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Sample records for previous structure determinations

  1. Determining root correspondence between previously and newly detected objects

    Science.gov (United States)

    Paglieroni, David W.; Beer, N Reginald

    2014-06-17

    A system that applies attribute and topology based change detection to networks of objects that were detected on previous scans of a structure, roadway, or area of interest. The attributes capture properties or characteristics of the previously detected objects, such as location, time of detection, size, elongation, orientation, etc. The topology of the network of previously detected objects is maintained in a constellation database that stores attributes of previously detected objects and implicitly captures the geometrical structure of the network. A change detection system detects change by comparing the attributes and topology of new objects detected on the latest scan to the constellation database of previously detected objects.

  2. Crystal structure determination of Efavirenz

    International Nuclear Information System (INIS)

    Popeneciu, Horea; Dumitru, Ristoiu; Tripon, Carmen; Borodi, Gheorghe; Pop, Mihaela Maria

    2015-01-01

    Needle-shaped single crystals of the title compound, C 14 H 9 ClF 3 NO 2 , were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring

  3. Determinants of capital structure.

    Science.gov (United States)

    McCue, M J; Ozcan, Y A

    1992-01-01

    This study analyzes the determinants of hospital capital structure in a new market setting that are created by the financial pressures of prospective payment and the intense price competition among hospitals. Using California data, the study found hospital system affiliation, bed size, growth rate in revenues, operating risk, and asset structure affected both short- and long-term debt borrowings. In addition, percentage of uncompensated care, profitability, and payer mix influenced short-term borrowings while market conditions and ownership affected long-term borrowings. Most significant of all is the finding that smaller hospitals tend to borrow more, possibly because they cannot generate funds internally.

  4. Determination of the Boltzmann constant with cylindrical acoustic gas thermometry: new and previous results combined

    Science.gov (United States)

    Feng, X. J.; Zhang, J. T.; Lin, H.; Gillis, K. A.; Mehl, J. B.; Moldover, M. R.; Zhang, K.; Duan, Y. N.

    2017-10-01

    We report a new determination of the Boltzmann constant k B using a cylindrical acoustic gas thermometer. We determined the length of the copper cavity from measurements of its microwave resonance frequencies. This contrasts with our previous work (Zhang et al 2011 Int. J. Thermophys. 32 1297, Lin et al 2013 Metrologia 50 417, Feng et al 2015 Metrologia 52 S343) that determined the length of a different cavity using two-color optical interferometry. In this new study, the half-widths of the acoustic resonances are closer to their theoretical values than in our previous work. Despite significant changes in resonator design and the way in which the cylinder length is determined, the value of k B is substantially unchanged. We combined this result with our four previous results to calculate a global weighted mean of our k B determinations. The calculation follows CODATA’s method (Mohr and Taylor 2000 Rev. Mod. Phys. 72 351) for obtaining the weighted mean value of k B that accounts for the correlations among the measured quantities in this work and in our four previous determinations of k B. The weighted mean {{\\boldsymbol{\\hat{k}}}{B}} is 1.380 6484(28)  ×  10-23 J K-1 with the relative standard uncertainty of 2.0  ×  10-6. The corresponding value of the universal gas constant is 8.314 459(17) J K-1 mol-1 with the relative standard uncertainty of 2.0  ×  10-6.

  5. Spectrophotometric determination of uranium by previous extraction chromatography separation in polimetalic mineral, phosphorites and technological licours

    International Nuclear Information System (INIS)

    Moreno Bermudez, J.; Cabrera Quevedo, C.; Alfonso Mendez, L.; Rodriguez Aguilera, M.

    1994-01-01

    The development of an analytical procedure for spectrophotometric determination of uranium in polimetalic mineral, phosphorites and technological licours is described. The method is based on the previous separation of interfering elements by extraction chromatography and on spectrophotometric determination of uranium (IV) with arsenazo III in concentrated hydrochloric acid. Tributyl phosphate impregnate on politetrafluoroethylene is used as stationary phase and 5.5 M nitric acid is used as movie phase. The influence of matrix-component elements was studies. The development procedure was applied to real samples, being the results compared with those obtained by other well established analytical methods like gamma-spectrometry, laser fluorimetric, spectrophotometry previous uranium separation by liquid liquid extraction and anion exchange. The reproducibility is evaluated and the detection limited has been established for each studied matrix. A procedure for correcting the thorium interference has been developed for samples with a Th/ 3U8O higher than 0.2

  6. Navigation and Comprehension of Digital Expository Texts: Hypertext Structure, Previous Domain Knowledge, and Working Memory Capacity

    Science.gov (United States)

    Burin, Debora I.; Barreyro, Juan P.; Saux, Gastón; Irrazábal, Natalia C.

    2015-01-01

    Introduction: In contemporary information societies, reading digital text has become pervasive. One of the most distinctive features of digital texts is their internal connections via hyperlinks, resulting in non-linear hypertexts. Hypertext structure and previous knowledge affect navigation and comprehension of digital expository texts. From the…

  7. Technique for sparing previously irradiated critical normal structures in salvage proton craniospinal irradiation

    International Nuclear Information System (INIS)

    McDonald, Mark W; Wolanski, Mark R; Simmons, Joseph W; Buchsbaum, Jeffrey C

    2013-01-01

    Cranial reirradiation is clinically appropriate in some cases but cumulative radiation dose to critical normal structures remains a practical concern. The authors developed a simple technique in 3D conformal proton craniospinal irradiation (CSI) to block organs at risk (OAR) while minimizing underdosing of adjacent target brain tissue. Two clinical cases illustrate the use of proton therapy to provide salvage CSI when a previously irradiated OAR required sparing from additional radiation dose. The prior radiation plan was coregistered to the treatment planning CT to create a planning organ at risk volume (PRV) around the OAR. Right and left lateral cranial whole brain proton apertures were created with a small block over the PRV. Then right and left lateral “inverse apertures” were generated, creating an aperture opening in the shape of the area previously blocked and blocking the area previously open. The inverse aperture opening was made one millimeter smaller than the original block to minimize the risk of dose overlap. The inverse apertures were used to irradiate the target volume lateral to the PRV, selecting a proton beam range to abut the 50% isodose line against either lateral edge of the PRV. Together, the 4 cranial proton fields created a region of complete dose avoidance around the OAR. Comparative photon treatment plans were generated with opposed lateral X-ray fields with custom blocks and coplanar intensity modulated radiation therapy optimized to avoid the PRV. Cumulative dose volume histograms were evaluated. Treatment plans were developed and successfully implemented to provide sparing of previously irradiated critical normal structures while treating target brain lateral to these structures. The absence of dose overlapping during irradiation through the inverse apertures was confirmed by film. Compared to the lateral X-ray and IMRT treatment plans, the proton CSI technique improved coverage of target brain tissue while providing the least

  8. Structural determination of organic compounds

    International Nuclear Information System (INIS)

    Kintzinger, J.P.

    1991-01-01

    This paper reports that the current methods available in high-field NMR spectroscopy are such that the tridimensional structure determination of any rigid molecule containing only carbon and hydrogen atoms may be achieved. The connectivities between carbon-carbon, carbon-hydrogen, and hydrogen-hydrogen atoms are determined by multipulse and two-dimensional (2D) experiments. These connectivity patterns or maps allow a step-by-step reconstruction of the molecular structures. From the carbon-carbon connectivity map, the carbon framework of the molecule is obtained, whereas the carbon-hydrogen pattern allows determination of the positions of the hydrogen atoms on their corresponding carbon atoms. High-field spectrometers are then necessary to remove fortuitous degeneracy and to reduce the proton spectra to a nearly first-order one, allowing an easy measurement of the chemical shifts and the coupling constants

  9. Investigating physiological methods to determine previous exposure of immature insects to ionizing radiation

    International Nuclear Information System (INIS)

    Mansour, M.Y.

    2001-01-01

    Effect of gamma radiation on phenoloxidase activity in codling moth, Cydia pomonella L., larvae was investigated. Phenoloxidase activity was determined spectrophotometrically by measuring the increase in optical density at 490 nm, or by observing the degree of melanization in larvae killed by freezing. Results showed that, in unirradiated larvae, phenoloxidase activity could be detected in 7 day old larvae and activity continued to increase throughout the larval stage. This increase was not observed when larvae were irradiated with a minimum dose of 50 Gy during the 1st week of their development. However, irradiating larvae in which enzyme activity was already high (24 week old) did not eliminate the activity but reduced further increase. Larval melanization studies were in general agreement with the results of the phenoloxidase assay. (author)

  10. Structure determination of enterovirus 71

    Energy Technology Data Exchange (ETDEWEB)

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G. (Purdue); (Sentinext)

    2013-02-20

    Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.

  11. Microbial community structure of relict niter-beds previously used for saltpeter production.

    Directory of Open Access Journals (Sweden)

    Takashi Narihiro

    Full Text Available From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA. The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3-, Cl-, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB and "Ca. Nitrososphaera"-type ammonia-oxidizing archaea (AOA, respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.

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

    Science.gov (United States)

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

    2014-01-01

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

  13. Spectrophotometric determination of uranium with arsenazo previous liquid-liquid extraction and colour development in organic medium

    International Nuclear Information System (INIS)

    Palomares Delgado, F.; Vera Palomino, J.; Petrement Eguiluz, J. C.

    1964-01-01

    The determination of uranium with arsenazo is hindered by a great number of cation which form stable complexes with the reactive and may given rise to serious interferences. By studying the optimum conditions of uranium the extraction be means of tributylphosphate solutions dissolved in methylisobuthylketone, under conditions for previous masking of the interfering cations, an organic extract was obtained containing all the uranium together with small amounts of iron. The possible interference derived from the latter element is avoided by reduction with hydroxylammoniumchlorid followed by complex formation of the Fe(II)-ortophenantroline compound in alcoholic medium. (Author) 17 refs

  14. Solution NMR structure determination of proteins revisited

    International Nuclear Information System (INIS)

    Billeter, Martin; Wagner, Gerhard; Wuethrich, Kurt

    2008-01-01

    This 'Perspective' bears on the present state of protein structure determination by NMR in solution. The focus is on a comparison of the infrastructure available for NMR structure determination when compared to protein crystal structure determination by X-ray diffraction. The main conclusion emerges that the unique potential of NMR to generate high resolution data also on dynamics, interactions and conformational equilibria has contributed to a lack of standard procedures for structure determination which would be readily amenable to improved efficiency by automation. To spark renewed discussion on the topic of NMR structure determination of proteins, procedural steps with high potential for improvement are identified

  15. Determinants of Glycosaminoglycan (GAG Structure

    Directory of Open Access Journals (Sweden)

    Kristian Prydz

    2015-08-01

    Full Text Available Proteoglycans (PGs are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG chains in the secretory pathway of animal cells. The most common GAG attachment site is a serine residue followed by a glycine (-ser-gly-, from which a linker tetrasaccharide extends and may continue as a heparan sulfate, a heparin, a chondroitin sulfate, or a dermatan sulfate GAG chain. Which type of GAG chain becomes attached to the linker tetrasaccharide is influenced by the structure of the protein core, modifications occurring to the linker tetrasaccharide itself, and the biochemical environment of the Golgi apparatus, where GAG polymerization and modification by sulfation and epimerization take place. The same cell type may produce different GAG chains that vary, depending on the extent of epimerization and sulfation. However, it is not known to what extent these differences are caused by compartmental segregation of protein cores en route through the secretory pathway or by differential recruitment of modifying enzymes during synthesis of different PGs. The topic of this review is how different aspects of protein structure, cellular biochemistry, and compartmentalization may influence GAG synthesis.

  16. Patterns and Determinants of Treatment Seeking among Previously Untreated Psychotic Patients in Aceh Province, Indonesia: A Qualitative Study

    Directory of Open Access Journals (Sweden)

    Marthoenis Marthoenis

    2016-01-01

    Full Text Available Immediate treatment of first-episode psychosis is essential in order to achieve a positive outcome. However, Indonesian psychiatric patients often delay accessing health services, the reason for which is not yet fully understood. The current study aimed to understand patterns of treatment seeking and to reveal determinants of the delay in accessing psychiatric care among first-time user psychotic patients. Qualitative interviews were conducted with sixteen family members who accompanied the patients to a psychiatric hospital. Many families expressed beliefs that mental illness appertains to village sickness and not hospital sickness; therefore, they usually take the patients to traditional or religious healers before taking them to a health professional. They also identified various factors that potentially delay accessing psychiatric treatment: low literacy and beliefs about the cause of the illness, stigmatisation, the role of extended family, financial problems, and long distance to the psychiatric hospital. On the other hand, the family mentioned various factors related to timely help seeking, including being a well-educated family, living closer to health facilities, previous experience of successful psychotic therapy, and having more positive symptoms of psychosis. The findings call for mental health awareness campaigns in the community.

  17. Structure of catalase determined by MicroED

    Science.gov (United States)

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

    2014-01-01

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

  18. Monte Carlo determination of heteroepitaxial misfit structures

    DEFF Research Database (Denmark)

    Baker, J.; Lindgård, Per-Anker

    1996-01-01

    We use Monte Carlo simulations to determine the structure of KBr overlayers on a NaCl(001) substrate, a system with large (17%) heteroepitaxial misfit. The equilibrium relaxation structure is determined for films of 2-6 ML, for which extensive helium-atom scattering data exist for comparison...

  19. Structural determinants of students' employability: Influence of ...

    African Journals Online (AJOL)

    Structural determinants of students' employability: Influence of career ... greatest influence on students' employability, followed by decision-making skills, and ... efforts in developing app-ropriate strategies so as to engage undergraduates with ...

  20. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  1. Vascular structure determines pulmonary blood flow distribution

    Science.gov (United States)

    Hlastala, M. P.; Glenny, R. W.

    1999-01-01

    Scientific knowledge develops through the evolution of new concepts. This process is usually driven by new methodologies that provide observations not previously available. Understanding of pulmonary blood flow determinants advanced significantly in the 1960s and is now changing rapidly again, because of increased spatial resolution of regional pulmonary blood flow measurements.

  2. Capital Structure Determinants and Governance Structure Variety in Franchising

    NARCIS (Netherlands)

    T. Jiang (Tao)

    2009-01-01

    textabstractThis thesis investigates two questions: the determinants of capital structure in franchising and its subsequent impact on the franchise financing decisions; and the efficient governance structure choice in franchising. We posit that firms franchise in order to benefit from the reduced

  3. Structural Study and Evaluation of Previous Restoration Work of Mohammad 'Ali Pasha Mosque at the Citadel in Cairo

    Directory of Open Access Journals (Sweden)

    dr.Yaser Yehya Amin Abdel-Aty

    2011-01-01

    Full Text Available Mohammad 'Ali Pasha Mosque at the Citadel in Cairo is considered one of the main landmarks in Egypt. It majestically stands at a northwestern bend of the Citadel and it is visible from numerous locations in Cairo. It has become the symbol of the Citadel, to the point that its name is given to the whole complex in the colloquial Egyptian parlance. This paper studies analytically the static and dynamic structural behavior of this great mosque using computer numerical modeling techniques, to reach the main reasons for past cracking and failures in its domed-roof and other structural elements, which occurred by the end of 19th Century. A number of 3D-models are analyzed to study the mosque, in both original and after restoration conditions, under static (i.e. dead and live loads and dynamic (i.e. Eigenvector modal analysis, response-spectrum and time-history cases of loading. Besides, structural evaluation of major restoration project, in 1930s, is conducted to determine the current structural safety status of the mosque

  4. Advances on surface structural determination by LEED

    International Nuclear Information System (INIS)

    Soares, Edmar A; De Carvalho, Vagner E; De Castilho, Caio M C

    2011-01-01

    In the last 40 years, low energy electron diffraction (LEED) has proved to be the most reliable quantitative technique for surface structural determination. In this review, recent developments related to the theory that gives support to LEED structural determination are discussed under a critical analysis of the main theoretical approximation-the muffin-tin calculation. The search methodologies aimed at identifying the best matches between theoretical and experimental intensity versus voltage curves are also considered, with the most recent procedures being reviewed in detail. (topical review)

  5. Representing Personal Determinants in Causal Structures.

    Science.gov (United States)

    Bandura, Albert

    1984-01-01

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

  6. Blood donations from previously transfused or pregnant donors: a multicenter study to determine the frequency of alloexposure.

    Science.gov (United States)

    Rios, Jorge A; Schlumpf, Karen S; Kakaiya, Ram M; Triulzi, Darrell J; Roback, John D; Kleinman, Steve H; Murphy, Edward L; Gottschall, Jerome L; Carey, Patricia M

    2011-06-01

    Transfusion-related acute lung injury (TRALI) mitigation strategies include the deferral of female donors from apheresis platelet (PLT) donations and the distribution of plasma for transfusion from male donors only. We studied the implications of these policies in terms of component loss at six blood centers in the United States. We collected data from allogeneic blood donors making whole blood and blood component donations during calendar years 2006 through 2008. We analyzed the distribution of donations in terms of the sex, transfusion and pregnancy histories, and blood type. A TRALI mitigation policy that would not allow plasma from female whole blood donors to be prepared into transfusable plasma components would result in nearly a 50% reduction in the units of whole blood available for plasma manufacturing and would decrease the number of type AB plasma units that could be made from whole blood donations by the same amount. Deferral of all female apheresis PLT donors, all female apheresis PLT donors with histories of prior pregnancies, or all female apheresis PLT donors with histories of prior pregnancies and positive screening test results for antibodies to human leukocyte antigens (HLAs) will result in a loss of 37.1, 22.5, and 5.4% of all apheresis PLT donations, respectively. A TRALI mitigation policy that only defers female apheresis PLT donors with previous pregnancies and HLAs would result in an approximately 5% decrease in the inventory of apheresis PLTs, but would eliminate a large proportion of components that are associated with TRALI. © 2010 American Association of Blood Banks.

  7. Capital Structure Determinants and Governance Structure Variety in Franchising

    OpenAIRE

    Jiang, Tao

    2009-01-01

    textabstractThis thesis investigates two questions: the determinants of capital structure in franchising and its subsequent impact on the franchise financing decisions; and the efficient governance structure choice in franchising. We posit that firms franchise in order to benefit from the reduced franchisees’ operational risks by limiting the debt level, such that the franchisor can bear more debt and gain tax-deduction benefits. Specific hypotheses are based on various theories like resource...

  8. Investigating physiological methods to determine previous exposure of immature insects to ionizing radiation and estimating the exposure dose

    International Nuclear Information System (INIS)

    Mansour, M.

    1998-10-01

    Effects of gamma radiation on pupation and adult emergence in mature (diapausing and non-diapausing) codling moth, Cydia pomonella L., larvae and on phenoloxidase activity in larvae killed by freezing were investigated. Results showed that, a dose of 50 Gy reduced adult emergence (and pupation) significantly and 200 Gy completely prevented it. Diapausing larvae were more susceptible to irradiation that non-diapausing larvae and female moths were more susceptible to irradiation injury than males. Phenoloxidase activity in codling moth larvae was determined spectrophotometrically by measuring the increase in optical density at 490 nm, or by observing the degree of melanization in larvae killed by freezing. Results showed that, in un-irradiated larvae, phenoloxidase activity can be detected in 7 day old larvae and activity continued to accumulate throughout the larval stage. This accumulation was not observed when larvae were irradiated with a minimum dose of 50 Gy during the 1st week of their development. However, irradiating larvae in which enzyme activity was already high (2-3 week old) did not remove activity but only reduced further accumulation. Larval melanization studies were in agreement with results of the phenoloxidase assay. (author)

  9. In cellulo structure determination of a novel cypovirus polyhedrin

    International Nuclear Information System (INIS)

    Axford, Danny; Ji, Xiaoyun; Stuart, David I.; Sutton, Geoff

    2014-01-01

    The crystal structure of a previously unsolved type of cypovirus polyhedrin has been determined from data collected directly from frozen live insect cells. This work demonstrates that with the use of a microfocus synchrotron beam the structure of a novel viral polyhedrin could be successfully determined from microcrystals within cells, removing the preparatory step of sample isolation and maintaining a favourable biological environment. The data obtained are of high quality, comparable to that obtained from isolated crystals, and enabled a facile structure determination. A small but significant difference is observed between the unit-cell parameters and the mosaic spread of in cellulo and isolated crystals, suggesting that even these robust crystals are adversely affected by removal from the cell

  10. Capital Structure Determinants of Small and Medium Enterprises in Croatia

    Directory of Open Access Journals (Sweden)

    Nataša Šarlija

    2016-09-01

    Full Text Available Most of the research about capital structure is focused towards two theories: trade off theory (TOT and pecking order theory (POT. The idea is to explore which theory works better in certain conditions and identify the key determinants that affect the capital structure of the company. However, in different countries different determinants with opposite relation to the leverage are found to be significant. Besides, most of the previous researches are oriented on listed companies. The aim of this paper is to analyse the capital structure of small and medium enterprises in Croatia through the analysis of the fundamental determinants of the capital structure. The research was conducted on a data sample of 500 SMEs in Croatia in the period of 2005–2011. On the unbalanced panel data set a linear regression is applied. Influence of determinants on leverage is estimated by a static panel model with random effect and with fixed effect estimation. Four capital structure determinants are analysed: growth, size, profitability and tangible assets. The results of this research support the pecking order theory confirming that SMEs in Croatia are primarily financed frominternally generated funds that affect profitability, growth, tangible assets and enterprise size.

  11. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

    2005-01-01

    at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...

  12. High Resolution Powder Diffraction and Structure Determination

    International Nuclear Information System (INIS)

    Cox, D. E.

    1999-01-01

    It is clear that high-resolution synchrotrons X-ray powder diffraction is a very powerful and convenient tool for material characterization and structure determination. Most investigations to date have been carried out under ambient conditions and have focused on structure solution and refinement. The application of high-resolution techniques to increasingly complex structures will certainly represent an important part of future studies, and it has been seen how ab initio solution of structures with perhaps 100 atoms in the asymmetric unit is within the realms of possibility. However, the ease with which temperature-dependence measurements can be made combined with improvements in the technology of position-sensitive detectors will undoubtedly stimulate precise in situ structural studies of phase transitions and related phenomena. One challenge in this area will be to develop high-resolution techniques for ultra-high pressure investigations in diamond anvil cells. This will require highly focused beams and very precise collimation in front of the cell down to dimensions of 50 (micro)m or less. Anomalous scattering offers many interesting possibilities as well. As a means of enhancing scattering contrast it has applications not only to the determination of cation distribution in mixed systems such as the superconducting oxides discussed in Section 9.5.3, but also to the location of specific cations in partially occupied sites, such as the extra-framework positions in zeolites, for example. Another possible application is to provide phasing information for ab initio structure solution. Finally, the precise determination of f as a function of energy through an absorption edge can provide useful information about cation oxidation states, particularly in conjunction with XANES data. In contrast to many experiments at a synchrotron facility, powder diffraction is a relatively simple and user-friendly technique, and most of the procedures and software for data analysis

  13. Use of nuclear filters in the determination of thorium with previous separation by precipitation with fluoride ions and latter liquid-liquid extraction with TOPO

    International Nuclear Information System (INIS)

    Estevez, J.; Betancourt, M.

    1988-01-01

    A method for the determination of thorium in phosphorites, that includes a previous separation of some interfering elements was elaborated. Thorium was precipitated with fluoride ions and the insoluble compound formed was separated by using nuclear filters. Latter and extraction was made with Xilene-TOPO and colour was developed with Ars III in organic phase. 19 refs

  14. Shallow lunar structure determined from the passive seismic experiment

    International Nuclear Information System (INIS)

    Nakamura, Y.; Dorman, J.; Duennebier, F.; Lammlein, D.; Latham, G.

    1975-01-01

    Data relevant to the shallow structure of the Moon obtained at the Apollo seismic stations are compared with previously published results of the active seismic experiments. It is concluded that the lunar surface is covered by a layer of low seismic velocity (Vsub(p) approximately equal to 100 ms -1 ), which appears to be equivalent to the lunar regolith defined previously by geological observations. This layer is underlain by a zone of distinctly higher seismic velocity at all of the Apollo landing sites. The regolith thicknesses at the Apollo 11, 12, and 15 sites are estimated from the shear-wave resonance to be 4.4, 3.7, and 4.4m, respectively. These thicknesses and those determined at the other Apollo sites by the active seismic experiments appear to be correlated with the age determinations and the abundances of extra-lunar components at the sites. (Auth.)

  15. Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Yann Reynaud

    Full Text Available Mycobacterium tuberculosis genetic structure, and evolutionary history have been studied for years by several genotyping approaches, but delineation of a few sublineages remains controversial and needs better characterization. This is particularly the case of T group within lineage 4 (L4 which was first described using spoligotyping to pool together a number of strains with ill-defined signatures. Although T strains were not traditionally considered as a real phylogenetic group, they did contain a few phylogenetically meaningful sublineages as shown using SNPs. We therefore decided to investigate if this observation could be corroborated using other robust genetic markers. We consequently made a first assessment of genetic structure using 24-loci MIRU-VNTRs data extracted from the SITVIT2 database (n = 607 clinical isolates collected in Russia, Albania, Turkey, Iraq, Brazil and China. Combining Minimum Spanning Trees and Bayesian population structure analyses (using STRUCTURE and TESS softwares, we distinctly identified eight tentative phylogenetic groups (T1-T8 with a remarkable correlation with geographical origin. We further compared the present structure observed with other L4 sublineages (n = 416 clinical isolates belonging to LAM, Haarlem, X, S sublineages, and showed that 5 out of 8 T groups seemed phylogeographically well-defined as opposed to the remaining 3 groups that partially mixed with other L4 isolates. These results provide with novel evidence about phylogeographically specificity of a proportion of ill-defined T group of M. tuberculosis. The genetic structure observed will now be further validated on an enlarged worldwide dataset using Whole Genome Sequencing (WGS.

  16. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1977-01-01

    Crystallography may be described as the science of the structure of materi­ als, using this word in its widest sense, and its ramifications are apparent over a broad front of current scientific endeavor. It is not surprising, therefore, to find that most universities offer some aspects of crystallography in their undergraduate courses in the physical sciences. It is the principal aim of this book to present an introduction to structure determination by X-ray crystal­ lography that is appropriate mainly to both final-year undergraduate studies in crystallography, chemistry, and chemical physics, and introductory post­ graduate work in this area of crystallography. We believe that the book will be of interest in other disciplines, such as physics, metallurgy, biochemistry, and geology, where crystallography has an important part to play. In the space of one book, it is not possible either to cover all aspects of crystallography or to treat all the subject matter completely rigorously. In particular, certain ...

  17. Determination of the Basin Structure Beneath European Side of Istanbul

    Science.gov (United States)

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

    2016-04-01

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

  18. Synthesis and Structural Determination of Temocapril Sulfoxide Hydrochlorides

    International Nuclear Information System (INIS)

    Seong, Seok Bong; Moon, Jong Taik; Kim, Jung Ahn; Choo, Dong Joon; Lee, Jae Yeol

    2012-01-01

    Impurity (or related substance) control in pharmaceutical products is a primary goal of drug development. Stringent international regulatory requirements have been in place for several years as outlined in the International Conference on Harmonization (ICH) Guidelines Q3A (R), Q3B (R) and Q3C. According to ICH guidelines, impurities associated with the manufacture of a drug substance, also known as an active pharmaceutical ingredient (API), are classified into the following categories: (1) organic impurities (process and drug-related); (2) inorganic impurities (3) residual solvents. Many potential impurities result from the API manufacturing process including starting materials, isomers, intermediates, reagents, solvents, catalysts and reaction by-products. These potential impurities should be investigated to determine process control mechanisms for their removal and the need for specification controls at appropriate points in the process. The suggested structures of the impurities can be synthesized and will provide the final evidence for their structures, previously determined by spectroscopic methods. Therefore it is essential to know the structure of these impurities in the bulk drug in order to alter the reaction condition and to reduce the quantity of impurity to an acceptable level. Isolation, identification and quantification of impurities help the pharmaceutical company to obtain a pure substance with less toxicity and safety in drug therapy

  19. Determining the crystal structure of fibrinogen.

    Science.gov (United States)

    Doolittle, R F

    2004-05-01

    Summary. I have enjoyed reading previous historical sketches that have appeared in Journal of Thrombosis and Haemostasis, and especially those by Ted Tuddenham on factor VIII and Bjorn Dahlback on activated protein C resistance. Like those authors, I have tried to capture some of the excitement-as well as the disappointments-that occurred along the way to a long-term goal.

  20. Overcoming barriers to membrane protein structure determination.

    Science.gov (United States)

    Bill, Roslyn M; Henderson, Peter J F; Iwata, So; Kunji, Edmund R S; Michel, Hartmut; Neutze, Richard; Newstead, Simon; Poolman, Bert; Tate, Christopher G; Vogel, Horst

    2011-04-01

    After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new approaches to solving membrane protein structures based on recent technological advances. Rational approaches to overcoming the bottlenecks in the field are urgently required as membrane proteins, which typically comprise ~30% of the proteomes of organisms, are dramatically under-represented in the structural database of the Protein Data Bank.

  1. Investigations of nephrotoxicity caused by ionic and non-ionic contrast media in rats with previously damaged and not previously damaged kidneys and special view to urinary enzyme determinations

    International Nuclear Information System (INIS)

    Hofmeister, R.

