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Sample records for protein backbone torsion

  1. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

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

    2013-07-15

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

  2. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2007-01-01

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ 1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ 1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C', respectively, including outliers

  3. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

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

    2009-08-15

    NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between {sup 13}C, {sup 15}N and {sup 1}H chemical shifts and backbone torsion angles {phi} and {psi} (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted {phi} and {psi} angles, equals {+-}13{sup o}. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.

  4. Assignment of protein backbone resonances using connectivity, torsion angles and 13Cα chemical shifts

    International Nuclear Information System (INIS)

    Morris, Laura C.; Valafar, Homayoun; Prestegard, James H.

    2004-01-01

    A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just 13 C α chemical shifts (δ( 13 C α )) and data restricting the φ and ψ backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in δ( 13 C α ), φ, and ψ space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and 13 C α chemical shift data are available

  5. MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data

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    Mantsyzov, Alexey B. [M.V. Lomonosov Moscow State University, Faculty of Fundamental Medicine (Russian Federation); Shen, Yang; Lee, Jung Ho [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Hummer, Gerhard [Max Planck Institute of Biophysics (Germany); Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2015-09-15

    MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts ({sup 15}N, {sup 13}C{sup α}, and {sup 13}C′), six types of J couplings ({sup 3}J{sub HNHα}, {sup 3}J{sub C′C′}, {sup 3}J{sub C′Hα}, {sup 1}J{sub HαCα}, {sup 2}J{sub CαN} and {sup 1}J{sub CαN}), as well as the {sup 15}N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3.

  6. Deep learning methods for protein torsion angle prediction.

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    Li, Haiou; Hou, Jie; Adhikari, Badri; Lyu, Qiang; Cheng, Jianlin

    2017-09-18

    Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012, it has achieved success in a number of areas such as protein residue-residue contact prediction, secondary structure prediction, and fold recognition. In this work, we developed deep learning methods to improve the prediction of torsion (dihedral) angles of proteins. We design four different deep learning architectures to predict protein torsion angles. The architectures including deep neural network (DNN) and deep restricted Boltzmann machine (DRBN), deep recurrent neural network (DRNN) and deep recurrent restricted Boltzmann machine (DReRBM) since the protein torsion angle prediction is a sequence related problem. In addition to existing protein features, two new features (predicted residue contact number and the error distribution of torsion angles extracted from sequence fragments) are used as input to each of the four deep learning architectures to predict phi and psi angles of protein backbone. The mean absolute error (MAE) of phi and psi angles predicted by DRNN, DReRBM, DRBM and DNN is about 20-21° and 29-30° on an independent dataset. The MAE of phi angle is comparable to the existing methods, but the MAE of psi angle is 29°, 2° lower than the existing methods. On the latest CASP12 targets, our methods also achieved the performance better than or comparable to a state-of-the art method. Our experiment demonstrates that deep learning is a valuable method for predicting protein torsion angles. The deep recurrent network architecture performs slightly better than deep feed-forward architecture, and the predicted residue contact number and the error distribution of torsion angles extracted from sequence fragments are useful features for improving prediction accuracy.

  7. Mars - robust automatic backbone assignment of proteins

    International Nuclear Information System (INIS)

    Jung, Young-Sang; Zweckstetter, Markus

    2004-01-01

    MARS a program for robust automatic backbone assignment of 13 C/ 15 N labeled proteins is presented. MARS does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds and it can work with a wide variety of NMR experiments. Using only 13 C α / 13 C β connectivity information, MARS allows automatic, error-free assignment of 96% of the 370-residue maltose-binding protein. MARS can successfully be used when data are missing for a substantial portion of residues or for proteins with very high chemical shift degeneracy such as partially or fully unfolded proteins. Other sources of information, such as residue specific information or known assignments from a homologues protein, can be included into the assignment process. MARS exports its result in SPARKY format. This allows visual validation and integration of automated and manual assignment

  8. Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

    Directory of Open Access Journals (Sweden)

    Bordner Andrew J

    2010-04-01

    Full Text Available Abstract Background Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However, backbone-only scoring functions do not require computationally intensive structure optimization and so are well suited to protein design, which requires fast score evaluation. Furthermore, scoring functions that account for the distinctive relative position and orientation preferences of residue pairs are expected to be more accurate than those that depend only on the separation distance. Results Residue pair scoring functions for fixed backbone protein design were derived using only backbone geometry. Unlike previous studies that used spherical harmonics to fit 2D angular distributions, Gaussian Mixture Models were used to fit the full 3D (position only and 6D (position and orientation distributions of residue pairs. The performance of the 1D (residue separation only, 3D, and 6D scoring functions were compared by their ability to identify correct threading solutions for a non-redundant benchmark set of protein backbone structures. The threading accuracy was found to steadily increase with increasing dimension, with the 6D scoring function achieving the highest accuracy. Furthermore, the 3D and 6D scoring functions were shown to outperform side chain-dependent empirical potentials from three other studies. Next, two computational methods that take advantage of the speed and pairwise form of these new backbone-only scoring functions were investigated. The first is a procedure that exploits available sequence data by averaging scores over threading solutions for homologs. This was evaluated by applying it to the challenging problem of identifying interacting transmembrane alpha-helices and found to further improve prediction accuracy. The second is a protein design method for determining the optimal sequence for a backbone structure by applying Belief Propagation

  9. Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure.

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    Li, Tao; Li, Qian-Zhong

    2012-11-07

    RNA-protein interactions play important roles in various biological processes. The precise detection of RNA-protein interaction sites is very important for understanding essential biological processes and annotating the function of the proteins. In this study, based on various features from amino acid sequence and structure, including evolutionary information, solvent accessible surface area and torsion angles (φ, ψ) in the backbone structure of the polypeptide chain, a computational method for predicting RNA-binding sites in proteins is proposed. When the method is applied to predict RNA-binding sites in three datasets: RBP86 containing 86 protein chains, RBP107 containing 107 proteins chains and RBP109 containing 109 proteins chains, better sensitivities and specificities are obtained compared to previously published methods in five-fold cross-validation tests. In order to make further examination for the efficiency of our method, the RBP107 dataset is used as training set, RBP86 and RBP109 datasets are used as the independent test sets. In addition, as examples of our prediction, RNA-binding sites in a few proteins are presented. The annotated results are consistent with the PDB annotation. These results show that our method is useful for annotating RNA binding sites of novel proteins.

  10. High-resolution protein design with backbone freedom.

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    Harbury, P B; Plecs, J J; Tidor, B; Alber, T; Kim, P S

    1998-11-20

    Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.

  11. Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

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    Zhang, Qian; Xu, Zhijian; Shi, Jiye; Zhu, Weiliang

    2017-07-24

    Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (R F ) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too. Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 Å resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.

  12. Backbone dynamics of the EIAV-Tat protein from 15N relaxation studies

    International Nuclear Information System (INIS)

    Ejchart, A.; Herrmann, F.; Roesch, P.; Sticht, H.; Willbold, D.

    1994-01-01

    The work investigates the mobility of EIAV-Tat protein backbone by measuring the relaxation parameters of the 15 N nitrogens. High degree of the flexibility, non-typical of rigid, well structured proteins was shown

  13. Determination of protein global folds using backbone residual dipolar coupling and long-range NOE restraints

    International Nuclear Information System (INIS)

    Giesen, Alexander W.; Homans, Steve W.; Brown, Jonathan Miles

    2003-01-01

    We report the determination of the global fold of human ubiquitin using protein backbone NMR residual dipolar coupling and long-range nuclear Overhauser effect (NOE) data as conformational restraints. Specifically, by use of a maximum of three backbone residual dipolar couplings per residue (N i -H N i , N i -C' i-1 , H N i - C' i-1 ) in two tensor frames and only backbone H N -H N NOEs, a global fold of ubiquitin can be derived with a backbone root-mean-square deviation of 1.4 A with respect to the crystal structure. This degree of accuracy is more than adequate for use in databases of structural motifs, and suggests a general approach for the determination of protein global folds using conformational restraints derived only from backbone atoms

  14. Selective backbone labelling of ILV methyl labelled proteins

    International Nuclear Information System (INIS)

    Sibille, Nathalie; Hanoulle, Xavier; Bonachera, Fanny; Verdegem, Dries; Landrieu, Isabelle; Wieruszeski, Jean-Michel; Lippens, Guy

    2009-01-01

    Adding the 13 C labelled 2-keto-isovalerate and 2-oxobutanoate precursors to a minimal medium composed of 12 C labelled glucose instead of the commonly used ( 2 D, 13 C) glucose leads not only to the 13 C labelling of (I, L, V) methyls but also to the selective 13 C labelling of the backbone C α and CO carbons of the Ile and Val residues. As a result, the backbone ( 1 H, 15 N) correlations of the Ile and Val residues and their next neighbours in the (i + 1) position can be selectively identified in HN(CA) and HN(CO) planes. The availability of a selective HSQC spectrum corresponding to the sole amide resonances of the Ile and Val residues allows connecting them to their corresponding methyls by the intra-residue NOE effect, and should therefore be applicable to larger systems

  15. Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

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    Colin A Smith

    Full Text Available Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface, interactions between and within parts of the structure (e.g. domains can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

  16. Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

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    Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

    2016-02-01

    Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.

  17. Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy

    International Nuclear Information System (INIS)

    Lopez del Amo, Juan-Miguel; Fink, Uwe; Reif, Bernd

    2010-01-01

    We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual 15 N-T 1 timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5 s -1 . Backbone amide 15 N longitudinal relaxation times that we determined previously are not significantly affected for most residues, yielding no systematic artifacts upon quantification of backbone dynamics (Chevelkov et al. 2008b). Significant exchange was observed for the backbone amides of R21, S36 and K60, as well as for the sidechain amides of N38, N35 and for W41ε. These residues could not be fit in our previous motional analysis, demonstrating that amide proton chemical exchange needs to be considered in the analysis of protein dynamics in the solid-state, in case D 2 O is employed as a solvent for sample preparation. Due to the intrinsically long 15 N relaxation times in the solid-state, the approach proposed here can expand the range of accessible HDX rates in the intermediate regime that is not accessible so far with exchange quench and MEXICO type experiments.

  18. Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling

    International Nuclear Information System (INIS)

    Knight, Jennifer L.; Zhou, Zhiyong; Gallicchio, Emilio; Himmel, Daniel M.; Friesner, Richard A.; Arnold, Eddy; Levy, Ronald M.

    2008-01-01

    Torsion-angle sampling, as implemented in the Protein Local Optimization Program (PLOP), is used to generate multiple structurally variable single-conformer models which are in good agreement with X-ray data. An ensemble-refinement approach to differentiate between positional uncertainty and conformational heterogeneity is proposed. Modeling structural variability is critical for understanding protein function and for modeling reliable targets for in silico docking experiments. Because of the time-intensive nature of manual X-ray crystallographic refinement, automated refinement methods that thoroughly explore conformational space are essential for the systematic construction of structurally variable models. Using five proteins spanning resolutions of 1.0–2.8 Å, it is demonstrated how torsion-angle sampling of backbone and side-chain libraries with filtering against both the chemical energy, using a modern effective potential, and the electron density, coupled with minimization of a reciprocal-space X-ray target function, can generate multiple structurally variable models which fit the X-ray data well. Torsion-angle sampling as implemented in the Protein Local Optimization Program (PLOP) has been used in this work. Models with the lowest R free values are obtained when electrostatic and implicit solvation terms are included in the effective potential. HIV-1 protease, calmodulin and SUMO-conjugating enzyme illustrate how variability in the ensemble of structures captures structural variability that is observed across multiple crystal structures and is linked to functional flexibility at hinge regions and binding interfaces. An ensemble-refinement procedure is proposed to differentiate between variability that is a consequence of physical conformational heterogeneity and that which reflects uncertainty in the atomic coordinates

  19. Automated backbone assignment of labeled proteins using the threshold accepting algorithm

    International Nuclear Information System (INIS)

    Leutner, Michael; Gschwind, Ruth M.; Liermann, Jens; Schwarz, Christian; Gemmecker, Gerd; Kessler, Horst

    1998-01-01

    The sequential assignment of backbone resonances is the first step in the structure determination of proteins by heteronuclear NMR. For larger proteins, an assignment strategy based on proton side-chain information is no longer suitable for the use in an automated procedure. Our program PASTA (Protein ASsignment by Threshold Accepting) is therefore designed to partially or fully automate the sequential assignment of proteins, based on the analysis of NMR backbone resonances plus C β information. In order to overcome the problems caused by peak overlap and missing signals in an automated assignment process, PASTA uses threshold accepting, a combinatorial optimization strategy, which is superior to simulated annealing due to generally faster convergence and better solutions. The reliability of this algorithm is shown by reproducing the complete sequential backbone assignment of several proteins from published NMR data. The robustness of the algorithm against misassigned signals, noise, spectral overlap and missing peaks is shown by repeating the assignment with reduced sequential information and increased chemical shift tolerances. The performance of the program on real data is finally demonstrated with automatically picked peak lists of human nonpancreatic synovial phospholipase A 2 , a protein with 124 residues

  20. On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

    Science.gov (United States)

    Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

    2015-05-01

    Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. © 2015 Wiley Periodicals, Inc.

  1. Protein backbone angle restraints from searching a database for chemical shift and sequence homology

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    Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    1999-03-15

    Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C{alpha}, 13C{beta}, 13C', 1H{alpha} and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar {phi} and {psi} backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 deg. Approximately 3% of the predictions made by TALOS are found to be in error.

  2. Structural test of the parameterized-backbone method for protein design.

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    Plecs, Joseph J; Harbury, Pehr B; Kim, Peter S; Alber, Tom

    2004-09-03

    Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families of structures. We report the crystal structure of RH3, a right-handed, three-helix coiled coil that was designed using a parameterized backbone and detailed modeling of core packing. This crystal structure was determined using another rationally designed feature, a metal-binding site that permitted experimental phasing of the X-ray data. RH3 adopted the intended fold, which has not been observed previously in biological proteins. Unanticipated structural asymmetry in the trimer was a principal source of variation within the RH3 structure. The sequence of RH3 differs from that of a previously characterized right-handed tetramer, RH4, at only one position in each 11 amino acid sequence repeat. This close similarity indicates that the design method is sensitive to the core packing interactions that specify the protein structure. Comparison of the structures of RH3 and RH4 indicates that both steric overlap and cavity formation provide strong driving forces for oligomer specificity.

  3. Prediction of backbone dihedral angles and protein secondary structure using support vector machines

    Directory of Open Access Journals (Sweden)

    Hirst Jonathan D

    2009-12-01

    Full Text Available Abstract Background The prediction of the secondary structure of a protein is a critical step in the prediction of its tertiary structure and, potentially, its function. Moreover, the backbone dihedral angles, highly correlated with secondary structures, provide crucial information about the local three-dimensional structure. Results We predict independently both the secondary structure and the backbone dihedral angles and combine the results in a loop to enhance each prediction reciprocally. Support vector machines, a state-of-the-art supervised classification technique, achieve secondary structure predictive accuracy of 80% on a non-redundant set of 513 proteins, significantly higher than other methods on the same dataset. The dihedral angle space is divided into a number of regions using two unsupervised clustering techniques in order to predict the region in which a new residue belongs. The performance of our method is comparable to, and in some cases more accurate than, other multi-class dihedral prediction methods. Conclusions We have created an accurate predictor of backbone dihedral angles and secondary structure. Our method, called DISSPred, is available online at http://comp.chem.nottingham.ac.uk/disspred/.

  4. Correlation between protein secondary structure, backbone bond angles, and side-chain orientations

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    Lundgren, Martin; Niemi, Antti J.

    2012-08-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central Cα carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the Cβ carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the Cα-Cβ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

  5. Hidden Markov model approach for identifying the modular framework of the protein backbone.

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    Camproux, A C; Tuffery, P; Chevrolat, J P; Boisvieux, J F; Hazout, S

    1999-12-01

    The hidden Markov model (HMM) was used to identify recurrent short 3D structural building blocks (SBBs) describing protein backbones, independently of any a priori knowledge. Polypeptide chains are decomposed into a series of short segments defined by their inter-alpha-carbon distances. Basically, the model takes into account the sequentiality of the observed segments and assumes that each one corresponds to one of several possible SBBs. Fitting the model to a database of non-redundant proteins allowed us to decode proteins in terms of 12 distinct SBBs with different roles in protein structure. Some SBBs correspond to classical regular secondary structures. Others correspond to a significant subdivision of their bounding regions previously considered to be a single pattern. The major contribution of the HMM is that this model implicitly takes into account the sequential connections between SBBs and thus describes the most probable pathways by which the blocks are connected to form the framework of the protein structures. Validation of the SBBs code was performed by extracting SBB series repeated in recoding proteins and examining their structural similarities. Preliminary results on the sequence specificity of SBBs suggest promising perspectives for the prediction of SBBs or series of SBBs from the protein sequences.

  6. On the purported "backbone fluorescence" in protein three-dimensional fluorescence spectra

    DEFF Research Database (Denmark)

    Bortolotti, Annalisa; Wong, Yin How; Korsholm, Stine S.

    2016-01-01

    In this study, several proteins (albumin, lysozyme, insulin) and model compounds (Trp, Tyr, homopolypeptides) were used to demonstrate the origin of the fluorescence observed upon their excitation at 220-230 nm. In the last 10 years we have observed a worrying increase in the number of articles...... as any traditional protein emission spectrum. The many papers in reputable journals erroneously reporting this peak assignment, contradicting 5 decades of prior knowledge, have led to the creation of a new dogma, where many authors and reviewers now take the purported backbone fluorescence...... as an established fact. We hope the current paper helps counter this new situation and leads to a reassessment of those papers that make this erroneous claim....

  7. Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

    DEFF Research Database (Denmark)

    Eildal, Jonas N N; Hultqvist, Greta; Balle, Thomas

    2013-01-01

    -protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains...... of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding...... to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1...

  8. Chemical synthesis of membrane proteins by the removable backbone modification method.

    Science.gov (United States)

    Tang, Shan; Zuo, Chao; Huang, Dong-Liang; Cai, Xiao-Ying; Zhang, Long-Hua; Tian, Chang-Lin; Zheng, Ji-Shen; Liu, Lei

    2017-12-01

    Chemical synthesis can produce membrane proteins bearing specifically designed modifications (e.g., phosphorylation, isotope labeling) that are difficult to obtain through recombinant protein expression approaches. The resulting homogeneously modified synthetic membrane proteins are valuable tools for many advanced biochemical and biophysical studies. This protocol describes the chemical synthesis of membrane proteins by condensation of transmembrane peptide segments through native chemical ligation. To avoid common problems encountered due to the poor solubility of transmembrane peptides in almost any solvent, we describe an effective procedure for the chemical synthesis of membrane proteins through the removable-backbone modification (RBM) strategy. Two key steps of this protocol are: (i) installation of solubilizing Arg4-tagged RBM groups into the transmembrane peptides at any primary amino acid through Fmoc (9-fluorenylmethyloxycarbonyl) solid-phase peptide synthesis and (ii) native ligation of the full-length sequence, followed by removal of the RBM tags by TFA (trifluoroacetic acid) cocktails to afford the native protein. The installation of RBM groups is achieved by using 4-methoxy-5-nitrosalicyladehyde by reduction amination to incorporate an activated O-to-N acyl transfer auxiliary. The Arg4-tag-modified membrane-spanning peptide segments behave like water-soluble peptides to facilitate their purification, ligation and mass characterization.

  9. APSY-NMR for protein backbone assignment in high-throughput structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

    2015-01-15

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

  10. Cross-correlated relaxation rates between protein backbone H–X dipolar interactions

    International Nuclear Information System (INIS)

    Vögeli, Beat

    2017-01-01

    The relaxation interference between dipole–dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive H N –N and H α –C α dipole–dipole interactions. Here, we provide a detailed account of the measurement of the four types of CCR rates. All rates were obtained from at least two different pulse sequences, of which the yet unpublished ones are presented. Detailed comparisons between the different methods and corrections for unwanted pathways demonstrate that the averaged CCR rates are highly accurate and precise with errors of 1.5–3% of the entire value ranges.

  11. Cross-correlated relaxation rates between protein backbone H–X dipolar interactions

    Energy Technology Data Exchange (ETDEWEB)

    Vögeli, Beat, E-mail: beat.vogeli@ucdenver.edu [University of Colorado Denver, Department of Biochemistry and Molecular Genetics (United States)

    2017-03-15

    The relaxation interference between dipole–dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive H{sup N}–N and H{sup α}–C{sup α} dipole–dipole interactions. Here, we provide a detailed account of the measurement of the four types of CCR rates. All rates were obtained from at least two different pulse sequences, of which the yet unpublished ones are presented. Detailed comparisons between the different methods and corrections for unwanted pathways demonstrate that the averaged CCR rates are highly accurate and precise with errors of 1.5–3% of the entire value ranges.

  12. A new strategy for backbone resonance assignment in large proteins using a MQ-HACACO experiment

    International Nuclear Information System (INIS)

    Pervushin, Konstantin; Eletsky, Alexander

    2003-01-01

    A new strategy of backbone resonance assignment is proposed based on a combination of the most sensitive TROSY-type triple resonance experiments such as TROSY-HNCA and TROSY-HNCO with a new 3D multiple-quantum HACACO experiment. The favourable relaxation properties of the multiple-quantum coherences and signal detection using the 13 C' antiphase coherences optimize the performance of the proposed experiment for application to larger proteins. In addition to the 1 H N , 15 N, 13 C α and 13 C' chemical shifts the 3D multiple-quantum HACACO experiment provides assignment for the 1 H α resonances in contrast to previously proposed experiments for large proteins. The strategy is demonstrated with the 44 kDa uniformly 15 N, 13 C-labeled and fractionally 35% deuterated trimeric B. subtilis Chorismate Mutase measured at 20 deg. C and 9 deg. C. Measurements at the lower temperature indicate that the new strategy can be applied to even larger proteins with molecular weights up to 80 kDa

  13. 4D experiments measured with APSY for automated backbone resonance assignments of large proteins

    International Nuclear Information System (INIS)

    Krähenbühl, Barbara; Boudet, Julien; Wider, Gerhard

    2013-01-01

    Detailed structural and functional characterization of proteins by solution NMR requires sequence-specific resonance assignment. We present a set of transverse relaxation optimization (TROSY) based four-dimensional automated projection spectroscopy (APSY) experiments which are designed for resonance assignments of proteins with a size up to 40 kDa, namely HNCACO, HNCOCA, HNCACB and HN(CO)CACB. These higher-dimensional experiments include several sensitivity-optimizing features such as multiple quantum parallel evolution in a ‘just-in-time’ manner, aliased off-resonance evolution, evolution-time optimized APSY acquisition, selective water-handling and TROSY. The experiments were acquired within the concept of APSY, but they can also be used within the framework of sparsely sampled experiments. The multidimensional peak lists derived with APSY provided chemical shifts with an approximately 20 times higher precision than conventional methods usually do, and allowed the assignment of 90 % of the backbone resonances of the perdeuterated primase-polymerase ORF904, which contains 331 amino acid residues and has a molecular weight of 38.4 kDa.

  14. PASA - A Program for Automated Protein NMR Backbone Signal Assignment by Pattern-Filtering Approach

    International Nuclear Information System (INIS)

    Xu Yizhuang; Wang Xiaoxia; Yang Jun; Vaynberg, Julia; Qin Jun

    2006-01-01

    We present a new program, PASA (Program for Automated Sequential Assignment), for assigning protein backbone resonances based on multidimensional heteronuclear NMR data. Distinct from existing programs, PASA emphasizes a per-residue-based pattern-filtering approach during the initial stage of the automated 13 C α and/or 13 C β chemical shift matching. The pattern filter employs one or multiple constraints such as 13 C α /C β chemical shift ranges for different amino acid types and side-chain spin systems, which helps to rule out, in a stepwise fashion, improbable assignments as resulted from resonance degeneracy or missing signals. Such stepwise filtering approach substantially minimizes early false linkage problems that often propagate, amplify, and ultimately cause complication or combinatorial explosion of the automation process. Our program (http://www.lerner.ccf.org/moleccard/qin/) was tested on four representative small-large sized proteins with various degrees of resonance degeneracy and missing signals, and we show that PASA achieved the assignments efficiently and rapidly that are fully consistent with those obtained by laborious manual protocols. The results demonstrate that PASA may be a valuable tool for NMR-based structural analyses, genomics, and proteomics

  15. Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure

    International Nuclear Information System (INIS)

    Wang Lincong; Donald, Bruce Randall

    2004-01-01

    We have derived a quartic equation for computing the direction of an internuclear vector from residual dipolar couplings (RDCs) measured in two aligning media, and two simple trigonometric equations for computing the backbone (φ,ψ) angles from two backbone vectors in consecutive peptide planes. These equations make it possible to compute, exactly and in constant time, the backbone (φ,ψ) angles for a residue from RDCs in two media on any single backbone vector type. Building upon these exact solutions we have designed a novel algorithm for determining a protein backbone substructure consisting of α-helices and β-sheets. Our algorithm employs a systematic search technique to refine the conformation of both α-helices and β-sheets and to determine their orientations using exclusively the angular restraints from RDCs. The algorithm computes the backbone substructure employing very sparse distance restraints between pairs of α-helices and β-sheets refined by the systematic search. The algorithm has been demonstrated on the protein human ubiquitin using only backbone NH RDCs, plus twelve hydrogen bonds and four NOE distance restraints. Further, our results show that both the global orientations and the conformations of α-helices and β-strands can be determined with high accuracy using only two RDCs per residue. The algorithm requires, as its input, backbone resonance assignments, the identification of α-helices and β-sheets as well as sparse NOE distance and hydrogen bond restraints.Abbreviations: NMR - nuclear magnetic resonance; RDC - residual dipolar coupling; NOE - nuclear Overhauser effect; SVD - singular value decomposition; DFS - depth-first search; RMSD - root mean square deviation; POF - principal order frame; PDB - protein data bank; SA - simulated annealing; MD - molecular dynamics

  16. The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

    Science.gov (United States)

    Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

    2015-11-01

    The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. © 2015 Wiley Periodicals, Inc.

  17. The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain.

    Directory of Open Access Journals (Sweden)

    Søren W. Pedersen

    Full Text Available Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.

  18. Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein

    International Nuclear Information System (INIS)

    Żerko, Szymon; Byrski, Piotr; Włodarczyk-Pruszyński, Paweł; Górka, Michał; Ledolter, Karin; Masliah, Eliezer; Konrat, Robert; Koźmiński, Wiktor

    2016-01-01

    New experiments dedicated for large IDPs backbone resonance assignment are presented. The most distinctive feature of all described techniques is the employment of MOCCA-XY16 mixing sequences to obtain effective magnetization transfers between carbonyl carbon backbone nuclei. The proposed 4 and 5 dimensional experiments provide a high dispersion of obtained signals making them suitable for use in the case of large IDPs (application to 354 a. a. residues of Tau protein 3x isoform is presented) as well as provide both forward and backward connectivities. What is more, connecting short chains interrupted with proline residues is also possible. All the experiments employ non-uniform sampling.

  19. Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein

    Energy Technology Data Exchange (ETDEWEB)

    Żerko, Szymon; Byrski, Piotr; Włodarczyk-Pruszyński, Paweł; Górka, Michał [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland); Ledolter, Karin [University of Vienna, Department of Computational and Structural Biology, Max F. Perutz Laboratories (Austria); Masliah, Eliezer [University of California, San Diego, Departments of Neuroscience and Pathology (United States); Konrat, Robert [University of Vienna, Department of Computational and Structural Biology, Max F. Perutz Laboratories (Austria); Koźmiński, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland)

    2016-08-15

    New experiments dedicated for large IDPs backbone resonance assignment are presented. The most distinctive feature of all described techniques is the employment of MOCCA-XY16 mixing sequences to obtain effective magnetization transfers between carbonyl carbon backbone nuclei. The proposed 4 and 5 dimensional experiments provide a high dispersion of obtained signals making them suitable for use in the case of large IDPs (application to 354 a. a. residues of Tau protein 3x isoform is presented) as well as provide both forward and backward connectivities. What is more, connecting short chains interrupted with proline residues is also possible. All the experiments employ non-uniform sampling.

  20. 5D {sup 13}C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion

    Energy Technology Data Exchange (ETDEWEB)

    Novacek, Jiri [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic); Zawadzka-Kazimierczuk, Anna [University of Warsaw, Faculty of Chemistry (Poland); Papouskova, Veronika; Zidek, Lukas, E-mail: lzidek@chemi.muni.cz [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic); Sanderova, Hana; Krasny, Libor [Institute of Microbiology, Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology (Czech Republic); Kozminski, Wiktor [University of Warsaw, Faculty of Chemistry (Poland); Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)

    2011-05-15

    Two novel 5D NMR experiments (CACONCACO, NCOCANCO) for backbone assignment of disordered proteins are presented. The pulse sequences exploit relaxation properties of the unstructured proteins and combine the advantages of {sup 13}C-direct detection, non-uniform sampling, and longitudinal relaxation optimization to maximize the achievable resolution and minimize the experimental time. The pulse sequences were successfully tested on the sample of partially disordered delta subunit from RNA polymerase from Bacillus subtilis. The unstructured part of this 20 kDa protein consists of 81 amino acids with frequent sequential repeats. A collection of 0.0003% of the data needed for a conventional experiment with linear sampling was sufficient to perform an unambiguous assignment of the disordered part of the protein from a single 5D spectrum.

  1. Transforming between discrete and continuous angle distribution models: application to protein χ1 torsions

    International Nuclear Information System (INIS)

    Schmidt, Jürgen M.

    2012-01-01

    Two commonly employed angular-mobility models for describing amino-acid side-chain χ 1 torsion conformation, the staggered-rotamer jump and the normal probability density, are discussed and performance differences in applications to scalar-coupling data interpretation highlighted. Both models differ in their distinct statistical concepts, representing discrete and continuous angle distributions, respectively. Circular statistics, introduced for describing torsion-angle distributions by using a universal circular order parameter central to all models, suggest another distribution of the continuous class, here referred to as the elliptic model. Characteristic of the elliptic model is that order parameter and circular variance form complementary moduli. Transformations between the parameter sets that describe the probability density functions underlying the different models are provided. Numerical aspects of parameter optimization are considered. The issues are typified by using a set of χ 1 related 3 J coupling constants available for FK506-binding protein. The discrete staggered-rotamer model is found generally to produce lower order parameters, implying elevated rotatory variability in the amino-acid side chains, whereas continuous models tend to give higher order parameters that suggest comparatively less variation in angle conformations. The differences perceived regarding angular mobility are attributed to conceptually different features inherent to the models.

  2. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.

    Directory of Open Access Journals (Sweden)

    Kevin Drew

    Full Text Available Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones, oligooxopiperazines, oligo-peptoids, [Formula: see text]-peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org. This work helps address the peptidomimetic community's need for an automated and expandable

  3. A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

    Energy Technology Data Exchange (ETDEWEB)

    Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

    2007-01-15

    Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the {alpha} and {beta} regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

  4. Protein backbone motions viewed by intraresidue and sequential H{sup N}-H{sup {alpha}} residual dipolar couplings

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-05-15

    Triple resonance E.COSY-based techniques were used to measure intra-residue and sequential H{sup N}-H{sup {alpha}} residual dipolar couplings (RDCs) for the third IgG-binding domain of protein G (GB3), aligned in Pf1 medium. Measurements closely correlate with values predicted on the basis of an NMR structure, previously determined on the basis of a large number of one-bond backbone RDCs measured in five alignment media. However, in particular the sequential H{sup N}-H{sup {alpha}} RDCs are smaller than predicted for a static structure, suggesting a degree of motion for these internuclear vectors that exceeds that of the backbone amide N-H vectors. Of all experimentally determined GB3 structures available, the best correlation between experimental {sup 1}H-{sup 1}H couplings is observed for a GB3 ensemble, previously derived to generate a realistic picture of the conformational space sampled by GB3 (Clore and Schwieters, J Mol Biol 355:879-886, 2006). However, for both NMR and X-ray-derived structures the {sup 1}H-{sup 1}H couplings are found to be systematically smaller than expected on the basis of alignment tensors derived from {sup 15}N-{sup 1}H amide RDCs, assuming librationally corrected N-H bond lengths of 1.041 A.

  5. Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network.

    Science.gov (United States)

    Lyons, James; Dehzangi, Abdollah; Heffernan, Rhys; Sharma, Alok; Paliwal, Kuldip; Sattar, Abdul; Zhou, Yaoqi; Yang, Yuedong

    2014-10-30

    Because a nearly constant distance between two neighbouring Cα atoms, local backbone structure of proteins can be represented accurately by the angle between C(αi-1)-C(αi)-C(αi+1) (θ) and a dihedral angle rotated about the C(αi)-C(αi+1) bond (τ). θ and τ angles, as the representative of structural properties of three to four amino-acid residues, offer a description of backbone conformations that is complementary to φ and ψ angles (single residue) and secondary structures (>3 residues). Here, we report the first machine-learning technique for sequence-based prediction of θ and τ angles. Predicted angles based on an independent test have a mean absolute error of 9° for θ and 34° for τ with a distribution on the θ-τ plane close to that of native values. The average root-mean-square distance of 10-residue fragment structures constructed from predicted θ and τ angles is only 1.9Å from their corresponding native structures. Predicted θ and τ angles are expected to be complementary to predicted ϕ and ψ angles and secondary structures for using in model validation and template-based as well as template-free structure prediction. The deep neural network learning technique is available as an on-line server called Structural Property prediction with Integrated DEep neuRal network (SPIDER) at http://sparks-lab.org. Copyright © 2014 Wiley Periodicals, Inc.

  6. Three-Dimensional Protein Fold Determination from Backbone Amide Pseudocontact Shifts Generated by Lanthanide Tags at Multiple Sites

    KAUST Repository

    Yagi, Hiromasa

    2013-06-01

    Site-specific attachment of paramagnetic lanthanide ions to a protein generates pseudocontact shifts (PCS) in the nuclear magnetic resonance (NMR) spectra of the protein that are easily measured as changes in chemical shifts. By labeling the protein with lanthanide tags at four different sites, PCSs are observed for most amide protons and accurate information is obtained about their coordinates in three-dimensional space. The approach is demonstrated with the chaperone ERp29, for which large differences have been reported between X-ray and NMR structures of the C-terminal domain, ERp29-C. The results unambiguously show that the structure of rat ERp29-C in solution is similar to the crystal structure of human ERp29-C. PCSs of backbone amides were the only structural restraints required. Because these can be measured for more dilute protein solutions than other NMR restraints, the approach greatly widens the range of proteins amenable to structural studies in solution. © 2013 Elsevier Ltd. All rights reserved.

  7. Backbone resonance assignments for G protein α(i3) subunit in the GDP-bound state.

    Science.gov (United States)

    Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

    2014-10-01

    Guanine-nucleotide binding proteins (G proteins) serve as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of the G protein α subunit with GDP (Gα·GDP) and the G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP-GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα·GTP) and Gβγ. Then, Gα·GTP and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. The G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Here, we established the backbone resonance assignments of human Gαi3, a member of the i/o family with a molecular weight of 41 K, in complex with GDP. The chemical shifts were compared with those of Gα(i3) in complex with a GTP-analogue, GTPγS, which we recently reported, indicating that the residues with significant chemical shift differences are mostly consistent with the regions with the structural differences between the GDP- and GTPγS-bound states, as indicated in the crystal structures. The assignments of Gα(i3)·GDP would be useful for the analyses of the dynamics of Gα(i3) and its interactions with various target molecules.

  8. Backbone assignment and secondary structure of the PsbQ protein from Photosystem II

    Czech Academy of Sciences Publication Activity Database

    Horničáková, M.; Kohoutová, Jaroslava; Schlagnitweit, J.; Wohlschlager, Ch.; Ettrich, Rüdiger; Fiala, R.; Schoefberger, W.; Müller, N.

    2011-01-01

    Roč. 5, č. 2 (2011), s. 169-175 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LC06010 Institutional research plan: CEZ:AV0Z60870520 Keywords : Photosystem II * PsbQ * Missing link * NMR resonance assignment * Protein-protein interaction Subject RIV: BO - Biophysics Impact factor: 0.720, year: 2011 http://www.springerlink.com/content/3n38075w5h1l1082/fulltext.pdf

  9. Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design.

    Directory of Open Access Journals (Sweden)

    Elisabeth Humphris-Narayanan

    Full Text Available Predicting which mutations proteins tolerate while maintaining their structure and function has important applications for modeling fundamental properties of proteins and their evolution; it also drives progress in protein design. Here we develop a computational model to predict the tolerated sequence space of HIV-1 protease reachable by single mutations. We assess the model by comparison to the observed variability in more than 50,000 HIV-1 protease sequences, one of the most comprehensive datasets on tolerated sequence space. We then extend the model to a second protein, reverse transcriptase. The model integrates multiple structural and functional constraints acting on a protein and uses ensembles of protein conformations. We find the model correctly captures a considerable fraction of protease and reverse-transcriptase mutational tolerance and shows comparable accuracy using either experimentally determined or computationally generated structural ensembles. Predictions of tolerated sequence space afforded by the model provide insights into stability-function tradeoffs in the emergence of resistance mutations and into strengths and limitations of the computational model.

  10. Density functional calculations of backbone 15N shielding tensors in beta-sheet and turn residues of protein G

    International Nuclear Information System (INIS)

    Cai Ling; Kosov, Daniel S.; Fushman, David

    2011-01-01

    We performed density functional calculations of backbone 15 N shielding tensors in the regions of beta-sheet and turns of protein G. The calculations were carried out for all twenty-four beta-sheet residues and eight beta-turn residues in the protein GB3 and the results were compared with the available experimental data from solid-state and solution NMR measurements. Together with the alpha-helix data, our calculations cover 39 out of the 55 residues (or 71%) in GB3. The applicability of several computational models developed previously (Cai et al. in J Biomol NMR 45:245–253, 2009) to compute 15 N shielding tensors of alpha-helical residues is assessed. We show that the proposed quantum chemical computational model is capable of predicting isotropic 15 N chemical shifts for an entire protein that are in good correlation with experimental data. However, the individual components of the predicted 15 N shielding tensor agree with experiment less well: the computed values show much larger spread than the experimental data, and there is a profound difference in the behavior of the tensor components for alpha-helix/turns and beta-sheet residues. We discuss possible reasons for this.

  11. Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

    KAUST Repository

    Maadooliat, Mehdi; Gao, Xin; Huang, Jianhua Z.

    2012-01-01

    Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.

  12. Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

    KAUST Repository

    Maadooliat, Mehdi

    2012-08-27

    Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.

  13. High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Zawadzka-Kazimierczuk, Anna; Kozminski, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry (Poland); Sanderova, Hana; Krasny, Libor [Institute of Microbiology, Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria, Department of Bacteriology (Czech Republic)

    2012-04-15

    Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using {delta} subunit (20 kDa) of Bacillus subtilis RNA polymerase that has an 81-amino acid disordered part containing various repetitive sequences.

  14. Backbone and sidechain methyl Ile (δ1), Leu and Val chemical shift assignments of RDE-4 (1-243), an RNA interference initiation protein in C. elegans.

    Science.gov (United States)

    Chiliveri, Sai Chaitanya; Kumar, Sonu; Marelli, Udaya Kiran; Deshmukh, Mandar V

    2012-10-01

    The RNAi pathway of several organisms requires presence of double stranded RNA binding proteins for functioning of Dicer in gene regulation. In C. elegans, a double stranded RNA binding protein, RDE-4 (385 aa, 44 kDa) recognizes long exogenous dsRNA and initiates the RNAi pathway. We have achieved complete backbone and stereospecific methyl sidechain Ile (δ1), Leu and Val chemical shifts of first 243 amino acids of RDE-4, namely RDE-4ΔC.

  15. A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

    Science.gov (United States)

    Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John Z H

    2013-09-01

    Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

  16. Appendicular Torsion

    Directory of Open Access Journals (Sweden)

    Siddharth Pramod Dubhashi

    2016-01-01

    Full Text Available Torsion of the vermiform appendix is a rare condition detectable only at operation. It can be primary or secondary. This is a case report of 52-year-old female with 180° anti-clockwise rotation of the appendix. Torsion can further leads to strangulation and infarction of the organ. Appendicular torsion could be included in the differential diagnosis of pain in right iliac fossa.

  17. Beta-scission of alkoxyl radicals on peptides and proteins can give rise to backbone cleavage and loss of side-chains

    International Nuclear Information System (INIS)

    Headlam, H.A.; Davies, M.J.; Mortimer, A.; Easton, C.J.

    2000-01-01

    Full text: Exposure of proteins to radicals in the presence of O 2 brings about multiple changes including side-chain oxidation, backbone fragmentation, cross-linking, unfolding, changes in hydrophobicity and conformation, altered susceptibility to proteolytic enzymes and formation of new reactive groups (e.g. hydroperoxides and 3,4-dihydroxyphenylalanine). All of these processes can result in loss of structural or enzymatic activity. The mechanisms that give rise to backbone cleavage are only partly understood. Whilst it is known that direct hydrogen atom abstraction at a-carbon sites gives backbone cleavages it has also been proposed that initial attack at side-chain sites might also give rise to backbone cleavage. In this study we have examined whether initial attack at the β- (C-3) position can give rise to α-carbon radicals (and hence backbone cleavage) via the formation, and subsequent β- scission, of C-3 alkoxyl radicals. This process has been observed previously with protected amino acids in organic solvents (J. Chem. Soc. Perkin Trans. 2, 1997, 503-507) but the occurrence of such reactions with proteins in aqueous solution has not been explored. Alkoxyl radicals were generated at the C-3 position of a variety of protected amino acids and small peptides by two methods: metal-ion catalysed decomposition of hydroperoxides formed as a result of γ-radiolysis in the presence of O 2 , and UV photolysis of nitrate esters. In most cases radicals have been detected by EPR spectroscopy using nitroso and nitrone spin traps, which can be assigned by comparison with literature data to α-carbon radicals; in some case assignments were confirmed by the generation of the putative species by other routes. With Ala peptide hydroperoxides and nitrate esters, and MNP as the spin trap, the major radical detected in each case has been assigned to the adduct of an α-carbon radical with partial structure - NH- . CH-C(O) - consistent with the rapid occurrence of the above

  18. CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

    International Nuclear Information System (INIS)

    Swain, Monalisa; Atreya, Hanudatta S.

    2009-01-01

    Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1 H α and 13 C' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment

  19. Appendicular Torsion

    African Journals Online (AJOL)

    A‑2/103, Shivranjan Towers, Someshwarwadi, Pashan, Pune ‑ 411 008,. Maharashtra, India. E‑mail: spdubhashi@gmail.com. INTRODUCTION. Acute appendicitis presents with pain in right iliac fossa. Torsion of the vermiform appendix, though rare, also presents in a similar fashion, and it is detectable only at operation.[1].

  20. Empirical correlation between protein backbone {sup 15}N and {sup 13}C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

    Energy Technology Data Exchange (ETDEWEB)

    Wang Liya [Cold Spring Harbor Laboratory (United States); Markley, John L. [University of Wisconsin, Biochemistry Department (United States)], E-mail: markley@nmrfam.wisc.edu

    2009-06-15

    The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting {sup 13}C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to {sup 15}N NMR data from proteins, so as to enable the detection and correction of inconsistencies in chemical shift referencing for this nucleus. The approach is based on our finding that the secondary {sup 15}N chemical shift of the backbone nitrogen atom of residue i is strongly correlated with the secondary chemical shift difference (experimental minus random coil) between the alpha and beta carbons of residue i - 1. Thus once alpha and beta {sup 13}C chemical shifts are available (their difference is referencing error-free), the {sup 15}N referencing can be validated, and an appropriate offset correction can be derived. This approach can be implemented prior to a structure determination and can be used to analyze potential referencing problems in database data not associated with three-dimensional structure. Application of the LACS algorithm to the current BMRB protein chemical shift database, revealed that nearly 35% of the BMRB entries have {delta}{sup 15}N values mis-referenced by over 0.7 ppm and over 25% of them have {delta}{sup 1}H{sup N} values mis-referenced by over 0.12 ppm. One implication of the findings reported here is that a backbone {sup 15}N chemical shift provides a better indicator of the conformation of the preceding residue than of the residue itself.

  1. Testing Backbone.js

    CERN Document Server

    Roemer, Ryan

    2013-01-01

    This book is packed with the step by step tutorial and instructions in recipe format helping you setup test infrastructure and gradually advance your skills to plan, develop, and test your backbone applications.If you are a JavaScript developer looking for recipes to create and implement test support for your backbone application, then this book is ideal for you.

  2. Backbone amide linker strategy

    DEFF Research Database (Denmark)

    Shelton, Anne Pernille Tofteng; Jensen, Knud Jørgen

    2013-01-01

    In the backbone amide linker (BAL) strategy, the peptide is anchored not at the C-terminus but through a backbone amide, which leaves the C-terminal available for various modifications. This is thus a very general strategy for the introduction of C-terminal modifications. The BAL strategy...

  3. Testicular torsion

    DEFF Research Database (Denmark)

    Brasso, K; Andersen, L; Kay, L

    1993-01-01

    Thirty-five patients were examined 6-11 years after operation for torsion of the testis. Loss of testicular tissue was significantly associated with long preoperative duration of symptoms and with low postoperative sperm counts. The sex hormones were normal in the majority of patients...... to the sperm count and concentration. Measurement of carnitine levels in seminal plasma, as a sign of vas deferens obstruction or dysfunction of epididymis, and of autoantibodies against spermatozoa revealed no significant findings....

  4. Optimized set of two-dimensional experiments for fast sequential assignment, secondary structure determination, and backbone fold validation of 13C/15N-labelled proteins

    International Nuclear Information System (INIS)

    Bersch, Beate; Rossy, Emmanuel; Coves, Jacques; Brutscher, Bernhard

    2003-01-01

    NMR experiments are presented which allow backbone resonance assignment, secondary structure identification, and in favorable cases also molecular fold topology determination from a series of two-dimensional 1 H- 15 N HSQC-like spectra. The 1 H- 15 N correlation peaks are frequency shifted by an amount ± ω X along the 15 N dimension, where ω X is the C α , C β , or H α frequency of the same or the preceding residue. Because of the low dimensionality (2D) of the experiments, high-resolution spectra are obtained in a short overall experimental time. The whole series of seven experiments can be performed in typically less than one day. This approach significantly reduces experimental time when compared to the standard 3D-based methods. The here presented methodology is thus especially appealing in the context of high-throughput NMR studies of protein structure, dynamics or molecular interfaces

  5. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    Science.gov (United States)

    Wilburn, Damien B; Bowen, Kathleen E; Doty, Kari A; Arumugam, Sengodagounder; Lane, Andrew N; Feldhoff, Pamela W; Feldhoff, Richard C

    2014-01-01

    In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique

  6. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    Directory of Open Access Journals (Sweden)

    Damien B Wilburn

    Full Text Available In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s without the immediate need for complementary mutations. Consequently

  7. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

    DEFF Research Database (Denmark)

    Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

    2008-01-01

    . Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...

  8. Local Backbone Flexibility as a Determinant of the Apparent pKa Values of Buried Ionizable Groups in Proteins.

    Science.gov (United States)

    Peck, Meredith T; Ortega, Gabriel; De Luca-Johnson, Javier N; Schlessman, Jamie L; Robinson, Aaron C; García-Moreno E, Bertrand

    2017-10-10

    Ionizable groups buried in the hydrophobic interior of proteins are essential for energy transduction. These groups can have highly anomalous pK a values that reflect the incompatibility between charges and dehydrated environments. A systematic study of pK a values of buried ionizable groups in staphylococcal nuclease (SNase) suggests that these pK a values are determined in part by conformational reorganization of the protein. Lys-66 is one of the most deeply buried residues in SNase. We show that its apparent pK a of 5.7 reflects the average of the pK a values of Lys-66 in different conformational states of the protein. In the fully folded state, Lys-66 is deeply buried in the hydrophobic core of SNase and must titrate with a pK a of ≪5.7. In other states, the side chain of Lys-66 is fully solvent-exposed and has a normal pK a of ≈10.4. We show that the pK a of Lys-66 can be shifted from 5.7 toward a more normal value of 7.1 via the insertion of flanking Gly residues at positions 64 and 67 to promote an "open" conformation of SNase. Crystal structures and nuclear magnetic resonance spectroscopy show that in these Gly-containing variants Lys-66 can access bulk water as a consequence of overwinding of the C-terminal end of helix 1. These data illustrate that the apparent pK a values of buried groups in proteins are governed in part by the difference in free energy between different conformational states of the protein and by differences in the pK a values of the buried groups in the different conformations.

  9. A ‘just-in-time’ HN(CA)CO experiment for the backbone assignment of large proteins with high sensitivity

    Science.gov (United States)

    Werner-Allen, Jon W.; Jiang, Ling; Zhou, Pei

    2006-07-01

    Among the suite of commonly used backbone experiments, HNCACO presents an unresolved sensitivity limitation due to fast 13CO transverse relaxation and passive 13Cα-13Cβ coupling. Here, we present a high-sensitivity 'just-in-time' (JIT) HN(CA)CO pulse sequence that uniformly refocuses 13Cα-13Cβ coupling while collecting 13CO shifts in real time. Sensitivity comparisons of the 3-D JIT HN(CA)CO, a CT-HMQC-based control, and a HSQC-based control with selective 13Cα inversion pulses were performed using a 2H/13C/15N labeled sample of the 29 kDa HCA II protein at 15 °C. The JIT experiment shows a 42% signal enhancement over the CT-HMQC-based experiment. Compared to the HSQC-based experiment, the JIT experiment is 16% less sensitive for residues experiencing proper 13Cα refocusing and 13Cα-13Cβ decoupling. However, for the remaining residues, the JIT spectrum shows a 106% average sensitivity gain over the HSQC-based experiment. The high-sensitivity JIT HNCACO experiment should be particularly beneficial for studies of large proteins to provide 13CO resonance information regardless of residue type.

  10. Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15N or 13C′ chemical shifts of multiple contiguous residues in highly resolved 3D spectra

    International Nuclear Information System (INIS)

    Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A.

    2015-01-01

    Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone 1 H N , 15 N H , and 13 C′ resonance assignments to be completed from a single pair of 3D experiments

  11. 1990s: High Capacity Backbones

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. 1990s: High Capacity Backbones. Backbone capacities increased from 2.5 Gb/s to 100s of Gb/s during the 1990's. Wavelength division multiplexing with 160 waves of 10 Gb/s was commercially available. Several high-capacity backbones built in the US and Europe.

  12. Ribosomal proteins L11 and L10.(L12)4 and the antibiotic thiostrepton interact with overlapping regions of the 23 S rRNA backbone in the ribosomal GTPase centre

    DEFF Research Database (Denmark)

    Rosendahl, G; Douthwaite, S

    1993-01-01

    RNA, and to investigate how this interaction is influenced by other ribosomal components. Complexes were characterized in both naked 23 S rRNA and ribosomes from an E. coli L11-minus strain, before and after reconstitution with L11. The protein protects 17 riboses between positions 1058 and 1085 in the naked 23 S r......The Escherichia coli ribosomal protein (r-protein) L11 and its binding site on 23 S ribosomal RNA (rRNA) are associated with ribosomal hydrolysis of guanosine 5'-triphosphate (GTP). We have used hydroxyl radical footprinting to map the contacts between L11 and the backbone riboses in 23 S r......)4 and other proteins within the ribosome. The antibiotics thiostrepton and micrococcin inhibit the catalytic functions of this region by slotting in between the accessible loops and interacting with nucleotides there....

  13. Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm

    International Nuclear Information System (INIS)

    Hefke, Frederik; Bagaria, Anurag; Reckel, Sina; Ullrich, Sandra Johanna; Dötsch, Volker; Glaubitz, Clemens; Güntert, Peter

    2011-01-01

    We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273–6279 (1982)), types of amino acids are labeled with 13 C or/and 15 N such that cross peaks between 13 CO(i – 1) and 15 NH(i) result only for pairs of sequentially adjacent amino acids of which the first is labeled with 13 C and the second with 15 N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. Our computer algorithm UPLABEL for optimal unique pair labeling, implemented in the program CYANA and in a standalone program, and also available through a web portal, uses combinatorial optimization to find for a given amino acid sequence labeling patterns that maximize the number of unique pair assignments with a minimal number of differently labeled protein samples. Various auxiliary conditions, including labeled amino acid availability and price, previously known partial assignments, and sequence regions of particular interest can be taken into account when determining optimal amino acid type-specific labeling patterns. The method is illustrated for the assignment of the human G-protein coupled receptor bradykinin B2 (B 2 R) and applied as a starting point for the backbone assignment of the membrane protein proteorhodopsin.

