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Sample records for surface folding index

  1. Gyral Folding Pattern Analysis via Surface Profiling

    Science.gov (United States)

    Li, Kaiming; Guo, Lei; Li, Gang; Nie, Jingxin; Faraco, Carlos; Cui, Guangbin; Zhao, Qun; Miller, L. Stephen; Liu, Tianming

    2010-01-01

    Folding is an essential shape characteristic of the human cerebral cortex. Descriptors of cortical folding patterns have been studied for decades. However, many previous studies are either based on local shape descriptors such as curvature, or based on global descriptors such as gyrification index or spherical wavelets. This paper proposes a gyrus-scale folding pattern analysis technique via cortical surface profiling. Firstly, we sample the cortical surface into 2D profiles and model them using a power function. This step provides both the flexibility of representing arbitrary shape by profiling and the compactness of representing shape by parametric modeling. Secondly, based on the estimated model parameters, we extract affine-invariant features on the cortical surface, and apply the affinity propagation clustering algorithm to parcellate the cortex into cortical regions with strict hierarchy and smooth transitions among them. Finally, a second-round surface profiling is performed on the parcellated cortical surface, and the number of hinges is detected to describe the gyral folding pattern. We have applied the surface profiling method to two normal brain datasets and a Schizophrenia patient dataset. The experimental results demonstrate that the proposed method can accurately classify human gyri into 2-hinge, 3-hinge and 4-hinge patterns. The distribution of these folding patterns on brain lobes and the relationship between fiber density and gyral folding patterns are further investigated. Results from the Schizophrenia dataset are consistent with commonly found abnormality in former studies by others, which demonstrates the potential clinical applications of the proposed technique. PMID:20472071

  2. Plant surfaces with cuticular folds are slippery for beetles.

    Science.gov (United States)

    Prüm, Bettina; Seidel, Robin; Bohn, Holger Florian; Speck, Thomas

    2012-01-07

    Plant surfaces covered with three-dimensional (3D) waxes are known to strongly reduce insect adhesion, leading to slippery surfaces. Besides 3D epicuticular waxes, cuticular folds are a common microstructure found on plant surfaces, which have not been quantitatively investigated with regard to their influence on insect adhesion. We performed traction experiments with Colorado potato beetles on five plant surfaces with cuticular folds of different magnitude. For comparison, we also tested (i) smooth plant surfaces and (ii) plant surfaces possessing 3D epicuticular waxes. Traction forces on surfaces with medium cuticular folds, of about 0.5 µm in both height and thickness and a spacing of 0.5-1.5 µm, were reduced by an average of 88 per cent in comparison to smooth plant surfaces. Traction forces were reduced by the same order of magnitude as on plant surfaces covered with 3D epicuticular waxes. For surface characterization, we performed static contact angle measurements, which proved a strong effect of cuticular folds also on surface wettability. Surfaces possessing cuticular folds of greater magnitude showed higher contact angles up to superhydrophobicity. We hypothesize that cuticular folds reduce insect adhesion mainly due to a critical roughness, reducing the real contact area between the surface and the insect's adhesive devices.

  3. Interaction of β-sheet folds with a gold surface.

    Directory of Open Access Journals (Sweden)

    Martin Hoefling

    Full Text Available The adsorption of proteins on inorganic surfaces is of fundamental biological importance. Further, biomedical and nanotechnological applications increasingly use interfaces between inorganic material and polypeptides. Yet, the underlying adsorption mechanism of polypeptides on surfaces is not well understood and experimentally difficult to analyze. Therefore, we investigate here the interactions of polypeptides with a gold(111 surface using computational molecular dynamics (MD simulations with a polarizable gold model in explicit water. Our focus in this paper is the investigation of the interaction of polypeptides with β-sheet folds. First, we concentrate on a β-sheet forming model peptide. Second, we investigate the interactions of two domains with high β-sheet content of the biologically important extracellular matrix protein fibronectin (FN. We find that adsorption occurs in a stepwise mechanism both for the model peptide and the protein. The positively charged amino acid Arg facilitates the initial contact formation between protein and gold surface. Our results suggest that an effective gold-binding surface patch is overall uncharged, but contains Arg for contact initiation. The polypeptides do not unfold on the gold surface within the simulation time. However, for the two FN domains, the relative domain-domain orientation changes. The observation of a very fast and strong adsorption indicates that in a biological matrix, no bare gold surfaces will be present. Hence, the bioactivity of gold surfaces (like bare gold nanoparticles will critically depend on the history of particle administration and the proteins present during initial contact between gold and biological material. Further, gold particles may act as seeds for protein aggregation. Structural re-organization and protein aggregation are potentially of immunological importance.

  4. Liminal transformations: folding the surface of the photograph

    Directory of Open Access Journals (Sweden)

    Nour Dados

    2010-04-01

    Full Text Available At once a material object and a multitude of paths, the photograph is a useful place to begin thinking about the threshold. In the photograph we might dwell on the nuances of the threshold, its ability to be an ‘inbetween’ and a gateway to a ‘beyond’ simultaneously. Indeed, the photograph offers both possibilities. The work of Bhabha, Benjamin and Sontag elucidates this slippage. In this uncertainty, ‘inbetween’ and ‘beyond’ signal another productive intersection.  The liminality of the threshold marks this terrain as a spatial transgression that ushers in a temporal disjuncture. The threshold is a shadow zone, as ordinary as a stairwell and as transformative as a breakthrough. In attempting to map the threshold, the paper borrows from Deleuze and Marks on enfolding and unfolding as a means through which knowledge becomes accessible, or remains concealed. To some extent, mapping the threshold is a process that begins unfolding from the discussion of surface, gaze and perception. Yet despite these markers, mapping the threshold of photographs proves difficult and elusive. In this respect, Wittgenstein’s notion of ‘seeing aspects’ helps explain the way that the threshold always exceeds our attempts at mapping and defies perception. The paper examines this impasse through the ‘fold of the surface’, an action which transgresses the flatness of the image without altering it. Perhaps this is the closest we can be to the threshold without holding it.À la fois objet matériel et multitude de chemins, la photographie est un lieu privilégié pour commencer à réfléchir sur le seuil. Dans la photo, nous pouvons nous attarder sur les nuances du seuil, son caractère simultané d’« entre-deux » et de portail vers un « au-delà » en même temps. En effet, la photo offre en effet ces deux possibilités. Les travaux de Bhabha, Benjamin et Sontag éclaircissent ce glissement. Dans cet incertain, l’« entre-deux » et

  5. Liquid refractive index sensor based on a 2D 10-fold photonic quasicrystal

    Science.gov (United States)

    Wang, Shuai; Sun, XiaoHong; Wang, Cong; Peng, Gangding; Qi, Yongle; Wang, XiShi

    2017-09-01

    A liquid refractive index sensor is designed and optimized by using silicon-rods based on a 10-fold photonic quasicrystal without defects. The resonant mode with high Q value is chosen as the sensing wavelength in the transmission spectrum. By changing the radius of the silicon pillars, the sensor size and the refractive index of the background media, different types of sensors are designed and investigated. On the other hand, the performance of the sensor is investigated including the measurement range, sensitivity, etc. In the detection limit of spectral instruments, 0.02 nm, the sensing accuracy is 10-4 refractive index unit with a figure of merit of 1478. The measurement range is from 1.2731 to 1.4185. This will provide a new method for the design and fabrication of lab-on-chip, microfluidic optical elements and integrated optical circuits.

  6. Competition between surface adsorption and folding of fibril-forming polypeptides.

    Science.gov (United States)

    Ni, Ran; Kleijn, J Mieke; Abeln, Sanne; Cohen Stuart, Martien A; Bolhuis, Peter G

    2015-02-01

    Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse-grained model, we systematically studied the folding and adsorption behavior of a β-roll forming polypeptide. We find that there are two different folding pathways depending on the temperature: (i) at low temperature, the polypeptide folds in solution into a β-roll before adsorbing onto the attractive surface; (ii) at higher temperature, the polypeptide first adsorbs in a disordered state and folds while on the surface. The folding temperature increases with increasing attraction as the folded β-roll is stabilized by the surface. Surprisingly, further increasing the attraction lowers the folding temperature again, as strong attraction also stabilizes the adsorbed disordered state, which competes with folding of the polypeptide. Our results suggest that to enhance the folding, one should use a weakly attractive surface. They also explain the recent experimental observation of the nonmonotonic effect of charge on the fibril formation on an oppositely charged surface [C. Charbonneau et al., ACS Nano 8, 2328 (2014)].

  7. Competition between surface adsorption and folding of fibril-forming polypeptides

    Science.gov (United States)

    Ni, Ran; Kleijn, J. Mieke; Abeln, Sanne; Cohen Stuart, Martien A.; Bolhuis, Peter G.

    2015-02-01

    Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse-grained model, we systematically studied the folding and adsorption behavior of a β -roll forming polypeptide. We find that there are two different folding pathways depending on the temperature: (i) at low temperature, the polypeptide folds in solution into a β -roll before adsorbing onto the attractive surface; (ii) at higher temperature, the polypeptide first adsorbs in a disordered state and folds while on the surface. The folding temperature increases with increasing attraction as the folded β -roll is stabilized by the surface. Surprisingly, further increasing the attraction lowers the folding temperature again, as strong attraction also stabilizes the adsorbed disordered state, which competes with folding of the polypeptide. Our results suggest that to enhance the folding, one should use a weakly attractive surface. They also explain the recent experimental observation of the nonmonotonic effect of charge on the fibril formation on an oppositely charged surface [C. Charbonneau et al., ACS Nano 8, 2328 (2014), 10.1021/nn405799t].

  8. 2d index and surface operators

    International Nuclear Information System (INIS)

    Gadde, Abhijit; Gukov, Sergei

    2014-01-01

    In this paper we compute the superconformal index of 2d (2,2) supersymmetric gauge theories. The 2d superconformal index, a.k.a. flavored elliptic genus, is computed by a unitary matrix integral much like the matrix integral that computes the 4d superconformal index. We compute the 2d index explicitly for a number of examples. In the case of abelian gauge theories we see that the index is invariant under flop transition and under CY-LG correspondence. The index also provides a powerful check of the Seiberg-type duality for non-abelian gauge theories discovered by Hori and Tong. In the later half of the paper, we study half-BPS surface operators in N=2 superconformal gauge theories. They are engineered by coupling the 2d (2,2) supersymmetric gauge theory living on the support of the surface operator to the 4d N=2 theory, so that different realizations of the same surface operator with a given Levi type are related by a 2d analogue of the Seiberg duality. The index of this coupled system is computed by using the tools developed in the first half of the paper. The superconformal index in the presence of surface defect is expected to be invariant under generalized S-duality. We demonstrate that it is indeed the case. In doing so the Seiberg-type duality of the 2d theory plays an important role

  9. Quantum Nuclear Extension of Electron Nuclear Dynamics on Folded Effective-Potential Surfaces

    DEFF Research Database (Denmark)

    Hall, B.; Deumens, E.; Ohrn, Y.

    2014-01-01

    A perennial problem in quantum scattering calculations is accurate theoretical treatment of low energy collisions. We propose a method of extracting a folded, nonadiabatic, effective potential energy surface from electron nuclear dynamics (END) trajectories; we then perform nuclear wave packet...

  10. Effects of surface processes on multilayer detachment folding: a numerical approach

    Science.gov (United States)

    Collignon, M.; May, D.; Kaus, B.; Fernandez, N.

    2013-12-01

    Over the past decades, the interaction between surface processes and development of mountain belts has been extensively studied. While syntectonic sedimentation appears to control the external development of the fold-and-thrust belts, erosion strongly influences the evolution of internal regions within mountain belts. The effects of surface processes on brittle deformation have been thoroughly studied using analogue and numerical models of accretionary wedges, however, most of the numerical studies used a 2D model of deformation and/or a simple formulation for the surface processes, where both sedimentation and erosion are rarely present together. Coupled analogue models of deformation and surface processes are challenging, due to material and scaling issues, and often only reproduce two end-member cases (no erosion vs very strong erosion, where all the material is removed), but fail to investigate the transitional cases. In contrast, interactions between surface processes and ductile deformation (e.g. multilayer detachment folding) have been poorly investigated. Thin-skinned fold and thrust belts are seen as the result of compressional deformation of a sediment pile over a weak layer acting as a décollement level. The resulting surface expression has often been interpreted, based on geometrical criteria in terms of fault bend folds, propagation folds and/or detachment folds. A few analogue studies have demonstrated that fold morphology can be influenced by erosion rates or preferential localization of sedimentation, and additionally, that the fold growth can be stopped by increasing the supply of sediments. Here we aim to numerically investigate the effects of surface processes and multilayer folding in three dimensions. For this purpose, we have developed a finite-element based landscape evolution model (both erosion and sedimentation) using PETSc, and coupled it to the 3D mechanical code LaMEM. The landscape evolution model uses a non-linear diffusion

  11. Analysis of the free-energy surface of proteins from reversible folding simulations.

    Directory of Open Access Journals (Sweden)

    Lucy R Allen

    2009-07-01

    Full Text Available Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

  12. FoldIndex((c)) : a simple tool to predict whether a given protein sequence is intrinsically unfolded

    NARCIS (Netherlands)

    Prilusky, J; Felder, CE; Zeev-Ben-Mordehai, T; Rydberg, EH; Man, O; Beckmann, J.S.; Silman, I.; Sussman, J.L.

    2005-01-01

    An easy-to-use, versatile and freely available graphic web server, FoldIndex© is described: it predicts if a given protein sequence is intrinsically unfolded implementing the algorithm of Uversky and co-workers, which is based on the average residue hydrophobicity and net charge of the sequence.

  13. Determination of strain field on the superior surface of excised larynx vocal folds using DIC.

    Science.gov (United States)

    Bakhshaee, Hani; Young, Jonathan; Yang, Justin C W; Mongeau, Luc; Miri, Amir K

    2013-11-01

    The objective of the present study was to quantify the mechanical strain and stress in excised porcine larynges during self-oscillation using digital image correlation (DIC) method. The use of DIC in the excised larynx setup may yield accurate measurements of the vocal fold displacement field. Ex vivo animal larynx. Measurements were performed using excised porcine larynges on a humidified flow bench, equipped with two high-speed cameras and a commercially available DIC software. Surface deformations were calculated from digital images recorded at 3000 frames per second during continuous self-oscillation for four excised porcine larynges. Larynx preparation consisted of removing the supraglottal wall and the false folds. DIC yielded the deformation field on the superior visible surface of the vocal folds. Measurement data for adducted and freely suspended vocal folds were also used to estimate the distribution of the initial prephonatory strain field. An isotropic constitutive law, the polymer eight-chain model, was used to estimate the surface distributions of planar stresses from the strain data. The Lagrangian normal strain values were between ∼16% and ∼29% along the anterior-posterior direction. The motion of material points on the vocal fold surface described an elliptical trajectory during oscillation. A phase difference was observed between the anterior-posterior and the medial-lateral component of the displacement. The strain data and eight-chain model yielded a maximum stress of ∼4 kPa along the medial-lateral direction on the superior surface. DIC allowed the strain field over the superior surface of an excised porcine larynx to be quantified during self-oscillation. The approach allowed the determination of the trajectory of specific points on the vocal fold surface. The results for the excised larynx were found to be significantly different than previous results obtained using synthetic replicas. The present study provides suggestions for future

  14. Competition between surface adsorption and folding of fibril-forming polypeptides

    NARCIS (Netherlands)

    Ni, R.; Kleijn, J.M.; Cohen Stuart, M.A.; Bolhuis, P.G.

    2015-01-01

    Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse-grained model, we systematically studied the folding and adsorption behavior of a ß -roll forming polypeptide. We find that there are two

  15. Competition between surface adsorption and folding of fibril-forming polypeptides

    NARCIS (Netherlands)

    Ni, R.; de Kleijn, M.; Abeln, S.; Cohen Stuart, M.A.; Bolhuis, P.G.

    2015-01-01

    Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse-grained model, we systematically studied the folding and adsorption behavior of a β-roll forming polypeptide. We find that there are two different

  16. Competition between surface adsorption and folding of fibril-forming polypeptides

    NARCIS (Netherlands)

    Ni, R.; Kleijn, J.M.; Abeln, S.; Cohen Stuart, M.A.; Bolhuis, P.G.

    2015-01-01

    Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse-grained model, we systematically studied the folding and adsorption behavior of a beta-roll forming polypeptide. We find that there are two

  17. Effect of graphite on folded metal occurrence in honed surfaces of grey and compacted cast irons

    Science.gov (United States)

    do Vale, João Luiz; da Silva, Carlos Henrique; Pintaúde, Giuseppe

    2017-09-01

    Grey cast iron (GCI) and compacted graphite iron (CGI) are the most employed materials to manufacture cylinder liners. The use of diamond tools to hone the surfaces resulted in an increase of the so-called folded metal occurrence. This irregularity can reduce the performance of engines and investigations to understand it have been made. In this sense, the current study aims to correlate the variation of graphite and the folded metal occurrence. Different samples of GCI and CGI were extracted directly of engine blocks, resulting in four metallurgical conditions. Topographical analysis was conducted in an optical interferometer and a dedicated routine to count the folded metal was developed using 3D images. Folded metal occurrence can be associated to a specific region of topography and to an increase in the graphite area fraction. Experimental evidences were provided revealing cross-sectional images of grooves using a scanning electron microscope. In addition, the present investigation shows that a larger amount of folded metal was related to the microstructure of thicker walls of compact graphite iron.

  18. Normal Incidence for Graded Index Surfaces

    Science.gov (United States)

    Khankhoje, Uday K.; Van Zyl, Jakob

    2011-01-01

    A plane wave is incident normally from vacuum (eta(sub 0) = 1) onto a smooth surface. The substrate has three layers; the top most layer has thickness d(sub 1) and permittivity epsilon(sub 1). The corresponding numbers for the next layer are d(sub 2); epsilon(sub 2), while the third layer which is semi-in nite has index eta(sub 3). The Hallikainen model [1] is used to relate volumetric soil moisture to the permittivity. Here, we consider the relation for the real part of the permittivity for a typical loam soil: acute epsilon(mv) = 2.8571 + 3.9678 x mv + 118:85 x mv(sup 2).

  19. Simultaneous formation of multiscale hierarchical surface morphologies through sequential wrinkling and folding

    Science.gov (United States)

    Wang, Yu; Sun, Qingyang; Xiao, Jianliang

    2018-02-01

    Highly organized hierarchical surface morphologies possess various intriguing properties that could find important potential applications. In this paper, we demonstrate a facile approach to simultaneously form multiscale hierarchical surface morphologies through sequential wrinkling. This method combines surface wrinkling induced by thermal expansion and mechanical strain on a three-layer structure composed of an aluminum film, a hard Polydimethylsiloxane (PDMS) film, and a soft PDMS substrate. Deposition of the aluminum film on hard PDMS induces biaxial wrinkling due to thermal expansion mismatch, and recovering the prestrain in the soft PDMS substrate leads to wrinkling of the hard PDMS film. In total, three orders of wrinkling patterns form in this process, with wavelength and amplitude spanning 3 orders of magnitude in length scale. By increasing the prestrain in the soft PDMS substrate, a hierarchical wrinkling-folding structure was also obtained. This approach can be easily extended to other thin films for fabrication of multiscale hierarchical surface morphologies with potential applications in different areas.

  20. Surface states in crystals with low-index surfaces

    International Nuclear Information System (INIS)

    Wang Hui-Ping; Tao Rui-Bao

    2015-01-01

    For most of the conventional crystals with low-index surfaces, the hopping between the nearest neighbor (1NN) crystal planes (CPs) is dominant and the ones from the nNN (2 ≤ n < ∞) CPs are relatively weak, considered as small perturbations. The recent theoretical analysis [1] has demonstrated the absence of surface states at the level of the hopping approximation between the 1NN CPs when the original infinite crystal has the geometric reflection symmetry (GRS) for each CP. Meanwhile, based on the perturbation theory, it has also been shown that small perturbations from the hopping between the nNN (2 ≤ n < ∞) CPs and surface relaxation have no impact on the above conclusion. However, for the crystals with strong intrinsic spin-orbit coupling (SOC), the dominant terms of intrinsic SOC associate with two 1NN bond hoppings. Thus SOC will significantly contribute the hoppings from the 1NN and/or 2NN CPs except the ones within each CP. Here, we will study the effect of the hopping between the 2NN CPs on the surface states in model crystals with three different type structures (Type I: “···–P–P–P–P–···”, Type II: “···–P–Q–P–Q–···” and Type III: “···–P=Q–P=Q–···” where P and Q indicate CPs and the signs “−” and “=” mark the distance between the 1NN CPs). In terms of analytical and numerical calculations, we study the behavior of surface states in three types after the symmetric/asymmetric hopping from the 2NN CPs is added. We analytically prove that the symmetric hopping from the 2NN CPs cannot induce surface states in Type I when each CP has only one electron mode. The numerical calculations also provide strong support for the conclusion, even up to 5NN. However, in general, the coupling from the 2NN CPs (symmetric and asymmetric) is favorable to generate surface states except Type I with single electron mode only. (paper)

  1. Fracture zones constrained by neutral surfaces in a fault-related fold: Insights from the Kelasu tectonic zone, Kuqa Depression

    Science.gov (United States)

    Sun, Shuai; Hou, Guiting; Zheng, Chunfang

    2017-11-01

    Stress variation associated with folding is one of the controlling factors in the development of tectonic fractures, however, little attention has been paid to the influence of neutral surfaces during folding on fracture distribution in a fault-related fold. In this study, we take the Cretaceous Bashijiqike Formation in the Kuqa Depression as an example and analyze the distribution of tectonic fractures in fault-related folds by core observation and logging data analysis. Three fracture zones are identified in a fault-related fold: a tensile zone, a transition zone and a compressive zone, which may be constrained by two neutral surfaces of fold. Well correlation reveals that the tensile zone and the transition zone reach the maximum thickness at the fold hinge and get thinner in the fold limbs. A 2D viscoelastic stress field model of a fault-related fold was constructed to further investigate the mechanism of fracturing. Statistical and numerical analysis reveal that the tensile zone and the transition zone become thicker with decreasing interlimb angle. Stress variation associated with folding is the first level of control over the general pattern of fracture distribution while faulting is a secondary control over the development of local fractures in a fault-related fold.

  2. Quantitative Study for the Surface Dehydration of Vocal Folds Based on High-Speed Imaging.

    Science.gov (United States)

    Li, Lin; Zhang, Yu; Maytag, Allison L; Jiang, Jack J

    2015-07-01

    From the perspective of the glottal area and mucosal wave, quantitatively estimate the differences of vocal fold on laryngeal activity during phonation at three different dehydration levels. Controlled three sets of tests. A dehydration experiment for 10 excised canine larynges was conducted at 16 cm H2O. According to the dehydration cycle time (H), dehydration levels were divided into three degrees (0% H, 50% H, 75% H). The glottal area and mucosal wave under three dehydration levels were extracted from high-speed images and digital videokymography (DKG) image sequences. Direct and non-direct amplitude components were derived from glottal areas. The amplitude and frequency of mucosal wave were calculated from DKG image sequences. These parameters in condition of three dehydration levels were compared for statistical analysis. The results showed a significant difference in direct (P = 0.001; P = 0.005) and non-direct (P = 0.005; P = 0.016) components of glottal areas between every two different dehydration levels. Considering the right-upper, right-lower, left-upper, and left-lower of vocal fold, the amplitudes of mucosal waves consistently decreased with increasing of dehydration levels. But, there was no significant difference in frequency. Surface dehydration could give rise to complex variation of vocal fold on tissues and vibratory mechanism, which should need analyzing from multiple perspectives. The results suggested that the combination of glottal area and mucosal wave could be better to research the change of vocal fold at different dehydrations. It would become a better crucial research tool for the clinical treatment of dehydration-induced laryngeal pathologies. Copyright © 2015 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  3. Comparison between body mass index, triceps skin fold thickness and mid-arm muscle circumference in Saudi adolescents

    International Nuclear Information System (INIS)

    Abdalkhail, B.; Shawky, S.

    2002-01-01

    Adolescence is an important period in an individual's life. Overweight and obesity are fraught with several health problems even late in life. The objective of this study was estimate the overweight, obesity, body fat and muscle content of Saudi adolescents as compared to a recognized reference population. Data were collected from a sample of Saudi adolescents in Jeddah from 42 boys' and 42 girls' school during the month of April 2000. Data collection was done by personal interviews to collect sociodemograhic factors and by direct measurement of weight, height, triceps skin fold thickness (TSF) and mid-arm circumference (MAC). The 50th, 85th and 95th percentiles(P50, P85 and P95) for body mass index (BMI) and triceps skin fold thickness (TSF) were taken, then the 50th, 90th, and 95th percentiles (P50, P90 and P95) for the mid-arm muscle circumference (MAMC) were calculated. These measurements were compared with corresponding values of the National Health and Nutrition Examination Survey I (NHANES I). The P85 and P95 for the BMI and TSF were higher for Saudi adolescents than the NHANES I and the difference was wider for P95. Conversely, there was a lower MAMC at P90 and P95thane the NHANES I reference population curves. The lower MAMC curves were less marked in girls than in boys. On the other hand Saudi boys and girls showed on average similar body mass index indicated by MBI at P50, which was misleading, since those adolescents showing similar body mass index had more fatness than of average reference population indicated by TSF and P50, and less muscularity on average than reference population indicated MAMC at P-50. Overweight and obesity with increased body fat content and decreased body muscle content appear to be widespread among Saudi adolescents even among those adolescents showing average body index. Public health interventions are required to improve quality of food, encourage physical, activity and exercise, as well as correct the perception of

  4. Key indexes of the effectiveness of mask surface treatments

    Science.gov (United States)

    Lin, Chen-Yang; Liu, Chung-Hsuan; Lin, Kuan-Wen; Lu, Chi-Lun; Hsu, Luke; Chin, Angus; Yen, Anthony

    2015-10-01

    A proper surface treatment, such as O2 plasma, helps to improve particle removal efficiency (PRE) because of the formation of hydrogen bonding between particles, water and the mask surface after treatment. The effectiveness of surface treatments cannot be determined only by the static wettability after processes. More key indexes should be considered. In this paper, we report our findings on the relationship between surface treatments on photomasks and the resulting wettability. In addition, added defects after the treatment and the cleaning process were inspected with a 193- nm KLA inspector on 193-nm immersion and EUV photomasks, which consist of SiO2, MoSi, Cr, Ta-based absorber and Ru. Based on our work, three indexes can be built for determining the effectiveness of surface treatments. The first is to check whether the surface becomes super-hydrophilic after treatment. The second is to determine the efficiency of surface treatments on enhancing wettability. The last is to quantify the added watermark count after the surface treatment and the cleaning process. With a proper surface treatment, watermarks can be greatly eased. These three indexes can quickly determine possible effective methods for treating the surfaces of different materials.

  5. A surface refractive index scanning system and method

    DEFF Research Database (Denmark)

    2015-01-01

    The invention relates to a surface refractive index scanning system for characterization of a sample. The system comprises a grating device for holding or receiving the sample, the device comprising at least a first grating region having a first grating width along a transverse direction, and a s......The invention relates to a surface refractive index scanning system for characterization of a sample. The system comprises a grating device for holding or receiving the sample, the device comprising at least a first grating region having a first grating width along a transverse direction...

  6. A new burn severity index based on land surface temperature and enhanced vegetation index

    Science.gov (United States)

    Zheng, Zhong; Zeng, Yongnian; Li, Songnian; Huang, Wei

    2016-03-01

    Remotely sensed data have already become one of the major resources for estimating the burn severity of forest fires. Recently, Land Surface Temperature (LST) calculated from remote sensing data has been considered as a potential indicator for estimating burn severity. However, using the LST-based index alone may not be sufficient for estimating burn severity in the areas that has unburned trees and vegetation. In this paper, a new index is proposed by considering LST and enhanced vegetation index (EVI) together. The accuracy of the proposed index was evaluated by using 264 composite burn index (CBI) field sample data of the five fires across different regional eco-type areas in the Western United States. Results show that the proposed index performed equally well for post-fire areas covered with both sparse vegetation and dense vegetation and relatively better than some commonly-used burn severity indices. This index also has high potential of estimating burn severity if more accurate surface temperatures can be obtained in the future.

  7. Mapping of near surface fold structures with GPR and ERT near Steinbrunn (Northern Burgenland, Austria)

    Science.gov (United States)

    Kreutzer, Ingrid; Chwatal, Werner; Häusler, Hermann; Scheibz, Jürgen; Steirer, Fritz

    2014-05-01

    In the transition zone between the southern Vienna Basin and the Eisenstadt basin, close to Wr. Neustadt, spectacular fold structures are exposed in the former sand pit of Steinbrunn. The succession of Upper Pannonian age consists of decimetre to meter thick sandy, silty and clayey beds, which are overlain by sandstone beds (Grundtner et al., 2009). The anticline and syncline structures were interpreted as of gravitational origin by Exner et al. (2009), and reinterpreted as of tectonic origin by Häusler (2012a). In order to gain a more detailed insight to the three dimensional distribution and orientation of the folds high resolution geophysics such as electrical resistivity tomography (ERT), ground penetrating radar (GPR) and electromagnetics (EM) were applied to map the surroundings of the sandpit. The ERT- and EM-profiles show that the uppermost layer is more clayey northwest and sandier southeast of the sandpit. This is important for the GPR because clay attenuates the radar signals and therefore no clear layering of the subsurface could be mapped in these areas. In order to directly compare ERT and GPR results with the lithology of the fold structures observed in the sandpit, a reference profile on top of the 140 m long wall of the sandpit was performed. Both methods clearly reveal fold structures paralleling the folded Pannonian strata of the outcrop. While the GPR data displays boundaries and their geometry in the succession, the resistivities in the ERT portrays a more smoothened image of the observed fold structure. In almost all GPR profiles wavelike structures are visible with axes in northern direction and dome-shaped structures with axes in eastern direction, deepening towards the west. In conclusion this pattern is comparable to sections of rounded buckle folds. Although there are clayey areas wave-like and dome-like reflections can be followed in the GPR profiles over a distance of several hundred meters. This is confirmed by the ERT profiles

  8. Representation of geographic terrain surface using global indexing

    DEFF Research Database (Denmark)

    Kolar, Jan

    2004-01-01

    in the domain. Handling entire terrain is inherently coupled with global spatial index. This problem is overviewed and a solution is proposed. Afterwards the data representation of the essential surface in geography is introduced. The representation deals with the problem of LOD and is suitable for use...

  9. Quantification of acute vocal fold epithelial surface damage with increasing time and magnitude doses of vibration exposure.

    Directory of Open Access Journals (Sweden)

    Tsuyoshi Kojima

    Full Text Available Because the vocal folds undergo repeated trauma during continuous cycles of vibration, the epithelium is routinely susceptible to damage during phonation. Excessive and prolonged vibration exposure is considered a significant predisposing factor in the development of vocal fold pathology. The purpose of the present study was to quantify the extent of epithelial surface damage following increased time and magnitude doses of vibration exposure using an in vivo rabbit phonation model. Forty-five New Zealand white breeder rabbits were randomized to nine groups and received varying phonation time-doses (30, 60, or 120 minutes and magnitude-doses (control, modal intensity phonation, or raised intensity phonation of vibration exposure. Scanning electron microscopy and transmission electron microscopy was used to quantify the degree of epithelial surface damage. Results revealed a significant reduction in microprojection density, microprojection height, and depth of the epithelial surface with increasing time and phonation magnitudes doses, signifying increased epithelial surface damage risk with excessive and prolonged vibration exposure. Destruction to the epithelial cell surface may provide significant insight into the disruption of cell function following prolonged vibration exposure. One important goal achieved in the present study was the quantification of epithelial surface damage using objective imaging criteria. These data provide an important foundation for future studies of long-term tissue recovery from excessive and prolonged vibration exposure.

  10. Cell surface area and membrane folding in glioblastoma cell lines differing in PTEN and p53 status.

    Directory of Open Access Journals (Sweden)

    Simon Memmel

    Full Text Available Glioblastoma multiforme (GBM is characterized by rapid growth, invasion and resistance to chemo-/radiotherapy. The complex cell surface morphology with abundant membrane folds, microvilli, filopodia and other membrane extensions is believed to contribute to the highly invasive behavior and therapy resistance of GBM cells. The present study addresses the mechanisms leading to the excessive cell membrane area in five GBM lines differing in mutational status for PTEN and p53. In addition to scanning electron microscopy (SEM, the membrane area and folding were quantified by dielectric measurements of membrane capacitance using the single-cell electrorotation (ROT technique. The osmotic stability and volume regulation of GBM cells were analyzed by video microscopy. The expression of PTEN, p53, mTOR and several other marker proteins involved in cell growth and membrane synthesis were examined by Western blotting. The combined SEM, ROT and osmotic data provided independent lines of evidence for a large variability in membrane area and folding among tested GBM lines. Thus, DK-MG cells (wild type p53 and wild type PTEN exhibited the lowest degree of membrane folding, probed by the area-specific capacitance C m = 1.9 µF/cm(2. In contrast, cell lines carrying mutations in both p53 and PTEN (U373-MG and SNB19 showed the highest C m values of 3.7-4.0 µF/cm(2, which corroborate well with their heavily villated cell surface revealed by SEM. Since PTEN and p53 are well-known inhibitors of mTOR, the increased membrane area/folding in mutant GBM lines may be related to the enhanced protein and lipid synthesis due to a deregulation of the mTOR-dependent downstream signaling pathway. Given that membrane folds and extensions are implicated in tumor cell motility and metastasis, the dielectric approach presented here provides a rapid and simple tool for screening the biophysical cell properties in studies on targeting chemo- or radiotherapeutically the

  11. Single-Molecule Protein Folding: A Study of the Surface-Mediated Conformational Dynamics of a Model Amphipathic Peptide

    Science.gov (United States)

    Cunningham, Joy; English, Douglas

    2004-03-01

    Most surface-active polypeptides, composed of 10-50 amino acids, are devoid of well-defined tertiary structure. The conformation of these proteins is greatly dependent upon their environment and may assume totally different characteristics in an aqueous environment, in a detergent micelle, or in an organic solvent. Most antimicrobial peptides are helix-forming and are activated upon interaction with a membrane-mimicking environment. We are seeking to physically characterize the mechanism of membrane-peptide interaction through studying a simple model peptide, MT-1. MT-1 was designed as a nonhomologous analogue of melittin, the principle component in bee venom. We are using single molecule spectroscopy to examine the induction of secondary structure upon interaction of MT-1 with various membrane-mimicking interfaces. Specifically, we monitor coil-to-helix transition through single molecule fluorescence resonance energy transfer (sm-FRET) to determine conformational distributions of folded and unfolded peptides at an interface. Studies with MT-1 will focus upon the biologically relevant issues of orientation, aggregation, and folding at surfaces using both ensemble and single molecule experiments.

  12. A simple interpretation of the surface temperature/vegetation index space for assessment of surface moisture status

    DEFF Research Database (Denmark)

    Sandholt, Inge; Rasmussen, Kjeld; Andersen, Jens Asger

    2002-01-01

    A simplified land surface dryness index (Temperature-Vegetation Dryness Index, TVDI) based on an empirical parameterisation of the relationship between surface temperature (T-s) and vegetation index (NDVI) is suggested. The index is related to soil moisture and, in comparison to existing interpre......A simplified land surface dryness index (Temperature-Vegetation Dryness Index, TVDI) based on an empirical parameterisation of the relationship between surface temperature (T-s) and vegetation index (NDVI) is suggested. The index is related to soil moisture and, in comparison to existing...... interpretations of the T-s/NDVI space, the index is conceptually and computationally straightforward. It is based on satellite derived information only, and the potential for operational application of the index is therefore large. The spatial pattern and temporal evolution in TVDI has been analysed using 37 NOAA...

  13. Using extremely halophilic bacteria to understand the role of surface charge and surface hydration in protein evolution, folding, and function

    Science.gov (United States)

    Hoff, Wouter; Deole, Ratnakar; Osu Collaboration

    2013-03-01

    Halophilic Archaea accumulate molar concentrations of KCl in their cytoplasm as an osmoprotectant, and have evolved highly acidic proteomes that only function at high salinity. We examine osmoprotection in the photosynthetic Proteobacteria Halorhodospira halophila. We find that H. halophila has an acidic proteome and accumulates molar concentrations of KCl when grown in high salt media. Upon growth of H. halophila in low salt media, its cytoplasmic K + content matches that of Escherichia coli, revealing an acidic proteome that can function in the absence of high cytoplasmic salt concentrations. These findings necessitate a reassessment of two central aspects of theories for understanding extreme halophiles. We conclude that proteome acidity is not driven by stabilizing interactions between K + ions and acidic side chains, but by the need for maintaining sufficient solvation and hydration of the protein surface at high salinity through strongly hydrated carboxylates. We propose that obligate protein halophilicity is a non-adaptive property resulting from genetic drift in which constructive neutral evolution progressively incorporates weakly stabilizing K + binding sites on an increasingly acidic protein surface.

  14. Extreme Folding

    Science.gov (United States)

    Demaine, Erik

    2012-02-01

    Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

  15. Correlation among the dysphonia severity index (DSI), the RBH voice perceptual evaluation, and minimum glottal area in female patients with vocal fold nodules.

    Science.gov (United States)

    Hussein Gaber, Ammar Gaber; Liang, Fa-Ya; Yang, Jin-Shan; Wang, Ya-Jing; Zheng, Yi-Qing

    2014-01-01

    To investigate the clinical significance and correlation of the dysphonia severity index (DSI), the RBH (roughness [R]; breathiness [B]; hoarseness [H]) perceptual voice quality evaluation, and minimum glottal area (MGA) in patients with vocal fold nodules and validate the practicality of the DSI further. The DSI evaluation, the voice RBH perceptual evaluation, and the MGA were performed on 30 female patients with vocal fold nodules (the patient group) and 30 female volunteers with normal voices (the control group). The DSI determination was calculated using the following formula: DSI = 0.13 × MPT + 0.0053 × F(0)-High - 0.26 × I-Low - 1.18 × Jitter(%) + 12.4. The RBH evaluation was graded according to four scales. The MGA was measured by KayPENTAX Kips (7105) software. The differences among the DSI, the RBH grade, and MGA of the patients were compared. The median DSI values of the patient group and the control group were -0.81 and 3.79, respectively, and the difference was statistically significant (P dysphonia in female patients with vocal nodules has significant clinical application and good correlation with MGA measurement. Copyright © 2014 The Voice Foundation. All rights reserved.

  16. A simple interpretation of the surface tenperature/vegetation index space for assessment of soil moisture status

    DEFF Research Database (Denmark)

    Sandholt, Inge; Andersen, J.; Rasmussen, Kjeld

    2002-01-01

    Remote Sensing, soil moisture, surface temperature, vegetation index, hydrology, Africa, Senegal, semiarid......Remote Sensing, soil moisture, surface temperature, vegetation index, hydrology, Africa, Senegal, semiarid...

  17. Biological Surface Adsorption Index of Nanomaterials: Modelling Surface Interactions of Nanomaterials with Biomolecules.

    Science.gov (United States)

    Chen, Ran; Riviere, Jim E

    2017-01-01

    Quantitative analysis of the interactions between nanomaterials and their surrounding environment is crucial for safety evaluation in the application of nanotechnology as well as its development and standardization. In this chapter, we demonstrate the importance of the adsorption of surrounding molecules onto the surface of nanomaterials by forming biocorona and thus impact the bio-identity and fate of those materials. We illustrate the key factors including various physical forces in determining the interaction happening at bio-nano interfaces. We further discuss the mathematical endeavors in explaining and predicting the adsorption phenomena, and propose a new statistics-based surface adsorption model, the Biological Surface Adsorption Index (BSAI), to quantitatively analyze the interaction profile of surface adsorption of a large group of small organic molecules onto nanomaterials with varying surface physicochemical properties, first employing five descriptors representing the surface energy profile of the nanomaterials, then further incorporating traditional semi-empirical adsorption models to address concentration effects of solutes. These Advancements in surface adsorption modelling showed a promising development in the application of quantitative predictive models in biological applications, nanomedicine, and environmental safety assessment of nanomaterials.

  18. Diabatic Molecular Orbitals, Potential Energies, and Potential Energy Surface Couplings by the 4-fold Way for Photodissociation of Phenol.

    Science.gov (United States)

    Xu, Xuefei; Yang, Ke R; Truhlar, Donald G

    2013-08-13

    Complete-active-space self-consistent-field (CASSCF) calculations provide useful reference wave functions for configuration interaction or perturbation theory calculations of excited-state potential energy surfaces including dynamical electron correlation. However, the canonical molecular orbitals (MOs) of CASSCF calculations usually have mixed character in regions of strong interaction of two or more electronic states; therefore, they are unsuitable for diabatization using the configurational uniformity approach. Here, CASSCF diabatic MOs for phenol have been obtained by the 4-fold way, and comparison to the CASSCF canonical MOs shows that they are much smoother. Using these smooth CASSCF diabatic MOs, we performed direct diabatization calculations for the three low-lying states ((1)ππ, (1)ππ*, and (1)πσ*) and their diabatic (scalar) couplings at the dynamically correlated multiconfiguration quasidegenerate perturbation theory (MC-QDPT) level. We present calculations along the O-H stretching and C-C-O-H torsion coordinates for the nonadiabatic photodissociation of phenol to the phenoxyl radical and hydrogen atom. The seams of (1)ππ*/(1)πσ* and (1)ππ/(1)πσ* diabatic crossings are plotted as functions of these coordinates. We also present diabatization calculations for displacements along the out-of-plane ring distortion modes 16a and 16b of the phenyl group. The dominant coupling modes of the two conical intersections ((1)ππ*/(1)πσ* and (1)ππ/(1)πσ*) are discussed. The present diabatization method is confirmed to be valid even for significantly distorted ring structures by diabatization calculations along a reaction path connecting the planar equilibrium geometry of phenol to its strongly distorted prefulvenic form. The present work provides insight into the mode specificity of phenol photodissociation and shows that diabatization at the MC-QDPT level employing CASSCF diabatic MOs can be a good starting point for multidimensional dynamics

  19. Geotechnical properties of surface sediments in the INDEX area

    Digital Repository Service at National Institute of Oceanography (India)

    Khadge, N.H.

    As a part of the environmental impact assessment studies, geotechnical properties of sediments were determined in the Central Indian Basin. The undrained shear strength and index properties of the siliceous sediments were determined on 20 box cores...

  20. Surface folding-induced attraction and motion of particles in a soft elastic gel: cooperative effects of surface tension, elasticity, and gravity.

    Science.gov (United States)

    Chakrabarti, Aditi; Chaudhury, Manoj K

    2013-12-17

    We report some experimental observations regarding a new type of long-range interaction between rigid particles that prevails when they are suspended in an ultrasoft elastic gel. A denser particle submerges itself to a considerable depth inside the gel and becomes elasto-buoyant by balancing its weight against the elastic force exerted by the surrounding medium. By virtue of a large elasto-capillary length, the surface of the gel wraps around the particle and closes to create a line singularity connecting the particle to the free surface of the gel. A substantial amount of tensile strain is thus developed in the gel network parallel to the free surface that penetrates to a significant depth inside the gel. The field of this tensile strain is rather long-range because of a large gravito-elastic correlation length and sufficiently strong to pull two submerged particles into contact. The particles move toward each other with an effective force following an inverse linear distance law. When more monomers or dimers of the particles are released inside the gel, they orient rather freely inside the capsules where they are located and attract each other to form closely packed clusters. Eventually, these clusters themselves interact and coalesce. This is an emergent phenomenon in which gravity, capillarity, and elasticity work in tandem to create a long-range interaction. We also present the results of a related experiment, in which a particle suspended inside a thickness-graded gel moves accompanied by the continuous folding and the relaxation of the gel's surface.

  1. Surface antireflection properties of GaN nanostructures with various effective refractive index profiles.

    Science.gov (United States)

    Han, Lu; Zhao, Hongping

    2014-12-29

    GaN nanostructures with various effective refractive index profiles (Linear, Cubic, and Quintic functions) were numerically studied as broadband omnidirectional antireflection structures for concentrator photovoltaics by using three-dimensional finite difference time domain (3D-FDTD) method. Effective medium theory was used to design the surface structures corresponding to different refractive index profiles. Surface antireflection properties were calculated and analyzed for incident light with wavelength, polarization and angle dependences. The surface antireflection properties of GaN nanostructures based on six-sided pyramid with both uniform and non-uniform patterns were also investigated. Results indicate a significant dependence of the surface antireflection on the refractive index profiles of surface nanostructures as well as their pattern uniformity. The GaN nanostructures with linear refractive index profile show the best performance to be used as broadband omnidirectional antireflection structures.

  2. Indexing Glomerular Filtration Rate to Body Surface Area

    DEFF Research Database (Denmark)

    Redal-Baigorri, Belén; Rasmussen, Knud; Heaf, James Goya

    2014-01-01

    BACKGROUND: Kidney function is mostly expressed in terms of glomerular filtration rate (GFR). A common feature is the expression as ml/min per 1.73 m(2) , which represents the adjustment of the individual kidney function to a standard body surface area (BSA) to allow comparison between individuals...

  3. Surface plasmon resonance optical cavity enhanced refractive index sensing

    Czech Academy of Sciences Publication Activity Database

    Giorgini, A.; Avino, S.; Malara, P.; Gagliardi, G.; Casalino, M.; Coppola, G.; Iodice, M.; Adam, Pavel; Chadt, Karel; Homola, Jiří; De Natale, P.

    2013-01-01

    Roč. 38, č. 11 (2013), s. 1951-1953 ISSN 0146-9592 R&D Projects: GA ČR GBP205/12/G118 Institutional support: RVO:67985882 Keywords : Resonators * Surface plasmons * Optical sensing and sensors Subject RIV: BH - Optics, Masers, Lasers Impact factor: 3.179, year: 2013

  4. Overview of total beta activity index and beta rest in surface waters of the Spanish rivers

    International Nuclear Information System (INIS)

    Pujol, L.; Payeras, J.; Pablo, M. A. de

    2013-01-01

    This work aims to give an overview of the index of total beta activity and the activity index beta rest in surface waters of the main Spanish rivers. These indices are a parameter over water quality that CEDEX comes determined by order of the Ministry of Agriculture, Food and Environment, in water policy. (Author)

  5. Indexing aortic valve area by body surface area increases the prevalence of severe aortic stenosis

    DEFF Research Database (Denmark)

    Jander, Nikolaus; Gohlke-Bärwolf, Christa; Bahlmann, Edda

    2014-01-01

    To account for differences in body size in patients with aortic stenosis, aortic valve area (AVA) is divided by body surface area (BSA) to calculate indexed AVA (AVAindex). Cut-off values for severe stenosis are......To account for differences in body size in patients with aortic stenosis, aortic valve area (AVA) is divided by body surface area (BSA) to calculate indexed AVA (AVAindex). Cut-off values for severe stenosis are...

  6. Atomic scale structure of the 5-fold surface of an AlPdMn quasicrystal: A quantitative X-Ray photoelectron diffraction analysis

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Jin-Cheng; Huan, C.H.A.; Wee, A.T.S.; Van Hove, M.A.; Fadley, C.S.; Shi, F.J.; Rotenberg, E.; Barman, S.R.; Paggel, J.J.; Horn, K.; Ebert, Ph.; Urban, K.

    2004-02-11

    The atomic scale structure of the 5-fold symmetric surface of an AlPdMn quasicrystal is investigated quantitatively by comparing x-ray photoelectron diffraction (XPD) simulations to experiment. The observed 5-fold symmetry of the diffraction patterns indicates that the surface is quasicrystalline with no hint of a reconstruction from the bulk structure. In analyzing the experimental data, many possible bulk terminations have been tested. Those few that fit best to the data have in common that they contain an Al-rich surface layer followed by a dense mixed Al/Pd/Mn layer. These best terminations, while not identical to each other, are suggested to form terraces coexisting on a real surface. Structural relaxations of the quasicrystal surface are also analyzed: mixing several best-fit terminations gives average best-fit interlayer spacing changes of Dd12 = -0.057 Angstrom, Dd24 = +0.159 Angstrom. These results are in good agreement with a prior structure determination by LEED on a sample that was prepared in a different manner.

  7. A topological screening heuristic for low-energy, high-index surfaces

    Science.gov (United States)

    Sun, Wenhao; Ceder, Gerbrand

    2018-03-01

    Robust ab initio investigations of nanoparticle surface properties require a method to identify candidate low-energy surface facets a priori. By assuming that low-energy surfaces are planes with high atomic density, we devise an efficient algorithm to screen for low-energy surface orientations, even if they have high (hkl) miller indices. We successfully predict the observed low-energy, high-index { 10 12 bar } and { 10 1 bar 4 } surfaces of hematite α-Fe2O3, the {311} surfaces of cuprite Cu2O, and the {112} surfaces of anatase TiO2. We further tabulate candidate low-energy surface orientations for nine of the most common binary oxide structures. Screened surfaces are found to be generally applicable across isostructural compounds with varying chemistries, although relative surface energies between facets may vary based on the preferred coordination of the surface atoms.

  8. Simulation of imperfections in plastic lenses - transferring local refractive index changes into surface shape modifications

    Science.gov (United States)

    Arasa, Josep; Pizarro, Carles; Blanco, Patricia

    2016-06-01

    Injection molded plastic lenses have continuously improved their performance regarding optical quality and nowadays are as usual as glass lenses in image forming devices. However, during the manufacturing process unavoidable fluctuations in material density occur, resulting in local changes in the distribution of refractive index, which degrade the imaging properties of the polymer lens. Such material density fluctuations correlate to phase delays, which opens a path for their mapping. However, it is difficult to transfer the measured variations in refractive index into conventional optical simulation tool. Thus, we propose a method to convert the local variations in refractive index into local changes of one surface of the lens, which can then be described as a free-form surface, easy to introduce in conventional simulation tools. The proposed method was tested on a commercial gradient index (GRIN) lens for a set of six different object positions, using the MTF sagittal and tangential cuts to compare the differences between the real lens and a lens with homogenous refractive index, and the last surface converted into a free-form shape containing the internal refractive index changes. The same procedure was used to reproduce the local refractive index changes of an injected plastic lens with local index changes measured using an in-house built polariscopic arrangement, showing the capability of the method to provide successful results.

  9. Surface-length index: a novel index for rapid detection of right ventricles with abnormal ejection fraction using cardiac MRI.

    Science.gov (United States)

    Bonnemains, Laurent; Mandry, Damien; Menini, Anne; Stos, Bertrand; Felblinger, Jacques; Marie, Pierre-Yves; Vuissoz, Pierre-Andre

    2013-09-01

    To validate a new index, the surface-length index (SLI) based on area change in a short-axis view and length reduction in the horizontal long-axis view, which is used to quickly (right ventricles with an abnormal ejection fraction (EF) during a cardiac MRI examination. SLI can be used to avoid a complete delineation of the endocardial contours of normal right ventricles. Sixty patients (group A) were retrospectively included to calibrate the SLI formula by optimisation of the area under the ROC curves and SLI thresholds were chosen to obtain 100 % sensitivity. Another 340 patients (group B) were prospectively recruited to test SLI's capacity to detect right ventricles (RVs) with an abnormal EF (right ventricle ejection fraction (RVEF) with cine-MRI is time consuming. • Therefore, RVEF is not always assessed during cardiac MRI. • Surface-length index (SLI) allows rapid detection of abnormal RVEF during cardiac MRI. • SLI saves one third of the operator time. • Every cardiac MRI could include RVEF assessment by means of SLI.

  10. Structure and energetics of high index Fe, Al, Cu and Ni surfaces using equivalent crystal theory

    Science.gov (United States)

    Rodriguez, Agustin M.; Bozzolo, Guillermo; Ferrante, John

    1993-01-01

    Equivalent crystal theory (ECT) is applied to the study of multilayer relaxations and surface energies of high-index faces of Fe, Al, Ni, and Cu. Changes in interplanar spacing as well as registry of planes close to the surface and the ensuing surface energies changes are discussed in reference to available experimental data and other theoretical calculations. Since ECT is a semiempirical method, the dependence of the results on the variation of the input used was investigated.

  11. Structural and electronic properties of low-index stoichiometric BiOI surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Wen-Wu; Zhao, Zong-Yan, E-mail: zzy@kmust.edu.cn

    2017-06-01

    As promising photocatalyst driven by visible-light, BiOI has attracted more and more attention in the past years. However, the surface structure and properties of BiOI that is the most important place for the photocatalytic have not been investigated in details. To this end, density functional theory was performed to calculate the structural and electronic properties of four low-index stoichiometric surfaces of BiOI. It is found that the relaxation of the low-index BiOI surfaces are relatively small, especially the (001) surface. Thus, the surface energies of BiOI are very relatively small. Moreover, there are a few surface states below the bottom of conduction band in the first layer except the (001) surface, which maybe capture the photo-excited carriers. In all of the most stable terminated planes, all the dangling bonds are cleaved from the broken Bi-O bonds. In the case of (001) surface, the dangling bond density of Bi atoms for the (001) surface is zero per square nano. Therefore, the (001) surface is thermodynamically lowest-energy surface of BiOI, and it is the predominant surface (51.4%). As a final remark, the dangling bonds density of bismuth atoms determines not only the surface energy, but also the surface relaxation. Finally, the equilibrium morphology of BiOI was also proposed and provided, which is determined through the Wulff construction. These results will help us to better understand the underlying photocatalytic mechanism that is related to BiOI surfaces, and provide theoretical support for some experimental studies about BiOI-based photocatalyst in future. - Highlights: • Four low-index BiOI surfaces have been calculated by DFT method. • The relaxations of the low-index BiOI surfaces are relatively small. • There are a few surface states below the bottom of conduction band in the first layer. • The dangling bonds density of bismuth atoms determines not only the surface energy, but also the surface relaxation. • The thermodynamic

  12. 50-Fold EQE Improvement up to 6.27% of Solution-Processed All-Inorganic Perovskite CsPbBr3 QLEDs via Surface Ligand Density Control.

    Science.gov (United States)

    Li, Jianhai; Xu, Leimeng; Wang, Tao; Song, Jizhong; Chen, Jiawei; Xue, Jie; Dong, Yuhui; Cai, Bo; Shan, Qingsong; Han, Boning; Zeng, Haibo

    2017-02-01

    Solution-processed CsPbBr 3 quantum-dot light-emitting diodes with a 50-fold external quantum efficiency improvement (up to 6.27%) are achieved through balancing surface passivation and carrier injection via ligand density control (treating with hexane/ethyl acetate mixed solvent), which induces the coexistence of high levels of ink stability, photoluminescence quantum yields, thin-film uniformity, and carrier-injection efficiency. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Ordering and growth of rare gas films (Xe, Kr, Ar, and Ne) on the pseudo-ten-fold quasicrystalline approximant Al₁₃Co₄(100) surface.

    Science.gov (United States)

    Petucci, J; Karimi, M; Huang, Y-T; Curtarolo, S; Diehl, R D

    2014-03-05

    Adsorption of the rare gases Kr, Ar, and Ne on the complex alloy surface Al₁₃Co₄(100) was studied using grand canonical Monte Carlo (GCMC) computer simulations. This surface is an approximant to the ten-fold decagonal Al-Ni-Co quasicrystalline surface, on which rare gas adsorption was studied previously. Comparison of adsorption results on the periodic Al₁₃Co₄(100) surface with those of the quasiperiodic Al-Ni-Co surface indicates some similarities, such as layer-by-layer growth, and some dissimilarities, such as the formation of Archimedes tiling phases (Mikhael et al 2008 Nature 454 501, Shechtman et al 1984 Phys. Rev. Lett. 53 1951, Macia 2006 Rep. Prog. Phys. 69 397, Schmiedeberg et al 2010 Eur. Phys. J. E 32 25-34, Kromer et al 2012 Phys. Rev. Lett. 108 218301, Schmiedeberg and Stark 2008 Phys. Rev. Lett. 101 218302). The conditions under which Archimedes tiling phases (ATP) emerge on Al₁₃Co₄(100) are examined and their presence is related to the gas-gas and gas-surface interaction parameters.

  14. Indexed

    CERN Document Server

    Hagy, Jessica

    2008-01-01

    Jessica Hagy is a different kind of thinker. She has an astonishing talent for visualizing relationships, capturing in pictures what is difficult for most of us to express in words. At indexed.blogspot.com, she posts charts, graphs, and Venn diagrams drawn on index cards that reveal in a simple and intuitive way the large and small truths of modern life. Praised throughout the blogosphere as “brilliant,” “incredibly creative,” and “comic genius,” Jessica turns her incisive, deadpan sense of humor on everything from office politics to relationships to religion. With new material along with some of Jessica’s greatest hits, this utterly unique book will thrill readers who demand humor that makes them both laugh and think.

  15. Reflection-based fibre-optic refractive index sensor using surface plasmon resonance

    Czech Academy of Sciences Publication Activity Database

    Hlubina, P.; Kadulová, M.; Ciprian, D.; Sobota, Jaroslav

    2014-01-01

    Roč. 9, August 19 (2014), 14033:1-5 ISSN 1990-2573 R&D Projects: GA MŠk(CZ) LO1212 Keywords : surface plasmon resonance * fibre -optic sensor * spectral interrogation technique * aqueous solutions of ethanol * refractive index Subject RIV: BH - Optics, Masers, Lasers Impact factor: 1.231, year: 2014

  16. Reassessment of MxiH subunit orientation and fold within native Shigella T3SS needles using surface labelling and solid-state NMR.

    Science.gov (United States)

    Verasdonck, Joeri; Shen, Da-Kang; Treadgold, Alexander; Arthur, Christopher; Böckmann, Anja; Meier, Beat H; Blocker, Ariel J

    2015-12-01

    T3SSs are essential virulence determinants of many Gram-negative bacteria, used to inject bacterial effectors of virulence into eukaryotic host cells. Their major extracellular portion, a ∼50 nm hollow, needle-like structure, is essential to host cell sensing and the conduit for effector secretion. It is formed of a small, conserved subunit arranged as a helical polymer. The structure of the subunit has been studied by electron cryomicroscopy within native polymers and by solid-state NMR in recombinant polymers, yielding two incompatible atomic models. To resolve this controversy, we re-examined the native polymer used for electron cryomicroscopy via surface labelling and solid-state NMR. Our data show the orientation and overall fold of the subunit within this polymer is as established by solid-state NMR for recombinant polymers. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  17. Surface-Based Body Shape Index and Its Relationship with All-Cause Mortality.

    Directory of Open Access Journals (Sweden)

    Syed Ashiqur Rahman

    Full Text Available Obesity is a global public health challenge. In the US, for instance, obesity prevalence remains high at more than one-third of the adult population, while over two-thirds are obese or overweight. Obesity is associated with various health problems, such as diabetes, cardiovascular diseases (CVDs, depression, some forms of cancer, sleep apnea, osteoarthritis, among others. The body mass index (BMI is one of the best known measures of obesity. The BMI, however, has serious limitations, for instance, its inability to capture the distribution of lean mass and adipose tissue, which is a better predictor of diabetes and CVDs, and its curved ("U-shaped" relationship with mortality hazard. Other anthropometric measures and their relation to obesity have been studied, each with its advantages and limitations. In this work, we introduce a new anthropometric measure (called Surface-based Body Shape Index, SBSI that accounts for both body shape and body size, and evaluate its performance as a predictor of all-cause mortality.We analyzed data on 11,808 subjects (ages 18-85, from the National Health and Human Nutrition Examination Survey (NHANES 1999-2004, with 8-year mortality follow up. Based on the analysis, we introduce a new body shape index constructed from four important anthropometric determinants of body shape and body size: body surface area (BSA, vertical trunk circumference (VTC, height (H and waist circumference (WC. The surface-based body shape index (SBSI is defined as follows: SBSI = ((H(7/4(WC(5/6/(BSA VTC (1 SBSI has negative correlation with BMI and weight respectively, no correlation with WC, and shows a generally linear relationship with age. Results on mortality hazard prediction using both the Cox proportionality model, and Kaplan-Meier curves each show that SBSI outperforms currently popular body shape indices (e.g., BMI, WC, waist-to-height ratio (WHtR, waist-to-hip ratio (WHR, A Body Shape Index (ABSI in predicting all

  18. The atomic structure of low-index surfaces of the intermetallic compound InPd

    Energy Technology Data Exchange (ETDEWEB)

    McGuirk, G. M.; Ledieu, J.; Gaudry, É.; Weerd, M.-C.; Fournée, V. de, E-mail: vincent.fournee@univ-lorraine.fr [Institut Jean Lamour (UMR 7198 CNRS-Université de Lorraine), Parc de Saurupt, F-54011 Nancy Cedex (France); Hahne, M.; Gille, P. [Department of Earth and Environmental Sciences, Crystallography Section, Ludwig-Maximilians-Universität München, Theresienstrasse 41, D-80333 München (Germany); Ivarsson, D. C. A.; Armbrüster, M. [Faculty of Natural Sciences, Institute of Chemistry, Materials for Innovative Energy Concepts, Technische Universität Chemnitz, D-09107 Chemnitz (Germany); Ardini, J.; Held, G. [Department of Chemistry, University of Reading, Reading RG6 6AD (United Kingdom); Diamond Light Source Ltd, Didcot OX11 0DE (United Kingdom); Maccherozzi, F. [Diamond Light Source Ltd, Didcot OX11 0DE (United Kingdom); Bayer, A. [Lehrstuhl für Physikalische Chemie II, Universität Erlangen-Nürnberg, Egerlandstraße 3, D-91058 Erlangen (Germany); Lowe, M. [Surface Science Research Centre and Department of Physics, The University of Liverpool, Liverpool L69 3BX (United Kingdom); Pussi, K. [Department of Mathematics and Physics, Lappeenranta University of Technology, P.O. Box 20, FIN-53851 Lappeenranta (Finland); Diehl, R. D. [Department of Physics, Penn State University, University Park, Pennsylvania 16802 (United States)

    2015-08-21

    The intermetallic compound InPd (CsCl type of crystal structure with a broad compositional range) is considered as a candidate catalyst for the steam reforming of methanol. Single crystals of this phase have been grown to study the structure of its three low-index surfaces under ultra-high vacuum conditions, using low energy electron diffraction (LEED), X-ray photoemission spectroscopy (XPS), and scanning tunneling microscopy (STM). During surface preparation, preferential sputtering leads to a depletion of In within the top few layers for all three surfaces. The near-surface regions remain slightly Pd-rich until annealing to ∼580 K. A transition occurs between 580 and 660 K where In segregates towards the surface and the near-surface regions become slightly In-rich above ∼660 K. This transition is accompanied by a sharpening of LEED patterns and formation of flat step-terrace morphology, as observed by STM. Several superstructures have been identified for the different surfaces associated with this process. Annealing to higher temperatures (≥750 K) leads to faceting via thermal etching as shown for the (110) surface, with a bulk In composition close to the In-rich limit of the existence domain of the cubic phase. The Pd-rich InPd(111) is found to be consistent with a Pd-terminated bulk truncation model as shown by dynamical LEED analysis while, after annealing at higher temperature, the In-rich InPd(111) is consistent with an In-terminated bulk truncation, in agreement with density functional theory (DFT) calculations of the relative surface energies. More complex surface structures are observed for the (100) surface. Additionally, individual grains of a polycrystalline sample are characterized by micro-spot XPS and LEED as well as low-energy electron microscopy. Results from both individual grains and “global” measurements are interpreted based on comparison to our single crystals findings, DFT calculations and previous literature.