    1988-01-01

    In this study ionic (meglumine amidotrizoate) and non-ionic contrast media (SHH 340 AB, Iohexol, Iopromide, Iosimide and Iopamidol) were tested for their nephrotoxicity in rats. During the experiment detections of urea nitrogen, serum creatinine and urinary enzymes as well as histological examinations of the kidneys were carried out for the diagnosis of acute renal damage. The results obtained in this study demonstrate that rats are not very sensitive to non-ionic contrast media with regard to kidney damage and determinations of urinary enzymes are valuable for the diagnosis of contrast media induced acute kidney damage in living animals. (orig./MG) [de

  2. A use of Ramachandran potentials in protein solution structure determinations

    International Nuclear Information System (INIS)

    Bertini, Ivano; Cavallaro, Gabriele; Luchinat, Claudio; Poli, Irene

    2003-01-01

    A strategy is developed to use database-derived φ-ψ constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived φ-ψ constraints are enforced for all aminoacids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the φ-ψ values for each residue are examined. In the second and final run, the database-derived φ-ψ constraints are enforced only for those residues which in the first run have ended in one and the same favored φ-ψ region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints

  3. determination of verticality of reservoir engineering structure

    African Journals Online (AJOL)

    user

    applications is 3D survey and management of oil and gas facilities and other engineering structures. This recent .... also affect ground water contamination. 2. VERTICALITY ...... The soil, water and concrete in a Reservoir at the foundation bed ...

  4. DETERMINANTS OF FINANCIAL STRUCTURE OF GREEK COMPANIES

    Directory of Open Access Journals (Sweden)

    Gargalis PANAGIOTIS

    2016-06-01

    Full Text Available Capital structure is essential for the survival, growth and performance of a firm. There has been a growing interest worldwide in identifying the factors associated with debt leverage. This article aims to investigate the factors affecting the capital structure of companies listed on the Athens Stock Exchange (ASE. The data set used is composed of indicators reflecting the financial position and performance of 40 firms listed on the ASE in 2014. Using a regression model we estimate in what extent the financial structure of companies is affected by performance indicators and other specific factors like the field of activity or the size of the firms. The results obtained show an important influence of share of tangible assets in total assets of the company on the financial leverage, as main variable selected in order to reflect the capital structure of Greek companies.

  5. Science achievement determinants: factorial structure of family ...

    African Journals Online (AJOL)

    The family plays an important role in determining the academic achievement ... parents' assistance, expectation, and encouragement in their children's mathematics ... suggested that cultural upbringing is a strong factor contributing to the.

  6. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1995-01-01

    X-ray crystallography provides us with the most accurate picture we can get of atomic and molecular structures in crystals. It provides a hard bedrock of structural results in chemistry and in mineralogy. In biology, where the structures are not fully crystalline, it can still provide valuable results and, indeed, the impact here has been revolutionary. It is still an immense field for young workers, and no doubt will provide yet more striking develop­ ments of a major character. It does, however, require a wide range of intellectual application, and a considerable ability in many fields. This book will provide much help. It is a very straightforward and thorough guide to every aspect of the subject. The authors are experienced both as research workers themselves and as teachers of standing, and this is shown in their clarity of exposition. There are plenty of iliustrations and worked examples to aid the student to obtain a real grasp of the subject.

  7. Structural determinants in the bulk heterojunction.

    Science.gov (United States)

    Acocella, Angela; Höfinger, Siegfried; Haunschmid, Ernst; Pop, Sergiu C; Narumi, Tetsu; Yasuoka, Kenji; Yasui, Masato; Zerbetto, Francesco

    2018-02-21

    Photovoltaics is one of the key areas in renewable energy research with remarkable progress made every year. Here we consider the case of a photoactive material and study its structural composition and the resulting consequences for the fundamental processes driving solar energy conversion. A multiscale approach is used to characterize essential molecular properties of the light-absorbing layer. A selection of bulk-representative pairs of donor/acceptor molecules is extracted from the molecular dynamics simulation of the bulk heterojunction and analyzed at increasing levels of detail. Significantly increased ground state energies together with an array of additional structural characteristics are identified that all point towards an auxiliary role of the material's structural organization in mediating charge-transfer and -separation. Mechanistic studies of the type presented here can provide important insights into fundamental principles governing solar energy conversion in next-generation photovoltaic devices.

  8. Some structural determinants of melody recall.

    Science.gov (United States)

    Boltz, M

    1991-05-01

    Sophisticated musicians were asked to recall, using musical notation, a set of unfamiliar folk tunes that varied in rhythmic structure and referents of tonality. The results showed that memory was facilitated by tonic triad members marking phrase endings, but only when their presence was highlighted by a corresponding pattern of temporal accents. Conversely, recall significantly declined when tonal information was either absent or obscured by rhythmic structure. Error analyses further revealed that the retention of overall pitch contour and information at phrase ending points varied as a function of these manipulations. The results are discussed in terms of a framework that links the acts of perceiving and remembering to a common attentional scheme.

  9. Overcoming barriers to membrane protein structure determination

    NARCIS (Netherlands)

    Bill, Roslyn M.; Henderson, Peter J. F.; Iwata, So; Kunji, Edmund R. S.; Michel, Hartmut; Neutze, Richard; Newstead, Simon; Poolman, Bert; Tate, Christopher G.; Vogel, Horst

    After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new

  10. Structural determination and gynecological tumor diagnosis using ...

    African Journals Online (AJOL)

    covalent bonding patterns and branched structures. Studies have shown that changes in protein glycosylation at the cell surface during tumorigenesis are closely related to the occurrence and development of some cancers, including pancreatic cancer, mammary cancer, prostatic cancer, colon cancer, and gastric cancer [1].

  11. Determining the structure of Carbon-60

    International Nuclear Information System (INIS)

    Wif, D.

    1994-01-01

    Carbon-60 is the most stable and best known of the carbon cage structures known collectively as the fullerenes. It is a remarkable molecule that forms a fascinating solid. Although the molecular shape of C sub 6 sub 0 is familiar - it is simply the shape of a soccer ball with 12 pentagons and 20 hexagons - the manner in which it forms a crystal structure is by no means obvious. This talk will focus on the insights which neutron scattering at ISIS has brought to our understanding of solid C sub6 sub 0. At room temperature, the structure may be regarded as forming as essentially ideal cubic-close packed molecular b ubble-raft : each molecule is reorienting so rapidly that a time-averaged picture, over as little as a nanosecond, reveals a closely spherical shell of atomic density. At 260 K, a rather unusual structural transition occurs. The molecules order but still retain cubic symmetry. Although this may not appear to be a rather dramatic change, detailed considerations show that a profound transition has occurred that bears close similarities to a solid-liquid phase transition but in two dimensions. Below 260 K, reorientation still occurs but at a dramatically reduced rate as the temperature is lowered. Indeed at around 90 K, The reorientation is so slow that thermodynamic equilibrium cannot be achieved in a reasonable timescale an orientational glass transition occurs. Although the behaviour of solid C sub 6 sub 0 undergoes dramatic changes as a function of temperature, a coherent description has evolved in which neutron scattering plays a central role. Close analogies are to be found in the study of systems as diverse as solid H sub 2 and human-rhinovirus structures. These analogies and the central role played by neutron scattering at ISIS will be emphasised in this paper. 5 figs., 10 refs. (author)

  12. Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus: Purification, Crystallization and Structure Determination

    International Nuclear Information System (INIS)

    Clemons, William M. Jr.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki

    2001-01-01

    We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 (angstrom) resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 (angstrom) resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

  13. Three-Dimensional Structure Determination of Botulinum Toxin

    National Research Council Canada - National Science Library

    Stevens, Ray

    1997-01-01

    ...) Based on the structure of the neurotoxin, understand the toxins mechanism of action. We have accomplished the first goal of determining the three-dimensional structure of the 150 kD botulinum neurotoxin serotype...

  14. Three-Dimensional Structure Determination of Botulinum Toxin

    National Research Council Canada - National Science Library

    Stevens, Ray

    1998-01-01

    ...) Based on the structure of the neurotoxin, understand the toxins mechanism of action. We have accomplished the first goal of determining the three-dimensional structure of the 150 kD botulinum neurotoxin serotype...

  15. The determinants of capital structure: evidence from Dutch panel data

    OpenAIRE

    Chen, Linda H.; Lensink, Robert; Sterken, Elmer

    1999-01-01

    This paper studies the determinants of capital structure choice of Dutch firms. Our main objective is to investigate whether and to what extent the main capital structure theories can explain capital structure choice of Dutch firms. A better understanding of the capital structure determinants in a rela-tively small yet open industrialized economy is essential not only for enrich-ing empirical studies in this field, but also for the purpose of cross country asset evaluation. By estimating a pa...

  16. How structure determines correlations in neuronal networks.

    Directory of Open Access Journals (Sweden)

    Volker Pernice

    2011-05-01

    Full Text Available Networks are becoming a ubiquitous metaphor for the understanding of complex biological systems, spanning the range between molecular signalling pathways, neural networks in the brain, and interacting species in a food web. In many models, we face an intricate interplay between the topology of the network and the dynamics of the system, which is generally very hard to disentangle. A dynamical feature that has been subject of intense research in various fields are correlations between the noisy activity of nodes in a network. We consider a class of systems, where discrete signals are sent along the links of the network. Such systems are of particular relevance in neuroscience, because they provide models for networks of neurons that use action potentials for communication. We study correlations in dynamic networks with arbitrary topology, assuming linear pulse coupling. With our novel approach, we are able to understand in detail how specific structural motifs affect pairwise correlations. Based on a power series decomposition of the covariance matrix, we describe the conditions under which very indirect interactions will have a pronounced effect on correlations and population dynamics. In random networks, we find that indirect interactions may lead to a broad distribution of activation levels with low average but highly variable correlations. This phenomenon is even more pronounced in networks with distance dependent connectivity. In contrast, networks with highly connected hubs or patchy connections often exhibit strong average correlations. Our results are particularly relevant in view of new experimental techniques that enable the parallel recording of spiking activity from a large number of neurons, an appropriate interpretation of which is hampered by the currently limited understanding of structure-dynamics relations in complex networks.

  17. Determining building interior structures using compressive sensing

    Science.gov (United States)

    Lagunas, Eva; Amin, Moeness G.; Ahmad, Fauzia; Nájar, Montse

    2013-04-01

    We consider imaging of the building interior structures using compressive sensing (CS) with applications to through-the-wall imaging and urban sensing. We consider a monostatic synthetic aperture radar imaging system employing stepped frequency waveform. The proposed approach exploits prior information of building construction practices to form an appropriate sparse representation of the building interior layout. We devise a dictionary of possible wall locations, which is consistent with the fact that interior walls are typically parallel or perpendicular to the front wall. The dictionary accounts for the dominant normal angle reflections from exterior and interior walls for the monostatic imaging system. CS is applied to a reduced set of observations to recover the true positions of the walls. Additional information about interior walls can be obtained using a dictionary of possible corner reflectors, which is the response of the junction of two walls. Supporting results based on simulation and laboratory experiments are provided. It is shown that the proposed sparsifying basis outperforms the conventional through-the-wall CS model, the wavelet sparsifying basis, and the block sparse model for building interior layout detection.

  18. Language structure is partly determined by social structure.

    Directory of Open Access Journals (Sweden)

    Gary Lupyan

    Full Text Available BACKGROUND: Languages differ greatly both in their syntactic and morphological systems and in the social environments in which they exist. We challenge the view that language grammars are unrelated to social environments in which they are learned and used. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a statistical analysis of >2,000 languages using a combination of demographic sources and the World Atlas of Language Structures--a database of structural language properties. We found strong relationships between linguistic factors related to morphological complexity, and demographic/socio-historical factors such as the number of language users, geographic spread, and degree of language contact. The analyses suggest that languages spoken by large groups have simpler inflectional morphology than languages spoken by smaller groups as measured on a variety of factors such as case systems and complexity of conjugations. Additionally, languages spoken by large groups are much more likely to use lexical strategies in place of inflectional morphology to encode evidentiality, negation, aspect, and possession. Our findings indicate that just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche in which they are being learned and used. As adults learn a language, features that are difficult for them to acquire, are less likely to be passed on to subsequent learners. Languages used for communication in large groups that include adult learners appear to have been subjected to such selection. Conversely, the morphological complexity common to languages used in small groups increases redundancy which may facilitate language learning by infants. CONCLUSIONS/SIGNIFICANCE: We hypothesize that language structures are subjected to different evolutionary pressures in different social environments. Just as biological organisms are shaped by ecological niches, language structures appear to adapt to the

  19. Microwave Determination of the Structure of Pyridine

    Energy Technology Data Exchange (ETDEWEB)

    Bak, B.; Hansen, L.; Rastrup-Andersen, J. [Chemical Laboratory of the University of Copenhagen, Copenhagen (Denmark)

    1954-12-15

    2‐, 3‐, and 4‐mono‐deutero‐pyridine have been prepared and the microwave spectra recorded. For each of the isotopic species 11—12 transitions (Q‐ and R‐branch lines) were localized, a number of which could be identified by their Stark effect. For all three species rotational constants of high precision were calculated. The material so provided in connection with known rotational constants for ordinary pyridine is insufficient for a complete determination of the ten geometrical parameters of the molecule. Seven models with a choice of C – H distances close to the correct value (1.075‐1.085 A) were considered one of which was shown to be consistent with electron‐diffraction work and current valence theory. In this model d(N – C(2)) = 1.340±0.005; d(C(2) – C(3)) = 1.390±0.005; d(C(3) – C(4)) = 1.400±0.005 A. The valence angles in the aromatic ring (starting with the C(6) – N – C(2) angle) are: 116° 42′; 124° 00′; 118° 36′; 118° 06′.

  20. Determination of atomic cluster structure with cluster fusion algorithm

    DEFF Research Database (Denmark)

    Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2005-01-01

    We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....

  1. Structural analysis of eight novel and 112 previously reported missense mutations in the interactive FXI mutation database reveals new insight on FXI deficiency.

    Science.gov (United States)

    Saunders, Rebecca E; Shiltagh, Nuha; Gomez, Keith; Mellars, Gillian; Cooper, Carolyn; Perry, David J; Tuddenham, Edward G; Perkins, Stephen J

    2009-08-01

    Factor XI (FXI) functions in blood coagulation. FXI is composed of four apple (Ap) domains and a serine protease (SP) domain. Deficiency of FXI leads to an injury-related bleeding disorder, which is remarkable for the lack of correlation between bleeding symptoms and FXI coagulant activity (FXI:C). The number of mutations previously reported in our interactive web database (http://www.FactorXI.org) is now significantly increased to 183 through our new patient studies and from literature surveys. Eight novel missense mutations give a total of 120 throughout the FXI gene (F11). The most abundant defects in FXI are revealed to be those from low-protein plasma levels (Type I: CRM-) that originate from protein misfolding, rather than from functional defects (Type II: CRM+). A total of 70 Ap missense mutations were analysed using a consensus Ap domain structure generated from the FXI dimer crystal structure. This showed that all parts of the Ap domain were affected. The 47 SP missense mutations were also distributed throughout the SP domain structure. The periphery of the Ap beta-sheet structure is sensitive to structural perturbation caused by residue changes throughout the Ap domain, yet this beta-sheet is crucial for FXI dimer formation. Residues located at the Ap4:Ap4 interface in the dimer are much less directly involved. We conclude that the abundance of Type I defects in FXI results from the sensitivity of the Ap domain folding to residue changes within this, and discuss how structural knowledge of the mutations improves our understanding of FXI deficiencies.

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

    Science.gov (United States)

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

    2018-04-03

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

  3. Rapid and reliable protein structure determination via chemical shift threading.

    Science.gov (United States)

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

    2018-01-01

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

  4. De novo protein structure determination using sparse NMR data

    International Nuclear Information System (INIS)

    Bowers, Peter M.; Strauss, Charlie E.M.; Baker, David

    2000-01-01

    We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models are built from these fragments by minimizing an energy function that favors hydrophobic burial, strand pairing, and satisfaction of NOE constraints. Models generated using this procedure with ∼1 NOE constraint per residue are in some cases closer to the corresponding X-ray structures than the published NMR solution structures. The method requires only the sparse constraints available during initial stages of NMR structure determination, and thus holds promise for increasing the speed with which protein solution structures can be determined

  5. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

    Science.gov (United States)

    Fromm, S A; Sachse, C

    2016-01-01

    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. © 2016 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Stokes-Rees, Ian; Sliz, Piotr

    2010-12-14

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

  7. Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics.

    Science.gov (United States)

    Dong, Zirui; Wang, Huilin; Chen, Haixiao; Jiang, Hui; Yuan, Jianying; Yang, Zhenjun; Wang, Wen-Jing; Xu, Fengping; Guo, Xiaosen; Cao, Ye; Zhu, Zhenzhen; Geng, Chunyu; Cheung, Wan Chee; Kwok, Yvonne K; Yang, Huanming; Leung, Tak Yeung; Morton, Cynthia C; Cheung, Sau Wai; Choy, Kwong Wai

    2017-11-02

    PurposeRecent studies demonstrate that whole-genome sequencing enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in the 1000 Genomes Project without knowing which bands were affected.MethodsThe 1000 Genomes Project provides an unprecedented integrated map of structural variants in phenotypically normal subjects, but there is no information on potential inclusion of subjects with apparent BCAs akin to those traditionally detected in diagnostic cytogenetics laboratories. We applied our analytical tool to 1,166 genomes from the 1000 Genomes Project with sufficient physical coverage (8.25-fold).ResultsWith this approach, we detected four reciprocal balanced translocations and four inversions, ranging in size from 57.9 kb to 13.3 Mb, all of which were confirmed by cytogenetic methods and polymerase chain reaction studies. One of these DNAs has a subtle translocation that is not readily identified by chromosome analysis because of the similarity of the banding patterns and size of exchanged segments, and another results in disruption of all transcripts of an OMIM gene.ConclusionOur study demonstrates the extension of utilizing low-pass whole-genome sequencing for unbiased detection of BCAs including translocations and inversions previously unknown in the 1000 Genomes Project.GENETICS in MEDICINE advance online publication, 2 November 2017; doi:10.1038/gim.2017.170.

  8. Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase .

    Science.gov (United States)

    Hall, Richard S; Agarwal, Rakhi; Hitchcock, Daniel; Sauder, J Michael; Burley, Stephen K; Swaminathan, Subramanyam; Raushel, Frank M

    2010-05-25

    Two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. The genes encoding these two enzymes, NYSGXRC-9339a ( gi|44585104 ) and NYSGXRC-9236b ( gi|44611670 ), were first identified from DNA isolated from the Sargasso Sea as part of the Global Ocean Sampling Project. The genes were synthesized, and the proteins were subsequently expressed and purified. The X-ray structure of Sgx9339a was determined at 2.7 A resolution (Protein Data Bank entry 2PAJ ). This protein folds as a distorted (beta/alpha)(8) barrel and contains a single zinc ion in the active site. These enzymes are members of the amidohydrolase superfamily and belong to cog0402 within the clusters of orthologous groups (COG). Enzymes in cog0402 have previously been shown to catalyze the deamination of guanine, cytosine, S-adenosylhomocysteine, and 8-oxoguanine. A small compound library of pteridines, purines, and pyrimidines was used to probe catalytic activity. The only substrates identified in this search were isoxanthopterin and pterin 6-carboxylate. The kinetic constants for the deamination of isoxanthopterin with Sgx9339a were determined to be 1.0 s(-1), 8.0 muM, and 1.3 x 10(5) M(-1) s(-1) (k(cat), K(m), and k(cat)/K(m), respectively). The active site of Sgx9339a most closely resembles the active site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9 ). A model for substrate recognition of isoxanthopterin by Sgx9339a was proposed on the basis of the binding of guanine and xanthine in the active site of guanine deaminase. Residues critical for substrate binding appear to be conserved glutamine and tyrosine residues that form hydrogen bonds with the carbonyl oxygen at C4, a conserved threonine residue that forms hydrogen bonds with N5, and another conserved threonine residue that forms hydrogen bonds with the carbonyl group at C7. These conserved active site residues were used to identify 24 other genes

  9. Discovery and Structure Determination of the Orphan Enzyme Isoxanthopterin Deaminase

    Energy Technology Data Exchange (ETDEWEB)

    Hall, R.S.; Swaminathan, S.; Agarwal, R.; Hitchcock, D.; Sauder, J. M.; Burley, S. K.; Raushel, F. M.

    2010-05-25

    Two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. The genes encoding these two enzymes, NYSGXRC-9339a (gi|44585104) and NYSGXRC-9236b (gi|44611670), were first identified from DNA isolated from the Sargasso Sea as part of the Global Ocean Sampling Project. The genes were synthesized, and the proteins were subsequently expressed and purified. The X-ray structure of Sgx9339a was determined at 2.7 {angstrom} resolution (Protein Data Bank entry 2PAJ). This protein folds as a distorted ({beta}/{alpha}){sub 8} barrel and contains a single zinc ion in the active site. These enzymes are members of the amidohydrolase superfamily and belong to cog0402 within the clusters of orthologous groups (COG). Enzymes in cog0402 have previously been shown to catalyze the deamination of guanine, cytosine, S-adenosylhomocysteine, and 8-oxoguanine. A small compound library of pteridines, purines, and pyrimidines was used to probe catalytic activity. The only substrates identified in this search were isoxanthopterin and pterin 6-carboxylate. The kinetic constants for the deamination of isoxanthopterin with Sgx9339a were determined to be 1.0 s{sup -1}, 8.0 {micro}M, and 1.3 x 10{sup 5} M{sup -1} s{sup -1} (k{sub cat}, K{sub m}, and k{sub cat}/K{sub m}, respectively). The active site of Sgx9339a most closely resembles the active site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9). A model for substrate recognition of isoxanthopterin by Sgx9339a was proposed on the basis of the binding of guanine and xanthine in the active site of guanine deaminase. Residues critical for substrate binding appear to be conserved glutamine and tyrosine residues that form hydrogen bonds with the carbonyl oxygen at C4, a conserved threonine residue that forms hydrogen bonds with N5, and another conserved threonine residue that forms hydrogen bonds with the carbonyl group at C7. These conserved active site

  10. Determinants of capital structure and financial crisis impact: evidence

    OpenAIRE

    Proença, Pedro Miguel Correia

    2012-01-01

    Mestrado em contabilidade The objectives of this empirical work are to investigate the determinants of Portuguese SMEs capital structure, evaluate whether and how the impacts of those determinants affect the debt ratios and examine the effects of financial crisis and industry on Portuguese SMEs capital structure. The sample used considers the period 2007-2010, resulting in 12.857 Portugues e SMEs per year observations. R...

  11. Transaction cost determinants of credit governance structures of ...

    African Journals Online (AJOL)

    This paper explores transaction cost determinants of credit governance structures (CGS) of commercial banks in Tanzania. Descriptive statistics, linear regression model, binary and multinomial logistic regression models were employed for analysis. Findings revealed four modes of credit governance structures that are ...

  12. The Determinants of Capital Structure: Some Evidence from Banks

    OpenAIRE

    Heider, Florian; Gropp, Reint

    2008-01-01

    This paper documents that standard cross-sectional determinants of firm leverage also apply to the capital structure of large banks in the United States and Europe. We find a remarkable consistency in sign, significance and economic magnitude. Like non-financial firms, banks appear to have stable capital structures at levels that are specific to each individual bank. The results suggest that capital requirements may only be of second-order importance for banks’ capital structures and confirm ...

  13. Labor Market Structure and Salary Determination among Professional Basketball Players.

    Science.gov (United States)

    Wallace, Michael

    1988-01-01

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

  14. Denotational, Causal, and Operational Determinism in Event Structures

    NARCIS (Netherlands)

    Rensink, Arend; Kirchner, H.

    1996-01-01

    Determinism of labelled transition systems and trees is a concept of theoretical and practical importance. We study its generalisation to event structures. It turns out that the result depends on what characterising property of tree determinism one sets out to generalise. We present three distinct

  15. Denotational, Causal, and Operational Determinism in Event Structures

    NARCIS (Netherlands)

    Rensink, Arend

    Determinism is a theoretically and practically important concept in labelled transition systems and trees. We study its generalisation to event structures. It turns out that the result depends on what characterising property of tree determinism one sets out to generalise. We present three distinct

  16. An Empirical Study on Capital Structure Determinants of Selected ASEAN Countries

    OpenAIRE

    Ngo, Hoang Anh

    2013-01-01

    Capital structure has been a controversial topic for decades. Conflicting arguments in theories and mixed findings in empirical work require further studies on this subject. More importantly, most previous studies have focused on developed countries and little attention is paid to emerging economies, especially ASEAN. Therefore, this study attempts to fill the gap by examining effects of capital structure's determinants on different measures of leverage of listed manufacturing companies in se...

  17. Integral membrane protein structure determination using pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: dn206@cam.ac.uk [University of Cambridge, Department of Biochemistry (United Kingdom)

    2015-04-15

    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

  18. Structural determination of intact proteins using mass spectrometry

    Science.gov (United States)

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

    2008-05-06

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

  19. BIRTHDAY CAKE ACTIVITY STRUCTURED ARRANGEMENT FOR HELPING CHILDREN DETERMINING QUANTITIES

    Directory of Open Access Journals (Sweden)

    Neni Mariana

    2010-07-01

    Full Text Available Few researches have been concerned about relation between children’s spatialthinking and number sense. Narrowing for this small research, we focused onone component of spatial thinking, that is structuring objects, and onecomponent of number senses, that is cardinality by determining quantities. Thisstudy focused on a design research that was conducted in Indonesia in which weinvestigated pre-school children’s (between 2 and 3.5 years old ability inmaking structured arrangement and their ability to determine the quantities bylooking at the arrangements. The result shows us that some of the children wereable to make such arrangement. However, the children found difficulties eitherto determine quantities from those arrangements or to compare some structuresto easily recognize number of objects.Keywords: structures, structured arrangement, cardinality DOI: http://dx.doi.org/10.22342/jme.1.1.790.53-70

  20. Energy group structure determination using particle swarm optimization

    International Nuclear Information System (INIS)

    Yi, Ce; Sjoden, Glenn

    2013-01-01

    Highlights: ► Particle swarm optimization is applied to determine broad group structure. ► A graph representation of the broad group structure problem is introduced. ► The approach is tested on a fuel-pin model. - Abstract: Multi-group theory is widely applied for the energy domain discretization when solving the Linear Boltzmann Equation. To reduce the computational cost, fine group cross libraries are often down-sampled into broad group cross section libraries. Cross section data collapsing generally involves two steps: Firstly, the broad group structure has to be determined; secondly, a weighting scheme is used to evaluate the broad cross section library based on the fine group cross section data and the broad group structure. A common scheme is to average the fine group cross section weighted by the fine group flux. Cross section collapsing techniques have been intensively researched. However, most studies use a pre-determined group structure, open based on experience, to divide the neutron energy spectrum into thermal, epi-thermal, fast, etc. energy range. In this paper, a swarm intelligence algorithm, particle swarm optimization (PSO), is applied to optimize the broad group structure. A graph representation of the broad group structure determination problem is introduced. And the swarm intelligence algorithm is used to solve the graph model. The effectiveness of the approach is demonstrated using a fuel-pin model

  1. Development of XAFS Into a Structure Determination Technique

    Science.gov (United States)

    Stern, E. A.

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

  2. Solution structure of apamin determined by nuclear magnetic resonance and distance geometry

    Energy Technology Data Exchange (ETDEWEB)

    Pease, J.H.B.; Wemmer, D.E.

    1988-11-01

    The solution structure of the bee venom neurotoxin apamin has been determined with a distance geometry program using distance constraints derived from NMR. Twenty embedded structures were generated and refined by using the program DSPACE. After error minimization using both conjugate gradient and dynamics algorithms, six structures had very low residual error. Comparisons of these show that the backbone of the peptide is quite well-defined with the largest rms difference between backbone atoms in these structures of 1.34 /Angstrom/. The side chains have far fewer constraints and show greater variability in their positions. The structure derived here is generally consistent with the qualitative model previously described, with most differences occurring in the loop between the ..beta..-turn (residues 2-5) and the C-terminal ..cap alpha..-helix (residues 9-17). Comparisons are made with previously derived models from NMR data and other methods.

  3. Solution structure of apamin determined by nuclear magnetic resonance and distance geometry

    International Nuclear Information System (INIS)

    Pease, J.H.B.; Wemmer, D.E.

    1988-01-01

    The solution structure of the bee venom neurotoxin apamin has been determined with a distance geometry program using distance constraints derived from NMR. Twenty embedded structures were generated and refined by using the program DSPACE. After error minimization using both conjugate gradient and dynamics algorithms, six structures had very low residual error. Comparisons of these show that the backbone of the peptide is quite well-defined with the largest rms difference between backbone atoms in these structures of 1.34 /Angstrom/. The side chains have far fewer constraints and show greater variability in their positions. The structure derived here is generally consistent with the qualitative model previously described, with most differences occurring in the loop between the β-turn (residues 2-5) and the C-terminal α-helix (residues 9-17). Comparisons are made with previously derived models from NMR data and other methods

  4. WHAT DETERMINES THE CAPITAL STRUCTURE OF LISTED FIRMS IN ROMANIA

    Directory of Open Access Journals (Sweden)

    Floriniţa Duca

    2012-10-01

    Full Text Available This paper examines the relative importance of four factors in the capital structure decisions of Romanian listed firms. The existing empirical research on capital structure has been largely confined to developed countries. The Romanian Financial Market has been developing at an exponential rate and dedicated research in the field is required. We used 100 firms listed in 2010 at the Bucharest Stock Exchange. The objective of this paper is to build on previous studies model all the important factors affecting capital structure decisions. We find that factors such as tangibility of assets, firm size, liquidity, and profitability have significant influences on the leverage structure chosen by firms.These results are believed to have significant implications for the theory of finance and to be of importance to the corporate treasure in choice of new financing and to the financial analyst.