  14. Intermittent Testicular Torsion

    African Journals Online (AJOL)

    2017-06-02

    Jun 2, 2017 ... had prior episodes of testicular pain, suggesting that they may have had intermittent torsion before .... None of the patients had antecedent history of sexual exposure, fever, or urinary tract infection .... torsion of the spermatic cord portends an increased risk of acute testicular infarction. J Urol 2008;180 4 ...

  15. Temperature-dependent spectral density analysis applied to monitoring backbone dynamics of major urinary protein-I complexed with the pheromone 2-sec-butyl-4,5-dihydrothiazole

    International Nuclear Information System (INIS)

    Krizova, Hana; Zidek, Lukas; Stone, Martin J.; Novotny, Milos V.; Sklenar, Vladimir

    2004-01-01

    Backbone dynamics of mouse major urinary protein I (MUP-I) was studied by 15 N NMR relaxation. Data were collected at multiple temperatures for a complex of MUP-I with its natural pheromonal ligand, 2-sec-4,5-dihydrothiazole, and for the free protein. The measured relaxation rates were analyzed using the reduced spectral density mapping. Graphical analysis of the spectral density values provided an unbiased qualitative picture of the internal motions. Varying temperature greatly increased the range of analyzed spectral density values and therefore improved reliability of the analysis. Quantitative parameters describing the dynamics on picosecond to nanosecond time scale were obtained using a novel method of simultaneous data fitting at multiple temperatures. Both methods showed that the backbone flexibility on the fast time scale is slightly increased upon pheromone binding, in accordance with the previously reported results. Zero-frequency spectral density values revealed conformational changes on the microsecond to millisecond time scale. Measurements at different temperatures allowed to monitor temperature depencence of the motional parameters

  16. Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space.

    Science.gov (United States)

    Stegemann, Björn; Klebe, Gerhard

    2012-02-01

    Small molecules are recognized in protein-binding pockets through surface-exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein-ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise to unexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein-cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein-binding pockets, and the local folding patterns next to the cofactor-binding site. State-of-the-art clustering techniques have been applied to group the different protein-cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process. Copyright © 2011 Wiley Periodicals, Inc.

  17. Some torsion potentials

    Energy Technology Data Exchange (ETDEWEB)

    Grundberg, J; Lindstrom, U

    1986-10-01

    Using the notion of torsion potentials, the duality between antisymmetric tensor fields and scalar fields is discussed. First-order actions with these fields, the connection and the metric as independent variables are presented.

  18. Testicular Torsion (For Parents)

    Science.gov (United States)

    ... Parents Kids Teens Hernias Ultrasound: Scrotum Undescended Testicles Male Reproductive System PQ: I have a lump on one of ... to Do a Testicular Self-Exam (Slideshow) Varicocele Male Reproductive System Testicular Torsion View more About Us Contact Us ...

  19. Induced quantum torsion

    International Nuclear Information System (INIS)

    Denardo, G.; Spallucci, E.

    1985-07-01

    We study pregeometry in the framework of a Poincare gauge field theory. The Riemann-Cartan space-time is shown to be an ''effective geometry'' for this model in the low energy limit. By using Heat Kernel techniques we find the induced action for curvature and torsion. We obtain in this way the usual Einstein-Hilbert action plus an axial Maxwell term describing the propagation of a massless, axial vector torsion field. (author)

  20. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

    Science.gov (United States)

    Armen, Roger S; Chen, Jianhan; Brooks, Charles L

    2009-10-13

    Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

  1. Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios

    Science.gov (United States)

    Fernández, Ariel; Colubri, Andrés; Berry, R. Stephen

    2001-04-01

    This work presents a method to portray protein folding dynamics at a coarse resolution, based on a pattern-recognition-and-feedback description of the evolution of torsional motions of the backbone chain in the hydrophobic collapse of the protein. The approach permits theory and computation to treat the search of conformation space from picoseconds to the millisecond time scale or longer, the time scales of adiabatic evolution of soft-mode dynamics. The procedure tracks the backbone torsional coordinates modulo the basins of attraction to which they belong in the Ramachandran maps. The state and history of the backbone are represented in a map of local torsional states and hydrophobicity/hydrophilicity matching of the residues comprising the chain, the local topology matrix (LTM). From this map, we infer allowable structural features by recognizing patterns in the LTM as topologically compatible with particular structural forms within a level of frustration tolerance. Each such 3D realization of an LTM leads to a contact map, from which one can infer one or more structures. Introduction of energetic and entropic terms allow elimination of all but the most favored of these structures at each new juncture. The method's predictive power is first established by comparing "final," stable LTMs for natural sequences of intermediate length (N⩽120) with PDB data. The method is extended further to β-lactoglobulin (β-LG, N=162), the quintessential nonhierarchical folder.

  2. Backbone and sidechain 1H, 13C and 15N resonance assignments of the human brain-type fatty acid binding protein (FABP7) in its apo form and the holo forms binding to DHA, oleic acid, linoleic acid and elaidic acid

    DEFF Research Database (Denmark)

    Oeemig, Jesper S; Jørgensen, Mathilde L; Hansen, Mikka S

    2009-01-01

    In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid.......In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid....

  3. Higher Franz-Reidemeister torsion

    CERN Document Server

    Igusa, Kiyoshi

    2002-01-01

    The book is devoted to the theory of topological higher Franz-Reidemeister torsion in K-theory. The author defines the higher Franz-Reidemeister torsion based on Volodin's K-theory and Borel's regulator map. He describes its properties and generalizations and studies the relation between the higher Franz-Reidemeister torsion and other torsions used in K-theory: Whitehead torsion and Ray-Singer torsion. He also presents methods of computing higher Franz-Reidemeister torsion, illustrates them with numerous examples, and describes various applications of higher Franz-Reidemeister torsion, particularly for the study of homology of mapping class groups. Packed with up-to-date information, the book provides a unique research and reference tool for specialists working in algebraic topology and K-theory.

  4. Measurement of backbone hydrogen-deuterium exchange in the type III secretion system needle protein PrgI by solid-state NMR

    Science.gov (United States)

    Chevelkov, Veniamin; Giller, Karin; Becker, Stefan; Lange, Adam

    2017-10-01

    In this report we present site-specific measurements of amide hydrogen-deuterium exchange rates in a protein in the solid state phase by MAS NMR. Employing perdeuteration, proton detection and a high external magnetic field we could adopt the highly efficient Relax-EXSY protocol previously developed for liquid state NMR. According to this method, we measured the contribution of hydrogen exchange on apparent 15N longitudinal relaxation rates in samples with differing D2O buffer content. Differences in the apparent T1 times allowed us to derive exchange rates for multiple residues in the type III secretion system needle protein.

  5. Gallbladder torsion. Case report

    DEFF Research Database (Denmark)

    Brasso, K; Rasmussen, O V

    1991-01-01

    Gallbladder torsion is a rare surgical emergency occurring primarily in elderly women. The anatomical background is a variation in the attachment of the gallbladder to the inferior margin of the liver. Increasing life span will probably lead to an increasing number of cases, and gallbladder torsion...... must be kept in mind in patients with sudden onset of pain in the upper right quadrant, nausea, vomiting, and a palpable mass. None of the laboratory routines or non-invasive examinations enables one to make the right preoperative diagnosis. Treatment is cholecystectomy. Promptly treated, the prognosis...

  6. Torsional heterotic geometries

    International Nuclear Information System (INIS)

    Becker, Katrin; Sethi, Savdeep

    2009-01-01

    We construct new examples of torsional heterotic backgrounds using duality with orientifold flux compactifications. We explain how duality provides a perturbative solution to the type I/heterotic string Bianchi identity. The choice of connection used in the Bianchi identity plays an important role in the construction. We propose the existence of a much larger landscape of compact torsional geometries using string duality. Finally, we present some quantum exact metrics that correspond to NS5-branes placed on an elliptic space. These metrics describe how torus isometries are broken by NS flux.

  7. Inferential backbone assignment for sparse data

    International Nuclear Information System (INIS)

    Vitek, Olga; Bailey-Kellogg, Chris; Craig, Bruce; Vitek, Jan

    2006-01-01

    This paper develops an approach to protein backbone NMR assignment that effectively assigns large proteins while using limited sets of triple-resonance experiments. Our approach handles proteins with large fractions of missing data and many ambiguous pairs of pseudoresidues, and provides a statistical assessment of confidence in global and position-specific assignments. The approach is tested on an extensive set of experimental and synthetic data of up to 723 residues, with match tolerances of up to 0.5 ppm for C α and C β resonance types. The tests show that the approach is particularly helpful when data contain experimental noise and require large match tolerances. The keys to the approach are an empirical Bayesian probability model that rigorously accounts for uncertainty in the data at all stages in the analysis, and a hybrid stochastic tree-based search algorithm that effectively explores the large space of possible assignments

  8. Deuterium isotope shifts for backbone {sup 1}H, {sup 15}N and {sup 13}C nuclei in intrinsically disordered protein {alpha}-synuclein

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-10-15

    Intrinsically disordered proteins (IDPs) are abundant in nature and characterization of their potential structural propensities remains a widely pursued but challenging task. Analysis of NMR secondary chemical shifts plays an important role in such studies, but the output of such analyses depends on the accuracy of reference random coil chemical shifts. Although uniform perdeuteration of IDPs can dramatically increase spectral resolution, a feature particularly important for the poorly dispersed IDP spectra, the impact of deuterium isotope shifts on random coil values has not yet been fully characterized. Very precise {sup 2}H isotope shift measurements for {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 15}N, and {sup 1}H{sup N} have been obtained by using a mixed sample of protonated and uniformly perdeuterated {alpha}-synuclein, a protein with chemical shifts exceptionally close to random coil values. Decomposition of these isotope shifts into one-bond, two-bond and three-bond effects as well as intra- and sequential residue contributions shows that such an analysis, which ignores conformational dependence, is meaningful but does not fully describe the total isotope shift to within the precision of the measurements. Random coil {sup 2}H isotope shifts provide an important starting point for analysis of such shifts in structural terms in folded proteins, where they are known to depend strongly on local geometry.

  9. Torsion in superstrings

    International Nuclear Information System (INIS)

    Bars, I.; Nemeschansky, D.; Yankielowicz, S.

    1986-01-01

    In this paper the authors discuss string theories on a background manifold with torsion. In the first part, candidate vacuum configurations for ten-dimensional superstrings are discussed. The authors compactify these on M/sub 4/xK, where M/sub 4/ is four-dimensional and K some compact six-dimensional manifold. In particular they are interested in investigating the existence of solutions with non-zero torsion on K. The compactification problem is approached both from the effective field theory point of view and directly using string considerations. The second part of the talk is devoted to the construction of string theories in curved space with torsion. The authors discuss both the Neveu-Schwarz-Ramond type string and the Green-Schwarz type string. Particular emphasis is put on the resulting constraints on space-time supersymmetry in the Green-Schwarz approach. This study uses two-dimensional non-linear sigma models to describe the propagation of strings in background geometries with torsion. The background field can be understood as arising from condensation of infinite number of strings

  10. Torsion induces gravity

    International Nuclear Information System (INIS)

    Aros, Rodrigo; Contreras, Mauricio

    2006-01-01

    In this work the Poincare-Chern-Simons and anti-de Sitter-Chern-Simons gravities are studied. For both, a solution that can be cast as a black hole with manifest torsion is found. Those solutions resemble Schwarzschild and Schwarzschild-AdS solutions, respectively

  11. Testicular torsion repair

    Science.gov (United States)

    ... the Procedure is Performed Testicular torsion is an emergency. In most cases, surgery is needed right away to relieve pain ... RM, Hockberger RS, Gausche-Hill M, eds. Rosen's Emergency Medicine: Concepts and Clinical Practice . 9th ed. Philadelphia, PA: Elsevier; 2018:chap ...

  12. Tibiotalar torsion: bioengineering paradigm.

    Science.gov (United States)

    Michele, A A; Nielsen, P M

    1976-10-01

    1. Medial tibiotalar torsion is the most common disorder peculiar to mankind. 2. The pathogonomic findings are (a) an axial medially rotated and adducted distal third of the shaft of the tibia, (b) the plafond of the tibia with its mortise containing the "track-bound" talus, which is deflected strongly toward the tibial side, (c) an exaggerated midtarsal equinus, (d) ostensible restriction of dorsiflexion of the hindfoot against the tibia, (e) mild separation of the distal tibiofibular articulation, and (f) forward displacement of the gravitational axis to the naviculocunei-form joint. 3. Faulty leg crossing in utero resulting in an abnormal pelvofemoral-tibial design is discussed and its important consequences in the vulnerable 40 per cent of the population are emphasized. 4. The kinesiomechanics of the leg, ankle and foot is reviewed. 5. The radiographic parameters of medial tibiotalar torsion are presented, as well as the multiple facets of the clinical examination. 6. Methods of treatment depending on age and severity of the disorder are recommended. Surgery, detortional casts, and corrective footwear are discussed. Shoes presently available are inadequate for tibiotalar torsion and therefore engineering principles must be applied in the design and construction of all footwear, including sneakers and sportswear. This can be done only if the pathological biomechanics of this group of disorders is recognized. Biplane proximal tibial osteotomy is recommended in refractory cases, especially when tibiotalar torsion is demonstrated. 7. After 30 years of experience, the author finds that results with these patients have been uniformly good to excellent, depending on age and mode of treatment. 8. In medial tibiotalar torsion, the consequent adaptive changes are readily observed, but rarely are they recognized as the inevitable sequelae of medial tibiotalar torsion. 9. Adaptive compensating disorders are identified and their mechanism described. 10. The management of

  13. Solution Structure and Backbone Dynamics of the Pleckstrin Homology Domain of the Human Protein Kinase B (PKB/Akt). Interaction with Inositol Phosphates

    International Nuclear Information System (INIS)

    Auguin, Daniel; Barthe, Philippe; Auge-Senegas, Marie-Therese; Stern, Marc-Henri; Noguchi, Masayuki; Roumestand, Christian

    2004-01-01

    The programmed cell death occurs as part of normal mammalian development. The induction of developmental cell death is a highly regulated process and can be suppressed by a variety of extracellular stimuli. Recently, the ability of trophic factors to promote survival have been attributed, at least in part, to the phosphatidylinositide 3'-OH kinase (PI3K)/Protein Kinase B (PKB, also named Akt) cascade. Several targets of the PI3K/PKB signaling pathway have been identified that may underlie the ability of this regulatory cascade to promote cell survival. PKB possesses a N-terminal Pleckstrin Homology (PH) domain that binds specifically and with high affinity to PtIns(3,4,5)P 3 and PtIns(3,4)P 2 , the PI3K second messengers. PKB is then recruited to the plasma membrane by virtue of its interaction with 3'-OH phosphatidylinositides and activated. Recent evidence indicates that PKB is active in various types of human cancer; constitutive PKB signaling activation is believed to promote proliferation and increased cell survival, thereby contributing to cancer progression. Thus, it has been shown that induction of PKB activity is augmented by the TCL1/MTCP1 oncoproteins through a physical association requiring the PKB PH domain. Here we present the three-dimensional solution structure of the PH domain of the human protein PKB (isoform β). PKBβ-PH is an electrostatically polarized molecule that adopts the same fold and topology as other PH-domains, consisting of a β-sandwich of seven strands capped on one top by an α-helix. The opposite face presents three variable loops that appear poorly defined in the NMR structure. Measurements of 15 N spin relaxation times and heteronuclear 15 N{ 1 H}NOEs showed that this poor definition is due to intrinsic flexibility, involving complex motions on different time scales. Chemical shift mapping studies correctly defined the binding site of Ins(1,3,4,5)P 4 (the head group of PtIns(3,4,5)P 3 ), as was previously proposed from a

  14. Backbone upgrades and DEC equipment replacement

    Science.gov (United States)

    Vancamp, Warren

    1991-01-01

    The NASA Science Internet (NSI) dual protocol backbone is outlined. It includes DECnet link upgrades to match TCP/IP link performance. It also includes the integration of backbone resources and central management. The phase 1 transition process is outlined.

  15. DNA-to-protein crosslinks and backbone breaks caused by far- and near-ultraviolet, and visible light radiations in mammalian cells

    International Nuclear Information System (INIS)

    Peak, M.J.; Peak, J.G.

    1986-01-01

    Spectral responses for DNA damages caused by far-uv, near-uv, and visible light radiations have been studied. The near congruence of the spectra for far-uv damages and the spectrum of DNA is good evidence that the mechanism is the same for the induction of breaks, crosslinks, and pyrimidine dimers. For near-uv, the different spectra imply that at least several nonDNA sensitizer molecules act as primary chromophores, but that DNA damage eventually results. With the understanding that near-uv and visible radiations produce a variety of chemically potent reactive oxygen species within the cell, we recognize the possibility for many types of DNA damage. If we assume that SSBs and DNA-to-protein crosslinks are random single events along the genome, it is possible to compute the number of events per cell genome per lethal event caused by the different energies used. In the near-uv and visible region, many more breaks and crosslinks are formed per lethal event than by far-uv. About 20 times more SSBs per lethal event are caused by 365-nm radiation than by x-rays, strong evidence that these breaks are effectively repaired. It is therefore likely that SSBs are not a serious event with regard to cellular lethality. The role of crosslinks and their repair in lethal events is less clear. The lack of any correlation at all between the action spectra for SSBs, or crosslinks, and lethality and mutagenesis in the same cells is evidence that another lesion or lesions are involved in these events. The multitude of chemical events that can be caused in cellular metabolites by the reactive species generated by these long wavelengths of radiation means that death is attributable to the total spectrum of changed chemicals delivered by a lethal dose, only some of which are DNA changes leading to SSBs and crosslinks. 43 refs., 3 figs., 2 tabs

  16. Stability in quadratic torsion theories

    Energy Technology Data Exchange (ETDEWEB)

    Vasilev, Teodor Borislavov; Cembranos, Jose A.R.; Gigante Valcarcel, Jorge; Martin-Moruno, Prado [Universidad Complutense de Madrid, Departamento de Fisica Teorica I, Madrid (Spain)

    2017-11-15

    We revisit the definition and some of the characteristics of quadratic theories of gravity with torsion. We start from a Lagrangian density quadratic in the curvature and torsion tensors. By assuming that General Relativity should be recovered when the torsion vanishes and investigating the behaviour of the vector and pseudo-vector torsion fields in the weak-gravity regime, we present a set of necessary conditions for the stability of these theories. Moreover, we explicitly obtain the gravitational field equations using the Palatini variational principle with the metricity condition implemented via a Lagrange multiplier. (orig.)

  17. Stability in quadratic torsion theories

    International Nuclear Information System (INIS)

    Vasilev, Teodor Borislavov; Cembranos, Jose A.R.; Gigante Valcarcel, Jorge; Martin-Moruno, Prado

    2017-01-01

    We revisit the definition and some of the characteristics of quadratic theories of gravity with torsion. We start from a Lagrangian density quadratic in the curvature and torsion tensors. By assuming that General Relativity should be recovered when the torsion vanishes and investigating the behaviour of the vector and pseudo-vector torsion fields in the weak-gravity regime, we present a set of necessary conditions for the stability of these theories. Moreover, we explicitly obtain the gravitational field equations using the Palatini variational principle with the metricity condition implemented via a Lagrange multiplier. (orig.)

  18. Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility.

    Science.gov (United States)

    Heffernan, Rhys; Yang, Yuedong; Paliwal, Kuldip; Zhou, Yaoqi

    2017-09-15

    The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some 'short to intermediate' non-local interactions. Here, we employed Long Short-Term Memory (LSTM) Bidirectional Recurrent Neural Networks (BRNNs) which are capable of capturing long range interactions without using a window. We showed that the application of LSTM-BRNN to the prediction of protein structural properties makes the most significant improvement for residues with the most long-range contacts (|i-j| >19) over a previous window-based, deep-learning method SPIDER2. Capturing long-range interactions allows the accuracy of three-state secondary structure prediction to reach 84% and the correlation coefficient between predicted and actual solvent accessible surface areas to reach 0.80, plus a reduction of 5%, 10%, 5% and 10% in the mean absolute error for backbone ϕ , ψ , θ and τ angles, respectively, from SPIDER2. More significantly, 27% of 182724 40-residue models directly constructed from predicted C α atom-based θ and τ have similar structures to their corresponding native structures (6Å RMSD or less), which is 3% better than models built by ϕ and ψ angles. We expect the method to be useful for assisting protein structure and function prediction. The method is available as a SPIDER3 server and standalone package at http://sparks-lab.org . yaoqi.zhou@griffith.edu.au or yuedong.yang@griffith.edu.au. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email

  19. Future High Capacity Backbone Networks

    DEFF Research Database (Denmark)

    Wang, Jiayuan

    are proposed. The work focuses on energy efficient routing algorithms in a dynamic optical core network environment, with Generalized MultiProtocol Label Switching (GMPLS) as the control plane. Energy ef- ficient routing algorithms for energy savings and CO2 savings are proposed, and their performance...... aiming for reducing the dynamic part of the energy consumption of the network may increase the fixed part of the energy consumption meanwhile. In the second half of the thesis, the conflict between energy efficiency and Quality of Service (QoS) is addressed by introducing a novel software defined......This thesis - Future High Capacity Backbone Networks - deals with the energy efficiency problems associated with the development of future optical networks. In the first half of the thesis, novel approaches for using multiple/single alternative energy sources for improving energy efficiency...

  20. Torsional Rigidity of Minimal Submanifolds

    DEFF Research Database (Denmark)

    Markvorsen, Steen; Palmer, Vicente

    2006-01-01

    We prove explicit upper bounds for the torsional rigidity of extrinsic domains of minimal submanifolds $P^m$ in ambient Riemannian manifolds $N^n$ with a pole $p$. The upper bounds are given in terms of the torsional rigidities of corresponding Schwarz symmetrizations of the domains in warped...

  1. Oophoropexy for Recurrent Ovarian Torsion

    Directory of Open Access Journals (Sweden)

    Jennifer Hartley

    2018-01-01

    Full Text Available A 31-year-old nulliparous patient presents with a three-day history of right sided colicky abdominal pain and associated nausea. This patient has previously presented twice with right sided ovarian torsion with the background of polycystic ovaries in the last two consecutive years. Blood tests were normal. Due to previous history, there was a high index of clinical suspicion that this may be a further torsion. Therefore, the patient was taken to theatre for a diagnostic laparoscopy and a further right sided ovarian torsion was noted. At this time, oophoropexy was performed to the uterosacral ligament to prevent further torsion in order to preserve the patients’ fertility. In this article, we detail this case and also provide a discussion of ovarian torsion including risk factors, presentation, and current thoughts on management.

  2. Torsion testing of bed joints

    DEFF Research Database (Denmark)

    Hansen, Klavs Feilberg; Pedersen, Carsten Mørk

    2008-01-01

    This paper describes a simple test method for determining the torsion strength of a single bed joint between two bricks and presents results from testing using this test method. The setup for the torsion test is well defined, require minimal preparation of the test specimen and the test can...... be carried out directly in a normal testing machine. The torsion strength is believed to be the most important parameter in out-of-plane resistance of masonry walls subjected to bending about an axis perpendicular to the bed joints. The paper also contains a few test results from bending of small walls about...... an axis perpendicular to the bed joints, which indicate the close connection between these results and results from torsion tests. These characteristics make the torsion strength well suited to act as substitute parameter for the bending strength of masonry about an axis perpendicular to the bed joints....

  3. Data Acquisition Backbone Core DABC

    International Nuclear Information System (INIS)

    Adamczewski, J; Essel, H G; Kurz, N; Linev, S

    2008-01-01

    For the new experiments at FAIR new concepts of data acquisition systems have to be developed like the distribution of self-triggered, time stamped data streams over high performance networks for event building. The Data Acquisition Backbone Core (DABC) is a software package currently under development for FAIR detector tests, readout components test, and data flow investigations. All kinds of data channels (front-end systems) are connected by program plug-ins into functional components of DABC like data input, combiner, scheduler, event builder, analysis and storage components. After detailed simulations real tests of event building over a switched network (InfiniBand clusters with up to 110 nodes) have been performed. With the DABC software more than 900 MByte/s input and output per node can be achieved meeting the most demanding requirements. The software is ready for the implementation of various test beds needed for the final design of data acquisition systems at FAIR. The development of key components is supported by the FutureDAQ project of the European Union (FP6 I3HP JRA1)

  4. Torsion in extra-dimensions

    International Nuclear Information System (INIS)

    Wali, Kameshwar C

    2010-01-01

    We consider a variant of the 5 dimensional Kaluza-Klein theory within the framework of Einstein-Cartan formalism. By imposing a set of constraints on torsion and Ricci rotation coefficients, we show that the torsion components are completely expressed in terms of the metric. and the Ricci tensor in 5D corresponds exactly to what one would obtain from torsion-free general relativity on a 4D hypersurface. The contributions of the scalar and vector fields of the standard K-K theory to the Ricci tensor and the affine connections are completely nullified by the contributions from the torsion. As a consequence, geodesic motions do not distinguish the torsion free 4D space-time from a hypersurface of 5D space-time with torsion satisfying the constraints. Since torsion is not an independent dynamical variable in this formalism, the modified Einstein equations are different from those in the general Einstein-Cartan theory. This leads to important cosmological consequences such as the emergence of cosmic acceleration.

  5. Ovarian torsion: Echographic discoveries

    International Nuclear Information System (INIS)

    Triana R, Gustavo; Navas O, Claudia

    1994-01-01

    Patient of 31 years who consulted to the even service of urgencies to present of two hours of evolution intense pain in flank and region lumbar left, associated to vomit, present square similar 5 previous days to the entrance in the right side. Go Po, plans with DIU FUR, 8 previous days to the square. It is practiced Tran abdominal pelvic echography that shows left ovary of 6 x 5 x 3 cms, with multiple follicular images, of thick walls, with I liquidate free abdominal, highly suggestive of ovarian torsion although the patient didn't present square of sharp abdomen. It decides to suspend analgesic and to value it, presented sharp abdominal pain, reason why laparotomy was practiced, finding mass of 6 x 6 cms. of necrotic aspect, corresponding to the left ovary, which presented three turns on their axis. It is taken finish left salpingooferectomy

  6. Re-torsion of the ovaries

    DEFF Research Database (Denmark)

    Hyttel, Trine E W; Bak, Geske S; Larsen, Solveig B

    2015-01-01

    The increasing use of de-torsion of the ovaries may result in re-torsion. This review addresses risk of re-torsion and describes preventive strategies to avoid re-torsion in pre-menarcheal girls, and fertile and pregnant women. We clinically reviewed PubMed, Embase, Trip and Cochrane databases. T...

  7. Hematosalpinx torsion in an adolescent

    Directory of Open Access Journals (Sweden)

    Inês Vaz

    2016-02-01

    Full Text Available Introduction: Isolated fallopian tube torsion is an uncommon cause of acute lower abdominal pain. Ectopic pregnancy, hydro or hematosalpinx, endometriosis, adnexal masses and other causes of adnexal disease are predisposing factors. The diagnosis is difficult and often delayed due to the lack of pathognomonic symptoms, characteristic physical signs, and specific imaging and laboratory studies. Defi nitive diagnosis requires a surgical approach. Case report: The authors present a case of hematosalpinx and its tubal torsion in a virgin teenager with no prior predisposing factors. Discussion: This rare case may highlight a new insight into pathophysiology of tubal torsion and recalls hematosalpinx as a differential diagnosis.

  8. Effect of backbone structure on charge transport along isolated conjugated polymer chains

    International Nuclear Information System (INIS)

    Siebbeles, Laurens D.A.; Grozema, Ferdinand C.; Haas, Matthijs P. de; Warman, John M.

    2005-01-01

    Fast charge transport in conjugated polymers is essential for their application in opto-electronic devices. In the present paper, measurements and theoretical modeling of the mobility of excess charges along isolated chains of conjugated polymers in dilute solution are presented. Charge carriers were produced by irradiation of the polymer solution with 3-MeV electrons from a Van de Graaff accelerator. The mobilities of the charges along the polymer chains were obtained from time-resolved microwave conductivity measurements. The mobilities are strongly dependent on the chemical nature of the polymer backbone. Comparison of the experimental data with results from ab initio quantum mechanical calculations shows that the measured mobilities are strongly limited by torsional disorder, chemical defects and chain ends. Improvement of the structure of polymer backbones is therefore expected to significantly enhance the performance of these materials in 'plastic electronics'

  9. 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.

  10. Isolated penile torsion in newborns.

    Science.gov (United States)

    Eroglu, Egemen; Gundogdu, Gokhan

    2015-01-01

    We reported on the incidence of isolated penile torsion among our healthy children and our approach to this anomaly. Between 2011 and 2014, newborn babies with penile torsion were classified according to the angle of torsion. Surgical correction (penile degloving and reattachment for moderate cases and dorsal dartos flap technique in case of resistance) after 6 months was advised to the babies with rotations more than 45°. Among 1000 newborn babies, 200 isolated penile torsions were found, and among these, 43 had torsions more than 45°, and 4 of these had angles greater than 90°. The mean angle of the rotations was found 30.45° (median: 20°). In total, 8 children with 60° torsions were previously circumcised. Surgery was performed on 19 patients, with a mean patient age of 12 ± 2 months. Of these 19, 13 babies were corrected with degloving and reattachment. This technique was not enough on the remaining 6 patients; therefore, derotational dorsal dartos flap was added to correct the torsion. After a mean of 15.6 ± 9.8 months, residual penile rotation, less than 15°, was found only in 2 children. The incidence of isolated penile torsion is 20% in newborns. However, rotation more than 45° angles are seen in 4.3% of male babies. Correction is not necessary in mild degrees, and penile degloving with reattachment is enough in most cases. If the initial correction is insufficient, dorsal dartos flap rotation is easy and effective. Prior circumcision neither disturbs the operative procedure nor affects the outcomes.

  11. Optical burst switching based satellite backbone network

    Science.gov (United States)

    Li, Tingting; Guo, Hongxiang; Wang, Cen; Wu, Jian

    2018-02-01

    We propose a novel time slot based optical burst switching (OBS) architecture for GEO/LEO based satellite backbone network. This architecture can provide high speed data transmission rate and high switching capacity . Furthermore, we design the control plane of this optical satellite backbone network. The software defined network (SDN) and network slice (NS) technologies are introduced. Under the properly designed control mechanism, this backbone network is flexible to support various services with diverse transmission requirements. Additionally, the LEO access and handoff management in this network is also discussed.

  12. Backbone dynamics of a model membrane protein: measurement of individual amide hydrogen-exchange rates in detergent-solubilized M13 coat protein using 13C NMR hydrogen/deuterium isotope shifts

    International Nuclear Information System (INIS)

    Henry, G.D.; Weiner, J.H.; Sykes, B.D.

    1987-01-01

    Hydrogen-exchange rates have been measured for individual assigned amide protons in M13 coat protein, a 50-residue integral membrane protein, using a 13 C nuclear magnetic resonance (NMR) equilibrium isotope shift technique. The locations of the more rapidly exchanging amides have been determined. In D 2 O solutions, a peptide carbonyl resonance undergoes a small upfield isotope shift (0.08-0.09 ppm) from its position in H 2 O solutions; in 1:1 H 2 O/D 2 O mixtures, the carbonyl line shape is determined by the exchange rate at the adjacent nitrogen atom. M13 coat protein was labeled biosynthetically with 13 C at the peptide carbonyls of alanine, glycine, phenylalanine, proline, and lysine, and the exchange rates of 12 assigned amide protons in the hydrophilic regions were measured as a function of pH by using the isotope shift method. This equilibrium technique is sensitive to the more rapidly exchanging protons which are difficult to measure by classical exchange-out experiments. In proteins, structural factors, notably H bonding, can decrease the exchange rate of an amide proton by many orders of magnitude from that observed in the freely exposed amides of model peptides such as poly(DL-alanine). With corrections for sequence-related inductive effects, the retardation of amide exchange in sodium dodecyl sulfate solubilized coat protein has been calculated with respect to poly(DL-alanine). The most rapidly exchanging protons, which are retarded very little or not at all, are shown to occur at the N- and C-termini of the molecule. A model of the detergent-solubilized coat protein is constructed from these H-exchange data which is consistent with circular dichroism and other NMR results

  13. Torsional carbon nanotube artificial muscles.

    Science.gov (United States)

    Foroughi, Javad; Spinks, Geoffrey M; Wallace, Gordon G; Oh, Jiyoung; Kozlov, Mikhail E; Fang, Shaoli; Mirfakhrai, Tissaphern; Madden, John D W; Shin, Min Kyoon; Kim, Seon Jeong; Baughman, Ray H

    2011-10-28

    Rotary motors of conventional design can be rather complex and are therefore difficult to miniaturize; previous carbon nanotube artificial muscles provide contraction and bending, but not rotation. We show that an electrolyte-filled twist-spun carbon nanotube yarn, much thinner than a human hair, functions as a torsional artificial muscle in a simple three-electrode electrochemical system, providing a reversible 15,000° rotation and 590 revolutions per minute. A hydrostatic actuation mechanism, as seen in muscular hydrostats in nature, explains the simultaneous occurrence of lengthwise contraction and torsional rotation during the yarn volume increase caused by electrochemical double-layer charge injection. The use of a torsional yarn muscle as a mixer for a fluidic chip is demonstrated.

  14. Torsional rigidity, isospectrality and quantum graphs

    International Nuclear Information System (INIS)

    Colladay, Don; McDonald, Patrick; Kaganovskiy, Leon

    2017-01-01

    We study torsional rigidity for graph and quantum graph analogs of well-known pairs of isospectral non-isometric planar domains. We prove that such isospectral pairs are distinguished by torsional rigidity. (paper)

  15. Dirac operators and Killing spinors with torsion

    International Nuclear Information System (INIS)

    Becker-Bender, Julia

    2012-01-01

    On a Riemannian spin manifold with parallel skew torsion, we use the twistor operator to obtain an eigenvalue estimate for the Dirac operator with torsion. We consider the equality case in dimensions four and six. In odd dimensions we describe Sasaki manifolds on which equality in the estimate is realized by Killing spinors with torsion. In dimension five we characterize all Killing spinors with torsion and obtain certain naturally reductive spaces as exceptional cases.

  16. The odd side of torsion geometry

    DEFF Research Database (Denmark)

    Conti, Diego; Madsen, Thomas Bruun

    2014-01-01

    We introduce and study a notion of `Sasaki with torsion structure' (ST) as an odd-dimensional analogue of Kähler with torsion geometry (KT). These are normal almost contact metric manifolds that admit a unique compatible connection with 3-form torsion. Any odd-dimensional compact Lie group is sho...

  17. Pediatric ovarian torsion: an uncommon clinical entity

    OpenAIRE

    Rajwani, Kapil M; Mahomed, Anies

    2014-01-01

    Key Clinical Message Pediatric ovarian torsion is an infrequent diagnosis and it often mimics acute appendicitis. Most cases are due to underlying ovarian pathology and if left untreated, ovarian torsion may eventually cause peritonitis. Emergency exploratory laparoscopy represents a valuable diagnostic and therapeutic tool in suspected ovarian torsion.

  18. Green Network Planning Model for Optical Backbones

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir; Jensen, Michael

    2010-01-01

    on the environment in general. In network planning there are existing planning models focused on QoS provisioning, investment minimization or combinations of both and other parameters. But there is a lack of a model for designing green optical backbones. This paper presents novel ideas to be able to define......Communication networks are becoming more essential for our daily lives and critically important for industry and governments. The intense growth in the backbone traffic implies an increment of the power demands of the transmission systems. This power usage might have a significant negative effect...

  19. Saccular impact on ocular torsion

    NARCIS (Netherlands)

    Graaf, B. de; Bos, J.E.; Groen, E.L.

    1996-01-01

    When someone is tilted laterally the sheer force on the maculae of the utriculus and the sacculus is described by the sine and the cosine of the angle of tilt, respectively. So both the sacculus and the utriculus are stimulated, but in the litera-ture ocular torsion is normally attributed to

  20. Torsion (volvulus) of the lung

    International Nuclear Information System (INIS)

    Felson, B.

    1986-01-01

    Torsion or volvulus of the lung is a relatively rare but serious condition that can often be recognized or at least suspected radiographically. It occurs under three different sets of circumstances: spontaneously, usually in association with some other pulmonary abnormality; with traumatic pneumothorax; and as a complication of thoracic surgery. The author studied nine cases of torsion of the lung, including examples from each of these categories. The radiographic signs of torsion are as follows: a collapsed or consolidated lobe that occupies an unusual position, hilar displacement in a direction inappropriate for an apparently collapsed lobe, alteration of the normal position and sweep of the pulmonary vasculature, raid opacification of an ipsilateral lobe after trauma or lobectomy, marked change in position of an opacified lobe on sequential films, bronchial cutoff with no evidence of a mass, abnormal position of an affected lobe (shown on CT, angiography, or bronchography), and lobar air trapping. Mortality is high if the torsion goes unrecognized and operation is delayed

  1. “Pinning strategy”: a novel approach for predicting the backbone ...

    Indian Academy of Sciences (India)

    Prakash

    To assess the quality of the strategy, we define two measures. The first one ...... modular framework of the protein backbone; Protein Eng. 12. 1063–1073 .... Richardson J S, Getzoff E D and Richardson D C 1978 The beta bulge: a common ...

  2. Backbone Diversity Analysis in Catalyst Design

    NARCIS (Netherlands)

    Maldonado, A.G.; Hageman, J.A.; Mastroianni, S.; Rothenberg, G.

    2009-01-01

    We present a computer-based heuristic framework for designing libraries of homogeneous catalysts. In this approach, a set of given bidentate ligand-metal complexes is disassembled into key substructures (building blocks). These include metal atoms, ligating groups, backbone groups, and residue

  3. ExScal Backbone Network Architecture

    Science.gov (United States)

    2005-01-01

    802.11 battery powered nodes was laid over the sensor network. We adopted the Stargate platform for the backbone tier to serve as the basis for...its head. XSS Hardware and Network: XSS stands for eXtreme Scaling Stargate . A stargate is a linux-based single board computer. It has a 400 MHz

  4. Versatile phosphite ligands based on silsesquioxane backbones

    NARCIS (Netherlands)

    van der Vlugt, JI; Ackerstaff, J; Dijkstra, TW; Mills, AM; Kooijman, H; Spek, AL; Meetsma, A; Abbenhuis, HCL; Vogt, D

    Silsesquioxanes are employed as ligand backbones for the synthesis of novel phosphite compounds with 3,3'-5,5'-tetrakis(tert-butyl)-2,2'-di-oxa-1,1'-biphenyl substituents. Both mono- and bidentate phosphites are prepared in good yields. Two types of silsesquioxanes are employed as starting

  5. TORSION OF THE VERMIFORM APPENDIX: A CASE REPORT

    Directory of Open Access Journals (Sweden)

    Dr. Imtiaz Wani

    2009-07-01

    Full Text Available Torsion of the vermiform appendix is a rare condition with few cases reported in the literature. Various factors predispose to torsion. Various factors predispose to torsion. We report a case of primary torsion of the vermiform appendix. The clinical presentation was indistinguishable from acute appendicitis and the diagnosis was made at operation. Appendix was preileal in position and the direction of torsion was anticlockwise. There was intrinsic torsion with no obvious factor for torsion identified. Appendectomy was performed.

  6. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

    Science.gov (United States)

    Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

    2015-01-01

    Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from

  7. Torsional oscillations of the sun

    International Nuclear Information System (INIS)

    Snodgrass, H.B.; Howard, R.; National Solar Observatory, Tucson, AZ)

    1985-01-01

    The sun's differential rotation has a cyclic pattern of change that is tightly correlated with the sunspot, or magnetic activity, cycle. This pattern can be described as a torsional oscillation, in which the solar rotation is periodically sped up or slowed down in certain zones of latitude while elsewhere the rotation remains essentially steady. The zones of anomalous rotation move on the sun in wavelike fashion, keeping pace with and flanking the zones of magnetic activity. It is uncertain whether this torsional oscillation is a globally coherent ringing of the sun or whether it is a local pattern caused by and causing local changes in the magnetic fields. In either case, it may be an important link in the connection between the rotation and the cycle that is widely believed to exist but is not yet understood. 46 references

  8. Torsions of 3-dimensional manifolds

    CERN Document Server

    Wurzbacher, T

    2002-01-01

    From the reviews: "This is an excellent exposition about abelian Reidemeister torsions for three-manifolds." ―Zentralblatt Math "This monograph contains a wealth of information many topologists will find very handy. …Many of the new points of view pioneered by Turaev are gradually becoming mainstream and are spreading beyond the pure topology world. This monograph is a timely and very useful addition to the scientific literature." ―Mathematical Reviews

  9. Moduli space of torsional manifolds

    International Nuclear Information System (INIS)

    Becker, Melanie; Tseng, L.-S.; Yau, S.-T.

    2007-01-01

    We characterize the geometric moduli of non-Kaehler manifolds with torsion. Heterotic supersymmetric flux compactifications require that the six-dimensional internal manifold be balanced, the gauge bundle be Hermitian Yang-Mills, and also the anomaly cancellation be satisfied. We perform the linearized variation of these constraints to derive the defining equations for the local moduli. We explicitly determine the metric deformations of the smooth flux solution corresponding to a torus bundle over K3

  10. Using torsion to manipulate spin currents

    Science.gov (United States)

    Fumeron, Sébastien; Berche, Bertrand; Medina, Ernesto; Santos, Fernando A. N.; Moraes, Fernando

    2017-02-01

    We address the problem of quantum particles moving on a manifold characterised by the presence of torsion along a preferential axis. In fact, such a torsion may be taylored by the presence of a single screw dislocation, whose Burgers vector measures the torsion amplitude. The problem, first treated in the relativistic limit describing fermions that couple minimally to torsion, is then analysed in the Pauli limit. We show that torsion induces a geometric potential and also that it couples generically to the phase of the wave function, giving rise to the possibility of using torsion to manipulate spin currents in the case of spinor wave functions. These results emerge as an alternative strategy for using screw dislocations in the design of spintronic-based devices.

  11. Newton-Cartan gravity and torsion

    Science.gov (United States)

    Bergshoeff, Eric; Chatzistavrakidis, Athanasios; Romano, Luca; Rosseel, Jan

    2017-10-01

    We compare the gauging of the Bargmann algebra, for the case of arbitrary torsion, with the result that one obtains from a null-reduction of General Relativity. Whereas the two procedures lead to the same result for Newton-Cartan geometry with arbitrary torsion, the null-reduction of the Einstein equations necessarily leads to Newton-Cartan gravity with zero torsion. We show, for three space-time dimensions, how Newton-Cartan gravity with arbitrary torsion can be obtained by starting from a Schrödinger field theory with dynamical exponent z = 2 for a complex compensating scalar and next coupling this field theory to a z = 2 Schrödinger geometry with arbitrary torsion. The latter theory can be obtained from either a gauging of the Schrödinger algebra, for arbitrary torsion, or from a null-reduction of conformal gravity.

  12. Experiments with a cryogenic torsion balance

    International Nuclear Information System (INIS)

    Newman, R.D.

    1983-01-01

    The torsion balance is a remarkably capable instrument for the measurement of slowly varying exceedingly small forces; indeed its potential abilities are still largely untapped. The author outlines some of the virtues (and limitations) of the torsion balance, and presents a menu of gravitation-related experiments to which it may be applied. He discusses plans for developing torsion balances operating at cryogenic temperatures, and describes an experiment to search for anomalous long-range interactions associated with intrinsic spin. (Auth.)

  13. Dirac operators and Killing spinors with torsion; Dirac-Operatoren und Killing-Spinoren mit Torsion

    Energy Technology Data Exchange (ETDEWEB)

    Becker-Bender, Julia

    2012-12-17

    On a Riemannian spin manifold with parallel skew torsion, we use the twistor operator to obtain an eigenvalue estimate for the Dirac operator with torsion. We consider the equality case in dimensions four and six. In odd dimensions we describe Sasaki manifolds on which equality in the estimate is realized by Killing spinors with torsion. In dimension five we characterize all Killing spinors with torsion and obtain certain naturally reductive spaces as exceptional cases.

  14. Primary splenic torsion in a Boston terrier.

    Science.gov (United States)

    OHTA, Hiroshi; TAKAGI, Satoshi; MURAKAMI, Masahiro; SASAKI, Noboru; YOSHIKAWA, Muneyoshi; NAKAMURA, Kensuke; HWANG, Shiang-Jyi; YAMASAKI, Masahiro; TAKIGUCHI, Mitsuyoshi

    2009-11-01

    A 7-year-old female Boston terrier was referred to Hokkaido University Veterinary Teaching Hospital with a history of hemoglobinuria and anemia for several days. Abdominal radiographs showed splenomegaly, and ultrasonography revealed a hypoechoic splenic parenchyma with interspersed linear echoes consistent with the ultrasonographic appearance of splenic torsion. Ultrasonography and computed tomography (CT) indicated a C-shaped spleen. Exploratory laparotomy confirmed the diagnosis of splenic torsion. A splenectomy was performed, and the dog recovered well without complications. This is the first report of splenic torsion in Boston terriers, and the usefulness of ultrasonographic and CT findings of the splenic torsion was also confirmed.

  15. Primary splenic torsion in a Boston terrier

    International Nuclear Information System (INIS)

    Ohta, H.; Takagi, S.; Murakami, M.; Sasaki, N.; Yoshikawa, M.; Nakamura, K.; Hwang, S.J.; Yamasaki, M.; Takiguchi, M.

    2009-01-01

    A 7-year-old female Boston terrier was referred to Hokkaido University Veterinary Teaching Hospital with a history of hemoglobinuria and anemia for several days. Abdominal radiographs showed splenomegaly, and ultrasonography revealed a hypoechoic splenic parenchyma with interspersed linear echoes consistent with the ultrasonographic appearance of splenic torsion. Ultrasonography and computed tomography (CT) indicated a C-shaped spleen. Exploratory laparotomy confirmed the diagnosis of splenic torsion. A splenectomy was performed, and the dog recovered well without complications. This is the first report of splenic torsion in Boston terriers, and the usefulness of ultrasonographic and CT findings of the splenic torsion was also confirmed

  16. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus sidechain groups to chain expansion via chemical denaturation

    Science.gov (United States)

    Holehouse, Alex S.; Garai, Kanchan; Lyle, Nicholas; Vitalis, Andreas; Pappu, Rohit V.

    2015-01-01

    In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones and therefore backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of sidechains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that sidechains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of sidechain-mediated interactions as determinants of the

  17. Porous solid backbone impregnation for electrochemical energy conversion systems

    KAUST Repository

    Boulfrad, Samir

    2013-09-19

    An apparatus and method for impregnating a porous solid backbone. The apparatus may include a platform for holding a porous solid backbone, an ink jet nozzle configured to dispense a liquid solution onto the porous solid backbone, a positioning mechanism configured to position the ink jet nozzle proximate to a plurality of locations of the porous solid backbone, and a control unit configured to control the positioning mechanism to position the ink jet nozzle proximate to the plurality of locations and cause the ink jet nozzle to dispense the liquid solution onto the porous solid backbone.

  18. Porous solid backbone impregnation for electrochemical energy conversion systems

    KAUST Repository

    Boulfrad, Samir; Jabbour, Ghassan

    2013-01-01

    An apparatus and method for impregnating a porous solid backbone. The apparatus may include a platform for holding a porous solid backbone, an ink jet nozzle configured to dispense a liquid solution onto the porous solid backbone, a positioning mechanism configured to position the ink jet nozzle proximate to a plurality of locations of the porous solid backbone, and a control unit configured to control the positioning mechanism to position the ink jet nozzle proximate to the plurality of locations and cause the ink jet nozzle to dispense the liquid solution onto the porous solid backbone.

  19. Torsion of a growing shaft

    Directory of Open Access Journals (Sweden)

    Alexander V. Manzhirov

    2017-12-01

    Full Text Available The torsion of a shaft by rigid disks is considered. The shaft has the form of circular cylinder. Two rigid disks are attached to its end faces. The process of continuous growth of such shaft under the influence of twisting torques applied to the disks is studied. Dual series equations which reflect the mathematical content of the problem at the different stages of the growing process are derived and solved. Results of the numerical analysis and singularities of the qualitative mechanical behaviour of the fundamental characteristics are discussed.

  20. Peptoid-Peptide hybrid backbone architectures

    DEFF Research Database (Denmark)

    Olsen, Christian Adam

    2010-01-01

    Peptidomimetic oligomers and foldamers have received considerable attention for over a decade, with beta-peptides and the so-called peptoids (N-alkylglycine oligomers) representing prominent examples of such architectures. Lately, hybrid or mixed backbones consisting of both alpha- and beta......-amino acids (alpha/beta-peptides) have been investigated in some detail as well. The present Minireview is a survey of the literature concerning hybrid structures of alpha-amino acids and peptoids, including beta-peptoids (N-alkyl-beta-alanine oligomers), and is intended to give an overview of this area...

  1. Instant Backbone.js application development

    CERN Document Server

    Hunter, Thomas

    2013-01-01

    Get to grips with a new technology, understand what it is and what it can do for you, and then get to work with the most important features and tasks. This book is a practical, step-by-step tutorial that will teach you to build Backbone.js applications quickly and efficiently.This book is targeted towards developers. It is assumed that you have at least a basic understanding of JavaScript and jQuery selectors. If you are interested in building dynamic Single Page Applications that interact heavily with a backend server, then this is the book for you.

  2. Teenage testicular torsion. | Onuigbo | International Journal of ...

    African Journals Online (AJOL)

    Aim: To study testicular torsion in teenagers in the Igbo community. Method: A retrospective study was carried out as regards requests for pathological examination of specimens received at a Regional Reference Laboratory based in Enugu. Results: Over a period of 30 years, 28 surgical specimens of testicular torsion in ...

  3. Right paratesticular abscess mimicking neonatal testicular torsion ...

    African Journals Online (AJOL)

    U.O. Ezomike

    Abstract. The clinical presentation of neonatal paratesticular abscess may closely resemble that of, neonatal testicular torsion and the use of scrotal ultrasonography to differentiate the two has low, sensitivity. We propose early operative treatment of suspected neonatal testicular torsion to salvage, the testicle in cases of ...

  4. Simultaneous acute appendicitis with right testicular torsion

    Directory of Open Access Journals (Sweden)

    Tanveer Akhtar

    2012-01-01

    Full Text Available We present a child with both acute appendicitis and torsion of the right testis presenting at the same time. Testicular torsion possibly occurring due to vomiting in acute appendicitis so far has not been reported in the literature.

  5. Appendicular Torsion | Dubhashi | Nigerian Journal of Surgery

    African Journals Online (AJOL)

    . It can be primary or secondary. This is a case report of 52-year-old female with 180° anti-clockwise rotation of the appendix. Torsion can further leads to strangulation and infarction of the organ. Appendicular torsion could be included in the ...

  6. Optically probing torsional superelasticity in spider silks

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Bhupesh; Thakur, Ashish; Panda, Biswajit; Singh, Kamal P. [Department of Physical Sciences, IISER Mohali, Sector 81, Manauli, Mohali 140306 (India)

    2013-11-11

    We investigate torsion mechanics of various spider silks using a sensitive optical technique. We find that spider silks are torsionally superelastic in that they can reversibly withstand great torsion strains of over 10{sup 2−3} rotations per cm before failure. Among various silks from a spider, we find the failure twist-strain is greatest in the sticky capture silk followed by dragline and egg-case silk. Our in situ laser-diffraction measurements reveal that torsional strains on the silks induce a nano-scale transverse compression in its diameter that is linear and reversible. These unique torsional properties of the silks could find applications in silk-based materials and devices.

  7. Optically probing torsional superelasticity in spider silks

    International Nuclear Information System (INIS)

    Kumar, Bhupesh; Thakur, Ashish; Panda, Biswajit; Singh, Kamal P.

    2013-01-01

    We investigate torsion mechanics of various spider silks using a sensitive optical technique. We find that spider silks are torsionally superelastic in that they can reversibly withstand great torsion strains of over 10 2−3 rotations per cm before failure. Among various silks from a spider, we find the failure twist-strain is greatest in the sticky capture silk followed by dragline and egg-case silk. Our in situ laser-diffraction measurements reveal that torsional strains on the silks induce a nano-scale transverse compression in its diameter that is linear and reversible. These unique torsional properties of the silks could find applications in silk-based materials and devices

  8. Structural insights into the backbone-circularized granulocyte colony-stimulating factor containing a short connector.