  19. Potential impacts of robust surface roughness indexes on DTM-based segmentation

    Science.gov (United States)

    Trevisani, Sebastiano; Rocca, Michele

    2017-04-01

    In this study, we explore the impact of robust surface texture indexes based on MAD (median absolute differences), implemented by Trevisani and Rocca (2015), in the unsupervised morphological segmentation of an alpine basin. The area was already object of a geomorphometric analysis, consisting in the roughness-based segmentation of the landscape (Trevisani et al. 2012); the roughness indexes were calculated on a high resolution DTM derived by means of airborne Lidar using the variogram as estimator. The calculated roughness indexes have been then used for the fuzzy clustering (Odeh et al., 1992; Burrough et al., 2000) of the basin, revealing the high informative geomorphometric content of the roughness-based indexes. However, the fuzzy clustering revealed a high fuzziness and a high degree of mixing between textural classes; this was ascribed both to the morphological complexity of the basin and to the high sensitivity of variogram to non-stationarity and signal-noise. Accordingly, we explore how the new implemented roughness indexes based on MAD affect the morphological segmentation of the studied basin. References Burrough, P.A., Van Gaans, P.F.M., MacMillan, R.A., 2000. High-resolution landform classification using fuzzy k-means. Fuzzy Sets and Systems 113, 37-52. Odeh, I.O.A., McBratney, A.B., Chittleborough, D.J., 1992. Soil pattern recognition with fuzzy-c-means: application to classification and soil-landform interrelationships. Soil Sciences Society of America Journal 56, 505-516. Trevisani, S., Cavalli, M. & Marchi, L. 2012, "Surface texture analysis of a high-resolution DTM: Interpreting an alpine basin", Geomorphology, vol. 161-162, pp. 26-39. Trevisani, S. & Rocca, M. 2015, "MAD: Robust image texture analysis for applications in high resolution geomorphometry", Computers and Geosciences, vol. 81, pp. 78-92.

  20. Downscaling Satellite Land Surface Temperatures in Urban Regions for Surface Energy Balance Study and Heat Index Development

    Science.gov (United States)

    Norouzi, H.; Bah, A.; Prakash, S.; Nouri, N.; Blake, R.

    2017-12-01

    A great percentage of the world's population reside in urban areas that are exposed to the threats of global and regional climate changes and associated extreme weather events. Among them, urban heat islands have significant health and economic impacts due to higher thermal gradients of impermeable surfaces in urban regions compared to their surrounding rural areas. Therefore, accurate characterization of the surface energy balance in urban regions are required to predict these extreme events. High spatial resolution Land surface temperature (LST) in the scale of street level in the cities can provide wealth of information to study surface energy balance and eventually providing a reliable heat index. In this study, we estimate high-resolution LST maps using combination of LandSat 8 and infrared based satellite products such as Moderate Resolution Imaging Spectroradiometer (MODIS) and newly launched Geostationary Operational Environmental Satellite-R Series (GOES-R). Landsat 8 provides higher spatial resolution (30 m) estimates of skin temperature every 16 days. However, MODIS and GOES-R have lower spatial resolution (1km and 4km respectively) with much higher temporal resolution. Several statistical downscaling methods were investigated to provide high spatiotemporal LST maps in urban regions. The results reveal that statistical methods such as Principal Component Analysis (PCA) can provide reliable estimations of LST downscaling with 2K accuracy. Other methods also were tried including aggregating (up-scaling) the high-resolution data to a coarse one to examine the limitations and to build the model. Additionally, we deployed flux towers over distinct materials such as concrete, asphalt, and rooftops in New York City to monitor the sensible and latent heat fluxes through eddy covariance method. To account for the incoming and outgoing radiation, a 4-component radiometer is used that can observe both incoming and outgoing longwave and shortwave radiation. This

  1. Refractive index dispersion of swift heavy ion irradiated BFO thin films using Surface Plasmon Resonance technique

    Energy Technology Data Exchange (ETDEWEB)

    Paliwal, Ayushi [Department of Physics and Astrophysics, University of Delhi, Delhi 110007 (India); Sharma, Savita [Department of Applied Physics, Delhi Technological University, Delhi (India); Tomar, Monika [Physics Department, Miranda House, University of Delhi, Delhi 110007 (India); Singh, Fouran [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110075 (India); Gupta, Vinay, E-mail: drguptavinay@gmail.com [Department of Physics and Astrophysics, University of Delhi, Delhi 110007 (India)

    2016-07-15

    Highlights: • Investigated the optical properties of BiFeO{sub 3} (BFO) thin films after irradiation using SPR. • Otto configuration has been used to excite the surface plasmons using gold metal thin film. • BFO thin films were prepared by sol–gel spin coating technique. • Examined the refractive index dispersion of pristine and irradiated BFO thin film. - Abstract: Swift heavy ion irradiation (SHI) is an effective technique to induce defects for possible modifications in the material properties. There is growing interest in studying the optical properties of multiferroic BiFeO{sub 3} (BFO) thin films for optoelectronic applications. In the present work, BFO thin films were prepared by sol–gel spin coating technique and were irradiated using the 15 UD Pelletron accelerator with 100 MeV Au{sup 9+} ions at a fluence of 1 × 10{sup 12} ions cm{sup −2}. The as-grown films became rough and porous on ion irradiation. Surface Plasmon Resonance (SPR) technique has been identified as a highly sensitive and powerful technique for studying the optical properties of a dielectric material. Optical properties of BFO thin films, before and after irradiation were studied using SPR technique in Otto configuration. Refractive index is found to be decreasing from 2.27 to 2.14 on ion irradiation at a wavelength of 633 nm. Refractive index dispersion of BFO thin film (from 405 nm to 633 nm) before and after ion radiation was examined.

  2. The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold [v2; ref status: indexed, http://f1000r.es/1nx

    Directory of Open Access Journals (Sweden)

    Daniel J Rigden

    2013-08-01

    Full Text Available We report the crystal structure solution of the Intracellular Protease Inhibitor (IPI protein from Bacillus subtilis, which has been reported to be an inhibitor of the intracellular subtilisin Isp1 from the same organism. The structure of IPI is a variant of the all-beta, immunoglobulin (Ig fold. It is possible that IPI is important for protein-protein interactions, of which inhibition of Isp1 is one. The intracellular nature of ISP is questioned, because an alternative ATG codon in the ipi gene would produce a protein with an N-terminal extension containing a signal peptide. It is possible that alternative initiation exists, producing either an intracellular inhibitor or a secreted form that may be associated with the cell surface.  Homologues of the IPI protein from other species are multi-domain proteins, containing signal peptides and domains also associated with the bacterial cell-surface. The cysteine peptidase inhibitors chagasin and amoebiasin also have Ig-like folds, but their topology differs significantly from that of IPI, and they share no recent common ancestor. A model of IPI docked to Isp1 shows similarities to other subtilisin:inhibitor complexes, particularly where the inhibitor interacts with the peptidase active site.

  3. Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit.

    Directory of Open Access Journals (Sweden)

    Franck Tarendeau

    Full Text Available Understanding how avian influenza viruses adapt to human hosts is critical for the monitoring and prevention of future pandemics. Host specificity is determined by multiple sites in different viral proteins, and mutation of only a limited number of these sites can lead to inter-species transmission. Several of these sites have been identified in the viral polymerase, the best characterised being position 627 in the PB2 subunit. Efficient viral replication at the relatively low temperature of the human respiratory tract requires lysine 627 rather than the glutamic acid variant found systematically in avian viruses. However, the molecular mechanism by which any of these host specific sites determine host range are unknown, although adaptation to host factors is frequently evoked. We used ESPRIT, a library screening method, to identify a new PB2 domain that contains a high density of putative host specific sites, including residue 627. The X-ray structure of this domain (denoted the 627-domain exhibits a novel fold with the side-chain of Lys627 solvent exposed. The structure of the K627E mutated domain shows no structural differences but the charge reversal disrupts a striking basic patch on the domain surface. Five other recently proposed host determining sites of PB2 are also located on the 627-domain surface. The structure of the complete C-terminal region of PB2 comprising the 627-domain and the previously identified NLS-domain, which binds the host nuclear import factor importin alpha, was also determined. The two domains are found to pack together with a largely hydrophilic interface. These data enable a three-dimensional mapping of approximately half of PB2 sites implicated in cross-species transfer onto a single structural unit. Their surface location is consistent with roles in interactions with other viral proteins or host factors. The identification and structural characterization of these well-defined PB2 domains will help design

  4. Effect of surface roughness variation on the transmission characteristics of D-shaped fibers with ambient index change

    International Nuclear Information System (INIS)

    Kim, Hyun-Joo; Kwon, Oh-Jang; Han, Young-Geun

    2010-01-01

    The influence of surface roughness on the sensitivity of D-shaped fibers to changes in the ambient index was investigated. In order to obtain D-shaped fibers with different surface roughness, we polished one side of the fibers by using different abrasive grits. The topographies of the surfaces of the polished D-shaped fibers were then observed by using atomic force microscopy (AFM). The light scattered from the rough surfaces of the D-shaped fibers was measured by using optical microscopy. The effect of an ambient index change on the transmission characteristics of D-shaped fibers was measured for various values of the surface roughness. The experimental results indicate that variations in the surface roughness have a considerable influence on the sensitivity of the transmission characteristics of D-shaped fibers to changes in the ambient index.

  5. A Robust Inversion Algorithm for Surface Leaf and Soil Temperatures Using the Vegetation Clumping Index

    Directory of Open Access Journals (Sweden)

    Zunjian Bian

    2017-07-01

    Full Text Available The inversion of land surface component temperatures is an essential source of information for mapping heat fluxes and the angular normalization of thermal infrared (TIR observations. Leaf and soil temperatures can be retrieved using multiple-view-angle TIR observations. In a satellite-scale pixel, the clumping effect of vegetation is usually present, but it is not completely considered during the inversion process. Therefore, we introduced a simple inversion procedure that uses gap frequency with a clumping index (GCI for leaf and soil temperatures over both crop and forest canopies. Simulated datasets corresponding to turbid vegetation, regularly planted crops and randomly distributed forest were generated using a radiosity model and were used to test the proposed inversion algorithm. The results indicated that the GCI algorithm performed well for both crop and forest canopies, with root mean squared errors of less than 1.0 °C against simulated values. The proposed inversion algorithm was also validated using measured datasets over orchard, maize and wheat canopies. Similar results were achieved, demonstrating that using the clumping index can improve inversion results. In all evaluations, we recommend using the GCI algorithm as a foundation for future satellite-based applications due to its straightforward form and robust performance for both crop and forest canopies using the vegetation clumping index.

  6. Glazed ceramic roof tiles: influence of surface features in the solar reflectance index

    International Nuclear Information System (INIS)

    Bortoli, Leitcia Silva de; Stapait, Camila Cristina; Marinoski, Deivis Luis; Fredel, Marcio Celso; Schabbach, Luciana M.

    2016-01-01

    In this study the influence of surface features of ceramic roof tiles in the solar reflectance index were evaluated. Two glazed ceramic roof tiles (type stoneware) with the same color (ivory) but with different appearance (matte and brilliant) were the focus of the analysis. The Solar Reflectance Index (SRI) of the roofs tiles were determined by the solar reflectance values (UV-VIS-NIR) and emittance, measured in laboratory. The samples showed SRI> 39 in accordance with LEED certification criteria (Leadership in Energy and Environmental Design), contributing to minimizing the Heat Island Effects. Although the matte roof tile shows a slightly higher SRI value (82) than the brilliant one (78), the results for the variables that composes the SRI value (reflectance and emittance) were very similar. Analysis of XRD, SEM and EDS performed on the surfaces of the two roofs indicated for the matte glaze the presence of microcrystals (with barium and zinc) that can contribute to the slightly highest value of SRI. The roughness (optical interferometer white light) and the brightness (brightness meter) of the samples were also measured. (author)

  7. Surface Plasmon Scattering in Exposed Core Optical Fiber for Enhanced Resolution Refractive Index Sensing.

    Science.gov (United States)

    Klantsataya, Elizaveta; François, Alexandre; Ebendorff-Heidepriem, Heike; Hoffmann, Peter; Monro, Tanya M

    2015-09-29

    Refractometric sensors based on optical excitation of surface plasmons on the side of an optical fiber is an established sensing architecture that has enabled laboratory demonstrations of cost effective portable devices for biological and chemical applications. Here we report a Surface Plasmon Resonance (SPR) configuration realized in an Exposed Core Microstructured Optical Fiber (ECF) capable of optimizing both sensitivity and resolution. To the best of our knowledge, this is the first demonstration of fabrication of a rough metal coating suitable for spectral interrogation of scattered plasmonic wave using chemical electroless plating technique on a 10 μm diameter exposed core of the ECF. Performance of the sensor in terms of its refractive index sensitivity and full width at half maximum (FWHM) of SPR response is compared to that achieved with an unstructured bare core fiber with 140 μm core diameter. The experimental improvement in FWHM, and therefore the detection limit, is found to be a factor of two (75 nm for ECF in comparison to 150 nm for the large core fiber). Refractive index sensitivity of 1800 nm/RIU was achieved for both fibers in the sensing range of aqueous environment (1.33-1.37) suitable for biosensing applications.

  8. Implied and Local Volatility Surfaces for South African Index and Foreign Exchange Options

    Directory of Open Access Journals (Sweden)

    Antonie Kotzé

    2015-01-01

    Full Text Available Certain exotic options cannot be valued using closed-form solutions or even by numerical methods assuming constant volatility. Many exotics are priced in a local volatility framework. Pricing under local volatility has become a field of extensive research in finance, and various models are proposed in order to overcome the shortcomings of the Black-Scholes model that assumes a constant volatility. The Johannesburg Stock Exchange (JSE lists exotic options on its Can-Do platform. Most exotic options listed on the JSE’s derivative exchanges are valued by local volatility models. These models needs a local volatility surface. Dupire derived a mapping from implied volatilities to local volatilities. The JSE uses this mapping in generating the relevant local volatility surfaces and further uses Monte Carlo and Finite Difference methods when pricing exotic options. In this document we discuss various practical issues that influence the successful construction of implied and local volatility surfaces such that pricing engines can be implemented successfully. We focus on arbitrage-free conditions and the choice of calibrating functionals. We illustrate our methodologies by studying the implied and local volatility surfaces of South African equity index and foreign exchange options.

  9. Covering folded shapes

    Directory of Open Access Journals (Sweden)

    Oswin Aichholzer

    2014-05-01

    Full Text Available Can folding a piece of paper flat make it larger? We explore whether a shape S must be scaled to cover a flat-folded copy of itself. We consider both single folds and arbitrary folds (continuous piecewise isometries \\(S\\to\\mathbb{R}^2\\. The underlying problem is motivated by computational origami, and is related to other covering and fixturing problems, such as Lebesgue's universal cover problem and force closure grasps. In addition to considering special shapes (squares, equilateral triangles, polygons and disks, we give upper and lower bounds on scale factors for single folds of convex objects and arbitrary folds of simply connected objects.

  10. Optimization of VCSELs incorporating monolithic subwavelength high-refractive-index contrast surface grating mirrors

    Science.gov (United States)

    Gebski, Marcin; Marciniak, Magdalena; Dems, Maciej; Czyszanowski, Tomasz; Lott, James A.

    2017-02-01

    We present results of computer simulations of vertical cavity surface emitting lasers (VCSELs) using novel, highreflectivity monolithic high refractive-index contrast grating (MHCG) mirrors and their more advanced version, partially covered by a thin metal layer - metallic MHCG (mMHCG) mirrors. The first experimental realization of this new class of mirrors is presented and discussed. We show that the metal layer does not deteriorate the high reflectivity of an mMHCG mirror, but in contrary, is a crucial element which allows high reflectivity and additionally opens a way for a more efficient electrical pumping of a VCSEL. Comparison of results of thermal-electrical-carrier-gain self-consistent simulations of both MHCG- and mMHCG-based VCSELs is presented and discussed. It is shown that using mHCG mirror as a top mirror of a VCSEL improves electrical characteristics and greatly decreases the differential resistance of the device.

  11. Refractive index dispersion of swift heavy ion irradiated BFO thin films using Surface Plasmon Resonance technique

    Science.gov (United States)

    Paliwal, Ayushi; Sharma, Savita; Tomar, Monika; Singh, Fouran; Gupta, Vinay

    2016-07-01

    Swift heavy ion irradiation (SHI) is an effective technique to induce defects for possible modifications in the material properties. There is growing interest in studying the optical properties of multiferroic BiFeO3 (BFO) thin films for optoelectronic applications. In the present work, BFO thin films were prepared by sol-gel spin coating technique and were irradiated using the 15 UD Pelletron accelerator with 100 MeV Au9+ ions at a fluence of 1 × 1012 ions cm-2. The as-grown films became rough and porous on ion irradiation. Surface Plasmon Resonance (SPR) technique has been identified as a highly sensitive and powerful technique for studying the optical properties of a dielectric material. Optical properties of BFO thin films, before and after irradiation were studied using SPR technique in Otto configuration. Refractive index is found to be decreasing from 2.27 to 2.14 on ion irradiation at a wavelength of 633 nm. Refractive index dispersion of BFO thin film (from 405 nm to 633 nm) before and after ion radiation was examined.

  12. Assessment of metals contamination in Klang River surface sediments by using different indexes

    Directory of Open Access Journals (Sweden)

    Abolfazl Naji

    2011-01-01

    Full Text Available Surface sediments (0-5 cm from 21 stations throughout Klang River were sampled for metal concentration as well sediment's pH, total organic carbon (TOC and particles sizes to obtain an overall classification of metal contaminations in the area. The concentration of metals (µg∕g, Fe%, dw were as follows: 0.57- 2.19 Cd; 31.89-272.33 Zn; 5.96-24.47 Ni; 10.57- 52.87 Cu; 24.23-64.11 Pb and 1.56-3.03 Fe. The degree of sediment contaminations were computed using an enrichment factor (EF and geoaccumulation index (Igeo. The results suggested that enrichment factor and geoaccumulation values of Cd were greatest among the studied metals. Pearson's correlation indicated that effectiveness of TOC in controlling the distribution and enrichment of metals was a more important factor than that of the grain size (< 63µm. The study revealed that on the basis of computed indexes, Klang River is classified as moderately polluted river.

  13. MODELS OF PROTEIN FOLDING

    Directory of Open Access Journals (Sweden)

    Unnati Ahluwalia

    2012-12-01

    Full Text Available In an attempt to explore the understanding of protein folding mechanism, various models have been proposed in the literature. Advances in recent experimental and computational techniques rationalized our understanding on some of the fundamental features of the protein folding pathways. The goal of this review is to revisit the various models and outline the essential aspects of the folding reaction.

  14. Multiview Rectification of Folded Documents.

    Science.gov (United States)

    You, Shaodi; Matsushita, Yasuyuki; Sinha, Sudipta; Bou, Yusuke; Ikeuchi, Katsushi

    2018-02-01

    Digitally unwrapping images of paper sheets is crucial for accurate document scanning and text recognition. This paper presents a method for automatically rectifying curved or folded paper sheets from a few images captured from multiple viewpoints. Prior methods either need expensive 3D scanners or model deformable surfaces using over-simplified parametric representations. In contrast, our method uses regular images and is based on general developable surface models that can represent a wide variety of paper deformations. Our main contribution is a new robust rectification method based on ridge-aware 3D reconstruction of a paper sheet and unwrapping the reconstructed surface using properties of developable surfaces via conformal mapping. We present results on several examples including book pages, folded letters and shopping receipts.

  15. Equivalent complex conductivities representing the effects of T-tubules and folded surface membranes on the electrical admittance and impedance of skeletal muscles measured by external-electrode method

    Science.gov (United States)

    Sekine, Katsuhisa

    2017-12-01

    In order to represent the effects of T-tubules and folded surface membranes on the electrical admittance and impedance of skeletal muscles measured by the external-electrode method, analytical relations for the equivalent complex conductivities of hypothetical smooth surface membranes were derived. In the relations, the effects of each tubule were represented by the admittance of a straight cable. The effects of the folding of a surface membrane were represented by the increased area of surface membranes. The equivalent complex conductivities were represented as summation of these effects, and the effects of the T-tubules were different between the transversal and longitudinal directions. The validity of the equivalent complex conductivities was supported by the results of finite-difference method (FDM) calculations made using three-dimensional models in which T-tubules and folded surface membranes were represented explicitly. FDM calculations using the equivalent complex conductivities suggested that the electrically inhomogeneous structure due to the existence of muscle cells with T-tubules was sufficient for explaining the experimental results previously obtained using the external-electrode method. Results of FDM calculations in which the structural changes caused by muscle contractions were taken into account were consistent with the reported experimental results.

  16. Heavy metal contamination in surface sediments of Yangtze River intertidal zone: An assessment from different indexes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Weiguo [State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062 (China); Feng Huan, E-mail: fengh@mail.montclair.ed [Department of Earth and Environmental Studies, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043 (United States); Chang Jinna; Qu Jianguo; Xie Hongxia; Yu Lizhong [State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062 (China)

    2009-05-15

    Surface sediments (0-5 cm) from 59 stations within the Yangtze River intertidal zone (YRIZ) were sampled for metal contamination analysis in April and August 2005. The concentrations ranged (in mg kg{sup -1} dry weight): Al, 40,803-97,213; Fe, 20,538-49,627; Cd, 0.12-0.75; Cr, 36.9-173; Cu, 6.87-49.7; Mn, 413-1,112; Ni, 17.6-48.0; Pb, 18.3-44.1; and Zn, 47.6-154; respectively. Among the 59 sampling stations, enrichment factors (EF) indicate enrichment of Cd (52 stations), Cr (54 stations), Cu (5 stations), Ni (26 stations), Pb (5 stations) and Zn (5 stations). Geoaccumulation indexes (I{sub geo}) also suggest individual metal contamination in localized areas. This study indicates that Cd, Cr and Ni enrichment in the YRIZ sediment is widespread whereas Cu, Mn, Pb and Zn enrichment is localized or nonexistent. Factor and cluster analyses indicate that Cd is associated with total organic carbon whereas Cu, Cr, Ni, Pb and Zn have a close association with Mn. - Surface sediment metal enrichment is evidenced for Cd, Cr and Ni in the Yangtze River intertidal zone.

  17. Extended T-index models for glacier surface melting: a case study from Chorabari Glacier, Central Himalaya, India

    Science.gov (United States)

    Karakoti, Indira; Kesarwani, Kapil; Mehta, Manish; Dobhal, D. P.

    2016-10-01

    Two enhanced temperature-index (T-index) models are proposed by incorporating meteorological parameters viz. relative humidity, wind speed and net radiation. The models are an attempt to explore different climatic variables other than temperature affecting glacier surface melting. Weather data were recorded at Chorabari Glacier using an automatic weather station during the summers of 2010 (July 10 to September 10) and 2012 (June 10 to October 25). The modelled surface melt is validated against the measured point surface melting at the snout. Performance of the developed models is evaluated by comparing with basic temperature-index model and is quantified through different efficiency criteria. The results suggest that proposed models yield considerable improvement in surface melt simulation . Consequently, the study reveals that glacier surface melt depends not only on temperature but also on weather parameters viz. relative humidity, wind speed and net radiation play a significant role in glacier surface melting. This approach provides a major improvement on basic temperature-index method and offers an alternative to energy balance model.

  18. Towards a geomechanics classification of folded layered rock masses

    Science.gov (United States)

    Agliardi, Federico; Zanchi, Andrea; Bianchi, Federico; Crosta, Giovanni B.

    2016-04-01

    Several schemes have been proposed in the last decades to account for the effects of structure and alteration of rock masses on their geo-mechanical properties. Among these, the Geological Strength Index (GSI) turned out as the most effective to account for complex geological conditions, including heavily fractured, heterogeneous (e.g. flysch-like) or tectonically disturbed rock masses. It is well known that folding has a direct impact on the type and degree of fracturing. Nevertheless, no classification scheme has been developed to introduce explicitly the effects of folding and associated fracturing on rock mass strength and deformability. In this perspective, we carried out an exploratory study aimed at establishing relationships between outcrop-scale folding and GSI in layered carbonate rock masses, exceptionally well exposed in a quarry near Bergamo (Lombardia, Southern Alps). A N-S trending, 350m long and 115m high benched rock face exposes a complete cross section of a sub-horizontal inclined fold involving Lower Jurassic cherty mudstones (Moltrasio Lms.) and marly limestones successions (Domaro Lms.). The main fold has an axial surface moderately dipping to the north and is characterised by polyharmonic folds at scales of metres to tens of metres. The site was documented by producing a digital outcrop through a high-resolution terrestrial photogrammetric survey from distances ranging from 70 to 130 m (18 camera stations, 395 pictures), using RTK GNSS measurements for camera station geo-referencing. Data processing by Structure-from-Motion (SfM) techniques resulted in detailed point clouds covering the entire slope with a cm-scale accuracy. In order to establish relationships between lithology, folding styles, and geomechanical properties of folded rock masses we performed a detailed structural analysis at 25 survey stations spread over all the different fold sectors. These surveys include: lithology, bedding attitude and thickness, brittle structures (e

  19. Digital processing of SEM images for the assessment of evaluation indexes of cleaning interventions on Pentelic marble surfaces

    International Nuclear Information System (INIS)

    Moropoulou, A.; Delegou, E.T.; Vlahakis, V.; Karaviti, E.

    2007-01-01

    In this work, digital processing of scanning-electron-microscopy images utilized to assess cleaning interventions applied on the Pentelic marble surfaces of the National Archaeological Museum and National Library in Athens, Greece. Beside mineralogical and chemical characterization that took place by scanning-electron-microscopy with Energy Dispersive X-ray Spectroscopy, the image-analysis program EDGE was applied for estimating three evaluation indexes of the marble micro-structure. The EDGE program was developed by the U.S. Geological Survey for the evaluation of cleaning interventions applied on Philadelphia City Hall. This computer program analyzes scanning-electron-microscopy images of stone specimens cut in cross-section for measuring the fractal dimension of the exposed surfaces, the stone near-surface fracture density, the shape factor (a surface roughness factor) and the friability index which represents the physico-chemical and physico-mechanical stability of the stone surface. The results indicated that the evaluation of the marble surface micro-structure before and after cleaning is achieved by the suggested indexes, while the performance of cleaning interventions on the marble surfaces can be assessed

  20. A Near-Zero Refractive Index Meta-Surface Structure for Antenna Performance Improvement

    Science.gov (United States)

    Ullah, Mohammad Habib; Islam, Mohammad Tariqul; Faruque, Mohammad Rashed Iqbal

    2013-01-01

    A new meta-surface structure (MSS) with a near-zero refractive index (NZRI) is proposed to enhance the performance of a square loop antenna array. The main challenge to improve the antenna performance is increment of the overall antenna volume that is mitigated by assimilating the planar NZRI MSS at the back of the antenna structure. The proposed NZRI MSS-loaded CPW-fed (Co-Planar Waveguide) four-element array antenna is designed on ceramic-bioplastic-ceramic sandwich substrate using high-frequency structure simulator (HFSS), a finite-element-method-based simulation tool. The gain and directivity of the antenna are significantly enhanced by incorporating the NZRI MSS with a 7 × 6 set of elements at the back of the antenna structure. Measurement results show that the maximum gains of the antenna increased from 6.21 dBi to 8.25 dBi, from 6.52 dBi to 9.05 dBi and from 10.54 dBi to 12.15 dBi in the first, second and third bands, respectively. The effect of the slot configuration in the ground plane on the reflection coefficient of the antenna was analyzed and optimized. The overall performance makes the proposed antenna appropriate for UHFFM (Ultra High Frequency Frequency Modulation) telemetry-based space applications as well as mobile satellite, microwave radiometry and radio astronomy applications. PMID:28788376

  1. Multi-pollutant surface objective analyses and mapping of air quality health index over North America.

    Science.gov (United States)

    Robichaud, Alain; Ménard, Richard; Zaïtseva, Yulia; Anselmo, David

    2016-01-01

    Air quality, like weather, can affect everyone, but responses differ depending on the sensitivity and health condition of a given individual. To help protect exposed populations, many countries have put in place real-time air quality nowcasting and forecasting capabilities. We present in this paper an optimal combination of air quality measurements and model outputs and show that it leads to significant improvements in the spatial representativeness of air quality. The product is referred to as multi-pollutant surface objective analyses (MPSOAs). Moreover, based on MPSOA, a geographical mapping of the Canadian Air Quality Health Index (AQHI) is also presented which provides users (policy makers, public, air quality forecasters, and epidemiologists) with a more accurate picture of the health risk anytime and anywhere in Canada and the USA. Since pollutants can also behave as passive atmospheric tracers, they provide information about transport and dispersion and, hence, reveal synoptic and regional meteorological phenomena. MPSOA could also be used to build air pollution climatology, compute local and national trends in air quality, and detect systematic biases in numerical air quality (AQ) models. Finally, initializing AQ models at regular time intervals with MPSOA can produce more accurate air quality forecasts. It is for these reasons that the Canadian Meteorological Centre (CMC) in collaboration with the Air Quality Research Division (AQRD) of Environment Canada has recently implemented MPSOA in their daily operations.

  2. Square array photonic crystal fiber-based surface plasmon resonance refractive index sensor

    Science.gov (United States)

    Liu, Min; Yang, Xu; Zhao, Bingyue; Hou, Jingyun; Shum, Ping

    2017-12-01

    Based on surface plasmon resonance (SPR), a novel refractive index (RI) sensor comprising a square photonic crystal fiber (PCF) is proposed to realize the detection of the annular analyte. Instead of hexagon structure, four large air-holes in a square array are introduced to enhance the sensitivity by allowing two polarization directions of the core mode to be more sensitive. The gold is used as the only plasmonic material. The design purpose is to reduce the difficulty in gold deposition and enhance the RI sensitivity. The guiding properties and the effects of the parameters on the performance of the sensor are numerically investigated by the Finite Element Method (FEM). By optimizing the structure, the sensor can exhibit remarkable sensitivity up to 7250 nm/RIU and resolution of 1.0638 × 10‑5 RIU with only one plasmonic material, which is very competitive compared with the other reported externally coated and single-layer coated PCF-based SPR (PCF-SPR) sensors, to our best knowledge.

  3. A Near-Zero Refractive Index Meta-Surface Structure for Antenna Performance Improvement

    Directory of Open Access Journals (Sweden)

    Mohammad Habib Ullah

    2013-11-01

    Full Text Available A new meta-surface structure (MSS with a near-zero refractive index (NZRI is proposed to enhance the performance of a square loop antenna array. The main challenge to improve the antenna performance is increment of the overall antenna volume that is mitigated by assimilating the planar NZRI MSS at the back of the antenna structure. The proposed NZRI MSS-loaded CPW-fed (Co-Planar Waveguide four-element array antenna is designed on ceramic-bioplastic-ceramic sandwich substrate using high-frequency structure simulator (HFSS, a finite-element-method-based simulation tool. The gain and directivity of the antenna are significantly enhanced by incorporating the NZRI MSS with a 7 × 6 set of elements at the back of the antenna structure. Measurement results show that the maximum gains of the antenna increased from 6.21 dBi to 8.25 dBi, from 6.52 dBi to 9.05 dBi and from 10.54 dBi to 12.15 dBi in the first, second and third bands, respectively. The effect of the slot configuration in the ground plane on the reflection coefficient of the antenna was analyzed and optimized. The overall performance makes the proposed antenna appropriate for UHFFM (Ultra High Frequency Frequency Modulation telemetry-based space applications as well as mobile satellite, microwave radiometry and radio astronomy applications.

  4. Joint spatiotemporal variability of global sea surface temperatures and global Palmer drought severity index values

    Science.gov (United States)

    Apipattanavis, S.; McCabe, G.J.; Rajagopalan, B.; Gangopadhyay, S.

    2009-01-01

    Dominant modes of individual and joint variability in global sea surface temperatures (SST) and global Palmer drought severity index (PDSI) values for the twentieth century are identified through a multivariate frequency domain singular value decomposition. This analysis indicates that a secular trend and variability related to the El Niño–Southern Oscillation (ENSO) are the dominant modes of variance shared among the global datasets. For the SST data the secular trend corresponds to a positive trend in Indian Ocean and South Atlantic SSTs, and a negative trend in North Pacific and North Atlantic SSTs. The ENSO reconstruction shows a strong signal in the tropical Pacific, North Pacific, and Indian Ocean regions. For the PDSI data, the secular trend reconstruction shows high amplitudes over central Africa including the Sahel, whereas the regions with strong ENSO amplitudes in PDSI are the southwestern and northwestern United States, South Africa, northeastern Brazil, central Africa, the Indian subcontinent, and Australia. An additional significant frequency, multidecadal variability, is identified for the Northern Hemisphere. This multidecadal frequency appears to be related to the Atlantic multidecadal oscillation (AMO). The multidecadal frequency is statistically significant in the Northern Hemisphere SST data, but is statistically nonsignificant in the PDSI data.

  5. Self versus examiner administration of the Ocular Surface Disease Index©.

    Science.gov (United States)

    Ngo, William; Srinivasan, Sruthi; Keech, Adam; Keir, Nancy; Jones, Lyndon

    To compare the difference in Ocular Surface Disease Index © (OSDI) scores when participants were given the OSDI to complete on their own (self-guided, SG), versus under the guidance of the examiner (examiner-guided, EG). 100 participants enrolled in this prospective two-visit study (fifty under-45 years old, 38F/12M; and fifty 45 years-and-older, 42F/8M). Participants who scored ≥1 on the Subjective Evaluation of Symptoms of Dryness (SESoD) were included in this study. Participants completed the OSDI SG during the first visit. Participants returned the next day and repeated the OSDI, but with EG (with standardized instructions). Participants were under deception and believed that they were comparing the OSDI to the SESoD. The mean OSDI score of the SG and EG administration was 32.0±17.3 and 33.8±19.6 respectively (p>0.05) with 95% limits of agreement between -20.6 and +24.2. The correlation between SG and EG administration was Spearman's r=0.81, p0.05) for both the under-45 group, and 45-and-older group. The 95% limits of agreement for the under-45 group were smaller than the 45-and-older group (under-45: [-15.5, +13.1,], 45-and-older: [-23.3, +32.2]). A significant difference was found between 8 of the 12 questions items (all p≤0.01). However, the mean difference for each was <0.6 and was not considered to be clinically significant. There was no clinically significant difference in OSDI score between SG and EG administration, however having instructions provided with EG administration affected variability of scores in the older group more than the younger group. Copyright © 2016 Spanish General Council of Optometry. Published by Elsevier España, S.L.U. All rights reserved.

  6. Vocal Fold Paralysis

    Science.gov (United States)

    ... decades-long project to develop an electrical stimulation technology to help people avoid having a tracheotomy when both vocal folds are paralyzed. The device, which currently is being tested in animals and people, uses an implanted pacemaker to stimulate ...

  7. Spherical images and inextensible curved folding

    Science.gov (United States)

    Seffen, Keith A.

    2018-02-01

    In their study, Duncan and Duncan [Proc. R. Soc. London A 383, 191 (1982), 10.1098/rspa.1982.0126] calculate the shape of an inextensible surface folded in two about a general curve. They find the analytical relationships between pairs of generators linked across the fold curve, the shape of the original path, and the fold angle variation along it. They present two special cases of generator layouts for which the fold angle is uniform or the folded curve remains planar, for simplifying practical folding in sheet-metal processes. We verify their special cases by a graphical treatment according to a method of Gauss. We replace the fold curve by a piecewise linear path, which connects vertices of intersecting pairs of hinge lines. Inspired by the d-cone analysis by Farmer and Calladine [Int. J. Mech. Sci. 47, 509 (2005), 10.1016/j.ijmecsci.2005.02.013], we construct the spherical images for developable folding of successive vertices: the operating conditions of the special cases in Duncan and Duncan are then revealed straightforwardly by the geometric relationships between the images. Our approach may be used to synthesize folding patterns for novel deployable and shape-changing surfaces without need of complex calculation.

  8. A probability index for surface zonda wind occurrence at Mendoza city through vertical sounding principal components analysis

    Science.gov (United States)

    Otero, Federico; Norte, Federico; Araneo, Diego

    2018-01-01

    The aim of this work is to obtain an index for predicting the probability of occurrence of zonda event at surface level from sounding data at Mendoza city, Argentine. To accomplish this goal, surface zonda wind events were previously found with an objective classification method (OCM) only considering the surface station values. Once obtained the dates and the onset time of each event, the prior closest sounding for each event was taken to realize a principal component analysis (PCA) that is used to identify the leading patterns of the vertical structure of the atmosphere previously to a zonda wind event. These components were used to construct the index model. For the PCA an entry matrix of temperature ( T) and dew point temperature (Td) anomalies for the standard levels between 850 and 300 hPa was build. The analysis yielded six significant components with a 94 % of the variance explained and the leading patterns of favorable weather conditions for the development of the phenomenon were obtained. A zonda/non-zonda indicator c can be estimated by a logistic multiple regressions depending on the PCA component loadings, determining a zonda probability index \\widehat{c} calculable from T and Td profiles and it depends on the climatological features of the region. The index showed 74.7 % efficiency. The same analysis was performed by adding surface values of T and Td from Mendoza Aero station increasing the index efficiency to 87.8 %. The results revealed four significantly correlated PCs with a major improvement in differentiating zonda cases and a reducing of the uncertainty interval.

  9. Water erosion in surface soil conditions: runoff velocity, concentration and D50 index of sediments in runoff

    Directory of Open Access Journals (Sweden)

    Júlio César Ramos

    2016-06-01

    Full Text Available ABSTRACT Water erosion and contamination of water resources are influenced by concentration and diameter of sediments in runoff. This study aimed to quantify runoff velocity and concentration and the D50 index of sediments in runoff under different soil surface managements, in the following treatments: i cropped systems: no-tilled soil covered by ryegrass (Lolium multiflorum Lam. residue, with high soil cover and minimal roughness (HCR; no tilled soil covered by vetch (Vicia sativa L. residue, with high soil cover and minimal roughness (HCV; chiseled soil after ryegrass crop removing the above-ground residues and keeping only the root system, with high roughness (HRR; chiseled soil after vetch crop removing the above-ground residues and keeping only the root system, with high roughness (HRV; ii bare and chiseled soil, with high roughness (BHR. The research was conducted on a Humic Dystrupept under simulated rainfall. The design was completely randomized and each treatment was replicated twice. Eight rainfall events of controlled intensity (65 mm h−1 were applied to each treatment for 90 minutes. The D50 index, runoff velocity and sediment concentration were influenced by crop and soil management. Runoff velocity was more intensely reduced by cover crop residues than by surface roughness. Regardless of surface condition, the D50 index and concentration of sediment in runoff were lower under ryegrass than vetch crop. Runoff velocity and the D50 index were exponentially and inversely correlated with soil cover by residues and with surface roughness, while the D50 index was positively and exponentially correlated with runoff velocity.

  10. Maxillomandibular relationship record for implant complete mouth rehabilitation with elastomeric material and facial surface index of existing denture

    Directory of Open Access Journals (Sweden)

    Pravinkumar G Patil

    2015-01-01

    Full Text Available Introduction: The maxillomandibular relationship (MMR record is a critical step to establish the new occlusion in implant supported complete mouth rehabilitation. Using patients existing denture for recording the MMR requires implant definitive cast to be modified extensively to completely seat the denture (with unaltered flanges on it. This may influence the correct seating of the denture on the implant definitive cast causing faulty recording of the MMR. Materials and Method: Elastomeric record bases, reinforced with the resin framework, are fabricated and relined with the light body elastomeric material when all the healing abutments are in place. The MMR is recorded with these elastomeric record bases using vacuum formed facial surface index of the occluded existing dentures as a guideline. Results: The elastomeric record bases with facial surface index of the existing dentures can allow clinicians to record MMR records without removing the healing abutments from the mouth with acceptable accuracy. This can save chair-side time of the procedure. The record of facial surfaces of existing complete denture in the form of vacuum formed sheet helps to set the occlusal vertical dimension. Conclusion: Use of facial surface index together with the elastomeric record bases can be the useful alternative technique to record the MMR in patients with implant supported full mouth rehabilitation. Further study is required to prove its routine clinical utility.

  11. BigFoot Leaf Area Index Surfaces for North and South American Sites, 2000-2003

    Data.gov (United States)

    National Aeronautics and Space Administration — The BigFoot project gathered leaf area index (LAI) data for nine EOS Land Validation Sites located from Alaska to Brazil from 2000 to 2003. Each site is...

  12. BigFoot Leaf Area Index Surfaces for North and South American Sites, 2000-2003

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: The BigFoot project gathered leaf area index (LAI) data for nine EOS Land Validation Sites located from Alaska to Brazil from 2000 to 2003. Each site is...

  13. A one-layer satellite surface energy balance for estimating evapotranspiration rates and crop water stress indexes.

    Science.gov (United States)

    Barbagallo, Salvatore; Consoli, Simona; Russo, Alfonso

    2009-01-01

    Daily evapotranspiration fluxes over the semi-arid Catania Plain area (Eastern Sicily, Italy) were evaluated using remotely sensed data from Landsat Thematic Mapper TM5 images. A one-source parameterization of the surface sensible heat flux exchange using satellite surface temperature has been used. The transfer of sensible and latent heat is described by aerodynamic resistance and surface resistance. Required model inputs are brightness, temperature, fractional vegetation cover or leaf area index, albedo, crop height, roughness lengths, net radiation, air temperature, air humidity and wind speed. The aerodynamic resistance (r(ah)) is formulated on the basis of the Monin-Obukhov surface layer similarity theory and the surface resistance (r(s)) is evaluated from the energy balance equation. The instantaneous surface flux values were converted into evaporative fraction (EF) over the heterogeneous land surface to derive daily evapotranspiration values. Remote sensing-based assessments of crop water stress (CWSI) were also made in order to identify local irrigation requirements. Evapotranspiration data and crop coefficient values obtained from the approach were compared with: (i) data from the semi-empirical approach "K(c) reflectance-based", which integrates satellite data in the visible and NIR regions of the electromagnetic spectrum with ground-based measurements and (ii) surface energy flux measurements collected from a micrometeorological tower located in the experiment area. The expected variability associated with ET flux measurements suggests that the approach-derived surface fluxes were in acceptable agreement with the observations.

  14. Near field evidence of backward surface plasmon polaritons on negative index material boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Cuevas, Mauro, E-mail: cuevas@df.uba.ar [Facultad de Ingeniería y Tecnología Informática, Universidad de Belgrano, Villanueva 1324, C1426BMJ, Buenos Aires (Argentina); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Argentina); Grunhut, Vivian [Facultad de Ingeniería, Universidad Austral (Argentina); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Argentina); Depine, Ricardo A. [Grupo de Electromagnetismo Aplicado, Departamento de Física, FCEN, Universidad de Buenos Aires and IFIBA, Ciudad Universitaria, Pabellón I, C1428EHA, Buenos Aires (Argentina); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Argentina)

    2016-12-09

    Highlights: • Electromagnetic scattering from a localized defect on a NIM surface is presented. • The electromagnetic response strongly depends on the SPPs excited. • Near field distribution reveals the forward or backward character of SPPs excited. - Abstract: We present a detailed analysis about the electromagnetic response of a metamaterial surface with a localized defect. The excitation of electromagnetic surface waves leads to a near-field distribution showing a periodic dependence along the metamaterial surface. We find that this periodic pattern provides a direct demonstration of the forward or backward surface wave propagation.

  15. Vocal Fold Collision Modeling

    DEFF Research Database (Denmark)

    Granados, Alba; Brunskog, Jonas; Misztal, M. K.

    2015-01-01

    When vocal folds vibrate at normal speaking frequencies, collisions occurs. The numerics and formulations behind a position-based continuum model of contact is an active field of research in the contact mechanics community. In this paper, a frictionless three-dimensional finite element model...... of the vocal fold collision is proposed, which incorporates different procedures used in contact mechanics and mathematical optimization theories. The penalty approach and the Lagrange multiplier method are investigated. The contact force solution obtained by the penalty formulation is highly dependent...

  16. First-principles study of the interactions of hydrogen with low-index surfaces of PdCu ordered alloy

    Directory of Open Access Journals (Sweden)

    Min Tang

    2017-12-01

    Full Text Available PdCu catalysts play a key role in several hydrogen-involved processes. Among these reactions, the interaction of hydrogen with PdCu essentially determines the catalytic performance. However, the response of PdCu to surrounding hydrogen has been poorly investigated, especially for specific facets of PdCu at different environment. In this work, taking temperature and hydrogen pressure into account, we studied the hydrogen-surface interactions for four low-index surfaces of PdCu through first-principles calculations. It was found that H-PdCu adsorption strong relies on the facets, hydrogen coverage, and reaction environment (temperature and H-pressure. Our work highlights the importance of the environment on the nature of catalyst surfaces and reactions and offers a plausible way to investigate the interactions between gas and the surfaces of nanocatalysts in real reactions.

  17. Optically pumped GaN vertical cavity surface emitting laser with high index-contrast nanoporous distributed Bragg reflector.

    Science.gov (United States)

    Lee, Seung-Min; Gong, Su-Hyun; Kang, Jin-Ho; Ebaid, Mohamed; Ryu, Sang-Wan; Cho, Yong-Hoon

    2015-05-04

    Laser operation of a GaN vertical cavity surface emitting laser (VCSEL) is demonstrated under optical pumping with a nanoporous distributed Bragg reflector (DBR). High reflectivity, approaching 100%, is obtained due to the high index-contrast of the nanoporous DBR. The VCSEL system exhibits low threshold power density due to the formation of high Q-factor cavity, which shows the potential of nanoporous medium for optical devices.

  18. Analysis of local concentration in stomach fold pattern by using abdominal X-ray CT image

    International Nuclear Information System (INIS)

    Watanabe, Shigeto; Hasegawa, Jun-ichi; Mekada, Yoshito; Mori, Kensaku; Nawano, Shigeru

    2004-01-01

    The paper presents a method for analysis of stomach folds pattern in abdominal X-ray CT images. Many stomach cancers have local concentration of folds at cancer lesions. Therefore, in stomach diagnosis, it is very important to evaluate quantitatively such fold concentration. In this paper, a method for calculation of concentration index for line figure on a curved surface is proposed first. Then, using this method a processing procedure for detection of stomach cancer from an abdominal X-ray CT image is developed. In the experiment using practical X-ray CT images, it is shown that by the proposed procedure, higher values of concentration index are obtained at cancer area. (author)

  19. Improved localized surface plasmon resonance index sensitivity based on chemically-synthesized gold nanoparticles on indium tin oxide surfaces

    Science.gov (United States)

    Zhu, Jin; Li, Xiaolong; Zheng, Wei; Wang, Biao; Tian, Yubo

    2018-02-01

    The results of this reported work indicated that gold nanoparticle arrays self-assembled on indium tin oxide (ITO) glasses can obtain broader localized surface plasmon resonance (LSPR) wavelength range and higher sensitivity than the bare quartz. The results of surface electric field calculated using finite difference time domain showed that the electric field of nanoparticles on ITO glasses is enhanced and the repulsive forces within each particle is weakened. According to the dipolar interaction mechanism, a weakened repulsive forces within each particle lead to a lower resonance frequency and a strong redshift of the LSPR spectra.

  20. Folds and Etudes

    Science.gov (United States)

    Bean, Robert

    2007-01-01

    In this article, the author talks about "Folds" and "Etudes" which are images derived from anonymous typing exercises that he found in a used copy of "Touch Typing Made Simple". "Etudes" refers to the musical tradition of studies for a solo instrument, which is a typewriter. Typing exercises are repetitive attempts to type words and phrases…

  1. Folding worlds between pages

    CERN Document Server

    Meier, Matthias

    2010-01-01

    "We all remember pop-up books form our childhood. As fascinated as we were back then, we probably never imagined how much engineering know-how went into these books. Pop-up engineer Anton Radevsky has even managed to fold a 27-kilometre particle accelerator into a book" (4 pages)

  2. New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface

    Science.gov (United States)

    Zorgani, Mohamed Amine; Patron, Kevin; Desvaux, Mickaël

    2014-07-01

    Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

  3. Long-chain alkaenone unsaturation index as sea surface temperature proxy in southwest Bay of Bengal

    Digital Repository Service at National Institute of Oceanography (India)

    Sarma, N.S.; Pasha, S.K.G.; SriRamKrishna, M.; Shirodkar, P.V.; Yadava, M.G.; Rao, K.M.

    . The LCA unsaturation index (U k minute37 ) d e- fined by eq. (1) 6 is a new proxy that is frequently an a- lysed at present globally, as the i n dex does not suffer from disadvantages associated with other methods, e.g. melt water 1 and salinity...

  4. Ion bombardment induced topography evolution on low index crystal surfaces of Cu and Pb

    International Nuclear Information System (INIS)

    Tanovic, L.; Tanovic, N.; Carter, G.; Nobes, M.J.

    1993-01-01

    (100), (110) and (111) oriented single crystal surfaces of Cu and Pb have been bombarded with inert gas ions, self ions, ions of the other substrate species and Bi in the energy range 50-150 keV and in the fluence range 10 15 -10 18 ions.cm 2 . The evolving surface topography was observed by scanning electron microscopy. This topography was observed to be strongly influenced by ion species and surface orientation but the habit of the topography was delineated at low fluences and the features increased in size and density with increasing fluence with some mutation to the more stable of the features. As an example Bi and Pb bombardment of (100) Cu leads to little topographic evolution, (110) Cu develops a system of parallel ridges with (100) facets and (111) Cu develops a prismatic surface, each prism possessing (100) facets. These, and the more general, results cannot be explained by surface erosion by sputtering theory alone (this predicts surface stability of the lowest sputtering yield orientation (110), nor by surface free energy density minimisation criteria (this predicts stability of (111) surfaces). It is proposed that the observed topography is most strongly related to the crystallographic form of precipitates of implanted species. (orig.)

  5. Ion bombardment induced topography evolution on low index crystal surfaces of Cu and Pb

    International Nuclear Information System (INIS)

    Tanovic, L.; Tanovic, N.; Carter, G.; Nobes, M.J.

    1994-01-01

    (100), (110) and (111) oriented single crystal surfaces of Cu and Pb have been bombarded with inert gas ions, self ions, ions of the other substrate species and Bi in the energy range 50-150 keV and in the fluence range 10 15 -10 18 ions cm 2 . The evolving surface topography was observed by scanning electron microscopy. This topography was observed to be strongly influenced by ion species and surface orientation but the habit of the topography was delineated at low fluences and the features increased in size and density with increasing fluence with some mutation to the more stable of the features. As an example Bi and Pb bombardment of (100) Cu leads to little topographic evolution, (110) Cu develops a system of parallel ridges with (100) facets and (111) Cu develops a prismatic surface, each prism possessing (100) facets. These, and the more general, results cannot be explained by surface erosion by sputtering theory alone (this predicts surface stability of the lowest sputtering yield orientation (110), nor by surface free energy density minimisation criteria (this predicts stability of (111) surfaces). It is proposed that the observed topography is most strongly related to the crystallographic form of precipitates of implanted species. (orig.)

  6. Electrophoretic deposition of carbon nanotubes on a carbon fiber surface with different index graphitization

    International Nuclear Information System (INIS)

    Almeida, E.C.; Baldan, M.R.; Ferreira, N.G.; Edwards, E.R.

    2009-01-01

    Full text: The purpose of this work is to examine the electrophoretic deposition of carbon nanotubes powder on carbon fibers, produced at different heat treatments temperatures. Besides, a systematic study of the effects of graphitization index from substrate on the structure and morphology of CNTs has been available. Carbon fibers were produced from polyacrylonitrile at three different heat treatments temperatures, 1000, 1500 and 2000 deg C. The carbon fibers microstructure or its graphitization index may be controlled by the heat treatments temperatures. The electrophoretic deposition of carbon nanotubes was obtained with the powder of carbon nanotubes dispersed in water by ultrasonication to obtain dispersions of 0.05 mg/mL. The carbon fibers were immersed in the nanotube dispersion, and a positive potential of 10 V/cm was applied. Morphology and microstructure of carbon nanotubes on carbon fibers were obtained by scanning electron microscopy, Raman spectroscopy and X-ray photoelectron spectroscopy. (author)

  7. Class frequency distribution for a surface raw water quality index in ...

    African Journals Online (AJOL)

    A harmonised in-stream water quality guideline was constructed to develop a water quality index for the Upper and Middle Vaal Water Management Areas, in the Vaal basin of South Africa. The study area consisted of 12 water quality monitoring points; V1, S1, B1, S4, K9, T1, R2, L1, V7, V9, V12, and V17. These points are ...

  8. Improving the performance of temperature index snowmelt model of SWAT by using MODIS land surface temperature data.

    Science.gov (United States)

    Yang, Yan; Onishi, Takeo; Hiramatsu, Ken

    2014-01-01

    Simulation results of the widely used temperature index snowmelt model are greatly influenced by input air temperature data. Spatially sparse air temperature data remain the main factor inducing uncertainties and errors in that model, which limits its applications. Thus, to solve this problem, we created new air temperature data using linear regression relationships that can be formulated based on MODIS land surface temperature data. The Soil Water Assessment Tool model, which includes an improved temperature index snowmelt module, was chosen to test the newly created data. By evaluating simulation performance for daily snowmelt in three test basins of the Amur River, performance of the newly created data was assessed. The coefficient of determination (R (2)) and Nash-Sutcliffe efficiency (NSE) were used for evaluation. The results indicate that MODIS land surface temperature data can be used as a new source for air temperature data creation. This will improve snow simulation using the temperature index model in an area with sparse air temperature observations.

  9. The Folded Horn Antenna

    Science.gov (United States)

    Farr, E. G.; Bowen, L. H.; Baum, C. E.; Prather, W. D.

    Antennas for radiating high-power mesoband (medium-bandwidth) electromagnetic signals are critical to the mission of upsetting electronics at a distance. When operated at frequencies of a few hundred megahertz, RF weapons require highly efficient antennas that can fit into a small volume. Most of the existing antennas, such as pyramidal horns, are too large to fit onto certain platforms of interest. To address this challenge, we investigate the folded horn, which has aperture dimensions of 0.5 × 2 wavelengths, and a depth of 1.5-2 wavelengths. This antenna has a nearly focused aperture field, due to a parabolic fold in the H-plane. We report here on the fabrication and testing of the first folded horn, operating at 3 GHz. After a number of iterations, we obtained a realized gain of at least 10 dBi over 3-5 GHz, an aperture efficiency of 80%, and a return loss below -10 dB over 2.8-3.35 GHz. This design could be adapted to high-voltages, and it could work well in a two-antenna array, with two antennas positioned back to back, driven by a differential source.

  10. Evaluation And Characterization Of Trace Metals Contamination In The Surface Sediment Using Pollution Load Index PLI And Geo-Accumulation Index Igeo Of Ona River Western Nigeria

    Directory of Open Access Journals (Sweden)

    Andem

    2015-01-01

    Full Text Available Abstract Evaluation and Characterization of Trace Metal Contamination in the Surface Sediment Using Pollution Load Index PLI and Geo-accumulation Index Igeo Index of Ona River was conducted for six months. From the result of this study the mean values of lead ranged between 0.004 mgkg and 0.330 mgkg while the mean iron was highest 5.05 mgkg in station 4 and lowest 2.26 mgkg in station 5. The mean chromium value ranged from 0.007 mgkg station 1 and 2 to 0.021 mgkg station 3 and 4. The mean copper was highest 3.97 mgkg in station 1 and lowest 0.008 mgkg in station 2. Analysis of variance ANOVA revealed the same trend in spatial variation of these heavy metals. There was a significant difference P 0.05 in lead chromium and copper among the study sampling stations and insignificant difference P0.05 in iron among the study sampling station. The PLI values recorded for all the stations were below 1. Thus the sediment of the study stretch that Ona River is unpolluted. The Igeo values for chromium and iron fall in class 0 in all the five sampling stations indicating that there is no pollution from these metals in the Ona River sediments lead fall in class 3 in station 4indicating moderately to heavily contaminated condition and class 0in station 1 2 3 and 5 and copper fall in class 3 in station 4 and 5 in class 6 in station 3 indicating extremely contaminated condition. The Igeo values were consistent with those derived for PLI. All trace metals had concentrations below the EPA regulatory limits for sediment except iron. From the results of this study sediment quality reflects the impacts of anthropogenic activities on quality of the river. However the continuous build-up of the metal contaminants can be checked if relevant government agencies ensure strict compliant of industrial standards which stipulate treatment of industrial waste before discharging such contaminated effluentswastes into River. Therefore perpetual assessment is highly recommended

  11. Surface morphology of refractive-index waveguide gratings fabricated in polymer films

    Science.gov (United States)

    Dong, Yi; Song, Yan-fang; Ma, Lei; Gao, Fang-fang

    2016-09-01

    The characteristic modifications are reported on the surface of polymeric waveguide film in the process of volume- grating fabrication. The light from a mode-locked 76 MHz femtosecond laser with pulse duration of 200 fs and wavelength of 800 nm is focused normal to the surface of the sample. The surface morphology modifications are ascribed to a fact that surface swelling occurs during the process. Periodic micro-structure is inscribed with increasing incident power. The laser-induced swelling threshold on the grating, which is higher than that of two-photon initiated photo-polymerization (TPIP) (8 mW), is verified to be about 20 mW. It is feasible to enhance the surface smoothness of integrated optics devices for further encapsulation. The variation of modulation depth is studied for different values of incident power and scan spacing. Ablation accompanied with surface swelling appears when the power is higher. By optimizing the laser carving parameters, highly efficient grating devices can be fabricated.

  12. IDENTIFYING RECENT SURFACE MINING ACTIVITIES USING A NORMALIZED DIFFERENCE VEGETATION INDEX (NDVI) CHANGE DETECTION METHOD

    Science.gov (United States)

    Coal mining is a major resource extraction activity on the Appalachian Mountains. The increased size and frequency of a specific type of surface mining, known as mountain top removal-valley fill, has in recent years raised various environmental concerns. During mountainto...

  13. Baseline studies and evaluation of effects of surface discharge of deep-sea mining - INDEX area

    Digital Repository Service at National Institute of Oceanography (India)

    DeSousa, S.N.; Sardessai, S.

    . An evaluation of possible effects of surface discharge of mining fines - a slurry consisting of fine nodule fragments, bottom water and sediments - suggests that the discharge, with an expected solid content of 50 g/l, will induce increased primary production...

  14. Class frequency distribution for a surface raw water quality index in ...

    African Journals Online (AJOL)

    2013-01-01

    Jan 1, 2013 ... applied in raw water pricing structures, provide equity on tar- iffs among surface raw water users, in addition to .... target values for receiving water quality objectives (Fig. 6). The process of deriving quality .... The corresponding parameter could be viewed as a target for future impact mitigation measures.

  15. Surface meteorological conditions at benthic disturbance experiment site - INDEX area during austral winter 1997

    Digital Repository Service at National Institute of Oceanography (India)

    Suryanarayana, A.; Murty, V.S.N.; RameshBabu, V.; Beena, B.S.

    fluxes and net surface heat gain. Maximum sunshine duration was 1 hour/day in June and 30 minutes/day in August. SST decreased from 28.2 degrees C in June to 25.8 degrees C in August. Southeasterly winds of speed 10 m/s during June contributed to a mean...

  16. Kinematics of large scale asymmetric folds and associated smaller ...

    Indian Academy of Sciences (India)

    active-hinge folding (involving lateral migration of active axial surfaces, e.g., Suppe 1983) are invoked to explain finite fold development. Any inference about fold kinematics is based on the analysis of distributions of diagnostic deformation features (Stewart and Alvarez 1991; Fischer et al. Keywords. Kinematic history ...

  17. Refractive index sensing and surface-enhanced Raman spectroscopy using silver–gold layered bimetallic plasmonic crystals

    Directory of Open Access Journals (Sweden)

    Somi Kang

    2017-11-01

    Full Text Available Herein we describe the fabrication and characterization of Ag and Au bimetallic plasmonic crystals as a system that exhibits improved capabilities for quantitative, bulk refractive index (RI sensing and surface-enhanced Raman spectroscopy (SERS as compared to monometallic plasmonic crystals of similar form. The sensing optics, which are bimetallic plasmonic crystals consisting of sequential nanoscale layers of Ag coated by Au, are chemically stable and useful for quantitative, multispectral, refractive index and spectroscopic chemical sensing. Compared to previously reported homometallic devices, the results presented herein illustrate improvements in performance that stem from the distinctive plasmonic features and strong localized electric fields produced by the Ag and Au layers, which are optimized in terms of metal thickness and geometric features. Finite-difference time-domain (FDTD simulations theoretically verify the nature of the multimode plasmonic resonances generated by the devices and allow for a better understanding of the enhancements in multispectral refractive index and SERS-based sensing. Taken together, these results demonstrate a robust and potentially useful new platform for chemical/spectroscopic sensing.

