absorption data. The two experimental findings can be explained consistently in the same context of mixed-atomic valence states and intrinsic electronic defects.

Two-Fold Anisotropy Governs Morphological Evolution and Stress Generation in Sodiated Black Phosphorus for Sodium Ion Batteries.

PubMed

Chen, Tianwu; Zhao, Peng; Guo, Xu; Zhang, Sulin

2017-04-12

Phosphorus represents a promising anode material for sodium ion batteries owing to its extremely high theoretical capacity. Recent in situ transmission electron microscopy studies evidenced anisotropic swelling in sodiated black phosphorus, which may find an origin from the two intrinsic anisotropic properties inherent to the layered structure of black phosphorus: sodium diffusional directionality and insertion strain anisotropy. To understand the morphological evolution and stress generation in sodiated black phosphorus, we develop a chemo-mechanical model by incorporating the intrinsic anisotropic properties into the large elasto-plastic deformation. Our modeling results reveal that the apparent morphological evolution in sodiated black phosphorus is critically controlled by the coupled effect of the two intrinsic anisotropic properties. In particular, sodium diffusional directionality generates sharp interphases along the [010] and [001] directions, which constrain anisotropic development of the insertion strain. The coupled effect renders distinctive stress-generation and fracture mechanisms when sodiation starts from different crystal facets. In addition to providing a powerful modeling framework for sodiation and lithiation of layered structures, our findings shed significant light on the sodiation-induced chemo-mechanical degradation of black phosphorus as a promising anode for the next-generation sodium ion batteries.

The α-Helical Structure of Prodomains Promotes Translocation of Intrinsically Disordered Neuropeptide Hormones into the Endoplasmic Reticulum*

PubMed Central

Dirndorfer, Daniela; Seidel, Ralf P.; Nimrod, Guy; Miesbauer, Margit; Ben-Tal, Nir; Engelhard, Martin; Zimmermann, Richard; Winklhofer, Konstanze F.; Tatzelt, Jörg

2013-01-01

Different neuropeptide hormones, which are either too small to adopt a stable conformation or are predicted to be intrinsically disordered, are synthesized as larger precursors containing a prodomain in addition to an N-terminal signal peptide. We analyzed the biogenesis of three unstructured neuropeptide hormones and observed that translocation of these precursors into the lumen of the endoplasmic reticulum (ER) is critically dependent on the presence of the prodomain. The hormone domains could be deleted from the precursors without interfering with ER import and secretion, whereas constructs lacking the prodomain remained in the cytosol. Domain-swapping experiments revealed that the activity of the prodomains to promote productive ER import resides in their ability to adopt an α-helical structure. Removal of the prodomain from the precursor did not interfere with co-translational targeting of the nascent chain to the Sec61 translocon but with its subsequent productive translocation into the ER lumen. Our study reveals a novel function of prodomains to enable import of small or intrinsically disordered secretory proteins into the ER based on their ability to adopt an α-helical conformation. PMID:23532840

The α-helical structure of prodomains promotes translocation of intrinsically disordered neuropeptide hormones into the endoplasmic reticulum.

PubMed

Dirndorfer, Daniela; Seidel, Ralf P; Nimrod, Guy; Miesbauer, Margit; Ben-Tal, Nir; Engelhard, Martin; Zimmermann, Richard; Winklhofer, Konstanze F; Tatzelt, Jörg

2013-05-17

Different neuropeptide hormones, which are either too small to adopt a stable conformation or are predicted to be intrinsically disordered, are synthesized as larger precursors containing a prodomain in addition to an N-terminal signal peptide. We analyzed the biogenesis of three unstructured neuropeptide hormones and observed that translocation of these precursors into the lumen of the endoplasmic reticulum (ER) is critically dependent on the presence of the prodomain. The hormone domains could be deleted from the precursors without interfering with ER import and secretion, whereas constructs lacking the prodomain remained in the cytosol. Domain-swapping experiments revealed that the activity of the prodomains to promote productive ER import resides in their ability to adopt an α-helical structure. Removal of the prodomain from the precursor did not interfere with co-translational targeting of the nascent chain to the Sec61 translocon but with its subsequent productive translocation into the ER lumen. Our study reveals a novel function of prodomains to enable import of small or intrinsically disordered secretory proteins into the ER based on their ability to adopt an α-helical conformation.

Identification of protein secondary structures by laser induced autofluorescence: A study of urea and GnHCl induced protein denaturation

NASA Astrophysics Data System (ADS)

Siddaramaiah, Manjunath; Satyamoorthy, Kapaettu; Rao, Bola Sadashiva Satish; Roy, Suparna; Chandra, Subhash; Mahato, Krishna Kishore

2017-03-01

In the present study an attempt has been made to interrogate the bulk secondary structures of some selected proteins (BSA, HSA, lysozyme, trypsin and ribonuclease A) under urea and GnHCl denaturation using laser induced autofluorescence. The proteins were treated with different concentrations of urea (3 M, 6 M, 9 M) and GnHCl (2 M, 4 M, 6 M) and the corresponding steady state autofluorescence spectra were recorded at 281 nm pulsed laser excitations. The recorded fluorescence spectra of proteins were then interpreted based on the existing PDB structures of the proteins and the Trp solvent accessibility (calculated using "Scratch protein predictor" at 30% threshold). Further, the influence of rigidity and conformation of the indole ring (caused by protein secondary structures) on the intrinsic fluorescence properties of proteins were also evaluated using fluorescence of ANS-HSA complexes, CD spectroscopy as well as with trypsin digestion experiments. The outcomes obtained clearly demonstrated GnHCl preferably disrupt helix as compared to the beta β-sheets whereas, urea found was more effective in disrupting β-sheets as compared to the helices. The other way round the proteins which have shown detectable change in the intrinsic fluorescence at lower concentrations of GnHCl were rich in helices whereas, the proteins which showed detectable change in the intrinsic fluorescence at lower concentrations of urea were rich in β-sheets. Since high salt concentrations like GnHCl and urea interfere in the secondary structure analysis by circular dichroism Spectrometry, the present method of analyzing secondary structures using laser induced autofluorescence will be highly advantageous over existing tools for the same.

Seismic imaging of Q structures by a trans-dimensional coda-wave analysis

NASA Astrophysics Data System (ADS)

Takahashi, Tsutomu

2017-04-01

Wave scattering and intrinsic attenuation are important processes to describe incoherent and complex wave trains of high frequency seismic wave (>1Hz). The multiple lapse time window analysis (MLTWA) has been used to estimate scattering and intrinsic Q values by assuming constant Q in a study area (e.g., Hoshiba 1993). This study generalizes this MLTWA to estimate lateral variations of Q values under the Bayesian framework in dimension variable space. Study area is partitioned into small areas by means of the Voronoi tessellation. Scattering and intrinsic Q in each small area are constant. We define a misfit function for spatiotemporal variations of wave energy as with the original MLTWA, and maximize the posterior probability with changing not only Q values but the number and spatial layout of the Voronoi cells. This maximization is conducted by means of the reversible jump Markov chain Monte Carlo (rjMCMC) (Green 1995) since the number of unknown parameters (i.e., dimension of posterior probability) is variable. After a convergence to the maximum posterior, we estimate Q structures from the ensemble averages of MCMC samples around the maximum posterior probability. Synthetic tests showed stable reconstructions of input structures with reasonable error distributions. We applied this method for seismic waveform data recorded by ocean bottom seismograms at the outer-rise area off Tohoku, and estimated Q values at 4-8Hz, 8-16Hz and 16-32Hz. Intrinsic Q are nearly constant at all frequency bands, and scattering Q shows two distinct strong scattering regions at petit spot area and high seismicity area. These strong scattering are probably related to magma inclusions and fractured structure, respectively. Difference between these two areas becomes clear at high frequencies. It means that scale dependences of inhomogeneities or smaller scale inhomogeneity is important to discuss medium property and origins of structural variations. While the generalized MLTWA is based on a classical waveform modeling in constant Q medium, this method can be a fundamental basis for Q structure imaging in the crust.

Numerical study of the intrinsic recombination carriers lifetime in extended short-wavelength infrared detector materials: A comparison between InGaAs and HgCdTe

NASA Astrophysics Data System (ADS)

Wen, Hanqing; Bellotti, Enrico

2016-05-01

Intrinsic carrier lifetime due to radiative and Auger recombination in HgCdTe and strained InGaAs has been computed in the extended short-wavelength infrared (ESWIR) spectrum from 1.7 μm to 2.7 μm. Using the Green's function theory, both direct and phonon-assisted indirect Auger recombination rates as well as the radiative recombination rates are calculated for different cutoff wavelengths at 300 K with full band structures of the materials. In order to properly model the full band structures of strained InGaAs, an empirical pseudo-potential model for the alloy is fitted using the virtual crystal approximation with spin-orbit coupling included. The results showed that for InxGa1-xAs grown on InP substrate, the compressive strain, which presents in the film when the cutoff wavelength is longer than 1.7 μm, leads to decrease of Auger recombination rate and increase of radiative recombination rate. Since the dominant intrinsic recombination mechanism in this spectral range is radiative recombination, the overall intrinsic carrier lifetime in the strained InGaAs alloys is shorter than that in the relaxed material. When compared to the relaxed HgCdTe, both relaxed and compressively strained InGaAs alloys show shorter intrinsic carrier lifetime at the same cutoff wavelength in room temperature which confirms the potential advantage of HgCdTe as wide-band infrared detector material. While HgCdTe offers superior performance, ultimately the material of choice for ESWIR application will also depend on material quality and cost.

Numerical study of the intrinsic recombination carriers lifetime in extended short-wavelength infrared detector materials: A comparison between InGaAs and HgCdTe

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

Wen, Hanqing; Bellotti, Enrico, E-mail: bellotti@bu.edu

2016-05-28

Intrinsic carrier lifetime due to radiative and Auger recombination in HgCdTe and strained InGaAs has been computed in the extended short-wavelength infrared (ESWIR) spectrum from 1.7 μm to 2.7 μm. Using the Green's function theory, both direct and phonon-assisted indirect Auger recombination rates as well as the radiative recombination rates are calculated for different cutoff wavelengths at 300 K with full band structures of the materials. In order to properly model the full band structures of strained InGaAs, an empirical pseudo-potential model for the alloy is fitted using the virtual crystal approximation with spin-orbit coupling included. The results showed that for In{sub x}Ga{submore » 1−x}As grown on InP substrate, the compressive strain, which presents in the film when the cutoff wavelength is longer than 1.7 μm, leads to decrease of Auger recombination rate and increase of radiative recombination rate. Since the dominant intrinsic recombination mechanism in this spectral range is radiative recombination, the overall intrinsic carrier lifetime in the strained InGaAs alloys is shorter than that in the relaxed material. When compared to the relaxed HgCdTe, both relaxed and compressively strained InGaAs alloys show shorter intrinsic carrier lifetime at the same cutoff wavelength in room temperature which confirms the potential advantage of HgCdTe as wide-band infrared detector material. While HgCdTe offers superior performance, ultimately the material of choice for ESWIR application will also depend on material quality and cost.« less

Structural disorder within sendai virus nucleoprotein and phosphoprotein: insight into the structural basis of molecular recognition.

PubMed

Jensen, Malene Ringkjøbing; Bernadó, Pau; Houben, Klaartje; Blanchard, Laurence; Marion, Dominque; Ruigrok, Rob W H; Blackledge, Martin

2010-08-01

Intrinsically disordered regions of significant length are present throughout eukaryotic genomes, and are particularly prevalent in viral proteins. Due to their inherent flexibility, these proteins inhabit a conformational landscape that is too complex to be described by classical structural biology. The elucidation of the role that conformational flexibility plays in molecular function will redefine our understanding of the molecular basis of biological function, and the development of appropriate technology to achieve this aim remains one of the major challenges for the future of structural biology. NMR is the technique of choice for studying intrinsically disordered proteins, providing information about structure, flexibility and interactions at atomic resolution even in completely disordered proteins. In particular residual dipolar couplings (RDCs) are sensitive and powerful tools for determining local and long-range structural behaviour in flexible proteins. Here we describe recent applications of the use of RDCs to quantitatively describe the level of local structure in intrinsically disordered proteins involved in replication and transcription in Sendai virus.

Structured self-reflection as a tool to enhance perceived performance and maintain effort in adult recreational salsa dancers

USDA-ARS?s Scientific Manuscript database

The purpose of this study was to determine if the use of structured self-reflection in community dance classes would influence achievement goal orientations, levels of intrinsic motivation, or perceived dance performance. The Task and Ego Orientation in Sport Questionnaire (TEOSQ) and the Intrinsic...

Sequences required for transcription termination at the intrinsic lambdatI terminator.

PubMed

Martínez-Trujillo, Miguel; Sánchez-Trujillo, Alejandra; Ceja, Víctor; Avila-Moreno, Federico; Bermúdez-Cruz, Rosa María; Court, Donald; Montañez, Cecilia

2010-02-01

The lambdatI terminator is located approximately 280 bp beyond the lambdaint gene, and it has a typical structure of an intrinsic terminator. To identify sequences required for lambdatI transcription termination a set of deletion mutants were generated, either from the 5' or the 3' end onto the lambdatI region. The termination efficiency was determined by measuring galactokinase (galK) levels by Northern blot assays and by in vitro transcription termination. The importance of the uridines and the stability of the stem structure in the termination were demonstrated. The nontranscribed DNA beyond the 3' end also affects termination. Additionally, sequences upstream have a small effect on transcription termination. The in vivo RNA termination sites at lambdatI were determined by S1 mapping and were located at 8 different positions. Processing of transcripts from the 3' end confirmed the importance of the hairpin stem in protection against exonuclease.

Intrinsic folding of small peptide chains: spectroscopic evidence for the formation of beta-turns in the gas phase.

PubMed

Chin, Wutharath; Dognon, Jean-Pierre; Piuzzi, François; Tardivel, Benjamin; Dimicoli, Iliana; Mons, Michel

2005-01-19

Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.

Allotropes of Phosphorus with Remarkable Stability and Intrinsic Piezoelectricity

NASA Astrophysics Data System (ADS)

Li, Zhenqing; He, Chaoyu; Ouyang, Tao; Zhang, Chunxiao; Tang, Chao; Römer, Rudolf A.; Zhong, Jianxin

2018-04-01

We construct a class of two-dimensional (2D) phosphorus allotropes by assembling a previously proposed ultrathin metastable phosphorus nanotube into planar structures in different stacking orientations. Based on first-principles methods, the structures, stabilities, and fundamental electronic properties of these allotropes are systematically investigated. Our results show that these 2D van der Waals phosphorene allotropes possess remarkable stabilities due to the strong intertube van der Waals interactions, which cause an energy release of about 30 - 70 meV /atom , depending on their stacking details. Most of them are confirmed to be energetically more favorable than the experimentally viable α -P and β -P . Three of them, showing a relatively higher probability of being synthesized in the future, are further confirmed to be dynamically stable semiconductors with strain-tunable band gaps and intrinsic piezoelectricity, which may have potential applications in nanosized sensors, piezotronics, and energy harvesting in portable electronic nanodevices.

Segregation and Phase Transformations Along Superlattice Intrinsic Stacking Faults in Ni-Based Superalloys

NASA Astrophysics Data System (ADS)

Smith, T. M.; Esser, B. D.; Good, B.; Hooshmand, M. S.; Viswanathan, G. B.; Rae, C. M. F.; Ghazisaeidi, M.; McComb, D. W.; Mills, M. J.

2018-06-01

In this study, local chemical and structural changes along superlattice intrinsic stacking faults combine to represent an atomic-scale phase transformation. In order to elicit stacking fault shear, creep tests of two different single crystal Ni-based superalloys, ME501 and CMSX-4, were performed near 750 °C using stresses of 552 and 750 MPa, respectively. Through high-resolution scanning transmission electron microscopy (STEM) and state-of-the-art energy dispersive X-ray spectroscopy, ordered compositional changes were measured along SISFs in both alloys. For both instances, the elemental segregation and local crystal structure present along the SISFs are consistent with a nanoscale γ' to D019 phase transformation. Other notable observations are prominent γ-rich Cottrell atmospheres and new evidence of more complex reordering processes responsible for the formation of these faults. These findings are further supported using density functional theory calculations and high-angle annular dark-field (HAADF)-STEM image simulations.

Slow-light transmission with high group index and large normalized delay bandwidth product through successive defect rods on intrinsic photonic crystal waveguide

NASA Astrophysics Data System (ADS)

Elshahat, Sayed; Khan, Karim; Yadav, Ashish; Bibbò, Luigi; Ouyang, Zhengbiao

2018-07-01

We proposed a strategy with successive cavities as energy reservoirs of electromagnetic energy and light-speed reducers introduced in the first and second rows of rods on the walls of an intrinsic photonic crystal waveguide (PCW) for slow-light transmission in the PCW concerning applications for optical communication, optical computation and optical signal processing. Subsequently, plane-wave expansion method (PWE) is used for studying slow-light properties and finite-difference time-domain (FDTD) method to demonstrate the slow-light propagating property of our proposed structure. We obtained group index as exceedingly large as 6123 with normalized delay bandwidth product (NDBP) as high as 0.48. We designed a facile but more generalized structure that may provide a vital theoretical basis for further enhancing the storage capacity properties of slow light with wideband and high NDBP.

Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins*

PubMed Central

2016-01-01

Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally heterogeneous, and can be considered an important part of the structure-function continuum. Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged in various interactions characterized by a wide spectrum of binding scenarios and an even wider spectrum of structural and functional outputs. PMID:26851286

Intrinsic line shape of electromagnetic radiation from a stack of intrinsic Josephson junctions synchronized by an internal cavity resonance

NASA Astrophysics Data System (ADS)

Koshelev, Alexei

2013-03-01

Stacks of intrinsic Josephson-junctions are realized in mesas fabricated out of layered superconducting single crystals, such as Bi2Sr2CaCu2O8 (BSCCO). Synchronization of phase oscillations in different junctions can be facilitated by the coupling to the internal cavity mode leading to powerful and coherent electromagnetic radiation in the terahertz frequency range. An important characteristic of this radiation is the shape of the emission line. A finite line width appears due to different noise sources leading to phase diffusion. We investigated the intrinsic line shape caused by the thermal noise for a mesa fabricated on the top of a BSCCO single crystal. In the ideal case of fully synchronized stack the finite line width is coming from two main contributions, the quasiparticle-current noise inside the mesa and the fluctuating radiation in the base crystal. We compute both contributions and conclude that for realistic mesa's parameters the second mechanism typically dominates. The role of the cavity quality factor in the emission line spectrum is clarified. Analytical results were verified by numerical simulations. In real mesa structures part of the stack may not be synchronized and chaotic dynamics of unsynchronized junctions may determine the real line width. Work supported by UChicago Argonne, LLC, under contract No. DE-AC02-06CH11357.

Identification of a residue in helix 2 of rice plasma membrane intrinsic proteins that influences water permeability.

PubMed

Zhang, Minhua; Lü, Shouqin; Li, Guowei; Mao, Zhilei; Yu, Xin; Sun, Weining; Tang, Zhangcheng; Long, Mian; Su, Weiai

2010-12-31

Molecular selection, ion exclusion, and water permeation are well known regulatory mechanisms in aquaporin. Water permeability was found to be diverse in different subgroups of plasma membrane intrinsic proteins (PIPs), even though the residues surrounding the water holes remained the same across the subgroups. Upon homology modeling and structural comparison, a conserved Ala/Ile(Val) residue difference was identified in helix 2 that affected the conformation of the NPA region and consequently influenced the water permeability. The residue difference was found to be conservative within the two subgroups of PIPs in rice as well as in other plants. Functional tests further confirmed the prediction via site-directed mutagenesis where replacement of Ala(103) or Ala(102) in respective OsPIP1;1 or OsPIP1;3 with Val yielded 7.0- and 2.2-fold increases in water transportation, and substitution of Ile(98) or Val(95) in respective OsPIP2;3 or OsPIP2;7 with Ala resulted in 73 or 52% reduction of water transportation. Based on structural analyses and molecular dynamics simulations, we proposed that the difference in water permeability was attributed to the orientation variations of helix 2 that modified water-water and water-protein interactions.

Understanding structure-stability relationships of Candida antartica lipase B in ionic liquids.

PubMed

De Diego, Teresa; Lozano, Pedro; Gmouh, Said; Vaultier, Michel; Iborra, José L

2005-01-01

Two different water-immiscible ionic liquids (ILs), 1-ethyl-3-methylimidizolium bis(trifluoromethylsulfonyl)imide and butyltrimethylammonium bis(trifluoromethylsulfonyl)imide, were used for butyl butyrate synthesis from vinyl butyrate catalyzed by Candida antarctica lipase B (CALB) at 2% (v/v) water content and 50 degrees C. Both the synthetic activity and stability of the enzyme in these ILs were enhanced as compared to those in hexane. Circular dichroism and intrinsic fluorescence spectroscopic techniques have been used over a period of 4 days to determine structural changes in the enzyme associated with differences in its stability for each assayed medium. CALB showed a loss in residual activity higher than 75% after 4 days of incubation in both water and hexane media at 50 degrees C, being related to great changes in both alpha-helix and beta-strand secondary structures. The stabilization of CALB, which was observed in the two ILs studied, was associated with both the maintenance of the 50% of initial alpha-helix content and the enhancement of beta-strands. Furthermore, intrinsic fluorescence studies clearly showed how a classical enzyme unfolding was occurring with time in both water and hexane media. However, the structural changes associated with the incubation of the enzyme in both ILs might be attributed to a compact and active enzyme conformation, resulting in an enhancement of the stability in these nonaqueous environments.

Conformational Dynamics of Titin PEVK Explored with FRET Spectroscopy

PubMed Central

Huber, Tamás; Grama, László; Hetényi, Csaba; Schay, Gusztáv; Fülöp, Lívia; Penke, Botond; Kellermayer, Miklós S.Z.

2012-01-01

The proline-, glutamate-, valine-, and lysine-rich (PEVK) domain of the giant muscle protein titin is thought to be an intrinsically unstructured random-coil segment. Various observations suggest, however, that the domain may not be completely devoid of internal interactions and structural features. To test the validity of random polymer models for PEVK, we determined the mean end-to-end distances of an 11- and a 21-residue synthetic PEVK peptide, calculated from the efficiency of the fluorescence resonance energy transfer (FRET) between an N-terminal intrinsic tryptophan donor and a synthetically added C-terminal IAEDANS acceptor obtained in steady-state and time-resolved experiments. We find that the contour-length scaling of mean end-to-end distance deviates from predictions of a purely statistical polymer chain. Furthermore, the addition of guanidine hydrochloride decreased, whereas the addition of salt increased the FRET efficiency, pointing at the disruption of structure-stabilizing interactions. Increasing temperature between 10 and 50°C increased the normalized FRET efficiency in both peptides but with different trajectories, indicating that their elasticity and conformational stability are different. Simulations suggest that whereas the short PEVK peptide displays an overall random structure, the long PEVK peptide retains residual, loose helical configurations. Transitions in the local structure and dynamics of the PEVK domain may play a role in the modulation of passive muscle mechanics. PMID:23062340

Recombinant Intrinsically Disordered Proteins for NMR: Tips and Tricks.

PubMed

Calçada, Eduardo O; Korsak, Magdalena; Kozyreva, Tatiana

2015-01-01

The growing recognition of the several roles that intrinsically disordered proteins play in biology places an increasing importance on protein sample availability to allow the characterization of their structural and dynamic properties. The sample preparation is therefore the limiting step to allow any biophysical method being able to characterize the properties of an intrinsically disordered protein and to clarify the links between these properties and the associated biological functions. An increasing array of tools has been recruited to help prepare and characterize the structural and dynamic properties of disordered proteins. This chapter describes their sample preparation, covering the most common drawbacks/barriers usually found working in the laboratory bench. We want this chapter to be the bedside book of any scientist interested in preparing intrinsically disordered protein samples for further biophysical analysis.

Intrinsic and Extrinsic Motivation Among Adolescent Ten-Pin Bowlers in Kuala Lumpur, Malaysia

PubMed Central

Teo, Eng-Wah; Khoo, Selina; Wong, Rebecca; Wee, Eng-Hoe; Lim, Boon-Hooi; Rengasamy, Shabesan Sit

2015-01-01

Motivation has long been associated with sports engagement. However, to date no research has been performed to understand the domain of motivation among ten-pin bowlers. The purpose of this study was to investigate different types of motivation (i.e., intrinsic vs. extrinsic) based on self-determination theory from the perspective of gender and the bowler type (competitive vs. casual). A total of 240 bowlers (104 male, 136 female; 152 competitive, 88 casual) with a mean age of 16.61 ± 0.78 years were recruited in Kuala Lumpur. The Sport Motivation Scale, a 28-item self-report questionnaire measuring seven subscales (i.e., intrinsic motivation to know, intrinsic motivation to accomplish, intrinsic motivation to experience stimulation, extrinsic motivation to identify regulation, extrinsic motivation for introjection regulation, extrinsic motivation to external regulation, and amotivation) was administered. Results showed significant differences (t=10.43, df=239, p=0.01) between total scores of intrinsic and extrinsic motivation among ten-pin bowlers. There were significant gender differences with respect to intrinsic motivation to know, intrinsic motivation to accomplish, intrinsic motivation to experience stimulation, and extrinsic motivation to identify regulation. However, no significant bowler type differences were found for either the intrinsic (t=−1.15, df=238, p=0.25) or extrinsic (t=−0.51, df=238, p=0.61) motivation dimensions. In conclusion, our study demonstrated substantial intrinsic motivation for gender effects, but no bowler type effects among adolescent ten-pin bowlers. PMID:25964827

Intrinsic and extrinsic motivation among adolescent ten-pin bowlers in kuala lumpur, malaysia.

PubMed

Teo, Eng-Wah; Khoo, Selina; Wong, Rebecca; Wee, Eng-Hoe; Lim, Boon-Hooi; Rengasamy, Shabesan Sit

2015-03-29

Motivation has long been associated with sports engagement. However, to date no research has been performed to understand the domain of motivation among ten-pin bowlers. The purpose of this study was to investigate different types of motivation (i.e., intrinsic vs. extrinsic) based on self-determination theory from the perspective of gender and the bowler type (competitive vs. casual). A total of 240 bowlers (104 male, 136 female; 152 competitive, 88 casual) with a mean age of 16.61 ± 0.78 years were recruited in Kuala Lumpur. The Sport Motivation Scale, a 28-item self-report questionnaire measuring seven subscales (i.e., intrinsic motivation to know, intrinsic motivation to accomplish, intrinsic motivation to experience stimulation, extrinsic motivation to identify regulation, extrinsic motivation for introjection regulation, extrinsic motivation to external regulation, and amotivation) was administered. Results showed significant differences (t=10.43, df=239, p=0.01) between total scores of intrinsic and extrinsic motivation among ten-pin bowlers. There were significant gender differences with respect to intrinsic motivation to know, intrinsic motivation to accomplish, intrinsic motivation to experience stimulation, and extrinsic motivation to identify regulation. However, no significant bowler type differences were found for either the intrinsic (t=-1.15, df=238, p=0.25) or extrinsic (t=-0.51, df=238, p=0.61) motivation dimensions. In conclusion, our study demonstrated substantial intrinsic motivation for gender effects, but no bowler type effects among adolescent ten-pin bowlers.

Thin film solar cell including a spatially modulated intrinsic layer

DOEpatents

Guha, Subhendu; Yang, Chi-Chung; Ovshinsky, Stanford R.

1989-03-28

One or more thin film solar cells in which the intrinsic layer of substantially amorphous semiconductor alloy material thereof includes at least a first band gap portion and a narrower band gap portion. The band gap of the intrinsic layer is spatially graded through a portion of the bulk thickness, said graded portion including a region removed from the intrinsic layer-dopant layer interfaces. The band gap of the intrinsic layer is always less than the band gap of the doped layers. The gradation of the intrinsic layer is effected such that the open circuit voltage and/or the fill factor of the one or plural solar cell structure is enhanced.

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

PubMed

Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

2015-10-26

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

NMR relaxation studies on the hydrate layer of intrinsically unstructured proteins.

PubMed

Bokor, Mónika; Csizmók, Veronika; Kovács, Dénes; Bánki, Péter; Friedrich, Peter; Tompa, Peter; Tompa, Kálmán

2005-03-01

Intrinsically unstructured/disordered proteins (IUPs) exist in a disordered and largely solvent-exposed, still functional, structural state under physiological conditions. As their function is often directly linked with structural disorder, understanding their structure-function relationship in detail is a great challenge to structural biology. In particular, their hydration and residual structure, both closely linked with their mechanism of action, require close attention. Here we demonstrate that the hydration of IUPs can be adequately approached by a technique so far unexplored with respect to IUPs, solid-state NMR relaxation measurements. This technique provides quantitative information on various features of hydrate water bound to these proteins. By freezing nonhydrate (bulk) water out, we have been able to measure free induction decays pertaining to protons of bound water from which the amount of hydrate water, its activation energy, and correlation times could be calculated. Thus, for three IUPs, the first inhibitory domain of calpastatin, microtubule-associated protein 2c, and plant dehydrin early responsive to dehydration 10, we demonstrate that they bind a significantly larger amount of water than globular proteins, whereas their suboptimal hydration and relaxation parameters are correlated with their differing modes of function. The theoretical treatment and experimental approach presented in this article may have general utility in characterizing proteins that belong to this novel structural class.

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

PubMed Central

Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

2015-01-01

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer’s disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements. PMID:26498066

Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins

PubMed Central

Perez, Romel B.; Tischer, Alexander; Auton, Matthew; Whitten, Steven T.

2014-01-01

Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins, mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline and alanine to glycine substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (Rh) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the glycine substitutions decreased polyproline II (PPII) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in Rh were not associated with folding. The experiments showed that changes in local PPII structure cause changes in Rh that are variable and that depend on the intrinsic chain propensities of proline and alanine residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed proline and alanine effects on the structures of intrinsically disordered proteins. PMID:25244701

Enhancing the intrinsic work motivation of community nutrition educators: how supportive supervision and job design foster autonomy.

PubMed

Dickin, Katherine L; Dollahite, Jamie S; Habicht, Jean-Pierre

2011-01-01

Mixed-methods research investigated the work motivation of paraprofessional community nutrition educators (CNEs) delivering a long-running public health nutrition program. In interviews, CNEs (n = 9) emphasized "freedom," supportive supervision, and "making a difference" as key sources of motivation. Community nutrition educator surveys (n = 115) confirmed high levels of autonomy, which was associated with supervisors' delegation and support, CNE decision-making on scheduling and curricula, and job satisfaction. Supervisors (n = 32) rated CNEs' job design as having inherently motivating characteristics comparable to professional jobs. Supervisory strategies can complement job design to create structured, supportive contexts that maintain fidelity, while granting autonomy to paraprofessionals to enhance intrinsic work motivation.

Cell cycle regulation by the intrinsically disordered proteins p21 and p27.

PubMed

Yoon, Mi-Kyung; Mitrea, Diana M; Ou, Li; Kriwacki, Richard W

2012-10-01

Today, it is widely accepted that proteins that lack highly defined globular three-dimensional structures, termed IDPs (intrinsically disordered proteins), play key roles in myriad biological processes. Our understanding of how intrinsic disorder mediates biological function is, however, incomplete. In the present paper, we review disorder-mediated cell cycle regulation by two intrinsically disordered proteins, p21 and p27. A structural adaptation mechanism involving a stretchable dynamic linker helix allows p21 to promiscuously recognize the various Cdk (cyclin-dependent kinase)-cyclin complexes that regulate cell division. Disorder within p27 mediates transmission of an N-terminal tyrosine phosphorylation signal to a C-terminal threonine phosphorylation, constituting a signalling conduit. These mechanisms are mediated by folding upon binding p21/p27's regulatory targets. However, residual disorder within the bound state contributes critically to these functional mechanisms. Our studies provide insights into how intrinsic protein disorder mediates regulatory processes and opportunities for designing drugs that target cancer-associated IDPs.

Evolution of intrinsic disorder in eukaryotic proteins.

PubMed

Ahrens, Joseph B; Nunez-Castilla, Janelle; Siltberg-Liberles, Jessica

2017-09-01

Conformational flexibility conferred though regions of intrinsic structural disorder allows proteins to behave as dynamic molecules. While it is well-known that intrinsically disordered regions can undergo disorder-to-order transitions in real-time as part of their function, we also are beginning to learn more about the dynamics of disorder-to-order transitions along evolutionary time-scales. Intrinsically disordered regions endow proteins with functional promiscuity, which is further enhanced by the ability of some of these regions to undergo real-time disorder-to-order transitions. Disorder content affects gene retention after whole genome duplication, but it is not necessarily conserved. Altered patterns of disorder resulting from evolutionary disorder-to-order transitions indicate that disorder evolves to modify function through refining stability, regulation, and interactions. Here, we review the evolution of intrinsically disordered regions in eukaryotic proteins. We discuss the interplay between secondary structure and disorder on evolutionary time-scales, the importance of disorder for eukaryotic proteome expansion and functional divergence, and the evolutionary dynamics of disorder.

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

Perriot, Romain; Uberuaga, Blas P.

We use molecular dynamics simulations to investigate the role of cation disorder on oxygen diffusion in Gd 2Zr 2O 7 (GZO) and Gd 2Ti 2O 7 (GTO) pyrochlores, a class of complex oxides which contain a structural vacancy relative to the basic fluorite structure. The introduction of disorder has distinct effects depending on the chemistry of the material, increasing the mobility of structural carriers by up to four orders of magnitude in GZO. In contrast, in GTO, there is no mobility at zero or low disorder on the ns timescale, but higher disorder liberates the otherwise immobile carriers, allowing diffusionmore » with rates comparable to GZO for the fully disordered material. Here, we show that the cation disorder enhances the diffusivity by both increasing the concentration of mobile structural carriers and their individual mobility. The disorder also influences the diffusion in materials containing intrinsic carriers, such as additional vacancies VO or oxygen interstitials OI. And while in ordered GZO and GTO the contribution of the intrinsic carriers dominates the overall diffusion of oxygen, OI in GZO contributes along with structural carriers, and the total diffusion rate can be calculated by assuming simple additive contributions from the two sources. Although the disorder in the materials with intrinsic defects usually enhances the diffusivity as in the defect-free case, in low concentrations, cation antisites AB or BA, where A = Gd and B = Zr or Ti, can act as traps for fast intrinsic defects. The trapping results in a lowering of the diffusivity, and causes a non-monotonic behavior of the diffusivity with disorder. Conversely, in the case of slow intrinsic defects, the main effect of the disorder is to liberate the structural carriers, resulting in an increase of the diffusivity regardless of the defect trapping.« less

Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding

PubMed Central

Smirnov, Alexey; Zubrienė, Asta; Manakova, Elena; Gražulis, Saulius

2018-01-01

The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure. PMID:29503769

Functional Anthology of Intrinsic Disorder. I. Biological Processes and Functions of Proteins with Long Disordered Regions

PubMed Central

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Uversky, Vladimir N.; Obradovic, Zoran

2008-01-01

Identifying relationships between function, amino acid sequence and protein structure represents a major challenge. In this study we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our statistical approach, outlines the major findings and provides illustrative examples of biological processes and functions positively and negatively correlated with intrinsic disorder. PMID:17391014

Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions.

PubMed

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Uversky, Vladimir N; Obradovic, Zoran

2007-05-01

Identifying relationships between function, amino acid sequence, and protein structure represents a major challenge. In this study, we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from the Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins, and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our statistical approach, outlines the major findings, and provides illustrative examples of biological processes and functions positively and negatively correlated with intrinsic disorder.

High-Throughput Characterization of Intrinsic Disorder in Proteins from the Protein Structure Initiative

PubMed Central

Johnson, Derrick E.; Xue, Bin; Sickmeier, Megan D.; Meng, Jingwei; Cortese, Marc S.; Oldfield, Christopher J.; Le Gall, Tanguy; Dunker, A. Keith; Uversky, Vladimir N.

2012-01-01

The identification of intrinsically disordered proteins (IDPs) among the targets that fail to form satisfactory crystal structures in the Protein Structure Initiative represent a key to reducing the costs and time for determining three-dimensional structures of proteins. To help in this endeavor, several Protein Structure Initiative Centers were asked to send samples of both crystallizable proteins and proteins that failed to crystallize. The abundance of intrinsic disorder in these proteins was evaluated via computational analysis using Predictors of Natural Disordered Regions (PONDR®) and the potential cleavage sites and corresponding fragments were determined. Then, the target proteins were analyzed for intrinsic disorder by their resistance to limited proteolysis. The rates of tryptic digestion of sample target proteins were compared to those of lysozyme/myoglobin, apo-myoglobin and α-casein as standards of ordered, partially disordered and completely disordered proteins, respectively. At the next stage, the protein samples were subjected to both far-UV and near-UV circular dichroism (CD) analysis. For most of the samples, a good agreement between CD data, predictions of disorder and the rates of limited tryptic digestion was established. Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins. PMID:22651963

Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles

PubMed Central

2013-01-01

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein–protein interaction prediction and design methods. PMID:24250278

VizieR Online Data Catalog: Structure of young stellar clusters. II. (Kuhn+, 2015)

NASA Astrophysics Data System (ADS)

Kuhn, M. A.; Getman, K. V.; Feigelson, E. D.

2015-07-01

We investigate the intrinsic stellar populations (estimated total numbers of OB and pre-main-sequence stars down to 0.1Mȯ) that are present in 17 massive star-forming regions (MSFRs) surveyed by the MYStIX project. The study is based on the catalog of >31000 MYStIX Probable Complex Members with both disk-bearing and disk-free populations, compensating for extinction, nebulosity, and crowding effects. Correction for observational sensitivities is made using the X-ray luminosity function and the near-infrared initial mass function --a correction that is often not made by infrared surveys of young stars. The resulting maps of the projected structure of the young stellar populations, in units of intrinsic stellar surface density, allow direct comparison between different regions. Several regions have multiple dense clumps, similar in size and density to the Orion Nebula Cluster. The highest projected density of ~34000 stars/pc2 is found in the core of the RCW 38 cluster. Histograms of surface density show different ranges of values in different regions, supporting the conclusion of Bressert et al. (B10; 2010MNRAS.409L..54B) that no universal surface-density threshold can distinguish between clustered and distributed star formation. However, a large component of the young stellar population of MSFRs resides in dense environments of 200-10000 stars/pc2 (including within the nearby Orion molecular clouds), and we find that there is no evidence for the B10 conclusion that such dense regions form an extreme "tail" of the distribution. Tables of intrinsic populations for these regions are used in our companion study of young cluster properties and evolution. (3 data files).

Learning to learn – intrinsic plasticity as a metaplasticity mechanism for memory formation

PubMed Central

Sehgal, Megha; Song, Chenghui; Ehlers, Vanessa L.; Moyer, James R.

2013-01-01

“Use it or lose it” is a popular adage often associated with use-dependent enhancement of cognitive abilities. Much research has focused on understanding exactly how the brain changes as a function of experience. Such experience-dependent plasticity involves both structural and functional alterations that contribute to adaptive behaviors, such as learning and memory, as well as maladaptive behaviors, including anxiety disorders, phobias, and posttraumatic stress disorder. With the advancing age of our population, understanding how use-dependent plasticity changes across the lifespan may also help to promote healthy brain aging. A common misconception is that such experience-dependent plasticity (e.g., associative learning) is synonymous with synaptic plasticity. Other forms of plasticity also play a critical role in shaping adaptive changes within the nervous system, including intrinsic plasticity – a change in the intrinsic excitability of a neuron. Intrinsic plasticity can result from a change in the number, distribution or activity of various ion channels located throughout the neuron. Here, we review evidence that intrinsic plasticity is an important and evolutionarily conserved neural correlate of learning. Intrinsic plasticity acts as a metaplasticity mechanism by lowering the threshold for synaptic changes. Thus, learning-related intrinsic changes can facilitate future synaptic plasticity and learning. Such intrinsic changes can impact the allocation of a memory trace within a brain structure, and when compromised, can contribute to cognitive decline during the aging process. This unique role of intrinsic excitability can provide insight into how memories are formed and, more interestingly, how neurons that participate in a memory trace are selected. Most importantly, modulation of intrinsic excitability can allow for regulation of learning ability – this can prevent or provide treatment for cognitive decline not only in patients with clinical disorders but also in the aging population. PMID:23871744

Molecular interactions within the halophilic, thermophilic, and mesophilic prokaryotic ribosomal complexes: clues to environmental adaptation.

PubMed

Mallik, Saurav; Kundu, Sudip

2015-01-01

Using the available crystal structures of 50S ribosomal subunits from three prokaryotic species: Escherichia coli (mesophilic), Thermus thermophilus (thermophilic), and Haloarcula marismortui (halophilic), we have analyzed different structural features of ribosomal RNAs (rRNAs), proteins, and of their interfaces. We have correlated these structural features with the environmental adaptation strategies of the corresponding species. While dense intra-rRNA packing is observed in thermophilic, loose intra-rRNA packing is observed in halophilic (both compared to mesophilic). Interestingly, protein-rRNA interfaces of both the extremophiles are densely packed compared to that of the mesophilic. The intersubunit bridge regions are almost devoid of cavities, probably ensuring the proper formation of each bridge (by not allowing any loosely packed region nearby). During rRNA binding, the ribosomal proteins experience some structural transitions. Here, we have analyzed the intrinsically disordered and ordered regions of the ribosomal proteins, which are subjected to such transitions. The intrinsically disordered and disorder-to-order transition sites of the thermophilic and mesophilic ribosomal proteins are simultaneously (i) highly conserved and (ii) slowly evolving compared to rest of the protein structure. Although high conservation is observed at such sites of halophilic ribosomal proteins, but slow rate of evolution is absent. Such differences between thermophilic, mesophilic, and halophilic can be explained from their environmental adaptation strategy. Interestingly, a universal biophysical principle evident by a linear relationship between the free energy of interface formation, interface area, and structural changes of r-proteins during assembly is always maintained, irrespective of the environmental conditions.

Understanding motivational structures that differentially predict engagement and achievement in middle school science

NASA Astrophysics Data System (ADS)

Lee, Christine S.; Hayes, Kathryn N.; Seitz, Jeffery; DiStefano, Rachelle; O'Connor, Dawn

2016-01-01

Middle school has been documented as the period in which a drop in students' science interest and achievement occurs. This trend indicates a lack of motivation for learning science; however, little is known about how different aspects of motivation interact with student engagement and science learning outcomes. This study examines the relationships among motivational factors, engagement, and achievement in middle school science (grades 6-8). Data were obtained from middle school students in the United States (N = 2094). The theoretical relationships among motivational constructs, including self-efficacy, and three types of goal orientations (mastery, performance approach, and performance avoid) were tested. The results showed that motivation is best modeled as distinct intrinsic and extrinsic factors; lending evidence that external, performance based goal orientations factor separately from self-efficacy and an internal, mastery based goal orientation. Second, a model was tested to examine how engagement mediated the relationships between intrinsic and extrinsic motivational factors and science achievement. Engagement mediated the relationship between intrinsic motivation and science achievement, whereas extrinsic motivation had no relationship with engagement and science achievement. Implications for how classroom practice and educational policy emphasize different student motivations, and in turn, can support or hinder students' science learning are discussed.

Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities

PubMed Central

Tomasso, Maria E.; Tarver, Micheal J.; Devarajan, Deepa; Whitten, Steven T.

2016-01-01

The properties of disordered proteins are thought to depend on intrinsic conformational propensities for polyproline II (PP II) structure. While intrinsic PP II propensities have been measured for the common biological amino acids in short peptides, the ability of these experimentally determined propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs) has not been established. Presented here are results from molecular simulations of disordered proteins showing that the hydrodynamic radius (R h) can be predicted from experimental PP II propensities with good agreement, even when charge-based considerations are omitted. The simulations demonstrate that R h and chain propensity for PP II structure are linked via a simple power-law scaling relationship, which was tested using the experimental R h of 22 IDPs covering a wide range of peptide lengths, net charge, and sequence composition. Charge effects on R h were found to be generally weak when compared to PP II effects on R h. Results from this study indicate that the hydrodynamic dimensions of IDPs are evidence of considerable sequence-dependent backbone propensities for PP II structure that qualitatively, if not quantitatively, match conformational propensities measured in peptides. PMID:26727467

A Hierarchical structure of key performance indicators for operation management and continuous improvement in production systems

PubMed Central

Kang, Ningxuan; Zhao, Cong; Li, Jingshan; Horst, John A.

2018-01-01

Key performance indicators (KPIs) are critical for manufacturing operation management and continuous improvement (CI). In modern manufacturing systems, KPIs are defined as a set of metrics to reflect operation performance, such as efficiency, throughput, availability, from productivity, quality and maintenance perspectives. Through continuous monitoring and measurement of KPIs, meaningful quantification and identification of different aspects of operation activities can be obtained, which enable and direct CI efforts. A set of 34 KPIs has been introduced in ISO 22400. However, the KPIs in a manufacturing system are not independent, and they may have intrinsic mutual relationships. The goal of this paper is to introduce a multi-level structure for identification and analysis of KPIs and their intrinsic relationships in production systems. Specifically, through such a hierarchical structure, we define and layer KPIs into levels of basic KPIs, comprehensive KPIs and their supporting metrics, and use it to investigate the relationships and dependencies between KPIs. Such a study can provide a useful tool for manufacturing engineers and managers to measure and utilize KPIs for CI. PMID:29398722

A Hierarchical structure of key performance indicators for operation management and continuous improvement in production systems.

PubMed

Kang, Ningxuan; Zhao, Cong; Li, Jingshan; Horst, John A

2016-01-01

Key performance indicators (KPIs) are critical for manufacturing operation management and continuous improvement (CI). In modern manufacturing systems, KPIs are defined as a set of metrics to reflect operation performance, such as efficiency, throughput, availability, from productivity, quality and maintenance perspectives. Through continuous monitoring and measurement of KPIs, meaningful quantification and identification of different aspects of operation activities can be obtained, which enable and direct CI efforts. A set of 34 KPIs has been introduced in ISO 22400. However, the KPIs in a manufacturing system are not independent, and they may have intrinsic mutual relationships. The goal of this paper is to introduce a multi-level structure for identification and analysis of KPIs and their intrinsic relationships in production systems. Specifically, through such a hierarchical structure, we define and layer KPIs into levels of basic KPIs, comprehensive KPIs and their supporting metrics, and use it to investigate the relationships and dependencies between KPIs. Such a study can provide a useful tool for manufacturing engineers and managers to measure and utilize KPIs for CI.

Optimal Superpositioning of Flexible Molecule Ensembles

PubMed Central

Gapsys, Vytautas; de Groot, Bert L.

2013-01-01

Analysis of the internal dynamics of a biological molecule requires the successful removal of overall translation and rotation. Particularly for flexible or intrinsically disordered peptides, this is a challenging task due to the absence of a well-defined reference structure that could be used for superpositioning. In this work, we started the analysis with a widely known formulation of an objective for the problem of superimposing a set of multiple molecules as variance minimization over an ensemble. A negative effect of this superpositioning method is the introduction of ambiguous rotations, where different rotation matrices may be applied to structurally similar molecules. We developed two algorithms to resolve the suboptimal rotations. The first approach minimizes the variance together with the distance of a structure to a preceding molecule in the ensemble. The second algorithm seeks for minimal variance together with the distance to the nearest neighbors of each structure. The newly developed methods were applied to molecular-dynamics trajectories and normal-mode ensembles of the Aβ peptide, RS peptide, and lysozyme. These new (to our knowledge) superpositioning methods combine the benefits of variance and distance between nearest-neighbor(s) minimization, providing a solution for the analysis of intrinsic motions of flexible molecules and resolving ambiguous rotations. PMID:23332072

Intrinsic, Functional, and Structural Properties of β-Thymosins and β-Thymosin/WH2 Domains in the Regulation and Coordination of Actin Self-Assembly Dynamics and Cytoskeleton Remodeling.

PubMed

Renault, L

2016-01-01

β-Thymosins are a family of heat-stable multifunctional polypeptides that are expressed as small proteins of about 5kDa (~45 amino acids) almost exclusively in multicellular animals. They were first isolated from the thymus. As full-length or truncated polypeptides, they appear to stimulate a broad range of extracellular activities in various signaling pathways, including tissue repair and regeneration, inflammation, cell migration, and immune defense. However, their cell surface receptors and structural mechanisms of regulations in these multiple pathways remain still poorly understood. Besides their extracellular activities, they belong to a larger family of small, intrinsically disordered actin-binding domains called WH2/β-thymosin domains that have been identified in more than 1800 multidomain proteins found in different taxonomic domains of life and involved in various actin-based motile processes including cell morphogenesis, motility, adhesions, tissue development, intracellular trafficking, or pathogen infections. This review briefly surveys the main recent findings to understand how these small, intrinsically disordered but functional domains can interact with many unrelated partners and can thus integrate and coordinate various intracellular activities in actin self-assembly dynamics and cell signaling pathways linked to their cytoskeleton remodeling. © 2016 Elsevier Inc. All rights reserved.

Temporal variations in a phytoplankton community in a subtropical reservoir: An interplay of extrinsic and intrinsic community effects.

PubMed

Yang, Wen; Zheng, Zhongming; Zheng, Cheng; Lu, Kaihong; Ding, Dewen; Zhu, Jinyong

2018-01-15

The phytoplankton community structure is potentially influenced by both extrinsic effects originating from the surrounding environment and intrinsic effects relying on interspecific interactions between two species. However, few studies have simultaneously considered both types of effects and assessed the relative importance of these factors. In this study, we used data collected over nine months (August 2012-May 2013) from a typical subtropical reservoir in southeast China to analyze the temporal variation of its phytoplankton community structure and develop a quantitative understanding of the extrinsic and intrinsic effects on phytoplankton community dynamics. Significant temporal variations were observed in environmental variables as well as the phytoplankton and zooplankton communities, whereas their variational trajectories and directions were entirely different. Variance partitioning analysis showed that extrinsic factors significantly explained only 31% of the variation in the phytoplankton community, thus suggesting that these factors were incomplete predictors of the community structure. Random forest-based models showed that 48% of qualified responsible phytoplankton species were more accurately predicted by phytoplankton-only models, which revealed clear effects of interspecific species-to-species interactions. Furthermore, we used association networks to model the interactions among phytoplankton, zooplankton and the environment. Network comparisons indicated that interspecific interactions were widely present in the phytoplankton community and dominated the network rather than those between phytoplankton and extrinsic factors. These findings expand the current understanding of the underlying mechanisms that govern phytoplankton community dynamics. Copyright © 2017 Elsevier B.V. All rights reserved.

[Comparison of Physico-chemical Aspects between E. coli and Human Dihydrofolate Reductase: an Equilibrium Unfolding Study].

PubMed

Thapliyal, Charu; Jain, Neha; Chaudhuri, Pratima

2015-01-01

A protein, differing in origin, may exhibit variable physicochemical behaviour, difference in sequence homology, fold and function. Thus studying structure-function relationship of proteins from altered sources is meaningful in the sense that it may give rise to comparative aspects of their sequence-structure-function relationship. Dihydrofolate reductase is an enzyme involved in cell cycle regulation. It is a significant enzyme as.a target for developing anticancer drugs. Hence, detailed understanding of structure-function relationships of wide variants of the enzyme dihydrofolate reductase would be important for developing an inhibitor or an antagonist against the enzyme involved in the cellular developmental processes. In this communication, we have reported the comparative structure-function relationship between E. coli and human dihydrofolate reductase. The differences in the unfolding behaviour of these two proteins have been investigated to understand various properties of these two proteins like relative' stability differences and variation in conformational changes under identical denaturing conditions. The equilibrium unfolding mechanism of dihydrofolate reductase proteins using guanidine hydrochloride as a denaturant in the presence of various types of osmolytes has been monitored using loss in enzymatic activity, intrinsic tryptophan fluorescence and an extrinsic fluorophore 8-anilino-1-naphthalene-sulfonic acid as probes. It has been observed that osmolytes, such as 1M sucrose, and 30% glycerol, provided enhanced stability to both variants of dihydrofolate reductase. Their level of stabilisation has been observed to be dependent on intrinsic protein stability. It was observed that 100 mM proline does not show any 'significant stabilisation to either of dihydrofolate reductases. In the present study, it has been observed that the human protein is relatively less stable than the E.coli counterpart.

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.

PubMed

Wells, Stephen A; van der Kamp, Marc W; McGeagh, John D; Mulholland, Adrian J

2015-01-01

Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes.

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions

PubMed Central

McGeagh, John D.; Mulholland, Adrian J.

2015-01-01

Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes. PMID:26241964

Adolescent-perceived parent and teacher overestimation of mathematics ability: Developmental implications for students' mathematics task values.

PubMed

Gniewosz, Burkhard; Watt, Helen M G

2017-07-01

This study examines whether and how student-perceived parents' and teachers' overestimation of students' own perceived mathematical ability can explain trajectories for adolescents' mathematical task values (intrinsic and utility) controlling for measured achievement, following expectancy-value and self-determination theories. Longitudinal data come from a 3-cohort (mean ages 13.25, 12.36, and 14.41 years; Grades 7-10), 4-wave data set of 1,271 Australian secondary school students. Longitudinal structural equation models revealed positive effects of student-perceived overestimation of math ability by parents and teachers on students' intrinsic and utility math task values development. Perceived parental overestimations predicted intrinsic task value changes between all measurement occasions, whereas utility task value changes only were predicted between Grades 9 and 10. Parental influences were stronger for intrinsic than utility task values. Teacher influences were similar for both forms of task values and commenced after the curricular school transition in Grade 8. Results support the assumptions that the perceived encouragement conveyed by student-perceived mathematical ability beliefs of parents and teachers, promote positive mathematics task values development. Moreover, results point to different mechanisms underlying parents' and teachers' support. Finally, the longitudinal changes indicate transition-related increases in the effects of student-perceived overestimations and stronger effects for intrinsic than utility values. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Intrinsic motivation and sportsmanship: mediating role of interpersonal relationships.

PubMed

Núñez, Juan L; Martín-Albo, José; Navarro, José G; Sánchez, Juana M; González-Cutre, David

2009-06-01

This study analyzed the mediating role of interpersonal relations between intrinsic motivation and sportsmanship. Athletes (98 men, 97 women), ages 11 to 43 years, completed measures of intrinsic motivation toward sports, self-concept of social and family relations, and sportsmanship orientation. A structural equation model indicated that self-concept of interpersonal relations mediated the relation between intrinsic motivation and sportsmanship. Also, intrinsic motivation was directly and positively associated with self-concept of interpersonal relations, which, in turn, was positively and significantly related to sportsmanship. Variances explained by self-concept of interpersonal relations and by sportsmanship were 32 and 56%, respectively. The motivational interaction between the context of interpersonal relations and the sports context proposed in the hierarchical model of intrinsic and extrinsic motivation was discussed.

Imitating intrinsic alignments: a bias to the CMB lensing-galaxy shape cross-correlation power spectrum induced by the large-scale structure bispectrum

NASA Astrophysics Data System (ADS)

Merkel, Philipp M.; Schäfer, Björn Malte

2017-10-01

Cross-correlating the lensing signals of galaxies and comic microwave background (CMB) fluctuations is expected to provide valuable cosmological information. In particular, it may help tighten constraints on parameters describing the properties of intrinsically aligned galaxies at high redshift. To access the information conveyed by the cross-correlation signal, its accurate theoretical description is required. We compute the bias to CMB lensing-galaxy shape cross-correlation measurements induced by non-linear structure growth. Using tree-level perturbation theory for the large-scale structure bispectrum, we find that the bias is negative on most angular scales, therefore mimicking the signal of intrinsic alignments. Combining Euclid-like galaxy lensing data with a CMB experiment comparable to the Planck satellite mission, the bias becomes significant only on smallest scales (ℓ ≳ 2500). For improved CMB observations, however, the corrections amount to 10-15 per cent of the CMB lensing-intrinsic alignment signal over a wide multipole range (10 ≲ ℓ ≲ 2000). Accordingly, the power spectrum bias, if uncorrected, translates into 2σ and 3σ errors in the determination of the intrinsic alignment amplitude in the case of CMB stage III and stage IV experiments, respectively.

Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins.

PubMed

Uversky, Vladimir N

2016-03-25

Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally heterogeneous, and can be considered an important part of the structure-function continuum. Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged in various interactions characterized by a wide spectrum of binding scenarios and an even wider spectrum of structural and functional outputs. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural and functional localization of airway effects from episodic exposure of infant monkeys to allergen and/or ozone

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

Joad, Jesse P.; Kott, Kayleen S.; Bric, John M.