  5. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    Directory of Open Access Journals (Sweden)

    Neni Mariana

    2010-07-01

    Full Text Available Few researches have been concerned about relation between children’s spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was conducted in Indonesia in which we investigated pre-school children’s (between 2 and 3.5 years old ability in making structured arrangement and their ability to determine the quantities by looking at the arrangements. The result shows us that some of the children were able to make such arrangement. However, the children found difficulties either to determine quantities from those arrangements or to compare some structures to easily recognize number of objects.

  6. Nucleic acid helix structure determination from NMR proton chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-06-15

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

  7. Determinants of Capital Structure in Non-Financial Companies

    OpenAIRE

    Kühnhausen, Fabian; Stieber, Harald W.

    2014-01-01

    In this paper, we evaluate firm-, industry- and country-specific factors determining a firm's capital structure. The empirical validity of several capital structure theories has been ambiguous so far. We shed light on the main drivers of leverage and depict differences in industry and country characteristics. Using a short panel data set with a large cross-section, we are able to show that firm size, industry leverage, industry growth and tax shield positively affect leverage ratios, while pr...

  8. A study on determinants of capital structure in India

    Directory of Open Access Journals (Sweden)

    Anshu Handoo

    2014-09-01

    Full Text Available The paper identifies the most important determinants of capital structure of 870 listed Indian firms comprising both private sector companies and government companies for the period 2001–2010. Ten independent variables and three dependent variables have been tested using regression analysis. It has been concluded that factors such as profitability, growth, asset tangibility, size, cost of debt, tax rate, and debt serving capacity have significant impact on the leverage structure chosen by firms in the Indian context.

  9. Sulfated oligosaccharide structures, as determined by NMR techniques

    International Nuclear Information System (INIS)

    Noseda, M.D.; Duarte, M.E.R.; Tischer, C.A.; Gorin, P.A.J.; Cerezo, A.S.

    1997-01-01

    Carrageenans are sulfated polysaccharides, produced by red seaweeds (Rhodophyta), that have important biological and physico-chemical properties. Using partial autohydrolysis, we obtained sulfated oligosaccharides from a λ-carrageenan (Noseda and Cerezo, 1993). These oligosaccharides are valuable not only for the study of the structures of the parent carrageenans but also for their possible biological activities. In this work we determined the chemical structure of one of the sulfated oligosaccharides using 1D and 2D NMR techniques. (author)

  10. Determinants of Market Structure and the Airline Industry

    Science.gov (United States)

    Raduchel, W.

    1972-01-01

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

  11. Generative probabilistic models extend the scope of inferential structure determination

    DEFF Research Database (Denmark)

    Olsson, Simon; Boomsma, Wouter; Frellsen, Jes

    2011-01-01

    demonstrate that the use of generative probabilistic models instead of physical forcefields in the Bayesian formalism is not only conceptually attractive, but also improves precision and efficiency. Our results open new vistas for the use of sophisticated probabilistic models of biomolecular structure......Conventional methods for protein structure determination from NMR data rely on the ad hoc combination of physical forcefields and experimental data, along with heuristic determination of free parameters such as weight of experimental data relative to a physical forcefield. Recently, a theoretically...

  12. Rotational characterization of methyl methacrylate: Internal dynamics and structure determination

    Science.gov (United States)

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

    2018-01-01

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

  13. Organizational Structure as a Determinant of Job Burnout.

    Science.gov (United States)

    Bilal, Atif; Ahmed, Hafiz Mushtaq

    2017-03-01

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

  14. Determination of glycaemic index; some methodological aspects related to the analysis of carbohydrate load and characteristics of the previous evening meal.

    Science.gov (United States)

    Granfeldt, Y; Wu, X; Björck, I

    2006-01-01

    To determine the possible differences in glycaemic index (GI) depending on (1) the analytical method used to calculate the 'available carbohydrate' load, that is, using carbohydrates by difference (total carbohydrate by difference, minus dietary fibre (DF)) as available carbohydrates vs available starch basis (total starch minus resistant starch (RS)) of a food rich in intrinsic RS and (2) the effect of GI characteristics and/or the content of indigestible carbohydrates (RS and DF) of the evening meal prior to GI testing the following morning. Blood glucose and serum insulin responses were studied after subjects consuming (1) two levels of barley kernels rich in intrinsic RS (15.2%, total starch basis) and (2) after a standard breakfast following three different evening meals varying in GI and/or indigestible carbohydrates: pasta, barley kernels and white wheat bread, respectively. Healthy adults with normal body mass index. (1) Increasing the portion size of barley kernels from 79.6 g (50 g 'available carbohydrates') to 93.9 g (50 g available starch) to adjust for its RS content did not significantly affect the GI or insulin index (11). (2) The low GI barley evening meal, as opposed to white wheat bread and pasta evening meals, reduced the postprandial glycaemic and insulinaemic (23 and 29%, respectively, P base carbohydrate load on specific analyses of the available carbohydrate content. (2) A low GI barley evening meal containing high levels of indigestible carbohydrates (RS and DF) substantially reduced the GI and II of white wheat bread determined at a subsequent breakfast meal.

  15. Revisiting chlorophyll extraction methods in biological soil crusts - methodology for determination of chlorophyll a and chlorophyll a + b as compared to previous methods

    Science.gov (United States)

    Caesar, Jennifer; Tamm, Alexandra; Ruckteschler, Nina; Lena Leifke, Anna; Weber, Bettina

    2018-03-01

    Chlorophyll concentrations of biological soil crust (biocrust) samples are commonly determined to quantify the relevance of photosynthetically active organisms within these surface soil communities. Whereas chlorophyll extraction methods for freshwater algae and leaf tissues of vascular plants are well established, there is still some uncertainty regarding the optimal extraction method for biocrusts, where organism composition is highly variable and samples comprise major amounts of soil. In this study we analyzed the efficiency of two different chlorophyll extraction solvents, the effect of grinding the soil samples prior to the extraction procedure, and the impact of shaking as an intermediate step during extraction. The analyses were conducted on four different types of biocrusts. Our results show that for all biocrust types chlorophyll contents obtained with ethanol were significantly lower than those obtained using dimethyl sulfoxide (DMSO) as a solvent. Grinding of biocrust samples prior to analysis caused a highly significant decrease in chlorophyll content for green algal lichen- and cyanolichen-dominated biocrusts, and a tendency towards lower values for moss- and algae-dominated biocrusts. Shaking of the samples after each extraction step had a significant positive effect on the chlorophyll content of green algal lichen- and cyanolichen-dominated biocrusts. Based on our results we confirm a DMSO-based chlorophyll extraction method without grinding pretreatment and suggest the addition of an intermediate shaking step for complete chlorophyll extraction (see Supplement S6 for detailed manual). Determination of a universal chlorophyll extraction method for biocrusts is essential for the inter-comparability of publications conducted across all continents.

  16. Revisiting chlorophyll extraction methods in biological soil crusts – methodology for determination of chlorophyll a and chlorophyll a + b as compared to previous methods

    Directory of Open Access Journals (Sweden)

    J. Caesar

    2018-03-01

    Full Text Available Chlorophyll concentrations of biological soil crust (biocrust samples are commonly determined to quantify the relevance of photosynthetically active organisms within these surface soil communities. Whereas chlorophyll extraction methods for freshwater algae and leaf tissues of vascular plants are well established, there is still some uncertainty regarding the optimal extraction method for biocrusts, where organism composition is highly variable and samples comprise major amounts of soil. In this study we analyzed the efficiency of two different chlorophyll extraction solvents, the effect of grinding the soil samples prior to the extraction procedure, and the impact of shaking as an intermediate step during extraction. The analyses were conducted on four different types of biocrusts. Our results show that for all biocrust types chlorophyll contents obtained with ethanol were significantly lower than those obtained using dimethyl sulfoxide (DMSO as a solvent. Grinding of biocrust samples prior to analysis caused a highly significant decrease in chlorophyll content for green algal lichen- and cyanolichen-dominated biocrusts, and a tendency towards lower values for moss- and algae-dominated biocrusts. Shaking of the samples after each extraction step had a significant positive effect on the chlorophyll content of green algal lichen- and cyanolichen-dominated biocrusts. Based on our results we confirm a DMSO-based chlorophyll extraction method without grinding pretreatment and suggest the addition of an intermediate shaking step for complete chlorophyll extraction (see Supplement S6 for detailed manual. Determination of a universal chlorophyll extraction method for biocrusts is essential for the inter-comparability of publications conducted across all continents.

  17. High-throughput determination of RNA structure by proximity ligation.

    Science.gov (United States)

    Ramani, Vijay; Qiu, Ruolan; Shendure, Jay

    2015-09-01

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

  18. Orientation determination of interfacial beta-sheet structures in situ.

    Science.gov (United States)

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

    2010-07-01

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

  19. Direct electron crystallographic determination of zeolite zonal structures

    International Nuclear Information System (INIS)

    Dorset, Douglas L.; Gilmore, Christopher J.; Jorda, Jose Luis; Nicolopoulos, Stavros

    2007-01-01

    The prospect for improving the success of ab initio zeolite structure investigations with electron diffraction data is evaluated. First of all, the quality of intensities obtained by precession electron diffraction at small hollow cone illumination angles is evaluated for seven representative materials: ITQ-1, ITQ-7, ITQ-29, ZSM-5, ZSM-10, mordenite, and MCM-68. It is clear that, for most examples, an appreciable fraction of a secondary scattering perturbation is removed by precession at small angles. In one case, ZSM-10, it can also be argued that precession diffraction produces a dramatically improved 'kinematical' data set. There seems to no real support for application of a Lorentz correction to these data and there is no reason to expect for any of these samples that a two-beam dynamical scattering relationship between structure factor amplitude and observed intensity should be valid. Removal of secondary scattering by the precession mode appears to facilitate ab initio structure analysis. Most zeolite structures investigated could be solved by maximum entropy and likelihood phasing via error-correcting codes when precession data were used. Examples include the projected structure of mordenite that could not be determined from selected area data alone. One anomaly is the case of ZSM-5, where the best structure determination in projection is made from selected area diffraction data. In a control study, the zonal structure of SSZ-48 could be determined from selected area diffraction data by either maximum entropy and likelihood or traditional direct methods. While the maximum entropy and likelihood approach enjoys some advantages over traditional direct methods (non-dependence on predicted phase invariant sums), some effort must be made to improve the figures of merit used to identify potential structure solutions

  20. Document boundary determination using structural and lexical analysis

    Science.gov (United States)

    Taghva, Kazem; Cartright, Marc-Allen

    2009-01-01

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

  1. New method to determine structures in thermonuclear plasmas

    International Nuclear Information System (INIS)

    Tanzi, C.P.

    1998-01-01

    The information from tomographic methods is not always sufficient to determine fast changing structures, e.g. very hot plasmas. A new method has been developed by means of which, among other things, physical mechanisms of plasma instability can be disentangled. 4 refs

  2. Dynamic Capital Structure: Dynamics, Determinants and Speed of Adjustment

    NARCIS (Netherlands)

    Tamirat, A.S.; Trujillo Barrera, A.A.; Pennings, J.M.E.

    2017-01-01

    The corporate finance literature has focused on explaining the determinants of firms target capital structure and speed of adjustment using the well-established theories such as pecking order, signaling and trade-off theories. However, less attention has been paid to understanding the financing

  3. Farm Target Capital Structure: Dynamics, Determinants and Speed of Adjustment

    NARCIS (Netherlands)

    Tamirat, A.S.; Trujillo Barrera, A.A.; Pennings, J.M.E.

    2017-01-01

    The corporate finance literature has focused on explaining the determinants of firms target capital structure and speed of adjustment using the well-established theories such as pecking order, signaling and trade-off theories. However, less attention has been paid to understanding the financing

  4. A Laboratory Exercise in the Determination of Carbohydrate Structures.

    Science.gov (United States)

    White, Bernard J.; Robyt, John F.

    1988-01-01

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

  5. Determining modulus of elasticity of ancient structural timber

    Science.gov (United States)

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

    2011-01-01

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

  6. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    Science.gov (United States)

    Mariana, Neni

    2010-01-01

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

  7. Macromolecular structure determination in the post-genome era

    International Nuclear Information System (INIS)

    Kuhn, P.; Soltis, S.M.

    2001-01-01

    Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system for the structure determination steps of this process, starting with the initial characterization of the frozen sample, followed by data collection, data reduction, phase determination, and model building. This paper focuses on the data collection elements of this high-throughput system

  8. From bacterial to human dihydrouridine synthase: automated structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Whelan, Fiona, E-mail: fiona.whelan@york.ac.uk; Jenkins, Huw T., E-mail: fiona.whelan@york.ac.uk [The University of York, Heslington, York YO10 5DD (United Kingdom); Griffiths, Samuel C. [University of Oxford, Headington, Oxford OX3 7BN (United Kingdom); Byrne, Robert T. [Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich (Germany); Dodson, Eleanor J.; Antson, Alfred A., E-mail: fiona.whelan@york.ac.uk [The University of York, Heslington, York YO10 5DD (United Kingdom)

    2015-06-30

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

  9. From bacterial to human dihydrouridine synthase: automated structure determination

    International Nuclear Information System (INIS)

    Whelan, Fiona; Jenkins, Huw T.; Griffiths, Samuel C.; Byrne, Robert T.; Dodson, Eleanor J.; Antson, Alfred A.

    2015-01-01

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer

  10. Using photoelectron diffraction to determine complex molecular adsorption structures

    International Nuclear Information System (INIS)

    Woodruff, D P

    2010-01-01

    Backscattering photoelectron diffraction, particularly in the energy-scan mode, is now an established technique for determining in a quantitative fashion the local structure of adsorbates on surfaces, and has been used successfully for ∼100 adsorbate phases. The elemental and chemical-state specificity afforded by the characteristic core level photoelectron binding energies means that it has particular advantages for molecular adsorbates, as the local geometry of inequivalent atoms in the molecule can be determined in a largely independent fashion. On the other hand, polyatomic molecules present a general problem for all methods of surface structure determination in that a mismatch of intramolecular distances with interatomic distances on the substrate surface means that the atoms in the adsorbed molecule are generally in low-symmetry sites. The quantities measured experimentally then represent an incoherent sum of the properties of each structural domain that is inequivalent with respect to the substrate point group symmetry. This typically leads to greater ambiguity or precision in the structural solutions. The basic principles of the method are described and illustrated with a simple example involving molecule/substrate bonding through only one constituent atom (TiO 2 -(110)/H 2 O). This example demonstrates the importance of obtaining quantitative local structural information. Further examples illustrate both the successes and the problems of this approach when applied to somewhat more complex molecular adsorbates.

  11. Macromolecular structure determination in the post-genome era

    CERN Document Server

    Kuhn, P

    2001-01-01

    Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system...

  12. Direct experimental determination of the atomic structure at internal interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Browning, N.D. [Oak Ridge National Lab., TN (United States)]|[Illinois Univ., Chicago, IL (United States); Pennycook, S.J. [Oak Ridge National Lab., TN (United States)

    1995-07-01

    A crucial first step in understanding the effect that internal interfaces have on the properties of materials is the ability to determine the atomic structure at the interface. As interfaces can contain atomic disorder, dislocations, segregated impurities and interphases, sensitivity to all of these features is essential for complete experimental characterization. By combining Z-contrast imaging and electron energy loss spectroscopy (EELS) in a dedicated scanning transmission electron microscope (STEM), the ability to probe the structure, bonding and composition at interfaces with the necessary atomic resolution has been obtained. Experimental conditions can be controlled to provide, simultaneously, both incoherent imaging and spectroscopy. This enables interface structures observed in the image to be interpreted intuitively and the bonding in a specified atomic column to be probed directly by EELS. The bonding and structure information can then be correlated using bond-valence sum analysis to produce structural models. This technique is demonstrated for 25{degrees}, 36{degrees} and 67{degrees} symmetric and 45{degrees} and 25{degrees} asymmetric [001] tilt grain boundaries in SrTiO{sub 3} The structures of both types of boundary were found to contain partially occupied columns in the boundary plane. From these experimental results, a series of structural units were identified which could be combined, using continuity of gain boundary structure principles, to construct all [001] tilt boundaries in SrTiO{sub 3}. Using these models, the ability of this technique to address the issues of vacancies and dopant segregation at grain boundaries in electroceramics is discussed.

  13. Global search in photoelectron diffraction structure determination using genetic algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Viana, M L [Departamento de Fisica, Icex, UFMG, Belo Horizonte, Minas Gerais (Brazil); Muino, R Diez [Donostia International Physics Center DIPC, Paseo Manuel de Lardizabal 4, 20018 San Sebastian (Spain); Soares, E A [Departamento de Fisica, Icex, UFMG, Belo Horizonte, Minas Gerais (Brazil); Hove, M A Van [Department of Physics and Materials Science, City University of Hong Kong, Hong Kong (China); Carvalho, V E de [Departamento de Fisica, Icex, UFMG, Belo Horizonte, Minas Gerais (Brazil)

    2007-11-07

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

  14. CAPITAL STRUCTURE DETERMINANTS: EVIDENCE FROM PALESTINE AND EGYPT STOCK EXCHANGES

    Directory of Open Access Journals (Sweden)

    Abdul Razak Abdul Hadi

    2017-04-01

    Full Text Available Abstract -This study is driven by the motivation to examine the capital structure determinants for Palestine Stock Exchange (PEX and Egypt Stock Exchange (EGX. Within the framework of capital structure theories, this study uses Generalized Method of Moments (GMM,1982 as an estimation model employing quarterly panel data analysis during the observed period from 2008 till 2012. The test results from GMM indicate that all the examined determinants have significant relationship with leverage. It has a negative value with liquidity, non-debt tax shield, profitability, size and growth. The Egyptian firms have some uniqueness in its trend. Current assets, debt ratio and liquidity behave positively with leverage except for growth. The other tested determinants in Egyptian companies are found to be not significant.

  15. X-ray structure determination and deuteration of nattokinase

    International Nuclear Information System (INIS)

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

    2013-01-01

    X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D 2 O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D 2 O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis

  16. X-ray structure determination and deuteration of nattokinase

    Energy Technology Data Exchange (ETDEWEB)

    Yanagisawa, Yasuhide [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Chatake, Toshiyuki [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki [Kurashiki University of Science and the Arts, 2640 Nishinoura, Tsurajima-cho, Kurashiki, Okayama 712-8505 (Japan); Kawaguchi, Akio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Chiba-Kamosida, Kaori [Nippon Advanced Technology Co. Ltd, J-PARC, 2-4 Shirane Shirakata, Tokai, Ibaraki 319-1195 (Japan); Ogawa, Megumi; Adachi, Tatsumi [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Morimoto, Yukio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan)

    2013-11-01

    X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D{sub 2}O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D{sub 2}O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

  17. Overconfidence, Managerial Optimism, and the Determinants of Capital Structure

    Directory of Open Access Journals (Sweden)

    Alexandre di Miceli da Silveira

    2008-12-01

    Full Text Available This research examines the determinants of the capital structure of firms introducing a behavioral perspective that has received little attention in corporate finance literature. The following central hypothesis emerges from a set of recently developed theories: firms managed by optimistic and/or overconfident people will choose more levered financing structures than others, ceteris paribus. We propose different proxies for optimism/overconfidence, based on the manager’s status as an entrepreneur or non-entrepreneur, an idea that is supported by theories and solid empirical evidence, as well as on the pattern of ownership of the firm’s shares by its manager. The study also includes potential determinants of capital structure used in earlier research. We use a sample of Brazilian firms listed in the Sao Paulo Stock Exchange (Bovespa in the years 1998 to 2003. The empirical analysis suggests that the proxies for the referred cognitive biases are important determinants of capital structure. We also found as relevant explanatory variables: profitability, size, dividend payment and tangibility, as well as some indicators that capture the firms’ corporate governance standards. These results suggest that behavioral approaches based on human psychology research can offer relevant contributions to the understanding of corporate decision making.

  18. Experimental determination of the structure of H3+

    International Nuclear Information System (INIS)

    Gaillard, M.J.; Gemmell, D.S.; Goldring, G.; Levine, I.; Pietsch, W.J.; Poizat, J.C.; Ratkowski, A.J.; Remillieux, J.; Vager, Z.; Zabransky, B.J.

    1978-01-01

    Three different measurements on the structure of the H 3 + molecular ion are reported. The measurements all make use of a new technique: the foil-induced dissociation of a fast molecular-ion beam. It is shown that the structure is equilaterally triangular in shape. The most probable length of side of the triangle is determined by the three measurements to be 0.97 +- 0.03 A, 0.95 +- 0.06 A, and 1.2 +- 0.2 A, respectively

  19. Sulfated oligosaccharide structures, as determined by NMR techniques

    Energy Technology Data Exchange (ETDEWEB)

    Noseda, M.D.; Duarte, M.E.R.; Tischer, C.A.; Gorin, P.A.J. [Parana Univ., Curitiba, PR (Brazil). Dept. De Bioquimica; Cerezo, A.S. [Buenos Aires Univ. Nacional (Argentina). Dept. de Quimica Organica

    1997-12-31

    Carrageenans are sulfated polysaccharides, produced by red seaweeds (Rhodophyta), that have important biological and physico-chemical properties. Using partial autohydrolysis, we obtained sulfated oligosaccharides from a {lambda}-carrageenan (Noseda and Cerezo, 1993). These oligosaccharides are valuable not only for the study of the structures of the parent carrageenans but also for their possible biological activities. In this work we determined the chemical structure of one of the sulfated oligosaccharides using 1D and 2D NMR techniques. (author) 4 refs., 8 figs., 1 tabs.

  20. Taking MAD to the extreme: ultrafast protein structure determination

    International Nuclear Information System (INIS)

    Walsh, M.A.; Dementieva, I.; Evans, G.; Sanishvili, R.; Joachimiak, A.

    1999-01-01

    Multiwavelength anomalous diffraction data were measured in 23 min from a 16 kDa selenomethionyl-substituted protein, producing experimental phases to 2.25 (angstrom) resolution. The data were collected on a mosaic 3 x 3 charge-coupled device using undulator radiation from the Structural Biology Center 19ID beamline at the Argonne National Laboratory's Advanced Photon Source. The phases were independently obtained semiautomatically by two crystallographic program suites, CCP4 and CNS. The quality and speed of this data acquisition exemplify the opportunities at third-generation synchrotron sources for high-throughput protein crystal structure determination

  1. Implantation measurements to determine tritium permeation in first wall structures

    International Nuclear Information System (INIS)

    Holland, D.F.; Causey, R.A.

    1983-01-01

    A principal safety concern for a D-T burning fusion reactor is release of tritium during routine operation. Tritium implantation into first wall structures, and subsequent permeation into coolants, is potentially an important source of tritium loss. This paper reports on an experiment in which an ion accelerator was used to implant deuterium atoms in a stainless steel disk to simulate tritium implantation in first wall structures. The permeation rate was measured under various operating conditions. These results were used in the TMAP computer code to determine potential tritium loss rates for fusion reactors

  2. DETERMINANT FACTORS OF THE CAPITAL STRUCTURE OF BRAZILIAN TECHNOLOGY COMPANIES

    Directory of Open Access Journals (Sweden)

    Camila Freitas Sant´Ana

    2015-12-01

    Full Text Available The purpose of this study is to identify determinant factors of the capital structure of Brazilian technology companies. The research was characterized as descriptive, document and quantitative, consisting of 21 companies in the communications, telecommunications and digital industry, according to the Exame magazine ranking. The analysis was established from 2009 to 2013 using panel data regression. The results indicate that the growth rate of capital and control type have a positive relationship with the general and long-term debt. However, it was found that company size, profitability and type of capital point to a negative relationship with the capital structure.

  3. Structure determination of T-cell protein-tyrosine phosphatase

    DEFF Research Database (Denmark)

    Iversen, L.F.; Møller, K. B.; Pedersen, A.K.

    2002-01-01

    Protein-tyrosine phosphatase 1B (PTP1B) has recently received much attention as a potential drug target in type 2 diabetes. This has in particular been spurred by the finding that PTP1B knockout mice show increased insulin sensitivity and resistance to diet-induced obesity. Surprisingly, the highly...... homologous T cell protein-tyrosine phosphatase (TC-PTP) has received much less attention, and no x-ray structure has been provided. We have previously co-crystallized PTP1B with a number of low molecular weight inhibitors that inhibit TC-PTP with similar efficiency. Unexpectedly, we were not able to co...... the high degree of functional and structural similarity between TC-PTP and PTP1B, we have been able to identify areas close to the active site that might be addressed to develop selective inhibitors of each enzyme....

  4. Fortuitous structure determination of ‘as-isolated’ Escherichia coli bacterioferritin in a novel crystal form

    International Nuclear Information System (INIS)

    Eerde, André van; Wolterink-van Loo, Suzanne; Oost, John van der; Dijkstra, Bauke W.

    2006-01-01

    E. coli bacterioferritin was crystallized in a novel crystal form from different conditions and the structure was solved. The crystals belonged to space group P2 1 3 and diffracted to a resolution of 2.5 Å. Escherichia coli bacterioferritin was serendipitously crystallized in a novel cubic crystal form and its structure could be determined to 2.5 Å resolution despite a high degree of merohedral twinning. This is the first report of crystallographic data on ‘as-isolated’ E. coli bacterioferritin. The ferroxidase active site contains positive difference density consistent with two metal ions that had co-purified with the protein. X-ray fluorescence studies suggest that the metal composition is different from that of previous structures and is a mix of zinc and native iron ions. The ferroxidase-centre configuration displays a similar flexibility as previously noted for other bacterioferritins

  5. The potential for biological structure determination with pulsed neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, C.C. [CLRC Rutherford Appleton Laboratory, Chilton Didcot Oxon (United Kingdom)

    1994-12-31

    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed.

  6. The potential for biological structure determination with pulsed neutrons

    International Nuclear Information System (INIS)

    Wilson, C.C.

    1994-01-01

    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed

  7. Determining the helicity structure of third generation resonances

    International Nuclear Information System (INIS)

    Papaefstathiou, Andreas

    2011-11-01

    We examine methods that have been proposed for determining the helicity structure of decays of new resonances to third generation quarks and/or leptons. We present analytical and semi-analytical predictions and assess the applicability of the relevant variables in realistic reconstruction scenarios using Monte Carlo-generated events, including the effects of QCD radiation and multiple parton interactions, combinatoric ambiguities and fast detector simulation. (orig.)

  8. MOTIVATION INTERNALIZATION AND SIMPLEX STRUCTURE IN SELF-DETERMINATION THEORY.

    Science.gov (United States)

    Ünlü, Ali; Dettweiler, Ulrich

    2015-12-01

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

  9. Determinants of capital structure: evidence from the Czech automotive industry

    Directory of Open Access Journals (Sweden)

    Pavlína Pinková

    2012-01-01

    Full Text Available The objective of the paper is to identify the determinants influencing the capital structure of large and medium-sized enterprises of the automotive industry in the Czech Republic. The sample consists of 100 companies belonging to NACE division 29. The data come from financial statements of selected companies and cover a period from 2006 to 2010. For the purpose of the paper quantitative research is used. The selection of appropriate dependent and independent is realized on the basis of secondary research on studies of capital structure. The analysis of variance, correlation and regression analyses have been performed to see the nature of relationship between variables. Size, tangibility, profitability and liquidity appear to be relevant determinants of capital structure. Growth is not a statistically significant determinant of leverage. It has been observed that the maturity of debt has to be considered, since the investigation of total debt only does not provide precious results. The findings do not unequivocally support either the static trade-off theory or the pecking order theory.

  10. Local magnetic structure determination using polarized neutron holography

    International Nuclear Information System (INIS)

    Szakál, Alex; Markó, Márton; Cser, László

    2015-01-01

    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems

  11. DNA nanotubes for NMR structure determination of membrane proteins.

    Science.gov (United States)

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

    2013-04-01

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

  12. Structural determinants and mechanism of HIV-1 genome packaging.

    Science.gov (United States)

    Lu, Kun; Heng, Xiao; Summers, Michael F

    2011-07-22

    Like all retroviruses, the human immunodeficiency virus selectively packages two copies of its unspliced RNA genome, both of which are utilized for strand-transfer-mediated recombination during reverse transcription-a process that enables rapid evolution under environmental and chemotherapeutic pressures. The viral RNA appears to be selected for packaging as a dimer, and there is evidence that dimerization and packaging are mechanistically coupled. Both processes are mediated by interactions between the nucleocapsid domains of a small number of assembling viral Gag polyproteins and RNA elements within the 5'-untranslated region of the genome. A number of secondary structures have been predicted for regions of the genome that are responsible for packaging, and high-resolution structures have been determined for a few small RNA fragments and protein-RNA complexes. However, major questions regarding the RNA structures (and potentially the structural changes) that are responsible for dimeric genome selection remain unanswered. Here, we review efforts that have been made to identify the molecular determinants and mechanism of human immunodeficiency virus type 1 genome packaging. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. Defining an essence of structure determining residue contacts in proteins.

    Science.gov (United States)

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

    2009-12-01

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

  14. Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

    Science.gov (United States)

    Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

    2016-04-01

    Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions.