  18. First principles study of elemental mercury (Hg0) adsorption on low index CoMnO3 surfaces

    International Nuclear Information System (INIS)

    Ji, Wenchao; Su, Pingru; Tang, Qingli; Cheng, Zhiwen; Shen, Zhemin; Fan, Maohong

    2017-01-01

    Highlights: • Hg 0 adsorption on low index CoMnO 3 surface was predicted by DFT method. • Hg 0 is adsorbed on the CoMnO 3 surface with chemisorption interaction. • Hg 0 has highest adsorption energy on CoMnO 3 (1 0 0) surface with Hg-Mn mechanism. • The electron transfer of Hg 0 has positive relationship with adsorption energy. - Abstract: The density functional theory (DFT) is applied to predict elemental mercury (Hg 0 ) adsorption on CoMnO 3 surface for the first time. GGA/PBE functional were selected to determine the potential Hg 0 capture mechanisms. The results show that Hg 0 has good affinity with CoMnO 3 surfaces with chemical adsorption. The adsorption energy of Hg 0 -CoMnO 3 (1 0 0), Hg 0 -CoMnO 3 (1 0 1) and Hg 0 -CoMnO 3 (1 1 0) are −85.225, −72.305 and −70.729 kJ/mol, respectively. The Hg-Mn and Hg-Co mechanisms were revealed on low index surfaces. Hg 0 was oxidized to its valence state of 0.236 on Mn site in CoMnO 3 (1 0 0) surface. The Hg-Co interaction mechanism occurred on Hg 0 -CoMnO 3 (1 0 1) and Hg 0 -CoMnO 3 (1 1 0) with 0.209e − and 0.189e − transformation, respectively. The PDOS analysis shows that Hg-Mn interaction depends on the hybridization of Hg(s- and d-orbitals) and Mn (s-, p- and d- orbitals). However, Hg-Co interaction stems from s- and d- orbitals of Hg, which only overlapping with d- and p- orbital of Co. Both the adsorption energy and electronic structure analysis indicated that CoMnO 3 catalyst performed excellent in Hg 0 oxidation. Exposing CoMnO 3 (1 0 0) is most favorable in Hg 0 control, which provides theoretical instruction on certain crystal plane synthesis in experiment.

  19. Coarsely resolved topography along protein folding pathways

    Science.gov (United States)

    Fernández, Ariel; Kostov, Konstantin S.; Berry, R. Stephen

    2000-03-01

    The kinetic data from the coarse representation of polypeptide torsional dynamics described in the preceding paper [Fernandez and Berry, J. Chem. Phys. 112, 5212 (2000), preceding paper] is inverted by using detailed balance to obtain a topographic description of the potential-energy surface (PES) along the dominant folding pathway of the bovine pancreatic trypsin inhibitor (BPTI). The topography is represented as a sequence of minima and effective saddle points. The dominant folding pathway displays an overall monotonic decrease in energy with a large number of staircaselike steps, a clear signature of a good structure-seeker. The diversity and availability of alternative folding pathways is analyzed in terms of the Shannon entropy σ(t) associated with the time-dependent probability distribution over the kinetic ensemble of contact patterns. Several stages in the folding process are evident. Initially misfolded states form and dismantle revealing no definite pattern in the topography and exhibiting high Shannon entropy. Passage down a sequence of staircase steps then leads to the formation of a nativelike intermediate, for which σ(t) is much lower and fairly constant. Finally, the structure of the intermediate is refined to produce the native state of BPTI. We also examine how different levels of tolerance to mismatches of side chain contacts influence the folding kinetics, the topography of the dominant folding pathway, and the Shannon entropy. This analysis yields upper and lower bounds of the frustration tolerance required for the expeditious and robust folding of BPTI.

  20. Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)

    Science.gov (United States)

    Bartl, Nikolaus; Bretis, Bernhard; Grasemann, Bernhard; Lockhart, Duncan

    2010-05-01

    basins (spacing and elongation ratio, circularity index and shape factor) of different parts in the fore and back-limb of the anticlines demonstrate that the basins have a low maturity and that fold growth is still highly active. Most importantly, the results of this geomorphological investigations demonstrates that the subcylindrical folds have developed from several non-cylindrical embryonic folds, which have merged during progressive fold growth.

  1. Photo-induced refractive index and topographical surface gratings in functionalized nanocarbon solid film

    Energy Technology Data Exchange (ETDEWEB)

    McGee, David J.; Ferrie, John; Plachy, Aljoscha [Department of Physics, The College of New Jersey, Ewing, New Jersey 08628 (United States); Joo, Yongho; Choi, Jonathan; Kanimozhi, Catherine; Gopalan, Padma, E-mail: pgopalan@cae.wisc.edu [Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States)

    2015-11-02

    We demonstrate that a single-walled carbon nanotube network noncovalently coupled with a pyrene-modified azo-benzene chromophore functions as a host matrix for a broad range of photo-orientation and photomechanical effects. The chromophore could be efficiently reoriented through repeated trans-cis-trans isomerization under linearly polarized 480 nm light, with Δn of 0.012 at 650 nm and fast characteristic rise-times of 0.12 s. Erasable phase diffraction gratings could also be written, with permanent surface relief gratings forming at sufficiently long irradiation times. In addition to demonstrating a mechanism for photo-manipulation of single-walled carbon nanotubes, these results show photo-orientation of chromophores in azo-functionalized single-walled carbon nanotube networks as a path towards the photosensitive tuning of the electrostatic environment of the nanotube.

  2. Photo-induced refractive index and topographical surface gratings in functionalized nanocarbon solid film

    International Nuclear Information System (INIS)

    McGee, David J.; Ferrie, John; Plachy, Aljoscha; Joo, Yongho; Choi, Jonathan; Kanimozhi, Catherine; Gopalan, Padma

    2015-01-01

    We demonstrate that a single-walled carbon nanotube network noncovalently coupled with a pyrene-modified azo-benzene chromophore functions as a host matrix for a broad range of photo-orientation and photomechanical effects. The chromophore could be efficiently reoriented through repeated trans-cis-trans isomerization under linearly polarized 480 nm light, with Δn of 0.012 at 650 nm and fast characteristic rise-times of 0.12 s. Erasable phase diffraction gratings could also be written, with permanent surface relief gratings forming at sufficiently long irradiation times. In addition to demonstrating a mechanism for photo-manipulation of single-walled carbon nanotubes, these results show photo-orientation of chromophores in azo-functionalized single-walled carbon nanotube networks as a path towards the photosensitive tuning of the electrostatic environment of the nanotube

  3. Photo-induced refractive index and topographical surface gratings in functionalized nanocarbon solid film

    Science.gov (United States)

    McGee, David J.; Ferrie, John; Plachy, Aljoscha; Joo, Yongho; Choi, Jonathan; Kanimozhi, Catherine; Gopalan, Padma

    2015-11-01

    We demonstrate that a single-walled carbon nanotube network noncovalently coupled with a pyrene-modified azo-benzene chromophore functions as a host matrix for a broad range of photo-orientation and photomechanical effects. The chromophore could be efficiently reoriented through repeated trans-cis-trans isomerization under linearly polarized 480 nm light, with Δn of 0.012 at 650 nm and fast characteristic rise-times of 0.12 s. Erasable phase diffraction gratings could also be written, with permanent surface relief gratings forming at sufficiently long irradiation times. In addition to demonstrating a mechanism for photo-manipulation of single-walled carbon nanotubes, these results show photo-orientation of chromophores in azo-functionalized single-walled carbon nanotube networks as a path towards the photosensitive tuning of the electrostatic environment of the nanotube.

  4. Index of stations: surface-water data-collection network of Texas, September 1995

    Science.gov (United States)

    Gandara, S.C.; Jones, R.E.

    1996-01-01

    As of September 30, 1995, the surface-water data-collection network of Texas (table 1) included 305 continuous-recording streamflow stations (D), 28 gageheight record only stations (G), 23 crest-stage partialrecord stations (C), 42 flood-hydrograph partial-record stations (H), 33 low-flow partial-record stations (L), 19 continuous-recording temperature and conductivity stations (M2), 5 continuous-recording temperature, conductivity, and dissolved oxygen stations (M3), 17 continuous-recording temperature, conductivity, dissolved oxygen, and pH stations (M4), 6 daily chemicalquality stations (Q), 143 periodic chemical-quality stations (Qp), 20 reservoir/lake surveys for water quality (Qs), and 64 continuous or daily reservoir-content stations (R). Plate 1 identifies the major river basins in Texas and shows the location of the stations listed in table 1.

  5. Defining an Abrasion Index for Lunar Surface Systems as a Function of Dust Interaction Modes and Variable Concentration Zones

    Science.gov (United States)

    Kobrick, Ryan L.; Klaus, David M.; Street, Kenneth W., Jr.

    2010-01-01

    Unexpected issues were encountered during the Apollo era of lunar exploration due to detrimental abrasion of materials upon exposure to the fine-grained, irregular shaped dust on the surface of the Moon. For critical design features involving contact with the lunar surface and for astronaut safety concerns, operational concepts and dust tolerance must be considered in the early phases of mission planning. To systematically define material selection criteria, dust interaction can be characterized by two-body or three-body abrasion testing, and subcategorically by physical interactions of compression, rolling, sliding and bending representing specific applications within the system. Two-body abrasion occurs when a single particle or asperity slides across a given surface removing or displacing material. Three-body abrasion occurs when multiple particles interact with a solid surface, or in between two surfaces, allowing the abrasives to freely rotate and interact with the material(s), leading to removal or displacement of mass. Different modes of interaction are described in this paper along with corresponding types of tests that can be utilized to evaluate each configuration. In addition to differential modes of abrasion, variable concentrations of dust in different zones can also be considered for a given system design and operational protocol. These zones include: (1) outside the habitat where extensive dust exposure occurs, (2) in a transitional zone such as an airlock or suitport, and (3) inside the habitat or spacesuit with a low particle count. These zones can be used to help define dust interaction frequencies, and corresponding risks to the systems and/or crew can be addressed by appropriate mitigation strategies. An abrasion index is introduced that includes the level of risk, R, the hardness of the mineralogy, H, the severity of the abrasion mode, S, and the frequency of particle interactions, F.

  6. A 30-Year Multi-Sensor Vegetation Index and Land Surface Phenology Data Record: Methods Challenges and Potentials

    Science.gov (United States)

    Didan, K.; Barreto-munoz, A.; Miura, T.; Tsend-Ayush, J.

    2013-12-01

    During the last five years the Vegetation Index and Phenology Lab. (vip.arizona.edu) embarked on an effort to process a global multi-sensor Earth Science Data Record of NDVI, EVI2, and land surface Phenology. Data from AVHRR, MODIS, and SPOT-VGT, covering the period 1981 to present, were processed into a seamless and sensor independent record using a suite of community algorithms for data filtering, across-sensor continuity, Vegetation Index (NDVI and EVI2), land surface Phenology, and spatial and temporal gap filling. Currently at Version 3.0 these ESDRs are suitable for the study of land surface vegetation dynamics, long term change and trends, anomalies, and can support various ecosystem and climate modeling efforts by providing key parameters. While adapting the various algorithms to processing this new data record many challenges emerged, ranging from excessive missing and poor quality data to complex and temporally dependent divergence across the various sensors making continuity quite difficult. The first step to addressing these challenges was the adoption of very strict and low tolerance to noise data filters, where the intrinsic input data quality is used along with the long term expected dynamic range to screen for outliers and poor quality. A sophisticated and explicit per-pixel and seasonally dependent across-sensor translation algorithm was developed to address the continuity more properly. To generate the land surface phenology we adapted various community algorithms to work with and take advantage of this new record. Both the standard MODIS Vegetation dynamic algorithm and an in-house homogeneous cluster algorithm were applied to the data. We've also completed a spatially and temporally explicit error and uncertainty characterization of this record. Results indicate a VI error in the range of 5-10% VI units and a 5-40 days error in the date dependent phenology parameters, with an average error of 15 days. This VIP record accounts now for more than

  7. Effects of vegetation types on soil moisture estimation from the normalized land surface temperature versus vegetation index space

    Science.gov (United States)

    Zhang, Dianjun; Zhou, Guoqing

    2015-12-01

    Soil moisture (SM) is a key variable that has been widely used in many environmental studies. Land surface temperature versus vegetation index (LST-VI) space becomes a common way to estimate SM in optical remote sensing applications. Normalized LST-VI space is established by the normalized LST and VI to obtain the comparable SM in Zhang et al. (Validation of a practical normalized soil moisture model with in situ measurements in humid and semiarid regions [J]. International Journal of Remote Sensing, DOI: 10.1080/01431161.2015.1055610). The boundary conditions in the study were set to limit the point A (the driest bare soil) and B (the wettest bare soil) for surface energy closure. However, no limitation was installed for point D (the full vegetation cover). In this paper, many vegetation types are simulated by the land surface model - Noah LSM 3.2 to analyze the effects on soil moisture estimation, such as crop, grass and mixed forest. The locations of point D are changed with vegetation types. The normalized LST of point D for forest is much lower than crop and grass. The location of point D is basically unchanged for crop and grass.

  8. The Complexity of Folding Self-Folding Origami

    Directory of Open Access Journals (Sweden)

    Menachem Stern

    2017-12-01

    Full Text Available Why is it difficult to refold a previously folded sheet of paper? We show that even crease patterns with only one designed folding motion inevitably contain an exponential number of “distractor” folding branches accessible from a bifurcation at the flat state. Consequently, refolding a sheet requires finding the ground state in a glassy energy landscape with an exponential number of other attractors of higher energy, much like in models of protein folding (Levinthal’s paradox and other NP-hard satisfiability (SAT problems. As in these problems, we find that refolding a sheet requires actuation at multiple carefully chosen creases. We show that seeding successful folding in this way can be understood in terms of subpatterns that fold when cut out (“folding islands”. Besides providing guidelines for the placement of active hinges in origami applications, our results point to fundamental limits on the programmability of energy landscapes in sheets.

  9. The Complexity of Folding Self-Folding Origami

    Science.gov (United States)

    Stern, Menachem; Pinson, Matthew B.; Murugan, Arvind

    2017-10-01

    Why is it difficult to refold a previously folded sheet of paper? We show that even crease patterns with only one designed folding motion inevitably contain an exponential number of "distractor" folding branches accessible from a bifurcation at the flat state. Consequently, refolding a sheet requires finding the ground state in a glassy energy landscape with an exponential number of other attractors of higher energy, much like in models of protein folding (Levinthal's paradox) and other NP-hard satisfiability (SAT) problems. As in these problems, we find that refolding a sheet requires actuation at multiple carefully chosen creases. We show that seeding successful folding in this way can be understood in terms of subpatterns that fold when cut out ("folding islands"). Besides providing guidelines for the placement of active hinges in origami applications, our results point to fundamental limits on the programmability of energy landscapes in sheets.

  10. How the genome folds

    Science.gov (United States)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  11. Index of stations: surface-water data-collection network of Texas, September 1999

    Science.gov (United States)

    Gandara, Susan C.; Barbie, Dana L.

    2001-01-01

    As of September 30, 1999, the surface-water data-collection network of Texas (table 1) included 321 continuous-record streamflow stations (D), 20 continuous-record gage-height only stations (G), 24 crest-stage partial-record stations (C), 40 floodhydrograph partial-record stations (H), 25 low-flow partial-record stations (L), 1 continuous-record temperature station (M1), 25 continuous-record temperature and specific conductance stations (M2), 17 continuous-record temperature, specific conductance, dissolved oxygen, and pH stations (M4), 4 daily water-quality stations (Qd), 115 periodic water-quality stations (Qp), 17 reservoir/lake surveys for water quality stations (Qs), 85 continuous or daily reservoircontent stations (R), and 10 daily precipitation stations (Pd). Plate 1 identifies the major river basins in Texas and shows the location of the stations listed in table 1. Table 1 shows the station number and name, latitude and longitude, type of station, and office responsible for the collection of the data and maintenance of the record. An 8-digit permanent numerical designation for all gaging stations has been adopted on a nationwide basis; stations are numbered and listed in downstream order. In the downstream direction along the main stem, all stations on a tributary entering between two main-stem stations are listed between these two stations. A similar order is followed in listing stations by first rank, second rank, and other ranks of tributaries. The rank of any tributary, with respect to the stream to which it is an immediate tributary, is indicated by an indention in the table. Each indention represents one rank. This downstream order and system of indention shows which gaging stations are on tributaries between any two stations on a main stem and the rank of the tributary on which each gaging station is situated.

  12. Assessment of metal contamination in estuarine surface sediments from Dongying City, China: Use of a modified ecological risk index.

    Science.gov (United States)

    Liu, Qunqun; Wang, Feifei; Meng, Fanping; Jiang, Lei; Li, Guangjing; Zhou, Rongguang

    2018-01-01

    Surface sediments and clam Meretrix meretrix were collected from a northern estuarine region in Dongying City, China. Sediments were analysed for heavy metals (Hg, As, Cd, Cr, Cu, Pb, and Zn) and the clams were tested for metallothioneins (MTs) and lysosomal membrane stability (LMS). The heavy metal total concentrations decreased in the order of Cr>Zn>Cu>Pb>As>Cd>Hg. The results of Bureau Communautaire de Référence (BCR) sequential extraction of heavy metals showed that the geochemical speciation of all heavy metals was dominated by residual fraction. According to the responses of biomarkers in M. meretrix, the modified potential ecological risk index (PERI-B) can more accurately reflect heavy metals pollution. PERI-B showed all sediment samples have low or moderate risk, except at site S10 (considerable risk), and the main contribution of ecological risk heavy metals were Cd and Hg. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Development of a 3-D urbanization index using digital terrain models for surface urban heat island effects

    Science.gov (United States)

    Wu, Chih-Da; Lung, Shih-Chun Candice; Jan, Jihn-Fa

    2013-07-01

    This study assesses surface urban heat island (SUHI) effects during heat waves in subtropical areas. Two cities in northern Taiwan, Taipei metropolis and its adjacent medium-sized city, Yilan, were selected for this empirical study. Daytime and night time surface temperature and SUHI intensity of both cities in five heat wave cases were obtained from MODIS Land-Surface Temperature (LST) and compared. In order to assess SUHI in finer spatial scale, an innovated three-dimensional Urbanization Index (3DUI) with a 5-m spatial resolution was developed to quantify urbanization from a 3-D perspective using Digital Terrain Models (DTMs). The correlation between 3DUI and surface temperatures were also assessed. The results obtained showed that the highest SUHI intensity in daytime was 10.2 °C in Taipei and 7.5 °C in Yilan. The SUHI intensity was also higher than that in non-heat-wave days (about 5 °C) in Taipei. The difference in SUHI intensity of both cities could be as small as only 1.0 °C, suggesting that SUHI intensity was enhanced in both large and medium-sized cities during heat waves. Moreover, the surface temperatures of rural areas in Taipei and Yilan were elevated in the intense heat wave cases, suggesting that the SUHI may reach a plateau when the heat waves get stronger and last longer. In addition, the correlation coefficient between 3DUI and surface temperature was greater than 0.6. The innovative 3DUI can be employed to assess the spatial variation of temperatures and SUHI intensity in much finer spatial resolutions than measurements obtained from remote sensing and weather stations. In summary, the empirical results demonstrated intensified SUHI in large and medium-sized cities in subtropical areas during heat waves which could result in heat stress risks of residents. The innovative 3DUI can be employed to identify vulnerable areas in fine spatial resolutions for formulation of heat wave adaptation strategies.

  14. RNA folding: structure prediction, folding kinetics and ion electrostatics.

    Science.gov (United States)

    Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

    2015-01-01

    Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

  15. The review on tessellation origami inspired folded structure

    Science.gov (United States)

    Chu, Chai Chen; Keong, Choong Kok

    2017-10-01

    Existence of folds enhances the load carrying capacity of a folded structure which makes it suitable to be used for application where large open space is required such as large span roof structures and façade. Folded structure is closely related to origami especially the tessellation origami. Tessellation origami provides a folded configuration with facetted surface as a result from repeated folding pattern. Besides that, tessellation origami has flexible folding mechanism that produced a variety of 3-dimensional folded configurations. Despite the direct relationship between fold in origami and folded structure, the idea of origami inspired folded structure is not properly reviewed in the relevant engineering field. Hence, this paper aims to present the current studies from related discipline which has direct relation with application of tessellation origami in folded structure. First, tessellation origami is properly introduced and defined. Then, the review covers the topic on the origami tessellation design suitable for folded structure, its modeling and simulation method, and existing studies and applications of origami as folded structure is presented. The paper also includes the discussion on the current issues related to each topic.

  16. Use of weather research and forecasting model outputs to obtain near-surface refractive index structure constant over the ocean.

    Science.gov (United States)

    Qing, Chun; Wu, Xiaoqing; Li, Xuebin; Zhu, Wenyue; Qiao, Chunhong; Rao, Ruizhong; Mei, Haipin

    2016-06-13

    The methods to obtain atmospheric refractive index structure constant (Cn2) by instrument measurement are limited spatially and temporally and they are more difficult and expensive over the ocean. It is useful to forecast Cn2 effectively from Weather Research and Forecasting Model (WRF) outputs. This paper introduces a method that WRF Model is used to forecast the routine meteorological parameters firstly, and then Cn2 is calculated based on these parameters by the Bulk model from the Monin-Obukhov similarity theory (MOST) over the ocean near-surface. The corresponding Cn2 values measured by the micro-thermometer which is placed on the ship are compared with the ones forecasted by WRF model to determine how this method performs. The result shows that the forecasted Cn2 is consistent with the measured Cn2 in trend and the order of magnitude as a whole, as well as the correlation coefficient is up to 77.57%. This method can forecast some essential aspects of Cn2 and almost always captures the correct magnitude of Cn2, which experiences fluctuations of two orders of magnitude. Thus, it seems to be a feasible and meaningful method that using WRF model to forecast near-surface Cn2 value over the ocean.

  17. Leaf Area Index Estimation in Vineyards from Uav Hyperspectral Data, 2d Image Mosaics and 3d Canopy Surface Models

    Science.gov (United States)

    Kalisperakis, I.; Stentoumis, Ch.; Grammatikopoulos, L.; Karantzalos, K.

    2015-08-01

    The indirect estimation of leaf area index (LAI) in large spatial scales is crucial for several environmental and agricultural applications. To this end, in this paper, we compare and evaluate LAI estimation in vineyards from different UAV imaging datasets. In particular, canopy levels were estimated from i.e., (i) hyperspectral data, (ii) 2D RGB orthophotomosaics and (iii) 3D crop surface models. The computed canopy levels have been used to establish relationships with the measured LAI (ground truth) from several vines in Nemea, Greece. The overall evaluation indicated that the estimated canopy levels were correlated (r2 > 73%) with the in-situ, ground truth LAI measurements. As expected the lowest correlations were derived from the calculated greenness levels from the 2D RGB orthomosaics. The highest correlation rates were established with the hyperspectral canopy greenness and the 3D canopy surface models. For the later the accurate detection of canopy, soil and other materials in between the vine rows is required. All approaches tend to overestimate LAI in cases with sparse, weak, unhealthy plants and canopy.

  18. Two-dimensional echocardiographic right ventricle measurements adjusted to body mass index and surface area in a normal population.

    Science.gov (United States)

    Eslami, Masood; Larti, Farnoush; Larry, Mehrdad; Molaee, Parisa; Badkoobeh, Roya Sattarzadeh; Tavoosi, Anahita; Safari, Saeed; Parsa, Amir Farhang Zand

    2017-05-01

    To determine reference echocardiographic values in a normal population and assess their correlation with body mass index (BMI) and body surface area. An expert cardiologist performed two-dimensional echocardiography with triplicate right ventricle (RV) size measurements in 80 subjects with normal heart condition. Results were correlated with anthropometric data. Base-to-apex length in four-chamber view (RVD3) and above-pulmonic valve in short-axis view in males, as well as mid-RV diameter in standard four-chamber view (RVD), basal RV diameter, and mid RV diameter in RV-focused four-chamber view in females, were significantly correlated with BMI. All RV variables were significantly correlated with BMI in 20-30-year-old subjects. All RV variables except RVD3 and above-aortic valve in short-axis view (proximal) were significantly correlated with BMI in 35-55-year-old subjects. All RV parameters were significantly correlated with body surface area, except for RVD and in 20-35-year-old subjects. RV echocardiographic values must be adjusted to anthropometric characteristics for proper diagnosis and management of cardiac disorders. © 2016 Wiley Periodicals, Inc. J Clin Ultrasound 45:204-210, 2017. © 2016 Wiley Periodicals, Inc.

  19. Evolutionary optimization of protein folding.

    Directory of Open Access Journals (Sweden)

    Cédric Debès

    Full Text Available Nature has shaped the make up of proteins since their appearance, [Formula: see text]3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last [Formula: see text]1.5 billion years that began during the "big bang" of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions.

  20. Loss of surface horizon of an irrigated soil detected by radiometric images of normalized difference vegetation index.

    Science.gov (United States)

    Fabian Sallesses, Leonardo; Aparicio, Virginia Carolina; Costa, Jose Luis

    2017-04-01

    The use of the soil in the Humid Pampa of Argentina has changed since the mid-1990s from agricultural-livestock production (that included pastures with direct grazing) to a purely agricultural production. Also, in recent years the area under irrigation by central pivot has been increased to 150%. The waters used for irrigation are sodium carbonates. The combination of irrigation and rain increases the sodium absorption ratio of soil (SARs), consequently raising the clay dispersion and reducing infiltration. This implies an increased risk of soil loss. A reduction in the development of white clover crop (Trifolium repens L.) was observed at an irrigation plot during 2015 campaign. The clover was planted in order to reduce the impact of two maize (Zea mays L.) campaigns under irrigation, which had increased soil SAR and deteriorated soil structure. SPOT-5 radiometric normalized difference vegetation index (NDVI) images were used to determine two zones of high and low production. In each zone, four random points were selected for further geo-referenced field sampling. Two geo-referenced measures of effective depth and surface soil sampling were carried out in each point. Texture of soil samples was determined by Pipette Method of Sedimentation Analysis. Data exploratory analysis showed that low production zone had a media effective depth = 80 cm and silty clay loam texture, while high production zone had a media effective depth > 140 cm and silt loam texture. The texture class of the low production zone did not correspond to prior soil studies carried out by the INTA (National Institute of Agricultural Technology), which showed that those soil textures were silt loam at surface and silty clay loam at sub-surface. The loss of the A horizon is proposed as a possible explanation, but further research is required. Besides, the need of a soil cartography actualization, which integrates new satellite imaging technologies and geo-referenced measurements with soil sensors is

  1. Kinetics of Peptide Folding in Lipid Membranes

    Science.gov (United States)

    Oh, Kwang-Im; Smith-Dupont, Kathryn B.; Markiewicz, Beatrice N.; Gai, Feng

    2015-01-01

    Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments. PMID:25808575

  2. The reliability of three psoriasis assessment tools: Psoriasis area and severity index, body surface area and physician global assessment.

    Science.gov (United States)

    Bożek, Agnieszka; Reich, Adam

    2017-08-01

    A wide variety of psoriasis assessment tools have been proposed to evaluate the severity of psoriasis in clinical trials and daily practice. The most frequently used clinical instrument is the psoriasis area and severity index (PASI); however, none of the currently published severity scores used for psoriasis meets all the validation criteria required for an ideal score. The aim of this study was to compare and assess the reliability of 3 commonly used assessment instruments for psoriasis severity: the psoriasis area and severity index (PASI), body surface area (BSA) and physician global assessment (PGA). On the scoring day, 10 trained dermatologists evaluated 9 adult patients with plaque-type psoriasis using the PASI, BSA and PGA. All the subjects were assessed twice by each physician. Correlations between the assessments were analyzed using the Pearson correlation coefficient. Intra-class correlation coefficient (ICC) was calculated to analyze intra-rater reliability, and the coefficient of variation (CV) was used to assess inter-rater variability. Significant correlations were observed among the 3 scales in both assessments. In all 3 scales the ICCs were > 0.75, indicating high intra-rater reliability. The highest ICC was for the BSA (0.96) and the lowest one for the PGA (0.87). The CV for the PGA and PASI were 29.3 and 36.9, respectively, indicating moderate inter-rater variability. The CV for the BSA was 57.1, indicating high inter-rater variability. Comparing the PASI, PGA and BSA, it was shown that the PGA had the highest inter-rater reliability, whereas the BSA had the highest intra-rater reliability. The PASI showed intermediate values in terms of interand intra-rater reliability. None of the 3 assessment instruments showed a significant advantage over the other. A reliable assessment of psoriasis severity requires the use of several independent evaluations simultaneously.

  3. Pavement Condition Assessment Using IRI from Roadroid and Surface Distress Index Method on National Road in Sumenep Regency

    Science.gov (United States)

    Arianto, T.; Suprapto, M.; Syafi’i

    2018-03-01

    The pavement condition will decrease due to the influence of traffic and environment, so that the maintenance effort is needed to maintain the road condition during the service period. In order to carry out road maintenance activities right on target, there needs to be a plan based on accurate pavement condition data. Road roughness is the most commonly used condition parameter in evaluating pavement conditions objectively because road roughness data is relatively easy to obtain, well correlated with vehicle operating costs and the most relevant parameter in road functional performance measurement. The Roadroid is an Android-based application that measures road roughness by using vibration sensors on a smartphone so it is possible to get an International Roughness Index (IRI) value as an indicator of pavement conditions more easily and efficiently. Besides based on road roughness, pavement condition evaluation can also be done visually by using Surface Distress Index (SDI) method that uses the total crack area parameters, average crack width, total number of potholes and the average depth of rutting. This study attempts to assess the condition of Jenderal Sudirman-Kalianget road by combining IRI Roadroid value and SDI value which will be used as the basis to determine the required road maintenance. This road segment is one of the national strategic road connecting the center of Sumenep regency with the Kalianget harbor. Based on IRI measurement and SDI calculation, the pavement condition of Jenderal Sudirman-Kalianget road can be described 4.2 kilometers (37.17%) were good and 2.3 kilometers (20.35%) were fair that need routine maintenance. While 2.1 kilometers (18.58%) were bad and 2.7 kilometers (23.89%) were poor that need periodical maintenance and reconstruction.

  4. Equi-Gaussian curvature folding

    Indian Academy of Sciences (India)

    have the same equi-Gaussian curvature 1/a2, where a is the radius of the sphere. Now let f : S2 → Pn be a cellular folding. Then we have the following possibilities: Firstly, there are no cellular foldings f : S2 → Pn, for any n > 3 [2]. Secondly, any cellular folding f : S2 → P3 for which Gf forms a regular graph is equivalent to ...

  5. Teaching computers to fold proteins

    DEFF Research Database (Denmark)

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages...

  6. Simulating the Refractive Index Structure Constant ({C}_{n}^{2}) in the Surface Layer at Antarctica with a Mesoscale Model

    Science.gov (United States)

    Qing, Chun; Wu, Xiaoqing; Li, Xuebin; Tian, Qiguo; Liu, Dong; Rao, Ruizhong; Zhu, Wenyue

    2018-01-01

    In this paper, we introduce an approach wherein the Weather Research and Forecasting (WRF) model is coupled with the bulk aerodynamic method to estimate the surface layer refractive index structure constant (C n 2) above Taishan Station in Antarctica. First, we use the measured meteorological parameters to estimate C n 2 using the bulk aerodynamic method, and second, we use the WRF model output parameters to estimate C n 2 using the bulk aerodynamic method. Finally, the corresponding C n 2 values from the micro-thermometer are compared with the C n 2 values estimated using the WRF model coupled with the bulk aerodynamic method. We analyzed the statistical operators—the bias, root mean square error (RMSE), bias-corrected RMSE (σ), and correlation coefficient (R xy )—in a 20 day data set to assess how this approach performs. In addition, we employ contingency tables to investigate the estimation quality of this approach, which provides complementary key information with respect to the bias, RMSE, σ, and R xy . The quantitative results are encouraging and permit us to confirm the fine performance of this approach. The main conclusions of this study tell us that this approach provides a positive impact on optimizing the observing time in astronomical applications and provides complementary key information for potential astronomical sites.

  7. Dynamics of folding: Impact of fault bend folds on earthquake cycles

    Science.gov (United States)

    Sathiakumar, S.; Barbot, S.; Hubbard, J.

    2017-12-01

    Earthquakes in subduction zones and subaerial convergent margins are some of the largest in the world. So far, forecasts of future earthquakes have primarily relied on assessing past earthquakes to look for seismic gaps and slip deficits. However, the roles of fault geometry and off-fault plasticity are typically overlooked. We use structural geology (fault-bend folding theory) to inform fault modeling in order to better understand how deformation is accommodated on the geological time scale and through the earthquake cycle. Fault bends in megathrusts, like those proposed for the Nepal Himalaya, will induce folding of the upper plate. This introduces changes in the slip rate on different fault segments, and therefore on the loading rate at the plate interface, profoundly affecting the pattern of earthquake cycles. We develop numerical simulations of slip evolution under rate-and-state friction and show that this effect introduces segmentation of the earthquake cycle. In crustal dynamics, it is challenging to describe the dynamics of fault-bend folds, because the deformation is accommodated by small amounts of slip parallel to bedding planes ("flexural slip"), localized on axial surface, i.e. folding axes pinned to fault bends. We use dislocation theory to describe the dynamics of folding along these axial surfaces, using analytic solutions that provide displacement and stress kernels to simulate the temporal evolution of folding and assess the effects of folding on earthquake cycles. Studies of the 2015 Gorkha earthquake, Nepal, have shown that fault geometry can affect earthquake segmentation. Here, we show that in addition to the fault geometry, the actual geology of the rocks in the hanging wall of the fault also affect critical parameters, including the loading rate on parts of the fault, based on fault-bend folding theory. Because loading velocity controls the recurrence time of earthquakes, these two effects together are likely to have a strong impact on the

  8. TBI server: a web server for predicting ion effects in RNA folding.

    Directory of Open Access Journals (Sweden)

    Yuhong Zhu

    Full Text Available Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²⁺, are essential for RNA tertiary structure formation. These ions can possibly become strongly correlated in the close vicinity of RNA surface. Most of the currently available software packages, which have widespread success in predicting ion effects in biomolecular systems, however, do not explicitly account for the ion correlation effect. Therefore, it is important to develop a software package/web server for the prediction of ion electrostatics in RNA folding by including ion correlation effects.The TBI web server http://rna.physics.missouri.edu/tbi_index.html provides predictions for the total electrostatic free energy, the different free energy components, and the mean number and the most probable distributions of the bound ions. A novel feature of the TBI server is its ability to account for ion correlation and ion distribution fluctuation effects.By accounting for the ion correlation and fluctuation effects, the TBI server is a unique online tool for computing ion-mediated electrostatic properties for given RNA structures. The results can provide important data for in-depth analysis for ion effects in RNA folding including the ion-dependence of folding stability, ion uptake in the folding process, and the interplay between the different energetic components.

  9. TBI server: a web server for predicting ion effects in RNA folding.

    Science.gov (United States)

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

    2015-01-01

    Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²⁺, are essential for RNA tertiary structure formation. These ions can possibly become strongly correlated in the close vicinity of RNA surface. Most of the currently available software packages, which have widespread success in predicting ion effects in biomolecular systems, however, do not explicitly account for the ion correlation effect. Therefore, it is important to develop a software package/web server for the prediction of ion electrostatics in RNA folding by including ion correlation effects. The TBI web server http://rna.physics.missouri.edu/tbi_index.html provides predictions for the total electrostatic free energy, the different free energy components, and the mean number and the most probable distributions of the bound ions. A novel feature of the TBI server is its ability to account for ion correlation and ion distribution fluctuation effects. By accounting for the ion correlation and fluctuation effects, the TBI server is a unique online tool for computing ion-mediated electrostatic properties for given RNA structures. The results can provide important data for in-depth analysis for ion effects in RNA folding including the ion-dependence of folding stability, ion uptake in the folding process, and the interplay between the different energetic components.

  10. VIS and NIR land surface albedo sensitivity of the Ent Terrestrial Biosphere Model to forcing leaf area index

    Science.gov (United States)

    Montes, C.; Kiang, N. Y.; Ni-Meister, W.; Yang, W.; Schaaf, C.; Aleinov, I. D.; Jonas, J.; Zhao, F. A.; Yao, T.; Wang, Z.; Sun, Q.; Carrer, D.

    2016-12-01

    Land surface albedo is a major controlling factor in vegetation-atmosphere transfers, modifying the components of the energy budget, the ecosystem productivity and patterns of regional and global climate. General Circulation Models (GCMs) are coupled to Dynamic Global Vegetation Models (DGVMs) to solve vegetation albedo by using simple schemes prescribing albedo based on vegetation classification, and approximations of canopy radiation transport for multiple plant functional types (PFTs). In this work, we aim at evaluating the sensitivity of the NASA Ent Terrestrial Biosphere Model (TBM), a demographic DGVM coupled to the NASA Goddard Institute for Space Studies (GISS) GCM, in estimating VIS and NIR surface albedo by using variable forcing leaf area index (LAI). The Ent TBM utilizes a new Global Vegetation Structure Dataset (GVSD) to account for geographically varying vegetation tree heights and densities, as boundary conditions to the gap-probability based Analytical Clumped Two-Stream (ACTS) canopy radiative transfer scheme (Ni-Meister et al., 2010). Land surface and vegetation characteristics for the Ent GVSD are obtained from a number of earth observation platforms and algorithms, including the Moderate Resolution Imaging Spectroradiometer (MODIS) land cover and plant functional types (PFTs) (Friedl et al., 2010), soil albedo derived from MODIS (Carrer et al., 2014), and vegetation height from the Geoscience Laser Altimeter System (GLAS) on board ICESat (Ice, Cloud, and land Elevation Satellite) (Simard et al., 2011; Tang et al., 2014). Three LAI products are used as input to ACTS/Ent TBM: MODIS MOD15A2H product (Yang et al., 2006), Beijing Normal University LAI (Yuan et al., 2011), and Global Data Sets of Vegetation (LAI3g) (Zhu et al. 2013). The sensitivity of the Ent TBM VIS and NIR albedo to the three LAI products is assessed, compared against the previous GISS GCM vegetation classification and prescribed Lambertian albedoes (Matthews, 1984), and against

  11. RELEVANCE OF OCULAR SURFACE DISEASE INDEX (OSDI QUESTIONNAIRE IN MINIMISING OPTIC NERVE DAMAGE AMONG GLAUCOMA POPULATION IN THE COMMUNITY

    Directory of Open Access Journals (Sweden)

    Subhra Sarkar

    2017-11-01

    Full Text Available BACKGROUND Glaucoma is one of the leading causes of blindness worldwide. Majority of these patients need lifelong medical therapy in the form of topical medications. Most of these medications contain preservatives, which have deleterious effects on eyes of patients causing Ocular Surface Disorder (OSD. When left undiagnosed, OSD can lead to noncompliance further deteriorating the situation and causing progression of glaucoma. Dry eye symptoms in glaucoma patients under topical medications can be ascertained with a simple 12-query OSDI (ocular surface disease index questionnaire. But, it needs to be assessed whether this can be relied on to establish a clinical diagnosis. The aim of the study is to correlate subjective OSDI scores with objective clinical findings in glaucoma patients using topical medications. MATERIALS AND METHODS 110 patients of primary open-angle glaucoma on antiglaucoma medications for >3 months underwent OSDI scoring and three clinical tests, Tear Film Break-Up Time (TBUT, Schirmer-1 Test and Lissamine-Green (LG staining of ocular surface. A clinical diagnosis of dry eye was considered if either eye showed TBUT <10 seconds or on Schirmer-1 test <10 mm or positive LG staining. Statistical analysis was done to know the correlation between OSDI scores and clinical diagnosis. Setting and Design- Prospective, single visit, comparative study carried in a tertiary care hospital. RESULTS 44 patients (40% had OSDI scores ≥13 indicating dry eye disease. 54 patients (49.1% had TBUT <10 seconds, 41 patients (37.27% had Schirmer-1 test <10 mm and 18 patients (16.36% had positive Lissamine-Green staining. So, dry eye was diagnosed in 54 patients (49.1%. We found that OSDI scores have a sensitivity of 81.48% and specificity of 100% in diagnosing dry eye. On Chi-square test, OSDI scores and diagnosis of dry eye have statistically significant correlation (p value <0.0001. CONCLUSION In our study, OSDI scores significantly correlates with

  12. A framework for consistent estimation of leaf area index, fraction of absorbed photosynthetically active radiation, and surface albedo from MODIS time-series data

    DEFF Research Database (Denmark)

    Xiao, Zhiqiang; Liang, Shunlin; Wang, Jindi

    2015-01-01

    model and the MODIS surface reflectance data. The estimated LAI values were then input into the ACRM to calculate the surface albedo and the fraction of absorbed photosynthetically active radiation (FAPAR). For snow-covered areas, the surface albedo was calculated as the underlying vegetation canopy...... albedo plus the weighted distance between the underlying vegetation canopy albedo and the albedo over deep snow. The LAI/FAPAR and surface albedo values estimated using this framework were compared with MODIS collection 5 eight-day 1-km LAI/FAPAR products (MOD15A2) and 500-m surface albedo product (MCD43......-series MODerate Resolution Imaging Spectroradiometer (MODIS) surface reflectance data. If the reflectance data showed snow-free areas, an ensemble Kalman filter (EnKF) technique was used to estimate leaf area index (LAI) for a two-layer canopy reflectance model (ACRM) by combining predictions from a phenology...

  13. [Is body surface area (BSA) suitable for indexing renal and dialysis clearances and other physiological parameters? A theoretical approach and a critical analysis (Part 2)].

    Science.gov (United States)

    Ruggieri, G

    2009-01-01

    Many parameters of biological functions, interesting different branches of medicine, have to be indexed by the same value for each other comparison between single individuals or between-within groups.Body Surface Area (BSA) and 1.73 m2 reference value are probably the most used tools for indexation, but a growing number of scientific papers emphasize the risk of under or over estimates of data by BSA indexation in overweight-obese or on the contrary underweight individuals. This study has been planned to evaluate such a problem: a) by a theoretical approach, indexing to 1.73 m2 the creatinine clearance(CtCl) in an ideal population, and b) analysing and debating the doubts and problems about the indexation by BSA in many fields, the possibilities of indexation by other methods, or to use BSA with different approach, to reduce the risk of bias, evaluating the possibility of this target in a real population of 45 men and 84 women undergoing Peritoneal Dialysis (PD) - II - The feasibility to agree to an identical value of normal or abnormal renal function for every age or, on the contrary, to have a normal range for each age, are analysed and discussed.About BSA as indexing tool, it is pointed out: a) the lack of significative correlation between BSA and GFR and other parameters b) the increasing gap during years between 1.73 m2 BSA and the average BSA.

  14. [Is body surface area (BSA) suitable for indexing renal and dialysis clearances and other physiological parameters? A theoretical approach and a critical analysis (Part 1)].

    Science.gov (United States)

    Ruggieri, G

    2009-01-01

    Many parameters of biological functions, interesting different branches of medicine, have to be indexed by the same value for each other comparison between single individuals or between-within groups. Body Surface Area (BSA) and 1.73 m2 reference value are probably the most used tools for indexation, but a growing number of scientific papers emphasize the risk of under or over estimates of data by BSA indexation in overweight--obese or on the contrary underweight individuals. This study has been planned to evaluate this problem: a) by a theoretical approach, indexing to 1.73 m2 the creatinine clearance (CtCl) in an ideal population and b) analysing and debating the doubts and problems about the indexation by BSA in many fields, the possibilities of indexation by other methods, or to use BSA with different approach, to reduce the risk of bias, evaluating the possibility of this target in a real population of 45 men and 84 women undergoing Peritoneal Dialysis (PD). The effects of indexing 1.73 m2, according different weights on the CtCl of the ideal population and on the values of BSA estimation according different formulae. Results, methods, and the problems due to abnormal fluctuation of weight compared to normal range of standard value according height are analyzed and discussed.

  15. Self-folding graphene-polymer bilayers

    International Nuclear Information System (INIS)

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.

    2015-01-01

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting

  16. On the Folded Normal Distribution

    Directory of Open Access Journals (Sweden)

    Michail Tsagris

    2014-02-01

    Full Text Available The characteristic function of the folded normal distribution and its moment function are derived. The entropy of the folded normal distribution and the Kullback–Leibler from the normal and half normal distributions are approximated using Taylor series. The accuracy of the results are also assessed using different criteria. The maximum likelihood estimates and confidence intervals for the parameters are obtained using the asymptotic theory and bootstrap method. The coverage of the confidence intervals is also examined.

  17. PREFACE Protein folding: lessons learned and new frontiers Protein folding: lessons learned and new frontiers

    Science.gov (United States)

    Pappu, Rohit V.; Nussinov, Ruth

    2009-03-01

    theories predict that evolved sequences (functional proteins as opposed to random sequences) find their native folds by minimizing geometric (topological) frustration (i.e. avoiding entropic bottlenecks/kinetic traps). In some cases, following a dominant pathway is the optimal way to minimize frustration, whereas in extreme cases, proteins may fold without encountering bottlenecks. Experimental studies of two-state proteins led in turn to the development of quantitative descriptors that have allowed specific testing of theoretical predictions. These include methods such as phi value analysis to characterize transition state ensembles and descriptors that measure the effects of geometry/topology on folding rates. Interestingly, there exists a striking inverse correlation between the relative contact order (the distance in sequence space between spatially proximal contacts made in the native state) and the folding rates of several two-state proteins. The relative contact order provides a rough estimate of the net entropic cost associated with realizing the folded state, and theories have been developed to explain the observed correlation between the contact order and folding rates. Despite its maturity as a field, there are several areas that come under the rubric of protein folding that are just beginning to receive attention. For example, how do complications in vivo such as macromolecular crowding, confinement, the presence of cosolutes, membrane anchoring, and tethering to surfaces influence protein stabilities and folding dynamics? While we are accustomed to studying proteins at concentrations that are amenable to investigation via probes whose signal intensities grow with protein concentration, this does not make these readouts relevant to the in vivo setting. In cells, protein concentrations are tightly regulated and are likely to be orders of magnitude lower than what we are accustomed to using within in vitro experimental setups. Protein folding in vivo is a complex

  18. Multivariate assimilation of coarse scale soil moisture, cosmic-ray soil moisture, land surface temperature and leaf area index in CLM4.5

    Science.gov (United States)

    Han, Xujun; Hendricks Franssen, Harrie-Jan; Schalge, Bernd; Baroni, Gabriele; Rihani, Jehan; Kollet, Stefan; Vereecken, Harry; Simmer, Clemens

    2017-04-01

    The land surface plays a central role in the atmosphere - land surface - subsurface continuum. Surface soil moisture for instance impacts the partitioning of absorbed radiation in heating ground and atmosphere and thus impacts resulting evapotranspiration. The land surface also drives partitioning of rainfall between infiltration which ends up as groundwater recharge and surface runoff contributing to stream discharge. It is therefore expected that the use of observations for characterizing and predicting the land surface state also leads to improved state estimations and predictions in all the other sub-compartments of the system we consider: groundwater, stream discharge and atmosphere. To test this hypothesis requires efficient data assimilation schemes that are capable to take up specific requirements of different compartments, such as different time windows of observations. In this study we will derive such data assimilation methods and quantify the improvement of predictions in the different compartments due to assimilation of multiple observations, and evaluate to what extent assimilation of land surface observations will also improve predictions of land surface states and fluxes for atmosphere and groundwater. We argue that improvements can be achieved by implementing a data assimilation methodology that is capable of simultaneous assimilation of many data sources (remote sensing soil moisture, cosmic-ray measurement for soil moisture, land surface temperature and leaf area index) at different spatial scales ranging from 102 m to 104 m. The multivariate data assimilation system for the land-surface component will be developed and extended to assimilate the coarse scale remote sensing soil moisture, cosmic-ray soil moisture, land surface temperature and leaf area index, and their different combinations using the local ensemble transform Kalman filter. The multivariate data assimilation will be evaluated using a synthetic study which mimics the Neckar

  19. Self-folding micropatterned polymeric containers.

    Science.gov (United States)

    Azam, Anum; Laflin, Kate E; Jamal, Mustapha; Fernandes, Rohan; Gracias, David H

    2011-02-01

    We demonstrate self-folding of precisely patterned, optically transparent, all-polymeric containers and describe their utility in mammalian cell and microorganism encapsulation and culture. The polyhedral containers, with SU-8 faces and biodegradable polycaprolactone (PCL) hinges, spontaneously assembled on heating. Self-folding was driven by a minimization of surface area of the liquefying PCL hinges within lithographically patterned two-dimensional (2D) templates. The strategy allowed for the fabrication of containers with variable polyhedral shapes, sizes and precisely defined porosities in all three dimensions. We provide proof-of-concept for the use of these polymeric containers as encapsulants for beads, chemicals, mammalian cells and bacteria. We also compare accelerated hinge degradation rates in alkaline solutions of varying pH. These optically transparent containers resemble three-dimensional (3D) micro-Petri dishes and can be utilized to sustain, monitor and deliver living biological components.

  20. Perceptions and concerns about dental fluorosis as assessed by tooth surface index of fluorosis among high school children in an area of endemic fluorosis--Kaiwara.

    Science.gov (United States)

    Bhagyajyothi, Chokkadi Sreepathi; Pushpanjali, Krishnappa

    2009-01-01

    The aim of this study was to assess the perceptions and concerns about dental fluorosis among high school children in an area that is endemic to fluorosis, and to correlate the children's perceptions of dental fluorosis with different scores of tooth surface index of fluorosis. The study was conducted among 155 children affected with fluorosis, aged between 12 and 16 years, studying in all four high schools of Kaiwara, Karnataka, India. Fluorosis was assessed on labial surfaces of maxillary anterior teeth using tooth surface index of fluorosis, and the data were collected using a self-administered pretested questionnaire that was given to the study subjects. Analysis was performed using frequency distribution, chi-square test and Spearman's correlation coefficients. Significant high correlations were found between tooth surface index of fluorosis scores and the perception of the importance of the condition (r = 0.226, chi2 = 72.065, P dental fluorosis among this age group of children appear to be of aesthetic concern making it essential to focus on this issue and to intervene.

  1. NoFold: RNA structure clustering without folding or alignment.

    Science.gov (United States)

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  2. Unexpected Covariant Behavior of the Aegean and Ionian Seas in the Period 1987-2008 by Means of a Nondimensional Sea Surface Height Index

    Science.gov (United States)

    Reale, M.; Salon, S.; Crise, A.; Farneti, R.; Mosetti, R.; Sannino, G.

    2017-10-01

    In this work, we use a set of recent multiyear simulations to develop a simplified sea surface height index (SSH). The index characterizes the dynamics of Ionian upper layer circulation and its links with sea surface height and salinity in the Southern Adriatic and Aegean Seas during the period 1987-2008. The analysis highlights a covariant behavior between Ionian Sea and Aegean Sea associated with a mutual zonal exchange of water masses with different salinity characteristics. Our analysis confirms that the variability observed in the period 1987-2008 in the upper layer circulation of the Ionian was driven by the salinity variability in the Southern Adriatic and Aegean Sea. This study supports and reinforces the hypothesis that two observed BiOS-like reversals reflect the existence of multiple equilibrium states in the Mediterranean Thermohaline circulation in the Eastern Mediterranean and that a complete characterization of observed variability needs to take into account a fully coupled Adriatic-Ionian-Aegean System.

  3. [Is body surface area (BSA) suitable for indexing renal and dialysis clearances and other physiological parameters? A theoretical approach and a critical analysis (part 3)].

    Science.gov (United States)

    Ruggieri, G

    2009-01-01

    Many parameters of biological functions, interesting different branches of medicine, have to be indexed by the same value for each other comparison between single individuals or between-within groups. Body Surface Area (BSA) and 1.73 m2 reference value are probably the most used tools for indexation, but a growing number of scientific papers emphasize the risk of under or over estimates of data by BSA indexation in overweight--obese or on the contrary underweight individuals. This study has been planned to evaluate this problem a) by a theoretical approach, indexing to 1.73 m2 the creatinine clearance (CtCl) in an ideal population and b) analysing and debating the doubts and problems about the indexation by BSA in many fields, the possibilities of indexation by other methods, or to use BSA with different approach, to reduce the risk of bias, evaluating the possibility of this target in a real population of 45 men and 84 women undergoing Peritoneal Dialysis (PD)--III--There is a lack of significative correlation between BSA and GFR, this one on the contrary significantly correlated with lean body mass and body water, possible alternatives to BSA. Researches performed to validate the indirect estimates of above variables by creatinine excretion and bioimpedance don't seem up till now to give sufficient evidences for a general acceptance. In conclusion, it would be advisable or to drop the indexing by BSA or, if necessary, to use it by different methods, as theoretically shown in this paper.

  4. Effects of Near-Surface Atmospheric Stability and Moisture on Wildfire Behavior and Consequences for Haines Index

    Science.gov (United States)

    Ruiyu Sun; Mary Ann Jenkins

    2003-01-01

    Since the 1950s, extensive research has been conducted to investigate the relationship between near-surface atmospheric conditions and large wildfire growth and occurrence. Observational studies have demonstrated that near-surface dryness (e-g., Fahnestock 1965) and atmospheric instability (e-g., Brotak and Reifsnyder 1977) are correlated with large wildfire growth and...

  5. Folded supersymmetry with a twist

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, Timothy [Department of Physics, Princeton University,Princeton, NJ 08544 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, NJ 08540 (United States); Institute of Theoretical Science, University of Oregon,Eugene, OR 97403 (United States); Craig, Nathaniel [Department of Physics, University of California,Santa Barbara, CA 93106 (United States); Lou, Hou Keong [Department of Physics, Princeton University,Princeton, NJ 08544 (United States); Pinner, David [Princeton Center for Theoretical Science, Princeton University,Princeton, NJ 08544 (United States)

    2016-03-30

    Folded supersymmetry (f-SUSY) stabilizes the weak scale against radiative corrections from the top sector via scalar partners whose gauge quantum numbers differ from their Standard Model counterparts. This non-trivial pairing of states can be realized in extra-dimensional theories with appropriate supersymmetry-breaking boundary conditions. We present a class of calculable f-SUSY models that are parametrized by a non-trivial twist in 5D boundary conditions and can accommodate the observed Higgs mass and couplings. Although the distinctive phenomenology associated with the novel folded states should provide strong evidence for this mechanism, the most stringent constraints are currently placed by conventional supersymmetry searches. These models remain minimally fine-tuned in light of LHC8 data and provide a range of both standard and exotic signatures accessible at LHC13.

  6. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...... of proteins) are natural consequences of the suggested wring mode model. Native (folded) proteins are found to possess an intrinsic standing wring mode....

  7. Equi-Gaussian curvature folding

    Indian Academy of Sciences (India)

    curvature kf (p) i.e., kp = kf (p). In this case f will map curves to curves with equal equi-. Gaussian curvature at corresponding points. It will also map area with sectional curvature k(σ, p) into areas with the same sectional curvature, and so on. The set of all equi-Gaussian curvature foldings of M into N will be denoted by.

  8. Calculation of the surface water pollution index in the evaluation of environmental component of product life cycle

    Directory of Open Access Journals (Sweden)

    Олег Аскольдович Проскурнин

    2015-05-01

    Full Text Available The assessment feasibility of the combined effect of the product life cycle on the environment is grounded. As an example, the pollution of surface waters at the production stage is considered in the article. A mechanism of ranking indicators of surface water pollution according to their importance is proposed. An algorithm for checking the consistency of the statistical expert judgment in determining weight coefficient for the indicators of pollution, based on the use of the concordance coefficient, is given

  9. 100-fold but not 50-fold dystrophin overexpression aggravates electrocardiographic defects in the mdx model of Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Yongping Yue

    2016-01-01

    Full Text Available Dystrophin gene replacement holds the promise of treating Duchenne muscular dystrophy. Supraphysiological expression is a concern for all gene therapy studies. In the case of Duchenne muscular dystrophy, Chamberlain and colleagues found that 50-fold overexpression did not cause deleterious side effect in skeletal muscle. To determine whether excessive dystrophin expression in the heart is safe, we studied two lines of transgenic mdx mice that selectively expressed a therapeutic minidystrophin gene in the heart at 50-fold and 100-fold of the normal levels. In the line with 50-fold overexpression, minidystrophin showed sarcolemmal localization and electrocardiogram abnormalities were corrected. However, in the line with 100-fold overexpression, we not only detected sarcolemmal minidystrophin expression but also observed accumulation of minidystrophin vesicles in the sarcoplasm. Excessive minidystrophin expression did not correct tachycardia, a characteristic feature of Duchenne muscular dystrophy. Importantly, several electrocardiogram parameters (QT interval, QRS duration and the cardiomyopathy index became worse than that of mdx mice. Our data suggests that the mouse heart can tolerate 50-fold minidystrophin overexpression, but 100-fold overexpression leads to cardiac toxicity.

  10. Evaluation of Surface Water Quality by Using GIS and a Heavy Metal Pollution Index (HPI) Model in a Coal Mining Area, India.

    Science.gov (United States)

    Tiwari, Ashwani Kumar; De Maio, Marina; Singh, Prasoon Kumar; Mahato, Mukesh Kumar

    2015-09-01

    Twenty eight surface water samples were collected from fourteen sites of the West Bokaro coalfield, India. The concentration of Mn, Cu, Zn, Ni, As, Se, Al, Cr, Ba, and Fe were analyzed using inductively coupled plasma mass spectrometry (ICP-MS) for determination of seasonal fluctuations and a heavy metal pollution index (HPI). The HPI values were below the critical pollution index value of 100. Metal concentrations were higher in the pre-monsoon season as compared to the post-monsoon season. The Zn, Ni, Mn, As, Se, Al, Ba, Cu, and Cr concentrations did not exceed the desirable limits for drinking water in either season. However, at many sites, concentrations of Fe were above the desirable limit of the WHO (2006) and Indian drinking water standard (BIS 2003) in both seasons. The water that contained higher concentrations of Fe would require treatment before domestic use.

  11. Synovial folds in equine articular process joints

    DEFF Research Database (Denmark)

    Thomsen, Line Nymann; Berg, Lise Charlotte; Markussen, Bo

    2013-01-01

    Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses.......Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses....

  12. Adolescent brain maturation and cortical folding: evidence for reductions in gyrification.

    Directory of Open Access Journals (Sweden)

    Daniel Klein

    Full Text Available Evidence from anatomical and functional imaging studies have highlighted major modifications of cortical circuits during adolescence. These include reductions of gray matter (GM, increases in the myelination of cortico-cortical connections and changes in the architecture of large-scale cortical networks. It is currently unclear, however, how the ongoing developmental processes impact upon the folding of the cerebral cortex and how changes in gyrification relate to maturation of GM/WM-volume, thickness and surface area. In the current study, we acquired high-resolution (3 Tesla magnetic resonance imaging (MRI data from 79 healthy subjects (34 males and 45 females between the ages of 12 and 23 years and performed whole brain analysis of cortical folding patterns with the gyrification index (GI. In addition to GI-values, we obtained estimates of cortical thickness, surface area, GM and white matter (WM volume which permitted correlations with changes in gyrification. Our data show pronounced and widespread reductions in GI-values during adolescence in several cortical regions which include precentral, temporal and frontal areas. Decreases in gyrification overlap only partially with changes in the thickness, volume and surface of GM and were characterized overall by a linear developmental trajectory. Our data suggest that the observed reductions in GI-values represent an additional, important modification of the cerebral cortex during late brain maturation which may be related to cognitive development.

  13. Quality index of the surface water of Amazonian rivers in industrial areas in Pará, Brazil.

    Science.gov (United States)

    Medeiros, Adaelson Campelo; Faial, Kleber Raimundo Freitas; do Carmo Freitas Faial, Kelson; da Silva Lopes, Iris Danielly; de Oliveira Lima, Marcelo; Guimarães, Raphael Mendonça; Mendonça, Neyson Martins

    2017-10-15

    In this study was to evaluate the waters quality of the Murucupi River, located in urban agglomerate area and intense industrial activity in Barcarena City, Pará State. The Arapiranga River in Abaetetuba City was used as control area (Background), next to Barcarena. Was used the Water Quality Index (WQI) based on nine variables analized. Waters quality of the Arapiranga and Murucupi rivers were regular to good and bad to good, respectively. Anthropogenic influence on the Murucupi River was higher, mainly by the disposal of domestic effluents from the urban agglomerate and of the industrial waste tailing basins upstream of this river. Due to its less inhabited environment and further away from the area urban and industrial, the Arapiranga River was more preserved. Waters pollution of around these area is increasingly intense, and restricted its uses for various purposes. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. First principles study of elemental mercury (Hg{sup 0}) adsorption on low index CoMnO{sub 3} surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Wenchao; Su, Pingru; Tang, Qingli; Cheng, Zhiwen [School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240 (China); Shen, Zhemin, E-mail: zmshen@sjtu.edu.cn [School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240 (China); Fan, Maohong [Department of Chemical and Petroleum Engineering, University of Wyoming, Laramie, Wyoming, 82071 (United States); School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332 (United States)

    2017-06-30

    Highlights: • Hg{sup 0} adsorption on low index CoMnO{sub 3} surface was predicted by DFT method. • Hg{sup 0} is adsorbed on the CoMnO{sub 3} surface with chemisorption interaction. • Hg{sup 0} has highest adsorption energy on CoMnO{sub 3} (1 0 0) surface with Hg-Mn mechanism. • The electron transfer of Hg{sup 0} has positive relationship with adsorption energy. - Abstract: The density functional theory (DFT) is applied to predict elemental mercury (Hg{sup 0}) adsorption on CoMnO{sub 3} surface for the first time. GGA/PBE functional were selected to determine the potential Hg{sup 0} capture mechanisms. The results show that Hg{sup 0} has good affinity with CoMnO{sub 3} surfaces with chemical adsorption. The adsorption energy of Hg{sup 0}-CoMnO{sub 3} (1 0 0), Hg{sup 0}-CoMnO{sub 3} (1 0 1) and Hg{sup 0}-CoMnO{sub 3} (1 1 0) are −85.225, −72.305 and −70.729 kJ/mol, respectively. The Hg-Mn and Hg-Co mechanisms were revealed on low index surfaces. Hg{sup 0} was oxidized to its valence state of 0.236 on Mn site in CoMnO{sub 3} (1 0 0) surface. The Hg-Co interaction mechanism occurred on Hg{sup 0}-CoMnO{sub 3} (1 0 1) and Hg{sup 0}-CoMnO{sub 3} (1 1 0) with 0.209e{sup −} and 0.189e{sup −} transformation, respectively. The PDOS analysis shows that Hg-Mn interaction depends on the hybridization of Hg(s- and d-orbitals) and Mn (s-, p- and d- orbitals). However, Hg-Co interaction stems from s- and d- orbitals of Hg, which only overlapping with d- and p- orbital of Co. Both the adsorption energy and electronic structure analysis indicated that CoMnO{sub 3} catalyst performed excellent in Hg{sup 0} oxidation. Exposing CoMnO{sub 3} (1 0 0) is most favorable in Hg{sup 0} control, which provides theoretical instruction on certain crystal plane synthesis in experiment.