2006-08-01

Both allergen and ozone exposure increase asthma symptoms and airway responsiveness in children. Little is known about how these inhalants may differentially modify airway responsiveness in large proximal as compared to small distal airways. We evaluated whether bronchi and respiratory bronchioles from infant monkeys exposed episodically to allergen and/or ozone differentially develop intrinsic hyperresponsiveness to methacholine and whether eosinophils and/or pulmonary neuroendocrine cells play a role. Infant monkeys were exposed episodically for 5 months to: (1) filtered air, (2) aerosolized house dust mite allergen, (3) ozone 0.5 ppm, or (4) house dust mite allergen + ozone. Studying the function/structure relationshipmore » of the same lung slices, we evaluated methacholine airway responsiveness and histology of bronchi and respiratory bronchioles. In bronchi, intrinsic responsiveness was increased by allergen exposure, an effect reduced by bombesin antagonist. In respiratory bronchioles, intrinsic airway responsiveness was increased by allergen + ozone exposure. Eosinophils were increased by allergen and allergen + ozone exposure in bronchi and by allergen exposure in respiratory bronchioles. In both airways, exposure to allergen + ozone resulted in fewer tissue eosinophils than did allergen exposure alone. In bronchi, but not in respiratory bronchioles, the number of eosinophils and neuroendocrine cells correlated with airway responsiveness. We conclude that episodically exposing infant monkeys to house dust mite allergen with or without ozone increased intrinsic airway responsiveness to methacholine in bronchi differently than in respiratory bronchioles. In bronchi, eosinophils and neuroendocrine cells may play a role in the development of airway hyperresponsiveness.« less

Human long intrinsically disordered protein regions are frequent targets of positive selection.

PubMed

Afanasyeva, Arina; Bockwoldt, Mathias; Cooney, Christopher R; Heiland, Ines; Gossmann, Toni I

2018-06-01

Intrinsically disordered regions occur frequently in proteins and are characterized by a lack of a well-defined three-dimensional structure. Although these regions do not show a higher order of structural organization, they are known to be functionally important. Disordered regions are rapidly evolving, largely attributed to relaxed purifying selection and an increased role of genetic drift. It has also been suggested that positive selection might contribute to their rapid diversification. However, for our own species, it is currently unknown whether positive selection has played a role during the evolution of these protein regions. Here, we address this question by investigating the evolutionary pattern of more than 6600 human proteins with intrinsically disordered regions and their ordered counterparts. Our comparative approach with data from more than 90 mammalian genomes uses a priori knowledge of disordered protein regions, and we show that this increases the power to detect positive selection by an order of magnitude. We can confirm that human intrinsically disordered regions evolve more rapidly, not only within humans but also across the entire mammalian phylogeny. They have, however, experienced substantial evolutionary constraint, hinting at their fundamental functional importance. We find compelling evidence that disordered protein regions are frequent targets of positive selection and estimate that the relative rate of adaptive substitutions differs fourfold between disordered and ordered protein regions in humans. Our results suggest that disordered protein regions are important targets of genetic innovation and that the contribution of positive selection in these regions is more pronounced than in other protein parts. © 2018 Afanasyeva et al.; Published by Cold Spring Harbor Laboratory Press.

Remote sensing image segmentation using local sparse structure constrained latent low rank representation

NASA Astrophysics Data System (ADS)

Tian, Shu; Zhang, Ye; Yan, Yimin; Su, Nan; Zhang, Junping

2016-09-01

Latent low-rank representation (LatLRR) has been attached considerable attention in the field of remote sensing image segmentation, due to its effectiveness in exploring the multiple subspace structures of data. However, the increasingly heterogeneous texture information in the high spatial resolution remote sensing images, leads to more severe interference of pixels in local neighborhood, and the LatLRR fails to capture the local complex structure information. Therefore, we present a local sparse structure constrainted latent low-rank representation (LSSLatLRR) segmentation method, which explicitly imposes the local sparse structure constraint on LatLRR to capture the intrinsic local structure in manifold structure feature subspaces. The whole segmentation framework can be viewed as two stages in cascade. In the first stage, we use the local histogram transform to extract the texture local histogram features (LHOG) at each pixel, which can efficiently capture the complex and micro-texture pattern. In the second stage, a local sparse structure (LSS) formulation is established on LHOG, which aims to preserve the local intrinsic structure and enhance the relationship between pixels having similar local characteristics. Meanwhile, by integrating the LSS and the LatLRR, we can efficiently capture the local sparse and low-rank structure in the mixture of feature subspace, and we adopt the subspace segmentation method to improve the segmentation accuracy. Experimental results on the remote sensing images with different spatial resolution show that, compared with three state-of-the-art image segmentation methods, the proposed method achieves more accurate segmentation results.

Study of gain homogeneity and radiation effects of Low Gain Avalanche Pad Detectors

NASA Astrophysics Data System (ADS)

Gallrapp, C.; Fernández García, M.; Hidalgo, S.; Mateu, I.; Moll, M.; Otero Ugobono, S.; Pellegrini, G.

2017-12-01

Silicon detectors with intrinsic charge amplification implementing a n++-p+-p structure are considered as a sensor technology for future tracking and timing applications in high energy physics experiments. The performance of the intrinsic gain in Low Gain Avalanche Detectors (LGAD) after irradiation is crucial for the characterization of radiation hardness and timing properties in this technology. LGAD devices irradiated with reactor neutrons or 800 MeV protons reaching fluences of 2.3 × 1016 neq/cm2 were characterized using Transient Current Technique (TCT) measurements with red and infra-red laser pulses. Leakage current variations observed in different production lots and within wafers were investigated using Thermally Stimulated Current (TSC). Results showed that the intrinsic charge amplification is reduced with increasing fluence up to 1015 neq/cm2 which is related to an effective acceptor removal. Further relevant issues were charge collection homogeneity across the detector surface and leakage current performance before and after irradiation.

Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I, II, VII, XII, and XIII

PubMed Central

Kišonaitė, Miglė; Zubrienė, Asta; Čapkauskaitė, Edita; Smirnov, Alexey; Smirnovienė, Joana; Kairys, Visvaldas; Michailovienė, Vilma; Manakova, Elena; Gražulis, Saulius; Matulis, Daumantas

2014-01-01

The early stage of drug discovery is often based on selecting the highest affinity lead compound. To this end the structural and energetic characterization of the binding reaction is important. The binding energetics can be resolved into enthalpic and entropic contributions to the binding Gibbs free energy. Most compound binding reactions are coupled to the absorption or release of protons by the protein or the compound. A distinction between the observed and intrinsic parameters of the binding energetics requires the dissection of the protonation/deprotonation processes. Since only the intrinsic parameters can be correlated with molecular structural perturbations associated with complex formation, it is these parameters that are required for rational drug design. Carbonic anhydrase (CA) isoforms are important therapeutic targets to treat a range of disorders including glaucoma, obesity, epilepsy, and cancer. For effective treatment isoform-specific inhibitors are needed. In this work we investigated the binding and protonation energetics of sixteen [(2-pyrimidinylthio)acetyl]benzenesulfonamide CA inhibitors using isothermal titration calorimetry and fluorescent thermal shift assay. The compounds were built by combining four sulfonamide headgroups with four tailgroups yielding 16 compounds. Their intrinsic binding thermodynamics showed the limitations of the functional group energetic additivity approach used in fragment-based drug design, especially at the level of enthalpies and entropies of binding. Combined with high resolution crystal structural data correlations were drawn between the chemical functional groups on selected inhibitors and intrinsic thermodynamic parameters of CA-inhibitor complex formation. PMID:25493428

Intrinsic physiological properties of rat retinal ganglion cells with a comparative analysis.

PubMed

Wong, Raymond C S; Cloherty, Shaun L; Ibbotson, Michael R; O'Brien, Brendan J

2012-10-01

Mammalian retina contains 15-20 different retinal ganglion cell (RGC) types, each of which is responsible for encoding different aspects of the visual scene. The encoding is defined by a combination of RGC synaptic inputs, the neurotransmitter systems used, and their intrinsic physiological properties. Each cell's intrinsic properties are defined by its morphology and membrane characteristics, including the complement and localization of the ion channels expressed. In this study, we examined the hypothesis that the intrinsic properties of individual RGC types are conserved among mammalian species. To do so, we measured the intrinsic properties of 16 morphologically defined rat RGC types and compared these data with cat RGC types. Our data demonstrate that in the rat different morphologically defined RGC types have distinct patterns of intrinsic properties. Variation in these properties across cell types was comparable to that found for cat RGC types. When presumed morphological homologs in rat and cat retina were compared directly, some RGC types had very similar properties. The rat A2 cell exhibited patterns of intrinsic properties nearly identical to the cat alpha cell. In contrast, rat D2 cells (ON-OFF directionally selective) had a very different pattern of intrinsic properties than the cat iota cell. Our data suggest that the intrinsic properties of RGCs with similar morphology and suspected visual function may be subject to variation due to the behavioral needs of the species.

JPRS Report, Science & Technology, USSR: Life Sciences

DTIC Science & Technology

1989-03-07

BIOORGANICHESKAYA KHIMIYA, Vol 14 No 4, Apr 88] 19 Intrinsic Fluorescence Studies on Effects of pH on Structure of Mistletoe Lectin [T. L. Bushuyeva, A. G...Figures 2; references 15: 3 Russian, 12 Western. UDC 576.8.097.29:547.962.3 Intrinsic Fluorescence Studies on Effects of pH on Structure of Mistletoe ...characteristics of the mistletoe lectin I (MLI), a molecule consisting of A (29 kD) and a B (34 kD) subunit, were used in assessing the structural

Determination of critical diameters for intrinsic carrier diffusion-length of GaN nanorods with cryo-scanning near-field optical microscopy

PubMed Central

Chen, Y. T.; Karlsson, K. F.; Birch, J.; Holtz, P. O.

2016-01-01

Direct measurements of carrier diffusion in GaN nanorods with a designed InGaN/GaN layer-in-a-wire structure by scanning near-field optical microscopy (SNOM) were performed at liquid-helium temperatures of 10 K. Without an applied voltage, intrinsic diffusion lengths of photo-excited carriers were measured as the diameters of the nanorods differ from 50 to 800 nm. The critical diameter of nanorods for carrier diffusion is concluded as 170 nm with a statistical approach. Photoluminescence spectra were acquired for different positions of the SNOM tip on the nanorod, corresponding to the origins of the well-defined luminescence peaks, each being related to recombination-centers. The phenomenon originated from surface oxide by direct comparison of two nanorods with similar diameters in a single map has been observed and investigated. PMID:26876009

RECONSTRUCTING THREE-DIMENSIONAL JET GEOMETRY FROM TWO-DIMENSIONAL IMAGES

NASA Astrophysics Data System (ADS)

Avachat, Sayali; Perlman, Eric S.; Li, Kunyang; Kosak, Katie

2018-01-01

Relativistic jets in AGN are one of the most interesting and complex structures in the Universe. Some of the jets can be spread over hundreds of kilo parsecs from the central engine and display various bends, knots and hotspots. Observations of the jets can prove helpful in understanding the emission and particle acceleration processes from sub-arcsec to kilo parsec scales and the role of magnetic field in it. The M87 jet has many bright knots as well as regions of small and large bends. We attempt to model the jet geometry using the observed 2 dimensional structure. The radio and optical images of the jet show evidence of presence of helical magnetic field throughout. Using the observed structure in the sky frame, our goal is to gain an insight into the intrinsic 3 dimensional geometry in the jets frame. The structure of the bends in jet's frame may be quite different than what we see in the sky frame. The knowledge of the intrinsic structure will be helpful in understanding the appearance of the magnetic field and hence polarization morphology. To achieve this, we are using numerical methods to solve the non-linear equations based on the jet geometry. We are using the Log Likelihood method and algorithm based on Markov Chain Monte Carlo (MCMC) simulations.

Different effects of the TAR structure on HIV-1 and HIV-2 genomic RNA translation

PubMed Central

Soto-Rifo, Ricardo; Limousin, Taran; Rubilar, Paulina S.; Ricci, Emiliano P.; Décimo, Didier; Moncorgé, Olivier; Trabaud, Mary-Anne; André, Patrice; Cimarelli, Andrea; Ohlmann, Théophile

2012-01-01

The 5′-untranslated region (5′-UTR) of the genomic RNA of human immunodeficiency viruses type-1 (HIV-1) and type-2 (HIV-2) is composed of highly structured RNA motifs essential for viral replication that are expected to interfere with Gag and Gag-Pol translation. Here, we have analyzed and compared the properties by which the viral 5′-UTR drives translation from the genomic RNA of both human immunodeficiency viruses. Our results showed that translation from the HIV-2 gRNA was very poor compared to that of HIV-1. This was rather due to the intrinsic structural motifs in their respective 5′-UTR without involvement of any viral protein. Further investigation pointed to a different role of TAR RNA, which was much inhibitory for HIV-2 translation. Altogether, these data highlight important structural and functional differences between these two human pathogens. PMID:22121214

Development and validation of the goal content for exercise questionnaire.

PubMed

Sebire, Simon J; Standage, Martyn; Vansteenkiste, Maarten

2008-08-01

Self-determination theory (SDT; Deci & Ryan, 2000) proposes that intrinsic, relative to extrinsic, goal content is a critical predictor of the quality of an individual's behavior and psychological well-being. Through three studies, we developed and psychometrically tested a measure of intrinsic and extrinsic goal content in the exercise context: the Goal Content for Exercise Questionnaire (GCEQ). In adults, exploratory (N = 354; Study 1) and confirmatory factor analyses (N = 312; Study 2) supported a 20-item solution consisting of 5 lower order factors (i.e., social affiliation, health management, skill development, image and social recognition) that could be subsumed within a 2-factor higher order structure (i.e., intrinsic and extrinsic). Evidence for external validity, temporal stability, gender invariance, and internal consistency of the GCEQ was found. An independent sample (N = 475; Study 3) provided further support for the lower order structure of the GCEQ and some support for the higher order structure. The GCEQ was supported as a measure of exercise-based goal content, which may help understand how intrinsic and extrinsic goals can motivate exercise behavior.

Toward Modeling the Intrinsic Complexity of Test Problems

ERIC Educational Resources Information Center

Shoufan, Abdulhadi

2017-01-01

The concept of intrinsic complexity explains why different problems of the same type, tackled by the same problem solver, can require different times to solve and yield solutions of different quality. This paper proposes a general four-step approach that can be used to establish a model for the intrinsic complexity of a problem class in terms of…

Intrinsic gray-matter connectivity of the brain in adults with autism spectrum disorder

PubMed Central

Ecker, Christine; Ronan, Lisa; Feng, Yue; Daly, Eileen; Murphy, Clodagh; Ginestet, Cedric E.; Brammer, Michael; Fletcher, Paul C.; Bullmore, Edward T.; Suckling, John; Baron-Cohen, Simon; Williams, Steve; Loth, Eva; Murphy, Declan G. M.; Bailey, A. J.; Baron-Cohen, S.; Bolton, P. F.; Bullmore, E. T.; Carrington, S.; Chakrabarti, B.; Daly, E. M.; Deoni, S. C.; Ecker, C.; Happe, F.; Henty, J.; Jezzard, P.; Johnston, P.; Jones, D. K.; Lai, M. C.; Lombardo, M. V.; Madden, A.; Mullins, D.; Murphy, C. M.; Murphy, D. G.; Pasco, G.; Sadek, S.; Spain, D.; Steward, R.; Suckling, J.; Wheelwright, S.; Williams, S. C.

2013-01-01

Autism spectrum disorders (ASD) are a group of neurodevelopmental conditions that are accompanied by atypical brain connectivity. So far, in vivo evidence for atypical structural brain connectivity in ASD has mainly been based on neuroimaging studies of cortical white matter. However, genetic studies suggest that abnormal connectivity in ASD may also affect neural connections within the cortical gray matter. Such intrinsic gray-matter connections are inherently more difficult to describe in vivo but may be inferred from a variety of surface-based geometric features that can be measured using magnetic resonance imaging. Here, we present a neuroimaging study that examines the intrinsic cortico-cortical connectivity of the brain in ASD using measures of “cortical separation distances” to assess the global and local intrinsic “wiring costs” of the cortex (i.e., estimated length of horizontal connections required to wire the cortex within the cortical sheet). In a sample of 68 adults with ASD and matched controls, we observed significantly reduced intrinsic wiring costs of cortex in ASD, both globally and locally. Differences in global and local wiring cost were predominantly observed in fronto-temporal regions and also significantly predicted the severity of social and repetitive symptoms (respectively). Our study confirms that atypical cortico-cortical “connectivity” in ASD is not restricted to the development of white-matter connections but may also affect the intrinsic gray-matter architecture (and connectivity) within the cortical sheet. Thus, the atypical connectivity of the brain in ASD is complex, affecting both gray and white matter, and forms part of the core neural substrates underlying autistic symptoms. PMID:23878213

Intrinsic gray-matter connectivity of the brain in adults with autism spectrum disorder.

PubMed

Ecker, Christine; Ronan, Lisa; Feng, Yue; Daly, Eileen; Murphy, Clodagh; Ginestet, Cedric E; Brammer, Michael; Fletcher, Paul C; Bullmore, Edward T; Suckling, John; Baron-Cohen, Simon; Williams, Steve; Loth, Eva; Murphy, Declan G M

2013-08-06

Autism spectrum disorders (ASD) are a group of neurodevelopmental conditions that are accompanied by atypical brain connectivity. So far, in vivo evidence for atypical structural brain connectivity in ASD has mainly been based on neuroimaging studies of cortical white matter. However, genetic studies suggest that abnormal connectivity in ASD may also affect neural connections within the cortical gray matter. Such intrinsic gray-matter connections are inherently more difficult to describe in vivo but may be inferred from a variety of surface-based geometric features that can be measured using magnetic resonance imaging. Here, we present a neuroimaging study that examines the intrinsic cortico-cortical connectivity of the brain in ASD using measures of "cortical separation distances" to assess the global and local intrinsic "wiring costs" of the cortex (i.e., estimated length of horizontal connections required to wire the cortex within the cortical sheet). In a sample of 68 adults with ASD and matched controls, we observed significantly reduced intrinsic wiring costs of cortex in ASD, both globally and locally. Differences in global and local wiring cost were predominantly observed in fronto-temporal regions and also significantly predicted the severity of social and repetitive symptoms (respectively). Our study confirms that atypical cortico-cortical "connectivity" in ASD is not restricted to the development of white-matter connections but may also affect the intrinsic gray-matter architecture (and connectivity) within the cortical sheet. Thus, the atypical connectivity of the brain in ASD is complex, affecting both gray and white matter, and forms part of the core neural substrates underlying autistic symptoms.

Studies of the Intrinsic Complexities of Magnetotail Ion Distributions: Theory and Observations

NASA Technical Reports Server (NTRS)

Ashour-Abdalla, Maha

1998-01-01

This year we have studied the relationship between the structure seen in measured distribution functions and the detailed magnetospheric configuration. Results from our recent studies using time-dependent large-scale kinetic (LSK) calculations are used to infer the sources of the ions in the velocity distribution functions measured by a single spacecraft (Geotail). Our results strongly indicate that the different ion sources and acceleration mechanisms producing a measured distribution function can explain this structure. Moreover, individual structures within distribution functions were traced back to single sources. We also confirmed the fractal nature of ion distributions.

Protein intrinsic disorder in plants.

PubMed

Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto

2013-09-12

To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

Protein intrinsic disorder in plants

PubMed Central

Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A.; Solano, Roberto

2013-01-01

To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks. PMID:24062761

Process development and tooling design for intrinsic hybrid composites

NASA Astrophysics Data System (ADS)

Riemer, M.; Müller, R.; Drossel, W. G.; Landgrebe, D.

2017-09-01

Hybrid parts, which combine the advantages of different material classes, are moving into the focus of lightweight applications. This development is amplified by their high potential for usage in the field of crash relevant structures. By the current state of the art, hybrid parts are mainly made in separate, subsequent forming and joining processes. By using the concept of an intrinsic hybrid, the shaping of the part and the joining of the different materials are performed in a single process step for shortening the overall processing time and thereby the manufacturing costs. The investigated hybrid part is made from continuous fibre reinforced plastic (FRP), in which a metallic reinforcement structure is integrated. The connection between these layered components is realized by a combination of adhesive bonding and a geometrical form fit. The form fit elements are intrinsically generated during the forming process. This contribution regards the development of the forming process and the design of the forming tool for the single step production of a hybrid part. To this end a forming tool, which combines the thermo-forming and the metal forming process, is developed. The main challenge by designing the tool is the temperature management of the tool elements for the variothermal forming process. The process parameters are determined in basic tests and finite element (FE) simulation studies. On the basis of these investigations a control concept for the steering of the motion axes and the tool temperature is developed. Forming tests are carried out with the developed tool and the manufactured parts are analysed by computer assisted tomography (CT) scans.

Proton-conducting ionic liquid-based Proton Exchange Membrane Fuel Cell membranes: The key role of ionomer-ionic liquid interaction

NASA Astrophysics Data System (ADS)

Martinez, Mathieu; Molmeret, Yannick; Cointeaux, Laure; Iojoiu, Cristina; Leprêtre, Jean-Claude; El Kissi, Nadia; Judeinstein, Patrick; Sanchez, Jean-Yves

The paper deals with the synthesis and characterisation of proton-conducting ionic liquids (PCILs) and their polymer electrolytes obtained by blending modified Nafion membranes with different concentrations of PCILs. The PCILs are obtained by the neutralization of triethylamine with different organic acids. The first part of the paper studies the influence of acidity and acid structure on PCIL thermal and electrochemical performance, while the second part examines membrane conductivity and reveals it to depend more on PCIL structure than on its intrinsic conductivity. At 130 °C, conductivities exceeding 10 mS cm -1 were obtained in fully anhydrous conditions.

Targeted Basic Studies of Ferroelectric and Ferroelastic Materials for Piezoelectric Transducer Applications.

DTIC Science & Technology

1983-03-01

PLZT ceramics. Low temperature studies on pure and doped PZTs have given the first clear indi- cation of the intrinsic (averaged) single domain...8217 11 4.0 PYROELECTRIC MATERIALS 27 4.1 Micro Composites 27 4.2 ’ Doped ’ Tungsten Bronze and TGS Structure Single Crystals 28 5.0 FERROELECTRIC...differences in piezo- electric activity, coupling constant and permittivity between differently doped PZTs are extrinsic and freeze out at 4°K. Extending

Linear parameter varying identification of ankle joint intrinsic stiffness during imposed walking movements.

PubMed

Sobhani Tehrani, Ehsan; Jalaleddini, Kian; Kearney, Robert E

2013-01-01

This paper describes a novel model structure and identification method for the time-varying, intrinsic stiffness of human ankle joint during imposed walking (IW) movements. The model structure is based on the superposition of a large signal, linear, time-invariant (LTI) model and a small signal linear-parameter varying (LPV) model. The methodology is based on a two-step algorithm; the LTI model is first estimated using data from an unperturbed IW trial. Then, the LPV model is identified using data from a perturbed IW trial with the output predictions of the LTI model removed from the measured torque. Experimental results demonstrate that the method accurately tracks the continuous-time variation of normal ankle intrinsic stiffness when the joint position changes during the IW movement. Intrinsic stiffness gain decreases from full plantarflexion to near the mid-point of plantarflexion and then increases substantially as the ankle is dosriflexed.

X-ray induced chemical reaction revealed by in-situ X-ray diffraction and scanning X-ray microscopy in 15 nm resolution (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ge, Mingyuan; Liu, Wenjun; Bock, David; De Andrade, Vincent; Yan, Hanfei; Huang, Xiaojing; Marschilok, Amy; Takeuchi, Esther; Xin, Huolin; Chu, Yong S.

2016-09-01

The detection sensitivity of synchrotron-based X-ray techniques has been largely improved due to the ever increasing source brightness, which have significantly advanced ex-situ and in-situ research for energy materials, such as lithium-ion batteries. However, the strong beam-matter interaction arisen from the high beam flux can significantly modify the material structure. The parasitic beam-induced effect inevitably interferes with the intrinsic material property, which brings difficulties in interpreting experimental results, and therefore requires comprehensive evaluation. Here we present a quantitative in-situ study of the beam-effect on one electrode material Ag2VO2PO4 using four different X-ray probes with different radiation dose rate. The material system we reported exhibits interesting and reversible radiation-induced thermal and chemical reactions, which was further evaluated under electron microscopy to illustrate the underlying mechanism. The work we presented here will provide a guideline in using synchrotron X-rays to distinguish the materials' intrinsic behavior from extrinsic structure changed induced by X-rays, especially in the case of in-situ and operando study where the materials are under external field of either temperature or electric field.

Microstructure and corrosion resistance of sputter-deposited titanium-chromium alloy coatings

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

Landolt, D.; Robyr, C.; Mettraux, P.

1998-10-01

Titanium, chromium, and titanium-chromium alloy coatings were sputter-deposited to study their corrosion behaviors in relation to microstructure and composition. Silicon substrates were used to study the effect of alloying on intrinsic corrosion resistance of the coating materials, and brass substrates were used to study the effect of alloying on the penetrating porosity of the coatings. Corrosion behavior was characterized using linear sweep voltammetry. The crystal structure of the coatings was examined by x-ray diffraction (XRD) and the microstructure by scanning electron microscopy (SEM). Electrochemical impedance spectroscopy (EIS) was used to estimate the real surface area of the coatings. Results showedmore » alloying of titanium with chromium greatly influenced microstructure of the coatings. Alloying led to deposits of higher apparent density and, in some cases, to an x-ray amorphous structure. Alloy coatings showed significantly lower corrosion currents than the constituting metals. The effect was attributed to a smoother surface topography. When corrected of differences in real surface area, the intrinsic corrosion rate of the alloy coatings did not differ significantly from that of the constituting metals. Alloy coatings deposited on brass exhibited a lower porosity than titanium or chromium metal coatings produced under identical conditions.« less

Scattering images from autocorrelation functions of P-wave seismic velocity images: the case of Tenerife Island (Canary Islands, Spain)

NASA Astrophysics Data System (ADS)

García-Yeguas, A.; Sánchez-Alzola, A.; De Siena, L.; Prudencio, J.; Díaz-Moreno, A.; Ibáñez, J. M.

2018-03-01

We present a P-wave scattering image of the volcanic structures under Tenerife Island using the autocorrelation functions of P-wave vertical velocity fluctuations. We have applied a cluster analysis to total quality factor attenuation ( {Q}_t^{-1} ) and scattering quality factor attenuation ( {Q}_{PSc}^{-1} ) images to interpret the structures in terms of intrinsic and scattering attenuation variations on a 2D plane, corresponding to a depth of 2000 m, and check the robustness of the scattering imaging. The results show that scattering patterns are similar to total attenuation patterns in the south of the island. There are two main areas where patterns differ: at Cañadas-Teide-Pico Viejo Complex, high total attenuation and average-to-low scattering values are observed. We interpret the difference as induced by intrinsic attenuation. In the Santiago Ridge Zone (SRZ) region, high scattering values correspond to average total attenuation. In our interpretation, the anomaly is induced by an extended scatterer, geometrically related to the surficial traces of Garachico and El Chinyero historical eruptions and the area of highest seismic activity during the 2004-2008 seismic crises.

Synchrotron x-ray microdiffraction reveals intrinsic structural features of amyloid deposits in situ.

PubMed

Briki, Fatma; Vérine, Jérôme; Doucet, Jean; Bénas, Philippe; Fayard, Barbara; Delpech, Marc; Grateau, Gilles; Riès-Kautt, Madeleine

2011-07-20

Amyloidoses are increasingly recognized as a major public health concern in Western countries. All amyloidoses share common morphological, structural, and tinctorial properties. These consist of staining by specific dyes, a fibrillar aspect in electron microscopy and a typical cross-β folding in x-ray diffraction patterns. Most studies that aim at deciphering the amyloid structure rely on fibers generated in vitro or extracted from tissues using protocols that may modify their intrinsic structure. Therefore, the fine details of the in situ architecture of the deposits remain unknown. Here, we present to our knowledge the first data obtained on ex vivo human renal tissue sections using x-ray microdiffraction. The typical cross-β features from fixed paraffin-embedded samples are similar to those formed in vitro or extracted from tissues. Moreover, the fiber orientation maps obtained across glomerular sections reveal an intrinsic texture that is correlated with the glomerulus morphology. These results are of the highest importance to understanding the formation of amyloid deposits and are thus expected to trigger new incentives for tissue investigation. Moreover, the access to intrinsic structural parameters such as fiber size and orientation using synchrotron x-ray microdiffraction, could provide valuable information concerning in situ mechanisms and deposit formation with potential benefits for diagnostic and therapeutic purposes. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Thin film solar cells with Si nanocrystallites embedded in amorphous intrinsic layers by hot-wire chemical vapor deposition.

PubMed

Park, Seungil; Parida, Bhaskar; Kim, Keunjoo

2013-05-01

We investigated the thin film growths of hydrogenated silicon by hot-wire chemical vapor deposition with different flow rates of SiH4 and H2 mixture ambient and fabricated thin film solar cells by implementing the intrinsic layers to SiC/Si heterojunction p-i-n structures. The film samples showed the different infrared absorption spectra of 2,000 and 2,100 cm(-1), which are corresponding to the chemical bonds of SiH and SiH2, respectively. The a-Si:H sample with the relatively high silane concentration provides the absorption peak of SiH bond, but the microc-Si:H sample with the relatively low silane concentration provides the absorption peak of SiH2 bond as well as SiH bond. Furthermore, the microc-Si:H sample showed the Raman spectral shift of 520 cm(-1) for crystalline phase Si bonds as well as the 480 cm(-1) for the amorphous phase Si bonds. These bonding structures are very consistent with the further analysis of the long-wavelength photoconduction tail and the formation of nanocrystalline Si structures. The microc-Si:H thin film solar cell has the photovoltaic behavior of open circuit voltage similar to crystalline silicon thin film solar cell, indicating that microc-Si:H thin film with the mixed phase of amorphous and nanocrystalline structures show the carrier transportation through the channel of nanocrystallites.

A new non-degradative method to purify glycogen.

PubMed

Tan, Xinle; Sullivan, Mitchell A; Gao, Fei; Li, Shihan; Schulz, Benjamin L; Gilbert, Robert G

2016-08-20

Liver glycogen, a complex branched glucose polymer containing a small amount of protein, is important for maintaining glucose homeostasis (blood-sugar control) in humans. It has recently been found that glycogen molecular structure is impaired in diabetes. Isolating the carbohydrate polymer and any intrinsically-attached protein(s) is an essential prerequisite for studying this structural impairment. This requires an effective, non-degradative and efficient purification method to exclude the many other proteins present in liver. Proteins and glycogen have different ranges of molecular sizes. Despite the plethora of proteins that might still be present in significant abundance after other isolation techniques, SEC (size exclusion chromatography, also known as GPC), which separates by molecular size, should separate those extraneous to glycogen from glycogen with any intrinsically associated protein(s). A novel purification method is developed for this, based on preparative SEC following sucrose gradient centrifugation. Proteomics is used to show that the new method compares favourably with current methods in the literature. Copyright © 2016 Elsevier Ltd. All rights reserved.

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Relationship between individual neuron and network spontaneous activity in developing mouse cortex.

PubMed

Barnett, Heather M; Gjorgjieva, Julijana; Weir, Keiko; Comfort, Cara; Fairhall, Adrienne L; Moody, William J

2014-12-15

Spontaneous synchronous activity (SSA) that propagates as electrical waves is found in numerous central nervous system structures and is critical for normal development, but the mechanisms of generation of such activity are not clear. In previous work, we showed that the ventrolateral piriform cortex is uniquely able to initiate SSA in contrast to the dorsal neocortex, which participates in, but does not initiate, SSA (Lischalk JW, Easton CR, Moody WJ. Dev Neurobiol 69: 407-414, 2009). In this study, we used Ca(2+) imaging of cultured embryonic day 18 to postnatal day 2 coronal slices (embryonic day 17 + 1-4 days in culture) of the mouse cortex to investigate the different activity patterns of individual neurons in these regions. In the piriform cortex where SSA is initiated, a higher proportion of neurons was active asynchronously between waves, and a larger number of groups of coactive cells was present compared with the dorsal cortex. When we applied GABA and glutamate synaptic antagonists, asynchronous activity and cellular clusters remained, while synchronous activity was eliminated, indicating that asynchronous activity is a result of cell-intrinsic properties that differ between these regions. To test the hypothesis that higher levels of cell-autonomous activity in the piriform cortex underlie its ability to initiate waves, we constructed a conductance-based network model in which three layers differed only in the proportion of neurons able to intrinsically generate bursting behavior. Simulations using this model demonstrated that a gradient of intrinsic excitability was sufficient to produce directionally propagating waves that replicated key experimental features, indicating that the higher level of cell-intrinsic activity in the piriform cortex may provide a substrate for SSA generation. Copyright © 2014 the American Physiological Society.

Contributions of intrinsic and extrinsic polarization species to energy storage properties of Ba0.95Ca0.05Zr0.2Ti0.8O3 ceramics

NASA Astrophysics Data System (ADS)

Zhan, Di; Xu, Qing; Huang, Duan-Ping; Liu, Han-Xing; Chen, Wen; Zhang, Feng

2018-03-01

Ba0.95Ca0.05Zr0.2Ti0.8O3 ceramics were prepared at different sintering temperatures by citrate precursor and solid-state reaction methods, respectively. The crystal structure and microstructure of the specimens were characterized. In view of energy storage capacitor utilizations, the dielectric properties of the specimens were investigated at room temperature as a function of frequency and applied electric field. Moreover, the nature of mobile charge carriers in the specimens was diagnosed by complex impedance spectroscopy at elevated temperatures. While the dielectric constants of the specimens prepared by different methods are quite different (4.4 × 103-2.2 × 104 at 10 kHz) at zero electric field, the energy storage densities at an identical strong electric field are similar (e.g. 0.32-0.41 J/cm3 at 120 kV/cm). The dielectric constants under bias electric field were fitted to a multipolarization mechanism model to resolve the contributions of intrinsic and extrinsic polarization mechanisms. It turned out that the extrinsic contributions fade out within low electric field range (<20 kV/cm) and thereby the intrinsic lattice polarization governs the overall dielectric responses at higher fields. Based on the fitting result, the energy storage properties of the specimens were interpreted.

Genetic and Diagnostic Biomarker Development in ASD Toddlers Using Resting State Functional MRI

DTIC Science & Technology

2017-11-01

and activation-based fMRI from the Courchesne lab report the presence of structural and functional abnormality in these structures by ages 1 to 2...young ages. With this invaluable resource, we will identify early developmental patterns of intrinsic functional network abnormalities in ASD infants...all infants and toddlers, analyses also investigate whether there may be subtypes of abnormal intrinsic connectivity patterns based on early clinical

NMR studies of a channel protein without membranes: structure and dynamics of water-solubilized KcsA.

PubMed

Ma, Dejian; Tillman, Tommy S; Tang, Pei; Meirovitch, Eva; Eckenhoff, Roderic; Carnini, Anna; Xu, Yan

2008-10-28

Structural studies of polytopic membrane proteins are often hampered by the vagaries of these proteins in membrane mimetic environments and by the difficulties in handling them with conventional techniques. Designing and creating water-soluble analogues with preserved native structures offer an attractive alternative. We report here solution NMR studies of WSK3, a water-soluble analogue of the potassium channel KcsA. The WSK3 NMR structure (PDB ID code 2K1E) resembles the KcsA crystal structures, validating the approach. By more stringent comparison criteria, however, the introduction of several charged residues aimed at improving water solubility seems to have led to the possible formations of a few salt bridges and hydrogen bonds not present in the native structure, resulting in slight differences in the structure of WSK3 relative to KcsA. NMR dynamics measurements show that WSK3 is highly flexible in the absence of a lipid environment. Reduced spectral density mapping and model-free analyses reveal dynamic characteristics consistent with an isotropically tumbling tetramer experiencing slow (nanosecond) motions with unusually low local ordering. An altered hydrogen-bond network near the selectivity filter and the pore helix, and the intrinsically dynamic nature of the selectivity filter, support the notion that this region is crucial for slow inactivation. Our results have implications not only for the design of water-soluble analogues of membrane proteins but also for our understanding of the basic determinants of intrinsic protein structure and dynamics.

Different thermostabilities of sarcoplasmic reticulum (Ca2+ + Mg2+)-ATPases from rabbit and trout muscles.

PubMed

de Toledo, F G; Albuquerque, M C; Goulart, B H; Chini, E N

1995-05-01

Trout and rabbit (Ca2+ + Mg2+)-ATPases from sarcoplasmic reticulum were compared for differences in thermal inactivation and susceptibility to trypsin digestion. The trout ATPase is more heat-sensitive than the rabbit ATPase and is stabilized by Ca2+, Na+, K+ and nucleotides. Solubilization of both ATPases shows that the two ATPases have different protein-intrinsic inactivation kinetics. When digested by trypsin, the two ATPases display different cleavage patterns. The present results indicate that the trout and rabbit ATPases have dissimilarities in protein structure that may explain the differences in thermal inactivation kinetics.

THE LIMITED EFFECT OF COINCIDENT ORIENTATION ON THE CHOICE OF INTRINSIC AXIS (.).

PubMed

Li, Jing; Su, Wei

2015-06-01

The allocentric system computes and represents general object-to-object spatial relationships to provide a spatial frame of reference other than the egocentric system. The intrinsic frame-of-reference system theory, which suggests people learn the locations of objects based upon an intrinsic axis, is important in research about the allocentric system. The purpose of the current study was to determine whether the effect of coincident orientation on the choice of intrinsic axis was limited. Two groups of participants (24 men, 24 women; M age = 24 yr., SD = 2) encoded different spatial layouts in which the objects shared the coincident orientation of 315° and 225° separately at learning perspective (0°). The response pattern of partial-scene-recognition task following learning reflected different strategies for choosing the intrinsic axis under different conditions. Under the 315° object-orientation condition, the objects' coincident orientation was as important as the symmetric axis in the choice of the intrinsic axis. However, participants were more likely to choose the symmetric axis as the intrinsic axis under the 225° object-orientation condition. The results suggest the effect of coincident orientation on the choice of intrinsic axis is limited.

Abundance of intrinsic structural disorder in the histone H1 subtypes.

PubMed

Kowalski, Andrzej

2015-12-01

The intrinsically disordered proteins consist of partially structured regions linked to the unstructured stretches, which consequently form the transient and dynamic conformational ensembles. They undergo disorder to order transition upon binding their partners. Intrinsic disorder is attributed to histones H1, perceived as assemblers of chromatin structure and the regulators of DNA and proteins activity. In this work, the comparison of intrinsic disorder abundance in the histone H1 subtypes was performed both by the analysis of their amino acid composition and by the prediction of disordered stretches, as well as by identifying molecular recognition features (MoRFs) and ANCHOR protein binding regions (APBR) that are responsible for recognition and binding. Both human and model organisms-animals, plants, fungi and protists-have H1 histone subtypes with the properties typical of disordered state. They possess a significantly higher content of hydrophilic and charged amino acid residues, arranged in the long regions, covering over half of the whole amino acid residues in chain. Almost complete disorder corresponds to histone H1 terminal domains, including MoRFs and ANCHOR. Those motifs were also identified in a more ordered histone H1 globular domain. Compared to the control (globular and fibrous) proteins, H1 histones demonstrate the increased folding rate and a higher proportion of low-complexity segments. The results of this work indicate that intrinsic disorder is an inherent structural property of histone H1 subtypes and it is essential for establishing a protein conformation which defines functional outcomes affecting on DNA- and/or partner protein-dependent cell processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Intrinsic and extrinsic pinning in NdFeAs(O,F): vortex trapping and lock-in by the layered structure

NASA Astrophysics Data System (ADS)

Tarantini, C.; Iida, K.; Hänisch, J.; Kurth, F.; Jaroszynski, J.; Sumiya, N.; Chihara, M.; Hatano, T.; Ikuta, H.; Schmidt, S.; Seidel, P.; Holzapfel, B.; Larbalestier, D. C.

2016-10-01

Fe-based superconductors (FBS) present a large variety of compounds whose properties are affected to different extents by their crystal structures. Amongst them, the REFeAs(O,F) (RE1111, RE being a rare-earth element) is the family with the highest critical temperature Tc but also with a large anisotropy and Josephson vortices as demonstrated in the flux-flow regime in Sm1111 (Tc ∼ 55 K). Here we focus on the pinning properties of the lower-Tc Nd1111 in the flux-creep regime. We demonstrate that for H//c critical current density Jc at high temperatures is dominated by point-defect pinning centres, whereas at low temperatures surface pinning by planar defects parallel to the c-axis and vortex shearing prevail. When the field approaches the ab-planes, two different regimes are observed at low temperatures as a consequence of the transition between 3D Abrikosov and 2D Josephson vortices: one is determined by the formation of a vortex-staircase structure and one by lock-in of vortices parallel to the layers. This is the first study on FBS showing this behaviour in the full temperature, field, and angular range and demonstrating that, despite the lower Tc and anisotropy of Nd1111 with respect to Sm1111, this compound is substantially affected by intrinsic pinning generating a strong ab-peak in Jc.

The effects of hormones and physical exercise on hippocampal structural plasticity.

PubMed

Triviño-Paredes, Juan; Patten, Anna R; Gil-Mohapel, Joana; Christie, Brian R

2016-04-01

The hippocampus plays an integral role in certain aspects of cognition. Hippocampal structural plasticity and in particular adult hippocampal neurogenesis can be influenced by several intrinsic and extrinsic factors. Here we review how hormones (i.e., intrinsic modulators) and physical exercise (i.e., an extrinsic modulator) can differentially modulate hippocampal plasticity in general and adult hippocampal neurogenesis in particular. Specifically, we provide an overview of the effects of sex hormones, stress hormones, and metabolic hormones on hippocampal structural plasticity and adult hippocampal neurogenesis. In addition, we also discuss how physical exercise modulates these forms of hippocampal plasticity, giving particular emphasis on how this modulation can be affected by variables such as exercise regime, duration, and intensity. Understanding the neurobiological mechanisms underlying the modulation of hippocampal structural plasticity by intrinsic and extrinsic factors will impact the design of new therapeutic approaches aimed at restoring hippocampal plasticity following brain injury or neurodegeneration. Copyright © 2016 Elsevier Inc. All rights reserved.

NMR contributions to structural dynamics studies of intrinsically disordered proteins☆

PubMed Central

Konrat, Robert

2014-01-01

Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082

Intrinsic, Narrow N V Absorption Reveals a Clumpy Outflow in z < 0.4 Radio-Loud Quasars

NASA Astrophysics Data System (ADS)

DeMarcy, Bryan; Serra, Viktoriah; Culliton, Chris; Ganguly, Rajib; Runnoe, Jessie; Charlton, Jane; Eracleous, Michael; Misawa, Toru; Narayanan, Anand

2018-01-01

Quasar outflows are often invoked in models for galaxy evolution to inject energy and momentum into the gas in the host galaxy and influence its star formation history. Thus, the study of quasar outflows is essential for understanding galaxy evolution. N V absorption systems within the associated region (|Δv| ≤ 5000 km s-1) of the quasar are thought to be intrinsic since many show evidence for partial covering of the quasar. A recent archival study of quasar spectra taken with COS/G130M or G160M found 39/181 radio-quiet quasars show intrinsic N V absorption, while none of the 31 radio-loud quasars have N V absorption detected (Culliton et al. 2017). Further investigation of these radio-loud quasars showed a clear bias towards compact morphologies as revealed by FIRST 1.4 GHz imaging and comparatively flat radio spectra. This suggests we are viewing more face-on orientations which prevent us from seeing absorption outflows. The cause for such bias within the HST archive is still unknown; however, it could explain the lack of radio-loud intrinsic N V absorption seen by Culliton et al. (2017). Alternatively, the quasar wind structure may be fundamentally different between radio-loud and radio-quiet objects. We used COS/G130M or G160M to obtain rest-frame UV spectra (1195 Å - 1250 Å) of 14 low-redshift SDSS radio-loud quasars which show lobe-dominated FIRST morphologies to distinguish between these possibilities. Intrinsic N V absorption was detected in 6 of our 14 quasars. This suggests the lack of detections in the archival study was a result of an orientation effect/sampling bias rather than to differences in wind structure between radio-loud and radio-quiet quasars. Interestingly, we find significant overlap in radio core fractions between quasars with and without N V detection. Quasars in our sample with N V detection span a range of core fractions from < 0.01 up to 0.89 while those without detected N V range from 0.04 up to 0.93. A laminar outflow with a small opening angle would be difficult to explain given this overlap in radio core fractions. Our observations suggest a clumpy, sporadic outflow is the more likely explanation.

Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase

PubMed Central

Mittag, Tanja; Marsh, Joseph; Grishaev, Alexander; Orlicky, Stephen; Lin, Hong; Sicheri, Frank; Tyers, Mike; Forman-Kay, Julie D.

2010-01-01

Summary Intrinsically disordered proteins can form highly dynamic complexes with partner proteins. One such dynamic complex involves the intrinsically disordered Sic1 with its partner Cdc4 in regulation of yeast cell cycle progression. Phosphorylation of six N-terminal Sic1 sites leads to equilibrium engagement of each phosphorylation site with the primary binding pocket in Cdc4, the substrate recognition subunit of a ubiquitin ligase. ENSEMBLE calculations utilizing experimental NMR and small-angle x-ray scattering data reveal significant transient structure in both phosphorylation states of the isolated ensembles (Sic1 and pSic1) that modulates their electrostatic potential, suggesting a structural basis for the proposed strong contribution of electrostatics to binding. A structural model of the dynamic pSic1-Cdc4 complex demonstrates the spatial arrangements in the ubiquitin ligase complex. These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated. PMID:20399186

What's in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered.

PubMed

Dunker, A Keith; Babu, M Madan; Barbar, Elisar; Blackledge, Martin; Bondos, Sarah E; Dosztányi, Zsuzsanna; Dyson, H Jane; Forman-Kay, Julie; Fuxreiter, Monika; Gsponer, Jörg; Han, Kyou-Hoon; Jones, David T; Longhi, Sonia; Metallo, Steven J; Nishikawa, Ken; Nussinov, Ruth; Obradovic, Zoran; Pappu, Rohit V; Rost, Burkhard; Selenko, Philipp; Subramaniam, Vinod; Sussman, Joel L; Tompa, Peter; Uversky, Vladimir N

2013-01-01

"What's in a name? That which we call a rose By any other name would smell as sweet." From "Romeo and Juliet", William Shakespeare (1594) This article opens a series of publications on disambiguation of the basic terms used in the field of intrinsically disordered proteins. We start from the beginning, namely from the explanation of what the expression "intrinsically disordered protein" actually means and why this particular term has been chosen as the common denominator for this class of proteins characterized by broad structural, dynamic and functional characteristics.

Functional Anthology of Intrinsic Disorder. II. Cellular Components, Domains, Technical Terms, Developmental Processes and Coding Sequence Diversities Correlated with Long Disordered Regions

PubMed Central

Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

2008-01-01

Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes ~90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes and coding sequence diversities possessing strong positive and negative correlation with long disordered regions. PMID:17391015

Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions.

PubMed

Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Obradovic, Zoran; Uversky, Vladimir N

2007-05-01

Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes approximately 90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions.

Evolutionary theory and teleology.

PubMed

O'Grady, R T

1984-04-21

The order within and among living systems can be explained rationally by postulating a process of descent with modification, effected by factors which are extrinsic or intrinsic to the organisms. Because at the time Darwin proposed his theory of evolution there was no concept of intrinsic factors which could evolve, he postulated a process of extrinsic effects--natural selection. Biological order was thus seen as an imposed, rather than an emergent, property. Evolutionary change was seen as being determined by the functional efficiency (adaptedness) of the organism in its environment, rather than by spontaneous changes in intrinsically generated organizing factors. The initial incompleteness of Darwin's explanatory model, and the axiomatization of its postulates in neo-Darwinism, has resulted in a theory of functionalism, rather than structuralism. As such, it introduces an unnecessary teleology which confounds evolutionary studies and reduces the usefulness of the theory. This problem cannot be detected from within the neo-Darwinian paradigm because the different levels of end-directed activity--teleomatic, teleonomic, and teleological--are not recognized. They are, in fact, considered to influence one another. The theory of nonequilibrium evolution avoids these problems by returning to the basic principles of biological order and developing a structuralist explanation of intrinsically generated change. Extrinsic factors may affect the resultant evolutionary pattern, but they are neither necessary nor sufficient for evolution to occur.

Topology-based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions.

PubMed

Ganguly, Debabani; Chen, Jianhan

2011-04-01

Coupled binding and folding is frequently involved in specific recognition of so-called intrinsically disordered proteins (IDPs), a newly recognized class of proteins that rely on a lack of stable tertiary fold for function. Here, we exploit topology-based Gō-like modeling as an effective tool for the mechanism of IDP recognition within the theoretical framework of minimally frustrated energy landscape. Importantly, substantial differences exist between IDPs and globular proteins in both amino acid sequence and binding interface characteristics. We demonstrate that established Gō-like models designed for folded proteins tend to over-estimate the level of residual structures in unbound IDPs, whereas under-estimating the strength of intermolecular interactions. Such systematic biases have important consequences in the predicted mechanism of interaction. A strategy is proposed to recalibrate topology-derived models to balance intrinsic folding propensities and intermolecular interactions, based on experimental knowledge of the overall residual structure level and binding affinity. Applied to pKID/KIX, the calibrated Gō-like model predicts a dominant multistep sequential pathway for binding-induced folding of pKID that is initiated by KIX binding via the C-terminus in disordered conformations, followed by binding and folding of the rest of C-terminal helix and finally the N-terminal helix. This novel mechanism is consistent with key observations derived from a recent NMR titration and relaxation dispersion study and provides a molecular-level interpretation of kinetic rates derived from dispersion curve analysis. These case studies provide important insight into the applicability and potential pitfalls of topology-based modeling for studying IDP folding and interaction in general. Copyright © 2011 Wiley-Liss, Inc.

Intrinsic transmission magnetic circular dichroism spectra of GaMnAs

NASA Astrophysics Data System (ADS)

Terada, Hiroshi; Ohya, Shinobu; Tanaka, Masaaki

2018-03-01

Transmission magnetic circular dichroism (MCD) spectroscopy has been widely used to reveal the spin-dependent band structure of ferromagnetic semiconductors. In these previous studies, some band pictures have been proposed from the spectral shapes observed in transmission MCD; however, extrinsic signals originating from optical interference have not been appropriately considered. In this study, we calculate the MCD spectra taking into account the optical interference of the layered structure of samples and show that the spectral shape of MCD is strongly influenced by optical interference. To correctly understand the transmission MCD, we also calculate the intrinsic MCD spectra of GaMnAs that are not influenced by the optical interference. The spectral shape of the intrinsic MCD can be explained by the characteristic band structure of GaMnAs, that is, the spin-polarized valence band and the impurity band existing above the valence band top.

Faraday dispersion functions of galaxies

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

Ideguchi, Shinsuke; Tashiro, Yuichi; Takahashi, Keitaro

2014-09-01

The Faraday dispersion function (FDF), which can be derived from an observed polarization spectrum by Faraday rotation measure synthesis, is a profile of polarized emissions as a function of Faraday depth. We study intrinsic FDFs along sight lines through face-on Milky Way like galaxies by means of a sophisticated galactic model incorporating three-dimensional MHD turbulence, and investigate how much information the FDF intrinsically contains. Since the FDF reflects distributions of thermal and cosmic-ray electrons as well as magnetic fields, it has been expected that the FDF could be a new probe to examine internal structures of galaxies. We, however, findmore » that an intrinsic FDF along a sight line through a galaxy is very complicated, depending significantly on actual configurations of turbulence. We perform 800 realizations of turbulence and find no universal shape of the FDF even if we fix the global parameters of the model. We calculate the probability distribution functions of the standard deviation, skewness, and kurtosis of FDFs and compare them for models with different global parameters. Our models predict that the presence of vertical magnetic fields and the large-scale height of cosmic-ray electrons tend to make the standard deviation relatively large. In contrast, the differences in skewness and kurtosis are relatively less significant.« less

Novel Intrinsic Ignition Method Measuring Local-Global Integration Characterizes Wakefulness and Deep Sleep

PubMed Central

Tagliazucchi, Enzo; Sanjuán, Ana

2017-01-01

Abstract A precise definition of a brain state has proven elusive. Here, we introduce the novel local-global concept of intrinsic ignition characterizing the dynamical complexity of different brain states. Naturally occurring intrinsic ignition events reflect the capability of a given brain area to propagate neuronal activity to other regions, giving rise to different levels of integration. The ignitory capability of brain regions is computed by the elicited level of integration for each intrinsic ignition event in each brain region, averaged over all events. This intrinsic ignition method is shown to clearly distinguish human neuroimaging data of two fundamental brain states (wakefulness and deep sleep). Importantly, whole-brain computational modelling of this data shows that at the optimal working point is found where there is maximal variability of the intrinsic ignition across brain regions. Thus, combining whole brain models with intrinsic ignition can provide novel insights into underlying mechanisms of brain states. PMID:28966977

Novel Intrinsic Ignition Method Measuring Local-Global Integration Characterizes Wakefulness and Deep Sleep.

PubMed

Deco, Gustavo; Tagliazucchi, Enzo; Laufs, Helmut; Sanjuán, Ana; Kringelbach, Morten L

2017-01-01

A precise definition of a brain state has proven elusive. Here, we introduce the novel local-global concept of intrinsic ignition characterizing the dynamical complexity of different brain states. Naturally occurring intrinsic ignition events reflect the capability of a given brain area to propagate neuronal activity to other regions, giving rise to different levels of integration. The ignitory capability of brain regions is computed by the elicited level of integration for each intrinsic ignition event in each brain region, averaged over all events. This intrinsic ignition method is shown to clearly distinguish human neuroimaging data of two fundamental brain states (wakefulness and deep sleep). Importantly, whole-brain computational modelling of this data shows that at the optimal working point is found where there is maximal variability of the intrinsic ignition across brain regions. Thus, combining whole brain models with intrinsic ignition can provide novel insights into underlying mechanisms of brain states.

FORTRAN multitasking library for use on the ELXSI 6400 and the CRAY XMP

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

Montry, G.R.

1985-07-16

A library of FORTRAN-based multitasking routines has been written for the ELXSI 6400 and the CRAY XMP. This library is designed to make multitasking codes easily transportable between machines with different hardware configurations. The library provides enhanced error checking and diagnostics over vendor-supplied multitasking intrinsics. The library also contains multitasking control structures not normally supplied by the vendor.

Sibling rivalry: intrinsic luminescence from two xanthene dye monoanions, resorufin and fluorescein, provides evidence for excited-state proton transfer in the latter.

PubMed

Kjær, Christina; Brøndsted Nielsen, Steen; Stockett, Mark H

2017-09-20

While the emission spectrum of fluorescein monoanions isolated in vacuo displays a broad and featureless band, that of resorufin, also belonging to the xanthene family, has a sharp band maximum, clear vibronic structure, and experiences a small Stokes shift. Excited-state proton transfer in fluorescein can account for the differences.

Characterization and manipulation of individual defects in insulating hexagonal boron nitride using scanning tunnelling microscopy.

PubMed

Wong, Dillon; Velasco, Jairo; Ju, Long; Lee, Juwon; Kahn, Salman; Tsai, Hsin-Zon; Germany, Chad; Taniguchi, Takashi; Watanabe, Kenji; Zettl, Alex; Wang, Feng; Crommie, Michael F

2015-11-01

Defects play a key role in determining the properties and technological applications of nanoscale materials and, because they tend to be highly localized, characterizing them at the single-defect level is of particular importance. Scanning tunnelling microscopy has long been used to image the electronic structure of individual point defects in conductors, semiconductors and ultrathin films, but such single-defect electronic characterization remains an elusive goal for intrinsic bulk insulators. Here, we show that individual native defects in an intrinsic bulk hexagonal boron nitride insulator can be characterized and manipulated using a scanning tunnelling microscope. This would typically be impossible due to the lack of a conducting drain path for electrical current. We overcome this problem by using a graphene/boron nitride heterostructure, which exploits the atomically thin nature of graphene to allow the visualization of defect phenomena in the underlying bulk boron nitride. We observe three different defect structures that we attribute to defects within the bulk insulating boron nitride. Using scanning tunnelling spectroscopy we obtain charge and energy-level information for these boron nitride defect structures. We also show that it is possible to manipulate the defects through voltage pulses applied to the scanning tunnelling microscope tip.

Brain Structural Integrity and Intrinsic Functional Connectivity Forecast 6 Year Longitudinal Growth in Children's Numerical Abilities.