  15. Laparoscopy After Previous Laparotomy

    Directory of Open Access Journals (Sweden)

    Zulfo Godinjak

    2006-11-01

    Full Text Available Following the abdominal surgery, extensive adhesions often occur and they can cause difficulties during laparoscopic operations. However, previous laparotomy is not considered to be a contraindication for laparoscopy. The aim of this study is to present that an insertion of Veres needle in the region of umbilicus is a safe method for creating a pneumoperitoneum for laparoscopic operations after previous laparotomy. In the last three years, we have performed 144 laparoscopic operations in patients that previously underwent one or two laparotomies. Pathology of digestive system, genital organs, Cesarean Section or abdominal war injuries were the most common causes of previouslaparotomy. During those operations or during entering into abdominal cavity we have not experienced any complications, while in 7 patients we performed conversion to laparotomy following the diagnostic laparoscopy. In all patients an insertion of Veres needle and trocar insertion in the umbilical region was performed, namely a technique of closed laparoscopy. Not even in one patient adhesions in the region of umbilicus were found, and no abdominal organs were injured.

  16. Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei

    Energy Technology Data Exchange (ETDEWEB)

    Begley, Darren W.; Hartley, Robert C.; Davies, Douglas R.; Edwards, Thomas E.; Leonard, Jess T.; Abendroth, Jan; Burris, Courtney A.; Bhandari, Janhavi; Myler, Peter J.; Staker, Bart L.; Stewart, Lance J. (UWASH); (Emerald)

    2011-09-28

    As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.

  17. Assessment of carotid plaque vulnerability using structural and geometrical determinants

    International Nuclear Information System (INIS)

    Li, Z.Y.; Tang, T.; U-King-Im, J.; Graves, M.; Gillard, J.H.; Sutcliffe, M.

    2008-01-01

    Because many acute cerebral ischemic events are caused by rupture of vulnerable carotid atheroma and subsequent thrombosis, the present study used both idealized and patient-specific carotid atheromatous plaque models to evaluate the effect of structural determinants on stress distributions within plaque. Using a finite element method, structural analysis was performed using models derived from in vivo high-resolution magnetic resonance imaging (MRI) of carotid atheroma in 40 non-consecutive patients (20 symptomatic, 20 asymptomatic). Plaque components were modeled as hyper-elastic materials. The effects of varying fibrous cap thickness, lipid core size and lumen curvature on plaque stress distributions were examined. Lumen curvature and fibrous cap thickness were found to be major determinants of plaque stress. The size of the lipid core did not alter plaque stress significantly when the fibrous cap was relatively thick. The correlation between plaque stress and lumen curvature was significant for both symptomatic (p=0.01; correlation coefficient: 0.689) and asymptomatic patients (p=0.01; correlation coefficient: 0.862). Lumen curvature in plaques of symptomatic patients was significantly larger than those of asymptomatic patients (1.50±1.0 mm -1 vs 1.25±0.75 mm -1 ; p=0.01). Specific plaque morphology (large lumen curvature and thin fibrous cap) is closely related to plaque vulnerability. Structural analysis using high-resolution MRI of carotid atheroma may help in detecting vulnerable atheromatous plaque and aid the risk stratification of patients with carotid disease. (author)

  18. X-ray structure determination and deuteration of nattokinase.

    Science.gov (United States)

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

    2013-11-01

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

  19. What determines the structures of native folds of proteins?

    International Nuclear Information System (INIS)

    Trovato, Antonio; Hoang, Trinh X; Banavar, Jayanth R; Maritan, Amos; Seno, Flavio

    2005-01-01

    We review a simple physical model (Hoang et al 2004 Proc. Natl Acad. Sci. USA 101 7960, Banavar et al 2004 Phys. Rev. E at press) which captures the essential physico-chemical ingredients that determine protein structure, such as the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by hydrogen bonds, sterics, and hydrophobicity. Within this framework, marginally compact conformations resembling the native state folds of proteins emerge as competing minima in the free energy landscape. Here we demonstrate that a hydrophobic-polar (HP) sequence composed of regularly repeated patterns has as its ground state a β-helical structure remarkably similar to a known architecture in the Protein Data Bank

  20. Host Proteins Determine MRSA Biofilm Structure and Integrity

    DEFF Research Database (Denmark)

    Dreier, Cindy; Nielsen, Astrid; Jørgensen, Nis Pedersen

    Human extracellular matrix (hECM) proteins aids the initial attachment and initiation of an infection, by specific binding to bacterial cell surface proteins. However, the importance of hECM proteins in structure, integrity and antibiotic resilience of a biofilm is unknown. This study aims...... to determine how specific hECM proteins affect S. aureus USA300 JE2 biofilms. Biofilms were grown in the presence of synovial fluid from rheumatoid arteritis patients to mimic in vivo conditions, where bacteria incorporate hECM proteins into the biofilm matrix. Difference in biofilm structure, with and without...... addition of hECM to growth media, was visualized by confocal laser scanning microscopy. Two enzymatic degradation experiments were used to study biofilm matrix composition and importance of hECM proteins: enzymatic removal of specific hECM proteins from growth media, before biofilm formation, and enzymatic...

  1. Purification and primary structure determination of human lysosomal dipeptidase.

    Science.gov (United States)

    Dolenc, Iztok; Mihelic, Marko

    2003-02-01

    The lysosomal metallopeptidase is an enzyme that acts preferentially on dipeptides with unsubstituted N- and C-termini. Its activity is highest in slightly acidic pH. Here we describe the isolation and characterization of lysosomal dipeptidase from human kidney. The isolated enzyme has the amino-terminal sequence DVAKAIINLAVY and is a homodimer with a molecular mass of 100 kDa. So far no amino acid sequence has been determined for this metallopeptidase. The complete primary structure as deduced from the nucleotide sequence revealed that the isolated dipeptidase is similar to blood plasma glutamate carboxypeptidase.

  2. Structure determination of spider silk from X-ray images

    Energy Technology Data Exchange (ETDEWEB)

    Ulrich, Stephan; Zippelius, Annette [Universitaet Goettingen, Institut fuer Theoretische Physik (Germany); Meling, Martin [Max-Planck-Institut fuer biophysikalische Chemie, Goettingen (Germany); Glisovic, Anja; Salditt, Tim [Universitaet Goettingen, Institut fuer Roentgenphysik (Germany)

    2008-07-01

    Spider silk consists of interconnected crystallites, which are typically aligned along the fiber axis. We present a method to systematically determine the structure of these crystallites. Hereby we introduce a model that calculates the scattering function G(q) which is fitted to the measured X-ray image (silk from nephila clavipes). With it, the crystallites' size, the constitution and dimensions of their unit cell, as well as their tilt with respect to the fiber axis is identified, and furthermore the effect of coherent scattering from different crystallites is investigated. The shown methods and the presented model can easily be generalized to a wide class of composite materials.

  3. Precise equilibrium structure determination of hydrazoic acid (HN3) by millimeter-wave spectroscopy

    International Nuclear Information System (INIS)

    Amberger, Brent K.; Esselman, Brian J.; Woods, R. Claude; McMahon, Robert J.; Stanton, John F.

    2015-01-01

    The millimeter-wave spectrum of hydrazoic acid (HN 3 ) was analyzed in the frequency region of 235-450 GHz. Transitions from a total of 14 isotopologues were observed and fit using the A-reduced or S-reduced Hamiltonian. Coupled-cluster calculations were performed to obtain a theoretical geometry, as well as rotation-vibration interaction corrections. These calculated vibration-rotation correction terms were applied to the experimental rotational constants to obtain mixed theoretical/experimental equilibrium rotational constants (A e , B e , and C e ). These equilibrium rotational constants were then used to obtain an equilibrium (R e ) structure using a least-squares fitting routine. The R e structural parameters are consistent with a previously published R s structure, largely falling within the uncertainty limits of that R s structure. The present R e geometric parameters of HN 3 are determined with exceptionally high accuracy, as a consequence of the large number of isotopologues measured experimentally and the sophisticated (coupled-cluster theoretical treatment (CCSD(T))/ANO2) of the vibration-rotation interactions. The R e structure exhibits remarkable agreement with the CCSD(T)/cc-pCV5Z predicted structure, validating both the accuracy of the ab initio method and the claimed uncertainties of the theoretical/experimental structure determination

  4. Simple surface structure determination from Fourier transforms of angle-resolved photoemission extended fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y. [Pennsylvania State Univ., University Park, PA (United States)]|[Lawrence Berkeley Lab., CA (United States); Shirley, D.A. [Pennsylvania State Univ., University Park, PA (United States)

    1995-02-01

    The authors show by Fourier analyses of experimental data, with no further treatment, that the positions of all the strong peaks in Fourier transforms of angle-resolved photoemission extended fine structure (ARPEFS) from adsorbed surfaces can be explicitly predicted from a trial structure with an accuracy of about {+-} 0.3 {angstrom} based on a single-scattering cluster model together with the concept of a strong backscattering cone, and without any additional analysis. This characteristic of ARPEFS Fourier transforms can be developed as a simple method for determining the structures of adsorbed surfaces to an accuracy of about {+-} 0.1 {angstrom}.

  5. PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.

    Science.gov (United States)

    Lee, Woonghee; Kim, Jin Hae; Westler, William M; Markley, John L

    2011-06-15

    PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY ((13)C-edited and/or (15)N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/.

  6. Structure determination by photoelectron diffraction of small molecules on surfaces

    International Nuclear Information System (INIS)

    Booth, N.A.

    1998-05-01

    The synchrotron radiation based technique of Photoelectron Diffraction (PhD) has been applied to three adsorption systems. Structure determinations, are presented for each system which involve the adsorption of small molecules on the low index {110} plane of single crystal Cu and Ni substrates. For the NH 3 -Cu(110) system PhD was successful in determining a N-Cu bondlength of 2.05 ± 0.03 A as well as values for the anisotropic vibrational amplitudes of the N and an expansion of the 1st to 2nd Cu substrate layer spacing from the bulk value of 0.08 ± 0.08 A. The most significant and surprising structural parameter determined for this system was that the N atom occupies an asymmetric adsorption site. Rather than being situated in the expected high symmetry atop site the N atom was found to be offset parallel to the surface by 0.37 ± 0.12 A in the [001] azimuth. In studying the glycine-Cu(110) system the adsorption structure of an amino-acid has been quantified. The local adsorption geometries of all the atoms involved in the molecule to surface bond have been determined. The glycine molecule is found to be bonded to the surface via both its amino and carboxylate functional groups. The molecule straddles two [11-bar0] rows of the Cu substrate. The two O atoms are found to be in identical sites both approximately atop Cu atoms on the [11-bar0] rows offset parallel to the surface by 0.80 ± 0.05 A in the [001] azimuth, the O-Cu bondlength was found to be 2.03 ± 0.05 A. The N atom was also found to adsorb in an approximately atop geometry but offset parallel to the surface by 0.24 ± 0.10A in the [11-bar0] direction, the N-Cu bondlength was found to be 2.05± 0.05 A. PhD was unsuccessful in determining the positions of the two C atoms that form a bridge between the two functional groups bonded to the surface due to difficulties in separating the two inequivalent contributions to the final intensity modulation function. For the CN-Ni(110) system both PhD and Near Edge

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

    Science.gov (United States)

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

    2018-02-02

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

  8. Production, purification, crystallization and structure determination of H-1 Parvovirus

    International Nuclear Information System (INIS)

    Halder, Sujata; Nam, Hyun-Joo; Govindasamy, Lakshmanan; Vogel, Michèle; Dinsart, Christiane; Salomé, Nathalie; McKenna, Robert; Agbandje-McKenna, Mavis

    2012-01-01

    The production, purification, crystallization and crystallographic analysis of H-1 Parvovirus, a gene-therapy vector, are reported. Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7 Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 255.4, b = 350.4, c = 271.6 Å, β = 90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined

  9. Structure of HIV-1 protease determined by neutron crystallography

    International Nuclear Information System (INIS)

    Adachi, Motoyasu; Kuroki, Ryota

    2009-01-01

    HIV-1 protease is an aspartic protease, and plays an essential role in replication of HIV. To develop HIV-1 protease inhibitors through structure-based drug design, it is necessary to understand the catalytic mechanism and inhibitor recognition of HIV-1 protease. We have determined the crystal structure of HIV-1 protease in complex with KNI-272 to 1.9 A resolution by neutron crystallography in combination with 1.4 A resolution X-ray diffraction data. The results show that the carbonyl group of hydroxymethylcarbonyl (HMC) in KNI-272 forms a hydrogen bonding interaction with protonated Asp 25 and the hydrogen atom from the hydroxyl group of HMC forms a hydrogen bonding interaction with the deprotonated Asp125. This is the first neutron report for HIV-1/inhibitor complex and shows directly the locations of key hydrogen atoms in catalysis and in the binding of a transition-state analog. The results confirm key aspect of the presumed catalytic mechanism of HIV-1 protease and will aid in the further development of protease inhibitors. (author)

  10. Determination of subsurface geological structure with borehole gravimetry

    International Nuclear Information System (INIS)

    Clark, S.R.; Hearst, J.R.

    1983-07-01

    Conventional gamma-gamma and gravimetric density measurements are routinely gathered for most holes used for underground nuclear tests. The logs serve to determine the subsurface structural geology near the borehole. The gamma-gamma density log measures density of the rock within about 15 cm of the borehole wall. The difference in gravity measured at two depths in a borehole can be interpreted in terms of the density of an infinite, homogeneous, horizontal bed between those depths. When the gravimetric density matches the gamma-gamma density over a given interval it is assumed that the bed actualy exists, and that rocks far from the hole must be the same as those encountered adjacent to the borehole. Conversely, when the gravimetric density differs from the gamma-gamma density it is apparent that the gravimeter is being influenced by a rock mass of different density than that at the hole wall. This mismatch can be a powerful tool to deduce the local structural geology. The geology deduced from gravity mesurements in emplacement hole, U4al, and the associated exploratory hole, UE4al, is an excellent example of the power of the method

  11. Determination of scattering structures from spatial coherence measurements.

    Science.gov (United States)

    Zarubin, A M

    1996-03-01

    A new method of structure determination and microscopic imaging with short-wavelength radiations (charged particles, X-rays, neutrons), based on measurements of the modulus and the phase of the degree of spatial coherence of the scattered radiation, is developed. The underlying principle of the method--transfer of structural information about the scattering potential via spatial coherence of the secondary (scattering) source of radiation formed by this potential--is expressed by the generalization of the van Cittert-Zernike theorem to wave and particle scattering [A.M. Zarubin, Opt. Commun. 100 (1993) 491; Opt. Commun. 102 (1993) 543]. Shearing interferometric techniques are proposed for implementing the above measurements; the limits of spatial resolution attainable by reconstruction of the absolute square of a 3D scattering potential and its 2D projections from the measurements are analyzed. It is shown theoretically that 3D imaging with atomic resolution can be realized in a "synthetic aperture" electron or ion microscope and that a 3D resolution of about 6 nm can be obtained with a "synthetic aperture" X-ray microscope. A proof-of-principle optical experiment is presented.

  12. A Determination of the Neutron Spin Structure Function

    Energy Technology Data Exchange (ETDEWEB)

    Hughes, Emlyn W

    2003-08-18

    The authors report the results of the experiment E142 which measured the spin dependent structure function of the neutron, g{sub 1}{sup n}(x, Q{sup 2}). The experiment was carried out at the Stanford Linear Accelerator Center by measuring an asymmetry in the deep inelastic scattering of polarized electrons from a polarized {sup 3}He target, at electron energies from 19 to 26 GeV. The structure function was determined over the kinematic range 0.03 < BJorken x < 0.6 and 1.0 < Q{sup 2} < 5.5 (GeV/c){sup 2}. An evaluation of the integral {integral}{sub 0}{sup 1} g{sub 1}{sup n}(x,Q{sup 2})dx at fixed Q{sup 2} = 2 (GeV/c){sup 2} yields the final result {Lambda}{sub 1}{sup n} = -0.032 {+-} 0.006 (stat.) {+-} 0.009 (syst.). This result, when combined with the integral of the proton spin structure function measured in other experiments, confirms the fundamental Bjorken sum rule with O({alpha}{sub s}{sup 3}) corrections to within one standard deviation. This is a major success for perturbative Quantum Chromodynamics. Some ancillary results include the findings that the Ellis-Jaffe sum rule for the neutron is violated at the 2 {sigma} level, and that the total contribution of the quarks to the helicity of the nucleon is 0.36 {+-} 0.10. The strange sea polarization is estimated to be small and negative, {Delta}s = -0.07 {+-} 0.04.

  13. Determinants of the capital structure of Portuguese firms with investments in Angola

    Directory of Open Access Journals (Sweden)

    Jorge H.F. Mota

    2017-02-01

    Full Text Available Background: This article seeks to complement the previous literature and clarify the particularities of the capital structure policy of firms with foreign direct investment in Angola. Aim: This article seeks to identify the determinants of the capital structure of Portuguese firms with direct investment in Angola and to understand whether the determinants normally considered by standard finance theory are in line with those used by firms when structuring their capital structure policy to participate in the specific market of Angola. Setting: This article examines 26 large Portuguese firms with investments in Angola using econometric panel data for the period 2006–2010. Methods: The study applied fixed and random effects methods and panel-corrected standard errors that maintain efficiency and unbiased behaviour even in the presence of panel-level heteroscedasticity and contemporaneous correlation of observations among panels. Results: The results provide evidence that the determinants normally considered by standard finance theory are in fact – in terms of sign and coefficient dimension – those used by firms for structuring their capital structure policy when involved in the internationalisation process of entering Angola. Specifically, age, asset structure, return on assets and tangibility have a positive influence on the capital structure of Portuguese firms that have invested in Angola, while non-debt tax shields and liquidity have a negative influence on these companies’ leverage ratios. When comparing our results with studies that have analysed the capital structure determinants of listed Portuguese firms – firms belonging to the PSI 20 Index and large firms in the Portuguese corporate sector – we found similarities in the sign and coefficient dimension of the determinants of capital structure. However, the profitability coefficient sign is in line with the trade-off framework (i.e. profitability is positively related to debt but

  14. Determination of the crystalline structure of scale solids from the 16H evaporator gravity drain line to tank 38H

    Energy Technology Data Exchange (ETDEWEB)

    Oji, L. N. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-10-01

    August 2015, scale solids from the 16H Evaporator Gravity Drain Line (GDL) to the Tank 38H were delivered to SRNL for analysis. The desired analytical goal was to identify and confirm the crystalline structure of the scale material and determine if the form of the aluminosilicate mineral was consistent with previous analysis of the scale material from the GDL.

  15. Simulating liquid water for determining its structural and transport properties

    International Nuclear Information System (INIS)

    Arismendi-Arrieta, Daniel; Medina, Juan S.; Fanourgakis, George S.; Prosmiti, Rita; Delgado-Barrio, Gerardo

    2014-01-01

    Molecular dynamics simulations are carried out for calculating structural and transport properties of pure liquid water, such as radial distribution functions and self-diffusion and viscosity coefficients, respectively. We employed reparameterized versions of the ab initio water potential by Niesar, Clementi and Corongiu (NCC). In order to investigate the role of the electrostatic contribution, the partial charges of the NCC model are adjusted so that to reproduce the dipole moment values of the SPC/E, SPC/Fw and TIP4P/2005 water models. The single and collective transport coefficients are obtained by employing the Green–Kubo relations at various temperatures. Additionally, in order to overcome convergence difficulties arising from the long correlation times of the stress-tensor autocorrelation functions, a previously reported fitting scheme was employed. The present results indicate that there is a significant relationship between the dipole moment value of the model, and the calculated transport coefficients. We found that by adjusting the molecular dipole moment of the NCC to the value of the TIP4P/2005, the obtained values for the self-diffusion and viscosity coefficients are in better agreement with experiment, compared to the values obtained with the original NCC model. Even though the predictions of the present model exhibits an overall correct behavior, we conclude that further improvements are still required. In order to achieve that, a careful reparameterization of the repulsion–dispersion terms of the potential model is proposed. Also, the effect of the inclusion of many-body effects such as polarizability, should also be investigated. - Highlights: ► Transport properties of liquid water are important in bio-simulations. ► Self-diffusion coefficient, shear and bulk viscosities calculations from NVE molecular dynamics simulations. ► Their comparison with experimental data provides information on intermolecular forces, and serve to develop water

  16. Surface buckling of black phosphorus: Determination, origin, and influence on electronic structure

    Science.gov (United States)

    Dai, Zhongwei; Jin, Wencan; Yu, Jie-Xiang; Grady, Maxwell; Sadowski, Jerzy T.; Kim, Young Duck; Hone, James; Dadap, Jerry I.; Zang, Jiadong; Osgood, Richard M.; Pohl, Karsten

    2017-12-01

    The surface structure of black phosphorus materials is determined using surface-sensitive dynamical microspot low energy electron diffraction (μ LEED ) analysis using a high spatial resolution low energy electron microscopy (LEEM) system. Samples of (i) crystalline cleaved black phosphorus (BP) at 300 K and (ii) exfoliated few-layer phosphorene (FLP) of about 10 nm thickness which were annealed at 573 K in vacuum were studied. In both samples, a significant surface buckling of 0.22 Å and 0.30 Å, respectively, is measured, which is one order of magnitude larger than previously reported. As direct evidence for large buckling, we observe a set of (for the flat surface forbidden) diffraction spots. Using first-principles calculations, we find that the presence of surface vacancies is responsible for the surface buckling in both BP and FLP, and is related to the intrinsic hole doping of phosphoresce materials previously reported.

  17. Spectrophotometric determination of uranium with arsenazo previous liquid-liquid extraction and colour development in organic medium; Determinacion espectrofotometrica de uranio con arsenazo, previa extraccion y desarrollo del color en medio organico

    Energy Technology Data Exchange (ETDEWEB)

    Palomares Delgado, F; Vera Palomino, J; Petrement Eguiluz, J C

    1964-07-01

    The determination of uranium with arsenazo is hindered by a great number of cation which form stable complexes with the reactive and may given rise to serious interferences. By studying the optimum conditions of uranium the extraction be means of tributylphosphate solutions dissolved in methylisobuthylketone, under conditions for previous masking of the interfering cations, an organic extract was obtained containing all the uranium together with small amounts of iron. The possible interference derived from the latter element is avoided by reduction with hydroxylammoniumchlorid followed by complex formation of the Fe(II)-ortophenantroline compound in alcoholic medium. (Author) 17 refs.

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

    Science.gov (United States)

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

    2010-01-01

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

  19. Structural Determinants of Autoproteolysis of the Haemophilus influenzae Hap Autotransporter▿

    Science.gov (United States)

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

    2009-01-01

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

  20. Rapid fold and structure determination of the archaeal translation elongation factor 1β from Methanobacterium thermoautotrophicum

    International Nuclear Information System (INIS)

    Kozlov, Guennadi; Ekiel, Irena; Beglova, Natalia; Yee, Adelinda; Dharamsi, Akil; Engel, Asaph; Siddiqui, Nadeem; Nong, Andrew; Gehring, Kalle

    2000-01-01

    The tertiary fold of the elongation factor, aEF-1β, from Methanobacterium thermoautotrophicum was determined in a high-throughput fashion using a minimal set of NMR experiments. NMR secondary structure prediction, deuterium exchange experiments and the analysis of chemical shift perturbations were combined to identify the protein fold as an alpha-beta sandwich typical of many RNA binding proteins including EF-G. Following resolution of the tertiary fold, a high resolution structure of aEF-1β was determined using heteronuclear and homonuclear NMR experiments and a semi-automated NOESY assignment strategy. Analysis of the aEF-1β structure revealed close similarity to its human analogue, eEF-1β. In agreement with studies on EF-Ts and human EF-1β, a functional mechanism for nucleotide exchange is proposed wherein Phe46 on an exposed loop acts as a lever to eject GDP from the associated elongation factor G-protein, aEF-1α. aEF-1β was also found to bind calcium in the groove between helix α2 and strand β4. This novel feature was not observed previously and may serve a structural function related to protein stability or may play a functional role in archaeal protein translation

  1. Rapid fold and structure determination of the archaeal translation elongation factor 1{beta} from Methanobacterium thermoautotrophicum

    Energy Technology Data Exchange (ETDEWEB)

    Kozlov, Guennadi [McGill University, Department of Biochemistry (Canada); Ekiel, Irena [National Research Council of Canada, Biomolecular NMR Group, Sector of Pharmaceutical Biotechnology, Biotechnology Research Institute (Canada); Beglova, Natalia [McGill University, Department of Biochemistry (Canada); Yee, Adelinda; Dharamsi, Akil; Engel, Asaph [University of Toronto, Department of Medical Biophysics (Canada); Siddiqui, Nadeem; Nong, Andrew; Gehring, Kalle [McGill University, Department of Biochemistry (Canada)

    2000-07-15

    The tertiary fold of the elongation factor, aEF-1{beta}, from Methanobacterium thermoautotrophicum was determined in a high-throughput fashion using a minimal set of NMR experiments. NMR secondary structure prediction, deuterium exchange experiments and the analysis of chemical shift perturbations were combined to identify the protein fold as an alpha-beta sandwich typical of many RNA binding proteins including EF-G. Following resolution of the tertiary fold, a high resolution structure of aEF-1{beta} was determined using heteronuclear and homonuclear NMR experiments and a semi-automated NOESY assignment strategy. Analysis of the aEF-1{beta} structure revealed close similarity to its human analogue, eEF-1{beta}. In agreement with studies on EF-Ts and human EF-1{beta}, a functional mechanism for nucleotide exchange is proposed wherein Phe46 on an exposed loop acts as a lever to eject GDP from the associated elongation factor G-protein, aEF-1{alpha}. aEF-1{beta} was also found to bind calcium in the groove between helix {alpha}2 and strand {beta}4. This novel feature was not observed previously and may serve a structural function related to protein stability or may play a functional role in archaeal protein translation.

  2. The determinants of capital structure: the evidence from the European Union

    Directory of Open Access Journals (Sweden)

    Natalia Mokhova

    2013-01-01

    Full Text Available The aim of this study is to indicate the influence of several internal determinants on capital structure in different European countries and retrace its tendency taking into consideration the membership of the European Union. Nowadays there are a lot of debates according the future of the European Union. The recent global financial crisis and the following European debt crisis show the significance of the country financial stability and its impact on the private sector. The paper investigates 32 countries of European Union dividing them into three groups as (1 old EU members (15 countries, (2 new EU members (12 countries and (3 EU candidates (4 candidate countries and 1 acceding country.The managers make their financial decisions according to the source of financing and capital structure based on the macroeconomic conditions and country specifics and obviously on company’s advantages and disadvantages, i.e. its internal characteristics. Based on the analysis of previous studies we have chosen several significant internal determinants of capital structure as profitability, tangibility, growth opportunities, non-debt tax shields and firm’s size.The findings show that the country’s specifics, EU membership and corporate debt structure influence the relation between capital structure and its internal characteristics. The capital structure in all countries has tendency to increase, furthermore the old members rely more on debt then candidates or new members.There is no doubt that the majority of countries support Pecking Order Theory then Trade off Theory regarding investigated relations. In most countries the profitability and size have negative and significant influence on corporate capital structure. At the same time tangibility, growth opportunities and non-debt tax shields split up: selected countries experience positive impact, another part negative, supporting different theories.

  3. Purification, crystallization and structure determination of native GroEL from Escherichia coli lacking bound potassium ions

    International Nuclear Information System (INIS)

    Kiser, Philip D.; Lodowski, David T.; Palczewski, Krzysztof

    2007-01-01

    A 3.02 Å crystal structure of native GroEL from E. coli is presented. GroEL is a member of the ATP-dependent chaperonin family that promotes the proper folding of many cytosolic bacterial proteins. The structures of GroEL in a variety of different states have been determined using X-ray crystallography and cryo-electron microscopy. In this study, a 3.02 Å crystal structure of the native GroEL complex from Escherichia coli is presented. The complex was purified and crystallized in the absence of potassium ions, which allowed evaluation of the structural changes that may occur in response to cognate potassium-ion binding by comparison to the previously determined wild-type GroEL structure (PDB code http://www.rcsb.org/pdb/explore.do?structureId), in which potassium ions were observed in all 14 subunits. In general, the structure is similar to the previously determined wild-type GroEL crystal structure with some differences in regard to temperature-factor distribution

  4. CCDC 1416891: Experimental Crystal Structure Determination : Methyl-triphenyl-germanium

    KAUST Repository

    Bernatowicz, Piotr; Shkurenko, Aleksander; Osior, Agnieszka; Kamieński, Bohdan; Szymański, Sławomir

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from

  5. Structural determinants of phenotypic diversity and replication rate of human prions.

    Directory of Open Access Journals (Sweden)

    Jiri G Safar

    2015-04-01

    Full Text Available The infectious pathogen responsible for prion diseases is the misfolded, aggregated form of the prion protein, PrPSc. In contrast to recent progress in studies of laboratory rodent-adapted prions, current understanding of the molecular basis of human prion diseases and, especially, their vast phenotypic diversity is very limited. Here, we have purified proteinase resistant PrPSc aggregates from two major phenotypes of sporadic Creutzfeldt-Jakob disease (sCJD, determined their conformational stability and replication tempo in vitro, as well as characterized structural organization using recently emerged approaches based on hydrogen/deuterium (H/D exchange coupled with mass spectrometry. Our data clearly demonstrate that these phenotypically distant prions differ in a major way with regard to their structural organization, both at the level of the polypeptide backbone (as indicated by backbone amide H/D exchange data as well as the quaternary packing arrangements (as indicated by H/D exchange kinetics for histidine side chains. Furthermore, these data indicate that, in contrast to previous observations on yeast and some murine prion strains, the replication rate of sCJD prions is primarily determined not by conformational stability but by specific structural features that control the growth rate of prion protein aggregates.