    Science.gov (United States)

    Miyafusa, Takamitsu; Shibuya, Risa; Honda, Shinya

    2018-06-02

    Backbone circularization is a powerful approach for enhancing the structural stability of polypeptides. Herein, we present the crystal structure of the circularized variant of the granulocyte colony-stimulating factor (G-CSF) in which the terminal helical region was circularized using a short, two-amino acid connector. The structure revealed that the N- and C-termini were indeed connected by a peptide bond. The local structure of the C-terminal region transited from an α helix to 3 10 helix with a bend close to the N-terminal region, indicating that the structural change offset the insufficient length of the connector. This is the first-ever report of a crystal structure of the backbone of a circularized protein. It will facilitate the development of backbone circularization methodology. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Protonation–deprotonation of the glycine backbone as followed by Raman scattering and multiconformational analysis

    Energy Technology Data Exchange (ETDEWEB)

    Hernández, Belén; Pflüger, Fernando [Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex (France); Kruglik, Sergei G. [Laboratoire Jean Perrin, FRE 3231, Université Pierre et Marie Curie (Paris 6), Case courrier 138, 75252 Paris Cedex 05 (France); Ghomi, Mahmoud, E-mail: mahmoud.ghomi@univ-paris13.fr [Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex (France)

    2013-11-08

    Highlights: • New pH-dependent Raman spectra in the middle wavenumber region (1800-300 cm{sup −1}). • New quantum mechanical calculations for exploring the Gly conformational landscape. • Construction of muticonformation based theoretical Raman spectra. - Abstract: Because of the absence of the side chain in its chemical structure and its well defined Raman spectra, glycine was selected here to follow its backbone protonation–deprotonation. The scan of the recorded spectra in the 1800–300 cm{sup −1} region led us to assign those obtained at pH 1, 6 and 12 to the cationic, zwitterionic and anionic species, respectively. These data complete well those previously published by Bykov et al. (2008) [16] devoted to the high wavenumber Raman spectra (>2500 cm{sup −1}). To reinforce our discussion, DFT calculations were carried out on the clusters of glycine + 5H{sub 2}O, mimicking reasonably the first hydration shell of the amino acid. Geometry optimization of 141 initial clusters, reflecting plausible combinations of the backbone torsion angles, allowed exploration of the conformational features, as well as construction of the theoretical Raman spectra by considering the most stable clusters containing each glycine species.

  10. Nonribosomal biosynthesis of backbone-modified peptides

    Science.gov (United States)

    Niquille, David L.; Hansen, Douglas A.; Mori, Takahiro; Fercher, David; Kries, Hajo; Hilvert, Donald

    2018-03-01

    Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-β-Phe with near-native specificity and efficiency. A co-crystal structure with a non-hydrolysable aminoacyl-AMP analogue reveals the origins of the 40,000-fold α/β-specificity switch, illuminating subtle but precise remodelling of the active site. When the engineered catalyst was paired with downstream module(s), (S)-β-Phe-containing peptides were produced at preparative scale in vitro (~1 mmol) and high titres in vivo (~100 mg l-1), highlighting the potential of biosynthetic pathway engineering for the construction of novel nonribosomal β-frameworks.

  11. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.

    Science.gov (United States)

    Lapidoth, Gideon D; Baran, Dror; Pszolla, Gabriele M; Norn, Christoffer; Alon, Assaf; Tyka, Michael D; Fleishman, Sarel J

    2015-08-01

    Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity. © 2015 Wiley Periodicals, Inc.

  12. Studies of torsional properties of DNA and nucleosomes using angular optical trapping

    Science.gov (United States)

    Sheinin, Maxim Y.

    DNA in vivo is subjected to torsional stress due to the action of molecular motors and other DNA-binding proteins. Several decades of research have uncovered the fascinating diversity of DNA transformations under torsion and the important role they play in the regulation of vital cellular processes such as transcription and replication. Recent studies have also suggested that torsion can influence the structure and stability of nucleosomes---basic building blocks of the eukaryotic genome. However, our understanding of the impact of torsion is far from being complete due to significant experimental challenges. In this work we have used a powerful single-molecule experimental technique, angular optical trapping, to address several long-standing issues in the field of DNA and nucleosome mechanics. First, we utilized the high resolution and direct torque measuring capability of the angular optical trapping to precisely measure DNA twist-stretch coupling. Second, we characterized DNA melting under tension and torsion. We found that torsionally underwound DNA forms a left-handed structure, significantly more flexible compared to the regular B-DNA. Finally, we performed the first comprehensive investigation of the single nucleosome behavior under torque and force. Importantly, we discovered that positive torque causes significant dimer loss, which can have implications for transcription through chromatin.

  13. Extracting the information backbone in online system.

    Science.gov (United States)

    Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

    2013-01-01

    Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such "less can be more" feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency.

  14. Torsion of the vermiform appendix: A case report | Wani | Internet ...

    African Journals Online (AJOL)

    Torsion of the vermiform appendix is a rare condition with few cases reported in the literature. Various factors predispose to torsion. Various factors predispose to torsion. We report a case of primary torsion of the vermiform appendix. The clinical presentation was indistinguishable from acute appendicitis and the diagnosis ...

  15. Measurement of tibial torsion by computer tomography

    Energy Technology Data Exchange (ETDEWEB)

    Jend, H.H.; Heller, M.; Dallek, M.; Schoettle, H. (Hamburg Univ. (Germany, F.R.))

    1981-01-01

    A CT procedure for objective measurements of tibial torsion independent of axial rotation in the nearby joints is described. Transverse sections in defined planes of the tibia permit easy calculation of normal and abnormal congenital or posttraumatic angles of torsion. In 69 limbs normal tibial torsion was 40/sup 0/+-9/sup 0/. In a series of 42 limbs with complicated healing of a fracture of both bones of the leg it is shown that tibial maltorsion is a deformity which in most cases leads to arthrosis of the ankle joint.

  16. Torsion of wandering spleen and distal pancreas

    International Nuclear Information System (INIS)

    Sheflin, J.R.; Lee, C.M.; Kretchmar, K.A.

    1984-01-01

    Wandering spleen is the term applied to the condition in which a long pedicle allows the spleen to lie in an abnormal location. Torsion of a wandering spleen is an unusual cause of an acute abdomen and is rarely diagnosed preoperatively. Associated torsion of the distal pancreas is even more uncommon. The authors describe a patient with torsion of a wandering spleen and distal pancreas, who was correctly diagnosed, and define the merits of the imaging methods used. The initial examination should be 99 /sup m/Tc-sulfur colloid liner-spleen scanning

  17. Measurement of tibial torsion by computer tomography

    International Nuclear Information System (INIS)

    Jend, H.-H.; Heller, M.; Dallek, M.; Schoettle, H.

    1981-01-01

    A CT procedure for objective measurements of tibial torsion independent of axial rotation in the nearby joints is described. Transverse sections in defined planes of the tibia permit easy calculation of normal and abnormal congenital or posttraumatic angles of torsion. In 69 limbs normal tibial torsion was 40 0 +-9 0 . In a series of 42 limbs with complicated healing of a fracture of both bones of the leg it is shown that tibial maltorsion is a deformity which in most cases leads to arthrosis of the ankle joint. (Auth.)

  18. Global Transcriptional Regulation of Backbone Genes in Broad-Host-Range Plasmid RA3 from the IncU Group Involves Segregation Protein KorB (ParB Family).

    Science.gov (United States)

    Kulinska, Anna; Godziszewska, Jolanta; Wojciechowska, Anna; Ludwiczak, Marta; Jagura-Burdzy, Grazyna

    2016-04-01

    The KorB protein of the broad-host-range conjugative plasmid RA3 from the IncU group belongs to the ParB family of plasmid and chromosomal segregation proteins. As a partitioning DNA-binding factor, KorB specifically recognizes a 16-bp palindrome which is an essential motif in the centromere-like sequence parSRA3, forms a segrosome, and together with its partner IncC (ParA family) participates in active DNA segregation ensuring stable plasmid maintenance. Here we show that by binding to this palindromic sequence, KorB also acts as a repressor for the adjacent mobC promoter driving expression of the mobC-nicoperon, which is involved in DNA processing during conjugation. Three other promoters, one buried in the conjugative transfer module and two divergent promoters located at the border between the replication and stability regions, are regulated by KorB binding to additional KorB operators (OBs). KorB acts as a repressor at a distance, binding to OBs separated from their cognate promoters by between 46 and 1,317 nucleotides. This repressor activity is facilitated by KorB spreading along DNA, since a polymerization-deficient KorB variant with its dimerization and DNA-binding abilities intact is inactive in transcriptional repression. KorB may act as a global regulator of RA3 plasmid functions in Escherichia coli, since its overexpression in transnegatively interferes with mini-RA3 replication and stable maintenance of RA3. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  19. High Performance Infiltrated Backbones for Cathode-Supported SOFC's

    DEFF Research Database (Denmark)

    Gil, Vanesa; Kammer Hansen, Kent

    2014-01-01

    The concept of using highly ionic conducting backbones with subsequent infiltration of electronically conducting particles has widely been used to develop alternative anode-supported SOFC's. In this work, the idea was to develop infiltrated backbones as an alternative design based on cathode......, microstructural characterization and electrochemical testing are discussed. Data on polarization resistance, Rp, are obtained from impedance spectra recorded on quasi-symmetrical cells (YSZ backbones/YSZ/LSM-YSZ (screen printed)). The backbones are infiltrated with LSM and compared to a standard LSM-YSZ screen...

  20. Effects of temperature and torsion speed on torsional properties of single-walled carbon nanotubes

    International Nuclear Information System (INIS)

    Khoei, A.R.; Ban, E.; Banihashemi, P.; Abdolhosseini Qomi, M.J.

    2011-01-01

    Carbon nanotubes (CNTs) are excellent candidates for torsional elements used in nanoelectro-mechanical systems (NEMS). Simulations show that after being twisted to a certain angle, they buckle and lose their mechanical strength. In this paper, classical molecular dynamics simulations are performed on single-walled carbon nanotubes (CNTs) to investigate the effects of torsion speed and temperature on CNT torsional properties. The AIREBO potential is employed to describe the bonded interactions between carbon atoms. The MD simulations clearly show that the buckling of CNTs in torsion is a reversible process, in which by unloading the buckled CNT in opposite direction, it returns to its original configuration. In addition, the numerical results reveal that the torsional shear modulus of CNTs increases by increasing the temperature and decreasing the torsion speed. Furthermore, the buckling torsion angle of CNTs increases by increasing the torsion speed and decreasing the temperature. Finally, it is observed that torsional properties of CNTs are highly affected by speed of twist and temperature of the nanotubes.

  1. Torsion sensing based on patterned piezoelectric beams

    Science.gov (United States)

    Cha, Youngsu; You, Hangil

    2018-03-01

    In this study, we investigated the sensing characteristics of piezoelectric beams under torsional loads. We used partially patterned piezoelectric beams to sense torsion. In particular, the piezoelectric patches are located symmetrically with respect to the line of the shear center of the beam. The patterned piezoelectric beam is modeled as a slender beam, and its electrical responses are obtained by piezoelectric electromechanical equations. To validate the modeling framework, experiments are performed using a setup that forces pure torsional deformation. Three different geometric configurations of the patterned piezoelectric layer are used for the experiments. The frequency and amplitude of the forced torsional load are systematically varied in order to study the behavior of the piezoelectric sensor. Experimental results demonstrate that two voltage outputs of the piezoelectric beam are approximately out of phase with identical amplitude. Moreover, the length of the piezoelectric layers has a significant influence on the sensing properties. Our theoretical predictions using the model support the experimental findings.

  2. Torsion, supersymmetry, and the heterotic string

    International Nuclear Information System (INIS)

    Curtright, T.

    1985-01-01

    The dynamical effects of torsion are summarized for bosonic and supersymmetric sigma models in two spacetime dimensions. Analogous structure for the heterotic superstring is discussed, including the presence of nonlinear realizations of supersymmetry on the world-sheet. 27 refs

  3. Isolated torsion of fallopian tube. Radiological findings

    International Nuclear Information System (INIS)

    Tomas Fanjul, L.; Aldea Martinez, J.; Fernandez Matia, G.; Rodrigo Verguizas, J.; Fernandez Alvarez, G.; Galindo Vicente, M.C.

    1993-01-01

    Isolated tubal torsion is a very uncommon disorder that is rarely diagnosed preoperatively. We present a case and review the literature, which only provides ultrasonographic findings in 5 cases reported to date. 11 refs

  4. Doubly graded sigma model with torsion

    International Nuclear Information System (INIS)

    Kowalski-Glikman, J.

    1986-08-01

    Using the Hull-Witten construction we show how to introduce torsion to the doubly graded sigma model. This construction enables us to find a link between this model and the ten-dimensional supergravity theory in superspace. (Auth.)

  5. Electrostatically actuated torsional resonant sensors and switches

    KAUST Repository

    Younis, Mohammad I.

    2016-01-01

    Embodiments in accordance of a torsional resonant sensor disclosure is configured to actuate a beam structure using electrostatic actuation with an AC harmonic load (e.g., AC and DC voltage sources) that is activated upon detecting a particular

  6. Torsion and geometrostasis in covariant superstrings

    International Nuclear Information System (INIS)

    Zachos, C.

    1985-01-01

    The covariant action for freely propagating heterotic superstrings consists of a metric and a torsion term with a special relative strength. It is shown that the strength for which torsion flattens the underlying 10-dimensional superspace geometry is precisely that which yields free oscillators on the light cone. This is in complete analogy with the geometrostasis of two-dimensional sigma-models with Wess-Zumino interactions. 13 refs

  7. Torsion and geometrostasis in covariant superstrings

    Energy Technology Data Exchange (ETDEWEB)

    Zachos, C.

    1985-01-01

    The covariant action for freely propagating heterotic superstrings consists of a metric and a torsion term with a special relative strength. It is shown that the strength for which torsion flattens the underlying 10-dimensional superspace geometry is precisely that which yields free oscillators on the light cone. This is in complete analogy with the geometrostasis of two-dimensional sigma-models with Wess-Zumino interactions. 13 refs.

  8. Attentional Modulation of Eye Torsion Responses

    Science.gov (United States)

    Stevenson, Scott B.; Mahadevan, Madhumitha S.; Mulligan, Jeffrey B.

    2016-01-01

    Eye movements generally have both reflexive and voluntary aspects, but torsional eye movements are usually thought of as a reflexive response to image rotation around the line of sight (torsional OKN) or to head roll (torsional VOR). In this study we asked whether torsional responses could be modulated by attention in a case where two stimuli rotated independently, and whether attention would influence the latency of responses. The display consisted of rear-projected radial "pinwheel" gratings, with an inner annulus segment extending from the center to 22 degrees eccentricity, and an outer annulus segment extending from 22 degrees out to 45 degrees eccentricity. The two segments rotated around the center in independent random walks, stepping randomly 4 degrees clockwise or counterclockwise at 60 Hz. Subjects were asked to attend to one or the other while keeping fixation steady at the center of the display. To encourage attention on one or the other segment of the display, subjects were asked to move a joystick in synchrony with the back and forth rotations of one part of the image while ignoring the other. Eye torsion was recorded with the scleral search coil technique, sampled at 500 Hz. All four subjects showed roughly 50% stronger torsion responses to the attended compared to unattended segments. Latency varied from 100 to 150 msec across subjects and was unchanged by attention. These findings suggest that attention can influence eye movement responses that are not typically under voluntary control.

  9. Torsional Optomechanics of a Levitated Nonspherical Nanoparticle

    Science.gov (United States)

    Hoang, Thai M.; Ma, Yue; Ahn, Jonghoon; Bang, Jaehoon; Robicheaux, F.; Yin, Zhang-Qi; Li, Tongcang

    2016-09-01

    An optically levitated nanoparticle in vacuum is a paradigm optomechanical system for sensing and studying macroscopic quantum mechanics. While its center-of-mass motion has been investigated intensively, its torsional vibration has only been studied theoretically in limited cases. Here we report the first experimental observation of the torsional vibration of an optically levitated nonspherical nanoparticle in vacuum. We achieve this by utilizing the coupling between the spin angular momentum of photons and the torsional vibration of a nonspherical nanoparticle whose polarizability is a tensor. The torsional vibration frequency can be 1 order of magnitude higher than its center-of-mass motion frequency, which is promising for ground state cooling. We propose a simple yet novel scheme to achieve ground state cooling of its torsional vibration with a linearly polarized Gaussian cavity mode. A levitated nonspherical nanoparticle in vacuum will also be an ultrasensitive nanoscale torsion balance with a torque detection sensitivity on the order of 10-29 N m /√{Hz } under realistic conditions.

  10. Extracting the information backbone in online system.

    Directory of Open Access Journals (Sweden)

    Qian-Ming Zhang

    Full Text Available Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such "less can be more" feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency.

  11. Extracting the Information Backbone in Online System

    Science.gov (United States)

    Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

    2013-01-01

    Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such “less can be more” feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency. PMID:23690946

  12. Backbone dynamics of oxidized and reduced D. vulgaris flavodoxin in solution

    International Nuclear Information System (INIS)

    Hrovat, Andrea; Bluemel, Markus; Loehr, Frank; Mayhew, Stephen G.; Rueterjans, Heinz

    1997-01-01

    Recombinant Desulfovibrio vulgaris flavodoxin was produced in Escherichia coli. A complete backbone NMR assignment for the two-electron reduced protein revealed significant changes of chemical shift values compared to the oxidized protein, in particular for the flavine mononucleotide (FMN)-binding site. A comparison of homo- and heteronuclear NOESY spectra for the two redox states led to the assumption that reduction is not accompanied by significant changes of the global fold of the protein.The backbone dynamics of both the oxidized and reduced forms of D. vulgaris flavodoxin were investigated using two-dimensional 15 N- 1 H correlation NMR spectroscopy.T 1 , T 2 and NOE data are obtained for 95% of the backbone amide groups in both redox states. These values were analysed in terms of the 'model-free' approach introduced by Lipari and Szabo [(1982) J. Am. Chem. Soc., 104, 4546-;4559, 4559-;4570]. A comparison of the two redox states indicates that in the reduced species significantly more flexibility occurs in the two loop regions enclosing FMN.Also, a higher amplitude of local motion could be found for the N(3)H group of FMN bound to the reduced protein compared to the oxidized state

  13. Torsional oscillations of strange stars

    Directory of Open Access Journals (Sweden)

    Mannarelli Massimo

    2014-01-01

    Full Text Available Strange stars are one of the hypothetical compact stellar objects that can be formed after a supernova explosion. The existence of these objects relies on the absolute stability of strange collapsed quark matter with respect to standard nuclear matter. We discuss simple models of strange stars with a bare quark matter surface, thus standard nuclear matter is completely absent. In these models an electric dipole layer a few hundreds Fermi thick should exist close to the star surface. Studying the torsional oscillations of the electrically charged layer we estimate the emitted power, finding that it is of the order of 1045 erg/s, meaning that these objects would be among the brightest compact sources in the heavens. The associated relaxation times are very uncertain, with values ranging between microseconds and minutes, depending on the crust thickness. Although part of the radiated power should be absorbed by the electrosphere surrounding the strange star, a sizable fraction of photons should escape and be detectable.

  14. Solution structure and backbone dynamics of recombinant Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.

    Science.gov (United States)

    Liu, J; Prakash, O; Cai, M; Gong, Y; Huang, Y; Wen, L; Wen, J J; Huang, J K; Krishnamoorthi, R

    1996-02-06

    The solution structure of recombinant Cucurbita maxima trypsin inhibitor-V (rCMTI-V), whose N-terminal is unacetylated and carries an extra glycine residue, was determined by means of two-dimensional (2D) homo and 3D hetero NMR experiments in combination with a distance geometry and simulated annealing algorithm. A total of 927 interproton distances and 123 torsion angle constraints were utilized to generate 18 structures. The root mean squared deviation (RMSD) of the mean structure is 0.53 A for main-chain atoms and 0.95 A for all the non-hydrogen atoms of residues 3-40 and 49-67. The average structure of rCMTI-V is found to be almost the same as that of the native protein [Cai, M., Gong, Y., Kao, J.-L., & Krishnamoorthi, R. (1995) Biochemistry 34, 5201-5211]. The backbone dynamics of uniformly 15N-labeled rCMTI-V were characterized by 2D 1H-15N NMR methods. 15N spin-lattice and spin-spin relaxation rate constants (R1 and R2, respectively) and [1H]-15N steady-state heteronuclear Overhauser effect enhancements were measured for the peptide NH units and, using the model-free formalism [Lipari, G., & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559, 4559-4570], the following parameters were determined: overall tumbling correlation time for the protein molecule (tau m), generalized order parameters for the individual N-H vectors (S2), effective correlation times for their internal motions (tau e), and terms to account for motions on a slower time scale (second) due to chemical exchange and/or conformational averaging (R(ex)). Most of the backbone NH groups of rCMTI-V are found to be highly constrained ((S2) = 0.83) with the exception of those in the binding loop (residues 41-48, (S2) = 0.71) and the N-terminal region ((S2) = 0.73). Main-chain atoms in these regions show large RMSD values in the average NMR structure. Residues involved in turns also appear to have more mobility ((S2) = 0.80). Dynamical properties of rCMTI-V were compared with those of two other

  15. Hydroxyl free radical production during torsional phacoemulsification.

    Science.gov (United States)

    Aust, Steven D; Hebdon, Thomas; Humbert, Jordan; Dimalanta, Ramon

    2010-12-01

    To quantitate free radical generation during phacoemulsification using an ultrasonic phacoemulsification device that includes a torsional mode and evaluate tip designs specific to the torsional mode. Chemistry and Biochemistry Department, Utah State University, Logan, Utah, USA. Experimental study. Experiments were performed using the Infiniti Vision System and OZil handpiece. Hydroxyl radical concentrations in the aspirated irrigation solution during torsional phacoemulsification were quantitated as nanomolar malondialdehyde (nM MDA) and determined spectrophotometrically using the deoxyribose assay. The mean free radical production during phacoemulsification with torsional modality at 100% amplitude was 30.1 nM MDA ± 5.1 (SD) using a 0.9 mm 45-degree Kelman tapered ABS tip. With other tip designs intended for use with the torsional modality, free radical production was further reduced when fitted with the 0.9 mm 45-degree Kelman mini-flared ABS tip (13.2 ± 5.6 nM MDA) or the 0.9 mm 45-degree OZil-12 mini-flared ABS tip (14.3 ± 6.7 nM MDA). Although the measurements resulting from the use of the latter 2 tips were not statistically significantly different (P ≈ .25), they were different from those of the tapered tip (P<.0001). The MDA concentration in the aspirated irrigation solution using the torsional modality was approximately one half that reported for the handpiece's longitudinal modality in a previous study using the same bent-tip design (Kelman tapered, P<.0001). The level of MDA was further reduced approximately one half with torsional-specific tips. Copyright © 2010 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  16. Backbone resonance assignments of the outer membrane lipoprotein FrpD from Neisseria meningitidis

    Czech Academy of Sciences Publication Activity Database

    Bumba, Ladislav; Sviridova, E.; Kutá-Smatanová, Ivana; Řezáčová, Pavlína; Veverka, Václav

    2014-01-01

    Roč. 8, č. 1 (2014), s. 53-55 ISSN 1874-2718 R&D Projects: GA ČR(CZ) GAP207/11/0717; GA MŠk(CZ) LK11205 Institutional support: RVO:61388963 ; RVO:61388971 ; RVO:67179843 Keywords : Neisseria meningitidis * FrpC * FrpD * backbone assignments * NMR * iron-regulated protein Subject RIV: CE - Biochemistry Impact factor: 0.760, year: 2014

  17. Live Zika virus chimeric vaccine candidate based on a yellow fever 17-D attenuated backbone

    OpenAIRE

    Nougairede, Antoine; Klitting, Raphaelle; Aubry, Fabien; Gilles, Magali; Touret, Franck; De Lamballerie, Xavier

    2018-01-01

    Zika virus (ZIKV) recently dispersed throughout the tropics and sub-tropics causing epidemics associated with congenital disease and neurological complications. There is currently no commercial vaccine for ZIKV. Here we describe the initial development of a chimeric virus containing the prM/E proteins of a ZIKV epidemic strain incorporated into a yellow fever 17-D attenuated backbone. Using the versatile and rapid ISA (Infectious Subgenomic Amplicons) reverse genetics method, we compared diff...

  18. Radiation safety system (RSS) backbones: Design, engineering, fabrication and installation

    International Nuclear Information System (INIS)

    Wilmarth, J.E.; Sturrock, J.C.; Gallegos, F.R.

    1998-01-01

    The Radiation Safety System (RSS) Backbones are part of an electrical/electronic/mechanical system insuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS Backbones control the safety fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low energy beam transport. The Backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the Backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two Linac Backbone segments and experimental area segments form a continuous cable plant over 3,500 feet from beam plugs to the tip on the longest tail. The Backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely

  19. Ultimate Strength of Ship Hulls under Torsion

    DEFF Research Database (Denmark)

    Paik, Jeom Kee; Thayamballi, Anil K.; Pedersen, Preben Terndrup

    2001-01-01

    For a ship hull with large deck openings such as container vessels and some large bulk carriers, the analysis of warping stresses and hatch opening deformations is an essential part of ship structural analyses. It is thus of importance to better understand the ultimate torsional strength characte......For a ship hull with large deck openings such as container vessels and some large bulk carriers, the analysis of warping stresses and hatch opening deformations is an essential part of ship structural analyses. It is thus of importance to better understand the ultimate torsional strength...... characteristics of ships with large hatch openings. The primary aim of the present study is to investigate the ultimate strength characteristics of ship hulls with large hatch openings under torsion. Axial (warping) as well as shear stresses are normally developed for thin-walled beams with open cross sections...... subjected to torsion. A procedure for calculating these stresses is briefly described. As an illustrative example, the distribution and magnitude of warping and shear stresses for a typical container vessel hull cross section under unit torsion is calculated by the procedure. By theoretical and numerical...

  20. Heat production: Longitudinal versus torsional phacoemulsification.

    Science.gov (United States)

    Han, Young Keun; Miller, Kevin M

    2009-10-01

    To compare the heat production of longitudinal versus torsional phacoemulsification under strict laboratory test conditions. Department of Ophthalmology, David Geffen School of Medicine at UCLA, and Jules Stein Eye Institute, Los Angeles, California, USA. Two Infiniti phacoemulsification handpieces were inserted into silicone test chambers filled with a balanced salt solution and imaged serially using a thermal camera. Incision compression was simulated by suspending 25.3 g weights from the silicone chambers. To simulate occlusion of the phacoemulsification tip, the aspiration line was clamped. Peak temperatures were measured 0, 10, 30, 60, and 120 seconds after the commencement of continuous ultrasound power. The 2 handpieces, operating exclusively in longitudinal or torsional modes, were compared 3 ways: (1) using the same power displayed on the instrument console, (2) using identical stroke lengths, and (3) using the same applied energy, a product of stroke length and frequency. For all 3 comparisons, torsional phacoemulsification resulted in lower temperatures at each time point. At the same displayed power setting, the scenario most familiar to cataract surgeons, longitudinal phacoemulsification elevated temperatures up to 41.5 degrees C more than torsional phacoemulsification. Torsional phacoemulsification generated less heat than longitudinal phacoemulsification in all 3 comparison tests. Lower operating temperatures indicate lower heat generation within the same volume of fluid, and this may provide additional thermal protection during cataract surgery.

  1. Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism.

    Science.gov (United States)

    Reymer, Anna; Zakrzewska, Krystyna; Lavery, Richard

    2018-02-28

    Torsional restraints on DNA change in time and space during the life of the cell and are an integral part of processes such as gene expression, DNA repair and packaging. The mechanical behavior of DNA under torsional stress has been studied on a mesoscopic scale, but little is known concerning its response at the level of individual base pairs and the effects of base pair composition. To answer this question, we have developed a geometrical restraint that can accurately control the total twist of a DNA segment during all-atom molecular dynamics simulations. By applying this restraint to four different DNA oligomers, we are able to show that DNA responds to both under- and overtwisting in a very heterogeneous manner. Certain base pair steps, in specific sequence environments, are able to absorb most of the torsional stress, leaving other steps close to their relaxed conformation. This heterogeneity also affects the local torsional modulus of DNA. These findings suggest that modifying torsional stress on DNA could act as a modulator for protein binding via the heterogeneous changes in local DNA structure.

  2. High Performance Infiltrated Backbones for Cathode-Supported SOFC's

    DEFF Research Database (Denmark)

    Gil, Vanesa; Kammer Hansen, Kent

    2014-01-01

    A four-step infiltration method has been developed to infiltrate La0.75Sr0.25MnO3+δ (LSM25) nanoparticles into porous structures (YSZ or LSM-YSZ backbones). The pore size distribution in the backbones is obtained either by using PMMA and/or graphites as pore formers or by leaching treatment of sa...... of samples with Ni remained in the YSZ structure at high temperatures. All impregnated backbones, presented Rs comparable to a standard screen printed cathode, which proves that LSM nanoparticles forms a pathway for electron conduction....

  3. Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component.

    Science.gov (United States)

    Hernandez, Carina; Birktoft, Jens J; Ohayon, Yoel P; Chandrasekaran, Arun Richard; Abdallah, Hatem; Sha, Ruojie; Stojanoff, Vivian; Mao, Chengde; Seeman, Nadrian C

    2017-11-16

    There is an increasing appreciation for structural diversity of DNA that is of interest to both DNA nanotechnology and basic biology. Here, we have explored how DNA responds to torsional stress by building on a previously reported two-turn DNA tensegrity triangle and demonstrating that we could introduce an extra nucleotide pair (np) into the original sequence without affecting assembly and crystallization. The extra np imposes a significant torsional stress, which is accommodated by global changes throughout the B-DNA duplex and the DNA lattice. The work reveals a near-atomic structure of naked DNA under a torsional stress of approximately 14%, and thus provides an example of DNA distortions that occur without a requirement for either an external energy source or the free energy available from protein or drug binding. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Development of techniques in magnetic resonance and structural studies of the prion protein

    Energy Technology Data Exchange (ETDEWEB)

    Bitter, Hans-Marcus L. [Univ. of California, Berkeley, CA (United States)

    2000-07-01

    Magnetic resonance is the most powerful analytical tool used by chemists today. Its applications range from determining structures of large biomolecules to imaging of human brains. Nevertheless, magnetic resonance remains a relatively young field, in which many techniques are currently being developed that have broad applications. In this dissertation, two new techniques are presented, one that enables the determination of torsion angles in solid-state peptides and proteins, and another that involves imaging of heterogenous materials at ultra-low magnetic fields. In addition, structural studies of the prion protein via solid-state NMR are described. More specifically, work is presented in which the dependence of chemical shifts on local molecular structure is used to predict chemical shift tensors in solid-state peptides with theoretical ab initio surfaces. These predictions are then used to determine the backbone dihedral angles in peptides. This method utilizes the theoretical chemicalshift tensors and experimentally determined chemical-shift anisotropies (CSAs) to predict the backbone and side chain torsion angles in alanine, leucine, and valine residues. Additionally, structural studies of prion protein fragments are described in which conformationally-dependent chemical-shift measurements were made to gain insight into the structural differences between the various conformational states of the prion protein. These studies are of biological and pathological interest since conformational changes in the prion protein are believed to cause prion diseases. Finally, an ultra-low field magnetic resonance imaging technique is described that enables imaging and characterization of heterogeneous and porous media. The notion of imaging gases at ultra-low fields would appear to be very difficult due to the prohibitively low polarization and spin densities as well as the low sensitivities of conventional Faraday coil detectors. However, Chapter 5 describes how gas imaging

  5. Ultrasonographic diagnosis of torsion of testicular appendages

    International Nuclear Information System (INIS)

    Esparza, J.; Gonzalez, A.; Cordero, J. L.

    2000-01-01

    To determine the efficacy of ultrasound in boys presenting torsion of a testicular appendage. A series of 30 boys with acute scrotal pain due to torsion of a testicular appendage was studied. Nine patients underwent surgery. The clinical findings and course in the remaining 21 suggested the presence of this abnormality. All of them underwent conventional and color Doppler ultrasound using a 7.5 MHz transducer. In 15 boys, ultrasound images depicted the affected appendage as a mass between the epididymal head and the testicle. In 13 cases, only signs of a inflammatory reaction, with enlargement of the epididymal head and tunicas presenting hyperflow and hydrocele, mimicking acute epididymities. In two cases, the images were normal. There is no definitive, distinguishing ultrasound image corresponding to testicular appendage torsion. Therefore, this diagnostic technique should be accompanied by clinical assessment. (Author) 14 refs

  6. experimental and analytical comparison of torsion, bending moment

    African Journals Online (AJOL)

    HOD

    In structural analysis and design, the effects of torsion are usually neglected ... bending and torsion, using these codes and experimental work; and validates the ..... [7] Kharagpur, I. Structural Analysis: Civil Engineering. Course Material (Vol.

  7. Ozil IP torsional mode versus combined torsional/longitudinal microcoaxial phacoemulsification.

    Science.gov (United States)

    Helvacioglu, Firat; Tunc, Zeki; Yeter, Celal; Oguzhan, Hasan; Sencan, Sadik

    2012-01-01

    To compare the safety and efficacy of microcoaxial phacoemulsification surgeries performed with the Ozil Intelligent Phaco (IP) torsional mode and combined torsional/longitudinal ultrasound (US) mode using the Infiniti Vision System (Alcon Laboratories). In this prospective randomized comparative study, 60 eyes were assigned to 2.2-mm microcoaxial phacoemulsification using the Ozil IP torsional mode (group 1) or combined torsional/longitudinal US mode (group 2). The primary outcome measures were US time (UST), cumulative dissipated energy (CDE), longitudinal and torsional ultrasound amplitudes, mean operation time, mean volume of balanced salt solution (BSS) used, and surgical complications. Both groups included 30 eyes. Mean UST, CDE, and longitudinal and torsional ultrasound amplitudes in group 1 were 1 minute 15±34.33 seconds, 8.74±5.64, 0.43±0.74, and 25.56±8.56, respectively, and these parameters in group 2 were 1 minute 40±51.44 seconds, 9.28±5.99, 3.64±1.55, and 3.71±1.34, respectively. UST and longitudinal amplitudes were found to be significantly low in group 1 (p<0.001, p<0.001), whereas torsional amplitude was found to be significantly high in this group (p=0.001). Mean volumes of BSS used in groups 1 and 2 were 63.30±18.00 cc and 84.50±28.65 cc, respectively (p=0.001). The Ozil IP torsional mode may provide more effective lens removal than the combined torsional/longitudinal US mode with a lower UST and volume of BSS used.

  8. Dynamic power control for wireless backbone mesh networks: a survey

    CSIR Research Space (South Africa)

    Olwal, TO

    2010-01-01

    Full Text Available points of failures, and robust against RF interference, obstacles or power outage. This is because WMRs forming wireless backbone mesh networks (WBMNs) are built on advanced physical technologies. Such nodes perform both accessing and forwarding...

  9. Towards a natural classification and backbone tree for Sordariomycete

    Digital Repository Service at National Institute of Oceanography (India)

    Maharachchikumbura, S.S.N.; Hyde, K.D.; Jones, E.B.G.; McKenzie, E.H.C.; Huang, S.-K.; Abdel-Wahab, M.A.; Daranagama, D.A.; Dayarathne, M.; D'souza, M.J.; Goonasekara, I.D.; Hongsanan, S.; Jayawardena, R.S.; Kirk, P.M.; Konta, S.; Liu, J.-K.; Liu, Z.-Y.; Norphanphoun, C.; Pang, K.-L.; Perera, R.H.; Senanayake, I.C.; Shang, Q.; Shenoy, B.D.; Xiao, Y.; Bahkali, A.H.; Kang, J.; Somrothipol, S.; Suetrong, S.; Wen, T.; Xu, J.

    , lichenized or lichenicolous taxa The class includes freshwater, marine and terrestrial taxa and has a worldwide distribution This paper provides an updated outline of the Sordariomycetes and a backbone tree incorporating asexual and sexual genera in the class...

  10. APPECT: An Approximate Backbone-Based Clustering Algorithm for Tags

    DEFF Research Database (Denmark)

    Zong, Yu; Xu, Guandong; Jin, Pin

    2011-01-01

    algorithm for Tags (APPECT). The main steps of APPECT are: (1) we execute the K-means algorithm on a tag similarity matrix for M times and collect a set of tag clustering results Z={C1,C2,…,Cm}; (2) we form the approximate backbone of Z by executing a greedy search; (3) we fix the approximate backbone...... as the initial tag clustering result and then assign the rest tags into the corresponding clusters based on the similarity. Experimental results on three real world datasets namely MedWorm, MovieLens and Dmoz demonstrate the effectiveness and the superiority of the proposed method against the traditional...... Agglomerative Clustering on tagging data, which possess the inherent drawbacks, such as the sensitivity of initialization. In this paper, we instead make use of the approximate backbone of tag clustering results to find out better tag clusters. In particular, we propose an APProximate backbonE-based Clustering...

  11. On the geometrization of electromagnetism by torsion

    International Nuclear Information System (INIS)

    Fonseca Neto, J.B. da.

    1984-01-01

    The possibility of electromagnetism geometrization using an four dimension Cartan geometry is investigated. The Lagrangian density which presents dual invariance for dyons electrodynamics formulated in term of two potentials is constructed. This theory by association of two potentials with track and with torsion pseudo-track and of the field with torsion covariant divergent is described. The minimum coupling of particle gravitational field of scalar and spinorial fields with dyon geometry theory by the minimum coupling of these fields with Cartan geometry was obtained. (author)

  12. On Backbone Structure for a Future Multipurpose Network

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Cuevas, Ruben; Riaz, M. Tahir

    2008-01-01

    Telecommunications are evolving towards the unification of services and infrastructures. This unification must be achieved at the highest hierarchical level for a complete synergy of services. Therefore, one of the requirements is a multipurpose backbone network capable of supporting all the curr......Telecommunications are evolving towards the unification of services and infrastructures. This unification must be achieved at the highest hierarchical level for a complete synergy of services. Therefore, one of the requirements is a multipurpose backbone network capable of supporting all...

  13. Backbone dynamics of reduced plastocyanin from the cyanobacterium Anabaena variabilis: Regions involved in electron transfer have enhanced mobility

    DEFF Research Database (Denmark)

    Ma, L.X.; Hass, M.A.S.; Vierick, N.

    2003-01-01

    The dynamics of the backbone of the electron-transfer protein plastocyanin from the cyanobacterium Anabaena variabilis were determined from the N-15 and C-13(alpha) R-1 and R-2) relaxation rates and steady-state [H-1]-N-15 and [H-1]-C-13 nuclear Overhauser effects (NOEs) using the model...

  14. C(α) torsion angles as a flexible criterion to extract secrets from a molecular dynamics simulation.

    Science.gov (United States)

    Victor Paul Raj, Fredrick Robin Devadoss; Exner, Thomas E

    2014-04-01

    Given the increasing complexity of simulated molecular systems, and the fact that simulation times have now reached milliseconds to seconds, immense amounts of data (in the gigabyte to terabyte range) are produced in current molecular dynamics simulations. Manual analysis of these data is a very time-consuming task, and important events that lead from one intermediate structure to another can become occluded in the noise resulting from random thermal fluctuations. To overcome these problems and facilitate a semi-automated data analysis, we introduce in this work a measure based on C(α) torsion angles: torsion angles formed by four consecutive C(α) atoms. This measure describes changes in the backbones of large systems on a residual length scale (i.e., a small number of residues at a time). Cluster analysis of individual C(α) torsion angles and its fuzzification led to continuous time patches representing (meta)stable conformations and to the identification of events acting as transitions between these conformations. The importance of a change in torsion angle to structural integrity is assessed by comparing this change to the average fluctuations in the same torsion angle over the complete simulation. Using this novel measure in combination with other measures such as the root mean square deviation (RMSD) and time series of distance measures, we performed an in-depth analysis of a simulation of the open form of DNA polymerase I. The times at which major conformational changes occur and the most important parts of the molecule and their interrelations were pinpointed in this analysis. The simultaneous determination of the time points and localizations of major events is a significant advantage of the new bottom-up approach presented here, as compared to many other (top-down) approaches in which only the similarity of the complete structure is analyzed.

  15. Torsional Oscillations of the Earths's Core

    Science.gov (United States)

    Hide, Raymond; Boggs, Dale H.; Dickey, Jean O.

    1997-01-01

    Torsional oscillations of the Earth's liquid metallic outer core are investigated by diving the core into twenty imaginary e1qui-volume annuli coaxial with the axis of ratation of the Earth and determining temproal fluctuations in the axial component of angular memonetum of each annulus under the assumption of iso-rotation on cylindrical surfaces.

  16. Torsion of the gallbladder: a case report

    Directory of Open Access Journals (Sweden)

    Ijaz Samia

    2008-07-01

    Full Text Available Abstract Introduction Torsion of the gallbladder is a rare condition that most commonly affects the elderly. Pre-operative diagnosis is the exception rather than the rule. Any delay in treatment can be fatal as the gallbladder may rupture, leading to biliary peritonitis. Case presentation We present the case of an 80-year-old woman who was admitted with right upper quadrant pain initially thought to be secondary to acute cholecystitis. Subsequent ultrasound and computed tomography scans of the abdomen revealed signs suggestive of acute cholecystitis but neither modality detected any gallstones. As the patient's symptoms failed to resolve on conservative management, she was taken to theatre for an open cholecystectomy. Intra-operatively, the gallbladder had undergone complete torsion and appeared gangrenous. A routine cholecystectomy followed and she recovered from the operation without incident. Conclusion It is rare to diagnose torsion of the gallbladder pre-operatively despite advances in diagnostic imaging. However, this differential diagnosis should be borne in mind particularly in the elderly patient, without proven gallstones, who fails to improve on conservative management. An emergency cholecystectomy is indicated in the event of diagnosing torsion of the gallbladder to avert the potentially lethal sequelae of biliary peritonitis.

  17. The spectrum of axisymmetric torsional Alfven waves

    International Nuclear Information System (INIS)

    Sy, W.N.

    1977-03-01

    The spectrum of axisymmetric torsional Alfven waves propagating in a cylindrical, non-uniform, resistive plasma waveguide has been analysed by a method of singular perturbations. A simple condition has been derived which predicts whether the spectrum is continuous or discrete under given physical conditions. Application of this result to resolve an apparent discrepancy in experimental observations is briefly discussed. (Author)

  18. Conformal deformation of Riemann space and torsion

    International Nuclear Information System (INIS)

    Pyzh, V.M.

    1981-01-01

    Method for investigating conformal deformations of Riemann spaces using torsion tensor, which permits to reduce the second ' order equations for Killing vectors to the system of the first order equations, is presented. The method is illustrated using conformal deformations of dimer sphere as an example. A possibility of its use when studying more complex deformations is discussed [ru

  19. Adnexal torsion in 6 years old girl

    International Nuclear Information System (INIS)

    Plachkov, I.; Tzvetankov, K.; Dimova, M.; Dobreva, Tz.; Hadjidekov, G.

    2012-01-01

    MRI and US findings in Ovarian torsion in a premenarcheal girl are described. Adnexal torsion is an uncommon cause of severe lower abdominal pain in young women (mean age is 10-11), and in 50% of cases such symptoms are observed in pre-menarchal females. However, adnexal torsion should be considered in all premenarcheal girls admitted with acute abdominal pain and evidence of an ovarian mass. Accurate imaging is crucial after onset of early clinical symptoms to confirm the diagnosis and to preserve the viability of the affected ovary. A pelvic ovoid mass was visualised on ultrasound, suggesting several hypothesis -cystic mass, ovarian torsion, dermoid. Magnetic resonance imaging visualized edematous ovary enlargement and the presence of multiple follicules at the periphery due to congestion from the twisted vascular pedicule. Smooth wail thickening of the partially necrotic. Twisted ovary was seen in the subacute phase, which has been confirmed during laparoscopy. CT was not considered in this 6 years old girl due to ionizing radiation. (authors)

  20. Torsional Performance of Wind Turbine Blades

    DEFF Research Database (Denmark)

    Branner, Kim; Berring, Peter; Berggreen, Christian

    2007-01-01

    The present work investigates how well different finite element modeling techniques can predict bending and torsion behavior of a wind turbine blade. Two shell models are investigated. One model has element offsets and the other has the elements at the mid-thickness surfaces of the model. The las...

  1. Plant-based torsional actuator with memory

    Science.gov (United States)

    Nayomi Plaza; Samuel L. Zelinka; Don S. Stone; Joseph E. Jakes

    2013-01-01

    A bundle of a few loblolly pine (Pinus taeda) cells are moisture-activated torsional actuators that twist multiple revolutions per cm length in direct proportion to moisture content. The bundles generate 10 N m kg􀀀1 specific torque during both twisting and untwisting, which is higher than an electric motor. Additionally, the bundles exhibit a moisture-...

  2. Pseudotopological quasilocal energy of torsion gravity

    Science.gov (United States)

    Ko, Sheng-Lan; Lin, Feng-Li; Ning, Bo

    2017-08-01

    Torsion gravity is a natural extension to Einstein gravity in the presence of fermion matter sources. In this paper we adopt Wald's covariant method of calculating the Noether charge to construct the quasilocal energy of the Einstein-Cartan-fermion system, and find that its explicit expression is formally independent of the coupling constant between the torsion and axial current. This seemingly topological nature is unexpected and is reminiscent of the quantum Hall effect and topological insulators. However, a coupling dependence does arise when evaluating it on shell, and thus the situation is pseudotopological. Based on the expression for the quasilocal energy, we evaluate it for a particular solution on the entanglement wedge and find agreement with the holographic relative entropy obtained before. This shows the equivalence of these two quantities in the Einstein-Cartan-fermion system. Moreover, the quasilocal energy in this case is not always positive definite, and thus it provides an example of a swampland in torsion gravity. Based on the covariant Noether charge, we also derive the nonzero fermion effect on the Komar angular momentum. The implications of our results for future tests of torsion gravity in gravitational-wave astronomy are also discussed.

  3. Torsional ultrasound mode versus combined torsional and conventional ultrasound mode phacoemulsification for eyes with hard cataract.

    Science.gov (United States)

    Fakhry, Mohamed A; El Shazly, Malak I

    2011-01-01

    To compare torsional versus combined torsional and conventional ultrasound modes in hard cataract surgery regarding ultrasound energy and time and effect on corneal endothelium. Kasr El Aini hospital, Cairo University, and International Eye Hospital, Cairo, Egypt. Ninety-eight eyes of 63 patients were enrolled in this prospective comparative randomized masked clinical study. All eyes had nuclear cataracts of grades III and IV using the Lens Opacities Classification System III (LOCS III). Two groups were included, each having an equal number of eyes (49). The treatment for group A was combined torsional and conventional US mode phacoemulsification, and for group B torsional US mode phacoemulsification only. Pre- and post-operative assessments included best corrected visual acuity (BCVA), intraocular pressure (IOP), slit-lamp evaluation, and fundoscopic evaluation. Endothelial cell density (ECD) and central corneal thickness (CCT) were measured preoperatively, 1 day, 7 days, and 1 month postoperatively. All eyes were operated on using the Alcon Infiniti System (Alcon, Fort Worth, TX) with the quick chop technique. All eyes were implanted with AcrySof SA60AT (Alcon) intraocular lens (IOL). The main phaco outcome parameters included the mean ultrasound time (UST), the mean cumulative dissipated energy (CDE), and the percent of average torsional amplitude in position 3 (%TUSiP3). Improvement in BCVA was statistically significant in both groups (P < 0.001). Comparing UST and CDE for both groups revealed results favoring the pure torsional group (P = 0.002 and P < 0.001 for UST; P = 0.058 and P = 0.009 for CDE). As for %TUSiP3, readings were higher for the pure torsional group (P = 0.03 and P = 0.01). All changes of CCT, and ECD over time were found statistically significant using one-way ANOVA testing (P < 0.001). Both modes are safe in hard cataract surgery, however the pure torsional mode showed less US energy used.

  4. Torsion limits from t t macr production at the LHC

    Science.gov (United States)

    de Almeida, F. M. L.; de Andrade, F. R.; do Vale, M. A. B.; Nepomuceno, A. A.

    2018-04-01

    Torsion models constitute a well-known class of extended quantum gravity models. In this work, one investigates the phenomenological consequences of a torsion field interacting with top quarks at the LHC. A torsion field could appear as a new heavy state characterized by its mass and couplings to fermions. This new state would form a resonance decaying into a top antitop pair. The latest ATLAS t t ¯ production results from LHC 13 TeV data are used to set limits on torsion parameters. The integrated luminosity needed to observe torsion resonance at the next LHC upgrades are also evaluated, considering different values for the torsion mass and its couplings to Standard Model fermions. Finally, prospects for torsion exclusion at the future LHC phases II and III are obtained using fast detector simulations.

  5. Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

    Science.gov (United States)

    Haupt, V. Joachim; Schroeder, Michael; Labudde, Dirk

    2018-01-01

    The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes. PMID:29659563

  6. ADAR RNA editing below the backbone.

    Science.gov (United States)

    Keegan, Liam; Khan, Anzer; Vukic, Dragana; O'Connell, Mary

    2017-09-01

    ADAR RNA editing enzymes ( a denosine d e a minases acting on R NA) that convert adenosine bases to inosines were first identified biochemically 30 years ago. Since then, studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster , which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins. Drosophila ADAR is involved in the control of neuronal excitability and neurodegeneration and, intriguingly, in the control of neuronal plasticity and sleep. Drosophila ADAR also interacts strongly with RNA interference, a key antiviral defense mechanism in invertebrates. Recent crystal structures of human ADAR2 deaminase domain-RNA complexes help to interpret available information on Drosophila ADAR isoforms and on the evolution of ADARs from tRNA deaminase ADAT proteins. ADAR RNA editing is a paradigm for the now rapidly expanding range of RNA modifications in mRNAs and ncRNAs. Even with recent progress, much remains to be understood about these groundbreaking ADAR RNA modification systems. © 2017 Keegan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  7. Some fractal properties of the percolating backbone in two dimensions

    International Nuclear Information System (INIS)

    Laidlaw, D.; MacKay, G.; Jan, N.

    1987-01-01

    A new algorithm is presented, based on elements of artificial intelligence theory, to determine the fractal properties of the backbone of the incipient infinite cluster. It is found that fractal dimensionality of the backbone is d/sub f//sup BB/ = 1.61 +/- 0.01, the chemical dimensionality is d/sub t/ = 1.40 +/- 0.01, and the fractal dimension of the minimum path d/sub min/ = 1.15 +/- 0.02 for the two-dimensional triangular lattice

  8. Torsional ultrasound mode versus combined torsional and conventional ultrasound mode phacoemulsification for eyes with hard cataract

    Directory of Open Access Journals (Sweden)

    Fakhry MA

    2011-07-01

    Full Text Available Mohamed A Fakhry1,2, Malak I El Shazly11Department of Ophthalmology, Kasr El Aini Hospital, Cairo University, Cairo, Egypt; 2Cataract and Refractive Consultant, International Eye Hospital, Cairo, EgyptPurpose: To compare torsional versus combined torsional and conventional ultrasound modes in hard cataract surgery regarding ultrasound energy and time and effect on corneal endothelium.Settings: Kasr El Aini hospital, Cairo University, and International Eye Hospital, Cairo, Egypt.Methodology: Ninety-eight eyes of 63 patients were enrolled in this prospective comparative randomized masked clinical study. All eyes had nuclear cataracts of grades III and IV using the Lens Opacities Classification System III (LOCS III. Two groups were included, each having an equal number of eyes (49. The treatment for group A was combined torsional and conventional US mode phacoemulsification, and for group B torsional US mode phacoemulsification only. Pre- and post-operative assessments included best corrected visual acuity (BCVA, intraocular pressure (IOP, slit-lamp evaluation, and fundoscopic evaluation. Endothelial cell density (ECD and central corneal thickness (CCT were measured preoperatively, 1 day, 7 days, and 1 month postoperatively. All eyes were operated on using the Alcon Infiniti System (Alcon, Fort Worth, TX with the quick chop technique. All eyes were implanted with AcrySof SA60AT (Alcon intraocular lens (IOL. The main phaco outcome parameters included the mean ultrasound time (UST, the mean cumulative dissipated energy (CDE, and the percent of average torsional amplitude in position 3 (%TUSiP3.Results: Improvement in BCVA was statistically significant in both groups (P < 0.001. Comparing UST and CDE for both groups revealed results favoring the pure torsional group (P = 0.002 and P < 0.001 for UST; P = 0.058 and P = 0.009 for CDE. As for %TUSiP3, readings were higher for the pure torsional group (P = 0.03 and P = 0.01. All changes of CCT, and ECD

  9. Biothermal sensing of a torsional artificial muscle.

    Science.gov (United States)

    Lee, Sung-Ho; Kim, Tae Hyeob; Lima, Márcio D; Baughman, Ray H; Kim, Seon Jeong

    2016-02-14

    Biomolecule responsive materials have been studied intensively for use in biomedical applications as smart systems because of their unique property of responding to specific biomolecules under mild conditions. However, these materials have some challenging drawbacks that limit further practical application, including their speed of response and mechanical properties, because most are based on hydrogels. Here, we present a fast, mechanically robust biscrolled twist-spun carbon nanotube yarn as a torsional artificial muscle through entrapping an enzyme linked to a thermally sensitive hydrogel, poly(N-isopropylacrylamide), utilizing the exothermic catalytic reaction of the enzyme. The induced rotation reached an equilibrated angle in less than 2 min under mild temperature conditions (25-37 °C) while maintaining the mechanical properties originating from the carbon nanotubes. This biothermal sensing of a torsional artificial muscle offers a versatile platform for the recognition of various types of biomolecules by replacing the enzyme, because an exothermic reaction is a general property accompanying a biochemical transformation.