PubMed

Evans, Tanya M; Kochalka, John; Ngoon, Tricia J; Wu, Sarah S; Qin, Shaozheng; Battista, Christian; Menon, Vinod

2015-08-19

Early numerical proficiency lays the foundation for acquiring quantitative skills essential in today's technological society. Identification of cognitive and brain markers associated with long-term growth of children's basic numerical computation abilities is therefore of utmost importance. Previous attempts to relate brain structure and function to numerical competency have focused on behavioral measures from a single time point. Thus, little is known about the brain predictors of individual differences in growth trajectories of numerical abilities. Using a longitudinal design, with multimodal imaging and machine-learning algorithms, we investigated whether brain structure and intrinsic connectivity in early childhood are predictive of 6 year outcomes in numerical abilities spanning childhood and adolescence. Gray matter volume at age 8 in distributed brain regions, including the ventrotemporal occipital cortex (VTOC), the posterior parietal cortex, and the prefrontal cortex, predicted longitudinal gains in numerical, but not reading, abilities. Remarkably, intrinsic connectivity analysis revealed that the strength of functional coupling among these regions also predicted gains in numerical abilities, providing novel evidence for a network of brain regions that works in concert to promote numerical skill acquisition. VTOC connectivity with posterior parietal, anterior temporal, and dorsolateral prefrontal cortices emerged as the most extensive network predicting individual gains in numerical abilities. Crucially, behavioral measures of mathematics, IQ, working memory, and reading did not predict children's gains in numerical abilities. Our study identifies, for the first time, functional circuits in the human brain that scaffold the development of numerical skills, and highlights potential biomarkers for identifying children at risk for learning difficulties. Children show substantial individual differences in math abilities and ease of math learning. Early numerical abilities provide the foundation for future academic and professional success in an increasingly technological society. Understanding the early identification of poor math skills has therefore taken on great significance. This work provides important new insights into brain structure and connectivity measures that can predict longitudinal growth of children's math skills over a 6 year period, and may eventually aid in the early identification of children who might benefit from targeted interventions. Copyright © 2015 the authors 0270-6474/15/3511743-08$15.00/0.

Temporal structure of neuronal population oscillations with empirical model decomposition

NASA Astrophysics Data System (ADS)

Li, Xiaoli

2006-08-01

Frequency analysis of neuronal oscillation is very important for understanding the neural information processing and mechanism of disorder in the brain. This Letter addresses a new method to analyze the neuronal population oscillations with empirical mode decomposition (EMD). Following EMD of neuronal oscillation, a series of intrinsic mode functions (IMFs) are obtained, then Hilbert transform of IMFs can be used to extract the instantaneous time frequency structure of neuronal oscillation. The method is applied to analyze the neuronal oscillation in the hippocampus of epileptic rats in vivo, the results show the neuronal oscillations have different descriptions during the pre-ictal, seizure onset and ictal periods of the epileptic EEG at the different frequency band. This new method is very helpful to provide a view for the temporal structure of neural oscillation.

Local electrical properties of thermally grown oxide films formed on duplex stainless steel surfaces

NASA Astrophysics Data System (ADS)

Guo, L. Q.; Yang, B. J.; He, J. Y.; Qiao, L. J.

2018-06-01

The local electrical properties of thermally grown oxide films formed on ferrite and austenite surfaces of duplex stainless steel at different temperatures were investigated by Current sensing atomic force microscopy, X-ray Photoelectron Spectroscopy (XPS) and Auger Electron Spectroscopy (AES). The current maps and XPS/AES analyses show that the oxide films covering austenite and ferrite surfaces formed at different temperatures exhibit different local electrical characteristics, thickness and composition. The dependence of electrical conductivity of oxide films covering austenite and ferrite surface on the formation temperature is attributed to the film thickness and semiconducting structures, which is intrinsically related to thermodynamics and kinetics process of film grown at different temperature. This is well elucidated by corresponding semiconductor band structures of oxide films formed on austenite and ferrite phases at different temperature.

Small band gap superlattices as intrinsic long wavelength infrared detector materials

NASA Technical Reports Server (NTRS)

Smith, Darryl L.; Mailhiot, C.

1990-01-01

Intrinsic long wavelength (lambda greater than or equal to 10 microns) infrared (IR) detectors are currently made from the alloy (Hg, Cd)Te. There is one parameter, the alloy composition, which can be varied to control the properties of this material. The parameter is chosen to set the band gap (cut-off wavelength). The (Hg, Cd)Te alloy has the zincblend crystal structure. Consequently, the electron and light-hole effective masses are essentially inversely proportional to the band gap. As a result, the electron and light-hole effective masses are very small (M sub(exp asterisk)/M sub o approx. M sub Ih/M sub o approx. less than 0.01) whereas the heavy-hole effective mass is ordinary size (M sub hh(exp asterisk)/M sub o approx. 0.4) for the alloy compositions required for intrinsic long wavelength IR detection. This combination of effective masses leads to rather easy tunneling and relatively large Auger transition rates. These are undesirable characteristics, which must be designed around, of an IR detector material. They follow directly from the fact that (Hg, Cd)Te has the zincblend crystal structure and a small band gap. In small band gap superlattices, such as HgTe/CdTe, In(As, Sb)/InSb and InAs/(Ga,In)Sb, the band gap is determined by the superlattice layer thicknesses as well as by the alloy composition (for superlattices containing an alloy). The effective masses are not directly related to the band gap and can be separately varied. In addition, both strain and quantum confinement can be used to split the light-hole band away from the valence band maximum. These band structure engineering options can be used to reduce tunneling probabilities and Auger transition rates compared with a small band gap zincblend structure material. Researchers discuss the different band structure engineering options for the various classes of small band gap superlattices.

Intrinsic aspirations and personal meaning across adulthood: conceptual interrelations and age/sex differences.

PubMed

Morgan, Jessica; Robinson, Oliver

2013-05-01

The present study examined adult age and sex differences in self-reported aspirations and personal meaning. Young, midlife, and older adults (N = 2,557) from the United Kingdom or United States completed an online survey of their aspiration striving, aspiration importance, and personal meaning (subscales of Purposeful Life, Exciting Life, Accomplished Life, Principled Life, Valued Life). Predictions were made in line with humanistic and gerontology theories, which suggest that sources of personal meaning consolidate across the life span toward intrinsically motivated pursuits. Findings supported these predictions, showing that although there was a tendency for aspirations to decline with age, the proportion of intrinsically motivated aspirations increased, as did total meaning and the interrelationship between meaning and intrinsic aspirations. There were also gender differences in personal meaning and aspirations, which suggested a more pronounced midlife dip in intrinsic and purposive goal striving for men, and a greater focus on intrinsic aspirations in women. Developmental and cohort interpretations of these findings and directions for further research are discussed.

Assessing Individual-Level Factors Supporting Student Intrinsic Motivation in Online Discussions: A Qualitative Study

ERIC Educational Resources Information Center

Shroff, Ronnie H.; Vogel, Douglas R.; Coombes, John

2008-01-01

Research has established that intrinsic motivation has a positive effect on learning and academic achievement. However, little is known about the impact of different technology-supported learning activities on student intrinsic motivation or whether such learning activities significantly enhance student intrinsic motivation compared to traditional…

A fabrication guide for planar silicon quantum dot heterostructures

NASA Astrophysics Data System (ADS)

Spruijtenburg, Paul C.; Amitonov, Sergey V.; van der Wiel, Wilfred G.; Zwanenburg, Floris A.

2018-04-01

We describe important considerations to create top-down fabricated planar quantum dots in silicon, often not discussed in detail in literature. The subtle interplay between intrinsic material properties, interfaces and fabrication processes plays a crucial role in the formation of electrostatically defined quantum dots. Processes such as oxidation, physical vapor deposition and atomic-layer deposition must be tailored in order to prevent unwanted side effects such as defects, disorder and dewetting. In two directly related manuscripts written in parallel we use techniques described in this work to create depletion-mode quantum dots in intrinsic silicon, and low-disorder silicon quantum dots defined with palladium gates. While we discuss three different planar gate structures, the general principles also apply to 0D and 1D systems, such as self-assembled islands and nanowires.

Use of layer strains in strained-layer superlattices to make devices for operation in new wavelength ranges, E. G. , InAsSb at 8 to 12. mu. m. [InAs/sub 1-x/Sb/sub x/

DOEpatents

Osbourn, G.C.

1983-10-06

An intrinsic semiconductor electro-optical device comprises a p-n junction intrinsically responsive, when cooled, to electromagnetic radiation in the wavelength range of 8 to 12 ..mu..m. This radiation responsive p-n junction comprises a strained-layer superlattice (SLS) of alternating layers of two different III-V semiconductors. The lattice constants of the two semiconductors are mismatched, whereby a total strain is imposed on each pair of alternating semiconductor layers in the SLS structure, the proportion of the total strain which acts on each layer of the pair being proportional to the ratio of the layer thicknesses of each layer in the pair.

Compensatory Evolution of Intrinsic Transcription Terminators in Bacillus Cereus

PubMed Central

Safina, Ksenia R.; Mironov, Andrey A.

2017-01-01

Many RNA molecules possess complicated secondary structure critical to their function. Mutations in double-helical regions of RNA may disrupt Watson–Crick (WC) interactions causing structure destabilization or even complete loss of function. Such disruption can be compensated by another mutation restoring base pairing, as has been shown for mRNA, rRNA and tRNA. Here, we investigate the evolution of intrinsic transcription terminators between closely related strains of Bacillus cereus. While the terminator structure is maintained by strong natural selection, as evidenced by the low frequency of disrupting mutations, we observe multiple instances of pairs of disrupting-compensating mutations in RNA structure stems. Such two-step switches between different WC pairs occur very fast, consistent with the low fitness conferred by the intermediate non-WC variant. Still, they are not instantaneous, and probably involve transient fixation of the intermediate variant. The GU wobble pair is the most frequent intermediate, and remains fixed longer than other intermediates, consistent with its less disruptive effect on the RNA structure. Double switches involving non-GU intermediates are more frequent at the ends of RNA stems, probably because they are associated with smaller fitness loss. Together, these results show that the fitness landscape of bacterial transcription terminators is rather rugged, but that the fitness valleys associated with unpaired stem nucleotides are rather shallow, facilitating evolution. PMID:28201729

Phase space interrogation of the empirical response modes for seismically excited structures

NASA Astrophysics Data System (ADS)

Paul, Bibhas; George, Riya C.; Mishra, Sudib K.

2017-07-01

Conventional Phase Space Interrogation (PSI) for structural damage assessment relies on exciting the structure with low dimensional chaotic waveform, thereby, significantly limiting their applicability to large structures. The PSI technique is presently extended for structure subjected to seismic excitations. The high dimensionality of the phase space for seismic response(s) are overcome by the Empirical Mode Decomposition (EMD), decomposing the responses to a number of intrinsic low dimensional oscillatory modes, referred as Intrinsic Mode Functions (IMFs). Along with their low dimensionality, a few IMFs, retain sufficient information of the system dynamics to reflect the damage induced changes. The mutually conflicting nature of low-dimensionality and the sufficiency of dynamic information are taken care by the optimal choice of the IMF(s), which is shown to be the third/fourth IMFs. The optimal IMF(s) are employed for the reconstruction of the Phase space attractor following Taken's embedding theorem. The widely referred Changes in Phase Space Topology (CPST) feature is then employed on these Phase portrait(s) to derive the damage sensitive feature, referred as the CPST of the IMFs (CPST-IMF). The legitimacy of the CPST-IMF is established as a damage sensitive feature by assessing its variation with a number of damage scenarios benchmarked in the IASC-ASCE building. The damage localization capability, remarkable tolerance to noise contamination and the robustness under different seismic excitations of the feature are demonstrated.

The fragmented self: imbalance between intrinsic and extrinsic self-networks in psychotic disorders.

PubMed

Ebisch, Sjoerd J H; Aleman, André

2016-08-01

Self-disturbances are among the core features of schizophrenia and related psychotic disorders. The basic structure of the self could depend on the balance between intrinsic and extrinsic self-processing. We discuss studies on self-related processing in psychotic disorders that provide converging evidence for disrupted communication between neural networks subserving the so-called intrinsic self and extrinsic self. This disruption might be mainly caused by impaired integrity of key brain hubs. The intrinsic self has been associated with cortical midline structures involved in self-referential processing, autobiographical memory, and emotional evaluation. Additionally, we highlight central aspects of the extrinsic self in its interaction with the environment using sensorimotor networks, including self-experience in sensation and actions. A deficient relationship between these self-aspects because of disrupted between-network interactions offers a framework to explain core clinical features of psychotic disorders. In particular, we show how relative isolation and reduced modularity of networks subserving intrinsic and extrinsic self-processing might trigger the emergence of hallucinations and delusions, and why patients with psychosis typically have difficulties with self-other relationships and do not recognise mental problems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Partner-Mediated Polymorphism of an Intrinsically Disordered Protein.

PubMed

Bignon, Christophe; Troilo, Francesca; Gianni, Stefano; Longhi, Sonia

2017-11-29

Intrinsically disordered proteins (IDPs) recognize their partners through molecular recognition elements (MoREs). The MoRE of the C-terminal intrinsically disordered domain of the measles virus nucleoprotein (N TAIL ) is partly pre-configured as an α-helix in the free form and undergoes α-helical folding upon binding to the X domain (XD) of the viral phosphoprotein. Beyond XD, N TAIL also binds the major inducible heat shock protein 70 (hsp70). So far, no structural information is available for the N TAIL /hsp70 complex. Using mutational studies combined with a protein complementation assay based on green fluorescent protein reconstitution, we have investigated both N TAIL /XD and N TAIL /hsp70 interactions. Although the same N TAIL region binds the two partners, the binding mechanisms are different. Hsp70 binding is much more tolerant of MoRE substitutions than XD, and the majority of substitutions lead to an increased N TAIL /hsp70 interaction strength. Furthermore, while an increased and a decreased α-helicity of the MoRE lead to enhanced and reduced interaction strength with XD, respectively, the impact on hsp70 binding is negligible, suggesting that the MoRE does not adopt an α-helical conformation once bound to hsp70. Here, by showing that the α-helical conformation sampled by the free form of the MoRE does not systematically commit it to adopt an α-helical conformation in the bound form, we provide an example of partner-mediated polymorphism of an IDP and of the relative insensitiveness of the bound structure to the pre-recognition state. The present results therefore contribute to shed light on the molecular mechanisms by which IDPs recognize different partners. Copyright © 2017 Elsevier Ltd. All rights reserved.

Intrinsic group behaviour: Dependence of pedestrian dyad dynamics on principal social and personal features

PubMed Central

Yücel, Zeynep; Brščić, Dražen; Kanda, Takayuki; Hagita, Norihiro

2017-01-01

Being determined by human social behaviour, pedestrian group dynamics may depend on “intrinsic properties” such as the purpose of the pedestrians, their personal relation, gender, age, and body size. In this work we investigate the dynamical properties of pedestrian dyads (distance, spatial formation and velocity) by analysing a large data set of automatically tracked pedestrian trajectories in an unconstrained “ecological” setting (a shopping mall), whose apparent physical and social group properties have been analysed by three different human coders. We observed that females walk slower and closer than males, that workers walk faster, at a larger distance and more abreast than leisure oriented people, and that inter-group relation has a strong effect on group structure, with couples walking very close and abreast, colleagues walking at a larger distance, and friends walking more abreast than family members. Pedestrian height (obtained automatically through our tracking system) influences velocity and abreast distance, both growing functions of the average group height. Results regarding pedestrian age show that elderly people walk slowly, while active age adults walk at the maximum velocity. Groups with children have a strong tendency to walk in a non-abreast formation, with a large distance (despite a low abreast distance). A cross-analysis of the interplay between these intrinsic features, taking in account also the effect of an “extrinsic property” such as crowd density, confirms these major results but reveals also a richer structure. An interesting and unexpected result, for example, is that the velocity of groups with children increases with density, at least in the low-medium density range found under normal conditions in shopping malls. Children also appear to behave differently according to the gender of the parent. PMID:29095913

Intrinsic group behaviour: Dependence of pedestrian dyad dynamics on principal social and personal features.

PubMed

Zanlungo, Francesco; Yücel, Zeynep; Brščić, Dražen; Kanda, Takayuki; Hagita, Norihiro

2017-01-01

Being determined by human social behaviour, pedestrian group dynamics may depend on "intrinsic properties" such as the purpose of the pedestrians, their personal relation, gender, age, and body size. In this work we investigate the dynamical properties of pedestrian dyads (distance, spatial formation and velocity) by analysing a large data set of automatically tracked pedestrian trajectories in an unconstrained "ecological" setting (a shopping mall), whose apparent physical and social group properties have been analysed by three different human coders. We observed that females walk slower and closer than males, that workers walk faster, at a larger distance and more abreast than leisure oriented people, and that inter-group relation has a strong effect on group structure, with couples walking very close and abreast, colleagues walking at a larger distance, and friends walking more abreast than family members. Pedestrian height (obtained automatically through our tracking system) influences velocity and abreast distance, both growing functions of the average group height. Results regarding pedestrian age show that elderly people walk slowly, while active age adults walk at the maximum velocity. Groups with children have a strong tendency to walk in a non-abreast formation, with a large distance (despite a low abreast distance). A cross-analysis of the interplay between these intrinsic features, taking in account also the effect of an "extrinsic property" such as crowd density, confirms these major results but reveals also a richer structure. An interesting and unexpected result, for example, is that the velocity of groups with children increases with density, at least in the low-medium density range found under normal conditions in shopping malls. Children also appear to behave differently according to the gender of the parent.

Intrinsic and Extrinsic Motivational Orientations in the Classroom: Age Differences and Academic Correlates

ERIC Educational Resources Information Center

Lepper, Mark R.; Corpus, Jennifer Henderlong; Iyengar, Sheena S.

2005-01-01

Age differences in intrinsic and extrinsic motivation and the relationships of each to academic outcomes were examined in an ethnically diverse sample of 797 3rd-grade through 8th-grade children. Using independent measures, the authors found intrinsic and extrinsic motivation to be only moderately correlated, suggesting that they may be largely…

Motivational Profiles of Medical Students of Nepalese Army Institute of Health Sciences.

PubMed

Shrestha, Lochana; Pant, Shambhu Nath

2018-01-01

Students enter the medical study with different types of motives. Given the importance of academic motivation for good academic achievement of the students, the present study was designed to reveal the possible relationship between academic motivation and achievement in medical students. In this cross-sectional study medical students (N=364) of Nepalese Army institute of Health Sciences were participated and classified to different subgroups using intrinsic and controlled motivation scores. Cluster membership was used as an independent variable to assess differences in study strategies and academic performance. Four clusters were obtained: High Intrinsic High Controlled, Low Intrinsic High Controlled, High Intrinsic Low Controlled, and Low Intrinsic Low Controlled. High Intrinsic High Controlled and High Intrinsic Low Controlled profile students constituted 36.1%, 22.6% of the population, respectively. No significant differences were observed as regards to deep strategy and surface strategy between high interest status motivated and high interest-motivated students. However, both of the clusters had significantly deeper, surface strategy and better academic performance than status-motivated and low-motivation clusters (p < 0.001). The interest status motivated and interest-motivated medical students were associated with good deep and surface study strategy and good academic performance. Low-motivation and status-motivated students were associated with the least academic performance with less interest learning behaviors. This reflected that motivation is important required component for good learning outcomes for medical students Keywords: Academic performance; controlled motivation; clusters; intrinsic motivation; motivation.

Room Temperature Silicene Field-Effect Transistors

NASA Astrophysics Data System (ADS)

Akinwande, Deji

Silicene, a buckled Si analogue of graphene, holds significant promise for future electronics beyond traditional CMOS. In our predefined experiments via encapsulated delamination with native electrodes approach, silicene devices exhibit an ambipolar charge transport behavior, corroborating theories on Dirac band in Ag-free silicene. Monolayer silicene device has extracted field-effect mobility within the theoretical expectation and ON/OFF ratio greater than monolayer graphene, while multilayer silicene devices show decreased mobility and gate modulation. Air-stability of silicene devices depends on the number of layers of silicene and intrinsic material structure determined by growth temperature. Few or multi-layer silicene devices maintain their ambipolar behavior for days in contrast to minutes time scale for monolayer counterparts under similar conditions. Multilayer silicene grown at different temperatures below 300oC possess different intrinsic structures and yield different electrical property and air-stability. This work suggests a practical prospect to enable more air-stable silicene devices with layer and growth condition control, which can be leveraged for other air-sensitive 2D materials. In addition, we describe quantum and classical transistor device concepts based on silicene and related buckled materials that exploit the 2D topological insulating phenomenon. The transistor device physics offer the potential for ballistic transport that is robust against scattering and can be employed for both charge and spin transport. This work was supported by the ARO.

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient.

PubMed

Orihuela, Rodrigo L L; Peres, Carlos A; Mendes, Gabriel; Jarenkow, João A; Tabarelli, Marcelo

2015-01-01

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide.

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient

PubMed Central

Orihuela, Rodrigo L. L.; Peres, Carlos A.; Mendes, Gabriel; Jarenkow, João A.; Tabarelli, Marcelo

2015-01-01

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide. PMID:26309252

Factor VIII organisation on nanodiscs with different lipid composition.

PubMed

Grushin, Kirill; Miller, Jaimy; Dalm, Daniela; Stoilova-McPhie, Svetla

2015-04-01

Nanodiscs (ND) are lipid bilayer membrane patches held by amphiphilic scaffolding proteins (MSP) of ~10 nm in diameter. Nanodiscs have been developed as lipid nanoplatforms for structural and functional studies of membrane and membrane associated proteins. Their size and monodispersity have rendered them unique for electron microscopy (EM) and single particle analysis studies of proteins and complexes either spanning or associated to the ND membrane. Binding of blood coagulation factors and complexes, such as the Factor VIII (FVIII) and the Factor VIIIa - Factor IXa (intrinsic tenase) complex to the negatively charged activated platelet membrane is required for normal haemostasis. In this study we present our work on optimising ND, specifically designed to bind FVIII at close to physiological conditions. The binding of FVIII to the negatively charged ND rich in phosphatidylserine (PS) was followed by electron microscopy at three different PS compositions and two different membrane scaffolding protein (MSP1D1) to lipid ratios. Our results show that the ND with highest PS content (80 %) and lowest MSP1D1 to lipid ratio (1:47) are the most suitable for structure determination of the membrane-bound FVIII by single particle EM. Our preliminary FVIII 3D reconstruction as bound to PS containing ND demonstrates the suitability of the optimised ND for structural studies by EM. Further assembly of the activated FVIII form (FVIIIa) and the whole FVIIIa-FIXa complex on ND, followed by EM and single particle reconstruction will help to identify the protein-protein and protein-membrane interfaces critical for the intrinsic tenase complex assembly and function.

Direct Evidence of Intrinsic Blue Fluorescence from Oligomeric Interfaces of Human Serum Albumin.

PubMed

Bhattacharya, Arpan; Bhowmik, Soumitra; Singh, Amit K; Kodgire, Prashant; Das, Apurba K; Mukherjee, Tushar Kanti

2017-10-10

The molecular origin behind the concentration-dependent intrinsic blue fluorescence of human serum albumin (HSA) is not known yet. This unusual blue fluorescence is believed to be a characteristic feature of amyloid-like fibrils of protein/peptide and originates due to the delocalization of peptide bond electrons through the extended hydrogen bond networks of cross-β-sheet structure. Herein, by combining the results of spectroscopy, size exclusion chromatography, native gel electrophoresis, and confocal microscopy, we have shown that the intrinsic blue fluorescence of HSA exclusively originates from oligomeric interfaces devoid of any amyloid-like fibrillar structure. Our study suggests that this low energy fluorescence band is not due to any particular residue/sequence, but rather it is a common feature of self-assembled peptide bonds. The present findings of intrinsic blue fluorescence from oligomeric interfaces pave the way for future applications of this unique visual phenomenon for early stage detection of various protein aggregation related human diseases.

Bi-alkali antimonide photocathode growth: An X-ray diffraction study

DOE PAGES

Schubert, Susanne; Wong, Jared; Feng, Jun; ...

2016-07-21

Bi-alkali antimonide photocathodes are one of the best known sources of electrons for high current and/or high bunch charge applications like Energy Recovery Linacs or Free Electron Lasers. Despite their high quantum efficiency in visible light and low intrinsic emittance, the surface roughness of these photocathodes prohibits their use as low emittance cathodes in high accelerating gradient superconducting and normal conducting radio frequency photoguns and limits the minimum possible intrinsic emittance near the threshold. Also, the growth process for these materials is largely based on recipes obtained by trial and error and is very unreliable. In this paper, using X-raymore » diffraction, we investigate the different structural and chemical changes that take place during the growth process of the bi-alkali antimonide material K 2 CsSb. Our measurements give us a deeper understanding of the growth process of alkali-antimonide photocathodes allowing us to optimize it with the goal of minimizing the surface roughness to preserve the intrinsic emittance at high electric fields and increasing its reproducibility.« less

Claustrum of the short-tailed fruit bat, Carollia perspicillata: Alignment of cellular orientation and functional connectivity.

PubMed

Orman, Rena; Kollmar, Richard; Stewart, Mark

2017-04-15

The claustrum is a gray-matter structure that underlies neocortex and reciprocates connections with cortical and subcortical targets. In lower mammals, the claustrum is directly adjacent to neocortex, making the definition of claustral boundaries challenging. Latexin, an endogenous inhibitor of metallocarboxypeptidases, localizes to claustral cells, enabling a clear delineation of claustrum. Given its proportionately large claustrum, we hypothesized that the short-tailed fruit bat, Carollia perspicillata, can be a useful model for claustral structure-function relations. We used latexin immunohistochemistry to identify claustral boundaries and intrinsic structure and multielectrode recordings from brain slices to explore intrinsic excitatory connectivity of the claustrum. Carollia's claustrum contains cells whose intrinsic connectivity and alignment permit the generation of spontaneous, synchronous population events and mirror their pattern of spread in disinhibited brain slices over millimeters. Carollia shows cellular alignment and spontaneous population-activity spread along both horizontal and dorsoventral axes. Carollia claustrum possesses intrinsic excitatory connectivity sufficient to: 1) generate single, spontaneous, synchronized burst discharges, 2) support activity spread along axes where claustral cells are aligned, and 3), because of multiple axes for cell alignment, support activity spread along both rostrocaudal and dorsoventral axes. The smaller event sizes in bat claustrum compared with rat claustrum are consistent with events occurring in population subsets rather than the full claustral cell population. The overall size of claustrum, its pronounced vascularity, and its more complex intrinsic connectivity than rat suggest that the bat is an animal model for claustral structure and function that will permit unique access to claustrum's processing capabilities. J. Comp. Neurol. 525:1459-1474, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Study on CO2 gasification reactivity and physical characteristics of biomass, petroleum coke and coal chars.

PubMed

Huo, Wei; Zhou, Zhijie; Chen, Xueli; Dai, Zhenghua; Yu, Guangsuo

2014-05-01

Gasification reactivities of six different carbonaceous material chars with CO2 were determined by a Thermogravimetric Analyzer (TGA). Gasification reactivities of biomass chars are higher than those of coke and coal chars. In addition, physical structures and chemical components of these chars were systematically tested. It is found that the crystalline structure is an important factor to evaluate gasification reactivities of different chars and the crystalline structures of biomass chars are less order than those of coke and coal chars. Moreover, initial gasification rates of these chars were measured at high temperatures and with relatively large particle sizes. The method of calculating the effectiveness factor η was used to quantify the effect of pore diffusion on gasification. The results show that differences in pore diffusion effects among gasification with various chars are prominent and can be attributed to different intrinsic gasification reactivities and physical characteristics of different chars. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Subspace Approach to the Structural Decomposition and Identification of Ankle Joint Dynamic Stiffness.

PubMed

Jalaleddini, Kian; Tehrani, Ehsan Sobhani; Kearney, Robert E

2017-06-01

The purpose of this paper is to present a structural decomposition subspace (SDSS) method for decomposition of the joint torque to intrinsic, reflexive, and voluntary torques and identification of joint dynamic stiffness. First, it formulates a novel state-space representation for the joint dynamic stiffness modeled by a parallel-cascade structure with a concise parameter set that provides a direct link between the state-space representation matrices and the parallel-cascade parameters. Second, it presents a subspace method for the identification of the new state-space model that involves two steps: 1) the decomposition of the intrinsic and reflex pathways and 2) the identification of an impulse response model of the intrinsic pathway and a Hammerstein model of the reflex pathway. Extensive simulation studies demonstrate that SDSS has significant performance advantages over some other methods. Thus, SDSS was more robust under high noise conditions, converging where others failed; it was more accurate, giving estimates with lower bias and random errors. The method also worked well in practice and yielded high-quality estimates of intrinsic and reflex stiffnesses when applied to experimental data at three muscle activation levels. The simulation and experimental results demonstrate that SDSS accurately decomposes the intrinsic and reflex torques and provides accurate estimates of physiologically meaningful parameters. SDSS will be a valuable tool for studying joint stiffness under functionally important conditions. It has important clinical implications for the diagnosis, assessment, objective quantification, and monitoring of neuromuscular diseases that change the muscle tone.

A computational study of a novel graphene nanoribbon field effect transistor

NASA Astrophysics Data System (ADS)

Ghoreishi, Seyed Saleh; Yousefi, Reza

2017-04-01

In this paper, using gate structure engineering and modification of channel dopant profile, we propose a new double gate graphene nanoribbon field effect transistor (DG-GNRFET) mainly to suppress the band-to-band tunneling (BTBT) of carriers. In the new device, the intrinsic part of the channel is replaced by an intrinsic-lightly doped-intrinsic (I -N--I) configuration in a way that only the intrinsic parts are covered by the gate contact. Transport characteristics of the device are investigated theoretically using the nonequilibrium Green’s function (NEGF) formalism. Numerical simulations show that off-current, ambipolar behavior, on/off-current ratio and the switching characteristics such as intrinsic delay and power-delay product are improved. In addition, the new device demonstrates better sub-threshold swing and less drain-induced barrier lowering (DIBL).

Designing a Quantitative Structure-Activity Relationship for the Intrinsic Metabolic Clearance of Environmentally Relevant Chemicals

EPA Science Inventory

Toxicokinetic models serve a vital role in risk assessment by bridging the gap between chemical exposure and potentially toxic endpoints. While intrinsic metabolic clearance rates have a strong impact on toxicokinetics, limited data is available for environmentally relevant chemi...

Intention to Be Physically Active after School Graduation and Its Relationship to Three Types of Intrinsic Motivation

ERIC Educational Resources Information Center

Hein, Vello; Muur, Maret; Koka, Andre

2004-01-01

In this article the relationships between three different types of intrinsic motivation and students' intention to be physically active after school graduation were examined. The participants were 400 school children aged 14-18 years. The modified version of SMS was used to measure the three different types of intrinsic motivation. The intention…

Age-related changes in the plasticity and toughness of human cortical bone at multiple length-scales

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

Zimmermann, Elizabeth A.; Schaible, Eric; Bale, Hrishikesh

2011-08-10

The structure of human cortical bone evolves over multiple length-scales from its basic constituents of collagen and hydroxyapatite at the nanoscale to osteonal structures at nearmillimeter dimensions, which all provide the basis for its mechanical properties. To resist fracture, bone’s toughness is derived intrinsically through plasticity (e.g., fibrillar sliding) at structural-scales typically below a micron and extrinsically (i.e., during crack growth) through mechanisms (e.g., crack deflection/bridging) generated at larger structural-scales. Biological factors such as aging lead to a markedly increased fracture risk, which is often associated with an age-related loss in bone mass (bone quantity). However, we find that age-relatedmore » structural changes can significantly degrade the fracture resistance (bone quality) over multiple lengthscales. Using in situ small-/wide-angle x-ray scattering/diffraction to characterize sub-micron structural changes and synchrotron x-ray computed tomography and in situ fracture-toughness measurements in the scanning electron microscope to characterize effects at micron-scales, we show how these age-related structural changes at differing size-scales degrade both the intrinsic and extrinsic toughness of bone. Specifically, we attribute the loss in toughness to increased non-enzymatic collagen cross-linking which suppresses plasticity at nanoscale dimensions and to an increased osteonal density which limits the potency of crack-bridging mechanisms at micron-scales. The link between these processes is that the increased stiffness of the cross-linked collagen requires energy to be absorbed by “plastic” deformation at higher structural levels, which occurs by the process of microcracking.« less

Innervation of the rabbit cardiac ventricles.

PubMed

Pauziene, Neringa; Alaburda, Paulius; Rysevaite-Kyguoliene, Kristina; Pauza, Audrys G; Inokaitis, Hermanas; Masaityte, Aiste; Rudokaite, Gabriele; Saburkina, Inga; Plisiene, Jurgita; Pauza, Dainius H

2016-01-01

The rabbit is widely used in experimental cardiac physiology, but the neuroanatomy of the rabbit heart remains insufficiently examined. This study aimed to ascertain the architecture of the intrinsic nerve plexus in the walls and septum of rabbit cardiac ventricles. In 51 rabbit hearts, a combined approach involving: (i) histochemical acetylcholinesterase staining of intrinsic neural structures in total cardiac ventricles; (ii) immunofluorescent labelling of intrinsic nerves, nerve fibres (NFs) and neuronal somata (NS); and (iii) transmission electron microscopy of intrinsic ventricular nerves and NFs was used. Mediastinal nerves access the ventral and lateral surfaces of both ventricles at a restricted site between the root of the ascending aorta and the pulmonary trunk. The dorsal surface of both ventricles is supplied by several epicardial nerves extending from the left dorsal ganglionated nerve subplexus on the dorsal left atrium. Ventral accessing nerves are thicker and more numerous than dorsal nerves. Intrinsic ventricular NS are rare on the conus arteriosus and the root of the pulmonary trunk. The number of ventricular NS ranged from 11 to 220 per heart. Four chemical phenotypes of NS within ventricular ganglia were identified, i.e. ganglionic cells positive for choline acetyltransferase (ChAT), neuronal nitric oxide synthase (nNOS), and biphenotypic, i.e. positive for both ChAT/nNOS and for ChAT/tyrosine hydroxylase. Clusters of small intensely fluorescent cells are distributed within or close to ganglia on the root of the pulmonary trunk, but not on the conus arteriosus. The largest and most numerous intrinsic nerves proceed within the epicardium. Scarce nerves were found near myocardial blood vessels, but the myocardium contained only a scarce meshwork of NFs. In the endocardium, large numbers of thin nerves and NFs proceed along the bundle of His and both its branches up to the apex of the ventricles. The endocardial meshwork of fine NFs was approximately eight times denser than the myocardial meshwork. Adrenergic NFs predominate considerably in all layers of the ventricular walls and septum, whereas NFs of other neurochemical phenotypes were in the minority and their amount differed between the epicardium, myocardium and endocardium. The densities of NFs positive for nNOS and ChAT were similar in the epicardium and endocardium, but NFs positive for nNOS in the myocardium were eight times more abundant than NFs positive for ChAT. Potentially sensory NFs positive for both calcitonin gene-related peptide and substance P were sparse in the myocardial layer, but numerous in epicardial nerves and particularly abundant within the endocardium. Electron microscopic observations demonstrate that intrinsic ventricular nerves have a distinctive morphology, which may be attributed to remodelling of the peripheral nerves after their access into the ventricular wall. In conclusion, the rabbit ventricles display complex structural organization of intrinsic ventricular nerves, NFs and ganglionic cells. The results provide a basic anatomical background for further functional analysis of the intrinsic nervous system in the cardiac ventricles. © 2015 Anatomical Society.

Interactive Structure (EUCLID) For Static And Dynamic Representation Of Human Body

NASA Astrophysics Data System (ADS)

Renaud, Ch.; Steck, R.

1983-07-01

A specific software (EUCLID) for static and dynamic representation of human models is described. The data processing system is connected with ERGODATA and used in interactive mode by intrinsic or specific functions. More or less complex representations in 3-D view of models of the human body are developed. Biostereometric and conventional anthropometric raw data from the data bank are processed for different applications in ergonomy.

Solvation and Dynamics of Sodium and Potassium in Ethylene Carbonate from ab Initio Molecular Dynamics Simulations

DOE PAGES

Pham, Tuan Anh; Kweon, Kyoung E.; Samanta, Amit; ...

2017-09-18

The development of sodium and potassium batteries offers a promising way to meet the scaling and cost challenges of energy storage. However, compared to Li +, several intrinsic properties of Na + and K +, including their solvation and dynamics in typical organic electrolytes utilized in battery applications, are less well-understood. Here in this paper, we report a systematic investigation of Na + and K + in ethylene carbonate (EC) using first-principles molecular dynamics simulations. Our simulations reveal significant differences in the solvation structure and dynamical properties of Na + and K + compared to Li +. We find that,more » in contrast to Li + which exhibits a well-defined first solvation shell, the larger Na+ and K+ ions show more disordered and flexible solvation structures. These differences in solvation were found to significantly influence the ion dynamics, leading to larger diffusion coefficients of Na + and K + compared to Li +. Our simulations also reveal a clear and interesting analog in the behavior of the ions in EC and aqueous environments, particularly in the specific ion effects on the solvent dynamics. Lastly, this work provides fundamental understanding of the intrinsic properties of Na + and K + in organic electrolytes, which may ultimately influence the intercalation mechanism at the electrode–electrolyte interface and therefore battery performance, lifetime, and safety.« less

Concept for a fast analysis method of the energy dissipation at mechanical joints

NASA Astrophysics Data System (ADS)

Wolf, Alexander; Brosius, Alexander

2017-10-01

When designing hybrid parts and structures one major challenge is the design, production and quality assessment of the joining points. While the polymeric composites themselves have excellent material properties, the necessary joints are often the weak link in assembled structures. This paper presents a method of measuring and analysing the energy dissipation at mechanical joining points of hybrid parts. A simplified model is applied based on the characteristic response to different excitation frequencies and amplitudes. The dissipation from damage is the result of relative moments between joining partners und damaged fibres within the composite, whereas the visco-elastic material behaviour causes the intrinsic dissipation. The ambition is to transfer these research findings to the characterisation of mechanical joints in order to quickly assess the general quality of the joint with this non-destructive testing method. The inherent challenge for realising this method is the correct interpretation of the measured energy dissipation and its attribution to either a bad joining point or intrinsic material properties. In this paper the authors present the concept for energy dissipation measurements at different joining points. By inverse analysis a simplified fast semi-analytical model will be developed that allows for a quick basic quality assessment of a given joining point.

Advantages of synchrotron radiation circular dichroism spectroscopy to study intrinsically disordered proteins.

PubMed

Kumagai, Patricia S; DeMarco, Ricardo; Lopes, Jose L S

2017-10-01

The unordered secondary structural content of an intrinsically disordered protein (IDP) is susceptible to conformational changes induced by many different external factors, such as the presence of organic solvents, removal of water, changes in temperature, binding to partner molecules, and interaction with lipids and/or other ligands. In order to characterize the high-flexibility nature of an IDP, circular dichroism (CD) spectroscopy is a particularly useful method due to its capability of monitoring both subtle and remarkable changes in different environments, relative ease in obtaining measurements, the small amount of sample required, and the capability for sample recovery (sample not damaged) and others. Using synchrotron radiation as the light source for CD spectroscopy represents the state-of-the-art version of this technique with feasibility of accessing the lower wavelength UV region, and therefore presenting a series of advantages over conventional circular dichroism (cCD) to monitor a protein conformational behavior, check protein stability, detect ligand binding, and many others. In this paper, we have performed a comparative study using cCD and SRCD methods for investigating the secondary structure and the conformational behavior of natively unfolded proteins: MEG-14 and soybean trypsin inhibitor. We show that the SRCD technique greatly improves the analysis and accuracy of the studies on the conformations of IDPs.

Exploring the Specifications of Spatial Adjacencies and Weights in Bayesian Spatial Modeling with Intrinsic Conditional Autoregressive Priors in a Small-area Study of Fall Injuries

PubMed Central

Law, Jane

2016-01-01

Intrinsic conditional autoregressive modeling in a Bayeisan hierarchical framework has been increasingly applied in small-area ecological studies. This study explores the specifications of spatial structure in this Bayesian framework in two aspects: adjacency, i.e., the set of neighbor(s) for each area; and (spatial) weight for each pair of neighbors. Our analysis was based on a small-area study of falling injuries among people age 65 and older in Ontario, Canada, that was aimed to estimate risks and identify risk factors of such falls. In the case study, we observed incorrect adjacencies information caused by deficiencies in the digital map itself. Further, when equal weights was replaced by weights based on a variable of expected count, the range of estimated risks increased, the number of areas with probability of estimated risk greater than one at different probability thresholds increased, and model fit improved. More importantly, significance of a risk factor diminished. Further research to thoroughly investigate different methods of variable weights; quantify the influence of specifications of spatial weights; and develop strategies for better defining spatial structure of a map in small-area analysis in Bayesian hierarchical spatial modeling is recommended. PMID:29546147

Looking forward, not back: Supporting structuralism in the present.

PubMed

McKenzie, Kerry

2016-10-01

The view that the fundamental kind properties are intrinsic properties enjoys reflexive endorsement by most metaphysicians of science. But ontic structural realists deny that there are any fundamental intrinsic properties at all. Given that structuralists distrust intuition as a guide to truth, and given that we currently lack a fundamental physical theory that we could consult instead to order settle the issue, it might seem as if there is simply nowhere for this debate to go at present. However, I will argue that there exists an as-yet untapped resource for arguing for ontic structuralism - namely, the way that fundamentality is conceptualized in our most fundamental physical frameworks. By arguing that physical objects must be subject to the 'Goldilock's principle' if they are to count as fundamental at all, I argue that we can no longer view the majority of properties defining them as intrinsic. As such, ontic structural realism can be regarded as the most promising metaphysics for fundamental physics, and that this is so even though we do not yet claim to know precisely what that fundamental physics is. Copyright © 2016 Elsevier Ltd. All rights reserved.

Broadening of effective photonic band gaps in biological chiral structures: From intrinsic narrow band gaps to broad band reflection spectra

NASA Astrophysics Data System (ADS)

Vargas, W. E.; Hernández-Jiménez, M.; Libby, E.; Azofeifa, D. E.; Solis, Á.; Barboza-Aguilar, C.

2015-09-01

Under normal illumination with non-polarized light, reflection spectra of the cuticle of golden-like and red Chrysina aurigans scarabs show a structured broad band of left-handed circularly polarized light. The polarization of the reflected light is attributed to a Bouligand-type left-handed chiral structure found through the scarab's cuticle. By considering these twisted structures as one-dimensional photonic crystals, a novel approach is developed from the dispersion relation of circularly polarized electromagnetic waves traveling through chiral media, to show how the broad band characterizing these spectra arises from an intrinsic narrow photonic band gap whose spectral position moves through visible and near-infrared wavelengths.

High and Low Activity Rats: Elevated intrinsic physical activity drives resistance to diet induced obesity in non-bred rats

PubMed Central

Perez-Leighton, Claudio E.; Boland, Kelsey; Billington, Charles; Kotz, Catherine M.

2012-01-01

Humans and rodents show large variability in their individual sensitivity to diet-induced obesity, which has been associated with differences in intrinsic spontaneous physical activity (SPA). Evidence from genetic and out-bred rat obesity models shows that higher activity of the orexin peptides results in higher intrinsic SPA and protection against diet-induced obesity. Based on this, we hypothesized that naturally occurring variation in SPA and orexin signaling activity is sufficient to drive differences in sensitivity to diet-induced obesity. We analyzed orexin activity and sensitivity to diet-induced obesity in non-manipulated male Sprague Dawley rats selected for high and low intrinsic SPA. Our results defined a new model of differential DIO sensitivity, the high-activity and low activity-rats, and suggest that naturally occurring variations in intrinsic SPA cause differences in energy expenditure that are mediated by orexin signaling and alter DIO sensitivity. PMID:23404834

Aging Differences in Ethnic Skin

PubMed Central

Buainain De Castro Maymone, Mayra; Kundu, Roopal V.

2016-01-01

Aging is an inevitable and complex process that can be described clinically as features of wrinkles, sunspots, uneven skin color, and sagging skin. These cutaneous effects are influenced by both intrinsic and extrinsic factors and often are varied based on ethnic origin given underlying structural and functional differences. The authors sought to provide updated information on facets of aging and how it relates to ethnic variation given innate differences in skin structure and function. Publications describing structural and functional principles of ethnic and aging skin were primarily found through a PubMed literature search and supplemented with a review of textbook chapters. The most common signs of skin aging despite skin type are dark spots, loss of elasticity, loss of volume, and rhytides. Skin of color has many characteristics that make its aging process unique. Those of Asian, Hispanic, and African American descent have distinct facial structures. Differences in the concentration of epidermal melanin makes darkly pigmented persons more vulnerable to dyspigmentation, while a thicker and more compact dermis makes facial lines less noticeable. Ethnic skin comprises a large portion of the world population. Therefore, it is important to understand the unique structural and functional differences among ethnicities to adequately treat the signs of aging. PMID:26962390

Multimodal Investigation of Network Level Effects Using Intrinsic Functional Connectivity, Anatomical Covariance, and Structure-to-Function Correlations in Unmedicated Major Depressive Disorder

PubMed Central

Scheinost, Dustin; Holmes, Sophie E; DellaGioia, Nicole; Schleifer, Charlie; Matuskey, David; Abdallah, Chadi G; Hampson, Michelle; Krystal, John H; Anticevic, Alan; Esterlis, Irina

2018-01-01

Converging evidence suggests that major depressive disorder (MDD) affects multiple large-scale brain networks. Analyses of the correlation or covariance of regional brain structure and function applied to structural and functional MRI data may provide insights into systems-level organization and structure-to-function correlations in the brain in MDD. This study applied tensor-based morphometry and intrinsic connectivity distribution to identify regions of altered volume and intrinsic functional connectivity in data from unmedicated individuals with MDD (n=17) and healthy comparison participants (HC, n=20). These regions were then used as seeds for exploratory anatomical covariance and connectivity analyses. Reduction in volume in the anterior cingulate cortex (ACC) and lower structural covariance between the ACC and the cerebellum were observed in the MDD group. Additionally, individuals with MDD had significantly lower whole-brain intrinsic functional connectivity in the medial prefrontal cortex (mPFC). This mPFC region showed altered connectivity to the ventral lateral PFC (vlPFC) and local circuitry in MDD. Global connectivity in the ACC was negatively correlated with reported depressive symptomatology. The mPFC–vlPFC connectivity was positively correlated with depressive symptoms. Finally, we observed increased structure-to-function correlation in the PFC/ACC in the MDD group. Although across all analysis methods and modalities alterations in the PFC/ACC were a common finding, each modality and method detected alterations in subregions belonging to distinct large-scale brain networks. These exploratory results support the hypothesis that MDD is a systems level disorder affecting multiple brain networks located in the PFC and provide new insights into the pathophysiology of this disorder. PMID:28944772

Multimodal Investigation of Network Level Effects Using Intrinsic Functional Connectivity, Anatomical Covariance, and Structure-to-Function Correlations in Unmedicated Major Depressive Disorder.

PubMed

Scheinost, Dustin; Holmes, Sophie E; DellaGioia, Nicole; Schleifer, Charlie; Matuskey, David; Abdallah, Chadi G; Hampson, Michelle; Krystal, John H; Anticevic, Alan; Esterlis, Irina

2018-04-01

Converging evidence suggests that major depressive disorder (MDD) affects multiple large-scale brain networks. Analyses of the correlation or covariance of regional brain structure and function applied to structural and functional MRI data may provide insights into systems-level organization and structure-to-function correlations in the brain in MDD. This study applied tensor-based morphometry and intrinsic connectivity distribution to identify regions of altered volume and intrinsic functional connectivity in data from unmedicated individuals with MDD (n=17) and healthy comparison participants (HC, n=20). These regions were then used as seeds for exploratory anatomical covariance and connectivity analyses. Reduction in volume in the anterior cingulate cortex (ACC) and lower structural covariance between the ACC and the cerebellum were observed in the MDD group. Additionally, individuals with MDD had significantly lower whole-brain intrinsic functional connectivity in the medial prefrontal cortex (mPFC). This mPFC region showed altered connectivity to the ventral lateral PFC (vlPFC) and local circuitry in MDD. Global connectivity in the ACC was negatively correlated with reported depressive symptomatology. The mPFC-vlPFC connectivity was positively correlated with depressive symptoms. Finally, we observed increased structure-to-function correlation in the PFC/ACC in the MDD group. Although across all analysis methods and modalities alterations in the PFC/ACC were a common finding, each modality and method detected alterations in subregions belonging to distinct large-scale brain networks. These exploratory results support the hypothesis that MDD is a systems level disorder affecting multiple brain networks located in the PFC and provide new insights into the pathophysiology of this disorder.

Disorder in milk proteins: caseins, intrinsically disordered colloids.

PubMed

Redwan, Elrashdy M; Xue, Bin; Almehdar, Hussein A; Uversky, Vladimir N

2015-01-01

This article opens a series of reviews on the abundance and roles of intrinsic disorder in milk proteins. The focus of this introductory article on caseins is symbolic, since caseins were among the first recognized functional unfolded proteins and since they are definitely the most disordered, the most abundant, and the most studied of all milk proteins. In eutherian milks, the casein family includes at least three and usually four major members (αs1-, αs2-, β-, and κ-caseins) that are unrelated in sequence. However, in some species, two different αS2-casein genes are active, and therefore the total number of caseins can be as high as five. These proteins have found a number of uses in food industry. The functional repertoire of caseins ranges from nutritional function to involvement in the improving and/or maintaining cardiovascular health, to crucial contribution to the milk capacity to transport calcium phosphate, to serve as molecular chaperones, and to protect the mother's mammary gland against amyloidoses and ectopic calcification. An intricate feature of caseins is their ability to assemble to colloidal protein particles, casein micelles, serving to sequester and transport amorphous calcium phosphate. These and many other functions of caseins are obviously dependent on their intrinsically disordered nature and are controlled by various posttranslational modifications. Since various aspects of casein structure and function are rather well studied and since several recent reviews emphasized the functional roles of caseins' intrinsic disorder, the major goal of this article is to show how intrinsic disorder is encoded in the amino acid sequences of these proteins.

A preliminary investigation of Stroop-related intrinsic connectivity in cocaine dependence: Associations with treatment outcomes

PubMed Central

Mitchell, Marci R.; Balodis, Iris M.; DeVito, Elise E.; Lacadie, Cheryl M.; Yeston, Jon; Scheinost, Dustin; Constable, R. Todd; Carroll, Kathleen M.; Potenza, Marc N.

2013-01-01

Background Cocaine-dependent individuals demonstrate neural and behavioral differences compared to healthy comparison subjects when performing the Stroop color-word inference test. Stroop measures also relate to treatment outcome for cocaine dependence. Intrinsic connectivity analyses assess the extent to which task-related regional brain activations are related to each other in the absence of defining a priori regions-of-interest. Objective This study examined: 1) the extent to which cocaine-dependent and non-addicted individuals differed on measures of intrinsic connectivity during fMRI Stroop performance; and, 2) the relationships between fMRI Stroop intrinsic connectivity and treatment outcome in cocaine dependence. Methods Sixteen treatment-seeking cocaine-dependent patients and matched non-addicted comparison subjects completed an fMRI Stroop task. Between-group differences in intrinsic connectivity were assessed and related to self-reported and urine-toxicology-based cocaine-abstinence measures. Results Cocaine-dependent patients vs. comparison subjects showed less intrinsic connectivity in cortical and sub-cortical regions. When adjusting for individual degree of intrinsic connectivity, cocaine-dependent vs. comparison subjects showed relatively greater intrinsic connectivity in the ventral striatum, putamen, inferior frontal gyrus, anterior insula, thalamus, and substantia nigra. Non-mean-adjusted intrinsic-connectivity measures in the midbrain, thalamus, ventral striatum, substantia nigra, insula, and hippocampus negatively correlated with measures of cocaine abstinence. Conclusion The diminished intrinsic connectivity in cocaine-dependent vs. comparison subjects suggests poorer communication across brain regions during cognitive-control processes. In mean-adjusted analyses, the cocaine-dependent group displayed relatively greater Stroop-related connectivity in regions implicated in motivational processes in addictions. The relationships between treatment outcomes and connectivity in the midbrain and basal ganglia suggest that connectivity represents a potential treatment target. PMID:24200209

Intrinsic magnetic properties of L10 FeNi obtained from meteorite NWA 6259

NASA Astrophysics Data System (ADS)

Poirier, Eric; Pinkerton, Frederick E.; Kubic, Robert; Mishra, Raja K.; Bordeaux, Nina; Mubarok, Arif; Lewis, Laura H.; Goldstein, Joseph I.; Skomski, Ralph; Barmak, Katayun

2015-05-01

FeNi having the tetragonal L10 crystal structure is a promising new rare-earth-free permanent magnet material. Laboratory synthesis is challenging, however, tetragonal L10 FeNi—the mineral "tetrataenite"—has been characterized using specimens found in nickel-iron meteorites. Most notably, the meteorite NWA 6259 recovered from Northwest Africa is 95 vol. % tetrataenite with a composition of 43 at. % Ni. Hysteresis loops were measured as a function of sample orientation on a specimen cut from NWA 6259 in order to rigorously deduce the intrinsic hard magnetic properties of its L10 phase. Electron backscatter diffraction showed that NWA 6259 is strongly textured, containing L10 grains oriented along any one of the three equivalent cubic directions of the parent fcc structure. The magnetic structure was modeled as a superposition of the three orthonormal uniaxial variants. By simultaneously fitting first-quadrant magnetization data for 13 different orientations of the sample with respect to the applied field direction, the intrinsic magnetic properties were estimated to be saturation magnetization 4πMs = 14.7 kG and anisotropy field Ha = 14.4 kOe. The anisotropy constant K = 0.84 MJ/m3 is somewhat smaller than the value K = 1.3 MJ/m3 obtained by earlier researchers from nominally equiatomic FeNi prepared by neutron irradiation accompanied by annealing in a magnetic field, suggesting that higher Ni content (fewer Fe antisite defects) may improve the anisotropy. The fit also indicated that NWA 6259 contains one dominant variant (62% by volume), the remainder of the sample being a second variant, and the third variant being absent altogether.

Intrinsic magnetic properties of L1(0) FeNi obtained from meteorite NWA 6259

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

Poirier, E; Pinkerton, FE; Kubic, R

2015-05-07

FeNi having the tetragonal L1(0) crystal structure is a promising new rare-earth-free permanent magnet material. Laboratory synthesis is challenging, however, tetragonal L1(0) FeNi-the mineral "tetrataenite"-has been characterized using specimens found in nickel-iron meteorites. Most notably, the meteorite NWA 6259 recovered from Northwest Africa is 95 vol.% tetrataenite with a composition of 43 at.% Ni. Hysteresis loops were measured as a function of sample orientation on a specimen cut from NWA 6259 in order to rigorously deduce the intrinsic hard magnetic properties of its L1(0) phase. Electron backscatter diffraction showed that NWA 6259 is strongly textured, containing L1(0) grains oriented alongmore » any one of the three equivalent cubic directions of the parent fcc structure. The magnetic structure was modeled as a superposition of the three orthonormal uniaxial variants. By simultaneously fitting first-quadrant magnetization data for 13 different orientations of the sample with respect to the applied field direction, the intrinsic magnetic properties were estimated to be saturation magnetization 4 pi M-s = 14.7 kG and anisotropy field H-a = 14.4 kOe. The anisotropy constant K = 0.84 MJ/m(3) is somewhat smaller than the value K = 1.3 MJ/m(3) obtained by earlier researchers from nominally equiatomic FeNi prepared by neutron irradiation accompanied by annealing in a magnetic field, suggesting that higher Ni content (fewer Fe antisite defects) may improve the anisotropy. The fit also indicated that NWA 6259 contains one dominant variant (62% by volume), the remainder of the sample being a second variant, and the third variant being absent altogether. (C) 2015 AIP Publishing LLC.« less

Opposite consequences of two transcription pauses caused by an intrinsic terminator oligo(U): antitermination versus termination by bacteriophage T7 RNA polymerase.

PubMed

Lee, Sooncheol; Kang, Changwon

2011-05-06

The RNA oligo(U) sequence, along with an immediately preceding RNA hairpin structure, is an essential cis-acting element for bacterial class I intrinsic termination. This sequence not only causes a pause in transcription during the beginning of the termination process but also facilitates transcript release at the end of the process. In this study, the oligo(U) sequence of the bacteriophage T7 intrinsic terminator Tφ, rather than the hairpin structure, induced pauses of phage T7 RNA polymerase not only at the termination site, triggering a termination process, but also 3 bp upstream, exerting an antitermination effect. The upstream pause presumably allowed RNA to form a thermodynamically more stable secondary structure rather than a terminator hairpin and to persist because the 5'-half of the terminator hairpin-forming sequence could be sequestered by a farther upstream sequence via sequence-specific hybridization, prohibiting formation of the terminator hairpin and termination. The putative antiterminator RNA structure lacked several base pairs essential for termination when probed using RNases A, T1, and V1. When the antiterminator was destabilized by incorporation of IMP into nascent RNA at G residue positions, antitermination was abolished. Furthermore, antitermination strength increased with more stable antiterminator secondary structures and longer pauses. Thus, the oligo(U)-mediated pause prior to the termination site can exert a cis-acting antitermination activity on intrinsic terminator Tφ, and the termination efficiency depends primarily on the termination-interfering pause that precedes the termination-facilitating pause at the termination site.