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

    Directory of Open Access Journals (Sweden)

    Alexandre Presas

    2017-03-01

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

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

    Science.gov (United States)

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

    2017-03-22

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

  8. Application of molecular spectroscopy to the determination of organic structures

    International Nuclear Information System (INIS)

    Leicknam, J.P.

    1976-01-01

    Some brief accounts are presented followed by a discussion about various physico-chemical techniques: Raman spectrometry, infrared spectrometry, resonance Raman spectrometry, conformational analysis and polarized Rayleigh diffusion. Applications of the Nuclear Magnetic Resonance to nucleotide structure in aqueous solution are described as well as some applications of neutron scattering to the study of organic structures [fr

  9. CCDC 1408042: Experimental Crystal Structure Determination : 6,13-dimesitylpentacene

    KAUST Repository

    Shi, Xueliang

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  10. CCDC 1416891: Experimental Crystal Structure Determination : Methyl-triphenyl-germanium

    KAUST Repository

    Bernatowicz, Piotr

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  11. 5 THE DETERMINANTS OF FINANCIAL STRUCTURE IN THE ...

    African Journals Online (AJOL)

    these authors showed that the presence of imperfections in the market ... impact of financial structure on firm value, several theoretical and ... structure of for-profit organizations (Fama and French, 2000; .... compared to large companies to face the pressures that are generated .... assets' accounting value or the sales.

  12. Determining the Mechanical Properties of Lattice Block Structures

    Science.gov (United States)

    Wilmoth, Nathan

    2013-01-01

    Lattice block structures and shape memory alloys possess several traits ideal for solving intriguing new engineering problems in industries such as aerospace, military, and transportation. Recent testing at the NASA Glenn Research Center has investigated the material properties of lattice block structures cast from a conventional aerospace titanium alloy as well as lattice block structures cast from nickel-titanium shape memory alloy. The lattice block structures for both materials were sectioned into smaller subelements for tension and compression testing. The results from the cast conventional titanium material showed that the expected mechanical properties were maintained. The shape memory alloy material was found to be extremely brittle from the casting process and only compression testing was completed. Future shape memory alloy lattice block structures will utilize an adjusted material composition that will provide a better quality casting. The testing effort resulted in baseline mechanical property data from the conventional titanium material for comparison to shape memory alloy materials once suitable castings are available.

  13. Quantitative x-ray structure determination of superlattices and interfaces

    International Nuclear Information System (INIS)

    Schuller, I.K.; Fullerton, E.E.

    1990-01-01

    This paper presents a general procedure for quantitative structural refinement of superlattice structures. To analyze a wide range of superlattices, the authors have derived a general kinematical diffraction formula that includes random, continuous and discrete fluctuations from the average structure. By implementing a non-linear fitting algorithm to fit the entire x-ray diffraction profile, refined parameters that describe the average superlattice structure, and deviations from this average are obtained. The structural refinement procedure is applied to a crystalline/crystalline Mo/Ni superlattices and crystalline/amorphous Pb/Ge superlattices. Roughness introduced artificially during growth in Mo/Ni superlattices is shown to be accurately reproduced by the refinement

  14. The Determinants of Capital Structure: Evidence from Listed Companies in Balkan Countries

    Directory of Open Access Journals (Sweden)

    Ajla Ngjeliu

    2018-03-01

    Full Text Available As most of the empirical literature regarding the determinants of capital structure relies on developed economies, this study contributes to the existing literature by looking at listed companies in the Balkan region. It investigates 760 companies over a 6-year period from 2007 to 2013 using a random effect model. The leverage is specified as a function of firm-specific characteristics, and the results are in line with previous empirical studies. Respectively, it is seen that a positive correlation is significant for size, while a negative one is found for profitability. Observing the decomposition of leverage, it can be assessed that the Balkan companies rely mostly on short-term debt. Furthermore, this study aims and finds significant differences between the determinants of capital structure of the companies established in EU and those in non-EU countries. The z-score indicated that when looking at the total debt ratio there is only one determinant which is statically significant.

  15. Adsorption properties and porous structure of sulfuric acid treated bentonites determined - SHORT COMMUNICATION

    Directory of Open Access Journals (Sweden)

    SNEZANA BREZOVSKA

    2005-02-01

    Full Text Available In a previous paper adsorption isotherms of benzene vapor on natural bentonite from Ginovci, Macedonia, and forms acid activated with 10 % and 15 % solutions of hydrochloric were interpreted by means of the Dubinin–Radushkevich–Stoeckli and Dubinin–Astakhov equations; the investigation has been continued with bentonites acid activated with 10 % and 15 % solutions of sulfuric acid where X-ray analysis indicates smaller structural changes. Using the above equations, the heterogeneity of the micropores and the energetic heterogeneity of the bentonites were determined from the differential distribution of the micropore volume with respect to the structural parameter of the equations characterizing the microporous structure and to the molar free energy of adsorption. Activated bentonites obtain bigger pores but also a certain quantity of new small pores appear during acid activation with the higher concentration of acid. The micropore volumes, determined from the adsorption of benzene vapor, of bentonites activated with 10 % and 15 % solution of hydrochloric acid (144.60 cm3 kg-1 and 110.06 cm3 kg-1, respectively, decrease in comparison with that of natural bentonite (162.55 cm3 kgv.1 In contrast, the values of the micropore volume for bentonities treated with 10 % and 15 % solutions of sulfuric acids increase (169.19 cm3 kg-1 and 227.74 cm3 kg-1. That is due to the difference in the structural changes occurring during activation with hydrochloric and sulfuric acids. The values of the free energy of adsorption of benzene vapor for natural bentonite are higher than those of the acid acitivated bentonities, what is in accordance with the structural and porosity changes.

  16. Structural determinants of reductive terpene cyclization in iridoid biosynthesis

    DEFF Research Database (Denmark)

    Kries, Hajo; Caputi, Lorenzo; Stevenson, Clare E M

    2016-01-01

    The carbon skeleton of ecologically and pharmacologically important iridoid monoterpenes is formed in a reductive cyclization reaction unrelated to canonical terpene cyclization. Here we report the crystal structure of the recently discovered iridoid cyclase (from Catharanthus roseus) bound...

  17. Structure determination at room temperature and phase transition ...

    Indian Academy of Sciences (India)

    Unknown

    Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India. MS received 9 May 2002 ... exhibit a ferroelectric–paraelectric phase transition at ele- ..... The pattern decomposition and peak extraction methods ...

  18. Structural Determinants of Specific Lipid Binding to Potassium Channels

    NARCIS (Netherlands)

    Weingarth, M.H.|info:eu-repo/dai/nl/330985655; Prokofyev, A.; van der Cruijsen, E.A.W.|info:eu-repo/dai/nl/330826743; Nand, D.|info:eu-repo/dai/nl/337731403; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238; Pongs, O.; Baldus, M.|info:eu-repo/dai/nl/314410864

    2013-01-01

    We have investigated specific lipid binding to the pore domain of potassium channels KcsA and chimeric KcsAKv1.3 on the structural and functional level using extensive coarse-grained and atomistic molecular dynamics simulations, solid-state NMR, and single channel measurements. We show that, while

  19. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Unknown

    Although the method of structure completion when once the starting model is provided is ... In this article a survey of the recent development in this area is ..... The Monte Carlo method 4,9 differs from the traditional approaches as it operates in.

  20. Type of disturbance and ecological history determine structural stability.

    NARCIS (Netherlands)

    van der Wurff, A.W.G.; Kools, S.A.E.; Boivin, M.E.; van den Brink, P.J.; van den Megen, H.H.M.; Riksen, J.A.G.; Doroszuk, A.; Kammenga, J.E.

    2007-01-01

    This study aims to reveal whether complexity, namely, community and trophic structure, of chronically stressed soil systems is at increased risk or remains stable when confronted with a subsequent disturbance. Therefore, we focused on a grassland with a history of four centuries of patchy

  1. Type of disturbance and ecological history determine structural stability

    NARCIS (Netherlands)

    Wurff, van der A.W.G.; Kools, S.A.E.; Boivin, M.E.Y.; Brink, van den P.J.; Megen, van H.H.B.; Riksen, J.A.G.; Doroszuk, A.; Kammenga, J.E.

    2007-01-01

    This study aims to reveal whether complexity, namely, community and trophic structure, of chronically stressed soil systems is at increased risk or remains stable when confronted with a subsequent disturbance. Therefore, we focused on a grassland with a history of four centuries of patchy

  2. Heuristic Optimization Techniques for Determining Optimal Reserve Structure of Power Generating Systems

    DEFF Research Database (Denmark)

    Ding, Yi; Goel, Lalit; Wang, Peng

    2012-01-01

    cost of the system will also increase. The reserve structure of a MSS should be determined based on striking a balance between the required reliability and the reserve cost. The objective of reserve management for a MSS is to schedule the reserve at the minimum system reserve cost while maintaining......Electric power generating systems are typical examples of multi-state systems (MSS). Sufficient reserve is critically important for maintaining generating system reliabilities. The reliability of a system can be increased by increasing the reserve capacity, noting that at the same time the reserve...... the required level of supply reliability to its customers. In previous research, Genetic Algorithm (GA) has been used to solve most reliability optimization problems. However, the GA is not very computationally efficient in some cases. In this chapter a new heuristic optimization technique—the particle swarm...

  3. Structural insights into viral determinants of nematode mediated Grapevine fanleaf virus transmission.

    Directory of Open Access Journals (Sweden)

    Pascale Schellenberger

    2011-05-01

    Full Text Available Many animal and plant viruses rely on vectors for their transmission from host to host. Grapevine fanleaf virus (GFLV, a picorna-like virus from plants, is transmitted specifically by the ectoparasitic nematode Xiphinema index. The icosahedral capsid of GFLV, which consists of 60 identical coat protein subunits (CP, carries the determinants of this specificity. Here, we provide novel insight into GFLV transmission by nematodes through a comparative structural and functional analysis of two GFLV variants. We isolated a mutant GFLV strain (GFLV-TD poorly transmissible by nematodes, and showed that the transmission defect is due to a glycine to aspartate mutation at position 297 (Gly297Asp in the CP. We next determined the crystal structures of the wild-type GFLV strain F13 at 3.0 Å and of GFLV-TD at 2.7 Å resolution. The Gly297Asp mutation mapped to an exposed loop at the outer surface of the capsid and did not affect the conformation of the assembled capsid, nor of individual CP molecules. The loop is part of a positively charged pocket that includes a previously identified determinant of transmission. We propose that this pocket is a ligand-binding site with essential function in GFLV transmission by X. index. Our data suggest that perturbation of the electrostatic landscape of this pocket affects the interaction of the virion with specific receptors of the nematode's feeding apparatus, and thereby severely diminishes its transmission efficiency. These data provide a first structural insight into the interactions between a plant virus and a nematode vector.

  4. Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils.

    Science.gov (United States)

    Long, Xi-En; Yao, Huaiying; Wang, Juan; Huang, Ying; Singh, Brajesh K; Zhu, Yong-Guan

    2015-06-16

    Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.

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

    Science.gov (United States)

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

    2012-01-01

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

  6. Determination of Velocity And Acceleration of Structural Deformation ...

    African Journals Online (AJOL)

    This paper outlines the procedure of geodetic monitoring system of circular oil storage ... In this study, only tank 6 was used as case study scenario for the determination of ... In this study, deformation analysis by Kalman Filter technique of the ...

  7. Gap-closing test structures for temperature budget determination

    NARCIS (Netherlands)

    Faber, Erik Jouwert; Wolters, Robertus A.M.; Schmitz, Jurriaan

    2011-01-01

    We present the extension of a method for determining the temperature budget of the process side of silicon substrates and chips, employing silicide formation reactions. In this work, silicon-on-insulator type substrates are used instead of bulk silicon wafers. By an appropriate choice of the layer

  8. Advances in RNA Structure Determination | Center for Cancer Research

    Science.gov (United States)

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

  9. Determinants of fish assemblage structure in Northwestern Great Plains streams

    Science.gov (United States)

    Mullen, J.A.; Bramblett, R.G.; Guy, C.S.; Zale, A.V.; Roberts, D.W.

    2011-01-01

    Prairie streams are known for their harsh and stochastic physical conditions, and the fish assemblages therein have been shown to be temporally variable. We assessed the spatial and temporal variation in fish assemblage structure in five intermittent, adventitious northwestern Great Plains streams representing a gradient of watershed areas. Fish assemblages and abiotic conditions varied more spatially than temporally. The most important variables explaining fish assemblage structure were longitudinal position and the proportion of fine substrates. The proportion of fine substrates increased proceeding upstream, approaching 100% in all five streams, and species richness declined upstream with increasing fine substrates. High levels of fine substrate in the upper reaches appeared to limit the distribution of obligate lithophilic fish species to reaches further downstream. Species richness and substrates were similar among all five streams at the lowermost and uppermost sites. However, in the middle reaches, species richness increased, the amount of fine substrate decreased, and connectivity increased as watershed area increased. Season and some dimensions of habitat (including thalweg depth, absolute distance to the main-stem river, and watershed size) were not essential in explaining the variation in fish assemblages. Fish species richness varied more temporally than overall fish assemblage structure did because common species were consistently abundant across seasons, whereas rare species were sometimes absent or perhaps not detected by sampling. The similarity in our results among five streams varying in watershed size and those from other studies supports the generalization that spatial variation exceeds temporal variation in the fish assemblages of prairie and warmwater streams. Furthermore, given longitudinal position, substrate, and stream size, general predictions regarding fish assemblage structure and function in prairie streams are possible. ?? American

  10. The internal structure of magnetic nanoparticles determines the magnetic response

    Czech Academy of Sciences Publication Activity Database

    Pacáková, Barbara; Kubíčková, Simona; Salas, G.; Mantlíková, Alice; Marciello, M.; Morales, M.P.; Nižňanský, D.; Vejpravová, Jana

    2017-01-01

    Roč. 9, č. 16 (2017), s. 5129-5140 ISSN 2040-3364 R&D Projects: GA ČR(CZ) GA15-01953S Institutional support: RVO:68378271 Keywords : nanoparticles * single-domain * internal structure Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 7.367, year: 2016

  11. Structural similarity image quality reliability: Determining parameters and window size

    OpenAIRE

    Silvestre-Blanes, Javier

    2011-01-01

    The need to obtain objective values of the quality of distorted images with respect to the original is fundamental in multimedia and image processing applications. It is generally required that this value correlates well with the human vision system (HVS). In spite of the properties and the general use of the mean square error (MSE) measurement, this has a poor correlation with HSV, which has led to the development of methods such as structural similarity (SSIM). This metric improves the corr...

  12. Determination of the pion and kaon structure functions

    International Nuclear Information System (INIS)

    Aitkenhead, W.; Barton, D.S.; Brandenburg, G.W.; Busza, W.; Dobrowolski, T.; Friedman, J.I.; Kendall, H.W.; Lyons, T.; Nelson, B.; Rosenson, L.; Toy, W.; Verdier, R.; Votta, L.; Chiaradia, M.T.; DeMarzo, C.; Favuzzi, C.; Germinario, G.; Guerriero, L.; LaVopa, P.; Maggi, G.; Posa, F.; Selvaggi, G.; Spinelli, P.; Waldner, F.; Brenner, A.E.; Carey, D.C.; Elias, J.E.; Garbincius, P.H.; Mikenberg, G.; Polychronakos, V.A.; Meunier, R.; Cutts, D.; Dulude, R.S.; Lanou, R.E. Jr.; Massimo, J.T.

    1980-01-01

    Quark structure functions have been extracted from low-p/sub T/ inclusive hadron production data for the pion and kaon with use of the recombination model. n/sup π/=1.0 +- 0.1 and n/sup K/=2.5 +- 0.6 is obtained, where n is the leading (1-x) power of the nonstrange--valence-quark distribution. Both the pion and kaon nonstrange--sea-quark functions have napprox. =3.5

  13. Entry Regulations, Product Differentiation and Determinants of Market Structure

    OpenAIRE

    Maican, Florin; Orth, ´Matilda

    2013-01-01

    We use a dynamic oligopoly model of entry and exit to evaluate how entry regulations affect profitability and market structure in retail. The model incorporates demand and store-level heterogeneity. Based on unique data for all retail food stores in Sweden, we find that the average entry costs for small and large stores are 10 and 18 percent lower, respectively, in markets with liberal compared with restrictive regulations. Counterfactual simulations show that lower entry costs in restrictive...

  14. Entry regulations, welfare and determinants of market structure

    OpenAIRE

    Maican, Florin; Orth, Matilda

    2015-01-01

    We use a dynamic oligopoly model of entry and exit with store-type differentiation to evaluate how entry regulations affect profitability, market structure and welfare. Based on unique data for all retail food stores in Sweden, we estimate demand, recover variable profits, and estimate entry costs and fixed costs by store type. Counterfactual policy experiments show that welfare increases when competition is enhanced by lower entry costs. Protecting small stores by imposing licensing fees on ...

  15. Economic Liberalization in Nepal: Determinants, Structure, and Trends of FDI

    Directory of Open Access Journals (Sweden)

    Raghu Bir Bista

    2017-03-01

    Full Text Available This research examined the relationship between FDI (Foreign Direct Investment and GDP (Gross Domestic Product along with the impact of FDI determinants on FDI inflow in Nepal. This research used literature review by doing multiple regression models. This research used an econometric model based on Cobb Douglas Production Model and a theoretical growth model based on Solow Growth. The result indicates the positive relationship between GDP and FDI. Furthermore, liberalization and privatization policies are positive, but insecurity is disturbing.

  16. Structural determination of some uranyl compounds by vibrational spectroscopy

    International Nuclear Information System (INIS)

    Rodriguez S, A.; Martinez Q, E.

    1990-07-01

    The vibrational spectra of different uranyl compounds has been studied and of it spectral information has been used the fundamental asymmetric vibrational frequency, to determine the length and constant bond force U=O by means of the combination of the concept of absorbed energy and the mathematical expression of Badger modified by Jones. It is intended a factor that simplifies the mathematical treatment and the results are compared with the values obtained for other methods. (Author)

  17. Structural imaging in the presymptomatic stage of genetically determined parkinsonism

    DEFF Research Database (Denmark)

    Reetz, Kathrin; Tadic, Vera; Kasten, Meike

    2010-01-01

    Several genes associated with monogenic forms of Parkinson's disease (PD) have been discovered, opening up new avenues for the investigation of presymptomatic stages of PD. Using voxel-based morphometry in 30 asymptomatic mutation carriers (MC) with mutations in four different genes for PD and 100....... The observed striatal GMV increase might be the common structural correlate of compensatory mechanisms due to the latent dopaminergic deficit, reflecting the different, but probably interrelated pathogenic pathways resulting in nigral cell death. Asymptomatic PINK1 and LRRK2 MC also revealed smaller GMV...

  18. A General Chemistry Experiment Incorporating Synthesis and Structural Determination

    Science.gov (United States)

    van Ryswyk, Hal

    1997-07-01

    An experiment for the general chemistry laboratory is described wherein gas chromatography-mass spectroscopy (GC-MS) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) are used to characterize the products of a series of microscale reactions on vanillin. A single sophisticated instrument can be incorporated into the laboratory given sufficient attention to the use of sampling accessories and software macros. Synthetic experiments coupled with modern instrumental techniques can be used in the general chemistry laboratory to illustrate the concepts of synthesis, structure, bonding, and spectroscopy.

  19. Structure determination of organic compounds by 'electron pyrolysis'. Pt. 6

    International Nuclear Information System (INIS)

    Ege, G.; Gessner, K.; Schildknecht, H.

    1977-01-01

    By action of tritiated water on N-substituted 3-Amino-Δ 4 -thiazoline-2-ones and -2-thiones cleavage of the N-N-bond occurs with the formation of Δ 4 -thiazoline-2-ones and -2-thiones, respectively, and H 2 N-R 3 . Detection and identification of the fragments is performed by thin-layer chromatography and by comparison with authentic samples under the application of a radio-scanner. Such a fragmention is strong evidence for the five-membered ring structure. (orig.) [de

  20. 1. The determination of crystal and magnetic structures

    International Nuclear Information System (INIS)

    Elemans, J.B.A.A.

    1975-01-01

    A theoretical foundation of the technique of thermal neutron scattering by powders is outlined. A description of the experimental set-up is given. A beam of themalized neutrons emerges from the reactor (HFR at Petten) through a slit system. It is diffracted by a manochromator crystal with a finite mosaic structure, a Cu (111) crystal being used. After passing through 10 cm pyrolytic graphite with a ''window'' from 0.23 to 0.29 nm as a lambda/2 filter, resulting in a wave length of 0.257 nm, the neutrons are taken off at a predetermined angle defined by a second slit system, resulting in a beam in which the sample is bathed. The neutrons scattered by the sample are detected by a counter moving in an arc with the position of the sample as center. The standard measurement time for a 10 cm 3 sample was two days. A discussion of the mathematical procedures for deriving the magnetic structure from the observed counts is given

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

    Science.gov (United States)

    Potrzebowski, Wojciech; André, Ingemar

    2015-07-01

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

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

    Science.gov (United States)

    2014-12-01

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

  3. Quantitative X-ray determination of CFRP micro structures

    International Nuclear Information System (INIS)

    Hentschel, Manfred P.; Mueller, Bernd R.; Lange, Axel; Wald, Oliver

    2008-01-01

    Beyond imaging the mass distribution of materials by X-ray absorption techniques recent synchrotron and laboratory X-ray refraction techniques provide interface contrast imaging of micro structures. This is of specific relevance to carbon fibre composites (CFRP) which constitute advanced aerospace components. Apart from merely finding isolated flaws like cracks or pores within the natural high interface density only the quantitative measurement of the differences after defined mechanical treatment provides a reliable understanding of the related macroscopic properties. The contribution of the fibre matrix interface of CFRP laminates to the mechanical properties is investigated by relating the mechanical damage to the additional fibre debonding after impact and fatigue. Composites of industrially sized carbon fibres for aerospace applications and of unsized fibres are compared. (orig.)

  4. Budgetary Structure as a Determinant in Measuring Fiscal Transparency

    Directory of Open Access Journals (Sweden)

    Benito Furtado Mota

    2017-08-01

    Full Text Available National and International research studies often relate fiscal transparency to political, socio-economic and fiscal variables. Therefore, this study seeks to analyze how budget execution (revenues and expenses influence active fiscal transparency in municipalities in the state of Paraiba. Thus, Focco-PB (Forum on Fighting Corruption Paraíba reports were analyzed, with a view to identifying the  Active Fiscal Transparency Index in Paraíba’s municipalities in relation to this study’s dependent variable. Subsequently, independent variables were collected (intergovernmental transfer revenue, individual per capita revenue, spending on human resources, education and health in the TCE / PB database. Initially, a Pearson correlation test was performed and later an analysis of panel data  with a fixed effect. Furthermore, descriptive analyses of the dependent variables in relation to data for the years 2013, 2014 and 2015 were conducted. The results suggest that Income from Transfers and Health Expenditure  reflected a negative relation with respect to the Active Fiscal Transparency Index whilst (ITFA Individual Income Per Capita and Spending on Human Resources indicate a positive relation.   As proposed in this study, it can be concluded that most of the variables studied and which make up budgetary structure impact on the Active Fiscal Transparency Index in Paraíba’s municipalities.

  5. Benzofuranyl Esters: Synthesis, Crystal Structure Determination, Antimicrobial and Antioxidant Activities

    Directory of Open Access Journals (Sweden)

    C. S. Chidan Kumar

    2015-09-01

    Full Text Available A series of five new 2‐(1‐benzofuran‐2‐yl‐2‐oxoethyl 4-(un/substitutedbenzoates 4(a–e, with the general formula of C8H5O(C=OCH2O(C=OC6H4X, X = H, Cl, CH3, OCH3 or NO2, was synthesized in high purity and good yield under mild conditions. The synthesized products 4(a–e were characterized by FTIR, 1H-, 13C- and 1H-13C HMQC NMR spectroscopic analysis and their 3D structures were confirmed by single-crystal X-ray diffraction studies. These compounds were screened for their antimicrobial and antioxidant activities. The tested compounds showed antimicrobial ability in the order of 4b < 4a < 4c < 4d < 4e and the highest potency with minimum inhibition concentration (MIC value of 125 µg/mL was observed for 4e. The results of antioxidant activities revealed the highest activity for compound 4e (32.62% ± 1.34% in diphenyl-2-picrylhydrazyl (DPPH radical scavenging, 4d (31.01% ± 4.35% in ferric reducing antioxidant power (FRAP assay and 4a (27.11% ± 1.06% in metal chelating (MC activity.

  6. Determining the in situ concrete strength of existing structures for assessing their structural safety

    NARCIS (Netherlands)

    Steenbergen, R.D.J.M.; Vervuurt, A.H.J.M.

    2012-01-01

    EN 13791 applies when assessing the in situ compressive strength of structures and precast concrete components. According to the code itself, it may be adopted when doubt arises about the compressive strength of a concrete. For assessing the structural safety of existing structures, however, the

  7. Comparison of algorithms for determination of rotation measure and Faraday structure. I. 1100–1400 MHz

    International Nuclear Information System (INIS)

    Sun, X. H.; Akahori, Takuya; Anderson, C. S.; Farnes, J. S.; O’Sullivan, S. P.; Rudnick, L.; O’Brien, T.; Bell, M. R.; Bray, J. D.; Scaife, A. M. M.; Ideguchi, S.; Kumazaki, K.; Stepanov, R.; Stil, J.; Wolleben, M.; Takahashi, K.; Weeren, R. J. van

    2015-01-01

    Faraday rotation measures (RMs) and more general Faraday structures are key parameters for studying cosmic magnetism and are also sensitive probes of faint ionized thermal gas. A definition of which derived quantities are required for various scientific studies is needed, as well as addressing the challenges in determining Faraday structures. A wide variety of algorithms has been proposed to reconstruct these structures. In preparation for the Polarization Sky Survey of the Universe's Magnetism (POSSUM) to be conducted with the Australian Square Kilometre Array Pathfinder and the ongoing Galactic Arecibo L-band Feeds Array Continuum Transit Survey (GALFACTS), we run a Faraday structure determination data challenge to benchmark the currently available algorithms, including Faraday synthesis (previously called RM synthesis in the literature), wavelet, compressive sampling, and QU-fitting. The input models include sources with one Faraday thin component, two Faraday thin components, and one Faraday thick component. The frequency set is similar to POSSUM/GALFACTS with a 300 MHz bandwidth from 1.1 to 1.4 GHz. We define three figures of merit motivated by the underlying science: (1) an average RM weighted by polarized intensity, RM wtd , (2) the separation Δϕ of two Faraday components, and (3) the reduced chi-squared χ r 2 . Based on the current test data with a signal-to-noise ratio of about 32, we find the following. (1) When only one Faraday thin component is present, most methods perform as expected, with occasional failures where two components are incorrectly found. (2) For two Faraday thin components, QU-fitting routines perform the best, with errors close to the theoretical ones for RM wtd but with significantly higher errors for Δϕ. All other methods, including standard Faraday synthesis, frequently identify only one component when Δϕ is below or near the width of the Faraday point-spread function. (3) No methods as currently implemented work well

  8. Purification, crystal structure determination and functional characterization of type III antifreeze proteins from the European eelpout Zoarces viviparus

    DEFF Research Database (Denmark)

    Wilkens, Casper; Poulsen, Jens-Christian Navarro; Ramløv, Hans

    2014-01-01

    Antifreeze proteins (AFPs) are essential components of many organisms adaptation to cold temperatures. Fish type III AFPs are divided into two groups, SP isoforms being much less active than QAE1 isoforms. Two type III AFPs from Zoarces viviparus, a QAE1 (ZvAFP13) and an SP (ZvAFP6) isoform......, are here characterized and their crystal structures determined. We conclude that the higher activity of the QAE1 isoforms cannot be attributed to single residues, but rather a combination of structural effects. Furthermore both ZvAFP6 and ZvAFP13 crystal structures have water molecules around T18...... equivalent to the tetrahedral-like waters previously identified in a neutron crystal structure. Interestingly, ZvAFP6 forms dimers in the crystal, with a significant dimer interface. The presence of ZvAFP6 dimers was confirmed in solution by native electrophoresis and gel filtration. To our knowledge...

  9. Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.

    Science.gov (United States)

    Pedersen, Hege Lynum; Johnson, Kenneth A; McVey, Colin E; Leiros, Ingar; Moe, Elin

    2015-10-01

    Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues

  10. Structure and partitioning of bacterial DNA: determined by a balance of competion and expansion forces?

    DEFF Research Database (Denmark)

    Woldringh, C. L.; Jensen, Peter Ruhdal; Westerhoff, H. V.

    1995-01-01

    The mechanisms that determine chromosome structure and chromosome partitioning in bacteria are largely unknown. Here we discuss two hypotheses: (i) the structure of the Escherichia coli nucleoid is determined by DNA binding proteins and DNA supercoiling, representing a compaction force on the one...

  11. Structure and dynamics of porcine submaxillary mucin as determined by natural abundance carbon-13 NMR spectroscopy

    International Nuclear Information System (INIS)

    Gerken, T.A.; Jentoft, N.