  10. Electronic transport in torsional strained Weyl semimetals

    Science.gov (United States)

    Soto-Garrido, Rodrigo; Muñoz, Enrique

    2018-05-01

    In a recent paper (Muñoz and Soto-Garrido 2017 J. Phys.: Condens. Matter 29 445302) we have studied the effects of mechanical strain and magnetic field on the electronic transport properties in graphene. In this article we extended our work to Weyl semimetals (WSM). We show that although the WSM are 3D materials, most of the analysis done for graphene (2D material) can be carried out. In particular, we studied the electronic transport through a cylindrical region submitted to torsional strain and external magnetic field. We provide exact analytical expressions for the scattering cross section and the transmitted electronic current. In addition, we show the node-polarization effect on the current and propose a recipe to measure the torsion angle from transmission experiments.

  11. High-pressure torsion of hafnium

    International Nuclear Information System (INIS)

    Edalati, Kaveh; Horita, Zenji; Mine, Yoji

    2010-01-01

    Pure Hf (99.99%) is processed by high-pressure torsion (HPT) under pressures of 4 and 30 GPa to form an ultrafine-grained structure with a gain size of ∼180 nm. X-ray diffraction analysis shows that, unlike Ti and Zr, no ω phase formation is detected after HPT processing even under a pressure of 30 GPa. A hydride formation is detected after straining at the pressure of 4 GPa. The hydride phase decomposes either by application of a higher pressure as 30 GPa or by unloading for prolong time after HPT processing. Microhardness, tensile and bending tests show that a high hardness (360 Hv) and an appreciable ductility (8%) as well as high tensile and bending strength (1.15 and 2.75 GPa, respectively) are achieved following the high-pressure torsion.

  12. Torsional Tribological Behavior and Torsional Friction Model of Polytetrafluoroethylene against 1045 Steel

    Science.gov (United States)

    Wang, Shibo; Niu, Chengchao

    2016-01-01

    In this work, the plane-on-plane torsional fretting tribological behavior of polytetrafluoroethylene (PTFE) was studied. A model of a rigid, flat-ended punch acting on an elastic half-space was built according to the experimental conditions. The results indicate that the shape of T–θ curves was influenced by both the torsional angle and the normal load. The torsion friction torque and wear rate of PTFE exponentially decreased when the torsion angle rose. The torsional torque increased from 0.025 N·m under a normal load of 43 N to 0.082 N·m under a normal load of 123 N. With sequentially increasing normal load, the value of torque was maintained. With rising normal load, the wear mass loss of PTFE disks was increased and the wear rate was decreased. Good agreement was found with the calculated torque according to the model and the experimental torque except for that under a normal load of 163 N. The difference under a normal load of 163 N was caused by the coefficient of friction. Usually the coefficient of friction of a polymer decreases with increasing normal load, whereas a constant coefficient of friction was applied in the model. PMID:26799324

  13. Torsion method for measuring piezooptic coefficients

    Energy Technology Data Exchange (ETDEWEB)

    Skab, I.; Smaga, I.; Savaryn, V.; Vasylkiv, Yu.; Vlokh, R. [Institute of Physical Optics, Lviv (Ukraine)

    2011-01-15

    We develop and describe analytically a torsion method for measuring piezooptic coefficients associated with shear stresses. It is shown that the method enables to increase significantly the accuracy of determination of piezooptic coefficients. The method and the appropriate apparatus are verified experimentally on the example of LiNbO{sub 3} crystals. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  14. Torsional asymmetry in suspension bridge systems

    Czech Academy of Sciences Publication Activity Database

    Malík, Josef

    2015-01-01

    Roč. 60, č. 6 (2015), s. 677-701 ISSN 0862-7940 R&D Projects: GA MŠk ED2.1.00/03.0082 Institutional support: RVO:68145535 Keywords : suspension bridge * Hamilton principle * vertical and torsional oscillation * uniqueness * existence Subject RIV: BA - General Mathematics Impact factor: 0.507, year: 2015 http://link.springer.com/article/10.1007%2Fs10492-015-0117-3

  15. Electrostatically actuated torsional resonant sensors and switches

    KAUST Repository

    Younis, Mohammad I.

    2016-12-29

    Embodiments in accordance of a torsional resonant sensor disclosure is configured to actuate a beam structure using electrostatic actuation with an AC harmonic load (e.g., AC and DC voltage sources) that is activated upon detecting a particular agent having a mass above a predefined level. In various embodiments, the beam structure may be different types of resonant structures that is at least partially coated or layered with a selective material.

  16. Spacetime thermodynamics in the presence of torsion

    Science.gov (United States)

    Dey, Ramit; Liberati, Stefano; Pranzetti, Daniele

    2017-12-01

    It was shown by Jacobson in 1995 that the Einstein equation can be derived as a local constitutive equation for an equilibrium spacetime thermodynamics. With the aim to understand if such thermodynamical description is an intrinsic property of gravitation, many attempts have been made so far to generalize this treatment to a broader class of gravitational theories. Here we consider the case of the Einstein-Cartan theory as a prototype of theories with nonpropagating torsion. In doing so, we study the properties of Killing horizons in the presence of torsion, establish the notion of local causal horizon in Riemann-Cartan spacetimes, and derive the generalized Raychaudhuri equation for these kinds of geometries. Then, starting with the entropy that can be associated to these local causal horizons, we derive the Einstein-Cartan equation by implementing the Clausius equation. We outline two ways of proceeding with the derivation depending on whether we take torsion as a geometric field or as a matter field. In both cases we need to add internal entropy production terms to the Clausius equation as the shear and twist cannot be taken to be 0 a priori for our setup. This fact implies the necessity of a nonequilibrium thermodynamics treatment for the local causal horizon. Furthermore, it implies that a nonzero twist at the horizon in general contributes to the Hartle-Hawking tidal heating for black holes with possible implications for future observations.

  17. Isolated Fallopian Tube Torsion in Adolescents

    Directory of Open Access Journals (Sweden)

    S. Rajaram

    2013-01-01

    Full Text Available Background. Fallopian tube torsion is a rare cause of acute abdomen, occurring commonly in females of reproductive age. It lacks pathognomonic symptoms, signs, or imaging features, thus causing delay in surgical intervention. Case. We report two cases of isolated fallopian tube torsion in adolescent girls. In the first case a 19-year-old patient presented with acute pain in the left iliac region associated with episodes of vomiting for one day and mild tenderness on examination. Laparoscopy revealed left sided twisted fallopian tube associated with hemorrhagic cyst of ovary. The tube was untwisted and salvaged. In another case an 18-year-old virgin girl presented with similar complaints since one week, associated with mild tenderness in the lower abdomen and tender cystic mass on per rectal examination. On laparoscopy right twisted fallopian tube associated with a paratubal cyst was found. Salpingectomy was done as the tube was gangrenous. Conclusion. Fallopian tube torsion, though rare, should be considered in women of reproductive age with unilateral pelvic pain. Early diagnostic laparoscopy is important for an accurate diagnosis and could salvage the tube.

  18. Gauge fields in a torsion field

    International Nuclear Information System (INIS)

    Rosu, Ion

    2004-01-01

    In this paper we analyse the motion and the field equations in a non-null curvature and torsion space. In this 4-n dimensional space, the connection coefficients are γ bc a = 1/2S bc a + 1/2T bc a, where S bc a is the symmetrical part and T bc a are the components of the torsion tensor. We will consider that all the fields depend on x = x α , α = 1,2,3,4 and do not depend on y = y k , k=1,2,...,n. The factor S bc a depends on the components of the metric tensor g αβ (x) and on the gauge fields A ν s 0 (x) and the components of the torsion depend only on the gauge fields A ν s 0 (x). We take into consideration the particular case for which the geodesic equations coincide with the motion equations in the presence of the gravitational and the gauge fields. In this case the field equations are Einstein equations in a 4-n dimensional space. We show that both the geodesic equations and the field equations can be obtained from a variational principle. (author)

  19. Design of a nonlinear torsional vibration absorber

    Science.gov (United States)

    Tahir, Ammaar Bin

    Tuned mass dampers (TMD) utilizing linear spring mechanisms to mitigate destructive vibrations are commonly used in practice. A TMD is usually tuned for a specific resonant frequency or an operating frequency of a system. Recently, nonlinear vibration absorbers attracted attention of researchers due to some potential advantages they possess over the TMDs. The nonlinear vibration absorber, or the nonlinear energy sink (NES), has an advantage of being effective over a broad range of excitation frequencies, which makes it more suitable for systems with several resonant frequencies, or for a system with varying excitation frequency. Vibration dissipation mechanism in an NES is passive and ensures that there is no energy backflow to the primary system. In this study, an experimental setup of a rotational system has been designed for validation of the concept of nonlinear torsional vibration absorber with geometrically induced cubic stiffness nonlinearity. Dimensions of the primary system have been optimized so as to get the first natural frequency of the system to be fairly low. This was done in order to excite the dynamic system for torsional vibration response by the available motor. Experiments have been performed to obtain the modal parameters of the system. Based on the obtained modal parameters, the design optimization of the nonlinear torsional vibration absorber was carried out using an equivalent 2-DOF modal model. The optimality criterion was chosen to be maximization of energy dissipation in the nonlinear absorber attached to the equivalent 2-DOF system. The optimized design parameters of the nonlinear absorber were tested on the original 5-DOF system numerically. A comparison was made between the performance of linear and nonlinear absorbers using the numerical models. The comparison showed the superiority of the nonlinear absorber over its linear counterpart for the given set of primary system parameters as the vibration energy dissipation in the former is

  20. Fast Torsional Artificial Muscles from NiTi Twisted Yarns.

    Science.gov (United States)

    Mirvakili, Seyed M; Hunter, Ian W

    2017-05-17

    Torsional artificial muscles made of multiwalled carbon nanotube/niobium nanowire yarns have shown remarkable torsional speed and gravimetric torque. The muscle structure consists of a twisted yarn with half of its length infiltrated with a stimuli-responsive guest material such as paraffin wax. The volumetric expansion of the guest material creates the torsional actuation in the yarn. In the present work, we show that this type of actuation is not unique to wax-infiltrated carbon multiwalled nanotube (MWCNT) or niobium nanowire yarns and that twisted yarn of NiTi alloy fibers also produces fast torsional actuation. By gold-plating half the length of a NiTi twisted yarn and Joule heating it, we achieved a fully reversible torsional actuation of up to 16°/mm with peak torsional speed of 10 500 rpm and gravimetric torque of 8 N·m/kg. These results favorably compare to those of MWCNTs and niobium nanowire yarns.

  1. Isolated Penile Torsion in Brothers: A Case Report

    Directory of Open Access Journals (Sweden)

    Metin Gunduz

    2012-04-01

    Full Text Available Penile torsion can be congenital and associated with hypospadias and chordee, or can be acquired after circumcision. The incidence of isolated neonatal penile torsion was 1.7 to 27% in the literature. The majority were between 10 and deg; and 20 and deg;. Generally, torsion was to the left in cases. The techniques for correction of penile torsion described in the literature are penile de-gloving and reattaching of skin, resection of Buck's fascia incising the base of the penis and removing angular ellipses of corporeal tissue with subsequent plication of tunica, and dorsal dartos flap rotation in severe cases. In conclusion, penile torsion may be familial. Therefore, brothers should be examined carefully. The degloving and realignment technique is successful in isolated penile torsion. [Arch Clin Exp Surg 2012; 1(2.000: 122-124

  2. Performance of Flow-Aware Networking in LTE backbone

    DEFF Research Database (Denmark)

    Sniady, Aleksander; Soler, José

    2012-01-01

    technologies, such as Long Term Evolution (LTE). This paper proposes usage of a modified Flow Aware Networking (FAN) technique for enhancing Quality of Service (QoS) in the all-IP transport networks underlying LTE backbone. The results obtained with OPNET Modeler show that FAN, in spite of being relatively...

  3. The Graphical Representation of the Digital Astronaut Physiology Backbone

    Science.gov (United States)

    Briers, Demarcus

    2010-01-01

    This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

  4. Determination of backbone chain direction of PDA using FFM

    Science.gov (United States)

    Jo, Sadaharu; Okamoto, Kentaro; Takenaga, Mitsuru

    2010-01-01

    The effect of backbone chains on friction force was investigated on both Langmuir-Blodgett (LB) films of 10,12-heptacosadiynoic acid and the (0 1 0) surfaces of single crystals of 2,4-hexadiene-1,6-diol using friction force microscopy (FFM). It was observed that friction force decreased when the scanning direction was parallel to the [0 0 1] direction in both samples. Moreover, friction force decreased when the scanning direction was parallel to the crystallographic [1 0 2], [1 0 1], [1 0 0] and [1 0 1¯] directions in only the single crystals. For the LB films, the [0 0 1] direction corresponds to the backbone chain direction of 10,12-heptacosadiynoic acid. For the single crystals, both the [0 0 1] and [1 0 1] directions correspond to the backbone chain direction, and the [1 0 2], [1 0 0] and [1 0 1¯] directions correspond to the low-index crystallographic direction. In both the LB films and single crystals, the friction force was minimized when the directions of scanning and the backbone chain were parallel.

  5. Internet Backbone in the Democratic Republic of Congo : Feasibility ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Internet Backbone in the Democratic Republic of Congo : Feasibility Study and Advocacy. During 7-10 February 2005, representatives of five francophone African countries (Cameroon, Morocco, Niger, Sénégal, and the Democratic Republic of Congo - DRC) met to consider ways and means of galvanizing the appropriation ...

  6. Development of a simple computerized torsion test to quantify subjective ocular torsion.

    Science.gov (United States)

    Kim, Y D; Yang, H K; Hwang, J-M

    2017-11-01

    PurposeThe double Maddox-rod test (DMRT) and Lancaster red-green test (LRGT) are the most widely used tests worldwide to assess subjective ocular torsion. However, these tests require equipment and the quantified results of ocular torsion are only provided in rough values. Here we developed a novel computerized torsion test (CTT) for individual assessment of subjective ocular torsion and validated the reliability and accuracy of the test compared with those of the DMRT and LRGT.MethodsA total of 30 patients with cyclovertical strabismus and 30 controls were recruited. The CTT was designed using Microsoft Office PowerPoint. Subjects wore red-green filter spectacles and viewed gradually tilted red and cyan lines on an LCD monitor and pressed the keyboard to go through the slides, until both lines seemed parallel. All subjects underwent the CTT, DMRT, and LRGT. Intraclass correlation coefficients and Bland-Altman plots were analyzed to assess the acceptability of the CTT compared with that of the DMRT.ResultsBoth the DMRT and CTT showed no significant test-retest differences in the strabismus and control groups. The DMRT and CTT results demonstrated an acceptable agreement. The reliability of the CTT was better than that of the DMRT. The LRGT showed low sensitivity for the detection of ocular torsion compared with the DMRT (40.0%) and CTT (39.1%).ConclusionOur results suggest that the assessment of subjective ocular torsion using the CTT based on PowerPoint software is simple, reproducible, and accurate and can be applied in clinical practice.

  7. Painless inter epididymal testicular torsion of the spermatic cord

    Directory of Open Access Journals (Sweden)

    Salomon V. Romano

    2007-02-01

    Full Text Available Inter epididymal testicular torsion of the spermatic cord is extremely rare and usually diagnosed at surgery. We present an unusual case of spermatic cord torsion in a 14-year-old male patient. It is important to highlight that the torsion occurred only on the distal half of the epididymis leaving the head untwisted and edematous. In addition, the fact that this condition was painless made this case extremely rare and motivated our presentation.

  8. Painless inter epididymal testicular torsion of the spermatic cord

    OpenAIRE

    Salomon V. Romano; Haime S. Hernan; Norberto Fredotovich

    2007-01-01

    Inter epididymal testicular torsion of the spermatic cord is extremely rare and usually diagnosed at surgery. We present an unusual case of spermatic cord torsion in a 14-year-old male patient. It is important to highlight that the torsion occurred only on the distal half of the epididymis leaving the head untwisted and edematous. In addition, the fact that this condition was painless made this case extremely rare and motivated our presentation.

  9. Ultrasonographic features of prenatal testicular torsion: Case report

    Directory of Open Access Journals (Sweden)

    Elif Ağaçayak

    2013-01-01

    Full Text Available Although prenatal testicular torsion (PNTT is rarely observed,it is an important condition that can cause bilateralvanishing testis. Generally, PNTT cases observed asextravaginal torsion and treatment is emergency surgicalop-eration. In this article, 39 week presented a case diagnosedin the prenatal testicular torsion. PNTT diagnosiswas confirmed by Doppler ultrasonography and emergencysurgery was performed. Extravaginal left testiculartorsion gangrene and necrosis of the testis was observedin the operation. Left orchiectomy was performed andintrauter-ine ultrasonographic diagnosis was found to becorrect.Key words: Testicular torsion, prenatal diagnosis, features,ultrasonography

  10. Association of Torsion With Testicular Cancer: A Retrospective Study.

    Science.gov (United States)

    Uguz, Sami; Yilmaz, Sercan; Guragac, Ali; Topuz, Bahadır; Aydur, Emin

    2016-02-01

    Testicular torsion is a medical emergency that usually requires surgical exploration. However, testicular malignancy has been anecdotally reported with the association of torsion in surgical specimens, and the published data remain scant on the association of torsion with testicular tumors. By retrospective medical record review, we identified 32 patients who had been diagnosed with testicular torsion, 20 of whom had undergone orchiectomy. Of these 20 patients, 2 were diagnosed with a malignancy. Our study, the largest case series to date, has shown an association between testicular torsion and testicular cancer of 6.4%. Testicular torsion is a medical emergency that usually requires surgical exploration. However, testicular malignancy has been anecdotally reported in association with torsion in surgical specimens. However, the published data remain scant on the association between torsion and the presence of testicular tumors. The present retrospective study explored the association between torsion and testicular cancer in patients with testicular torsion undergoing orchiectomy during scrotal exploration. A medical record review was performed of patients who had had a diagnosis of testicular torsion from January 2003 to February 2015. The clinicopathologic characteristics of the patients were recorded. A total of 32 patients were identified. Their mean age was 21.1 years (range, 7-39 years). All the patients had unilateral testicular torsion, which affected the left side in 17 and the right side in 15. Manual detorsion was successful in 6 patients, and 26 patients underwent emergency surgery with testicular detorsion (6 fixation surgery and 20 orchiectomy). The type of incision was scrotal in 6, inguinal in 10, and unspecified in 4. Pathologic examination of the orchiectomy specimens showed malignancy in 2 cases (seminoma and malign mixed germ cell tumor). To the best of our knowledge, the present single-center case series is the largest case series to date of

  11. Secondary Torsion of Vermiform Appendix with Mucinous Cystadenoma

    Directory of Open Access Journals (Sweden)

    Maki Kitagawa

    2007-06-01

    Full Text Available Torsion of the vermiform appendix is a rare disorder, which causes abdominal symptoms indistinguishable from acute appendicitis. We report a case (a 34-year-old male of secondary torsion of the vermiform appendix with mucinous cystadenoma. This case was characterized by mild inflammatory responses, pentazocine-resistant abdominal pain, and appendiceal tumor, which was not enhanced by the contrast medium on computed tomography presumably because of reduced blood flow by the torsion. These findings may be helpful for the preoperative diagnosis of secondary appendiceal torsion.

  12. Structural Modifications for Torsional Vibration Control of Shafting Systems Based on Torsional Receptances

    Directory of Open Access Journals (Sweden)

    Zihao Liu

    2016-01-01

    Full Text Available Torsional vibration of shafts is a very important problem in engineering, in particular in ship engines and aeroengines. Due to their high levels of integration and complexity, it is hard to get their accurate structural data or accurate modal data. This lack of data is unhelpful to vibration control in the form of structural modifications. Besides, many parts in shaft systems are not allowed to be modified such as rotary inertia of a pump or an engine, which is designed for achieving certain functions. This paper presents a strategy for torsional vibration control of shaft systems in the form of structural modifications based on receptances, which does not need analytical or modal models of the systems under investigation. It only needs the torsional receptances of the system, which can be obtained by testing simple auxiliary structure attached to relevant locations of the shaft system and using the finite element model (FEM of the simple structure. An optimization problem is constructed to determine the required structural modifications, based on the actual requirements of modal frequencies and mode shapes. A numerical experiment is set up and the influence of several system parameters is analysed. Several scenarios of constraints in practice are considered. The numerical simulation results demonstrate the effectiveness of this method and its feasibility in solving torsional vibration problems in practice.

  13. Toward laboratory torsional spine magnetic reconnection

    Science.gov (United States)

    Chesny, David L.; Orange, N. Brice; Oluseyi, Hakeem M.; Valletta, David R.

    2017-12-01

    Magnetic reconnection is a fundamental energy conversion mechanism in nature. Major attempts to study this process in controlled settings on Earth have largely been limited to reproducing approximately two-dimensional (2-D) reconnection dynamics. Other experiments describing reconnection near three-dimensional null points are non-driven, and do not induce any of the 3-D modes of spine fan, torsional fan or torsional spine reconnection. In order to study these important 3-D modes observed in astrophysical plasmas (e.g. the solar atmosphere), laboratory set-ups must be designed to induce driven reconnection about an isolated magnetic null point. As such, we consider the limited range of fundamental resistive magnetohydrodynamic (MHD) and kinetic parameters of dynamic laboratory plasmas that are necessary to induce the torsional spine reconnection (TSR) mode characterized by a driven rotational slippage of field lines - a feature that has yet to be achieved in operational laboratory magnetic reconnection experiments. Leveraging existing reconnection models, we show that within a 3$ apparatus, TSR can be achieved in dense plasma regimes ( 24~\\text{m}-3$ ) in magnetic fields of -1~\\text{T}$ . We find that MHD and kinetic parameters predict reconnection in thin current sheets on time scales of . While these plasma regimes may not explicitly replicate the plasma parameters of observed astrophysical phenomena, studying the dynamics of the TSR mode within achievable set-ups signifies an important step in understanding the fundamentals of driven 3-D magnetic reconnection and the self-organization of current sheets. Explicit control of this reconnection mode may have implications for understanding particle acceleration in astrophysical environments, and may even have practical applications to fields such as spacecraft propulsion.

  14. Transverse posterior element fractures associated with torsion

    International Nuclear Information System (INIS)

    Abel, M.S.

    1989-01-01

    Six examples of a previously undescribed class of transverse vertebral element fractures are presented. These fractures differ from Chance and Smith fractures and their variants in the following respects: (1) the etiology is torsion and not flexion; (2) there is neither distraction of posterior ring fragments nor posterior ligament tears; (3) in contrast to Chance and Smith fractures, extension of the fracture into the vertebral body is absent or minimal; (4) the transverse process of the lumbar vertebra is avulsed at its base with a vertical fracture, not split horizontally. These fractures occur in cervical, lumbar, and sacral vertebrae in normal or compromised areas of the spine. (orig.)

  15. Possible role of torsion in gravitational theories

    International Nuclear Information System (INIS)

    Nieh, H.T.

    1983-01-01

    Torsion is of interest in an indirect way, in that it has the potential of being an important ingredient in a future successful quantum theory of gravitation. Einstein's theory of gravitation, despite its simplicity and elegance, and its successes in large-scale gravitational phenomena, can only be regarded as a macroscopic classical theory. It is a non-renormalizable quantum field theory, and, therefore, lacks the status of a good microscopic theory. It is the search for a successful quantum field theory of gravitation that poses as one of the great challenges to theoretical physics today. (Auth.)

  16. Torsion of the normal fallopian tube.

    Science.gov (United States)

    Provost, M W

    1972-01-01

    From 1961 to 1970 a number of cases of torsion of the Fallopian tube were seen at the Kaiser Foundation Hospital in San Francisco of which 3 cases are reported. Of the many theories of causation, pelvic congestion seemed the most likely. The only universal symptom is pain, located in the quadrant of the affected tube and sometimes radiating to the thigh or flank. Nausea and vomiting are frequent; temperature and white cell count are only slightly elevated or normal. A mass is often felt, depending on the amount of hemorrhage. Correct diagnosis is almost never made preoperatively. The only treatment is laparotomy and surgical correction.

  17. Dismal salvage of testicular torsion: A call to action! | Maranya ...

    African Journals Online (AJOL)

    ... were not subjected to orchidopexy. There was no occurrence of torsion after orchidopexy. Conclusion: Testicular torsions were associated with low salvage rates. Increased public awareness coupled with clinician, parental, teacher, teenage and adult male education with respect to the consequences of acute scrotal pain ...

  18. Quantum gravity effect in torsion driven inflation and CP violation

    Energy Technology Data Exchange (ETDEWEB)

    Choudhury, Sayantan [Department of Theoretical Physics, Tata Institute of Fundamental Research,Colaba, 1, Homi Bhabha Road, Mumbai 400005 (India); Pal, Barun Kumar [Inter-University Centre for Astronomy and Astrophysics,Ganeshkhind, Pune 411007 (India); Netaji Nagar College for Women,Regent Estate, Kolkata 700092 (India); Basu, Banasri; Bandyopadhyay, Pratul [Physics and Applied Mathematics Unit, Indian Statistical Institute,203 B.T. Road, Kolkata 700 108 (India)

    2015-10-28

    We have derived an effective potential for inflationary scenario from torsion and quantum gravity correction in terms of the scalar field hidden in torsion. A strict bound on the CP violating θ parameter, O(10{sup −10})<θ

  19. Torsion of the Spermatic Cord: Is Bilateral Orchidopexy Really ...

    African Journals Online (AJOL)

    Aim: To evaluate the rationale for bilateral orchidopexy as treatment for unilateral torsion of the testis, by determining how frequently the contralateral testis shows an abnormal pathology in unilateral testicular torsion. Patients and Methods:This is a retrospective study using adult urology patients treated for both acute and ...

  20. Comparison of torsional and longitudinal modes using phacoemulsification parameters.

    Science.gov (United States)

    Rekas, Marek; Montés-Micó, Robert; Krix-Jachym, Karolina; Kluś, Adam; Stankiewicz, Andrzej; Ferrer-Blasco, Teresa

    2009-10-01

    To compare phacoemulsification parameters of torsional and longitudinal ultrasound modes. Ophthalmology Department, Military Health Service Institute, Warsaw, Poland. This prospective study evaluated eyes 1, 7, and 30 days after phacoemulsification with an Infiniti Vision System using the torsional or longitudinal ultrasound (US) mode. Cataract classification was according to the Lens Opacities Classification System II. Nucleus fragmentation was by the phaco-chop and quick-chop methods. Primary outcome measures were phaco time, mean phaco power, mean torsional amplitude, and aspiration time. Total energy, defined as cumulative dissipated energy (CDE) x aspiration time, and the effective coefficient, defined as aspiration time/phaco time, were also calculated. Four hundred eyes were evaluated. The CDE was statistically significantly lower in the torsional mode for nucleus grades I, II, and III (P.05). Aspiration time was statistically significantly shorter in the torsional mode than in the longitudinal mode for nucleus grades III and IV (P<.05). Total energy was significantly lower in the torsional mode for all nucleus densities (P<.05). The effective coefficient was significantly lower in the longitudinal mode except for nucleus grade I (P<.05). Torsional phacoemulsification was more effective than longitudinal phacoemulsification in the amount of applied fluid and the quantity of US energy expended. With the torsional method, it was possible to maintain a constant ratio of amount of fluid flow to quantity of US energy used, regardless of nucleus density.

  1. Additivity for parametrized topological Euler characteristic and Reidemeister torsion

    OpenAIRE

    Badzioch, Bernard; Dorabiala, Wojciech

    2005-01-01

    Dwyer, Weiss, and Williams have recently defined the notions of parametrized topological Euler characteristic and parametrized topological Reidemeister torsion which are invariants of bundles of compact topological manifolds. We show that these invariants satisfy additivity formulas paralleling the additive properties of the classical Euler characteristic and Reidemeister torsion of finite CW-complexes.

  2. Perinatal testicular torsion: literature review and local experience ...

    African Journals Online (AJOL)

    The prognosis in TUDT is guarded and contralateral fixation was not practiced, except in a 5-week-old infant. Early orchiopexy at 3–6 months is recommended. Cooperation between surgeons, neonatologists, and parents is mandatory to avoid time delay. Keywords: intrauterine testicular torsion, postnatal testicular torsion, ...

  3. Mechanical origins of rightward torsion in early chick brain development

    Science.gov (United States)

    Chen, Zi; Guo, Qiaohang; Dai, Eric; Taber, Larry

    2015-03-01

    During early development, the neural tube of the chick embryo undergoes a combination of progressive ventral bending and rightward torsion. This torsional deformation is one of the major organ-level left-right asymmetry events in development. Previous studies suggested that bending is mainly due to differential growth, however, the mechanism for torsion remains poorly understood. Since the heart almost always loops rightwards that the brain twists, researchers have speculated that heart looping affects the direction of brain torsion. However, direct evidence is lacking, nor is the mechanical origin of such torsion understood. In our study, experimental perturbations show that the bending and torsional deformations in the brain are coupled and that the vitelline membrane applies an external load necessary for torsion to occur. Moreover, the asymmetry of the looping heart gives rise to the chirality of the twisted brain. A computational model and a 3D printed physical model are employed to help interpret these findings. Our work clarifies the mechanical origins of brain torsion and the associated left-right asymmetry, and further reveals that the asymmetric development in one organ can induce the asymmetry of another developing organ through mechanics, reminiscent of D'Arcy Thompson's view of biological form as ``diagram of forces''. Z.C. is supported by the Society in Science - Branco Weiss fellowship, administered by ETH Zurich. L.A.T acknowledges the support from NIH Grants R01 GM075200 and R01 NS070918.

  4. Torsional structural response from free-field ground motion

    International Nuclear Information System (INIS)

    Lam, P.C.; Scavuzzo, R.J.

    1979-01-01

    Torsional response of structures subjected to the action of both the free-field torsional inputs and external torque is investigated. By expanding the work of Scanlan, both lateral and torsional foundation inputs due to a travelling shear wave are derived from the free-field point motion. These free-field torsional motions are used as the basis of numerical studies. Response for different soil stiffness and structural characteristics are studied, as well as different dynamic models. In one dynamic model the structure is coupled to the soil using a compliance spring matrix and in the second model the structure coupled to an elastic half-space. Results of these two basic models are compared and found to be in good agreement. Finally, torsional structural response caused by torsional inputs is compared with lateral response caused by modified lateral inputs to determine the significance of torsional excitation on the seismic response of building structures. Numerical results show that these torsional seismic loads are as large or larger than those from modified lateral inputs. (orig.)

  5. Quantum gravity effect in torsion driven inflation and CP violation

    International Nuclear Information System (INIS)

    Choudhury, Sayantan; Pal, Barun Kumar; Basu, Banasri; Bandyopadhyay, Pratul

    2015-01-01

    We have derived an effective potential for inflationary scenario from torsion and quantum gravity correction in terms of the scalar field hidden in torsion. A strict bound on the CP violating θ parameter, O(10"−"1"0)<θ< O(10"−"9) has been obtained, using Planck+WMAP9 best fit cosmological parameters.

  6. Torsional stresses in the transverse fillet weld tubular joints

    NARCIS (Netherlands)

    Gunay, D.; Aydemir, A.; Özer, H.

    1996-01-01

    Torsional stresses, 'tre and tel , in tbe transverse fillet tubular weld joint subjected to torsional load have been analyzed by the finite element method using triangular and quadrilateral izoparametric axisymmetric fourier type torus finite elements. There is an axisymmetry with respect to

  7. Severe congenital penile torsion with anterior urethral diverticulum ...

    African Journals Online (AJOL)

    On examination, he was found to be a case of severe congenital penile torsion with diversion and rotation of median raphae in a counterclockwise fashion upto the midline dorsally confirming 180◦ torsion. During voiding, there was appearance of a swelling in distal penile region with passage of urinary drops while ...

  8. A Patient Presenting with Concurrent Testis Torsion and Epididymal Leiomyoma

    Directory of Open Access Journals (Sweden)

    E. Arpali

    2013-01-01

    Full Text Available Leiomyomas are the second most common tumors of epididymis. Patients with leiomyomas are sometimes misdiagnosed with testicular tumors. A Case of a patient with a scrotal mass presenting with testicular torsion is reported. Concurrent occurrence of testicular torsion and epididymal leiomyoma is an extremely rare condition.

  9. The Reidemeister torsion of 3-manifolds

    CERN Document Server

    Nicolaescu, Liviu I

    2003-01-01

    This is a state-of-the-art introduction to the work of Franz Reidemeister, Meng Taubes, Turaev, and the author on the concept of torsion and its generalizations. Torsion is the oldest topological (but not with respect to homotopy) invariant that in its almost eight decades of existence has been at the center of many important and surprising discoveries. During the past decade, in the work of Vladimir Turaev, new points of view have emerged, which turned out to be the "right ones" as far as gauge theory is concerned. The book features mostly the new aspects of this venerable concept. The theoretical foundations of this subject are presented in a style accessible to those, who wish to learn and understand the main ideas of the theory. Particular emphasis is upon the many and rather diverse concrete examples and techniques which capture the subleties of the theory better than any abstract general result. Many of these examples and techniques never appeared in print before, and their choice is often justified by ...

  10. Curvature and torsion in growing actin networks

    International Nuclear Information System (INIS)

    Shaevitz, Joshua W; Fletcher, Daniel A

    2008-01-01

    Intracellular pathogens such as Listeria monocytogenes and Rickettsia rickettsii move within a host cell by polymerizing a comet-tail of actin fibers that ultimately pushes the cell forward. This dense network of cross-linked actin polymers typically exhibits a striking curvature that causes bacteria to move in gently looping paths. Theoretically, tail curvature has been linked to details of motility by considering force and torque balances from a finite number of polymerizing filaments. Here we track beads coated with a prokaryotic activator of actin polymerization in three dimensions to directly quantify the curvature and torsion of bead motility paths. We find that bead paths are more likely to have low rather than high curvature at any given time. Furthermore, path curvature changes very slowly in time, with an autocorrelation decay time of 200 s. Paths with a small radius of curvature, therefore, remain so for an extended period resulting in loops when confined to two dimensions. When allowed to explore a three-dimensional (3D) space, path loops are less evident. Finally, we quantify the torsion in the bead paths and show that beads do not exhibit a significant left- or right-handed bias to their motion in 3D. These results suggest that paths of actin-propelled objects may be attributed to slow changes in curvature, possibly associated with filament debranching, rather than a fixed torque

  11. Physics of detecting torsion and placing limits on its effects

    International Nuclear Information System (INIS)

    Stoeger, W.R.

    1985-01-01

    The essential principles of torsion-detection physics are presented, and an evaluation is conducted of several conceivable types of experiments and observations for actually detecting torsion fields, reemphasizing also the evident impossibility of successfully searching for its manifestations among cosmological relics. In particular, a polarized body, with net intrinsic (fundamental-particle) spin, is essential for detecting a torsion field. One which possesses only orbital angular momentum - rotation - or an unpolarized intrinsic spin density will not feel torsion. The fundamental problem in searching for such fields is the extremely small basic unit of the coupling or interaction energy between the torsion field and spin. The best way of maximizing the total interaction energy is to increase the spin density of the source sigma-s and at the same time the spin number SD of the detector. 15 references

  12. Krukenberg Tumor: A Rare Cause of Ovarian Torsion

    Directory of Open Access Journals (Sweden)

    Sameer Sandhu

    2012-01-01

    Full Text Available Ovarian torsion is the fifth most common gynecological surgical emergency. Ovarian torsion is usually associated with a cyst or a tumor, which is typically benign. The most common is mature cystic teratoma. We report the case of a 43-year-old woman who came to the Emergency Department with rare acute presentation of bilateral Krukenberg tumors, due to unilateral ovarian torsion. In this case report, we highlight the specific computed tomography (CT features of ovarian torsion and demonstrate the unique radiological findings on CT imaging. Metastasis to the ovary is not rare and 5 to 10% of all ovarian malignancies are metastatic. The stomach is the common primary site in most Krukenberg tumors (70%; an acute presentation of metastatic Krukenberg tumors with ovarian torsion is rare and not previously reported in radiology literature.

  13. Peculiar torsion dynamical response of spider dragline silk

    Science.gov (United States)

    Liu, Dabiao; Yu, Longteng; He, Yuming; Peng, Kai; Liu, Jie; Guan, Juan; Dunstan, D. J.

    2017-07-01

    The torsional properties of spider dragline silks from Nephila edulis and Nephila pilipes spiders are investigated by using a torsion pendulum technique. A permanent torsional deformation is observed after even small torsional strain. This behaviour is quite different from that of the other materials tested here, i.e., carbon fiber, thin metallic wires, Kevlar fiber, and human hair. The spider dragline thus displays a strong energy dissipation upon the initial excitation (around 75% for small strains and more for a larger strain), which correspondingly reduces the amplitude of subsequent oscillations around the new equilibrium position. The variation of torsional stiffness in relaxation dynamics of spider draglines for different excitations is also determined. The experimental result is interpreted in the light of the hierarchical structure of dragline silk.

  14. Induced helical backbone conformations of self-organizable dendronized polymers.

    Science.gov (United States)

    Rudick, Jonathan G; Percec, Virgil

    2008-12-01

    Control of function through the primary structure of a molecule presents a significant challenge with valuable rewards for nanoscience. Dendritic building blocks encoded with information that defines their three-dimensional shape (e.g., flat-tapered or conical) and how they associate with each other are referred to as self-assembling dendrons. Self-organizable dendronized polymers possess a flat-tapered or conical self-assembling dendritic side chain on each repeat unit of a linear polymer backbone. When appended to a covalent polymer, the self-assembling dendrons direct a folding process (i.e., intramolecular self-assembly). Alternatively, intermolecular self-assembly of dendrons mediated by noncovalent interactions between apex groups can generate a supramolecular polymer backbone. Self-organization, as we refer to it, is the spontaneous formation of periodic and quasiperiodic arrays from supramolecular elements. Covalent and supramolecular polymers jacketed with self-assembling dendrons self-organize. The arrays are most often comprised of cylindrical or spherical objects. The shape of the object is determined by the primary structure of the dendronized polymer: the structure of the self-assembling dendron and the length of the polymer backbone. It is therefore possible to predictably generate building blocks for single-molecule nanotechnologies or arrays of supramolecules for bottom-up self-assembly. We exploit the self-organization of polymers jacketed with self-assembling dendrons to elucidate how primary structure determines the adopted conformation and fold (i.e., secondary and tertiary structure), how the supramolecules associate (i.e., quaternary structure), and their resulting functions. A combination of experimental techniques is employed to interrogate the primary, secondary, tertiary, and quaternary structure of the self-organizable dendronized polymers. We refer to the process by which we interpolate between the various levels of structural

  15. Torsional actuation with extension-torsion composite coupling and a magnetostrictive actuator

    Science.gov (United States)

    Bothwell, Christopher M.; Chandra, Ramesh; Chopra, Inderjit

    1995-04-01

    An analytical-experimental study of using magnetostrictive actuators in conjunction with an extension-torsion coupled composite tube to actuate a rotor blade trailing-edge flap to actively control helicopter vibration is presented. Thin walled beam analysis based on Vlasov theory was used to predict the induced twist and extension in a composite tube with magnetostrictive actuation. The study achieved good correlation between theory and experiment. The Kevlar-epoxy systems showed good correlation between measured and predicted twist values.

  16. Experimental investigation of torsional vibration isolation using Magneto Rheological Elastomer

    Directory of Open Access Journals (Sweden)

    Praveen Shenoy K

    2018-01-01

    Full Text Available Rotating systems suffer from lateral and torsional vibrations which have detrimental effect on the roto-dynamic performance. Many available technologies such as vibration isolators and vibration absorbers deal with the torsional vibrations to a certain extent, however passive isolators and absorbers find less application when the input conditions are dynamic. The present work discusses use of a smart material called as Magneto Rheological Elastomer (MRE, whose properties can be changed based on magnetic field input, as a potential isolator for torsional vibrations under dynamic loading conditions. Carbonyl Iron Particles (CIP of average size 5 μm were mixed with RTV Silicone rubber to form the MRE. The effect of magnetic field on the system parameters was comprehended under impulse loading conditions using a custom built in-house system. Series arrangement of accelerometers were used to differentiate between the torsional and the bending modes of vibration of the system. Impact hammer tests were carried out on the torsional system to study its response, in the presence and absence of magnetic field. The tests revealed a shift in torsional frequency in the presence of magnetic field which elucidates the ability of MRE to work as a potential vibration isolator for torsional systems.

  17. Online Identification and Verification of the Elastic Coupling Torsional Stiffness

    Directory of Open Access Journals (Sweden)

    Wanyou Li

    2016-01-01

    Full Text Available To analyze the torsional vibration of a diesel engine shaft, the torsional stiffness of the flexible coupling is a key kinetic parameter. Since the material properties of the elastic element of the coupling might change after a long-time operation due to the severe working environment or improper use and the variation of such properties will change dynamic feature of the coupling, it will cause a relative large calculation error of torsional vibration to the shaft system. Moreover, the torsional stiffness of the elastic coupling is difficult to be determined, and it is inappropriate to measure this parameter by disassembling the power unit while it is under normal operation. To solve these problems, this paper comes up with a method which combines the torsional vibration test with the calculation of the diesel shafting and uses the inherent characteristics of shaft torsional vibration to identify the dynamic stiffness of the elastic coupling without disassembling the unit. Analysis results show that it is reasonable and feasible to identify the elastic coupling dynamic torsional stiffness with this method and the identified stiffness is accurate. Besides, this method provides a convenient and practical approach to examine the dynamic behavior of the long running elastic coupling.

  18. Dynamic Bending and Torsion Stiffness Derivation from Modal Curvatures and Torsion Rates

    Science.gov (United States)

    MAECK, J.; DE ROECK, G.

    1999-08-01

    In order to maintain the reliability of civil engineering structures, considerable effort is currently spent on developing a non-destructive vibration testing method for monitoring the structural integrity of constructions. The technique must be able to observe damage, secondly to localize the damage; and finally to give an idea of the severity of the damage. Within the framework of relating changes of measured modal parameters to changes in the integrity of the structure, it is important to be able to determine the dynamic stiffness in each section of the structure from measured modal characteristics.A damaged structure results in a dynamic stiffness reduction of the cracked sections. The dynamic stiffnesses provide directly an indication of the extension of the cracked zones in the structure. The dynamic stiffness reduction can also be associated with a degree of cracking in a particular zone.In an experimental programme, a concrete beam of 6 m length is subjected to an increasing static load to produce cracks. After each static perload, the beam is tested dynamically in a free-free set-up. The change in modal parameters is then related to damage in the beam.The technique that will be presented in the paper to predict the damage location and intensity is a direct stiffness derivation from measured modal displacement derivatives. Using the bending modes, the dynamic bending stiffness can be derived from modal curvatures. Using the torsional modes, the dynamic torsion stiffness can be derived from modal torsion rates.

  19. Experimental study on pure titanium during the positive-torsion and positive-negative-torsion

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Han; Li, Fuguo, E-mail: fuguolx@nwpu.edu.cn; Li, Jinghui; Zhao, Zhen; Zhou, Shunshun; Wan, Qiong

    2016-09-30

    The results of the mechanical properties, microstructure and fracture analysis of the pure titanium deformed by positive-torsion (PT) and positive-negative-torsion (PNT) are investigated by uniaxial tensile (UT) test, micro-indentation (MI) test, optical microscope (OM), transmission electron microscope (TEM) and scanning electron microscope (SEM). The UT test indicates that the strength increases obviously with the increase of torsion radian during PT. However, the strength firstly increases quickly, and then tends to steady with the increase of deformation during PNT. The similar phenomena are also shown through MI hardness analysis. The results from geometrically necessary dislocations (GNDs) and statistically stored dislocations (SSDs) indicate that the dislocation density varies differently with the increase of deformation during PT and PNT. OM observation shows the grains are elongated and large numbers of deformation twins are observed during PT while the equiaxial grains are always presented during PNT. The variations of dislocation density during PT and PNT are verified by TEM. Besides, quantities of subgrains (SGs) are observed owing to the accumulated larger plastic strain during PNT while large numbers of deformation twins intersect with each other during PT. The fracture analysis indicates that large numbers of micro-voids distribute non-uniformly on fracture surface of sample twisted by PNT. However, the characteristics of ductile and brittle fracture are observed on fracture surface of sample twisted by PT.

  20. Torsion based universal MEMS logic device

    KAUST Repository

    Ilyas, Saad; Carreno, Armando Arpys Arevalo; Bayes, Ernesto; Foulds, Ian G.; Younis, Mohammad I.

    2015-01-01

    In this work we demonstrate torsion based complementary MEMS logic device, which is capable, of performing INVERTER, AND, NAND, NOR, and OR gates using one physical structure within an operating range of 0-10 volts. It can also perform XOR and XNOR with one access inverter using the same structure with different electrical interconnects. The paper presents modeling, fabrication and experimental calculations of various performance features of the device including lifetime, power consumption and resonance frequency. The fabricated device is 535 μm by 150 μm with a gap of 1.92 μm and a resonant frequency of 6.51 kHz. The device is capable of performing the switching operation with a frequency of 1 kHz.

  1. ZNxZM orbifolds and discrete torsion

    International Nuclear Information System (INIS)

    Font, A.; Quevedo, F.

    1989-01-01

    We extend previous work on Z N -orbifolds to the general Z N xZ M abelian case for both (2, 2) and (0, 2) models. We classify the corresponding (2, 2) compactifications and show that a number of models obtained by tensoring minimal N = 2 superconformal theories can be constructed as Z N xZ M -orbifolds. Furthermore, Z N xZ M -orbifolds allow the addition of discrete torsion which leads to new (2, 2) compactifications not considered previously. Some of the latter have negative Euler characteristics and Betti numbers equal to those of some complete intersection Calabi-Yau (CICY) manifolds. This suggests the existence of a previously overlooked connection between CICY models and orbifolds. (orig.)

  2. Torsion based universal MEMS logic device

    KAUST Repository

    Ilyas, Saad

    2015-10-28

    In this work we demonstrate torsion based complementary MEMS logic device, which is capable, of performing INVERTER, AND, NAND, NOR, and OR gates using one physical structure within an operating range of 0-10 volts. It can also perform XOR and XNOR with one access inverter using the same structure with different electrical interconnects. The paper presents modeling, fabrication and experimental calculations of various performance features of the device including lifetime, power consumption and resonance frequency. The fabricated device is 535 μm by 150 μm with a gap of 1.92 μm and a resonant frequency of 6.51 kHz. The device is capable of performing the switching operation with a frequency of 1 kHz.

  3. Covariant formulation of scalar-torsion gravity

    Science.gov (United States)

    Hohmann, Manuel; Järv, Laur; Ualikhanova, Ulbossyn

    2018-05-01

    We consider a generalized teleparallel theory of gravitation, where the action contains an arbitrary function of the torsion scalar and a scalar field, f (T ,ϕ ) , thus encompassing the cases of f (T ) gravity and a nonminimally coupled scalar field as subclasses. The action is manifestly Lorentz invariant when besides the tetrad one allows for a flat but nontrivial spin connection. We derive the field equations and demonstrate how the antisymmetric part of the tetrad equations is automatically satisfied when the spin connection equation holds. The spin connection equation is a vital part of the covariant formulation, since it determines the spin connection associated with a given tetrad. We discuss how the spin connection equation can be solved in general and provide the cosmological and spherically symmetric examples. Finally, we generalize the theory to an arbitrary number of scalar fields.

  4. Torsional malalignment, how much significant in the trochanteric fractures?

    Science.gov (United States)

    Kim, Tae Young; Lee, Yong Beom; Chang, Jun Dong; Lee, Sang Soo; Yoo, Jae Hyun; Chung, Kook Jin; Hwang, Ji Hyo

    2015-11-01

    The rotational alignment is definitely important in the long bones such as tibias and femurs. We also predict the importance of rotational alignment in the trochanteric fractures. So we measured torsional malalignment in trochanteric fracture and anlaysed their risk factors and their clinical significance. A total of 109 inpatients who had undergone internal fixation following trochanteric fracture and a postoperative pelvic CT scan between 2008 and 2013, with at least one year follow-up, were selected. Factors that affect torsional malalignment, such as age, gender, fracture stability, injured area, operative time, time of surgery after admission, and ASA status, were investigated. Factors that affect the patients' clinical results in malrotation, including ambulation time after surgery, postoperative complication rates, pain assessment of VAS one year postoperatively and Koval score, were also investigated. Of the 109 subjects, torsional malalignment was observed in 28 (25.7%) subjects with a mean torsional malalignment angle of 20.7° (range: -31.2° to 27.1°). Torsional malalignment risk factors were fracture stability (p=0.021) and operative time (p=0.043). In terms of the time to ambulation after surgery, the postoperative complication rates, and the VAS and Koval scores at one year postoperatively, no statistically significant difference was observed between the torsional malalignment patients and the non-deformity patients. In this study, 25.7% of the patients who had undergone internal fixation following trochanteric fracture experienced torsional malalignment. Major factors of the torsional malalignment were an unstable fracture and the consequent delay in the operative time. But the torsional malalignment was deemed to have no effect on clinical results. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

    Science.gov (United States)

    Fortin, Connor H; Schulze, Katharina V; Babbitt, Gregory A

    2015-01-01

    It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity. We present TRX-LOGOS, an R software package and Perl wrapper code that interfaces the JASPAR database for computational regulatory genomics. TRX-LOGOS extends the traditional sequence logo plot to include Shannon information content calculated with regard to the dinucleotide-based BI-BII conformation shifts in phosphate linkages on the DNA backbone, thereby adding a visual measure of intrinsic DNA flexibility that can be critical for many DNA-protein interactions. TRX-LOGOS is available as an R graphics module offered at both SourceForge and as a download supplement at this journal. To demonstrate the general utility of TRX logo plots, we first calculated the information content for 416 Saccharomyces cerevisiae transcription factor binding sites functionally confirmed in the Yeastract database and matched to previously published yeast genomic alignments. We discovered that flanking regions contain significantly elevated information content at phosphate linkages than can be observed at nucleobases. We also examined broader transcription factor classifications defined by the JASPAR database, and discovered that many general signatures of transcription factor binding are locally more information rich at the level of DNA backbone dynamics than nucleobase sequence. We used TRX-logos in combination with MEGA 6.0 software

  6. Torsion as a dynamic degree of freedom of quantum gravity

    International Nuclear Information System (INIS)

    Kim, Sang-Woo; Pak, D G

    2008-01-01

    The gauge approach to gravity based on the local Lorentz group with a general independent affine connection A μcd is developed. We consider SO(1, 3) gauge theory with a Lagrangian quadratic in curvature as a simple model of quantum gravity. The torsion is proposed to represent a dynamic degree of freedom of quantum gravity at scales above the Planckian energy. The Einstein-Hilbert theory is induced as an effective theory due to quantum corrections of torsion via generating a stable gravito-magnetic condensate. We conjecture that torsion possesses an intrinsic quantum nature and can be confined

  7. Dynamics of continuous medium in space with torsion

    International Nuclear Information System (INIS)

    Krechet, V.G.

    1985-01-01

    In frames of Einstein-Cartan gravitation theory general properties of continuous media dynamics using description formalism of continuous medium steam-line congruence geometry are investigated. Raichaudhuri type equations in space with torsion applied to study the problem of singularities in gravitation theory are derived. It is shown that space-time torsion tensor trace may immediately affect volumetric autoparallel divergence and torsion pseudo trace - rotation of continuous medium steam-line congruences. Using formalism considered metrics of homogeneous rotation nonstationary cosmological model is determined and investigated

  8. Generalised discrete torsion and mirror symmetry for G2 manifolds

    International Nuclear Information System (INIS)

    Gaberdiel, Matthias R.; Kaste, Peter

    2004-01-01

    A generalisation of discrete torsion is introduced in which different discrete torsion phases are considered for the different fixed points or twist fields of a twisted sector. The constraints that arise from modular invariance are analysed carefully. As an application we show how all the different resolutions of the T 7 /Z 2 3 orbifold of Joyce have an interpretation in terms of such generalised discrete torsion orbifolds. Furthermore, we show that these manifolds are pairwise identified under G 2 mirror symmetry. From a conformal field theory point of view, this mirror symmetry arises from an automorphism of the extended chiral algebra of the G 2 compactification. (author)

  9. Ultrafine grained Cu processed by compression with oscillatory torsion

    OpenAIRE

    K. Rodak

    2007-01-01

    Purpose: The aim of this work is a study of Cu microstructure after severe plastic deformation process by usingcompression with oscillatory torsion test.Design/methodology/approach: Cu samples were deformed at torsion frequency (f) changed from 0 Hz(compression) to 1.8 Hz under a constant torsion angle (α) ≈8° and compression speed (v)=0.1mm/s. Structuralinvestigations were conducted by using light microscopy (LM) and transmission electron microscopy (TEM).Findings: The structural analysis ma...