Effect of intrinsic motivation on affective responses during and after exercise: latent curve model analysis.

PubMed

Shin, Myoungjin; Kim, Inwoo; Kwon, Sungho

2014-12-01

Understanding the relationship between affect and exercise is helpful in predicting human behavior with respect to exercise participation. The goals of the present study were to investigate individual differences in affective response during and after exercise and to identify the role of intrinsic motivation in affective changes. 30 active male college students (M age = 21.4 yr.) who regularly participated in sports activities volunteered to answer a questionnaire measuring intrinsic motivation toward running activities and performed a 20-min. straight running protocol at heavy intensity (about 70% of VO2max). Participants' affective responses were measured every 5 min. from the beginning of the run to 10 min. after completing the run. Latent curve model analysis indicated that individuals experienced different changes in affective state during exercise, moderated by intrinsic motivation. Higher intrinsic motivation was associated with more positive affect during exercise. There were no significant individual differences in the positive tendency of the participants' affective responses after exercise over time. Intrinsic motivation seems to facilitate positive feelings during exercise and encourages participation in exercise.

New intrinsic mechanism on gum-like superelasticity of multifunctional alloys

PubMed Central

Liu, Jia-Peng; Wang, Yan-Dong; Hao, Yu-Lin; Wang, Yunzhi; Nie, Zhi-Hua; Wang, Dong; Ren, Yang; Lu, Zhao-Ping; Wang, Jinguo; Wang, Haoliang; Hui, Xidong; Lu, Ning; Kim, Moon J.; Yang, Rui

2013-01-01

Ti-Nb-based Gum Metals exhibit extraordinary superelasticity with ultralow elastic modulus, superior strength and ductility, and a peculiar dislocation-free deformation behavior, most of which challenge existing theories of crystal strength. Additionally, this kind of alloys actually displays even more anomalous mechanical properties, such as the non-linear superelastic behavior, accompanied by a pronounced tension-to-compression asymmetry, and large ductility with a low Poisson's ratio. Two main contradictory arguments exist concerning the deformation mechanisms of those alloys, i.e., formation of reversible nanodisturbance and reversible martensitic transformation. Herein we used the in-situ synchrotron high-energy X-ray scattering technique to reveal the novel intrinsic physical origin of all anomalous mechanical properties of the Ti-24Nb-4Zr-8Sn-0.10O alloy, a typical gum-like metal. Our experiments provide direct evidence on two different kinds of interesting, stress-induced, reversible nanoscale martensitic transitions, i.e., the austenitic regions with B2 structure transform to α″ martensite and those with BCC structure transform to δ martensite. PMID:23831664

Robust Sub-harmonic Mixer at 340 GHz Using Intrinsic Resonances of Hammer-Head Filter and Improved Diode Model

NASA Astrophysics Data System (ADS)

Wang, Cheng; He, Yue; Lu, Bin; Jiang, Jun; Miao, Li; Deng, Xian-Jin; Xiong, Yong-zhong; Zhang, Jian

2017-11-01

This paper presents a sub-harmonic mixer at 340 GHz based on anti-parallel Schottky diodes (SBDs). Intrinsic resonances in low-pass hammer-head filter have been adopted to enhance the isolation for different harmonic components, while greatly minimizing the transmission loss. The application of new DC grounding structure, impedance matching structure, and suspended micro-strip mitigates the negative influences of fabrication errors from metal cavity, quartz substrate, and micro-assembly. An improved lumped element equivalent circuit model of SBDs guarantees the accuracy of simulation, which takes current-voltage (I/V) behavior, capacitance-voltage (C/V) behavior, carrier velocity saturation, DC series resistor, plasma resonance, skin effect, and four kinds of noise generation mechanisms into consideration thoroughly. The measurement indicates that with local oscillating signal of 2 mW, the lowest double sideband conversion loss is 5.5 dB at 339 GHz; the corresponding DSB noise temperature is 757 K. The 3 dB bandwidth of conversion loss is 50 GHz from 317 to 367 GHz.

Intrinsic Defect Ferromagnetism: The case of Hafnium Oxide

NASA Astrophysics Data System (ADS)

Das Pemmaraju, Chaitanya

2005-03-01

In view of the recent experimental reports of intrinsic ferromagnetism in Hafnium Oxide (HfO2) thin film systems ootnotetextM. Venkatesan, C. B. Fitzgerald, J. M. D. Coey Nature 430, 630 (2004) Brief Communications, we carried out first principles investigations to look for magnetic structure in HfO2 possibly brought about by the presence of small concentrations of intrinsic point defects. Ab initio electronic structure calculations using Density Functional Theory (DFT) show that isolated cation vacancy sites in HfO2 lead to the formation of high spin defect states which couple ferromagnetically to each other. Interestingly, these high spin states are observed in the low symmetry monoclinic and tetragonal phases while the highly symmetric cubic flourite phase exhibits a non-magnetic ground state. Detailed studies of the electronic structure of cation vacancies in the three crystalline phases of Hafnia show that symmetry leading to orbitally degenerate defect levels is not a pre-requsite for ferromagnetism and that the interplay between Kinetic, Coulomb and Exchange energy together with favourable coupling to the Crystalline environment can lead to high spin ferromagnetic ground states even in extreme low symmetry systems like monoclinic HfO2. These findings open up a much wider class of systems to the possibility of intrinsic defect ferromagnetism.

The Mediating Effect of Intrinsic Motivation to Learn on the Relationship between Student´s Autonomy Support and Vitality and Deep Learning.

PubMed

Núñez, Juan L; León, Jaime

2016-07-18

Self-determination theory has shown that autonomy support in the classroom is associated with an increase of students' intrinsic motivation. Moreover, intrinsic motivation is related with positive outcomes. This study examines the relationships between autonomy support, intrinsic motivation to learn and two motivational consequences, deep learning and vitality. Specifically, the hypotheses were that autonomy support predicts the two types of consequences, and that autonomy support directly and indirectly predicts the vitality and the deep learning through intrinsic motivation to learn. Participants were 276 undergraduate students. The mean age was 21.80 years (SD = 2.94). Structural equation modeling was used to test the relationships between variables and delta method was used to analyze the mediating effect of intrinsic motivation to learn. Results indicated that student perception of autonomy support had a positive effect on deep learning and vitality (p < .001). In addition, these associations were mediated by intrinsic motivation to learn. These findings suggest that teachers are key elements in generating of autonomy support environment to promote intrinsic motivation, deep learning, and vitality in classroom. Educational implications are discussed.

From Sequence and Forces to Structure, Function and Evolution of Intrinsically Disordered Proteins

PubMed Central

Forman-Kay, Julie D.; Mittag, Tanja

2015-01-01

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales and compactness is shaping a unified understanding of structure-dynamics-disorder/function relationships. On the 20th anniversary of this journal, Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional and evolutionary properties. PMID:24010708

From sequence and forces to structure, function, and evolution of intrinsically disordered proteins.

PubMed

Forman-Kay, Julie D; Mittag, Tanja

2013-09-03

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics, and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales, and compactness are shaping a unified understanding of structure-dynamics-disorder/function relationships. In the 20(th) anniversary of Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional, and evolutionary properties. Copyright © 2013 Elsevier Ltd. All rights reserved.

Wide-line NMR and DSC studies on intrinsically disordered p53 transactivation domain and its helically pre-structured segment

PubMed Central

Tompa, Peter; Han, Kyou-Hoon; Bokor, Mónika; Kamasa, Pawel; Tantos, Ágnes; Fritz, Beáta; Kim, Do-Hyoung; Lee, Chewook; Verebélyi, Tamás; Tompa, Kálmán

2016-01-01

Wide-line 1H NMR intensity and differential scanning calorimetry measurements were carried out on the intrinsically disordered 73-residue full transactivation domain (TAD) of the p53 tumor suppressor protein and two peptides: one a wild type p53 TAD peptide with a helix pre-structuring property, and a mutant peptide with a disabled helix-forming propensity. Measurements were carried out in order to characterize their water and ion binding characteristics. By quantifying the number of hydrate water molecules, we provide a microscopic description for the interactions of water with a wild-type p53 TAD and two p53 TAD peptides. The results provide direct evidence that intrinsically disordered proteins (IDPs) and a less structured peptide not only have a higher hydration capacity than globular proteins, but are also able to bind a larger amount of charged solute ions. [BMB Reports 2016; 49(9): 497-501] PMID:27418282

Folding propensity of intrinsically disordered proteins by osmotic stress

DOE PAGES

Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.; ...

2016-10-11

Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scatteringmore » (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.« less

Folding propensity of intrinsically disordered proteins by osmotic stress

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

Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.

Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scatteringmore » (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.« less

Conformational Dissection of a Viral Intrinsically Disordered Domain Involved in Cellular Transformation

PubMed Central

Perrone, Sebastián; Salvay, Andres G.; Chemes, Lucía B.; de Prat-Gay, Gonzalo

2013-01-01

Intrinsic disorder is abundant in viral genomes and provides conformational plasticity to its protein products. In order to gain insight into its structure-function relationships, we carried out a comprehensive analysis of structural propensities within the intrinsically disordered N-terminal domain from the human papillomavirus type-16 E7 oncoprotein (E7N). Two E7N segments located within the conserved CR1 and CR2 regions present transient α-helix structure. The helix in the CR1 region spans residues L8 to L13 and overlaps with the E2F mimic linear motif. The second helix, located within the highly acidic CR2 region, presents a pH-dependent structural transition. At neutral pH the helix spans residues P17 to N29, which include the retinoblastoma tumor suppressor LxCxE binding motif (residues 21–29), while the acidic CKII-PEST region spanning residues E33 to I38 populates polyproline type II (PII) structure. At pH 5.0, the CR2 helix propagates up to residue I38 at the expense of loss of PII due to charge neutralization of acidic residues. Using truncated forms of HPV-16 E7, we confirmed that pH-induced changes in α-helix content are governed by the intrinsically disordered E7N domain. Interestingly, while at both pH the region encompassing the LxCxE motif adopts α-helical structure, the isolated 21–29 fragment including this stretch is unable to populate an α-helix even at high TFE concentrations. Thus, the E7N domain can populate dynamic but discrete structural ensembles by sampling α-helix-coil-PII-ß-sheet structures. This high plasticity may modulate the exposure of linear binding motifs responsible for its multi-target binding properties, leading to interference with key cell signaling pathways and eventually to cellular transformation by the virus. PMID:24086265

Tool Wear Feature Extraction Based on Hilbert Marginal Spectrum

NASA Astrophysics Data System (ADS)

Guan, Shan; Song, Weijie; Pang, Hongyang

2017-09-01

In the metal cutting process, the signal contains a wealth of tool wear state information. A tool wear signal’s analysis and feature extraction method based on Hilbert marginal spectrum is proposed. Firstly, the tool wear signal was decomposed by empirical mode decomposition algorithm and the intrinsic mode functions including the main information were screened out by the correlation coefficient and the variance contribution rate. Secondly, Hilbert transform was performed on the main intrinsic mode functions. Hilbert time-frequency spectrum and Hilbert marginal spectrum were obtained by Hilbert transform. Finally, Amplitude domain indexes were extracted on the basis of the Hilbert marginal spectrum and they structured recognition feature vector of tool wear state. The research results show that the extracted features can effectively characterize the different wear state of the tool, which provides a basis for monitoring tool wear condition.

Intrinsic Chirality Origination in Carbon Nanotubes.

PubMed

Pierce, Neal; Chen, Gugang; P Rajukumar, Lakshmy; Chou, Nam Hawn; Koh, Ai Leen; Sinclair, Robert; Maruyama, Shigeo; Terrones, Mauricio; Harutyunyan, Avetik R

2017-10-24

Elucidating the origin of carbon nanotube chirality is key for realizing their untapped potential. Currently, prevalent theories suggest that catalyst structure originates chirality via an epitaxial relationship. Here we studied chirality abundances of carbon nanotubes grown on floating liquid Ga droplets, which excludes the influence of catalyst features, and compared them with abundances grown on solid Ru nanoparticles. Results of growth on liquid droplets bolsters the intrinsic preference of carbon nuclei toward certain chiralities. Specifically, the abundance of the (11,1)/χ = 4.31° tube can reach up to 95% relative to (9,4)/χ = 17.48°, although they have exactly the same diameter, (9.156 Å). However, the comparative abundances for the pair, (19,3)/χ = 7.2° and (17,6)/χ = 14.5°, with bigger diameter, (16.405 Å), fluctuate depending on synthesis temperature. The abundances of the same pairs of tubes grown on floating solid polyhedral Ru nanoparticles show completely different trends. Analysis of abundances in relation to nucleation probability, represented by a product of the Zeldovich factor and the deviation interval of a growing nuclei from equilibrium critical size, explain the findings. We suggest that the chirality in the nanotube in general is a result of interplay between intrinsic preference of carbon cluster and induction by catalyst structure. This finding can help to build the comprehensive theory of nanotube growth and offers a prospect for chirality-preferential synthesis of carbon nanotubes by the exploitation of liquid catalyst droplets.

Intrinsic thermodynamics of inhibitor binding to human carbonic anhydrase IX.

PubMed

Linkuvienė, Vaida; Matulienė, Jurgita; Juozapaitienė, Vaida; Michailovienė, Vilma; Jachno, Jelena; Matulis, Daumantas

2016-04-01

Human carbonic anhydrase 9th isoform (CA IX) is an important marker of numerous cancers and is increasingly interesting as a potential anticancer drug target. Various synthetic aromatic sulfonamide-bearing compounds are being designed as potent inhibitors of CA IX. However, sulfonamide compound binding to CA IX is linked to several reactions, the deprotonation of the sulfonamide amino group and the protonation of the CA active site Zn(II)-bound hydroxide. These linked reactions significantly affect the affinities and other thermodynamic parameters such as enthalpies and entropies of binding. The observed and intrinsic affinities of compound binding to CA IX were determined by the fluorescent thermal shift assay. The enthalpies and entropies of binding were determined by the isothermal titration calorimetry. The pKa of CA IX was determined to be 6.8 and the enthalpy of CA IX-Zn(II)-bound hydroxide protonation was -24 kJ/mol. These values enabled the analysis of intrinsic thermodynamics of a library of compounds binding to CA IX. The most strongly binding compounds exhibited the intrinsic affinity of 0.01 nM and the observed affinity of 2 nM. The intrinsic thermodynamic parameters of compound binding to CA IX helped to draw the compound structure to thermodynamics relationship. It is important to distinguish the intrinsic from observed parameters of any disease target protein interaction with its inhibitors as drug candidates when drawing detailed compound structure to thermodynamics correlations. Copyright © 2016 Elsevier B.V. All rights reserved.

Sequence periodicity in nucleosomal DNA and intrinsic curvature.

PubMed

Nair, T Murlidharan

2010-05-17

Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA.

The Impact of Curiosity and External Regulation on Intrinsic Motivation: An Empirical Study in Hong Kong Education

ERIC Educational Resources Information Center

Hon-keung, Yau; Man-shan, Kan; Lai-fong, Cheng Alison

2012-01-01

The purposes of this paper are to identify: (1) the factors affecting the intrinsic motivation of university students in Hong Kong; and (2) gender differences in the perception of intrinsic motivation in Hong Kong higher education environment. The factors of curiosity and external regulation with intrinsic motivation are taken into investigation…

Non-destructive detection of cross-sectional strain and defect structure in an individual Ag five-fold twinned nanowire by 3D electron diffraction mapping.

PubMed

Fu, Xin; Yuan, Jun

2017-07-24

Coherent x-ray diffraction investigations on Ag five-fold twinned nanowires (FTNWs) have drawn controversial conclusions concerning whether the intrinsic 7.35° angular gap could be compensated homogeneously through phase transformation or inhomogeneously by forming disclination strain field. In those studies, the x-ray techniques only provided an ensemble average of the structural information from all the Ag nanowires. Here, using three-dimensional (3D) electron diffraction mapping approach, we non-destructively explore the cross-sectional strain and the related strain-relief defect structures of an individual Ag FTNW with diameter about 30 nm. The quantitative analysis of the fine structure of intensity distribution combining with kinematic electron diffraction simulation confirms that for such a Ag FTNW, the intrinsic 7.35° angular deficiency results in an inhomogeneous strain field within each single crystalline segment consistent with the disclination model of stress-relief. Moreover, the five crystalline segments are found to be strained differently. Modeling analysis in combination with system energy calculation further indicates that the elastic strain energy within some crystalline segments, could be partially relieved by the creation of stacking fault layers near the twin boundaries. Our study demonstrates that 3D electron diffraction mapping is a powerful tool for the cross-sectional strain analysis of complex 1D nanostructures.

Characteristics of zero-absenteeism in hospital care.

PubMed

Schreuder, J A H; Roelen, C A M; van der Klink, J J L; Groothoff, J W

2013-06-01

Literature on sickness presenteeism is emerging, but still little is known about employees who are never absent from work due to injuries or illness. Insight into the determinants and characteristics of such zero-absentees may provide clues for preventing sickness absence. To investigate the characteristics of zero-absentees, defined as employees without sickness absence over a period of 5 years. A mixed-method qualitative study comprising semi-structured interviews and focus groups for which Azjen and Fishbein's theory of planned behaviour was used as a framework. Zero-absentees working in hospital care were invited for semi-structured interviews until saturation was reached. The results of semi-structured interviews were validated in two focus groups. Of 1053 hospital employees, 47 were zero-absentees of whom 31 (66%) agreed to participate in the study. After 16 semi-structured interviews, no new insights or information were gathered from the interviews. The remaining 15 employees were invited to two (n = 8 and n = 7) focus groups. Personal attitudes and self-efficacy were more important in zero-absenteeism than social pressures of managers, colleagues or patients. Zero-absentees were found to be intrinsically motivated to try attending work when ill. In the present study population of hospital employees, we found indications that zero-absenteeism and sickness presenteeism might be different types of work attendance. Managers should realize that zero-absentees are driven by intrinsic motivation rather than social pressures to attend work.

Intrinsic delay of permeable base transistor

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

Chen, Wenchao; Guo, Jing; So, Franky

2014-07-28

Permeable base transistors (PBTs) fabricated by vacuum deposition or solution process have the advantages of easy fabrication and low power operation and are a promising device structure for flexible electronics. Intrinsic delay of PBT, which characterizes the speed of the transistor, is investigated by solving the three-dimensional Poisson equation and drift-diffusion equation self-consistently using finite element method. Decreasing the emitter thickness lowers the intrinsic delay by improving on-current, and a thinner base is also preferred for low intrinsic delay because of fewer carriers in the base region at off-state. The intrinsic delay exponentially decreases as the emitter contact Schottky barriermore » height decreases, and it linearly depends on the carrier mobility. With an optimized emitter contact barrier height and device geometry, a sub-nano-second intrinsic delay can be achieved with a carrier mobility of ∼10 cm{sup 2}/V/s obtainable in solution processed indium gallium zinc oxide, which indicates the potential of solution processed PBTs for GHz operations.« less

Substrate temperature effect on the structural anisotropy in amorphous Tb-Fe films

NASA Astrophysics Data System (ADS)

Harris, V. G.; Hellman, F.; Elam, W. T.; Koon, N. C.

1993-05-01

Using extended x-ray absorption fine structures (EXAFS) measurements we have investigated the atomic environment around the Fe atom in a series of amorphous Tb0.26Fe0.74 films having different magnetic anisotropy energies owing to different deposition temperatures. The polarization properties of synchrotron radiation allowed the separate study of structure parallel and perpendicular to the sample plane. An anisotropy between these two structures was observed. Modeling results indicate this anisotropy is due to anisotropic pair correlations where the Fe-Fe pairs are statistically preferred in-plane and the Fe-Tb pairs out-of-plane. The amplitude of this anisotropy scales with both the substrate temperature and the magnetic anisotropy energy. A ≊1% in-plane compression of the Fe-Fe distance was measured between the in-plane and out-of-plane structure of the sample grown at 77 K. This sample had no detectable local chemical anisotropy suggesting that intrinsic stress plays an important role in determining its magnetic anisotropy.

Changes of Water Hydrogen Bond Network with Different Externalities

PubMed Central

Zhao, Lin; Ma, Kai; Yang, Zi

2015-01-01

It is crucial to uncover the mystery of water cluster and structural motif to have an insight into the abundant anomalies bound to water. In this context, the analysis of influence factors is an alternative way to shed light on the nature of water clusters. Water structure has been tentatively explained within different frameworks of structural models. Based on comprehensive analysis and summary of the studies on the response of water to four externalities (i.e., temperature, pressure, solutes and external fields), the changing trends of water structure and a deduced intrinsic structural motif are put forward in this work. The variations in physicochemical and biological effects of water induced by each externality are also discussed to emphasize the role of water in our daily life. On this basis, the underlying problems that need to be further studied are formulated by pointing out the limitations attached to current study techniques and to outline prominent studies that have come up recently. PMID:25884333

An antisymmetric cell structure for high-performance zinc bromine flow battery

NASA Astrophysics Data System (ADS)

Kim, Yongbeom; Jeon, Joonhyeon

2017-12-01

Zinc-bromine flow batteries (ZBBs) remain a problem of designing a cell with high coulombic efficiency and stability. This problem is caused intrinsically by different phase transition in each side of the half-cells during charge-discharge process. This paper describes a ZBB with an antisymmetric cell structure, which uses anode and cathode with different surface morphologies, for high-discharge capacity and reliability. The structure of the antisymmetric ZBB cell contains a carbon-surface electrode and a carbon-volume electrode in zinc and bromine half cells, respectively. To demonstrate the effectiveness of this proposed ZBB cell structure, Cyclic Voltammetry measurement is performed on a graphite foil and a carbon felt which are used as the surface and electrodes. Charge and discharge cyclic operations are also carried out with symmetric and antisymmetric ZBB cells combined with the two electrode types. Experimental results show that the arrangement of antisymmetric cell structure in ZBB provides a solution to the high performance and durability.

Resolution of structural heterogeneity in dynamic crystallography.

PubMed

Ren, Zhong; Chan, Peter W Y; Moffat, Keith; Pai, Emil F; Royer, William E; Šrajer, Vukica; Yang, Xiaojing

2013-06-01

Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

Diffusion of vaporous guests into a seemingly non-porous organic crystal

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

Herbert, Simon A.; Janiak, Agnieszka; Thallapally, Praveen K.

2014-10-07

In this research, the tetragonal apohost phase of p-tert-butyltetramethoxythiacalix[4]arene absorbs hydrochloric acid and iodine. These guest molecules occupy different sites in the solid-state structure -- either within the small intrinsic voids of the macrocycle or within the interstitial spaces between the host molecules. This study illustrates the dynamic deformation of the host, providing strong mechanistic insight into the diffusion of guests into this seemingly non-porous material.

Intrinsic Motivation, Learning Goals, Engagement, and Achievement in a Diverse High School

ERIC Educational Resources Information Center

Froiland, John Mark; Worrell, Frank C.

2016-01-01

Using structural equation models, with gender, parent education, and prior grade point average (GPA) as control variables, we examined the relationships among intrinsic motivation to learn, learning goals, behavioral engagement at school, and academic performance (measured by GPA) in 1,575 students in an ethnically and racially diverse high…

Intramolecular three-colour single pair FRET of intrinsically disordered proteins with increased dynamic range.

PubMed

Milles, Sigrid; Koehler, Christine; Gambin, Yann; Deniz, Ashok A; Lemke, Edward A

2012-10-01

Single molecule observation of fluorescence resonance energy transfer can be used to provide insight into the structure and dynamics of proteins. Using a straightforward triple-colour labelling strategy, we present a measurement and analysis scheme that can simultaneously study multiple regions within single intrinsically disordered proteins.

Intramolecular Three-Colour Single Pair FRET of Intrinsically Disordered Proteins with Increased Dynamic Range

PubMed Central

Milles, Sigrid; Koehler, Christine; Gambin, Yann

2012-01-01

Single molecule observation of fluorescence resonance energy transfer can be used to provide insights into the structure and dynamics of proteins. Using a straightforward triple-colour labelling strategy, we present a measurement and analysis scheme that can simultaneously study multiple regions within single intrinsically disordered proteins. PMID:22739670

COMPENSATION FOR VARIABLE INTRINSIC NEURONAL EXCITABILITY BY CIRCUIT-SYNAPTIC INTERACTIONS

PubMed Central

Grashow, Rachel; Brookings, Ted; Marder, Eve

2010-01-01

Recent theoretical and experimental work indicates that neurons tune themselves to maintain target levels of excitation by modulating ion channel expression and synaptic strengths. As a result, functionally equivalent circuits can produce similar activity despite disparate underlying network and cellular properties. To experimentally test the extent to which synaptic and intrinsic conductances can produce target activity in the presence of variability in neuronal intrinsic properties, we used the dynamic clamp to create hybrid two-cell circuits built from four types of stomatogastric (STG) neurons coupled to the same model Morris-Lecar neuron by reciprocal inhibition. We measured six intrinsic properties (input resistance, minimum membrane potential, firing rate in response to +1nA of injected current, slope of the FI curve, spike height and spike voltage threshold) of Dorsal Gastric (DG), Gastric Mill (GM), Lateral Pyloric (LP) and Pyloric Dilator (PD) neurons from male crabs, Cancer borealis. The intrinsic properties varied two to seven-fold in each cell type. We coupled each biological neuron to the Morris-Lecar model with seven different values of inhibitory synaptic conductance, and also used the dynamic clamp to add seven different values of an artificial h-conductance, thus creating 49 different circuits for each biological neuron. Despite the variability in intrinsic excitability, networks formed from each neuron produced similar circuit performance at some values of synaptic and h-conductances. This work experimentally confirms results from previous modeling studies; tuning synaptic and intrinsic conductances can yield similar circuit output from neurons with variable intrinsic excitability. PMID:20610748

Exploring the relevance of gas-phase structures to biology: cold ion spectroscopy of the decapeptide neurokinin A.

PubMed

Pereverzev, A Y; Boyarkin, O V

2017-02-01

Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with solvents, to some extent mimicking a hydrophobic environment. Intrinsic structures therefore may resemble native ones for peptides that in vivo reside in a hydrophobic environment (e.g., binding pockets of receptors). In this study, we investigate doubly protonated neurokinin A (NKA) using IR-UV double resonance cold ion spectroscopy and find only five conformers of this decapeptide in the gas phase. In contrast, NMR data show that in aqueous solutions, NKA exhibits high conformational heterogeneity, which reduces to a few well-defined structures in hydrophobic micelles. Do the gas-phase structures of NKA resemble these native structures? The IR spectra reported here allow the validation of future structural calculations that may answer this question.

Basal Ganglia Shape Abnormalities in the Unaffected Siblings of Schizophrenia Patients

PubMed Central

Mamah, Daniel; Harms, Michael P.; Wang, Lei; Barch, Deanna; Thompson, Paul; Kim, Jaeyun; Miller, Michael I.; Csernansky, John G.

2008-01-01

Objective Abnormalities of basal ganglia structure in schizophrenia have been attributed to the effects of antipsychotic drugs. Our aim was to test the hypothesis that abnormalities of basal ganglia structure are intrinsic features of schizophrenia, by assessing basal ganglia volume and shape in the unaffected siblings of schizophrenia subjects. Method The study involved 25 pairs of schizophrenia subjects and their unaffected siblings and 40 pairs of healthy controls and their siblings. Large deformation, high-dimensional brain mapping was used to obtain surface representations of the caudate, putamen, and globus pallidus. Surfaces were derived from transformations of anatomical templates and shapes were analyzed using reduced-dimensional measures of surface variability (i.e. principal components and canonical analysis). Canonical functions were derived using schizophrenia and control groups, and were then used to compare shapes in the sibling groups. To visualize shape differences, maps of the estimated surface displacement between groups were created. Results In the caudate, putamen and globus pallidus, the degree of shape abnormality observed in the siblings of the schizophrenia subjects was intermediate between the schizophrenia subjects and the controls. In the schizophrenia subjects, significant correlations were observed between measures of caudate, putamen and globus pallidus structure and the selected measures of lifetime psychopathology. Conclusions Attenuated abnormalities of basal ganglia structure are present in the unaffected siblings of schizophrenia subjects. This finding implies that basal ganglia structural abnormalities observed in subjects with schizophrenia are at least in part an intrinsic feature of the illness. PMID:18295189

Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment

PubMed Central

Mollica, Luca; Bessa, Luiza M.; Hanoulle, Xavier; Jensen, Malene Ringkjøbing; Blackledge, Martin; Schneider, Robert

2016-01-01

In recent years, protein science has been revolutionized by the discovery of intrinsically disordered proteins (IDPs). In contrast to the classical paradigm that a given protein sequence corresponds to a defined structure and an associated function, we now know that proteins can be functional in the absence of a stable three-dimensional structure. In many cases, disordered proteins or protein regions become structured, at least locally, upon interacting with their physiological partners. Many, sometimes conflicting, hypotheses have been put forward regarding the interaction mechanisms of IDPs and the potential advantages of disorder for protein-protein interactions. Whether disorder may increase, as proposed, e.g., in the “fly-casting” hypothesis, or decrease binding rates, increase or decrease binding specificity, or what role pre-formed structure might play in interactions involving IDPs (conformational selection vs. induced fit), are subjects of intense debate. Experimentally, these questions remain difficult to address. Here, we review experimental studies of binding mechanisms of IDPs using NMR spectroscopy and transient kinetic techniques, as well as the underlying theoretical concepts and numerical methods that can be applied to describe these interactions at the atomic level. The available literature suggests that the kinetic and thermodynamic parameters characterizing interactions involving IDPs can vary widely and that there may be no single common mechanism that can explain the different binding modes observed experimentally. Rather, disordered proteins appear to make combined use of features such as pre-formed structure and flexibility, depending on the individual system and the functional context. PMID:27668217

Mutations in actin used for structural studies partially disrupt β-thymosin/WH2 domains interaction.

PubMed

Deville, Célia; Girard-Blanc, Christine; Assrir, Nadine; Nhiri, Naïma; Jacquet, Eric; Bontems, François; Renault, Louis; Petres, Stéphane; van Heijenoort, Carine

2016-10-01

Understanding the structural basis of actin cytoskeleton remodeling requires stabilization of actin monomers, oligomers, and filaments in complex with partner proteins, using various biochemical strategies. Here, we report a dramatic destabilization of the dynamic interaction with a model β-thymosin/WH2 domain induced by mutations in actin. This result underlines that mutant actins should be used with prudence to characterize interactions with intrinsically disordered partners as destabilization of dynamic interactions, although identifiable by NMR, may be invisible to other structural techniques. It also highlights how both β-thymosin/WH2 domains and actin tune local structure and dynamics in regulatory processes involving intrinsically disordered domains. © 2016 Federation of European Biochemical Societies.

Electrostatic differences: A possible source for the functional differences between MCF7 and brain microtubules.

PubMed

Feizabadi, Mitra Shojania; Rosario, Brandon; Hernandez, Marcos A V

2017-11-04

Recent studies suggested a link between diversity of beta tubulin isotypes in microtubule structures and the regulatory roles that they play not only on microtubules' intrinsic dynamic, but also on the translocation characteristics of some of the molecular motors along microtubules. Remarkably, unlike porcine brain microtubules, MCF7 microtubules are structured from a different beta tubulin distribution. These types of cancer microtubules show a relatively stable and slow dynamic. In addition, the translocation parameters of some molecular motors are distinctly different along MCF7 as compared to those parameters on brain microtubules. It is known that the diversity of beta tubulin isotypes differ predominantly in the specifications and the electric charge of their carboxy-terminal tails. A key question is to identify whether the negative electrostatic charge of tubulin isotypes and, consequently, microtubules, can potentially be considered as one of the sources of functional differences in MCF7 vs. brain microtubules. We tested this possibility experimentally by monitoring the electro-orientation of these two types of microtubules inside a uniform electric field. Through this evaluation, we quantified and compared the average normalized polarization coefficient of MCF7 vs. Porcine brain microtubules. The higher value obtained for the polarization of MCF7 microtubules, which is associated to the higher negative charge of these types of microtubules, is significant as it can further explain the slow intrinsic dynamic that has been recently reported for single MCF7 microtubules in vitro. Furthermore, it can be potentially considered as a factor that can directly impact the translocation parameters of some molecular motors along MCF7 microtubules, by altering the mutual electrostatic interactions between microtubules and molecular motors. Copyright © 2017 Elsevier Inc. All rights reserved.

Spectral and photoelectric characteristics of the gamma irradiated intrinsic oxide-ІnSe heterostructures obtained under different conditions

NASA Astrophysics Data System (ADS)

Sydor, O. M.

2016-09-01

The investigations of photoelectric characteristics and photoresponce spectral dependences were carried out for intrinsic oxide-InSe heterostructures (HSs) and their changes induced by bremsstrahlung γ-quanta with an energy of 1-34 MeV at fluences of 1012-1015 cm-2. The thermal oxidation of the p-InSe:Cd substrates was carried out at a temperature of 420 °С. For three selected groups of samples the duration of the process was 15 min, 60 min, and 96 h. At a short-term oxidation (15 and 60 min) a layer of In2O3 appears. The only difference between the samples of these two groups is a higher photosensitivity in the range of energy 1.25-2.8 eV of the HSs obtained after the 60 min oxidation. At the long-term oxidation the photoresponce spectra η(hν) of the obtained HSs are characterized with a sharp short-wavelength decrease at hν≅2.0 eV. It is established that the intrinsic oxide films act as transparent barrier electrodes in the corresponding HSs and are low-sensitive to γ-irradiation in the all range of fluences. The shape of the photoresponce spectra for all the gamma irradiated HSs remains practically the same. However, it was found: (i) some decrease of photosensitivity at the long-wavelength edge, (ii) decreasing the width of η(hν) at half-height, (iii) the appearance of the exciton peak, (iv) the improvement of a slope of the low-energy edge of the photoresponce spectra with increasing irradiation dose whereas at the maximum fluence this parameter decreases, and (v) the slight extension of the spectral sensitivity to the short-wavelength range for the structures obtained after oxidation for 96 h. The photoelectric parameters of the intrinsic oxide-p-InSe HSs, open circuit voltage Voc, short-circuit current Jsc, current SIλmax and voltage SVλmax sensitivities become only improved after irradiation with the fluences 1012-1013 cm-2. At the maximum fluence a small decreasing of the values of Voc and Jsc was detected except for the structures obtained after oxidation for 15 min. An increase of the SIλmax and SVλmax sensitivities in comparison with the initial value were found for all the HSs even at the maximum fluence except for the structures obtained by a long-term oxidation.

Backbone conformational preferences of an intrinsically disordered protein in solution.

PubMed

Espinoza-Fonseca, L Michel; Ilizaliturri-Flores, Ian; Correa-Basurto, José

2012-06-01

We have performed a 4-μs molecular dynamics simulation to investigate the native conformational preferences of the intrinsically disordered kinase-inducible domain (KID) of the transcription factor CREB in solution. There is solid experimental evidence showing that KID does not possess a bound-like structure in solution; however, it has been proposed that coil-to-helix transitions upon binding to its binding partner (CBP) are template-driven. While these studies indicate that IDPs possess a bias towards the bound structure, they do not provide direct evidence on the time-dependent conformational preferences of IDPs in atomic detail. Our simulation captured intrinsic conformational characteristics of KID that are in good agreement with experimental data such as a very small percentage of helical structure in its segment α(B) and structural disorder in solution. We used dihedral principal component analysis dPCA to map the conformations of KID in the microsecond timescale. By using principal components as reaction coordinates, we further constructed dPCA-based free energy landscapes of KID. Analysis of the free energy landscapes showed that KID is best characterized as a conformational ensemble of rapidly interconverting conformations. Interestingly, we found that despite the conformational heterogeneity of the backbone and the absence of substantial secondary structure, KID does not randomly sample the conformational space in solution: analysis of the (Φ, Ψ) dihedral angles showed that several individual residues of KID possess a strong bias toward the helical region of the Ramachandran plot. We suggest that the intrinsic conformational preferences of KID provide a bias toward the folded state without having to populate bound-like conformations before binding. Furthermore, we argue that these conformational preferences do not represent actual structural constraints which drive binding through a single pathway, which allows for specific interactions with multiple binding partners. Based on this evidence, we propose that the backbone conformational preferences of KID provide a thermodynamic advantage for folding and binding without negatively affecting the kinetics of binding. We further discuss the relation of our results to previous studies to rationalize the functional implications of the conformational preferences of IDPs, such as the optimization of structural disorder in protein-protein interactions. This study illustrates the importance in obtaining atomistic information of intrinsically disordered proteins in real time to reveal functional features arising from their complex conformational space.

Effect of q-profile structure on intrinsic torque reversals

NASA Astrophysics Data System (ADS)

Lu, Zhixin

2014-10-01

Intrinsic toroidal rotation plays an important role in mitigating macroinstability and regulating turbulent transport in ITER, where neutral beams are not sufficient to provide the requisite torque. Recent experiments on C-Mod with LHCD observed rotation reversal related to a change in the q profile. In this work, we focus on understanding the physics of intrinsic rotation reversals in LHCD plasmas, using nonlinear, global gyro-kinetic simulations and analysis of mode structure and spectrum symmetry breaking. The sensitive dependence of turbulent residual stress on magnetic shear is identified and characterized. The basic residual stress is non-vanishing when the k-parallel spectrum symmetry is broken, e.g., by E × B shear induced radial shift, non-uniformity in turbulence intensity, etc.. It is found that at low magnetic shear, the poloidal harmonics can shift strongly in the radial direction, as a feature of non-local effects, due to radial propagation and amplitude variation of the mode. This new symmetry breaking mechanism leads to a change in the sign of spectrum averaged parallel wave vector and thus the direction of intrinsic torque. Theoretical study shows that the competition between magnetic drift and ion kinetic effects determines the non-local effects and the structure of the asymmetry. Specifically, it is found that the direction of the intrinsic torque changes from counter- to co-current in the core, when magnetic shear decreases through a critical value. A critical shear ŝR = 0 . 2 ~ 0 . 5 for reversal of CTEM-induced intrinsic torque found by simulation is consistent with that from the LHCD C-Mod reversal experiments. In addition, simulations indicate ŝR = 1 ~ 2 for the reversal of ITG-induced torque, a prediction which can be tested by experiments. This work is supported by CER and CMTFO, UCSD and U.S. DOE-PPPL Contract DE-AC02-09CH11466.

Compaction and binding properties of the intrinsically disordered C-terminal domain of Henipavirus nucleoprotein as unveiled by deletion studies.

PubMed

Blocquel, David; Habchi, Johnny; Gruet, Antoine; Blangy, Stéphanie; Longhi, Sonia

2012-01-01

Henipaviruses are recently emerged severe human pathogens within the Paramyxoviridae family. Their genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that recruits the polymerase complex via the phosphoprotein (P). We have previously shown that in Henipaviruses the N protein possesses an intrinsically disordered C-terminal domain, N(TAIL), which undergoes α-helical induced folding in the presence of the C-terminal domain (P(XD)) of the P protein. Using computational approaches, we previously identified within N(TAIL) four putative molecular recognition elements (MoREs) with different structural propensities, and proposed a structural model for the N(TAIL)-P(XD) complex where the MoRE encompassing residues 473-493 adopt an α-helical conformation at the P(XD) surface. In this work, for each N(TAIL) protein, we designed four deletion constructs bearing different combinations of the predicted MoREs. Following purification of the N(TAIL) truncated proteins from the soluble fraction of E. coli, we characterized them in terms of their conformational, spectroscopic and binding properties. These studies provided direct experimental evidence for the structural state of the four predicted MoREs, and showed that two of them have clear α-helical propensities, with the one spanning residues 473-493 being strictly required for binding to P(XD). We also showed that Henipavirus N(TAIL) and P(XD) form heterologous complexes, indicating that the P(XD) binding regions are functionally interchangeable between the two viruses. By combining spectroscopic and conformational analyses, we showed that the content in regular secondary structure is not a major determinant of protein compaction.

Changes in self-perceptions of competence and intrinsic motivation among elementary schoolchildren.

PubMed

Bouffard, Thérèse; Marcoux, Marie-France; Vezeau, Carole; Bordeleau, Luce

2003-06-01

Children's perceived competence and intrinsic motivation are assumed to be very high at the outset of schooling. However, how they change and how they relate to each other and to academic achievement across early schooling years remain open to question. This 3-year longitudinal study was aimed at examining the following questions. Do children's perceived competence and intrinsic motivation about reading and mathematics change across the first 3 years of schooling? Do their perceived competence and intrinsic motivation differ according to academic domains? Do their perceived competence and intrinsic motivation relate to their academic achievement in each academic domain? A total of 115 elementary schoolchildren (63 boys and 52 girls) were examined in first grade (mean age = 84,5 months, SD =.67) and for the next 2 years. Children responded to questionnaires about their perceived competence and intrinsic motivation in reading and mathematics. Year-end grades in these two subjects were used as a measure of performance. Changes in perceived competence and intrinsic motivation, and between-year intercorrelations, were observed to differ according to academic domains and gender. Intrinsic motivation did not make a significant contribution to academic achievement at either school grade or in any academic domain, whereas perceived competence was significantly related to achievement at each school grade in both reading and mathematics. Differences between boys and girls observed in this study were not linked to a specific domain and cannot be attributed to gender-role stereotypes. Girls appeared to be more precocious in differentiating their competence and intrinsic motivation according to academic domain, as well as in being able to process and integrate information about their ability from past performances in a domain to judge their competence in the same domain.

Nucleation Process of a Fibril Precursor in the C-Terminal Segment of Amyloid-β

NASA Astrophysics Data System (ADS)

Baftizadeh, Fahimeh; Pietrucci, Fabio; Biarnés, Xevi; Laio, Alessandro

2013-04-01

By extended atomistic simulations in explicit solvent and bias-exchange metadynamics, we study the aggregation process of 18 chains of the C-terminal segment of amyloid-β, an intrinsically disordered protein involved in Alzheimer’s disease and prone to form fibrils. Starting from a disordered aggregate, we are able to observe the formation of an ordered nucleus rich in beta sheets. The rate limiting step in the nucleation pathway involves crossing a barrier of approximately 40kcal/mol and is associated with the formation of a very specific interdigitation of the side chains belonging to different sheets. This structural pattern is different from the one observed experimentally in a microcrystal of the same system, indicating that the structure of a “nascent” fibril may differ from the one of an “extended” fibril.

Intrinsic motivation and amotivation in first episode and prolonged psychosis.

PubMed

Luther, Lauren; Lysaker, Paul H; Firmin, Ruth L; Breier, Alan; Vohs, Jenifer L

2015-12-01

The deleterious functional implications of motivation deficits in psychosis have generated interest in examining dimensions of the construct. However, there remains a paucity of data regarding whether dimensions of motivation differ over the course of psychosis. Therefore, this study examined two motivation dimensions, trait-like intrinsic motivation, and the negative symptom of amotivation, and tested the impact of illness phase on the 1) levels of these dimensions and 2) relationship between these dimensions. Participants with first episode psychosis (FEP; n=40) and prolonged psychosis (n=66) completed clinician-rated measures of intrinsic motivation and amotivation. Analyses revealed that when controlling for group differences in gender and education, the FEP group had significantly more intrinsic motivation and lower amotivation than the prolonged psychosis group. Moreover, intrinsic motivation was negatively correlated with amotivation in both FEP and prolonged psychosis, but the magnitude of the relationship did not statistically differ between groups. These findings suggest that motivation deficits are more severe later in the course of psychosis and that low intrinsic motivation may be partially independent of amotivation in both first episode and prolonged psychosis. Clinically, these results highlight the importance of targeting motivation in early intervention services. Copyright © 2015 Elsevier B.V. All rights reserved.

Examining intrinsic versus extrinsic exercise goals: cognitive, affective, and behavioral outcomes.

PubMed

Sebire, Simon J; Standage, Martyn; Vansteenkiste, Maarten

2009-04-01

Grounded in self-determination theory (SDT), this study had two purposes: (a) examine the associations between intrinsic (relative to extrinsic) exercise goal content and cognitive, affective, and behavioral outcomes; and (b) test the mediating role of psychological need satisfaction in the Exercise Goal Content --> Outcomes relationship. Using a sample of 410 adults, hierarchical regression analysis showed relative intrinsic goal content to positively predict physical self-worth, self-reported exercise behavior, psychological well-being, and psychological need satisfaction and negatively predict exercise anxiety. Except for exercise behavior, the predictive utility of relative intrinsic goal content on the dependent variables of interest remained significant after controlling for participants' relative self-determined exercise motivation. Structural equation modeling analyses showed psychological need satisfaction to partially mediate the effect of relative intrinsic goal content on the outcome variables. Our findings support further investigation of exercise goals commensurate with the goal content perspective advanced in SDT.

Origins of retinal intrinsic signals: a series of experiments on retinas of macaque monkeys.

PubMed

Tsunoda, Kazushige; Hanazono, Gen; Inomata, Koichi; Kazato, Yoko; Suzuki, Wataru; Tanifuji, Manabu

2009-07-01

Diffuse flash stimuli applied to the ocular fundus evoke light reflectance decreases of the fundus illuminated with infrared observation light. This phenomenon, which is independent of the photopigment bleaching observed as an increase in the reflectance of visible light, is called intrinsic signals. Intrinsic signals, in general, are stimulus-evoked light reflectance changes of neural tissues due to metabolic changes, and they have been extensively investigated in the cerebral cortex. This noninvasive objective technique of functional imaging has good potential as a tool for the early detection of retinal dysfunction. Once the signal properties were studied in detail, however, it became apparent that the intrinsic signals observed in the retina have uniquely interesting properties of their own due to the characteristic layered structure of the retina. Experiments on anesthetized macaque monkeys are reviewed, and the possible origins of the intrinsic signals of the retina are discussed.

Neural predictors of individual differences in response to math tutoring in primary-grade school children

PubMed Central

Supekar, Kaustubh; Swigart, Anna G.; Tenison, Caitlin; Jolles, Dietsje D.; Rosenberg-Lee, Miriam; Fuchs, Lynn; Menon, Vinod

2013-01-01

Now, more than ever, the ability to acquire mathematical skills efficiently is critical for academic and professional success, yet little is known about the behavioral and neural mechanisms that drive some children to acquire these skills faster than others. Here we investigate the behavioral and neural predictors of individual differences in arithmetic skill acquisition in response to 8-wk of one-to-one math tutoring. Twenty-four children in grade 3 (ages 8–9 y), a critical period for acquisition of basic mathematical skills, underwent structural and resting-state functional MRI scans pretutoring. A significant shift in arithmetic problem-solving strategies from counting to fact retrieval was observed with tutoring. Notably, the speed and accuracy of arithmetic problem solving increased with tutoring, with some children improving significantly more than others. Next, we examined whether pretutoring behavioral and brain measures could predict individual differences in arithmetic performance improvements with tutoring. No behavioral measures, including intelligence quotient, working memory, or mathematical abilities, predicted performance improvements. In contrast, pretutoring hippocampal volume predicted performance improvements. Furthermore, pretutoring intrinsic functional connectivity of the hippocampus with dorsolateral and ventrolateral prefrontal cortices and the basal ganglia also predicted performance improvements. Our findings provide evidence that individual differences in morphometry and connectivity of brain regions associated with learning and memory, and not regions typically involved in arithmetic processing, are strong predictors of responsiveness to math tutoring in children. More generally, our study suggests that quantitative measures of brain structure and intrinsic brain organization can provide a more sensitive marker of skill acquisition than behavioral measures. PMID:23630286

Neural predictors of individual differences in response to math tutoring in primary-grade school children.

PubMed

Supekar, Kaustubh; Swigart, Anna G; Tenison, Caitlin; Jolles, Dietsje D; Rosenberg-Lee, Miriam; Fuchs, Lynn; Menon, Vinod

2013-05-14

Now, more than ever, the ability to acquire mathematical skills efficiently is critical for academic and professional success, yet little is known about the behavioral and neural mechanisms that drive some children to acquire these skills faster than others. Here we investigate the behavioral and neural predictors of individual differences in arithmetic skill acquisition in response to 8-wk of one-to-one math tutoring. Twenty-four children in grade 3 (ages 8-9 y), a critical period for acquisition of basic mathematical skills, underwent structural and resting-state functional MRI scans pretutoring. A significant shift in arithmetic problem-solving strategies from counting to fact retrieval was observed with tutoring. Notably, the speed and accuracy of arithmetic problem solving increased with tutoring, with some children improving significantly more than others. Next, we examined whether pretutoring behavioral and brain measures could predict individual differences in arithmetic performance improvements with tutoring. No behavioral measures, including intelligence quotient, working memory, or mathematical abilities, predicted performance improvements. In contrast, pretutoring hippocampal volume predicted performance improvements. Furthermore, pretutoring intrinsic functional connectivity of the hippocampus with dorsolateral and ventrolateral prefrontal cortices and the basal ganglia also predicted performance improvements. Our findings provide evidence that individual differences in morphometry and connectivity of brain regions associated with learning and memory, and not regions typically involved in arithmetic processing, are strong predictors of responsiveness to math tutoring in children. More generally, our study suggests that quantitative measures of brain structure and intrinsic brain organization can provide a more sensitive marker of skill acquisition than behavioral measures.

Nonlinear optical properties of semiconductor nanocrystals

NASA Astrophysics Data System (ADS)

Ricard, Gianpiero Banfi Vittorio Degiorgio Daniel

1998-05-01

This review is devoted to the description of recent experimental results concerning the nonlinear optical properties of semiconductor-doped glasses SDGs with particular emphasis on the regime in which the energy of the incident photon is smaller than the energy gap. A considerable theoretical and experimental effort has been devoted in the last 10years to the fundamental aspects of quantumconfined structures, which have properties somewhat intermediate between the bulk crystals and atoms or molecules. From this point of view, SDGs represent an easily available test system, and optical techniques have been a major diagnostic tool. Luminescence and absorption spectroscopy were extensively used to characterize the electronic states. The experiments aimed at the measurement of the real and imaginary parts of the third-order optical susceptibility of SDGs below the bandgap are described in some detail, and the results obtained with different techniques are compared. Besides the intrinsic fast nonlinearity due to bound electrons, SDGs may present a larger but much slower nonlinearity due to the free carriers generated by two-photon absorption. This implies that experiments have to be properly designed for separation of the two effects. In this article we stress the importance of a detailed structural characterization of the samples. Knowledge of the volume fraction occupied by the nanocrystals is necessary in order to derive from the experimental data the intrinsic nonlinearity and to compare it with the bulk nonlinearity. We discuss recent experiments in which the dependence of the intrinsic nonlinearity on the crystal size is derived by performing, on the samples, measurements of the real part and imaginary part of the nonlinear optical susceptibility and measurements of crystal size and volume fraction. Structural characterization is of interest also for a better understanding of the physical processes underlying the growth of crystallites in SDGs. The average size of nanocrystals can be tailored by controlling the temperature or time of the treatment. The major problem is the size dispersion of the crystallites, which is intrinsic to the diffusion process. At present, this is the major source of the undesired inhomogeneous broadening of the optical transition lines of the SDGs. Efforts are at present being made to fabricate materials, SDGs included, which embed nanocrystals with a reduced spread of sizes. The interest in the nonlinear optical properties is due not only to fundamental reasons but also to possible applications for optical devices. Generally speaking, resonant nonlinearities are much larger than non-resonant nonlinearities, but they are not necessarily the most interesting for applications because materials at resonance absorb the incident radiation and also present long response times. The studies below the bandgap seem to indicate that the values of the intrinsic nonlinearities of nanocrystals in the structures which are at present available are similar to those of the bulk. New and better controlled structures are now under development and have to be tested from the viewpoint of optical nonlinearities. In several situations SDGs cannot be modelled as an ensemble of freely standing nanocrystals, with the glass matrix playing the role of an inert support. Phenomena such as trapping and darkening, which are very probably connected with electronic states at the glasssemiconductor interface, may play a role in determining the optical response. They might give rise to an extrinsic optical nonlinearity which can be even larger than the intrinsic nonlinearity. The physical processes which are involved in these extrinsic nonlinearities are poorly understood and at present being investigated.

Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins.

PubMed

Perez, Romel B; Tischer, Alexander; Auton, Matthew; Whitten, Steven T

2014-12-01

Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins (IDPs), mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline (PRO) and alanine (ALA) to glycine (GLY) substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (R(h)) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the GLY substitutions decreased polyproline II (PP(II)) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in R(h) were not associated with folding. The experiments showed that changes in local PP(II) structure cause changes in R(h) that are variable and that depend on the intrinsic chain propensities of PRO and ALA residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed PRO and alanine effects on the structures of IDPs. © 2014 Wiley Periodicals, Inc.

Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations.

PubMed

Ithuralde, Raúl Esteban; Roitberg, Adrián Enrique; Turjanski, Adrián Gustavo

2016-07-20

Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15.6 μs. Our results show that c-myb folds very fast upon binding to CBP with no unique pathway for binding. The process can proceed through both structured or unstructured TS's with similar probabilities. This finding reconciles previous seemingly different experimental results. We also performed Go-type coarse-grained MD of several structured and unstructured models that indicate that coupled folding and binding follows a native contact mechanism. To the best of our knowledge, this is the first atomistic MD simulation that samples the free energy surface of the coupled folding and binding processes of IDPs.

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

Zhou Juefei; Szafruga, Urszula B.; Kuzyk, Mark G.

We use numerical optimization to study the properties of (1) the class of one-dimensional potential energy functions and (2) systems of point nuclei in two dimensions that yield the largest intrinsic hyperpolarizabilities, which we find to be within 30% of the fundamental limit. In all cases, we use a one-electron model. It is found that a broad range of optimized potentials, each of very different character, yield the same intrinsic hyperpolarizability ceiling of 0.709. Furthermore, all optimized potential energy functions share common features such as (1) the value of the normalized transition dipole moment to the dominant state, which forcesmore » the hyperpolarizability to be dominated by only two excited states and (2) the energy ratio between the two dominant states. All optimized potentials are found to obey the three-level ansatz to within about 1%. Many of these potential energy functions may be implementable in multiple quantum well structures. The subset of potentials with undulations reaffirm that modulation of conjugation may be an approach for making better organic molecules, though there appear to be many others. Additionally, our results suggest that one-dimensional molecules may have larger diagonal intrinsic hyperpolarizability {beta}{sub xxx}{sup int} than higher-dimensional systems.« less

Observation of Kelvin-Helmholtz instabilities and gravity waves in the summer mesopause above Andenes in Northern Norway

NASA Astrophysics Data System (ADS)

Stober, Gunter; Sommer, Svenja; Schult, Carsten; Latteck, Ralph; Chau, Jorge L.

2018-05-01

We present observations obtained with the Middle Atmosphere Alomar Radar System (MAARSY) to investigate short-period wave-like features using polar mesospheric summer echoes (PMSEs) as a tracer for the neutral dynamics. We conducted a multibeam experiment including 67 different beam directions during a 9-day campaign in June 2013. We identified two Kelvin-Helmholtz instability (KHI) events from the signal morphology of PMSE. The MAARSY observations are complemented by collocated meteor radar wind data to determine the mesoscale gravity wave activity and the vertical structure of the wind field above the PMSE. The KHIs occurred in a strong shear flow with Richardson numbers Ri < 0.25. In addition, we observed 15 wave-like events in our MAARSY multibeam observations applying a sophisticated decomposition of the radial velocity measurements using volume velocity processing. We retrieved the horizontal wavelength, intrinsic frequency, propagation direction, and phase speed from the horizontally resolved wind variability for 15 events. These events showed horizontal wavelengths between 20 and 40 km, vertical wavelengths between 5 and 10 km, and rather high intrinsic phase speeds between 45 and 85 m s-1 with intrinsic periods of 5-10 min.

Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations.

PubMed

Bernetti, Mattia; Masetti, Matteo; Pietrucci, Fabio; Blackledge, Martin; Jensen, Malene Ringkjobing; Recanatini, Maurizio; Mollica, Luca; Cavalli, Andrea

2017-10-19

Intrinsically disordered proteins (IDPs) are emerging as an important class of the proteome. Being able to interact with different molecular targets, they participate in many physiological and pathological activities. However, due to their intrinsically heterogeneous nature, determining the equilibrium properties of IDPs is still a challenge for biophysics. Herein, we applied state-of-the-art enhanced sampling methods to Sev N TAIL , a test case of IDPs, and constructed a bin-based kinetic model to unveil the underlying kinetics. To validate our simulation strategy, we compared the predicted NMR properties against available experimental data. Our simulations reveal a rough free-energy surface comprising multiple local minima, which are separated by low energy barriers. Moreover, we identified interconversion rates between the main kinetic states, which lie in the sub-μs time scales, as suggested in previous works for Sev N TAIL . Therefore, the emerging picture is in agreement with the atomic-level properties possessed by the free IDP in solution. By providing both a thermodynamic and kinetic characterization of this IDP test case, our study demonstrates how computational methods can be effective tools for studying this challenging class of proteins.