  15. Glazed ceramic roof tiles: influence of surface features in the solar reflectance index; Influencia das caracteristicas da superficie no indice de refletancia solar de telhas ceramicas esmaltadas

    Energy Technology Data Exchange (ETDEWEB)

    Bortoli, Leitcia Silva de; Stapait, Camila Cristina; Marinoski, Deivis Luis; Fredel, Marcio Celso; Schabbach, Luciana M., E-mail: luciana.maccarini@ufsc.br [Universidade Federal de Santa Catarina (UFSC), Blumenau, SC (Brazil)

    2016-07-01

    In this study the influence of surface features of ceramic roof tiles in the solar reflectance index were evaluated. Two glazed ceramic roof tiles (type stoneware) with the same color (ivory) but with different appearance (matte and brilliant) were the focus of the analysis. The Solar Reflectance Index (SRI) of the roofs tiles were determined by the solar reflectance values (UV-VIS-NIR) and emittance, measured in laboratory. The samples showed SRI> 39 in accordance with LEED certification criteria (Leadership in Energy and Environmental Design), contributing to minimizing the Heat Island Effects. Although the matte roof tile shows a slightly higher SRI value (82) than the brilliant one (78), the results for the variables that composes the SRI value (reflectance and emittance) were very similar. Analysis of XRD, SEM and EDS performed on the surfaces of the two roofs indicated for the matte glaze the presence of microcrystals (with barium and zinc) that can contribute to the slightly highest value of SRI. The roughness (optical interferometer white light) and the brightness (brightness meter) of the samples were also measured. (author)

  16. Non-symmetric localized fold of a floating sheet

    Science.gov (United States)

    Rivetti, Marco

    2013-03-01

    An elastic sheet lying on the surface of a liquid, if axially compressed, shows a transition from a smooth sinusoidal pattern to a well-localized fold. This wrinkle-to-fold transition is a manifestation of a localized buckling. The symmetric and antisymmetric shapes of the fold have recently been described by Diamant and Witten (2011), who found two exact solutions of the nonlinear equilibrium equations. In this Note, we show that these solutions can be generalized to a continuous family of solutions, which yields non-symmetric shapes of the fold. We prove that non-symmetric solutions also describe the shape of a soft strip withdrawn from a liquid bath, a physical problem that allows us to easily observe portions of non-symmetric profiles.

  17. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested that prot......The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...

  18. Bodies Folded in Migrant Crypts

    DEFF Research Database (Denmark)

    Galis, Vasilis; Tzokas, Spyros; Tympas, Aristotle

    2016-01-01

    , and to performing mobility in general. Dis/ability and migration have not been associated in the literature. We adopt an analytical symmetry between humans and non-humans, in this case between bodies and crypts. By suggesting an infected, ambivalent, and hybrid approach to the human subject, the body......This article considers media narratives that suggest that hiding in trucks, buses, and other vehicles to cross borders has, in fact, been a common practice in the context of migration to, and within, Europe. We aim to problematize how the tension between the materiality of bordering practices...... and human migrants generates a dis/abled subject. In this context, dis/ability may be a cause or consequence of migration, both in physical/material (the folding of bodies in the crypt) and cultural/semiotic terms, and may become a barrier to accessing protection, to entering and/or crossing a country...

  19. Fluoroangiographic picture of chorioretinal folds

    International Nuclear Information System (INIS)

    Kalvodova, B.; Karel, I.

    1988-01-01

    Fluoroangiographic pictures of chorioretinal folds (CRF) were analyzed in 13 eyes of 12 patients. The orbital origin of CRF was present in 8 eyes (orbital tumors in 7 eyes and thyroid ophthalmopathy in one eye), the intraocular origin in 5 eyes (hypotonic postoperative syndrome caused by the detachment of the choroid in 3 eyes, Irwine-Gass syndrome in 2 eyes, scleral bucle used for retinal detachment repair in one eye). The fluoroangiographic findings of CRF were determined by changes in the pigmented epithelium and choroid of a different degree, which modified the clinical picture of the basic disease. Fluorescein angiography is a very useful method for the differentiation of retinal and choroid detachments but with a limited possibility to determine the etiological factor of the disease. (author). 6 figs., 2 tabs., 32 refs

  20. Overview of total beta activity index and beta rest in surface waters of the Spanish rivers; Vision general del indice de actividad beta total y beta resto en las aguas superficiales de los rios espanoles

    Energy Technology Data Exchange (ETDEWEB)

    Pujol, L.; Payeras, J.; Pablo, M. A. de

    2013-07-01

    This work aims to give an overview of the index of total beta activity and the activity index beta rest in surface waters of the main Spanish rivers. These indices are a parameter over water quality that CEDEX comes determined by order of the Ministry of Agriculture, Food and Environment, in water policy. (Author)

  1. Chemisorption of oxygen and subsequent reactions on low index surfaces of β-Mo2C

    DEFF Research Database (Denmark)

    Shi, Xue Rong; Wang, Shengguang; Wang, Jianguo

    2016-01-01

    Oxygen chemisorption on β-Mo2C surfaces, the subsequent CO/CO2 desorption and oxygen diffusion to the carbon vacancy have been investigated by density-functional theory. The most stable structures together with the energetics of oxygen stepwise adsorption, CO/CO2 desorption and oxygen diffusion...... to the carbon vacancy were identified. We examined the effect of oxygen coverage on the morphology of β-Mo2C by plotting the equilibrium crystal shape. Thermodynamic effect of temperature and reactant or product pressure on the CO/CO2 desorption were investigated. The CO/CO2 desorption is more favorable...

  2. Atomic structure of a stable high-index Ge surface: G2(103)-(4x1)

    DEFF Research Database (Denmark)

    Seehofer, L.; Bunk, O.; Falkenberg, G.

    1997-01-01

    Based on scanning tunneling microscopy and surface X-ray diffraction, we propose a complex structural model for the Ge(103)-(4 x 1) reconstruction. Each unit cell contains two (103) double steps, which gives rise to the formation of stripes of Ge atoms oriented in the [] direction....... The stripes and the spaces between them are covered with threefold-coordinated Ge adatoms. Charge is transferred from the bulk-like edge atoms of the double steps to the adatoms. The formation of the reconstruction can be explained in terms of stress relief, charge transfer, and minimization of the dangling...

  3. Amyloid Beta Peptide Folding in Reverse Micelles.

    Science.gov (United States)

    Eskici, Gözde; Axelsen, Paul H

    2017-07-19

    Previously published experimental studies have suggested that when the 40-residue amyloid beta peptide is encapsulated in a reverse micelle, it folds into a structure that may nucleate amyloid fibril formation (Yeung, P. S.-W.; Axelsen, P. H. J. Am. Chem. Soc. 2012, 134, 6061 ). The factors that induce the formation of this structure have now been identified in a multi-microsecond simulation of the same reverse micelle system that was studied experimentally. Key features of the polypeptide-micelle interaction include the anchoring of a hydrophobic residue cluster into gaps in the reverse micelle surface, the formation of a beta turn at the anchor point that brings N- and C-terminal segments of the polypeptide into proximity, high ionic strength that promotes intramolecular hydrogen bond formation, and deformation of the reverse micelle surface to facilitate interactions with the surface along the entire length of the polypeptide. Together, these features cause the simulation-derived vibrational spectrum to red shift in a manner that reproduces the red-shift previously reported experimentally. On the basis of these findings, a new mechanism is proposed whereby membranes nucleate fibril formation and facilitate the in-register alignment of polypeptide strands that is characteristic of amyloid fibrils.

  4. The surgical anatomy of the nasolabial fold.

    Science.gov (United States)

    Pogrel, M A; Shariati, S; Schmidt, B; Faal, Z H; Regezi, J

    1998-10-01

    The purpose of this cadaver dissection study was to investigate the anatomy of the nasolabial fold with a view to explaining the problems of surgical softening or elimination of the fold. Ten formalin-fixed cadavers and 6 fresh-frozen cadavers were used for this study. In 12 cadavers (8 formalin-fixed, 4 fresh-frozen), the nasolabial fold was sectioned at right angles to the fold for histologic examination, and in 4 cadavers (2 formalin-fixed, 2 fresh-frozen) the epithelium was dissected off the fold to allow for more detailed gross examination of the underlying musculature. The fold was clearly identified on 14 of the cadavers but was indistinct on 2 on gross examination. Beneath the fold were 2 muscle bundles. The more superficial muscle runs parallel to the fold whereas a deeper muscle runs at right angles to it. The buccal fat pad lies above the fold and appears to be retained by horizontal septae in the fat pad and also by the musculature of the fold. Cadavers showing a poorly defined nasolabial fold had fewer muscle bundles to support the fat and fewer fibrous septae running through the fat. The nasolabial fold is defined by structures that support the buccal fat pad and hold it above the fold. This appears to be a combination of muscle bundles that run both across and parallel to the fold and also by fibrous septae supporting the fat pad. This has implications for the development of surgical procedures to soften or eliminate the fold, which must separate the muscles from the dermis of the fold and allow the fat to descend and soften the fold.

  5. The parallel universe of RNA folding.

    Science.gov (United States)

    Batey, R T; Doudna, J A

    1998-05-01

    How do large RNA molecules find their active conformations among a universe of possible structures? Two recent studies reveal that RNA folding is a rapid and ordered process, with surprising similarities to protein folding mechanisms.

  6. Self-organized critical model for protein folding

    Science.gov (United States)

    Moret, M. A.

    2011-09-01

    The major factor that drives a protein toward collapse and folding is the hydrophobic effect. At the folding process a hydrophobic core is shielded by the solvent-accessible surface area of the protein. We study the fractal behavior of 5526 protein structures present in the Brookhaven Protein Data Bank. Power laws of protein mass, volume and solvent-accessible surface area are measured independently. The present findings indicate that self-organized criticality is an alternative explanation for the protein folding. Also we note that the protein packing is an independent and constant value because the self-similar behavior of the volumes and protein masses have the same fractal dimension. This power law guarantees that a protein is a complex system. From the analyzed data, q-Gaussian distributions seem to fit well this class of systems.

  7. How the cortex gets its folds: an inside-out, connectivity-driven model for the scaling of mammalian cortical folding

    OpenAIRE

    Bruno eMota; Bruno eMota; Suzana eHerculano-Houzel; Suzana eHerculano-Houzel

    2012-01-01

    Larger mammalian cerebral cortices tend to have increasingly folded surfaces, often considered to result from the lateral expansion of the grey matter (GM), which, in a volume constrained by the cranium, causes mechanical compression that is relieved by inward folding of the white matter (WM), or to result from differential expansion of cortical layers. Across species, thinner cortices, presumably more pliable, would offer less resistance and hence become more folded than thicker cortices of ...

  8. Vocal fold ion transport and mucin expression following acrolein exposure.

    Science.gov (United States)

    Levendoski, Elizabeth Erickson; Sivasankar, M Preeti

    2014-05-01

    The vocal fold epithelium is exposed to inhaled particulates including pollutants during breathing in everyday environments. Yet, our understanding of the effects of pollutants on vocal fold epithelial function is extremely limited. The objective of this study was to investigate the effect of the pollutant acrolein on two vocal fold epithelial mechanisms: ion transport and mucin (MUC) synthesis. These mechanisms were chosen as each plays a critical role in vocal defense and in maintaining surface hydration which is necessary for optimal voice production. Healthy, native porcine vocal folds (N = 85) were excised and exposed to an acrolein or sham challenge. A 60-min acrolein, but not sham challenge significantly reduced ion transport and inhibited cyclic adenosine monophosphate-dependent, increases in ion transport. Decreases in ion transport were associated with reduced sodium absorption. Within the same timeline, no significant acrolein-induced changes in MUC gene or protein expression were observed. These results improve our understanding of the effects of acrolein on key vocal fold epithelial functions and inform the development of future investigations that seek to elucidate the impact of a wide range of pollutant exposures on vocal fold health.

  9. The role of hydration in vocal fold physiology.

    Science.gov (United States)

    Sivasankar, Mahalakshmi; Leydon, Ciara

    2010-06-01

    Increased vocal fold hydration is a popular target in the prevention and management of voice disorders. Current intervention strategies focus on enhancing both systemic (internal) and superficial (surface) hydration. We review relevant bench and human research on the role of hydration in vocal fold physiology. Bench and human studies provide converging evidence that systemic and superficial dehydration are detrimental to vocal fold physiology. Dehydration challenges increase the viscous properties of excised vocal fold tissue. Systemic, superficial, and combined drying challenges increase aerodynamic and acoustic measures of voice production in speakers. Emerging theoretical and clinical data suggest that increasing both systemic and superficial hydration levels may benefit voice production; however, robust evidence for positive outcomes of hydration treatments is lacking. Increased systemic and superficial vocal fold hydration as a component of vocal hygiene may improve overall health and efficiency of the vocal apparatus. However, continued exploration of biological mechanisms regulating vocal fold hydration is needed to optimize clinical hydration interventions. Specifically, the development of hydration treatments that maximize positive phonatory outcomes will necessitate understanding of the signaling pathways linking systemic and superficial hydration.

  10. Disaggregation of SMOS soil moisture over West Africa using the Temperature and Vegetation Dryness Index based on SEVIRI land surface parameters

    DEFF Research Database (Denmark)

    Tagesson, T.; Horion, S.; Nieto, H.

    2018-01-01

    The overarching objective of this study was to produce a disaggregated SMOS Soil Moisture (SM) product using land surface parameters from a geostationary satellite in a region covering a diverse range of ecosystem types. SEVIRI data at 15 minute temporal resolution were used to derive the Tempera...... resolution of SMOS SM, with potential application for local drought/flood monitoring of importance for the livelihood of the population of West Africa....... the Temperature and Vegetation Dryness Index (TVDI) that served as SM proxy within the disaggregation process. West Africa (3 N, 26 W; 28 N, 26 E) was selected as a case study as it presents both an important North-South climate gradient and a diverse range of ecosystem types. The main challenge was to set up...

  11. Effect of sediments load on growth folds in thin-skinned fold-and-thrust belt: a numerical approach.

    Science.gov (United States)

    Collignon, Marine; Fernandez, Naiara; May, Dave A.; Kaus, Boris J. P.

    2013-04-01

    Over the past decades, the interaction between surface processes and development of mountain belts has been extensively studied. While syntectonic sedimentation appears to control the external development of the fold-and-thrust belts, erosion strongly influences the evolution of internal regions within mountain belts. The effects of sedimentation on brittle deformation have been thoroughly studied using analogue and numerical models of accretionary wedges, however, most of the numerical studies used a 2D model of deformation and/or a simple formulation for the surface processes, where both sedimentation and erosion are rarely present together. Coupled analogue models of deformation and erosion/sedimentation are challenging, due to material and scaling issues, and often only reproduce two end-member cases (no erosion vs very strong erosion, where all the material is removed), but fail to investigate the transitional cases. In contrast, the influence of sedimentation on ductile deformation has not been examined in detail. Thin-skinned fold and thrust belts are seen as the result of compressional deformation of a sediment pile over a weak layer acting as a décollement level. The resulting surface expression has often been interpreted, based on geometrical criteria in terms of fault bend folds, propagation folds or/and detachment folds. Several analogue studies have demonstrated that fold morphology can be influenced by erosion rates or preferential localization of sedimentation, and additionally, that the fold growth can be stopped by increasing the supply of sediments. Here we aim to numerically investigate the effects of sedimentation on the growth of folds in three dimensions. In order to study the feedback between sedimentation and ductile deformation, we have developed a finite-element based landscape evolution model (both erosion and sedimentation) using PETSc, and coupled it to the 3D mechanical code LaMEM. The landscape evolution model uses a non

  12. Anatomy and Histology of an Epicanthal Fold.

    Science.gov (United States)

    Park, Jae Woo; Hwang, Kun

    2016-06-01

    The aim of this study is to elucidate the precise anatomical and histological detail of the epicanthal fold.Thirty-two hemifaces of 16 Korean adult cadavers were used in this study (30 hemifaces with an epicanthal fold, 2 without an epicanthal fold). In 2 patients who had an epicanthoplasty, the epicanthal folds were sampled.In a dissection, the periorbital skin and subcutaneous tissues were removed and the epicanthal fold was observed in relation to each part of the orbicularis oculi muscle. Specimens including the epicanthal fold were embeddedin in paraffin, sectioned at 10 um, and stained with Hematoxylin-Eosin. The horizontal section in the level of the paplebral fissure was made and the prepared slides were observed under a light microscope.In the specimens without an epicanthal fold, no connection between the upper preseptal muscle and the lower preseptal muscle was found. In the specimens with an epicanthal fold, a connection of the upper preseptal muscle to the lower preseptal muscle was observed. It was present in all 15 hemifaces (100%). There was no connection between the pretarsal muscles. In a horizontal section, the epicanthal fold was composed of 3 compartments: an outer skin lining, a core structure, and an innerskin lining. The core structure was mainly composed of muscular fibers and fibrotic tissue and they were intermingled.Surgeons should be aware of the anatomical details of an epicanthal fold. In removing or reconstructing an epicanthal fold, the fibromuscular core band should also be removed or reconstructed.

  13. Air temperature thresholds to evaluate snow melting at the surface of Alpine glaciers by T-index models: the case study of Forni Glacier (Italy)

    Science.gov (United States)

    Senese, A.; Maugeri, M.; Vuillermoz, E.; Smiraglia, C.; Diolaiuti, G.

    2014-03-01

    The glacier melt conditions (i.e.: null surface temperature and positive energy budget) can be assessed by analyzing meteorological and energy data acquired by a supraglacial Automatic Weather Station (AWS). In the case this latter is not present the assessment of actual melting conditions and the evaluation of the melt amount is difficult and simple methods based on T-index (or degree days) models are generally applied. These models require the choice of a correct temperature threshold. In fact, melt does not necessarily occur at daily air temperatures higher than 273.15 K. In this paper, to detect the most indicative threshold witnessing melt conditions in the April-June period, we have analyzed air temperature data recorded from 2006 to 2012 by a supraglacial AWS set up at 2631 m a.s.l. on the ablation tongue of the Forni Glacier (Italian Alps), and by a weather station located outside the studied glacier (at Bormio, a village at 1225 m a.s.l.). Moreover we have evaluated the glacier energy budget and the Snow Water Equivalent (SWE) values during this time-frame. Then the snow ablation amount was estimated both from the surface energy balance (from supraglacial AWS data) and from T-index method (from Bormio data, applying the mean tropospheric lapse rate and varying the air temperature threshold) and the results were compared. We found that the mean tropospheric lapse rate permits a good and reliable reconstruction of glacier air temperatures and the major uncertainty in the computation of snow melt is driven by the choice of an appropriate temperature threshold. From our study using a 5.0 K lower threshold value (with respect to the largely applied 273.15 K) permits the most reliable reconstruction of glacier melt.

  14. Estimating the surface layer refractive index structure constant over snow and sea ice using Monin-Obukhov similarity theory with a mesoscale atmospheric model.

    Science.gov (United States)

    Qing, Chun; Wu, Xiaoqing; Huang, Honghua; Tian, Qiguo; Zhu, Wenyue; Rao, Ruizhong; Li, Xuebin

    2016-09-05

    Since systematic direct measurements of refractive index structure constant ( Cn2) for many climates and seasons are not available, an indirect approach is developed in which Cn2 is estimated from the mesoscale atmospheric model outputs. In previous work, we have presented an approach that a state-of-the-art mesoscale atmospheric model called Weather Research and Forecasting (WRF) model coupled with Monin-Obukhov Similarity (MOS) theory which can be used to estimate surface layer Cn2 over the ocean. Here this paper is focused on surface layer Cn2 over snow and sea ice, which is the extending of estimating surface layer Cn2 utilizing WRF model for ground-based optical application requirements. This powerful approach is validated against the corresponding 9-day Cn2 data from a field campaign of the 30th Chinese National Antarctic Research Expedition (CHINARE). We employ several statistical operators to assess how this approach performs. Besides, we present an independent analysis of this approach performance using the contingency tables. Such a method permits us to provide supplementary key information with respect to statistical operators. These methods make our analysis more robust and permit us to confirm the excellent performances of this approach. The reasonably good agreement in trend and magnitude is found between estimated values and measurements overall, and the estimated Cn2 values are even better than the ones obtained by this approach over the ocean surface layer. The encouraging performance of this approach has a concrete practical implementation of ground-based optical applications over snow and sea ice.

  15. Viscoelastic properties of the false vocal fold

    Science.gov (United States)

    Chan, Roger W.

    2004-05-01

    The biomechanical properties of vocal fold tissues have been the focus of many previous studies, as vocal fold viscoelasticity critically dictates the acoustics and biomechanics of phonation. However, not much is known about the viscoelastic response of the ventricular fold or false vocal fold. It has been shown both clinically and in computer simulations that the false vocal fold may contribute significantly to the aerodynamics and sound generation processes of human voice production, with or without flow-induced oscillation of the false fold. To better understand the potential role of the false fold in phonation, this paper reports some preliminary measurements on the linear and nonlinear viscoelastic behavior of false vocal fold tissues. Linear viscoelastic shear properties of human false fold tissue samples were measured by a high-frequency controlled-strain rheometer as a function of frequency, and passive uniaxial tensile stress-strain response of the tissue samples was measured by a muscle lever system as a function of strain and loading rate. Elastic moduli (Young's modulus and shear modulus) of the false fold tissues were calculated from the measured data. [Work supported by NIH.

  16. Identification of Major Risk Sources for Surface Water Pollution by Risk Indexes (RI) in the Multi-Provincial Boundary Region of the Taihu Basin, China.

    Science.gov (United States)

    Yao, Hong; Li, Weixin; Qian, Xin

    2015-08-21

    Environmental safety in multi-district boundary regions has been one of the focuses in China and is mentioned many times in the Environmental Protection Act of 2014. Five types were categorized concerning the risk sources for surface water pollution in the multi-provincial boundary region of the Taihu basin: production enterprises, waste disposal sites, chemical storage sites, agricultural non-point sources and waterway transportations. Considering the hazard of risk sources, the purification property of environmental medium and the vulnerability of risk receptors, 52 specific attributes on the risk levels of each type of risk source were screened out. Continuous piecewise linear function model, expert consultation method and fuzzy integral model were used to calculate the integrated risk indexes (RI) to characterize the risk levels of pollution sources. In the studied area, 2716 pollution sources were characterized by RI values. There were 56 high-risk sources screened out as major risk sources, accounting for about 2% of the total. The numbers of sources with high-moderate, moderate, moderate-low and low pollution risk were 376, 1059, 101 and 1124, respectively, accounting for 14%, 38%, 5% and 41% of the total. The procedure proposed could be included in the integrated risk management systems of the multi-district boundary region of the Taihu basin. It could help decision makers to identify major risk sources in the risk prevention and reduction of surface water pollution.

  17. Identification of Major Risk Sources for Surface Water Pollution by Risk Indexes (RI in the Multi-Provincial Boundary Region of the Taihu Basin, China

    Directory of Open Access Journals (Sweden)

    Hong Yao

    2015-08-01

    Full Text Available Environmental safety in multi-district boundary regions has been one of the focuses in China and is mentioned many times in the Environmental Protection Act of 2014. Five types were categorized concerning the risk sources for surface water pollution in the multi-provincial boundary region of the Taihu basin: production enterprises, waste disposal sites, chemical storage sites, agricultural non-point sources and waterway transportations. Considering the hazard of risk sources, the purification property of environmental medium and the vulnerability of risk receptors, 52 specific attributes on the risk levels of each type of risk source were screened out. Continuous piecewise linear function model, expert consultation method and fuzzy integral model were used to calculate the integrated risk indexes (RI to characterize the risk levels of pollution sources. In the studied area, 2716 pollution sources were characterized by RI values. There were 56 high-risk sources screened out as major risk sources, accounting for about 2% of the total. The numbers of sources with high-moderate, moderate, moderate-low and low pollution risk were 376, 1059, 101 and 1124, respectively, accounting for 14%, 38%, 5% and 41% of the total. The procedure proposed could be included in the integrated risk management systems of the multi-district boundary region of the Taihu basin. It could help decision makers to identify major risk sources in the risk prevention and reduction of surface water pollution.

  18. Hybrid-Mode-Assisted Long-Distance Excitation of Short-Range Surface Plasmons in a Nanotip-Enhanced Step-Index Fiber.

    Science.gov (United States)

    Tuniz, Alessandro; Chemnitz, Mario; Dellith, Jan; Weidlich, Stefan; Schmidt, Markus A

    2017-02-08

    We propose and experimentally demonstrate a monolithic nanowire-enhanced fiber-based nanoprobe for the broadband delivery of light (550-730 nm) to a deep subwavelength scale using short-range surface plasmons. The geometry is formed by a step index fiber with an integrated gold nanowire in its core and a protruding gold nanotip with sub-10 nm apex radius. We present a novel coupling scheme to excite short-range surface plasmons, whereby the radially polarized hybrid mode propagating inside the nanowire section excites the plasmonic mode close to the fiber endface, which is in turn superfocused down to nanoscale dimensions at the tip apex. We show that in this all-integrated fiber-plasmonic coupling scheme the wire length can be orders of magnitude longer than the attenuation length of short-range plasmon polaritons, yielding a broadband plasmon excitation and reducing demands in fabrication. We observe that the scattered light in the far-field from the nanotip is axially polarized and preferentially excited by a radially polarized input, unambiguously revealing that it originates from a short-range plasmon propagating on the nanotip, in agreement with simulations. This novel excitation scheme will have important applications in near-field microscopy and nanophotonics and potentially offers significantly improved resolution compared to current delivery near-field probes.

  19. Identification of Major Risk Sources for Surface Water Pollution by Risk Indexes (RI) in the Multi-Provincial Boundary Region of the Taihu Basin, China

    Science.gov (United States)

    Yao, Hong; Li, Weixin; Qian, Xin

    2015-01-01

    Environmental safety in multi-district boundary regions has been one of the focuses in China and is mentioned many times in the Environmental Protection Act of 2014. Five types were categorized concerning the risk sources for surface water pollution in the multi-provincial boundary region of the Taihu basin: production enterprises, waste disposal sites, chemical storage sites, agricultural non-point sources and waterway transportations. Considering the hazard of risk sources, the purification property of environmental medium and the vulnerability of risk receptors, 52 specific attributes on the risk levels of each type of risk source were screened out. Continuous piecewise linear function model, expert consultation method and fuzzy integral model were used to calculate the integrated risk indexes (RI) to characterize the risk levels of pollution sources. In the studied area, 2716 pollution sources were characterized by RI values. There were 56 high-risk sources screened out as major risk sources, accounting for about 2% of the total. The numbers of sources with high-moderate, moderate, moderate-low and low pollution risk were 376, 1059, 101 and 1124, respectively, accounting for 14%, 38%, 5% and 41% of the total. The procedure proposed could be included in the integrated risk management systems of the multi-district boundary region of the Taihu basin. It could help decision makers to identify major risk sources in the risk prevention and reduction of surface water pollution. PMID:26308032

  20. Relative Path Impact Index (RPII): a morphometric approach to quantify the effect of anthropogenic features on surface flow processes in agricultural landscapes

    Science.gov (United States)

    Tarolli, P.; Prosdocimi, M.; Sofia, G.; Preti, F.; Dalla Fontana, G.

    2014-12-01

    Soil erosion in cultivated land is one of the main critical issue because of its significant economic consequences, especially whether it occurs in hilly and mountainous environments. Among the cultivated lands, vineyards deserve a particular attention. In fact, they not only represent one of the most important crop in terms of income and employment, but they also constitute the form of agricultural land use that causes the highest soil loss. In these cultivated lands, the construction of terraces is one of the most widely used system for soil and water conservation measures. However, while favoring agricultural activities, terraces may cause local instabilities as well, if they are not properly maintained. Terraced fields are also served by agricultural roads and the construction of these anthropogenic features can have deep effects on water flows and instabilities. In fact, the plane surface of roads can intercept the overland and the subsurface flow and can modify the natural flow directions expanding the drainage network. The main objective of this work is to use high-resolution topography derived from lidar technology for a hydro-geomorphological analysis of terraced vineyards. We considered few case studies located in Italy. At first, the Relative Path Impact Index (RPII) is used to identify likely sections of terraces and agricultural roads subject to potential landsliding or erosion. Statistical thresholds of RPII are then defined to label the most critical areas. Afterwards, using the index and the defined thresholds, different scenarios of soil conservation measures are simulated, to establish the optimal solution for erosion reduction. The results prove the effectiveness of high-resolution topography in the analysis of surface erosion in terraced vineyards, when the surface water flow is the main factor triggering the instabilities. This preliminary analysis can help in scheduling a suitable planning to mitigate the consequences of the anthropogenic

  1. A comparison of RNA folding measures

    DEFF Research Database (Denmark)

    Freyhult, E.; Gardner, P. P.; Moulton, V.

    2005-01-01

    Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare...... the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. Results Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE) than...... random sequences with the same dinucleotide frequency. Moreover, even when the MFE is significant, many ncRNAs appear to not have a unique fold, but rather several alternative folds, at least when folded in silico. Furthermore, we find that the six investigated measures are correlated to varying degrees...

  2. Adaptive Origami for Efficiently Folded Structures

    Science.gov (United States)

    2016-02-01

    AFRL-RQ-WP-TR-2016-0020 ADAPTIVE ORIGAMI FOR EFFICIENTLY FOLDED STRUCTURES James J. Joo and Greg Reich Design and Analysis Branch... ORIGAMI FOR EFFICIENTLY FOLDED STRUCTURES 5a. CONTRACT NUMBER In-house 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S) James J...NOTES PA Case Number: 88ABW-2016-0843; Clearance Date: 25 February 2016. 14. ABSTRACT Origami , the art of paper folding, transforms a flat sheet into

  3. Primary cortical folding in the human newborn: an early marker of later functional development

    Science.gov (United States)

    Benders, M.; Borradori-Tolsa, C.; Cachia, A.; Lazeyras, F.; Ha-Vinh Leuchter, R.; Sizonenko, S. V.; Warfield, S. K.; Mangin, J. F.; Hüppi, P. S.

    2008-01-01

    In the human brain, the morphology of cortical gyri and sulci is complex and variable among individuals, and it may reflect pathological functioning with specific abnormalities observed in certain developmental and neuropsychiatric disorders. Since cortical folding occurs early during brain development, these structural abnormalities might be present long before the appearance of functional symptoms. So far, the precise mechanisms responsible for such alteration in the convolution pattern during intra-uterine or post-natal development are still poorly understood. Here we compared anatomical and functional brain development in vivo among 45 premature newborns who experienced different intra-uterine environments: 22 normal singletons, 12 twins and 11 newborns with intrauterine growth restriction (IUGR). Using magnetic resonance imaging (MRI) and dedicated post-processing tools, we investigated early disturbances in cortical formation at birth, over the developmental period critical for the emergence of convolutions (26–36 weeks of gestational age), and defined early ‘endophenotypes’ of sulcal development. We demonstrated that twins have a delayed but harmonious maturation, with reduced surface and sulcation index compared to singletons, whereas the gyrification of IUGR newborns is discordant to the normal developmental trajectory, with a more pronounced reduction of surface in relation to the sulcation index compared to normal newborns. Furthermore, we showed that these structural measurements of the brain at birth are predictors of infants’ outcome at term equivalent age, for MRI-based cerebral volumes and neurobehavioural development evaluated with the assessment of preterm infant's behaviour (APIB). PMID:18587151

  4. Green (In,Ga,Al)P-GaP light-emitting diodes grown on high-index GaAs surfaces

    Science.gov (United States)

    Ledentsov, N. N.; Shchukin, V. A.; Lyytikäinen, J.; Okhotnikov, O.; Cherkashin, N. A.; Shernyakov, Yu M.; Payusov, A. S.; Gordeev, N. Y.; Maximov, M. V.; Schlichting, S.; Nippert, F.; Hoffmann, A.

    2015-03-01

    We report on green (550-560 nm) electroluminescence (EL) from (Al0.5Ga0.5)0.5In0.5P-(Al0.8Ga0.2)0.5In0.5P double p-i-n heterostructures with monolayer-scale tensile strained GaP insertions in the cladding layers and light-emitting diodes (LEDs) based thereupon. The structures are grown side-by-side on high-index and (100) GaAs substrates by molecular beam epitaxy. Cross-sectional transmission electron microscopy studies indicate that GaP insertions are flat, thus the GaP-barrier substrate orientation-dependent heights should match the predictions of the flat model. At moderate current densities (~500 A/cm2) the EL intensity of the structures is comparable for all substrate orientations. Opposite to the (100)-grown strictures, the EL spectra of (211) and (311)-grown devices are shifted towards shorter wavelengths (~550 nm at room temperature). At high current densities (>1 kA/cm2) a much higher EL intensity is achieved for the devices grown on high-index substrates. The integrated intensity of (311)-grown structures gradually saturates at current densities above 4 kA/cm2, whereas no saturation is revealed for (211)-grown structures up to the current densities above 14 kA/cm2. We attribute the effect to the surface orientation-dependent engineering of the GaP band structure which prevents the escape of the nonequilibrium electrons into the indirect conduction band minima of the p- doped (Al0.8Ga0.2)0.5In0.5P cladding layers.

  5. Green (In,Ga,Al)P-GaP light-emitting diodes grown on high-index GaAs surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ledentsov, N. N., E-mail: nikolay.ledentsov@v-i-systems.com; Shchukin, V. A. [VI Systems GmbH, Hardenbergstr. 7, Berlin D-10623 (Germany); Lyytikäinen, J.; Okhotnikov, O. [Optoelectronics Research Centre, Tampere University of Technology, Tampere FI-33720 (Finland); Shernyakov, Yu. M.; Payusov, A. S.; Gordeev, N. Yu.; Maximov, M. V. [A. F. Ioffe Physical Technical Institute of the Russian Academy of Sciences, Politekhnicheskaya 26, St. Petersburg 194021 (Russian Federation); Schlichting, S.; Nippert, F.; Hoffmann, A. [Institut für Festkörperphysik, Technische Universität Berlin, Hardenbergstrasse 36, Berlin D-10623 (Germany)

    2014-11-03

    We report on green (550–560 nm) electroluminescence (EL) from (Al{sub 0.5}Ga{sub 0.5}){sub 0.5}In{sub 0.5}P-(Al{sub 0.8}Ga{sub 0.2}){sub 0.5}In{sub 0.5}P double p-i-n heterostructures with monolayer-scale GaP insertions in the cladding layers and light-emitting diodes based thereupon. The structures are grown side-by-side on high-index and (100) GaAs substrates by molecular beam epitaxy. At moderate current densities (∼500 A/cm{sup 2}), the EL intensity of the structures is comparable for all substrate orientations. Opposite to the (100)-grown strictures, the EL spectra of (211) and (311)-grown devices are shifted towards shorter wavelengths (∼550 nm at room temperature). At high current densities (>1 kA/cm{sup 2}), a much higher EL intensity is achieved for the devices grown on high-index substrates. The integrated intensity of (311)-grown structures gradually saturates at current densities above 4 kA/cm{sup 2}, whereas no saturation is revealed for (211)-grown structures up to the current densities above 14 kA/cm{sup 2}. We attribute the effect to the surface orientation-dependent engineering of the GaP band structure, which prevents the escape of the nonequilibrium electrons into the indirect conduction band minima of the p-doped (Al{sub 0.8}Ga{sub 0.2}){sub 0.5}In{sub 0.5}P cladding layers.

  6. Comparing MODIS and near-surface vegetation indexes for monitoring tropical dry forest phenology along a successional gradient using optical phenology towers

    Science.gov (United States)

    Rankine, C.; Sánchez-Azofeifa, G. A.; Guzmán, J. Antonio; Espirito-Santo, M. M.; Sharp, Iain

    2017-10-01

    Tropical dry forests (TDFs) present strong seasonal greenness signals ideal for tracking phenology and primary productivity using remote sensing techniques. The tightly synchronized relationship these ecosystems have with water availability offer a valuable natural experiment for observing the complex interactions between the atmosphere and the biosphere in the tropics. To investigate how well the MODIS vegetation indices (normalized difference vegetation index (NDVI) and the enhanced vegetation index (EVI)) represented the phenology of different successional stages of naturally regenerating TDFs, within a widely conserved forest fragment in the semi-arid southeast of Brazil, we installed several canopy towers with radiometric sensors to produce high temporal resolution near-surface vegetation greenness indices. Direct comparison of several years of ground measurements with a combined Aqua/Terra 8 day satellite product showed similar broad temporal trends, but MODIS often suffered from cloud contamination during the onset of the growing season and occasionally during the peak growing season. The strength of the in-situ and MODIS linear relationship was greater for NDVI than for EVI across sites but varied with forest stand age. Furthermore, we describe the onset dates and duration of canopy development phases for three years of in-situ monitoring. A seasonality analysis revealed significant discrepancies between tower and MODIS phenology transitions dates, with up to five weeks differences in growing season length estimation. Our results indicate that 8 and 16 day MODIS satellite vegetation monitoring products are suitable for tracking general patterns of tropical dry forest phenology in this region but are not temporally sufficient to characterize inter-annual differences in phenology phase onset dates or changes in productivity due to mid-season droughts. Such rapid transitions in canopy greenness are important indicators of climate change sensitivity of these

  7. Protein disulfide-isomerase interacts with a substrate protein at all stages along its folding pathway.

    Directory of Open Access Journals (Sweden)

    Alistair G Irvine

    Full Text Available In contrast to molecular chaperones that couple protein folding to ATP hydrolysis, protein disulfide-isomerase (PDI catalyzes protein folding coupled to formation of disulfide bonds (oxidative folding. However, we do not know how PDI distinguishes folded, partly-folded and unfolded protein substrates. As a model intermediate in an oxidative folding pathway, we prepared a two-disulfide mutant of basic pancreatic trypsin inhibitor (BPTI and showed by NMR that it is partly-folded and highly dynamic. NMR studies show that it binds to PDI at the same site that binds peptide ligands, with rapid binding and dissociation kinetics; surface plasmon resonance shows its interaction with PDI has a Kd of ca. 10(-5 M. For comparison, we characterized the interactions of PDI with native BPTI and fully-unfolded BPTI. Interestingly, PDI does bind native BPTI, but binding is quantitatively weaker than with partly-folded and unfolded BPTI. Hence PDI recognizes and binds substrates via permanently or transiently unfolded regions. This is the first study of PDI's interaction with a partly-folded protein, and the first to analyze this folding catalyst's changing interactions with substrates along an oxidative folding pathway. We have identified key features that make PDI an effective catalyst of oxidative protein folding - differential affinity, rapid ligand exchange and conformational flexibility.

  8. Treatment of vocal fold bowing using neuromuscular electrical stimulation.

    Science.gov (United States)

    Lagorio, Lisa A; Carnaby-Mann, Giselle D; Crary, Michael A

    2010-04-01

    To investigate the clinical effectiveness and safety of a novel behavioral voice therapy program combining structured vocal exercise with adjunctive neuromuscular electrical stimulation for rehabilitating dysphonia secondary to vocal fold bowing. Prospective interventional clinical case series with a 3-month follow-up. Outpatient speech and hearing clinic in an academic medical center. Convenience sample of 7 patients diagnosed by an otolaryngologist as having chronic dysphonia for at least 3 months due to bilateral vocal fold bowing. A novel voice therapy program incorporating exercise principles and sustained phonations of increasing length, volume, and pitch paired with concurrent transcutaneous neuromuscular electrical stimulation. Change in maximum phonation time, highest attainable pitch, glottal closure, supraglottic compression, and Voice Handicap Index. Maximum phonation time for /i/ increased significantly (z = -2.201, P vocal fold bowing, resulting in improved acoustic, laryngeal, and patient-centered outcomes. Maximum phonation time and glottal closure results imply increased vocal fold tension secondary to enhanced thyroarytenoid or cricothyroid muscle function after voice therapy.

  9. Guiding the folding pathway of DNA origami.

    Science.gov (United States)

    Dunn, Katherine E; Dannenberg, Frits; Ouldridge, Thomas E; Kwiatkowska, Marta; Turberfield, Andrew J; Bath, Jonathan

    2015-09-03

    DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

  10. Integrating ASCAT surface soil moisture and GEOV1 leaf area index into the SURFEX modelling platform: a land data assimilation application over France

    Directory of Open Access Journals (Sweden)

    A. L. Barbu

    2014-01-01

    Full Text Available The land monitoring service of the European Copernicus programme has developed a set of satellite-based biogeophysical products, including surface soil moisture (SSM and leaf area index (LAI. This study investigates the impact of joint assimilation of remotely sensed SSM derived from Advanced Scatterometer (ASCAT backscatter data and the Copernicus Global Land GEOV1 satellite-based LAI product into the the vegetation growth version of the Interactions between Soil Biosphere Atmosphere (ISBA-A-gs land surface model within the the externalised surface model (SURFEX modelling platform of Météo-France. The ASCAT data were bias corrected with respect to the model climatology by using a seasonal-based CDF (Cumulative Distribution Function matching technique. A multivariate multi-scale land data assimilation system (LDAS based on the extended Kalman Filter (EKF is used for monitoring the soil moisture, terrestrial vegetation, surface carbon and energy fluxes across the domain of France at a spatial resolution of 8 km. Each model grid box is divided into a number of land covers, each having its own set of prognostic variables. The filter algorithm is designed to provide a distinct analysis for each land cover while using one observation per grid box. The updated values are aggregated by computing a weighted average. In this study, it is demonstrated that the assimilation scheme works effectively within the ISBA-A-gs model over a four-year period (2008–2011. The EKF is able to extract useful information from the data signal at the grid scale and distribute the root-zone soil moisture and LAI increments throughout the mosaic structure of the model. The impact of the assimilation on the vegetation phenology and on the water and carbon fluxes varies from one season to another. The spring drought of 2011 is an interesting case study of the potential of the assimilation to improve drought monitoring. A comparison between simulated and in situ soil

  11. Stretched versus compressed exponential kinetics in α-helix folding

    International Nuclear Information System (INIS)

    Hamm, Peter; Helbing, Jan; Bredenbeck, Jens

    2006-01-01

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

  12. Merging monads and folds for functional programming

    NARCIS (Netherlands)

    Meijer, E.; Jeuring, J.T.

    1995-01-01

    These notes discuss the simultaneous use of generalised fold operators and monads to structure functional programs. Generalised fold operators structure programs after the decomposition of the value they consume. Monads structure programs after the computation of the value they produce. Our programs

  13. Folded tandem ion accelerator facility at Trombay

    Indian Academy of Sciences (India)

    Keywords. Folded tandem ion accelerator; carbon beam; magnets; electrostatic deflector; quadrupole lenses; foil/gas strippers; Rutherford back scattering. Abstract. The folded tandem ion accelerator (FOTIA) project at BARC has been commissioned. The analysed carbon beams of 40 nA(3+) and 25 nA(4+), at terminal ...

  14. Accelerated molecular dynamics simulations of protein folding.

    Science.gov (United States)

    Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew

    2015-07-30

    Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.

  15. THE ALPHA/BETA-HYDROLASE FOLD

    NARCIS (Netherlands)

    OLLIS, DL; CHEAH, E; CYGLER, M; FROLOW, F; FRANKEN, SM; HAREL, M; REMINGTON, SJ; SILMAN, [No Value; SCHRAG, J; SUSSMAN, JL; VERSCHUEREN, KHG; GOLDMAN, A

    We have identified a new protein fold-the alpha/beta-hydrolase fold-that is common to several hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is similar: an alpha/beta-sheet, not barrel, of eight beta-sheets connected by alpha-helices. These

  16. Graph-representation of oxidative folding pathways

    Directory of Open Access Journals (Sweden)

    Kaján László

    2005-01-01

    Full Text Available Abstract Background The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS which can also be isolated and characterized. Each DIS corresponds to a family of folding states (conformations that the given DIS can adopt in three dimensions. Results The oxidative folding space can be represented as a network of DIS states interconnected by disulfide interchange reactions that can either create/abolish or rearrange disulfide bridges. We propose a simple 3D representation wherein the states having the same number of disulfide bridges are placed on separate planes. In this representation, the shuffling transitions are within the planes, and the redox edges connect adjacent planes. In a number of experimentally studied cases (bovine pancreatic trypsin inhibitor, insulin-like growth factor and epidermal growth factor, the observed intermediates appear as part of contiguous oxidative folding pathways. Conclusions Such networks can be used to visualize folding pathways in terms of the experimentally observed intermediates. A simple visualization template written for the Tulip package http://www.tulip-software.org/ can be obtained from V.A.

  17. Fold and Fit: Space Conserving Shape Editing

    KAUST Repository

    Ibrahim, Mohamed

    2017-09-01

    We present a framework that folds man-made objects in a structure-aware manner for space-conserving storage and transportation. Given a segmented 3D mesh of a man-made object, our framework jointly optimizes for joint locations, the folding order, and folding angles for each part of the model, enabling it to transform into a spatially efficient configuration while keeping its original functionality as intact as possible. That is, if a model is supposed to withstand several forces in its initial state to serve its functionality, our framework places the joints between the parts of the model such that the model can withstand forces with magnitudes that are comparable to the magnitudes applied on the unedited model. Furthermore, if the folded shape is not compact, our framework proposes further segmentation of the model to improve its compactness in its folded state.

  18. Geometric U-folds in four dimensions

    Science.gov (United States)

    Lazaroiu, C. I.; Shahbazi, C. S.

    2018-01-01

    We describe a general construction of geometric U-folds compatible with a non-trivial extension of the global formulation of four-dimensional extended supergravity on a differentiable spin manifold. The topology of geometric U-folds depends on certain flat fiber bundles which encode how supergravity fields are globally glued together. We show that smooth non-trivial U-folds of this type can exist only in theories where both the scalar and space-time manifolds have non-trivial fundamental group and in addition the scalar map of the solution is homotopically non-trivial. Consistency with string theory requires smooth geometric U-folds to be glued using subgroups of the effective discrete U-duality group, implying that the fundamental group of the scalar manifold of such solutions must be a subgroup of the latter. We construct simple examples of geometric U-folds in a generalization of the axion-dilaton model of \

  19. Fan-fold shielded electrical leads

    Science.gov (United States)

    Rohatgi, Rajeev R.; Cowan, Thomas E.

    1996-01-01

    Fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate.

  20. Multi-objective room acoustic optimization of timber folded plate structure

    DEFF Research Database (Denmark)

    Skov, Rasmus; Parigi, Dario; Damkilde, Lars

    2017-01-01

    This paper investigates the application of multi-objective optimization in the design of timber folded plate structures in the scope of the architectural design process. Considering contrasting objectives of structural displacement, early decay time (EDT), clarity (C50) and sound strength (G......), the methodology applied in two benchmarks tests, encompasses both structural and acoustic performance when determining folding characteristics and directionality of surfaces in a timber folded plate structure....

  1. Abstracts and parameter index database for reports pertaining to the unsaturated zone and surface water-ground water interactions at the Idaho National Engineering Laboratory

    International Nuclear Information System (INIS)

    Bloomsburg, G.; Finnie, J.; Horn, D.; King, B.; Liou, J.

    1993-05-01

    This report is a product generated by faculty at the University of Idaho in support of research and development projects on Unsaturated Zone Contamination and Transport Processes, and on Surface Water-Groundwater Interactions and Regional Groundwater Flow at the Idaho National Engineering Laboratory. These projects are managed by the State of Idaho's INEL Oversight Program under a grant from the US Department of Energy. In particular, this report meets project objectives to produce a site-wide summary of hydrological information based on a literature search and review of field, laboratory and modeling studies at INEL, including a cross-referenced index to site-specific physical, chemical, mineralogic, geologic and hydrologic parameters determined from these studies. This report includes abstracts of 149 reports with hydrological information. For reports which focus on hydrological issues, the abstracts are taken directly from those reports; for reports dealing with a variety of issues beside hydrology, the abstracts were generated by the University of Idaho authors concentrating on hydrology-related issues. Each abstract is followed by a ''Data'' section which identifies types of technical information included in a given report, such as information on parameters or chemistry, mineralogy, stream flows, water levels. The ''Data'' section does not include actual values or data

  2. Monitoring change in refractive index of cytosol of animal cells on affinity surface under osmotic stimulus for label-free measurement of viability.

    Science.gov (United States)

    Park, Jina; Jin, Sung Il; Kim, Hyung Min; Ahn, Junhyoung; Kim, Yeon-Gu; Lee, Eun Gyo; Kim, Min-Gon; Shin, Yong-Beom

    2015-02-15

    We demonstrated that a metal-clad waveguide (MCW)-based biosensor can be applied to label-free measurements of viability of adherent animal cells with osmotic stimulation in real time. After Chinese hamster ovary (CHO) and human embryonic kidney cell 293 (HEK293) cells were attached to a Concanavalin A (Con A)-modified sensor surface, the magnitudes of cell responses to non-isotonic stimulation were compared between live and dead cells. The live cells exhibited a change in the refractive index (RI) of the cytosol caused by a redistribution of water through the cell membrane, which was induced by the osmotic stimulus, but the dead cells did not. Moreover, the normalized change in the RI measured via the MCW sensor was linearly proportional to the viability of attached cells and the resolution in monitoring cell viability was about 0.079%. Therefore, the viability of attached animal cells can be measured without labels by observing the relative differences in the RI of cytosol in isotonic and non-isotonic buffers. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. High-Efficiency and High-Color-Rendering-Index Semitransparent Polymer Solar Cells Induced by Photonic Crystals and Surface Plasmon Resonance.

    Science.gov (United States)

    Shen, Ping; Wang, Guoxin; Kang, Bonan; Guo, Wenbin; Shen, Liang

    2018-02-21

    Semitransparent polymer solar cells (ST-PSCs) show attractive potential in power-generating windows or building-integrated photovoltaics. However, the development of ST-PSCs is lagging behind opaque PSCs because of the contradiction between device efficiency and transmission. Herein, Ag/Au alloy nanoparticles and photonic crystals (PCs) were simultaneously introduced into ST-PSCs, acting compatibly as localized surface plasmon resonances and distributed Bragg reflectors to enhance light absorption and transmission. As a result, ST-PSCs based on a hybrid PTB7-Th:PC 71 BM active layer contribute an efficiency as high as 7.13 ± 0.15% and an average visible transmission beyond 20%, which are superior to most of the reported results. Furthermore, PCs can partly compensate valley range of transmission by balancing reflection and transmission regions, yielding a high color rendering index of 95. We believe that the idea of two light management methods compatibly enhancing the performance of ST-PSCs can offer a promising path to develop photovoltaic applications.

  4. Self-folding polymeric containers for encapsulation and delivery of drugs.

    Science.gov (United States)

    Fernandes, Rohan; Gracias, David H

    2012-11-01

    Self-folding broadly refers to self-assembly processes wherein thin films or interconnected planar templates curve, roll-up or fold into three dimensional (3D) structures such as cylindrical tubes, spirals, corrugated sheets or polyhedra. The process has been demonstrated with metallic, semiconducting and polymeric films and has been used to curve tubes with diameters as small as 2nm and fold polyhedra as small as 100nm, with a surface patterning resolution of 15nm. Self-folding methods are important for drug delivery applications since they provide a means to realize 3D, biocompatible, all-polymeric containers with well-tailored composition, size, shape, wall thickness, porosity, surface patterns and chemistry. Self-folding is also a highly parallel process, and it is possible to encapsulate or self-load therapeutic cargo during assembly. A variety of therapeutic cargos such as small molecules, peptides, proteins, bacteria, fungi and mammalian cells have been encapsulated in self-folded polymeric containers. In this review, we focus on self-folding of all-polymeric containers. We discuss the mechanistic aspects of self-folding of polymeric containers driven by differential stresses or surface tension forces, the applications of self-folding polymers in drug delivery and we outline future challenges. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Shallow seismic imaging of folds above the Puente Hills blind-thrust fault, Los Angeles, California

    Science.gov (United States)

    Pratt, Thomas L.; Shaw, John H.; Dolan, James F.; Christofferson, Shari A.; Williams, Robert A.; Odum, Jack K.; Plesch, Andreas

    2002-05-01

    High-resolution seismic reflection profiles image discrete folds in the shallow subsurface (Puente Hills blind-thrust fault system, Los Angeles basin, California. The profiles demonstrate late Quaternary activity at the fault tip, precisely locate the axial surfaces of folds within the upper 100 m, and constrain the geometry and kinematics of recent folding. The Santa Fe Springs segment of the Puente Hills fault zone shows an upward-narrowing kink band with an active anticlinal axial surface, consistent with fault-bend folding above an active thrust ramp. The Coyote Hills segment shows an active synclinal axial surface that coincides with the base of a 9-m-high scarp, consistent with tip-line folding or the presence of a backthrust. The seismic profiles pinpoint targets for future geologic work to constrain slip rates and ages of past events on this important fault system.

  6. Lithological Controls on 3D Fold Geometry in Mechanically Layered Rocks

    Science.gov (United States)

    Pearce, M. A.; Jones, R. R.; Rock, G.

    2010-12-01

    Folding and thrusting are key processes in accommodating shortening in evolving orogens. In the outer parts of mountain belts, the combination of tectonism and sedimentation often leads to viable petroleum systems where folds trap migrating hydrocarbons. A key aspect of the success of these traps is the 3D fold geometry, which must prevent up-plunge hydrocarbon escape. Fold shapes in a multilayered system are governed by the fold mechanism, and the rheology of the layers. In sedimentary environments where laterally heterogeneous thicknesses of interbedded carbonates, clastics, and evaporates may be present, predicting the sub-surface geometry of structures is challenging. We present field data combined with satellite and seismic interpretation from the Zagros fold and thrust belt of SE Turkey where Neogene shortening has affected an Ordovician to Miocene aged sedimentary pile comprising shales, sandstones, carbonates and minor evaporites. Miocene carbonates capping the sequence allow 3D fold geometries to be ascertained at surface with a high degree of confidence, whilst the underlying ~1km of shales and mudstones allows folds to develop that depart substantially from standard “text-book” geometries. Beneath these incompetent units a further 1.7km of carbonates and clastics overlie Ordovician shales up to 1.5km thick. In relatively low strain sections asymmetric, angular, kink-like folds form long wavelength structures and thrust faults rarely reach the surface. With increasing strain, the wavelength/amplitude ratio decreases and thrusts cut through the fold limbs. Folds are interpreted to detach above a thick sequence of Ordovician shales. They originate by buckling of the competent units within the two weaker horizons, with initial perturbations probably provided by sedimentary heterogeneities. As the folds amplify, thrusts form in the more competent units above the shale. These then propagate upwards with fold amplification dominated by fault-tip

  7. Combining optimal control theory and molecular dynamics for protein folding.

    Science.gov (United States)

    Arkun, Yaman; Gur, Mert

    2012-01-01

    A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG) protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD) which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.

  8. Combining optimal control theory and molecular dynamics for protein folding.

    Directory of Open Access Journals (Sweden)

    Yaman Arkun

    Full Text Available A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD. In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the Cα atoms. In turn, MD simulation provides an all-atom conformation whose Cα positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the Cα atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages.

  9. Performance of isolated and folded footings

    Directory of Open Access Journals (Sweden)

    Mahmoud Samir El-kady

    2017-04-01

    Full Text Available Folded foundations have been used as an alternative to the conventional flat shallow foundations, in situations involving heavy loads or weak soils. They can be geometrically shaped in many forms especially for isolated footings. The purpose of this paper is introducing an alternative foundation shape that reduces the cost of foundations by reducing the amount of reinforcing steel by minimizing or even eliminating the tension zones in the folded isolated footings. Also, achieving lower soil stresses through changing the isolated footing shape will consequently reduce the expected settlements and the footing stresses. Experimental and numerical studies are performed on five (5 quarter scale footings of which one (1 footing of flat shape is tested as a reference sample and four (4 footings are of folded shape by folding angles of 10°, 20°, 30°, and 40° with the horizontal. Results showed that the folded isolated footings achieve economic design by decreasing the quantities of reinforcement. It also induced less soil settlements, and stresses. In addition, the tensile stresses in the reinforced concrete footing body are also less in folded isolated footings than the flat one. Results show that the folded isolated footing have a better load carrying capacity when compared with the conventional slab/flat footing of similar cross sectional area for both cases of experimental and numerical analysis.

  10. Mapping the Universe of RNA Tetraloop Folds.

    Science.gov (United States)

    Bottaro, Sandro; Lindorff-Larsen, Kresten

    2017-07-25

    We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the relationship among the different folds. The cluster analysis also identifies 20 novel tetraloop folds that are peculiar to specific positions in ribosomal RNAs and that are stabilized by tertiary interactions. In our RNA tetraloop database we find a significant number of non-GNRA and non-UNCG sequences adopting the canonical GNRA and UNCG folds. Conversely, we find a significant number of GNRA and UNCG sequences adopting non-GNRA and non-UNCG folds. Our analysis demonstrates that there is not a simple one-to-one, but rather a many-to-many mapping between tetraloop sequence and tetraloop fold. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  11. A versatile selection system for folding competent proteins using genetic complementation in a eukaryotic host

    DEFF Research Database (Denmark)

    Lyngsø, C.; Kjaerulff, S.; Muller, S.

    2010-01-01

    -control systems to retain misfolded proteins in the ER and redirect them for cytosolic degradation, thereby only allowing folded proteins to reach the cell surface. Accordingly, the folding potential of the tested protein determines the ability of autotrophic colony growth. This system was successfully...

  12. Folded Plate Structures as Building Envelopes

    DEFF Research Database (Denmark)

    Falk, Andreas; Buelow, Peter von; Kirkegaard, Poul Henning

    2012-01-01

    This paper treats applications of cross-laminated timber (CLT) in structural systems for folded façade solutions. Previous work on CLT-based systems for folded roofs has shown a widening range of structural possibilities to develop timber-based shells. Geometric and material properties play...... CLT-based systems, which are studied and analysed by using a combination of digital tools for structural and environmental design and analysis. The results show gainful, rational properties of folded systems and beneficial effects from an integration of architectural and environmental performance...... criteria in the design of CLT-based façades....

  13. A bidirectional shape memory alloy folding actuator

    International Nuclear Information System (INIS)

    Paik, Jamie K; Wood, Robert J

    2012-01-01

    This paper presents a low-profile bidirectional folding actuator based on annealed shape memory alloy sheets applicable for meso- and microscale systems. Despite the advantages of shape memory alloys—high strain, silent operation, and mechanical simplicity—their application is often limited to unidirectional operation. We present a bidirectional folding actuator that produces two opposing 180° motions. A laser-patterned nickel alloy (Inconel 600) heater localizes actuation to the folding sections. The actuator has a thin ( < 1 mm) profile, making it appropriate for use in robotic origami. Various design parameters and fabrication variants are described and experimentally explored in the actuator prototype. (paper)

  14. Melody discrimination and protein fold classification

    Directory of Open Access Journals (Sweden)

    Robert P. Bywater

    2016-10-01

    Full Text Available One of the greatest challenges in theoretical biophysics and bioinformatics is the identification of protein folds from sequence data. This can be regarded as a pattern recognition problem. In this paper we report the use of a melody generation software where the inputs are derived from calculations of evolutionary information, secondary structure, flexibility, hydropathy and solvent accessibility from multiple sequence alignment data. The melodies so generated are derived from the sequence, and by inference, of the fold, in ways that give each fold a sound representation that may facilitate analysis, recognition, or comparison with other sequences.

  15. Mechanical Models of Fault-Related Folding

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  16. Self-folding miniature elastic electric devices

    International Nuclear Information System (INIS)

    Miyashita, Shuhei; Meeker, Laura; Rus, Daniela; Tolley, Michael T; Wood, Robert J

    2014-01-01

    Printing functional materials represents a considerable impact on the access to manufacturing technology. In this paper we present a methodology and validation of print-and-self-fold miniature electric devices. Polyvinyl chloride laminated sheets based on metalized polyester film show reliable self-folding processes under a heat application, and it configures 3D electric devices. We exemplify this technique by fabricating fundamental electric devices, namely a resistor, capacitor, and inductor. Namely, we show the development of a self-folded stretchable resistor, variable resistor, capacitive strain sensor, and an actuation mechanism consisting of a folded contractible solenoid coil. Because of their pre-defined kinematic design, these devices feature elasticity, making them suitable as sensors and actuators in flexible circuits. Finally, an RLC circuit obtained from the integration of developed devices is demonstrated, in which the coil based actuator is controlled by reading a capacitive strain sensor. (paper)

  17. Folded Resonant Horns for Power Ultrasonic Applications

    Science.gov (United States)

    Sherrit, Stewart; Askins, Stephen; Gradziel, Michael; Bao, Xiaoqi; Chang, Zensheu; Dolgin, Benjamin; Bar-Cohen, Yoseph; Peterson, Tom

    2003-01-01

    Folded horns have been conceived as alternatives to straight horns used as resonators and strain amplifiers in power ultrasonic systems. Such systems are used for cleaning, welding, soldering, cutting, and drilling in a variety of industries. In addition, several previous NASA Tech Briefs articles have described instrumented drilling, coring, and burrowing machines that utilize combinations of sonic and ultrasonic vibrational actuation. The main advantage of a folded horn, relative to a straight horn of the same resonance frequency, is that the folded horn can be made shorter (that is, its greatest linear dimension measured from the outside can be made smaller). Alternatively, for a given length, the resonance frequency can be reduced. Hence, the folded-horn concept affords an additional degree of design freedom for reducing the length of an ultrasonic power system that includes a horn.