  10. Gastric dilatation-volvulus after splenic torsion in two dogs.

    Science.gov (United States)

    Millis, D L; Nemzek, J; Riggs, C; Walshaw, R

    1995-08-01

    Two dogs developed gastric dilatation-volvulus 2 and 17 months, respectively, after splenectomy for treatment of splenic torsion. Splenic displacement and torsion may stretch the gastric ligaments, allowing increased mobility of the stomach. After splenectomy, an anatomic void may be created in the cranioventral part of the abdomen, contributing to the mobility of the stomach. Veterinarians treating dogs with isolated splenic torsion may wish to consider prophylactic gastropexy at splenectomy, to reduce the chance of future gastric dilatation-volvulus. Prophylactic gastropexy should be done only if the dog's hemodynamic status is stable enough to allow for performance of the additional surgery.

  11. 5D Lovelock gravity: New exact solutions with torsion

    Science.gov (United States)

    Cvetković, B.; Simić, D.

    2016-10-01

    Five-dimensional Lovelock gravity is investigated in the first order formalism. A new class of exact solutions is constructed: the Bañados, Teitelboim, Zanelli black rings with and without torsion. We show that our solution with torsion exists in a different sector of the Lovelock gravity, as compared to the Lovelock Chern-Simons sector or the one investigated by Canfora et al. The conserved charges of the solutions are found using Nester's formula, and the results are confirmed by the canonical method. We show that the theory linearized around the background with torsion possesses two additional degrees of freedom with respect to general relativity.

  12. Backbone dynamics of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue, by 15N NMR relaxation methods

    International Nuclear Information System (INIS)

    Canales-Mayordomo, Angeles; Fayos, Rosa; Angulo, Jesus; Ojeda, Rafael; Martin-Pastor, Manuel; Nieto, Pedro M.; Martin-Lomas, Manuel; Lozano, Rosa; Gimenez-Gallego, Guillermo; Jimenez-Barbero, Jesus

    2006-01-01

    The binding site and backbone dynamics of a bioactive complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed heparin hexasaccharide has been investigated by HSQC and relaxation NMR methods. The comparison of the relaxation data for the free and bound states has allowed showing that the complex is monomeric, and still induces mutagenesis, and that the protein backbone presents reduced motion in different timescale in its bound state, except in certain points that are involved in the interaction with the fibroblast growth factor receptor (FGFR)

  13. Backbone dynamics of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue, by {sup 15}N NMR relaxation methods

    Energy Technology Data Exchange (ETDEWEB)

    Canales-Mayordomo, Angeles; Fayos, Rosa [Centro de Investigaciones Biologicas, CSIC, Departamento de Estructura y Funcion de Proteinas (Spain); Angulo, Jesus; Ojeda, Rafael [Instituto de Investigaciones Quimicas, CSIC, Grupo de Carbohidratos (Spain); Martin-Pastor, Manuel [Unidad de RM y Unidad de RMN de Biomoleculas Asociada al CSIC, Laboratorio de Estructura e Estructura de Biomoleculas Jose Carracido (Spain); Nieto, Pedro M.; Martin-Lomas, Manuel [Instituto de Investigaciones Quimicas, CSIC, Grupo de Carbohidratos (Spain); Lozano, Rosa; Gimenez-Gallego, Guillermo; Jimenez-Barbero, Jesus [Centro de Investigaciones Biologicas, CSIC, Departamento de Estructura y Funcion de Proteinas (Spain)], E-mail: jjbarbero@cib.csic.es

    2006-08-15

    The binding site and backbone dynamics of a bioactive complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed heparin hexasaccharide has been investigated by HSQC and relaxation NMR methods. The comparison of the relaxation data for the free and bound states has allowed showing that the complex is monomeric, and still induces mutagenesis, and that the protein backbone presents reduced motion in different timescale in its bound state, except in certain points that are involved in the interaction with the fibroblast growth factor receptor (FGFR)

  14. Transitional Failure of Carbon Nanotube Systems under a Combination of Tension and Torsion

    OpenAIRE

    Jeong, Byeong-Woo

    2012-01-01

    Transitional failure envelopes of single- and double-walled carbon nanotubes under combined tension-torsion are predicted using classical molecular dynamics simulations. The observations reveal that while the tensile failure load decreases with combined torsion, the torsional buckling moment increases with combined tension. As a result, the failure envelopes under combined tension-torsion are definitely different from those under pure tension or torsion. In such combined loading, there is a m...

  15. Constructing Battery-Aware Virtual Backbones in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Yang Yuanyuan

    2007-01-01

    Full Text Available A critical issue in battery-powered sensor networks is to construct energy efficient virtual backbones for network routing. Recent study in battery technology reveals that batteries tend to discharge more power than needed and reimburse the over-discharged power if they are recovered. In this paper we first provide a mathematical battery model suitable for implementation in sensor networks. We then introduce the concept of battery-aware connected dominating set (BACDS and show that in general the minimum BACDS (MBACDS can achieve longer lifetime than the previous backbone structures. Then we show that finding a MBACDS is NP-hard and give a distributed approximation algorithm to construct the BACDS. The resulting BACDS constructed by our algorithm is at most opt size, where is the maximum node degree and opt is the size of an optimal BACDS. Simulation results show that the BACDS can save a significant amount of energy and achieve up to longer network lifetime than previous schemes.

  16. Constructing Battery-Aware Virtual Backbones in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Chi Ma

    2007-05-01

    Full Text Available A critical issue in battery-powered sensor networks is to construct energy efficient virtual backbones for network routing. Recent study in battery technology reveals that batteries tend to discharge more power than needed and reimburse the over-discharged power if they are recovered. In this paper we first provide a mathematical battery model suitable for implementation in sensor networks. We then introduce the concept of battery-aware connected dominating set (BACDS and show that in general the minimum BACDS (MBACDS can achieve longer lifetime than the previous backbone structures. Then we show that finding a MBACDS is NP-hard and give a distributed approximation algorithm to construct the BACDS. The resulting BACDS constructed by our algorithm is at most (8+Δopt size, where Δ is the maximum node degree and opt is the size of an optimal BACDS. Simulation results show that the BACDS can save a significant amount of energy and achieve up to 30% longer network lifetime than previous schemes.

  17. pi-Turns: types, systematics and the context of their occurrence in protein structures.

    Science.gov (United States)

    Dasgupta, Bhaskar; Chakrabarti, Pinak

    2008-09-22

    For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue gamma-turn to six-residue pi-turn. The Schellman motif occurring at the C-terminal end of alpha-helices is a classical example of hydrogen bonded pi-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded beta- and alpha-turns have been identified previously; likewise, a systematic characterization of pi-turns would provide valuable insight into turn structures. An analysis of protein structures indicates that at least 20% of pi-turns occur independent of the Schellman motif. The two categories of pi-turns, designated as pi-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length beta- and alpha-turns, pi-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal C alpha-atoms, and this resulted in a comparable number of non-hydrogen-bonded pi-turns (pi-NHB). The presence of shorter beta- and alpha-turns within all categories of pi-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. pi-turns have been characterized, first using hydrogen bond and the distance between C alpha atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the pi-HB turns, being located on surface cavities, have functional role and there is also sequence

  18. Contribution of peptide backbone to Anti-citrulline-dependent antibody reactivity

    DEFF Research Database (Denmark)

    Trier, Nicole Hartwig; Dam, Catharina; Olsen, Dorthe

    2015-01-01

    for ACPA reactivity and to be cross-reactive between the selected citrullinated peptides. The remaining amino acids within the citrullinated peptides were found to be of less importance for antibody reactivity. Moreover, these findings indicated that the Cit-Gly motif in combination with peptide backbone...... found in up to 70% of RA patients’ sera, have received much attention. Several citrullinated proteins are associated with RA, suggesting that ACPAs may react with different sequence patterns, separating them from traditional antibodies, whose reactivity usually is specific towards a single target...... homology rather than sequence homology are favored between citrullinated epitopes. These findings are important in relation to clarifying the etiology of RA and to determine the nature of ACPAs, e.g. why some Cit-Gly-containing sequences are not targeted by ACPAs....

  19. Sequential backbone assignment based on dipolar amide-to-amide correlation experiments

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus, E-mail: rali@nmr.mpibpc.mpg.de [Max Planck Institute for Biophysical Chemistry, Department for NMR-Based Structural Biology (Germany)

    2015-07-15

    Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common {sup 13}C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR.

  20. 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.

  1. Sequential backbone assignment based on dipolar amide-to-amide correlation experiments

    International Nuclear Information System (INIS)

    Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus

    2015-01-01

    Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common 13 C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR

  2. NMR backbone resonance assignments of the prodomain variants of BDNF in the urea denatured state.

    Science.gov (United States)

    Wang, Jing; Bains, Henrietta; Anastasia, Agustin; Bracken, Clay

    2018-04-01

    Brain derived neurotrophic factor (BDNF) is a member of the neurotrophin family of proteins which plays a central role in neuronal survival, growth, plasticity and memory. A single Val66Met variant has been identified in the prodomain of human BDNF that is associated with anxiety, depression and memory disorders. The structural differences within the full-length prodomain Val66 and Met66 isoforms could shed light on the mechanism of action of the Met66 and its impact on the development of neuropsychiatric-associated disorders. In the present study, we report the backbone 1 H, 13 C, and 15 N NMR assignments of both full-length Val66 and Met66 prodomains in the presence of 2 M urea. These conditions were utilized to suppress residual structure and aid subsequent native state structural investigations aimed at mapping and identifying variant-dependent conformational differences under native-state conditions.

  3. Wet-Spun Biofiber for Torsional Artificial Muscles.

    Science.gov (United States)

    Mirabedini, Azadeh; Aziz, Shazed; Spinks, Geoffrey M; Foroughi, Javad

    2017-12-01

    The demands for new types of artificial muscles continue to grow and novel approaches are being enabled by the advent of new materials and novel fabrication strategies. Self-powered actuators have attracted significant attention due to their ability to be driven by elements in the ambient environment such as moisture. In this study, we demonstrate the use of twisted and coiled wet-spun hygroscopic chitosan fibers to achieve a novel torsional artificial muscle. The coiled fibers exhibited significant torsional actuation where the free end of the coiled fiber rotated up to 1155 degrees per mm of coil length when hydrated. This value is 96%, 362%, and 2210% higher than twisted graphene fiber, carbon nanotube torsional actuators, and coiled nylon muscles, respectively. A model based on a single helix was used to evaluate the torsional actuation behavior of these coiled chitosan fibers.

  4. Isolated adnexal torsion in a 20-week spontaneous twin pregnancy

    Directory of Open Access Journals (Sweden)

    Ilker Kahramanoglu

    2016-01-01

    Discussion: Adnexal torsion as a cause of acute abdomen may be kept in mind in pregnants, even if there is no predisposing factor. Laparoscopy may be performed safely in 2nd trimester for acute abdomen.

  5. Incidence and predictive factors of isolated neonatal penile glanular torsion.

    Science.gov (United States)

    Sarkis, Pierrot E; Sadasivam, Muthurajan

    2007-12-01

    To determine the incidence of isolated neonatal penile glanular torsion, describe the basic characteristics, and explore the relationship between foreskin and glans torsion. A prospective survey was conducted of all male newborns admitted to nursery after delivery, or neonates less than 3 months presenting for circumcision. Cases with associated genital malformations were excluded. The incidence of isolated neonatal penile torsion was 27% (95% CI: 22.2%-31.84%), to the left in 99% of cases. In 3.5% of cases, the penis had an angle 20 degrees. Using Spearman's correlational coefficient, deviation of penile raphe from the midline at the foreskin tip had a better correlation with glans torsion than deviation of raphe at the coronal sulcus (0.727 vs 0.570; both significant at pscope of the study.

  6. Torsional Newton–Cartan geometry from Galilean gauge theory

    International Nuclear Information System (INIS)

    Banerjee, Rabin; Mukherjee, Pradip

    2016-01-01

    Using the recently advanced Galilean gauge theory (GGT) we give a comprehensive construction of torsional Newton–Cartan (NC) geometry. The coupling of a Galilean symmetric model with background NC geometry following GGT is illustrated by a free nonrelativistic scalar field theory. The issue of spatial diffeomorphism (Son and Wingate 2006 Ann. Phys. 321 197–224; Banerjee et al 2015 Phys. Rev. D 91 084021) is focussed from a new angle. The expression of the torsionful connection is worked out, which is in complete parallel with the relativistic theory. Also, smooth transition of the connection to its well known torsionless expression is demonstrated. A complete (implicit) expression of the torsion tensor for the NC spacetime is provided where the first-order variables occur in a suggestive way. The well known result for the temporal part of torsion is reproduced from our expression. (paper)

  7. Timoshenko-Wagner-Kappus Torsion Bending Theory and Wind ...

    Indian Academy of Sciences (India)

    Theory and Wind Tunnel Balance Design. S P Govinda ... The study of torsion and bending has always been a favourite ... Since it was difficult to work quietlyin Petersburg, .... should be stiff and strong to endure shocks and ensure long life.

  8. Spin-torsion effects in the hyperfine structure of methanol

    International Nuclear Information System (INIS)

    Coudert, L. H.; Gutlé, C.; Huet, T. R.; Grabow, J.-U.; Levshakov, S. A.

    2015-01-01

    The magnetic hyperfine structure of the non-rigid methanol molecule is investigated experimentally and theoretically. 12 hyperfine patterns are recorded using molecular beam microwave spectrometers. These patterns, along with previously recorded ones, are analyzed in an attempt to evidence the effects of the magnetic spin-torsion coupling due to the large amplitude internal rotation of the methyl group [J. E. M. Heuvel and A. Dymanus, J. Mol. Spectrosc. 47, 363 (1973)]. The theoretical approach setup to analyze the observed data accounts for this spin-torsion in addition to the familiar magnetic spin-rotation and spin-spin interactions. The theoretical approach relies on symmetry considerations to build a hyperfine coupling Hamiltonian and spin-rotation-torsion wavefunctions compatible with the Pauli exclusion principle. Although all experimental hyperfine patterns are not fully resolved, the line position analysis yields values for several parameters including one describing the spin-torsion coupling

  9. Outcomes of Surgery for Posterior Polar Cataract Using Torsional Ultrasound

    Directory of Open Access Journals (Sweden)

    Selçuk Sızmaz

    2013-10-01

    Full Text Available Purpose: The aim of this study is to report outcomes of surgery for posterior polar cataract using torsional ultrasound. Material and Method: Medical records of 26 eyes of 21 consecutive patients with posterior polar cataract who had cataract surgery using the torsional phacoemulsification were evaluated retrospectively. The surgical procedure used, phacoemulsification parameters, intraoperative complications, and postoperative visual outcome were recorded. Results: Of the 26 eyes, 24 (92.3% had small to medium posterior polar opacity. Two eyes had large opacity. All surgeries were performed using the torsional handpiece. Posterior capsule rupture occurred in 4 (15.3% eyes. The mean visual acuity improved significantly after surgery (p<0.001. The postoperative visual acuity was worse than 20/20 in 5 eyes. The cause of the low acuity was amblyopia. Discussion: Successful surgical results and good visual outcome can be achieved with phacoemulsification using the torsional handpiece. (Turk J Ophthalmol 2013; 43: 345-7

  10. Torsional Dynamics of Steerable Needles: Modeling and Fluoroscopic Guidance

    Science.gov (United States)

    Swensen, John P.; Lin, MingDe; Okamura, Allison M.; Cowan, Noah J.

    2017-01-01

    Needle insertions underlie a diversity of medical interventions. Steerable needles provide a means by which to enhance existing needle-based interventions and facilitate new ones. Tip-steerable needles follow a curved path and can be steered by twisting the needle base during insertion, but this twisting excites torsional dynamics that introduce a discrepancy between the base and tip twist angles. Here, we model the torsional dynamics of a flexible rod—such as a tip-steerable needle—during subsurface insertion and develop a new controller based on the model. The torsional model incorporates time-varying mode shapes to capture the changing boundary conditions inherent during insertion. Numerical simulations and physical experiments using two distinct setups—stereo camera feedback in semi-transparent artificial tissue and feedback control with real-time X-ray imaging in optically opaque artificial tissue— demonstrate the need to account for torsional dynamics in control of the needle tip. PMID:24860026

  11. Torsion effect on fully developed flow in a helical pipe

    Science.gov (United States)

    Kao, Hsiao C.

    1987-01-01

    Two techniques, a series expansion method of perturbed Poiseuille flow valid for low Dean numbers and a solution of the complete Navier-Stokes equation applicable to intermediate Dean values, are used to investigate the torsion effect on the fully developed laminar flow in a helical pipe of constant circular cross section. For the secondary flow patterns, the results show that the presence of torsion can produce a significant effect if the ratio of the curvature to the torsion is of order unity. The secondary flow is distorted in these cases. It is noted that the torsion effect is, however, usually small, and that the secondary flow has the usual pattern of a pair of counter-rotating vortices of nearly equal strength.

  12. Marburg virus VP35 can both fully coat the backbone and cap the ends of dsRNA for interferon antagonism.

    Directory of Open Access Journals (Sweden)

    Shridhar Bale

    2012-09-01

    Full Text Available Filoviruses, including Marburg virus (MARV and Ebola virus (EBOV, cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (dsRNA-binding domain (RBD of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules.

  13. Standardized education and parental awareness are lacking for testicular torsion.

    Science.gov (United States)

    Friedman, Ariella A; Ahmed, Haris; Gitlin, Jordan S; Palmer, Lane S

    2016-06-01

    Testicular torsion leads to orchiectomy in 30-50% of cases, which may cause psychological upset and parental guilt over a potentially avertable outcome. Presentation delay is an important modifiable cause of orchiectomy; yet, families are not routinely educated about torsion or its urgency. The present study assessed parental knowledge regarding acute scrotal pain. An anonymous survey was distributed to parents in Urology and ENT offices, asking about their children's gender and scrotal pain history, urgency of response to a child's acute scrotal pain, and familiarity with testicular torsion. Surveys of 479 urology and 59 ENT parents were analyzed. The results between the two were not statistically different. Among the urology parents, 34% had heard of testicular twisting/torsion, most commonly through friends, relatives or knowing someone with torsion (35%); only 17% were informed by pediatricians (Summary Figure). Parents presenting for a child's scrotal pain were significantly more likely to have heard of torsion (69%) than those presenting for other reasons (30%, OR 5.24, P parents of boys had spoken with their children about torsion. Roughly three quarters of them would seek emergent medical attention - by day (75%) or night (82%) - for acute scrotal pain. However, urgency was no more likely among those who knew about torsion. This was the first study to assess parental knowledge of the emergent nature of acute scrotal pain in a non-urgent setting, and most closely approximating their level of knowledge at the time of pain onset. It also assessed parents' hypothetical responses to the scenario, which was markedly different than documented presentation times, highlighting a potential area for improvement in presentation times. Potential limitations included lack of respondent demographic data, potential sampling bias of a population with greater healthcare knowledge or involvement, and assessment of parents only. Parental knowledge of testicular torsion was

  14. Model of Structural Fragmentation Induced by High Pressure Torsion

    Czech Academy of Sciences Publication Activity Database

    Kratochvíl, J.; Kružík, Martin; Sedláček, R.

    2010-01-01

    Roč. 25, č. 1 (2010), s. 88-98 ISSN 1606-5131 Institutional research plan: CEZ:AV0Z10750506 Keywords : High-pressure torsion * intergranular glide * homogeneous deformation mode Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.649, year: 2010 http://library.utia.cas.cz/separaty/2010/MTR/kruzik-model of structural fragmentation induced by high pressure torsion.pdf

  15. Torsional Moment Measurement on Bucket Wheel Shaft of Giant Machine

    Directory of Open Access Journals (Sweden)

    Jiří FRIES

    2011-06-01

    Full Text Available Bucket wheel loading at the present time (torsional moment on wheel shaft, peripheral cutting force is determined from electromotor incoming power or reaction force measured on gearbox hinge. Both methods together are weighted by steel construction absorption of driving units and by inertial forces of motor rotating parts. In the article is described direct method of the torsional moment measurement, which eliminates mentioned unfavourable impacts except absorption of steel construction of bucket wheel itself.

  16. Resolution of torsional vibration issue for large turbine generators

    International Nuclear Information System (INIS)

    Evans, D.G.; Giesecke, H.D.; Willman, E.C.; Moffitt, S.P.

    1995-01-01

    The excitation of turbine generator torsional natural frequencies in the region near 120 Hz by electrical transients in the power system has resulted in blade failures for several large 1,800 rpm nuclear turbines. At Cleveland Electric's Perry Nuclear Power plant a combination of advanced measurement techniques and analyses were used to identify and resolve a potential torsional vibration problem without adverse impact on the plant availability. The Perry turbine generator consists of a high pressure turbine, three low pressure turbines with 43 inch last stage blades, and a 1,250 MWe four pole generator operating at 1,800 rpm. Torsional vibration measurements obtained from random vibration during operation were acquired just prior to the 1994 refueling outage. The measurements indicated that the 26th torsional mode of vibration was just under 120 Hz and within the range of frequencies for which the manufacturer recommends modifying the unit to shift the problem torsional natural frequency. Extensive analytical modeling was used to design a modification to shift the torsional natural frequencies away from 120 Hertz and the modification was implemented during the refueling outage without affecting outage critical path. An off-line ramp test and additional on-line monitoring performed at the conclusion of the outage confirmed that the on-line method provided accurate measurements of the torsional natural frequencies and demonstrated that, with the modification, the torsional natural frequencies were sufficiently removed from 120 Hertz to allow turbine generator operation. The modification, which involved brazing of the tie wires on all last stage blades, also significantly reduces the stress on the last stage blades that result from negative sequence currents, further increasing the operating margin of the turbine generator with respect to electrical transients and faults

  17. Intravitreal Phacoemulsification Using Torsional Handpiece for Retained Lens Fragments

    OpenAIRE

    Kumar, Vinod; Takkar, Brijesh

    2016-01-01

    Purpose: To evaluate the results of intravitreal phacoemulsification with torsional hand piece in eyes with posteriorly dislocated lens fragments. Methods: In this prospective, interventional case series, 15 eyes with retained lens fragments following phacoemulsification were included. All patients underwent standard three-port pars plana vitrectomy and intravitreal phacoemulsification using sleeveless, torsional hand piece (OZiL™, Alcon's Infiniti Vision System). Patients were followed up...

  18. Muscular Basis of Whisker Torsion in Mice and Rats.

    Science.gov (United States)

    Haidarliu, Sebastian; Bagdasarian, Knarik; Shinde, Namrata; Ahissar, Ehud

    2017-09-01

    Whisking mammals move their whiskers in the rostrocaudal and dorsoventral directions with simultaneous rolling about their long axes (torsion). Whereas muscular control of the first two types of whisker movement was already established, the anatomic muscular substrate of the whisker torsion remains unclear. Specifically, it was not clear whether torsion is induced by asymmetrical operation of known muscles or by other largely unknown muscles. Here, we report that mystacial pads of newborn and adult rats and mice contain oblique intrinsic muscles (OMs) that connect diagonally adjacent vibrissa follicles. Each of the OMs is supplied by a cluster of motor end plates. In rows A and B, OMs connect the ventral part of the rostral follicle with the dorsal part of the caudal follicle. In rows C-E, in contrast, OMs connect the dorsal part of the rostral follicle to the ventral part of the caudal follicle. This inverse architecture is consistent with previous behavioral observations [Knutsen et al.: Neuron 59 (2008) 35-42]. In newborn mice, torsion occurred in irregular single twitches. In adult anesthetized rats, microelectrode mediated electrical stimulation of an individual OM that is coupled with two adjacent whiskers was sufficient to induce a unidirectional torsion of both whiskers. Torsional movement was associated with protracting movement, indicating that in the vibrissal system, like in the ocular system, torsional movement is mechanically coupled to horizontal and vertical movements. This study shows that torsional whisker rotation is mediated by specific OMs whose morphology and attachment sites determine rotation direction and mechanical coupling, and motor innervation determines rotation dynamics. Anat Rec, 300:1643-1653, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  19. Torsion of the greater omentum: A rare preoperative diagnosis

    International Nuclear Information System (INIS)

    Tandon, Ankit Anil; Lim, Kian Soon

    2010-01-01

    Torsion of the greater omentum is a rare acute abdominal condition that is seldom diagnosed preoperatively. We report the characteristic computed tomography (CT) scan findings and the clinical implications of this unusual diagnosis in a 41-year-old man, who also had longstanding right inguinal hernia. Awareness of omental torsion as a differential diagnosis in the acute abdomen setting is necessary for correct patient management

  20. Bicavitary effusion secondary to liver lobe torsion in a dog

    Directory of Open Access Journals (Sweden)

    Khan Z

    2016-04-01

    Full Text Available Zaheda Khan,1 Kathryn Gates,2 Stephen A Simpson,31Emergency and Critical Care, Animal Specialty and Emergency Center, Los Angeles, CA, 2Emergency and Critical Care, Advanced Critical Care, Emergency and Specialty Services, Culver City, CA 3Emergency and Critical Care, Southern California Veterinary Specialty Hospital, Irvine, CA, USA Abstract: We described the diagnosis and successful treatment of pleural and peritoneal effusion secondary to liver lobe torsion in a dog. A 12-year-old female spayed Borzoi dog was referred for heart failure. Emergency room thoracic and abdominal ultrasound showed a large volume of pleural effusion with mild peritoneal effusion and an abdominal mass. Pleural fluid analysis classified the effusion as exudative. A complete ultrasound revealed mild peritoneal effusion and decreased blood flow to the right liver lobe. Other causes of bicavitary effusion were ruled out based on blood work, ultrasound, echocardiogram, and computed tomography. The patient was taken to surgery and diagnosed with caudate liver lobe torsion and had a liver lobectomy. At the 2-week postoperative recheck, the patient was doing well and there was complete resolution of the pleural effusion. Liver lobe torsion is a rare occurrence in dogs and can be difficult to diagnose. Clinical signs are nonspecific for liver lobe torsion and patients may present in respiratory distress with significant pleural fluid accumulation. When assessing patients with pleural and peritoneal effusion, liver lobe torsion should be considered as a differential diagnosis.Keywords: pleural effusion, peritoneal effusion, hepatic torsion

  1. ESTIMATING TORSION OF DIGITAL CURVES USING 3D IMAGE ANALYSIS

    Directory of Open Access Journals (Sweden)

    Christoph Blankenburg

    2016-04-01

    Full Text Available Curvature and torsion of three-dimensional curves are important quantities in fields like material science or biomedical engineering. Torsion has an exact definition in the continuous domain. However, in the discrete case most of the existing torsion evaluation methods lead to inaccurate values, especially for low resolution data. In this contribution we use the discrete points of space curves to determine the Fourier series coefficients which allow for representing the underlying continuous curve with Cesàro’s mean. This representation of the curve suits for the estimation of curvature and torsion values with their classical continuous definition. In comparison with the literature, one major advantage of this approach is that no a priori knowledge about the shape of the cyclic curve parts approximating the discrete curves is required. Synthetic data, i.e. curves with known curvature and torsion, are used to quantify the inherent algorithm accuracy for torsion and curvature estimation. The algorithm is also tested on tomographic data of fiber structures and open foams, where discrete curves are extracted from the pore spaces.

  2. Torsional Vibration of a Shafting System under Electrical Disturbances

    Directory of Open Access Journals (Sweden)

    Ling Xiang

    2012-01-01

    Full Text Available Torsional vibration responses of a nonlinear shafting system are studied by a modified Riccati torsional transfer matrix combining with the Newmark-β method. Firstly, the system is modeled as a chain consisting of an elastic spring with concentrated mass points, from which a multi-segment lumped mass model is established. Secondly, accumulated errors are eliminated from the eigenfrequencies and responses of the system's torsional vibration by this newly developed procedure. The incremental transfer matrix method, combining the modified Riccati torsional transfer matrix with Newmark-β method, is further applied to solve the dynamical equations for the torsional vibration of the nonlinear shafting system. Lastly, the shafting system of a turbine-generator is employed as an illustrating example, and simulation analysis has been performed on the transient responses of the shaft's torsional vibrations during typical power network disturbances, such as three-phase short circuit, two-phase short circuit and asynchronous juxtaposition. The results validate the present method and are instructive for the design of a turbo-generator shaft.

  3. A new hybrid longitudinal–torsional magnetostrictive ultrasonic transducer

    International Nuclear Information System (INIS)

    Karafi, Mohammad Reza; Hojjat, Yousef; Sassani, Farrokh

    2013-01-01

    In this paper, a novel hybrid longitudinal–torsional magnetostrictive ultrasonic transducer (HL–TMUT) is introduced. The transducer is composed of a magnetostrictive exponential horn and a stainless steel tail mass. In this transducer a spiral magnetic field made up of longitudinal and circumferential magnetic fields is applied to the magnetostrictive horn. As a result, the magnetostrictive horn oscillates simultaneously both longitudinally and torsionally in accordance with the Joule and Wiedemann effects. The magnetostrictive exponential horn is designed in such a manner that it has the same longitudinal and torsional resonant frequency. It is made up of ‘2V Permendur’, which has isotropic magnetic properties. The differential equations of the torsional and longitudinal vibration of the horn are derived, and a HL–TMUT is designed with a resonant frequency of 20 573 Hz. The natural frequency and mode shapes of the transducer are considered theoretically and numerically. The experimental results show that this transducer resonates torsionally and longitudinally with frequencies of 20 610 Hz and 20 830 Hz respectively. The maximum torsional displacement is 1.5 mrad m −1 and the maximum longitudinal displacement is 0.6 μm. These are promising features for industrial applications. (paper)

  4. Effectiveness of lycopene on experimental testicular torsion.

    Science.gov (United States)

    Güzel, Mahmut; Sönmez, Mehmet Fatih; Baştuğ, Osman; Aras, Necip Fazıl; Öztürk, Ayşe Betül; Küçükaydın, Mustafa; Turan, Cüneyt

    2016-07-01

    We aimed to demonstrate the long term effectiveness of lycopene, a precursor of vitamin A, on the testes for ischemia-reperfusion injury. Seventy male Wistar albino rats were used for this experiment. The rats were divided into seven groups. Group 1 served as the control group; group 2 was sham-operated; group 3 received 20mg/kg/day lycopene (intraperitoneally); in group 4, the right testes of rats were kept torted for 2hours and then were detorted and the animals lived for three days; in group 5, the right testes of rats were kept torted for 2hours and then were detorted and the animals lived for ten days; in group 6, the right testes of the rats were kept torted for 2hours and then detorted and the animals received 20mg/kg/day lycopene (intraperitoneally) for three days; in group 7, the right testes of the rats were kept torted for 2hours and then were detorted and the animals received 20mg/kg/day lycopene (intraperitoneally) for ten days. Lycopene was used intraperitoneally. Some of the testes tissues were used for biochemical analyses and the other tissues were used for histological procedures. The Johnsen's score was used for seminiferous tubule deterioration. The TUNEL method was utilized to show apoptosis of testicular tissue. Testosterone levels were measured from blood samples and SOD, MDA, TNF-α, IL-1β and IL-6 measurements were recorded from tissue samples. The results were analyzed statistically. In groups 1, 2 and 3 there was normal testicular structure. Rats in groups 4 and 5 had damaged testicular tissues. In groups 6 and 7, in which we used lycopene, the testes were not better than those in groups 4 and 5. The MSTD and JTBS values were better in group 6, but not in group 7 among the torsion groups. As a result, MDA, SOD, TNF-α and IL-1β were increased and serum testosterone and IL-6 levels were decreased in groups 4 and 5 compared to group 1. There was no improvement in the groups treated with lycopene for therapeutic purposes. It was shown that

  5. The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

    Directory of Open Access Journals (Sweden)

    Manuel Michaël

    2010-02-01

    Full Text Available Abstract Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving

  6. Magnetic resonance imaging findings in adnexial torsion

    Energy Technology Data Exchange (ETDEWEB)

    Trindade, Ronald Meira Castro; Quadros, Marianne Siquara de [Hospital Albert Einstein, Sao Paulo, SP (Brazil). Instituto de Ensino e Pesquisa], e-mail: rtrindade@einstein.br; Baroni, Ronaldo Hueb; Rosemberg, Michelle; Racy, Marcelo de Castro Jorge; Tachibana, Adriano [Hospital Albert Einstein, Sao Paulo, SP (Brazil); Funari, Marcelo Buarque de Gusmao [Hospital Albert Einstein, Sao Paulo, SP (Brazil). Imaging Service

    2010-01-15

    Adnexial torsion is an unusual event, but a major cause of abdominal pain in women. It is often associated with ovarian tumor or cyst, but can occur in normal ovaries, especially in children. The twisting of adnexial structures may involve the ovary or tube, but frequently affects both. In most cases, it is unilateral, with slight predilection for the right size. In imaging findings, increased ovarian volume and adnexial masses are observed, with reduced or absent vascularisation. In cases of undiagnosed or untreated complete twist, hemorrhagic necrosis may occur leading to complications; in that, peritonitis is the most frequent. Early diagnosis helps preventing irreversible damage with conservative treatment, thereby saving the ovary. Limitations in performing physical examination, possible inconclusive results in ultrasound and exposure to radiation in computed tomography makes magnetic resonance imaging a valuable tool in emergency assessment of gynecological diseases. The objective of this study was to report two confirmed cases of adnexial twist, emphasizing the contribution of magnetic resonance imaging in the diagnosis of this condition. (author)

  7. Transforming plastic surfaces with electrophilic backbones from hydrophobic to hydrophilic.

    Science.gov (United States)

    Kim, Samuel; Bowen, Raffick A R; Zare, Richard N

    2015-01-28

    We demonstrate a simple nonaqueous reaction scheme for transforming the surface of plastics from hydrophobic to hydrophilic. The chemical modification is achieved by base-catalyzed trans-esterification with polyols. It is permanent, does not release contaminants, and causes no optical or mechanical distortion of the plastic. We present contact angle measurements to show successful modification of several types of plastics including poly(ethylene terephthalate) (PET) and polycarbonate (PC). Its applicability to blood analysis is explored using chemically modified PET blood collection tubes and found to be quite satisfactory. We expect this approach will reduce the cost of manufacturing plastic devices with optimized wettability and can be generalized to other types of plastic materials having an electrophilic linkage as its backbone.

  8. Design of an IPTV Multicast System for Internet Backbone Networks

    Directory of Open Access Journals (Sweden)

    T. H. Szymanski

    2010-01-01

    Full Text Available The design of an IPTV multicast system for the Internet backbone network is presented and explored through extensive simulations. In the proposed system, a resource reservation algorithm such as RSVP, IntServ, or DiffServ is used to reserve resources (i.e., bandwidth and buffer space in each router in an IP multicast tree. Each router uses an Input-Queued, Output-Queued, or Crosspoint-Queued switch architecture with unity speedup. A recently proposed Recursive Fair Stochastic Matrix Decomposition algorithm used to compute near-perfect transmission schedules for each IP router. The IPTV traffic is shaped at the sources using Application-Specific Token Bucker Traffic Shapers, to limit the burstiness of incoming network traffic. The IPTV traffic is shaped at the destinations using Application-Specific Playback Queues, to remove residual network jitter and reconstruct the original bursty IPTV video streams at each destination. All IPTV traffic flows are regenerated at the destinations with essentially zero delay jitter and essentially-perfect QoS. The destination nodes deliver the IPTV streams to the ultimate end users using the same IPTV multicast system over a regional Metropolitan Area Network. It is shown that all IPTV traffic is delivered with essentially-perfect end-to-end QoS, with deterministic bounds on the maximum delay and jitter on each video frame. Detailed simulations of an IPTV distribution system, multicasting several hundred high-definition IPTV video streams over several essentially saturated IP backbone networks are presented.

  9. Backbone dynamics of the human CC-chemokine eotaxin

    Energy Technology Data Exchange (ETDEWEB)

    Ye Jiqing; Mayer, Kristen L.; Stone, Martin J. [Indiana University, Department of Chemistry (United States)

    1999-10-15

    Eotaxin is a CC chemokine with potent chemoattractant activity towards eosinophils. {sup 15}N NMR relaxation data have been used to characterize the backbone dynamics of recombinant human eotaxin. {sup 15}N longitudinal (R{sub 1}) and transverse (R{sub 2}) auto relaxation rates, heteronuclear {sup 1}H-{sup 15}N steady-state NOEs, and transverse cross-relaxation rates ({eta}{sub xy}) were obtained at 30 deg. C for all resolved backbone secondary amide groups using {sup 1} H-detected two-dimensional NMR experiments. Ratios of transverse auto and cross relaxation rates were used to identify NH groups influenced by slow conformational rearrangement. Relaxation data were fit to the extended model free dynamics formalism, yielding parameters describing axially symmetric molecular rotational diffusion and the internal dynamics of each NH group. The molecular rotational correlation time ({tau}{sub m}) is 5.09{+-}0.02 ns, indicating that eotaxin exists predominantly as a monomer under the conditions of the NMR study. The ratio of diffusion rates about unique and perpendicular axes (D{sub parallel}/D{sub perpendicular}) is 0.81{+-}0.02. Residues with large amplitudes of subnanosecond motion are clustered in the N-terminal region (residues 1-19), the C-terminus (residues 68-73) and the loop connecting the first two {beta}-strands (residues 30-37). N-terminal flexibility appears to be conserved throughout the chemokine family and may have implications for the mechanism of chemokine receptor activation. Residues exhibiting significant dynamics on the microsecond-millisecond time scale are located close to the two conserved disulfide bonds, suggesting that these motions may be coupled to disulfide bond isomerization.

  10. AUTOBA: automation of backbone assignment from HN(C)N suite of experiments.

    Science.gov (United States)

    Borkar, Aditi; Kumar, Dinesh; Hosur, Ramakrishna V

    2011-07-01

    Development of efficient strategies and automation represent important milestones of progress in rapid structure determination efforts in proteomics research. In this context, we present here an efficient algorithm named as AUTOBA (Automatic Backbone Assignment) designed to automate the assignment protocol based on HN(C)N suite of experiments. Depending upon the spectral dispersion, the user can record 2D or 3D versions of the experiments for assignment. The algorithm uses as inputs: (i) protein primary sequence and (ii) peak-lists from user defined HN(C)N suite of experiments. In the end, one gets H(N), (15)N, C(α) and C' assignments (in common BMRB format) for the individual residues along the polypeptide chain. The success of the algorithm has been demonstrated, not only with experimental spectra recorded on two small globular proteins: ubiquitin (76 aa) and M-crystallin (85 aa), but also with simulated spectra of 27 other proteins using assignment data from the BMRB.

  11. On unified field theories, dynamical torsion and geometrical models: II

    International Nuclear Information System (INIS)

    Cirilo-Lombardo, D.J.

    2011-01-01

    We analyze in this letter the same space-time structure as that presented in our previous reference (Part. Nucl, Lett. 2010. V.7, No.5. P.299-307), but relaxing now the condition a priori of the existence of a potential for the torsion. We show through exact cosmological solutions from this model, where the geometry is Euclidean RxO 3 ∼ RxSU(2), the relation between the space-time geometry and the structure of the gauge group. Precisely this relation is directly connected with the relation of the spin and torsion fields. The solution of this model is explicitly compared with our previous ones and we find that: i) the torsion is not identified directly with the Yang-Mills type strength field, ii) there exists a compatibility condition connected with the identification of the gauge group with the geometric structure of the space-time: this fact leads to the identification between derivatives of the scale factor a with the components of the torsion in order to allow the Hosoya-Ogura ansatz (namely, the alignment of the isospin with the frame geometry of the space-time), and iii) of two possible structures of the torsion the 'tratorial' form (the only one studied here) forbid wormhole configurations, leading only to cosmological instanton space-time in eternal expansion

  12. Torsion of wandering spleen in patient with horseshoe kidney

    International Nuclear Information System (INIS)

    Molski, St.; Zurada, A.; Meder, G.; Lasek, W.

    2005-01-01

    Wandering spleen is rare pathology, mostly occurring in young women. Disease may be congenital or acquired. Absence or laxity of ligaments leads to spleen pathologic mobility and may cause torsion of its pedicle, resulting in ischemia or infarct even haemorrhagic shock and patients death. We report a case of young woman previously diagnosed (and treated nonoperative) with wandering spleen who presented acute abdomen after minor blunt trauma. She was evaluated with abdominal ultrasound (US) and spiral computed tomography (CT). Torsion of splenic pedicle and splenic rupture was diagnosed and a horseshoe kidney as well. Laparotomy followed by splenectomy confirmed the existence of an intrapelvic torsioned wandering spleen. The only definitive treatment of wandering spleen is operative since nonoperative treatment is associated with high complication rate. Earlier diagnosis of wandering spleen in asymptomatic patients lets to direct diagnosis when patient starts to present with acute abdomen. CT and abdominal US play most important role in diagnosing splenic pedicle torsion. To our knowledge this is a first case of torsion of splenic pedicle in patient with horseshoe kidney. We consider this coincidence to be a congenital defect as both conditions may develop in second month gestation. (author)

  13. Torsion of abdominal appendages presenting with acute abdominal pain

    International Nuclear Information System (INIS)

    Al-Jaberi, Tareq M.; Gharabeih, Kamal I.; Yaghan, Rami J.

    2000-01-01

    Diseases of abnormal appendages are rare causes of abdominal pain in all age groups. Nine patients with torsion and infraction of abdominal appendages were retrospectively reviewed. Four patients had torsion and infarction of the appendices epiploicae, four patients had torsion and infarction of the falciform ligament. The patient with falciform ligament disease represents the first reported case of primary torsion and infarction of the falciform ligament, and the patient with the transverse colon epiplocia represents the first reported case of vibration-induced appendix epiplocia torsion and infarction. The patient with the falciform ligament disease presented with a tender upper abdominal mass and the remaining patients were operated upon with the preoperative diagnosis of acute appendicitis. The presence of normal appendix with free serosanguinous fluid in the peritoneal cavity should raise the possibility of a disease and calls for further evaluation of the intra-abdominal organs. If the diagnosis is suspected preoperatively, CT scan and ultrasound may lead to a correct diagnosis and possibly conservative management. Laparoscopy is playing an increasing diagnostic and therapeutic role in such situations. (author)

  14. Prune belly syndrome, splenic torsion, and malrotation: a case report.

    Science.gov (United States)

    Tran, Sifrance; Grossman, Eric; Barsness, Katherine A

    2013-02-01

    An 18 year old male with a history of prune belly syndrome (PBS) presented with acute abdominal pain and palpable left upper quadrant mass. Computed tomography (CT) of the abdomen revealed a medialized spleen with a "whirl sign" in the splenic vessels, consistent with splenic torsion. Coincidentally, the small bowel was also noted to be on the right side of the abdomen, while the colon was located on the left, indicative of malrotation. Emergent diagnostic laparoscopy confirmed splenic torsion and intestinal malrotation. Successful laparoscopic reduction of the splenic torsion was achieved, however, conversion to an open procedure by a vertical midline incision was necessary owing to the patient's unique anatomy. Open splenopexy with a mesh sling and Ladd's procedure were subsequently performed. Malrotation and wandering spleen are known, rare associated anomalies in PBS; however, both have not been reported concurrently in a patient with PBS in the literature. In patients with PBS, acute abdominal pain, and an abdominal mass, high clinical suspicion for gastrointestinal malformations and prompt attention can result in spleen preservation and appropriate malrotation management. We present a case of a teenager who presented with a history of PBS, acute abdominal pain, and a palpable abdominal mass. The patient was found to have splenic torsion and intestinal malrotation. The clinical findings, diagnostic imaging, and surgical treatment options of splenic torsion are reviewed. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Elevated temperature axial and torsional fatigue behavior of Haynes 188

    Science.gov (United States)

    Bonacuse, Peter J.; Kalluri, Sreeramesh

    1992-06-01

    The results of high-temperature axial and torsional low-cycle fatigue experiments performed on Haynes 188, a wrought cobalt-base superalloy, are reported. Fatigue tests were performed at 760 C in air on thin-walled tubular specimens at various ranges under strain control. Data are also presented for coefficient of thermal expansion, elastic modulus, and shear modulus at various temperatures from room to 1000 C, and monotonic and cyclic stress-strain curves in tension and in shear at 760 C. The data set is used to evaluate several multiaxial fatigue life models (most were originally developed for room temperature multiaxial life prediction) including von Mises equivalent strain range (ASME boiler and pressure vessel code), Manson-Halford, Modified Multiaxiality Factor (proposed here), Modified Smith-Watson-Topper, and Fatemi-Socie-Kurath. At von Mises equivalent strain ranges (the torsional strain range divided by the square root of 3, taking the Poisson's ratio to be 0.5), torsionally strained specimens lasted, on average, factors of 2 to 3 times longer than axially strained specimens. The Modified Multiaxiality Factor approach shows promise as a useful method of estimating torsional fatigue life from axial fatigue data at high temperatures. Several difficulties arose with the specimen geometry and extensometry used in these experiments. Cracking at extensometer probe indentations was a problem at smaller strain ranges. Also, as the largest axial and torsional strain range fatigue tests neared completion, a small amount of specimen buckling was observed.

  16. Residual torsional properties of composite shafts subjected to impact loadings

    International Nuclear Information System (INIS)

    Sevkat, Ercan; Tumer, Hikmet

    2013-01-01

    Highlights: • Impact loading reduces the torsional strength of composite shaft. • Impact energy level determines the severity of torsional strength reduction. • Hybrid composite shafts can be manufactured by mixing two types of filament. • Maximum torque capacity of shafts can be estimated using finite element method. - Abstract: This paper presents an experimental and numerical study to investigate residual torsional properties of composite shafts subjected to impact loadings. E-glass/epoxy, carbon/epoxy and E-glass–carbon/epoxy hybrid composite shafts were manufactured by filament winding method. Composite shafts were impacted at 5, 10, 20 and 40 J energy levels. Force–time and energy–time histories of impact tests were recorded. One composite shaft with no impact, and four composite shafts with impact damage, five in total, were tested under torsion. Torque-twisting angle relations for each test were obtained. Reduction at maximum torque and maximum twisting angle induced by impact loadings were calculated. While 5 J impact did not cause significant reduction at maximum torque and maximum twisting angle, remaining impact loadings caused 34–67% reduction at maximum torque, and 30–61% reduction at maximum twisting angle. Reductions increased with increasing energy levels and varied depending on the material of composite shafts. The 3-D finite element (FE) software, Abaqus, incorporated with an elastic orthotropic model, was then used to simulate the torsion tests. Good agreement between experimental and numerical results was achieved

  17. Torsion as a dark matter candidate from the Higgs portal

    Science.gov (United States)

    Belyaev, Alexander S.; Thomas, Marc C.; Shapiro, Ilya L.

    2017-05-01

    Torsion is a metric-independent component of gravitation, which may provide a more general geometry than the one taking place within general relativity. On the other hand, torsion could lead to interesting phenomenology in both particle physics and cosmology. In the present work it is shown that a torsion field interacting with the SM Higgs doublet and having a negligible coupling to standard model (SM) fermions is protected from decaying by a Z2 symmetry, and therefore becomes a promising dark matter (DM) candidate. This model provides a good motivation for Higgs portal vector DM scenario. We evaluate the DM relic density and explore direct DM detection and collider constraints on this model to understand its consistency with experimental data and establish the most up-to-date limits on its parameter space. We have found in the model when the Higgs boson is only partly responsible for the generation of torsion mass, there is a region of parameter space where torsion contributes 100% to the DM budget of the Universe. Furthermore, we present the first results on the potential of the LHC to probe the parameter space of minimal scenario with Higgs portal vector DM using mono-jet searches and have found that LHC at high luminosity will be sensitive to the substantial part of model parameter space which cannot be probed by other experiments.

  18. Crack path in aeronautical titanium alloy under ultrasonic torsion loading

    Directory of Open Access Journals (Sweden)

    A. Nikitin

    2016-01-01

    Full Text Available This paper discusses features of fatigue crack initiation and growth in aeronautical VT3-1 titanium alloy under pure torsion loading in gigacycle regime. Two materials: extruded and forged VT3-1 titanium alloys were studied. Torsion fatigue tests were performed up to fatigue life of 109 cycles. The results of the torsion tests were compared with previously obtained results under fully reversed axial loading on the same alloys. It has been shown that independently on production process as surface as well subsurface crack initiation may appear under ultrasonic torsion loading despite the maximum stress amplitude located at the specimen surface. In the case of surface crack initiation, a scenario of crack initiation and growth is similar to HCF regime except an additional possibility for internal crack branching. In the case of subsurface crack, the initiation site is located below the specimen surface (about 200 μm and is not clearly related to any material flaw. Internal crack initiation is produced by shear stress in maximum shear plane and early crack growth is in Mode II. Crack branching is limited in the case of internal crack initiation compared to surface one. A typical ‘fish-eye’ crack can be observed at the torsion fracture surface, but mechanism of crack initiation seems not to be the same than under axial fatigue loading.

  19. Direct torsional actuation of microcantilevers using magnetic excitation

    Energy Technology Data Exchange (ETDEWEB)

    Gosvami, Nitya Nand; Nalam, Prathima C.; Tam, Qizhan; Carpick, Robert W., E-mail: carpick@seas.upenn.edu [Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (United States); Exarhos, Annemarie L.; Kikkawa, James M. [Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (United States)

    2014-09-01

    Torsional mode dynamic force microscopy can be used for a wide range of studies including mapping lateral contact stiffness, torsional frequency or amplitude modulation imaging, and dynamic friction measurements of various materials. Piezo-actuation of the cantilever is commonly used, but it introduces spurious resonances, limiting the frequency range that can be sampled, and rendering the technique particularly difficult to apply in liquid medium where the cantilever oscillations are significantly damped. Here, we demonstrate a method that enables direct torsional actuation of cantilevers with high uniformity over wide frequency ranges by attaching a micrometer-scale magnetic bead on the back side of the cantilever. We show that when beads are magnetized along the width of the cantilever, efficient torsional actuation of the cantilevers can be achieved using a magnetic field produced from a solenoid placed underneath the sample. We demonstrate the capability of this technique by imaging atomic steps on graphite surfaces in tapping mode near the first torsional resonance of the cantilever in dodecane. The technique is also applied to map the variations in the lateral contact stiffness on the surface of graphite and polydiacetylene monolayers.

  20. [Torsion of wandering spleen in a teenager: about a case].

    Science.gov (United States)

    Dème, Hamidou; Akpo, Léra Géraud; Fall, Seynabou; Badji, Nfally; Ka, Ibrahima; Guèye, Mohamadou Lamine; Touré, Mouhamed Hamine; Niang, El Hadj

    2016-01-01

    Wandering or migrating spleen is a rare anomaly which is usually described in children. Complications, which include pedicle torsion, are common and can be life-threatening. We report the case of a 17 year-old patient with a long past medical history of epigastric pain suffering from wandering spleen with chronic torsion of the pedicle. The clinical picture was marked by spontaneously painful epigastric mass, evolved over the past 48 hours. Abdominal ultrasound objectified heterogeneous hypertrophied ectopic spleen in epigastric position and a subcapsular hematoma. Doppler showed a torsion of splenic pedicle which was untwisted 2 turns and a small blood stream on the splenic artery. Abdominal CT scan with contrast injection showed a lack of parenchymal enhancement of large epigastric ectopic spleen and a subcapsular hematoma. The diagnosis of wandering spleen with chronic torsion of the pedicle complicated by necrosis and subcapsular hematoma was confirmed. The patient underwent splenectomy. The postoperative course was uneventful. We here discuss the contribution of ultrasound and CT scan in the diagnosis of wandering spleen with chronic torsion of the pedicle.

  1. 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...