    1987-01-01

    Nearly all of the resonances in the 13 C NMR spectrum of porcine submaxillary mucin glycoprotein (PSM) have been assigned to the peptide core carbons and to the carbons in the eight different oligosaccharide side chains that arise from the incomplete biosynthesis of the sialylated A blood group pentasaccharide. By use of these assignments, a nearly complete structural analysis of intact PSM has been performed without resorting to degradative chemical methods. Considerable structural variability in the carbohydrate side chains was observed between mucins obtained from different animals, while no variability was observed between glands in a single animal. The dynamics of the PSM core and carbohydrate side chains were examined by using the carbon-13 nuclear magnetic resonance relaxation times and nuclear Overhauser enhancements of each assigned carbon resonance. The peptide core of PSM exhibits internal segmental flexibility that is virtually identical with that of ovine submaxillary mucin (OSM), whose carbohydrate side chain consists of the α-NeuNAc(2-6)α-Ga1NAc disaccharide. These results differ from most reports of glycoprotein dynamics, which typically find the terminal carbohydrate residues to be undergoing rapid internal rotation about their terminal glycosidic bonds. The results reported here are consistent with previous studies on the conformations of the A and H determinants derived from model oligosaccharides and further indicate that the conformations of these determinants are unchanged when covalently bound to the mucin peptide core. In spite of their carbohydrate side-chain heterogeneity, mucins appear to be ideal glycoproteins for the study of O-linked oligosaccharide conformation and dynamics and for the study of the effects of glycosylation on polypeptide conformation and dynamics

  12. Structural determinants for antagonist pharmacology that distinguish the rho1 GABAC receptor from GABAA receptors.

    Science.gov (United States)

    Zhang, Jianliang; Xue, Fenqin; Chang, Yongchang

    2008-10-01

    GABA receptor (GABAR) types C (GABACR) and A (GABAAR) are both GABA-gated chloride channels that are distinguished by their distinct competitive antagonist properties. The structural mechanism underlying these distinct properties is not well understood. In this study, using previously identified binding residues as a guide, we made individual or combined mutations of nine binding residues in the rho1 GABACR subunit to their counterparts in the alpha1beta2gamma2 GABAAR or reverse mutations in alpha1 or beta2 subunits. The mutants were expressed in Xenopus laevis oocytes and tested for sensitivities of GABA-induced currents to the GABAA and GABAC receptor antagonists. The results revealed that bicuculline insensitivity of the rho1 GABACR was mainly determined by Tyr106, Phe138 and Phe240 residues. Gabazine insensitivity of the rho1 GABACR was highly dependent on Tyr102, Tyr106, and Phe138. The sensitivity of the rho1 GABACR to 3-aminopropyl-phosphonic acid and its analog 3-aminopropyl-(methyl)phosphinic acid mainly depended on residues Tyr102, Val140, FYS240-242, and Phe138. Thus, the residues Tyr102, Tyr106, Phe138, and Phe240 in the rho1 GABACR are major determinants for its antagonist properties distinct from those in the GABAAR. In addition, Val140 in the GABACR contributes to 3-APA binding. In conclusion, we have identified the key structural elements underlying distinct antagonist properties for the GABACR. The mechanistic insights were further extended and discussed in the context of antagonists docking to the homology models of GABAA or GABAC receptors.

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

    Science.gov (United States)

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

    1973-01-01

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

  14. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors

    NARCIS (Netherlands)

    Nabuurs, S.B.; Spronk, C.A.E.M.; Vuister, G.W.; Vriend, G.

    2006-01-01

    One of the major goals of structural genomics projects is to determine the three-dimensional structure of representative members of as many different fold families as possible. Comparative modeling is expected to fill the remaining gaps by providing structural models of homologs of the

  15. Effective cross-section for dimuon production and experimental determination of the hadronic structure functions

    International Nuclear Information System (INIS)

    Weisz, S.

    1982-07-01

    High mass dimuon hadronic production is studied. This study is aimed at pion structure determination. The device is presented. The accessible luminosity is more than one scale order beyond the preceeding experiment one. The performant beam, the great acceptance and the good high mass dimuon selection are described. Parton model is introduced. Drell-Yann mechanism is reviewed. Hadronic structure, revealed during high mass muon pair production, is presented. In particular, pion structure is determined [fr

  16. Rapid increase of near atomic resolution virus capsid structures determined by cryo-electron microscopy.

    Science.gov (United States)

    Ho, Phuong T; Reddy, Vijay S

    2018-01-01

    The recent technological advances in electron microscopes, detectors, as well as image processing and reconstruction software have brought single particle cryo-electron microscopy (cryo-EM) into prominence for determining structures of bio-molecules at near atomic resolution. This has been particularly true for virus capsids, ribosomes, and other large assemblies, which have been the ideal specimens for structural studies by cryo-EM approaches. An analysis of time series metadata of virus structures on the methods of structure determination, resolution of the structures, and size of the virus particles revealed a rapid increase in the virus structures determined by cryo-EM at near atomic resolution since 2010. In addition, the data highlight the median resolution (∼3.0 Å) and size (∼310.0 Å in diameter) of the virus particles determined by X-ray crystallography while no such limits exist for cryo-EM structures, which have a median diameter of 508 Å. Notably, cryo-EM virus structures in the last four years have a median resolution of 3.9 Å. Taken together with minimal sample requirements, not needing diffraction quality crystals, and being able to achieve similar resolutions of the crystal structures makes cryo-EM the method of choice for current and future virus capsid structure determinations. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2016-04-01

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

  18. Adsorption site and structure determination of c(2x2) N{sub 2}/Ni(100) using angle-resolved photoemission extended fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Moler, E.J.; Kellar, S.A.; Huff, W.R.A. [Lawrence Berkeley National Lab., CA (United States)] [and others

    1997-04-01

    The authors have determined the atomic spatial structure of c(2x2) N2Ni(100) with Angle-Resolved Photoemission Extended Fine Structure (ARPEFS) from the nitrogen 1s core level using monochromatized x-rays from beamline 6.1 at SSRL and beamline 9.3.2 at the ALS. The chemically shifted N 1s peak intensities were summed together to obtain ARPEFS curves for both nitrogen atoms in the molecule. They used a new, highly-optimized program based on the Rehr-Albers scattering matrix formalism to find the adsorption site and to quantitatively determine the bond-lengths. The nitrogen molecule stands upright at an atop site, with a N-Ni bond length of 2.25(1) {angstrom}, a N-N bond length of 1.10(7) {angstrom}, and a first layer Ni-Ni spacing of 1.76(4) {angstrom}. The shake-up peak shows an identical ARPEFS diffraction pattern, confirming its intrinsic nature and supporting a previous use of this feature to decompose the peak into contributions from the chemically inequivalent nitrogen atoms. Comparison to a previously published theoretical treatment of N-N-Ni and experimental structures of analogous adsorbate systems demonstrates the importance of adsorbate-adsorbate interactions in weakly chemisorbed systems.

  19. Structure determination of modulated structures by powder X-ray diffraction and electron diffraction

    Czech Academy of Sciences Publication Activity Database

    Zhou, Z.Y.; Palatinus, Lukáš; Sun, J.L.

    2016-01-01

    Roč. 3, č. 11 (2016), s. 1351-1362 ISSN 2052-1553 Institutional support: RVO:68378271 Keywords : electron diffraction * incommensurate structure * powder diffraction Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.036, year: 2016

  20. Preoperative screening: value of previous tests.

    Science.gov (United States)

    Macpherson, D S; Snow, R; Lofgren, R P

    1990-12-15

    To determine the frequency of tests done in the year before elective surgery that might substitute for preoperative screening tests and to determine the frequency of test results that change from a normal value to a value likely to alter perioperative management. Retrospective cohort analysis of computerized laboratory data (complete blood count, sodium, potassium, and creatinine levels, prothrombin time, and partial thromboplastin time). Urban tertiary care Veterans Affairs Hospital. Consecutive sample of 1109 patients who had elective surgery in 1988. At admission, 7549 preoperative tests were done, 47% of which duplicated tests performed in the previous year. Of 3096 previous results that were normal as defined by hospital reference range and done closest to the time of but before admission (median interval, 2 months), 13 (0.4%; 95% CI, 0.2% to 0.7%), repeat values were outside a range considered acceptable for surgery. Most of the abnormalities were predictable from the patient's history, and most were not noted in the medical record. Of 461 previous tests that were abnormal, 78 (17%; CI, 13% to 20%) repeat values at admission were outside a range considered acceptable for surgery (P less than 0.001, frequency of clinically important abnormalities of patients with normal previous results with those with abnormal previous results). Physicians evaluating patients preoperatively could safely substitute the previous test results analyzed in this study for preoperative screening tests if the previous tests are normal and no obvious indication for retesting is present.

  1. SMEs capital structure determinants during severe economic crisis: The case of Greece

    Directory of Open Access Journals (Sweden)

    D. Balios

    2016-12-01

    Full Text Available The objective of this paper was to explore whether and how the main capital structure determinants of SMEs affected capital structure determination in different ways during the years of economic crisis. We used panel data of 8,052 SMEs operating in Greece during 2009–2012. We found that the effect of capital structure determinants on leverage does not change in an environment of economic crisis; larger SMEs continued to show higher debt ratios, the relationship between profitability and tangibility of assets with leverage continued to be negative, and growth was positively related to leverage.

  2. Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

    International Nuclear Information System (INIS)

    Montalvao, Rinaldo W.; De Simone, Alfonso; Vendruscolo, Michele

    2012-01-01

    Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.

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

    Science.gov (United States)

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

    2013-10-21

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

  4. Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.

    Science.gov (United States)

    Feng, Yingang

    2017-01-01

    The use of NMR methods to determine the three-dimensional structures of carbohydrates and glycoproteins is still challenging, in part because of the lack of standard protocols. In order to increase the convenience of structure determination, the topology and parameter files for carbohydrates in the program Crystallography & NMR System (CNS) were investigated and new files were developed to be compatible with the standard simulated annealing protocols for proteins and nucleic acids. Recalculating the published structures of protein-carbohydrate complexes and glycosylated proteins demonstrates that the results are comparable to the published structures which employed more complex procedures for structure calculation. Integrating the new carbohydrate parameters into the standard structure calculation protocol will facilitate three-dimensional structural study of carbohydrates and glycosylated proteins by NMR spectroscopy.

  5. Halo structure of 8B determined from intermediate energy proton elastic scattering in inverse kinematics

    Science.gov (United States)

    Korolev, G. A.; Dobrovolsky, A. V.; Inglessi, A. G.; Alkhazov, G. D.; Egelhof, P.; Estradé, A.; Dillmann, I.; Farinon, F.; Geissel, H.; Ilieva, S.; Ke, Y.; Khanzadeev, A. V.; Kiselev, O. A.; Kurcewicz, J.; Le, X. C.; Litvinov, Yu. A.; Petrov, G. E.; Prochazka, A.; Scheidenberger, C.; Sergeev, L. O.; Simon, H.; Takechi, M.; Tang, S.; Volkov, V.; Vorobyov, A. A.; Weick, H.; Yatsoura, V. I.

    2018-05-01

    The absolute differential cross section for small-angle proton elastic scattering on the proton-rich 8B nucleus has been measured in inverse kinematics for the first time. The experiment was performed using a secondary radioactive beam with an energy of 0.7 GeV/u at GSI, Darmstadt. The active target, namely hydrogen-filled time projection ionization chamber IKAR, was used to measure the energy, angle and vertex point of the recoil protons. The scattering angle of the projectiles was simultaneously determined by the tracking detectors. The measured differential cross section is analyzed on the basis of the Glauber multiple scattering theory using phenomenological nuclear-density distributions with two free parameters. The radial density distribution deduced for 8B exhibits a halo structure with the root-mean-square (rms) matter radius Rm = 2.58 (6) fm and the rms halo radius Rh = 4.24 (25) fm. The results on 8B are compared to those on the mirror nucleus 8Li investigated earlier by the same method. A comparison is also made with previous experimental results and theoretical predictions for both nuclei.

  6. On the Tengiz petroleum deposit previous study

    International Nuclear Information System (INIS)

    Nysangaliev, A.N.; Kuspangaliev, T.K.

    1997-01-01

    Tengiz petroleum deposit previous study is described. Some consideration about structure of productive formation, specific characteristic properties of petroleum-bearing collectors are presented. Recommendation on their detail study and using of experience on exploration and development of petroleum deposit which have analogy on most important geological and industrial parameters are given. (author)

  7. Portable neutron moisture gage for the moisture determination of structure parts

    International Nuclear Information System (INIS)

    Harnisch, M.

    1985-01-01

    For determining the moisture of structure parts during building or before repairing a portable neutron moisture gage consisting of a neutron probe and pulse analyzer has been developed. The measuring process, calibration, and prerequisites of application are briefly discussed

  8. Determinants of the microbial community structure of eutrophic, hyporheic river sediments polluted with chlorinated aliphatic hydrocarbons

    NARCIS (Netherlands)

    Hamonts, K.; Ryngaert, A.; Smidt, H.; Springael, D.; Dejonghe, W.

    2014-01-01

    Chlorinated aliphatic hydrocarbons (CAHs) often discharge into rivers as contaminated groundwater baseflow. As biotransformation of CAHs in the impacted river sediments might be an effective remediation strategy, we investigated the determinants of the microbial community structure of eutrophic,

  9. Directions for Determining Buffer Zone Distances for Commodity and Structural Fumigation with Methyl Bromide

    Science.gov (United States)

    Buffer zones for commodity and food handling structural applications are distributed across numerous tables. This document provides directions for determining the factors to use to identify the correct table for a given application.

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

    Science.gov (United States)

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

    2015-08-24

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

  11. Using molecular principal axes for structural comparison: determining the tertiary changes of a FAB antibody domain induced by antigenic binding

    Directory of Open Access Journals (Sweden)

    Silverman B David

    2007-11-01

    Full Text Available Abstract Background Comparison of different protein x-ray structures has previously been made in a number of different ways; for example, by visual examination, by differences in the locations of secondary structures, by explicit superposition of structural elements, e.g. α-carbon atom locations, or by procedures that utilize a common symmetry element or geometrical feature of the structures to be compared. Results A new approach is applied to determine the structural changes that an antibody protein domain experiences upon its interaction with an antigenic target. These changes are determined with the use of two different, however comparable, sets of principal axes that are obtained by diagonalizing the second-order tensors that yield the moments-of-geometry as well as an ellipsoidal characterization of domain shape, prior to and after interaction. Determination of these sets of axes for structural comparison requires no internal symmetry features of the domains, depending solely upon their representation in three-dimensional space. This representation may involve atomic, Cα, or residue centroid coordinates. The present analysis utilizes residue centroids. When the structural changes are minimal, the principal axes of the domains, prior to and after interaction, are essentially comparable and consequently may be used for structural comparison. When the differences of the axes cannot be neglected, but are nevertheless slight, a smaller relatively invariant substructure of the domains may be utilized for comparison. The procedure yields two distance metrics for structural comparison. First, the displacements of the residue centroids due to antigenic binding, referenced to the ellipsoidal principal axes, are noted. Second, changes in the ellipsoidal distances with respect to the non-interacting structure provide a direct measure of the spatial displacements of the residue centroids, towards either the interior or exterior of the domain

  12. Determining the Velocity Fine Structure by a Laser Anemometer with Fixed Orientation

    DEFF Research Database (Denmark)

    Kristensen, Leif; Kirkegaard, Peter; Mikkelsen, Torben

    We have studied the velocity structure functions and spectra which can be determined by a CW-laser anemometer and a (pulsed) lidar anemometer. We have found useful theoretical expressions for both types of anemometers and compared their filtering of the alongbeam turbulent velocity. The purpose h...... been to establish a basis for remote determining of turbulence fine-structure in terms of the rate of dissipation of specific kinetic energy in the atmospheric boundary layer....

  13. Determining the velocity fine structure by a laser anemometer with fixed orientation

    Energy Technology Data Exchange (ETDEWEB)

    Kristensen, Leif; Kirkegaard, P.; Mikkelsen, Torben

    2011-02-15

    We have studied the velocity structure functions and spectra which can be determined by a CW-laser anemometer and a (pulsed) lidar anemometer. We have found useful theoretical expressions for both types of anemometers and compared their filtering of the along-beam turbulent velocity. The purpose has been to establish a basis for remote determining of turbulence fine-structure in terms of the rate of dissipation of specific kinetic energy in the atmospheric boundary layer. (Author)

  14. Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing

    OpenAIRE

    Feng, Yingang

    2017-01-01

    The use of NMR methods to determine the three-dimensional structures of carbohydrates and glycoproteins is still challenging, in part because of the lack of standard protocols. In order to increase the convenience of structure determination, the topology and parameter files for carbohydrates in the program Crystallography & NMR System (CNS) were investigated and new files were developed to be compatible with the standard simulated annealing protocols for proteins and nucleic acids. Recalculat...

  15. Invisible detergents for structure determination of membrane proteins by small-angle neutron scattering

    DEFF Research Database (Denmark)

    Midtgaard, Søren Roi; Darwish, Tamim A.; Pedersen, Martin Cramer

    2018-01-01

    A novel and generally applicable method for determining structures of membrane proteins in solution via small-angle neutron scattering (SANS) is presented. Common detergents for solubilizing membrane proteins were synthesized in isotope-substituted versions for utilizing the intrinsic neutron sca...... solution structure determination of membrane proteins by SANS and subsequent data analysis available to non-specialists. This article is protected by copyright. All rights reserved....

  16. Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase

    International Nuclear Information System (INIS)

    Almeida, Wagner B. de

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

  17. EXAFS, Determination of Short Range Order and Local Structures in Materials

    NARCIS (Netherlands)

    Koningsberger, D.C.; Prins, R.

    1981-01-01

    Extended X-ray Absorption Fine Structure (EXAFS) is a powerful method of determining short range order and local structures in materials using X-ray photons produced by a synchrotron light source, or in-house by a high intensity rotating anode X-ray generator. The technique has provided valuable

  18. Profitability of Western European banking systems: panel evidence on structural and cyclical determinants

    OpenAIRE

    Beckmann, Rainer

    2007-01-01

    This paper analyses structural and cyclical determinants of banking profitability in 16 Western European countries. We find that financial structure matters, particularly through the beneficial effect of the capital market orientation in the respective national financial system. Furthermore, higher diversification regarding banks' income sources shows a positive effect. The industry concentration of national banking systems, though, does not significantly affect aggregate profitability. Busin...

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

    Science.gov (United States)

    Çinar, Derya

    2015-01-01

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

  20. Blind testing of routine, fully automated determination of protein structures from NMR data.

    NARCIS (Netherlands)

    Rosato, A.; Aramini, J.M.; Arrowsmith, C.; Bagaria, A.; Baker, D.; Cavalli, A.; Doreleijers, J.; Eletsky, A.; Giachetti, A.; Guerry, P.; Gutmanas, A.; Guntert, P.; He, Y.; Herrmann, T.; Huang, Y.J.; Jaravine, V.; Jonker, H.R.; Kennedy, M.A.; Lange, O.F.; Liu, G.; Malliavin, T.E.; Mani, R.; Mao, B.; Montelione, G.T.; Nilges, M.; Rossi, P.; Schot, G. van der; Schwalbe, H.; Szyperski, T.A.; Vendruscolo, M.; Vernon, R.; Vranken, W.F.; Vries, S.D. de; Vuister, G.W.; Wu, B.; Yang, Y.; Bonvin, A.M.

    2012-01-01

    The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by

  1. Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

    NARCIS (Netherlands)

    Rosato, A.; Aramini, J.M.; van der Schot, G.; de Vries, S.J.|info:eu-repo/dai/nl/304837717; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238

    2012-01-01

    The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by

  2. Determinants of Rural Industrial Entrepreneurship of Farmers in West Bengal : A Structural Equations Approach

    NARCIS (Netherlands)

    Folmer, Henk; Dutta, Subrata; Oud, Han

    2010-01-01

    This article presents a structural equations model of rural industrial entrepreneurship (RIE) among farmers in the Bardhaman district, West Bengal, India. It identifies the determinants of RIE but also analyzes impacts of RIE on its endogenous determinants. Age, education, marital status, number of

  3. Determinants of rural industrial entrepreneurship of farmers in West Bengal: A structural equations approach

    NARCIS (Netherlands)

    Folmer, H.; Dutta, S.; Oud, J.H.L.

    2010-01-01

    This article presents a structural equations model of rural industrial entrepreneurship (RIE) among farmers in the Bardhaman district, West Bengal, India. It identifies the determinants of RIE but also analyzes impacts of RIE on its endogenous determinants. Age, education, marital status, number of

  4. Single-crystal structure determination of hydrous minerals and insights into a wet deep lower mantle

    Science.gov (United States)

    Zhang, L.; Yuan, H.; Meng, Y.; Popov, D.

    2017-12-01

    Water enters the Earth's interior through hydrated subducting slabs. How deep within the lower mantle (670-2900 km depth) can water be transported down and stored depends upon the availability of hydrous phases that is thermodynamically stable under the high P-T conditions and have a sufficiently high density to sink through the lower mantle. Phase H [MgSiH2O4] (1) and the δ-AlOOH (2) form solid solutions that are stable in the deep lower mantle (3), but the solid solution phase is 10% lighter than the corresponding lower mantle. Recent experimental discoveries of the pyrite (Py) structured FeO2 and FeOOH (4-6) suggest that these Fe-enriched phases can be transported to the deepest lower mantle owing to their high density. We have further discovered a very dense hydrous phase in (Fe,Al)OOH with a previously unknown hexagonal symmetry and this phase is stable relative to the Py-phase under extreme high P-T conditions in the deep lower mantle. Through in situ multigrain analysis (7) and single-crystal structure determination of the hydrous minerals at P-Tconditions of the deep lower mantle, we can obtain detailed structure information of the hydrous phases and therefore provide insights into the hydration mechanism in the deep lower mantle. These highly stable hydrous minerals extend the water cycle at least to the depth of 2900 km. 1. M. Nishi et al., Nature Geoscience 7, 224-227 (2014). 2. E. Ohtani, K. Litasov, A. Suzuki, T. Kondo, Geophysical Research Letters 28, 3991-3993 (2001). 3. I. Ohira et al., Earth and Planetary Science Letters 401, 12-17 (2014). 4. Q. Hu et al., Proceedings of the National Academy of Sciences of the United States of America 114, 1498-1501 (2017). 5. M. Nishi, Y. Kuwayama, J. Tsuchiya, T. Tsuchiya, Nature 547, 205-208 (2017). 6. Q. Hu et al., Nature 534, 241-244 (2016). 7. L. Zhang et al., American Mineralogist 101, 231-234 (2016).

  5. Determination of the three-dimensional structure for weakly aligned biomolecules by NMR spectroscopy

    International Nuclear Information System (INIS)

    Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G

    2002-01-01

    The key achievements and the potential of NMR spectroscopy for weakly aligned biomolecules are considered. Due to weak alignment, it becomes possible to determine a number of NMR parameters dependent on the orientation of biomolecules, which are averaged to zero in usual isotropic media. The addition of new orientational constraints to standard procedures of 3D structure determination markedly increases the achievable accuracy. The possibility of structure determination for biomolecules using only orientation-dependent parameters without invoking other NMR data is discussed. The methods of orientation, experimental techniques, and calculation methods are systematised. The main results obtained and the prospects of using NMR spectroscopy of weakly aligned systems to study different classes of biomolecules and to solve various problems of molecular biology are analysed. Examples of biomolecules whose structures have been determined using orientation-dependent parameters are given. The bibliography includes 508 references.

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

    Science.gov (United States)

    Talich, Milan

    2017-12-01

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

  7. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

    International Nuclear Information System (INIS)

    Lee, Woonghee; Petit, Chad M.; Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L.

    2016-01-01

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

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

    Science.gov (United States)

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

    2016-05-10

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

  9. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States); Petit, Chad M. [University of Alabama at Birmingham, Department of Biochemistry and Molecular Genetics (United States); Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

    2016-06-15

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

  10. Previously unknown species of Aspergillus.

    Science.gov (United States)

    Gautier, M; Normand, A-C; Ranque, S

    2016-08-01

    The use of multi-locus DNA sequence analysis has led to the description of previously unknown 'cryptic' Aspergillus species, whereas classical morphology-based identification of Aspergillus remains limited to the section or species-complex level. The current literature highlights two main features concerning these 'cryptic' Aspergillus species. First, the prevalence of such species in clinical samples is relatively high compared with emergent filamentous fungal taxa such as Mucorales, Scedosporium or Fusarium. Second, it is clearly important to identify these species in the clinical laboratory because of the high frequency of antifungal drug-resistant isolates of such Aspergillus species. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been shown to enable the identification of filamentous fungi with an accuracy similar to that of DNA sequence-based methods. As MALDI-TOF MS is well suited to the routine clinical laboratory workflow, it facilitates the identification of these 'cryptic' Aspergillus species at the routine mycology bench. The rapid establishment of enhanced filamentous fungi identification facilities will lead to a better understanding of the epidemiology and clinical importance of these emerging Aspergillus species. Based on routine MALDI-TOF MS-based identification results, we provide original insights into the key interpretation issues of a positive Aspergillus culture from a clinical sample. Which ubiquitous species that are frequently isolated from air samples are rarely involved in human invasive disease? Can both the species and the type of biological sample indicate Aspergillus carriage, colonization or infection in a patient? Highly accurate routine filamentous fungi identification is central to enhance the understanding of these previously unknown Aspergillus species, with a vital impact on further improved patient care. Copyright © 2016 European Society of Clinical Microbiology and

  11. Determination of dimensions and theoretical evaluation of the performance of electron accelerator structures

    International Nuclear Information System (INIS)

    Fuhrmann, C.; Setrao, V.A.

    1987-03-01

    A method to calculate the dimensions of a constant gradient disk-loaded structure of a linear accelerator is presented. The method is based on a description of the RF power flux along the structure axis and involves a particular dispersion that includes details of the iris geometry. The dimensions of the v p = c structure and of the buncher section of the CURUMIM linear accelerator, have been determined as an application of the above method. The theoretical performance of the accelerating structure has been evaluated for electron pulse widths ranging from 10 ns to 2 μs and for peak currents up to 10 A. (author) [pt

  12. Determination of crystallographic and macroscopic orientation of planar structures in TEM

    DEFF Research Database (Denmark)

    Huang, X.; Liu, Q.

    1998-01-01

    With the aid of a double-tilt holder in a transmission electron microscope (TEM), simple methods are described for determination of the crystallographic orientation of a planar structure and for calculation of the macroscopic orientation of the planar structure. The correlation between a planar...... structure and a crystallographic plane can be found by comparing the differences in their trace directions on the projection plane and inclination angles with respect to that plane. The angles between the traces of planar structures and the sample axis measured from the TEM micrographs, which have been...

  13. Solution structures of α-conotoxin G1 determined by two-dimensional NMR spectroscopy

    International Nuclear Information System (INIS)

    Pardi, A.; Galdes, A.; Florance, J.; Maniconte, D.

    1989-01-01

    Two-dimensional NMR data have been used to generate solution structures of α-conotoxin G1, a potent peptide antagonist of the acetylcholine receptor. Structural information was obtained in the form of proton-proton internuclear distance constraints, and initial structures were produced with a distance geometry algorithm. Energetically more favorable structures were generated by using the distance geometry structures as input for a constrained energy minimization program. The results of both of these calculations indicate that the overall backbone conformation of the molecule is well-defined by the NMR data whereas the side-chain conformations are generally less well-defined. The main structural features derived from the NMR data were the presence of tight turns centered on residues Pro 5 and Arg 9 . The solution structures are compared with previous proposed models of conotoxin G1, and the NMR data are interpreted in conjunction with chemical modification studies and structural properties of other antagonists of the acetylcholine receptor to gain insight into structure-activity relationships in these peptide toxins

  14. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    Energy Technology Data Exchange (ETDEWEB)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D., E-mail: jdfv2009@gmail.com [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil). Grupo de Ressonância Magnética Nuclear e Química Medicinal

    2017-07-01

    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  15. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    International Nuclear Information System (INIS)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D.

    2017-01-01

    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  16. Determination of the structure function F{sub 2} at HERMES

    Energy Technology Data Exchange (ETDEWEB)

    Gabbert, Dominik D.

    2008-11-15

    In this thesis we present the first measurement of inclusive proton and deuteron deep-inelastic scattering cross sections at the HERMES experiment. The measurement is performed using the 27.6 GeV lepton beam provided by the HERA storage ring in conjunction with hydrogen and deuterium gas targets internal to the beam pipe. The relevant systematic effects such as radiative corrections, detector smearing, acceptance, particle misidentification, misalignment, tracking related effects and trigger efficiencies are taken into account. Based on these results, the structure functions F{sup p}{sub 2} and F{sup d}{sub 2} are determined using the parameterization R{sub 1998} for the longitudinal-to-transverse virtual-photon absorption cross section R. A phenomenological fit of the proton deep-inelastic scattering cross section is performed based on all available data and using photoproduction data in order to pin down the low Q{sup 2} region. A second fit is performed to the world data on the deuteron-to-proton cross section ratio in order to study its Q{sup 2} evolution, the difference between higher twist contributions in proton and deuteron, and the difference between R as obtained from the two targets. It can be confirmed that R obtained for proton and deuteron is in agreement. The Gottfried integral is evaluated from the fit at different values of Q{sup 2}. The result at Q{sup 2}=4 GeV{sup 2} agrees with previous measurements by NMC and no indication for a Q{sup 2} dependence of the Gottfried integral is found. (orig.)

  17. A novel strategy for NMR resonance assignment and protein structure determination

    International Nuclear Information System (INIS)

    Lemak, Alexander; Gutmanas, Aleksandras; Chitayat, Seth; Karra, Murthy; Farès, Christophe; Sunnerhagen, Maria; Arrowsmith, Cheryl H.