  18. Cycle 24 COS/NUV Fold Distribution

    Science.gov (United States)

    Wheeler, Thomas; Welty, Alan

    2018-02-01

    We summarize the Cycle 24 COS/NUV Fold Distribution for the Cosmic Origins Spectrograph's (COS) MAMA detector on the Hubble Space Telescope. The detector micro-channel plate's health state is determined and the results presented.

  19. Topology Explains Why Automobile Sunshades Fold Oddly

    Science.gov (United States)

    Feist, Curtis; Naimi, Ramin

    2009-01-01

    Automobile sunshades always fold into an "odd" number of loops. The explanation why involves elementary topology (braid theory and linking number, both explained in detail here with definitions and examples), and an elementary fact from algebra about symmetric group.

  20. Origami: Paper Folding--The Algorithmic Way.

    Science.gov (United States)

    Heukerott, Pamela Beth

    1988-01-01

    Describes origami, the oriental art of paper folding as an activity to teach upper elementary students concepts and skills in geometry involving polygons, angles, measurement, symmetry, and congruence. (PK)

  1. Vocal Fold Pathologies and Three-Dimensional Flow Separation Phenomena

    Science.gov (United States)

    Apostoli, Adam G.; Weiland, Kelley S.; Plesniak, Michael W.

    2013-11-01

    Polyps and nodules are two different pathologies, which are geometric abnormalities that form on the medial surface of the vocal folds, and have been shown to significantly disrupt a person's ability to communicate. Although the mechanism by which the vocal folds self-oscillate and the three-dimensional nature of the glottal jet has been studied, the effect of irregularities caused by pathologies is not fully understood. Examining the formation and evolution of vortical structures created by a geometric protuberance is important, not only for understanding the aerodynamic forces exerted by these structures on the vocal folds, but also in the treatment of the above-mentioned pathological conditions. Using a wall-mounted prolate hemispheroid with a 2:1 aspect ratio in cross flow, the present investigation considers three-dimensional flow separation induced by a model vocal fold polyp. Building on previous work using skin friction line visualization, both the velocity flow field and wall pressure measurements around the model polyp are presented and compared. Supported by the National Science Foundation, Grant No. CBET-1236351 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  2. Surface cover infiltration index: a suggested method to assess infiltration capacity for intrinsic vulnerability in karstic areas in absence of quantitative data

    Directory of Open Access Journals (Sweden)

    Tezcan Levent

    2004-12-01

    Full Text Available Karst is a hydrogeological environment of importance not only for its water resources potential but also for its scenic and economic potential, thereby increasing the intensity of human impact. The uniqueness of karst in this regard stems from its high sensitivity and vulnerability to imposed pressures and its distinctive response to these pressures. Therefore, a clear definition and formulation of the concept of ‘intrinsic vulnerability’ is essential for the design of vulnerability and/or management criteria of the karstic system as a resource. In this regard, the recharge rate, the amount of water passing through the unsaturated zone into the aquifer, is among the principal attributes of the intrinsic vulnerability. Where data and measurements are available for even large areas, recharge can be evaluated quantitatively on the basis of field measurements and the water balance equation. However, particularly for countries suffering from lack of essential data for a quantitative evaluation of the net recharge rate, the recharge can be estimated using some derived parameters such as the so called ‘Surface Cover Infiltration Index’ proposed in this paper. The DRASTIC method which is modified by using SCI, soil thickness and precipitation, allows the unique hydrological behavior of karst to be considered by redistributing of the intrinsic vulnerability values on the basis of hydrologic connections between neighboring cells. Following a detailed description of the SCI index and the modification of DRASTIC method for karst aquifers, a case study carried out to demonstrate this method is presented in this paper whose objective is to discuss and thus elaborate the suggested methodology. The Olimpos National Park area was selected because the great variation in lithology, landuse and topography. It was found that the relative vulnerability may vary particularly in the neighborhood of the highly vulnerable cells covered by carbonate rocks. The

  3. Comparison of Two Questionnaires for Dry Eye Symptom Assessment: The Ocular Surface Disease Index and the Symptom Assessment in Dry Eye.

    Science.gov (United States)

    Amparo, Francisco; Schaumberg, Debra A; Dana, Reza

    2015-07-01

    The aim of this study was to compare patient-reported symptoms of dry eye disease (DED) as assessed by the Ocular Surface Disease Index (OSDI), a 12-item symptom frequency-based questionnaire, and the Symptom Assessment iN Dry Eye (SANDE), a 2-item frequency- and severity-based visual analog scale. Clinic-based evaluation of a diagnostic test. A total of 114 patients with DED. Patients were administered the OSDI and SANDE questionnaires at baseline and follow-up visits to evaluate DED-related symptoms. The correlations between both questionnaires' scores were evaluated using the Spearman coefficient, and their clinical differences were assessed using Bland-Altman analysis. Baseline and follow-up visit OSDI and SANDE dry eye symptom scores. At the baseline visit, the OSDI and SANDE questionnaire scores were significantly correlated (R = 0.64; P < 0.001). Moreover, a significant correlation was found between changes in the OSDI and SANDE scores from baseline to follow-up visits (R = 0.47; P < 0.001). A Bland-Altman analysis, after score normalization, revealed a difference (bias) of less than 2 centesimal units between the scores of the 2 questionnaires. Data collected from the SANDE questionnaire showed a significant correlation and negligible score differences with those from the OSDI, suggesting that the SANDE visual analog scale-based questionnaire has the potential to provide clinicians with a short, quick, and reliable measure for DED symptoms. Copyright © 2015 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

  4. Characterizing ecosystem response to water supply changes inferred from GRACE drought severity index and surface soil moisture anomalies from ESA CCI and SMAP

    Science.gov (United States)

    Zhao, M.; Velicogna, I.; Kimball, J. S.

    2017-12-01

    Climate change such as more frequent heatwaves and drought is threatening our food security and ecosystem by reducing water supply to vegetation. Characterizing vegetation response to water supply changes is not only important for evaluating and mitigating climatic change impacts on ecosystem functions and services, but also to determine the feedback mechanisms that ecosystem response may generate on the climate itself. However, such characterization is not well-known at the global scale partly because large scale observations of underground water supply changes are limited. Satellite observations of soil moisture (SM) datasets such as from Soil Moisture Active and Passive (SMAP) and European Space Agency Climate Change Initiative (ESA CCI) do not penetrate more than a few centimeters and do not capture the entire root-zone. Here we employ a newly developed Drought Severity Index from Gravity Recovery and Climate Experiment (GRACE-DSI) to complement SM observations by informing total water supply changes in the entire terrestrial hydrological cycle. We use MODIS vegetation indices as proxies for vegetation growth and investigate their seasonal and interannual variability in relation to GRACE-DSI. We find that total water supply constrains vegetation growth across the entire continental US. Water constraint begins at an earlier date of year and lasts for a longer period in the lower latitude than in the higher latitude. We also find that water constraint occurs at different phenological stages depending on vegetation type. For instance, water constrain forest growth during reproductive period in eastern US but constrain shrub land growth during green-up in Arizona (Fig. 1). In western United States, eastern Australia and the horn of Africa, we find that vegetation growth changes closely follows GRACE-DSI but can have 16-day to one-month delay with respect to SM anomalies from SMAP and ESA CCI. This suggests that in these regions, vegetation is sensitive to water

  5. "Wet" Versus "Dry" Folding of Polyproline

    Science.gov (United States)

    Shi, Liuqing; Holliday, Alison E.; Bohrer, Brian C.; Kim, Doyong; Servage, Kelly A.; Russell, David H.; Clemmer, David E.

    2016-06-01

    When the all- cis polyproline-I helix (PPI, favored in 1-propanol) of polyproline-13 is introduced into water, it folds into the all- trans polyproline-II (PPII) helix through at least six intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we show that the solvent-free intermediates refold into the all- cis PPI helix with high (>90%) efficiency. Moreover, in the absence of solvent, each intermediate appears to utilize the same small set of pathways observed for the solution-phase PPII → PPI transition upon immersion of PPIIaq in 1-propanol. That folding in solution (under conditions where water is displaced by propanol) and folding in vacuo (where energy required for folding is provided by collisional activation) occur along the same pathway is remarkable. Implicit in this statement is that 1-propanol mimics a "dry" environment, similar to the gas phase. We note that intermediates with structures that are similar to PPIIaq can form PPII under the most gentle activation conditions—indicating that some transitions observed in water (i.e. , "we t" folding, are accessible (albeit inefficient) in vacuo. Lastly, these "dry" folding experiments show that PPI (all cis) is favored under "dry" conditions, which underscores the role of water as the major factor promoting preference for trans proline.

  6. Large gastric folds arising in polyposis syndromes

    Directory of Open Access Journals (Sweden)

    Xiang-Yang Wangz

    2013-08-01

    Full Text Available Large gastric folds (LGF can be caused by benign conditions as well as malignancies. Unfortunately, endoscopic features and biopsy results are often equivocal, making the diagnosis and management of large gastric folds difficult. Polyposis syndromes encompass a group of conditions in which multiple gastrointestinal polyps occur in the lumen of the gut. Large gastric folds are extremely rare in these syndromes. We present the case of a patient with polyposis who was found to have large gastric folds in the entire gastric fundus and body, mimicking malignancy. The patient's medical history and endoscopic ultrasonography (EUS with mucosal resection confirmed the diagnosis of a pre-malignant disease. The lesion was monitored by serial endoscopic ultrasonography and biopsy, abdominal computed tomography (CT, and positron emission and computed tomography (PET-CT for 6 years. The lesion remained stable, with the exception of abnormal fluorodeoxyglucose uptake on PET-CT in the gastric folds, which was determined to be a false-positive sign. To date, the patient remains healthy. We further discuss the mechanisms underlying the formation of large gastric folds caused by polyposis syndromes. Helicobacter pylori (H. pylori or cytomegalovirus (CMV is unnecessary for this progression. Immunohistochemistry (IHC staining suggested that overexpression of transforming growth factor alpha (TGF-α and down-regulation of myocyte enhancer-binding factor 2 (MEF2 may be involved in this case.

  7. In-Situ Observation of Membrane Protein Folding during Cell-Free Expression.

    Directory of Open Access Journals (Sweden)

    Axel Baumann

    Full Text Available Proper insertion, folding and assembly of functional proteins in biological membranes are key processes to warrant activity of a living cell. Here, we present a novel approach to trace folding and insertion of a nascent membrane protein leaving the ribosome and penetrating the bilayer. Surface Enhanced IR Absorption Spectroscopy selectively monitored insertion and folding of membrane proteins during cell-free expression in a label-free and non-invasive manner. Protein synthesis was performed in an optical cell containing a prism covered with a thin gold film with nanodiscs on top, providing an artificial lipid bilayer for folding. In a pilot experiment, the folding pathway of bacteriorhodopsin via various secondary and tertiary structures was visualized. Thus, a methodology is established with which the folding reaction of other more complex membrane proteins can be observed during protein biosynthesis (in situ and in operando at molecular resolution.

  8. Frnakenstein: multiple target inverse RNA folding

    Directory of Open Access Journals (Sweden)

    Lyngsø Rune B

    2012-10-01

    Full Text Available Abstract Background RNA secondary structure prediction, or folding, is a classic problem in bioinformatics: given a sequence of nucleotides, the aim is to predict the base pairs formed in its three dimensional conformation. The inverse problem of designing a sequence folding into a particular target structure has only more recently received notable interest. With a growing appreciation and understanding of the functional and structural properties of RNA motifs, and a growing interest in utilising biomolecules in nano-scale designs, the interest in the inverse RNA folding problem is bound to increase. However, whereas the RNA folding problem from an algorithmic viewpoint has an elegant and efficient solution, the inverse RNA folding problem appears to be hard. Results In this paper we present a genetic algorithm approach to solve the inverse folding problem. The main aims of the development was to address the hitherto mostly ignored extension of solving the inverse folding problem, the multi-target inverse folding problem, while simultaneously designing a method with superior performance when measured on the quality of designed sequences. The genetic algorithm has been implemented as a Python program called Frnakenstein. It was benchmarked against four existing methods and several data sets totalling 769 real and predicted single structure targets, and on 292 two structure targets. It performed as well as or better at finding sequences which folded in silico into the target structure than all existing methods, without the heavy bias towards CG base pairs that was observed for all other top performing methods. On the two structure targets it also performed well, generating a perfect design for about 80% of the targets. Conclusions Our method illustrates that successful designs for the inverse RNA folding problem does not necessarily have to rely on heavy biases in base pair and unpaired base distributions. The design problem seems to become more

  9. Upright folding during extensional and transtensional tectonics

    Science.gov (United States)

    Teyssier, Christian; Fossen, Haakon; Rey, Patrice F.; Whitney, Donna L.

    2017-04-01

    Upright folds are common structures that develop in response to horizontal shortening in layered material, for example in foreland basins that surround orogens. While the contractional nature of these folds is not in doubt, interpretation of their tectonic setting needs careful consideration. Here we focus on two examples: (1) folds developed in transtension; and (2) folds developed during the flow of deep crust in response to lithospheric extension. In both cases we consider folding of nearly horizontal layers that are either primary (bedding) or secondary (foliation). Strain theory inspired by John Ramsay's work makes predictions for the behavior of material lines and planes as well as strain axes (instantaneous, finite) during transtensional deformation. Results show: folds can form in transtension; fold hinges rotate toward the direction of divergence (and not the shear zone boundary as they do in transpression), providing unique insight into ancient plate motions; fold tightness is controlled by the obliquity of divergence and not finite strain; hinge parallel stretching is always greater than hinge-perpendicular shortening, resulting in constriction strain and boudinage of fold hinges. Taken together these results provide a rigorous framework for interpreting field observations where structures are complex and boundary conditions unclear. These principles are applied to various tectonic settings ranging from active tectonic regions of oblique divergence in western North America to ancient folding that developed during oblique extension of the Western Gneiss Region, deposition of Devonian basins, and exhumation of ultrahigh-pressure rocks in the Norwegian Caledonides. The other class of upright folds that form during extension may require revision of the tectonic interpretation of structural overprints in orogenic cores, for example in gneiss/migmatite domes. Dynamic modeling of extension of thick/hot crust predicts a positive feedback between extension of

  10. Side chain and backbone contributions of Phe508 to CFTR folding

    Energy Technology Data Exchange (ETDEWEB)

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  11. Afghanistan Index

    DEFF Research Database (Denmark)

    Linnet, Poul Martin

    2007-01-01

    The Afghanistan index is a compilation of quantitative and qualitative data on the reconstruction and security effort in Afghanistan. The index aims at providing data for benchmarking of the international performance and thus provides the reader with a quick possibility to retrieve valid...... information on progress or lack of progress in the reconstruction of the post Taliban Afghanistan. The index is mainly based on information collected on the internet in order to provide quick access to the original source. The index is under development and thus new information will be added on a continuous...

  12. ParkIndex

    DEFF Research Database (Denmark)

    Kaczynski, Andrew T; Schipperijn, Jasper; Hipp, J Aaron

    2016-01-01

    , planners, and citizens to evaluate the potential for park use for a given area. Data used for developing ParkIndex were collected in 2010 in Kansas City, Missouri (KCMO). Adult study participants (n=891) reported whether they used a park within the past month, and all parks in KCMO were mapped and audited...... using ArcGIS 9.3 and the Community Park Audit Tool. Four park summary variables - distance to nearest park, and the number of parks, amount of park space, and average park quality index within 1 mile were analyzed in relation to park use using logistic regression. Coefficients for significant park...... summary variables were used to create a raster surface (ParkIndex) representing the probability of park use for all 100m×100m cells in KCMO. Two park summary variables were positively associated with park use - the number of parks and the average park quality index within 1 mile. The ParkIndex probability...

  13. Viral infections of the folds (intertriginous areas).

    Science.gov (United States)

    Adışen, Esra; Önder, Meltem

    2015-01-01

    Viruses are considered intracellular obligates with a nucleic acid, either RNA or DNA. They have the ability to encode proteins involved in viral replication and production of the protective coat within the host cells but require host cell ribosomes and mitochondria for translation. The members of the families Herpesviridae, Poxviridae, Papovaviridae, and Picornaviridae are the most commonly known agents for the cutaneous viral diseases, but other virus families, such as Adenoviridae, Togaviridae, Parvoviridae, Paramyxoviridae, Flaviviridae, and Hepadnaviridae, can also infect the skin. Though the cutaneous manifestations of viral infections are closely related to the type and the transmission route of the virus, viral skin diseases may occur in almost any part of the body. In addition to friction caused by skin-to-skin touch, skin folds are warm and moist areas of the skin that have limited air circulation. These features provide a fertile breeding ground for many kinds of microorganisms, including bacteria and fungi. In contrast to specific bacterial and fungal agents that have an affinity for the skin folds, except for viral diseases of the anogenital area, which have well-known presentations, viral skin infections that have a special affinity to the skin folds are not known. Many viral exanthems may affect the skin folds during the course of the infection, but here we focus only on the ones that usually affect the fold areas and also on the less well-known conditions or recently described associations. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Bifurcation of self-folded polygonal bilayers

    Science.gov (United States)

    Abdullah, Arif M.; Braun, Paul V.; Hsia, K. Jimmy

    2017-09-01

    Motivated by the self-assembly of natural systems, researchers have investigated the stimulus-responsive curving of thin-shell structures, which is also known as self-folding. Self-folding strategies not only offer possibilities to realize complicated shapes but also promise actuation at small length scales. Biaxial mismatch strain driven self-folding bilayers demonstrate bifurcation of equilibrium shapes (from quasi-axisymmetric doubly curved to approximately singly curved) during their stimulus-responsive morphing behavior. Being a structurally instable, bifurcation could be used to tune the self-folding behavior, and hence, a detailed understanding of this phenomenon is appealing from both fundamental and practical perspectives. In this work, we investigated the bifurcation behavior of self-folding bilayer polygons. For the mechanistic understanding, we developed finite element models of planar bilayers (consisting of a stimulus-responsive and a passive layer of material) that transform into 3D curved configurations. Our experiments with cross-linked Polydimethylsiloxane samples that change shapes in organic solvents confirmed our model predictions. Finally, we explored a design scheme to generate gripper-like architectures by avoiding the bifurcation of stimulus-responsive bilayers. Our research contributes to the broad field of self-assembly as the findings could motivate functional devices across multiple disciplines such as robotics, artificial muscles, therapeutic cargos, and reconfigurable biomedical devices.

  15. Kinetics and Thermodynamics of Membrane Protein Folding

    Directory of Open Access Journals (Sweden)

    Ernesto A. Roman

    2014-03-01

    Full Text Available Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.

  16. AUTHOR INDEX

    Indian Academy of Sciences (India)

    the Delhi Fold Belt, NW India. 627. Pandya M R. Simulation of at-sensor radiance over land for proposed thermal channels of Imager payload onboard INSAT-3D satellite using MODTRAN model. 19. Panigrahy S see Pandya M R. 19. Pant Vimlesh see Siingh Devendraa. 735. Panwar V see Sapra R. 807. Papa Fabrice.

  17. MULTI-TEMPORAL CROP SURFACE MODELS COMBINED WITH THE RGB VEGETATION INDEX FROM UAV-BASED IMAGES FOR FORAGE MONITORING IN GRASSLAND

    Directory of Open Access Journals (Sweden)

    M. Possoch

    2016-06-01

    Full Text Available Remote sensing of crop biomass is important in regard to precision agriculture, which aims to improve nutrient use efficiency and to develop better stress and disease management. In this study, multi-temporal crop surface models (CSMs were generated from UAV-based dense imaging in order to derive plant height distribution and to determine forage mass. The low-cost UAV-based RGB imaging was carried out in a grassland experiment at the University of Bonn, Germany, in summer 2015. The test site comprised three consecutive growths including six different nitrogen fertilizer levels and three replicates, in sum 324 plots with a size of 1.5×1.5 m. Each growth consisted of six harvesting dates. RGB-images and biomass samples were taken at twelve dates nearly biweekly within two growths between June and September 2015. Images were taken with a DJI Phantom 2 in combination of a 2D Zenmuse gimbal and a GoPro Hero 3 (black edition. Overlapping images were captured in 13 to 16 m and overview images in approximately 60 m height at 2 frames per second. The RGB vegetation index (RGBVI was calculated as the normalized difference of the squared green reflectance and the product of blue and red reflectance from the non-calibrated images. The post processing was done with Agisoft PhotoScan Professional (SfM-based and Esri ArcGIS. 14 ground control points (GCPs were located in the field, distinguished by 30 cm × 30 cm markers and measured with a RTK-GPS (HiPer Pro Topcon with 0.01 m horizontal and vertical precision. The errors of the spatial resolution in x-, y-, z-direction were in a scale of 3-4 cm. From each survey, also one distortion corrected image was georeferenced by the same GCPs and used for the RGBVI calculation. The results have been used to analyse and evaluate the relationship between estimated plant height derived with this low-cost UAV-system and forage mass. Results indicate that the plant height seems to be a suitable indicator for forage mass

  18. Multi-Temporal Crop Surface Models Combined with the RGB Vegetation Index from Uav-Based Images for Forage Monitoring in Grassland

    Science.gov (United States)

    Possoch, M.; Bieker, S.; Hoffmeister, D.; Bolten, A.; Schellberg, J.; Bareth, G.

    2016-06-01

    Remote sensing of crop biomass is important in regard to precision agriculture, which aims to improve nutrient use efficiency and to develop better stress and disease management. In this study, multi-temporal crop surface models (CSMs) were generated from UAV-based dense imaging in order to derive plant height distribution and to determine forage mass. The low-cost UAV-based RGB imaging was carried out in a grassland experiment at the University of Bonn, Germany, in summer 2015. The test site comprised three consecutive growths including six different nitrogen fertilizer levels and three replicates, in sum 324 plots with a size of 1.5×1.5 m. Each growth consisted of six harvesting dates. RGB-images and biomass samples were taken at twelve dates nearly biweekly within two growths between June and September 2015. Images were taken with a DJI Phantom 2 in combination of a 2D Zenmuse gimbal and a GoPro Hero 3 (black edition). Overlapping images were captured in 13 to 16 m and overview images in approximately 60 m height at 2 frames per second. The RGB vegetation index (RGBVI) was calculated as the normalized difference of the squared green reflectance and the product of blue and red reflectance from the non-calibrated images. The post processing was done with Agisoft PhotoScan Professional (SfM-based) and Esri ArcGIS. 14 ground control points (GCPs) were located in the field, distinguished by 30 cm × 30 cm markers and measured with a RTK-GPS (HiPer Pro Topcon) with 0.01 m horizontal and vertical precision. The errors of the spatial resolution in x-, y-, z-direction were in a scale of 3-4 cm. From each survey, also one distortion corrected image was georeferenced by the same GCPs and used for the RGBVI calculation. The results have been used to analyse and evaluate the relationship between estimated plant height derived with this low-cost UAV-system and forage mass. Results indicate that the plant height seems to be a suitable indicator for forage mass. There is a

  19. Ultrasound measured testicular volume in Nigerian adults: Relationship of the three formulae with height, body weight, body-surface area, and body-mass index

    Directory of Open Access Journals (Sweden)

    Madubogwu Chimezie Innocent

    2016-01-01

    Full Text Available Background: Measurement of testicular volume is one of the ways of assessing testicular function. Ultrasonography is an important and accurate radiological method for measurement of testicular volume. Objective: This study was aimed at evaluating the relationship of ultrasound measured testicular volume using the three formulae with the subjects' height, body weight, body surface area (BSA, and body mass index (BMI in adults. Methodology: One hundred twenty-five adult male subjects comprising staff and students of a University Teaching Hospital were recruited into the study. Height and body weight were measured while the BMI and BSA were calculated. Ultrasound measurement of the height, length, and width of both testes were done and used to calculate the volumes using the three formulae. Results: The subjects' age ranged from 19 to 29 years with a mean of 23.48 ± 2.26 yrs. The mean ultrasound measured volumes for the right and left testes were 15.38 ± 3.29 ml and 15.29 ± 3.89 ml using the prolate ellipsoid formula; 22.86 ± 5.43 ml and 23.54 ± 6.88 ml by the prolate spheroid formula; 21.20 ± 5.28 ml and 20.87 ± 5.35 ml by the Lambert formula, respectively. The calculated mean for height, body weight, BMI, and BSA were 174.64 ± 6.36 cm, 68.68 ± 8.25 kg, 22.48 ± 2.17 kg/m2, and 1.82 ± 0.13 m2, respectively. The right testes showed a negative correlation, while the left and combined testicular volumes showed a positive correlation with the subjects' height, body weight, BMI, and BSA for all the three formulae. Conclusion: The right testicular volume showed negative correlation, while the left and combined testicular volumes showed a positive correlation with the height, body weight, BSA, and BMI in Nigerian adults.

  20. SDEM modelling of fault-propagation folding

    DEFF Research Database (Denmark)

    Clausen, O.R.; Egholm, D.L.; Poulsen, Jane Bang

    2009-01-01

    Understanding the dynamics and kinematics of fault-propagation-folding is important for evaluating the associated hydrocarbon play, for accomplishing reliable section balancing (structural reconstruction), and for assessing seismic hazards. Accordingly, the deformation style of fault-propagation-......Understanding the dynamics and kinematics of fault-propagation-folding is important for evaluating the associated hydrocarbon play, for accomplishing reliable section balancing (structural reconstruction), and for assessing seismic hazards. Accordingly, the deformation style of fault......-propagation-folding has already been the topic of a large number of empirical studies as well as physical and computational model experiments. However, with the newly developed Stress-based Discrete Element Method (SDEM), we have, for the first time, explored computationally the link between self-emerging fault patterns...

  1. Improvement of a Vocal Fold Imaging System

    Energy Technology Data Exchange (ETDEWEB)

    Krauter, K. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-02-01

    Medical professionals can better serve their patients through continual update of their imaging tools. A wide range of pathologies and disease may afflict human vocal cords or, as they’re also known, vocal folds. These diseases can affect human speech hampering the ability of the patient to communicate. Vocal folds must be opened for breathing and the closed to produce speech. Currently methodologies to image markers of potential pathologies are difficult to use and often fail to detect early signs of disease. These current methodologies rely on a strobe light and slower frame rate camera in an attempt to obtain images as the vocal folds travel over the full extent of their motion.

  2. Extreme Mechanics: Self-Folding Origami

    Science.gov (United States)

    Santangelo, Christian D.

    2017-03-01

    Origami has emerged as a tool for designing three-dimensional structures from flat films. Because they can be fabricated by lithographic or roll-to-roll processing techniques, they have great potential for the manufacture of complicated geometries and devices. This article discusses the mechanics of origami and kirigami with a view toward understanding how to design self-folding origami structures. Whether an origami structure can be made to fold autonomously depends strongly on the geometry and kinematics of the origami fold pattern. This article collects some of the results on origami rigidity into a single framework, and discusses how these aspects affect the foldability of origami. Despite recent progress, most problems in origami and origami design remain completely open.

  3. AP Index

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Planetary Amplitude index - Bartels 1951. The a-index ranges from 0 to 400 and represents a K-value converted to a linear scale in gammas (nanoTeslas)--a scale that...

  4. Towards a systematic classification of protein folds

    DEFF Research Database (Denmark)

    Lindgård, Per-Anker; Bohr, Henrik

    1997-01-01

    structures are given a unique name, which simultaneously represent a linear string of physical coupling constants describing hinge spin interactions. We have defined a metric and a precise distance measure between the fold classes. An automated procedure is constructed in which any protein structure...... magic number of secondary structures. Thermodynamic arguments for the increased abundance and a phase diagram for the folding scenario are given. This includes an intermediate high symmetry phase, the parent structures, between the molten globule and the native states. We have made an exhaustive...

  5. Symmetric Circular Matchings and RNA Folding

    DEFF Research Database (Denmark)

    Hofacker, Ivo L.; Reidys, Christian; Stadler, Peter F.

    2012-01-01

    or the co-folding of two or more identical RNAs. Here, we show that the RNA folding problem with symmetry terms can still be solved with polynomial-time algorithms. Empirically, the fraction of symmetric ground state structures decreases with chain length, so that the error introduced by neglecting......RNA secondary structures can be computed as optimal solutions of certain circular matching problems. An accurate treatment of this energy minimization problem has to account for the small --- but non-negligible --- entropic destabilization of secondary structures with non-trivial automorphisms...

  6. Stretching and folding mechanism in foams

    Energy Technology Data Exchange (ETDEWEB)

    Tufaile, Alberto [Escola de Artes, Ciencias e Humanidades, Soft Matter Laboratory, Universidade de Sao Paulo, 03828-000 Sao Paulo, SP (Brazil)], E-mail: tufaile@usp.br; Pedrosa Biscaia Tufaile, Adriana [Escola de Artes, Ciencias e Humanidades, Soft Matter Laboratory, Universidade de Sao Paulo, 03828-000 Sao Paulo, SP (Brazil)

    2008-10-13

    We have described the stretching and folding of foams in a vertical Hele-Shaw cell containing air and a surfactant solution, from a sequence of upside-down flips. Besides the fractal dimension of the foam, we have observed the logistic growth for the soap film length. The stretching and folding mechanism is present during the foam formation, and this mechanism is observed even after the foam has reached its respective maximum fractal dimension. Observing the motion of bubbles inside the foam, large bubbles present power spectrum associated with random walk motion in both directions, while the small bubbles are scattered like balls in a Galton board.

  7. How the Cortex Gets Its Folds: An Inside-Out, Connectivity-Driven Model for the Scaling of Mammalian Cortical Folding

    Science.gov (United States)

    Mota, Bruno; Herculano-Houzel, Suzana

    2012-01-01

    Larger mammalian cerebral cortices tend to have increasingly folded surfaces, often considered to result from the lateral expansion of the gray matter (GM), which, in a volume constrained by the cranium, causes mechanical compression that is relieved by inward folding of the white matter (WM), or to result from differential expansion of cortical layers. Across species, thinner cortices, presumably more pliable, would offer less resistance and hence become more folded than thicker cortices of a same size. However, such models do not acknowledge evidence in favor of a tension-based pull onto the GM from the inside, holding it in place even when the constraint imposed by the cranium is removed. Here we propose a testable, quantitative model of cortical folding driven by tension along the length of axons in the WM that assumes that connections through the WM are formed early in development, at the same time as the GM becomes folded, and considers that axonal connections through the WM generate tension that leads to inward folding of the WM surface, which pulls the GM surface inward. As an important necessary simplifying hypothesis, we assume that axons leaving or entering the WM do so approximately perpendicularly to the WM–GM interface. Cortical folding is thus driven by WM connectivity, and is a function of the fraction of cortical neurons connected through the WM, the average length, and the average cross-sectional area of the axons in the WM. Our model predicts that the different scaling of cortical folding across mammalian orders corresponds to different combinations of scaling of connectivity, axonal cross-sectional area, and tension along WM axons, instead of being a simple function of the number of GM neurons. Our model also explains variations in average cortical thickness as a result of the factors that lead to cortical folding, rather than as a determinant of folding; predicts that for a same tension, folding increases with connectivity through the WM and

  8. Sill Emplacement and Forced Folding in the Canterbury Basin, offshore SE New Zealand

    Science.gov (United States)

    Reeves, Jennifer; Magee, Craig; Jackson, Christopher

    2017-04-01

    Sill-complexes are common in sedimentary basins worldwide. The geometry of sill-complexes and their associated deformation can be used to unravel tectono-magmatic events. For example, intruding magma may uplift the overburden and the free surface to produce forced folds that are typically either dome-shaped or flat-topped. These four-way dip closures can form suitable hydrocarbon traps and dating of onlapping of sedimentary strata allows the timing of emplacement, relative to hydrocarbon generation and migration to be assessed. Furthermore, these forced folds directly overlie the forcing intrusion and their volume is commonly assumed to equal that of the emplaced magma. This relationship between folds, which may be expressed that the Earth's surface, and magma volume is fundamental for volcano predication due to the use of ground deformation as a proxy for the location and magnitude of future eruptions. However, recent studies have demonstrated that fluidization of weak host rock can accommodate magma during non-brittle emplacement, producing little or no overburden deformation. Assessing the mechanics of intrusion-induced forced folding is therefore critical to a variety of Earth Science disciplines. Here, we use 3D seismic reflection data map four sills at a high-resolution within the underexplored Canterbury Basin, offshore SE New Zealand. We demonstrate that: (i) despite similar emplacement levels, forced folds are only developed above two of the sills, with no apparent uplift above the other two sills; (ii) onlap of sedimentary onto forced folds and associated hydrothermal vents indicates two episodes of sill emplacement in the Whaingaroan (34.6-31.8 Ma) and Opoitian (5.33-3.7 Ma); and (iii) intra-fold thickness is variable, with lower intervals within the folds displaying a flat-topped geometry overlain by sedimentary strata displaying dome-shaped folding. We discuss the formation of these forced folds as assess the role of non-brittle and inelastic

  9. Glueballs as rotating folded closed strings

    Science.gov (United States)

    Sonnenschein, Jacob; Weissman, Dorin

    2015-12-01

    In previous papers [1, 2] we argued that mesons and baryons can be described as rotating open strings in holographic backgrounds. Now we turn to closed strings, which should be the duals of glueballs. We look at the rotating folded closed string in both flat and curved backgrounds.

  10. Vocal fold nodules: morphological and immunohistochemical investigations.

    Science.gov (United States)

    Martins, Regina Helena Garcia; Defaveri, Julio; Custódio Domingues, Maria Aparecida; de Albuquerque E Silva, Rafael; Fabro, Alexandre

    2010-09-01

    The objective of this study was to investigate the morphological and immunohistochemical characteristics of vocal fold nodules. The study design was prospective and retrospective. For the histological study, we reviewed 15 slides from the surgical cases of vocal fold nodules, in which we analyzed epithelium, basal membrane (bm), and lamina propria. For the transmission and scanning electron microscopy (TEM, SEM) studies, five new cases on vocal fold nodules were included. Immunohistochemistry study was carried out in the 15 specimens, using antifibronectin, antilaminin, and anticollagen IV antibodies. The main histological alterations were epithelial hyperplasia (73.33%), basement membrane thickening (86.66%), edema, and fibrosis (93.33%). SEM--reduction in mucous lacing and increase in the desquamating cells, without epithelial erosion. TEM--hyperplasia of the epithelium, enlargement of the intercellular junctions, which was filled by fluid, subepithelial thickening of the lamina reticularis, and break points in the basal membrane. Immunohistochemistry--we identified greater immunoexpression of fibronectin on the basal membrane, on the lamina propria, and around the vessels. Antilaminin and anticollagen IV antibodies showed higher pigmentation on the endothelium of the vessels than that on the basal membrane. In vocal fold nodules, combined assessment using light microscopy, electron microscopy, and immunohistochemistry can reveal important morphological details useful in characterizing these lesions. 2010 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

  11. Assessment of thyroplasty for vocal fold paralysis

    DEFF Research Database (Denmark)

    Grøntved, Ågot Møller; Faber, Christian; Jakobsen, John

    2009-01-01

    INTRODUCTION: Thyroplasty with silicone rubber implantation is a surgical procedure for treatment of patients with vocal fold paralysis. The aim of the present study was to evaluate the outcome of the operation and to monitor which of the analyses were the more beneficial. MATERIAL AND METHODS...

  12. MARATHON DESPITE UNILATERAL VOCAL FOLD PARALYSIS

    Directory of Open Access Journals (Sweden)

    Matthias Echternach

    2008-06-01

    Full Text Available The principal symptoms of unilateral vocal fold paralysis are hoarseness and difficulty in swallowing. Dyspnea is comparatively rare (Laccourreye et al., 2003. The extent to which unilateral vocal fold paralysis may lead to respiratory problems at all - in contrast to bilateral vocal fold paralysis- has not yet well been determined. On the one hand, inspiration is impaired with unilateral vocal fold paralysis; on the other hand, neither the position of the vocal fold paralysis nor the degree of breathiness correlates with respiratory parameters (Cantarella et al., 2003; 2005. The question of what respiratory stress a patient with a vocal fold paresis can endure has not yet been dealt with.A 43 year-old female patient was suffering from recurrent unspecific respiratory complaints for four months after physical activity. During training for a marathon, she experienced no difficulty in breathing. These unspecific respiratory complaints occurred only after athletic activity and persisted for hours. The patient observed neither an increased coughing nor a stridor. Her voice remained unaltered during the attacks, nor were there any signs of a symptomatic gastroesophageal reflux or infectious disease. A cardio-pulmonary and a radiological examination by means of an X-ray of the thorax also revealed no pathological phenomena. As antiallergic and antiobstructive therapy remained unsuccessful, a laryngological examination was performed in order to exclude a vocal cord dysfunction.Surprisingly enough, the laryngostroboscopy showed, as an initial description, a vocal fold paralysis of the left vocal fold in median position (Figure 1. The anamnestic background for the cause was unclear. The only clue was a thoracotomy on the left side due to a pleuritis in childhood. A subsequent laryngoscopic examination had never been performed. Good mucosa waves and amplitudes were shown bilateral with complete glottal closure. Neither in the acoustic analysis, nor in the

  13. Engineering Biology by Controlling Tissue Folding.

    Science.gov (United States)

    Hookway, Tracy A

    2018-04-01

    Achieving complex self-organization in vitro has remained a fundamental challenge in tissue engineering. A recent study in Developmental Cell by Hughes and colleagues uses computational and experimental approaches to understand and control the morphogenic process of tissue folding. These approaches provide an engineering framework to reproducibly control tissue shape. Copyright © 2018 Elsevier Ltd. All rights reserved.

  14. Mapping the universe of RNA tetraloop folds

    DEFF Research Database (Denmark)

    Bottaro, Sandro; Lindorff-Larsen, Kresten

    2017-01-01

    We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG fold...

  15. Fold in Origami and Unfold Math

    Science.gov (United States)

    Georgeson, Joseph

    2011-01-01

    Students enjoy origami and like making everything from paper cranes to footballs out of small, colorful squares of paper. They can invent their own shapes and are intrigued by the polyhedrons that they can construct. Paper folding is fun, but where is the math? Unless teachers develop lessons that address mathematical objectives, origami could be…

  16. Folding of multidomain proteins: biophysical consequences of tethering even in apparently independent folding.

    Science.gov (United States)

    Arviv, Oshrit; Levy, Yaakov

    2012-12-01

    Most eukaryotic and a substantial fraction of prokaryotic proteins are composed of more than one domain. The tethering of these evolutionary, structural, and functional units raises, among others, questions regarding the folding process of conjugated domains. Studying the folding of multidomain proteins in silico enables one to identify and isolate the tethering-induced biophysical determinants that govern crosstalks generated between neighboring domains. For this purpose, we carried out coarse-grained and atomistic molecular dynamics simulations of two two-domain constructs from the immunoglobulin-like β-sandwich fold. Each of these was experimentally shown to behave as the "sum of its parts," that is, the thermodynamic and kinetic folding behavior of the constituent domains of these constructs seems to occur independently, with the folding of each domain uncoupled from the folding of its partner in the two-domain construct. We show that the properties of the individual domains can be significantly affected by conjugation to another domain. The tethering may be accompanied by stabilizing as well as destabilizing factors whose magnitude depends on the size of the interface, the length, and the flexibility of the linker, and the relative stability of the domains. Accordingly, the folding of a multidomain protein should not be viewed as the sum of the folding patterns of each of its parts, but rather, it involves abrogating several effects that lead to this outcome. An imbalance between these effects may result in either stabilization or destabilization owing to the tethering. Copyright © 2012 Wiley Periodicals, Inc.

  17. ETIOLOGICAL FACTORS FOR VOCAL FOLD POLYP FORMATION

    Directory of Open Access Journals (Sweden)

    DAŠA GLUVAJIĆ

    2016-05-01

    Full Text Available Background: Vocal fold polyp is one of the most common causes for hoarseness. Many different etiological factors contribute to vocal fold polyp formation. The aim of the study was to find out whether the etiological factors for polyp formation have changed in the last 30 years.Methods: Eighty-one patients with unilateral vocal fold polyp were included in the study. A control group was composed of 50 volunteers without voice problems who matched the patients by age and gender. The data about etiological factors and the findings of phoniatric examination were obtained from the patients' medical documentation and from the questionnaires for the control group. The incidence of etiological factors was compared between the two groups. The program SPSS, Version 18 was used for statistical analysis.Results: The most frequent etiological factors were occupational voice load, GER, allergy and smoking. In 79% of patients 2 – 6 contemporary acting risk factors were found. Occupational voice load (p=0,018 and GER (p=0,004 were significantly more frequent in the patients than in the controls. The other factors did not significantly influence the polyp formation.Conclusions: There are several factors involved simultaneously in the formation of vocal fold polyps both nowadays and 30 years ago. Some of the most common factors remain the same (voice load, smoking, others are new (GER, allergy, which is probably due to the different lifestyle and working conditions than 30 years ago. Occupational voice load and GER were significantly more frequently present in the patients with polyp than in the control group. Regarding the given results it is important to instruct workers with professional vocal load about etiological factors for vocal fold polyp formation.

  18. Inverse folding of RNA pseudoknot structures

    Directory of Open Access Journals (Sweden)

    Li Linda YM

    2010-06-01

    Full Text Available Abstract Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can deal with 3-noncrossing, canonical pseudoknot structures. Results In this paper we present the inverse folding algorithm Inv. We give a detailed analysis of Inv, including pseudocodes. We show that Inv allows to design in particular 3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures-a class which is difficult to construct via dynamic programming routines. Inv is freely available at http://www.combinatorics.cn/cbpc/inv.html. Conclusions The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures. In comparison with RNAinverse it uses new ideas, for instance by considering sets of competing structures. As a result, Inv is not only able to find novel sequences even for RNA secondary structures, it does so in the context of competing structures that potentially exhibit cross-serial interactions.

  19. Folding and Fracturing of Rocks: the background

    Science.gov (United States)

    Ramsay, John G.

    2017-04-01

    This book was generated by structural geology teaching classes at Imperial College. I was appointed lecturer during 1957 and worked together with Dr Gilbert Wilson teaching basic structural geology at B.Sc level. I became convinced that the subject, being essentially based on geometric field observations, required a firm mathematical basis for its future development. In particular it seemed to me to require a very sound understanding of stress and strain. My field experience suggested that a knowledge of two- and three-demensional strain was critical in understanding natural tectonic processes. I found a rich confirmation for this in early publications of deformed fossils, oolitic limestones and spotted slates made by several geologists around the beginning of the 20th century (Sorby, Philips, Haughton, Harker) often using surprisingly sophisticated mathematical methods. These methods were discussed and elaborated in Folding and Fracturing of Rocks in a practical way. The geometric features of folds were related to folding mechanisms and the fold related small scale structures such as cleavage, schistosity and lineation explained in terms of rock strain. My work in the Scottish Highlands had shown just how repeated fold superposition could produce very complex geometric features, while further work in other localities suggested that such geometric complications are common in many orogenic zones. From the development of structural geological studies over the past decades it seems that the readers of this book have found many of the ideas set out are still of practical application. The mapping of these outcrop-scale structures should be emphasised in all field studies because they can be seen as ''fingerprints'' of regional scale tectonic processes. My own understanding of structural geology has been inspired by field work and I am of the opinion that future progress in understanding will be likewise based on careful observation and measurement of the features of

  20. AA Index

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The geomagnetic aa index provides a long climatology of global geomagnetic activity using 2 antipodal observatories at Greenwich and Melbourne- IAGA Bulletin 37,...

  1. Diversity Index

    Data.gov (United States)

    Town of Chapel Hill, North Carolina — This map service summarizes racial and ethnic diversity in the United States in 2012.The Diversity Index shows the likelihood that two persons chosen at random from...

  2. Walkability Index

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Walkability Index dataset characterizes every Census 2010 block group in the U.S. based on its relative walkability. Walkability depends upon characteristics of...

  3. Intelligent indexing

    International Nuclear Information System (INIS)

    Farkas, J.

    1992-01-01

    In this paper we discuss the relevance of artificial intelligence to the automatic indexing of natural language text. We describe the use of domain-specific semantically-based thesauruses and address the problem of creating adequate knowledge bases for intelligent indexing systems. We also discuss the relevance of the Hilbert space ι 2 to the compact representation of documents and to the definition of the similarity of natural language texts. (author). 17 refs., 2 figs

  4. Positive therapy of andrographolide in vocal fold leukoplakia.

    Science.gov (United States)

    Xu, Jue; Xue, Tao; Bao, Ying; Wang, Dong-Hai; Ma, Bing-Liang; Yin, Chen-Yi; Yang, Guang-Hui; Ren, Gang; Lan, Long-Jiang; Wang, Jian-Qiu; Zhang, Xiao-Lan; Zhao, Yu-Qin

    2014-01-01

    Vocal fold leukoplakia is a premalignant precursor of squamous cell carcinoma. Although many efforts have been contributed to therapy of this disease, none exhibits a satisfactory result. The aims of this study were to investigate the effectiveness and feasibility of andrographolide therapy in vocal fold leukoplakia and to explore the preliminary mechanism underlying. Forty-one eligible patients were enrolled in the study. The patients were treated for 10-minute exposures of 5 ml (25mg/ml) andrographolide injection aerosols twice a day, and 2 weeks was considered as one treatment course. Electronic laryngoscope was used to observe the condition of vocal fold leukoplakia during the treatment. Every patient received one or two treatment courses, and the follow-up was carried out for 12 months. Toxic reactions of treatments were evaluated on the basis of the standards of the United States MD Anderson Cancer Center. Moreover, laryngeal carcinoma cell line Hep2 was applied to explore the mechanism of effect of andrographolide. Anti-proliferative effect on Hep2, cell nuclear morphology, express of mitogen-activated protein kinases (MAPK) and pro-apoptotic protein were detected after andrographolide treatment. We found that andrographolide exhibited significant curative effects on treatments, which were accompanied by thinning of the lesion of leukoplakia, reduction in the whitish surface area, and return of pink or red epithelium. A complete response up to 85% was observed, and no toxic side effect events occurred during the study. No patient with a complete response had a recurrence in the follow-up. Moreover, cellular experiments in Hep2 indicated that andrographolide activated MAPK pathway and caspase cascade, and finally induced apoptosis in laryngeal carcinoma cell. The advantages of andrographolide are connected with minimally invasive and localized character of the treatment and no damage of collagenous tissue structures, which are more convenient and less painful

  5. Folding in a Cooling Crust with Elasto-visco-plastic Rheology: An Example from Venus

    Science.gov (United States)

    Ghent, R.; Phillips, R. J.; Hansen, V.

    2001-12-01

    We investigate the effects of simultaneous shortening and cooling on fold wavelengths in a crust with elasto-visco-plastic (EVP) rheology, in order to better understand the interplay between rates of shortening and cooling on the anelastic response of the crust. We apply our techniques to Venusian crustal plateaus, which show ubiquitous, low-amplitude folds with a continuous range of wavelengths from 30 km. Previous studies have proposed that these folds (and other characteristic crustal plateau structures) originated during crustal plateau formation by interaction of large mantle plumes with the surface during a time of globally thin lithosphere [1]. In this scenario, a plume arriving at the lithosphere erases existing structures and produces a mechanically homogeneous surface by heating and/or melting the crust. Subsequent cooling results in a surface layer that is capable of recording strains and that thickens with time. We investigate the conditions under which folds matching those observed in Venusian crustal plateaus are created in a finite element model simulating concurrent shortening and cooling, as motivated by the tectonic scenario in [1]. Our models are novel because a) the EVP rheology more accurately represents the actual crust than viscous or viscoelastic models; and b) other models generally specify a priori a folding layer thickness and geometry, with material properties different from those of the surrounding rock, and this pre-determines the resulting fold wavelength(s). By contrast, our models incorporate spatially uniform material properties but temperature-dependent rheology [2], so that the strength profile through the crust evolves with cooling. This allows the thermal and stress conditions to determine the instantaneous effective folding layer thickness at each time step, which in turn determines surface fold wavelengths. We investigate conditions under which short wavelength folds are initiated when the effective folding layer is very thin

  6. Automated Water Extraction Index

    DEFF Research Database (Denmark)

    Feyisa, Gudina Legese; Meilby, Henrik; Fensholt, Rasmus

    2014-01-01

    of various sorts of environmental noise and at the same time offers a stable threshold value. Thus we introduced a new Automated Water Extraction Index (AWEI) improving classification accuracy in areas that include shadow and dark surfaces that other classification methods often fail to classify correctly...

  7. Comparison of fractional inhibitory concentration index with response surface modeling for characterization of in vitro interaction of antifungals against itraconazole-susceptible and -resistant Aspergillus fumigatus isolates.

    NARCIS (Netherlands)

    Dorsthorst, D.T.A. te; Verweij, P.E.; Meis, J.F.G.M.; Punt, N.C.; Mouton, J.W.

    2002-01-01

    Although the fractional inhibitory concentration (FIC) index is most frequently used to define or to describe drug interactions, it has some important disadvantages when used for drugs against filamentous fungi. This includes observer bias in the determination of the MIC and no agreement on the

  8. Folding pathways explored with artificial potential functions

    International Nuclear Information System (INIS)

    Ulutaş, B; Bozma, I; Haliloglu, T

    2009-01-01

    This paper considers the generation of trajectories to a given protein conformation and presents a novel approach based on artificial potential functions—originally proposed for multi-robot navigation. The artificial potential function corresponds to a simplified energy model, but with the novelty that—motivated by work on robotic navigation—a nonlinear compositional scheme of constructing the energy model is adapted instead of an additive formulation. The artificial potential naturally gives rise to a dynamic system for the protein structure that ensures collision-free motion to an equilibrium point. In cases where the equilibrium point is the native conformation, the motion trajectory corresponds to the folding pathway. This framework is used to investigate folding in a variety of protein structures, and the results are compared with those of other approaches including experimental studies

  9. Ca-Dependent Folding of Human Calumenin

    Science.gov (United States)

    Mazzorana, Marco; Hussain, Rohanah; Sorensen, Thomas

    2016-01-01

    Human calumenin (hCALU) is a six EF-hand protein belonging to the CREC family. As other members of the family, it is localized in the secretory pathway and regulates the activity of SERCA2a and of the ryanodine receptor in the endoplasmic reticulum (ER). We have studied the effects of Ca2+ binding to the protein and found it to attain a more compact structure upon ion binding. Circular Dichroism (CD) measurements suggest a major rearrangement of the protein secondary structure, which reversibly switches from disordered at low Ca2+ concentrations to predominantly alpha-helical when Ca2+ is added. SAXS experiments confirm the transition from an unfolded to a compact structure, which matches the structural prediction of a trilobal fold. Overall our experiments suggest that calumenin is a Ca2+ sensor, which folds into a compact structure, capable of interacting with its molecular partners, when Ca2+ concentration within the ER reaches the millimolar range. PMID:26991433

  10. Thermostable exoshells fold and stabilize recombinant proteins.

    Science.gov (United States)

    Deshpande, Siddharth; Masurkar, Nihar D; Girish, Vallerinteavide Mavelli; Desai, Malan; Chakraborty, Goutam; Chan, Juliana M; Drum, Chester L

    2017-11-13

    The expression and stabilization of recombinant proteins is fundamental to basic and applied biology. Here we have engineered a thermostable protein nanoparticle (tES) to improve both expression and stabilization of recombinant proteins using this technology. tES provides steric accommodation and charge complementation to green fluorescent protein (GFPuv), horseradish peroxidase (HRPc), and Renilla luciferase (rLuc), improving the yields of functional in vitro folding by ~100-fold. Encapsulated enzymes retain the ability to metabolize small-molecule substrates, presumably via four 4.5-nm pores present in the tES shell. GFPuv exhibits no spectral shifts in fluorescence compared to a nonencapsulated control. Thermolabile proteins internalized by tES are resistant to thermal, organic, chaotropic, and proteolytic denaturation and can be released from the tES assembly with mild pH titration followed by proteolysis.

  11. Cutting and Folding for Tunable Materials Properties

    Science.gov (United States)

    Damasceno, Pablo; Dodd, Paul; Shyu, Terry; Shlian, Matthew; Shtein, Max; Kotov, Nicholas; Glotzer, Sharon

    2014-03-01

    Despite the small set of building blocks used for their assembly, naturally occurring materials such as proteins show remarkable diversity in their mechanical properties ranging from something resembling rubber-low stiffness, high resilience and extensibility-to silk-high stiffness and strength. Moreover, their self-folding properties inspire the design of structures capable of tunable reconfiguration. Motivated by such versatility, we report on simulations and experiments for the design of nanocomposites sheets whose mechanical properties can be made tunable via ``secondary structures'' patterning. Our simulations reveal the main cutting features needed to obtain desired material extensibility. Additionally, we study how similar sheets could self-fold into their desired ``native'' structure via stochastic forces. Our results open the possibilities for manufacture of flexible and reconfigurable materials with targeted strength and extensibility. Research supported by the National Science Foundation, Emerging Frontiers in Research and Innovation Award # EFRI-1240264.

  12. Unit operations of tissue development: epithelial folding.

    Science.gov (United States)

    Zartman, Jeremiah J; Shvartsman, Stanislav Y

    2010-01-01

    The development of multicellular organisms relies on a small set of construction techniques-assembly, sculpting, and folding-that are spatially and temporally regulated in a combinatorial manner to produce the diversity of tissues within the body. These basic processes are well conserved across tissue types and species at the level of both genes and mechanisms. Here we review the signaling, patterning, and biomechanical transformations that occur in two well-studied model systems of epithelial folding to illustrate both the complexity and modularity of tissue development. In particular, we discuss the possibility of a spatial code specifying morphogenesis. To decipher this code, engineers and scientists need to establish quantitative experimental systems and to develop models that address mechanisms at multiple levels of organization, from gene sequence to tissue biomechanics. In turn, quantitative models of embryogenesis can inspire novel methods for creating synthetic organs and treating degenerative tissue diseases.

  13. Modulation of frustration in folding by sequence permutation

    Science.gov (United States)

    Nobrega, R. Paul; Arora, Karunesh; Kathuria, Sagar V.; Graceffa, Rita; Barrea, Raul A.; Guo, Liang; Chakravarthy, Srinivas; Bilsel, Osman; Irving, Thomas C.; Brooks, Charles L.; Matthews, C. Robert

    2014-01-01

    Folding of globular proteins can be envisioned as the contraction of a random coil unfolded state toward the native state on an energy surface rough with local minima trapping frustrated species. These substructures impede productive folding and can serve as nucleation sites for aggregation reactions. However, little is known about the relationship between frustration and its underlying sequence determinants. Chemotaxis response regulator Y (CheY), a 129-amino acid bacterial protein, has been shown previously to populate an off-pathway kinetic trap in the microsecond time range. The frustration has been ascribed to premature docking of the N- and C-terminal subdomains or, alternatively, to the formation of an unproductive local-in-sequence cluster of branched aliphatic side chains, isoleucine, leucine, and valine (ILV). The roles of the subdomains and ILV clusters in frustration were tested by altering the sequence connectivity using circular permutations. Surprisingly, the stability and buried surface area of the intermediate could be increased or decreased depending on the location of the termini. Comparison with the results of small-angle X-ray–scattering experiments and simulations points to the accelerated formation of a more compact, on-pathway species for the more stable intermediate. The effect of chain connectivity in modulating the structures and stabilities of the early kinetic traps in CheY is better understood in terms of the ILV cluster model. However, the subdomain model captures the requirement for an intact N-terminal domain to access the native conformation. Chain entropy and aliphatic-rich sequences play crucial roles in biasing the early events leading to frustration in the folding of CheY. PMID:25002512

  14. Protein Folding: Search for Basic Physical Models

    Directory of Open Access Journals (Sweden)

    Ivan Y. Torshin

    2003-01-01

    Full Text Available How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context of in vivo protein folding (which has been studied only for a few proteins, the roles of the fundamental physical forces in the in vitro folding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces. Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

  15. Folding Membrane Proteins by Deep Transfer Learning

    KAUST Repository

    Wang, Sheng

    2017-08-29

    Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here, we describe a high-throughput deep transfer learning method that first predicts MP contacts by learning from non-MPs and then predicts 3D structure models using the predicted contacts as distance restraints. Tested on 510 non-redundant MPs, our method has contact prediction accuracy at least 0.18 better than existing methods, predicts correct folds for 218 MPs, and generates 3D models with root-mean-square deviation (RMSD) less than 4 and 5 Å for 57 and 108 MPs, respectively. A rigorous blind test in the continuous automated model evaluation project shows that our method predicted high-resolution 3D models for two recent test MPs of 210 residues with RMSD ∼2 Å. We estimated that our method could predict correct folds for 1,345–1,871 reviewed human multi-pass MPs including a few hundred new folds, which shall facilitate the discovery of drugs targeting at MPs.

  16. Araguaia fold belt, new geochronological data

    International Nuclear Information System (INIS)

    Lafon, J.M.; Macambira, J.B.; Macambira, M.J.B.; Moura, C.A.V.; Souza, A.C.C.

    1990-01-01

    The northern part of the Araguaia Fold Belt (AFB) outcrops in a N-S direction for about 400 km in the state of Tocantins. Dome-like structures occur in this fold belt also in a N-S direction. Both deformation and metamorphism increase from the West to the East. The basement of the AFB consist of Colmeia complex and Cantao gneiss, which crop out mainly in the core of the dome-like structures. The supracrustals rocks of the fold belt belongs to the Baixo Araguaia supergroup which is divided into the lower Estrondo group and the upper Tocantins group. Preliminary Sm-Nd data from the Colmeia complex (Grota Rica dome) gave Archean model ages of 2.8 Ga (TNd sub(DM)) while Rb-Sr data in the same rocks give an age of 2530 ± 200 Ma. In the others dome-like structures, the Rb-Sr systematics gave ages for the Colmeia a complex of 2239 ± 47 Ma (Colmeia structure) and 1972 ± 46 Ma (Lontra structure). These younger ages are believed to represent partial to total isotopic resetting of the Rb-Sr system during the Transamazonian Event. The Rb-Sr studies of the Cantao gneiss gave an age of 1774 ± 31 Ma. (author)

  17. The energy landscape, folding pathways and the kinetics of a knotted protein.

    Directory of Open Access Journals (Sweden)

    Michael C Prentiss

    2010-07-01

    Full Text Available The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N or C terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N terminus portion of the knot and a rate-determining step where the C terminus is incorporated. The low-lying minima with the N terminus knotted and the C terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N and C termini into the knot occurs late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.

  18. Fold and thrust systems in Mass Transport Deposits

    Science.gov (United States)

    Alsop, G. I.; Marco, S.; Levi, T.; Weinberger, R.

    2017-01-01

    reduces to 35% in overlying beds. A 23% reduction in shortening by folding and thrusting along individual thrusts suggests that heterogeneous lateral compaction may increase by ∼10% towards the sediment surface. Thrust systems cutting unlithified sediments display distinct steps in cumulative displacement-distance plots representing increased rates of slip along the floor thrust, while displacement-distance plots along individual thrusts also reveal 'horizontal steps' relating to lithological variation. Competent units cut by thrust ramps may display the greatest displacement, which then progressively reduces both upward and sometimes downward along the ramp. This relationship demonstrates that ramps do not necessarily propagate upwards from the underlying flat as in some traditional models, but rather initiate by offset of competent horizons in the hangingwall of the detachment. Critical taper angles in MTDs may be an order of magnitude less than in accretionary complexes or lithified rocks. Overall, thrusts cutting unlithified sediments in MTDs display more variable displacement, and more pronounced displacement gradients toward fault tips, compared to thrusts cutting lithified sequences.

  19. Indexing mechanisms

    International Nuclear Information System (INIS)

    Wood, A.G.; Parker, G.E.; Berry, R.

    1976-01-01

    It is stated that the indexing mechanism described can be used in a nuclear reactor fuel element inspection rig. It comprises a tubular body adapted to house a canister containing a number of fuel elements located longtitudinally, and has two chucks spaced apart for displacing the fuel elements longitudinally in a stepwise manner, together with a plunger mechanism for displacing them successively into the chucks. A measuring unit is located between the chucks for measuring the diameter of the fuel elements at intervals about their circumferences, and a secondary indexing mechanism is provided for rotating the measuring unit in a stepwise manner. (U.K.)

  20. Author Index

    Indian Academy of Sciences (India)

    Author Index. Alshaary, A. A. see Sharaf, M. A., 9. Banajh, M. A. see Sharaf, M. A., 9. Burbidge Geoffrey see Narlikar Jayant, V., 67. Chen, H. D. see Li, K. J., 147. Chen, Y. Q. see Huang, C., 139. Cui Wenyuan Evolution of the Distribution of Neutron Exposures in the Galaxy. Disc: An Analytical Model, 55. Dhurde Samir see ...

  1. Author Index

    Indian Academy of Sciences (India)

    Author Index. Alecian, E. see Samadhi, R., 171; see Goupil, M.-J., 249. Antia, H. M. Helioseismology, 161. Ashoka, B. N. see Seetha, S., 301. Baudin, F. see Samadhi, R., 171. Boehm, T. see Goupil, M.-J., 249. Catala, C. see Goupil, M.-J., 249. Cunha Margarida S. Asteroseismic Theory of Rapidly Oscillating Ap Stars, 213.

  2. SUBJECT INDEX

    Indian Academy of Sciences (India)

    Unknown

    SUBJECT INDEX. Absorption. Effect of NaCl on the spectral and kinetic properties of cresyl violet (CV)-sodium dodecyl sulphate (SDS) complex. 299. Acid catalysts. Temperature-programmed desorption of water and ammonia on sulphated zirconia catalysts for measuring their strong acidity and acidity distribution. 281.

  3. Author Index

    Indian Academy of Sciences (India)

    J. Astrophys. Astr. (2008) 29, 405–409. Author Index. Aggarwal Malini see Jain Rajmal, 125; X-ray Emission Characteristics of Flares. Associated with CMEs, 195. Alyana Radharani see Rathod Jatin, 293; see Reddy Chandrasekhar, A., 313. Ambastha Ashok Helioseismic Effects of Energetic Transients, 93; see Maurya.