  2. Thin Films Formed from Conjugated Polymers with Ionic, Water-Soluble Backbones

    NARCIS (Netherlands)

    Voortman, Thomas P; Chiechi, Ryan C

    2015-01-01

    This paper compares the morphologies of films of conjugated polymers in which the backbone (main chain) and pendant groups are varied between ionic/hydrophilic and aliphatic/hydrophobic. We observe that conjugated polymers in which the pendant groups and backbone are matched, either ionic-ionic or

  3. A Case of Torsion of Gravid Uterus Caused by Leiomyoma

    Directory of Open Access Journals (Sweden)

    Gururaj Deshpande

    2011-01-01

    Full Text Available Uterine torsion during pregnancy is only sporadically reported in the literature. Here we present a case of leiomyoma causing uterine torsion in pregnancy and review the literature on etiology, diagnosis, and management. A 25-years-old primigravida with leiomyoma complicating pregnancy was admitted in our hospital with abdominal pain and uterine tenderness. She underwent emergency LSCS (lower segment cesarean section for fetal bradycardia. Intraoperatively, the uterus was rotated 180 degrees left to right. Inadvertent incision on the posterior wall was avoided by proper delineation of anatomy. Torsion was corrected by exteriorization of leiomyoma and uterus, and lower segment cesarean was carried out safely. Prompt recognition and management of this condition is necessary for better maternal and fetal outcome.

  4. Torsional Topological Invariants (and their relevance for real life)

    CERN Document Server

    Chandia, O; Chandia, Osvaldo; Zanelli, Jorge

    1997-01-01

    The existence of topological invariants analogous to Chern/Pontryagin classes for a standard $SO(D)$ or SU(N) connection, but constructed out of the torsion tensor, is discussed. These invariants exhibit many of the features of the Chern/Pontryagin invariants: they can be expressed as integrals over the manifold of local densities and take integer values on compact spaces without boundary; their spectrum is determined by the homotopy groups determined by the connection bundle but depend also on the bundle of local orthonormal frames on the tangent space of the manifold. It is shown that in spacetimes with nonvanishing torsion there can occur topologically stable configurations associated with the frame bundle which are independent of the curvature. Explicit examples of topologically stable configurations carrying nonvanishing instanton number in four and eight dimensions are given, and they can be conjectured to exist in dimension $4k$. It is also shown that the chiral anomaly in a spacetime with torsion rece...

  5. Simple currents versus orbifolds with discrete torsion -- a complete classification

    CERN Document Server

    Kreuzer, M

    1994-01-01

    We give a complete classification of all simple current modular invariants, extending previous results for $(\\Zbf_p)^k$ to arbitrary centers. We obtain a simple explicit formula for the most general case. Using orbifold techniques to this end, we find a one-to-one correspondence between simple current invariants and subgroups of the center with discrete torsions. As a by-product, we prove the conjectured monodromy independence of the total number of such invariants. The orbifold approach works in a straightforward way for symmetries of odd order, but some modifications are required to deal with symmetries of even order. With these modifications the orbifold construction with discrete torsion is complete within the class of simple current invariants. Surprisingly, there are cases where discrete torsion is a necessity rather than a possibility.

  6. Mechanical Design of AM Fabricated Prismatic Rods under Torsion

    Directory of Open Access Journals (Sweden)

    Manzhirov Alexander V.

    2017-01-01

    Full Text Available We study the stress-strain state of viscoelastic prismatic rods fabricated or repaired by additive manufacturing technologies under torsion. An adequate description of the processes involved is given by methods of a new scientific field, mechanics of growing solids. Three main stages of the deformation process (before the beginning of growth, in the course of growth, and after the termination of growth are studied. Two versions of statement of two problems are given: (i given the torque, find the stresses, displacements, and torsion; (ii given the torsion, find the stresses, displacements, and torque. Solution methods using techniques of complex analysis are presented. The results can be used in mechanical and instrument engineering.

  7. Intravitreal Phacoemulsification Using Torsional Handpiece for Retained Lens Fragments.

    Science.gov (United States)

    Kumar, Vinod; Takkar, Brijesh

    2016-01-01

    To evaluate the results of intravitreal phacoemulsification with torsional hand piece in eyes with posteriorly dislocated lens fragments. In this prospective, interventional case series, 15 eyes with retained lens fragments following phacoemulsification were included. All patients underwent standard three-port pars plana vitrectomy and intravitreal phacoemulsification using sleeveless, torsional hand piece (OZiL™, Alcon's Infiniti Vision System). Patients were followed up for a minimum of six months to evaluate the visual outcomes and complications. The preoperative best-corrected visual acuity (BCVA) ranged from light perception to 0.3. No complications such as thermal burns of the scleral wound, retinal damage due to flying lens fragments, or difficult lens aspiration occurred during intravitreal phacoemulsification. Mean post-operative BCVA at the final follow-up was 0.5. Two eyes developed cystoid macular edema, which was managed medically. No retinal detachment was noted. Intravitreal phacoemulsification using torsional hand piece is a safe and effective alternative to conventional longitudinal phacofragmentation.

  8. Standing torsional waves in a fully saturated, porous, circular cylinder

    CERN Document Server

    Solorza, S; 10.1111/j.1365-246X.2004.02198.x

    2004-01-01

    For dynamic measurement of the elastic moduli of a porous material saturated with viscous fluid using the resonance-bar technique, one also observes attenuation. In this article we have carried out the solution of the boundary-value problem associated with standing torsional oscillations of a finite, poroelastic, circular cylinder cast in the framework of volume-averaged theory of poroelasticity. Analysing this solution by eigenvalue perturbation approach we are able to develop expressions for torsional resonance and temporal attenuation frequencies in which the dependence upon the material properties are transparent. It shows how the attenuation is controlled by the permeability and the fluid properties, and how the resonance frequency drops over its value for the dry solid-frame due to the drag effect of fluid mass. Based upon this work we have a firm basis to determine solid-frame shear modulus, permeability, and tortuosity factor from torsional oscillation experiments.

  9. Simple currents versus orbifolds with discrete torsion - a complete classification

    International Nuclear Information System (INIS)

    Kreuzer, M.; Schellekens, A.N.

    1993-01-01

    We give a complete classification of all simple current modular invariants, extending previous results for (Z p ) k to arbitrary centers. We obtain a simple explicit formula for the most general case. Using orbifold techniques to this end, we find a one-to-one correspondence between simple current invariants and subgroups of the center with discrete torsions. As a by-product, we prove the conjectured monodromy independence of the total number of such invariants. The orbifold approach works in a straightforward way for symmetries of odd order, but some modifications are required to deal with symmetries of even order. With these modifications the orbifold construction with discrete torsion is complete within the class of simple current invariants. Surprisingly, there are cases where discrete torsion is a necessity rather than a possibility. (orig.)

  10. Backbone of complex networks of corporations: The flow of control

    Science.gov (United States)

    Glattfelder, J. B.; Battiston, S.

    2009-09-01

    We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

  11. Data Acquisition Backbone Core DABC release v1.0

    International Nuclear Information System (INIS)

    Adamczewski-Musch, J; Kurz, N; Linev, S; Essel, H G

    2010-01-01

    The Data Acquisition Backbone Core (DABC) is a general purpose software framework designed for the implementation of a wide-range of data acquisition systems - from various small detector test beds to high performance systems. DABC consists of a compact data-flow kernel and a number of plug-ins for various functional components like data inputs, device drivers, user functional modules and applications. DABC provides configurable components for implementing event building over fast networks like InfiniBand or Gigabit Ethernet. A generic Java GUI provides the dynamic control and visualization of control parameters and commands, provided by DIM servers. A first set of application plug-ins has been implemented to use DABC as event builder for the front-end components of the GSI standard DAQ system MBS (Multi Branch System). Another application covers the connection to DAQ readout chains from detector front-end boards (N-XYTER) linked to read-out controller boards (ROC) over UDP into DABC for event building, archiving and data serving. This was applied for data taking in the September 2008 test beamtime for the CBM experiment at GSI. DABC version 1.0 is released and available from the website.

  12. Solid state radiation chemistry of the DNA backbone

    International Nuclear Information System (INIS)

    Bernhard, W.A.

    1989-09-01

    The long term goal of this program is to determine the fundamental rules needed to predict the type and yield of damage produced in DNA due to direct effects of ionizing radiation. The focus is on damage to the sugar-phosphate backbone, damage that would lead to strand breaks. Model systems have been chosen that permit various aspects of this problem to be investigated. The emphasis will be on single crystals of monosaccharides, nucleosides, and nucleotides but will also include some powder work on polynucleotides. In these model systems, free radical products and reactions are observed by electron spin resonance (ESR) and electron nuclear double resonance (ENDOR) techniques. The information thus gained is used in constructing rules that predict what primary free radicals are formed in single crystals of model compounds and the reactions stemming from the primary radicals. The formulation of a set of rules that work in model systems will represent a major advance toward formulating a set of rules that predict the direct damage in DNA itself. In a broader context this program is part of the effort to understand and predict the effects of exposure to ionizing radiation received at low dose rates over long periods of time. Assessment of low dose effects requires a basic understanding of the action of radiation at the molecular level. By contributing to that basic understanding, this program will help solve the problems of risk assessment under low dose conditions. 5 refs., 3 figs

  13. Data acquisition backbone core DABC release v1.0

    Energy Technology Data Exchange (ETDEWEB)

    Adamczewski-Musch, Joern; Essel, Hans G.; Kurz, Nikolaus; Linev, S. [GSI Helmholtzzentrum fuer Schwerionenforschung, Darmstadt (Germany)

    2010-07-01

    The new experiments at FAIR require new concepts of data acquisition systems for the distribution of self-triggered, time stamped data streams over high performance networks for event building. The Data Acquisition Backbone Core (DABC) is a general purpose software framework developed for the implementation of such data acquisition systems. A DABC application consists of functional components like data input, combiner, scheduler, event builder, filter, analysis and storage which can be configured at runtime. Application specific code including the support of all kinds of data channels (front-end systems) is implemented by C++ program plug-ins. DABC is also well suited as environment for various detector and readout components test beds. A set of DABC plug-ins has been developed for the FAIR experiment CBM (Compressed Baryonic Matter) at GSI. This DABC application is used as DAQ system for test beamtimes. Front-end boards equipped with n-XYTER ASICs and ADCs are connected to read-out controller boards (ROC). From there the data is sent over Ethernet (UDP), or over optics and PCIe interface cards into Linux PCs. DABC does the controlling, event building, archiving and data serving. The first release of DABC was published in 2009 and is available under GPL license.

  14. The Impact of O-Glycan Chemistry on the Stability of Intrinsically Disordered Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Beckham, Gregg T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Prates, Erica T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Crowley, Michael F [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Guan, Xiaoyang [University of Colorado; Li, Yaohao [University of Colorado; Wang, Xinfeng [University of Colorado; Chaffey, Patrick K. [University of Colorado; Skaf, Munir S. [University of Campinas; Tan, Zhongping [University of Colorado

    2018-03-02

    Protein glycosylation is a diverse post-translational modification that serves myriad biological functions. O-linked glycans in particular vary widely in extent and chemistry in eukaryotes, with secreted proteins from fungi and yeast commonly exhibiting O-mannosylation in intrinsically disordered regions of proteins, likely for proteolysis protection, among other functions. However, it is not well understood why mannose is often the preferred glycan, and more generally, if the neighboring protein sequence and glycan have coevolved to protect against proteolysis in glycosylated intrinsically disordered proteins (IDPs). Here, we synthesized variants of a model IDP, specifically a natively O-mannosylated linker from a fungal enzyme, with a-O-linked mannose, glucose, and galactose moieties, along with a non-glycosylated linker. Upon exposure to thermolysin, O-mannosylation, by far, provides the highest extent of proteolysis protection. To explain this observation, extensive molecular dynamics simulations were conducted, revealing that the axial configuration of the C2-hydroxyl group (2-OH) of a-mannose adjacent to the glycan-peptide bond strongly influences the conformational features of the linker. Specifically, a-mannose restricts the torsions of the IDP main chain more than other glycans whose equatorial 2-OH groups exhibit interactions that favor perpendicular glycan-protein backbone orientation. We suggest that IDP stiffening due to O-mannosylation impairs protease action, with contributions from protein-glycan interactions, protein flexibility, and protein stability. Our results further imply that resistance to proteolysis is an important driving force for evolutionary selection of a-mannose in eukaryotic IDPs, and more broadly, that glycan motifs for proteolysis protection likely coevolve with the protein sequence to which they attach.

  15. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

    Czech Academy of Sciences Publication Activity Database

    Zgarbová, M.; Šponer, Jiří; Otyepka, M.; Cheatham III, T. E.; Galindo-Murillo, R.; Jurečka, P.

    2015-01-01

    Roč. 11, č. 12 (2015), s. 5723-5736 ISSN 1549-9618 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * NUCLEIC-ACID STRUCTURES * QUANTUM-CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 5.301, year: 2015

  16. Primary decomposition of torsion R[X]-modules

    Directory of Open Access Journals (Sweden)

    William A. Adkins

    1994-01-01

    Full Text Available This paper is concerned with studying hereditary properties of primary decompositions of torsion R[X]-modules M which are torsion free as R-modules. Specifically, if an R[X]-submodule of M is pure as an R-submodule, then the primary decomposition of M determines a primary decomposition of the submodule. This is a generalization of the classical fact from linear algebra that a diagonalizable linear transformation on a vector space restricts to a diagonalizable linear transformation of any invariant subspace. Additionally, primary decompositions are considered under direct sums and tensor product.

  17. Singularities and n-dimensional black holes in torsion theories

    Energy Technology Data Exchange (ETDEWEB)

    Cembranos, J.A.R.; Valcarcel, J. Gigante; Torralba, F.J. Maldonado, E-mail: cembra@fis.ucm.es, E-mail: jorgegigante@ucm.es, E-mail: fmaldo01@ucm.es [Departamento de Física Teórica I, Universidad Complutense de Madrid, E-28040 Madrid (Spain)

    2017-04-01

    In this work we have studied the singular behaviour of gravitational theories with non symmetric connections. For this purpose we introduce a new criteria for the appearance of singularities based on the existence of black/white hole regions of arbitrary codimension defined inside a spacetime of arbitrary dimension. We discuss this prescription by increasing the complexity of the particular torsion theory under study. In this sense, we start with Teleparallel Gravity, then we analyse Einstein-Cartan theory, and finally dynamical torsion models.

  18. Elastic torsional buckling of thin-walled composite cylinders

    Science.gov (United States)

    Marlowe, D. E.; Sushinsky, G. F.; Dexter, H. B.

    1974-01-01

    The elastic torsional buckling strength has been determined experimentally for thin-walled cylinders fabricated with glass/epoxy, boron/epoxy, and graphite/epoxy composite materials and composite-reinforced aluminum and titanium. Cylinders have been tested with several unidirectional-ply orientations and several cross-ply layups. Specimens were designed with diameter-to-thickness ratios of approximately 150 and 300 and in two lengths of 10 in. and 20 in. The results of these tests were compared with the buckling strengths predicted by the torsional buckling analysis of Chao.

  19. Torsion tensor and covector in a unified field theory

    International Nuclear Information System (INIS)

    Chernikov, N.A.

    1976-01-01

    The Einstein unified field theory is used to solve a tensor equation to provide the unambiguous definition of affine connectedness. In the process of solving the Einstein equation limitations imposed by symmetry on the tensor and the torsion covector as well as on affine connectedness are elucidated. It is demonstrated that in a symmetric case the connectedness is unambiguously determined by the Einstein equation. By means of the Riemann geometry a formula for the torsion covector is derived. The equivalence of Einstein equations to those of the nonlinear Born-Infeld electrodynamics is proved

  20. Torsional osteotomies of the tibia in patellofemoral dysbalance.

    Science.gov (United States)

    Dickschas, Jörg; Tassika, Aliki; Lutter, Christoph; Harrer, Jörg; Strecker, Wolf

    2017-02-01

    Anterior knee pain or patellofemoral instability is common symptom of patellofemoral dysbalance or maltracking. Tibial torsional deformities can be the reason of this pathology. After appropriate diagnostic investigation, the treatment of choice is a torsional osteotomy. This study addresses the diagnostic investigation, treatment, and the outcome of torsional osteotomies of the tibia. Does this treatment result in patellofemoral stability and provide pain relief? Forty-nine tibial torsional osteotomies were included. The major symptoms were patellofemoral instability in 19 cases and anterior knee pain in 42 cases. In addition to clinical and radiographic analysis, a torsional angle CT scan was performed pre-operatively. A visual analog scale (VAS), the Japanese Knee Society score, the Tegner activity score, and the Lysholm score were assessed pre-operatively and at the 42-month follow-up. Mean tibial external torsion was 47.4° (SD 5.41; range 37°-66°; standard value 34°). Surgical treatment consisted of an acute supratuberositary tibial internal torsional osteotomy (mean 10.8°; SD 3.01°; range 5°-18°). At the follow-up investigation, the Tegner activity score was increased 0.4 points (p value 0.014) from 3.9 (SD 1.33; range 2-7) to 4.3 (SD 1.25; range 0-7). The Lysholm score increased 26 points (SD 16.32; p value 0.001) from 66 (SD 14.94; range 32-94) to 92 (SD 9.29; range 70-100) and the Japanese Knee Society score increased 18 points (SD 14.70; p value 0.001) from 72 (SD 13.72, range 49-100) to 90 (SD 9.85, range 60-100). VAS was reduced 3.4 points (SD 2.89; p value 0.001) from 5.7 (SD 2.78; range 0-10) to 2.3 (SD 1.83; range 0-7). As regards patellofemoral instability, no redislocation occurred in the follow-up period. The results of this study show that in cases of tibial maltorsion, a torsional osteotomy can lead to patellofemoral stability and pain relief, and should be considered as a treatment option. The improved clinical scores in the present

  1. Spontaneous compactification and Ricci-flat manifolds with torsion

    International Nuclear Information System (INIS)

    McInnes, B.

    1985-06-01

    The Freund-Rubin mechanism is based on the equation Rsub(ik)=lambdagsub(ik) (where lambda>0), which, via Myers' Theorem, implies ''spontaneous'' compactification. The difficulties connected with the cosmological constant in this approach can be resolved if torsion is introduced and lambda set equal to zero, but then compactification ''by hand'' is necessary, since the equation Rsub(ik)=0 can be satisfied both on compact and on non-compact manifolds. In this paper we discuss the global geometry of Ricci-flat manifolds with torsion, and suggest ways of restoring the ''spontaneity'' of the compactification. (author)

  2. Torsion of cracked nanorods using a nonlocal elasticity model

    International Nuclear Information System (INIS)

    Loya, J A; Aranda-Ruiz, J; Fernández-Sáez, J

    2014-01-01

    This paper presents a nonlocal cracked-rod model from which we have analysed the torsional vibrations of a carbon nanotube with a circumferential crack. Several types of boundary conditions, including the consideration of a buckyball at the end of the nanotube, have been studied. The nonlocal Eringen elasticity theory is used to formulate the problem. The cracked rod is modelled by dividing the cracked element into two segments connected by a torsional linear spring whose stiffness is related to the crack severity. The effect of the nonlocal small-scale parameter, crack severity, cracked section position, different boundary conditions and attached mass are examined in this work. (paper)

  3. Massless fermions and Kaluza--Klein theory with torsion

    International Nuclear Information System (INIS)

    Wu, Y.; Zee, A.

    1984-01-01

    A pure Kaluza--Klein theory contains no massless fermion in four-dimensional theory. We investigate the effect of introducing torsion on the internal manifold and find that there are massless fermions. The hope is that given an isometry group the representation to which these fermions belong is fixed, in contrast to the situation in Yang--Mills theory. We show that this is indeed the case, but the representations do not appear to be the ones favored by current theoretical prejudice. The cases with parallelizable torsions on a group manifold as the internal manifold are analyzed in detail

  4. A black hole with torsion in 5D Lovelock gravity

    Science.gov (United States)

    Cvetković, B.; Simić, D.

    2018-03-01

    We analyze static spherically symmetric solutions of five dimensional (5D) Lovelock gravity in the first order formulation. In the Riemannian sector, when torsion vanishes, the Boulware–Deser black hole represents a unique static spherically symmetric black hole solution for the generic choice of the Lagrangian parameters. We show that a special choice of the Lagrangian parameters, different from the Lovelock Chern–Simons gravity, leads to the existence of a static black hole solution with torsion, the metric of which is asymptotically anti-de Sitter (AdS). We calculate the conserved charges and thermodynamical quantities of this black hole solution.

  5. Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.

    Science.gov (United States)

    Babbitt, Gregory A; Alawad, Mohammed A; Schulze, Katharina V; Hudson, André O

    2014-01-01

    While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (≈GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an 'accessory' during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. A 55-Year-Old Man with Right Testicular Pain: Too Old for Torsion?

    Science.gov (United States)

    Tang, Yu Ho; Yeung, Victor Hip Wo; Chu, Peggy Sau Kwan; Man, Chi Wai

    2017-02-01

    Testicular torsion is predominantly a disease of adolescence, but age itself should not be an exclusion criterion for the diagnosis. A lack of suspicion for testicular torsion in older patients may result in a missed or delayed diagnosis which jeopardizes the chance of testicular salvage. In this article, we report a case of testicular torsion in a 55-year-old Chinese man.

  7. Aerodynamic stability of long span suspension bridges with low torsional natural frequencies

    DEFF Research Database (Denmark)

    Andersen, Michael Styrk; Johansson, Jens; Brandt, Anders

    2016-01-01

    tests where the torsional frequency was lower than the vertical. But too low torsional stiffness caused large static displacements of the girder at medium–high wind speeds and steady state oscillations driven by a combination of torsional divergence and stalling behavior at the critical wind seed...

  8. DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations.

    Science.gov (United States)

    Zhitnikova, M Y; Shestopalova, A V

    2017-11-01

    The structural adjustments of the sugar-phosphate DNA backbone (switching of the γ angle (O5'-C5'-C4'-C3') from canonical to alternative conformations and/or C2'-endo → C3'-endo transition of deoxyribose) lead to the sequence-specific changes in accessible surface area of both polar and non-polar atoms of the grooves and the polar/hydrophobic profile of the latter ones. The distribution of the minor groove electrostatic potential is likely to be changing as a result of such conformational rearrangements in sugar-phosphate DNA backbone. Our analysis of the crystal structures of the short free DNA fragments and calculation of their electrostatic potentials allowed us to determine: (1) the number of classical and alternative γ angle conformations in the free B-DNA; (2) changes in the minor groove electrostatic potential, depending on the conformation of the sugar-phosphate DNA backbone; (3) the effect of the DNA sequence on the minor groove electrostatic potential. We have demonstrated that the structural adjustments of the DNA double helix (the conformations of the sugar-phosphate backbone and the minor groove dimensions) induce changes in the distribution of the minor groove electrostatic potential and are sequence-specific. Therefore, these features of the minor groove sizes and distribution of minor groove electrostatic potential can be used as a signal for recognition of the target DNA sequence by protein in the implementation of the indirect readout mechanism.

  9. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences.

    Science.gov (United States)

    Walsh, Patrick S; Dean, Jacob C; McBurney, Carl; Kang, Hyuk; Gellman, Samuel H; Zwier, Timothy S

    2016-04-28

    The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase. This work seeks a bottom-up understanding of the role played by glutamine residues in directing peptide structures that lead to neurodegenerative diseases. Resonant ion-dip infrared (RIDIR) spectroscopy is used to record single-conformation infrared spectra in the NH stretch, amide I and amide II regions. Comparison of the experimental spectra with the predictions of calculations carried out at the DFT M05-2X/6-31+G(d) level of theory lead to firm assignments for the H-bonding architectures of a total of eight conformers of four molecules, including three in Z-Gln-OH, one in Z-Gln-NHMe, three in Ac-Gln-NHBn, and one in Ac-Ala-Gln-NHBn. The Gln side chain engages actively in forming H-bonds with nearest-neighbor amide groups, forming C8 H-bonds to the C-terminal side, C9 H-bonds to the N-terminal side, and an amide-stacked geometry, all with an extended (C5) peptide backbone about the Gln residue. The Gln side chain also stabilizes an inverse γ-turn in the peptide backbone by forming a pair of H-bonds that bridge the γ-turn and stabilize it. Finally, the entire conformer population of Ac-Ala-Gln-NHBn is funneled into a single structure that incorporates the peptide backbone in a type I β-turn, stabilized by the Gln side chain forming a C7 H-bond to the central amide group in the β-turn not otherwise involved in a hydrogen bond. This β-turn backbone structure is nearly identical to that observed in a series of X-(AQ)-Y β-turns in the protein data bank, demonstrating that the gas-phase structure is robust to perturbations imposed by the crystalline protein environment.

  10. Determination of the Glass-Transition Temperature of GRPS and CFRPS Using a Torsion Pendulum in Regimes of Freely Damped Vibrations and Quasi-Stastic Torsion of Specimens

    Science.gov (United States)

    Startsev, V. O.; Lebedev, M. P.; Molokov, M. V.

    2018-03-01

    A method to measure the glass-transition temperature of polymers and polymeric matrices of composite materials with the help of an inverse torsion pendulum over a wide range of temperatures is considered combining the method of free torsional vibrations and a quasi-static torsion of specimens. The glass-transition temperature Tg of a KMKS-1-80. T10 fiberglass, on increasing the frequency of freely damped torsional vibrations from 0.7 to 9.6 Hz, was found to increase from 132 to 140°C. The value of Tg of these specimens, determined by measuring the work of their torsion through a small fixed angle was 128.6°C ± 0.8°C. It is shown that the use of a torsion pendulum allows one to determine the glass-transition temperature of polymeric or polymer matrices of PCMs in dynamic and quasi-static deformation regimes of specimens.

  11. MCBT: Multi-Hop Cluster Based Stable Backbone Trees for Data Collection and Dissemination in WSNs

    Directory of Open Access Journals (Sweden)

    Tae-Jin Lee

    2009-07-01

    Full Text Available We propose a stable backbone tree construction algorithm using multi-hop clusters for wireless sensor networks (WSNs. The hierarchical cluster structure has advantages in data fusion and aggregation. Energy consumption can be decreased by managing nodes with cluster heads. Backbone nodes, which are responsible for performing and managing multi-hop communication, can reduce the communication overhead such as control traffic and minimize the number of active nodes. Previous backbone construction algorithms, such as Hierarchical Cluster-based Data Dissemination (HCDD and Multicluster, Mobile, Multimedia radio network (MMM, consume energy quickly. They are designed without regard to appropriate factors such as residual energy and degree (the number of connections or edges to other nodes of a node for WSNs. Thus, the network is quickly disconnected or has to reconstruct a backbone. We propose a distributed algorithm to create a stable backbone by selecting the nodes with higher energy or degree as the cluster heads. This increases the overall network lifetime. Moreover, the proposed method balances energy consumption by distributing the traffic load among nodes around the cluster head. In the simulation, the proposed scheme outperforms previous clustering schemes in terms of the average and the standard deviation of residual energy or degree of backbone nodes, the average residual energy of backbone nodes after disseminating the sensed data, and the network lifetime.

  12. Solution, solid phase and computational structures of apicidin and its backbone-reduced analogs.

    Science.gov (United States)

    Kranz, Michael; Murray, Peter John; Taylor, Stephen; Upton, Richard J; Clegg, William; Elsegood, Mark R J

    2006-06-01

    The recently isolated broad-spectrum antiparasitic apicidin (1) is one of the few naturally occurring cyclic tetrapeptides (CTP). Depending on the solvent, the backbone of 1 exhibits two gamma-turns (in CH(2)Cl(2)) or a beta-turn (in DMSO), differing solely in the rotation of the plane of one of the amide bonds. In the X-ray crystal structure, the peptidic C==Os and NHs are on opposite sides of the backbone plane, giving rise to infinite stacks of cyclotetrapeptides connected by three intermolecular hydrogen bonds between the backbones. Conformational searches (Amber force field) on a truncated model system of 1 confirm all three backbone conformations to be low-energy states. The previously synthesized analogs of 1 containing a reduced amide bond exhibit the same backbone conformation as 1 in DMSO, which is confirmed further by the X-ray crystal structure of a model system of the desoxy analogs of 1. This similarity helps in explaining why the desoxy analogs retain some of the antiprotozoal activities of apicidin. The backbone-reduction approach designed to facilitate the cyclization step of the acyclic precursors of the CTPs seems to retain the conformational preferences of the parent peptide backbone.

  13. Torsion of the spleen with incomplete infarction: case report

    International Nuclear Information System (INIS)

    Lernau, O.Z.; Baron, J.; Nissan, S.

    1977-01-01

    Torsion and infarction of a ''wandering spleen'' is a rare disease which is often confused with other acute abdominal crises. A correct preoperative diagnosis, when made, has usually been determined by arteriographic studies. A child is described in whom changes in the TcSC scan made a correct diagnosis possible by non-invasive methods

  14. Ocular torsion before and after 1 hour centrifugation

    NARCIS (Netherlands)

    Groen, E.; Graaf, B. de; Bles, W.; Bos, J.E.

    1996-01-01

    To assess a possible otolith contribution to effects observed following prolonged expo-sure to hyper gravity, we used video-oculography to measure ocular torsion during static and dynamic conditions of lateral body tilt (roll) before and after one hour of centrifugation with a Gx-load of 3G. Static

  15. Ocular torsion before and after 1 hour centrifugation

    NARCIS (Netherlands)

    Groen, Eric; De Graaf, Bernd; Bles, Willem; Bos, Jelte E.

    1996-01-01

    To assess a possible otolith contribution to effects observed following prolonged exposure to hypergravity, we used video oculography to measure ocular torsion during static and dynamic conditions of lateral body tilt (roll) before and after t h of centrifugation with a G(x)-load of 3 G. Static tilt

  16. Lung lobe torsion in dogs: 22 cases (1981-1999).

    Science.gov (United States)

    Neath, P J; Brockman, D J; King, L G

    2000-10-01

    To identify breed disposition, postoperative complications, and outcome in dogs with lung lobe torsion. Retrospective study. 22 client-owned dogs. Information on signalment; history; clinical findings; results of clinicopathologic testing, diagnostic imaging, and pleural fluid analysis; surgical treatment; intra- and postoperative complications; histologic findings; and outcome were obtained from medical records. All 22 dogs had pleural effusion; dyspnea was the most common reason for examination. Fifteen dogs were large deep-chested breeds; 5 were toy breeds. Afghan Hounds were overrepresented, compared with the hospital population. One dog was euthanatized without treatment; the remaining dogs underwent exploratory thoracotomy and lung lobectomy. Eleven dogs recovered from surgery without complications, but 3 of these later died of thoracic disease. Four dogs survived to discharge but had clinically important complications within 2 months, including chylothorax, mediastinal mesothelioma, gastric dilatation, and a second lung lobe torsion. Six dogs died or were euthanatized within 2 weeks after surgery because of acute respiratory distress syndrome, pneumonia, septic shock, pneumothorax, or chylothorax. Chylothorax was diagnosed in 8 of the 22 dogs, including 4 Afghan Hounds. Results suggest that lung lobe torsion is rare in dogs and develops most frequently in large deep-chested dogs, particularly Afghan Hounds. Other predisposing causes were not identified, but an association with chylothorax was evident, especially in Afghan Hounds. Prognosis for dogs with lung lobe torsion was fair to guarded.

  17. In vitro transcription of a torsionally constrained template

    DEFF Research Database (Denmark)

    Bentin, Thomas; Nielsen, Peter E

    2002-01-01

    of torsionally constrained DNA by free RNAP. We asked whether or not a newly synthesized RNA chain would limit transcription elongation. For this purpose we developed a method to immobilize covalently closed circular DNA to streptavidin-coated beads via a peptide nucleic acid (PNA)-biotin conjugate in principle...

  18. f(R) gravity, torsion and non-metricity

    International Nuclear Information System (INIS)

    Sotiriou, Thomas P

    2009-01-01

    For both f(R) theories of gravity with an independent symmetric connection (no torsion), usually referred to as Palatini f(R) gravity theories, and for f(R) theories of gravity with torsion but no non-metricity, called U4 theories, it has been shown that the independent connection can actually be eliminated algebraically, as long as this connection does not couple to matter. Remarkably, the outcome in both cases is the same theory, which is dynamically equivalent with an ω 0 = -3/2 Brans-Dicke theory. It is shown here that even for the most general case of an independent connection with both non-metricity and torsion, one arrives at exactly the same theory as in the more restricted cases. This generalizes the previous results and explains why assuming that either the torsion or the non-metricity vanishing ultimately leads to the same theory. It also demonstrates that f(R) actions cannot support an independent connection which carries dynamical degrees of freedom, irrespective of how general this connection is, at least as long as there is no connection-matter coupling. (fast track communication)

  19. Torsional Newton-Cartan geometry and the Schrodinger algebra

    NARCIS (Netherlands)

    Bergshoeff, Eric A.; Hartong, Jelle; Rosseel, Jan

    2015-01-01

    We show that by gauging the Schrodinger algebra with critical exponent z and imposing suitable curvature constraints, that make diffeomorphisms equivalent to time and space translations, one obtains a geometric structure known as (twistless) torsional Newton-Cartan geometry (TTNC). This is a version

  20. Burden and seasonality of testicular torsion in tropical Africa ...

    African Journals Online (AJOL)

    Jibril O. Bello

    2018-02-14

    Feb 14, 2018 ... Department of Surgery, University of Ilorin Teaching Hospital, Ilorin, Nigeria ... Cases occurred 91% higher than average during the cold season (November to .... tion strategies through the education of school staff and students on .... torsion and weather conditions: analysis of 21,289 cases in Brazil. Int.

  1. Portal Venous Thrombosis Developing after Torsion of a Wandering ...

    African Journals Online (AJOL)

    2017-03-06

    Mar 6, 2017 ... Department of General Surgery, YüzüncüYıl University. Faculty of ... an emergency surgery. The spleen was ... exist in acute, subacute or chronic forms, depending on the development ... of spleen infarction, sepsis and acute pancreatitis. ... In cases of torsion of wandering spleen, the treatment principally ...

  2. Lateral-torsional buckling resistance of cellular beams

    NARCIS (Netherlands)

    Sonck, Delphine; Belis, Jan

    The evenly spaced circular web openings in I-section cellular beams have an advantageous effect on the material use if these beams are loaded in strong-axis bending. However, not all aspects of the behaviour of such beams have been studied adequately, such as the lateral–torsional buckling failure.

  3. Hardening and softening mechanisms of pearlitic steel wire under torsion

    International Nuclear Information System (INIS)

    Zhao, Tian-Zhang; Zhang, Shi-Hong; Zhang, Guang-Liang; Song, Hong-Wu; Cheng, Ming

    2014-01-01

    Highlights: • Mechanical behavior of pearlitic steel wire is studied using torsion. • Work hardening results from refinement lamellar pearlitic structure. • Softening results from recovery, shear bands and lamellar fragmentations. • A microstructure based analytical flow stress model is established. - Abstract: The mechanical behaviors and microstructure evolution of pearlitic steel wires under monotonic shear deformation have been investigated by a torsion test and a number of electron microscopy techniques including scanning electron microscopy (SEM) and transmission electron microscopy (TEM), with an aim to reveal the softening and hardening mechanisms of a randomly oriented pearlitic structure during a monotonic stain path. Significantly different from the remarkable strain hardening in cold wire drawing, the strain hardening rate during torsion drops to zero quickly after a short hardening stage. The microstructure observations indicate that the inter-lamellar spacing (ILS) decreases and the dislocations accumulate with strain, which leads to hardening of the material. Meanwhile, when the strain is larger than 0.154, the enhancement of dynamic recovery, shear bands (SBs) and cementite fragmentations results in the softening and balances the strain hardening. A microstructure based analytical flow stress model with considering the influence of ILS on the mean free path of dislocations and the softening caused by SBs and cementite fragmentations, has been established and the predicted flow shear curve meets well with the measured curve in the torsion test

  4. Torsion of an Epiploic Appendix Pretending as Acute Appendicitis

    Directory of Open Access Journals (Sweden)

    Kamran Ahmad Malik

    2010-07-01

    Full Text Available Torsion of an epiploic appendix is a rare surgical entity. Its unusual symptomatology, wide variation in physical findings and the absence of helpful laboratory and radiological studies makes it very difficult to diagnose pre-operatively. This is a report of this rare entity found in a patient upon diagnostic laparoscopy performed for suspected acute appendicitis

  5. Axial Torsion of Gangrenous Meckel's Diverticulum Causing Small ...

    African Journals Online (AJOL)

    dividing the band. Resection and anastomosis of the small bowel including the MD was performed. We hereby report a rare and unusual complication of a MD. Although treatment outcome is generally good, pre-operative diagnosis is often difficult. Key words: Axial torsion, Meckel's diverticulum, small bowel obstruction.

  6. Direct excitation of resonant torsional Alfven waves by footpoint motions

    NARCIS (Netherlands)

    Ruderman, M. S.; Berghmans, D.; Goossens, M.; Poedts, S.

    1997-01-01

    The present paper studies the heating of coronal loops by linear resonant Alfven waves that are excited by the motions of the photospheric footpoints of the magnetic field lines. The analysis is restricted to torsionally polarised footpoint motions in an axially symmetric system so that only

  7. Determination of ocular torsion by means of automatic pattern recognition

    NARCIS (Netherlands)

    Groen, E.L.; Bos, J.E.; Nacken, P.F.M.; Graaf, B. de

    1996-01-01

    A new, automatic method for determination of human ocular torsion (OT) was devel-oped based on the tracking of iris patterns in digitized video images. Instead of quanti-fying OT by means of cross-correlation of circular iris samples, a procedure commonly applied, this new method automatically

  8. Determination of ocular torsion by means of automatic pattern recognition

    NARCIS (Netherlands)

    Groen, Eric; Bos, Jelte E.; Nacken, Peter F M; De Graaf, Bernd

    A new, automatic method for determination of human ocular torsion (OT) was developed based on the tracking of iris patterns in digitized video images. Instead of quantifying OT by means of cross-correlation of circular iris samples, a procedure commonly applied, this new method automatically selects

  9. Absence of torsion for NK_1(R) over associative rings

    OpenAIRE

    Basu, Rabeya

    2010-01-01

    When R is a commutative ring with identity, and if k is a natural number with kR = R, then C. Weibel proved that SK_1(R[X]) has no k-torsion. We reprove his result for any associative ring R with identity in which kR = R.

  10. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

    International Nuclear Information System (INIS)

    Marassi, Francesca M.; Ding, Yi; Schwieters, Charles D.; Tian, Ye; Yao, Yong

    2015-01-01

    The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential

  11. Unilateral testicular torsion following ejaculation by manual sexual stimulation in an adolescent: A case report

    Directory of Open Access Journals (Sweden)

    Omer Faruk Yagli

    2018-05-01

    Full Text Available Testicular torsion is one of the most common causes of acute scrotum in children and adolescents. The bell-clapper deformity, which detected in 12% of males, is the most important reason that leads to testicular torsion. In our case, a 14 years old male admitted to our clinic due to testicular torsion developed after ejaculation with manual sexual stimulation of the penis. The most important criteria in determining the loss of testis is the degree and duration of torsion. Here, we discussed the rare cause of testicular torsion along with diagnostic and therapeutic characteristics.

  12. Uganda's National Transmission Backbone Infrastructure Project: Technical Challenges and the Way Forward

    Science.gov (United States)

    Bulega, T.; Kyeyune, A.; Onek, P.; Sseguya, R.; Mbabazi, D.; Katwiremu, E.

    2011-10-01

    Several publications have identified technical challenges facing Uganda's National Transmission Backbone Infrastructure project. This research addresses the technical limitations of the National Transmission Backbone Infrastructure project, evaluates the goals of the project, and compares the results against the technical capability of the backbone. The findings of the study indicate a bandwidth deficit, which will be addressed by using dense wave division multiplexing repeaters, leasing bandwidth from private companies. Microwave links for redundancy, a Network Operation Center for operation and maintenance, and deployment of wireless interoperability for microwave access as a last-mile solution are also suggested.

  13. Cytocompatibility evaluation and surface characterization of TiNi deformed by high-pressure torsion

    Energy Technology Data Exchange (ETDEWEB)

    Awang Shri, Dayangku Noorfazidah, E-mail: AWANGSHRI.Dayangku@nims.go.jp [Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577 (Japan); Structural Materials Unit, National Institute for Materials Science, Tsukuba, Ibaraki 305-0047 (Japan); Tsuchiya, Koichi [Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577 (Japan); Structural Materials Unit, National Institute for Materials Science, Tsukuba, Ibaraki 305-0047 (Japan); Yamamoto, Akiko [Biomaterials Unit, International Center for Material Nanoarchitectonics (WPI-MANA), National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044 (Japan)

    2014-10-01

    Effect of high-pressure torsion (HPT) deformation on biocompatibility and surface chemistry of TiNi was systematically investigated. Ti–50 mol% Ni was subjected to HPT straining for different numbers of turns, N = 0.25, 0.5, 1, 5 and 10 at a rotation speed of 1 rpm. X-ray photoelectron spectroscopy observations after 7 days of cell culture revealed the changes in the surface oxide composition, enrichment of Ti and detection of nitrogen derived from organic molecules in the culture medium. Plating efficiency of L929 cells was slightly increased by HPT deformation though no significant difference was observed. Albumin adsorption was higher in HPT-deformed samples, while vitronectin adsorption was peaked at N = 1. HPT deformation was also found to effectively suppress the Ni ion release from the TiNi samples into the cell culture medium even after the low degree of deformation at N = 0.25. - Highlights: • Nanostructured Ti–50 mol%Ni alloy was produced using high-pressure torsion. • HPT deformation improved L929 growth on TiNi samples. • Changes in surface chemistry were observed in HPT deformed samples. • Protein adsorption behavior was influenced by the surface chemistry. • Ni ion release was suppressed in HPT deformed samples.

  14. Development of a chimeric Zika vaccine using a licensed live-attenuated flavivirus vaccine as backbone.

    Science.gov (United States)

    Li, Xiao-Feng; Dong, Hao-Long; Wang, Hong-Jiang; Huang, Xing-Yao; Qiu, Ye-Feng; Ji, Xue; Ye, Qing; Li, Chunfeng; Liu, Yang; Deng, Yong-Qiang; Jiang, Tao; Cheng, Gong; Zhang, Fu-Chun; Davidson, Andrew D; Song, Ya-Jun; Shi, Pei-Yong; Qin, Cheng-Feng

    2018-02-14

    The global spread of Zika virus (ZIKV) and its unexpected association with congenital defects necessitates the rapid development of a safe and effective vaccine. Here we report the development and characterization of a recombinant chimeric ZIKV vaccine candidate (termed ChinZIKV) that expresses the prM-E proteins of ZIKV using the licensed Japanese encephalitis live-attenuated vaccine SA14-14-2 as the genetic backbone. ChinZIKV retains its replication activity and genetic stability in vitro, while exhibiting an attenuation phenotype in multiple animal models. Remarkably, immunization of mice and rhesus macaques with a single dose of ChinZIKV elicits robust and long-lasting immune responses, and confers complete protection against ZIKV challenge. Significantly, female mice immunized with ChinZIKV are protected against placental and fetal damage upon ZIKV challenge during pregnancy. Overall, our study provides an alternative vaccine platform in response to the ZIKV emergency, and the safety, immunogenicity, and protection profiles of ChinZIKV warrant further clinical development.

  15. A systematic analysis of backbone amide assignments achieved via combinatorial selective labelling of amino acids

    Energy Technology Data Exchange (ETDEWEB)

    Jeremy Craven, C. [University of Sheffield, Department of Biotechnology and Molecular Biology (United Kingdom); Al-Owais, Moza; Parker, Martin J. [University of Leeds, Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology (United Kingdom)], E-mail: m.j.parker@leeds.ac.uk

    2007-06-15

    With the advent of high-yield cell-free expressions systems, many researchers are exploiting selective isotope labelling of amino acids to increase the efficiency and accuracy of the NMR assignment process. We developed recently a combinatorial selective labelling (CSL) method capable of yielding large numbers of residue-type and sequence-specific backbone amide assignments, which involves comparing cross-peak intensities in {sup 1}H-{sup 15}N HSQC and 2D {sup 1}H-{sup 15}N HNCO spectra collected for five samples containing different combinations of {sup 13}C- and {sup 15}N-labelled amino acids [Parker MJ, Aulton-Jones M, Hounslow A, Craven C J (2004) J Am Chem Soc 126:5020-5021]. In this paper we develop a robust method for establishing the reliability of these assignments. We have performed a detailed statistical analysis of the CSL data collected for a model system (the B1 domain of protein G from Streptococcus), developing a scoring method which allows the confidence in assignments to be assessed, and which enables the effects of overlap on assignment fidelity to be predicted. To further test the scoring method and also to assess the performance of CSL in relation to sample quality, we have applied the method to the CSL data collected for GFP in our previous study.

  16. A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

    Directory of Open Access Journals (Sweden)

    Maurer Till

    2005-04-01

    Full Text Available Abstract Background We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral angles and their standard deviations are used which are calculated with an algorithm described earlier by Döker et al. (1999, BBRC, 257, 348–350. The overall long-range contacts are established via a small number of distance restraints between atoms involved in hydrogen bonds and backbone atoms of conserved residues. Employing the restraints generated by PERMOL three-dimensional structures are obtained using standard molecular dynamics programs such as DYANA or CNS. Results To test this modeling approach it has been used for predicting the structure of the histidine-containing phosphocarrier protein HPr from E. coli and the structure of the human peroxisome proliferator activated receptor γ (Ppar γ. The divergence between the modeled HPr and the previously determined X-ray structure was comparable to the divergence between the X-ray structure and the published NMR structure. The modeled structure of Ppar γ was also very close to the previously solved X-ray structure with an RMSD of 0.262 nm for the backbone atoms. Conclusion In summary, we present a new method for homology modeling capable of producing high-quality structure models. An advantage of the method is that it can be used in combination with incomplete NMR data to obtain reasonable structure models in accordance with the experimental data.

  17. Transitional Failure of Carbon Nanotube Systems under a Combination of Tension and Torsion

    Directory of Open Access Journals (Sweden)

    Byeong-Woo Jeong

    2012-01-01

    Full Text Available Transitional failure envelopes of single- and double-walled carbon nanotubes under combined tension-torsion are predicted using classical molecular dynamics simulations. The observations reveal that while the tensile failure load decreases with combined torsion, the torsional buckling moment increases with combined tension. As a result, the failure envelopes under combined tension-torsion are definitely different from those under pure tension or torsion. In such combined loading, there is a multitude of failure modes (tensile failure and torsional buckling, and the failure consequently exhibits the feature of transitional failure envelopes. In addition, the safe region of double-walled carbon nanotubes is significantly larger than that of single-walled carbon nanotubes due to the differences in the onset of torsional buckling.

  18. Green IGP Link Weights for Energy-efficiency and Load-balancing in IP Backbone Networks

    OpenAIRE

    Francois, Frederic; Wang, Ning; Moessner, Klaus; Georgoulas, Stylianos; Xu, Ke

    2013-01-01

    The energy consumption of backbone networks has become a primary concern for network operators and regulators due to the pervasive deployment of wired backbone networks to meet the requirements of bandwidth-hungry applications. While traditional optimization of IGP link weights has been used in IP based load-balancing operations, in this paper we introduce a novel link weight setting algorithm, the Green Load-balancing Algorithm (GLA), which is able to jointly optimize both energy efficiency ...

  19. Backbone assignment of the little finger domain of a Y-family DNA polymerase.

    Science.gov (United States)

    Ma, Dejian; Fowler, Jason D; Suo, Zucai

    2011-10-01

    Sulfolobus solfataricus DNA polymerase IV (Dpo4), a prototype Y-family DNA polymerase, contains a unique little finger domain besides a catalytic core. Here, we report the chemical shift assignments for the backbone nitrogens, α and β carbons, and amide protons of the little finger domain of Dpo4. This work and our published backbone assignment for the catalytic core provide the basis for investigating the conformational dynamics of Dpo4 during catalysis using solution NMR spectroscopy.

  20. Chemical characteristics and antithrombotic effect of chondroitin sulfates from sturgeon skull and sturgeon backbone.

    Science.gov (United States)

    Gui, Meng; Song, Juyi; Zhang, Lu; Wang, Shun; Wu, Ruiyun; Ma, Changwei; Li, Pinglan

    2015-06-05

    Chondroitin sulfates (CSs) were extracted from sturgeon skull and backbone, and their chemical composition, anticoagulant, anti-platelet and thrombolysis activities were evaluated. The average molecular weights of CS from sturgeon skull and backbone were 38.5kDa and 49.2kDa, respectively. Disaccharide analysis indicated that the sturgeon backbone CS was primarily composed of disaccharide monosulfated in position four of the GalNAc (37.8%) and disaccharide monosulfated in position six of the GalNAc (59.6%) while sturgeon skull CS was primarily composed of nonsulfated disaccharide (74.2%). Sturgeon backbone CS showed stronger antithrombotic effect than sturgeon skull CS. Sturgeon backbone CS could significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT), inhibited ADP-induced platelet aggregation and dissolved platelet plasma clots in vitro. The results suggested that sturgeon backbone CS can be explored as a functional food with antithrombotic function. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Torsion of the fallopian the mimicking appendicitis in a pregnant woman; Torsion de la trompa de Falopio en una mujer gestante simulando apendicitis

    Energy Technology Data Exchange (ETDEWEB)

    Tapia-Vine, M.; Pedrosa, I.; Escribano, N. [Hospital Clinico San Carlos (Spain)

    2000-07-01

    Isolated torsion of the fallopian tube is an uncommon entity. Given the difficulties involved in the preoperative diagnosis, the ultrasound findings characteristic of this anomaly are not widely known. We present a case of tubal torsion associated with a cyst, describing the ultrasound images in our case and those reported in the literature. (Author) 18 refs.

  2. Experimental evaluation of torsional fatigue strength of welded bellows and application to design of fusion device

    International Nuclear Information System (INIS)

    Takatsu, Hideyuki; Yamamoto, Masahiro; Shimizu, Masatsugu; Suzuki, Kazuo; Sonobe, Tadashi; Hayashi, Yuzo; Mizuno, Gen-ichiro.

    1984-01-01

    Torsional fatigue strength of the welded bellows was evaluated experimentally, aiming the application to a port of a fusion device. The welded bellows revealed elastic torsional buckling and spiral distorsion even under a small angle of torsion. Twisting load never leads the welded bellows to fracture easily so far as the angle of torsion is not excessively large, and the welded bellows has the torsional fatigue strength much larger than that expected so far. Two formulae were proposed to evaluate the stress of the welded bellows under the forced angle of torsion; shearing stress evaluation formula in the case that torsional buckling does not occur and the axial bending stress evaluation formula in the case that torsional buckling occurs. And the results of the torsional fatigue experiments showed that the former is reasonably conservative and simulates the actual behavior of the welded bellows better than the latter in the high cycle fatigue region and vice versa in the low cycle fatigue region from the viewpoint of the mechanical design. The present evaluation method of the torsional fatigue strength was applied to the welded bellows for the port of the JT-60 vacuum vessel and its structural integrity was confirmed under the design load condition. (author)

  3. Testicular torsion and weather conditions: analysis of 21,289 cases in Brazil

    Directory of Open Access Journals (Sweden)

    Fernando Korkes

    2012-04-01

    Full Text Available PURPOSE: The hypothesis of association between testicular torsion and hyperactive cremasteric reflex, worsened by cold weather, has not been proved. Thirteen studies in the literature evaluated this issue, with inconclusive results. The aim of the present study was to evaluate the seasonality of testicular torsion in a large subset of patients surgically treated in Brazil, and additionally to estimate the incidence of testicular torsion. MATERIALS AND METHODS: Brazilian Public Health System Database was assessed from 1992-2010 to evaluate hospital admissions associated with treatment of testicular torsion. Average monthly temperature between 1992-2010 was calculated for each region. RESULTS: We identified 21,289 hospital admissions for treatment of testicular torsion. There was a higher number of testicular torsions during colder months (p = 0.002. To estimate the incidence of testicular torsion, we have related our findings to data from the last Brazilian census (2010. In 2010, testicular torsion occurred in 1.4:100,000 men in Brazil. CONCLUSIONS:Testicular torsion occurred at an annual incidence of approximately 1.4:100,000 men in Brazil in 2010. Seasonal variations do occur, with a significant increase of events during winter. Our findings support the theory of etiological role of cold weather to the occurrence of testicular torsion. Strategies to prevent these events can be based on these findings.

  4. A torsional artificial muscle from twisted nitinol microwire

    Science.gov (United States)

    Mirvakili, Seyed M.; Hunter, Ian W.

    2017-04-01

    Nitinol microwires of 25 μm in diameter can have tensile actuation of up to 4.5% in less than 100 ms. A work density of up to 480 MPa can be achieved from these microwires. In the present work, we are showing that by twisting the microwires in form of closed-loop two-ply yarn we can create a torsional actuator. We achieved a revisable torsional stroke of 46°/mm with peak rotational speed of up to 10,000 rpm. We measured a gravimetric torque of up to 28.5 N•m/kg which is higher than the 3 - 6 N•m/kg for direct-drive commercial electric motors. These remarkable performance results are comparable to those of guest-infiltrated carbon nanotube twisted yarns.