    2011-01-01

    The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution – especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

  18. Developments of the neutron scattering analysis method for the determination of magnetic structures

    Energy Technology Data Exchange (ETDEWEB)

    Park, Je-Geun; Chung, Jae Gwan; Park, Jung Hwan; Kong, Ung Girl [Inha Univ., Incheon (Korea); So, Ji Yong [Seoul National University, Seoul(Korea)

    2001-04-01

    Neutron diffraction is up to now almost the only and very important experimental method of determining the magnetic structure of materials. Unlike the studies of crystallographic structure, however to use neutron diffraction for magnetic structure determination is not easily accessible to non-experts because of the complexity of magnetic group theory: which is very important in the magnetic structure analysis. With the recent development of computer code for magnetic group, it is now time to rethink of these difficulties. In this work, we have used the computer code of the magnetic group (Mody-2) and Fullprof refinement program in order to study the magnetic structure of YMnO{sub 3} and other interesting materials. YMnO{sub 3} forms in the hexagonal structure and show both ferroelectric and antiferromagnetic phase transitions. Since it was recently found that YMnO{sub 3} can be used as a nonvolatile memory device, there has been many numbers of applied research on this material. We used neutron diffraction to determine the magnetic structure, and, in particular, to investigate the correlation between the order parameters of the ferroelectric and antiferromagnetic phase transitions. From this study, we have demonstrated that with a proper use of the computer code of the magnetic group one can overcome most of difficulties arising from the magnetic group theory. 4 refs., 8 figs., 5 tabs. (Author)

  19. Structure determination of helical filaments by solid-state NMR spectroscopy

    Science.gov (United States)

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

    2016-01-01

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

  20. Accuracy Assessment in Determining the Location of Corners of Building Structures Using a Combination of Various Measurement Methods

    Science.gov (United States)

    Krzyżek, Robert; Przewięźlikowska, Anna

    2017-12-01

    When surveys of corners of building structures are carried out, surveyors frequently use a compilation of two surveying methods. The first one involves the determination of several corners with reference to a geodetic control using classical methods of surveying field details. The second method relates to the remaining corner points of a structure, which are determined in sequence from distance-distance intersection, using control linear values of the wall faces of the building, the so-called tie distances. This paper assesses the accuracy of coordinates of corner points of a building structure, determined using the method of distance-distance intersection, based on the corners which had previously been determined by the conducted surveys tied to a geodetic control. It should be noted, however, that such a method of surveying the corners of building structures from linear measures is based on the details of the first-order accuracy, while the regulations explicitly allow such measurement only for the details of the second- and third-order accuracy. Therefore, a question arises whether this legal provision is unfounded, or whether surveyors are acting not only against the applicable standards but also without due diligence while performing surveys? This study provides answers to the formulated problem. The main purpose of the study was to verify whether the actual method which is used in practice for surveying building structures allows to obtain the required accuracy of coordinates of the points being determined, or whether it should be strictly forbidden. The results of the conducted studies clearly demonstrate that the problem is definitely more complex. Eventually, however, it might be assumed that assessment of the accuracy in determining a location of corners of a building using a combination of two different surveying methods will meet the requirements of the regulation [MIA, 2011), subject to compliance with relevant baseline criteria, which have been

  1. The structure of melon necrotic spot virus determined at 2.8 Å resolution

    International Nuclear Information System (INIS)

    Wada, Yasunobu; Tanaka, Hideaki; Yamashita, Eiki; Kubo, Chikako; Ichiki-Uehara, Tamaki; Nakazono-Nagaoka, Eiko; Omura, Toshihiro; Tsukihara, Tomitake

    2007-01-01

    The structure of melon necrotic spot virus is reported. The structure of melon necrotic spot virus (MNSV) was determined at 2.8 Å resolution. Although MNSV is classified into the genus Carmovirus of the family Tombusviridae, the three-dimensional structure of MNSV showed a higher degree of similarity to tomato bushy stunt virus (TBSV), which belongs to the genus Tombusvirus, than to carnation mottle virus (CMtV), turnip crinkle virus (TCV) or cowpea mottle virus (CPMtV) from the genus Carmovirus. Thus, the classification of the family Tombusviridae at the genus level conflicts with the patterns of similarity among coat-protein structures. MNSV is one of the viruses belonging to the genera Tombusvirus or Carmovirus that are naturally transmitted in the soil by zoospores of fungal vectors. The X-ray structure of MNSV provides us with a representative structure of viruses transmitted by fungi

  2. Document turn-over analysis to determine need of NPP construction in build-up structures of reinforced concrete

    International Nuclear Information System (INIS)

    Vojpe, D.K.; Lyubavin, V.K.

    1986-01-01

    Document turn-over to determine used of NPP construction in build-up structures of reinforced concrete is carried out. Ways of improving determination of needs of NPP construction board in the mentioned structures are pointed out

  3. An approach for high-throughput structure determination of proteins by NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Medek, Ales; Olejniczak, Edward T.; Meadows, Robert P.; Fesik, Stephen W. [Abbott Laboratories, Pharmaceutical Discovery Division (United States)

    2000-11-15

    An approach is described for rapidly determining protein structures by NMR that utilizes proteins containing {sup 13}C-methyl labeled Val, Leu, and Ile ({delta}1) and protonated Phe and Tyr in a deuterated background. Using this strategy, the key NOEs that define the hydrophobic core and overall fold of the protein are easily obtained. NMR data are acquired using cryogenic probe technology which markedly reduces the spectrometer time needed for data acquisition. The approach is demonstrated by determining the overall fold of the antiapoptotic protein, Bcl-xL, from data collected in only 4 days. Refinement of the Bcl-xL structure to a backbone rmsd of 0.95 A was accomplished with data collected in an additional 3 days. A distance analysis of 180 different proteins and structure calculations using simulated data suggests that our method will allow the global folds of a wide variety of proteins to be determined.

  4. Ab initio structure determination and quantitative disorder analysis on nanoparticles by electron diffraction tomography.

    Science.gov (United States)

    Krysiak, Yaşar; Barton, Bastian; Marler, Bernd; Neder, Reinhard B; Kolb, Ute

    2018-03-01

    Nanoscaled porous materials such as zeolites have attracted substantial attention in industry due to their catalytic activity, and their performance in sorption and separation processes. In order to understand the properties of such materials, current research focuses increasingly on the determination of structural features beyond the averaged crystal structure. Small particle sizes, various types of disorder and intergrown structures render the description of structures at atomic level by standard crystallographic methods difficult. This paper reports the characterization of a strongly disordered zeolite structure, using a combination of electron exit-wave reconstruction, automated diffraction tomography (ADT), crystal disorder modelling and electron diffraction simulations. Zeolite beta was chosen for a proof-of-principle study of the techniques, because it consists of two different intergrown polymorphs that are built from identical layer types but with different stacking sequences. Imaging of the projected inner Coulomb potential of zeolite beta crystals shows the intergrowth of the polymorphs BEA and BEB. The structures of BEA as well as BEB could be extracted from one single ADT data set using direct methods. A ratio for BEA/BEB = 48:52 was determined by comparison of the reconstructed reciprocal space based on ADT data with simulated electron diffraction data for virtual nanocrystals, built with different ratios of BEA/BEB. In this way, it is demonstrated that this smart interplay of the above-mentioned techniques allows the elaboration of the real structures of functional materials in detail - even if they possess a severely disordered structure.

  5. NMR in a crystallography-based high-throughput protein structure-determination environment

    International Nuclear Information System (INIS)

    Wüthrich, Kurt

    2010-01-01

    As an introduction to three papers on comparisons of corresponding crystal and NMR solution structures determined by the Joint Center for Structural Genomics (JCSG), an outline is provided of the JCSG strategy for combined use of the two techniques. A special commentary addresses the potentialities of the concept of ‘reference crystal structures’, which is introduced in the following three papers. An introduction is provided to three papers which compare corresponding protein crystal and NMR solution structures determined by the Joint Center for Structural Genomics (JCSG). Special mention is made of the JCSG strategy for combined use of the two techniques, and of potential applications of the concept of ‘reference crystal structures’, which is introduced in the following three papers

  6. The use of magnetic Barkhausen noise analysis for nondestructive determination of stresses in structural elements

    International Nuclear Information System (INIS)

    Silva Junior, Silverio Ferreira da; Mansur, Tanius Rodrigues; Cruz, Julio Ricardo Barreto

    2007-01-01

    The knowledge about the stress state acting in structural elements has significant importance in the structural integrity evaluation of a specific component. The magnetic Barkhausen noise analysis can be used for this purpose. As a nondestructive testing method, it presents the advantage of not promote any changes in the tested component. In this paper, a study about the use of this new nondestructive test method for stress measurements is presented. The test system configuration and the reference standards used for this purpose, as well as the optimum test parameters determination are discussed. The experiments were carried out in ASTM A-36 steel, used for structural components manufacturing. A structure of this material was loaded and the resulting stresses were determined from strain gage measurements and Barkhausen noise analysis. The results obtained have showed a good sensitivity of the magnetic Barkhausen noise to stress changes occurred in the material. The main advantages and limitations of this test method for stress measurements are presented. (author)

  7. Molecular structure determination of cyclootane by ab initio and electron diffraction methods in the gas phase

    OpenAIRE

    De Almeida, Wagner B.

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can ma...

  8. Kendall’s tau and agglomerative clustering for structure determination of hierarchical Archimedean copulas

    Directory of Open Access Journals (Sweden)

    Górecki J.

    2017-01-01

    Full Text Available Several successful approaches to structure determination of hierarchical Archimedean copulas (HACs proposed in the literature rely on agglomerative clustering and Kendall’s correlation coefficient. However, there has not been presented any theoretical proof justifying such approaches. This work fills this gap and introduces a theorem showing that, given the matrix of the pairwise Kendall correlation coefficients corresponding to a HAC, its structure can be recovered by an agglomerative clustering technique.

  9. Determination of the Steady State Leakage Current in Structures with Ferroelectric Ceramic Films

    Science.gov (United States)

    Podgornyi, Yu. V.; Vorotilov, K. A.; Sigov, A. S.

    2018-03-01

    Steady state leakage currents have been investigated in capacitor structures with ferroelectric solgel films of lead zirconate titanate (PZT) formed on silicon substrates with a lower Pt electrode. It is established that Pt/PZT/Hg structures, regardless of the PZT film thickness, are characterized by the presence of a rectifying contact similar to p-n junction. The steady state leakage current in the forward direction increases with a decrease in the film thickness and is determined by the ferroelectric bulk conductivity.

  10. Identification and determination of solitary wave structures in nonlinear wave propagation

    International Nuclear Information System (INIS)

    Newman, W.I.; Campbell, D.K.; Hyman, J.M.

    1991-01-01

    Nonlinear wave phenomena are characterized by the appearance of ''solitary wave coherent structures'' traveling at speeds determined by their amplitudes and morphologies. Assuming that these structures are briefly noninteracting, we propose a method for the identification of the number of independent features and their respective speeds. Using data generated from an exact two-soliton solution to the Korteweg-de-Vries equation, we test the method and discuss its strengths and limitations. 41 refs., 2 figs

  11. Determinants of capital structure in small and medium sized enterprises in Malaysia

    OpenAIRE

    Mat Nawi, Hafizah

    2015-01-01

    This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London This study aims to investigate the determinants of capital structure in small and medium-sized enterprises (SMEs) in Malaysia and their effect on firms’ performance. The study addresses the following primary question: What are the factors that influence the capital structure of SMEs in Malaysia? The sample of this research is SMEs in the east coast region of Malaysia. Adopting a posi...

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

    International Nuclear Information System (INIS)

    Axford, Danny; Foadi, James; Hu, Nien-Jen; Choudhury, Hassanul Ghani; Iwata, So; Beis, Konstantinos; Evans, Gwyndaf; Alguel, Yilmaz

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Axford, Danny [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Hu, Nien-Jen; Choudhury, Hassanul Ghani [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Kyoto University, Kyoto 606-8501 (Japan); Beis, Konstantinos [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom)

    2015-05-14

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

  14. DETERMINANTS OF CAPITAL STRUCTURE OF CROATIAN ENTERPRISES BEFORE AND DURING THE FINANCIAL CRISIS

    Directory of Open Access Journals (Sweden)

    Ena Mostarac

    2013-06-01

    Full Text Available This paper analysis capital structure determinants of Croatian enterprises based on a cross-sectional data for pre-recession 2007 and recession 2010 comprising about 10,000 firms. Determinants are selected with reference to the relevant capital structure theories and include asset tangibility, profitability, firm size and business risk. The results indicate highly positive significant impact of tangibility and negative significant impact of profitability on financial leverage in both observed years. Firm size seems to be statistically significant at higher level in crisis period, but at the same time no relationship can be found between business risk and financial leverage that is of economic significance.

  15. Breaking symmetry in the structure determination of (large) symmetric protein dimers

    Energy Technology Data Exchange (ETDEWEB)

    Gaponenko, Vadim; Altieri, Amanda S.; Li, Jess; Byrd, R. Andrew [National Cancer Institute, Structural Biophysics Laboratory (United States)], E-mail: rabyrd@ncifcrf.gov

    2002-10-15

    We demonstrate a novel methodology to disrupt the symmetry in the NMR spectra of homodimers. A paramagnetic probe is introduced sub-stoichiometrically to create an asymmetric system with the paramagnetic probe residing on only one monomer within the dimer. This creates sufficient magnetic anisotropy for resolution of symmetry-related overlapped resonances and, consequently, detection of pseudocontact shifts and residual dipolar couplings specific to each monomeric component. These pseudocontact shifts can be readily incorporated into existing structure refinement calculations and enable determination of monomer orientation within the dimeric protein. This methodology can be widely used for solution structure determination of symmetric dimers.

  16. Determination of dynamic characteristics of multi-layer carbon plastic structures of high-resolution scanner

    Directory of Open Access Journals (Sweden)

    В. Н. Маслей

    2017-10-01

    Full Text Available The comparative analysis results for the numerical determination of the dynamic characteristics of multi-layer carbon-fiber plates of the space vehicle scanner design by various types of finite element approximation of the physico-mechanical properties of the composite material are presented. Using the topological structure of the construction of reinforcing layers material in the plate package plane, experimental data for the elastic and mass characteristics of homogeneous carbon-fiber fibers, equivalent structural and orthotropic stiffness and elastic characteristics of the material of composite plates are determined.

  17. Experimental determination of the π meson structure functions by the Drell-Yan mechanism

    International Nuclear Information System (INIS)

    Badier, J.; Bourotte, J.; Mine, P.; Vanderhaghen, R.; Weisz, S.; Boucrot, J.; Callot, O.; Decamp, D.; Karyotakis, Y.; Lefrancois, J.; Crozon, M.; Delpierre, P.; Leray, T.; Maillard, J.; Tilquin, A.; Valentin, J.

    1983-01-01

    We have studied high statistics samples of dimuon events (proportional35,000) produced from πsup(+-) on platinum target in the mass interval 4.2 2 sigma/dx 1 dx 2 to π + and π - data. At 200 GeV, the simultaneous use of π + and π - data allows a separate determination of the valence and sea structure functions of the π. Furthermore, the 150 and 280 GeV data allow an accurate determination of the shape of the valence structure function and give an estimate of its evolution between Q 2 =25 and 50 GeV 2 . (orig.)

  18. Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods

    Science.gov (United States)

    Mandal, Kalyaneswar; Pentelute, Brad L; Tereshko, Valentina; Thammavongsa, Vilasak; Schneewind, Olaf; Kossiakoff, Anthony A; Kent, Stephen B H

    2009-01-01

    We describe the use of racemic crystallography to determine the X-ray structure of the natural product plectasin, a potent antimicrobial protein recently isolated from fungus. The protein enantiomers l-plectasin and d-plectasin were prepared by total chemical synthesis; interestingly, l-plectasin showed the expected antimicrobial activity, while d-plectasin was devoid of such activity. The mirror image proteins were then used for racemic crystallization. Synchrotron X-ray diffraction data were collected to atomic resolution from a racemic plectasin crystal; the racemate crystallized in the achiral centrosymmetric space group with one l-plectasin molecule and one d-plectasin molecule forming the unit cell. Dimer-like intermolecular interactions between the protein enantiomers were observed, which may account for the observed extremely low solvent content (13%–15%) and more highly ordered nature of the racemic crystals. The structure of the plectasin molecule was well defined for all 40 amino acids and was generally similar to the previously determined NMR structure, suggesting minimal impact of the crystal packing on the plectasin conformation. PMID:19472324

  19. Atomic structure of large angle grain boundaries determined by quantitative X-ray diffraction techniques

    International Nuclear Information System (INIS)

    Fitzsimmons, M.R.; Sass, S.L.

    1988-01-01

    Quantitative X-ray diffraction techniques have been used to determine the atomic structure of the Σ = 5 and 13 [001] twist boundaries in Au with a resolution of 0.09 Angstrom or better. The reciprocal lattices of these boundaries were mapped out using synchrotron radiation. The atomic structures were obtained by testing model structures against the intensity observations with a chi square analysis. The boundary structure were modeled using polyhedra, including octahedra, special configurations of tetrahedra and Archimedian anti-prisms, interwoven together by the boundary symmetry. The results of this work point to the possibility of obtaining general rules for grain boundary structure based on X-ray diffraction observations that give the atomic positions with high resolution

  20. Ownership and Determinants Capital Structure of Public Listed Companies in Indonesia: a Panel Data Analysis

    Directory of Open Access Journals (Sweden)

    Arief Tri Hardiyanto

    2013-04-01

    Full Text Available Capital structure is a mix of debts and equities used by a company to finance its investment. Debt offers benefit of tax shield from interest expenses that can be deducted in calculating company income tax. Unfortunately, company can not use debts in unlimited amount because it will lead to risk of bankcrupt. Therefore, company needs to establish a target (unobserved capital structure which will optimize the value of the firm. The purpose of this study is to investigate the determinant of capital structure and ownership in public listed companies in Indonesia Stock Exchange using Time-Series Cross-Section Regression (TSCSREG and supported with a balanced panel data. Data used are financial statements of 228 public listed companies from group of eight industry sectors. Research finding confirms that tax shield and fixed financial burden are significantly influence the capital structure and state ownership also significantly influence the capital structure of the state owned enterprises.

  1. Ownership and Determinants Capital Structure of Public Listed Companies in Indonesia: a Panel Data Analysis

    Directory of Open Access Journals (Sweden)

    Arief Tri Hardiyanto

    2013-04-01

    Full Text Available Capital structure is a mix of debts and equities used by a company to finance its investment. Debt offers benefit of tax shield from interest expenses that can be deducted in calculating company income tax. Unfortunately, company can not use debts in unlimited amount because it will lead to risk of bankcrupt. Therefore, company needs to establish a target (unobserved capital structure which will optimize the value of the firm. The purpose of this study is to investigate the determinant of capital structure and ownership in public listed companies in Indonesia Stock Exchange using Time-Series CrossSection Regression (TSCSREG and supported with a balanced panel data. Data used are financial statements of 228 public listed companies from group of eight industry sectors. Research finding confirms that tax shield and fixed financial burden are significantly influence the capital structure and state ownership also significantly influence the capital structure of the state owned enterprises.

  2. Solvation structure determination of nickel(II) ion in six nitriles using extended X-ray absorption fine structure spectroscopy

    International Nuclear Information System (INIS)

    Inada, Yasuhiro; Funahashi, Shigenobu

    1997-01-01

    The solvation structures of the nickel(II) ion in six nitriles have been determined using X-ray absorption fine structure spectroscopy. The coordination number and the Ni-N bond length are 6 and 206.9 ± 0.6 pm in acetonitrile, 5.9 ± 0.2 and 206.9 ± 0.6 pm in propionitrile, 6.0 ± 0.2 and 206.8 ± 0.6 pm in butyronitrile, 6.0 ± 0.2 and 206.8 ± 0.6 pm in isobutyronitrile, 6.0 ± 0.2 and 206.8 ± 0.6 pm in valeronitrile, and 6.0 ± 0.2 and 206.5 ± 0.7 pm in benzonitrile, respectively. The structure parameters around the nickel(II) ion in all the nitriles are not affected by the bulkiness of the nitrile molecules. On the basis of the obtained structure parameters, we have discussed the structural characteristics around the nickel(II) ion with nitrogen and oxygen donor solvents and the reaction mechanisms for nitrile exchange on the nickel(II) ion. (author)

  3. Population structure of humpback whales in the western and central South Pacific Ocean as determined by vocal exchange among populations.

    Science.gov (United States)

    Garland, Ellen C; Goldizen, Anne W; Lilley, Matthew S; Rekdahl, Melinda L; Garrigue, Claire; Constantine, Rochelle; Hauser, Nan Daeschler; Poole, M Michael; Robbins, Jooke; Noad, Michael J

    2015-08-01

    For cetaceans, population structure is traditionally determined by molecular genetics or photographically identified individuals. Acoustic data, however, has provided information on movement and population structure with less effort and cost than traditional methods in an array of taxa. Male humpback whales (Megaptera novaeangliae) produce a continually evolving vocal sexual display, or song, that is similar among all males in a population. The rapid cultural transmission (the transfer of information or behavior between conspecifics through social learning) of different versions of this display between distinct but interconnected populations in the western and central South Pacific region presents a unique way to investigate population structure based on the movement dynamics of a song (acoustic) display. Using 11 years of data, we investigated an acoustically based population structure for the region by comparing stereotyped song sequences among populations and years. We used the Levenshtein distance technique to group previously defined populations into (vocally based) clusters based on the overall similarity of their song display in space and time. We identified the following distinct vocal clusters: western cluster, 1 population off eastern Australia; central cluster, populations around New Caledonia, Tonga, and American Samoa; and eastern region, either a single cluster or 2 clusters, one around the Cook Islands and the other off French Polynesia. These results are consistent with the hypothesis that each breeding aggregation represents a distinct population (each occupied a single, terminal node) in a metapopulation, similar to the current understanding of population structure based on genetic and photo-identification studies. However, the central vocal cluster had higher levels of song-sharing among populations than the other clusters, indicating that levels of vocal connectivity varied within the region. Our results demonstrate the utility and value of

  4. Determinants of Regional Female Labour Market Participation in the Netherlands : A Spatial Structural Equation Modeling Approach

    NARCIS (Netherlands)

    Liu, An; Noback, Inge

    2011-01-01

    The paper analyses the determinants of female labour participation. Structural equation modelling is used to handle theoretical concepts and to solve the typical problem of multicollinearity. The proposed methodology is applied to a dataset for the year 2002 made up of a sample of 278 municipalities

  5. The determination of the in situ structure by nuclear spin contrast variation

    Energy Technology Data Exchange (ETDEWEB)

    Stuhrmann, H.B. [GKSS Forschungszentrum, Geesthacht (Germany); Nierhaus, K.H. [Max-Planch-Institut fuer Molekulare Genetik, Berlin (Germany)

    1994-12-31

    Polarized neutron scattering from polarized nuclear spins in hydrogenous substances opens a new way of contrast variation. The enhanced contrast due to proton spin polarization was used for the in situ structure determination of tRNA of the functional complex of the E.coli ribosome.

  6. Crystal structure determination from powder diffraction data of the coumarin vanillin chalcone

    Czech Academy of Sciences Publication Activity Database

    Ghouili, A.; Rohlíček, Jan; Ayed, T.B.; Hassen, R.B.

    2014-01-01

    Roč. 29, č. 4 (2014), s. 361-365 ISSN 0885-7156 Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : chalcone * absorption spectra * powder diffraction * crystal structure determination * coumarin derivatives Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.636, year: 2014

  7. Instruction in text-structure as a determinant of senior secondary ...

    African Journals Online (AJOL)

    The study determined the effectiveness of instruction in text-structure on achievement of students in English narrative text. The pretest-posttest control group quasi experimental design was adopted for the study. The participants were 120 students in intact classes from four purposively selected senior secondary schools in ...

  8. Structure determination and compositional modification of body-centered tetragonal PX-phase lead titanate

    Czech Academy of Sciences Publication Activity Database

    Wang, J.; Schenk, K.; Carvalho, A.; Wylie-van Eerd, B.; Trodahl, J.; Sandu, C.S.; Bonin, M.; Gregora, Ivan; He, Z.; Yamada, T.; Funakubo, H.; Briddon, P.R.; Setter, N.

    2011-01-01

    Roč. 23, č. 10 (2011), s. 2529-2535 ISSN 0897-4756 R&D Projects: GA AV ČR KAN301370701 Institutional research plan: CEZ:AV0Z10100520 Keywords : lead titanate * fibrous PX phase * structure determination * open channels * Raman scattering Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 7.286, year: 2011

  9. Synthesis and Single Crystal X-Ray Structure Determination of 3,3',5 ...

    African Journals Online (AJOL)

    Single crystal structure determination at 100 K revealed needle-like crystals in an orthorhombic crystal system. The asymmetric unit of the cell consists of an isolated chloride ion, one half of a tetrahedral [MnCl4]2- anion, a [H2Me4bpz]2+ dication and one half of a molecule of water. Keywords: Crystal Engineering, Hydrogen ...

  10. Magnetic Resonance Determinations of Structure and Reaction Kinetics of Epoxy/Amine Systems.

    Science.gov (United States)

    1981-12-31

    AD- AISA 542 MCDONNELL DOUGLAS RESEARCH LABS ST LOUIS MO FIG 7/4 MAGNETIC RESONANCE DETERMINATIONS OF STRUCTURE AND REACTION KIN--ETC (U) DEC Al I M...solvent content (methylene chloride). DD I JAN73 1473 EDITION OF I NOV 65 IS OBSOLETE UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE (When Doe Fntered

  11. Kendall’s tau and agglomerative clustering for structure determination of hierarchical Archimedean copulas

    Czech Academy of Sciences Publication Activity Database

    Górecki, J.; Hofert, M.; Holeňa, Martin

    2017-01-01

    Roč. 5, č. 1 (2017), s. 75-87 ISSN 2300-2298 R&D Projects: GA ČR GA17-01251S Institutional support: RVO:67985807 Keywords : structure determination * agglomerative clustering * Kendall’s tau * Archimedean copula Subject RIV: IN - Informatics, Computer Science OBOR OECD: Statistics and probability

  12. Determination of the pion structure function from muon-pair production

    International Nuclear Information System (INIS)

    Newman, C.B.; Anderson, K.J.; Coleman, R.N.; Hogan, G.E.; Karhi, K.P.; McDonald, K.T.; Pilcher, J.E.; Rosenberg, E.I.; Sanders, G.H.; Smith, A.J.S.; Thaler, J.J.

    1979-01-01

    Data on muon-pair production by pions are used to determine the momentum distribution for valence quarks in the pion. The shape of a nucleon structure function is also obtained and is compared with a calculation based on existing data

  13. Determination of the Nonlinearity Parameter in the TNM Model of Structural Recovery

    Science.gov (United States)

    Bari, Rozana; Simon, Sindee

    Structural recovery of non-equilibrium glassy materials takes place by evolution of volume and enthalpy as the glass attempts to reach to equilibrium. Structural recovery is nonlinear, nonexponential, and depends on thermal history and the process can be described by phenomenological models of structural recovery, such as the Tool-Narayanaswamy-Moynihan (TNM) and the Kovacs-Aklonis-Hutchinson-Ramos (KAHR) models. The goal of the present work is to analyze methods to determine the nonlinearity parameter x and activation energy Δh/R. The methods to determine x includes the inflectional analysis, time-temperature superposition, and two-step temperature jump methods. The activation energy Δh/R can also be obtained by the first two methods. The TNM model is used to simulate structural recovery data, which are then used to test the accuracy of the methods to determine x and Δh/R, with a particular interest in data obtained after cooling at high rates as can be obtained in the Flash DSC. The nonlinearity parameter x by the inflectional analysis and two-step temperature methods are accurate for exponential recovery. However, for real systems with nonexponential relaxation, methods to determine x are not reliable. The activation energy is well estimated by both the time-temperature superposition and inflectional analysis methods, with the former being slightly better.

  14. The determination of the in situ structure by nuclear spin contrast variation

    International Nuclear Information System (INIS)

    Stuhrmann, H.B.; Nierhaus, K.H.

    1994-01-01

    Polarized neutron scattering from polarized nuclear spins in hydrogenous substances opens a new way of contrast variation. The enhanced contrast due to proton spin polarization was used for the in situ structure determination of tRNA of the functional complex of the E.coli ribosome

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

    Science.gov (United States)

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

    1986-01-01

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

  16. Unbiased determination of the proton structure function F2p with faithful uncertainty estimation

    International Nuclear Information System (INIS)

    Del Debbio, Luigi; Forte, Stefano; Latorre, Jose I.; Rojo, Joan; Piccione, Andrea

    2005-01-01

    We construct a parametrization of the deep-inelastic structure function of the proton F 2 (x,Q 2 ) based on all available experimental information from charged lepton deep-inelastic scattering experiments. The parametrization effectively provides a bias-free determination of the probability measure in the space of structure functions, which retains information on experimental errors and correlations. The result is obtained in the form of a Monte Carlo sample of neural networks trained on an ensemble of replicas of the experimental data. We discuss in detail the techniques required for the construction of bias-free parameterizations of large amounts of structure function data, in view of future applications to the determination of parton distributions based on the same method. (author)

  17. Structure determination of human Lck unique and SH3 domains by nuclear magnetic resonance spectroscopy

    Directory of Open Access Journals (Sweden)

    Willbold Dieter

    2003-05-01

    Full Text Available Abstract Background Protein tyrosine kinases are involved in signal transduction pathways that regulate cell growth, differentiation, activation and transformation. Human lymphocyte specific kinase (Lck is a 56 kDa protein involved in T-cell- and IL2-receptor signaling. Three-dimensional structures are known for SH3, SH2 and kinase domains of Lck as well as for other tyrosine kinases. No structure is known for the unique domain of any Src-type tyrosine kinase. Results Lck(1–120 comprising unique and SH3 domains was structurally investigated by nuclear magnetic resonance spectroscopy. We found the unique domain, in contrast to the SH3 part, to have basically no defined structural elements. The solution structure of the SH3 part could be determined with very high precision. It does not show significant differences to Lck SH3 in the absence of the unique domain. Minor differences were observed to the X-ray structure of Lck SH3. Conclusion The unique domain of Lck does not contain any defined structure elements in the absence of ligands and membranes. Presence of the unique domain is not relevant to the three-dimensional structure of the Lck SH3 domain.