  4. SUBJECT INDEX

    Indian Academy of Sciences (India)

    Unknown

    SUBJECT INDEX. Ab initio calculations. Basis set effects on energy and hardness profiles of the hydrogen fluoride dimer. 549. Activation by calcinations. Highly active and reusable catalyst from Fe-Mg- hydrotalcite anionic clay for Friedel–Crafts type benzyla- tion reactions. 635. Adsorption. Adsorption studies of iron(III) on ...

  5. Author Index

    Indian Academy of Sciences (India)

    Author Index. Aggarwal Malini see Jain Rajmal, 155. Aghaee, A. Determination of the Mean Hi Absorption of the Intergalactic. Medium, 59. Agrawal, S. P. see Singh Ambika, 89. Biesiada Marek Could the Optical Transient SCP 06F6 be due to Micro- lensing?, 213. C¸ aliskan, S . see Küçük, ˙I., 135. Evans Lloyd, T. Carbon ...

  6. Author Index

    Indian Academy of Sciences (India)

    Author Index. Ahmad Farooq see Iqbal Naseer, 373. Ali Syed Salman Study of a Large Helical Eruptive Prominence Associated with. Double CME on 21 April 2001, 347; see Uddin Wahab, 267. Ali, A. Chemistry of Carbon Rich Star IRAS 15194–5115, 399. Ambastha Ashok Photospheric, Chromospheric and Helioseismic ...

  7. Subject Index

    Indian Academy of Sciences (India)

    J. Astrophys. Astr. (2006) 27, 469–472. Subject Index. Astrophysical Processes. Spatial Damping of Linear Compressional Magnetoacoustic Waves in Quiescent. Prominences (K. A. P. Singh), 321. Report on the Dynamical Evolution of an Axially Symmetric Quasar Model. (N. J. Papadopoulos & N. D. Caranicolas), 389.

  8. SUBJECT INDEX

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    SUBJECT INDEX. 1D inversion. A direct inversion scheme for deep resistivity sound- ing data using artificial neural networks. 49. 40. Ar-. 39. Ar thermochronology. Tectono-thermal evolution of the India-Asia colli- sion zone based on. 40. Ar-. 39. Ar thermochronology in. Ladakh, India. 737. ANN. Artificial neural network ...

  9. Index Fossils

    Indian Academy of Sciences (India)

    stricted geologic time range, easily preservable, of short species duration and found in multiple environment. Index fossils are used by geologists and palaeontologists as significant aids to determine the correlation and age of rock sequences [2]. Geologists use both large fossils or 'macrofossils' and microscopic fossils or ...

  10. Author Index

    Indian Academy of Sciences (India)

    user1

    Yan, X. L. see Deng, L. H., 221. Phase Relationship Between Sunspot Number, Flare Index and Solar Radio. Flux, 387. ZANINETTI, L. Revisiting the Cosmological Principle in a Cellular Framework, 399. ZHAO XIAN-FENG. Constraints on the Moment of Inertia of a Proto Neutron Star from the Hyperon Coupling Constants, ...

  11. Index Fossils

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 10. Index Fossils - Evidences from Plant Sources. Dipanjan Ghosh. General Article ... Author Affiliations. Dipanjan Ghosh1. Biological Science Department Kirnahar Shib Chandra High School Kirnahar, Birbhum 731302, West Bengal, India.

  12. Life Experience of Patients With Unilateral Vocal Fold Paralysis.

    Science.gov (United States)

    Francis, David O; Sherman, Ariel E; Hovis, Kristen L; Bonnet, Kemberlee; Schlundt, David; Garrett, C Gaelyn; Davies, Louise

    2018-04-05

    Clinicians and patients benefit when they have a clear understanding of how medical conditions influence patients' life experiences. Patients' perspectives on life with unilateral vocal fold paralysis have not been well described. To promote patient-centered care by characterizing the patient experiences of living with unilateral vocal fold paralysis. This study used mixed methods: surveys using the voice and dysphagia handicap indexes (VHI and DHI) and semistructured interviews with adults with unilateral vocal cord paralysis recruited from a tertiary voice center. Recorded interviews were transcribed, coded using a hierarchical coding system, and analyzed using an iterative inductive-deductive approach. Symptom domains of the patient experience. In 36 patients (26 [72%] were female, and the median age and interquartile range [IQR] were 63 years [48-68 years]; median interview duration, 42 minutes), median VHI and DHI scores were 96 (IQR, 77-108) and 55.5 (IQR, 35-89) at the time of interviews, respectively. Frustration, isolation, fear, and altered self-identity were primary themes permeating patients' experiences. Frustrations related to limitations in communication, employment, and the medical system. Sources of fear included a loss of control, fear of further dysfunction or permanent disability, concern for health consequences (eg, aspiration pneumonia), and/or an inability to call for help in emergency situations. These experiences were modified by the following factors: resilience, self-efficacy, perceived sense of control, and social support systems. Effects of unilateral vocal fold paralysis extend beyond impaired voice and other somatic symptoms. Awareness of the extent to which these patients experience frustration, isolation, fear, and altered self-identity is important. A patient-centered approach to optimizing unilateral vocal fold paralysis treatment is enhanced by an understanding of both the physical dimension of this condition and how patients

  13. Understanding the folding process of synthetic polymers by small ...

    Indian Academy of Sciences (India)

    This two-point interaction between the folding agent and the polymer backbone leads to a folding of the polymer chain, which was readily monitored by NMR titrations. The effect of various parameters, such as structures of the folding agent and polymer, and the solvent composition, on the folding propensities of the polymer ...

  14. Comparison of fault-related folding algorithms to restore a fold-and-thrust-belt

    Science.gov (United States)

    Brandes, Christian; Tanner, David

    2017-04-01

    Fault-related folding means the contemporaneous evolution of folds as a consequence of fault movement. It is a common deformation process in the upper crust that occurs worldwide in accretionary wedges, fold-and-thrust belts, and intra-plate settings, in either strike-slip, compressional, or extensional regimes. Over the last 30 years different algorithms have been developed to simulate the kinematic evolution of fault-related folds. All these models of fault-related folding include similar simplifications and limitations and use the same kinematic behaviour throughout the model (Brandes & Tanner, 2014). We used a natural example of fault-related folding from the Limón fold-and-thrust belt in eastern Costa Rica to test two different algorithms and to compare the resulting geometries. A thrust fault and its hanging-wall anticline were restored using both the trishear method (Allmendinger, 1998; Zehnder & Allmendinger, 2000) and the fault-parallel flow approach (Ziesch et al. 2014); both methods are widely used in academia and industry. The resulting hanging-wall folds above the thrust fault are restored in substantially different fashions. This is largely a function of the propagation-to-slip ratio of the thrust, which controls the geometry of the related anticline. Understanding the controlling factors for anticline evolution is important for the evaluation of potential hydrocarbon reservoirs and the characterization of fault processes. References: Allmendinger, R.W., 1998. Inverse and forward numerical modeling of trishear fault propagation folds. Tectonics, 17, 640-656. Brandes, C., Tanner, D.C. 2014. Fault-related folding: a review of kinematic models and their application. Earth Science Reviews, 138, 352-370. Zehnder, A.T., Allmendinger, R.W., 2000. Velocity field for the trishear model. Journal of Structural Geology, 22, 1009-1014. Ziesch, J., Tanner, D.C., Krawczyk, C.M. 2014. Strain associated with the fault-parallel flow algorithm during kinematic fault

  15. Organic Matter Fractions and Quality of the Surface Layer of a Constructed and Vegetated Soil After Coal Mining. II - Physical Compartments and Carbon Management Index

    Directory of Open Access Journals (Sweden)

    Otávio dos Anjos Leal

    2015-06-01

    Full Text Available Soils constructed after mining often have low carbon (C stocks and low quality of organic matter (OM. Cover crops are decisive for the recovery process of these stocks, improving the quality of constructed soils. Therefore, the goal of this study was to evaluate the effect of cover crops on total organic C (TOC stocks, C distribution in physical fractions of OM and the C management index (CMI of a soil constructed after coal mining. The experiment was initiated in 2003 with six treatments: Hemarthria altissima (T1, Paspalum notatum (T2, Cynodon dactylon (T3, Urochloa brizantha (T4, bare constructed soil (T5, and natural soil (T6. Soil samples were collected in 2009 from the 0.00-0.03 m layer, and the TOC and C stocks in the physical particle size fractions (carbon in the coarse fraction - CCF, and mineral-associated carbon - MAC and density fractions (free light fraction - FLF; occluded light fraction - OLF, and heavy fraction - HF of OM were determined. The CMI components: carbon pool index (CPI, lability (L and lability index (LI were estimated by both fractionation methods. No differences were observed between TOC, CCF and MAC stocks. The lowest C stocks in FLF and OLF fractions were presented by T2, 0.86 and 0.61 Mg ha-1, respectively. The values of TOC stock, C stock in physical fractions and CMI were intermediate, greater than T5 and lower than T6 in all treatments, indicating the partial recovery of soil quality. As a result of the better adaptation of the species Hemarthria and Brizantha, resulting in greater accumulation of labile organic material, the CPI, L, LI and CMI values were higher in these treatments, suggesting a greater potential of these species for recovery of constructed soils.

  16. Assessment of thyroplasty for vocal fold paralysis

    DEFF Research Database (Denmark)

    Grøntved, Ågot Møller; Faber, Christian; Jakobsen, John

    2009-01-01

    -Dimensional Voice Program. Furthermore, patients answered the Voice Handicap Index (VHI) questionnaire. RESULTS: The capacity and intensity of the voice were significantly increased with an improvement of the highest intensity of 13 dB. The capacity of the voice was increased more than 2.5 times. The voice quality...... was improved significantly as measured by the jitter percentage, shimmer percentage and voice turbulence index. The VHI was decreased by 40, from a mean preoperative value of 82. A total of 90% of patients were satisfied. CONCLUSION: Besides videostroboscopy, a phonetogram is the most important analysis...

  17. Perspectives in using a remotely sensed dryness index in distributed hydrological models at river basin scale

    DEFF Research Database (Denmark)

    Andersen, J.; Sandholt, Inge; Jensen, Karsten Høgh

    2002-01-01

    Remote Sensing, hydrological modelling, dryness index, surface temperature, vegetation index, Africa, Senegal, soil moisture......Remote Sensing, hydrological modelling, dryness index, surface temperature, vegetation index, Africa, Senegal, soil moisture...

  18. Pattern Analysis of El Nino and La Nina Phenomenon Based on Sea Surface Temperature (SST) and Rainfall Intensity using Oceanic Nino Index (ONI) in West Java Area

    Science.gov (United States)

    Prasetyo, Yudo; Nabilah, Farras

    2017-12-01

    Climate change occurs in 1998-2016 brings significant alteration in the earth surface. It is affects an extremely anomaly temperature such as El Nino and La Nina or mostly known as ENSO (El Nino Southern Oscillation). West Java is one of the regions in Indonesia that encounters the impact of this phenomenon. Climate change due to ENSO also affects food production and other commodities. In this research, processing data method is conducted using programming language to process SST data and rainfall data from 1998 to 2016. The data are sea surface temperature from NOAA satellite, SST Reynolds (Sea Surface Temperature) and daily rainfall temperature from TRMM satellite. Data examination is done using analysis of rainfall spatial pattern and sea surface temperature (SST) where is affected by El Nino and La Nina phenomenon. This research results distribution map of SST and rainfall for each season to find out the impacts of El Nino and La Nina around West Java. El Nino and La Nina in Java Sea are occurring every August to February. During El Nino, sea surface temperature is between 27°C - 28°C with average temperature on 27.71°C. Rainfall intensity is 1.0 mm/day – 2.0 mm/day and the average are 1.63 mm/day. During La Nina, sea surface temperature is between 29°C - 30°C with average temperature on 29.06°C. Rainfall intensity is 9.0 mm/day - 10 mm/day, and the average is 9.74 mm/day. The correlation between rainfall and SST is 0,413 which is expresses a fairly strong correlation between parameters. The conclusion is, during La Nina SST and rainfall increase. While during El Nino SST and rainfall decrease. Hopefully this research could be a guideline to plan disaster mitigation in West Java region that is related extreme climate change.

  19. Ptolemaic indexing

    Directory of Open Access Journals (Sweden)

    Magnus Lie Hetland

    2015-07-01

    Full Text Available This paper discusses a new family of bounds for use in similarity search, related to those used in metric indexing, but based on Ptolemy's inequality, rather than the metric axioms. Ptolemy's inequality holds for the well-known Euclidean distance, but is also shown here to hold for quadratic form metrics in general, with Mahalanobis distance as an important special case. The inequality is examined empirically on both synthetic and real-world data sets and is also found to hold approximately, with a very low degree of error, for important distances such as the angular pseudometric and several Lp norms. Indexing experiments are performed on several data sets, demonstrating a highly increased filtering power when using certain forms of Ptolemaic filtering, compared to existing, triangular methods. It is also shown that combining the Ptolemaic and triangular filtering can lead to better results than using either approach on its own.

  20. Image analysis of vocal fold histology

    Science.gov (United States)

    Reinisch, Lou; Garrett, C. Gaelyn

    2001-05-01

    To visualize the concentration gradients of collagen, elastin and ground substance in histologic sections of vocal folds, an image enhancement scheme was devised. Slides stained with Movat's solution were viewed on a light microscope. The image was digitally photographed. Using commercially available software, all pixels within a color range are selected from the mucosa presented on the image. Using the Movat's pentachrome stain, yellow to yellow-brown pixels represented mature collagen, blue to blue-green pixels represented young collagen (collagen that is not fully cross-linked) and black to dark violet pixels represented elastin. From each of the color range selections, a black and white image was created. The pixels not within the color range were black. The selected pixels within the color range were white. The image was averaged and smoothed to produce 256 levels of gray with less spatial resolution. This new grey-scale image showed the concentration gradient. These images were further enhanced with contour lines surrounding equivalent levels of gray. This technique is helpful to compare the micro-anatomy of the vocal folds. For instance, we find large concentration of the collagen deep in the mucosa and adjacent to the vocalis muscle.

  1. Numerical modeling of fold-and-thrust belts: Applications to Kuqa foreland fold belt, China

    Science.gov (United States)

    Yin, H.; Morgan, J. K.; Zhang, J.; Wang, Z.

    2009-12-01

    We constructed discrete element models to simulate the evolution of fold-and-thrust belts. The impact of rock competence and decollement strength on the geometric pattern and deformation mechanics of fold-and-thrust belts has been investigated. The models reproduced some characteristic features of fold-and-thrust belts, such as faulted detachment folds, pop-ups, far-traveled thrust sheets, passive-roof duplexes, and back thrusts. In general, deformation propagates farther above a weak decollement than above a strong decollement. Our model results confirm that fold-and-thrust belts with strong frictional decollements develop relatively steep and narrow wedges formed by closely spaced imbricate thrust slices, whereas fold belts with weak decollements form wide low-taper wedges composed of faulted detachment folds, pop-ups, and back thrusts. Far-traveled thrust sheets and passive-roof duplexes are observed in the model with a strong lower decollement and a weak upper detachment. Model results also indicate that the thickness of the weak layer is critical. If it is thick enough, it acts as a ductile layer that is able to flow under differential stress, which helps to partition deformation above and below it. The discrete element modeling results were used to interpret the evolution of Kuqa Cenozoic fold-and-thrust belt along northern Tarim basin, China. Seismic and well data show that the widely distributed Paleogene rock salt has a significant impact on the deformation in this area. Structures beneath salt are closely spaced imbricate thrust and passive-roof duplex systems. Deformation above salt propagates much farther than below the salt. Faults above salt are relatively wide spaced. A huge controversy over the Kuqa fold-and-thrust belt is whether it is thin-skinned or thick-skinned. With the insights from DEM results, we suggest that Kuqa structures are mostly thin-skinned with Paleogene salt as decollement, except for the rear part near the backstop, where the

  2. Gauge Theory and Calibrated Geometry for Calabi-Yau 4-folds

    Science.gov (United States)

    Cao, Yalong

    Floer theory in the sense of Fukaya-Oh-Ohta-Ono for Calabi-Yau 4-folds. 5. We study Kapustin-Witten type (KWC) equations on Calabi-Yau 4-folds. In particular, we investigate their ellipticity, relations with complex ASD equations for complex gauge groups and local Kuranishi models for moduli spaces of corresponding solutions. We also give some vanishing results when the complex vector bundle satisfies certain topological conditions. Dimensional reductions of KWC equations to Calabi-Yau 3-folds and Kahler surfaces are also discussed.

  3. Nitrogen adsorption on Fe(111), (100), and (110) surfaces

    DEFF Research Database (Denmark)

    Mortensen, Jens Jørgen; Ganduglia-Pirovano, Veronica; Hansen, Lars Bruno

    1999-01-01

    Adsorption energies and structures for N atoms on three low-index surfaces of Fe have been calculated using density functional theory (DFT) and the generalized gradient approximation (GGA). At low N coverage the adsorption energy on Fe(100) is found to be similar to 0.7 eV higher than on the (111......) and (110) surfaces - particularly the c(2 x 2)-N/Fe(100) structure with the N atoms in four-fold sites is very stable. We attribute the differences in adsorption energy to the lack of four-fold sites on the (111) and (110) surfaces, We suggest that at higher N coverages, islands with a structure similar...

  4. Temporalis Fascia Transplantation for Sulcus Vocalis and Vocal Fold Scar: Long-Term Outcomes.

    Science.gov (United States)

    Karle, William E; Helman, Samuel N; Cooper, Amy; Zhang, Yuan; Pitman, Michael J

    2018-04-01

    Sulcus vocalis and vocal fold scar involve derangement of the superficial lamina propria of the vocal fold, which results in significant dysphonia. Many options exist for treatment, most of which have unsatisfactory and unpredictable outcomes. Autologous transplantation of temporalis fascia into the vocal fold (ATFV) has the potential to be a better treatment option, but long-term outcomes have not been well studied. Retrospective chart review and patient survey. Twenty-one patients diagnosed with vocal fold scar or sulcus vocalis and treated with ATFV with at least 1-year follow-up were included. Voice Handicap Index 10 (VHI-10) questionnaires were collected preoperatively and 6 months postoperatively. Patients were reached at the time of the study to complete another VHI-10 and a Likert scale survey. The mean decrease in VHI-10 scores between preoperation and 6 months postoperation was 8.35 ( P fascia into the vocal fold for the treatment of vocal fold scar and sulcus vocalis is a safe surgery with good long-term outcomes and high patient satisfaction.

  5. Chondroitin sulphate-mediated fusion of brain neural folds in rat embryos.

    Science.gov (United States)

    Alonso, M I; Moro, J A; Martín, C; de la Mano, A; Carnicero, E; Martínez-Alvarez, C; Navarro, N; Cordero, J; Gato, A

    2009-01-01

    Previous studies have demonstrated that during neural fold fusion in different species, an apical extracellular material rich in glycoconjugates is involved. However, the composition and the biological role of this material remain undetermined. In this paper, we show that this extracellular matrix in rat increases notably prior to contact between the neural folds, suggesting the dynamic behaviour of the secretory process. Immunostaining has allowed us to demonstrate that this extracellular matrix contains chondroitin sulphate proteoglycan (CSPG), with a spatio-temporal distribution pattern, suggesting a direct relationship with the process of adhesion. The degree of CSPG involvement in cephalic neural fold fusion in rat embryos was determined by treatment with specific glycosidases.In vitro rat embryo culture and microinjection techniques were employed to carry out selective digestion, with chondroitinase AC, of the CSPG on the apical surface of the neural folds; this was done immediately prior to the bonding of the cephalic neural folds. In all the treated embryos, cephalic defects of neural fold fusion could be detected. These results show that CSPG plays an important role in the fusion of the cephalic neural folds in rat embryos, which implies that this proteoglycan could be involved in cellular recognition and adhesion. (c) 2008 S. Karger AG, Basel.

  6. Improving decoy databases for protein folding algorithms

    KAUST Repository

    Lindsey, Aaron

    2014-01-01

    Copyright © 2014 ACM. Predicting protein structures and simulating protein folding are two of the most important problems in computational biology today. Simulation methods rely on a scoring function to distinguish the native structure (the most energetically stable) from non-native structures. Decoy databases are collections of non-native structures used to test and verify these functions. We present a method to evaluate and improve the quality of decoy databases by adding novel structures and removing redundant structures. We test our approach on 17 different decoy databases of varying size and type and show significant improvement across a variety of metrics. We also test our improved databases on a popular modern scoring function and show that they contain a greater number of native-like structures than the original databases, thereby producing a more rigorous database for testing scoring functions.

  7. Noise Folding in Completely Perturbed Compressed Sensing

    Directory of Open Access Journals (Sweden)

    Limin Zhou

    2016-01-01

    Full Text Available This paper first presents a new generally perturbed compressed sensing (CS model y=(A+E(x+u+e, which incorporated a general nonzero perturbation E into sensing matrix A and a noise u into signal x simultaneously based on the standard CS model y=Ax+e and is called noise folding in completely perturbed CS model. Our construction mainly will whiten the new proposed CS model and explore in restricted isometry property (RIP and coherence of the new CS model under some conditions. Finally, we use OMP to give a numerical simulation which shows that our model is feasible although the recovered value of signal is not exact compared with original signal because of measurement noise e, signal noise u, and perturbation E involved.

  8. Neutron structural biology. Beyond the folding structure

    International Nuclear Information System (INIS)

    Niimura, Nobuo

    2009-01-01

    Hydrogen atoms and water molecules around proteins and nucleic acids play a crucial role in many physiological functions. Neutron diffraction provides an experimental method of directly locating hydrogen atoms. (a) Since almost all the H atom positions can be identified experimentally, the geometrical details of certain types of H-bonds can be visualized and (b) as far as mechanistic implications are concerned, the identification of protonation and deprotonation states of certain important amino acid residues can be carried out. (c) The hydration structure around proteins and the hydration networks around DNA oligomers have been successfully characterized in several outstanding cases. These will open the new field beyond the folding structure of bio-macromolecules such as: 1) Recognition of proteins and nucleic acids through the network structure of water molecules surrounding bio-macromolecules, and 2) The nature of chemical bond in proteins and nucleic acids elucidated by the accumulation of accurate structural information of hydrogen atoms. (author)

  9. Electrotransfection of Polyamine Folded DNA Origami Structures.

    Science.gov (United States)

    Chopra, Aradhana; Krishnan, Swati; Simmel, Friedrich C

    2016-10-12

    DNA origami structures are artificial molecular nanostructures in which DNA double helices are forced into a closely packed configuration by a multitude of DNA strand crossovers. We show that three different types of origami structures (a flat sheet, a hollow tube, and a compact origami block) can be formed in magnesium-free buffer solutions containing low (origami folding is proportional to the DNA concentration. At excessive amounts, the structures aggregate and precipitate. In contrast to origami structures formed in conventional buffers, the resulting structures are stable in the presence of high electric field pulses, such as those commonly used for electrotransfection experiments. We demonstrate that spermidine-stabilized structures are stable in cell lysate and can be delivered into mammalian cells via electroporation.

  10. Microscopic Phonosurgery in Benign Vocal Fold Lesions

    Directory of Open Access Journals (Sweden)

    Sukamal Das

    2014-06-01

    Thirty out of 32 patients showed objective improvement in fibreoptic laryngoscopy post treatment. Two patients were noncompliant to voice therapy and showed recurrence of their pathologies.Mean VHI 10 score showed significant improvement from 8 in the preoperative period to 3 in the postoperative period. Conclusion : Phonosurgery is a quick and effective treatment with uncommon and transient post-operative complications. Pre and postoperative voice therapy plays an integral role in combination with phono-micro surgery enhances the outcome in patients with benign vocal fold lesions. Objective assessment of the voice pre- and postoperatively should be used consistently to evaluate the additional impact of pre- and postoperative voice therapy.

  11. Unexpected fold in the circumsporozoite protein target of malaria vaccines

    Energy Technology Data Exchange (ETDEWEB)

    Doud, Michael B.; Koksal, Adem C.; Mi, Li-Zhi; Song, Gaojie; Lu, Chafen; Springer, Timothy A. (Harvard-Med)

    2012-10-09

    Circumsporozoite (CS) protein is the major surface component of Plasmodium falciparum sporozoites and is essential for host cell invasion. A vaccine containing tandem repeats, region III, and thrombospondin type-I repeat (TSR) of CS is efficacious in phase III trials but gives only a 35% reduction in severe malaria in the first year postimmunization. We solved crystal structures showing that region III and TSR fold into a single unit, an '{alpha}TSR' domain. The {alpha}TSR domain possesses a hydrophobic pocket and core, missing in TSR domains. CS binds heparin, but {alpha}TSR does not. Interestingly, polymorphic T-cell epitopes map to specialized {alpha}TSR regions. The N and C termini are unexpectedly close, providing clues for sporozoite sheath organization. Elucidation of a unique structure of a domain within CS enables rational design of next-generation subunit vaccines and functional and medicinal chemical investigation of the conserved hydrophobic pocket.

  12. On the folding of graphs-theory and application

    International Nuclear Information System (INIS)

    Nada, S.I.; Hamouda, E.H.

    2009-01-01

    In this article, we recall the definition of graph folding in the sense of El-kholy and El-Esawy [El-kholy E, El-Esawy A. Graph folding of some special graphs. J Math Stat 2005;1(1):66-70.] and study the limit of folding of some graphs. Also we define the folding number and give a formula to compute the number of folding maps f: P n → P n , where P n is a path with n edges. We also discuss application of folding from Orgami to buckling and high energy physics.

  13. Glycoprotein folding and quality-control mechanisms in protein-folding diseases

    Directory of Open Access Journals (Sweden)

    Sean P. Ferris

    2014-03-01

    Full Text Available Biosynthesis of proteins – from translation to folding to export – encompasses a complex set of events that are exquisitely regulated and scrutinized to ensure the functional quality of the end products. Cells have evolved to capitalize on multiple post-translational modifications in addition to primary structure to indicate the folding status of nascent polypeptides to the chaperones and other proteins that assist in their folding and export. These modifications can also, in the case of irreversibly misfolded candidates, signal the need for dislocation and degradation. The current Review focuses on the glycoprotein quality-control (GQC system that utilizes protein N-glycosylation and N-glycan trimming to direct nascent glycopolypeptides through the folding, export and dislocation pathways in the endoplasmic reticulum (ER. A diverse set of pathological conditions rooted in defective as well as over-vigilant ER quality-control systems have been identified, underlining its importance in human health and disease. We describe the GQC pathways and highlight disease and animal models that have been instrumental in clarifying our current understanding of these processes.

  14. SUBJECT INDEX

    Indian Academy of Sciences (India)

    Surface waves. Elastic waves along a cylindrical borehole in a poroelastic medium saturated by two immiscible fluids. 225. Talchir Basin. Facies characteristics of the basal part of the. Talchir Formation, Talchir Basin, India – deposi- tional history revisited. 15. Talchir Formation. Facies characteristics of the basal part of the.

  15. AUTHOR INDEX

    Indian Academy of Sciences (India)

    Cline J M. Mimicking trans-Planckian effects in the. CMB with conventional physics. 749. Das C R see Parida M K. 647. Das Niranjan. Note on the surface wave due to the pre- scribed elevation. 135. Das Subinoy see Konar Sushan. 1241. Dasgupta Mrinal. On de-globalization in quantum chromo- dynamics. 675. Dash P C.

  16. Author Index

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    system for Langmuir-Blodgett film deposition set-up. 213. Pal Chandra Prakash. Effect of dynamic visco-elasticity on vertical and torsional vibrations of half-space. 371 ... mounted rib. Part1: Turbulent structure char- acterisation. 387. Fundamentally excited flow past a surface- mounted rib.Part II: Kinetic energy budget details.

  17. SUBJECT INDEX

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    A direct inversion scheme for deep resistivity sound- ing data using artificial neural networks. 49. 40. Ar-. 39. Ar thermochronology. Tectono-thermal evolution of the India-Asia colli- sion zone based on. 40. Ar-. 39. Ar thermochronology in. Ladakh, India. 737. ANN. Artificial neural network approach for estima- tion of surface ...

  18. Type I gore-tex laryngoplasty for glottic incompetence in mobile vocal folds.

    Science.gov (United States)

    Buckmire, Robert A; Bryson, Paul C; Patel, Mihir R

    2011-05-01

    To determine the effectiveness of gore-tex medialization thyroplasty for the management of glottic incompetence (GI) in patients with mobile vocal folds. Twenty patients with glottic incompetence (GI) and mobile vocal folds were retrospectively analyzed after gore-tex medialization laryngoplasty. Pre- and postoperative outcome measures including grade, roughness, breathiness, asthenia, strain of the voice (GRBAS), glottal function index (GFI), and voice-related quality of life (VRQOL) were compared to detect surgical effectiveness. Two anesthetic subgroups were identified and compared: general anesthesia, via laryngeal mask airway (LMA) anesthetic, and local anesthesia. Statistically significant differences were identified between pre- and postoperative VRQOL (PGore-tex thyroplasty provides reliable medium-term improvement in both perceptual and subjective voice parameters in the setting of GI with mobile vocal folds. Copyright © 2011 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

  19. Role of early voice therapy in patients affected by unilateral vocal fold paralysis.

    Science.gov (United States)

    D'Alatri, L; Galla, S; Rigante, M; Antonelli, O; Buldrini, S; Marchese, M R

    2008-09-01

    To evaluate the functional results obtained after voice therapy in patients with unilateral vocal fold paralysis caused by different aetiologies. Prospective analysis of the outcome of unilateral vocal fold paralysis cases treated at our speech and language rehabilitation service from November 2003 to January 2006. Thirty cases underwent behavioural treatment, between two and six weeks after unilateral vocal fold paralysis onset. A multi-dimensional assessment was carried out before, immediately after and six months after treatment. After behavioural therapy, the prevalence of complete glottal closure increased significantly (p voice range profile analysis showed a significant decrease of lowest voice frequency and a significant increase of the number of semitones (p < 0.05). Mean values for grade, instability, breathiness, asthenia and voice handicap index scores were significantly decreased both immediately and six months after treatment, compared with pre-treatment values (p < 0.05). Early voice therapy may enable significant improvement in vocal function, allowing the patient to avoid surgery.

  20. (In,Ga,Al)P-GaP laser diodes grown on high-index GaAs surfaces emitting in the green, yellow and bright red spectral range

    Science.gov (United States)

    Ledentsov, N. N.; Shchukin, V. A.; Shernyakov, Yu M.; Kulagina, M. M.; Payusov, A. S.; Gordeev, N. Yu; Maximov, M. V.; Cherkashin, N. A.

    2017-02-01

    We report on low threshold current density (<400 A cm-2) injection lasing in (Al x Ga1-x )0.5In0.5P-GaAs-based diodes down to the green spectral range (<570 nm). The epitaxial structures are grown on high-index (611)A and (211)A GaAs substrates by metal-organic vapor phase epitaxy and contain tensile-strained GaP-enriched insertions aimed at reflection of the injected nonequilibrium electrons preventing their escape from the active region. Extended waveguide concept results in a vertical beam divergence with a full width at half maximum of 15° for (611)A substrates. The lasing at the wavelength of 569 nm is realized at 85 K. In an orange-red laser diode structure low threshold current density (190 A cm-2) in the orange spectral range (598 nm) is realized at 85 K. The latter devices demonstrated room temperature lasing at 628 nm at ˜2 kA cm-2 and a total power above 3 W. The red laser diodes grown on (211)A substrates demonstrated a far field characteristic for vertically multimode lasing indicating a lower optical confinement factor for the fundamental mode as compared to the devices grown on (611)A. However, as expected from previous research, the temperature stability of the threshold current and the wavelength stability were significantly higher for (211)A-grown structures.

  1. Self-folding origami at any energy scale

    Science.gov (United States)

    Pinson, Matthew B.; Stern, Menachem; Carruthers Ferrero, Alexandra; Witten, Thomas A.; Chen, Elizabeth; Murugan, Arvind

    2017-05-01

    Programmable stiff sheets with a single low-energy folding motion have been sought in fields ranging from the ancient art of origami to modern meta-materials research. Despite such attention, only two extreme classes of crease patterns are usually studied; special Miura-Ori-based zero-energy patterns, in which crease folding requires no sheet bending, and random patterns with high-energy folding, in which the sheet bends as much as creases fold. We present a physical approach that allows systematic exploration of the entire space of crease patterns as a function of the folding energy. Consequently, we uncover statistical results in origami, finding the entropy of crease patterns of given folding energy. Notably, we identify three classes of Mountain-Valley choices that have widely varying `typical' folding energies. Our work opens up a wealth of experimentally relevant self-folding origami designs not reliant on Miura-Ori, the Kawasaki condition or any special symmetry in space.

  2. Phonosurgery of vocal fold polyps, cysts and nodules is beneficial

    DEFF Research Database (Denmark)

    Jensen, Jane Bjerg; Rasmussen, Niels

    2013-01-01

    This study reports our experience with microscopic phonosurgery (PS) of benign lesions of the vocal folds.......This study reports our experience with microscopic phonosurgery (PS) of benign lesions of the vocal folds....

  3. Multidimensional Analysis on the Effect of Vocal Function Exercises on Aged Vocal Fold Atrophy.

    Science.gov (United States)

    Kaneko, Mami; Hirano, Shigeru; Tateya, Ichiro; Kishimoto, Yo; Hiwatashi, Nao; Fujiu-Kurachi, Masako; Ito, Juichi

    2015-09-01

    Age-related voice change is characterized as weak, harsh, and breathy. These changes are caused by histologic alteration of the lamina propria of the vocal fold mucosa as well as atrophy of the thyroarytenoid muscle. Several therapeutic strategies involving laryngeal framework surgery and injection laryngoplasty have been tried, but effects have been limited. Vocal function exercises (VFE) have been used to treat age-related vocal fold atrophy although the effectiveness has been shown with limited analysis. The present study aims to determine the effectiveness of VFE for the treatment of aged atrophy using multidimensional analysis. This is a retrospective study. Sixteen patients with vocal fold atrophy aged 65-81 years underwent voice therapy using VFE. Six patients with vocal fold atrophy aged 65-85 years were involved as a historical control group. The grade, roughness, breathiness, asthenia, strain (GRBAS) scale, stroboscopic examinations, aerodynamic assessment, acoustic analysis, and Voice Handicap Index-10 (VHI-10) were performed before and after VFE. Normalized mucosal wave amplitude (NMWA), normalized glottal gap (NGG), and bowing index (BI) were measured by image analysis during stroboscopic examinations. After VFE, significant improvements were shown in GRBAS, maximum phonation time, jitter, NMWA, NGG, and VHI-10 although BI has not changed significantly. There were no significant improvements in the historical control. The data suggest that VFE produces significant improvement in subjective, objective, and patient self-evaluation and deserves further attention as a treatment for aged atrophy of the vocal fold. It was also suggested that VFE does not improve the vocal fold bowing but may improve muscular function during voicing. Copyright © 2015 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  4. 3D fold growth rates in transpressional tectonic settings

    Science.gov (United States)

    Frehner, Marcel

    2015-04-01

    Geological folds are inherently three-dimensional (3D) structures; hence, they also grow in 3D. In this study, fold growth in all three dimensions is quantified numerically using a finite-element algorithm for simulating deformation of Newtonian media in 3D. The presented study is an extension and generalization of the work presented in Frehner (2014), which only considered unidirectional layer-parallel compression. In contrast, the full range from strike slip settings (i.e., simple shear) to unidirectional layer-parallel compression is considered here by varying the convergence angle of the boundary conditions; hence the results are applicable to general transpressional tectonic settings. Only upright symmetrical single-layer fold structures are considered. The horizontal higher-viscous layer exhibits an initial point-like perturbation. Due to the mixed pure- and simple shear boundary conditions a mechanical buckling instability grows from this perturbation in all three dimensions, described by: Fold amplification (vertical growth): Fold amplification describes the growth from a fold shape with low limb-dip angle to a shape with higher limb-dip angle. Fold elongation (growth parallel to fold axis): Fold elongation describes the growth from a dome-shaped (3D) structure to a more cylindrical fold (2D). Sequential fold growth (growth perpendicular to fold axial plane): Sequential fold growth describes the growth of secondary (and further) folds adjacent to the initial isolated fold. The term 'lateral fold growth' is used as an umbrella term for both fold elongation and sequential fold growth. In addition, the orientation of the fold axis is tracked as a function of the convergence angle. Even though the absolute values of all three growth rates are markedly reduced with increasing simple-shear component at the boundaries, the general pattern of the quantified fold growth under the studied general-shear boundary conditions is surprisingly similar to the end

  5. Factors that affect coseismic folds in an overburden layer

    Science.gov (United States)

    Zeng, Shaogang; Cai, Yongen

    2018-03-01

    Coseismic folds induced by blind thrust faults have been observed in many earthquake zones, and they have received widespread attention from geologists and geophysicists. Numerous studies have been conducted regarding fold kinematics; however, few have studied fold dynamics quantitatively. In this paper, we establish a conceptual model with a thrust fault zone and tectonic stress load to study the factors that affect coseismic folds and their formation mechanisms using the finite element method. The numerical results show that the fault dip angle is a key factor that controls folding. The greater the dip angle is, the steeper the fold slope. The second most important factor is the overburden thickness. The thicker the overburden is, the more gradual the fold. In this case, folds are difficult to identify in field surveys. Therefore, if a fold can be easily identified with the naked eye, the overburden is likely shallow. The least important factors are the mechanical parameters of the overburden. The larger the Young's modulus of the overburden is, the smaller the displacement of the fold and the fold slope. Strong horizontal compression and vertical extension in the overburden near the fault zone are the main mechanisms that form coseismic folds.

  6. 76 FR 74704 - Folded Self-Mailers and Unenveloped Mailpieces

    Science.gov (United States)

    2011-12-01

    ... as an oblong. The final folded edge of an oblong folded self-mailer must be the leading (right) edge... POSTAL SERVICE 39 CFR Part 111 Folded Self-Mailers and Unenveloped Mailpieces AGENCY: Postal... self-mailers (FSM) and unenveloped mailpieces that are mailed at automation or machinable prices. To...

  7. Folds in multilayered rocks of Proterozoic age, Rajasthan, India

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Johnson and Johnson 2002 etc) shows that the fold shape modification may be brought about by buckling and flattening operating simultaneously throughout the development of fold. In the present paper a series of F1 folds devel- oped in slates with interlayered alternations with quartzite of Proterozoic age and unaffected ...

  8. Nomenclature proposal to describe vocal fold motion impairment

    NARCIS (Netherlands)

    Rosen, Clark A.; Mau, Ted; Remacle, Marc; Hess, Markus; Eckel, Hans E.; Young, VyVy N.; Hantzakos, Anastasios; Yung, Katherine C.; Dikkers, Frederik G.

    2016-01-01

    The terms used to describe vocal fold motion impairment are confusing and not standardized. This results in a failure to communicate accurately and to major limitations of interpreting research studies involving vocal fold impairment. We propose standard nomenclature for reporting vocal fold

  9. Nomenclature proposal to describe vocal fold motion impairment

    NARCIS (Netherlands)

    Rosen, Clark A.; Mau, Ted; Remacle, Marc; Hess, Markus; Eckel, Hans E.; Young, VyVy N.; Hantzakos, Anastasios; Yung, Katherine C.; Dikkers, Frederik G.

    The terms used to describe vocal fold motion impairment are confusing and not standardized. This results in a failure to communicate accurately and to major limitations of interpreting research studies involving vocal fold impairment. We propose standard nomenclature for reporting vocal fold

  10. α/β Hydrolase fold enzymes: the family keeps growing

    NARCIS (Netherlands)

    Nardini, Marco; Dijkstra, B W

    1999-01-01

    The alpha/beta hydrolase fold is a typical example of a tertiary fold adopted by proteins that have no obvious sequence similarity, but nevertheless, in the course of evolution, diverged from a common ancestor. Recently solved structures demonstrate a considerably increased variability in fold

  11. Probing folding free energy landscape of small proteins through ...

    Indian Academy of Sciences (India)

    Unknown

    lattice and off-lattice models of proteins have been used to study the statistical and dynamical aspects of folding.12,13 Levitt pioneered in the computational studies of protein folding using off-lattice protein models.14 A recent off-lattice model study of HP-36 based on hydrophobicity tried to correlate the folding with many ...

  12. 77 FR 74513 - Folding Gift Boxes From China

    Science.gov (United States)

    2012-12-14

    ... COMMISSION Folding Gift Boxes From China Determination On the basis of the record \\1\\ developed in the... antidumping duty order on folding gift boxes from China would be likely to lead to continuation or recurrence... Commission are contained in USITC Publication 4365 (November 2012), entitled Folding Gift Boxes from China...

  13. Kinetics of folding of the myosin rod.

    Science.gov (United States)

    Bechet, J J; Nozais, M

    1997-02-15

    The kinetics of the unfolding and refolding of the myosin rod have been studied by fluorescence and circular dichroism techniques, at different concentrations of protein and guanidine hydrochloride. The unfolding of the myosin rod was fast and at least biphasic in 2-3 M denaturant, with an initial immediate phase followed by a slower low-amplitude first-order phase. The refolding of the rod in 0.4-2 M guanidine hydrochloride was also at least biphasic; an initial immediate phase preceded a slow second-order phase. At the final denaturant concentration of 0.8 M, the amplitude of the burst phase was weakly dependent on the protein concentration and the rate constant of the refolding slow phase was optimal. These data are incorporated into a folding mechanism with at least three states. The high rates of the first steps of unfolding and refolding may be relevant for the functioning of the native myosin molecule by allowing a transient separation of the two strands of the myosin tail.

  14. Hydrophobic-hydrophilic forces in protein folding.

    Science.gov (United States)

    Durell, Stewart R; Ben-Naim, Arieh

    2017-08-01

    The process of protein folding is obviously driven by forces exerted on the atoms of the amino-acid chain. These forces arise from interactions with other parts of the protein itself (direct forces), as well as from interactions with the solvent (solvent-induced forces). We present a statistical-mechanical formalism that describes both these direct and indirect, solvent-induced thermodynamic forces on groups of the protein. We focus on 2 kinds of protein groups, commonly referred to as hydrophobic and hydrophilic. Analysis of this result leads to the conclusion that the forces on hydrophilic groups are in general stronger than on hydrophobic groups. This is then tested and verified by a series of molecular dynamics simulations, examining both hydrophobic alkanes of different sizes and hydrophilic moieties represented by polar-neutral hydroxyl groups. The magnitude of the force on assemblies of hydrophilic groups is dependent on their relative orientation: with 2 to 4 times larger forces on groups that are able to form one or more direct hydrogen bonds. © 2017 Wiley Periodicals, Inc.

  15. Folding very short peptides using molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Bosco K Ho

    2006-04-01

    Full Text Available Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides, the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

  16. Compression strain-induced folding at intersecting deformation macrobands on the copper single crystals

    Science.gov (United States)

    Chumaevskii, A. V.; Lychagin, D. V.; Tarasov, S. Yu.

    2017-12-01

    Compression strain-induced surface pattern on copper single crystal faces was studied by means of optical, confocal laser and scanning electron microscopies. It was shown that apart from work-hardening effect of previously formed deformation macrobands there is a pure geometrical (size) effect which serves for changing the conditions for further deformation within the deformation macroband zones by folded structure formation.

  17. Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation.

    Science.gov (United States)

    Mikulecky, Peter J; Feig, Andrew L

    2004-01-01

    In proteins, empirical correlations have shown that changes in heat capacity (DeltaC(P)) scale linearly with the hydrophobic surface area buried upon folding. The influence of DeltaC(P) on RNA folding has been widely overlooked and is poorly understood. In addition to considerations of solvent reorganization, electrostatic effects might contribute to DeltaC(P)s of folding in polyanionic species such as RNAs. Here, we employ a perturbation method based on electrostatic theory to probe the hot and cold denaturation behavior of the hammerhead ribozyme. This treatment avoids much of the error associated with imposing two-state folding models on non-two-state systems. Ribozyme stability is perturbed across a matrix of solvent conditions by varying the concentration of NaCl and methanol co-solvent. Temperature-dependent unfolding is then monitored by circular dichroism spectroscopy. The resulting array of unfolding transitions can be used to calculate a DeltaC(P) of folding that accurately predicts the observed cold denaturation temperature. We confirm the accuracy of the calculated DeltaC(P) by using isothermal titration calorimetry, and also demonstrate a methanol-dependence of the DeltaC(P). We weigh the strengths and limitations of this method for determining DeltaC(P) values. Finally, we discuss the data in light of the physical origins of the DeltaC(P)s for RNA folding and consider their impact on biological function.

  18. Multiple routes and milestones in the folding of HIV-1 protease monomer.

    Directory of Open Access Journals (Sweden)

    Massimiliano Bonomi

    Full Text Available Proteins fold on a time scale incompatible with a mechanism of random search in conformational space thus indicating that somehow they are guided to the native state through a funneled energetic landscape. At the same time the heterogeneous kinetics suggests the existence of several different folding routes. Here we propose a scenario for the folding mechanism of the monomer of HIV-1 protease in which multiple pathways and milestone events coexist. A variety of computational approaches supports this picture. These include very long all-atom molecular dynamics simulations in explicit solvent, an analysis of the network of clusters found in multiple high-temperature unfolding simulations and a complete characterization of free-energy surfaces carried out using a structure-based potential at atomistic resolution and a combination of metadynamics and parallel tempering. Our results confirm that the monomer in solution is stable toward unfolding and show that at least two unfolding pathways exist. In our scenario, the formation of a hydrophobic core is a milestone in the folding process which must occur along all the routes that lead this protein towards its native state. Furthermore, the ensemble of folding pathways proposed here substantiates a rational drug design strategy based on inhibiting the folding of HIV-1 protease.

  19. Self-organization and mismatch tolerance in protein folding: General theory and an application

    Science.gov (United States)

    Fernández, Ariel; Berry, R. Stephen

    2000-03-01

    The folding of a protein is a process both expeditious and robust. The analysis of this process presented here uses a coarse, discretized representation of the evolving form of the backbone chain, based on its torsional states. This coarse description consists of discretizing the torsional coordinates modulo the Ramachandran basins in the local softmode dynamics. Whenever the representation exhibits "contact patterns" that correspond to topological compatibilities with particular structural forms, secondary and then tertiary, the elements constituting the pattern are effectively entrained by a reduction of their rates of exploration of their discretized configuration space. The properties "expeditious and robust" imply that the folding protein must have some tolerance to both torsional "frustrated" and side-chain contact mismatches which may occur during the folding process. The energy-entropy consequences of the staircase or funnel topography of the potential surface should allow the folding protein to correct these mismatches, eventually. This tolerance lends itself to an iterative pattern-recognition-and-feedback description of the folding process that reflects mismatched local torsional states and hydrophobic/polar contacts. The predictive potential of our algorithm is tested by application to the folding of bovine pancreatic trypsin inhibitor (BPTI), a protein whose ability to form its active structure is contingent upon its frustration tolerance.

  20. Finite element analysis of electroactive polymer and magnetoactive elastomer based actuation for origami folding

    Science.gov (United States)

    Zhang, Wei; Ahmed, Saad; Masters, Sarah; Ounaies, Zoubeida; Frecker, Mary

    2017-10-01

    The incorporation of smart materials such as electroactive polymers and magnetoactive elastomers in origami structures can result in active folding using external electric and magnetic stimuli, showing promise in many origami-inspired engineering applications. In this study, 3D finite element analysis (FEA) models are developed using COMSOL Multiphysics software for three configurations that incorporate a combination of active and passive material layers, namely: (1) a single-notch unimorph folding configuration actuated using only external electric field, (2) a double-notch unimorph folding configuration actuated using only external electric field, and (3) a bifold configuration which is actuated using multi-field (electric and magnetic) stimuli. The objectives of the study are to verify the effectiveness of the FEA models to simulate folding behavior and to investigate the influence of geometric parameters on folding quality. Equivalent mechanical pressure and surface stress are used as external loads in the FEA to simulate electric and magnetic fields, respectively. Compared quantitatively with experimental data, FEA captured the folding performance of electric actuation well for notched configurations and magnetic actuation for a bifold structure, but underestimated electric actuation for the bifold structure. By investigating the impact of geometric parameters and locations to place smart materials, FEA can be used in design, avoiding trial-and-error iterations of experiments.

  1. Cricothyroid muscle dysfunction impairs vocal fold vibration in unilateral vocal fold paralysis.

    Science.gov (United States)

    Pei, Yu-Cheng; Fang, Tuan-Jen; Li, Hsueh-Yu; Wong, Alice M K

    2014-01-01

    The relevance of the cricothyroid (CT) muscle in patients with unilateral vocal fold paralysis (UVFP) remains controversial. To clarify the functional significance of the CT muscle in patients with UVFP, the confounding effect of the severity of recurrent laryngeal nerve injury should be taken into consideration. In the present study, quantitative laryngeal electromyography (LEMG) was used to measure the severity of paralysis of the thyroarytenoid-lateral cricoarytenoid (TA-LCA) muscle complex to allow the functional contribution of the CT muscle to be determined. Cross-sectional study performed in an otolaryngology outpatient clinic. Thirty-one patients with a main diagnosis of UVFP were recruited. The main outcome measures included LEMG examination, quantitative LEMG analysis of the TA-LCA muscle complex, UVFP-related quality-of-life questionnaire (Voice Outcome Survey [VOS]), voice acoustics analysis, videolaryngostroboscopy, and general quality-of-life questionnaire (Short Form-36 Health Survey [SF-36]) assessments. The vocal cord position did not differ between patients with and without CT muscle impairment. Patients with both TA-LCA and CT paralysis showed poorer vocal fold vibration (P = .048) and higher fundamental frequency (P = .02), and the VOS and SF-36 were both poorer compared with patients with only TA-LCA paralysis. Although the vocal cord position was not influenced by CT muscle function, coexisting CT muscle paralysis may damage the voice by impairing vocal fold vibration in UVFP patients. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

  2. Folding and membrane insertion of the pore-forming peptide gramicidin occur as a concerted process.

    Science.gov (United States)

    Hicks, Matthew R; Damianoglou, Angeliki; Rodger, Alison; Dafforn, Timothy R

    2008-11-07

    Many antibiotic peptides function by binding and inserting into membranes. Understanding this process provides an insight into the fundamentals of both membrane protein folding and antibiotic peptide function. For the first time, in this work, flow-aligned linear dichroism (LD) is used to study the folding of the antibiotic peptide gramicidin. LD provides insight into the combined processes of peptide folding and insertion and has the advantage over other similar techniques of being insensitive to off-membrane aggregation events. By combining LD data with conventional measurements of protein fluorescence and circular dichroism, the mechanism of gramicidin insertion is elucidated. The mechanism consists of five separately assignable steps that include formation of a water-insoluble gramicidin aggregate, dissociation from the aggregate, partitioning of peptide to the membrane surface, oligomerisation on the surface and concerted insertion and folding of the peptide to the double-helical form of gramicidin. Measurement of the rates of each step shows that although changes in the fluorescence signal cease 10 s after the initiation of the process, the insertion of the peptide into the membrane is actually not complete for a further 60 min. This last membrane insertion phase is only apparent by measurement of LD and circular dichroism signal changes. In summary, this study demonstrates the importance of multi-technique approaches, including LD, in studies of membrane protein folding.

  3. Protein-Folding Landscapes in Multi-Chain Systems

    Energy Technology Data Exchange (ETDEWEB)

    Cellmer, Troy; Bratko, Dusan; Prausnitz, John M.; Blanch, Harvey

    2005-06-20

    Computational studies of proteins have significantly improved our understanding of protein folding. These studies are normally carried out using chains in isolation. However, in many systems of practical interest, proteins fold in the presence of other molecules. To obtain insight into folding in such situations, we compare the thermodynamics of folding for a Miyazawa-Jernigan model 64-mer in isolation to results obtained in the presence of additional chains. The melting temperature falls as the chain concentration increases. In multi-chain systems, free-energy landscapes for folding show an increased preference for misfolded states. Misfolding is accompanied by an increase in inter-protein interactions; however, near the folding temperature, the transition from folded chains to misfolded and associated chains isentropically driven. A majority of the most probable inter-protein contacts are also native contacts, suggesting that native topology plays a role in early stages of aggregation.

  4. Development of Forest Drought Index and Forest Water Use Prediction in Gyeonggi Province, Korea Using High-Resolution Weather Research and Forecast Data and Localized JULES Land Surface Model

    Science.gov (United States)

    Lee, H.; Park, J.; Cho, S.; Lee, S. J.; Kim, H. S.

    2017-12-01

    Forest determines the amount of water available to low land ecosystems, which use the rest of water after evapotranspiration by forests. Substantial increase of drought, especially for seasonal drought, has occurred in Korea due to climate change, recently. To cope with this increasing crisis, it is necessary to predict the water use of forest. In our study, forest water use in the Gyeonggi Province in Korea was estimated using high-resolution (spatial and temporal) meteorological forecast data and localized Joint UK Land Environment Simulator (JULES) which is one of the widely used land surface models. The modeled estimation was used for developing forest drought index. The localization of the model was conducted by 1) refining the existing two tree plant functional types (coniferous and deciduous trees) into five (Quercus spp., other deciduous tree spp., Pinus spp., Larix spp., and other coniferous spp.), 2) correcting moderate resolution imaging spectroradiometer (MODIS) leaf area index (LAI) through data assimilation with in situ measured LAI, and 3) optimizing the unmeasured plant physiological parameters (e.g. leaf nitrogen contents, nitrogen distribution within canopy, light use efficiency) based on sensitivity analysis of model output values. The high-resolution (hourly and 810 × 810 m) National Center for AgroMeteorology-Land-Atmosphere Modeling Package (NCAM-LAMP) data were employed as meteorological input data in JULES. The plant functional types and soil texture of each grid cell in the same resolution with that of NCAM-LAMP was also used. The performance of the localized model in estimating forest water use was verified by comparison with the multi-year sapflow measurements and Eddy covariance data of Taehwa Mountain site. Our result can be used as referential information to estimate the forest water use change by the climate change. Moreover, the drought index can be used to foresee the drought condition and prepare to it.

  5. Geomorphology of the Southwest Coast of County Cork, Ireland: A Look into the Rocks, Folds, and Glacial Scours

    Science.gov (United States)

    Bowden, S.; Wireman, R.; Sautter, L.; Beutel, E. K.

    2015-12-01

    Bathymetric data were collected off the southwest coast of County Cork, Ireland by the joint INFOMAR project between the Marine Institute of Ireland and the Geologic Survey of Ireland. Data were collected using a Kongsberg EM2040 multibeam sonar on the R/V Celtic Voyager, in August and September 2014, and were post-processed with CARIS HIPS and SIPS 8.1 and 9.0 software to create 2D and 3D bathymetric surfaces. From the computer generated images, some of the lithologic formations were relatively aged and observed. The studied regions range in depth from 20 to 118 m, with shallower areas to the northeast. Several large rock outcrops occur, the larger of which shows a vertical rise of nearly 20 m. These outcrops are oriented in a northeast-southwest direction, and exhibit significant bed folding, regional folding, tilted beds, and cross joints. The folds studied are plunging chevron folds. These folds have a northeast-southwest fold axis orthogonal to the cross joints and are older relative to the jointing systems. The NE-SW joints are older than the NW-SE joints due to their correlation with drainage and erosion patterns. Regional folding is the youngest feature due to its superposition on the chevron folding and jointing systems. The interaction of cross jointing and folding is consistent with the geologic history of the area, and creates a unique bathymetry worthy of further study.

  6. Evaluation of topographic index in relation to terrain roughness and ...

    Indian Academy of Sciences (India)

    comparing the topographic index surface with respect to reference data (10 m grid spacing topographic index surface). The RMSE and mean error of topographic index surface increases in larger grid spacing and the effect is more in rugged terrain. 1. Introduction. Terrain relief is the first order control on the vari- ous natural ...

  7. Cellular scaling rules for the brain of Artiodactyla include a highly folded cortex with few neurons

    Science.gov (United States)

    Kazu, Rodrigo S.; Maldonado, José; Mota, Bruno; Manger, Paul R.; Herculano-Houzel, Suzana

    2014-01-01

    Quantitative analysis of the cellular composition of rodent, primate, insectivore, and afrotherian brains has shown that non-neuronal scaling rules are similar across these mammalian orders that diverged about 95 million years ago, and therefore appear to be conserved in evolution, while neuronal scaling rules appear to be free to vary in a clade-specific manner. Here we analyze the cellular scaling rules that apply to the brain of artiodactyls, a group within the order Cetartiodactyla, believed to be a relatively recent radiation from the common Eutherian ancestor. We find that artiodactyls share non-neuronal scaling rules with all groups analyzed previously. Artiodactyls share with afrotherians and rodents, but not with primates, the neuronal scaling rules that apply to the cerebral cortex and cerebellum. The neuronal scaling rules that apply to the remaining brain areas are, however, distinct in artiodactyls. Importantly, we show that the folding index of the cerebral cortex scales with the number of neurons in the cerebral cortex in distinct fashions across artiodactyls, afrotherians, rodents, and primates, such that the artiodactyl cerebral cortex is more convoluted than primate cortices of similar numbers of neurons. Our findings suggest that the scaling rules found to be shared across modern afrotherians, glires, and artiodactyls applied to the common Eutherian ancestor, such as the relationship between the mass of the cerebral cortex as a whole and its number of neurons. In turn, the distribution of neurons along the surface of the cerebral cortex, which is related to its degree of gyrification, appears to be a clade-specific characteristic. If the neuronal scaling rules for artiodactyls extend to all cetartiodactyls, we predict that the large cerebral cortex of cetaceans will still have fewer neurons than the human cerebral cortex. PMID:25429261

  8. Cellular scaling rules for the brain of Artiodactyla include a highly folded cortex with few neurons

    Directory of Open Access Journals (Sweden)

    Rodrigo eSiqueira Kazu

    2014-11-01

    Full Text Available Quantitative analysis of the cellular composition of rodent, primate, insectivore and afrotherian brains has shown that nonneuronal scaling rules are similar across these mammalian orders that diverged about 95 million years ago, and therefore appear to be conserved in evolution, while neuronal scaling rules appear to be free to vary in a clade-specific manner. Here we analyze the cellular scaling rules that apply to the brain of artiodactyls, a group within the order Cetartiodactyla, believed to be a relatively recent radiation from the common Eutherian ancestor. We find that artiodactyls share nonneuronal scaling rules with all groups analyzed previously. Artiodactyls share with afrotherians and rodents, but not with primates, the neuronal scaling rules that apply to the cerebral cortex and cerebellum. The neuronal scaling rules that apply to the remaining brain areas are however distinct in artiodactyls. Importantly, we show that the folding index of the cerebral cortex scales with the number of neurons in the cerebral cortex in distinct fashions across artiodactyls, afrotherians, rodents, and primates, such that the artiodactyl cerebral cortex is more convoluted than primate cortices of similar numbers of neurons. Our findings suggest that the scaling rules found to be shared across modern afrotherians, glires and artiodactyls applied to the common Eutherian ancestor, such as the relationship between the mass of the cerebral cortex as a whole and its number of neurons. In turn, the distribution of neurons along the surface of the cerebral cortex, which is related to its degree of gyrification, appears to be a clade-specific characteristic. If the neuronal scaling rules for artiodactyls extend to all cetartiodactyls, we predict that the large cerebral cortex of cetaceans will still have fewer neurons than the human cerebral cortex.

  9. Form Exploration of Folded Plate Timber Structures based on Performance Criteria

    DEFF Research Database (Denmark)

    Falk, Andreas; Von Buelow, Peter

    2011-01-01

    This paper presents an explorative study on applications of cross-laminated timber (CLT) elements in shell structures. Previous studies of plate tensegrity, folded plate roofs interacting with stabilising steel-based systems and studies inspired by origami show a widening range of possibilities...... experimental. Folded plate structures which are the focus of this paper present several issues of structural importance – potential mechanisms, subdivision of surfaces etc. – and the hereby presented study aims at exploring developed typologies, using computer tools for developed optimisation procedures...... with interaction from the designer....

  10. The relation of vocal fold lesions and voice quality to voice handicap and psychosomatic well-being.

    Science.gov (United States)

    Smits, R; Marres, H; de Jong, Felix

    2012-07-01

    Voice disorders have a multifactorial genesis and may be present in various ways. They can cause a significant communication handicap and impaired quality of life. To assess the effect of vocal fold lesions and voice quality on voice handicap and psychosomatic well-being. Female patients, aged 18-65 years, who were referred to the outpatient clinic with voice problems were subsequently assessed. Laryngostroboscopic examination and acoustic voice analysis were carried out, and the patients were asked to fill in the Voice Handicap Index (VHI) and Symptom Check List-90 questionnaires. Eighty-two patients were included. In 43 patients (52.4%), a vocal fold lesion was observed. The VHI and psychosomatic well-being did not differ significantly between patients with and without a vocal fold lesion. The patients with a vocal fold lesion showed lower scores on the Dysphonia Severity Index (DSI) compared with those without a vocal fold lesion. However, the DSI was not correlated with voice handicap and psychosomatic well-being, except for the VHI physical subscale. Objective measurement does not necessarily correlate with the subjective appraisal of the patient's voice handicap and psychosomatic well-being. Furthermore, the criterion of the presence of a vocal fold lesion as the base of indemnity that is applied by health insurance institutions should be questioned. Copyright © 2012 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

  11. Restrictions to protein folding determined by the protein size.

    Science.gov (United States)

    Finkelstein, Alexei V; Bogatyreva, Natalya S; Garbuzynskiy, Sergiy O

    2013-06-27

    Experimentally measured rates of spontaneous folding of single-domain globular proteins range from microseconds to hours: the difference (11 orders of magnitude!) is akin to the difference between the life span of a mosquito and the age of the Universe. We show that physical theory with biological constraints outlines the possible range of folding rates for single-domain globular proteins of various size and stability, and that the experimentally measured folding rates fall within this narrow "golden triangle" built without any adjustable parameters, filling it almost completely. This "golden triangle" also successfully predicts the maximal allowed size of the "foldable" protein domains, as well as the maximal size of protein domains that fold under solely thermodynamic (rather than kinetic) control. In conclusion, we give a phenomenological formula for dependence of the folding rate on the size, shape and stability of the protein fold. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  12. Cotranslational Protein Folding inside the Ribosome Exit Tunnel

    Directory of Open Access Journals (Sweden)

    Ola B. Nilsson

    2015-09-01

    Full Text Available At what point during translation do proteins fold? It is well established that proteins can fold cotranslationally outside the ribosome exit tunnel, whereas studies of folding inside the exit tunnel have so far detected only the formation of helical secondary structure and collapsed or partially structured folding intermediates. Here, using a combination of cotranslational nascent chain force measurements, inter-subunit fluorescence resonance energy transfer studies on single translating ribosomes, molecular dynamics simulations, and cryoelectron microscopy, we show that a small zinc-finger domain protein can fold deep inside the vestibule of the ribosome exit tunnel. Thus, for small protein domains, the ribosome itself can provide the kind of sheltered folding environment that chaperones provide for larger proteins.