  5. Omental torsion in a captive polar bear (Ursus maritimus).

    Science.gov (United States)

    Mendez-Angulo, Jose L; Funes, Francisco J; Trent, Ava M; Willette, Michelle; Woodhouse, Kerry; Renier, Anna C

    2014-03-01

    This is the first case report of an omental torsion in a polar bear (Ursus maritimus). A captive, 23-yr-old, 250-kg, intact female polar bear presented to the University of Minnesota Veterinary Medical Center with a 2-day history of lethargy, depression, and vomiting. Abdominal ultrasound identified large amounts of hyperechoic free peritoneal fluid. Ultrasound-guided abdominocentesis was performed and yielded thick serosanguinous fluid compatible with a hemoabdomen. An exploratory laparotomy revealed a large amount of malodorous, serosanguineous fluid and multiple necrotic blood clots associated with a torsion of the greater omentum and rupture of a branch of the omental artery. A partial omentectomy was performed to remove the necrotic tissue and the abdomen was copiously lavaged. The polar bear recovered successfully and is reported to be clinically well 6 mo later. This condition should be considered as a differential in bears with clinical signs of intestinal obstruction and hemoabdomen.

  6. Scalar-metric and scalar-metric-torsion gravitational theories

    International Nuclear Information System (INIS)

    Aldersley, S.J.

    1977-01-01

    The techniques of dimensional analysis and of the theory of tensorial concomitants are employed to study field equations in gravitational theories which incorporate scalar fields of the Brans-Dicke type. Within the context of scalar-metric gravitational theories, a uniqueness theorem for the geometric (or gravitational) part of the field equations is proven and a Lagrangian is determined which is uniquely specified by dimensional analysis. Within the context of scalar-metric-torsion gravitational theories a uniqueness theorem for field Lagrangians is presented and the corresponding Euler-Lagrange equations are given. Finally, an example of a scalar-metric-torsion theory is presented which is similar in many respects to the Brans-Dicke theory and the Einstein-Cartan theory

  7. MR evaluation of femoral neck version and tibial torsion

    Energy Technology Data Exchange (ETDEWEB)

    Koenig, James Karl; Dwek, Jerry R. [University of California, San Diego, Children' s Hospital and Health Center, Department of Radiology, San Diego, CA (United States); Pring, Maya E. [Rady Children' s Hospital, Department of Pediatric Orthopedic Surgery, San Diego, CA (United States)

    2012-01-15

    Abnormalities of femoral neck version have been associated with a number of hip abnormalities in children, including slipped capital femoral epiphysis, proximal femoral focal deficiency, coxa vara, a deep acetabulum and, rarely, developmental dysplasia of the hip. Orthopedic surgeons also are interested in quantifying the femoral neck anteversion or retroversion in children especially to plan derotational osteotomies. Historically, the angle of femoral version and tibial torsion has been measured with the use of radiography and later by CT. Both methods carry with them the risks associated with ionizing radiation. Techniques that utilize MR are used less often because of the associated lengthy imaging times. This article describes a technique using MRI to determine femoral neck version and tibial torsion with total scan times of approximately 10 min. (orig.)

  8. Direct observation of vibrational energy dispersal via methyl torsions.

    Science.gov (United States)

    Gardner, Adrian M; Tuttle, William D; Whalley, Laura E; Wright, Timothy G

    2018-02-28

    Explicit evidence for the role of methyl rotor levels in promoting energy dispersal is reported. A set of coupled zero-order vibration/vibration-torsion (vibtor) levels in the S 1 state of para -fluorotoluene ( p FT) are investigated. Two-dimensional laser-induced fluorescence (2D-LIF) and two-dimensional zero-kinetic-energy (2D-ZEKE) spectra are reported, and the assignment of the main features in both sets of spectra reveals that the methyl torsion is instrumental in providing a route for coupling between vibrational levels of different symmetry classes. We find that there is very localized, and selective, dissipation of energy via doorway states, and that, in addition to an increase in the density of states, a critical role of the methyl group is a relaxation of symmetry constraints compared to direct vibrational coupling.

  9. In vitro transcription of a torsionally constrained template

    DEFF Research Database (Denmark)

    Bentin, Thomas; Nielsen, Peter E

    2002-01-01

    RNA polymerase (RNAP) and the DNA template must rotate relative to each other during transcription elongation. In the cell, however, the components of the transcription apparatus may be subject to rotary constraints. For instance, the DNA is divided into topological domains that are delineated...... of torsionally constrained DNA by free RNAP. We asked whether or not a newly synthesized RNA chain would limit transcription elongation. For this purpose we developed a method to immobilize covalently closed circular DNA to streptavidin-coated beads via a peptide nucleic acid (PNA)-biotin conjugate in principle...... constrained. We conclude that transcription of a natural bacterial gene may proceed with high efficiency despite the fact that newly synthesized RNA is entangled around the template in the narrow confines of torsionally constrained supercoiled DNA....

  10. Nonlinear modulation of torsional waves in elastic rod. [Instability

    Energy Technology Data Exchange (ETDEWEB)

    Hirao, M; Sugimoto, N [Osaka Univ., Toyonaka (Japan). Faculty of Engineering Science

    1977-06-01

    Nonlinear Schroedinger equation, which describes the nonlinear modulation of dispersive torsional waves in an elastic rod of circular cross-section, is derived by the derivative expansion method. It is found, for the lowest dispersive mode, that the modulational instability occurs except in the range of the carrier wavenumber, 2.799torsional and its second-harmonic longitudinal modes.

  11. Torsion of a Wandering Spleen Presenting as Acute Abdomen

    International Nuclear Information System (INIS)

    Chauhan, Narvir Singh; Kumar, Satish

    2016-01-01

    Wandering spleen is a rare condition which if uncorrected, can result in torsion and infarction. Clinical presentation of a wandering spleen can vary from asymptomatic abdominal mass to acute abdominal pain. Radiological investigations play a pivotal role in diagnosis as the clinical diagnosis is usually impossible. We present a case of wandering spleen with torsion and complete infarction that occurred in a 32-year-old multiparous female. The diagnosis was established preoperatively on colour Doppler and CT of the abdomen with subsequent confirmation on surgery. Wandering spleen is a rare clinical condition which can present as acute abdomen. An increased awareness of this entity together with the timely use of ultrasound and CT of the abdomen can play an important role in preoperative diagnosis and surgical management

  12. General relativity with spin and torsion: Foundations and prospects

    International Nuclear Information System (INIS)

    Hehl, F.W.; von der Heyde, P.; Kerlick, G.D.; Nester, J.M.

    1976-01-01

    A generalization of Einstein's gravitational theory is discussed in which the spin of matter as well as its mass plays a dynamical role. The spin of matter couples to a non-Riemannian structure in space-time, Cartan's torsion tensor. The theory which emerges from taking this coupling into account, the U 4 theory of gravitation, predicts, in addition to the usual infinite-range gravitational interaction mediated by the metric field, a new, very weak, spin contact interaction of gravitational origin. We summarize here all the available theoretical evidence that argues for admitting spin and torsion into a relativistic gravitational theory. Not least among this evidence is the demonstration that the U 4 theory arises as a local gauge theory for the Poincare group in space-time. The deviations of the U 4 theory from standard general relativity are estimated, and the prospects for further theoretical development are assessed

  13. Redox-controlled backbone dynamics of human cytochrome c revealed by 15N NMR relaxation measurements

    International Nuclear Information System (INIS)

    Sakamoto, Koichi; Kamiya, Masakatsu; Uchida, Takeshi; Kawano, Keiichi; Ishimori, Koichiro

    2010-01-01

    Research highlights: → The dynamic parameters for the backbone dynamics in Cyt c were determined. → The backbone mobility of Cyt c is highly restricted due to the covalently bound heme. → The backbone mobility of Cyt c is more restricted upon the oxidation of the heme. → The redox-dependent dynamics are shown in the backbone of Cyt c. → The backbone dynamics of Cyt c would regulate the electron transfer from Cyt c. -- Abstract: Redox-controlled backbone dynamics in cytochrome c (Cyt c) were revealed by 2D 15 N NMR relaxation experiments. 15 N T 1 and T 2 values and 1 H- 15 N NOEs of uniformly 15 N-labeled reduced and oxidized Cyt c were measured, and the generalized order parameters (S 2 ), the effective correlation time for internal motion (τ e ), the 15 N exchange broadening contributions (R ex ) for each residue, and the overall correlation time (τ m ) were estimated by model-free dynamics formalism. These dynamic parameters clearly showed that the backbone dynamics of Cyt c are highly restricted due to the covalently bound heme that functions as the stable hydrophobic core. Upon oxidation of the heme iron in Cyt c, the average S 2 value was increased from 0.88 ± 0.01 to 0.92 ± 0.01, demonstrating that the mobility of the backbone is further restricted in the oxidized form. Such increases in the S 2 values were more prominent in the loop regions, including amino acid residues near the thioether bonds to the heme moiety and positively charged region around Lys87. Both of the regions are supposed to form the interaction site for cytochrome c oxidase (CcO) and the electron pathway from Cyt c to CcO. The redox-dependent mobility of the backbone in the interaction site for the electron transfer to CcO suggests an electron transfer mechanism regulated by the backbone dynamics in the Cyt c-CcO system.

  14. Radiation, photon orbits, and torsion in strongly curved spacetimes

    International Nuclear Information System (INIS)

    Sandberg, V.D.

    1975-01-01

    Four topics on the strong field aspects of general relativity are presented. These are the role of constraining forces for ultrarelativistic particle motion as a source of gravitational radiation, the study of electromagnetic radiation due to space-time oscillations, the light scattering properties of a class of naked singularities, and the relation of gravitation theories with torsion to general relativity. The astrophysical implications and unusual physical phenomena associated with very intense gravitational fields are discussed for these four topics

  15. Elasto-plastic torsion problem as an infinity Laplace's equation

    Directory of Open Access Journals (Sweden)

    Ahmed Addou

    2006-12-01

    Full Text Available In this paper, we study a perturbed infinity Laplace's equation, the perturbation corresponds to an Leray-Lions operator with no coercivity assumption. We consider the case where data are distributions or $L^{1}$ elements. We show that this problem has an unique solution which is the solution to the variational inequality arising in the elasto-plastic torsion problem, associated with an operator $A$.

  16. Human tibial torsion - Morphometric assessment and clinical relevance

    Directory of Open Access Journals (Sweden)

    Swati Gandhi

    2014-02-01

    Full Text Available Background: Tibial torsion is an important anatomical parameter in clinical practice and displays variability among individuals. These variations are extremely significant in view of alignment guides such as those related to rotational landmarks of tibia in total knee arthroplasty. Further, precise knowledge and information pertaining to angle of tibial torsion also helps in correction of traumatic malunion or congenital maltorsion of tibia. Methods: The present study was carried out to determine the angle of tibial torsion in 100 adult dry tibia bones in the Department of Anatomy, Government Medical College, Amritsar. The study group comprised 50 males and 50 females with equal number of right- and left-sided bones. The measurements were meticulously recorded and the data were subjected to statistical analysis. The results were analyzed and discussed in the light of existing literature. Results: On the right side, it was found to be 29.84° ± 4.86°° (range = 22.00° -38.00° in males and 28.92° ± 5.10°° (range = 15.00°-38.00° in females. On the left side, it was found to be 28.00° ± 4.94°° (range = 20.00°-40.00°° in males and 28.12° ± 4.28°° (range = 20.00°-37.00°° in females. Conclusion: The present study is an endeavor to provide baseline data with reference to the angle of tibial torsion in the Indian population. The results of the study assume special importance in view of the technical advancements in reconstructive surgical procedures in orthopedic practice.

  17. On Polya's inequality for torsional rigidity and first Dirichlet eigenvalue

    OpenAIRE

    Berg, M. van den; Ferone, V.; Nitsch, C.; Trombetti, C.

    2016-01-01

    Let $\\Omega$ be an open set in Euclidean space with finite Lebesgue measure $|\\Omega|$. We obtain some properties of the set function $F:\\Omega\\mapsto \\R^+$ defined by $$ F(\\Omega)=\\frac{T(\\Omega)\\lambda_1(\\Omega)}{|\\Omega|} ,$$ where $T(\\Omega)$ and $\\lambda_1(\\Omega)$ are the torsional rigidity and the first eigenvalue of the Dirichlet Laplacian respectively. We improve the classical P\\'olya bound $F(\\Omega)\\le 1,$ and show that $$F(\\Omega)\\le 1- \

  18. Compactification over coset spaces with torsion and vanishing cosmological constant

    International Nuclear Information System (INIS)

    Batakis, N.A.

    1989-01-01

    We consider the compactification of ten-dimensional Einstein-Yang-Mills theories over non-symmetric, six-dimensional homogeneous coset spaces with torsion. We examine the Einstein-Yang-Mills equations of motion requiring vanishing cosmological constant at ten and four dimensions and we present examples of compactifying solutions. It appears that the introduction of more than one radii in the coset space, when possible, may be mandatory for the existence of compactifying solutions. (orig.)

  19. Spectral Action for Torsion with and without Boundaries

    DEFF Research Database (Denmark)

    Iochum, B.; Levy, Cyril Olivier; Vassilevich, D.

    2012-01-01

    We derive a commutative spectral triple and study the spectral action for a rather general geometric setting which includes the (skew-symmetric) torsion and the chiral bag conditions on the boundary. The spectral action splits into bulk and boundary parts. In the bulk, we clarify certain issues...... of the boundary conditions, and show that θ = 0 is a critical point of the action in any dimension and at all orders of the expansion....

  20. Compactification over coset spaces with torsion and vanishing cosmological constant

    Energy Technology Data Exchange (ETDEWEB)

    Batakis, N.A.; Farakos, K.; Koutsoumbas, G.; Zoupanos, G.; Kapetanakis, D.

    1989-04-13

    We consider the compactification of ten-dimensional Einstein-Yang-Mills theories over non-symmetric, six-dimensional homogeneous coset spaces with torsion. We examine the Einstein-Yang-Mills equations of motion requiring vanishing cosmological constant at ten and four dimensions and we present examples of compactifying solutions. It appears that the introduction of more than one radii in the coset space, when possible, may be mandatory for the existence of compactifying solutions.

  1. Torsion and curvature in higher dimensional supergravity theories

    International Nuclear Information System (INIS)

    Smith, A.W.; Pontificia Univ. Catolica do Rio de Janeiro

    1983-01-01

    This work is an extension of Dragon's theorems to higher dimensional space-time. It is shown that the first set of Bianchi identities allow us to express the curvature components in terms of torsion components and its covariant derivatives. It is also shown that the second set of Bianchi identities does not give any new information which is not already contained in the first one. (Author) [pt

  2. Effect of bilateral superior oblique split lengthening on torsion

    Directory of Open Access Journals (Sweden)

    Jitendra Jethani

    2015-01-01

    Full Text Available Introduction: Superior oblique split lengthening (SOSL is done for weakening of superior oblique. It corrects the superior oblique overaction (SOOA and A pattern. Its effect on the torsion of the eye is not known. We present our data on the effect of this particular procedure on torsion. Materials and Methods: We did a study of 16 patients (32 eyes who underwent bilateral SOSL and compared the disc foveal angle (DFA preoperatively and postoperatively. The split lengthening was done from 4 mm to 7 mm depending upon the overaction of superior oblique. Results: The mean age was 15.3 ± 8.4 years. Mean preoperative DFA in the right eye (RE was −3.9° and in the left eye (LE was −2.9°. Mean postoperative DFA in RE was 0.2° and in LE was 0.9°. The mean change in the DFA for RE was 4.1° ± 1.3° and for LE was 3.8° ± 1.2°. All the patients were aligned horizontally within 6 prism diopter and no pattern and no diplopia postoperatively. The A pattern was corrected in all the patient postsurgery. For each mm of surgery, an improvement of 0.8° was seen in the DFA. Conclusion: We report the effect of SOSL on torsion. The SOSL reduces intorsion postsurgery and is, therefore, a valuable procedure in SOOA where both pattern and in torsion needs to be corrected.

  3. Tachyonless models of relativistic particles with curvature and torsion

    International Nuclear Information System (INIS)

    Kuznetsov, Yu.A.; Plyushchaj, M.S.

    1992-01-01

    The problem of construction (2+1)-dimensional tachyonless models of relativistic particles with an action depending on the world-trajectory curvature and torsion is investigated. The special class of models, described by maximum symmetric action and comprising only spin internal degrees of freedom is found. The examples of systems from the special class are given, whose classical and quantum spectra contain only massive states. 23 refs

  4. A supersymmetric R2-action in six dimensions and torsion

    International Nuclear Information System (INIS)

    Bergshoeff, E.; Salam, A.; Sezgin, E.

    1986-01-01

    We give the superconformal extension of (Rsub(μνab)) 2 in six dimensions. We show that in a superconformal gauge the 3-form field Hsub(μνrho) has a natural torsion interpretation. We also give partial results on the superconformal extension of the Gauss-Bonnet combination: Rsub(μνab) 2 -4Rsub(μa) 2 +R 2 . (author)

  5. Einstein gravity with torsion induced by the scalar field

    Science.gov (United States)

    Özçelik, H. T.; Kaya, R.; Hortaçsu, M.

    2018-06-01

    We couple a conformal scalar field in (2+1) dimensions to Einstein gravity with torsion. The field equations are obtained by a variational principle. We could not solve the Einstein and Cartan equations analytically. These equations are solved numerically with 4th order Runge-Kutta method. From the numerical solution, we make an ansatz for the rotation parameter in the proposed metric, which gives an analytical solution for the scalar field for asymptotic regions.

  6. On discrete symmetries and torsion homology in F-theory

    Energy Technology Data Exchange (ETDEWEB)

    Mayrhofer, Christoph [Arnold-Sommerfeld-Center, Ludwig-Maximilians-Universität München,München (Germany); Palti, Eran; Till, Oskar; Weigand, Timo [Institut für Theoretische Physik, Ruprecht-Karls-Universität Heidelberg,Heidelberg (Germany)

    2015-06-04

    We study the relation between discrete gauge symmetries in F-theory compactifications and torsion homology on the associated Calabi-Yau manifold. Focusing on the simplest example of a ℤ{sub 2} symmetry, we show that there are two physically distinct ways that such a discrete gauge symmetry can arise. First, compactifications of M-Theory on Calabi-Yau threefolds which support a genus-one fibration with a bi-section are known to be dual to six-dimensional F-theory vacua with a ℤ{sub 2} gauge symmetry. We show that the resulting five-dimensional theories do not have a ℤ{sub 2} symmetry but that the latter emerges only in the F-theory decompactification limit. Accordingly the genus-one fibred Calabi-Yau manifolds do not exhibit torsion in homology. Associated to the bi-section fibration is a Jacobian fibration which does support a section. Compactifying on these related but distinct varieties does lead to a ℤ{sub 2} symmetry in five dimensions and, accordingly, we find explicitly an associated torsion cycle. We identify the expected particle and membrane system of the discrete symmetry in terms of wrapped M2 and M5 branes and present a field-theory description of the physics for both cases in terms of circle reductions of six-dimensional theories. Our results and methods generalise straightforwardly to larger discrete symmetries and to four-dimensional compactifications.

  7. Boundary integral method for torsion of composite shafts

    International Nuclear Information System (INIS)

    Chou, S.I.; Mohr, J.A.

    1987-01-01

    The Saint-Venant torsion problem for homogeneous shafts with simply or multiply-connected regions has received a great deal of attention in the past. However, because of the mathematical difficulties inherent in the problem, very few problems of torsion of shafts with composite cross sections have been solved analytically. Muskhelishvili (1963) studied the torsion problem for shafts with cross sections having several solid inclusions surrounded by an elastic material. The problem of a circular shaft reinforced by a non-concentric round inclusion, a rectangular shaft composed of two rectangular parts made of different materials were solved. In this paper, a boundary integral equation method, which can be used to solve problems more complex than those considered by Katsikadelis et. al., is developed. Square shaft with two dissimilar rectangular parts, square shaft with a square inclusion are solved and the results compared with those given in the reference cited above. Finally, a square shaft composed of two rectangular parts with circular inclusion is solved. (orig./GL)

  8. Discussion on massive gravitons and propagating torsion in arbitrary dimensions

    International Nuclear Information System (INIS)

    Hernaski, C.A.; Vargas-Paredes, A.A.; Helayel-Neto, J.A.

    2009-01-01

    Full text. Massive gravity has been an issue of particular interest since the early days of Quantum Gravity. More recently, in connection with models based on brane-world scenarios, the discussion of massive gravitons is drawing a great deal of attention, in view of the possibility of their production at LHC and the feasibility of detection of quantum gravity effects at the TeV scale. In this paper, we reassess a particular R 2 -type gravity action in D dimensions, recently studied by Nakasone and Oda, taking now torsion effects into account. Considering that the vielbein and the spin connection carry independent propagating degrees of freedom, we conclude that ghosts and tachyons are absent only if torsion is non-propagating, and we also conclude that there is no room for massive gravitons. To include these excitations, we understand how to enlarge Nakasone-Oda's model by means of explicit torsion terms in the action and we discuss the unitarity of the enlarged model for arbitrary dimensions. To make this we construct a complete basis of operators that projects the degrees of freedom of the dynamical fields of the model in their irreducible spin decomposition. The outcome is that we find a set of Lagrangians with a massive graviton that, in D=4, reproduce those already studied in the literature. (author)

  9. Intravitreal Phacoemulsification Using Torsional Handpiece for Retained Lens Fragments

    Science.gov (United States)

    Kumar, Vinod; Takkar, Brijesh

    2016-01-01

    Purpose: To evaluate the results of intravitreal phacoemulsification with torsional hand piece in eyes with posteriorly dislocated lens fragments. Methods: In this prospective, interventional case series, 15 eyes with retained lens fragments following phacoemulsification were included. All patients underwent standard three-port pars plana vitrectomy and intravitreal phacoemulsification using sleeveless, torsional hand piece (OZiL™, Alcon's Infiniti Vision System). Patients were followed up for a minimum of six months to evaluate the visual outcomes and complications. Results: The preoperative best-corrected visual acuity (BCVA) ranged from light perception to 0.3. No complications such as thermal burns of the scleral wound, retinal damage due to flying lens fragments, or difficult lens aspiration occurred during intravitreal phacoemulsification. Mean post-operative BCVA at the final follow-up was 0.5. Two eyes developed cystoid macular edema, which was managed medically. No retinal detachment was noted. Conclusion: Intravitreal phacoemulsification using torsional hand piece is a safe and effective alternative to conventional longitudinal phacofragmentation. PMID:27621783

  10. Diffusive intergranular cavity growth in creep in tension and torsion

    International Nuclear Information System (INIS)

    Stanzl, S.E.; Argon, A.S.; Tschegg, E.K.

    1983-01-01

    Creep experiments were performed at 500 C in tension and torsion on high conductivity copper tubes with a uniform initial coverage of implanted water vapor bubbles on all grain boundaries. No significant differences were found in the times to fracture over a wide stress range when the results were correlated according to the maximum principal tensile stress in the two fields. The results indicate that the cavities grow in a crack-like mode but at one tenth the rate predicted from the theoretical model of Pharr and Nix. This difference is attributed partly to load shedding from boundaries normal to the maximum principal tensile stress to slanted boundaries, and partly to a lack of knowledge about th surface diffusion constant. The results indicate further that the contribution to intergranular cavity growth by power-law creep in negligible in comparison to the contribution by diffusional flow. Complementary tension and torsion experiments performed in initially uncavitated samples results in shorter creep lives in torsion than in tension due to more effective cavity nucleation in the former. The times to fracture in both of these cases obey Monkman and Grant's law, indicating the presence of constraints on growth by the lagging deformations by power-law creep in the surroundings of the cavitating isolated grain facets

  11. Review of gastric torsion in eight guinea pigs (Cavia porcellus).

    Science.gov (United States)

    Nógrádi, Anna Linda; Cope, Iain; Balogh, Márton; Gál, János

    2017-12-01

    The authors present eight cases of gastric dilatation and volvulus (GDV) in guinea pigs from the Department and Clinic of Exotic Animal and Wildlife Medicine, University of Veterinary Medicine, Budapest, Hungary between 2012 and 2016. Seven animals were operated on and two survived. Gastric torsion has been noted in many mammalian species. Gastric volvulus has a high morbidity and high mortality rate with a guarded to poor prognosis in all of these species. How GDV develops is still not widely understood. Postmortem examinations, in both our cases and previously reported cases, have failed to reveal the exact causes of the gastric torsions. The aetiology of gastric torsion in guinea pigs is probably multifactorial. Feeding fewer meals per day, eating rapidly, decreased food particle size, exercise, stress after a meal, competition, age, and an aggressive or fearful temperament, are all likely and potential risk factors for GDV development in a similar fashion to dogs. Sex, breeding, dental diseases, anatomical abnormalities, pain and pregnancy may also be contributing factors.

  12. Backbone and stereospecific (13)C methyl Ile (δ1), Leu and Val side-chain chemical shift assignments of Crc.

    Science.gov (United States)

    Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V

    2015-04-01

    Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (δ1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W.

  13. Tensile and Torsional Structural Properties of the Native Scapholunate Ligament.

    Science.gov (United States)

    Pang, Eric Quan; Douglass, Nathan; Behn, Anthony; Winterton, Matthew; Rainbow, Michael J; Kamal, Robin N

    2018-02-17

    The ideal material for reconstruction of the scapholunate interosseous ligament (SLIL) should replicate the mechanical properties of the native SLIL to recreate normal kinematics and prevent posttraumatic arthritis. The purpose of our study was to evaluate the cyclic torsional and tensile properties of the native SLIL and load to failure tensile properties of the dorsal SLIL. The SLIL bone complex was resected from 10 fresh-frozen cadavers. The scaphoid and lunate were secured in polymethylmethacrylate and mounted on a test machine that incorporated an x-y stage and universal joint, which permitted translations perpendicular to the rotation/pull axis as well as nonaxial angulations. After a 1 N preload, specimens underwent cyclic torsional testing (±0.45 N m flexion/extension at 0.5 Hz) and tensile testing (1-50 N at 1 Hz) for 500 cycles. Lastly, the dorsal 10 mm of the SLIL was isolated and displaced at 10 mm/min until failure. During intact SLIL cyclic torsional testing, the neutral zone was 29.7° ± 6.6° and the range of rotation 46.6° ± 7.1°. Stiffness in flexion and extension were 0.11 ± 0.02 and 0.12 ± 0.02 N m/deg, respectively. During cyclic tensile testing, the engagement length was 0.2 ± 0.1 mm, the mean stiffness was 276 ± 67 N/mm, and the range of displacement was 0.4 ± 0.1 mm. The dorsal SLIL displayed a 0.3 ± 0.2 mm engagement length, 240 ± 65 N/mm stiffness, peak load of 270 ± 91 N, and displacement at peak load of 1.8 ± 0.3 mm. We report the torsional properties of the SLIL. Our novel test setup allows for free rotation and translation, which reduces out-of-plane force application. This may explain our observation of greater dorsal SLIL load to failure than previous reports. By matching the natural ligament with respect to its tensile and torsional properties, we believe that reconstructions will better restore the natural kinematics of the wrist and lead to improved outcomes. Future clinical studies should aim to investigate this

  14. Research on torsional vibration modelling and control of printing cylinder based on particle swarm optimization

    Science.gov (United States)

    Wang, Y. M.; Xu, W. C.; Wu, S. Q.; Chai, C. W.; Liu, X.; Wang, S. H.

    2018-03-01

    The torsional oscillation is the dominant vibration form for the impression cylinder of printing machine (printing cylinder for short), directly restricting the printing speed up and reducing the quality of the prints. In order to reduce torsional vibration, the active control method for the printing cylinder is obtained. Taking the excitation force and moment from the cylinder gap and gripper teeth open & closing cam mechanism as variable parameters, authors establish the dynamic mathematical model of torsional vibration for the printing cylinder. The torsional active control method is based on Particle Swarm Optimization(PSO) algorithm to optimize input parameters for the serve motor. Furthermore, the input torque of the printing cylinder is optimized, and then compared with the numerical simulation results. The conclusions are that torsional vibration active control based on PSO is an availability method to the torsional vibration of printing cylinder.

  15. Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients

    Directory of Open Access Journals (Sweden)

    Restelli U

    2017-06-01

    Full Text Available Umberto Restelli,1,2 Giuliano Rizzardini,3,4 Andrea Antinori,5 Adriano Lazzarin,6 Marzia Bonfanti,1 Paolo Bonfanti,7 Davide Croce1,2 1Centre for Research on Health Economics, Social and Health Care Management, LIUC – Università Cattaneo, Castellanza, Varese, Italy; 2School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; 3First and Second Divisions of Infectious Diseases, “Luigi Sacco” Hospital, Milan, Italy; 4School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; 5National Institute for Infectious Diseases “L Spallanzani”, Rome, 6Department of Infectious Diseases, San Raffaele Scientific Institute, 7Department of Infectious and Tropical Diseases, A Manzoni Hospital, Lecco, Italy Background: In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG, a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER of the use of DTG+backbone compared with raltegravir (RAL+backbone, darunavir (DRV+ritonavir(r+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service’s point of view.Materials and methods: A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD] and successive lines of therapy. The model considers costs (2014 and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies.Results: In

  16. An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

    Science.gov (United States)

    Kamisetty, Hetunandan; Bailey-Kellogg, Chris; Pandurangan, Gopal

    2006-01-15

    Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were 'close enough'. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for alpha-helices and beta-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise. This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental beta-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to

  17. Soluble and Membrane-Bound β-Glucosidases Are Involved in Trimming the Xyloglucan Backbone.

    Science.gov (United States)

    Sampedro, Javier; Valdivia, Elene R; Fraga, Patricia; Iglesias, Natalia; Revilla, Gloria; Zarra, Ignacio

    2017-02-01

    In many flowering plants, xyloglucan is a major component of primary cell walls, where it plays an important role in growth regulation. Xyloglucan can be degraded by a suite of exoglycosidases that remove specific sugars. In this work, we show that the xyloglucan backbone, formed by (1→4)-linked β-d-glucopyranosyl residues, can be attacked by two different Arabidopsis (Arabidopsis thaliana) β-glucosidases from glycoside hydrolase family 3. While BGLC1 (At5g20950; for β-glucosidase active against xyloglucan 1) is responsible for all or most of the soluble activity, BGLC3 (At5g04885) is usually a membrane-anchored protein. Mutations in these two genes, whether on their own or combined with mutations in other exoglycosidase genes, resulted in the accumulation of partially digested xyloglucan subunits, such as GXXG, GXLG, or GXFG. While a mutation in BGLC1 had significant effects on its own, lack of BGLC3 had only minor effects. On the other hand, double bglc1 bglc3 mutants revealed a synergistic interaction that supports a role for membrane-bound BGLC3 in xyloglucan metabolism. In addition, bglc1 bglc3 was complemented by overexpression of either BGLC1 or BGLC3 In overexpression lines, BGLC3 activity was concentrated in a microsome-enriched fraction but also was present in soluble form. Finally, both genes were generally expressed in the same cell types, although, in some cases, BGLC3 was expressed at earlier stages than BGLC1 We propose that functional specialization could explain the separate localization of both enzymes, as a membrane-bound β-glucosidase could specifically digest soluble xyloglucan without affecting the wall-bound polymer. © 2017 American Society of Plant Biologists. All Rights Reserved.

  18. Success of torsional correction surgery after failed surgeries for patellofemoral pain and instability

    OpenAIRE

    Stevens, Peter M.; Gililland, Jeremy M.; Anderson, Lucas A.; Mickelson, Jennifer B.; Nielson, Jenifer; Klatt, Joshua W.

    2013-01-01

    Torsional deformities of the femur and/or tibia often go unrecognized in adolescents and adults who present with anterior knee pain, and patellar maltracking or instability. While open and arthroscopic surgical techniques have evolved to address these problems, unrecognized torsion may compromise the outcomes of these procedures. We collected a group of 16 consecutive patients (23 knees), with mean age of 17, who had undergone knee surgery before torsion was recognized and subsequently treate...

  19. Isolated torsion of fallopian tube during pregnancy; report of two cases.

    Science.gov (United States)

    Yalcin, O T; Hassa, H; Zeytinoglu, S; Isiksoy, S

    1997-08-01

    Isolated torsion of fallopian tube is very uncommon during pregnancy. Predisposing factors for torsion are hydrosalpinx, prior tubal operation, pelvic congestion, ovarian and paraovarian masses and trauma. Although the most important clinical symptom is abdominal pain in lower quadrants, the diagnosis is usually established during the operation performed for acute abdomen and salpingectomy is almost always necessary. Two cases of torsion of fallopian tube during pregnancy, one with hydrosalpinx, the other with paratubal cyst are presented and symptoms and predisposing factors are discussed.

  20. Torsion of gallbladder: a diagnostic predicament

    International Nuclear Information System (INIS)

    Andrabi, S.I.H.; Ahmed, M.; Rathore, M.A.

    2007-01-01

    A 69 years old woman was admitted under the case of physicians with lethargy and anemia. While in-hospital, she developed severe pain in the right hypochondrium with vomiting. Past medical history included peripheral vascular disease, appendicectomy and tuberculous meningitis. On examination, she had tachycardia, hypotension was pale, apyrexic, clinically anicteric and markedly tender over right upper quadrant with mild guarding. Her hemoglobin was 8.5 gm/dl, white cell count was 25,000 per L and had a raised C Reactive Protein of 110. Her liver functions were normal. Plain abdominal radiograph revealed dilated small bowel in the upper abdomen. Provisional diagnosis of acute cholecystitis was made and conservative management was started initially, using intravenous cefuroxime. She deteriorated rapidly, developed metabolic acidosis and atrial fibrillation. CT scan did not reveal a significant abnormality. There were no gallstones and no evidence of acute cholecystitis. An emergency laparotomy revealed a gangrenous gallbladder and twisted more than 3600 anticlockwise on its pedicle. Cholecystectomy was performed and she was managed in intensive care unit. She developed abdominal compartment syndrome requiring re-exploration and a laparostomy. On the fifth post-op day her abdomen was successfully closed with a mesh. Despite intensive monitoring and vigorous management, she developed multi-organ failure and died five weeks after her first operation. Histology confirmed venous infarction of an acalculous gallbladder without cholelithiasis. (author)

  1. Gender features of functional condition of backbone of teenagers with scoliotic posture

    Directory of Open Access Journals (Sweden)

    Sergiy Afanasiev

    2016-10-01

    Full Text Available Purpose: to study mobility of backbone, endurance of muscles of a trunk and to define gender features of functional condition of backbone at children of the middle school age with scoliotic posture depending on the direction of the top of arch of curvature of spine. Material & Methods: 40 girls and 40 boys, including 18 girls and 18 boys with the right-side deformation of backbone in the thoracic department, the left-side – 22 girls and 22 boys are examined. Results: features of changes of indicators, depending on sex of children and frontage of the top of arch of curvature of spine column, are revealed when studying the level of flexibility of backbone and endurance of muscles of a trunk at children of the middle school age with scoliotic posture. Conclusions: it is established that the level of decrease in flexibility of backbone is higher at boys, than at girls, whereas indicators of contractile ability and tone of muscles of "muscular corset" are higher at boys.

  2. Tibial torsion in non-arthritic Indian adults: A computer tomography study of 100 limbs

    Directory of Open Access Journals (Sweden)

    Mullaji Arun

    2008-01-01

    Full Text Available Background: Knowledge of normal tibial torsion is mandatory during total knee replacement (TKR, deformity correction and fracture management of tibia. Different values of tibial torsion have been found in different races due to biological and mechanical factors. Value of normal tibial torsion in Indian limbs is not known, hence this study to determine the norm of tibial torsional value in normal Indian population. Materials and Methods: Computer tomography (CT scans were performed in 100 non-arthritic limbs of 50 Indian adults (42 males, eight females; age 26-40 years. Value of tibial torsion was measured using dorsal tangent to tibial condyles proximally and bimalleolar axis distally. Results: Normal tibial torsion was found to be 21.6 ± 7.6 (range 4.8 to 39.5 with none of the values in internal rotation. Right tibia was externally rotated by 2 degrees as compared to the left side ( P 0.029. No significant difference was found in male and female subjects. Value of tibial torsion was less than in Caucasian limbs, but was comparable to Japanese limbs when studies using similar measurement technique were compared. Conclusions: Indian limbs have less tibial torsion than Caucasian limbs but the value of tibial torsion is comparable to Japanese limbs.

  3. Running coupling in electroweak interactions of leptons from f(R)-gravity with torsion

    International Nuclear Information System (INIS)

    Capozziello, Salvatore; De Laurentis, Mariafelicia; Fabbri, Luca; Vignolo, Stefano

    2012-01-01

    The f(R)-gravitational theory with torsion is considered for one family of leptons; it is found that the torsion tensor gives rise to interactions having the structure of the weak forces, while the intrinsic non-linearity of the f(R) function provides an energy-dependent coupling: in this way, torsional f(R) gravity naturally generates both structure and strength of the electroweak interactions among leptons. This implies that the weak interactions among the lepton fields could be addressed as a geometric effect due to the interactions among spinors induced by the presence of torsion in the most general f(R) gravity. Phenomenological considerations are given. (orig.)

  4. Unusual cause of acute abdominal pain in a postmenopausal woman: adnexal torsion

    Directory of Open Access Journals (Sweden)

    Alper Biler

    2016-03-01

    Full Text Available Adnexal torsion is an infrequent but significant cause of acute lower abdominal pain in women. While adnexal torsion is generally considered in premenopausal women presenting with acute abdominal pain and a pelvic mass, it is a rare cause of acute abdominal pain during postmenopausal period. The diagnosis of adnexal torsion is often challenging due to nonspesific clinical, laboratory and physical examination findings. Causes of adnexal torsion is also different in premenopausal and postmenopausal women. While a simple functional cyst is often the cause of torsion in premenopausal women, it is more rarely the cause in postmenopausal women. Adnexal torsion is a surgical emergency. The surgery of adnexal torsion is performed either via conventional exploratory laparotomy or laparoscopic surgery. Adnexal torsion in postmenopausal women should be considered not only in the setting of sudden onset pain, but also in long-term abdominal discomfort. In this article, we presented a case with adnexal torsion that rarely cause acute abdominal pain in postmenopausal women. [Cukurova Med J 2016; 41(1.000: 167-170

  5. The accuracy of serum interleukin-6 and tumour necrosis factor as markers for ovarian torsion.

    Science.gov (United States)

    Cohen, S B; Wattiez, A; Stockheim, D; Seidman, D S; Lidor, A L; Mashiach, S; Goldenberg, M

    2001-10-01

    The aim of this study was to investigate a possible role for interleukin-6 (IL-6) and tumour necrosis factor (TNF-alpha) as pre-operative markers for the diagnosis of ovarian torsion. Twenty consecutive patients admitted to the gynaecological emergency room with suspected clinical diagnosis of ovarian torsion were prospectively assigned to the study. Blood samples were drawn pre-operatively and examined for serum concentrations of IL-6 and TNF-alpha. Surgeons were blinded to laboratory results prior to laparoscopy. The pre-operative diagnosis of ovarian torsion was confirmed during an urgent diagnostic laparoscopy in 8 (40%) patients. The surgical diagnosis among the remaining 12 patients was a large ovarian cyst not in torsion. In six out of eight (75.0%) patients with ovarian torsion serum IL-6 concentrations were elevated. None of the 12 patients without torsion had elevated serum IL-6 concentrations. This difference was statistically significant (P < 0.001). There was no significant difference in the proportion of women with elevated serum TNF-alpha concentrations, two of eight (25.0%) patients with torsion and four of 12 (33.3%) control cases. Elevated serum IL-6 concentrations, but not serum TNF-alpha concentrations, were significantly associated with the occurrence of ovarian torsion. In patients with vague clinical signs of ovarian torsion, serum IL-6 might help to distinguish which patients should undergo diagnostic laparoscopy.

  6. Isolated torsion of fallopian tube in a post-menopausal patient: a case report.

    Science.gov (United States)

    Ozgun, Mahmut Tuncay; Batukan, Cem; Turkyilmaz, Cagdas; Serin, Ibrahim Serdar

    2007-07-20

    Isolated fallopian tube torsion after menopause is a rare condition. Here we report the second case of isolated fallopian tube torsion in a post-menopausal woman. A 55-year-old post-menopausal woman presented with right lower abdominal pain. Sonography depicted a simple cystic mass adjacent to the right uterine border. Laparatomy revealed torsion of the right fallopian tube together with a paraovarian cyst. Total abdominal hysterectomy and bilateral salpingo-oophorectomy was performed. Histopathological examination revealed a simple paraovarian cyst with severe congestion, necrosis and hemorrhage. Tubal torsion should be considered in the differential diagnosis of acute lower abdominal pain, even in post-menopausal women.

  7. Acute torsion and ischemia of the appendix in a young child

    Directory of Open Access Journals (Sweden)

    Dhruvin H. Hirpara

    2018-04-01

    Full Text Available Torsion of the vermiform appendix is a rare diagnosis; its clinical and radiographic presentation can mimic that of acute appendicitis. We report the case of a two-year-old boy presenting with a one day history of lower abdominal pain and serial ultrasound examinations suspicious for atypical acute appendicitis. Operative findings revealed a necrotic and engorged appendix with a 720° clockwise torsion at its base. Final pathology was consistent with ischemic necrosis in the setting of lymphoid hyperplasia. A brief update on the current body of literature regarding pediatric torsion of the vermiform appendix is provided. Keywords: Appendicitis, Volvulus, Torsion

  8. A Rare Cause of Scrotal Mass in a Newborn: Antenatal Intravaginal Testicular Torsion

    Directory of Open Access Journals (Sweden)

    Ahmet Ali Tuncer

    2018-04-01

    Full Text Available Intravaginal testicular torsion is a very rare pathology in the neonatal period. However, it is the most common type of torsion in puberty. In this article, we present a male patient with testicular hyperemia and a mass in the testis. Ultrasonography revealed intravaginal testicular torsion and absence of testicular blood flow. This paper aims to draw attention to the importance of neonatal examination for the presence of testicular torsion which is a rare pathology in newborns with scrotal colour change or presence of an abnormal mass.

  9. Mnn10 Maintains Pathogenicity in Candida albicans by Extending α-1,6-Mannose Backbone to Evade Host Dectin-1 Mediated Antifungal Immunity.

    Directory of Open Access Journals (Sweden)

    Shi Qun Zhang

    2016-05-01

    Full Text Available The cell wall is a dynamic structure that is important for the pathogenicity of Candida albicans. Mannan, which is located in the outermost layer of the cell wall, has been shown to contribute to the pathogenesis of C. albicans, however, the molecular mechanism by which this occurs remains unclear. Here we identified a novel α-1,6-mannosyltransferase encoded by MNN10 in C. albicans. We found that Mnn10 is required for cell wall α-1,6-mannose backbone biosynthesis and polysaccharides organization. Deletion of MNN10 resulted in significant attenuation of the pathogenesis of C. albicans in a murine systemic candidiasis model. Inhibition of α-1,6-mannose backbone extension did not, however, impact the invasive ability of C. albicans in vitro. Notably, mnn10 mutant restored the invasive capacity in athymic nude mice, which further supports the notion of an enhanced host antifungal defense related to this backbone change. Mnn10 mutant induced enhanced Th1 and Th17 cell mediated antifungal immunity, and resulted in enhanced recruitment of neutrophils and monocytes for pathogen clearance in vivo. We also demonstrated that MNN10 could unmask the surface β-(1,3-glucan, a crucial pathogen-associated molecular pattern (PAMP of C. albicans recognized by host Dectin-1. Our results demonstrate that mnn10 mutant could stimulate an enhanced Dectin-1 dependent immune response of macrophages in vitro, including the activation of nuclear factor-κB, mitogen-activated protein kinase pathways, and secretion of specific cytokines such as TNF-α, IL-6, IL-1β and IL-12p40. In summary, our study indicated that α-1,6-mannose backbone is critical for the pathogenesis of C. albicans via shielding β-glucan from recognition by host Dectin-1 mediated immune recognition. Moreover, our work suggests that inhibition of α-1,6-mannose extension by Mnn10 may represent a novel modality to reduce the pathogenicity of C. albicans.

  10. Analysis of stationary availability factor of two-level backbone computer networks with arbitrary topology

    Science.gov (United States)

    Rahman, P. A.

    2018-05-01

    This scientific paper deals with the two-level backbone computer networks with arbitrary topology. A specialized method, offered by the author for calculation of the stationary availability factor of the two-level backbone computer networks, based on the Markov reliability models for the set of the independent repairable elements with the given failure and repair rates and the methods of the discrete mathematics, is also discussed. A specialized algorithm, offered by the author for analysis of the network connectivity, taking into account different kinds of the network equipment failures, is also observed. Finally, this paper presents an example of calculation of the stationary availability factor for the backbone computer network with the given topology.

  11. Impact of Backbone Fluorination on π-Conjugated Polymers in Organic Photovoltaic Devices: A Review

    Directory of Open Access Journals (Sweden)

    Nicolas Leclerc

    2016-01-01

    Full Text Available Solution-processed bulk heterojunction solar cells have experienced a remarkable acceleration in performances in the last two decades, reaching power conversion efficiencies above 10%. This impressive progress is the outcome of a simultaneous development of more advanced device architectures and of optimized semiconducting polymers. Several chemical approaches have been developed to fine-tune the optoelectronics and structural polymer parameters required to reach high efficiencies. Fluorination of the conjugated polymer backbone has appeared recently to be an especially promising approach for the development of efficient semiconducting polymers. As a matter of fact, most currently best-performing semiconducting polymers are using fluorine atoms in their conjugated backbone. In this review, we attempt to give an up-to-date overview of the latest results achieved on fluorinated polymers for solar cells and to highlight general polymer properties’ evolution trends related to the fluorination of their conjugated backbone.

  12. Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers.

    Science.gov (United States)

    Iadevaia, Giulia; Núñez-Villanueva, Diego; Stross, Alexander E; Hunter, Christopher A

    2018-06-06

    Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

  13. Protein oxidation and peroxidation

    DEFF Research Database (Denmark)

    Davies, Michael Jonathan

    2016-01-01

    Proteins are major targets for radicals and two-electron oxidants in biological systems due to their abundance and high rate constants for reaction. With highly reactive radicals damage occurs at multiple side-chain and backbone sites. Less reactive species show greater selectivity with regard...... to the residues targeted and their spatial location. Modification can result in increased side-chain hydrophilicity, side-chain and backbone fragmentation, aggregation via covalent cross-linking or hydrophobic interactions, protein unfolding and altered conformation, altered interactions with biological partners...... and modified turnover. In the presence of O2, high yields of peroxyl radicals and peroxides (protein peroxidation) are formed; the latter account for up to 70% of the initial oxidant flux. Protein peroxides can oxidize both proteins and other targets. One-electron reduction results in additional radicals...

  14. Polyolefin backbone substitution in binders for low temperature powder injection moulding feedstocks.

    Science.gov (United States)

    Hausnerova, Berenika; Kuritka, Ivo; Bleyan, Davit

    2014-02-27

    This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al₂O₃ feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions containing polyethylene glycol as the initial opening agent and governing the proper mechanism of the degradation process. Moreover, the replacement of synthetic polymer by the natural wax contributes to an increase of environmental sustainability of modern industrial technologies.

  15. Polyolefin Backbone Substitution in Binders for Low Temperature Powder Injection Moulding Feedstocks

    Directory of Open Access Journals (Sweden)

    Berenika Hausnerova

    2014-02-01

    Full Text Available This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al2O3 feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions containing polyethylene glycol as the initial opening agent and governing the proper mechanism of the degradation process. Moreover, the replacement of synthetic polymer by the natural wax contributes to an increase of environmental sustainability of modern industrial technologies.

  16. Electric field induced localization phenomena in a ladder network with superlattice configuration: Effect of backbone environment

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Paramita; Karmakar, S. N. [Condensed Matter Physics Division, Saha Institute of Nuclear Physics, Sector-I, Block-AF, Bidhannagar, Kolkata-700 064 (India); Maiti, Santanu K., E-mail: santanu.maiti@isical.ac.in [Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 Barrackpore Trunk Road, Kolkata-700 108 (India)

    2014-09-15

    Electric field induced localization properties of a tight-binding ladder network in presence of backbone sites are investigated. Based on Green's function formalism we numerically calculate two-terminal transport together with density of states for different arrangements of atomic sites in the ladder and its backbone. Our results lead to a possibility of getting multiple mobility edges which essentially plays a switching action between a completely opaque to fully or partly conducting region upon the variation of system Fermi energy, and thus, support in fabricating mesoscopic or DNA-based switching devices.

  17. Five Principles of Industrialized Transformation for Successfully Building an Operational Backbone

    DEFF Research Database (Denmark)

    Winkler, Till J.; Kettunen, Petteri

    2018-01-01

    approach that is underpinned by five principles—template-based, business-driven, matrix-organized, tight supplier steering and cascaded planning. The UPM case provides important lessons for transformation leaders seeking to build, expand or develop a value-adding operational backbone.......To move into the digital age, a globally operating company needs to have in place an operational backbone, but many struggle with achieving this and the associated transformation program. Based on the experience of UPM, a Finnish forest industry company, we describe an industrialized transformation...

  18. Protein and peptide alkoxyl radicals can give rise to C-terminal decarboxylation and backbone cleavage

    DEFF Research Database (Denmark)

    Davies, Michael Jonathan

    1996-01-01

    Previous studies have demonstrated that gamma-irradiation of some free amino acids in the presence of oxygen gives high yields of side-chain hydroperoxides. It is shown in the present study that N-acetyl amino acids and peptides also give high levels of hydroperoxides on gamma-irradiation, even...

  19. [The functional sport shoe parameter "torsion" within running shoe research--a literature review].

    Science.gov (United States)

    Michel, F I; Kälin, X; Metzger, A; Westphal, K; Schweizer, F; Campe, S; Segesser, B

    2009-12-01

    Within the sport shoe area torsion is described as the twisting and decoupling of the rear-, mid- and forefoot along the longitudinal axis of the foot. Studies have shown that running shoes restrict the torsion of the foot and thus they increase the pronation of the foot. Based on the findings, it is recommended to design running shoes, which allow the natural freedom of movement of the foot. The market introduction of the first torsion concept through adidas(R) took place in 1989. Independently of the first market introduction, only one epidemiological study was conducted in the running shoe area. The study should investigate the occurrence of Achilles tendon problems of the athletes running in the new "adidas Torsion(R) shoes". However, further studies quantifying the optimal region of torsionability concerning the reduction of injury incidence are still missing. Newer studies reveal that the criterion torsion only plays a secondary roll regarding the buying decision. Moreover, athletes are not able to perceive torsionability as a discrete functional parameter. It is to register, that several workgroups are dealing intensively with the detailed analysis of the foot movement based on kinematic multi-segment-models. However, scientific as well as popular scientific contributions display that the original idea of the torsion concept is still not completely understood. Hence, the "inverse" characteristic is postulated. The present literature review leads to the deduction that the functional characteristics of the torsion concept are not fully implemented within the running shoe area. This implies the necessity of scientific studies, which investigate the relevance of a functional torsion concept regarding injury prevention based on basic and applied research. Besides, biomechanical studies should analyse systematically the mechanism and the effects of torsion relevant technologies and systems.

  20. The model of the relativistic particle with torsion

    International Nuclear Information System (INIS)

    Plyushchay, M.S.

    1991-01-01

    The model of the relativistic particle with torsion, whose action appears in the Bose-Fermi transmutation mechanism, is canonically quantized in the Minkowski and euclidean spaces. In the Minkowski space there are massive, massless and tachyonic states in the spectrum of the model. In the massive sector the spectrum contains an infinite number of states, whose spin can take integer, half-integer, or fractional values. In the euclidean space, the spectrum is finite and the spin can only be integer, or half-integer. The reasons for the differences of the quantum theory of the model in the two spaces are elucidated. (orig.)

  1. Electromagnetic calibration system for sub-micronewton torsional thrust stand

    Science.gov (United States)

    Lam, J. K.; Koay, S. C.; Cheah, K. H.

    2017-12-01

    It is critical for a micropropulsion system to be evaluated. Thrust stands are widely recognised as the instrument to complete such tasks. This paper presents the development of an alternative electromagnetic calibration technique for thrust stands. Utilising the commercially made voice coils and permanent magnets, the proposed system is able to generate repeatable and also consistent steady-state calibration forces at over four orders of magnitude (30 - 23000 μN). The system is then used to calibrate a custom-designed torsional thrust stand, where its inherent ability in ease of setup is well demonstrated.

  2. Experimental and numerical research on forging with torsion

    Science.gov (United States)

    Petrov, Mikhail A.; Subich, Vadim N.; Petrov, Pavel A.