Defective boron nitride nanotubes: mechanical properties, electronic structures and failure behaviors

NASA Astrophysics Data System (ADS)

Wang, Huan; Ding, Ning; Zhao, Xian; Wu, Chi-Man Lawrence

2018-03-01

Due to their excellent physical and chemical characteristics, boron nitride nanotubes (BNNTs) are regarded as a complementary addition to carbon nanotubes. Pioneer studies have demonstrated that defects in carbon nanotubes are considered tools for tuning the physical properties of these materials. In the present work, investigation on the mechanical and electronic properties of pristine and defective BNNTs was performed using the density functional theory method. The analysis on the intrinsic strength, stiffness, and failure critical strain of different types of BNNTs was conducted systematically. The computing results showed that the intrinsic strength of BNNTs decreased linearly with the increased Stone-Wales (SW) defect density around the axis. The SW defect density along the axis played a minor role on the changing of mechanical properties of BNNTs. The BNNT with a B vacancy expressed higher intrinsic strength than that of the N vacancy model. The final failure of the pristine BNNTs was due to the fracture of the Type1 bonds under the mechanical strain. Defects like SW or vacancy are served as the initial break site of BNNTs. Applying strain or creating defects are both effective methods for reducing the band gap of BNNTs.

A tonoplast intrinsic protein in Gardenia jasminoides

NASA Astrophysics Data System (ADS)

Gao, Lan; Li, Hao-Ming

2017-08-01

Physiological and molecular studies proved that plasma membrane intrinsic proteins (PIPs) and tonoplast intrinsic proteins (TIPs) subfamily of aquaporins play key functions in plant water homeostasis. Five specialized subgroups (TIP1-5) of TIPs have been found in higher plants, in which the TIP1 and TIP2 isoforms are the largest arbitrary groups. TIPs have high water-transport activity than PIPs, some TIPs can transport other small molecule such as urea, ammonia, hydrogen peroxide, and carbon dioxide. In this work, the structure of the putative tonoplast aquaporin from Gardenia jasminoides (GjTIP) was analyzed. Its transcript level has increased during fruit maturation. A phylogenetic analysis indicates that the protein belongs to TIP1 subfamily. A three-dimensional model structure of GjTIP was built based on crystal structure of an ammonia-permeable AtTIP2-1 from Arabidopsis thaliana. The model structure displayed as a homo-tetramer, each monomer has six trans-membrane and two half-membrane-spanning α helices. The data suggests that the GjTIP has tendency to be a mixed function aquaporin, might involve in water, urea and hydrogen peroxide transport, and the gating machanism founded in some AQPs involving pH and phosphorylation response have not been proved in GjTIP.

Critical Role of Monoclinic Polarization Rotation in High-Performance Perovskite Piezoelectric Materials.

PubMed

Liu, Hui; Chen, Jun; Fan, Longlong; Ren, Yang; Pan, Zhao; Lalitha, K V; Rödel, Jürgen; Xing, Xianran

2017-07-07

High-performance piezoelectric materials constantly attract interest for both technological applications and fundamental research. The understanding of the origin of the high-performance piezoelectric property remains a challenge mainly due to the lack of direct experimental evidence. We perform in situ high-energy x-ray diffraction combined with 2D geometry scattering technology to reveal the underlying mechanism for the perovskite-type lead-based high-performance piezoelectric materials. The direct structural evidence reveals that the electric-field-driven continuous polarization rotation within the monoclinic plane plays a critical role to achieve the giant piezoelectric response. An intrinsic relationship between the crystal structure and piezoelectric performance in perovskite ferroelectrics has been established: A strong tendency of electric-field-driven polarization rotation generates peak piezoelectric performance and vice versa. Furthermore, the monoclinic M_{A} structure is the key feature to superior piezoelectric properties as compared to other structures such as monoclinic M_{B}, rhombohedral, and tetragonal. A high piezoelectric response originates from intrinsic lattice strain, but little from extrinsic domain switching. The present results will facilitate designing high-performance perovskite piezoelectric materials by enhancing the intrinsic lattice contribution with easy and continuous polarization rotation.

Thermodynamic study of the native and phosphorylated regulatory domain of the CFTR

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

Marasini, Carlotta, E-mail: marasini@ge.ibf.cnr.it; Galeno, Lauretta; Moran, Oscar

2012-07-06

Highlights: Black-Right-Pointing-Pointer CFTR mutations produce cystic fibrosis. Black-Right-Pointing-Pointer Chloride transport depends on the regulatory domain phosphorylation. Black-Right-Pointing-Pointer Regulatory domain is intrinsically disordered. Black-Right-Pointing-Pointer Secondary structure and protein stability change upon phosphorylation. -- Abstract: The regulatory domain (RD) of the cystic fibrosis transmembrane conductance regulator (CFTR), the defective protein in cystic fibrosis, is the region of the channel that regulates the CFTR activity with multiple phosphorylation sites. This domain is an intrinsically disordered protein, characterized by lack of stable or unique tertiary structure. The disordered character of a protein is directly correlated with its function. The flexibility of RD may bemore » important for its regulatory role: the continuous conformational change may be necessary for the progressive phosphorylation, and thus activation, of the channel. However, the lack of a defined and stable structure results in a considerable limitation when trying to in build a unique molecular model for the RD. Moreover, several evidences indicate significant structural differences between the native, non-phosphorylated state, and the multiple phosphorylated state of the protein. The aim of our work is to provide data to describe the conformations and the thermodynamic properties in these two functional states of RD. We have done the circular dichroism (CD) spectra in samples with a different degree of phosphorylation, from the non-phosphorylated state to a bona fide completely phosphorylated state. Analysis of CD spectra showed that the random coil and {beta}-sheets secondary structure decreased with the polypeptide phosphorylation, at expenses of an increase of {alpha}-helix. This observation lead to interpret phosphorylation as a mechanism favoring a more structured state. We also studied the thermal denaturation curves of the protein in the two conditions, monitoring the changes of the mean residue ellipticity measured at 222 nm as a function of temperature, between 20 and 95 Degree-Sign C. The thermodynamic analysis of the denaturation curves shows that phosphorylation of the protein induces a state of lower stability of R domain, characterized by a lower transition temperature, and by a smaller Gibbs free energy difference between the native and the unfolded states.« less

Identification of N-Terminal Lobe Motifs that Determine the Kinase Activity of the Catalytic Domains and Regulatory Strategies of Src and Csk Protein Tyrosine Kinases†

PubMed Central

Huang, Kezhen; Wang, Yue-Hao; Brown, Alex; Sun, Gongqin

2009-01-01

Csk and Src protein tyrosine kinases are structurally homologous, but use opposite regulatory strategies. The isolated catalytic domain of Csk is intrinsically inactive and is activated by interactions with the regulatory SH3 and SH2 domains, while the isolated catalytic domain of Src is intrinsically active and is suppressed by interactions with the regulatory SH3 and SH2 domains. The structural basis for why one isolated catalytic domain is intrinsically active while the other is inactive is not clear. In this current study, we identify the structural elements in the N-terminal lobe of the catalytic domain that render the Src catalytic domain active. These structural elements include the α-helix C region, a β-turn between the β-4 and β-5 strands, and an Arg residue at the beginning of the catalytic domain. These three motifs interact with each other to activate the Src catalytic domain, but the equivalent motifs in Csk directly interact with the regulatory domains that are important for Csk activation. The Src motifs can be grafted to the Csk catalytic domain to obtain an active Csk catalytic domain. These results, together with available Src and Csk tertiary structures, reveal an important structural switch that determines the kinase activity of a catalytic domain and dictates the regulatory strategy of a kinase. PMID:19244618

Extracting Intrinsic Functional Networks with Feature-Based Group Independent Component Analysis

ERIC Educational Resources Information Center

Calhoun, Vince D.; Allen, Elena

2013-01-01

There is increasing use of functional imaging data to understand the macro-connectome of the human brain. Of particular interest is the structure and function of intrinsic networks (regions exhibiting temporally coherent activity both at rest and while a task is being performed), which account for a significant portion of the variance in…

Drift paths of ions composing multiple-nose spectral structures near the inner edge of the plasma sheet

NASA Astrophysics Data System (ADS)

Ferradas, C. P.; Zhang, J.-C.; Spence, H. E.; Kistler, L. M.; Larsen, B. A.; Reeves, G.; Skoug, R.; Funsten, H.

2016-11-01

We present a case study of the H+, He+, and O+ multiple-nose structures observed by the Helium, Oxygen, Proton, and Electron instrument on board Van Allen Probe A over one complete orbit on 28 September 2013. Nose structures are observed near the inner edge of the plasma sheet and constitute the signatures of ion drift in the highly dynamic environment of the inner magnetosphere. We find that the multiple noses are intrinsically associated with variations in the solar wind. Backward ion drift path tracings show new details of the drift trajectories of these ions; i.e., multiple noses are formed by ions with a short drift time from the assumed source location to the inner region and whose trajectories (1) encircle the Earth different number of times or (2) encircle the Earth equal number of times but with different drift time, before reaching the observation site.

Ubiquitousness of link-density and link-pattern communities in real-world networks

NASA Astrophysics Data System (ADS)

Šubelj, L.; Bajec, M.

2012-01-01

Community structure appears to be an intrinsic property of many complex real-world networks. However, recent work shows that real-world networks reveal even more sophisticated modules than classical cohesive (link-density) communities. In particular, networks can also be naturally partitioned according to similar patterns of connectedness among the nodes, revealing link-pattern communities. We here propose a propagation based algorithm that can extract both link-density and link-pattern communities, without any prior knowledge of the true structure. The algorithm was first validated on different classes of synthetic benchmark networks with community structure, and also on random networks. We have further applied the algorithm to different social, information, technological and biological networks, where it indeed reveals meaningful (composites of) link-density and link-pattern communities. The results thus seem to imply that, similarly as link-density counterparts, link-pattern communities appear ubiquitous in nature and design.

How to assess communication, professionalism, collaboration and the other intrinsic CanMEDS roles in orthopedic residents: use of an objective structured clinical examination (OSCE)

PubMed Central

Dwyer, Tim; Takahashi, Susan Glover; Hynes, Melissa Kennedy; Herold, Jodi; Wasserstein, David; Nousiainen, Markku; Ferguson, Peter; Wadey, Veronica; Murnaghan, M. Lucas; Leroux, Tim; Semple, John; Hodges, Brian; Ogilvie-Harris, Darrell

2014-01-01

Background Assessing residents’ understanding and application of the 6 intrinsic CanMEDS roles (communicator, professional, manager, collaborator, health advocate, scholar) is challenging for postgraduate medical educators. We hypothesized that an objective structured clinical examination (OSCE) designed to assess multiple intrinsic CanMEDS roles would be sufficiently reliable and valid. Methods The OSCE comprised 6 10-minute stations, each testing 2 intrinsic roles using case-based scenarios (with or without the use of standardized patients). Residents were evaluated using 5-point scales and an overall performance rating at each station. Concurrent validity was sought by correlation with in-training evaluation reports (ITERs) from the last 12 months and an ordinal ranking created by program directors (PDs). Results Twenty-five residents from postgraduate years (PGY) 0, 3 and 5 participated. The interstation reliability for total test scores (percent) was 0.87, while reliability for each of the communicator, collaborator, manager and professional roles was greater than 0.8. Total test scores, individual station scores and individual CanMEDS role scores all showed a significant effect by PGY level. Analysis of the PD rankings of intrinsic roles demonstrated a high correlation with the OSCE role scores. A correlation was seen between ITER and OSCE for the communicator role, while the ITER medical expert and total scores highly correlated with the communicator, manager and professional OSCE scores. Conclusion An OSCE designed to assess the intrinsic CanMEDS roles was sufficiently valid and reliable for regular use in an orthopedic residency program. PMID:25078926

Effects of Formative Feedback on Intrinsic Motivation: Examining Ethnic Differences

ERIC Educational Resources Information Center

El, Ron Pat; Tillema, Harm; van Koppen, Sabine W. M.

2012-01-01

In this study we investigate the influence of ethnic differences on student motivation when learning from formative feedback. Interpersonal teacher behavior and student motivational needs are used to explain the effects of assessment for learning on intrinsic motivation by comparing students from different ethnic backgrounds. The final study's…

Incentives and intrinsic motivation in healthcare.

PubMed

Berdud, Mikel; Cabasés, Juan M; Nieto, Jorge

It has been established in the literature that workers within public organisations are intrinsically motivated. This paper is an empirical study of the healthcare sector using methods of qualitative analysis research, which aims to answer the following hypotheses: 1) doctors are intrinsically motivated; 2) economic incentives and control policies may undermine doctors' intrinsic motivation; and 3) well-designed incentives may encourage doctors' intrinsic motivation. We conducted semi-structured interviews à-la-Bewley with 16 doctors from Navarre's Healthcare Service (Servicio Navarro de Salud-Osasunbidea), Spain. The questions were based on current theories of intrinsic motivation and incentives to test the hypotheses. Interviewees were allowed to respond openly without time constraints. Relevant information was selected, quantified and analysed by using the qualitative concepts of saturation and codification. The results seem to confirm the hypotheses. Evidence supporting hypotheses 1 and 2 was gathered from all interviewees, as well as indications of the validity of hypothesis 3 based on interviewees' proposals of incentives. The conclusions could act as a guide to support the optimal design of incentive policies and schemes within health organisations when healthcare professionals are intrinsically motivated. Copyright © 2016 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

Content of intrinsic disorder influences the outcome of cell-free protein synthesis.

PubMed

Tokmakov, Alexander A; Kurotani, Atsushi; Ikeda, Mariko; Terazawa, Yumiko; Shirouzu, Mikako; Stefanov, Vasily; Sakurai, Tetsuya; Yokoyama, Shigeyuki

2015-09-11

Cell-free protein synthesis is used to produce proteins with various structural traits. Recent bioinformatics analyses indicate that more than half of eukaryotic proteins possess long intrinsically disordered regions. However, no systematic study concerning the connection between intrinsic disorder and expression success of cell-free protein synthesis has been presented until now. To address this issue, we examined correlations of the experimentally observed cell-free protein expression yields with the contents of intrinsic disorder bioinformatically predicted in the expressed sequences. This analysis revealed strong relationships between intrinsic disorder and protein amenability to heterologous cell-free expression. On the one hand, elevated disorder content was associated with the increased ratio of soluble expression. On the other hand, overall propensity for detectable protein expression decreased with disorder content. We further demonstrated that these tendencies are rooted in some distinct features of intrinsically disordered regions, such as low hydrophobicity, elevated surface accessibility and high abundance of sequence motifs for proteolytic degradation, including sites of ubiquitination and PEST sequences. Our findings suggest that identification of intrinsically disordered regions in the expressed amino acid sequences can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

Movement trajectories and habitat partitioning of small mammals in logged and unlogged rain forests on Borneo.

PubMed

Wells, Konstans; Pfeiffer, Martin; Lakim, Maklarin B; Kalko, Elisabeth K V

2006-09-01

1. Non-volant animals in tropical rain forests differ in their ability to exploit the habitat above the forest floor and also in their response to habitat variability. It is predicted that specific movement trajectories are determined both by intrinsic factors such as ecological specialization, morphology and body size and by structural features of the surrounding habitat such as undergrowth and availability of supportive structures. 2. We applied spool-and-line tracking in order to describe movement trajectories and habitat segregation of eight species of small mammals from an assemblage of Muridae, Tupaiidae and Sciuridae in the rain forest of Borneo where we followed a total of 13,525 m path. We also analysed specific changes in the movement patterns of the small mammals in relation to habitat stratification between logged and unlogged forests. Variables related to climbing activity of the tracked species as well as the supportive structures of the vegetation and undergrowth density were measured along their tracks. 3. Movement patterns of the small mammals differed significantly between species. Most similarities were found in congeneric species that converged strongly in body size and morphology. All species were affected in their movement patterns by the altered forest structure in logged forests with most differences found in Leopoldamys sabanus. However, the large proportions of short step lengths found in all species for both forest types and similar path tortuosity suggest that the main movement strategies of the small mammals were not influenced by logging but comprised generally a response to the heterogeneous habitat as opposed to random movement strategies predicted for homogeneous environments. 4. Overall shifts in microhabitat use showed no coherent trend among species. Multivariate (principal component) analysis revealed contrasting trends for convergent species, in particular for Maxomys rajah and M. surifer as well as for Tupaia longipes and T. tana, suggesting that each species was uniquely affected in its movement trajectories by a multiple set of environmental and intrinsic features.

Sequence periodicity in nucleosomal DNA and intrinsic curvature

PubMed Central

2010-01-01

Background Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Results Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. Conclusions The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA. PMID:20487515

Off-stoichiometric silver antimony telluride: An experimental study of transport properties with intrinsic and extrinsic doping

DOE PAGES

Nielsen, Michele D.; Jaworski, Christopher M.; Heremans, Joseph P.

2015-03-20

AgSbTe 2 is a thermoelectric semiconductor with an intrinsically low thermal conductivity and a valence band structure that is favorable to obtaining a high thermoelectric figure of merit zT. It also has a very small energy gap Eg ~ 7.6 ± 3 meV. As this gap is less than the thermal excitation energy at room temperature, near-intrinsic AgSbTe 2 is a two carrier system having both holes (concentration p) and electrons ( n). Good thermoelectric performance requires heavy p-type doping ( p > > n). This can be achieved with native defects or with extrinsic doping, e.g. with transition metalmore » element. The use of defect doping is complicated by the fact that many of the ternary Ag-Sb-Te and pseudo-binary Sb 2Te 3-Ag 2Te phase diagrams are contradictory. This paper determines the compositional region most favorable to creating a single phase material. Through a combination of intrinsic and extrinsic doping, values of zT > 1 are achieved, though not on single-phased material. In addition, we show that thermal conductivity is not affected by defects, further demonstrating that the low lattice thermal conductivity of I-V-VI 2 materials is due to an intrinsic mechanism, insensitive to changes in defect structure.« less

Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions

PubMed Central

Hu, Gang; Wu, Zhonghua

2017-01-01

Some of the intrinsically disordered proteins and protein regions are promiscuous interactors that are involved in one-to-many and many-to-one binding. Several studies have analyzed enrichment of intrinsic disorder among the promiscuous hub proteins. We extended these works by providing a detailed functional characterization of the disorder-enriched hub protein-protein interactions (PPIs), including both hubs and their interactors, and by analyzing their enrichment among disease-associated proteins. We focused on the human interactome, given its high degree of completeness and relevance to the analysis of the disease-linked proteins. We quantified and investigated numerous functional and structural characteristics of the disorder-enriched hub PPIs, including protein binding, structural stability, evolutionary conservation, several categories of functional sites, and presence of over twenty types of posttranslational modifications (PTMs). We showed that the disorder-enriched hub PPIs have a significantly enlarged number of disordered protein binding regions and long intrinsically disordered regions. They also include high numbers of targeting, catalytic, and many types of PTM sites. We empirically demonstrated that these hub PPIs are significantly enriched among 11 out of 18 considered classes of human diseases that are associated with at least 100 human proteins. Finally, we also illustrated how over a dozen specific human hubs utilize intrinsic disorder for their promiscuous PPIs. PMID:29257115

Mapping multivalency and differential affinities within large intrinsically disordered protein complexes with segmental motion analysis.

PubMed

Milles, Sigrid; Lemke, Edward A

2014-07-07

Intrinsically disordered proteins (IDPs) can bind to multiple interaction partners. Numerous binding regions in the IDP that act in concert through complex cooperative effects facilitate such interactions, but complicate studying IDP complexes. To address this challenge we developed a combined fluorescence correlation and time-resolved polarization spectroscopy approach to study the binding properties of the IDP nucleoporin153 (Nup153) to nuclear transport receptors (NTRs). The detection of segmental backbone mobility of Nup153 within the unperturbed complex provided a readout of local, region-specific binding properties that are usually masked in measurements of the whole IDP. The binding affinities of functionally and structurally diverse NTRs to distinct regions of Nup153 can differ by orders of magnitudes-a result with implications for the diversity of transport routes in nucleocytoplasmic transport. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Client Motivation for Therapy Scale: a measure of intrinsic motivation, extrinsic motivation, and amotivation for therapy.

PubMed

Pelletier, L G; Tuson, K M; Haddad, N K

1997-04-01

The purpose of this study was to examine the psychometric properties of a new measure of client motivation for therapy, the Client Motivation for Therapy Scale. This scale is designed to measure client's Intrinsic Motivation, four forms of regulation for Extrinsic Motivation (integrated, identified, introjected, and external regulation), and Amotivation for therapy. These subscales correspond to different forms of motivation identified by Deci and Ryan (1985) and fall along a self-determination continuum. An experimental version of the scale, along with related scales, was distributed to a total sample of 138 clients involved in therapy. The results supported the factor structure of the scale and revealed a satisfactory level of internal consistency. Correlations among the subscales revealed a simplex pattern that, in general, provides support for the self-determination continuum and the construct validity of the scale. Implications for research on client motivation for therapy are discussed.

Experimentally observed evolution between dynamic patterns and intrinsic localized modes in a driven nonlinear electrical cyclic lattice

NASA Astrophysics Data System (ADS)

Shige, S.; Miyasaka, K.; Shi, W.; Soga, Y.; Sato, M.; Sievers, A. J.

2018-02-01

Locked intrinsic localized modes (ILMs) and large amplitude lattice spatial modes (LSMs) have been experimentally measured for a driven 1-D nonlinear cyclic electric transmission line, where the nonlinear element is a saturable capacitor. Depending on the number of cells and electrical lattice damping an LSM of fixed shape can be tuned across the modal spectrum. Interestingly, by tuning the driver frequency away from this spectrum the LSM can be continuously converted into ILMs and vice versa. The differences in pattern formation between simulations and experimental findings are due to a low concentration of impurities. Through this novel nonlinear excitation and switching channel in cyclic lattices either energy balanced or unbalanced LSMs and ILMs may occur. Because of the general nature of these dynamical results for nonintegrable lattices applications are to be expected. The ultimate stability of driven aero machinery containing nonlinear periodic structures may be one example.

The direct and inverse problems of an air-saturated poroelastic cylinder submitted to acoustic radiation

NASA Astrophysics Data System (ADS)

Ogam, Erick; Fellah, Z. E. A.

2011-09-01

A wave-fluid saturated poroelastic structure interaction model based on the modified Biot theory (MBT) and plane-wave decomposition using orthogonal cylindrical functions is developed. The model is employed to recover from real data acquired in an anechoic chamber, the poromechanical properties of a soft cellular melamine cylinder submitted to an audible acoustic radiation. The inverse problem of acoustic diffraction is solved by constructing the objective functional given by the total square of the difference between predictions from the MBT interaction model and diffracted field data from experiment. The faculty of retrieval of the intrinsic poromechanical parameters from the diffracted acoustic fields, indicate that a wave initially propagating in a light fluid (air) medium, is able to carry in the absence of mechanical excitation of the specimen, information on the macroscopic mechanical properties which depend on the microstructural and intrinsic properties of the solid phase.

Present knowledge of electronic properties and charge transport of icosahedral boron-rich solids

NASA Astrophysics Data System (ADS)

Werheit, Helmut

2009-06-01

B12 icosahedra or related structure elements determine the different modifications of elementary boron and numerous boron-rich compounds from α-rhombohedral boron with 12 to YB66 type with about 1584 atoms per unit cell. Typical are well-defined high density intrinsic defects: Jahn-Teller distorted icosahedra, vacancies, incomplete occupancies, statistical occupancies and antisite defects. The correlation between intrinsic point defects and electron deficiencies solves the discrepancy between theoretically predicted metal and experimentally proved semiconducting character. The electron deficiencies generate split-off valence states, which are decisive for the electronic transport, a superposition of band-type and hopping-type conduction. Their share depends on actual conditions like temperature or pre-excitation. The theoretical model of bipolaron hopping is incompatible with numerous experiments. Technical application of the typically p-type icosahedral boron-rich solids requires suitable n-type counterparts; doping and other possibilities are discussed.

Optimizing the Learning Order of Chinese Characters Using a Novel Topological Sort Algorithm

PubMed Central

Wang, Jinzhao

2016-01-01

We present a novel algorithm for optimizing the order in which Chinese characters are learned, one that incorporates the benefits of learning them in order of usage frequency and in order of their hierarchal structural relationships. We show that our work outperforms previously published orders and algorithms. Our algorithm is applicable to any scheduling task where nodes have intrinsic differences in importance and must be visited in topological order. PMID:27706234

3D surface rendered MR images of the brain and its vasculature.

PubMed

Cline, H E; Lorensen, W E; Souza, S P; Jolesz, F A; Kikinis, R; Gerig, G; Kennedy, T E

1991-01-01

Both time-of-flight and phase contrast magnetic resonance angiography images are combined with stationary tissue images to provide data depicting two contrast relationships yielding intrinsic discrimination of brain matter and flowing blood. A computer analysis is based on nearest neighbor segmentation and the connection between anatomical structures to partition the images into different tissue categories: from which, high resolution brain parenchymal and vascular surfaces are constructed and rendered in juxtaposition, aiding in surgical planning.

NMR binding and crystal structure reveal that intrinsically-unstructured regulatory domain auto-inhibits PAK4 by a mechanism different from that of PAK1.

PubMed

Wang, Wei; Lim, Liangzhong; Baskaran, Yohendran; Manser, Ed; Song, Jianxing

2013-08-16

Six human PAK members are classified into groups I (PAKs 1-3) and II (PAK4-6). Previously, only group I PAKs were thought to be auto-inhibited but very recently PAK4, the prototype of group II PAKs, has also been shown to be auto-inhibited by its N-terminal regulatory domain. However, the complete auto-inhibitory domain (AID) sequence remains undefined and the mechanism underlying its auto-inhibition is largely elusive. Here, the N-terminal regulatory domain of PAK4 sufficient for auto-inhibiting and binding Cdc42/Rac was characterized to be intrinsically unstructured, but nevertheless we identified the entire AID sequence by NMR. Strikingly, an AID peptide was derived by deleting the binding-unnecessary residues, which has a Kd of 320 nM to the PAK4 catalytic domain. Consequently, the PAK4 crystal structure complexed with the entire AID has been determined, which reveals that the complete kinase cleft is occupied by 20 AID residuescomposed of an N-terminal α-helix and a previously-identified pseudosubstrate motif, thus achieving auto-inhibition. Our study reveals that PAK4 is auto-inhibited by a novel mechanism which is completely different from that for PAK1, thus bearing critical implications for design of inhibitors specific for group II PAKs. Copyright © 2013 Elsevier Inc. All rights reserved.

Thin silica shell coated Ag assembled nanostructures for expanding generality of SERS analytes

PubMed Central

Kang, Yoo-Lee; Lee, Minwoo; Kang, Homan; Kim, Jaehi; Pham, Xuan-Hung; Kim, Tae Han; Hahm, Eunil; Lee, Yoon-Sik; Jeong, Dae Hong

2017-01-01

Surface-enhanced Raman scattering (SERS) provides a unique non-destructive spectroscopic fingerprint for chemical detection. However, intrinsic differences in affinity of analyte molecules to metal surface hinder SERS as a universal quantitative detection tool for various analyte molecules simultaneously. This must be overcome while keeping close proximity of analyte molecules to the metal surface. Moreover, assembled metal nanoparticles (NPs) structures might be beneficial for sensitive and reliable detection of chemicals than single NP structures. For this purpose, here we introduce thin silica-coated and assembled Ag NPs (SiO2@Ag@SiO2 NPs) for simultaneous and quantitative detection of chemicals that have different intrinsic affinities to silver metal. These SiO2@Ag@SiO2 NPs could detect each SERS peak of aniline or 4-aminothiophenol (4-ATP) from the mixture with limits of detection (LOD) of 93 ppm and 54 ppb, respectively. E-field distribution based on interparticle distance was simulated using discrete dipole approximation (DDA) calculation to gain insight into enhanced scattering of these thin silica coated Ag NP assemblies. These NPs were successfully applied to detect aniline in river water and tap water. Results suggest that SiO2@Ag@SiO2 NP-based SERS detection systems can be used as a simple and universal detection tool for environment pollutants and food safety. PMID:28570633

HdeB chaperone activity is coupled to its intrinsic dynamic properties

PubMed Central

Ding, Jienv; Yang, Chengfeng; Niu, Xiaogang; Hu, Yunfei; Jin, Changwen

2015-01-01

Enteric bacteria encounter extreme acidity when passing through hosts’ stomach. Since the bacterial periplasmic space quickly equilibrates with outer environment, an efficient acid resistance mechanism is essential in preventing irreversible protein denaturation/aggregation and maintaining bacteria viability. HdeB, along with its homolog HdeA, was identified as a periplasmic acid-resistant chaperone. Both proteins exist as homodimers and share similar monomeric structures under neutral pH, while showing different dimeric packing interfaces. Previous investigations show that HdeA functions through an acid-induced dimer-to-monomer transition and partial unfolding at low pH (pH 2–3), resulting in exposure of hydrophobic surfaces that bind substrate proteins. In contrast, HdeB appears to have a much higher optimal activation pH (pH 4–5), under which condition the protein maintains a well-folded dimer and the mechanism for its chaperone activity remains elusive. Herein, we present an NMR study of HdeB to investigate its dynamic properties. Our results reveal that HdeB undergoes significant micro- to milli-second timescale conformational exchanges at neutral to near-neutral pH, under the later condition it exhibits optimal activity. The current study indicates that HdeB activation is coupled to its intrinsic dynamics instead of structural changes, and therefore its functional mechanism is apparently different from HdeA. PMID:26593705

Hydrogen-enhanced clusterization of intrinsic defects and impurities in silicon

NASA Astrophysics Data System (ADS)

Mukashev, B. N.; Abdullin, Kh. A.; Gorelkinskii, Yu. V.; Tamendarov, M. F.; Tokmoldin, S. Zh

2001-01-01

Formation of intrinsic and impurity defect complexes in hydrogenated monocrystalline silicon is studied. Hydrogen was incorporated into samples by different ways: either by proton implantation at 80 and 300 K, or by annealing at 1250°C for 30-60 min in a sealed quartz ampoule containing ∼10 -3 ml of distilled water, or by treatment in hydrogen plasma. Radiation defects were incorporated either during the hydrogen implantation or by additional irradiation with protons or α-particles. The measurements were performed by electron paramagnetic resonance (EPR), deep level transient spectroscopy (DLTS) and infrared absorption (IR) methods. Essential differences of defect formation processes in hydrogenated samples as compared with reference samples were detected. The main reasons responsible for the differences are (i) hydrogen precipitation in a supersaturated solution during thermal treatment; (ii) interaction of hydrogen with defects and impurities and hydrogen-induced formation of defects; (iii) ability of hydrogen to play the role of accelerator of impurities precipitation. These factors result in the formation of vacancy-related, interstitial-related and impurity clusters which are observed only in the presence of hydrogen. The nature of the clusters and possible models of their structure are discussed.

Quantitative spectral light scattering polarimetry for monitoring fractal growth pattern of Bacillus thuringiensis bacterial colonies

NASA Astrophysics Data System (ADS)

Banerjee, Paromita; Soni, Jalpa; Ghosh, Nirmalya; Sengupta, Tapas K.

2013-02-01

It is of considerable current interest to develop various methods which help to understand and quantify the cellular association in growing bacterial colonies and is also important in terms of detection and identification of a bacterial species. A novel approach is used here to probe the morphological structural changes occurring during the growth of the bacterial colony of Bacillus thuringiensis under different environmental conditions (in normal nutrient agar, in presence of glucose - acting as additional nutrient and additional 3mM arsenate as additional toxic material). This approach combines the quantitative Mueller matrix polarimetry to extract intrinsic polarization properties and inverse analysis of the polarization preserving part of the light scattering spectra to determine the fractal parameter H (Hurst exponent) using Born approximation. Interesting differences are observed in the intrinsic polarization parameters and also in the Hurst exponent, which is a measurement of the fractality of a pattern formed by bacteria while growing as a colony. These findings are further confirmed with optical microscopic studies of the same sample and the results indicate a very strong and distinct dependence on the environmental conditions during growth, which can be exploited to quantify different bacterial species and their growth patterns.

The influence of different cucumariosides on immunogenicity of OmpF porin from Yersinia pseudotuberulosis as a model protein antigen of tubular immunostimulating complex

NASA Astrophysics Data System (ADS)

Sanina, N. M.; Chopenko, N. S.; Davydova, L. A.; Mazeika, A. N.; Portnyagina, O. Yu.; Kim, N. Yu.; Golotin, V. A.; Kostetsky, E. Y.; Shnyrov, V. L.

2017-09-01

Nanoparticulate tubular immunostimulating complex (TI-complex) is a novel promising adjuvant carrier of antigens allowing to create safe and effective vaccines of new generation. The adjuvant activity of TI-complexes based on monogalactosyldyacylglycerol (MGDG) from the sea alga Ulva lactuca and different triterpene glycosides cucumariosides (CDs) from marine invertebrate Cucumaria japonica and their fractions was studied to assess effects of different CDs on the immunogenicity of porin OmpF from Yersinia pseudotuberculosis (YOmpF). TI-complexes with cucumarioside A2-2 (CDA2-2) maximally stimulated anti-porin antibody production. Studies of protein intrinsic fluorescence showed that all CDs had a relaxing effect on the conformation of YOmpF, loosening peripheral region of protein and promoting exposure of the protein antigenic determinants to the water environment. The greatest immunostimulating effect of TI-complexes comprising CDA2-2 was accompanied by mild effect of this CD on the tertiary structure of protein antigen YOmpF, whereas cucumarioside E (CDE) and cucumarioside A2-4 (CDA2-4) caused especially sharp redistribution of spectral form of the YOmpF corresponding to the emission of an intrinsic protein fluorophore tryptophan.

Ensemble-based evaluation for protein structure models.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-06-15

Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts' intuitive assessment of computational models and provides information of practical usefulness of models. https://bitbucket.org/mjamroz/flexscore dkihara@purdue.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Ensemble-based evaluation for protein structure models

PubMed Central

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2016-01-01

Motivation: Comparing protein tertiary structures is a fundamental procedure in structural biology and protein bioinformatics. Structure comparison is important particularly for evaluating computational protein structure models. Most of the model structure evaluation methods perform rigid body superimposition of a structure model to its crystal structure and measure the difference of the corresponding residue or atom positions between them. However, these methods neglect intrinsic flexibility of proteins by treating the native structure as a rigid molecule. Because different parts of proteins have different levels of flexibility, for example, exposed loop regions are usually more flexible than the core region of a protein structure, disagreement of a model to the native needs to be evaluated differently depending on the flexibility of residues in a protein. Results: We propose a score named FlexScore for comparing protein structures that consider flexibility of each residue in the native state of proteins. Flexibility information may be extracted from experiments such as NMR or molecular dynamics simulation. FlexScore considers an ensemble of conformations of a protein described as a multivariate Gaussian distribution of atomic displacements and compares a query computational model with the ensemble. We compare FlexScore with other commonly used structure similarity scores over various examples. FlexScore agrees with experts’ intuitive assessment of computational models and provides information of practical usefulness of models. Availability and implementation: https://bitbucket.org/mjamroz/flexscore Contact: dkihara@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307633

Ensemble models of proteins and protein domains based on distance distribution restraints.

PubMed

Jeschke, Gunnar

2016-04-01

Conformational ensembles of intrinsically disordered peptide chains are not fully determined by experimental observations. Uncertainty due to lack of experimental restraints and due to intrinsic disorder can be distinguished if distance distributions restraints are available. Such restraints can be obtained from pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy applied to pairs of spin labels. Here, we introduce a Monte Carlo approach for generating conformational ensembles that are consistent with a set of distance distribution restraints, backbone dihedral angle statistics in known protein structures, and optionally, secondary structure propensities or membrane immersion depths. The approach is tested with simulated restraints for a terminal and an internal loop and for a protein with 69 residues by using sets of sparse restraints for underlying well-defined conformations and for published ensembles of a premolten globule-like and a coil-like intrinsically disordered protein. © 2016 Wiley Periodicals, Inc.

Obesity and Cancer Metabolism: A Perspective on Interacting Tumor-Intrinsic and Extrinsic Factors.

PubMed

Doerstling, Steven S; O'Flanagan, Ciara H; Hursting, Stephen D

2017-01-01

Obesity is associated with increased risk and poor prognosis of many types of cancers. Several obesity-related host factors involved in systemic metabolism can influence tumor initiation, progression, and/or response to therapy, and these have been implicated as key contributors to the complex effects of obesity on cancer incidence and outcomes. Such host factors include systemic metabolic regulators including insulin, insulin-like growth factor 1, adipokines, inflammation-related molecules, and steroid hormones, as well as the cellular and structural components of the tumor microenvironment, particularly adipose tissue. These secreted and structural host factors are extrinsic to, and interact with, the intrinsic metabolic characteristics of cancer cells to influence their growth and spread. This review will focus on the interplay of these tumor cell-intrinsic and extrinsic factors in the context of energy balance, with the objective of identifying new intervention targets for preventing obesity-associated cancer.

Assemblages of animals around urban structures: testing hypotheses of patterns in sediments under boat-mooring pontoons.

PubMed

Lindegarth, M

2001-05-01

Assemblages of animals in soft-sediments were studied in relation to pontoons for mooring private boats in two estuaries near Sydney, Australia. Based on previously observed patterns around other types of artificial structures, it was predicted that assemblages of animals under pontoons would be different from those in similar areas away from pontoons. Hypotheses about overall differences in average abundance and composition between sites with and without pontoons were tested, as were hypotheses about variable differences among and within estuaries. Analyses revealed that there were fewer crustaceans under pontoons in one estuary. The most conspicuous patterns related to pontoons were, however, differences in variability among sites with pontoons compared to sites without pontoons. Differences in spatial variability were found for the overall multivariate structure using Bray-Curtis dissimilarities and for abundances of most major taxa. Total abundance was approximately 60 times more variable among sites without pontoons and number of taxa were seven times more variable among sites with pontoons. Such patterns indicate that impacts of pontoons occur at some sites but not at others. This may be explained by intrinsic differences among sites or by differences in practices for maintenance. Predictions from these two contrasting models need to be tested in order to achieve efficient management of this type of structure.

Relationships between Academic Intrinsic Motivation and Anxiety in Children and Young Adolescents.

ERIC Educational Resources Information Center

Gottfried, Adele Eskeles

1982-01-01

Investigates the relationship between academic intrinsic motivation and anxiety when these variables are differentiated into academic subject areas. Results showed fourth and seventh graders differed in the pattern of relationships. Results clearly show academic intrinsic motivation and anxiety are negatively related and differentiated according…

Design of catalysts by different substituent groups to the ;cut g-C3N4; single layer

NASA Astrophysics Data System (ADS)

Xu, Weiwei; Tang, Chao; Chen, Chongyang; Li, Youyong; Xu, Lai

2017-09-01

Graphitic carbon nitride has been wildly studied as a kind of promising photocatalysts for hydrogen evolution. However, it has a low intrinsic activity. Herein, we designed new periodic structures "cut g-C3N4", and adding the new substituent groups. We employed density functional theory to calculate the charge distribution and catalytic properties of hydrogen evolution on the structures. We got a theoretical view that introducing conjugate substituents can enhance the catalytic performance for hydrogen evolution. Furthermore, it provided a theoretical guidance for the reasonable design of two dimensional non-metallic photocatalysts, with lower activation barrier of the catalytic reaction.

Race-Conscious Professionalism and African American Representation in Academic Medicine.

PubMed

Powers, Brian W; White, Augustus A; Oriol, Nancy E; Jain, Sachin H

2016-07-01

African Americans remain substantially less likely than other physicians to hold academic appointments. The roots of these disparities stem from different extrinsic and intrinsic forces that guide career development. Efforts to ameliorate African American underrepresentation in academic medicine have traditionally focused on modifying structural and extrinsic barriers through undergraduate and graduate outreach, diversity and inclusion initiatives at medical schools, and faculty development programs. Although essential, these initiatives fail to confront the unique intrinsic forces that shape career development. America's ignoble history of violence, racism, and exclusion exposes African American physicians to distinct personal pressures and motivations that shape professional development and career goals. This article explores these intrinsic pressures with a focus on their historical roots; reviews evidence of their effect on physician development; and considers the implications of these trends for improving African American representation in academic medicine. The paradigm of "race-conscious professionalism" is used to understand the dual obligation encountered by many minority physicians not only to pursue excellence in their field but also to leverage their professional stature to improve the well-being of their communities. Intrinsic motivations introduced by race-conscious professionalism complicate efforts to increase the representation of minorities in academic medicine. For many African American physicians, a desire to have their work focused on the community will be at odds with traditional paths to professional advancement. Specific policy options are discussed that would leverage race-conscious professionalism as a draw to a career in academic medicine, rather than a force that diverts commitment elsewhere.

The Moderating Effects of Group Membership and Growth Need Strength on the Relationships between Job Characteristics and Job Satisfaction, Job Involvement, and Intrinsic Motivation.

DTIC Science & Technology

1979-12-01

STRENGTH ON THE RELATIONSHIPS BETWEEN JOB CHARACTERISTICS AND JOB SATISFACTION, JOB INVOLVEMENT AND INTRINSIC MOTIVATION Master’s Thesis / David L... Motivation -Hygiene Theory ...... ..... .. . 11 Job Characteristics and Individual Difference . . 13 An Interactive Approach. . . . .......... 14 Refinement of...characteristics and intrinsic motivation , job involvement, and job satisfaction. Measures used to describe the job characteristics and intrinsic motivation are

Evolution of haploid-diploid life cycles when haploid and diploid fitnesses are not equal.

PubMed

Scott, Michael F; Rescan, Marie

2017-02-01

Many organisms spend a significant portion of their life cycle as haploids and as diploids (a haploid-diploid life cycle). However, the evolutionary processes that could maintain this sort of life cycle are unclear. Most previous models of ploidy evolution have assumed that the fitness effects of new mutations are equal in haploids and homozygous diploids, however, this equivalency is not supported by empirical data. With different mutational effects, the overall (intrinsic) fitness of a haploid would not be equal to that of a diploid after a series of substitution events. Intrinsic fitness differences between haploids and diploids can also arise directly, for example because diploids tend to have larger cell sizes than haploids. Here, we incorporate intrinsic fitness differences into genetic models for the evolution of time spent in the haploid versus diploid phases, in which ploidy affects whether new mutations are masked. Life-cycle evolution can be affected by intrinsic fitness differences between phases, the masking of mutations, or a combination of both. We find parameter ranges where these two selective forces act and show that the balance between them can favor convergence on a haploid-diploid life cycle, which is not observed in the absence of intrinsic fitness differences. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Quantum Dot Nanotoxicity Assessment Using the Zebrafish Embryo

PubMed Central

King-Heiden, Tisha C.; Wiecinski, Paige N.; Mangham, Andrew N.; Metz, Kevin M.; Nesbit, Dorothy; Pedersen, Joel A.; Hamers, Robert J.; Heideman, Warren; Peterson, Richard E.

2009-01-01

Quantum dots (QDs) hold promise for several biomedical, life sciences and photovoltaic applications. Substantial production volumes and environmental release are anticipated. QD toxicity may be intrinsic to their physicochemical properties, or result from the release of toxic components during breakdown. We hypothesized that developing zebrafish could be used to identify and distinguish these different types of toxicity. Embryos were exposed to aqueous suspensions of CdSecore/ZnSshell QDs functionalized with either poly-L-lysine or poly(ethylene glycol) terminated with methoxy, carboxylate, or amine groups. Toxicity was influenced by the QD coating, which also contributed to the QD suspension stability. At sublethal concentrations, many QD preparations produced characteristic signs of Cd toxicity that weakly correlated with metallothionein expression, indicating that QDs are only slightly degraded in vivo. QDs also produced distinctly different toxicity that could not be explained by Cd release. Using the zebrafish model, we were able to distinguish toxicity intrinsic to QDs from that caused by released metal ions. We conclude that developing zebrafish provide a rapid, low- cost approach for assessing structure-toxicity relationships of nanoparticles. PMID:19350942

On the intrinsic flexibility of the opioid receptor through multiscale modeling approaches

NASA Astrophysics Data System (ADS)

Vercauteren, Daniel; FosséPré, Mathieu; Leherte, Laurence; Laaksonen, Aatto

Numerous releases of G protein-coupled receptors crystalline structures created the opportunity for computational methods to widely explore their dynamics. Here, we study the biological implication of the intrinsic flexibility properties of opioid receptor OR. First, one performed classical all-atom (AA) Molecular Dynamics (MD) simulations of OR in its apo-form. We highlighted that the various degrees of bendability of the α-helices present important consequences on the plasticity of the binding site. Hence, this latter adopts a wide diversity of shape and volume, explaining why OR interacts with very diverse ligands. Then, one introduces a new strategy for parameterizing purely mechanical but precise coarse-grained (CG) elastic network models (ENMs). The CG ENMs reproduced in a high accurate way the flexibility properties of OR versus the AA simulations. At last, one uses network modularization to design multi-grained (MG) models. They represent a novel type of low resolution models, different in nature versus CG models as being true multi-resolution models, i . e ., each MG grouping a different number of residues. The three parts constitute hierarchical and multiscale approach for tackling the flexibility of OR.

Emergence of evolutionary cycles in size-structured food webs.

PubMed

Ritterskamp, Daniel; Bearup, Daniel; Blasius, Bernd

2016-11-07

The interplay of population dynamics and evolution within ecological communities has been of long-standing interest for ecologists and can give rise to evolutionary cycles, e.g. taxon cycles. Evolutionary cycling was intensely studied in small communities with asymmetric competition; the latter drives the evolutionary processes. Here we demonstrate that evolutionary cycling arises naturally in larger communities if trophic interactions are present, since these are intrinsically asymmetric. To investigate the evolutionary dynamics of a trophic community, we use an allometric food web model. We find that evolutionary cycles emerge naturally for a large parameter ranges. The origin of the evolutionary dynamics is an intrinsic asymmetry in the feeding kernel which creates an evolutionary ratchet, driving species towards larger bodysize. We reveal different kinds of cycles: single morph cycles, and coevolutionary and mixed cycling of complete food webs. The latter refers to the case where each trophic level can have different evolutionary dynamics. We discuss the generality of our findings and conclude that ongoing evolution in food webs may be more frequent than commonly believed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Probing disorder in isometric pyrochlore and related complex oxides

NASA Astrophysics Data System (ADS)

Shamblin, Jacob; Feygenson, Mikhail; Neuefeind, Joerg; Tracy, Cameron L.; Zhang, Fuxiang; Finkeldei, Sarah; Bosbach, Dirk; Zhou, Haidong; Ewing, Rodney C.; Lang, Maik

2016-05-01

There has been an increased focus on understanding the energetics of structures with unconventional ordering (for example, correlated disorder that is heterogeneous across different length scales). In particular, compounds with the isometric pyrochlore structure, A2B2O7, can adopt a disordered, isometric fluorite-type structure, (A, B)4O7, under extreme conditions. Despite the importance of the disordering process there exists only a limited understanding of the role of local ordering on the energy landscape. We have used neutron total scattering to show that disordered fluorite (induced intrinsically by composition/stoichiometry or at far-from-equilibrium conditions produced by high-energy radiation) consists of a local orthorhombic structural unit that is repeated by a pseudo-translational symmetry, such that orthorhombic and isometric arrays coexist at different length scales. We also show that inversion in isometric spinel occurs by a similar process. This insight provides a new basis for understanding order-to-disorder transformations important for applications such as plutonium immobilization, fast ion conduction, and thermal barrier coatings.

m1A and m1G Potently Disrupt A-RNA Structure Due to the Intrinsic Instability of Hoogsteen Base Pairs

PubMed Central

Zhou, Huiqing; Kimsey, Isaac J.; Nikolova, Evgenia N.; Sathyamoorthy, Bharathwaj; Grazioli, Gianmarc; McSally, James; Bai, Tianyu; Wunderlich, Christoph H.; Kreutz, Christoph; Andricioaei, Ioan; Al-Hashimi, Hashim M.

2016-01-01

The B-DNA double helix can dynamically accommodate G–C and A–T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G–C+ and A–U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result, N1-methyl adenosine and N1-methyl guanosine, which occur in DNA as a form of alkylation damage, and in RNA as a posttranscriptional modification, have dramatically different consequences. They create G–C+ and A–U Hoogsteen base pairs in duplex DNA that maintain the structural integrity of the double helix, but block base pairing all together and induce local duplex melting in RNA, providing a mechanism for potently disrupting RNA structure through posttranscriptional modifications. The markedly different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help meet the opposing requirements of maintaining genome stability on one hand, and dynamically modulating the structure of the epitranscriptome on the other. PMID:27478929

Structure-property relationships in directionally solidified single crystal NiAl

NASA Technical Reports Server (NTRS)

Noebe, R. D.; Kim, J. T.; Gibala, R.

1987-01-01

The ordered intermetallic alloy NiAl is being considered as a potential high temperature structural material, but lack of ductility at ambient temperatures, especially in polycrystalline form, is presently a major obstacle in achieving this goal. Even general agreement of the intrinsic ductility that can be achieved in monocrystals is in dispute. In order to understand this problem, two directionally solidified ingots of NiAl which displayed known differences in ductility were characterized in sufficient detail to identify the corresponding microstructural differences. It was found that the type and size of casting defects, i.e., porosity, present in the material were the major factors in controlling ductility of NiAl single crystals and could explain the order of magnitude variance in fracture strains reported in the literature.

A Novel Intrinsic Interface State Controlled by Atomic Stacking Sequence at Interfaces of SiC/SiO2.

PubMed

Matsushita, Yu-Ichiro; Oshiyama, Atsushi

2017-10-11

On the basis of ab initio total-energy electronic-structure calculations, we find that electron states localized at the SiC/SiO 2 interface emerge in the energy region between 0.3 eV below and 1.2 eV above the bulk conduction-band minimum (CBM) of SiC, being sensitive to the sequence of atomic bilayers in SiC near the interface. These new interface states unrecognized in the past are due to the peculiar characteristics of the CBM states that are distributed along the crystallographic channels. We also find that the electron doping modifies the energetics among the different stacking structures. Implication for performance of electron devices fabricated on different SiC surfaces is discussed.

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

Amaro, Mariana; Wellbrock, Thorben; Birch, David J. S.

The fluorescence decay of beta-amyloid's (Aβ) intrinsic fluorophore tyrosine has been used for sensing the oligomer formation of dye-labelled Aβ monomers and the results compared with previously studied oligomerization of the non-labelled Aβ peptides. It has been demonstrated that two different sized, covalently bound probes 7-diethylaminocoumarin-3-carbonyl and Hilyte Fluor 488 (HLF), alter the rate and character of oligomerization to different extents. The ability of HLF to inhibit formation of highly ordered structures containing beta-sheets was also shown. The implications of our findings for using fluorescence methods in amyloidosis research are discussed and the advantages of this auto-fluorescence approach highlighted.

Moral Foundations Predict Religious Orientations in New Zealand

PubMed Central

Bulbulia, Joseph; Osborne, Danny; Sibley, Chris G.

2013-01-01

The interplay between religion, morality, and community-making is a core theme across human experience, yet scholars have only recently begun to quantify these links. Drawing on a sample of 1512 self-identified religious – mainly Christian (86.0%) – New Zealanders, we used structural equation modeling to test hypothesized associations between Religious Orientations (Quest, Intrinsic, Extrinsic Personal, Extrinsic Social) and Moral Foundations (Care/Harm, Fairness/Cheating, Loyalty/Betrayal, Authority/Subversion, Sanctity/Degradation). Our results show, for the first time in a comprehensive model, how different ways of valuing communities are associated with different ways of valuing religion. PMID:24339872

Validation Evidence of the Motivation for Teaching Scale in Secondary Education.

PubMed

Abós, Ángel; Sevil, Javier; Martín-Albo, José; Aibar, Alberto; García-González, Luis

2018-04-10

Grounded in self-determination theory, the aim of this study was to develop a scale with adequate psychometric properties to assess motivation for teaching and to explain some outcomes of secondary education teachers at work. The sample comprised 584 secondary education teachers. Analyses supported the five-factor model (intrinsic motivation, identified regulation, introjected regulation, external regulation and amotivation) and indicated the presence of a continuum of self-determination. Evidence of reliability was provided by Cronbach's alpha, composite reliability and average variance extracted. Multigroup confirmatory factor analyses supported the partial invariance (configural and metric) of the scale in different sub-samples, in terms of gender and type of school. Concurrent validity was analyzed by a structural equation modeling that explained 71% of the work dedication variance and 69% of the boredom at work variance. Work dedication was positively predicted by intrinsic motivation (ß = .56, p < .001) and external regulation (ß = .29, p < .001) and negatively predicted by introjected regulation (ß = -.22, p < .001) and amotivation (ß = -.49, p < .001). Boredom at work was negatively predicted by intrinsic motivation (ß = -.28, p < .005) and positively predicted by amotivation (ß = .68, p < .001). The Motivation for Teaching Scale in Secondary Education (Spanish acronym EME-ES, Escala de Motivación por la Enseñanza en Educación Secundaria) is discussed as a valid and reliable instrument. This is the first specific scale in the work context of secondary teachers that has integrated the five-factor structure together with their dedication and boredom at work.

Prediction of sport adherence through the influence of autonomy-supportive coaching among spanish adolescent athletes.

PubMed

Almagro, Bartolomé J; Sáenz-López, Pedro; Moreno, Juan A

2010-01-01

The purpose of this study was to test a motivational model of the coach-athlete relationship, based on self-determination theory and on the hierarchical model of intrinsic and extrinsic motivation. The sample comprised of 608 athletes (ages of 12-17 years) completed the following measures: interest in athlete's input, praise for autonomous behavior, perceived autonomy, intrinsic motivation, and the intention to be physically active. Structural equation modeling results demonstrated that interest in athletes' input and praise for autonomous behavior predicted perceived autonomy, and perceived autonomy positively predicted intrinsic motivation. Finally, intrinsic motivation predicted the intention to be physically active in the future. The results are discussed in relation to the importance of the climate of autonomy support created by the coach on intrinsic motivation and adherence to sport by adolescent athletes. Further, the results provide information related to the possible objectives of future interventions for the education of coaches, with the goal of providing them with tools and strategies to favor the development of intrinsic motivation among their athletes. In conclusion, the climate of autonomy support created by the coach can predict the autonomy perceived by the athletes which predicts the intrinsic motivation experienced by the athletes, and therefore, their adherence to athletic practice. Key pointsImportance of the climate of autonomy support created by the coach on intrinsic motivation and adherence to sport by adolescent athletes.Interest in athletes' input and praise for autonomous behavior predicted perceived autonomy, and perceived autonomy positively predicted intrinsic motivation.Intrinsic motivation predicted the intention to be physically active in the future.

Prediction of Sport Adherence Through the Influence of Autonomy-Supportive Coaching Among Spanish Adolescent Athletes

PubMed Central

Almagro, Bartolomé J.; Sáenz-López, Pedro; Moreno, Juan A.

2010-01-01

The purpose of this study was to test a motivational model of the coach-athlete relationship, based on self-determination theory and on the hierarchical model of intrinsic and extrinsic motivation. The sample comprised of 608 athletes (ages of 12-17 years) completed the following measures: interest in athlete's input, praise for autonomous behavior, perceived autonomy, intrinsic motivation, and the intention to be physically active. Structural equation modeling results demonstrated that interest in athletes' input and praise for autonomous behavior predicted perceived autonomy, and perceived autonomy positively predicted intrinsic motivation. Finally, intrinsic motivation predicted the intention to be physically active in the future. The results are discussed in relation to the importance of the climate of autonomy support created by the coach on intrinsic motivation and adherence to sport by adolescent athletes. Further, the results provide information related to the possible objectives of future interventions for the education of coaches, with the goal of providing them with tools and strategies to favor the development of intrinsic motivation among their athletes. In conclusion, the climate of autonomy support created by the coach can predict the autonomy perceived by the athletes which predicts the intrinsic motivation experienced by the athletes, and therefore, their adherence to athletic practice. Key points Importance of the climate of autonomy support created by the coach on intrinsic motivation and adherence to sport by adolescent athletes. Interest in athletes' input and praise for autonomous behavior predicted perceived autonomy, and perceived autonomy positively predicted intrinsic motivation. Intrinsic motivation predicted the intention to be physically active in the future. PMID:24149380

Special Workshop: Kolsky/Split Hopkinson Pressure Bar Testing of Ceramics

DTIC Science & Technology

2006-09-01

merit) control armor performance and how these properties are controlled/ influenced by intrinsic (crystal structure, phase transitions, and single...reproducibility uncertainties (estimates of precision) could be quantified and also identify key parameters that should be controlled in SHPB/Kolsky testing...control performance? Are there figures of merit? How are the mechanical properties influenced by intrinsic and extrinsic material characteristics

The Contributions of Intrinsic and Extrinsic Reading Motivation to the Development of Reading Competence over Summer Vacation

ERIC Educational Resources Information Center

Schaffner, Ellen; Schiefele, Ulrich

2016-01-01

This study addressed the role of reading motivation as a potential determinant of losses or gains in reading competence over six weeks of summer vacation (SV). Based on a sample of 223 third-grade elementary students, structural equation analyses showed that intrinsic reading motivation before SV contributed positively to both word and sentence…

Dynamical Coordination of Hand Intrinsic Muscles for Precision Grip in Diabetes Mellitus.