  13. Pulse shapes and surface effects in segmented germanium detectors

    Energy Technology Data Exchange (ETDEWEB)

    Lenz, Daniel

    2010-03-24

    It is well established that at least two neutrinos are massive. The absolute neutrino mass scale and the neutrino hierarchy are still unknown. In addition, it is not known whether the neutrino is a Dirac or a Majorana particle. The GERmanium Detector Array (GERDA) will be used to search for neutrinoless double beta decay of {sup 76}Ge. The discovery of this decay could help to answer the open questions. In the GERDA experiment, germanium detectors enriched in the isotope {sup 76}Ge are used as source and detector at the same time. The experiment is planned in two phases. In the first, phase existing detectors are deployed. In the second phase, additional detectors will be added. These detectors can be segmented. A low background index around the Q value of the decay is important to maximize the sensitivity of the experiment. This can be achieved through anti-coincidences between segments and through pulse shape analysis. The background index due to radioactive decays in the detector strings and the detectors themselves was estimated, using Monte Carlo simulations for a nominal GERDA Phase II array with 18-fold segmented germanium detectors. A pulse shape simulation package was developed for segmented high-purity germanium detectors. The pulse shape simulation was validated with data taken with an 19-fold segmented high-purity germanium detector. The main part of the detector is 18-fold segmented, 6-fold in the azimuthal angle and 3-fold in the height. A 19th segment of 5mm thickness was created on the top surface of the detector. The detector was characterized and events with energy deposited in the top segment were studied in detail. It was found that the metalization close to the end of the detector is very important with respect to the length of the of the pulses observed. In addition indications for n-type and p-type surface channels were found. (orig.)

  14. Evaluation of single and multi-threshold entropy-based algorithms for folded substrate analysis

    Directory of Open Access Journals (Sweden)

    Magdolna Apro

    2011-10-01

    Full Text Available This paper presents a detailed evaluation of two variants of Maximum Entropy image segmentation algorithm(single and multi-thresholding with respect to their performance on segmenting test images showing folded substrates.The segmentation quality was determined by evaluating values of four different measures: misclassificationerror, modified Hausdorff distance, relative foreground area error and positive-negative false detection ratio. Newnormalization methods were proposed in order to combine all parameters into a unique algorithm evaluation rating.The segmentation algorithms were tested on images obtained by three different digitalisation methods coveringfour different surface textures. In addition, the methods were also tested on three images presenting a perfect fold.The obtained results showed that Multi-Maximum Entropy algorithm is better suited for the analysis of imagesshowing folded substrates.

  15. The Complex Kinetics of Protein Folding in Wide Temperature Ranges

    OpenAIRE

    Wang, Jin

    2004-01-01

    The complex protein folding kinetics in wide temperature ranges is studied through diffusive dynamics on the underlying energy landscape. The well-known kinetic chevron rollover behavior is recovered from the mean first passage time, with the U-shape dependence on temperature. The fastest folding temperature T0 is found to be smaller than the folding transition temperature Tf. We found that the fluctuations of the kinetics through the distribution of first passage time show rather universal b...

  16. Iterative Controller Tuning for Process with Fold Bifurcations

    DEFF Research Database (Denmark)

    Huusom, Jakob Kjøbsted; Poulsen, Niels Kjølstad; Jørgensen, Sten Bay

    2007-01-01

    Processes involving fold bifurcation are notoriously difficult to control in the vicinity of the fold where most often optimal productivity is achieved . In cases with limited process insight a model based control synthesis is not possible. This paper uses a data driven approach with an improved...... version of iterative feedback tuning to optimizing a closed loop performance criterion, as a systematic tool for tuning process with fold bifurcations....

  17. The Ventricular-Fold Dynamics in Human Phonation

    OpenAIRE

    Bailly , Lucie; Henrich Bernardoni , Nathalie; Müller , Frank; Rohlfs , Anna-Katharina; Hess , Markus

    2014-01-01

    International audience; Purpose: In this study, the authors aimed (a) to provide a classification of the ventricular-fold dynamics during voicing, (b) to study the aerodynamic impact of these motions on vocal-fold vibrations, and (c) to assess whether ventricularfold oscillations could be sustained by aerodynamic coupling with the vocal folds. Method: A 72-sample database of vocal gestures accompanying different acoustical events comprised highspeed cinematographic, audio, and electroglottogr...

  18. Folding System for the Clothes by a Robot and Tools

    OpenAIRE

    大澤, 文明; 関, 啓明; 神谷, 好承

    2004-01-01

    The works of a home robot has the laundering. The purpose of this study is to find a means of folding of the clothes and store the clothes in a drawer by a home robot. Because the shape of cloth tends to change in various ways depending on the situation, it is difficult for robot hands to fold the clothes. In this paper, we propose a realistic folding system for the clothes by a robot and tools. The function of a tool is folding the clothes in half by inserting the clothes using two plates. T...

  19. Specific features of vocal fold paralysis in functional computed tomography

    International Nuclear Information System (INIS)

    Laskowska, K.; Mackiewicz-Nartowicz, H.; Serafin, Z.; Nawrocka, E.

    2008-01-01

    Vocal fold paralysis is usually recognized in laryngological examination, and detailed vocal fold function may be established based on laryngovideostroboscopy. Additional imaging should exclude any morphological causes of the paresis, which should be treated pharmacologically or surgically. The aim of this paper was to analyze the computed tomography (CT) images of the larynx in patients with unilateral vocal fold paralysis. CT examinations of the larynx were performed in 10 patients with clinically defined unilateral vocal fold paralysis. The examinations consisted of unenhanced acquisition and enhanced 3-phased acquisition: during free breathing, Valsalva maneuver, and phonation. The analysis included the following morphologic features of the paresis.the deepened epiglottic vallecula, the deepened piriform recess, the thickened and medially positioned aryepiglottic fold, the widened laryngeal pouch, the anteriorly positioned arytenoid cartilage, the thickened vocal fold, and the filled infraglottic space in frontal CT reconstruction. CT images were compared to laryngovideostroboscopy. The most common symptoms of vocal cord paralysis in CT were the deepened epiglottic vallecula and piriform recess, the widened laryngeal pouch with the filled infraglottic space, and the thickened aryepiglottic fold. Regarding the efficiency of the paralysis determination, the three functional techniques of CT larynx imaging used did not differ significantly, and laryngovideostroboscopy demonstrated its advantage over CT. CT of the larynx is a supplementary examination in the diagnosis of vocal fold paralysis, which may enable topographic analysis of the fold dysfunction. The knowledge of morphological CT features of the paralysis may help to prevent false-positive diagnosis of laryngeal cancer. (author)

  20. Protein folding and the organization of the protein topology universe

    DEFF Research Database (Denmark)

    Lindorff-Larsen,, Kresten; Røgen, Peter; Paci, Emanuele

    2005-01-01

    of protein folds that is based on the topological features of the polypeptide backbone, rather than the conventional view that depends on the arrangement of different types of secondary-structure elements. By linking the folding process to the organization of the protein structure universe, we propose......The mechanism by which proteins fold to their native states has been the focus of intense research in recent years. The rate-limiting event in the folding reaction is the formation of a conformation in a set known as the transition-state ensemble. The structural features present within...

  1. Fracture Toughness of Vocal Fold Tissue: A Preliminary Study.

    Science.gov (United States)

    Miri, Amir K; Chen, Lei Xi; Mongrain, Rosaire; Mongeau, Luc

    2016-05-01

    A customized mechanical tester that slices thin, soft samples was used to measure the fracture toughness of vocal fold tissue. Porcine vocal fold lamina propria was subjected to quasi-static, guillotine-like tests at three equally distanced regions along the anterior-posterior direction. The central one-third where high-velocity collisions between vocal folds occur was found to have the maximum fracture toughness. In contrast, the anterior one-third featured a lower toughness. Fracture toughness can be indicative of the risk of benign and malignant lesions in vocal fold tissue. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  2. Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a beta-Hairpin.

    Directory of Open Access Journals (Sweden)

    2005-06-01

    Full Text Available The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity cinRO((N + nm log n, where N is the size of the output patterns and (n x m is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1 The method recovers states previously obtained by visually analyzing free energy surfaces. (2 It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3 The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the

  3. Apico-basal forces exerted by apoptotic cells drive epithelium folding.

    Science.gov (United States)

    Monier, Bruno; Gettings, Melanie; Gay, Guillaume; Mangeat, Thomas; Schott, Sonia; Guarner, Ana; Suzanne, Magali

    2015-02-12

    Epithelium folding is a basic morphogenetic event that is essential in transforming simple two-dimensional epithelial sheets into three-dimensional structures in both vertebrates and invertebrates. Folding has been shown to rely on apical constriction. The resulting cell-shape changes depend either on adherens junction basal shift or on a redistribution of myosin II, which could be driven by mechanical signals. Yet the initial cellular mechanisms that trigger and coordinate cell remodelling remain largely unknown. Here we unravel the active role of apoptotic cells in initiating morphogenesis, thus revealing a novel mechanism of epithelium folding. We show that, in a live developing tissue, apoptotic cells exert a transient pulling force upon the apical surface of the epithelium through a highly dynamic apico-basal myosin II cable. The apoptotic cells then induce a non-autonomous increase in tissue tension together with cortical myosin II apical stabilization in the surrounding tissue, eventually resulting in epithelium folding. Together our results, supported by a theoretical biophysical three-dimensional model, identify an apoptotic myosin-II-dependent signal as the initial signal leading to cell reorganization and tissue folding. This work further reveals that, far from being passively eliminated as generally assumed (for example, during digit individualization), apoptotic cells actively influence their surroundings and trigger tissue remodelling through regulation of tissue tension.

  4. Characteristics of phonation onset in a two-layer vocal fold model.

    Science.gov (United States)

    Zhang, Zhaoyan

    2009-02-01

    Characteristics of phonation onset were investigated in a two-layer body-cover continuum model of the vocal folds as a function of the biomechanical and geometric properties of the vocal folds. The analysis showed that an increase in either the body or cover stiffness generally increased the phonation threshold pressure and phonation onset frequency, although the effectiveness of varying body or cover stiffness as a pitch control mechanism varied depending on the body-cover stiffness ratio. Increasing body-cover stiffness ratio reduced the vibration amplitude of the body layer, and the vocal fold motion was gradually restricted to the medial surface, resulting in more effective flow modulation and higher sound production efficiency. The fluid-structure interaction induced synchronization of more than one group of eigenmodes so that two or more eigenmodes may be simultaneously destabilized toward phonation onset. At certain conditions, a slight change in vocal fold stiffness or geometry may cause phonation onset to occur as eigenmode synchronization due to a different pair of eigenmodes, leading to sudden changes in phonation onset frequency, vocal fold vibration pattern, and sound production efficiency. Although observed in a linear stability analysis, a similar mechanism may also play a role in register changes at finite-amplitude oscillations.

  5. Three-Dimensional Flow Separation Induced by a Model Vocal Fold Polyp

    Science.gov (United States)

    Stewart, Kelley C.; Erath, Byron D.; Plesniak, Michael W.

    2012-11-01

    The fluid-structure energy exchange process for normal speech has been studied extensively, but it is not well understood for pathological conditions. Polyps and nodules, which are geometric abnormalities that form on the medial surface of the vocal folds, can disrupt vocal fold dynamics and thus can have devastating consequences on a patient's ability to communicate. A recent in-vitro investigation of a model polyp in a driven vocal fold apparatus demonstrated that such a geometric abnormality considerably disrupts the glottal jet behavior and that this flow field adjustment was a likely reason for the severe degradation of the vocal quality in patients. Understanding of the formation and propagation of vortical structures from a geometric protuberance, and their subsequent impact on the aerodynamic loadings that drive vocal fold dynamic, is a critical component in advancing the treatment of this pathological condition. The present investigation concerns the three-dimensional flow separation induced by a wall-mounted prolate hemispheroid with a 2:1 aspect ratio in cross flow, i.e. a model vocal fold polyp. Unsteady three-dimensional flow separation and its impact of the wall pressure loading are examined using skin friction line visualization and wall pressure measurements. Supported by the National Science Foundation, Grant No. CBET-1236351 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  6. SAXS study of transient pre-melting in chain-folded alkanes

    International Nuclear Information System (INIS)

    Ungar, G.; Wills, H.H.

    1990-01-01

    A pronounced pre-melting effect is observed in chain-folded crystals of pure monodisperse n-alkane C 246 H 494 . The effect is reversible on a short time scale, but at longer times the once-folded chain crystals are irreversibly lost as slow chain extension proceeds by solid diffusion well below the melting point. The melting process is thus monitored by rapid time-resolved small-angle X-ray (SAXS) measurements, using synchrotron radiation. The results show that the observed pronounced broadening of the DSC melting endotherm for chain-folded crystals is entirely due to genuine pre-melting of lamellar surfaces. Although a significant portion of material is already molten below the final melting point of chain-folded crystals T F , no recrystallization in the chain-extended form can occur until the cores of the crystalline lamellae melt at T F . Pre-melting of extended chain crystals is significantly less pronounced than that of folded chain crystals

  7. Travelling waves and fold localization in hovercraft seals

    Science.gov (United States)

    Wiggins, Andrew; Zalek, Steve; Perlin, Marc; Ceccio, Steve

    2013-11-01

    The seal system on hovercraft consists of a series of open-ended fabric cylinders that contact the free surface and, when inflated, form a compliant pressure barrier. Due to a shortening constraint imposed by neighboring seals, bow seals operate in a post-buckled state. We present results from large-scale experiments on these structures. These experiment show the hydroelastic response of seals to be characterized by striking stable and unstable post-buckling behavior. Using detailed 3-d measurements of the deformed seal shape, dominant response regimes are identified. These indicate that mode number decreases with wetted length, and that the form of the buckling packet becomes localized with increased velocity and decreased bending stiffness. Eventually, at a critical pressure, travelling waves emerge. To interpret the wide range of observed behavior, a 2-d nonlinear post-buckling model is developed and compared with the experimental studies. The model shows the importance of seal shortening and the buckling length, which is driven by the balance of hydrodynamic and bending energies. Preliminary scaling laws for the fold amplitude and mode number are presented. The experiments may ultimately provide insight into the bedeviling problem of seal wear. Sponsored by the Office of Naval Research under grant N00014-10-1-0302, Ms. Kelly B. Cooper, program manager.

  8. Exploring the correlation between the folding rates of proteins and the entanglement of their native states

    Science.gov (United States)

    Baiesi, Marco; Orlandini, Enzo; Seno, Flavio; Trovato, Antonio

    2017-12-01

    The folding of a protein towards its native state is a rather complicated process. However, there is empirical evidence that the folding time correlates with the contact order, a simple measure of the spatial organization of the native state of the protein. Contact order is related to the average length of the main chain loops formed by amino acids that are in contact. Here we argue that folding kinetics can also be influenced by the entanglement that loops may undergo within the overall three-dimensional protein structure. In order to explore such a possibility, we introduce a novel descriptor, which we call ‘maximum intrachain contact entanglement’. Specifically, we measure the maximum Gaussian entanglement between any looped portion of a protein and any other non-overlapping subchain of the same protein, which is easily computed by discretized line integrals on the coordinates of the Cα atoms. By analyzing experimental data sets of two-state and multi-state folders, we show that the new index is also a good predictor of the folding rate. Moreover, being only partially correlated with previous methods, it can be integrated with them to yield more accurate predictions.

  9. Earthquake-by-earthquake fold growth above the Puente Hills blind thrust fault, Los Angeles, California: Implications for fold kinematics and seismic hazard

    Science.gov (United States)

    Leon, Lorraine A.; Christofferson, Shari A.; Dolan, James F.; Shaw, John H.; Pratt, Thomas L.

    2007-03-01

    . Specifically, strata dip 0.4° at 4 m depth, 0.7° at 20 m depth, 8° at 90 m, 16° at 110 m, and 17° at 200 m. Moreover, structural restorations of the borehole data show that the locus of active folding (the anticlinal active axial surface) does not extend to the surface in exactly the same location from earthquake to earthquake. Rather, that the axial surfaces migrate from earthquake to earthquake, reflecting a component of fold growth by kink band migration. The incremental acquisition of bed dip in the growth triangle may reflect some combination of fold growth by limb rotation in addition to kink band migration, possibly through a component of trishear or shear fault bend folding. Alternatively, the component of limb rotation may result from curved hinge fault bend folding, and/or the mechanical response of loosely consolidated granular sediments in the shallow subsurface to folding at depth.

  10. Quantification of fold growth of frontal antiforms in the Zagros fold and thrust belt (Kurdistan, NE Iraq)

    Science.gov (United States)

    Bretis, Bernhard; Bartl, Nikolaus; Graseman, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros fold and thrust belt is a seismically active orogen, where actual kinematic models based on GPS networks suggest a north-south shortening between Arabian and Eurasian in the order of 1.5-2.5 cm/yr. Most of this deformation is partitioned in south-southwest oriented folding and thrusting with northwest-southeast to north-south trending dextral strike slip faults. The Zagros fold and thrust belt is of great economic interest because it has been estimated that this area contains about 15% of the global recoverable hydrocarbons. Whereas the SE parts of the Zagros have been investigated by detailed geological studies, the NW extent being part of the Republic of Iraq have experienced considerably less attention. In this study we combine field work and remote sensing techniques in order to investigate the interaction of erosion and fold growth in the area NE of Erbil (Kurdistan, Iraq). In particular we focus on the interaction of the transient development of drainage patterns along growing antiforms, which directly reflects the kinematics of progressive fold growth. Detailed geomorphological studies of the Bana Bawi-, Permam- and Safeen fold trains show that these anticlines have not developed from subcylindrical embryonic folds but they have merged from different fold segments that joined laterally during fold amplification. This fold segments with length between 5 and 25 km have been detected by mapping ancient and modern river courses that initially cut the nose of growing folds and eventually got defeated leaving behind a wind gap. Fold segments, propagating in different directions force rivers to join resulting in steep gorges, which dissect the merging fold noses. Along rapidly lateral growing folds (e.g. at the SE end of the Bana Bawi Anticline) we observed "curved wind gaps", a new type of abandoned river course, where form of the wind gap mimics a formed nose of a growing antiform. The inherited curved segments of uplifted curved river courses strongly

  11. Protein folding pathology in domestic animals.

    Science.gov (United States)

    Gruys, Erik

    2004-10-01

    Fibrillar proteins form structural elements of cells and the extracellular matrix. Pathological lesions of fibrillar microanatomical structures, or secondary fibrillar changes in globular proteins are well known. A special group concerns histologically amorphous deposits, amyloid. The major characteristics of amyloid are: apple green birefringence after Congo red staining of histological sections, and non-branching 7-10 nm thick fibrils on electron microscopy revealing a high content of cross beta pleated sheets. About 25 different types of amyloid have been characterised. In animals, AA-amyloid is the most frequent type. Other types of amyloid in animals represent: AIAPP (in cats), AApoAI, AApoAII, localised AL-amyloid, amyloid in odontogenic or mammary tumors and amyloid in the brain. In old dogs Abeta and in sheep APrPsc-amyloid can be encountered. AA-amyloidosis is a systemic disorder with a precursor in blood, acute phase serum amyloid A (SAA). In chronic inflammatory processes AA-amyloid can be deposited. A rapid crystallization of SAA to amyloid fibrils on small beta-sheeted fragments, the 'amyloid enhancing factor' (AEF), is known and the AEF has been shown to penetrate the enteric barrier. Amyloid fibrils can aggregate from various precursor proteins in vitro in particular at acidic pH and when proteolytic fragments are formed. Molecular chaperones influence this process. Tissue data point to amyloid fibrillogenesis in lysosomes and near cell surfaces. A comparison can be made of the fibrillogenesis in prion diseases and in enhanced AA-amyloidosis. In the reactive form, acute phase SAA is the supply of the precursor protein, whereas in the prion diseases, cell membrane proteins form a structural source. Abeta-amyloid in brain tissue of aged dogs showing signs of dementia forms a canine counterpart of senile dementia of the Alzheimer type (ccSDAT) in man. Misfolded proteins remain potential food hazards. Developments concerning prevention of amyloidogenesis

  12. Understanding the folding process of synthetic polymers by small ...

    Indian Academy of Sciences (India)

    WINTEC

    Understanding the folding process of synthetic polymers by small-molecule folding agents. S G RAMKUMAR and S RAMAKRISHNAN*. Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012 e-mail: raman@ipc.iisc.ernet.in. Abstract. Two acceptor containing polyimides PDI and NDI ...

  13. Spatially confined folding of chromatin in the interphase nucleus

    NARCIS (Netherlands)

    Mateos-Langerak, J.; Bohn, M.; de Leeuw, W.; Giromus, O.; Manders, E.M.M.; Verschure, P.J.; Indemans, M.H.G.; Gierman, H.J.; Heermann, D.W.; van Driel, R.; Goetze, S.

    2009-01-01

    Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a

  14. Landforms along transverse faults parallel to axial zone of folded ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Earth System Science; Volume 126; Issue 1. Landforms along transverse faults parallel to axial zone of folded mountain front, north-eastern Kumaun Sub-Himalaya, India. Khayingshing ... Keywords. Himalayan Frontal Thrust; outer Kumaun Himalaya; transverse structure; folded mountain front.

  15. Co-transcriptional folding is encoded within RNA genes

    Directory of Open Access Journals (Sweden)

    Miklós István

    2004-08-01

    Full Text Available Abstract Background Most of the existing RNA structure prediction programs fold a completely synthesized RNA molecule. However, within the cell, RNA molecules emerge sequentially during the directed process of transcription. Dedicated experiments with individual RNA molecules have shown that RNA folds while it is being transcribed and that its correct folding can also depend on the proper speed of transcription. Methods The main aim of this work is to study if and how co-transcriptional folding is encoded within the primary and secondary structure of RNA genes. In order to achieve this, we study the known primary and secondary structures of a comprehensive data set of 361 RNA genes as well as a set of 48 RNA sequences that are known to differ from the originally transcribed sequence units. We detect co-transcriptional folding by defining two measures of directedness which quantify the extend of asymmetry between alternative helices that lie 5' and those that lie 3' of the known helices with which they compete. Results We show with statistical significance that co-transcriptional folding strongly influences RNA sequences in two ways: (1 alternative helices that would compete with the formation of the functional structure during co-transcriptional folding are suppressed and (2 the formation of transient structures which may serve as guidelines for the co-transcriptional folding pathway is encouraged. Conclusions These findings have a number of implications for RNA secondary structure prediction methods and the detection of RNA genes.

  16. Analysis of protein folds using protein contact networks

    Indian Academy of Sciences (India)

    Proteins are important biomolecules, which perform diverse structural and functional roles in living systems. Starting from a linear chain of amino acids, proteins fold to different secondary structures, which then fold through short- and long-range interactions to give rise to the final three-dimensional shapes useful to carry out ...

  17. Competition between folding and glycosylation in the endoplasmic reticulum

    DEFF Research Database (Denmark)

    Holst, B; Bruun, A W; Kielland-Brandt, Morten

    1996-01-01

    Using carboxypeptidase Y in Saccharomyces cerevisiae as a model system, the in vivo relationship between protein folding and N-glycosylation was studied. Seven new sites for N-glycosylation were introduced at positions buried in the folded protein structure. The level of glycosylation of such new...

  18. Analyses of fold profiles by changing weight parameters of NURB ...

    Indian Academy of Sciences (India)

    Manash Pratim Gogoi

    2017-10-06

    Oct 6, 2017 ... try was not simulated earlier from linear viscous rheology, as per Cruikshank and Johnson (1993). Doming of fluid/ductile deforming rocks with a. Newtonian viscous rheology produces parabolic fold morphology (Johnson and Fletcher 1994). On the other hand, the parabolic fold profiles simu- lated in figure ...

  19. Status report on the folded tandem ion accelerator at BARC

    Indian Academy of Sciences (India)

    Folded tandem ion accelerator; charged particle beams; voltage stability; Rutherford backscattering; ion optics; beam lines. Abstract. The folded tandem ion accelerator (FOTIA) facility set up at BARC has become operational. At present, it is used for elemental analysis studies using the Rutherford backscattering technique.

  20. The dominant folding route minimizes backbone distortion in SH3.

    Directory of Open Access Journals (Sweden)

    Heiko Lammert

    Full Text Available Energetic frustration in protein folding is minimized by evolution to create a smooth and robust energy landscape. As a result the geometry of the native structure provides key constraints that shape protein folding mechanisms. Chain connectivity in particular has been identified as an essential component for realistic behavior of protein folding models. We study the quantitative balance of energetic and geometrical influences on the folding of SH3 in a structure-based model with minimal energetic frustration. A decomposition of the two-dimensional free energy landscape for the folding reaction into relevant energy and entropy contributions reveals that the entropy of the chain is not responsible for the folding mechanism. Instead the preferred folding route through the transition state arises from a cooperative energetic effect. Off-pathway structures are penalized by excess distortion in local backbone configurations and contact pair distances. This energy cost is a new ingredient in the malleable balance of interactions that controls the choice of routes during protein folding.

  1. Surfing the free energy landscape of flavodoxin folding

    NARCIS (Netherlands)

    Bollen, Y.J.M.

    2004-01-01

    The research described in this thesis has been carried out to obtain a better understanding of the fundamental rules describing protein folding. Protein folding is the process in which a linear chain of amino acids contracts to a compact state in which it is active. Flavodoxin from Azotobacter

  2. Vocal Fold Mucus Aggregation in Persons with Voice Disorders

    Science.gov (United States)

    Bonilha, Heather Shaw; White, Lisa; Kuckhahn, Kelsey; Gerlach, Terri Treman; Deliyski, Dimitar D.

    2012-01-01

    Mucus aggregation on the vocal folds is a common finding from laryngeal endoscopy. Patients with voice disorders report the presence of mucus aggregation. Patients also report that mucus aggregation causes them to clear their throat, a behavior believed to be harmful to vocal fold mucosa. Even though clinicians and patients report and discuss…

  3. Double folding model analysis of elastic scattering of halo nucleus ...

    Indian Academy of Sciences (India)

    barrier energy have been performed using a potential obtained from the double folding model and are compared with the ... In double folding (DF) model, the real nucleus–nucleus optical potential is given by the expression [9]. V DF(r) = ∫ dr1. ∫ ... expressed as a sum of three Yukawa terms. It is obtained from the fitting of ...

  4. BENIGN LESIONS OF THE VOCAL FOLDS - HISTOPATHOLOGY AND PHONOTRAUMA

    NARCIS (Netherlands)

    DIKKERS, FG; NIKKELS, PGJ

    Benign lesions of the vocal folds have various appearances. Histopathologic examination might provide the true diagnosis. Therefore, histologic slides of 74 patients (92 vocal folds) with clinically well-defined diagnoses were single-blind examined by a pathologist. Single histologic features did

  5. Analyses of fold profiles by changing weight parameters of NURB ...

    Indian Academy of Sciences (India)

    56

    Department of Geology, Sibsagar College, Joysagar, Sivasagar-785665, Assam, INDIA. 2. Department of Earth Sciences, Indian ..... 3rd degree (n=3) cubic NURB folds generated by increasing value of w1=w2=w from 0.1 to 9.9 and increasing R = hL-1. In all cases, h remains constant. 7*4 possibilities of fold geometries ...

  6. Fluorescence of Alexa Fluor dye tracks protein folding

    NARCIS (Netherlands)

    Lindhoud, S.; Westphal, A.H.; Borst, J.W.; Visser, A.J.W.G.; Mierlo, van C.P.M.

    2012-01-01

    Fluorescence spectroscopy is an important tool for the characterization of protein folding. Often, a protein is labeled with appropriate fluorescent donor and acceptor probes and folding-induced changes in Förster Resonance Energy Transfer (FRET) are monitored. However, conformational changes of the

  7. Method of generating ploynucleotides encoding enhanced folding variants

    Energy Technology Data Exchange (ETDEWEB)

    Bradbury, Andrew M.; Kiss, Csaba; Waldo, Geoffrey S.

    2017-05-02

    The invention provides directed evolution methods for improving the folding, solubility and stability (including thermostability) characteristics of polypeptides. In one aspect, the invention provides a method for generating folding and stability-enhanced variants of proteins, including but not limited to fluorescent proteins, chromophoric proteins and enzymes. In another aspect, the invention provides methods for generating thermostable variants of a target protein or polypeptide via an internal destabilization baiting strategy. Internally destabilization a protein of interest is achieved by inserting a heterologous, folding-destabilizing sequence (folding interference domain) within DNA encoding the protein of interest, evolving the protein sequences adjacent to the heterologous insertion to overcome the destabilization (using any number of mutagenesis methods), thereby creating a library of variants. The variants in the library are expressed, and those with enhanced folding characteristics selected.

  8. Co- and post-translational protein folding in the ER

    DEFF Research Database (Denmark)

    Ellgaard, Lars; McCaul, Nicholas; Chatsisvili, Anna

    2016-01-01

    The biophysical rules that govern folding of small, single-domain proteins in dilute solutions are now quite well understood. The mechanisms underlying co-translational folding of multidomain and membrane-spanning proteins in complex cellular environments are often less clear. The endoplasmic...... and the variety of ER-specific protein modifications. Here, we review chaperone-assisted co- and post-translational folding and assembly in the ER and underline the influence of protein modifications on these processes. We emphasize how method development has helped advance the field by allowing researchers...... to monitor the progression of folding as it occurs inside living cells, while at the same time probing the intricate relationship between protein modifications during folding....

  9. Folding propensity of intrinsically disordered proteins by osmotic stress

    International Nuclear Information System (INIS)

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

    2016-01-01

    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 scattering (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.

  10. Do mesoscale faults in a young fold belt indicate regional or local stress?

    Science.gov (United States)

    Kokado, Akihiro; Yamaji, Atsushi; Sato, Katsushi

    2017-04-01

    The result of paleostress analyses of mesoscale faults is usually thought of as evidence of a regional stress. On the other hand, the recent advancement of the trishear modeling has enabled us to predict the deformation field around fault-propagation folds without the difficulty of assuming paleo mechanical properties of rocks and sediments. We combined the analysis of observed mesoscale faults and the trishear modeling to understand the significance of regional and local stresses for the formation of mesoscale faults. To this end, we conducted the 2D trishear inverse modeling with a curved thrust fault to predict the subsurface structure and strain field of an anticline, which has a more or less horizontal axis and shows a map-scale plane strain perpendicular to the axis, in the active fold belt of Niigata region, central Japan. The anticline is thought to have been formed by fault-propagation folding under WNW-ESE regional compression. Based on the attitudes of strata and the positions of key tephra beds in Lower Pleistocene soft sediments cropping out at the surface, we obtained (1) a fault-propagation fold with the fault tip at a depth of ca. 4 km as the optimal subsurface structure, and (2) the temporal variation of deformation field during the folding. We assumed that mesoscale faults were activated along the direction of maximum shear strain on the faults to test whether the fault-slip data collected at the surface were consistent with the deformation in some stage(s) of folding. The Wallace-Bott hypothesis was used to estimate the consistence of faults with the regional stress. As a result, the folding and the regional stress explained 27 and 33 of 45 observed faults, respectively, with the 11 faults being consistent with the both. Both the folding and regional one were inconsistent with the remaining 17 faults, which could be explained by transfer faulting and/or the gravitational spreading of the growing anticline. The lesson we learnt from this work was

  11. Conical expansion of the outer subventricular zone and the role of neocortical folding in evolution and development

    Directory of Open Access Journals (Sweden)

    Eric eLewitus

    2013-08-01

    Full Text Available There is a basic rule to mammalian neocortical expansion: as it expands, so does it fold. The degree to which it folds, however, cannot strictly be attributed to its expansion. Across species, cortical volume does not keep pace with cortical surface area, but rather folds appear more rapidly than expected. As a result, larger brains quickly become disproportionately more convoluted than smaller brains. Both the absence (lissencephaly and presence (gyrencephaly of cortical folds is observed in all mammalian orders and, while there is likely some phylogenetic signature to the evolutionary appearance of gyri and sulci, there are undoubtedly universal trends to the acquisition of folds in an expanding neocortex. Whether these trends are governed by conical expansion of neocortical germinal zones, the distribution of cortical connectivity, or a combination of growth- and connectivity-driven forces remains an open question. But the importance of cortical folding for evolution of the uniquely mammalian neocortex, as well as for the incidence of neuropathologies in humans, is undisputed. In this hypothesis and theory article, we will summarize the development of cortical folds in the neocortex, consider the relative influence of growth- versus connectivity-driven forces for the acquisition of cortical folds between and within species, assess the genetic, cell-biological, and mechanistic implications for neocortical expansion, and discuss the significance of these implications for human evolution, development, and disease. We will argue that evolutionary increases in the density of neuron production, achieved via maintenance of a basal proliferative niche in the neocortical germinal zones, drive the conical migration of neurons towards the cortical surface and ultimately lead to the establishment of cortical folds in large-brained mammal species.

  12. Entropic formulation for the protein folding process: Hydrophobic stability correlates with folding rates

    Science.gov (United States)

    Dal Molin, J. P.; Caliri, A.

    2018-01-01

    Here we focus on the conformational search for the native structure when it is ruled by the hydrophobic effect and steric specificities coming from amino acids. Our main tool of investigation is a 3D lattice model provided by a ten-letter alphabet, the stereochemical model. This minimalist model was conceived for Monte Carlo (MC) simulations when one keeps in mind the kinetic behavior of protein-like chains in solution. We have three central goals here. The first one is to characterize the folding time (τ) by two distinct sampling methods, so we present two sets of 103 MC simulations for a fast protein-like sequence. The resulting sets of characteristic folding times, τ and τq were obtained by the application of the standard Metropolis algorithm (MA), as well as by an enhanced algorithm (Mq A). The finding for τq shows two things: (i) the chain-solvent hydrophobic interactions {hk } plus a set of inter-residues steric constraints {ci,j } are able to emulate the conformational search for the native structure. For each one of the 103MC performed simulations, the target is always found within a finite time window; (ii) the ratio τq / τ ≅ 1 / 10 suggests that the effect of local thermal fluctuations, encompassed by the Tsallis weight, provides to the chain an innate efficiency to escape from energetic and steric traps. We performed additional MC simulations with variations of our design rule to attest this first result, both algorithms the MA and the Mq A were applied to a restricted set of targets, a physical insight is provided. Our second finding was obtained by a set of 600 independent MC simulations, only performed with the Mq A applied to an extended set of 200 representative targets, our native structures. The results show how structural patterns should modulate τq, which cover four orders of magnitude; this finding is our second goal. The third, and last result, was obtained with a special kind of simulation performed with the purpose to explore a

  13. Multidimensional effects of voice therapy in patients affected by unilateral vocal fold paralysis due to cancer.

    Science.gov (United States)

    Barcelos, Camila Barbosa; Silveira, Paula Angélica Lorenzon; Guedes, Renata Lígia Vieira; Gonçalves, Aline Nogueira; Slobodticov, Luciana Dall'Agnol Siqueira; Angelis, Elisabete Carrara-de

    2017-08-24

    Patients with unilateral vocal fold paralysis may demonstrate different degrees of voice perturbation depending on the position of the paralyzed vocal fold. Understanding the effectiveness of voice therapy in this population may be an important coefficient to define the therapeutic approach. To evaluate the voice therapy effectiveness in the short, medium and long-term in patients with unilateral vocal fold paralysis and determine the risk factors for voice rehabilitation failure. Prospective study with 61 patients affected by unilateral vocal fold paralysis enrolled. Each subject had voice therapy with an experienced speech pathologist twice a week. A multidimensional assessment protocol was used pre-treatment and in three different times after voice treatment initiation: short-term (1-3 months), medium-term (4-6 months) and long-term (12 months); it included videoendoscopy, maximum phonation time, GRBASI scale, acoustic voice analysis and the portuguese version of the voice handicap index. Multiple comparisons for GRBASI scale and VHI revealed statistically significant differences, except between medium and long term (p<0.005). The data suggest that there is vocal improvement over time with stabilization results after 6 months (medium term). From the 28 patients with permanent unilateral vocal fold paralysis, 18 (69.2%) reached complete glottal closure following vocal therapy (p=0.001). The logistic regression method indicated that the Jitter entered the final model as a risk factor for partial improvement. For every unit of increased jitter, there was an increase of 0.1% (1.001) of the chance for partial improvement, which means an increase on no full improvement chance during rehabilitation. Vocal rehabilitation improves perceptual and acoustic voice parameters and voice handicap index, besides favor glottal closure in patients with unilateral vocal fold paralysis. The results were also permanent during the period of 1 year. The Jitter value, when elevated, is

  14. EJSCREEN Indexes 2015 Public

    Data.gov (United States)

    U.S. Environmental Protection Agency — There is an EJ Index for each environmental indicator. There are eight EJ Indexes in EJSCREEN reflecting the 8 environmental indicators. The EJ Index names are:...

  15. EJSCREEN Indexes 2016 Public

    Data.gov (United States)

    U.S. Environmental Protection Agency — There is an EJ Index for each environmental indicator. There are eleven EJ Indexes in EJSCREEN reflecting the 11 environmental indicators. The EJ Index names are:...

  16. Ion Mobility-Mass Spectrometry Reveals the Energetics of Intermediates that Guide Polyproline Folding

    Science.gov (United States)

    Shi, Liuqing; Holliday, Alison E.; Glover, Matthew S.; Ewing, Michael A.; Russell, David H.; Clemmer, David E.

    2016-01-01

    Proline favors trans-configured peptide bonds in native proteins. Although cis/ trans configurations vary for non-native and unstructured states, solvent also influences these preferences. Water induces the all- cis right-handed polyproline-I (PPI) helix of polyproline to fold into the all- trans left-handed polyproline-II (PPII) helix. Our recent work has shown that this occurs via a sequential mechanism involving six resolved intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we use ion mobility-mass spectrometry to make the first detailed thermodynamic measurements of the folding intermediates, which inform us about how and why this transition occurs. It appears that early intermediates are energetically favorable because of the hydration of the peptide backbone, whereas late intermediates are enthalpically unfavorable. However, folding continues, as the entropy of the system increases upon successive formation of each new structure. When PPII is immersed in 1-propanol, the PPII→PPI transition occurs, but this reaction occurs through a very different mechanism. Early on, the PPII population splits onto multiple pathways that eventually converge through a late intermediate that continues on to the folded PPI helix. Nearly every step is endothermic. Folding results from a stepwise increase in the disorder of the system, allowing a wide-scale search for a critical late intermediate. Overall, the data presented here allow us to establish the first experimentally determined energy surface for biopolymer folding as a function of solution environment.

  17. Effect of sugarcane biopolymer gel injected in rabbit vocal fold

    Directory of Open Access Journals (Sweden)

    Rodrigo Augusto de Souza Leão

    2014-06-01

    Full Text Available INTRODUCTION: Alterations in the vocal folds that involve volume reduction and glottal closure failure result in exaggerated air escape during speech. For such situations, the use of implants or grafts of different materials has been proposed. OBJECTIVE: To define the effect of sugarcane biopolymer gel when implanted in the vocal folds of rabbits. METHODS: This was an experimental study. The vocal folds of rabbits injected with sugarcane biopolymer and saline solution were histologically evaluated after 21 and 90 days. RESULTS: Mild to moderate inflammation and increased volume were observed in all vocal folds injected with biopolymer, when compared to controls. There were no cases of necrosis or calcification. DISCUSSION: This study showed higher inflammatory reaction in cases than in controls and biopolymer biointegration to the vocal fold. This fibrogenic response with absence of epithelial repercussions suggests that the biopolymer in its gel form can be bioactive and preserve the normal vibratory function of the epithelium. CONCLUSION: We show that in spite of producing an inflammatory reaction in vocal fold tissues, the material remained in vocal fold throughout the study period.

  18. Analyzing the effect of homogeneous frustration in protein folding.

    Science.gov (United States)

    Contessoto, Vinícius G; Lima, Debora T; Oliveira, Ronaldo J; Bruni, Aline T; Chahine, Jorge; Leite, Vitor B P

    2013-10-01

    The energy landscape theory has been an invaluable theoretical framework in the understanding of biological processes such as protein folding, oligomerization, and functional transitions. According to the theory, the energy landscape of protein folding is funneled toward the native state, a conformational state that is consistent with the principle of minimal frustration. It has been accepted that real proteins are selected through natural evolution, satisfying the minimum frustration criterion. However, there is evidence that a low degree of frustration accelerates folding. We examined the interplay between topological and energetic protein frustration. We employed a Cα structure-based model for simulations with a controlled nonspecific energetic frustration added to the potential energy function. Thermodynamics and kinetics of a group of 19 proteins are completely characterized as a function of increasing level of energetic frustration. We observed two well-separated groups of proteins: one group where a little frustration enhances folding rates to an optimal value and another where any energetic frustration slows down folding. Protein energetic frustration regimes and their mechanisms are explained by the role of non-native contact interactions in different folding scenarios. These findings strongly correlate with the protein free-energy folding barrier and the absolute contact order parameters. These computational results are corroborated by principal component analysis and partial least square techniques. One simple theoretical model is proposed as a useful tool for experimentalists to predict the limits of improvements in real proteins. Copyright © 2013 Wiley Periodicals, Inc.

  19. The role of the mesenchyme in cranial neural fold elevation

    Energy Technology Data Exchange (ETDEWEB)

    Morris-Wiman, J.A.

    1988-01-01

    It has been previously postulated that the expansion of an hyaluronate-rich extracellular matrix in the fold mesenchyme is responsible for neural fold elevation. In this study we provide evidence that such expansions may play an important role in cranial neural fold elevation by pushing the folds towards the dorsal midline to assist in their elevation. For mesenchymal expansion to result in fold elevation, hyaluronate (HA) and mesenchymal cells must be non-randomly distributed within the mesenchyme. Patterns of mesenchymal cell distribution and cell proliferation were analyzed using the computer-assisted method of smoothed spatial averaging. The distribution of Alcian blue-stained and {sup 3}H-glucosamine-labelled HA was also analyzed during cranial neural fold elevation using established image processing techniques. Analysis of the distribution of {sup 3}H-thymidine-labelled mesenchymal cells indicated that differential mitotic activity was not responsible for decreased mesenchymal cell density. Likewise, analysis of distribution patterns of {sup 3}H-glucosamine-labelled HA indicated that decreased HA concentration was not produced by regional differences in HA synthesis. These results suggest that decreases in mesenchymal cell density and HA concentration that occur during neural fold elevation are produced by mesenchymal expansion.

  20. The role of the mesenchyme in cranial neural fold elevation

    International Nuclear Information System (INIS)

    Morris-Wiman, J.A.

    1988-01-01

    It has been previously postulated that the expansion of an hyaluronate-rich extracellular matrix in the fold mesenchyme is responsible for neural fold elevation. In this study we provide evidence that such expansions may play an important role in cranial neural fold elevation by pushing the folds towards the dorsal midline to assist in their elevation. For mesenchymal expansion to result in fold elevation, hyaluronate (HA) and mesenchymal cells must be non-randomly distributed within the mesenchyme. Patterns of mesenchymal cell distribution and cell proliferation were analyzed using the computer-assisted method of smoothed spatial averaging. The distribution of Alcian blue-stained and 3 H-glucosamine-labelled HA was also analyzed during cranial neural fold elevation using established image processing techniques. Analysis of the distribution of 3 H-thymidine-labelled mesenchymal cells indicated that differential mitotic activity was not responsible for decreased mesenchymal cell density. Likewise, analysis of distribution patterns of 3 H-glucosamine-labelled HA indicated that decreased HA concentration was not produced by regional differences in HA synthesis. These results suggest that decreases in mesenchymal cell density and HA concentration that occur during neural fold elevation are produced by mesenchymal expansion

  1. Origami-Inspired Folding of Thick, Rigid Panels

    Science.gov (United States)

    Trease, Brian P.; Thomson, Mark W.; Sigel, Deborah A.; Walkemeyer, Phillip E.; Zirbel, Shannon; Howell, Larry; Lang, Robert

    2014-01-01

    To achieve power of 250 kW or greater, a large compression ratio of stowed-to-deployed area is needed. Origami folding patterns were used to inspire the folding of a solar array to achieve synchronous deployment; however, origami models are generally created for near-zero-thickness material. Panel thickness is one of the main challenges of origami-inspired design. Three origami-inspired folding techniques (flasher, square twist, and map fold) were created with rigid panels and hinges. Hinge components are added to the model to enable folding of thick, rigid materials. Origami models are created assuming zero (or near zero) thickness. When a material with finite thickness is used, the panels are required to bend around an increasingly thick fold as they move away from the center of the model. The two approaches for dealing with material thickness are to use membrane hinges to connect the panels, or to add panel hinges, or hinges of the same thickness, at an appropriate width to enable folding.

  2. Fluorescence of Alexa fluor dye tracks protein folding.

    Directory of Open Access Journals (Sweden)

    Simon Lindhoud

    Full Text Available Fluorescence spectroscopy is an important tool for the characterization of protein folding. Often, a protein is labeled with appropriate fluorescent donor and acceptor probes and folding-induced changes in Förster Resonance Energy Transfer (FRET are monitored. However, conformational changes of the protein potentially affect fluorescence properties of both probes, thereby profoundly complicating interpretation of FRET data. In this study, we assess the effects protein folding has on fluorescence properties of Alexa Fluor 488 (A488, which is commonly used as FRET donor. Here, A488 is covalently attached to Cys69 of apoflavodoxin from Azotobacter vinelandii. Although coupling of A488 slightly destabilizes apoflavodoxin, the three-state folding of this protein, which involves a molten globule intermediate, is unaffected. Upon folding of apoflavodoxin, fluorescence emission intensity of A488 changes significantly. To illuminate the molecular sources of this alteration, we applied steady state and time-resolved fluorescence techniques. The results obtained show that tryptophans cause folding-induced changes in quenching of Alexa dye. Compared to unfolded protein, static quenching of A488 is increased in the molten globule. Upon populating the native state both static and dynamic quenching of A488 decrease considerably. We show that fluorescence quenching of Alexa Fluor dyes is a sensitive reporter of conformational changes during protein folding.

  3. Fluorescence of Alexa fluor dye tracks protein folding.

    Science.gov (United States)

    Lindhoud, Simon; Westphal, Adrie H; Visser, Antonie J W G; Borst, Jan Willem; van Mierlo, Carlo P M

    2012-01-01

    Fluorescence spectroscopy is an important tool for the characterization of protein folding. Often, a protein is labeled with appropriate fluorescent donor and acceptor probes and folding-induced changes in Förster Resonance Energy Transfer (FRET) are monitored. However, conformational changes of the protein potentially affect fluorescence properties of both probes, thereby profoundly complicating interpretation of FRET data. In this study, we assess the effects protein folding has on fluorescence properties of Alexa Fluor 488 (A488), which is commonly used as FRET donor. Here, A488 is covalently attached to Cys69 of apoflavodoxin from Azotobacter vinelandii. Although coupling of A488 slightly destabilizes apoflavodoxin, the three-state folding of this protein, which involves a molten globule intermediate, is unaffected. Upon folding of apoflavodoxin, fluorescence emission intensity of A488 changes significantly. To illuminate the molecular sources of this alteration, we applied steady state and time-resolved fluorescence techniques. The results obtained show that tryptophans cause folding-induced changes in quenching of Alexa dye. Compared to unfolded protein, static quenching of A488 is increased in the molten globule. Upon populating the native state both static and dynamic quenching of A488 decrease considerably. We show that fluorescence quenching of Alexa Fluor dyes is a sensitive reporter of conformational changes during protein folding.

  4. Endoscopic Anatomy of the Tensor Fold and Anterior Attic.

    Science.gov (United States)

    Li, Bin; Doan, Phi; Gruhl, Robert R; Rubini, Alessia; Marchioni, Daniele; Fina, Manuela

    2018-02-01

    Objectives The objectives of the study were to (1) study the anatomical variations of the tensor fold and its anatomic relation with transverse crest, supratubal recess, and anterior epitympanic space and (2) explore the most appropriate endoscopic surgical approach to each type of the tensor fold variants. Study Design Cadaver dissection study. Setting Temporal bone dissection laboratory. Subjects and Methods Twenty-eight human temporal bones (26 preserved and 2 fresh) were dissected through an endoscopic transcanal approach between September 2016 and June 2017. The anatomical variations of the tensor fold, transverse crest, supratubal recess, and anterior epitympanic space were studied before and after removing ossicles. Results Three different tensor fold orientations were observed: vertical (type A, 11/28, 39.3%) with attachment to the transverse crest, oblique (type B, 13/28, 46.4%) with attachment to the anterior tegmen tympani, and horizontal (type C, 4/28, 14.3%) with attachment to the tensor tympani canal. The tensor fold was a complete membrane in 20 of 28 (71.4%) specimens, preventing direct ventilation between the supratubal recess and anterior epitympanic space. We identified 3 surgical endoscopic approaches, which allowed visualization of the tensor fold without removing the ossicles. Conclusions The orientation of the tensor fold is the determining structure that dictates the conformation and limits of the epitympanic space. We propose a classification of the tensor fold based on 3 anatomical variants. We also describe 3 different minimally invasive endoscopic approaches to identify the orientation of the tensor fold while maintaining ossicular chain continuity.

  5. A nomenclature paradigm for benign midmembranous vocal fold lesions.

    Science.gov (United States)

    Rosen, Clark A; Gartner-Schmidt, Jackie; Hathaway, Bridget; Simpson, C Blake; Postma, Gregory N; Courey, Mark; Sataloff, Robert T

    2012-06-01

    There is a significant lack of uniform agreement regarding nomenclature for benign vocal fold lesions (BVFLs). This confusion results in difficulty for clinicians communicating with their patients and with each other. In addition, BVFL research and comparison of treatment methods are hampered by the lack of a detailed and uniform BVFL nomenclature. Clinical consensus conferences were held to develop an initial BVFL nomenclature paradigm. Perceptual video analysis was performed to validate the stroboscopy component of the paradigm. The culmination of the consensus conferences and the video-perceptual analysis was used to evaluate the BVFL nomenclature paradigm using a retrospective review of patients with BVFL. An initial BVFL nomenclature paradigm was proposed utilizing detailed definitions relating to vocal fold lesion morphology, stroboscopy, response to voice therapy and intraoperative findings. Video-perceptual analysis of stroboscopy demonstrated that the proposed binary stroboscopy system used in the BVFL nomenclature paradigm was valid and widely applicable. Retrospective review of 45 patients with BVFL followed to the conclusion of treatment demonstrated that slight modifications of the initial BVFL nomenclature paradigm were required. With the modified BVFL nomenclature paradigm, 96% of the patients fit into the predicted pattern and definitions of the BVFL nomenclature system. This study has validated a multidimensional BVFL nomenclature paradigm. This vocal fold nomenclature paradigm includes nine distinct vocal fold lesions: vocal fold nodules, vocal fold polyp, pseudocyst, vocal fold cyst (subepithelial or ligament), nonspecific vocal fold lesion, vocal fold fibrous mass (subepithelial or ligament), and reactive lesion. Copyright © 2011 The American Laryngological, Rhinological, and Otological Society, Inc.

  6. 3D Fault modeling of the active Chittagong-Myanmar fold belt, Bangladesh

    Science.gov (United States)

    Peterson, D. E.; Hubbard, J.; Akhter, S. H.; Shamim, N.

    2013-12-01

    The Chittagong-Myanmar fold belt (CMFB), located in eastern Bangladesh, eastern India and western Myanmar, accommodates east-west shortening at the India-Burma plate boundary. Oblique subduction of the Indian Plate beneath the Burma Plate since the Eocene has led to the development of a large accretionary prism complex, creating a series of north-south trending folds. A continuous sediment record from ~55 Ma to the present has been deposited in the Bengal Basin by the Ganges-Brahmaputra-Meghna rivers, providing an opportunity to learn about the history of tectonic deformation and activity in this fold-and-thrust belt. Surface mapping indicates that the fold-and-thrust belt is characterized by extensive N-S-trending anticlines and synclines in a belt ~150-200 km wide. Seismic reflection profiles from the Chittagong and Chittagong Hill Tracts, Bangladesh, indicate that the anticlines mapped at the surface narrow with depth and extend to ~3.0 seconds TWTT (two-way travel time), or ~6.0 km. The folds of Chittagong and Chittagong Hill Tracts are characterized by doubly plunging box-shaped en-echelon anticlines separated by wide synclines. The seismic data suggest that some of these anticlines are cored by thrust fault ramps that extend to a large-scale décollement that dips gently to the east. Other anticlines may be the result of detachment folding from the same décollement. The décollement likely deepens to the east and intersects with the northerly-trending, oblique-slip Kaladan fault. The CMFB region is bounded to the north by the north-dipping Dauki fault and the Shillong Plateau. The tectonic transition from a wide band of E-W shortening in the south to a narrow zone of N-S shortening along the Dauki fault is poorly understood. We integrate surface and subsurface datasets, including topography, geological maps, seismicity, and industry seismic reflection profiles, into a 3D modeling environment and construct initial 3D surfaces of the major faults in this

  7. Molecular dynamics studies of protein folding and aggregation

    Science.gov (United States)

    Ding, Feng

    This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism

  8. Compression induced folding of a sheet: An integrable system

    Science.gov (United States)

    Diamant, Haim; Witten, Thomas A.

    2012-02-01

    The apparently intractable shape of a fold in a compressed elastic film lying on a fluid substrate is found to have an exact solution. Such systems buckle at a nonzero wave vector set by the bending stiffness of the film and the weight of the substrate fluid. Our solution describes the entire progression from a weakly displaced sinusoidal buckling to a single large fold that contacts itself. The pressure decrease is exactly quadratic in the lateral displacement. We demonstrate a subtle connection to the sine-Gordon problem, which reveals a new symmetry in the folding phenomenon.

  9. Adjustable thermal resistor by reversibly folding a graphene sheet.

    Science.gov (United States)

    Song, Qichen; An, Meng; Chen, Xiandong; Peng, Zhan; Zang, Jianfeng; Yang, Nuo

    2016-08-11

    Phononic (thermal) devices such as thermal diodes, thermal transistors, thermal logic gates, and thermal memories have been studied intensively. However, tunable thermal resistors have not been demonstrated yet. Here, we propose an instantaneously adjustable thermal resistor based on folded graphene. Through theoretical analysis and molecular dynamics simulations, we study the phonon-folding scattering effect and the dependence of thermal resistivity on the length between two folds and the overall length. Furthermore, we discuss the possibility of realizing instantaneously adjustable thermal resistors in experiment. Our studies bring new insights into designing thermal resistors and understanding the thermal modulation of 2D materials by adjusting basic structure parameters.

  10. Anisotropic Liquid Microcapsules from Biomimetic Self-Folding Polymer Films.

    Science.gov (United States)

    Zakharchenko, Svetlana; Ionov, Leonid

    2015-06-17

    We demonstrated a novel approach for the fabrication of anisotropic capsules with liquid content using biomimetic self-folding thermoresponsive polymer films. The behavior of self-folding films is very similar to actuation in plants, where nonhomogenous swelling results in complex movements such as twisting, bending, or folding. This approach allows the design of anisotropic liquid capsules with rodlike and dumbbell-like morphologies. We found that these capsules are able to assemble into different complex structures, such as nematic-like one and 3D network depending on their morphology.

  11. Miniaturization of Multiple-Layer Folded Patch Antennas

    DEFF Research Database (Denmark)

    Zhang, Jiaying; Breinbjerg, Olav

    2009-01-01

    layer patch is fabricated and measured to validate the design method. The theoretical analysis, design and simulations, fabrications, as well as the measurements are presented in this paper. All the results show that the folded patch antenna is a good candidate in making a highly miniaturized compact......A new folded patch antenna with multiple layers was developed in this paper, by folding the patch in a proper way, and a highly miniaturized antenna can be realized. The multiple layer patch with 4-layer and 6-layer are designed and evaluated at 2.4 GHz, 915 MHz, and 415 MHz respectively. Then a 4...

  12. Large sonic band gaps in 12-fold quasicrystals

    Science.gov (United States)

    Lai, Yun; Zhang, Xiangdong; Zhang, Zhao-Qing

    2002-05-01

    The sonic band-gap structures of 12-fold symmetry quasicrystals consisting of rigid cylinders in air are investigated by using the multiple scattering method. Large full gaps are found in this system owing to its high symmetry. At filling fractions between 0.2 and 0.4, this 12-fold square-triangle tiling is much better for the realization of sonic band gaps than the square or triangular lattice. This makes the 12-fold quasicrystal a promising structure for acoustic-wave band-gap materials.

  13. Water dynamics clue to key residues in protein folding

    International Nuclear Information System (INIS)

    Gao, Meng; Zhu, Huaiqiu; Yao, Xin-Qiu; She, Zhen-Su

    2010-01-01

    A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

  14. Competition between folding and glycosylation in the endoplasmic reticulum

    DEFF Research Database (Denmark)

    Holst, B; Bruun, A W; Kielland-Brandt, Morten

    1996-01-01

    Using carboxypeptidase Y in Saccharomyces cerevisiae as a model system, the in vivo relationship between protein folding and N-glycosylation was studied. Seven new sites for N-glycosylation were introduced at positions buried in the folded protein structure. The level of glycosylation of such new...... acceptor sites was analysed by pulse-labelling under two sets of conditions that are known to reduce the rate of folding: (i) addition of dithiothreitol to the growth medium and (ii) introduction of deletions in the propeptide. A variety of effects was observed, depending on the position of the new...

  15. Atmospheric stability index using radio occultation refractivity profiles

    Indian Academy of Sciences (India)

    A new stability index based on atmospheric refractivity at ∼500 hPa level and surface measurements of temperature, pressure and humidity is formulated. The new index named here as refractivity based lifted index (RLI) is designed to give similar results as traditionally used lifted index derived from radiosonde profiles of ...

  16. [Journal selection and indexing for Index Medicus and Chinese periodicals indexed in Index Medicus].

    Science.gov (United States)

    Zhou, Qing-Hui; Ling, Chang-Quan; Bai, Yu-Jin; Yin, Hui-Xia

    2005-01-01

    Index Medicus/MEDLINE/PubMed published by U. S. National Library of Medicine (NLM) is the most important and commonly used biomedical literature retrieval system in the world. According to the"List of Journals Indexed in Index Medicus (2004)", 4,098 journals are indexed for Index Medicus, including 70 journals from mainland China and Hong Kong and 9 journals from Taiwan. Journal of Chinese Integrative Medicine established in May, 2003 is indexed in Index Medicus in 2004. This article outlines the critical elements of journal selection for Index Medicus/MEDLINE and the journal selection process for indexing at NLM, and introduces some measures for the Journal of Chinese Integrative Medicine being indexed in Index Medicus/MEDLINE.

  17. Adipose-Derived Mesenchymal Stem Cells in the Regeneration of Vocal Folds: A Study on a Chronic Vocal Fold Scar

    Directory of Open Access Journals (Sweden)

    Angelou Valerie

    2016-01-01

    Full Text Available Background. The aim of the study was to assess the histological effects of autologous infusion of adipose-derived stem cells (ADSC on a chronic vocal fold scar in a rabbit model as compared to an untreated scar as well as in injection of hyaluronic acid. Study Design. Animal experiment. Method. We used 74 New Zealand rabbits. Sixteen of them were used as control/normal group. We created a bilateral vocal fold wound in the remaining 58 rabbits. After 18 months we separated our population into three groups. The first group served as control/scarred group. The second one was injected with hyaluronic acid in the vocal folds, and the third received an autologous adipose-derived stem cell infusion in the scarred vocal folds (ADSC group. We measured the variation of thickness of the lamina propria of the vocal folds and analyzed histopathologic changes in each group after three months. Results. The thickness of the lamina propria was significantly reduced in the group that received the ADSC injection, as compared to the normal/scarred group. The collagen deposition, the hyaluronic acid, the elastin levels, and the organization of elastic fibers tend to return to normal after the injection of ADSC. Conclusions. Autologous injection of adipose-derived stem cells on a vocal fold chronic scar enhanced the healing of the vocal folds and the reduction of the scar tissue, even when compared to other treatments.

  18. The Influence of Frontal and Lateral Ramps in Fold Thrust Belts on Structural Architecture and Erosion

    Science.gov (United States)

    Robinson, D. M.; McQuarrie, N.

    2016-12-01

    In fold thrust belts, horizontal and vertical motions (or flow) define the path that a particular rock or mineral takes to the surface of the Earth, which is dictated by the location of frontal and lateral ramps. Horizontal flow occurs between ramp locations while the vertical component of motion (or flow) dominates when rocks are traveling over the ramps. Frontal ramps are common features near the front (foreland) of a fold thrust belt. Foreland frontal ramps are the easiest to obtain data for, and from these data predict ramp geometry, because they are shallow and the ramp geometry is commonly expressed as changes in the dip of strata in the mapped geology. Less constrainable are the frontal ramps at depth in the hinterland of a fold thrust belt. However, these deep frontal ramps control the architecture of a fold thrust belt, influence the mapped surface geology, control active uplift and thus, are locations of focused erosion. We show kinematic models from Nepal that illustrate how the architecture (geometry of structures, dips of strata) changes in the fold thrust belt when the location of a frontal ramp is moved and how both thermochronologic data and accurate mapping limit the possibilities for the location of these hinterland frontal ramps. Lateral ramps at depth provide limits on the width of horizontal flow paths and encourage vertical flow paths that have orientations strongly oblique to the strike of the orogen. A challenge in fold thrust belts is to determine the most logical location for lateral ramps. We use examples from Nepal that highlight characteristics that can be used to define the location of lateral ramps. Both lateral and frontal ramps produce significant structural elevation and changes in topographic elevation and thus, are locations of focused erosion through time. Additionally, because material is moving both laterally and vertically in a brittle fold thrust belt, frontal and lateral ramps can control the origin of earthquakes as well

  19. Fast mapping of global protein folding states by multivariate NMR:

    DEFF Research Database (Denmark)

    Malmendal, Anders; Underhaug, Jarl; Otzen, Daniel

    2010-01-01

    that provides such an overview. GPS NMR exploits the unique ability of NMR to simultaneously record signals from individual hydrogen atoms in complex macromolecular systems and of multivariate analysis to describe spectral variations from these by a few variables for establishment of, and positioning in......, protein-folding state maps. The method is fast, sensitive, and robust, and it works without isotope-labelling. The unique capabilities of GPS NMR to identify different folding states and to compare different unfolding processes are demonstrated by mapping of the equilibrium folding space of bovine alpha......To obtain insight into the functions of proteins and their specific roles, it is important to establish efficient procedures for exploring the states that encapsulate their conformational space. Global Protein folding State mapping by multivariate NMR (GPS NMR) is a powerful high-throughput method...