    2017-10-01

    Increasing the efficiency of the technological operations of blank production is closely related to the computer-aided technologies (CAx). On the one hand, the practical result represents reality exactly. On the other hand, the development procedure of new process development demands unrestricted resources, which are limited on the SMEs. The tools of CAx were successfully applied for development of new process of forging with torsion and result analysis as well. It was shown, that the theoretical calculations find the confirmation both in praxis and during numerical simulation. The mostly used constructional materials were under study. The torque angles were stated. The simulated results were evaluated by experimental procedure.

  3. The evolution of space curves by curvature and torsion

    International Nuclear Information System (INIS)

    Richardson, G; King, J R

    2002-01-01

    We apply Lie group based similarity methods to the study of a new, and widely relevant, class of objects, namely motions of a space curve. In particular, we consider the motion of a curve evolving with a curvature κ and torsion τ dependent velocity law. We systematically derive the Lie point symmetries of all such laws of motion and use these to catalogue all their possible similarity reductions. This calculation reveals special classes of law with high degrees of symmetry (and a correspondingly large number of similarity reductions). Of particular note is one class which is invariant under general linear transformations in space. This has potential applications in pattern and signal recognition

  4. Validation of an Automated Torsional and Warping Stress Analysis Program

    Science.gov (United States)

    1992-08-19

    AT ftA NC[ VIPS’ Af $UPP69T ds (ZqOoo x,~)(23.6 ui7)( .000012433) 127672 P~s Af .SL Cq6"): dws (2qOOC KcI)(21Ci;)2)G-.OOOQQ 3623):’ -2uqO KSI AT M~C...TORSIONAL ,’KMENT .50000000 ENDING AT 1,2.04000 FMD • LE3 END PHIZ .00)OOE+00 PHI: .o0000Eo0f PHI2: .38240E-04 PHI3: -. 33�E-05 I"OR. SHR. WEL

  5. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard; Gao, Xin; Li, Ming

    2012-01-01

    Background: Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule's introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening.Results: We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.Conclusions: Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. 2012 Jang et al.; licensee BioMed Central Ltd.

  6. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2012-03-21

    Background: Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening.Results: We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.Conclusions: Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. 2012 Jang et al.; licensee BioMed Central Ltd.

  7. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

  8. Effect of cyclic torsional preloading on cyclic fatigue resistance of ProTaper Next and Mtwo nickel–titanium instruments

    Directory of Open Access Journals (Sweden)

    Eugenio Pedullà

    2015-06-01

    Conclusions: Torsional preloads reduced the cyclic fatigue resistance of M-wire and conventional (as ProTaper Next and Mtwo NiTi rotary instruments except for Mtwo with 25% or 50% of torsional preloading.

  9. Asymmetric magnetoimpedance in amorphous microwires due to bias current: Effect of torsional stress

    International Nuclear Information System (INIS)

    Buznikov, N.A.; Antonov, A.S.; Granovsky, A.B.

    2014-01-01

    The influence of torsional stress on the asymmetric magnetoimpedance in a glass-coated negative magnetostrictive amorphous microwire due to bias current is studied theoretically. The longitudinal and off-diagonal impedance components are found assuming a simplified spatial distribution of the magnetoelastic anisotropy induced by the torsional stress. The asymmetry in the field dependence of the impedance components is attributed to the combination of the circular magnetic field produced by the bias current and a helical anisotropy induced by the torsional stress. The asymmetry in the magnetoimpedance and the low-field hysteresis are analyzed as a function of the bias current and torsional stress. It is shown that the application of torsional stress significantly changes the value of the bias current required to suppress the hysteresis effect. The results obtained may be useful for applications in magnetic-field and stress sensors. - Highlights: • Effects of torsional stress on magnetoimpedance in amorphous microwire are studied. • Asymmetry in magnetoimpedance is analyzed as a function of bias current and stress. • Torsional stress changes the anisotropy and effects on the microwire impedance. • Field-dependence of impedance is anhysteretic when bias current exceeds threshold value. • Threshold bias current can be tuned by the application of torsional stress

  10. Asymmetric magnetoimpedance in amorphous microwires due to bias current: Effect of torsional stress

    Energy Technology Data Exchange (ETDEWEB)

    Buznikov, N.A., E-mail: n_buznikov@mail.ru [Scientific-Research Institute of Natural Gases and Gas Technologies – GAZPROM VNIIGAZ, Razvilka, Leninsky District, Moscow Region 142717 (Russian Federation); Antonov, A.S. [Institute for Theoretical and Applied Electrodynamics, Russian Academy of Sciences, Moscow 125412 (Russian Federation); Granovsky, A.B. [Faculty of Physics, M.V. Lomonosov Moscow State University, Moscow 119992 (Russian Federation)

    2014-04-15

    The influence of torsional stress on the asymmetric magnetoimpedance in a glass-coated negative magnetostrictive amorphous microwire due to bias current is studied theoretically. The longitudinal and off-diagonal impedance components are found assuming a simplified spatial distribution of the magnetoelastic anisotropy induced by the torsional stress. The asymmetry in the field dependence of the impedance components is attributed to the combination of the circular magnetic field produced by the bias current and a helical anisotropy induced by the torsional stress. The asymmetry in the magnetoimpedance and the low-field hysteresis are analyzed as a function of the bias current and torsional stress. It is shown that the application of torsional stress significantly changes the value of the bias current required to suppress the hysteresis effect. The results obtained may be useful for applications in magnetic-field and stress sensors. - Highlights: • Effects of torsional stress on magnetoimpedance in amorphous microwire are studied. • Asymmetry in magnetoimpedance is analyzed as a function of bias current and stress. • Torsional stress changes the anisotropy and effects on the microwire impedance. • Field-dependence of impedance is anhysteretic when bias current exceeds threshold value. • Threshold bias current can be tuned by the application of torsional stress.

  11. Contribution of the otoliths to the human torsional vestibulo-ocular reflex

    NARCIS (Netherlands)

    Groen, Eric; Bos, Jelte E.; De Graaf, Bernd

    1999-01-01

    The dynamic contribution of the otolith organs to the human ocular torsion response was examined during passive sinusoidal body roll about an earth-horizontal axis (varying otolith inputs) and about an earth-vertical axis (invariant otolith inputs). Torsional eye movements were registered in 5

  12. Torsion of the fallopian the mimicking appendicitis in a pregnant woman

    International Nuclear Information System (INIS)

    Tapia-Vine, M.; Pedrosa, I.; Escribano, N.

    2000-01-01

    Isolated torsion of the fallopian tube is an uncommon entity. Given the difficulties involved in the preoperative diagnosis, the ultrasound findings characteristic of this anomaly are not widely known. We present a case of tubal torsion associated with a cyst, describing the ultrasound images in our case and those reported in the literature. (Author) 18 refs

  13. Brans-Dicke theory in general space-time with torsion

    International Nuclear Information System (INIS)

    Kim, S.

    1986-01-01

    The Brans-Dicke theory in the general space-time endowed with torsion is investigated. Since the gradient of the scalar field as well as the intrinsic spin generate the torsion field, the interaction term of the spin-scalar field appears in the wave equation. The equations of motion are satisfied with the conservation laws

  14. Open string fluctuations in AdS space with and without torsion

    DEFF Research Database (Denmark)

    Larsen, A.L.; Lomholt, Michael Andersen

    2003-01-01

    The equations of motion and boundary conditions for the fluctuations around a classical open string, in a curved space-time with torsion, are considered in compact and world-sheet covariant form. The rigidly rotating open strings in anti-de Sitter space with and without torsion are investigated...

  15. Should Torsion Balance Technique Continue to be Taught to Pharmacy Students?

    Science.gov (United States)

    Bilger, Rhonda; Chereson, Rasma; Salama, Noha Nabil

    2017-06-01

    Objective. To determine the types of balances used in compounding pharmacies: torsion or digital. Methods. A survey was mailed to the pharmacist-in-charge at 698 pharmacies, representing 47% of the pharmacies in Missouri as of July 2013. The pharmacies were randomly selected and stratified by region into eight regions to ensure a representative sample. Information was gathered regarding the type and use of balances and pharmacists' perspectives on the need to teach torsion balance technique to pharmacy students. Results. The response rate for the survey was 53.3%. Out of the total responses received, those pharmacies having a torsion balance, digital balance or both were 46.8%, 27.4% and 11.8%, respectively. About 68.3% of respondents compound prescriptions. The study showed that 52% of compounding pharmacies use torsion balances in their practice. Of those with a balance in their pharmacy, 65.6% favored continuation of torsion balance instruction. Conclusions. Digital balances have become increasingly popular and have replaced torsion balances in some pharmacies, especially those that compound a significant number of prescriptions. The results of this study indicate that torsion balances remain integral to compounding practice. Therefore, students should continue being taught torsion balance technique at the college.

  16. Uterine Torsion in a West African Dwarf Ewe in Ibadan, Nigeria ...

    African Journals Online (AJOL)

    Keywords: Uterine torsion, West African Dwarf Ewe, Ibadan A case of uterine torsion in a 21/2 year old pluriparous West Africa Dwarf (WAD) ewe raised semi intensively with adequate veterinary care before the death of the dam and the lamb is presented. The dam had been off feed for 3 days and was found straining a night ...

  17. Theory of pure rotational transitions in doubly degenerate torsional states of ethane

    Science.gov (United States)

    Rosenberg, A.; Susskind, J.

    1979-01-01

    It is shown that pure rotational transitions in doubly degenerate torsional states of C2H6 (with selection rules Delta K = 0, plus or minus 1) are made allowed by Coriolis interaction between torsion and dipole-allowed vibrations. Expressions are presented for integrated intensities from which strengths of lines in the millimeter region can be calculated.

  18. Numerical Investigation of Damping of Torsional Beam Vibrations by Viscous Bimoments

    DEFF Research Database (Denmark)

    Hoffmeyer, David; Høgsberg, Jan Becker

    2017-01-01

    Damping of torsional beam vibrations of slender beam–structures with thin–walled cross–sections is investigated. Analytical results from solving the differential equation governing torsion with viscous bimoments imposed at the boundary, are compared with a numerical approach with three...

  19. Humeral torsion revisited: a functional and ontogenetic model for populational variation.

    Science.gov (United States)

    Cowgill, Libby W

    2007-12-01

    Anthropological interest in humeral torsion has a long history, and several functional explanations for observed variation in the orientation of the humeral head have been proposed. Recent clinical studies have revived this topic by linking patterns of humeral torsion to habitual activities such as overhand throwing. However, the precise functional implications and ontogenetic history of humeral torsion remain unclear. This study examines the ontogeny of humeral torsion in a large sample of primarily immature remains from six different skeletal collections (n = 407). The results of this research confirm that humeral torsion displays consistent developmental variation within all populations of growing children; neonates display relatively posteriorly oriented humeral heads, and the level of torsion declines steadily into adulthood. As in adults, variation in the angle of humeral torsion in immature individuals varies by population, and these differences arise early in development. However, when examined in the context of the developing muscles of the shoulder complex, it becomes apparent that variation in the angle of humeral torsion is not necessarily related to specific habitual activities. Variability in this feature is more likely caused by a generalized functional imbalance between muscles of medial and lateral rotation that can be produced by a wide variety of upper limb activity patterns during growth. (c) 2007 Wiley-Liss, Inc.

  20. Torsion zero-cycles and the Abel-Jacobi map over the real numbers

    NARCIS (Netherlands)

    Hamel, J. van

    1999-01-01

    This is a study of the torsion in the Chow group of zero-cycles on a variety over the real numbers. The first section recalls important results from the literature. The rest of the paper is devoted to the study of the Abel–Jacobi map a: A0XAlbXR restricted to torsion subgroups. Using Roitman’s

  1. Numerical Analysis on Variation of Dynamic Response of Girder Bridges with Torsional Reinforcement Panels

    Directory of Open Access Journals (Sweden)

    Kang Jae-Yoon

    2015-01-01

    Full Text Available The dynamic flexural behaviour of the railway bridge is influenced by its torsional behaviour. Especially, in the case of girder railway bridges, the dynamic response tends to amplify when the natural frequency in flexure (1st vibration mode is close to that in torsion (2nd vibration mode. In order to prevent such situation, it is necessary to adopt a flexural-to-torsional natural frequency ratio larger than 120%. This study proposes a solution shifting the natural frequency in torsion to high frequency range and restraining torsion by installing concrete panels on the bottom flange of the girder so as to prevent the superposition of the responses in the girder bridge. The applicability of this solution is examined by finite element analysis of the shift of the torsional natural frequency and change in the dynamic response according to the installation of the concrete panels. The analytical results for a 30 m-span girder railway bridge indicate that installing the concrete panels increases the natural frequency in torsion by restraining the torsional behaviour and reduces also the overall dynamic response. It is seen that the installation of 100 mm-thick concrete panels along a section of 4 m at both extremities of the girder can reduce the dynamic response by more than 30%.

  2. Study on reinforced lightweight coconut shell concrete beam behavior under torsion

    International Nuclear Information System (INIS)

    Gunasekaran, K.; Ramasubramani, R.; Annadurai, R.; Prakash Chandar, S.

    2014-01-01

    Highlights: • Use of coconut shell as aggregate in concrete production. • Behavior of coconut shell concrete under torsion. • Pre and post cracking behavior and analysis. • Torsional reinforcement and ductility. • Crack width and stiffness. - Abstract: This research investigates and evaluates the results of coconut shell concrete beams subjected to torsion and compared with conventional concrete beams. Eight beams, four with coconut shell concrete and four with conventional concrete were fabricated and tested. Study includes the general cracking characteristics, pre cracking behavior and analysis, post cracking behavior and analysis, minimum torsional reinforcement, torsional reinforcement, ductility, crack width and stiffness. It was observed that the torsional behavior of coconut shell concrete is comparable to that of conventional concrete. Compare to ACI prediction, equation suggested by Macgregor is more conservative in calculating cracking torsional resistance. But for the calculation of ultimate torque strength ACI prediction is more conservative compared to the equation suggested by Macgregor. Indian standard is also conservative in this regard, but it was under estimated compared to ACI and Macgregor equations. Minimum torsional reinforcement in beams is necessary to ensure that the beam do not fail at cracking. Compared to conventional concrete specimens, coconut shell concrete specimens have more ductility. Crack width at initial cracking torque for both conventional and coconut shell concrete with corresponding reinforcement ratios is almost similar

  3. Assignment by Negative-Ion Electrospray Tandem Mass Spectrometry of the Tetrasaccharide Backbones of Monosialylated Glycans Released from Bovine Brain Gangliosides

    Science.gov (United States)

    Chai, Wengang; Zhang, Yibing; Mauri, Laura; Ciampa, Maria G.; Mulloy, Barbara; Sonnino, Sandro; Feizi, Ten

    2018-05-01

    Gangliosides, as plasma membrane-associated sialylated glycolipids, are antigenic structures and they serve as ligands for adhesion proteins of pathogens, for toxins of bacteria, and for endogenous proteins of the host. The detectability by carbohydrate-binding proteins of glycan antigens and ligands on glycolipids can be influenced by the differing lipid moieties. To investigate glycan sequences of gangliosides as recognition structures, we have underway a program of work to develop a "gangliome" microarray consisting of isolated natural gangliosides and neoglycolipids (NGLs) derived from glycans released from them, and each linked to the same lipid molecule for arraying and comparative microarray binding analyses. Here, in the first phase of our studies, we describe a strategy for high-sensitivity assignment of the tetrasaccharide backbones and application to identification of eight of monosialylated glycans released from bovine brain gangliosides. This approach is based on negative-ion electrospray mass spectrometry with collision-induced dissociation (ESI-CID-MS/MS) of the desialylated glycans. Using this strategy, we have the data on backbone regions of four minor components among the monosialo-ganglioside-derived glycans; these are of the ganglio-, lacto-, and neolacto-series.

  4. Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

    Czech Academy of Sciences Publication Activity Database

    Kruse, H.; Mládek, Arnošt; Gkionis, Konstantinos; Hansen, A.; Grimme, S.; Šponer, Jiří

    2015-01-01

    Roč. 11, č. 10 (2015), s. 4972-4991 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DENSITY-FUNCTIONAL THEORY * SUGAR-PHOSPHATE BACKBONE Subject RIV: BO - Biophysics Impact factor: 5.301, year: 2015

  5. Comparing the Reliability of Regular Topologies on a Backbone Network. A Case Study

    DEFF Research Database (Denmark)

    Cecilio, Sergio Labeage; Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir

    2009-01-01

    The aim of this paper is to compare the reliability of regular topologies on a backbone network. The study is focused on a large-scale fiberoptic network. Different regular topological solutions as single ring, double ring or 4-Regular grid are applied to the case study, and compared in terms...

  6. Directional virtual backbone based data aggregation scheme for Wireless Visual Sensor Networks.

    Science.gov (United States)

    Zhang, Jing; Liu, Shi-Jian; Tsai, Pei-Wei; Zou, Fu-Min; Ji, Xiao-Rong

    2018-01-01

    Data gathering is a fundamental task in Wireless Visual Sensor Networks (WVSNs). Features of directional antennas and the visual data make WVSNs more complex than the conventional Wireless Sensor Network (WSN). The virtual backbone is a technique, which is capable of constructing clusters. The version associating with the aggregation operation is also referred to as the virtual backbone tree. In most of the existing literature, the main focus is on the efficiency brought by the construction of clusters that the existing methods neglect local-balance problems in general. To fill up this gap, Directional Virtual Backbone based Data Aggregation Scheme (DVBDAS) for the WVSNs is proposed in this paper. In addition, a measurement called the energy consumption density is proposed for evaluating the adequacy of results in the cluster-based construction problems. Moreover, the directional virtual backbone construction scheme is proposed by considering the local-balanced factor. Furthermore, the associated network coding mechanism is utilized to construct DVBDAS. Finally, both the theoretical analysis of the proposed DVBDAS and the simulations are given for evaluating the performance. The experimental results prove that the proposed DVBDAS achieves higher performance in terms of both the energy preservation and the network lifetime extension than the existing methods.

  7. Treatment Results of Injuries of Thoracic and Lumbar Backbone Departments at Osteoporosis Patients

    Directory of Open Access Journals (Sweden)

    D.Y. Sumin

    2009-06-01

    Full Text Available Information relates to radiologic (computer tomography manifestations providing the visualization of thoracic and lumbar backbone department injuries at osteoporotic patients. Contemporary methods of transcutaneous and trans-pedicle vertebroplasty with bone cement allows to obtain a stable positive healing effect against such pathologies.

  8. SEVA Linkers: A Versatile and Automatable DNA Backbone Exchange Standard for Synthetic Biology

    DEFF Research Database (Denmark)

    Kim, Se Hyeuk; Cavaleiro, Mafalda; Rennig, Maja

    2016-01-01

    flexibility, and different researchers prefer and master different molecular technologies. Here, we describe a new, highly versatile and automatable standard “SEVA linkers” for vector exchange. SEVA linkers enable backbone swapping with 20 combinations of classical enzymatic restriction/ligation, Gibson...

  9. Integrative technology of massage manipulations in physical rehabilitation of students with backbone pathology

    Directory of Open Access Journals (Sweden)

    V.I. Kotelevskiy

    2016-06-01

    Full Text Available Purpose:to analyze effectiveness of massage manipulations’ integrative technology in physical rehabilitation of higher educational establishments’ students with backbone pathology. Material: in the research 195 students of 19-20 years’ age participated. All students had periodical initial neurological symptoms of functional pathology and first stage osteochondrosis in different parts of backbone. We conducted a course of 10 sessions of therapeutic massage. Results: the sense of massage integrative technology is that every specialist shall have certain optimal set of skills and knowledge in technique of manipulation sessions of massage. Integrative technology of massage manipulations consists of psycho-corrective and manipulation parts. It considers psycho-somatic, mechanical and reflex rehabilitation aspects of patho-genesis of backbone functional disorders and vertebral osteochondrosis. Conclusions: depending on pathological process or backbone functional state of every person (peculiarities of his (her psycho-somatic status or, even, his (her bents. Individual approach in choice of strategy, tactic and methodological provisioning of massage session shall be used.

  10. Influence of structures of polymer backbones on cooperative photoreorientation behavior of p-cyanoazobenzene side chains

    DEFF Research Database (Denmark)

    Han, Mina; Kidowaki, Masatoshi; Ichimura, Kunihiro

    2001-01-01

    Photoinduced orientational behavior of a polymethacrylate (CN6) and a polyester (p6a12) with p-cyanoazobenzene side chains was studied to reveal the structural effect of the liquid crystalline polymer backbones. Irradiation with linearly polarized W light resulted in the reorientation of the azob...

  11. Acute abdomen due to primary omental torsion: case report.

    Science.gov (United States)

    Tsironis, Apostolos; Zikos, Nikolaos; Bali, Christina; Pappas-Gogos, George; Koulas, Spiridon; Katsamakis, Nikolaos

    2013-01-01

    Primary torsion of the greater omentum is an uncommon cause of acute abdominal pain that mainly affects adults in their fourth or fifth decade. It was first described by Eitel in 1899. Since then, more than 300 cases have been reported in the published literature. Clinical presentation and imaging findings are often of limited value in the diagnosis of primary omental torsion (POT). The patients usually undergo laparotomy for "acute appendicitis" or acute abdomen of poorly defined origin. To provide a detailed description of this rare cause of acute abdomen. We report a case of POT in a woman of reproductive age and discuss contemporary methods in diagnosis and management of the condition. Nowadays, laparoscopy is a safe and effective approach for the diagnosis and management of POT, with the advantages of reduced postoperative pain and hospital stay. Conservative management has also been advocated by some authors in selected patients with a preoperative diagnosis of POT based on computed tomography findings. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. Cosmology with torsion: An alternative to cosmic inflation

    International Nuclear Information System (INIS)

    Poplawski, Nikodem J.

    2010-01-01

    We propose a simple scenario which explains why our Universe appears spatially flat, homogeneous and isotropic. We use the Einstein-Cartan-Kibble-Sciama (ECKS) theory of gravity which naturally extends general relativity to include the spin of matter. The torsion of spacetime generates gravitational repulsion in the early Universe filled with quarks and leptons, preventing the cosmological singularity: the Universe expands from a state of minimum but finite radius. We show that the dynamics of the closed Universe immediately after this state naturally solves the flatness and horizon problems in cosmology because of an extremely small and negative torsion density parameter, Ω S ∼-10 -69 . Thus the ECKS gravity provides a compelling alternative to speculative mechanisms of standard cosmic inflation. This scenario also suggests that the contraction of our Universe preceding the bounce at the minimum radius may correspond to the dynamics of matter inside a collapsing black hole existing in another universe, which could explain the origin of the Big Bang.

  13. CT measurements of torsion and length in the lower extremities

    International Nuclear Information System (INIS)

    Waidelich, H.A.; Strecker, W.; Schneider, E.

    1992-01-01

    Complex corrective osteotomies in the lower extremities require precise preoperative planning. Fifty patients who had suffered fractures of the lower limbs and had been treated by osteosynthetic or conservative methods were studied, using a GE 9800 Quick CT; accurate and reproducible measurements of the angles of torsion of the femur and tibia were obtained. Digital images were produced to standardise the planes of measurement and to measure the length of the limb. The most important clinical measurement is the intra-individual difference of the torsional angles. Amongst normals this is 4.3 ± 2.3deg in the femur and 6.1 ± 4.5deg in the tibia. Radiation exposure was measured by a LiF-thermoluminescence dosimeter on an Alderson phantom. Skin dose was 6.3 ± 1.2 mGy and gonadal dose for females was 2.5 ± 0.3 mGy and for males 0.7 ± 0.1 mGy. (orig./GDG) [de

  14. Strengthening of Steel Columns under Load: Torsional-Flexural Buckling

    Directory of Open Access Journals (Sweden)

    Martin Vild

    2016-01-01

    Full Text Available The paper presents experimental and numerical research into the strengthening of steel columns under load using welded plates. So far, the experimental research in this field has been limited mostly to flexural buckling of columns and the preload had low effect on the column load resistance. This paper focuses on the local buckling and torsional-flexural buckling of columns. Three sets of three columns each were tested. Two sets corresponding to the base section (D and strengthened section (E were tested without preloading and were used for comparison. Columns from set (F were first preloaded to the load corresponding to the half of the load resistance of the base section (D. Then the columns were strengthened and after they cooled, they were loaded to failure. The columns strengthened under load (F had similar average resistance as the columns welded without preloading (E, meaning the preload affects even members susceptible to local buckling and torsional-flexural buckling only slightly. This is the same behaviour as of the tested columns from previous research into flexural buckling. The study includes results gained from finite element models of the problem created in ANSYS software. The results obtained from the experiments and numerical simulations were compared.

  15. A strain gradient plasticity theory with application to wire torsion

    KAUST Repository

    Liu, J. X.

    2014-06-05

    Based on the framework of the existing strain gradient plasticity theories, we have examined three kinds of relations for the plastic strain dependence of the material intrinsic length scale, and thus developed updated strain gradient plasticity versions with deformation-dependent characteristic length scales. Wire torsion test is taken as an example to assess existing and newly built constitutive equations. For torsion tests, with increasing plastic strain, a constant intrinsic length predicts too high a torque, while a decreasing intrinsic length scale can produce better predictions instead of the increasing one, different from some published observations. If the Taylor dislocation rule is written in the Nix-Gao form, the derived constitutive equations become singular when the hardening exponent gets close to zero, which seems questionable and calls for further experimental clarifications on the exact coupling of hardening due to statistically stored dislocations and geometrically necessary dislocations. Particularly, when comparing the present model with the mechanism-based strain gradient plasticity, the present model satisfies the reciprocity relation naturally and gives different predictions even under the same parameter setting. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  16. A MEMS torsion magnetic sensor with reflective blazed grating integration

    International Nuclear Information System (INIS)

    Long, Liang; Zhong, Shaolong

    2016-01-01

    A novel magnetic sensor based on a permanent magnet and blazed grating is presented in this paper. The magnetic field is detected by measuring the diffracted wavelength of the blazed grating which is changed by the torsion motion of a torsion sensitive micro-electromechanical system (MEMS) structure with a permanent magnet attached. A V-shape grating structure is obtained by wet etching on a (1 0 0) SOI substrate. When the magnet is magnetized in different directions, the in-plane or out-of-plane magnetic field is detected by a sensor. The MEMS magnetic sensor with a permanent magnet is fabricated after analytical design and bulk micromachining processes. The magnetic-sensing capability of the sensor is tested by fiber-optic detection system. The result shows the sensitivities of the in-plane and out-of-plane magnetic fields are 3.6 pm μ T −1 and 5.7 pm μ T −1 , respectively. Due to utilization of the permanent magnet and fiber-optic detection, the sensor shows excellent capability of covering the high-resolution detection of low-frequency signals. In addition, the sensitive direction of the magnetic sensor can be easily switched by varying the magnetized direction of the permanent magnet, which offers a simple way to achieve tri-axis magnetic sensor application. (paper)

  17. Acute gallbladder torsion - a continued pre-operative diagnostic dilemma

    Directory of Open Access Journals (Sweden)

    Desrochers Randal

    2011-04-01

    Full Text Available Abstract Acute gallbladder volvulus continues to remain a relatively uncommon process, manifesting itself usually during exploration for an acute surgical abdomen with a presumptive diagnosis of acute cholecystitis. The pathophysiology is that of mechanical organo-axial torsion along the gallbladder's longitudinal axis involving the cystic duct and cystic artery, and with a pre-requisite of local mesenteric redundancy. The demographic tendency is septua- and octo-genarians of the female sex, and its overall incidence is increasing, this being attributed to increasing life expectancy. We discuss two cases of elderly, fragile women presenting to the emergency department complaining of sudden onset right upper quadrant abdominal pain. Their subsequent evaluation suggested acute cholecystitis. Ultimately both were taken to the operating room where the correct diagnosis of gallbladder torsion was made. Pre-operative diagnosis continues to be a major challenge with only 4 cases reported in the literature diagnosed with pre-operative imaging; the remainder were found intra-operatively. Consequently, a delay in diagnosis can have devastating patient outcomes. Herein we propose a necessary high index of suspicion for gallbladder volvulus in the outlined patient demographic with symptoms and signs mimicking acute cholecystitis.

  18. Postoperative influences of the torsional phacoemulsification on foveal thickness and corneal edema

    Directory of Open Access Journals (Sweden)

    Lei Li

    2014-05-01

    Full Text Available AIM: To report the influences onfoveal thickness and corneal edema after torsional phacoemulsification.METHODS: Totally 52 patients(52 eyeswith age-related cataract were randomly assigned to phacoemulsification using torsional mode(26 eyesor conventional ultrasound mode(26 eyes. The foveal thickness examined by optical coherence tomography(OCTafter surgery at 1, 4 and 12wk and corneal edema was examined by slit lamp after surgery at 1d.RESULTS: The postoperative averagefoveal thickness datas of the two groups, comparing with corresponding preoperative datas, were significantly augmented at 1, 4 and 12wk(PPP>0.05. The effects of corneal edema in torsional group were slighter(PCONCLUSION: The postoperative influences onfoveal thickness and corneal edema with torsional mode are slighter than that with ultrasound mode, and the postoperative reactions with torsional mode are efficiently reduced.

  19. The physics of detecting torsion and placing limits on its effects

    International Nuclear Information System (INIS)

    Stoeger, W.R.

    1985-01-01

    The essential principles of torsion-detection physics are presented and several conceivable types of experiments and observations for actually detecting torsion fields are evaluated reemphasizing also the evident impossibility of successfully searching for its manifestations among cosmological relics. In particular, a polarized body, with net intrinsic (fundamental-particle) spin, is essential for detecting a torsion field. One which possesses only orbital angular momentum-rotation-or an unpolarized intrinsic spin density will not feel torsion. The fundamental problem in searching for such fields is the extremely small basic unit of the coupling or interaction energy between the torsion field and spin, epsilonapprox.(8πG'/c 2 )(h 2 /4). The best way of maximizing the total interaction energy is to increase the spin density of the source σ 5 and, at the same time the ''spin number'' Ssub(D) of the detector. (author)

  20. TEMPERATURE GRADIENTS IN THE SOLAR ATMOSPHERE AND THE ORIGIN OF CUTOFF FREQUENCY FOR TORSIONAL TUBE WAVES

    International Nuclear Information System (INIS)

    Routh, S.; Musielak, Z. E.; Hammer, R.

    2010-01-01

    Fundamental modes supported by a thin magnetic flux tube embedded in the solar atmosphere are typically classified as longitudinal, transverse, and torsional waves. If the tube is isothermal, then the propagation of longitudinal and transverse tube waves is restricted to frequencies that are higher than the corresponding global cutoff frequency for each wave. However, no such global cutoff frequency exists for torsional tube waves, which means that a thin and isothermal flux tube supports torsional tube waves of any frequency. In this paper, we consider a thin and non-isothermal magnetic flux tube and demonstrate that temperature gradients inside this tube are responsible for the origin of a cutoff frequency for torsional tube waves. The cutoff frequency is used to determine conditions for the wave propagation in the solar atmosphere, and the obtained results are compared to the recent observational data that support the existence of torsional tube waves in the Sun.

  1. Torsion of a nongravid uterus with a large ovarian cyst: usefulness of contrast MR image.

    Science.gov (United States)

    Matsumoto, Hiroki; Ohta, Tsuyoshi; Nakahara, Kenji; Kojimahara, Takanobu; Kurachi, Hirohisa

    2007-01-01

    Torsion of a nongravid uterus is extremely rare. Most cases of uterine torsion occur during pregnancy. Here we report a case of nongravid uterus torsion with a large adnexal mass. A 73-year-old woman presented at the emergency room with acute abdominal pain. A preoperative diagnosis of torsion of an ovarian cyst was made and laparotomy was performed. The left ovary was twisted 360 degrees in a clockwise rotation, and the uterine corpus had also undergone a 360 degrees rotation. Total abdominal hysterectomy and bilateral salpingo-oophorectomy were carried out. Although a preoperative diagnosis of uterine torsion was not possible, it is noteworthy that in the contrast-enhanced magnetic resonance images the uterine cervix was intensely enhanced, while the uterine corpus was not. This is the first report to show the magnetic resonance imaging findings of a twisted uterus. Copyright (c) 2007 S. Karger AG, Basel.

  2. Torsional Properties of TiNi Shape Memory Alloy Tape for Rotary Actuator

    Science.gov (United States)

    Takeda, K.; Tobushi, H.; Mitsui, K.; Nishimura, Y.; Miyamoto, K.

    2012-12-01

    In order to develop novel shape memory actuators, the torsional deformation of a shape memory alloy (SMA) tape and the actuator models driven by the tape were investigated. The results obtained can be summarized as follows. In the SMA tape subjected to torsion, the martensitic transformation appears along both edges of the tape due to elongation of these elements and grows to the central part. The fatigue life in both the pulsating torsion and alternating torsion is expressed by the unified relationship of the dissipated work in each cycle. Based on an opening and closing door model and a solar-powered active blind model, the two-way rotary driving actuator with a small and simple mechanism can be developed by using torsion of the SMA tape.

  3. Ionic polymer-metal composite torsional sensor: physics-based modeling and experimental validation

    Science.gov (United States)

    Aidi Sharif, Montassar; Lei, Hong; Khalid Al-Rubaiai, Mohammed; Tan, Xiaobo

    2018-07-01

    Ionic polymer-metal composites (IPMCs) have intrinsic sensing and actuation properties. Typical IPMC sensors are in the shape of beams and only respond to stimuli acting along beam-bending directions. Rod or tube-shaped IPMCs have been explored as omnidirectional bending actuators or sensors. In this paper, physics-based modeling is studied for a tubular IPMC sensor under pure torsional stimulus. The Poisson–Nernst–Planck model is used to describe the fundamental physics within the IPMC, where it is hypothesized that the anion concentration is coupled to the sum of shear strains induced by the torsional stimulus. Finite element simulation is conducted to solve for the torsional sensing response, where some of the key parameters are identified based on experimental measurements using an artificial neural network. Additional experimental results suggest that the proposed model is able to capture the torsional sensing dynamics for different amplitudes and rates of the torsional stimulus.

  4. Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching

    Directory of Open Access Journals (Sweden)

    Bron Peter A

    2012-09-01

    Full Text Available Abstract Background Specific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background. Results Through genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-κB reporter cells expressing Toll like receptor (TLR-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-α after stimulation with the WTA mutants as compared to the wild-type. Conclusions The study presented here correlates structural differences in WTA to their functional characteristics, thereby

  5. Markers of protein oxidation

    DEFF Research Database (Denmark)

    Headlam, Henrietta A; Davies, Michael Jonathan

    2004-01-01

    Exposure of proteins to radicals in the presence of O2 gives both side-chain oxidation and backbone fragmentation. These processes can be interrelated, with initial side-chain oxidation giving rise to backbone damage via transfer reactions. We have shown previously that alkoxyl radicals formed...... of this process depends on the extent of oxidation at C-3 compared with other sites. HO*, generated by gamma radiolysis, gave the highest total carbonyl yield, with protein-bound carbonyls predominating over released. In contrast, metal ion/H2O2 systems, gave more released than bound carbonyls, with this ratio...... modulated by EDTA. This is ascribed to metal ion-protein interactions affecting the sites of initial oxidation. Hypochlorous acid gave low concentrations of released carbonyls, but high yields of protein-bound material. The peroxyl radical generator 2,2'-azobis(2-amidinopropane) hydrochloride...

  6. Exact interior solutions for static spheres in the Einstein-Cartan theory with two sources of torsion

    CERN Document Server

    Gallakhmetov, A M

    2002-01-01

    In the framework of the problem of existence of exact interior solutions for static spherically symmetric configurations in the Einstein-Cartan theory (ECT), the distributions of perfect fluid and non-minimally coupled scalar field are considered. The exact solutions in the one-torsion ECT and two-torsion one are obtained. Some consequences of two sources of torsion are discussed.

  7. Rat disc torsional mechanics: effect of lumbar and caudal levels and axial compression load.

    Science.gov (United States)

    Espinoza Orías, Alejandro A; Malhotra, Neil R; Elliott, Dawn M

    2009-03-01

    Rat models with altered loading are used to study disc degeneration and mechano-transduction. Given the prominent role of mechanics in disc function and degeneration, it is critical to measure mechanical behavior to evaluate changes after model interventions. Axial compression mechanics of the rat disc are representative of the human disc when normalized by geometry, and differences between the lumbar and caudal disc have been quantified in axial compression. No study has quantified rat disc torsional mechanics. Compare the torsional mechanical behavior of rat lumbar and caudal discs, determine the contribution of combined axial load on torsional mechanics, and compare the torsional properties of rat discs to human lumbar discs. Cadaveric biomechanical study. Cyclic torsion without compressive load followed by cyclic torsion with a fixed compressive load was applied to rat lumbar and caudal disc levels. The apparent torsional modulus was higher in the lumbar region than in the caudal region: 0.081+/-0.026 (MPa/degrees, mean+/-SD) for lumbar axially loaded; 0.066+/-0.028 for caudal axially loaded; 0.091+/-0.033 for lumbar in pure torsion; and 0.056+/-0.035 for caudal in pure torsion. These values were similar to human disc properties reported in the literature ranging from 0.024 to 0.21 MPa/degrees. Use of the caudal disc as a model may be appropriate if the mechanical focus is within the linear region of the loading regime. These results provide support for use of this animal model in basic science studies with respect to torsional mechanics.

  8. The role of nonlinear torsional contributions on the stability of flexural-torsional oscillations of open-cross section beams

    Science.gov (United States)

    Di Egidio, Angelo; Contento, Alessandro; Vestroni, Fabrizio

    2015-12-01

    An open-cross section thin-walled beam model, already developed by the authors, has been conveniently simplified while maintaining the capacity of accounting for the significant nonlinear warping effects. For a technical range of geometrical and mechanical characteristics of the beam, the response is characterized by the torsional curvature prevailing over the flexural ones. A Galerkin discretization is performed by using a suitable expansion of displacements based on shape functions. The attention is focused on the dynamic response of the beam to a harmonic force, applied at the free end of the cantilever beam. The excitation is directed along the symmetry axis of the beam section. The stability of the one-component oscillations has been investigated using the analytical model, showing the importance of the internal resonances due to the nonlinear warping coupling terms. Comparison with the results provided by a computational finite element model has been performed. The good agreement among the results of the analytical and the computational models confirms the effectiveness of the simplified model of a nonlinear open-cross section thin-walled beam and overall the important role of the warping and of the torsional elongation in the study of the one-component dynamic oscillations and their stability.

  9. Lorentz violation bounds from torsion trace fermion sector and galaxy M51 data and chiral dynamos

    Energy Technology Data Exchange (ETDEWEB)

    Garcia de Andrade, L.C. [IF-UERJ, Departamento de Fisica Teorica, Rio de Janeiro, RJ (Brazil)

    2017-06-15

    Earlier we have computed a Lorentz violation (LV) bound for torsion terms via galactic dynamos and found bounds similar to the one obtained by Kostelecky et al. (Phys Rev Lett 100:111102, 2008) which is of the order of 10{sup -31} GeV. Their result was found making use of the axial torsion vector in terms of Dirac spinors and minimal torsion coupling in flat space-time of fermions. In this paper, a torsion dynamo equation obtained using the variation of the torsion trace and galaxy M51 data of 500 pc are used to place an upper bound of 10{sup -26} GeV in LV, which agrees with the one by Kostelecky and his group using an astrophysical framework background. Their lowest bound was obtained in earth laboratory using dual masers. One of the purposes of this paper is to apply the Faraday self-induction magnetic equation, recently extended to torsioned space-time, by the author to show that it lends support to physics in Riemann-Cartan space-time, in several distinct physical backgrounds. Backreaction magnetic effects are used to obtain the LV bounds. Previously Bamba et al. (JCAP 10:058, 2012) have used the torsion trace in their teleparallel investigation of the IGMF, with the argument that the torsion trace leads to less weaker effects than the other irreducible components of the torsion tensor. LV is computed in terms of a chiral-torsion-like current in the new dynamo equation analogous to the Dvornikov and Semikoz dynamo equation with chiral magnetic currents. Making use of the chiral-torsion dynamo equation we estimate the LV bounds in the early universe to be of the order of 10{sup -24} GeV, which was the order of the charged-lepton sector. Our main result is that it is possible to obtain more stringent bounds than the ones found in the fermion sector of astrophysics in the new revised 2017 data table for CPT and Lorentz violation by Kostelecky and Mewes. They found in several astrophysical backgrounds, orders of magnitude such as 10{sup -24} and 10{sup -23} Ge

  10. Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR

    International Nuclear Information System (INIS)

    Eddy, Matthew T.; Su, Yongchao; Silvers, Robert; Andreas, Loren; Clark, Lindsay; Wagner, Gerhard; Pintacuda, Guido; Emsley, Lyndon; Griffin, Robert G.

    2015-01-01

    The human voltage dependent anion channel 1 (VDAC) is a 32 kDa β-barrel integral membrane protein that controls the transport of ions across the outer mitochondrial membrane. Despite the determination of VDAC solution and diffraction structures, a structural basis for the mechanism of its function is not yet fully understood. Biophysical studies suggest VDAC requires a lipid bilayer to achieve full function, motivating the need for atomic resolution structural information of VDAC in a membrane environment. Here we report an essential step toward that goal: extensive assignments of backbone and side chain resonances for VDAC in DMPC lipid bilayers via magic angle spinning nuclear magnetic resonance (MAS NMR). VDAC reconstituted into DMPC lipid bilayers spontaneously forms two-dimensional lipid crystals, showing remarkable spectral resolution (0.5–0.3 ppm for 13 C line widths and <0.5 ppm 15 N line widths at 750 MHz). In addition to the benefits of working in a lipid bilayer, several distinct advantages are observed with the lipid crystalline preparation. First, the strong signals and sharp line widths facilitated extensive NMR resonance assignments for an integral membrane β-barrel protein in lipid bilayers by MAS NMR. Second, a large number of residues in loop regions were readily observed and assigned, which can be challenging in detergent-solubilized membrane proteins where loop regions are often not detected due to line broadening from conformational exchange. Third, complete backbone and side chain chemical shift assignments could be obtained for the first 25 residues, which comprise the functionally important N-terminus. The reported assignments allow us to compare predicted torsion angles for VDAC prepared in DMPC 2D lipid crystals, DMPC liposomes, and LDAO-solubilized samples to address the possible effects of the membrane mimetic environment on the conformation of the protein. Concluding, we discuss the strengths and weaknesses of the reported

  11. Transabdominal color doppler ultrasonography: A relevant approach for assessment of effects of uterine torsion in buffaloes

    Directory of Open Access Journals (Sweden)

    Devender

    2016-08-01

    Full Text Available Aim: The present study was conducted on advanced pregnant buffaloes suffering from uterine torsion to assess the status of fetus and uterus by transabdominal ultrasonography, and the findings were compared with normal advanced pregnant buffaloes. Materials and Methods: The study was conducted on 20 clinical cases of uterine torsion and 20 normal advanced pregnant buffaloes (control group. The lower ventral area just lateral to linea alba (on both sides of the udder in standing animals was scanned transabdominally by the two-dimensional convex transducer for various ultrasonographic findings. The data collected were statistically analyzed by “one-way ANOVA” and “independent sample t-test” using computerized SPSS 16.0 software program. Results: Transabdominal ultrasonography revealed dead fetus in 95% uterine torsion cases and proved useful in imaging internal structures of fetuses while no dead fetus was reported in the control group. Size of umbilicus was found significantly decreased (p0.05 in uterine torsion group. Average thickness of the uterine wall and mean pixel values of fetal fluids (echogenicity were found significantly increased (p<0.05 in uterine torsion affected buffaloes in comparison to control group. Conclusion: Status of fetus (whether live or dead, internal status of uterus, and its contents could be determined by transabdominal ultrasonography in uterine torsion cases and thus determining the prognosis of the uterine torsion cases before going for further manipulations. This will also help in taking all the precautions to avoid death of the fetus.

  12. Frequency-dependent solvent friction and torsional damping in liquid 1,2-difluoroethane

    Science.gov (United States)

    MacPhail, Richard A.; Monroe, Frances C.

    1991-04-01

    We have used Raman spectroscopy to study the torsional dynamics, rotational dynamics, and conformational solvation energy of liquid 1,2-difluoroethane. From the Raman intensities, we obtain Δ H(g-t) = -2.4±0.1 kcal/mol, indicating strong dipolar solvation of the gauche conformer. We analyze the Raman linewidths of the CCF bending bands to obtain the zero-frequency torsional damping coefficient or well friction for the gauche conformer, and from the linewidth of the torsion band we obtain the friction evaluated at the torsional frequency. The zero-frequency well friction shows deviations from hydrodynamic behavior reminiscent of those observed for barrier friction, whereas the high-frequency friction is considerably smaller in magnitude and independent of temperature and viscosity. The zero-frequency torsional friction correlates linearly with the rotational friction. It is argued that the small amplitude of the torsional fluctuations emphasizes the short distance, or high wavevector components of the solvent friction. Dielectric friction apparently does not contribute to the torsional friction at the observed frequencies.

  13. Plastic Behavior and Fracture of Aluminum and Copper in Torsion Tests

    International Nuclear Information System (INIS)

    Bressan, Jose Divo

    2007-01-01

    Present work investigates the plastic behavior, work hardening and the beginning of plastic instabilities, of cylindrical specimens deformed by high speed cold plastic torsion tests and at low speed tensile test. The tests were carried out in a laboratory torsion test equipment and an universal tensile test machine. The tensile tests were performed at room temperature in an universal testing machine at low strain rate of 0.034/s. Experimental torsion tests were carried out at constant angular speed that imposed a constant shear strain rate to the specimen. In the tests, the rotation speed were set to 62 rpm and 200 rpm which imposed high strain rates of about 2/s and 6.5/s respectively. The torsion tests performed at room temperature on annealed commercial pure copper and aluminum. Two types of torsion specimen for aluminum were used: solid and tubular. The solid aluminum specimen curves presented various points of maximum torque. The tubular copper specimens showed two points of maximum. Shear bands or shear strain localization at specimen were possibly the mechanism of maximum torque points formation. The work hardening coefficient n and the strain rate sensitivity parameter m were evaluated from the equivalent stress versus strain curve from tensile and torsion tests. The n-value remained constant whereas the m-value increased ten folds for aluminum specimens: from tensile test m= 0.027 and torsion test m= 0.27. However, the hardening curves were sigmoidal

  14. On the properties of torsions in Riemann-Cartan space-times

    International Nuclear Information System (INIS)

    Baker, W.M.; Atkins, W.K.; Davis, W.R.

    1978-01-01

    This paper is the first paper in a series of three papers dealing with the physical properties of torsions in Riemann-Cartan space-times (U 4 ). Paper one deals with the particular types of torsion that can be associated with the U 4 reinterpretation of a special class of null electromagnetic solutions of the standard form of Einstein's equations. In particular, for plane null electromagnetic solutions, three types of torsion solutions are associated with this type of reinterpretation. Two of these solutions, the trivector and semi-symmetric torsions, although rather special, serve as examples of what could be done to find the associated torsions in terms of simple requirements on identities in U 4 . The third class is obtained by relating the contorsion to the Lanczos ''spin'' tensor. Paper two, dealing with gravitational radiation, provides the proper background relating to the physical significance of the Lanczos tensor. This series of papers is primarily concerned with the question of the possible physical role of all types of torsion, compatible with an extension or an U 4 reinterpretation of Einstein's theory, consistent with the broadest possible interpretation of the present form of the Einstein-Cartan-Sciama-Kibble theory. However, in paper three some consideration will be given on theories with simpler metrical generalizations of U 4 and the related types of torsion. We emphasize that the content of paper one and two should be viewed mainly as special formal results that introduce the more general considerations of paper three

  15. Non-relativistic correspondence of Dirac equation with external electromagnetic field and space-time torsion

    International Nuclear Information System (INIS)

    Goncalves, Bruno; Dias Junior, Mario Marcio

    2013-01-01

    Full text: The discussion of experimental manifestations of torsion at low energies is mainly related to the torsion-spin interaction. In this respect the behavior of Dirac field and the spinning particle in an external torsion field deserves and received very special attention. In this work, we consider the combined action of torsion and magnetic field on the massive spinor field. In this case, the Dirac equation is not straightforward solved. We suppose that the spinor has two components. The equations have mixed terms between the two components. The electromagnetic field is introduced in the action by the usual gauge transformation. The torsion field is described by the field S μ . The main purpose of the work is to get an explicit form to the equation of motion that shows the possible interactions between the external fields and the spinor in a Hamiltonian that is independent to each component. We consider that S 0 is constant and is the unique non-vanishing term of S μ . This simplification is taken just to simplify the algebra, as our main point is not to describe the torsion field itself. In order to get physical analysis of the problem, we consider the non-relativistic approximation. The final result is a Hamiltonian that describes a half spin field in the presence of electromagnetic and torsion external fields. (author)

  16. Torsion of DNA modeled as a heterogeneous fluctuating rod

    Science.gov (United States)

    Argudo, David; Purohit, Prashant K.

    2014-01-01

    We discuss the statistical mechanics of a heterogeneous elastic rod with bending, twisting and stretching. Our model goes beyond earlier works where only homogeneous rods were considered in the limit of high forces and long lengths. Our methods allow us to consider shorter fluctuating rods for which boundary conditions can play an important role. We use our theory to study structural transitions in torsionally constrained DNA where there is coexistence of states with different effective properties. In particular, we examine whether a newly discovered left-handed DNA conformation called L-DNA is a mixture of two known states. We also use our model to investigate the mechanical effects of the binding of small molecules to DNA. For both these applications we make experimentally falsifiable predictions.

  17. Stick-slip and Torsional Friction Factors in Inclined Wellbores

    Directory of Open Access Journals (Sweden)

    Aarsnes Ulf Jakob F.

    2018-01-01

    The model is shown to have a good match with the surface and downhole behavior of two deviated wellbores for depths ranging from 1500 to 3000 meters. In particular, the model replicates the amplitude and period of the oscillations, in both the topside torque and the downhole RPM, as caused by the along-string stick slip. It is further shown that by using the surface behavior of the drill-string during rotational startup, an estimate of the static and dynamic friction factors along the wellbore can be obtained, even during stick-slip oscillations, if axial tension in the drillstring is considered. This presents a possible method to estimate friction factors in the field when off-bottom stick slip is encountered, and points in the direction of avoiding stick slip through the design of an appropriate torsional start-up procedure without the need of an explicit friction test.

  18. Electrodynamic wireless power transmission to a torsional receiver

    International Nuclear Information System (INIS)

    McEachern, K M; Arnold, D P

    2013-01-01

    This paper presents a wireless power transmission (WPT) concept that uses electrodynamic coupling and torsional motion of a permanent magnet in the receiver. The system is shown to transfer an average power of 3.09 mW (power density equal to 143 μW/cm 3 ) over a distance of 1 cm, an average power of 1.98 mW over a distance of 2 cm, and an average power of 126 μW over a distance of 7 cm. We also demonstrate unaltered power transmission through conductive media, including a human hand and an aluminum plate, highlighting a key advantage of the electrodynamic wireless power transmission approach

  19. High-pressure torsion for new hydrogen storage materials.

    Science.gov (United States)

    Edalati, Kaveh; Akiba, Etsuo; Horita, Zenji

    2018-01-01

    High-pressure torsion (HPT) is widely used as a severe plastic deformation technique to create ultrafine-grained structures with promising mechanical and functional properties. Since 2007, the method has been employed to enhance the hydrogenation kinetics in different Mg-based hydrogen storage materials. Recent studies showed that the method is effective not only for increasing the hydrogenation kinetics but also for improving the hydrogenation activity, for enhancing the air resistivity and more importantly for synthesizing new nanostructured hydrogen storage materials with high densities of lattice defects. This manuscript reviews some major findings on the impact of HPT process on the hydrogen storage performance of different titanium-based and magnesium-based materials.

  20. Quaternionic Kaehler and hyperkaehler manifolds with torsion and twistor spaces

    International Nuclear Information System (INIS)

    Ivanov, Stefan; Minchev, Ivan

    2001-12-01

    The target space of a (4,0) supersymmetric two-dimensional sigma model with Wess-Zumino term has a connection with totally skew-symmetric torsion and holonomy contained in Sp(n)Sp(l) (resp. Sp(n)), QKT (resp. HKT)-spaces. We study the geometry of QKT, HKT manifold and their twistor spaces. We show that the Swann bundle of a QKT manifold admits a HKT structure with special symmetry if and only if the twistor space of the QKT manifold admits an almost hermitian structure with totally skew-symmetric Nijenhuis tensor, thus connecting two structures arising from quantum field theories and supersymmetric sigma models with Wess- Zumino term. We discovered that a HKT manifold has always co-closed Lee form. Applying this property to compact HKT manifold we get information about the plurigenera. (author)