PubMed

Li, Ke; Wei, Na; Cheng, Mei; Hou, Xingguo; Song, Jun

2018-03-12

This study investigated the effects of diabetes mellitus (DM) on dynamical coordination of hand intrinsic muscles during precision grip. Precision grip was tested using a custom designed apparatus with stable and unstable loads, during which the surface electromyographic (sEMG) signals of the abductor pollicis brevis (APB) and first dorsal interosseous (FDI) were recorded simultaneously. Recurrence quantification analysis (RQA) was applied to quantify the dynamical structure of sEMG signals of the APB and FDI; and cross recurrence quantification analysis (CRQA) was used to assess the intermuscular coupling between the two intrinsic muscles. This study revealed that the DM altered the dynamical structure of muscle activation for the FDI and the dynamical intermuscular coordination between the APB and FDI during precision grip. A reinforced feedforward mechanism that compensates the loss of sensory feedbacks in DM may be responsible for the stronger intermuscular coupling between the APB and FDI muscles. Sensory deficits in DM remarkably decreased the capacity of online motor adjustment based on sensory feedback, rendering a lower adaptability to the uncertainty of environment. This study shed light on inherent dynamical properties underlying the intrinsic muscle activation and intermuscular coordination for precision grip and the effects of DM on hand sensorimotor function.

Identification of Atg3 as an intrinsically disordered polypeptide yields insights into the molecular dynamics of autophagy-related proteins in yeast.

PubMed

Popelka, Hana; Uversky, Vladimir N; Klionsky, Daniel J

2014-06-01

The mechanism of autophagy relies on complex cell signaling and regulatory processes. Each cell contains many proteins that lack a rigid 3-dimensional structure under physiological conditions. These dynamic proteins, called intrinsically disordered proteins (IDPs) and protein regions (IDPRs), are predominantly involved in cell signaling and regulation. Yet, very little is known about their presence among proteins of the core autophagy machinery. In this work, we characterized the autophagy protein Atg3 from yeast and human along with 2 variants to show that Atg3 is an IDPRs-containing protein and that disorder/order predicted for these proteins from their amino acid sequence corresponds to their experimental characteristics. Based on this consensus, we applied the same prediction methods to all known Atg proteins from Saccharomyces cerevisiae. The data presented here provide an insight into the structural dynamics of each Atg protein. They also show that intrinsic disorder at various levels has to be taken into consideration for about half of the Atg proteins. This work should become a useful tool that will facilitate and encourage exploration of protein intrinsic disorder in autophagy.

14 CFR 29.573 - Damage Tolerance and Fatigue Evaluation of Composite Rotorcraft Structures.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Composite Rotorcraft Structures. 29.573 Section 29.573 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION... Structures. (a) Each applicant must evaluate the composite rotorcraft structure under the damage tolerance..., types, and sizes of damage, considering fatigue, environmental effects, intrinsic and discrete flaws...

14 CFR 27.573 - Damage Tolerance and Fatigue Evaluation of Composite Rotorcraft Structures.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Composite Rotorcraft Structures. 27.573 Section 27.573 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION... Structures. (a) Each applicant must evaluate the composite rotorcraft structure under the damage tolerance..., types, and sizes of damage, considering fatigue, environmental effects, intrinsic and discrete flaws...

14 CFR 27.573 - Damage Tolerance and Fatigue Evaluation of Composite Rotorcraft Structures.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Composite Rotorcraft Structures. 27.573 Section 27.573 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION... Structures. (a) Each applicant must evaluate the composite rotorcraft structure under the damage tolerance..., types, and sizes of damage, considering fatigue, environmental effects, intrinsic and discrete flaws...

14 CFR 29.573 - Damage Tolerance and Fatigue Evaluation of Composite Rotorcraft Structures.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Composite Rotorcraft Structures. 29.573 Section 29.573 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION... Structures. (a) Each applicant must evaluate the composite rotorcraft structure under the damage tolerance..., types, and sizes of damage, considering fatigue, environmental effects, intrinsic and discrete flaws...

14 CFR 27.573 - Damage Tolerance and Fatigue Evaluation of Composite Rotorcraft Structures.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Composite Rotorcraft Structures. 27.573 Section 27.573 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION... Structures. (a) Each applicant must evaluate the composite rotorcraft structure under the damage tolerance..., types, and sizes of damage, considering fatigue, environmental effects, intrinsic and discrete flaws...

14 CFR 29.573 - Damage Tolerance and Fatigue Evaluation of Composite Rotorcraft Structures.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Composite Rotorcraft Structures. 29.573 Section 29.573 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION... Structures. (a) Each applicant must evaluate the composite rotorcraft structure under the damage tolerance..., types, and sizes of damage, considering fatigue, environmental effects, intrinsic and discrete flaws...

Acceleration of vascularized bone tissue-engineered constructs in a large animal model combining intrinsic and extrinsic vascularization.

PubMed

Weigand, Annika; Beier, Justus P; Hess, Andreas; Gerber, Thomas; Arkudas, Andreas; Horch, Raymund E; Boos, Anja M

2015-05-01

During the last decades, a range of excellent and promising strategies in Bone Tissue Engineering have been developed. However, the remaining major problem is the lack of vascularization. In this study, extrinsic and intrinsic vascularization strategies were combined for acceleration of vascularization. For optimal biomechanical stability of the defect site and simplifying future transition into clinical application, a primary stable and approved nanostructured bone substitute in clinically relevant size was used. An arteriovenous (AV) loop was microsurgically created in sheep and implanted, together with the bone substitute, in either perforated titanium chambers (intrinsic/extrinsic) for different time intervals of up to 18 weeks or isolated Teflon(®) chambers (intrinsic) for 18 weeks. Over time, magnetic resonance imaging and micro-computed tomography (CT) analyses illustrate the dense vascularization arising from the AV loop. The bone substitute was completely interspersed with newly formed tissue after 12 weeks of intrinsic/extrinsic vascularization and after 18 weeks of intrinsic/extrinsic and intrinsic vascularization. Successful matrix change from an inorganic to an organic scaffold could be demonstrated in vascularized areas with scanning electron microscopy and energy dispersive X-ray spectroscopy. Using the intrinsic vascularization method only, the degradation of the scaffold and osteoclastic activity was significantly lower after 18 weeks, compared with 12 and 18 weeks in the combined intrinsic-extrinsic model. Immunohistochemical staining revealed an increase in bone tissue formation over time, without a difference between intrinsic/extrinsic and intrinsic vascularization after 18 weeks. This study presents the combination of extrinsic and intrinsic vascularization strategies for the generation of an axially vascularized bone substitute in clinically relevant size using a large animal model. The additional extrinsic vascularization promotes tissue ingrowth and remodeling processes of the bone substitute. Extrinsic vessels contribute to faster vascularization and finally anastomose with intrinsic vasculature, allowing microvascular transplantation of the bone substitute after a shorter prevascularization time than using the intrinsic method only. It can be reasonably assumed that the usage of perforated chambers can significantly reduce the time until transplantation of bone constructs. Finally, this study paves the way for further preclinical testing for proof of the concept as a basis for early clinical applicability.

A VHDL Core for Intrinsic Evolution of Discrete Time Filters with Signal Feedback

NASA Technical Reports Server (NTRS)

Gwaltney, David A.; Dutton, Kenneth

2005-01-01

The design of an Evolvable Machine VHDL Core is presented, representing a discrete-time processing structure capable of supporting control system applications. This VHDL Core is implemented in an FPGA and is interfaced with an evolutionary algorithm implemented in firmware on a Digital Signal Processor (DSP) to create an evolvable system platform. The salient features of this architecture are presented. The capability to implement IIR filter structures is presented along with the results of the intrinsic evolution of a filter. The robustness of the evolved filter design is tested and its unique characteristics are described.

Fine structure in the transition region: reaction force analyses of water-assisted proton transfers.

PubMed

Yepes, Diana; Murray, Jane S; Santos, Juan C; Toro-Labbé, Alejandro; Politzer, Peter; Jaque, Pablo

2013-07-01

We have analyzed the variation of the reaction force F(ξ) and the reaction force constant κ(ξ) along the intrinsic reaction coordinates ξ of the water-assisted proton transfer reactions of HX-N = Y (X,Y = O,S). The profile of the force constant of the vibration associated with the reactive mode, k ξ (ξ), was also determined. We compare our results to the corresponding intramolecular proton transfers in the absence of a water molecule. The presence of water promotes the proton transfers, decreasing the energy barriers by about 12 - 15 kcal mol(-1). This is due in part to much smaller bond angle changes being needed than when water is absent. The κ(ξ) profiles along the intrinsic reaction coordinates for the water-assisted processes show striking and intriguing differences in the transition regions. For the HS-N = S and HO-N = S systems, two κ(ξ) minima are obtained, whereas for HO-N = O only one minimum is found. The k ξ (ξ) show similar behavior in the transition regions. We propose that this fine structure reflects the degree of synchronicity of the two proton migrations in each case.

Intrinsic Cell Stress is Independent of Organization in Engineered Cell Sheets.

PubMed

van Loosdregt, Inge A E W; Dekker, Sylvia; Alford, Patrick W; Oomens, Cees W J; Loerakker, Sandra; Bouten, Carlijn V C

2018-06-01

Understanding cell contractility is of fundamental importance for cardiovascular tissue engineering, due to its major impact on the tissue's mechanical properties as well as the development of permanent dimensional changes, e.g., by contraction or dilatation of the tissue. Previous attempts to quantify contractile cellular stresses mostly used strongly aligned monolayers of cells, which might not represent the actual organization in engineered cardiovascular tissues such as heart valves. In the present study, therefore, we investigated whether differences in organization affect the magnitude of intrinsic stress generated by individual myofibroblasts, a frequently used cell source for in vitro engineered heart valves. Four different monolayer organizations were created via micro-contact printing of fibronectin lines on thin PDMS films, ranging from strongly anisotropic to isotropic. Thin film curvature, cell density, and actin stress fiber distribution were quantified, and subsequently, intrinsic stress and contractility of the monolayers were determined by incorporating these data into sample-specific finite element models. Our data indicate that the intrinsic stress exerted by the monolayers in each group correlates with cell density. Additionally, after normalizing for cell density and accounting for differences in alignment, no consistent differences in intrinsic contractility were found between the different monolayer organizations, suggesting that the intrinsic stress exerted by individual myofibroblasts is independent of the organization. Consequently, this study emphasizes the importance of choosing proper architectural properties for scaffolds in cardiovascular tissue engineering, as these directly affect the stresses in the tissue, which play a crucial role in both the functionality and remodeling of (engineered) cardiovascular tissues.

The effects of using screencasting as a multimedia pre-training tool to manage the intrinsic cognitive load of chemical equilibrium instruction for advanced high school chemistry students

NASA Astrophysics Data System (ADS)

Musallam, Ramsey

Chemistry is a complex knowledge domain. Specifically, research notes that Chemical Equilibrium presents greater cognitive challenges than other topics in chemistry. Cognitive Load Theory describes the impact a subject, and the learning environment, have on working memory. Intrinsic load is the facet of Cognitive Load Theory that explains the complexity innate to complex subjects. The purpose of this study was to build on the limited research into intrinsic cognitive load, by examining the effects of using multimedia screencasts as a pre-training technique to manage the intrinsic cognitive load of chemical equilibrium instruction for advanced high school chemistry students. A convenience sample of 62 fourth-year high school students enrolled in an advanced chemistry course from a co-ed high school in urban San Francisco were given a chemical equilibrium concept pre-test. Upon conclusion of the pre-test, students were randomly assigned to two groups: pre-training and no pre-training. The pre-training group received a 10 minute and 52 second pre-training screencast that provided definitions, concepts and an overview of chemical equilibrium. After pre-training both group received the same 50-minute instructional lecture. After instruction, all students were given a chemical equilibrium concept post-test. Independent sample t-tests were conducted to examine differences in performance and intrinsic load. No significant differences in performance or intrinsic load, as measured by ratings of mental effort, were observed on the pre-test. Significant differences in performance, t(60)=3.70, p=.0005, and intrinsic load, t(60)=5.34, p=.0001, were observed on the post-test. A significant correlation between total performance scores and total mental effort ratings was also observed, r(60)=-0.44, p=.0003. Because no significant differences in prior knowledge were observed, it can be concluded that pre-training was successful at reducing intrinsic load. Moreover, a significant correlation between performance and mental effort strengthens the argument that performance measures can be used to approximate intrinsic cognitive load.

First-principles study of lattice thermal conductivity in ZrTe5 and HfTe5

NASA Astrophysics Data System (ADS)

Wang, Cong; Wang, Haifeng; Chen, Y. B.; Yao, Shu-Hua; Zhou, Jian

2018-05-01

Recently, the layered transition-metal pentatellurides ZrTe5 and HfTe5 have attracted increasing attention because of their interesting topological electronic properties. Nevertheless, some of their other good physical properties seem to be ignored now. Actually, both ZrTe5 and HfTe5 have high electric conductivities (>105 Ω-1 m-1) and Seebeck coefficients (> 100 μV/K) at room temperature, thus making them promising thermoelectric materials. However, the disadvantage is that the thermal conductivities of the two materials are relatively high according to the few available experiments; meanwhile, the detailed mechanism of the intrinsic thermal conductivity has not been studied yet. Based on the density functional theory and the Boltzmann transport theory, we present here the theoretical study of the intrinsic lattice thermal conductivities of ZrTe5 and HfTe5, which are found to be in the range of 5-8 W/mṡK at room temperature and well consistent with the experimental results. We also find that the thermal conductivities of the two materials are anisotropic, which are mainly caused by their anisotropic crystal structures. Based on the detailed analysis, we proposed that the thermal conductivities of the two materials could possibly be reduced by different kinds of structural engineering at the atomic and mesoscopic scales, such as alloying, doping, nano-structuring, and polycrystalline structuring, which could make ZrTe5 and HfTe5 good thermoelectric materials for room temperature thermoelectric applications.

How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein?

PubMed

Bonetti, Daniela; Troilo, Francesca; Brunori, Maurizio; Longhi, Sonia; Gianni, Stefano

2018-04-24

The mechanism of interaction of an intrinsically disordered protein (IDP) with its physiological partner is characterized by a disorder-to-order transition in which a recognition and a binding step take place. Even if the mechanism is quite complex, IDPs tend to bind their partner in a cooperative manner such that it is generally possible to detect experimentally only the disordered unbound state and the structured complex. The interaction between the disordered C-terminal domain of the measles virus nucleoprotein (N TAIL ) and the X domain (XD) of the viral phosphoprotein allows us to detect and quantify the two distinct steps of the overall reaction. Here, we analyze the robustness of the folding of N TAIL upon binding to XD by measuring the effect on both the folding and binding steps of N TAIL when the structure of XD is modified. Because it has been shown that wild-type XD is structurally heterogeneous, populating an on-pathway intermediate under native conditions, we investigated the binding to 11 different site-directed variants of N TAIL of one particular variant of XD (I504A XD) that populates only the native state. Data reveal that the recognition and the folding steps are both affected by the structure of XD, indicating a highly malleable pathway. The experimental results are briefly discussed in the light of previous experiments on other IDPs. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Computer Simulations of Intrinsically Disordered Proteins

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Chatterjee, Prathit; Ham, Sihyun

2017-05-01

The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields. Thus, achieving an accurate structural characterization of IDPs via simulations is a challenge. It is also daunting to perform a configuration-space integration over heterogeneous structural ensembles sampled by IDPs to extract, in particular, protein configurational entropy. In this review, we summarize recent efforts devoted to the development of force fields and the critical evaluations of their performance when applied to IDPs. We also survey recent advances in computational methods for protein configurational entropy that aim to provide a thermodynamic link between structural disorder and protein activity.

Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings.

PubMed

Jensen, Malene Ringkjøbing; Markwick, Phineus R L; Meier, Sebastian; Griesinger, Christian; Zweckstetter, Markus; Grzesiek, Stephan; Bernadó, Pau; Blackledge, Martin

2009-09-09

Intrinsically disordered proteins (IDPs) inhabit a conformational landscape that is too complex to be described by classical structural biology, posing an entirely new set of questions concerning the molecular understanding of functional biology. The characterization of the conformational properties of IDPs, and the elucidation of the role they play in molecular function, is therefore one of the major challenges remaining for modern structural biology. NMR is the technique of choice for studying this class of proteins, providing information about structure, flexibility, and interactions at atomic resolution even in completely disordered states. In particular, residual dipolar couplings (RDCs) have been shown to be uniquely sensitive and powerful tools for characterizing local and long-range structural behavior in disordered proteins. In this review we describe recent applications of RDCs to quantitatively describe the level of local structure and transient long-range order in IDPs involved in viral replication, neurodegenerative disease, and cancer.

Intrinsic hierarchical structural imperfections in a natural ceramic of bivalve shell with distinctly graded properties

PubMed Central

Jiao, Da; Liu, Zengqian; Zhang, Zhenjun; Zhang, Zhefeng

2015-01-01

Despite the extensive investigation on the structure of natural biological materials, insufficient attention has been paid to the structural imperfections by which the mechanical properties of synthetic materials are dominated. In this study, the structure of bivalve Saxidomus purpuratus shell has been systematically characterized quantitatively on multiple length scales from millimeter to sub-nanometer. It is revealed that hierarchical imperfections are intrinsically involved in the crossed-lamellar structure of the shell despite its periodically packed platelets. In particular, various favorable characters which are always pursued in synthetic materials, e.g. nanotwins and low-angle misorientations, have been incorporated herein. The possible contributions of these imperfections to mechanical properties are further discussed. It is suggested that the imperfections may serve as structural adaptations, rather than detrimental defects in the real sense, to help improve the mechanical properties of natural biological materials. This study may aid in understanding the optimizing strategies of structure and properties designed by nature, and accordingly, provide inspiration for the design of synthetic materials. PMID:26198844

Intrinsic hierarchical structural imperfections in a natural ceramic of bivalve shell with distinctly graded properties.

PubMed

Jiao, Da; Liu, Zengqian; Zhang, Zhenjun; Zhang, Zhefeng

2015-07-22

Despite the extensive investigation on the structure of natural biological materials, insufficient attention has been paid to the structural imperfections by which the mechanical properties of synthetic materials are dominated. In this study, the structure of bivalve Saxidomus purpuratus shell has been systematically characterized quantitatively on multiple length scales from millimeter to sub-nanometer. It is revealed that hierarchical imperfections are intrinsically involved in the crossed-lamellar structure of the shell despite its periodically packed platelets. In particular, various favorable characters which are always pursued in synthetic materials, e.g. nanotwins and low-angle misorientations, have been incorporated herein. The possible contributions of these imperfections to mechanical properties are further discussed. It is suggested that the imperfections may serve as structural adaptations, rather than detrimental defects in the real sense, to help improve the mechanical properties of natural biological materials. This study may aid in understanding the optimizing strategies of structure and properties designed by nature, and accordingly, provide inspiration for the design of synthetic materials.

Heat-resistant variants of the Chinese hamster ovary cell: alteration of cellular structure and expression of vimentin.

PubMed

Lee, Y J; Hou, Z Z; Curetty, L; Armour, E P; al-Saadi, A; Bernstein, J; Corry, P M

1992-04-01

Three heat-resistant mutant cell lines (78-1, 78-2, 78-3) were previously selected from Chinese hamster ovary cells. In this study, we investigated whether the differences in intrinsic thermal sensitivity result from alteration of stress protein levels or cellular structural changes. Although there was no significant difference in the levels of stress proteins, i.e., constitutive HSP70 in wild type and three heat-resistant mutant strains, there were marked differences in the amounts of vimentin among the cell lines. Two-dimensional gel electrophoresis and Western blot showed a 2.3-2.9-fold increase in the level of vimentin in the mutant cells under normal growth conditions. Northern blot also revealed higher amounts of vimentin mRNA in the mutant cells. Electron microscopy and immunofluorescence suggest that increased amounts of the vimentin-containing intermediate filaments are correlated with the heat-resistant phenotypes.

Computational modeling of intrinsic dissipation in nano-structure

NASA Astrophysics Data System (ADS)

Kunal, Kumar

In this work, using computational modeling, we study the different mechanisms of intrinsic dissipation in nano-electro mechanical systems (NEMS). We, first, use molecular dynamics (MD) simulation and gain an understanding of the underlying loss mechanisms. Using insights from the MD simulation, a multi-scale method to model intrinsic damping is developed. The high frequency vibration in NEMS have important applications. A few examples include the sensing of atomic mass, detection of biological molecules and observation of quantum effects in macroscopic objects. For all these potential applications, dissipation plays a limiting role. While a number of experimental and theoretical studies have been performed, the individual role of different mechanisms remains unclear. In this work, we attempt to isolate and understand the surface and size effect on some of the intrinsic mechanisms. We, first, consider the case of the Akhiezer damping. The Akhiezer dynamics is expected to play an important role in nano-resonators with frequencies in the GHz range. Using a judiciously devised MD set-up, we isolate Akhiezer dynamics. We show that the surfaces aid in reducing the dissipation rate through increasing the rate of thermalization of the phonons. We, next, study damping under the flexure mode of operation. A comparative analysis with the stretching mode shows that the flexure mode is less dissipative. A reduced order model is considered to understand this novel behavior. We, also, investigate the role of tension on the Q factor, a measure of the inverse of dissipation rate. From these studies, we conclude that Akhiezer dynamics plays a dominant role in nano-resonators. We, then, develop a quasi-harmonic based multi-scale method to model Akhiezer damping. A stress component, that characterizes the non-equilibrium phonon population, is derived. We obtain constitutive relation that governs the time evolution of the non-equilibrium stress. Different methods to parametrize the constitutive relation are discussed. Using the proposed formulation, we compute the dissipation rate for different cases. The results are compared with those obtained using MD. Next, we use the Boltzmann transport equation and investigate the Q factor due to the thermo-elastic dissipation (TED). The Q factor obtained shows deviations from the classical theory of TED. Correction to the classical formula, for the case of longitudinal modes, is provided. We, then, study damping is low dimensional structure. We first consider the case of two dimensional graphene sheet and under in-plane stretching. We show that the coupling between the in-plane and the out-of-plane motions plays an important role in the loss of mechanical energy. Further, a hysteresis behavior in the out-of-plane dynamics is observed. Next, we investigate the stretching motion of graphene nano-ribbon. A normal mode Langevin dynamics is devised to understand the results from the MD simulation.

Motivational profiles of medical students: association with study effort, academic performance and exhaustion.

PubMed

Kusurkar, Rashmi A; Croiset, Gerda; Galindo-Garré, Francisca; Ten Cate, Olle

2013-06-19

Students enter the medical study with internally generated motives like genuine interest (intrinsic motivation) and/or externally generated motives like parental pressure or desire for status or prestige (controlled motivation). According to Self-determination theory (SDT), students could differ in their study effort, academic performance and adjustment to the study depending on the endorsement of intrinsic motivation versus controlled motivation. The objectives of this study were to generate motivational profiles of medical students using combinations of high or low intrinsic and controlled motivation and test whether different motivational profiles are associated with different study outcomes. Participating students (N = 844) from University Medical Center Utrecht, the Netherlands, were classified to different subgroups through K-means cluster analysis using intrinsic and controlled motivation scores. Cluster membership was used as an independent variable to assess differences in study strategies, self-study hours, academic performance and exhaustion from study. Four clusters were obtained: High Intrinsic High Controlled (HIHC), Low Intrinsic High Controlled (LIHC), High Intrinsic Low Controlled (HILC), and Low Intrinsic Low Controlled (LILC). HIHC profile, including the students who are interest + status motivated, constituted 25.2% of the population (N = 213). HILC profile, including interest-motivated students, constituted 26.1% of the population (N = 220). LIHC profile, including status-motivated students, constituted 31.8% of the population (N = 268). LILC profile, including students who have a low-motivation and are neither interest nor status motivated, constituted 16.9% of the population (N = 143). Interest-motivated students (HILC) had significantly more deep study strategy (p < 0.001) and self-study hours (p < 0.05), higher GPAs (p < 0.001) and lower exhaustion (p < 0.001) than status-motivated (LIHC) and low-motivation (LILC) students. The interest-motivated profile of medical students (HILC) is associated with good study hours, deep study strategy, good academic performance and low exhaustion from study. The interest + status motivated profile (HIHC) was also found to be associated with a good learning profile, except that students with this profile showed higher surface strategy. Low-motivation (LILC) and status-motivated profiles (LIHC) were associated with the least desirable learning behaviours.

Poissonian renormalizations, exponentials, and power laws.

PubMed

Eliazar, Iddo

2013-05-01

This paper presents a comprehensive "renormalization study" of Poisson processes governed by exponential and power-law intensities. These Poisson processes are of fundamental importance, as they constitute the very bedrock of the universal extreme-value laws of Gumbel, Fréchet, and Weibull. Applying the method of Poissonian renormalization we analyze the emergence of these Poisson processes, unveil their intrinsic dynamical structures, determine their domains of attraction, and characterize their structural phase transitions. These structural phase transitions are shown to be governed by uniform and harmonic intensities, to have universal domains of attraction, to uniquely display intrinsic invariance, and to be intimately connected to "white noise" and to "1/f noise." Thus, we establish a Poissonian explanation to the omnipresence of white and 1/f noises.

Using seismic coda waves to resolve intrinsic and scattering attenuation

NASA Astrophysics Data System (ADS)

Wang, W.; Shearer, P. M.

2016-12-01

Seismic attenuation is caused by two factors, scattering and intrinsic absorption. Characterizing scattering and absorbing properties and the power spectrum of crustal heterogeneity is a fundamental problem for informing strong ground motion estimates at high frequencies, where scattering and attenuation effects are critical. Determining the relative amount of attenuation caused by scattering and intrinsic absorption has been a long-standing problem in seismology. The wavetrain following the direct body wave phases is called the coda, which is caused by scattered energy. Many studies have analyzed the coda of local events to constrain crustal and upper-mantle scattering strength and intrinsic attenuation. Here we examine two popular attenuation inversion methods, the Multiple Lapse Time Window Method (MLTWM) and the Coda Qc Method. First, based on our previous work on California attenuation structure, we apply an efficient and accurate method, the Monte Carlo Approach, to synthesize seismic envelope functions. We use this code to generate a series of synthetic data based on several complex and realistic forward models. Although the MLTWM assumes a uniform whole space, we use the MLTWM to invert for both scattering and intrinsic attenuation from the synthetic data to test how accurately it can recover the attenuation models. Results for the coda Qc method depend on choices for the length and starting time of the coda-wave time window. Here we explore the relation between the inversion results for Qc, the windowing parameters, and the intrinsic and scattering Q structure of our synthetic model. These results should help assess the practicality and accuracy of the Multiple Lapse Time Window Method and Coda Qc Method when applied to realistic crustal velocity and attenuation models.

Experimental validation of a structural damage detection method based on marginal Hilbert spectrum

NASA Astrophysics Data System (ADS)

Banerji, Srishti; Roy, Timir B.; Sabamehr, Ardalan; Bagchi, Ashutosh

2017-04-01

Structural Health Monitoring (SHM) using dynamic characteristics of structures is crucial for early damage detection. Damage detection can be performed by capturing and assessing structural responses. Instrumented structures are monitored by analyzing the responses recorded by deployed sensors in the form of signals. Signal processing is an important tool for the processing of the collected data to diagnose anomalies in structural behavior. The vibration signature of the structure varies with damage. In order to attain effective damage detection, preservation of non-linear and non-stationary features of real structural responses is important. Decomposition of the signals into Intrinsic Mode Functions (IMF) by Empirical Mode Decomposition (EMD) and application of Hilbert-Huang Transform (HHT) addresses the time-varying instantaneous properties of the structural response. The energy distribution among different vibration modes of the intact and damaged structure depicted by Marginal Hilbert Spectrum (MHS) detects location and severity of the damage. The present work investigates damage detection analytically and experimentally by employing MHS. The testing of this methodology for different damage scenarios of a frame structure resulted in its accurate damage identification. The sensitivity of Hilbert Spectral Analysis (HSA) is assessed with varying frequencies and damage locations by means of calculating Damage Indices (DI) from the Hilbert spectrum curves of the undamaged and damaged structures.

Distinct sensory representations of wind and near-field sound in the Drosophila brain

PubMed Central

Yorozu, Suzuko; Wong, Allan; Fischer, Brian J.; Dankert, Heiko; Kernan, Maurice J.; Kamikouchi, Azusa; Ito, Kei; Anderson, David J.

2009-01-01

Behavioral responses to wind are thought to play a critical role in controlling the dispersal and population genetics of wild Drosophila species1,2, as well as their navigation in flight3, but their underlying neurobiological basis is unknown. We show that Drosophila melanogaster, like wild-caught Drosophila strains4, exhibits robust wind-induced suppression of locomotion (WISL), in response to air currents delivered at speeds normally encountered in nature1,2. Here we identify wind-sensitive neurons in Johnston’s Organ (JO), an antennal mechanosensory structure previously implicated in near-field sound detection (reviewed in5,6). Using Gal4 lines targeted to different subsets of JO neurons7, and a genetically encoded calcium indicator8, we show that wind and near-field sound (courtship song) activate distinct populations of JO neurons, which project to different regions of the antennal and mechanosensory motor center (AMMC) in the central brain. Selective genetic ablation of wind-sensitive JO neurons in the antenna abolishes WISL behavior, without impairing hearing. Different neuronal subsets within the wind-sensitive population, moreover, respond to different directions of arista deflection caused by airflow and project to different regions of the AMMC, providing a rudimentary map of wind-direction in the brain. Importantly, sound- and wind-sensitive JO neurons exhibit different intrinsic response properties: the former are phasically activated by small, bi-directional, displacements of the aristae, while the latter are tonically activated by unidirectional, static deflections of larger magnitude. These different intrinsic properties are well suited to the detection of oscillatory pulses of near-field sound and laminar airflow, respectively. These data identify wind-sensitive neurons in JO, a structure that has been primarily associated with hearing, and reveal how the brain can distinguish different types of air particle movements, using a common sensory organ. PMID:19279637

Chimpanzees and bonobos differ in intrinsic motivation for tool use.

PubMed

Koops, Kathelijne; Furuichi, Takeshi; Hashimoto, Chie

2015-06-16

Tool use in nonhuman apes can help identify the conditions that drove the extraordinary expansion of hominin technology. Chimpanzees and bonobos are our closest living relatives. Whereas chimpanzees are renowned for their tool use, bonobos use few tools and none in foraging. We investigated whether extrinsic (ecological and social opportunities) or intrinsic (predispositions) differences explain this contrast by comparing chimpanzees at Kalinzu (Uganda) and bonobos at Wamba (DRC). We assessed ecological opportunities based on availability of resources requiring tool use. We examined potential opportunities for social learning in immature apes. Lastly, we investigated predispositions by measuring object manipulation and object play. Extrinsic opportunities did not explain the tool use difference, whereas intrinsic predispositions did. Chimpanzees manipulated and played more with objects than bonobos, despite similar levels of solitary and social play. Selection for increased intrinsic motivation to manipulate objects likely also played an important role in the evolution of hominin tool use.

The periodic table and the intrinsic barrier in s(n)2 reactions.

PubMed

Yi, Ren; Basch, Harold; Hoz, Shmaryahu

2002-08-23

The identity S(N)2 reactions on nitrogen (see eq 3) with nucleophiles having the general structure H(n)()X(-) where X belongs to the group of nonmetallic elements which do not border the line separating them from the metallic elements (X = F, Cl, Br, I, O, S, Se, N, P, and C) were studied at the G2+ level. The results show that, similarly to the previously observed phenomenon for S(N)2 reaction on carbon (J. Am. Chem. Soc. 1999, 121, 7724), the Periodic Table, through the valence of the element X, controls the intrinsic barrier for the reaction. The average intrinsic barriers obtained for nitrogen substrates were 20, 27, 39, and 57 kcal/mol for the mono-, di-, tri-, and tetravalent X's, respectively. It is also concluded that the intrinsic barriers are similar for N- and C-based substrates and dimethyl substitution on both raises the intrinsic barrier by ca. 10 kcal/mol.

Method for manufacturing solid-state thermal neutron detectors with simultaneous high thermal neutron detection efficiency (>50%) and neutron to gamma discrimination (>1.0E4)

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

Nikolic, Rebecca J.; Conway, Adam M.; Heineck, Daniel

2013-10-15

Methods for manufacturing solid-state thermal neutron detectors with simultaneous high thermal neutron detection efficiency (>50%) and neutron to gamma discrimination (>10.sup.4) are provided. A structure is provided that includes a p+ region on a first side of an intrinsic region and an n+ region on a second side of the intrinsic region. The thickness of the intrinsic region is minimized to achieve a desired gamma discrimination factor of at least 1.0E+04. Material is removed from one of the p+ region or the n+ region and into the intrinsic layer to produce pillars with open space between each pillar. The openmore » space is filed with a neutron sensitive material. An electrode is placed in contact with the pillars and another electrode is placed in contact with the side that is opposite of the intrinsic layer with respect to the first electrode.« less

Atomic Structure of Intrinsic and Electron-Irradiation-Induced Defects in MoTe2

PubMed Central

2018-01-01

Studying the atomic structure of intrinsic defects in two-dimensional transition-metal dichalcogenides is difficult since they damage quickly under the intense electron irradiation in transmission electron microscopy (TEM). However, this can also lead to insights into the creation of defects and their atom-scale dynamics. We first show that MoTe2 monolayers without protection indeed quickly degrade during scanning TEM (STEM) imaging, and discuss the observed atomic-level dynamics, including a transformation from the 1H phase into 1T′, 3-fold rotationally symmetric defects, and the migration of line defects between two 1H grains with a 60° misorientation. We then analyze the atomic structure of MoTe2 encapsulated between two graphene sheets to mitigate damage, finding the as-prepared material to contain an unexpectedly large concentration of defects. These include similar point defects (or quantum dots, QDs) as those created in the nonencapsulated material and two different types of line defects (or quantum wires, QWs) that can be transformed from one to the other under electron irradiation. Our density functional theory simulations indicate that the QDs and QWs embedded in MoTe2 introduce new midgap states into the semiconducting material and may thus be used to control its electronic and optical properties. Finally, the edge of the encapsulated material appears amorphous, possibly due to the pressure caused by the encapsulation. PMID:29503509

Structural Plasticity of Malaria Dihydroorotate Dehydrogenase Allows Selective Binding of Diverse Chemical Scaffolds

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

Deng, Xiaoyi; Gujjar, Ramesh; El Mazouni, Farah

Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes andmore » to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.« less

A prospective study on the variation in falling and fall risk among community-dwelling older citizens in 12 European countries

PubMed Central

Franse, Carmen B; Rietjens, Judith AC; Burdorf, Alex; van Grieken, Amy; Korfage, Ida J; van der Heide, Agnes; Mattace Raso, Francesco; van Beeck, Ed; Raat, Hein

2017-01-01

Objectives The rate of falling among older citizens appears to vary across different countries, but the underlying aspects causing this variation are unexplained. We aim to describe between-country variation in falling and explore whether intrinsic fall risk factors can explain possible variation. Design Prospective study on data from the cross-national Survey of Health, Ageing and Retirement in Europe (SHARE). Setting Twelve European countries (Austria, Belgium, Czech Republic, Denmark, Estonia, France, Germany, Italy, The Netherlands, Spain, Sweden, Switzerland). Participants Community-dwelling persons aged ≥65 years (n=18 596). Measurements Socio-demographic factors (age, gender, education level and living situation) and intrinsic fall risk factors (less than good self-rated health (SRH), mobility limitations, limitations with activities of daily living (ADL), dizziness, impaired vision, depression and impaired cognition) were assessed in a baseline interview. Falling was assessed 2 years later by asking whether the participant had fallen within the 6 months prior to the follow-up interview. Results There was significant between-country variation in the rate of falling (varying from 7.9% in Switzerland to 16.2% in the Czech Republic). The prevalence of intrinsic fall risk factors varied twofold to fourfold between countries. Associations between factors age ≥80 years, less than good SRH, mobility limitations, ADL limitations, dizziness and depression, and falling were different between countries (p<0.05). Between-country differences in falling largely persisted after adjusting for socio-demographic differences but strongly attenuated after adjusting for differences in intrinsic fall risk factors. Conclusion There is considerable variation in the rate of falling between European countries, which can largely be explained by between-country variation in the prevalence of intrinsic fall risk factors. There are also country-specific variations in the association between these intrinsic risk factors and falling. These findings emphasise the importance of addressing intrinsic fall risk in (inter)national fall-prevention strategies, while highlighting country-specific priorities. PMID:28667220

The preparation and structure of salty ice VII under pressure

NASA Astrophysics Data System (ADS)

Klotz, Stefan; Bove, Livia E.; Strässle, Thierry; Hansen, Thomas C.; Saitta, Antonino M.

2009-05-01

It is widely accepted that ice, no matter what phase, is unable to incorporate large amounts of salt into its structure. This conclusion is based on the observation that on freezing of salt water, ice expels the salt almost entirely as brine. Here, we show that this behaviour is not an intrinsic physico-chemical property of ice phases. We demonstrate by neutron diffraction that substantial amounts of dissolved LiCl can be built homogeneously into the ice VII structure if it is produced by recrystallization of its glassy (amorphous) state under pressure. Such `alloyed' ice VII has significantly different structural properties compared with pure ice VII, such as an 8% larger unit cell volume, 5 times larger displacement factors, an absence of a transition to an ordered ice VIII structure and plasticity. Our study suggests that there could be a whole new class of `salty' high-pressure ice forms.

The preparation and structure of salty ice VII under pressure.

PubMed

Klotz, Stefan; Bove, Livia E; Strässle, Thierry; Hansen, Thomas C; Saitta, Antonino M

2009-05-01

It is widely accepted that ice, no matter what phase, is unable to incorporate large amounts of salt into its structure. This conclusion is based on the observation that on freezing of salt water, ice expels the salt almost entirely as brine. Here, we show that this behaviour is not an intrinsic physico-chemical property of ice phases. We demonstrate by neutron diffraction that substantial amounts of dissolved LiCl can be built homogeneously into the ice VII structure if it is produced by recrystallization of its glassy (amorphous) state under pressure. Such 'alloyed' ice VII has significantly different structural properties compared with pure ice VII, such as an 8% larger unit cell volume, 5 times larger displacement factors, an absence of a transition to an ordered ice VIII structure and plasticity. Our study suggests that there could be a whole new class of 'salty' high-pressure ice forms.

Intrinsic operators for the electromagnetic nuclear current

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

J. Adam, Jr.; H. Arenhovel

1996-09-01

The intrinsic electromagnetic nuclear meson exchange charge and current operators arising from a separation of the center-of-mass motion are derived for a one-boson-exchange model for the nuclear interaction with scalar, pseudoscalar and vector meson exchange including leading order relativistic terms. Explicit expressions for the meson exchange operators corresponding to the different meson types are given in detail for a two-nucleon system. These intrinsic operators are to be evaluated between intrinsic wave functions in their center-of-mass frame.

Probing the fractal pattern and organization of Bacillus thuringiensis bacteria colonies growing under different conditions using quantitative spectral light scattering polarimetry

NASA Astrophysics Data System (ADS)

Banerjee, Paromita; Soni, Jalpa; Purwar, Harsh; Ghosh, Nirmalya; Sengupta, Tapas K.

2013-03-01

Development of methods for quantification of cellular association and patterns in growing bacterial colony is of considerable current interest, not only to help understand multicellular behavior of a bacterial species but also to facilitate detection and identification of a bacterial species in a given space and under a given set of condition(s). We have explored quantitative spectral light scattering polarimetry for probing the morphological and structural changes taking place during colony formations of growing Bacillus thuringiensis bacteria under different conditions (in normal nutrient agar representing favorable growth environment, in the presence of 1% glucose as an additional nutrient, and 3 mM sodium arsenate as toxic material). The method is based on the measurement of spectral 3×3 Mueller matrices (which involves linear polarization measurements alone) and its subsequent analysis via polar decomposition to extract the intrinsic polarization parameters. Moreover, the fractal micro-optical parameter, namely, the Hurst exponent H, is determined via fractal-Born approximation-based inverse analysis of the polarization-preserving component of the light scattering spectra. Interesting differences are noted in the derived values for the H parameter and the intrinsic polarization parameters (linear diattenuation d, linear retardance δ, and linear depolarization Δ coefficients) of the growing bacterial colonies under different conditions. The bacterial colony growing in presence of 1% glucose exhibit the strongest fractality (lowest value of H), whereas that growing in presence of 3 mM sodium arsenate showed the weakest fractality. Moreover, the values for δ and d parameters are found to be considerably higher for the colony growing in presence of glucose, indicating more structured growth pattern. These findings are corroborated further with optical microscopic studies conducted on the same samples.

Refining the intrinsic chimera flap: a review.

PubMed

Agarwal, Jayant P; Agarwal, Shailesh; Adler, Neta; Gottlieb, Lawrence J

2009-10-01

Reconstruction of complex tissue deficiencies in which each missing component is in a different spatial relationship to each other can be particularly challenging, especially in patients with limited recipient vessels. The chimera flap design is uniquely suited to reconstruct these deformities. Chimera flaps have been previously defined in many ways with 2 main categories: prefabricated or intrinsic. Herein we attempt to clarify the definition of a true intrinsic chimeric flap and provide examples of how these constructs provide a method for reconstruction of complex defects. The versatility of the intrinsic chimera flap and its procurement from 7 different vascular systems is described. A clarification of the definition of a true intrinsic chimera flap is described. In addition, construction of flaps from the lateral femoral circumflex, deep circumflex iliac, inferior gluteal, peroneal, subscapular, thoracodorsal, and radial arterial systems is described to showcase the versatility of these chimera flaps. A true intrinsic chimera flap must consist of more than a single tissue type. Each of the tissue components receives its blood flow from separate vascular branches or perforators that are connected to a single vascular source. These vascular branches must be of appropriate length to allow for insetting with 3-dimensional spatial freedom. There are a multitude of sites from which true intrinsic chimera flaps may be harvested.

Influential Effects of Intrinsic-Extrinsic Incentive Factors on Management Performance in New Energy Enterprises.

PubMed

Wang, Ping; Lu, Zhengnan; Sun, Jihong

2018-02-08

Background : New energy has become a key trend for global energy industry development. Talent plays a very critical role in the enhancement of new energy enterprise competitiveness. As a key component of talent, managers have been attracting more and more attention. The increase in job performance relies on, to a certain extent, incentive mechanism. Based on the Two-factor Theory, differences in influences and effects of different incentives on management performance have been checked in this paper from an empirical perspective. Methods : This paper selects the middle and low level managers in new energy enterprises as research samples and classifies the managers' performance into task performance, contextual performance and innovation performance. It uses manager performance questionnaires and intrinsic-extrinsic incentive factor questionnaires to investigate and study the effects and then uses Amos software to analyze the inner link between the intrinsic-extrinsic incentives and job performance. Results : Extrinsic incentives affect task performance and innovation performance positively. Intrinsic incentives impose active significant effects on task performance, contextual performance, and innovation performance. The intrinsic incentive plays a more important role than the extrinsic incentive. Conclusions : Both the intrinsic-extrinsic incentives affect manager performance positively and the intrinsic incentive plays a more important role than the extrinsic incentive. Several suggestions to management should be given based on these results.

Solution to certain problems in the failure of composite structures

NASA Astrophysics Data System (ADS)

Goodsell, Johnathan

The present work contains the solution of two problems in composite structures. In the first, an approximate elasticity solution for prediction of the displacement, stress and strain fields within the m-layer, symmetric and balanced angle-ply composite laminate of finite-width subjected anticlastic bending deformation is developed. The solution is shown to recover classical laminated plate theory predictions at interior regions of the laminate and thereby illustrates the boundary layer character of this interlaminar phenomenon. The results exhibit the anticipated response in congruence with the solutions for uniform axial extension and uniform temperature change, where divergence of the interlaminar shearing stress is seen to occur at the intersection of the free-edge and planes between lamina of +theta and -theta orientation. The analytical results show excellent agreement with the finite-element predictions for the same boundary-value problem and thereby provide an efficient and compact solution available for parametric studies of the influence of geometry and material properties. The solution is combined with previously developed solutions for uniform axial extension and uniform temperature change of the identical laminate and the combined solution is exercised to compare the relative magnitudes of free-edge phenomenon arising from the different loading conditions, to study very thick laminates and laminates where the laminate width is less than the laminate thickness. Significantly, it was demonstrated that the solution is valid for arbitrary stacking sequence and the solution was exercised to examine antisymmetric and non-symmetric laminates. Finally, the solution was exercised to determine the dimensions of the boundary layer for very large numbers of layers. It was found that the dimension of the boundary layer width in bending is approximately twice that in uniform axial extension and uniform temperature change. In the second, the intrinsic flaw concept is extended to the determination of the intrinsic flaw length and the prediction of performance variability in the 10-degree off-axis specimen. The intrinsic flaw is defined as a fracture mechanics-type, through-thickness planar crack extending in the fiber direction from the failure initiation site of length, a. The distribution of intrinsic flaw lengths is postulated from multiple tests of 10-degree off-axis specimens by calculating the length of flaw that would cause fracture at each measured failure site and failure load given the fracture toughness of the material. The intrinsic flaw lengths on the homogeneous and micromechanical scales for unnotched (no hole) and specimens containing a centrally-located, through-thickness circular hole are compared. 8 hole-diameters ranging from 1.00--12.7 mm are considered. On the micromechanical scale, the intrinsic flaw ranges between approximately 10 and 100 microns in length, on the order of the relevant microstructural dimensions. The intrinsic flaw lengths on the homogeneous scale are determined to be an order of magnitude greater than that on the micromechanical scale. The effect of variation in the fiber volume fraction on the intrinsic flaw length is also considered. In the strength predictions for the specimens, the intrinsic flaw crack geometry and probability density function of intrinsic flaw lengths calculated from the unnotched specimens allow fracture mechanics predictions of strength variability. The strength prediction is dependent on the flaw density, the number of flaws per unit length along the free-edge. The flaw density is established by matching the predicted strength with the experimental strength. The distribution of intrinsic flaw lengths is used with the strength variability of the unnotched and of open-hole specimens to determine the flaw density at each hole-size. The flaw density is shown to be related to the fabrication machining speed suggesting machining damage as a mechanism for the hole-size dependence of the flaw density. (Abstract shortened by UMI.)

Intrinsic magnetic properties of L1{sub 0} FeNi obtained from meteorite NWA 6259

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

Poirier, Eric; Pinkerton, Frederick E., E-mail: frederick.e.pinkerton@gm.com; Kubic, Robert

2015-05-07

FeNi having the tetragonal L1{sub 0} crystal structure is a promising new rare-earth-free permanent magnet material. Laboratory synthesis is challenging, however, tetragonal L1{sub 0} FeNi—the mineral “tetrataenite”—has been characterized using specimens found in nickel-iron meteorites. Most notably, the meteorite NWA 6259 recovered from Northwest Africa is 95 vol. % tetrataenite with a composition of 43 at. % Ni. Hysteresis loops were measured as a function of sample orientation on a specimen cut from NWA 6259 in order to rigorously deduce the intrinsic hard magnetic properties of its L1{sub 0} phase. Electron backscatter diffraction showed that NWA 6259 is strongly textured, containing L1{submore » 0} grains oriented along any one of the three equivalent cubic directions of the parent fcc structure. The magnetic structure was modeled as a superposition of the three orthonormal uniaxial variants. By simultaneously fitting first-quadrant magnetization data for 13 different orientations of the sample with respect to the applied field direction, the intrinsic magnetic properties were estimated to be saturation magnetization 4πM{sub s} = 14.7 kG and anisotropy field H{sub a} = 14.4 kOe. The anisotropy constant K = 0.84 MJ/m{sup 3} is somewhat smaller than the value K = 1.3 MJ/m{sup 3} obtained by earlier researchers from nominally equiatomic FeNi prepared by neutron irradiation accompanied by annealing in a magnetic field, suggesting that higher Ni content (fewer Fe antisite defects) may improve the anisotropy. The fit also indicated that NWA 6259 contains one dominant variant (62% by volume), the remainder of the sample being a second variant, and the third variant being absent altogether.« less

Intrinsic quantum anomalous Hall effect in the kagome lattice Cs 2LiMn 3F 12

DOE PAGES

Xu, Gang; Lian, Biao; Zhang, Shou -Cheng

2015-10-27

In a kagome lattice, the time reversal symmetry can be broken by a staggered magnetic flux emerging from ferromagnetic ordering and intrinsic spin-orbit coupling, leading to several well-separated nontrivial Chern bands and intrinsic quantum anomalous Hall effect. Based on this idea and ab initio calculations, we propose the realization of the intrinsic quantum anomalous Hall effect in the single layer Cs 2Mn 3F 12 kagome lattice and on the (001) surface of a Cs 2LiMn 3F 12 single crystal by modifying the carrier coverage on it, where the band gap is around 20 meV. Furthermore, a simplified tight binding modelmore » based on the in-plane ddσ antibonding states is constructed to understand the topological band structures of the system.« less

The role of stoichiometric vacancy periodicity in pressure-induced amorphization of the Ga{sub 2}SeTe{sub 2} semiconductor alloy

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

Abdul-Jabbar, N. M.; Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Kalkan, B.

2014-08-04

We observe that pressure-induced amorphization of Ga{sub 2}SeTe{sub 2} (a III-VI semiconductor) is directly influenced by the periodicity of its intrinsic defect structures. Specimens with periodic and semi-periodic two-dimensional vacancy structures become amorphous around 10–11 GPa in contrast to those with aperiodic structures, which amorphize around 7–8 GPa. The result is an instance of altering material phase-change properties via rearrangement of stoichiometric vacancies as opposed to adjusting their concentrations. Based on our experimental findings, we posit that periodic two-dimensional vacancy structures in Ga{sub 2}SeTe{sub 2} provide an energetically preferred crystal lattice that is less prone to collapse under applied pressure. This ismore » corroborated through first-principles electronic structure calculations, which demonstrate that the energy stability of III-VI structures under hydrostatic pressure is highly dependent on the configuration of intrinsic vacancies.« less

Genealogy of an ancient protein family: the Sirtuins, a family of disordered members.

PubMed

Costantini, Susan; Sharma, Ankush; Raucci, Raffaele; Costantini, Maria; Autiero, Ida; Colonna, Giovanni

2013-03-05

Sirtuins genes are widely distributed by evolution and have been found in eubacteria, archaea and eukaryotes. While prokaryotic and archeal species usually have one or two sirtuin homologs, in humans as well as in eukaryotes we found multiple versions and in mammals this family is comprised of seven different homologous proteins being all NAD-dependent de-acylases. 3D structures of human SIRT2, SIRT3, and SIRT5 revealed the overall conformation of the conserved core domain but they were unable to give a structural information about the presence of very flexible and dynamically disordered regions, the role of which is still structurally and functionally unclear. Recently, we modeled the 3D-structure of human SIRT1, the most studied member of this family, that unexpectedly emerged as a member of the intrinsically disordered proteins with its long disordered terminal arms. Despite clear similarities in catalytic cores between the human sirtuins little is known of the general structural characteristics of these proteins. The presence of disorder in human SIRT1 and the propensity of these proteins in promoting molecular interactions make it important to understand the underlying mechanisms of molecular recognition that reasonably should involve terminal segments. The mechanism of recognition, in turn, is a prerequisite for the understanding of any functional activity. Aim of this work is to understand what structural properties are shared among members of this family in humans as well as in other organisms. We have studied the distribution of the structural features of N- and C-terminal segments of sirtuins in all known organisms to draw their evolutionary histories by taking into account average length of terminal segments, amino acid composition, intrinsic disorder, presence of charged stretches, presence of putative phosphorylation sites, flexibility, and GC content of genes. Finally, we have carried out a comprehensive analysis of the putative phosphorylation sites in human sirtuins confirming those sites already known experimentally for human SIRT1 and 2 as well as extending their topology to all the family to get feedback of their physiological functions and cellular localization. Our results highlight that the terminal segments of the majority of sirtuins possess a number of structural features and chemical and physical properties that strongly support their involvement in activities of recognition and interaction with other protein molecules. We also suggest how a multisite phosphorylation provides a possible mechanism by which flexible and intrinsically disordered segments of a sirtuin supported by the presence of positively or negatively charged stretches might enhance the strength and specificity of interaction with a particular molecular partner.

Intrinsic time quantum geometrodynamics

NASA Astrophysics Data System (ADS)

Ita, Eyo Eyo; Soo, Chopin; Yu, Hoi-Lai

2015-08-01

Quantum geometrodynamics with intrinsic time development and momentric variables is presented. An underlying SU(3) group structure at each spatial point regulates the theory. The intrinsic time behavior of the theory is analyzed, together with its ground state and primordial quantum fluctuations. Cotton-York potential dominates at early times when the universe was small; the ground state naturally resolves Penrose's Weyl curvature hypothesis, and thermodynamic and gravitational "arrows of time" point in the same direction. Ricci scalar potential corresponding to Einstein's general relativity emerges as a zero-point energy contribution. A new set of fundamental commutation relations without Planck's constant emerges from the unification of gravitation and quantum mechanics.

High prevalence of luminal B breast cancer intrinsic subtype in Colombian women

PubMed Central

Serrano-Gomez, Silvia Juliana; Sanabria-Salas, Maria Carolina; Hernández-Suarez, Gustavo; García, Oscar; Silva, Camilo; Romero, Alejandro; Mejía, Juan Carlos; Miele, Lucio; Fejerman, Laura; Zabaleta, Jovanny

2016-01-01

Breast cancer is the most frequent malignancy in women worldwide. Distinct intrinsic subtypes of breast cancer have different prognoses, and their relative prevalence varies significantly among ethnic groups. Little is known about the prevalence of breast cancer intrinsic subtypes and their association with clinicopathological data and genetic ancestry in Latin Americans. Immunohistochemistry surrogates from the 2013 St. Gallen International Expert Consensus were used to classify breast cancers in 301 patients from Colombia into intrinsic subtypes. We analyzed the distribution of subtypes by clinicopathological variables. Genetic ancestry was estimated from a panel of 80 ancestry informative markers. Luminal B breast cancer subtype was the most prevalent in our population (37.2%) followed by luminal A (26.3%), non-basal triple negative (NBTN) (11.6%), basal like (9%), human epidermal growth factor receptor 2 (HER2) enriched (8.6%) and unknown (7.3%). We found statistical significant differences in distribution between Colombian region (P = 0.007), age at diagnosis (P = 0.0139), grade (P < 0.001) and recurrence (P < 0.001) according to intrinsic subtype. Patients diagnosed with HER2-enriched, basal-like and NBTN breast cancer had the highest African ancestry. Future studies analyzing the molecular profiles of breast cancer in Colombian women will help us understand the molecular basis of this subtype distribution and compare the molecular characteristics of the different intrinsic subtypes in Colombian patients. PMID:27207651

Small Modifications to Network Topology Can Induce Stochastic Bistable Spiking Dynamics in a Balanced Cortical Model

PubMed Central

McDonnell, Mark D.; Ward, Lawrence M.

2014-01-01

Abstract Directed random graph models frequently are used successfully in modeling the population dynamics of networks of cortical neurons connected by chemical synapses. Experimental results consistently reveal that neuronal network topology is complex, however, in the sense that it differs statistically from a random network, and differs for classes of neurons that are physiologically different. This suggests that complex network models whose subnetworks have distinct topological structure may be a useful, and more biologically realistic, alternative to random networks. Here we demonstrate that the balanced excitation and inhibition frequently observed in small cortical regions can transiently disappear in otherwise standard neuronal-scale models of fluctuation-driven dynamics, solely because the random network topology was replaced by a complex clustered one, whilst not changing the in-degree of any neurons. In this network, a small subset of cells whose inhibition comes only from outside their local cluster are the cause of bistable population dynamics, where different clusters of these cells irregularly switch back and forth from a sparsely firing state to a highly active state. Transitions to the highly active state occur when a cluster of these cells spikes sufficiently often to cause strong unbalanced positive feedback to each other. Transitions back to the sparsely firing state rely on occasional large fluctuations in the amount of non-local inhibition received. Neurons in the model are homogeneous in their intrinsic dynamics and in-degrees, but differ in the abundance of various directed feedback motifs in which they participate. Our findings suggest that (i) models and simulations should take into account complex structure that varies for neuron and synapse classes; (ii) differences in the dynamics of neurons with similar intrinsic properties may be caused by their membership in distinctive local networks; (iii) it is important to identify neurons that share physiological properties and location, but differ in their connectivity. PMID:24743633

The Role of Relative Intrinsic Aspirations in Chinese Adolescents' Prosocial Behaviors

ERIC Educational Resources Information Center

Fu, Xinyuan; Liu, Xiaolan; Yang, Ying; Zhang, Mengyuan; Kou, Yu

2018-01-01

We examined Chinese adolescents' aspirations and explored the relationship between relative intrinsic aspirations (RIA) and prosocial behaviors and whether adolescents with different levels of RIA have different emphases on self- and other-oriented considerations during prosocial decision making. In Study 1, 236 participants were recruited and…

Job Attitudes among Different Occupational Status Groups. An Economic Analysis.