  20. Protein folding and misfolding shining light by infrared spectroscopy

    CERN Document Server

    Fabian, Heinz

    2012-01-01

    Infrared spectroscopy is a new and innovative technology to study protein folding/misfolding events in the broad arsenal of techniques conventionally used in this field. The progress in understanding protein folding and misfolding is primarily due to the development of biophysical methods which permit to probe conformational changes with high kinetic and structural resolution. The most commonly used approaches rely on rapid mixing methods to initiate the folding event via a sudden change in solvent conditions. Traditionally, techniques such as fluorescence, circular dichroism or visible absorption are applied to probe the process. In contrast to these techniques, infrared spectroscopy came into play only very recently, and the progress made in this field up to date which now permits to probe folding events over the time scale from picoseconds to minutes has not yet been discussed in a book. The aim of this book is to provide an overview of the developments as seen by some of the main contributors to the field...

  1. New Analysis and Theory of Deployable Folded Structures, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — A recently developed mathematical folding theory has great value for deployable space structures and in situ manufacture of large beams, panels and cylinders. The...

  2. On the functioning of folded dipole antennas on conducting masts

    CSIR Research Space (South Africa)

    Mcnamara, DA

    1993-11-01

    Full Text Available The radiation properties of individual folded dipole antennas mounted at various radial distances from the centre of conducting masts of different diameters are described in compact fashion....

  3. Criteria for folding in structure-based models of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw (Poland)

    2016-05-14

    In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very low thermodynamic stability, especially when the contact map used is too sparse. We consider six different structure-based models and show that allowing for a small, but model-dependent, percentage of the native contacts not being established boosts the folding temperature substantially while affecting the time scales of folding only in a minor way. We also compare other properties of the six models. We show that the choice of the description of the backbone stiffness has a substantial effect on the values of characteristic temperatures that relate both to equilibrium and kinetic properties. Models without any backbone stiffness (like the self-organized polymer) are found to perform similar to those with the stiffness, including in the studies of stretching.

  4. Phonosurgery of the vocal folds : a classification proposal

    NARCIS (Netherlands)

    Remacle, M; Friedrich, G; Dikkers, FG; de Jong, F

    The Phonosurgery Committee of the European Laryngological Society (ELS) has examined the definition and technical description of phonosurgical procedures. Based on this review, the committee has proposed a working classification. The current presentation is restricted to vocal fold surgery (VFS)

  5. Kinematics of large scale asymmetric folds and associated smaller ...

    Indian Academy of Sciences (India)

    ductile structures in the Proterozoic Somnur Formation, Pranhita - Godavari valley, ... The development of structural elements and finite strain data are analysed to constrain kinematics of folds and faults at various scales within a Proterozoic ...

  6. Folding two dimensional crystals by swift heavy ion irradiation

    International Nuclear Information System (INIS)

    Ochedowski, Oliver; Bukowska, Hanna; Freire Soler, Victor M.; Brökers, Lara; Ban-d'Etat, Brigitte; Lebius, Henning; Schleberger, Marika

    2014-01-01

    Ion irradiation of graphene, the showcase model of two dimensional crystals, has been successfully applied to induce various modifications in the graphene crystal. One of these modifications is the formation of origami like foldings in graphene which are created by swift heavy ion irradiation under glancing incidence angle. These foldings can be applied to locally alter the physical properties of graphene like mechanical strength or chemical reactivity. In this work we show that the formation of foldings in two dimensional crystals is not restricted to graphene but can be applied for other materials like MoS 2 and hexagonal BN as well. Further we show that chemical vapour deposited graphene forms foldings after swift heavy ion irradiation while chemical vapour deposited MoS 2 does not

  7. Folding two dimensional crystals by swift heavy ion irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Ochedowski, Oliver; Bukowska, Hanna [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Freire Soler, Victor M. [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Departament de Fisica Aplicada i Optica, Universitat de Barcelona, E08028 Barcelona (Spain); Brökers, Lara [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Ban-d' Etat, Brigitte; Lebius, Henning [CIMAP (CEA-CNRS-ENSICAEN-UCBN), 14070 Caen Cedex 5 (France); Schleberger, Marika, E-mail: marika.schleberger@uni-due.de [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany)

    2014-12-01

    Ion irradiation of graphene, the showcase model of two dimensional crystals, has been successfully applied to induce various modifications in the graphene crystal. One of these modifications is the formation of origami like foldings in graphene which are created by swift heavy ion irradiation under glancing incidence angle. These foldings can be applied to locally alter the physical properties of graphene like mechanical strength or chemical reactivity. In this work we show that the formation of foldings in two dimensional crystals is not restricted to graphene but can be applied for other materials like MoS{sub 2} and hexagonal BN as well. Further we show that chemical vapour deposited graphene forms foldings after swift heavy ion irradiation while chemical vapour deposited MoS{sub 2} does not.

  8. Folding, stowage, and deployment of viscoelastic tape springs

    DEFF Research Database (Denmark)

    Kwok, Kawai; Pellegrino, Sergio

    2013-01-01

    This paper presents an experimental and numerical study of the folding, stowage, and deployment behavior of viscoelastic tape springs. Experiments show that during folding the relationship between load and displacement is nonlinear and varies with rate and temperature. In particular, the limit...... and propagation loads increase with the folding rate but decrease with temperature. During stowage, relaxation behavior leads to a reduction in internal forces that significantly impacts the subsequent deployment dynamics. The deployment behavior starts with a short, dynamic transient that is followed by a steady...... deployment and ends with a slow creep recovery. Unlike elastic tape springs, localized folds in viscoelastic tape springs do not move during deployment. Finite-element simulations based on a linear viscoelastic constitutive model with an experimentally determined relaxation modulus are shown to accurately...

  9. Exploring the mechanisms used by promiscuous chaperones to assist protein folding in the cell

    Science.gov (United States)

    Jewett, Andrew I.

    protein folding at relevant chaperone concentrations, chaperones must bind to and hold the protein weakly enough to allow it to change its conformation while bound. We suspect that during this time, the chaperone would also discourage aggregation by competing for aggregation-prone hydrophobic sites on the protein's surface.

  10. Can Local Probes Go Global? A Joint Experiment-Simulation Analysis of λ(6-85) Folding.

    Science.gov (United States)

    Sukenik, Shahar; Pogorelov, Taras V; Gruebele, Martin

    2016-06-02

    The process of protein folding is known to involve global motions in a cooperative affair; the structure of most of the protein sequences is gained or lost over a narrow range of temperature, denaturant, or pressure perturbations. At the same time, recent simulations and experiments reveal a complex structural landscape with a rich set of local motions and conformational changes. We couple experimental kinetic and thermodynamic measurements with specifically tailored analysis of simulation data to isolate local versus global folding probes. We find that local probes exhibit lower melting temperatures, smaller surface area changes, and faster kinetics compared to global ones. We also see that certain local probes of folding match the global behavior more closely than others. Our work highlights the importance of using multiple probes to fully characterize protein folding dynamics by theory and experiment.

  11. A Turing Reaction-Diffusion Model for Human Cortical Folding Patterns and Cortical Pattern Malformations

    Science.gov (United States)

    Hurdal, Monica K.; Striegel, Deborah A.

    2011-11-01

    Modeling and understanding cortical folding pattern formation is important for quantifying cortical development. We present a biomathematical model for cortical folding pattern formation in the human brain and apply this model to study diseases involving cortical pattern malformations associated with neural migration disorders. Polymicrogyria is a cortical malformation disease resulting in an excessive number of small gyri. Our mathematical model uses a Turing reaction-diffusion system to model cortical folding. The lateral ventricle (LV) and ventricular zone (VZ) of the brain are critical components in the formation of cortical patterning. In early cortical development the shape of the LV can be modeled with a prolate spheroid and the VZ with a prolate spheroid surface. We use our model to study how global cortex characteristics, such as size and shape of the LV, affect cortical pattern formation. We demonstrate increasing domain scale can increase the number of gyri and sulci formed. Changes in LV shape can account for sulcus directionality. By incorporating LV size and shape, our model is able to elucidate which parameters can lead to excessive cortical folding.

  12. Cross-tropopause Transport In Tropopause Folds: Mechanisms and Sensitivity To Model Resolution

    Science.gov (United States)

    Gray, S. L.

    The rate and processes of transfer of mass and chemical species between the strato- sphere and troposphere (stratosphere-troposphere exchange) are currently uncertain. In the midlatitudes exchange appears to be dominated by processes associated with tropopause folds and cut-off lows. The development of a tropopause fold is a reversible process and thus irreversible processes must occur for the permanent transfer of ma- terial across the tropopause boundary. Proposed processes include turbulent mixing, quasi-isentropic mixing, convectively breaking gravity waves, deep convection and radiative heating. Numerical models run at typical climate or regional-scale resolutions are unable to re- solve the fine-scale features observed in tropopause folds. It is hypothesised that both the rate of exchange and its partitioning into different processes, as derived from nu- merical model simulations, are sensitive to model resolution. This hypothesis is tested through simulations of a tropopause folding event associated with a vigorous surface cold front which tracked across the British Isles. Climate to high-mesoscale resolution simulations incorporating passive tracers are performed using the mesoscale version of the Met Office Unified Model. The mechanism by which the parametrized convec- tion leads to exchange is the subject of further examination.

  13. Climate Prediction Center Southern Oscillation Index

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This is one of the CPC?s Monthly Atmospheric and Sea Surface Temperature (SST)Indices. It contains Southern Oscillation Index which is standardized sea level...

  14. WW Domain Folding Complexity Revealed by Infrared Spectroscopy

    OpenAIRE

    Davis, Caitlin M.; Dyer, R. Brian

    2014-01-01

    Although the intrinsic tryptophan fluorescence of proteins offers a convenient probe of protein folding, interpretation of the fluorescence spectrum is often difficult because it is sensitive to both global and local changes. Infrared (IR) spectroscopy offers a complementary measure of structural changes involved in protein folding, because it probes changes in the secondary structure of the protein backbone. Here we demonstrate the advantages of using multiple probes, infrared and fluorescen...

  15. Morphometric Study of Vocal Folds in Indian Cadavers

    Directory of Open Access Journals (Sweden)

    Rawal J.D.

    2015-06-01

    Full Text Available Introduction: -The larynx is an air passage and a sphincteric device used in respiration and phonation. The larynx, from inside outwards has a framework of mucosa surrounded by fibro-elastic membrane which in turn is surrounded by cartilages and then a layer of muscles. Vocal folds are intrinsic ligament of larynx covered by mucosal folds. Larynx generates sound through rhythmic opening and closing of the vocal folds. The perceived pitch of human voice mainly depends upon fundamental frequency of sound generated by larynx. Aim: - The aim of present study is to measure various dimensions of vocal folds in Indian cadavers. Material & Methods: - 50 larynx were obtained from embalmed cadavers, of which 10 larynx were of females. Vocal cords were dissected from the larynx and morphometric analysis was done. Results and Conclusions: - The average total length of the vocal folds was found to be 16.11 mm. ± 2.62 mm. in male and 14.10 mm. ± 1.54 mm. in female cadavers. The average width of the vocal folds was found to be 4.38 mm. ± 0.74 mm. in male and 3.60 mm. ± 0.64 mm. in female cadavers. The average total length of the membranous part of the vocal folds was found to be 11.90 mm. ± 1.86 mm. in male and 10.45 mm. ± 1.81 mm. in female cadavers. The average ratio of the length of the membranous and the cartilaginous parts of the vocal folds was calculated to be 3.10 ± 0.96in male and 2.85 ± 0.73in female cadavers.

  16. RNA folding inside a virus capsid and dimensional reduction.

    Science.gov (United States)

    Ghafouri, Rouzbeh; Bruinsma, Robijn; Rudnick, Joseph

    2006-03-01

    As RNA folds on itself , in certain conditions, it takes the form of a branched polymer. So the problem of RNA folding in a virus capsid is essentially the problem of a branched polymer in a confined environment. In this paper we attack the problem using the technique of dimensional reduction which relates a branched polymer with self interation in D dimension to a hardcore classical gas in (D-2) dimension. We look for phase transitions and intersting physical quantities such as pressure.

  17. REMARKS ON MIURA-ORI, A JAPANESE FOLDING METHOD

    Directory of Open Access Journals (Sweden)

    Stachel Hellmuth

    2009-07-01

    Full Text Available Miura-ori is a Japanese folding technique named after Prof. Koryo Miura, the University of Tokyo. It is used for solar panels because it can be unfolded into its rectangular shape by pulling on one corner only. On the other hand it is used as kernel to stiffen sandwich structures. In this paper some insight will be given into the geometric structure of this folding method combined with an outlook to analogues and generalizations.

  18. A New CMOS Current-Mode Folding Amplifier

    Directory of Open Access Journals (Sweden)

    M.A Al-Absi

    2013-09-01

    Full Text Available In this paper, a new CMOS current-mode folding amplifier is proposed. The circuit is designed using MOSFETs operating in strong inversion. The design produces a nearly ideal saw-tooth input-output characteristic which is a mandatory requirement in folding analog-to-digital converters. The functionality of the proposed circuit was confirmed using Tanner simulation tools in 0.35 µm CMOS technology. Simulation results are in excellent agreement with the theory.

  19. Structural model of the eastern Achara-Trialeti fold and thrust belt using seismic reflection profiles

    Science.gov (United States)

    Alania, Victor; Chabukiani, Alexander; Enukidze, Onise; Razmadze, Alexander; Sosson, Marc; Tsereteli, Nino; Varazanashvili, Otar

    2017-04-01

    Our study focused on the structural geometry at the eastern Achara-Trialeti fold and thrust belt (ATFTB) located at the retro-wedge of the Lesser Caucasus orogen (Alania et al., 2016a). Our interpretation has integrated seismic reflection profiles, several oil-wells, and the surface geology data to reveal structural characteristics of the eastern ATFTB. Fault-related folding theories were used to seismic interpretation (Shaw et al., 2004). Seismic reflection data reveal the presence of basement structural wedge, south-vergent backthrust, north-vergent forethrust and some structural wedges (or duplex). The rocks are involved in the deformation range from Paleozoic basement rocks to Tertiary strata. Building of thick-skinned structures of eastern Achara-Trialeti was formed by basement wedges propagated from south to north along detachment horizons within the cover generating thin-skinned structures. The kinematic evolution of the south-vergent backthrust zone with respect to the northward propagating structural wedge (or duplexes). The main style of deformation within the backthrust belt is a series of fault-propagation folds. Frontal part of eastern ATFTB are represent by triangle zone (Alania et al., 2016b; Sosson et al., 2016). A detailed study was done for Tbilisi area: seismic refection profiles, serial balanced cross-sections, and earthquakes reveal the presence of an active blind thrust fault beneath Tbilisi. 2 & 3-D structural models show that 2002 Mw 4.5 Tbilisi earthquake related to a north-vergent blind thrust. Empirical relations between blind fault rupture area and magnitude suggest that these fault segments could generate earthquakes of Mw 6.5. The growth fault-propagation fold has been observed near Tbilisi in the frontal part of eastern ATFTB. Seismic reflection profile through Ormoiani syncline shows that south-vergent growth fault-propagation fold related to out-of-the-syncline thrust. The outcrop of fault-propagation fold shown the geometry of the

  20. Self-Folding Textiles through Manipulation of Knit Stitch Architecture

    Directory of Open Access Journals (Sweden)

    Chelsea E. Knittel

    2015-12-01

    Full Text Available This research presents a preliminary study on finding predictable methods of controlling the self-folding behaviors of weft knit textiles for use in the development of smart textiles and garment devices, such as those with shape memory, auxetic behavior or transformation abilities. In this work, Shima Seiki SDS-One Apex computer-aided knitting technology, Shima Seiki industrial knitting machines, and the study of paper origami tessellation patterns were used as tools to understand and predict the self-folding abilities of weft knit textiles. A wide range of self-folding weft knit structures was produced, and relationships between the angles and ratios of the knit and purl stitch types were determined. Mechanical testing was used as a means to characterize differences produced by stitch patterns, and to further understand the relationships between angles and folding abilities. By defining a formulaic method for predicting the nature of the folds that occur due to stitch architecture patterns, we can better design self-folding fabrics for smart textile applications.

  1. Metal ion coupled protein folding and allosteric motions

    Science.gov (United States)

    Wang, Wei

    2014-03-01

    Many proteins need the help of cofactors for their successful folding and functioning. Metal ions, i.e., Zn2+, Ca2+, and Mg2+ etc., are typical biological cofactors. Binding of metal ions can reshape the energy landscapes of proteins, thereby modifying the folding and allosteric motions. For example, such binding may make the intrinsically disordered proteins have funneled energy landscapes, consequently, ensures their spontaneous folding. In addition, the binding may activate certain biological processes by inducing related conformational changes of regulation proteins. However, how the local interactions involving the metal ion binding can induce the global conformational motions of proteins remains elusive. Investigating such question requires multiple models with different details, including quantum mechanics, atomistic models, and coarse grained models. In our recent work, we have been developing such multiscale methods which can reasonably model the metal ion binding induced charge transfer, protonation/deprotonation, and large conformational motions of proteins. With such multiscale model, we elucidated the zinc-binding induced folding mechanism of classical zinc finger and the calcium-binding induced dynamic symmetry breaking in the allosteric motions of calmodulin. In addition, we studied the coupling of folding, calcium binding and allosteric motions of calmodulin domains. In this talk, I will introduce the above progresses on the metal ion coupled protein folding and allosteric motions. We thank the finacial support from NSFC and the 973 project.

  2. Synthetic oligorotaxanes exert high forces when folding under mechanical load

    Science.gov (United States)

    Sluysmans, Damien; Hubert, Sandrine; Bruns, Carson J.; Zhu, Zhixue; Stoddart, J. Fraser; Duwez, Anne-Sophie

    2018-01-01

    Folding is a ubiquitous process that nature uses to control the conformations of its molecular machines, allowing them to perform chemical and mechanical tasks. Over the years, chemists have synthesized foldamers that adopt well-defined and stable folded architectures, mimicking the control expressed by natural systems1,2. Mechanically interlocked molecules, such as rotaxanes and catenanes, are prototypical molecular machines that enable the controlled movement and positioning of their component parts3-5. Recently, combining the exquisite complexity of these two classes of molecules, donor-acceptor oligorotaxane foldamers have been synthesized, in which interactions between the mechanically interlocked component parts dictate the single-molecule assembly into a folded secondary structure6-8. Here we report on the mechanochemical properties of these molecules. We use atomic force microscopy-based single-molecule force spectroscopy to mechanically unfold oligorotaxanes, made of oligomeric dumbbells incorporating 1,5-dioxynaphthalene units encircled by cyclobis(paraquat-p-phenylene) rings. Real-time capture of fluctuations between unfolded and folded states reveals that the molecules exert forces of up to 50 pN against a mechanical load of up to 150 pN, and displays transition times of less than 10 μs. While the folding is at least as fast as that observed in proteins, it is remarkably more robust, thanks to the mechanically interlocked structure. Our results show that synthetic oligorotaxanes have the potential to exceed the performance of natural folding proteins.

  3. Multi-crease Self-folding by Global Heating.

    Science.gov (United States)

    Miyashita, Shuhei; Onal, Cagdas D; Rus, Daniela

    2015-01-01

    This study demonstrates a new approach to autonomous folding for the body of a 3D robot from a 2D sheet, using heat. We approach this challenge by folding a 0.27-mm sheetlike material into a structure. We utilize the thermal deformation of a contractive sheet sandwiched by rigid structural layers. During this baking process, the heat applied on the entire sheet induces contraction of the contracting layer and thus forms an instructed bend in the sheet. To attain the targeted folding angles, the V-fold spans method is used. The targeted angle θout can be kinematically encoded into crease geometry. The realization of this angle in the folded structure can be approximately controlled by a contraction angle θin. The process is non-reversible, is reliable, and is relatively fast. Our method can be applied simultaneously to all the folds in multi-crease origami structures. We demonstrate the use of this method to create a lightweight mobile robot.

  4. Folding and Biogenesis of Mitochondrial Small Tim Proteins

    Directory of Open Access Journals (Sweden)

    Efrain Ceh-Pavia

    2013-08-01

    Full Text Available Correct and timely folding is critical to the function of all proteins. The importance of this is illustrated in the biogenesis of the mitochondrial intermembrane space (IMS “small Tim” proteins. Biogenesis of the small Tim proteins is regulated by dedicated systems or pathways, beginning with synthesis in the cytosol and ending with assembly of individually folded proteins into functional complexes in the mitochondrial IMS. The process is mostly centered on regulating the redox states of the conserved cysteine residues: oxidative folding is crucial for protein function in the IMS, but oxidized (disulfide bonded proteins cannot be imported into mitochondria. How the redox-sensitive small Tim precursor proteins are maintained in a reduced, import-competent form in the cytosol is not well understood. Recent studies suggest that zinc and the cytosolic thioredoxin system play a role in the biogenesis of these proteins. In the IMS, the mitochondrial import and assembly (MIA pathway catalyzes both import into the IMS and oxidative folding of the small Tim proteins. Finally, assembly of the small Tim complexes is a multistep process driven by electrostatic and hydrophobic interactions; however, the chaperone function of the complex might require destabilization of these interactions to accommodate the substrate. Here, we review how folding of the small Tim proteins is regulated during their biogenesis, from maintenance of the unfolded precursors in the cytosol, to their import, oxidative folding, complex assembly and function in the IMS.

  5. Laryngoplasty with hyaluronic acid in patients with unilateral vocal fold paralysis.

    Science.gov (United States)

    Reiter, Rudolf; Rudolf, Reiter; Brosch, Sibylle; Sibylle, Brosch

    2012-11-01

    Augmentation of vocal fold with hyaluronic acid (Restylane; Q-Med AB, Uppsala, Sweden) is used as a therapeutic option for insufficient glottic closure in unilateral vocal fold paralysis (UVP). Analysis of the optimal glottic width, effectiveness (long-term voice improvement as a consequence of longevity of Restylane), and safety of this new method was made. In a prospective clinical cohort study, 19 consecutive patients with UVP who received vocal fold augmentation with hyaluronic acid (Restylane) were examined preoperatively; 6 weeks, 6, and 12 months postoperatively by laryngostroboscopy; and their voice was evaluated by subjective, objective, and self-assessment (Voice Handicap Index). In 11 of 19 (58%) patients, a subjectively and objectively acceptable voice quality was observed in a follow-up of 12 months. Eight of 19 (42%) patients had a considerable impairment of the voice after 6 weeks (range: 1-24 weeks). Therefore, another intervention (eg, injection laryngoplasty or thyroplasty) was recommended. An impairment of voice was mainly observed if the preoperative glottal gap during phonation was more than 1 mm. A long duration (up to 12 months) of acceptable quality of voice was achieved by augmentation with Restylane, if the glottal gap was 1 mm or less videolaryngostroboscopically during phonation. The authors recommend this therapy for temporary voice improvement and to augment vocal therapy, if spontaneous recovery of voice is likely. Long-term results remain to be seen. Copyright © 2012 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

  6. Prospective multi-arm evaluation of surgical treatments for vocal fold scar and pathologic sulcus vocalis

    Science.gov (United States)

    Welham, Nathan V.; Choi, Seong Hee; Dailey, Seth H.; Ford, Charles N.; Jiang, Jack J.; Bless, Diane M.

    2011-01-01

    Objectives/Hypothesis The purpose of this study was to compare the clinical effectiveness of type I thyroplasty, injection laryngoplasty and graft implantation for the treatment of vocal fold scar and pathologic sulcus vocalis. Study Design Prospective, multi-arm, quasi-experimental research design. Methods Twenty-eight patients with newly diagnosed vocal fold scar and/or pathologic sulcus vocalis were assigned to one of three treatment modalities: Type I thyroplasty (n = 9), injection laryngoplasty (n = 9) and graft implantation (n = 10). Psychosocial, auditory-perceptual, acoustic, aerodynamic and videostroboscopic data were collected pre-treatment and at 1, 6, 12 and 18 months post-treatment. Results Type I thyroplasty and graft implantation both resulted in reduced voice handicap with no concomitant improvement in auditory-perceptual, acoustic, aerodynamic or vocal fold physiologic performance. Injection laryngoplasty resulted in no improvement on any vocal function index. Patients who underwent graft implantation exhibited the slowest improvement trajectory across the 18 month follow-up period. Conclusions A persistent challenge in this area is that no single treatment modality is successful for the majority of patients, and there is no evidence-based decision algorithm for matching a given treatment to a given patient. Progress therefore requires the identification and categorization of predictive clinical features that can drive evidence-based treatment assignment. PMID:21557241

  7. Laser induced temperature jump investigations of fast protein folding dynamics

    Science.gov (United States)

    Qiu, Linlin

    Protein folding has a large parameter space, diverse mechanism, and multipath kinetics. However, there are some common features many proteins share in their folding processes: all seem to fold at the rates much faster than the random conformation search, and all fold into the structures which have the highly regular motifs like alpha-helices, beta-sheets and turns. Understanding how fast proteins can fold is one of the central issues in solving the protein folding problem. Ultrafast folding kinetics had not been accessible until a few sub-millisecond probes were invented and applied lately. We constructed a laser induced temperature jump spectrometer which is a great utility in identifying the local structure and tertiary contact formation of proteins on the time scale from 10 -8 to 10-3 s with time resolution of 10 -9 s. With this spectrometer we studied the fast folding mini-protein, TrpCage and a few short stable beta-hairpins, the TrpZip series. Studying TrpCage was a major breakthrough it was a pioneer protein model which brought experiment and simulation very close: its structures measured by NMR and predicted by the molecular dynamics were amazingly alike. Our kinetic results showed that it folds in 4 mus at room temperature which turned out to be the fastest ever known for protein-like molecules. Also this folding time constant is consistent with what was later on simulated by distributed computation. TrpZips are among the smallest and stablest polypeptide chains which form secondary structures. They are slightly different from each other based on structural stability and by forming various types of beta-hairpins which are the minimum units of beta tertiary structure. The beta-hairpins form in the time range of 1--10 mus that confirms the theory that loop formation is controlled by the diffusion process (˜mus). We also investigated the kinetics of the protein chain collapse, a very controversial problem. By comparing the collapse of the foldable 104

  8. High-frequency viscoelastic shear properties of vocal fold tissues: implications for vocal fold tissue engineering.

    Science.gov (United States)

    Teller, Sean S; Farran, Alexandra J E; Xiao, Longxi; Jiao, Tong; Duncan, Randall L; Clifton, Rodney J; Jia, Xinqiao

    2012-10-01

    The biomechanical function of the vocal folds (VFs) depends on their viscoelastic properties. Many conditions can lead to VF scarring that compromises voice function and quality. To identify candidate replacement materials, the structure, composition, and mechanical properties of native tissues need to be understood at phonation frequencies. Previously, the authors developed the torsional wave experiment (TWE), a stress-wave-based experiment to determine the linear viscoelastic shear properties of small, soft samples. Here, the viscoelastic properties of porcine and human VFs were measured over a frequency range of 10-200 Hz. The TWE utilizes resonance phenomena to determine viscoelastic properties; therefore, the specimen test frequency is determined by the sample size and material properties. Viscoelastic moduli are reported at resonance frequencies. Structure and composition of the tissues were determined by histology and immunochemistry. Porcine data from the TWE are separated into two groups: a young group, consisting of fetal and newborn pigs, and an adult group, consisting of 6-9-month olds and 2+-year olds. Adult tissues had an average storage modulus of 2309±1394 Pa and a loss tangent of 0.38±0.10 at frequencies of 36-200 Hz. The VFs of young pigs were significantly more compliant, with a storage modulus of 394±142 Pa and a loss tangent of 0.40±0.14 between 14 and 30 Hz. No gender dependence was observed. Histological staining showed that adult porcine tissues had a more organized, layered structure than the fetal tissues, with a thicker epithelium and a more structured lamina propria. Elastin fibers in fetal VF tissues were immature compared to those in adult tissues. Together, these structural changes in the tissues most likely contributed to the change in viscoelastic properties. Adult human VF tissues, recovered postmortem from adult patients with a history of smoking or disease, had an average storage modulus of 756±439 Pa and a loss tangent of 0

  9. Downhill versus barrier-limited folding of BBL 2: mechanistic insights from kinetics of folding monitored by independent tryptophan probes.

    Science.gov (United States)

    Neuweiler, Hannes; Sharpe, Timothy D; Johnson, Christopher M; Teufel, Daniel P; Ferguson, Neil; Fersht, Alan R

    2009-04-10

    Barrier-free downhill folding has been proposed for the peripheral subunit-binding domain BBL. To date, ultrafast kinetic experiments on BBL, which are crucial for a mechanistic understanding of folding, have been hampered by the lack of good intrinsic spectroscopic probes. Here, we present a detailed kinetic characterization of three single-point tryptophan mutants of BBL that have suitable fluorescence properties for following microsecond and nanosecond folding kinetics using temperature jump fluorescence spectroscopy. Experiments were performed at pH 7, which is optimal for stability and minimizes complications that arise from the presence of an alternative native-state conformation of BBL at lower pH. We examined the dependence of rate and equilibrium constants on concentration of denaturant and found that they follow well-established laws allowing kinetic transients to be related to events in folding and compared with equilibrium data. Logarithms of rate constants versus denaturant concentration yielded plots (chevrons) that are characteristic of barrier-limited folding for all mutants investigated, including a truncated sequence that was previously used in the proposal of downhill folding. The thermodynamic quantities calculated from the rate constants were in excellent agreement with those directly determined from equilibrium denaturation based on empirical two-state equations. We found that sequence truncation of BBL as used in studies proposing downhill folding leads to a large loss in helical content and protein stability, which were exacerbated at the low pH used in those studies. The kinetics and equilibria of folding of BBL fit to conventional barrier-limited kinetics.

  10. To Index or Not To Index.

    Science.gov (United States)

    Veenema, Fred

    1996-01-01

    Describes an experiment comparing the performance of an automatic full-text indexing software for personal computers (i.e., the Quick-Finder facility in WordPerfect 6.1 for Windows) with the human intellectual assignment of indexing terms to each document in a collection. Results are discussed in terms of ease of use, the time factor, and recall…

  11. Structural Analysis of Protein Folding by the Long-Chain Archaeal Chaperone FKBP26

    Energy Technology Data Exchange (ETDEWEB)

    E Martinez-Hackert; W Hendrickson

    2011-12-31

    In the cell, protein folding is mediated by folding catalysts and chaperones. The two functions are often linked, especially when the catalytic module forms part of a multidomain protein, as in Methanococcus jannaschii peptidyl-prolyl cis/trans isomerase FKBP26. Here, we show that FKBP26 chaperone activity requires both a 50-residue insertion in the catalytic FKBP domain, also called 'Insert-in-Flap' or IF domain, and an 80-residue C-terminal domain. We determined FKBP26 structures from four crystal forms and analyzed chaperone domains in light of their ability to mediate protein-protein interactions. FKBP26 is a crescent-shaped homodimer. We reason that folding proteins are bound inside the large crescent cleft, thus enabling their access to inward-facing peptidyl-prolyl cis/trans isomerase catalytic sites and ipsilateral chaperone domain surfaces. As these chaperone surfaces participate extensively in crystal lattice contacts, we speculate that the observed lattice contacts reflect a proclivity for protein associations and represent substrate interactions by FKBP26 chaperone domains. Finally, we find that FKBP26 is an exceptionally flexible molecule, suggesting a mechanism for nonspecific substrate recognition.

  12. The nature of folded states of globular proteins.

    Science.gov (United States)

    Honeycutt, J D; Thirumalai, D

    1992-06-01

    We suggest, using dynamical simulations of a simple heteropolymer modelling the alpha-carbon sequence in a protein, that generically the folded states of globular proteins correspond to statistically well-defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several free energy minima separated by barriers of various heights such that the folded conformations of a polypeptide chain in each of the minima have similar structural characteristics but have different energies from one another. The calculated structural characteristics, such as bond angle and dihedral angle distribution functions, are assumed to arise from only those configurations belonging to a given minimum. The validity of this hypothesis is illustrated by simulations of a continuum model of a heteropolymer whose low temperature state is a well-defined beta-barrel structure. The simulations were done using a molecular dynamics algorithm (referred to as the "noisy" molecular dynamics method) containing both friction and noise terms. It is shown that for this model there are several distinct metastable minima in which the structural features are similar. Several new methods of analyzing fluctuations in structures belonging to two distinct minima are introduced. The most notable one is a dynamic measure of compactness that can in principle provide the time required for maximal compactness to be achieved. The analysis shows that for a given metastable state in which the protein has a well-defined folded structure the transition to a state of higher compactness occurs very slowly, lending credence to the notion that the system encounters a late barrier in the process of folding to the most compact structure. The examination of the fluctuations in the structures near the unfolding----folding transition temperature indicates that the transition state for the unfolding to folding process occurs closer to the folded state.

  13. Simulated Reflux Decreases Vocal Fold Epithelial Barrier Resistance

    Science.gov (United States)

    Erickson, Elizabeth; Sivasankar, Mahalakshmi

    2010-01-01

    Objectives/Hypothesis The vocal fold epithelium provides a barrier to the entry of inhaled and systemic challenges. However, the location of the epithelium makes it vulnerable to damage. Past research suggests, but does not directly demonstrate, that exposure to gastric reflux adversely affects the function of the epithelial barrier. Understanding the nature of reflux-induced epithelial barrier dysfunction is necessary to better recognize the mechanisms for vocal fold susceptibility to this disease. Therefore, we examined the effects of physiologically relevant reflux challenges on vocal fold transepithelial resistance and gross epithelial and subepithelial appearance. Study Design Ex vivo, mixed design with between-group and repeated-measures analyses. Methods Healthy, native porcine vocal folds (N = 52) were exposed to physiologically relevant acidic pepsin, acid-only, or pepsin-only challenges and examined with electrophysiology and light microscopy. For all challenges, vocal folds exposed to a neutral pH served as control. Results Acidic pepsin and acid-only challenges, but not pepsin-only or control challenges significantly reduced transepithelial resistance within 30 minutes. Reductions in transepithelial resistance were irreversible. Challenge exposure produced minimal gross changes in vocal fold epithelial or subepithelial appearance as evidenced by light microscopy. Conclusions These findings demonstrate that acidic environments characteristic of gastric reflux compromise epithelial barrier function without gross structural changes. In healthy, native vocal folds, reductions in transepithelial resistance could reflect reflux-related epithelial disruption. These results might guide the development of pharmacologic and therapeutic recommendations for patients with reflux, such as continued acid-suppression therapy and patient antireflux behavioral education. PMID:20564752

  14. Solitons and protein folding: An In Silico experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ilieva, N., E-mail: nevena.ilieva@parallel.bas.bg [Institute of Information and Communication Technologies, Bulgarian Aacademy of Sciences, Sofia (Bulgaria); Dai, J., E-mail: daijing491@gmail.com [School of Physics, Beijing Institute of Technology, Beijing (China); Sieradzan, A., E-mail: adams86@wp.pl [Faculty of Chemistry, University of Gdańsk, Gdańsk (Poland); Niemi, A., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden); LMPT–CNRS, Université de Tours, Tours (France)

    2015-10-28

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

  15. 3D Visualization of Sheath Folds in Roman Marble from Ephesus, Turkey

    Science.gov (United States)

    Wex, Sebastian; Passchier, Cornelis W.; de Kemp, Eric A.; Ilhan, Sinan

    2013-04-01

    Excavation of a palatial 2nd century AD house (Terrace House Two) in the ancient city of Ephesus, Turkey in the 1970s produced 10.313 pieces of colored, folded marble which belonged to 54 marble plates of 1.6 cm thickness that originally covered the walls of the banquet hall of the house. The marble plates were completely reassembled and restored by a team of workers over the last 6 years. The plates were recognized as having been sawn from two separate large blocks of "Cipollino verde", a green mylonitized marble from Karystos on the Island of Euboea, Greece. After restoration, it became clear that all slabs had been placed on the wall in approximately the sequence in which they had been cut off by a Roman stone saw. As a result, the marble plates give a full 3D insight in the folded internal structure of 1m3 block of mylonite. The restoration of the slabs was recognized as a first, unique opportunity for detailed reconstruction of the 3D geometry of m-scale folds in mylonitized marble. Photographs were taken of each slab and used to reconstruct their exact arrangement within the originally quarried blocks. Outlines of layers were digitized and a full 3D reconstruction of the internal structure of the block was created using ArcMap and GOCAD. Fold structures in the block include curtain folds and multilayered sheath folds. Several different layers showing these structures were digitized on the photographs of the slab surfaces and virtually mounted back together within the model of the marble block. Due to the serial sectioning into slabs, with cm-scale spacing, the visualization of the 3D geometry of sheath folds was accomplished with a resolution better than 4 cm. Final assembled 3D images reveal how sheath folds emerge from continuous layers and show their overall consistency as well as a constant hinge line orientation of the fold structures. Observations suggest that a single deformation phase was responsible for the evolution of "Cipollino verde" structures

  16. Strain Hardening and Size Effect in Five-fold Twinned Ag Nanowires.

    Science.gov (United States)

    Narayanan, Sankar; Cheng, Guangming; Zeng, Zhi; Zhu, Yong; Zhu, Ting

    2015-06-10

    Metallic nanowires usually exhibit ultrahigh strength but low tensile ductility owing to their limited strain hardening capability. Here we study the unique strain hardening behavior of the five-fold twinned Ag nanowires by nanomechanical testing and atomistic modeling. In situ tensile tests within a scanning electron microscope revealed strong strain hardening behavior of the five-fold twinned Ag nanowires. Molecular dynamics simulations showed that such strain hardening was critically controlled by twin boundaries and pre-existing defects. Strain hardening was size dependent; thinner nanowires achieved more hardening and higher ductility. The size-dependent strain hardening was found to be caused by the obstruction of surface-nucleated dislocations by twin boundaries. Our work provides mechanistic insights into enhancing the tensile ductility of metallic nanostructures by engineering the internal interfaces and defects.

  17. Form Exploration of Folded Plate Timber Structures based on Performance Criteria

    DEFF Research Database (Denmark)

    Falk, Andreas; Buelow, Peter Von

    2011-01-01

    This paper presents an explorative study on applications of cross-laminated timber (CLT) elements in shell structures. Previous studies of plate tensegrity, folded plate roofs interacting with stabilising steel-based systems and studies inspired by origami show a widening range of possibilities...... to develop timber-based shells. Steadily rising interest in rationality during pre-fabrication, transport and on-site construction in contemporary industrialised production increases the competitiveness of CLT-based elements and systems and the architectural applications are getting more common and more...... experimental. Folded plate structures which are the focus of this paper present several issues of structural importance – potential mechanisms, subdivision of surfaces etc. – and the hereby presented study aims at exploring developed typologies, using computer tools for developed optimisation procedures...

  18. WW domain folding complexity revealed by infrared spectroscopy.

    Science.gov (United States)

    Davis, Caitlin M; Dyer, R Brian

    2014-09-02

    Although the intrinsic tryptophan fluorescence of proteins offers a convenient probe of protein folding, interpretation of the fluorescence spectrum is often difficult because it is sensitive to both global and local changes. Infrared (IR) spectroscopy offers a complementary measure of structural changes involved in protein folding, because it probes changes in the secondary structure of the protein backbone. Here we demonstrate the advantages of using multiple probes, infrared and fluorescence spectroscopy, to study the folding of the FBP28 WW domain. Laser-induced temperature jumps coupled with fluorescence or infrared spectroscopy have been used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding IR bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe three kinetics phases, with the fastest process corresponding to the relaxation kinetics of the turns. In contrast, fluorescence measurements of the wild-type WW domain and tryptophan mutants exhibit single-exponential kinetics with a lifetime that corresponds to the slowest phase observed by infrared spectroscopy. Mutant sequences provide evidence of an intermediate dry molten globule state. The slowest step in the folding of this WW domain is the tight packing of the side chains in the transition from the dry molten globule intermediate to the native structure. This study demonstrates that using multiple complementary probes enhances the interpretation of protein folding dynamics.

  19. Modeling Vocal Fold Intravascular Flow using Synthetic Replicas

    Science.gov (United States)

    Terry, Aaron D.; Ricks, Matthew T.; Thomson, Scott L.

    2017-11-01

    Vocal fold vibration that is induced by air flowing from the lungs is believed to decrease blood flow through the vocal folds. This is important due to the critical role of blood flow in maintaining tissue health. However, the precise mechanical relationships between vocal fold vibration and blood perfusion remain understudied. A platform for studying liquid perfusion in a synthetic, life-size, self-oscillating vocal fold replica has recently been developed. The replicas are fabricated using molded silicone with material properties comparable to those of human vocal fold tissues and that include embedded microchannels through which liquid is perfused. The replicas are mounted on an air flow supply tube to initiate flow-induced vibration. A liquid reservoir is attached to the microchannel to cause liquid to perfuse through replica in the anterior-posterior direction. As replica vibration is initiated and amplitude increases, perfusion flow rate decreases. In this presentation, the replica design will be presented, along with data quantifying the relationships between parameters such as replica vibration amplitude, stiffness, microchannel diameter, and perfusion flow rate. This work was supported by Grant NIDCD R01DC005788 from the National Institutes of Health.

  20. A Case of Diabetic Macular Edema with Prominent Chorioretinal Folds

    Directory of Open Access Journals (Sweden)

    Takaki Sato

    2017-03-01

    Full Text Available Purpose: To report a case of diabetic macular edema with prominent chorioretinal folds. Case Report: This study involved a 55-year-old male with untreated bilateral diabetic retinopathy who had undergone cataract surgery at another clinic. Following that surgery, diabetic macular edema rapidly exacerbated, accentuating marked cystoid macular edema and radial chorioretinal folds in the macula. Investigation of his medical history revealed that in addition to diabetes, he had uncontrolled hypertension and severe diabetic nephropathy. Vitreous surgery was performed on both eyes due to a resistance to a subtenon injection of triamcinolone acetonide or intravitreal injection of an antivascular endothelial growth factor agent. After surgery, the macular edema and chorioretinal folds showed a tendency towards improvement. Thereafter, kidney transplant surgery was performed for renal failure, and a mild tendency of chorioretinal folds was observed. Conclusion: In the case presented in this study, we observed remarkable cystoid macular edema in the fovea centralis and theorize that distortion with the surrounding tissue might have occurred, thus leading to the formation of chorioretinal folds around the macula.

  1. Fold maps and positive topological quantum field theories

    Energy Technology Data Exchange (ETDEWEB)

    Wrazidlo, Dominik Johannes

    2017-04-12

    The notion of positive TFT as coined by Banagl is specified by an axiomatic system based on Atiyah's original axioms for TFTs. By virtue of a general framework that is based on the concept of Eilenberg completeness of semirings from computer science, a positive TFT can be produced rigorously via quantization of systems of fields and action functionals - a process inspired by Feynman's path integral from classical quantum field theory. The purpose of the present dissertation thesis is to investigate a new differential topological invariant for smooth manifolds that arises as the state sum of the fold map TFT, which has been constructed by Banagl as a example of a positive TFT. By eliminating an internal technical assumption on the fields of the fold map TFT, we are able to express the informational content of the state sum in terms of an extension problem for fold maps from cobordisms into the plane. Next, we use the general theory of generic smooth maps into the plane to improve known results about the structure of the state sum in arbitrary dimensions, and to determine it completely in dimension two. The aggregate invariant of a homotopy sphere, which is derived from the state sum, naturally leads us to define a filtration of the group of homotopy spheres in order to understand the role of indefinite fold lines beyond a theorem of Saeki. As an application, we show how Kervaire spheres can be characterized by indefinite fold lines in certain dimensions.

  2. Creating a placental inflammatory composite index that has a high prognostic relevance to child morbidity.

    Science.gov (United States)

    Chen, Yan; Zou, Lile; Zhao, Yanjun; Wu, Ting; Ye, Jiangfeng; Zhang, Huijuan; Zhang, Jun

    2017-07-01

    Selecting pathologic measures of placental inflammation that affect pregnancy and childhood health is largely empirical. We aimed to systematically select several core inflammation-related placental measures to construct a novel placental inflammatory evaluation criterion with a high prognostic relevance to child morbidity. We used data from the US Collaborative Perinatal Project (1959-1976), a longitudinal birth cohort study that recruited women during pregnancy and followed the children until 7 years of age. Bootstrap resampling, least absolute shrinkage and selection operator, and receiver-operator curve were used to select placental pathologic measures that were closely related to child morbidity to form a placental inflammatory composite index. Twenty-six candidate placental inflammation-related measures were ranked based on their close association with adverse neonatal outcomes. The top five placental measures were: (i) neutrophilic infiltration in umbilical artery; (ii) placental weight-birthweight ratio; (iii) necrosis in decidua capsularis; (iv) bacterial colony in epithelium of amnion; and (v) opacity of membranes and fetal surface. Several composite indexes were constructed. A five-measure composite index that had the highest prognostic relevance was chosen. Compared with subjects without any of the five abnormal measures, those with any lesion ranging from 1 to 5 had a 1.2- to 4.6-fold risk of adverse child outcomes, respectively. Our composite index is simple, evidence-based, and has predictive value for child morbidity. It may be used as a novel placental inflammatory evaluation criterion. © 2017 Japan Society of Obstetrics and Gynecology.

  3. Analysis in indexing

    DEFF Research Database (Denmark)

    Mai, Jens Erik

    2005-01-01

    The paper discusses the notion of steps in indexing and reveals that the document-centered approach to indexing is prevalent and argues that the document-centered approach is problematic because it blocks out context-dependent factors in the indexing process. A domain-centered approach to indexing...... is presented as an alternative and the paper discusses how this approach includes a broader range of analyses and how it requires a new set of actions from using this approach; analysis of the domain, users and indexers. The paper concludes that the two-step procedure to indexing is insufficient to explain...

  4. Supersymmetry and index theory

    International Nuclear Information System (INIS)

    Alvarez-Gaume, L.

    1985-01-01

    The author presents information mainly concerned with the fact that many of the ingredients and results in index theory have very simple analogs in supersymmetric quantum mechanical systems so that using elementary quantum mechanics one can obtain new proofs of the Atiyah-Singer index theorem and related results. Simple ideas on index theorems and characteristic classes are reviewed; simple results on fermion functional integrals are outlined; supersymmetric quantum mechanical systems which appear naturally in dealing with index problems are analyzed; proof of the classical index theorem is presented; the character valued index theorem is derived; and applications of the methods developed here for the computation of anomalies are presented

  5. Active Flexural-Slip Faulting: Controls Exerted by Stratigraphy, Geometry, and Fold Kinematics

    Science.gov (United States)

    Li, Tao; Chen, Jie; Thompson Jobe, Jessica A.; Burbank, Douglas W.

    2017-10-01

    Flexural slip plays an important role in accommodating fold growth, and its topographic expression, flexural-slip fault (FSF) scarps, may be one of the most commonly occurring secondary structures in areas dominated by active thrusts and folds. Where FSF scarps are present and what factors control their occurrence, however, are typically poorly known. Through an investigation of clearly expressed FSF scarps, well-preserved fluvial terraces, and well-exposed bedrock at eight sites in the Pamir-Tian Shan convergent zone and Kuche fold belt, NW China, we summarize the most favorable conditions for active flexural-slip faulting. Our study yields six key results. First, flexural slip operates commonly in well-layered beds, although uncommonly can occur in massive, poorly layered beds as well. Second, in well-layered beds, the slip surface is commonly located either (a) close to the contact of competent and incompetent beds or (b) within thin incompetent beds. Third, FSF scarps are always found overlying steep beds with dips of 30-100°. Fourth, slip surfaces are typically spaced between 10 and 440 m but can reach up to 600 m. Fifth, FSF scarps at most sites can be observed far away from the hinge-migrated fold scarps, suggesting that compared to hinge migration, limb rotation is generally required to accumulate flexural slip and produce associated topographic scarps. Finally, a higher regional convergent rate seems to facilitate the creation of FSF scarps more often than lower rates, whereas well-preserved, old terraces capped by thin deposits are more likely to record FSF scarps than unevenly preserved, young terraces with thick sedimentary caps.

  6. Folding wings like a cockroach: a review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania.

    Directory of Open Access Journals (Sweden)

    István Mikó

    Full Text Available We revise two relatively rare ensign wasp genera, whose species are restricted to Sub-Saharan Africa: Afrevania and Trissevania. Afrevania longipetiolata sp. nov., Trissevania heatherae sp. nov., T. hugoi sp. nov., T. mrimaensis sp. nov. and T. slideri sp. nov. are described, males and females of T. anemotis and Afrevania leroyi are redescribed, and an identification key for Trissevaniini is provided. We argue that Trissevania mrimaensis sp. nov. and T. heatherae sp. nov. populations are vulnerable, given their limited distributions and threats from mining activities in Kenya. We hypothesize that these taxa together comprise a monophyletic lineage, Trissevaniini, tr. nov., the members of which share the ability to fold their fore wings along two intersecting fold lines. Although wing folding of this type has been described for the hind wing of some insects four-plane wing folding of the fore wing has never been documented. The wing folding mechanism and the pattern of wing folds of Trissevaniini is shared only with some cockroach species (Blattodea. It is an interesting coincidence that all evaniids are predators of cockroach eggs. The major wing fold lines of Trissevaniini likely are not homologous to any known longitudinal anatomical structures on the wings of other Evaniidae. Members of the new tribe share the presence of a coupling mechanism between the fore wing and the mesosoma that is composed of a setal patch on the mesosoma and the retinaculum of the fore wing. While the setal patch is an evolutionary novelty, the retinaculum, which originally evolved to facilitate fore and hind wing coupling in Hymenoptera, exemplifies morphological exaptation. We also refine and clarify the Semantic Phenotype approach used in previous taxonomic revisions and explore the consequences of merging new with existing data. The way that semantic statements are formulated can evolve in parallel, alongside improvements to the ontologies themselves.

  7. Vocal Fold Injection: Review of Indications, Techniques, and Materials for Augmentation

    OpenAIRE

    Mallur, Pavan S.; Rosen, Clark A.

    2010-01-01

    Vocal fold injection is a procedure that has over a 100 year history but was rarely done as short as 20 years ago. A renaissance has occurred with respect to vocal fold injection due to new technologies (visualization and materials) and new injection approaches. Awake, un-sedated vocal fold injection offers many distinct advantages for the treatment of glottal insufficiency (vocal fold paralysis, vocal fold paresis, vocal fold atrophy and vocal fold scar). A review of materials available and ...

  8. IMPAIRED MOBILITY OF VOCAL FOLDS - etiology and symptoms

    Directory of Open Access Journals (Sweden)

    Karlo Pintarić

    2015-06-01

    Full Text Available Paresis or paralysis of one or both vocal cords affects some significant aspects of a human life: breathing, swallowing and speech. The major causes for reduced mobility or even immobility are innervation damage, less often fixation of vocal cord or impaired mobility of crycoarytenoid joint. An injury of the superior or/and inferior laryngeal nerve can be a consequence of different medical procedures, tumor growth, trauma, infection, neurological disorders, radiation exposure, toxic damage, impaired circulation of the area or it is idiopathic. The symptoms are different in the case of unilateral and bilateral paresis of the vocal folds. They also depend on the cause for the impaired mobility. In the patients with unilateral vocal fold paresis, hoarseness and aspiration during swallowing are the leading symptoms. In the bilateral vocal fold paralysis, dyspnea prevails. 

  9. Functional stimuli responsive hydrogel devices by self-folding

    International Nuclear Information System (INIS)

    Yoon, ChangKyu; Xiao, Rui; Nguyen, Thao D; Park, JaeHyun; Gracias, David H; Cha, Jaepyeong

    2014-01-01

    We describe a photolithographic approach to create functional stimuli responsive, self-folding, microscale hydrogel devices using thin, gradient cross-linked hinges and thick, fully cross-linked panels. The hydrogels are composed of poly (N-isopropylacrylamide-co-acrylic acid) (pNIPAM-AAc) with reversible stimuli responsive properties just below physiological temperatures. We show that a variety of three-dimensional structures can be formed and reversibly actuated by temperature or pH. We experimentally characterized the swelling and mechanical properties of pNIPAM-AAc and developed a finite element model to rationalize self-folding and its variation with hinge thickness and swelling ratio. Finally, we highlight applications of this approach in the creation of functional devices such as self-folding polymeric micro-capsules, untethered micro-grippers and thermally steered micro-mirror systems. (paper)

  10. Lymphotactin: How a protein can adopt two folds

    Science.gov (United States)

    Camilloni, Carlo; Sutto, Ludovico

    2009-12-01

    Metamorphic proteins such as lymphotactin are a notable exception of the empirical principle that structured natural proteins possess a unique three-dimensional structure. In particular, the human chemokine lymphotactin protein exists in two distinct conformations (one monomeric and one dimeric) under physiological conditions. In this work, we use a Cα Go¯ model to show how this very peculiar behavior can be reproduced. From the study of the thermodynamics and of the kinetics, we characterize the interconversion mechanism. In particular, this takes place through the docking of the two chains living in a third monomeric, partially unfolded, state which shows a residual structure involving a set of local contacts common to the two native conformations. The main feature of two fold proteins appears to be the sharing of a common set of local contacts between the two distinct folds as confirmed by the study of two designed two fold proteins. Metamorphic proteins may be more common than expected.

  11. The use of folding structures in fusion reactors

    International Nuclear Information System (INIS)

    Haines, T.

    1992-01-01

    Folding structures can be used with advantage in fusion machines. They have been used in Space for decades to extend antennas, sensors and solar panels; terrestrial versions have been used as retractable antennas and antennas masts. They have also been used in the Joint European Torus (JET) and other nuclear applications. In this paper, three types are described, together with concepts for use in fusion machines. The Storable Tubular Extendible Member (STEM) was conceived by the National Research Council of Canada and developed by Spar Aerospace Limited. The Astromast is a folding truss developed by Astro Aerospace Corporation, a US subsidiary of Spar. The X-Beam is an ultra-stiff folding truss

  12. A biomorphic origami actuator fabricated by folding a conducting paper

    International Nuclear Information System (INIS)

    Okuzaki, H; Saido, T; Suzuki, H; Hara, Y; Yan, H

    2008-01-01

    Cooperation between the electrical conductivity and hygroscopic nature of conducting polymers can provide an insight into the development of a new class of electro-active polymer (EAP) actuators or soft robots working in ambient air. In this paper, we describe an 'origami' actuator fabricated by folding a sheet of conducting 'paper'. The principle lies in the electrically induced changes in the elastic modulus of a humidosensitive conducting polymer film through reversible sorption and desorption of water vapor molecules, which is responsible for amplifying a contraction of the film (∼ 1%) to more than a 100-fold expansion (> 100%) of the origami actuator. Utilizing the origami technique, we have fabricated a biomorphic origami robot by folding an electrochemically synthesized polypyrrole film into the figure of an accordion shape, which can move with a caterpillar-like motion by repeated expansion and contraction at a velocity of 2 cm min -1 .

  13. Intraoperative handheld probe for 3D imaging of pediatric benign vocal fold lesions using optical coherence tomography (Conference Presentation)

    Science.gov (United States)

    Benboujja, Fouzi; Garcia, Jordan; Beaudette, Kathy; Strupler, Mathias; Hartnick, Christopher J.; Boudoux, Caroline

    2016-02-01

    Excessive and repetitive force applied on vocal fold tissue can induce benign vocal fold lesions. Children affected suffer from chronic hoarseness. In this instance, the vibratory ability of the folds, a complex layered microanatomy, becomes impaired. Histological findings have shown that lesions produce a remodeling of sup-epithelial vocal fold layers. However, our understanding of lesion features and development is still limited. Indeed, conventional imaging techniques do not allow a non-invasive assessment of sub-epithelial integrity of the vocal fold. Furthermore, it remains challenging to differentiate these sub-epithelial lesions (such as bilateral nodules, polyps and cysts) from a clinical perspective, as their outer surfaces are relatively similar. As treatment strategy differs for each lesion type, it is critical to efficiently differentiate sub-epithelial alterations involved in benign lesions. In this study, we developed an optical coherence tomography (OCT) based handheld probe suitable for pediatric laryngological imaging. The probe allows for rapid three-dimensional imaging of vocal fold lesions. The system is adapted to allow for high-resolution intra-operative imaging. We imaged 20 patients undergoing direct laryngoscopy during which we looked at different benign pediatric pathologies such as bilateral nodules, cysts and laryngeal papillomatosis and compared them to healthy tissue. We qualitatively and quantitatively characterized laryngeal pathologies and demonstrated the added advantage of using 3D OCT imaging for lesion discrimination and margin assessment. OCT evaluation of the integrity of the vocal cord could yield to a better pediatric management of laryngeal diseases.

  14. Protein folding: understanding the role of water and the low Reynolds number environment as the peptide chain emerges from the ribosome and folds.

    Science.gov (United States)

    Sen, Siddhartha; Voorheis, H Paul

    2014-12-21

    The mechanism of protein folding during early stages of the process has three determinants. First, moving water molecules obey the rules of low Reynolds number physics without an inertial component. Molecular movement is instantaneous and size insensitive. Proteins emerging from the ribosome move and rotate without an external force if they change shape, forming and propagating helical structures that increases translocational efficiency. Forward motion ceases when the shape change or propelling force ceases. Second, application of quantum field theory to water structure predicts the spontaneous formation of low density coherent units of fixed size that expel dissolved atmospheric gases. Structured water layers with both coherent and non-coherent domains, form a sheath around the new protein. The surface of exposed hydrophobic amino acids is protected from water contact by small nanobubbles of dissolved atmospheric gases, 5 or 6 molecules on average, that vibrate, attracting even widely separated resonating nanobubbles. This force results from quantum effects, appearing only when the system is within and interacts with an oscillating electromagnetic field. The newly recognized quantum force sharply bends the peptide and is part of a dynamic field determining the pathway of protein folding. Third, the force initiating the tertiary folding of proteins arises from twists at the position of each hydrophobic amino acid, that minimizes surface exposure of the hydrophobic amino acids and propagates along the protein. When the total bend reaches 360°, the leading segment of water sheath intersects the trailing segment. This steric self-intersection expels water from overlapping segments of the sheath and by Newton׳s second law moves the polypeptide chain in an opposite direction. Consequently, with very few exceptions that we enumerate and discuss, tertiary structures are absent from proteins without hydrophobic amino acids, which control the early stages of protein

  15. Compression induced folding of a sheet: an integrable system.

    Science.gov (United States)

    Diamant, Haim; Witten, Thomas A

    2011-10-14

    The apparently intractable shape of a fold in a compressed elastic film lying on a fluid substrate is found to have an exact solution. Such systems buckle at a nonzero wave vector set by the bending stiffness of the film and the weight of the substrate fluid. Our solution describes the entire progression from a weakly displaced sinusoidal buckling to a single large fold that contacts itself. The pressure decrease is exactly quadratic in the lateral displacement. We identify a complex wave vector whose magnitude remains invariant with compression.

  16. Fabrication of ten-fold photonic quasicrystalline structures

    Directory of Open Access Journals (Sweden)

    XiaoHong Sun

    2015-05-01

    Full Text Available Compared to periodic crystals, quasicrystals have higher point group symmetry and are more favorable in achieving complete band-gaps. In this report, a top-cut prism interferometer is designed to fabricate ten-fold photonic quasicrystalline structures. By optimizing the exposing conditions and material characteristics, appropriate quasicrystals have been obtained in the SU8 photoresist films. Atomic Force Microscopy and laser diffraction are used to characterize the fabricated structures. The measurement results show the consistence between the theoretical design and experiments. This will provide guidance for the large-area and fast production of ten-fold quasicrystalline structures with high quality.

  17. Protein folding and the organization of the protein topology universe

    DEFF Research Database (Denmark)

    Lindorff-Larsen,, Kresten; Røgen, Peter; Paci, Emanuele

    2005-01-01

    such ensembles have now been analysed for a series of proteins using data from a combination of biochemical and biophysical experiments together with computer-simulation methods. These studies show that the topology of the transition state is determined by a set of interactions involving a small number of key...... of protein folds that is based on the topological features of the polypeptide backbone, rather than the conventional view that depends on the arrangement of different types of secondary-structure elements. By linking the folding process to the organization of the protein structure universe, we propose...

  18. A folding algorithm for extended RNA secondary structures.

    Science.gov (United States)

    Höner zu Siederdissen, Christian; Bernhart, Stephan H; Stadler, Peter F; Hofacker, Ivo L

    2011-07-01

    RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction. All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.

  19. Folded MoS2 layers with reduced interlayer coupling

    OpenAIRE

    Castellanos-Gomez, Andres; van der Zant, Herre S. J.; Steele, Gary A.

    2013-01-01

    We study molybdenum disulfide (MoS2) structures generated by folding single- and bilayer MoS2 flakes. We find that this modified layer stacking leads to a decrease in the interlayer coupling and an enhancement of the photoluminescence emission yield. We additionally find that folded single-layer MoS2 structures show a contribution to photoluminescence spectra of both neutral and charged excitons, which is a characteristic feature of single-layer MoS2 that has not been observed in multilayer M...

  20. Western Alaska ESI: INDEX (Index Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains vector polygons representing the boundaries of all the hardcopy cartographic products produced as part of the Environmental Sensitivity Index...