ERIC Educational Resources Information Center

Ronen, Simcha; Sadan, Simcha

1984-01-01

An economic model is applied to employee attitudinal variables to compare the contribution of intrinsic and extrinsic factors to job satisfaction for skilled workers and managers in an electronics manufacturing organization. Intrinsic rewards are found to increase in importance as employment level increases, suggesting different frames of…

Converging on the function of intrinsically disordered nucleoporins in the nuclear pore complex.

PubMed

Peleg, Orit; Lim, Roderick Y H

2010-07-01

Several biological mechanisms involve proteins or proteinaceous components that are intrinsically disordered. A case in point pertains to the nuclear pore complex (NPC), which regulates molecular transport between the nucleus and the cytoplasm. NPC functionality is dependent on unfolded domains rich in Phe-Gly (FG) repeats (i.e., FG-domains) that collectively act to promote or hinder cargo translocation. To a large extent, our understanding of FG-domain behavior is limited to in vitro investigations given the difficulty to resolve them directly in the NPC. Nevertheless, recent findings indicate a collective convergence towards rationalizing FG-domain function. This review aims to glean further insight into this fascinating problem by taking an objective look at the boundary conditions and contextual details underpinning FG-domain behavior in the NPC. Here, we treat the FG-domains as being commensurate with polymeric chains to address ambiguities such as for instance, how FG-domains tethered to the central channel of the NPC would behave differently as compared with their free-floating counterparts in solution. By bringing such fundamental questions to the fore, this review seeks to illuminate the importance of how such parameters can hold influence over the structure-function relation of intrinsically disordered proteins in the NPC and beyond.

Composite mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1987-01-01

Recent research activities and accomplishments at Lewis Research Center on composite mechanics for engine structures are summarized. The activities focused mainly on developing procedures for the computational simulation of composite intrinsic and structural behavior. The computational simulation encompasses all aspects of composite mechanics, advanced three-dimensional finite-element methods, damage tolerance, composite structural and dynamic response, and structural tailoring and optimization.

Composite mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1989-01-01

Recent research activities and accomplishments at Lewis Research Center on composite mechanics for engine structures are summarized. The activities focused mainly on developing procedures for the computational simulation of composite intrinsic and structural behavior. The computational simulation encompasses all aspects of composite mechanics, advanced three-dimensional finite-element methods, damage tolerance, composite structural and dynamic response, and structural tailoring and optimization.

Intrinsic to extrinsic phonon lifetime transition in a GaAs-AlAs superlattice.

PubMed

Hofmann, F; Garg, J; Maznev, A A; Jandl, A; Bulsara, M; Fitzgerald, E A; Chen, G; Nelson, K A

2013-07-24

We have measured the lifetimes of two zone-center longitudinal acoustic phonon modes, at 320 and 640 GHz, in a 14 nm GaAs/2 nm AlAs superlattice structure. By comparing measurements at 296 and 79 K we separate the intrinsic contribution to phonon lifetime determined by phonon-phonon scattering from the extrinsic contribution due to defects and interface roughness. At 296 K, the 320 GHz phonon lifetime has approximately equal contributions from intrinsic and extrinsic scattering, whilst at 640 GHz it is dominated by extrinsic effects. These measurements are compared with intrinsic and extrinsic scattering rates in the superlattice obtained from first-principles lattice dynamics calculations. The calculated room-temperature intrinsic lifetime of longitudinal phonons at 320 GHz is in agreement with the experimentally measured value of 0.9 ns. The model correctly predicts the transition from predominantly intrinsic to predominantly extrinsic scattering; however the predicted transition occurs at higher frequencies. Our analysis indicates that the 'interfacial atomic disorder' model is not entirely adequate and that the observed frequency dependence of the extrinsic scattering rate is likely to be determined by a finite correlation length of interface roughness.

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

Lu, Z. X.; Wang, W. X.; Diamond, P. H.

We report that intrinsic torque, which can be generated by turbulent stresses, can induce toroidal rotation in a tokamak plasma at rest without direct momentum injection. Reversals in intrinsic torque have been inferred from the observation of toroidal velocity changes in recent lower hybrid current drive (LHCD) experiments. Here we focus on understanding the cause of LHCD-induced intrinsic torque reversal using gyrokinetic simulations and theoretical analyses. A new mechanism for the intrinsic torque reversal linked to magnetic shear (sˆ) effects on the turbulence spectrum is identified. This reversal is a consequence of the ballooning structure at weak sˆ . Basedmore » on realistic profiles from the Alcator C-Mod LHCD experiments, simulations demonstrate that the intrinsic torque reverses for weak sˆ discharges and that the value of sˆ crit is consistent with the experimental results sˆ exp crit [Rice et al., Phys. Rev. Lett. 111, 125003 (2013)]. In conclusion, the consideration of this intrinsic torque feature in our work is important for the understanding of rotation profile generation at weak and its consequent impact on macro-instability stabilization and micro-turbulence reduction, which is crucial for ITER. It is also relevant to internal transport barrier formation at negative or weakly positive sˆ .« less

Two-dimensional chiral asymmetry in unidirectional magnetic anisotropy structures

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

Perna, P., E-mail: paolo.perna@imdea.org; Guerrero, R.; Niño, M. A.

2016-05-15

We investigate the symmetry-breaking effects of magnetic nanostructures that present unidirectional (one-fold) magnetic anisotropy. Angular and field dependent transport and magnetic properties have been studied in two different exchange-biased systems, i.e. ferromagnetic (FM)/ antiferromagnetic (AFM) bilayer and spin-valve structures. We experimentally show the direct relationships between the magnetoresistance (MR) response and the magnetization reversal pathways for any field value and direction. We demonstrate that even though the MR signals are related to different transport phenomena, namely anisotropic magnetoresistance (AMR) and giant magnetoresistance (GMR), chiral asymmetries are found around the magnetization hard-axis direction, in both cases originated from the one-fold symmetrymore » of the interfacial exchange coupling. Our results indicate that the chiral asymmetry of transport and magnetic behaviors are intrinsic of systems with an unidirectional contribution.« less

Hippocampal Atrophy Is Associated with Altered Hippocampus-Posterior Cingulate Cortex Connectivity in Mesial Temporal Lobe Epilepsy with Hippocampal Sclerosis.

PubMed

Shih, Y C; Tseng, C E; Lin, F-H; Liou, H H; Tseng, W Y I

2017-03-01

Unilateral mesial temporal lobe epilepsy and hippocampal sclerosis have structural and functional abnormalities in the mesial temporal regions. To gain insight into the pathophysiology of the epileptic network in mesial temporal lobe epilepsy with hippocampal sclerosis, we aimed to clarify the relationships between hippocampal atrophy and the altered connection between the hippocampus and the posterior cingulate cortex in patients with mesial temporal lobe epilepsy with hippocampal sclerosis. Fifteen patients with left mesial temporal lobe epilepsy with hippocampal sclerosis and 15 healthy controls were included in the study. Multicontrast MR imaging, including high-resolution T1WI, diffusion spectrum imaging, and resting-state fMRI, was performed to measure the hippocampal volume, structural connectivity of the inferior cingulum bundle, and intrinsic functional connectivity between the hippocampus and the posterior cingulate cortex, respectively. Compared with controls, patients had decreased left hippocampal volume (volume ratio of the hippocampus and controls, 0.366% ± 0.029%; patients, 0.277% ± 0.063%, corrected P = .002), structural connectivity of the bilateral inferior cingulum bundle (generalized fractional anisotropy, left: controls, 0.234 ± 0.020; patients, 0.193 ± 0.022, corrected P = .0001, right: controls, 0.226 ± 0.022; patients, 0.208 ± 0.017, corrected P = .047), and intrinsic functional connectivity between the left hippocampus and the left posterior cingulate cortex (averaged z-value: controls, 0.314 ± 0.152; patients, 0.166 ± 0.062). The left hippocampal volume correlated with structural connectivity positively (standardized β = 0.864, P = .001), but it had little correlation with intrinsic functional connectivity (standardized β = -0.329, P = .113). On the contralesional side, the hippocampal volume did not show any significant correlation with structural connectivity or intrinsic functional connectivity ( F 2,12 = 0.284, P = .757, R 2 = 0.045). In left mesial temporal lobe epilepsy with hippocampal sclerosis, the left inferior cingulum bundle undergoes degeneration in tandem with the left hippocampal volume, whereas intrinsic functional connectivity seems to react by compensating the loss of connectivity. Such insight might be helpful in understanding the development of the epileptic network in left mesial temporal lobe epilepsy with hippocampal sclerosis. © 2017 by American Journal of Neuroradiology.

Lessons with Living Harvest Mice: An empirical study of their effects on intrinsic motivation and knowledge acquisition

NASA Astrophysics Data System (ADS)

Wilde, Matthias; Hußmann, Jona Samuel; Lorenzen, Simone; Meyer, Annika; Randler, Christoph

2012-12-01

The aim of this study was to evaluate the effects of living animals on pupils' intrinsic motivation and knowledge. Various studies from the late 1970s and 1980s stress the high effectiveness of authentic learning experiences in pupils' knowledge acquisition. However, there are only few current empirical studies on this topic. The research question of our study is to assess whether the use of living animals in the biology classroom supports intrinsic motivation and knowledge acquisition. In a pre-/post-test design, 185 fifth graders received two different treatments: the experimental group (N = 74) was taught with living harvest mice (Micromys minutus) and the control group (N = 111) received lessons with the same content which was presented in short film clips on laptop computers. Knowledge acquisition was assessed with open-ended and closed questions, while intrinsic motivation was tested with an adapted version of the Intrinsic Motivation Inventory (IMI). There were no differences in knowledge acquisition between the treatments. However, the results of the IMI showed significant differences in favour of the experimental group in interest/enjoyment, perceived competence, and perceived autonomy. Thus, living animals exert a positive influence on motivation.

Cancer/Testis Antigens: “Smart” Biomarkers for Diagnosis and Prognosis of Prostate and Other Cancers

PubMed Central

Kulkarni, Prakash; Uversky, Vladimir N.

2017-01-01

A clinical dilemma in the management of prostate cancer (PCa) is to distinguish men with aggressive disease who need definitive treatment from men who may not require immediate intervention. Accurate prediction of disease behavior is critical because radical treatment is associated with high morbidity. Here, we highlight the cancer/testis antigens (CTAs) as potential PCa biomarkers. The CTAs are a group of proteins that are typically restricted to the testis in the normal adult but are aberrantly expressed in several types of cancers. Interestingly, >90% of CTAs are predicted to belong to the realm of intrinsically disordered proteins (IDPs), which do not have unique structures and exist as highly dynamic conformational ensembles, but are known to play important roles in several biological processes. Using prostate-associated gene 4 (PAGE4) as an example of a disordered CTA, we highlight how IDP conformational dynamics may regulate phenotypic heterogeneity in PCa cells, and how it may be exploited both as a potential biomarker as well as a promising therapeutic target in PCa. We also discuss how in addition to intrinsic disorder and post-translational modifications, structural and functional variability induced in the CTAs by alternate splicing represents an important feature that might have different roles in different cancers. Although it is clear that significant additional work needs to be done in the outlined direction, this novel concept emphasizing (multi)functionality as an important trait in selecting a biomarker underscoring the theranostic potential of CTAs that is latent in their structure (or, more appropriately, the lack thereof), and casts them as next generation or “smart” biomarker candidates. PMID:28362316

Cross-Linking/Mass Spectrometry for Studying Protein Structures and Protein-Protein Interactions: Where Are We Now and Where Should We Go from Here?

PubMed

Sinz, Andrea

2018-05-28

Structural mass spectrometry (MS) is gaining increasing importance for deriving valuable three-dimensional structural information on proteins and protein complexes, and it complements existing techniques, such as NMR spectroscopy and X-ray crystallography. Structural MS unites different MS-based techniques, such as hydrogen/deuterium exchange, native MS, ion-mobility MS, protein footprinting, and chemical cross-linking/MS, and it allows fundamental questions in structural biology to be addressed. In this Minireview, I will focus on the cross-linking/MS strategy. This method not only delivers tertiary structural information on proteins, but is also increasingly being used to decipher protein interaction networks, both in vitro and in vivo. Cross-linking/MS is currently one of the most promising MS-based approaches to derive structural information on very large and transient protein assemblies and intrinsically disordered proteins. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intrinsic motivations drive learning of eye movements: an experiment with human adults.

PubMed

Caligiore, Daniele; Mustile, Magda; Cipriani, Daniele; Redgrave, Peter; Triesch, Jochen; De Marsico, Maria; Baldassarre, Gianluca

2015-01-01

Intrinsic motivations drive the acquisition of knowledge and skills on the basis of novel or surprising stimuli or the pleasure to learn new skills. In so doing, they are different from extrinsic motivations that are mainly linked to drives that promote survival and reproduction. Intrinsic motivations have been implicitly exploited in several psychological experiments but, due to the lack of proper paradigms, they are rarely a direct subject of investigation. This article investigates how different intrinsic motivation mechanisms can support the learning of visual skills, such as "foveate a particular object in space", using a gaze contingency paradigm. In the experiment participants could freely foveate objects shown in a computer screen. Foveating each of two "button" pictures caused different effects: one caused the appearance of a simple image (blue rectangle) in unexpected positions, while the other evoked the appearance of an always-novel picture (objects or animals). The experiment studied how two possible intrinsic motivation mechanisms might guide learning to foveate one or the other button picture. One mechanism is based on the sudden, surprising appearance of a familiar image at unpredicted locations, and a second one is based on the content novelty of the images. The results show the comparative effectiveness of the mechanism based on image novelty, whereas they do not support the operation of the mechanism based on the surprising location of the image appearance. Interestingly, these results were also obtained with participants that, according to a post experiment questionnaire, had not understood the functions of the different buttons suggesting that novelty-based intrinsic motivation mechanisms might operate even at an unconscious level.

Experimentally evaluating the origin of dilute magnetism in nanomaterials

NASA Astrophysics Data System (ADS)

Pereira, L. M. C.

2017-10-01

Reports of room-temperature ferromagnetism continue to emerge for an ever-growing range of nanomaterials with a small or even vanishing concentration of magnetic atoms. Dilute magnetic semiconductors (DMS) are the most representative class of such materials, but similar magnetic properties have been reported in many others. Challenging our understanding of magnetic order in solids, as well as our ability to experimentally assess it, these remarkable magnetic phenomena have become one of the most controversial topics in magnetism. Various non-intrinsic sources of ferromagnetism (e.g. instrumental artifacts and magnetic contamination) are becoming well documented, and rarely are all of them taken into account when room-temperature ferromagnetism is reported. This topical review is intended to serve as a guide when evaluating to what extent a given data set supports the claim of intrinsic ferromagnetism in dilute nanomaterials. It compiles the most relevant sources of non-intrinsic ferromagnetism which have been reported, as well as guidelines for how to minimize them. It also provides an overview of complementary structural and magnetic characterization techniques which can be combined to provide different levels of scrutiny of the intrinsic nature of experimentally observed ferromagnetism. In particular, it gives some notable examples of how comprehensive studies based on those techniques have led to a remarkably detailed understanding of model DMS materials, with strong evidence of absence of room-temperature ferromagnetism. Although mostly based on DMS research, this review provides a set of guidelines and cautionary notes of broader relevance, including some emerging new fields of dilute nanomagnetism such as magnetically doped 3D topological insulators, 3D Dirac semimetals, and 2D materials.

The Structures & Properties of Carbon

ERIC Educational Resources Information Center

Castellini, Olivia M.; Lisensky, George C.; Ehrlich, Jennifer; Zenner, Greta M.; Crone, Wendy C.

2006-01-01

The four main forms of carbon--diamond, graphite, buckyballs, and carbon nanotubes (CNTs)--are an excellent vehicle for teaching fundamental principles of chemical bonding, material structure, and properties. Carbon atoms form a variety of structures that are intrinsically connected to the properties they exhibit. Educators can take advantage of…

Influence of Deposition Pressure on the Properties of Round Pyramid Textured a-Si:H Solar Cells for Maglev.

PubMed

Lee, Jaehyeong; Choi, Wonseok; Lee, Kyuil; Lee, Daedong; Kang, Hyunil

2016-05-01

HIT (Heterojunction with Intrinsic Thin-layer) photovoltaic cells is one of the highest efficiencies in the commercial solar cells. The pyramid texturization for reducing surface reflectance of HIT solar cells silicon wafers is widely used. For the low leakage current and high shunt of solar cells, the intrinsic amorphous silicon (a-Si:H) on substrate must be uniformly thick of pyramid structure. However, it is difficult to control the thickness in the traditional pyramid texturing process. Thus, we textured the intrinsic a-Si:H thin films with the round pyramidal structure by using HNO3, HF, and CH3COOH solution. The characteristics of round pyramid a-Si:H solar cells deposited at pressure of 500, 1000, 1500, and 2000 mTorr by PECVD (Plasma Enhanced Chemical Vapor Deposition) was investigated. The lifetime, open circuit voltage, fill factor and efficiency of a-Si:H solar cells were investigated with respect to various deposition pressure.

A game theoretic framework for incentive-based models of intrinsic motivation in artificial systems

PubMed Central

Merrick, Kathryn E.; Shafi, Kamran

2013-01-01

An emerging body of research is focusing on understanding and building artificial systems that can achieve open-ended development influenced by intrinsic motivations. In particular, research in robotics and machine learning is yielding systems and algorithms with increasing capacity for self-directed learning and autonomy. Traditional software architectures and algorithms are being augmented with intrinsic motivations to drive cumulative acquisition of knowledge and skills. Intrinsic motivations have recently been considered in reinforcement learning, active learning and supervised learning settings among others. This paper considers game theory as a novel setting for intrinsic motivation. A game theoretic framework for intrinsic motivation is formulated by introducing the concept of optimally motivating incentive as a lens through which players perceive a game. Transformations of four well-known mixed-motive games are presented to demonstrate the perceived games when players' optimally motivating incentive falls in three cases corresponding to strong power, affiliation and achievement motivation. We use agent-based simulations to demonstrate that players with different optimally motivating incentive act differently as a result of their altered perception of the game. We discuss the implications of these results both for modeling human behavior and for designing artificial agents or robots. PMID:24198797

A game theoretic framework for incentive-based models of intrinsic motivation in artificial systems.

PubMed

Merrick, Kathryn E; Shafi, Kamran

2013-01-01

An emerging body of research is focusing on understanding and building artificial systems that can achieve open-ended development influenced by intrinsic motivations. In particular, research in robotics and machine learning is yielding systems and algorithms with increasing capacity for self-directed learning and autonomy. Traditional software architectures and algorithms are being augmented with intrinsic motivations to drive cumulative acquisition of knowledge and skills. Intrinsic motivations have recently been considered in reinforcement learning, active learning and supervised learning settings among others. This paper considers game theory as a novel setting for intrinsic motivation. A game theoretic framework for intrinsic motivation is formulated by introducing the concept of optimally motivating incentive as a lens through which players perceive a game. Transformations of four well-known mixed-motive games are presented to demonstrate the perceived games when players' optimally motivating incentive falls in three cases corresponding to strong power, affiliation and achievement motivation. We use agent-based simulations to demonstrate that players with different optimally motivating incentive act differently as a result of their altered perception of the game. We discuss the implications of these results both for modeling human behavior and for designing artificial agents or robots.

Motivation, strategy, and English as a foreign language vocabulary learning: A structural equation modelling study.

PubMed

Zhang, Yining; Lin, Chin-Hsi; Zhang, Dongbo; Choi, Yunjeong

2017-03-01

In spite of considerable advancements in our understanding of the different factors involved in achieving vocabulary-learning success, the overall pattern and interrelationships of critical factors involved in L2 vocabulary learning - particularly, the mechanisms through which learners regulate their motivation and learning strategies - remain unclear. This study examined L2 vocabulary learning, focusing on the joint influence of different motivational factors and learning strategies on the vocabulary breadth of adolescent learners of English as a foreign language (EFL) in China. The participants were 107 tenth graders (68 females, 39 males) in China. The data were collected via two questionnaires, one assessing students' motivation towards English-vocabulary learning and the other their English vocabulary-learning strategies, along with a test measuring vocabulary breadth. Structural equation modelling (SEM) indicated that learning strategy partially mediated the relationship between motivation (i.e., a composite score of intrinsic and extrinsic motivation) and vocabulary learning. Separate SEM analyses for intrinsic (IM) and extrinsic motivation (EM) revealed that there were significant and positive direct and indirect effects of IM on vocabulary knowledge; and while EM's direct effect over and above that of learning strategies did not achieve significance, its indirect effect was significant and positive. The findings suggest that vocabulary-learning strategies mediate the relationship between motivation and vocabulary knowledge. In addition, IM may have a greater influence on vocabulary learning in foreign-language contexts. © 2016 The British Psychological Society.

An RNA Origami Octahedron with Intrinsic siRNAs for Potent Gene Knockdown.

PubMed

Høiberg, Hans Christian; Sparvath, Steffen M; Andersen, Veronica L; Kjems, Jørgen; Andersen, Ebbe S

2018-05-26

The fields of DNA and RNA nanotechnology have established nucleic acids as valuable building blocks for functional nanodevices with applications in nanomedicine. Here, a simple method for designing and assembling a 3D scaffolded RNA origami wireframe structure with intrinsic functioning small interfering RNAs (siRNAs) embedded is introduced. Uniquely, the method uses an mRNA fragment as scaffold strand, which is folded by sequence-complementarity of nine shorter synthetic strands. High-yield production of the intended 3D structure is verified by transmission electron microscopy (TEM). Production of functional siRNAs is facilitated by incorporating recognition sites for Dicer at selected locations in the structure, and efficient silencing of a target reporter gene is demonstrated. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Poissonian renormalizations, exponentials, and power laws

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2013-05-01

This paper presents a comprehensive “renormalization study” of Poisson processes governed by exponential and power-law intensities. These Poisson processes are of fundamental importance, as they constitute the very bedrock of the universal extreme-value laws of Gumbel, Fréchet, and Weibull. Applying the method of Poissonian renormalization we analyze the emergence of these Poisson processes, unveil their intrinsic dynamical structures, determine their domains of attraction, and characterize their structural phase transitions. These structural phase transitions are shown to be governed by uniform and harmonic intensities, to have universal domains of attraction, to uniquely display intrinsic invariance, and to be intimately connected to “white noise” and to “1/f noise.” Thus, we establish a Poissonian explanation to the omnipresence of white and 1/f noises.

Intrinsic Decomposition of The Stretch Tensor for Fibrous Media

NASA Astrophysics Data System (ADS)

Kellermann, David C.

2010-05-01

This paper presents a novel mechanism for the description of fibre reorientation based on the decomposition of the stretch tensor according to a given material's intrinsic constitutive properties. This approach avoids the necessity for fibre directors, structural tensors or specialised model such as the ideal fibre reinforced model, which are commonly applied to the analysis of fibre kinematics in the finite deformation of fibrous media for biomechanical problems. The proposed approach uses Intrinsic-Field Tensors (IFTs) that build upon the linear orthotropic theory presented in a previous paper entitled Strongly orthotropic continuum mechanics and finite element treatment. The intrinsic decomposition of the stretch tensor therein provides superior capacity to represent the intermediary kinematics driven by finite orthotropic ratios, where the benefits are predominantly expressed in cases of large deformation as is typical in the biomechanical studies. Satisfaction of requirements such as Material Frame-Indifference (MFI) and Euclidean objectivity are demonstrated here—these factors being necessary for the proposed IFTs to be valid tensorial quantities. The resultant tensors, initially for the simplest case of linear elasticity, are able to describe the same fibre reorientation as would the contemporary approaches such as with use of structural tensors and the like, while additionally being capable of showing results intermediary to classical isotropy and the infinitely orthotropic representations. This intermediary case is previously unreported.

Intrinsic properties of high-spin band structures in triaxial nuclei

NASA Astrophysics Data System (ADS)

Jehangir, S.; Bhat, G. H.; Sheikh, J. A.; Palit, R.; Ganai, P. A.

2017-12-01

The band structures of 68,70Ge, 128,130,132,134Ce and 132,134,136,138Nd are investigated using the triaxial projected shell model (TPSM) approach. These nuclei depict forking of the ground-state band into several s-bands and in some cases, both the lowest two observed s-bands depict neutron or proton character. It was discussed in our earlier work that this anomalous behaviour can be explained by considering γ-bands based on two-quasiparticle configurations. As the parent band and the γ-band built on it have the same intrinsic structure, g-factors of the two bands are expected to be similar. In the present work, we have undertaken a detailed investigation of g-factors for the excited band structures of the studied nuclei and the available data for a few high-spin states are shown to be in fair agreement with the predicted values.

Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins.

PubMed

Schuler, Benjamin; Soranno, Andrea; Hofmann, Hagen; Nettels, Daniel

2016-07-05

The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.

Inhibition of beta-amyloid aggregation by fluorescent dye labels

NASA Astrophysics Data System (ADS)

Amaro, Mariana; Wellbrock, Thorben; Birch, David J. S.; Rolinski, Olaf J.

2014-02-01

The fluorescence decay of beta-amyloid's (Aβ) intrinsic fluorophore tyrosine has been used for sensing the oligomer formation of dye-labelled Aβ monomers and the results compared with previously studied oligomerization of the non-labelled Aβ peptides. It has been demonstrated that two different sized, covalently bound probes 7-diethylaminocoumarin-3-carbonyl and Hilyte Fluor 488 (HLF), alter the rate and character of oligomerization to different extents. The ability of HLF to inhibit formation of highly ordered structures containing beta-sheets was also shown. The implications of our findings for using fluorescence methods in amyloidosis research are discussed and the advantages of this auto-fluorescence approach highlighted.

Comparison of skin barrier function and sensory nerve electric current perception threshold between IgE-high extrinsic and IgE-normal intrinsic types of atopic dermatitis.

PubMed

Mori, T; Ishida, K; Mukumoto, S; Yamada, Y; Imokawa, G; Kabashima, K; Kobayashi, M; Bito, T; Nakamura, M; Ogasawara, K; Tokura, Y

2010-01-01

Background Two types of atopic dermatitis (AD) have been proposed, with different pathophysiological mechanisms underlying this seemingly heterogeneous disorder. The extrinsic type shows high IgE levels presumably as a consequence of skin barrier damage and feasible allergen permeation, whereas the intrinsic type exhibits normal IgE levels and is not mediated by allergen-specific IgE. Objectives To investigate the relationship between pruritus perception threshold and skin barrier function of patients with AD in a comparison between the extrinsic and intrinsic types. Methods Enrolled in this study were 32 patients with extrinsic AD, 17 with intrinsic AD and 24 healthy individuals. The barrier function of the stratum corneum was assessed by skin surface hydration and transepidermal water loss (TEWL), and pruritus perception was evaluated by the electric current perception threshold (CPT) of sensory nerves upon neuroselective transcutaneous electric stimulation. Results Skin surface hydration was significantly lower and TEWL was significantly higher in extrinsic AD than intrinsic AD or normal controls. Although there was no statistically significant difference in CPT among extrinsic AD, intrinsic AD and normal controls, CPT was significantly correlated with skin surface hydration and inversely with TEWL in intrinsic AD and normal controls, but not extrinsic AD. Finally, CPT was correlated with the visual analogue scale of itch in the nonlesional skin of patients with extrinsic but not intrinsic AD. Conclusions Patients with extrinsic AD have an impaired barrier, which increases the pre-existing pruritus but rather decreases sensitivity to external stimuli. In contrast, patients with intrinsic AD retain a normal barrier function and sensory reactivity to external pruritic stimuli.

The Intrinsically Disordered Regions of the Drosophila melanogaster Hox Protein Ultrabithorax Select Interacting Proteins Based on Partner Topology

PubMed Central

Hsiao, Hao-Ching; Gonzalez, Kim L.; Catanese, Daniel J.; Jordy, Kristopher E.; Matthews, Kathleen S.; Bondos, Sarah E.

2014-01-01

Interactions between structured proteins require a complementary topology and surface chemistry to form sufficient contacts for stable binding. However, approximately one third of protein interactions are estimated to involve intrinsically disordered regions of proteins. The dynamic nature of disordered regions before and, in some cases, after binding calls into question the role of partner topology in forming protein interactions. To understand how intrinsically disordered proteins identify the correct interacting partner proteins, we evaluated interactions formed by the Drosophila melanogaster Hox transcription factor Ultrabithorax (Ubx), which contains both structured and disordered regions. Ubx binding proteins are enriched in specific folds: 23 of its 39 partners include one of 7 folds, out of the 1195 folds recognized by SCOP. For the proteins harboring the two most populated folds, DNA-RNA binding 3-helical bundles and α-α superhelices, the regions of the partner proteins that exhibit these preferred folds are sufficient for Ubx binding. Three disorder-containing regions in Ubx are required to bind these partners. These regions are either alternatively spliced or multiply phosphorylated, providing a mechanism for cellular processes to regulate Ubx-partner interactions. Indeed, partner topology correlates with the ability of individual partner proteins to bind Ubx spliceoforms. Partners bind different disordered regions within Ubx to varying extents, creating the potential for competition between partners and cooperative binding by partners. The ability of partners to bind regions of Ubx that activate transcription and regulate DNA binding provides a mechanism for partners to modulate transcription regulation by Ubx, and suggests that one role of disorder in Ubx is to coordinate multiple molecular functions in response to tissue-specific cues. PMID:25286318

Intrinsic neuromodulation: altering neuronal circuits from within.

PubMed

Katz, P S; Frost, W N

1996-02-01

There are two sources of neuromodulation for neuronal circuits: extrinsic inputs and intrinsic components of the circuits themselves. Extrinsic neuromodulation is known to be pervasive in nervous systems, but intrinsic neuromodulation is less recognized, despite the fact that it has now been demonstrated in sensory and neuromuscular circuits and in central pattern generators. By its nature, intrinsic neuromodulation produces local changes in neuronal computation, whereas extrinsic neuromodulation can cause global changes, often affecting many circuits simultaneously. Studies in a number of systems are defining the different properties of these two forms of neuromodulation.

Intrinsic selectivity and structure sensitivity of Rhodium catalysts for C 2+ oxygenate production [On the intrinsic selectivity and structure sensitivity of Rhodium catalysts for C 2+ oxygenate production

DOE PAGES

Yang, Nuoya; Medford, Andrew J.; Liu, Xinyan; ...

2016-01-31

Synthesis gas (CO + H 2) conversion is a promising route to converting coal, natural gas, or biomass into synthetic liquid fuels. Rhodium has long been studied as it is the only elemental catalyst that has demonstrated selectivity to ethanol and other C 2+ oxygenates. However, the fundamentals of syngas conversion over rhodium are still debated. In this work a microkinetic model is developed for conversion of CO and H 2 into methane, ethanol, and acetaldehyde on the Rh (211) and (111) surfaces, chosen to describe steps and close-packed facets on catalyst particles. The model is based on DFT calculationsmore » using the BEEF-vdW functional. The mean-field kinetic model includes lateral adsorbate–adsorbate interactions, and the BEEF-vdW error estimation ensemble is used to propagate error from the DFT calculations to the predicted rates. The model shows the Rh(211) surface to be ~6 orders of magnitude more active than the Rh(111) surface, but highly selective toward methane, while the Rh(111) surface is intrinsically selective toward acetaldehyde. A variety of Rh/SiO 2 catalysts are synthesized, tested for catalytic oxygenate production, and characterized using TEM. The experimental results indicate that the Rh(111) surface is intrinsically selective toward acetaldehyde, and a strong inverse correlation between catalytic activity and oxygenate selectivity is observed. Furthermore, iron impurities are shown to play a key role in modulating the selectivity of Rh/SiO 2 catalysts toward ethanol. The experimental observations are consistent with the structure-sensitivity predicted from theory. As a result, this work provides an improved atomic-scale understanding and new insight into the mechanism, active site, and intrinsic selectivity of syngas conversion over rhodium catalysts and may also guide rational design of alloy catalysts made from more abundant elements.« less

Intrinsic selectivity and structure sensitivity of Rhodium catalysts for C 2+ oxygenate production [On the intrinsic selectivity and structure sensitivity of Rhodium catalysts for C 2+ oxygenate production

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

Yang, Nuoya; Medford, Andrew J.; Liu, Xinyan

Synthesis gas (CO + H 2) conversion is a promising route to converting coal, natural gas, or biomass into synthetic liquid fuels. Rhodium has long been studied as it is the only elemental catalyst that has demonstrated selectivity to ethanol and other C 2+ oxygenates. However, the fundamentals of syngas conversion over rhodium are still debated. In this work a microkinetic model is developed for conversion of CO and H 2 into methane, ethanol, and acetaldehyde on the Rh (211) and (111) surfaces, chosen to describe steps and close-packed facets on catalyst particles. The model is based on DFT calculationsmore » using the BEEF-vdW functional. The mean-field kinetic model includes lateral adsorbate–adsorbate interactions, and the BEEF-vdW error estimation ensemble is used to propagate error from the DFT calculations to the predicted rates. The model shows the Rh(211) surface to be ~6 orders of magnitude more active than the Rh(111) surface, but highly selective toward methane, while the Rh(111) surface is intrinsically selective toward acetaldehyde. A variety of Rh/SiO 2 catalysts are synthesized, tested for catalytic oxygenate production, and characterized using TEM. The experimental results indicate that the Rh(111) surface is intrinsically selective toward acetaldehyde, and a strong inverse correlation between catalytic activity and oxygenate selectivity is observed. Furthermore, iron impurities are shown to play a key role in modulating the selectivity of Rh/SiO 2 catalysts toward ethanol. The experimental observations are consistent with the structure-sensitivity predicted from theory. As a result, this work provides an improved atomic-scale understanding and new insight into the mechanism, active site, and intrinsic selectivity of syngas conversion over rhodium catalysts and may also guide rational design of alloy catalysts made from more abundant elements.« less

Intrinsic charge trapping in amorphous oxide films: status and challenges

NASA Astrophysics Data System (ADS)

Strand, Jack; Kaviani, Moloud; Gao, David; El-Sayed, Al-Moatasem; Afanas’ev, Valeri V.; Shluger, Alexander L.

2018-06-01

We review the current understanding of intrinsic electron and hole trapping in insulating amorphous oxide films on semiconductor and metal substrates. The experimental and theoretical evidences are provided for the existence of intrinsic deep electron and hole trap states stemming from the disorder of amorphous metal oxide networks. We start from presenting the results for amorphous (a) HfO2, chosen due to the availability of highest purity amorphous films, which is vital for studying their intrinsic electronic properties. Exhaustive photo-depopulation spectroscopy measurements and theoretical calculations using density functional theory shed light on the atomic nature of electronic gap states responsible for deep electron trapping observed in a-HfO2. We review theoretical methods used for creating models of amorphous structures and electronic structure calculations of amorphous oxides and outline some of the challenges in modeling defects in amorphous materials. We then discuss theoretical models of electron polarons and bi-polarons in a-HfO2 and demonstrate that these intrinsic states originate from low-coordinated ions and elongated metal-oxygen bonds in the amorphous oxide network. Similarly, holes can be captured at under-coordinated O sites. We then discuss electron and hole trapping in other amorphous oxides, such as a-SiO2, a-Al2O3, a-TiO2. We propose that the presence of low-coordinated ions in amorphous oxides with electron states of significant p and d character near the conduction band minimum can lead to electron trapping and that deep hole trapping should be common to all amorphous oxides. Finally, we demonstrate that bi-electron trapping in a-HfO2 and a-SiO2 weakens Hf(Si)–O bonds and significantly reduces barriers for forming Frenkel defects, neutral O vacancies and O2‑ ions in these materials. These results should be useful for better understanding of electronic properties and structural evolution of thin amorphous films under carrier injection conditions.

X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability.

PubMed

Kurpiewska, Katarzyna; Font, Josep; Ribó, Marc; Vilanova, Maria; Lewiński, Krzysztof

2009-11-15

To investigate the structural origin of decreased pressure and temperature stability, the crystal structure of bovine pancreatic ribonuclease A variants V47A, V54A, V57A, I81A, I106A, and V108A was solved at 1.4-2.0 A resolution and compared with the structure of wild-type protein. The introduced mutations had only minor influence on the global structure of ribonuclease A. The structural changes had individual character that depends on the localization of mutated residue, however, they seemed to expand from mutation site to the rest of the structure. Several different parameters have been evaluated to find correlation with decrease of free energy of unfolding DeltaDeltaG(T), and the most significant correlation was found for main cavity volume change. Analysis of the difference distance matrices revealed that the ribonuclease A molecule is organized into five relatively rigid subdomains with individual response to mutation. This behavior consistent with results of unfolding experiments is an intrinsic feature of ribonuclease A that might be surviving remnants of folding intermediates and reflects the dynamic nature of the molecule. 2009 Wiley-Liss, Inc.

Associations between adolescent siblings' relationship quality and similarity and differences in values.

PubMed

Kretschmer, Tina; Pike, Alison

2010-08-01

Theoretically framed by a self-determination perspective on value acquisition and taking into account research into sibling similarity and differences, the current study examined links between sibling relationship quality and adolescents' intrinsic values (benevolence and universalism) and extrinsic values (power, achievement, and materialism). Positive sibling experiences were expected to be positively linked to intrinsic values and negatively linked to extrinsic values, and negative experiences were hypothesized to fuel extrinsic values and thwart intrinsic values. Using a sample of 205 adolescent sibling pairs (older children M = 17.61 years, younger children M = 14.63 years) and multilevel modeling, we assessed within- and between-dyads differences to identify whether the sibling relationship functions as a correlate of values in a similar or different way for 2 siblings. Although siblings were not very similar in their values, sibling competition predicted sibling similarity in higher levels of extrinsic values and lower levels of intrinsic values. Implications for value acquisition research that so far has focused almost solely on parents and failed to acknowledge other processes within families are discussed.

Synthesis and characterization of hexaarylbenzenes with five or six different substituents enabled by programmed synthesis

NASA Astrophysics Data System (ADS)

Suzuki, Shin; Segawa, Yasutomo; Itami, Kenichiro; Yamaguchi, Junichiro

2015-03-01

Since its discovery in 1825, benzene has served as one of the most used and indispensable building blocks of chemical compounds, ranging from pharmaceuticals and agrochemicals to plastics and those used in organic electronic devices. Benzene has six hydrogen atoms that can each be replaced by different substituents, which means that the structural diversity of benzene derivatives is intrinsically extraordinary. The number of possible substituted benzenes from n different substituents is (2n + 2n2 + 4n3 + 3n4 + n6)/12. However, owing to a lack of general synthetic methods for making multisubstituted benzenes, this potentially huge structural diversity has not been fully exploited. Here, we describe a programmed synthesis of hexaarylbenzenes using C-H activation, cross-coupling and [4+2] cycloaddition reactions. The present method allows for the isolation and structure-property characterization of hexaarylbenzenes with distinctive aryl substituents at all positions for the first time. Moreover, the established protocol can be applied to the synthesis of tetraarylnaphthalenes and pentaarylpyridines.

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

Zhang, Libing; Lu, Zhou; Velarde Ruiz Esparza, Luis A.

Here we reported the first sub-wavenumber high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS) study on both the C-H and O-H region spectra of crystalline cellulose. HR-BB-SFG-VS has about 10 times better resolution than the conventional scanning SFG-VS and is known to be able to measure the intrinsic spectral lineshape and to resolve much more spectral details. With HR-BB-SFG-VS, we found that in cellulose from different sources, including Avicel and cellulose crystals isolated from algae Valonia (Iα) and tunicates (Iβ), the spectral signatures in the OH regions were unique for different allomorphs, i.e. Iα and Iβ, while the spectral signaturesmore » in the C-H regions varied in all samples examined. Even though the origin of the different behaviors of the crystalline cellulose in the O-H and C-H vibrational frequency regions is yet to be correlated to the structure of cellulose, these results provided new spectroscopic methods and opportunities to classify and understand the basic crystalline structure, as well as variations, in polymorphism of the crystalline cellulose structure.« less

Influential Effects of Intrinsic-Extrinsic Incentive Factors on Management Performance in New Energy Enterprises

PubMed Central

Wang, Ping; Lu, Zhengnan; Sun, Jihong

2018-01-01

Background: New energy has become a key trend for global energy industry development. Talent plays a very critical role in the enhancement of new energy enterprise competitiveness. As a key component of talent, managers have been attracting more and more attention. The increase in job performance relies on, to a certain extent, incentive mechanism. Based on the Two-factor Theory, differences in influences and effects of different incentives on management performance have been checked in this paper from an empirical perspective. Methods: This paper selects the middle and low level managers in new energy enterprises as research samples and classifies the managers’ performance into task performance, contextual performance and innovation performance. It uses manager performance questionnaires and intrinsic-extrinsic incentive factor questionnaires to investigate and study the effects and then uses Amos software to analyze the inner link between the intrinsic-extrinsic incentives and job performance. Results: Extrinsic incentives affect task performance and innovation performance positively. Intrinsic incentives impose active significant effects on task performance, contextual performance, and innovation performance. The intrinsic incentive plays a more important role than the extrinsic incentive. Conclusions: Both the intrinsic-extrinsic incentives affect manager performance positively and the intrinsic incentive plays a more important role than the extrinsic incentive. Several suggestions to management should be given based on these results. PMID:29419730

Characterization of the Intrinsic Water Wettability of Graphite Using Contact Angle Measurements: Effect of Defects on Static and Dynamic Contact Angles.

PubMed

Kozbial, Andrew; Trouba, Charlie; Liu, Haitao; Li, Lei

2017-01-31

Elucidating the intrinsic water wettability of the graphitic surface has increasingly attracted research interests, triggered by the recent finding that the well-established hydrophobicity of graphitic surfaces actually results from airborne hydrocarbon contamination. Currently, static water contact angle (WCA) is often used to characterize the intrinsic water wettability of graphitic surfaces. In the current paper, we show that because of the existence of defects, static WCA does not necessarily characterize the intrinsic water wettability. Freshly exfoliated graphite of varying qualities, characterized using atomic force microscopy and Raman spectroscopy, was studied using static, advancing, and receding WCA measurements. The results showed that graphite of different qualities (i.e., defect density) always has a similar advancing WCA, but it could have very different static and receding WCAs. This finding indicates that defects play an important role in contact angle measurements, and the static contact angle does not always represent the intrinsic water wettability of pristine graphite. On the basis of the experimental results, a qualitative model is proposed to explain the effect of defects on static, advancing, and receding contact angles. The model suggests that the advancing WCA reflects the intrinsic water wettability of pristine (defect-free) graphite. Our results showed that the advancing WCA for pristine graphite is 68.6°, which indicates that graphitic carbon is intrinsically mildly hydrophilic.

Drift paths of ions composing multiple-nose spectral structures near the inner edge of the plasma sheet

DOE PAGES

Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.; ...

2016-11-05

Here in this paper, we present a case study of the H +, He +, and O + multiple-nose structures observed by the Helium, Oxygen, Proton, and Electron instrument on board Van Allen Probe A over one complete orbit on 28 September 2013. Nose structures are observed near the inner edge of the plasma sheet and constitute the signatures of ion drift in the highly dynamic environment of the inner magnetosphere. We find that the multiple noses are intrinsically associated with variations in the solar wind. Backward ion drift path tracings show new details of the drift trajectories of thesemore » ions; i.e., multiple noses are formed by ions with a short drift time from the assumed source location to the inner region and whose trajectories (1) encircle the Earth different number of times or (2) encircle the Earth equal number of times but with different drift time, before reaching the observation site.« less

Drift paths of ions composing multiple-nose spectral structures near the inner edge of the plasma sheet

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

Ferradas, C. P.; Zhang, J. -C.; Spence, H. E.

Here in this paper, we present a case study of the H +, He +, and O + multiple-nose structures observed by the Helium, Oxygen, Proton, and Electron instrument on board Van Allen Probe A over one complete orbit on 28 September 2013. Nose structures are observed near the inner edge of the plasma sheet and constitute the signatures of ion drift in the highly dynamic environment of the inner magnetosphere. We find that the multiple noses are intrinsically associated with variations in the solar wind. Backward ion drift path tracings show new details of the drift trajectories of thesemore » ions; i.e., multiple noses are formed by ions with a short drift time from the assumed source location to the inner region and whose trajectories (1) encircle the Earth different number of times or (2) encircle the Earth equal number of times but with different drift time, before reaching the observation site.« less

Divergent regulation of the sarcomere and the cytoskeleton.

PubMed

Schevzov, Galina; Fath, Thomas; Vrhovski, Bernadette; Vlahovich, Nicole; Rajan, Sudarsan; Hook, Jeff; Joya, Josephine E; Lemckert, Frances; Puttur, Franz; Lin, Jim J-C; Hardeman, Edna C; Wieczorek, David F; O'Neill, Geraldine M; Gunning, Peter W

2008-01-04

The existence of a feedback mechanism regulating the precise amounts of muscle structural proteins, such as actin and the actin-associated protein tropomyosin (Tm), in the sarcomeres of striated muscles is well established. However, the regulation of nonmuscle or cytoskeletal actin and Tms in nonmuscle cell structures has not been elucidated. Unlike the thin filaments of striated muscles, the actin cytoskeleton in nonmuscle cells is intrinsically dynamic. Given the differing requirements for the structural integrity of the actin thin filaments of the sarcomere compared with the requirement for dynamicity of the actin cytoskeleton in nonmuscle cells, we postulated that different regulatory mechanisms govern the expression of sarcomeric versus cytoskeletal Tms, as key regulators of the properties of the actin cytoskeleton. Comprehensive analyses of tissues from transgenic and knock-out mouse lines that overexpress the cytoskeletal Tms, Tm3 and Tm5NM1, and a comparison with sarcomeric Tms provide evidence for this. Moreover, we show that overexpression of a cytoskeletal Tm drives the amount of filamentous actin.

Application of normal mode theory to seismic source and structure problems: Seismic investigations of upper mantle lateral heterogeneity. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Okal, E. A.

1978-01-01

The theory of the normal modes of the earth is investigated and used to build synthetic seismograms in order to solve source and structural problems. A study is made of the physical properties of spheroidal modes leading to a rational classification. Two problems addressed are the observability of deep isotropic seismic sources and the investigation of the physical properties of the earth in the neighborhood of the Core-Mantle boundary, using SH waves diffracted at the core's surface. Data sets of seismic body and surface waves are used in a search for possible deep lateral heterogeneities in the mantle. In both cases, it is found that seismic data do not require structural differences between oceans and continents to extend deeper than 250 km. In general, differences between oceans and continents are found to be on the same order of magnitude as the intrinsic lateral heterogeneity in the oceanic plate brought about by the aging of the oceanic lithosphere.

Two spin-canting textures in the antiferromagnetic phase AF1 of MnWO4 based on the new polar atomistic model in P2

NASA Astrophysics Data System (ADS)

Park, S.-H.; Liu, B.-Q.; Behal, D.; Pedersen, B.; Schneidewind, A.

2018-04-01

The low temperature antiferromagnetic (AF) phase of MnWO4 (the so-called AF1 phase) exhibits different spin-canting configurations at two Mn2+ sublattices of the (3  +  1)-dimensional magnetic structure. The suggested superspace group {{\\boldsymbol P}}2.1^\\prime(α, 1/2, γ)0s is a significant consequence of the polar space group {{\\boldsymbol P}} 2 true for the nuclear structure of MnWO4. Density functional theory calculations showed that its ground state prefers this two spin-canting system. The structural difference between two independent atomic sites for Mn (Mn a , Mn b ) is too small to allow microscopically detectable electric polarisation. However, this hidden intrinsic polar character allows AF1 two commensurately modulated spin-canting textures. This is considered as the prerequisite onset of the improper ferroelectricity enhanced by the helical spin order in the multiferroic phase AF2 of MnWO4.

A Structuralist Approach to Television Criticism.

ERIC Educational Resources Information Center

Robards, Brooks

Although television is highly dependent on language and semiotic analysis, its form can best be analyzed through the structural notion of transformation. The critic's task becomes the articulation of structural laws intrinsic to television. One such law has to do with how television structures time. Television programming transforms action into…

Differences in Intertidal Microbial Assemblages on Urban Structures and Natural Rocky Reef

PubMed Central

Tan, Elisa L.-Y.; Mayer-Pinto, Mariana; Johnston, Emma L.; Dafforn, Katherine A.

2015-01-01

Global seascapes are increasingly modified to support high levels of human activity in the coastal zone. Modifications include the addition of defense structures and boating infrastructure, such as seawalls and marinas that replace natural habitats. Artificial structures support different macrofaunal communities to those found on natural rocky shores; however, little is known about differences in microbial community structure or function in urban seascapes. Understanding how artificial constructions in marine environments influence microbial communities is important as these assemblages contribute to many basic ecological processes. In this study, the bacterial communities of intertidal biofilms were compared between artificial structures (seawalls) and natural habitats (rocky shores) within Sydney Harbour. Plots were cleared on each type of habitat at eight locations. After 3 weeks the newly formed biofilm was sampled and the 16S rRNA gene sequenced using the Illumina Miseq platform. To account for differences in orientation and substrate material between seawalls and rocky shores that might have influenced our survey, we also deployed recruitment blocks next to the habitats at all locations for 3 weeks and then sampled and sequenced their microbial communities. Intertidal bacterial community structure sampled from plots differed between seawalls and rocky shores, but when substrate material, age and orientation were kept constant (with recruitment blocks) then bacterial communities were similar in composition and structure among habitats. This suggests that changes in bacterial communities on seawalls are not related to environmental differences between locations, but may be related to other intrinsic factors that differ between the habitats such as orientation, complexity, or predation. This is one of the first comparisons of intertidal microbial communities on natural and artificial surfaces and illustrates substantial ecological differences with potential consequences for biofilm function and the recruitment of macrofauna. PMID:26635747

Autonomy, Competence, and Intrinsic Motivation in Science Education: A Self- Determination Theory Perspective

NASA Astrophysics Data System (ADS)

Painter, Jason

The purpose of this study was to examine a proposed motivational model of science achievement based on self-determination theory. The study relied on U.S. eighth-grade science data from the 2007 Third International Mathematics and Science Study to examine a structural model that hypothesized how perceived autonomy support, perceived competence in science, intrinsic motivation, and science achievement related to each other. Mother's education and student gender were used as controls. Findings showed that the hypothesized model provided a good fit to the data. The strongest direct effect on science achievement was students' perceived competence in science. Student intrinsic motivation was shown to have a surprisingly negative effect on science achievement. Autonomy support had positive direct effects on students' perceived competence in science and intrinsic motivation and had indirect positive effects to science achievement. Results and implications for science education are discussed.

Perceptions of motivational climate and teachers' strategies to sustain discipline as predictors of intrinsic motivation in physical education.

PubMed

Gutiérrez, Melchor; Ruiz, Luis-Miguel; López, Esther

2010-11-01

This study examined the relationship among pupils' perceptions of the motivational climate, pupils' perceptions of teachers' strategies to maintain discipline and pupils' intrinsic motivation in physical education. A sample of 2189 Spanish adolescents, ages 13 to 17 years, completed Spanish versions of the EPCM, SSDS, and IMI. Confirmatory factor analyses were carried out to confirm the factorial validity of the scales. Then, the relationship among the variables was explored through Structural Equation Modelling. The most important predictors of pupils' intrinsic motivation were the perceived mastery climate, and perceived teachers' emphasis on intrinsic reasons to maintain discipline. Perceived performance climate and perceived teachers' strategies to maintain discipline based on introjected reasons and indifference, predicted pupils' tension-pressure. Results are discussed in the context of theoretical propositions of self-determination theory and practical issues of enhancing adolescents' motivation in physical education.

Relations of perception of responsibility to intrinsic motivation and physical activity among Korean middle school students.

PubMed

Lee, Okseon; Kim, Younhee; Kim, Oung Jun

2012-12-01

To validate the Personal and Social Responsibility Questionnaire, the relations between perceived responsibility and intrinsic motivation were examined among Korean middle school students. The relations of change in stages of physical activity and students' perceived responsibility were also examined. Participants were 357 middle school students (160 boys, 197 girls) from three schools in the Seoul metropolitan area. Exploratory factor analysis supported a three-factor structure with effort and self-direction merged into one factor and the responsibilities of respect and caring for others constituted separate factors. Pearson correlations among factors showed perceptions of personal responsibility were associated with more intrinsic motivation toward physical education and a higher stage of physical activity. A moderate or low association between perceived social responsibility and intrinsic motivation implied a need to develop strategies for Korean students to use social responsibility for promoting physical activity.

Capacitance reduction for pillar structured devices

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

Shao, Qinghui; Conway, Adam; Nikolic, Rebecca J.

2017-05-09

In one embodiment, an apparatus includes: a first layer including a n+ dopant or p+ dopant; an intrinsic layer formed above the first layer, the intrinsic layer including a planar portion and pillars extending above the planar portion, cavity regions being defined between the pillars; and a second layer deposited on a periphery of the pillars thereby forming coated pillars, the second layer being substantially absent on the planar portion of the intrinsic layer between the coated pillars. The second layer includes an n+ dopant when the first layer includes a p+ dopant. The second layer includes a p+ dopantmore » when the first layer includes an n+ dopant. The apparatus includes a neutron sensitive material deposited between the coated pillars and above the planar portion of the intrinsic layer. In additional embodiments, an upper portion of each of the pillars includes a same type of dopant as the second layer.« less

Motivational profiles of medical students: Association with study effort, academic performance and exhaustion

PubMed Central

2013-01-01

Background Students enter the medical study with internally generated motives like genuine interest (intrinsic motivation) and/or externally generated motives like parental pressure or desire for status or prestige (controlled motivation). According to Self-determination theory (SDT), students could differ in their study effort, academic performance and adjustment to the study depending on the endorsement of intrinsic motivation versus controlled motivation. The objectives of this study were to generate motivational profiles of medical students using combinations of high or low intrinsic and controlled motivation and test whether different motivational profiles are associated with different study outcomes. Methods Participating students (N = 844) from University Medical Center Utrecht, the Netherlands, were classified to different subgroups through K-means cluster analysis using intrinsic and controlled motivation scores. Cluster membership was used as an independent variable to assess differences in study strategies, self-study hours, academic performance and exhaustion from study. Results Four clusters were obtained: High Intrinsic High Controlled (HIHC), Low Intrinsic High Controlled (LIHC), High Intrinsic Low Controlled (HILC), and Low Intrinsic Low Controlled (LILC). HIHC profile, including the students who are interest + status motivated, constituted 25.2% of the population (N = 213). HILC profile, including interest-motivated students, constituted 26.1% of the population (N = 220). LIHC profile, including status-motivated students, constituted 31.8% of the population (N = 268). LILC profile, including students who have a low-motivation and are neither interest nor status motivated, constituted 16.9% of the population (N = 143). Interest-motivated students (HILC) had significantly more deep study strategy (p < 0.001) and self-study hours (p < 0.05), higher GPAs (p < 0.001) and lower exhaustion (p < 0.001) than status-motivated (LIHC) and low-motivation (LILC) students. Conclusions The interest-motivated profile of medical students (HILC) is associated with good study hours, deep study strategy, good academic performance and low exhaustion from study. The interest + status motivated profile (HIHC) was also found to be associated with a good learning profile, except that students with this profile showed higher surface strategy. Low-motivation (LILC) and status-motivated profiles (LIHC) were associated with the least desirable learning behaviours. PMID:23782767

Fascin- and α-Actinin-Bundled Networks Contain Intrinsic Structural Features that Drive Protein Sorting.

PubMed

Winkelman, Jonathan D; Suarez, Cristian; Hocky, Glen M; Harker, Alyssa J; Morganthaler, Alisha N; Christensen, Jenna R; Voth, Gregory A; Bartles, James R; Kovar, David R

2016-10-24

Cells assemble and maintain functionally distinct actin cytoskeleton networks with various actin filament organizations and dynamics through the coordinated action of different sets of actin-binding proteins. The biochemical and functional properties of diverse actin-binding proteins, both alone and in combination, have been increasingly well studied. Conversely, how different sets of actin-binding proteins properly sort to distinct actin filament networks in the first place is not nearly as well understood. Actin-binding protein sorting is critical for the self-organization of diverse dynamic actin cytoskeleton networks within a common cytoplasm. Using in vitro reconstitution techniques including biomimetic assays and single-molecule multi-color total internal reflection fluorescence microscopy, we discovered that sorting of the prominent actin-bundling proteins fascin and α-actinin to distinct networks is an intrinsic behavior, free of complicated cellular signaling cascades. When mixed, fascin and α-actinin mutually exclude each other by promoting their own recruitment and inhibiting recruitment of the other, resulting in the formation of distinct fascin- or α-actinin-bundled domains. Subdiffraction-resolution light microscopy and negative-staining electron microscopy revealed that fascin domains are densely packed, whereas α-actinin domains consist of widely spaced parallel actin filaments. Importantly, other actin-binding proteins such as fimbrin and espin show high specificity between these two bundle types within the same reaction. Here we directly observe that fascin and α-actinin intrinsically segregate to discrete bundled domains that are specifically recognized by other actin-binding proteins. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ultrasound evaluation of intrinsic plantar muscles and fascia in hallux valgus

PubMed Central

Lobo, César Calvo; Marín, Alejandro Garrido; Sanz, David Rodríguez; López, Daniel López; López, Patricia Palomo; Morales, Carlos Romero; Corbalán, Irene Sanz

2016-01-01

Abstract A cross-sectional area (CSA) and thickness reduction of the abductor hallucis (AbH) is shown in subjects with hallux valgus (HV). To date, other soft-tissue structures have not been researched in relation with HV. The aim of this study was to compare the CSA and thickness of the intrinsic plantar muscles and fascia (PF) between feet with and without HV. Therefore, a cross-sectional and case-control study was performed using B-mode with an iU22 Philips ultrasound system and a 5 to 17-MHz transducer. The CSA and thickness were measured for the AbH, flexor digitorum brevis (FDB) and flexor hallucis brevis (FHB), and also the thickness for the anterior, middle, and posterior PF portions. A convenience sample of 40 feet, 20 with HV and 20 without HV, was recruited from a clinical and research center. A multivariate regression analysis using linear regression was performed to evaluate the ultrasound imaging measurements (α = 0.05). Consequently, statistically significant differences were observed between the groups (P < 0.05) for the AbH and FHB thickness, and CSA reduction, and also the plantar fascia thickness increase in favor of the HV group. On the contrary, the FDB thickness and CSA did not show statistically significant differences (P ≥ 0.05). In conclusion, the CSA and thickness of the AbH and FHB intrinsic plantar muscles are reduced, whereas the thickness of the anterior, middle, and posterior PF portions are increased, in subjects with HV compared with those without HV. PMID:27828846

Ultrasound evaluation of intrinsic plantar muscles and fascia in hallux valgus: A case-control study.

PubMed

Lobo, César Calvo; Marín, Alejandro Garrido; Sanz, David Rodríguez; López, Daniel López; López, Patricia Palomo; Morales, Carlos Romero; Corbalán, Irene Sanz

2016-11-01

A cross-sectional area (CSA) and thickness reduction of the abductor hallucis (AbH) is shown in subjects with hallux valgus (HV). To date, other soft-tissue structures have not been researched in relation with HV. The aim of this study was to compare the CSA and thickness of the intrinsic plantar muscles and fascia (PF) between feet with and without HV. Therefore, a cross-sectional and case-control study was performed using B-mode with an iU22 Philips ultrasound system and a 5 to 17-MHz transducer. The CSA and thickness were measured for the AbH, flexor digitorum brevis (FDB) and flexor hallucis brevis (FHB), and also the thickness for the anterior, middle, and posterior PF portions. A convenience sample of 40 feet, 20 with HV and 20 without HV, was recruited from a clinical and research center. A multivariate regression analysis using linear regression was performed to evaluate the ultrasound imaging measurements (α = 0.05). Consequently, statistically significant differences were observed between the groups (P < 0.05) for the AbH and FHB thickness, and CSA reduction, and also the plantar fascia thickness increase in favor of the HV group. On the contrary, the FDB thickness and CSA did not show statistically significant differences (P ≥ 0.05). In conclusion, the CSA and thickness of the AbH and FHB intrinsic plantar muscles are reduced, whereas the thickness of the anterior, middle, and posterior PF portions are increased, in subjects with HV compared with those without HV.

Co-production of GroELS discriminates between intrinsic and thermally-induced recombinant protein aggregation during substrate quality control

PubMed Central

2011-01-01

Background The effects and effectiveness of the chaperone pair GroELS on the yield and quality of recombinant polypeptides produced in Escherichia coli are matter of controversy, as the reported activities of this complex are not always consistent and eventually indicate undesired side effects. The divergence in the reported data could be due, at least partially, to different experimental conditions in independent research approaches. Results We have then selected two structurally different model proteins (namely GFP and E. coli β-galactosidase) and two derived aggregation-prone fusions to explore, in a systematic way, the eventual effects of GroELS co-production on yield, solubility and conformational quality. Host cells were cultured at two alternative temperatures below the threshold at which thermal stress is expected to be triggered, to minimize the involvement of independent stress factors. Conclusions From the analysis of protein yield, solubility and biological activity of the four model proteins produced alone or along the chaperones, we conclude that GroELS impacts on yield and quality of aggregation-prone proteins with intrinsic determinants but not on thermally induced protein aggregation. No effective modifications of protein solubility have been observed, but significant stabilization of small (encapsulable) substrates and moderate chaperone-induced degradation of larger (excluded) polypeptides. These findings indicate that the activities of this chaperone pair in the context of actively producing recombinant bacteria discriminate between intrinsic and thermally-induced protein aggregation, and that the side effects of GroELS overproduction might be determined by substrate size. PMID:21992454

The Next Generation Virgo Cluster Survey. VII. The Intrinsic Shapes of Low-luminosity Galaxies in the Core of the Virgo Cluster, and a Comparison with the Local Group

NASA Astrophysics Data System (ADS)

Sánchez-Janssen, Rubén; Ferrarese, Laura; MacArthur, Lauren A.; Côté, Patrick; Blakeslee, John P.; Cuillandre, Jean-Charles; Duc, Pierre-Alain; Durrell, Patrick; Gwyn, Stephen; McConnacchie, Alan W.; Boselli, Alessandro; Courteau, Stéphane; Emsellem, Eric; Mei, Simona; Peng, Eric; Puzia, Thomas H.; Roediger, Joel; Simard, Luc; Boyer, Fred; Santos, Matthew

2016-03-01

We investigate the intrinsic shapes of low-luminosity galaxies in the central 300 kpc of the Virgo Cluster using deep imaging obtained as part of the Next Generation Virgo Cluster Survey (NGVS). We build a sample of nearly 300 red-sequence cluster members in the yet-unexplored -14 < Mg < -8 mag range, and we measure their apparent axis ratios, q, through Sérsic fits to their two-dimensional light distribution, which is well described by a constant ellipticity parameter. The resulting distribution of apparent axis ratios is then fit by families of triaxial models with normally distributed intrinsic ellipticities, E = 1 - C/A, and triaxialities, T = (A2 - B2)/(A2 - C2). We develop a Bayesian framework to explore the posterior distribution of the model parameters, which allows us to work directly on discrete data, and to account for individual, surface-brightness-dependent axis ratio uncertainties. For this population we infer a mean intrinsic ellipticity \\bar{E} = {0.43}-0.02+0.02 and a mean triaxiality \\bar{T} = {0.16}-0.06+0.07. This implies that faint Virgo galaxies are best described as a family of thick, nearly oblate spheroids with mean intrinsic axis ratios 1:0.94:0.57. The core of Virgo lacks highly elongated low-luminosity galaxies, with 95% of the population having q > 0.45. We additionally attempt a study of the intrinsic shapes of Local Group (LG) satellites of similar luminosities. For the LG population we infer a slightly larger mean intrinsic ellipticity \\bar{E} = {0.51}-0.06+0.07, and the paucity of objects with round apparent shapes translates into more triaxial mean shapes, 1:0.76:0.49. Numerical studies that follow the tidal evolution of satellites within LG-sized halos are in good agreement with the inferred shape distributions, but the mismatch for faint galaxies in Virgo highlights the need for more adequate simulations of this population in the cluster environment. We finally compare the intrinsic shapes of NGVS low-mass galaxies with samples of more massive quiescent systems, and with field, star-forming galaxies of similar luminosities. We find that the intrinsic flattening in this low-luminosity regime is almost independent of the environment in which the galaxy resides, but there is a hint that objects may be slightly rounder in denser environments. The comparable flattening distributions of low-luminosity galaxies that have experienced very different degrees of environmental effects suggest that internal processes are the main drivers of galaxy structure at low masses, with external mechanisms playing a secondary role.

Intrinsic rewards, fruit and vegetable consumption, and habit strength: a three-wave study testing the associative-cybernetic model.

PubMed

Wiedemann, Amelie U; Gardner, Benjamin; Knoll, Nina; Burkert, Silke

2014-03-01

Habit formation is thought to lead to long-term maintenance of fruit and vegetable consumption. Habits develop through context-dependent repetition, but additional variables such as intrinsic reward of behaviour may influence habit strength. Drawing upon the Associative-Cybernetic Model, this exploratory study tested different pathways by which intrinsic reward may influence fruit and vegetable consumption habit strength. In a three-wave study of fruit and vegetable intake in adults (N = 127) from the general population, intrinsic reward, intention, and self-efficacy were assessed at baseline, fruit and vegetable consumption and intrinsic reward two weeks later, and habit strength another two weeks later. Direct, indirect, and moderation effects of intrinsic reward on habit strength were tested simultaneously in a moderated mediation model. Intrinsic reward had a positive indirect effect on habit strength through its influence on the frequency of fruit and vegetable consumption. Further, the relationship between fruit and vegetable consumption and habit was stronger where consumption was considered more intrinsically rewarding. Findings highlight the potential relevance of intrinsic reward to habit. We suggest that intrinsic rewards from behaviour may not only facilitate habit via behaviour frequency, but also reinforce the relationship between behavioural repetition and habit strength. © 2013 The International Association of Applied Psychology.

Amorphous and crystalline silicon based heterojunction solar cells

NASA Astrophysics Data System (ADS)

Schüttauf, J. A.

2011-10-01

In this thesis, research on amorphous and crystalline silicon heterojunction (SHJ) solar cells is described. Probably the most important feature of SHJ solar cells is a thin intrinsic amorphous silicion (a-Si:H) layer that is deposited before depositing the doped emitter and back surface field. The passivation properties of such intrinsic layers made by three different chemical vapor deposition (CVD) techniques have been investigated. For layers deposited at 130°C, all techniques show a strong reduction in surface recombination velocity (SRV) after annealing. Modelling indicates that dangling bond saturation by atomic hydrogen is the predominant mechanism. We obtain outstanding carrier lifetimes of 10.3 ms, corresponding to SRVs of 0.56 cm/s. For a-Si:H films made at 250°C, an as-deposited minority carrier lifetime of 2.0 ms is observed. In contrast to a-Si:H films fabricated at 130°C, however, no change in passivation quality upon thermal annealing is observed. These films were fabricated for the first time using a continuous in-line HWCVD mode. Wafer cleaning before a-Si:H deposition is a crucial step for c-Si surface passivation. We tested the influence of an atomic hydrogen treatment before a-Si:H deposition on the c-Si surface. The treatments were performed in a new virgin chamber to exclude Si deposition from the chamber walls. Subsequently, we deposited a-Si:H layers onto the c-Si wafers and measured the lifetime for different H treatment times. We found that increasing hydrogen treatment times led to lower effective lifetimes. Modelling of the measured minority carrier lifetime data shows that the decreased passivation quality is caused by an increased defect density at the amorphous-crystalline interface. Furtheremore, the passivation of different a-Si:H containing layers have been tested. For intrinsic films and intrinsic/n-type stacks, an improvement in passivation up to 255°C and 270°C is observed. This improvement is attributed to dangling bond saturation by H, whereas the decrease at higher temperatures is caused by H effusion. For intrinsic/n-type a-Si:H layer stacks, a record minority carrier lifetime of 13.3 ms is obtained. In contrast, for intrinsic/p-type a-Si:H layer stacks, a deterioration in passivation is observed over the whole temperature range, due to the asymmetric Fermi-level dependent defect formation enthalpy in n- and p-type a-Si:H. Comparing the lifetime values and trends for the different layer stacks to the performance of the corresponding cells, it is observed that the intrinsic/p-layer stack is limiting device performance. Based on these findings, the solar cells were prepared in a modified order, reaching an efficiency of 16.7% (VOC = 681 mV), versus 15.8% (VOC = 659 mV) in the ‘standard’ order. Finally, transparent conductive oxide (TCO) layers are studied for application into solar cells. It is observed that both types of TCO deposition have no significant influence on the passivation properties of standard a-Si:H layer stacks forming the emitter structure in the used SHJ cells. On flat wafers, a conversion efficiency of 16.7% has been obtained when ITO is used as TCO, versus an efficiency of 16.3% for ZnO:Al; slightly lower due to increased electrical losses.

Alteration of biomacromolecule in corn by steam flaking in relation to biodegradation kinetics in ruminant, revealed with vibrational molecular spectroscopy

NASA Astrophysics Data System (ADS)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-02-01

Large scale of steam flaked corn has been used in dairy ration to maintain high milk production level. This study aimed to determine effects of steam flaking on processing-induced intrinsic molecular structure changes that were associated with rumen degradation kinetics and nutrients supply. The advanced vibrational molecular spectroscopy was applied to reveal the processing-induced intrinsic structure changes on a molecular basis. The rumen degradation kinetics and nutrient supply were determined using in situ approach in ruminant livestock system. Raw corn grain (RC) and steam flaked corn grain (SFC) were obtained from two different processing plants. The results showed that (1) Compared to RC, SFC had greater truly digestible non-fiber carbohydrate [tdNFC: 86.8 versus 78.0% dry matter (DM)], but lower truly digestible crude protein [tdCP: 7.7 versus 9.0% DM]. (2) The steam flaking increased (P < 0.01) rumen degradable DM (RDDM) and starch (RDSt), but decreased (P < 0.01) rumen degradable protein (RDP). (3) Molecular absorbance intensities of most carbohydrate biopolymers were greater in SFC (P < 0.01), but protein amides associated molecular spectral intensities were lower (P < 0.01) in SFC. (4). The molecular structure and nutrient interactive study showed that carbohydrate spectral intensities were positively (P < 0.10) associated with RDDM and RDSt and protein amide spectral intensities were positively (P < 0.10) associated with RDP. This results indicated that the steam flaking induced molecular structure changes had an interactive relationship with rumen degradation kinetics.

Protein machines and self assembly in muscle organization

NASA Technical Reports Server (NTRS)

Barral, J. M.; Epstein, H. F.

1999-01-01

The remarkable order of striated muscle is the result of a complex series of protein interactions at different levels of organization. Within muscle, the thick filament and its major protein myosin are classical examples of functioning protein machines. Our understanding of the structure and assembly of thick filaments and their organization into the regular arrays of the A-band has recently been enhanced by the application of biochemical, genetic, and structural approaches. Detailed studies of the thick filament backbone have shown that the myosins are organized into a tubular structure. Additional protein machines and specific myosin rod sequences have been identified that play significant roles in thick filament structure, assembly, and organization. These include intrinsic filament components, cross-linking molecules of the M-band and constituents of the membrane-cytoskeleton system. Muscle organization is directed by the multistep actions of protein machines that take advantage of well-established self-assembly relationships. Copyright 1999 John Wiley & Sons, Inc.

Etude hydromecanique d'une fracture en cisaillement sous contrainte normale constante

NASA Astrophysics Data System (ADS)

Lamontagne, Eric

This research study deals with the effects of shear direction and injection flow rate on the flow directional anisotropy for a given normal stress. It presents experimental works on hydromechanical shear behaviour of a fracture under constant normal stress conditions that permits the characterisation of the intrinsic hydraulic transmissivity in relation with the directional anisotropy of the roughness morphology on the fracture surfaces. Tests were performed on mortar replicas of a natural fracture so that the fracture roughness and void space geometry were kept the same for each test. The experimental work program was performed through direct shear tests on the fracture replicas in four shear directions under four constant normal stress levels. The application of the normal stress was followed by several injections of fluid under constant flow rate. Then, for each defined shear displacement, several injections of fluid were done at different flow rate but under constant flow rate. The test results show that: (1) for the whole shear tests, the global intrinsic transmissivity is included within an enveloping zone of about one order of size. The transmissivity curves within the enveloping zone has a particularity to increase about two orders of size in the first millimetre of shear displacement and subsequently stabilised rapidly; (2) the highest dilatancy do not correspond necessarily with the highest intrinsic transmissivity so that, the behaviour of the global intrinsic transmissivity is not directly proportional to the fracture dilatancy during shear; (3) after the peak shear stress, the divergence is more marked between the global intrinsic transmissivity curves at various flow rate; (4) after peak shear strength and the beginning of asperity degradation, the gradual passage to residual friction shear behaviour causes a directional flow anisotropy and a reorientation of the flow chenalisation direction sub perpendicularly to the shear direction; (5) the anisotropy is not to develop equally between the two sense in the perpendicular direction to shear direction. In order to characterise the dynamics of the flow pattern in the fracture, a statistical analysis of the surfaces morphology of the fracture and the casting of void space geometry were performed before and after shear. A statistical analysis of asperity heights, on the global scale of the fracture surfaces, permits to characterise the fracture morphology and put in evidence a large morphological structure on which are superposed smaller asperities of variable dimensions. This large dimension structure generate a higher level landing occupying more than half of the fracture area. The study of the surfaces morphology of the fracture, performed with the geostatistical mean asperity heights variogram by direction before shearing, show the presence of two entangled morphologic structure families (28 and 15 mm). This same study done after shearing shows that the asperity degradation seems associated with the reduction of the global intrinsic transmissivity of the fracture. Finally, the void spaces morphology evaluated by casting techniques, during the shear tests, has permitted to verify the contacts evolution with the increasing shear displacement and visualised flow chenalisation during fracture shearing.

Probing Structural Transitions in the Intrinsically Disordered C-Terminal Domain of the Measles Virus Nucleoprotein by Vibrational Spectroscopy of Cyanylated Cysteines

PubMed Central

Bischak, Connor G.; Longhi, Sonia; Snead, David M.; Costanzo, Stéphanie; Terrer, Elodie; Londergan, Casey H.

2010-01-01

Four single-cysteine variants of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) were cyanylated at cysteine and their infrared spectra in the C≡N stretching region were recorded both in the absence and in the presence of one of the physiological partners of NTAIL, namely the C-terminal X domain (XD) of the viral phosphoprotein. Consistent with previous studies showing that XD triggers a disorder-to-order transition within NTAIL, the C≡N stretching bands of the infrared probe were found to be significantly affected by XD, with this effect being position-dependent. When the cyanylated cysteine side chain is solvent-exposed throughout the structural transition, its changing linewidth reflects a local gain of structure. When the probe becomes partially buried due to binding, its frequency reports on the mean hydrophobicity of the microenvironment surrounding the labeled side chain of the bound form. The probe moiety is small compared to other common covalently attached spectroscopic probes, thereby minimizing possible steric hindrance/perturbation at the binding interface. These results show for the first time to our knowledge the suitability of site-specific cysteine mutagenesis followed by cyanylation and infrared spectroscopy to document structural transitions occurring within intrinsically disordered regions, with regions involved in binding and folding being identifiable at the residue level. PMID:20816082

Intrinsic and Induced Arousal in the Short- and Long-Term Retention of Film Content by Elementary School Children in Puerto Rico. Technical Report No. 274.

ERIC Educational Resources Information Center

Santiago, Salvador; Farley, Frank H.

A study was designed to examine the contribution of intrinsic arousal (individual differences) and induced arousal to children's comprehension of film content with short- and long-term retention intervals. Intrinsic arousal was measured by a salivary response measure; induced arousal was manipulated by white auditory noise. The latter was…

Age and sex bias in the reconstruction of past population structures.

PubMed

Bello, Silvia M; Thomann, Aminte; Signoli, Michel; Dutour, Olivier; Andrews, Peter

2006-01-01

Palaeodemographical studies are founded on the assumption that the sex and age distribution of the skeletal sample reflects the constitution of the original population. It is becoming increasingly clear, however, that the type and amount of information that may be derived from osteoarchaeological collections are related to the state of preservation of remains. This work proposes a new method to evaluate bone preservation, to identify age and sex biases in the preservation of human skeletal remains, and to assess whether differences in preservation patterns are more dependent on factors intrinsic or extrinsic to anatomical features of human bones. Three osteological collections and over 600 skeletons were observed. The state of preservation of human bones was assessed using three preservation indexes: the anatomical preservation index (API), the bone representation index (BRI), and the qualitative bone index (QBI). The results suggest that subadult skeletons are generally more poorly preserved and with bones less well-represented than adult skeletons. Among subadults, female and male skeletons have different patterns of preservation according to their age. This pattern of preservation depends on intrinsic anatomical properties of bones themselves, while external factors can only increase these differences in the state of preservation and representation of osseous remains. It is concluded from this that failure to recognize these differences may lead to misleading interpretations of paleodemography of past human populations.

Cross-cultural consistency and diversity in intrinsic functional organization of Broca's Region.

PubMed

Zhang, Yu; Fan, Lingzhong; Caspers, Svenja; Heim, Stefan; Song, Ming; Liu, Cirong; Mo, Yin; Eickhoff, Simon B; Amunts, Katrin; Jiang, Tianzi

2017-04-15

As a core language area, Broca's region was consistently activated in a variety of language studies even across different language systems. Moreover, a high degree of structural and functional heterogeneity in Broca's region has been reported in many studies. This raised the issue of how the intrinsic organization of Broca's region effects by different language experiences in light of its subdivisions. To address this question, we used multi-center resting-state fMRI data to explore the cross-cultural consistency and diversity of Broca's region in terms of its subdivisions, connectivity patterns and modularity organization in Chinese and German speakers. A consistent topological organization of the 13 subdivisions within the extended Broca's region was revealed on the basis of a new in-vivo parcellation map, which corresponded well to the previously reported receptorarchitectonic map. Based on this parcellation map, consistent functional connectivity patterns and modularity organization of these subdivisions were found. Some cultural difference in the functional connectivity patterns was also found, for instance stronger connectivity in Chinese subjects between area 6v2 and the motor hand area, as well as higher correlations between area 45p and middle frontal gyrus. Our study suggests that a generally invariant organization of Broca's region, together with certain regulations of different language experiences on functional connectivity, might exists to support language processing in human brain. Copyright © 2017 Elsevier Inc. All rights reserved.

Intraoperative inspection of the ureteropelvic junction during pyeloplasty is not sufficient to distinguish between extrinsic and intrinsic causes of obstruction: Correlation with histological analysis.

PubMed

Mut, Tuna; Acar, Ömer; Oktar, Tayfun; Kılıçaslan, Işın; Esen, Tarık; Ander, Haluk; Ziylan, Orhan

2016-08-01

Based on current knowledge, it is possible to have an initial diagnosis of intrinsic or extrinsic ureteropelvic junction obstruction (UPJO) based solely on clinical and imaging findings. However, it may not be possible to strictly discriminate an intrinsic case with an additional extrinsic component from a primarily intrinsic stenosis because of lower pole aberrant vessels. These two disorders may coexist or trigger each other. Herein, we aimed to compare the histological changes observed in intrinsic and extrinsic types of UPJO. Our hypothesis is that inspecting the UPJ during pyeloplasty may not be a sufficient way to delineate the underlying cause of obstruction in every individual. We retrospectively reviewed the data of 56 patients who had dismembered pyeloplasty. The intrinsic and extrinsic groups consisted of 38 and 18 patients, respectively. Masson's trichrome stain, CD117, and connexin 43 (Cx43) antibody were used in histopathology and immunochemistry. Statistical calculations were done with chi-square and Mann-Whitney U tests. Connexin 43 staining pattern, CD117 positive cell count, and the extent of fibrosis did not differ significantly between extrinsic and intrinsic cases. However, the difference with regard to the degree of muscular hypertrophy was close to statistical significance. The exact pathophysiological mechanism underlying UPJO has yet to be elucidated. A study directly comparing both groups histologically is indeed rare. Our study showed that there are no significant differences between the intrinsic and extrinsic groups in terms of the pacemaker activity, gap junctional communication, and extent of fibrosis. Muscular hypertrophy, which was marginally higher in our extrinsic group, may persist despite successful relocation of the obstructing vessel. The main drawbacks of our study are; the absence of a control group and the retrospective study design with its inherent selection biases. Immunohistochemical profiles of intrinsic and extrinsic UPJOs resemble each other. Intraoperative inspection of the UPJ may not be enough for accurate discrimination for a surgical procedure that can correct only the extrinsic cause. Copyright © 2016 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

Investigating the intrinsic and extrinsic work values of 10th grade students in science-oriented charter schools

NASA Astrophysics Data System (ADS)

Ozer, Ozgur

The purpose of this study was to investigate to what extent gender, achievement level, and income level predict the intrinsic and extrinsic work values of 10th grade students. The study explored whether group differences were good predictors of scores in work values. The research was a descriptive, cross-sectional study conducted on 131 10th graders who attended science-oriented charter schools. Students took Super's Work Values Instrument, a Likert-type test that links to 15 work values, which can be categorized as intrinsic and extrinsic values (Super, 1970). Multiple regression analysis was employed as the main analysis followed by ANCOVA. Multiple regression analysis results indicated that there is evidence that 8.9% of the variance in intrinsic work values and 10.2% of the variance in extrinsic work values can be explained by the independent variables ( p < .05). Achievement Level and Income Level may help predict intrinsic work value scores; Achievement Level may also help predict extrinsic work values. Achievement Level was the covariate in ANCOVA. Results indicated that males (M = .174) in this sample have a higher mean of extrinsic work values than that of females (M = -.279). However, there was no statistically significant difference between the intrinsic work values by gender. One possible interpretation of this might be school choice; students in these science-oriented charter schools may have higher intrinsic work values regardless of gender. Results indicated that there was no statistically significant difference among the means of extrinsic work values by income level (p < .05). However, free lunch students (M = .268) have a higher mean of intrinsic work values than that of paid lunch students ( M = -.279). A possible interpretation of this might be that lower income students benefit greatly from the intrinsic work values in overcoming obstacles. Further research is needed in each of these areas. The study produced statistically significant results with little practical significance. Students, parents, teachers, and counselors may still be advised to consider the work value orientations of students during the career choice process.

A New One-dimensional Quantum Material - Ta2Pd3Se8 Atomic Chain

NASA Astrophysics Data System (ADS)

Liu, Xue; Liu, Jinyu; Hu, Jin; Yue, Chunlei; Mao, Zhiqiang; Wei, Jiang; Antipina, Liubov; Sorokin, Pavel; Sanchez, Ana

Since the discovery of carbon nanotube, there has been a persistent effort to search for other one dimensional (1D) quantum systems. However, only a few examples have been found. We report a new 1D example - semiconducting Ta2Pd3Se8. We demonstrate that the Ta2Pd3Se8 nanowire as thin as 1.3nm can be easily obtained by applying simple mechanical exfoliation from its bulk counterpart. High resolution TEM shows an intrinsic 1D chain-like crystalline morphology on these nano wires, indicating weak bonding between these atomic chains. Theoretical calculation shows a direct bandgap structure, which evolves from 0.53eV in the bulk to 1.04eV in single atomic chain. The field effect transistor based on Ta2Pd3Se8 nanowire achieved a promising performance with 104On/Off ratio and 80 cm2V-1s-1 mobility. Low temperature transport study reflects two different mechanisms, variable range hopping and thermal activation, which dominate the transport properties at different temperature regimes. Ta2Pd3Se8 nanowire provides an intrinsic 1D material system for the study low dimensional condensed matter physics.

Protonation linked equilibria and apparent affinity constants: the thermodynamic profile of the alpha-chymotrypsin-proflavin interaction.

PubMed

Bruylants, Gilles; Wintjens, René; Looze, Yvan; Redfield, Christina; Bartik, Kristin

2007-12-01

Protonation/deprotonation equilibria are frequently linked to binding processes involving proteins. The presence of these thermodynamically linked equilibria affects the observable thermodynamic parameters of the interaction (K(obs), DeltaH(obs)(0) ). In order to try and elucidate the energetic factors that govern these binding processes, a complete thermodynamic characterisation of each intrinsic equilibrium linked to the complexation event is needed and should furthermore be correlated to structural information. We present here a detailed study, using NMR and ITC, of the interaction between alpha-chymotrypsin and one of its competitive inhibitors, proflavin. By performing proflavin titrations of the enzyme, at different pH values, we were able to highlight by NMR the effect of the complexation of the inhibitor on the ionisable residues of the catalytic triad of the enzyme. Using ITC we determined the intrinsic thermodynamic parameters of the different equilibria linked to the binding process. The possible driving forces of the interaction between alpha-chymotrypsin and proflavin are discussed in the light of the experimental data and on the basis of a model of the complex. This study emphasises the complementarities between ITC and NMR for the study of binding processes involving protonation/deprotonation equilibria.

Interaction of flavan-3-ol derivatives and different caseins is determined by more than proline content and number of proline repeats.

PubMed

Bohin, Maxime C; Vincken, Jean-Paul; Westphal, Adrie H; Tripp, Annelise M; Dekker, Peter; van der Hijden, Harry T W M; Gruppen, Harry

2014-09-01

Interactions of Type A and B flavan-3-ol dimers (procyanidins) and several monomeric flavan-3-ols, with α-casein and β-casein, were investigated. Binding affinities measured were related to the ligands structure, including several properties (e.g. intrinsic flexibility (number of rotatable bonds) and hydrophobicity), and to the amino-acid composition of the caseins. A monomeric flavan-3-ol esterified with gallic acid (EGCG) had a five to ten times higher affinity to caseins compared to the non-galloylated dimeric flavan-3-ols. In this case, the larger number of rotatable bonds in EGCG might be accountable for this difference. Comparing flavan-3-ol dimers, intrinsic flexibility did not consistently promote interactions, as procyanidin A1 displayed a higher affinity to α-casein than the supposedly more flexible B-type dimers investigated. Despite its higher content of proline, compared to α-casein, β-casein did not always have a higher affinity for the ligands investigated (e.g. no interaction with procyanidin A1 detected). These results suggest that more factors than proline content and the number of proline repeats govern phenolic-casein interactions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Intrinsic differences in atomic ordering of calcium (alumino)silicate hydrates in conventional and alkali-activated cements

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

White, Claire E., E-mail: whitece@princeton.edu; Andlinger Center for Energy and the Environment, Princeton University, Princeton; Lujan Neutron Scattering Center, Los Alamos National Laboratory, Los Alamos

2015-01-15

The atomic structures of calcium silicate hydrate (C–S–H) and calcium (–sodium) aluminosilicate hydrate (C–(N)–A–S–H) gels, and their presence in conventional and blended cement systems, have been the topic of significant debate over recent decades. Previous investigations have revealed that synthetic C–S–H gel is nanocrystalline and due to the chemical similarities between ordinary Portland cement (OPC)-based systems and low-CO{sub 2} alkali-activated slags, researchers have inferred that the atomic ordering in alkali-activated slag is the same as in OPC–slag cements. Here, X-ray total scattering is used to determine the local bonding environment and nanostructure of C(–A)–S–H gels present in hydrated tricalcium silicatemore » (C{sub 3}S), blended C{sub 3}S–slag and alkali-activated slag, revealing the large intrinsic differences in the extent of nanoscale ordering between C–S–H derived from C{sub 3}S and alkali-activated slag systems, which may have a significant influence on thermodynamic stability, and material properties at higher length scales, including long term durability of alkali-activated cements.« less

Daple coordinates organ-wide and cell-intrinsic polarity to pattern inner-ear hair bundles

PubMed Central

Siletti, Kimberly; Hudspeth, A. J.

2017-01-01

The establishment of planar polarization by mammalian cells necessitates the integration of diverse signaling pathways. In the inner ear, at least two systems regulate the planar polarity of sensory hair bundles. The core planar cell polarity (PCP) proteins coordinate the orientations of hair cells across the epithelial plane. The cell-intrinsic patterning of hair bundles is implemented independently by the G protein complex classically known for orienting the mitotic spindle. Although the primary cilium also participates in each of these pathways, its role and the integration of the two systems are poorly understood. We show that Dishevelled-associating protein with a high frequency of leucine residues (Daple) interacts with PCP and cell-intrinsic signals. Regulated by the cell-intrinsic pathway, Daple is required to maintain the polarized distribution of the core PCP protein Dishevelled and to position the primary cilium at the abneural edge of the apical surface. Our results suggest that the primary cilium or an associated structure influences the domain of cell-intrinsic signals that shape the hair bundle. Daple is therefore essential to orient and pattern sensory hair bundles. PMID:29229865

Small Angle X-Ray Scattering from Lipid-Bound Myelin Basic Protein in Solution

PubMed Central

Haas, H.; Oliveira, C. L. P.; Torriani, I. L.; Polverini, E.; Fasano, A.; Carlone, G.; Cavatorta, P.; Riccio, P.

2004-01-01

The structure of myelin basic protein (MBP), purified from the myelin sheath in both lipid-free (LF-MBP) and lipid-bound (LB-MBP) forms, was investigated in solution by small angle x-ray scattering. The water-soluble LF-MBP, extracted at pH < 3.0 from defatted brain, is the classical preparation of MBP, commonly regarded as an intrinsically unfolded protein. LB-MBP is a lipoprotein-detergent complex extracted from myelin with its native lipidic environment at pH > 7.0. Under all conditions, the scattering from the two protein forms was different, indicating different molecular shapes. For the LB-MBP, well-defined scattering curves were obtained, suggesting that the protein had a unique, compact (but not globular) structure. Furthermore, these data were compatible with earlier results from molecular modeling calculations on the MBP structure which have been refined by us. In contrast, the LF-MBP data were in accordance with the expected open-coil conformation. The results represent the first direct structural information from x-ray scattering measurements on MBP in its native lipidic environment in solution. PMID:14695288

Structural perturbations on huntingtin N17 domain during its folding on 2D-nanomaterials

NASA Astrophysics Data System (ADS)

Zhang, Leili; Feng, Mei; Zhou, Ruhong; Luan, Binquan

2017-09-01

A globular protein’s folded structure in its physiological environment is largely determined by its amino acid sequence. Recently, newly discovered transformer proteins as well as intrinsically disordered proteins may adopt the folding-upon-binding mechanism where their secondary structures are highly dependent on their binding partners. Due to the various applications of nanomaterials in biological sensors and potential wearable devices, it is important to discover possible conformational changes of proteins on nanomaterials. Here, through molecular dynamics simulations, we show that the first 17 residues of the huntingtin protein (HTT-N17) exhibit appreciable differences during its folding on 2D-nanomaterials, such as graphene and MoS2 nanosheets. Namely, the protein is disordered on the graphene surface but is helical on the MoS2 surface. Despite that the amphiphilic environment at the nanosheet-water interface promotes the folding of the amphipathic proteins (such as HTT-N17), competitions between protein-nanosheet and intra-protein interactions yield very different protein conformations. Therefore, as engineered binding partners, nanomaterials might significantly affect the structures of adsorbed proteins.

Protein Flexibility Facilitates Quaternary Structure Assembly and Evolution

PubMed Central

Marsh, Joseph A.; Teichmann, Sarah A.

2014-01-01

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

Energy conversion modeling of the intrinsic persistent luminescence of solids via energy transfer paths between transition levels.

PubMed

Huang, Bolong; Sun, Mingzi

2017-04-05

An energy conversion model has been established for the intrinsic persistent luminescence in solids related to the native point defect levels, formations, and transitions. In this study, we showed how the recombination of charge carriers between different defect levels along the zero phonon line (ZPL) can lead to energy conversions supporting the intrinsic persistent phosphorescence in solids. This suggests that the key driving force for this optical phenomenon is the pair of electrons hopping between different charged defects with negative-U eff . Such a negative correlation energy will provide a sustainable energy source for electron-holes to further recombine in a new cycle with a specific quantum yield. This will help us to understand the intrinsic persistent luminescence with respect to native point defect levels as well as the correlations of electronics and energetics.

Ferroelectric properties of Pb(Zr,Ti)O3 films under ion-beam induced strain

NASA Astrophysics Data System (ADS)

Lee, Jung-Kun; Nastasi, Michael

2012-11-01

The influence of an ion-beam induced biaxial stress on the ferroelectric and dielectric properties of Pb(Zr,Ti)O3 (PZT) films is investigated using the ion beam process as a novel approach to control external stress. Tensile stress is observed to decrease the polarization, permittivity, and ferroelectric fatigue resistance of the PZT films whose structure is monoclinic. However, a compressive stress increases all of them in monoclinic PZT films. The dependence of the permittivity on stress is found not to follow the phenomenological theory relating external forces to intrinsic properties of ferroelectric materials. Changes in the ferroelectric and dielectric properties indicate that the application of a biaxial stress modulates both extrinsic and intrinsic properties of PZT films. Different degrees of dielectric non-linearity suggests the density and mobility of non-180o domain walls, and the domain switching can be controlled by an applied biaxial stress and thereby influence the ferroelectric and dielectric properties.

Self-determination and goal orientation in track and field.

PubMed

Chin, Ngien-Siong; Khoo, Selina; Low, Wah-Yun

2012-06-01

This study investigated gender, age group and locality differences in adolescent athletes' self-determination motivation and goal orientations in track and field. It also examined the relationship between the self-determination theory and achievement goal theory. A total of 632 (349 boys, 283 girls) adolescent athletes (aged 13-18 years) completed the Sports Motivation Scale and Task and Ego Orientation in Sport Questionnaire. Results indicated significant differences between gender on intrinsic motivation, extrinsic motivation, amotivation (t(630) = 4.10, p < 0.05) and ego orientation (t(630) = 2.48, p < 0.05). Male students reported higher intrinsic motivation, extrinsic motivation, amotivation and ego orientation. A significant difference was found between age groups on task orientation (t(630) = 1.94, p < 0.05) and locality on ego orientation (t(630) = 1.94, p < 0.05). Older athletes showed significantly higher task orientation. Rural athletes had higher ego orientation whereas urban athletes have higher intrinsic motivation. Task orientation was related to intrinsic motivation (r = 0.55, p < 0.01), extrinsic motivation (r = 0.55, p < 0.01), but weakly related to amotivation (r = 0.10, p < 0.01). Ego orientation was related to intrinsic motivation (r = 0.30, p < 0.01), extrinsic motivation (r = 0.36, p < 0.01) and amotivaion (r = 0.36, p < 0.01). Task orientation was related to ego orientation (r = 0.29, p < 0.01). Multiple regression analysis showed intrinsic motivation, extrinsic motivation and amotivation accounted for 30.5% of the variances in task orientation.

High prevalence of luminal B breast cancer intrinsic subtype in Colombian women.

PubMed

Serrano-Gomez, Silvia Juliana; Sanabria-Salas, Maria Carolina; Hernández-Suarez, Gustavo; García, Oscar; Silva, Camilo; Romero, Alejandro; Mejía, Juan Carlos; Miele, Lucio; Fejerman, Laura; Zabaleta, Jovanny

2016-07-01

Breast cancer is the most frequent malignancy in women worldwide. Distinct intrinsic subtypes of breast cancer have different prognoses, and their relative prevalence varies significantly among ethnic groups. Little is known about the prevalence of breast cancer intrinsic subtypes and their association with clinicopathological data and genetic ancestry in Latin Americans. Immunohistochemistry surrogates from the 2013 St. Gallen International Expert Consensus were used to classify breast cancers in 301 patients from Colombia into intrinsic subtypes. We analyzed the distribution of subtypes by clinicopathological variables. Genetic ancestry was estimated from a panel of 80 ancestry informative markers. Luminal B breast cancer subtype was the most prevalent in our population (37.2%) followed by luminal A (26.3%), non-basal triple negative (NBTN) (11.6%), basal like (9%), human epidermal growth factor receptor 2 (HER2) enriched (8.6%) and unknown (7.3%). We found statistical significant differences in distribution between Colombian region (P = 0.007), age at diagnosis (P = 0.0139), grade (P < 0.001) and recurrence (P < 0.001) according to intrinsic subtype. Patients diagnosed with HER2-enriched, basal-like and NBTN breast cancer had the highest African ancestry. Future studies analyzing the molecular profiles of breast cancer in Colombian women will help us understand the molecular basis of this subtype distribution and compare the molecular characteristics of the different intrinsic subtypes in Colombian patients. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Self-Determination and Goal Orientation in Track and Field

PubMed Central

Chin, Ngien-Siong; Khoo, Selina; Low, Wah-Yun

2012-01-01

This study investigated gender, age group and locality differences in adolescent athletes’ self-determination motivation and goal orientations in track and field. It also examined the relationship between the self-determination theory and achievement goal theory. A total of 632 (349 boys, 283 girls) adolescent athletes (aged 13–18 years) completed the Sports Motivation Scale and Task and Ego Orientation in Sport Questionnaire. Results indicated significant differences between gender on intrinsic motivation, extrinsic motivation, amotivation (t(630) = 4.10, p < 0.05) and ego orientation (t(630) = 2.48, p < 0.05). Male students reported higher intrinsic motivation, extrinsic motivation, amotivation and ego orientation. A significant difference was found between age groups on task orientation (t(630) = 1.94, p < 0.05) and locality on ego orientation (t(630) = 1.94, p < 0.05). Older athletes showed significantly higher task orientation. Rural athletes had higher ego orientation whereas urban athletes have higher intrinsic motivation. Task orientation was related to intrinsic motivation (r = 0.55, p < 0.01), extrinsic motivation (r = 0.55, p < 0.01), but weakly related to amotivation (r = 0.10, p < 0.01). Ego orientation was related to intrinsic motivation (r = 0.30, p < 0.01), extrinsic motivation (r = 0.36, p < 0.01) and amotivaion (r = 0.36, p < 0.01). Task orientation was related to ego orientation (r = 0.29, p < 0.01). Multiple regression analysis showed intrinsic motivation, extrinsic motivation and amotivation accounted for 30.5% of the variances in task orientation. PMID:23486244

Mono vs multilayer fibronectin coatings on polar/hydrophobic/ionic polyurethanes: Altering surface interactions with human monocytes.

PubMed

Gossart, Audrey; Battiston, Kyle G; Gand, Adeline; Pauthe, Emmanuel; Santerre, J Paul

2018-01-15

Monocyte interactions with materials that are biofunctionalized with fibronectin (Fn) are of interest because of the documented literature which associates this protein with white blood cell function at implant sites. A degradable-polar hydrophobic ionic polyurethane (D-PHI), has been reported to promote an anti-inflammatory response from human monocytes. The aim of the current work was to study the influence of intrinsic D-PHI material chemistry on Fn adsorption (mono and multi-layer structures), and to investigate the influence of such chemistry on the structural state of the Fn, as well as the latter's influence on the activity of human monocytes on the protein coated substrates. Significant differences in Fn adsorption, surface hydrophobicity and the availability of defined peptide sequences (N terminal, C terminal or Cell Binding Domain) for the Fn in mono vs multilayer structures were observed as a function of the changes in intrinsic material chemistry. A D-PHI-formulated polyurethane substrate with subtle changes in anionic and hydrophobic domain content relative to the polar non-ionic urethane/carbonate groups within the polymer matrix promoted the lowest activation of monocytes, in the presence of multi-layer Fn constructs. These results highlight the importance of chemical heterogeneity as a design parameter for biomaterial surfaces, and establishes a desired strategy for controlling human monocyte activity at the surface of devices, when these are coated with multi-layer Fn structures. The latter is an important step towards functionalizing the materials with multi-layer protein drug carriers as interventional therapeutic agents. The control of the behavior of monocytes, especially migration and activation, is of crucial interest to modulate the inflammatory response at the site of implanted biomaterial. Several studies report the influence of adsorbed serum proteins on the behavior of monocytes on biomaterials. However, few studies show the influence of surface chemical group distribution on the controlled adsorption and the subsequent induced conformation- of mono versus multi-layer assembled structures generated from specific proteins implicated in wound repair. The current research considered the role of Fn adsorption and conformation in thin films while interacting with the intrinsic chemistry of segmented block polyurethanes; and the influence of the former on modulation and activation of human monocytes. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Aggregation and structural changes of α(S1)-, β- and κ-caseins induced by homocysteinylation.

PubMed

Stroylova, Yulia Y; Zimny, Jaroslaw; Yousefi, Reza; Chobert, Jean-Marc; Jakubowski, Hieronim; Muronetz, Vladimir I; Haertlé, Thomas

2011-10-01

Elevated homocysteine levels are resulting in N-homocysteinylation of lysyl residues in proteins and they correlate with a number of human pathologies. However, the role of homocysteinylation of lysyl residues is still poorly known. In order to study the features of homocysteinylation of intrinsically unstructured proteins (IUP) bovine caseins were used as a model. α(S1)-, β- and κ-caseins, showing different aggregations and micelle formation, were modified with homocysteine-thiolactone and their physico-chemical properties were studied. Efficiency of homocysteine incorporation was estimated to be about 1.5, 2.1 and 1.3 homocysteyl residues per one β-, α(S1)-, and κ-casein molecule, respectively. Use of intrinsic and extrinsic fluorescent markers such as Trp, thioflavin T and ANS, reveal structural changes of casein structures after homocysteinylation reflected by an increase in beta-sheet content, which in some cases may be characteristic of amyloid-like transformations. CD spectra also show an increase in beta-sheet content of homocysteinylated caseins. Casein homocysteinylation leads in all cases to aggregation. The sizes of aggregates and aggregation rates were dependent on homocysteine thiolactone concentration and temperature. DLS and microscopic studies have revealed the formation of large aggregates of about 1-3μm. Homocysteinylation of α(S1)- and β-caseins results in formation of regular spheres. Homocysteinylated κ-casein forms thin unbranched fibrils about 400-800nm long. In case of κ-casein amyloidogenic effect of homocysteinylation was confirmed by Congo red spectra. Taken together, data indicate that N-homocysteinylation provokes significant changes in properties of native caseins. A comparison of amyloidogenic transformation of 3 different casein types, belonging to the IUP protein family, shows that the efficiency of amyloidogenic transformation upon homocysteinylation depends on micellization capacity, additional disulphide bonds and other structural features. Copyright © 2011 Elsevier B.V. All rights reserved.

Unraveling energy conversion modeling in the intrinsic persistent upconverted luminescence of solids: a study of native point defects in antiferromagnetic Er2O3.

PubMed

Huang, Bolong

2016-05-11

We investigated the mechanism of the intrinsic persistent luminescence of Er2O3 in the A-type lattice based on first-principles calculations. We found that the native point defects were engaged in mutual subtle interactions in the form of chemical reactions between different charge states. The release of energy related to lattice distortion facilitates the conversion of energy for electrons to be transported between the valence band and the trap levels or even between the deep trap levels so as to generate persistent luminescence. The defect transitions that take place along the zero-phonon line release energy to enable optical transitions, with the exact amount of negative effective correlation energy determined by the lattice distortions. Our calculations on the thermodynamic transition levels confirm that both the visible and NIR experimentally observed intrinsic persistent luminescence (phosphor or afterglow) are related to the thermodynamic transition levels of oxygen-related defects, and the thermodynamic transition levels within different charge states for these defects are independent of the chemical potentials of the given species. Lattice distortion defects such as anion Frenkel (a-Fr) pair defects play an important role in transporting O-related defects between different lattice sites. To obtain red persistent luminescence that matches the biological therapeutic window, it is suggested to increase the electron transition levels between high-coordinated O vacancies and related metastable a-Fr defects; a close-packed core-shell structure is required to quench low-coordinated O-related defects so as to reduce the green band luminescence. We further established a conversed chain reaction (CCR) model to interpret the energy conversion process of persistent luminescence in terms of the inter-reactions of native point defects between different charge states. It is advantageous to use the study of defect levels combined with formation energies to suggest limits to doping energy and explain photostimulated luminescence in terms of native point defects.

Intrinsic Kinetics Fluctuations as Cause of Growth Inhomogeneity in Protein Crystals

NASA Technical Reports Server (NTRS)

Vekilov, Peter G.; Rosenberger, Franz

1998-01-01

Intrinsic kinetics instabilities in the form of growth step bunching during the crystallization of the protein lysozyme from solution were characterized by in situ high-resolution optical interferometry. Compositional variations (striations) in the crystal, which potentially decrease its utility, e.g., for molecular structure studies by diffraction methods, were visualized by polarized light reflection microscopy. A spatiotemporal correlation was established between the sequence of moving step bunches and the striations.

A prospective study on the variation in falling and fall risk among community-dwelling older citizens in 12 European countries.

PubMed

Franse, Carmen B; Rietjens, Judith Ac; Burdorf, Alex; van Grieken, Amy; Korfage, Ida J; van der Heide, Agnes; Mattace Raso, Francesco; van Beeck, Ed; Raat, Hein

2017-06-30

The rate of falling among older citizens appears to vary across different countries, but the underlying aspects causing this variation are unexplained. We aim to describe between-country variation in falling and explore whether intrinsic fall risk factors can explain possible variation. Prospective study on data from the cross-national Survey of Health, Ageing and Retirement in Europe (SHARE). Twelve European countries (Austria, Belgium, Czech Republic, Denmark, Estonia, France, Germany, Italy, The Netherlands, Spain, Sweden, Switzerland). Community-dwelling persons aged ≥65 years (n=18 596). Socio-demographic factors (age, gender, education level and living situation) and intrinsic fall risk factors (less than good self-rated health (SRH), mobility limitations, limitations with activities of daily living (ADL), dizziness, impaired vision, depression and impaired cognition) were assessed in a baseline interview. Falling was assessed 2 years later by asking whether the participant had fallen within the 6 months prior to the follow-up interview. There was significant between-country variation in the rate of falling (varying from 7.9% in Switzerland to 16.2% in the Czech Republic). The prevalence of intrinsic fall risk factors varied twofold to fourfold between countries. Associations between factors age ≥80 years, less than good SRH, mobility limitations, ADL limitations, dizziness and depression, and falling were different between countries (p<0.05). Between-country differences in falling largely persisted after adjusting for socio-demographic differences but strongly attenuated after adjusting for differences in intrinsic fall risk factors. There is considerable variation in the rate of falling between European countries, which can largely be explained by between-country variation in the prevalence of intrinsic fall risk factors. There are also country-specific variations in the association between these intrinsic risk factors and falling. These findings emphasise the importance of addressing intrinsic fall risk in (inter)national fall-prevention strategies, while highlighting country-specific priorities. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Effect of molecular topology on the transport properties of dendrimers in dilute solution at Θ temperature: A Brownian dynamics study

NASA Astrophysics Data System (ADS)

Bosko, Jaroslaw T.; Ravi Prakash, J.

2008-01-01

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Θ conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.

Carbon nanotube and graphene device modeling and simulation

NASA Astrophysics Data System (ADS)

Yoon, Young Ki

The performance of the semiconductors has been improved and the price has gone down for decades. It has been continuously scaled down in size year by year, and now it encounters the fundamental scaling limit. We, therefore, should prepare a new era beyond the conventional semiconductor technologies. One of the most promising devices is possible by carbon nanotube (CNT) or graphene nanoribbon (GNR) in terms of its excellent charge transport properties. Their fundamental material properties and device physics are totally different to those of the conventional devices. In this nano-regime, more sophisticated device modeling and simulation are really needed to elucidate nano-device operation and to save our resources from errors. The numerical simulation works in this dissertation will provide novel view points on the emerging devices. In this dissertation, CNT and GNR devices are numerically studied. The first part of this work is on CNT devices, and a common structure of CNT device has CNT channel, metal source and drain contacts, and gate electrode. We investigate the strain, geometry, and scattering effects on the device performance of CNT field-effect transistors (FETs). It is shown that even a small amount of strain can result in a large effect on the performance of CNTFETs due to the variation of the bandgap and band-structure-limited velocity. A type of strain which produces a larger bandgap results in increased Schottky barrier (SB) height and decreased band-structure-limited velocity, and hence a smaller minimum leakage current, smaller on current, larger maximum achievable Ion/Ioff, and larger intrinsic delay. We also examine geometry effect of partial gate CNTFETs. In the growth process of vertical CNT, underlap between the gate and the bottom electrode is advantageous for transistor operation because it suppresses ambipolar conduction of SBFETs. Both n-type and p-type transistor operations with balanced performance metrics can be achieved on a single partial gate FET by using proper bias schemes. The effect of phonon scattering on the intrinsic delay and cut-off frequency of Schottky barrier CNTFETs is also examined. Carriers are mostly scattered by optical and zone boundary phonons beyond the beginning of the channel. The scattering has a small direct effect on the DC on current of the CNTFET, but it results in significant decrease of intrinsic cut-off frequency and increase of intrinsic delay. Semiconducting CNT is useful for the channel in CNTFETs, whereas metallic CNT can be used as an electrode. If a porous CNT film is used as a source electrode, vertical thin-film transistors (TFTs) can be constructed. Vertical organic FET (OFET) shows clear transistor switching behavior allowing orders of magnitude modulation of the source-drain current even in the presence of electrostatic screening by the source electrode. The channel length should be carefully engineered due to the trade-off between device characteristics in the subthreshold and above-threshold regions. The second subject is device simulations of GNRFETs. Even though GNR is also graphene-based quasi-1D nanostructure like CNT, the differences in shape, boundary condition, and existence of edges and dangling bonds make it operate in a different way. Atomistic 3D simulation study of the performance of GNR SBFETs is presented. The impacts of non-idealities on device performance have been investigated. The edges of GNR, which do not exist in CNT, can be advantages or disadvantages. If an appropriate control by different edge atoms is possible, it would be definitely positive. Totally new electronic band structure is obtained by different edge-termination atoms. In addition, only a fraction of impurity atom can also much affect on the material properties of GNR. In order to perform device simulations of non-uniform GNR devices, multiscale simulation scheme can be used in non-equilibrium Green's function (NEGF) formalism and density-functional method.

Intrinsic Motivations Drive Learning of Eye Movements: An Experiment with Human Adults

PubMed Central

Caligiore, Daniele; Mustile, Magda; Cipriani, Daniele; Redgrave, Peter; Triesch, Jochen; De Marsico, Maria; Baldassarre, Gianluca

2015-01-01

Intrinsic motivations drive the acquisition of knowledge and skills on the basis of novel or surprising stimuli or the pleasure to learn new skills. In so doing, they are different from extrinsic motivations that are mainly linked to drives that promote survival and reproduction. Intrinsic motivations have been implicitly exploited in several psychological experiments but, due to the lack of proper paradigms, they are rarely a direct subject of investigation. This article investigates how different intrinsic motivation mechanisms can support the learning of visual skills, such as “foveate a particular object in space”, using a gaze contingency paradigm. In the experiment participants could freely foveate objects shown in a computer screen. Foveating each of two “button” pictures caused different effects: one caused the appearance of a simple image (blue rectangle) in unexpected positions, while the other evoked the appearance of an always-novel picture (objects or animals). The experiment studied how two possible intrinsic motivation mechanisms might guide learning to foveate one or the other button picture. One mechanism is based on the sudden, surprising appearance of a familiar image at unpredicted locations, and a second one is based on the content novelty of the images. The results show the comparative effectiveness of the mechanism based on image novelty, whereas they do not support the operation of the mechanism based on the surprising location of the image appearance. Interestingly, these results were also obtained with participants that, according to a post experiment questionnaire, had not understood the functions of the different buttons suggesting that novelty-based intrinsic motivation mechanisms might operate even at an unconscious level. PMID:25775248

Are intrinsic motivational factors of work associated with functional incapacity similarly regardless of the country?

PubMed

Väänänen, A; Pahkin, K; Huuhtanen, P; Kivimäki, M; Vahtera, J; Theorell, T; Kalimo, R

2005-10-01

Many psychosocial models of wellbeing at work emphasise the role of intrinsic motivational factors such as job autonomy, job complexity, and innovativeness. However, little is known about whether the employees of multinational enterprises differ from country to country with regard to intrinsic motivational factors, and whether these factors are associated with wellbeing similarly in the different countries. The purpose of this study was to examine the level of intrinsic motivational factors and their impact on functional incapacity in different countries in a multinational corporation. In 2000, data were collected from a globally operating corporation with a questionnaire survey. The participants were 13 795 employees (response rate 59%; 56% under age 45; 80% men; 61% blue collar employees), who worked in similar industrial occupations in five countries (Canada, China, Finland, France, and Sweden). The Chinese employees reported higher autonomy and lower complexity at work than the employees from the other countries. After adjustment for age, sex, socioeconomic status, and physical work environment, job autonomy, and job complexity at work were associated with functional incapacity in most countries, whereas in China the impact was significantly stronger. In Finland and in China employees with low innovativeness at work were more prone to functional incapacity than corresponding employees in other countries. The level of intrinsic motivational factors varied between the Chinese employees and those in other countries. In line with theoretical notions, the relation between intrinsic motivational factors of work and functional incapacity followed a similar pattern in the different countries. However, these country specific results show that a culture specific approach to employee wellbeing should also be applied.