  18. Competition between intermolecular interaction and configuration entropy as the structure-determining factor for inclusion compounds

    Energy Technology Data Exchange (ETDEWEB)

    Subbotin, O.; Belosludov, V.; Adamova, T. [Russian Academy of Science, Novosibirsk (Russian Federation). Nikolaev Inst. of Inorganic Chemistry; Belosludov, R.; Kawazoe, Y. [Tohoku Univ., Aoba-ku, Sendai (Japan). Inst. for Materials Research; Kudoh, J.I. [Tohoku Univ., Aoba-ku, Sendai (Japan). Center for Northeast Asia Studies

    2008-07-01

    This paper presented a newly developed method to accurately predict the thermodynamic properties of clathrate hydrates, particularly their structural phase transitions under pressure. The method is based on the theory of Van-der-Waals and Platteeuw with some modifications that include the influence of guest molecules on the host lattice. The model was used to explain the exception from the established rule that small guest molecules form structure s1 and large molecules form structure s2 hydrates. In this study, the thermodynamic properties of argon (Ar) hydrate and methane hydrate, each in both cubic structure s1 and s2 were modelled. The model showed that two competing factors play a role in the formation of inclusions, notably the intermolecular interaction of guest molecules with water molecules, and the configuration entropy. Competition of these 2 factors determines the structure of hydrate formed at different pressures. The model provides an accurate description of the thermodynamic properties of gas hydrates and how they behave under pressure. For the argon hydrates, the structural phase transition from structure s2 to s1 at high pressure was predicted, while methane hydrates were predicted to be metastable in the s2 structure. The model can be used for other inclusion compounds with the same type of composition such as clathrate silicon, zeolites, and inclusion compounds of semiconductor elements. 17 refs., 5 figs.

  19. Effective Method for Determining Environmental Loads on Supporting Structures for Offshore Wind Turbines

    Directory of Open Access Journals (Sweden)

    Dymarski Paweł

    2016-01-01

    Full Text Available This paper presents a description of an effective method for determining loads due to waves and current acting on the supporting structures of the offshore wind turbines. This method is dedicated to the structures consisting of the cylindrical or conical elements as well as (truncates pyramids of polygon with a large number of sides (8 or more. The presented computational method is based on the Morison equation, which was originally developed only for cylindrically shaped structures. The new algorithm shown here uses the coefficients of inertia and drag forces that were calculated for non-cylindrical shapes. The analysed structure consists of segments which are truncated pyramids on the basis of a hex decagon. The inertia coefficients, CM, and drag coefficients, CD, were determined using RANSE-CFD calculations. The CFD simulations were performed for a specific range of variation of the period, and for a certain range of amplitudes of the velocity. In addition, the analysis of influence of the surface roughness on the inertia and drag coefficients was performed. In the next step, the computations of sea wave, current and wind load on supporting structure for the fifty-year storm were carried out. The simulations were performed in the time domain and as a result the function of forces distribution along the construction elements was obtained. The most unfavourable distribution of forces will be used, to analyse the strength of the structure, as the design load.

  20. Use of the CSD program package for structure determination from powder data

    International Nuclear Information System (INIS)

    Akselrud, L.G.; Zavalii, P.Yu.; Grin, Yu.N.; Pecharski, V.K.; Baumgartner, B.; Woelfel, E.

    1993-01-01

    Although Rietveld's method of full profile structure refinement of powder data is a much-used tool today, ab initio structure solution from powder data is still not a routine task. One of the reasons for this is that fully overlapped peaks usually cannot be handled by routine structure determination programs. This shortcoming is not present in the Crystal Structure Determination (CSD) package which accepts intensities from powder diagrams as well as single crystal data. In order to demonstrate the possibilities of the CSD package, powder diagrams of five substances with already known crystal structure were collected and evaluated with the CSD package. The samples were scheelite (CaWO 4 ), pentaerythritol (C(CH 2 OH) 4 ), sodium sulfite (Na 2 SO 3 ), copper sulfate pentahydrate (CuSO 4 .5H 2 O) and silver germanium phosphide (Ag 6 Ge 10 P 12 ) and showed problems typical for powder work like preferred orientation and heavy peak overlapping. For four of the samples, correct atomic positions for some atoms could be found from the automatic MULTAN solution, which were then used in subsequent least squares- and difference Fourier calculations to locate the remaining atoms. Surprisingly, the cubic Ag 6 Ge 10 P 12 posed the most problems for the structure solution although one third of the observed intensities was single-indexed and the final R-value was as low as 4%. (orig.)

  1. Structure and orientation of interfacial proteins determined by sum frequency generation vibrational spectroscopy: method and application.

    Science.gov (United States)

    Ye, Shuji; Wei, Feng; Li, Hongchun; Tian, Kangzhen; Luo, Yi

    2013-01-01

    In situ and real-time characterization of molecular structures and orientation of proteins at interfaces is essential to understand the nature of interfacial protein interaction. Such work will undoubtedly provide important clues to control biointerface in a desired manner. Sum frequency generation vibrational spectroscopy (SFG-VS) has been demonstrated to be a powerful technique to study the interfacial structures and interactions at the molecular level. This paper first systematically introduced the methods for the calculation of the Raman polarizability tensor, infrared transition dipole moment, and SFG molecular hyperpolarizability tensor elements of proteins/peptides with the secondary structures of α-helix, 310-helix, antiparallel β-sheet, and parallel β-sheet, as well as the methodology to determine the orientation of interfacial protein secondary structures using SFG amide I spectra. After that, recent progresses on the determination of protein structure and orientation at different interfaces by SFG-VS were then reviewed, which provides a molecular-level understanding of the structures and interactions of interfacial proteins, specially understanding the nature of driving force behind such interactions. Although this review has focused on analysis of amide I spectra, it will be expected to offer a basic idea for the spectral analysis of amide III SFG signals and other complicated molecular systems such as RNA and DNA. Copyright © 2013 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2018-03-01

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

  5. Power of isotopic fine structure for unambiguous determination of metabolite elemental compositions: In silico evaluation and metabolomic application

    International Nuclear Information System (INIS)

    Nagao, Tatsuhiko; Yukihira, Daichi; Fujimura, Yoshinori; Saito, Kazunori; Takahashi, Katsutoshi; Miura, Daisuke; Wariishi, Hiroyuki

    2014-01-01

    Graphical abstract: - Highlights: • We developed a method to determine elemental composition of metabolites. • The method was based on mass spectral data and empirical constraints. • In the validation study, the method succeeded for 70% of detected peaks. - Abstract: In mass spectrometry (MS)-based metabolomics studies, reference-free identification of metabolites is still a challenging issue. Previously, we demonstrated that the elemental composition (EC) of metabolites could be unambiguously determined using isotopic fine structure, observed by ultrahigh resolution MS, which provided the relative isotopic abundance (RIA) of 13 C, 15 N, 18 O, and 34 S. Herein, we evaluated the efficacy of the RIA for determining ECs based on the MS peaks of 20,258 known metabolites. The metabolites were simulated with a ≤25% error in the isotopic peak area to investigate how the error size effect affected the rate of unambiguous determination of the ECs. The simulation indicated that, in combination with reported constraint rules, the RIA led to unambiguous determination of the ECs for more than 90% of the tested metabolites. It was noteworthy that, in positive ion mode, the process could distinguish alkali metal-adduct ions ([M + Na] + and [M + K] + ). However, a significant degradation of the EC determination performance was observed when the method was applied to real metabolomic data (mouse liver extracts analyzed by infusion ESI), because of the influence of noise and bias on the RIA. To achieve ideal performance, as indicated in the simulation, we developed an additional method to compensate for bias on the measured ion intensities. The method improved the performance of the calculation, permitting determination of ECs for 72% of the observed peaks. The proposed method is considered a useful starting point for high-throughput identification of metabolites in metabolomic research

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

    Science.gov (United States)

    Khoo, Y; Singer, A; Cowburn, D

    2017-07-01

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

  7. Determination of the thickness of chemically removed thin layers on GaAs VPE structures

    Energy Technology Data Exchange (ETDEWEB)

    Somogyi, K.; Nemeth-Sallay, M.; Nemcsics, A. (Research Inst. for Technical Physics, Hungarian Academy of Sciences, Budapest (Hungary))

    1991-01-01

    Thinning of epitaxial GaAs layers was studied during the surface etching, with a special attention to submicron epitaxial structures, like MESFET or varactor-type structures. Each chemical treatment influences the crystal surface during the device preparation processes, though the possible thinning of the active layer is small. Therefore a method allowing determination of thicknesses as small as at about 20 nm of the layer removed by chemical etching from GaAs VPE structures was applied. Using special multilayered structures and a continuous electrochemical carrier concentration depth profiling, the influence of the layer thickness inhomogeneity and of some measurement errors can be minimized. Some frequently used etchants and the influence of different - so called - non-etching processes were compared in different combinations. It was shown that besides the direct etching a change of the surface conditions occurs, which influences the etch rate in the succeeding etching procedure. (orig.).

  8. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Yuanpeng Janet, E-mail: yphuang@cabm.rutgers.edu; Mao, Binchen; Xu, Fei; Montelione, Gaetano T., E-mail: gtm@rutgers.edu [Rutgers, The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium (United States)

    2015-08-15

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD–NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases {sup 15}N–{sup 1}H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD–NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta.

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

    Science.gov (United States)

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

    2018-02-01

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

  10. Application of in situ diffraction in high-throughput structure determination platforms.

    Science.gov (United States)

    Aller, Pierre; Sanchez-Weatherby, Juan; Foadi, James; Winter, Graeme; Lobley, Carina M C; Axford, Danny; Ashton, Alun W; Bellini, Domenico; Brandao-Neto, Jose; Culurgioni, Simone; Douangamath, Alice; Duman, Ramona; Evans, Gwyndaf; Fisher, Stuart; Flaig, Ralf; Hall, David R; Lukacik, Petra; Mazzorana, Marco; McAuley, Katherine E; Mykhaylyk, Vitaliy; Owen, Robin L; Paterson, Neil G; Romano, Pierpaolo; Sandy, James; Sorensen, Thomas; von Delft, Frank; Wagner, Armin; Warren, Anna; Williams, Mark; Stuart, David I; Walsh, Martin A

    2015-01-01

    Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.

  11. Method of magnetic susceptibility mapping of drilled cores. Experimental measurements for geologic structures determination

    International Nuclear Information System (INIS)

    Delrive, C.

    1993-01-01

    The evaluation of the safety of a deep geologic repository for dangerous materials requires the knowledge of the interstitial system of the surrounding host rock. A method is proposed for the determination of geologic structures (in particular fractures) from the magnetic susceptibility mapping of drilled cores. The feasibility of the method has been demonstrated using a SQUID magneto-gradient meter. A measurement tool using a new magnetic susceptibility captor and a testing bench have been developed. This tool allows the measurement of rocks with a magnetic susceptibility greater than 10 -5 SI units and can generate magnetic susceptibility maps with 4 x 4 mm 2 pixels. A magnetic visibility criterion has been defined which allows to foresee if a structure is visible or not. According to the measurements done, it is shown that any centimeter-scale structure with a sufficient magnetic contrast (20%) with respect to the matrix is visible. Therefore, the dip and the orientation of such structure can be determined with a 3 degree and a 5 degree precision, respectively. The position of the structure along the core axis is known with a 4 mm precision. On the other hand, about half of the magnetic contrasts observed do not correspond to the visual analyses and can be explained by very small variations of the mineralogic composition. This last point offers some interesting ways for future research using magnetic susceptibility mapping. (J.S.). 31 refs., 90 figs., 18 tabs., 2 photos., 6 appends

  12. Computational tools for experimental determination and theoretical prediction of protein structure

    Energy Technology Data Exchange (ETDEWEB)

    O`Donoghue, S.; Rost, B.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. The authors intend to review the state of the art in the experimental determination of protein 3D structure (focus on nuclear magnetic resonance), and in the theoretical prediction of protein function and of protein structure in 1D, 2D and 3D from sequence. All the atomic resolution structures determined so far have been derived from either X-ray crystallography (the majority so far) or Nuclear Magnetic Resonance (NMR) Spectroscopy (becoming increasingly more important). The authors briefly describe the physical methods behind both of these techniques; the major computational methods involved will be covered in some detail. They highlight parallels and differences between the methods, and also the current limitations. Special emphasis will be given to techniques which have application to ab initio structure prediction. Large scale sequencing techniques increase the gap between the number of known proteins sequences and that of known protein structures. They describe the scope and principles of methods that contribute successfully to closing that gap. Emphasis will be given on the specification of adequate testing procedures to validate such methods.

  13. Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling.

    Directory of Open Access Journals (Sweden)

    Lotta Berg

    Full Text Available Acetylcholinesterase (AChE is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used (inter alia to treat cholinergic deficiencies (e.g. in Alzheimer's disease, but may also act as dangerous toxins (e.g. nerve agents such as sarin. Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. We have screened a collection of organic molecules to assess their ability to inhibit the enzymatic activity of AChE, aiming to find lead compounds for further optimization leading to drugs with increased efficacy and/or decreased side effects. 124 inhibitors were discovered, with considerable chemical diversity regarding size, polarity, flexibility and charge distribution. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site (CAS. Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure-based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The complex formed between C5685 and Mus musculus AChE (C5685•mAChE is a representative structure for the general binding mode of the determined structures. The CAS binding part of C5685 could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule. We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical

  14. Crystal structure of core streptavidin determined from multi-wavelength anomalous diffraction of synchrotron radiation

    International Nuclear Information System (INIS)

    Hendrickson, W.A.; Paehler, A.; Smith, J.L.; Satow, Y.; Merritt, E.A.; Phizackerley, R.P.

    1989-01-01

    A three-dimensional crystal structure of the biotin-binding core of streptavidin has been determined at 3.1-angstrom resolution. The structure was analyzed from diffraction data measured at three wavelengths from a single crystal of the selenobiotinyl complex with streptavidin. Streptavidin is a tetramer with subunits arrayed in D 2 symmetry. Each protomer is an 8-stranded β-barrel with simple up-down topology. Biotin molecules are bound at one end of each barrel. This study demonstrates the effectiveness of multi-wavelength anomalous diffraction (MAD) procedures for macromolecular crystallography and provides a basis for detailed study of biotin-avidin interactions

  15. Implantation measurements to determine tritium permeation in first-wall structures

    International Nuclear Information System (INIS)

    Holland, D.F.; Causey, R.A.; Sattler, M.L.

    1983-01-01

    A principal safety concern for a D-T burning fusion reactor is release of tritium during routine operation. Tritium implantation into first-wall structures, and subsequent permeation into coolants, is potentially an important source of tritium loss. This paper reports on an experiment in which an ion accelerator was used to implant deuterium atoms in a stainless steel disk to simulate tritium implantation in first-wall structures. The permeation rate was measured under various operating conditions. These results were used in the TMAP computer code to determine potential tritium loss rates for fusion reactors

  16. Electron crystallography applied to the structure determination of Nb(Cu,Al,X) Laves phases.

    Science.gov (United States)

    Gigla, M; Lelatko, J; Krzelowski, M; Morawiec, H

    2006-09-01

    The presence of primary precipitates of the Laves phases considerably improves the mechanical properties and the resistance to thermal degradation of the high-temperature shape memory Cu-Al-Nb alloys. The structure analysis of the Laves phases was carried out on particles contained in the ternary and quaternary alloys as well on synthesized compounds related to the composition of the Nb(Cu,Al,X)(2) phase, where X = Ni, Co, Cr, Ti and Zr. The precise structure determination of the Laves phases was carried out by the electron crystallography method using the CRISP software.

  17. Structure of irregular galactic magnetic fields determined on the basis of cosmic ray measurements

    International Nuclear Information System (INIS)

    Somogyi, A.

    1975-02-01

    In the paper a method is described to determine the structural composition of random galactic fields on the basis of cosmic ray measurements, down to structures with characteristic length of the order of 0.001 to 1 pc. Assuming the diffusion mean free path of the particles to be independent of particle energy the spectral index of magnetic irregularities is estimated to be -(1.0+-0.5). The linear size of the confinement volume is found to be almost independent of particle energy. (Sz.Z.)

  18. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

    KAUST Repository

    Li, Jianping; Pilla, Kala Bharath; Li, Qingfeng; Zhang, Zhengfeng; Su, Xuncheng; Huber, Thomas; Yang, Jun

    2013-01-01

    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

  19. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

    KAUST Repository

    Li, Jianping

    2013-06-05

    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

  20. Determinants of Capital Structure:Evidence from UK Firm Panel Data

    OpenAIRE

    SONG, PING

    2015-01-01

    This study investigates the factors that determine firms’ the capital structures in the UK market. There 139 firms, in total, listed on FTSE 100 and FTSE 250 have been used as the sample set, and a 10-year time scale, from 2004 to 2013, is selected to constitute the panel data. Both firm-specific and macroeconomic determinants are included to be investigated whether they would pose impacts on total, long term and short term debt issuance. The fixed effects regression model is adopted to estim...

  1. Determination of Ni(II) crystal structure by powder x-ray diffraction ...

    African Journals Online (AJOL)

    X-ray powder diffraction pattern was used to determine the length of the unit cell, “a”, the lattice structure type, and the number of atoms per unit cell of Ni(II) crystal. The “a” value was determined to be 23.66 ± 0.005 Å, particle size of 34.87 nm, volume 13.24 Å and Strain value ε = 9.8 x 10-3. The cell search on PXRD patterns ...

  2. Determination of αS from scaling violations of truncated moments of structure functions

    International Nuclear Information System (INIS)

    Forte, Stefano; Latorre, J.I.; Magnea, Lorenzo; Piccione, Andrea

    2002-01-01

    We determine the strong coupling α S (M Z ) from scaling violations of truncated moments of the nonsinglet deep inelastic structure function F 2 . Truncated moments are determined from BCDMS and NMC data using a neural network parametrization which retains the full experimental information on errors and correlations. Our method minimizes all sources of theoretical uncertainty and bias which characterize extractions of α S from scaling violations. We obtain α S (M Z )=0.124 +0.004 -0.007 (exp.) +0.003 -0.004 (th.)

  3. Surface structural determination of UO2(111) using MeV ions

    International Nuclear Information System (INIS)

    Thompson, K.A.; Ellis, W.P.; Taylor, T.N.; Valone, S.M.; Maggiore, C.J.

    1983-01-01

    The UO 2 (111) surface was studied using MeV ions incident along the and directions. In addition, this surface was well characterized by LEED and Auger analysis. A resonance at 3.05 MeV for 4 He elastic scattering from 16 O made it possible to study the surface peaks for uranium and oxygen simultaneously. By combining previous surface studies with detailed analysis of the surface peaks and rocking curves for this compound material, an outward relaxation of 0.19 A +- 0.01 A was determined for uranium

  4. X-ray refractive index: A tool to determine the average composition in multilayer structures

    International Nuclear Information System (INIS)

    Miceli, P.F.; Neumann, D.A.; Zabel, H.

    1986-01-01

    We present a novel and simple method to determine the average composition of multilayers and superlattices by measuring the x-ray refractive index. Since these modulated structures exhibit Bragg reflections at small angles, by using a triple axis x-ray spectrometer we have accurately determined the peak shifts due to refraction in GaAs/Al/sub x/Ga/sub 1-x/As and Nb/Ta superlattices. Knowledge of the refractive index provides the average fractional composition of the periodic structure since the refractive index is a superposition of the refractive indices of the atomic constituents. We also present a critical discussion of the method and compare the values of the average fractional composition obtained in this manner to the values obtained from the lattice parameter change in the GaAs/Al/sub x/Ga/sub 1-x/As superlattices due to the Al

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

    Science.gov (United States)

    Benetti, Federico; Legname, Giuseppe

    2015-01-01

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

  6. Exploring the determinants of the graded structure of vocal emotion expressions.

    Science.gov (United States)

    Laukka, Petri; Audibert, Nicolas; Aubergé, Véronique

    2012-01-01

    We examined what determines the typicality, or graded structure, of vocal emotion expressions. Separate groups of judges rated acted and spontaneous expressions of anger, fear, and joy with regard to their typicality and three main determinants of the graded structure of categories: category members' similarity to the central tendency of their category (CT); category members' frequency of instantiation, i.e., how often they are encountered as category members (FI); and category members' similarity to ideals associated with the goals served by its category, i.e., suitability to express particular emotions. Partial correlations and multiple regression analysis revealed that similarity to ideals, rather than CT or FI, explained most variance in judged typicality. Results thus suggest that vocal emotion expressions constitute ideal-based goal-derived categories, rather than taxonomic categories based on CT and FI. This could explain how prototypical expressions can be acoustically distinct and highly recognisable but occur relatively rarely in everyday speech.

  7. Experimental model for neutron scattering in disordered systems: static structure factor determination of mode-softening

    International Nuclear Information System (INIS)

    Siegel, E.

    1982-01-01

    The generalized-disorder collective-boson mode-softening universality-principle (GDCBMSUP) for collective-boson mode dispersion in disordered systems (liquids, quantum liquids, glasses, powders, disordered magnets, plasmas...), a unified qualitative and semi-qualitative and semi-quantitative descriptive prescription for treating the properties of very differently disordered systems, is directly dependent upon a measurement (or calculation) of the static structure factor S(k) determined from a frequency average of the dynamic structure factor S(k,w), a multiple of the inelastic differential neutron scattering cross section d 2 sigma/dwdOMEGA. The prescription for this principle is given and, because of its universal applicability to disordered systems of any type with any type and/or degree of disorder, the neutron scattering determination of S(k) takes on renewed importance

  8. Neutron diffraction stress determination in W-laminates for structural divertor applications

    Directory of Open Access Journals (Sweden)

    R. Coppola

    2015-07-01

    Full Text Available Neutron diffraction measurements have been carried out to develop a non-destructive experimental tool for characterizing the crystallographic structure and the internal stress field in W foil laminates for structural divertor applications in future fusion reactors. The model sample selected for this study had been prepared by brazing, at 1085 °C, 13 W foils with 12 Cu foils. A complete strain distribution measurement through the brazed multilayered specimen and determination of the corresponding stresses has been obtained, assuming zero stress in the through-thickness direction. The average stress determined from the technique across the specimen (over both ‘phases’ of W and Cu is close to zero at −17 ± 32 MPa, in accordance with the expectations.

  9. Evidence against the continuum structure underlying motivation measures derived from self-determination theory.

    Science.gov (United States)

    Chemolli, Emanuela; Gagné, Marylène

    2014-06-01

    Self-determination theory (SDT) proposes a multidimensional conceptualization of motivation in which the different regulations are said to fall along a continuum of self-determination. The continuum has been used as a basis for using a relative autonomy index as a means to create motivational scores. Rasch analysis was used to verify the continuum structure of the Multidimensional Work Motivation Scale and of the Academic Motivation Scale. We discuss the concept of continuum against SDT's conceptualization of motivation and argue against the use of the relative autonomy index on the grounds that evidence for a continuum structure underlying the regulations is weak and because the index is statistically problematic. We suggest exploiting the full richness of SDT's multidimensional conceptualization of motivation through the use of alternative scoring methods when investigating motivational dynamics across life domains.

  10. Structure determination of LpxA from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii

    International Nuclear Information System (INIS)

    Badger, John; Chie-Leon, Barbara; Logan, Cheyenne; Sridhar, Vandana; Sankaran, Banumathi; Zwart, Peter H.; Nienaber, Vicki

    2012-01-01

    Crystal structures of the LpxA protein from A. baumannii were solved in apo forms that were suitable for structure-based antibacterial drug discovery. Acinetobacter baumannii is a Gram-negative pathogenic bacterium which is resistant to most currently available antibiotics and that poses a significant health threat to hospital patients. LpxA is a key enzyme in the biosynthetic pathway of the lipopolysaccharides that are components of the bacterial outer membrane. It is a potential target for antibacterial agents that might be used to fight A. baumannii infections. This paper describes the structure determination of the apo form of LpxA in space groups P2 1 2 1 2 1 and P6 3 . These crystal forms contained three and one protein molecules in the asymmetric unit and diffracted to 1.8 and 1.4 Å resolution, respectively. A comparison of the conformations of the independent protein monomers within and between the two crystal asymmetric units revealed very little structural variation across this set of structures. In the P6 3 crystal form the enzymatic site is exposed and is available for the introduction of small molecules of the type used in fragment-based drug discovery and structure-based lead optimization

  11. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

    International Nuclear Information System (INIS)

    Rosato, Antonio; Vranken, Wim; Fogh, Rasmus H.; Ragan, Timothy J.; Tejero, Roberto; Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H.; Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H.; Kennedy, Michael; Acton, Thomas B.; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T.; Vuister, Geerten W.

    2015-01-01

    The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged

  12. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

    Energy Technology Data Exchange (ETDEWEB)

    Rosato, Antonio [University of Florence, Department of Chemistry and Magnetic Resonance Center (Italy); Vranken, Wim [Vrije Universiteit Brussel, Structural Biology Brussels (Belgium); Fogh, Rasmus H.; Ragan, Timothy J. [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom); Tejero, Roberto [Universidad de Valencia, Departamento de Química Física (Spain); Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H. [University of Georgia, Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium (United States); Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H. [University of Toronto, Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium (Canada); Kennedy, Michael [Miami University, Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium (United States); Acton, Thomas B.; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T., E-mail: guy@cabm.rutgers.edu [The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers (United States); Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom)

    2015-08-15

    The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.

  13. Nondestructive determination of the load bearing capacity of rigid pavement structures. Zerstoerungsfreie Tragfaehigkeitsbestimmung fuer starre Deckenkonstruktionen

    Energy Technology Data Exchange (ETDEWEB)

    Heinrich, U. (Bauakademie, IHLGB, Berlin (Germany))

    1991-01-01

    Actual parameters of the bearing capacity of traffic areas are in case of intensive use an indispensable necessity for the determination of the remaining use value with the aim to optimize reinforcing layers and reconstruction periods. Until now there is only one adequate measuring method for flexible layers. With the Rollig load test (RLT) initial data can be gained for the calculation of the load bearing capacity of rigid pavement structures. The method is described with the example of an airplane runway. (BWI).

  14. Determination of gastric-emptying profiles in the rat: influence of oil structure and volume

    International Nuclear Information System (INIS)

    Palin, K.J.; Whalley, D.R.; Wilson, C.G.; Davis, S.S.; Phillips, A.J.

    1982-01-01

    A simple non-invasive technique was developed for the determination of the gastric-emptying rate of oils in rats, employing a gamma camera and 99m-Tc-sulphur colloid as the oil phase marker. Using this method the gastric emptying of 3 oils, arachis oil, Miglyol 812 and liquid paraffin, was investigated. It was shown that both the oil volume and chemcial structure altered the rate of gastric emptying. (Auth.)

  15. Determination of gastric-emptying profiles in the rat: influence of oil structure and volume

    Energy Technology Data Exchange (ETDEWEB)

    Palin, K.J.; Whalley, D.R.; Wilson, C.G.; Davis, S.S.; Phillips, A.J. (Nottingham Univ. (UK). Medical School)

    1982-11-01

    A simple non-invasive technique was developed for the determination of the gastric-emptying rate of oils in rats, employing a gamma camera and 99m-Tc-sulphur colloid as the oil phase marker. Using this method the gastric emptying of 3 oils, arachis oil, Miglyol 812 and liquid paraffin, was investigated. It was shown that both the oil volume and chemical structure altered the rate of gastric emptying.

  16. Spatial structure of transition metal complexes in solution determined by EXAFS spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Erenburg, S.B. E-mail: simon@che.nsk.su; Bausk, N.V.; Zemskova, S.M.; Mazalov, L.N

    2000-06-21

    CdK EXAFS, ZnK and CuK EXAFS and XANES spectra were measured for solutions of cadmium, zinc and copper dialkyldithiocarbamates in organic solvents with varying donating abilities: tributylphosphine, methylene chloride, benzene, dibutylsulfide, pyridine, dimethylsulfoxide and for some model compounds. The parameters of the local surroundings of the Cd, Zn and Cu atoms for complex forms in solutions were determined using EXAFS spectroscopy. Spatial structure models of the complex forms in a metal chelate - nonaqueous solvent system are suggested.

  17. Spatial structure of transition metal complexes in solution determined by EXAFS spectroscopy

    International Nuclear Information System (INIS)

    Erenburg, S.B.; Bausk, N.V.; Zemskova, S.M.; Mazalov, L.N.

    2000-01-01

    CdK EXAFS, ZnK and CuK EXAFS and XANES spectra were measured for solutions of cadmium, zinc and copper dialkyldithiocarbamates in organic solvents with varying donating abilities: tributylphosphine, methylene chloride, benzene, dibutylsulfide, pyridine, dimethylsulfoxide and for some model compounds. The parameters of the local surroundings of the Cd, Zn and Cu atoms for complex forms in solutions were determined using EXAFS spectroscopy. Spatial structure models of the complex forms in a metal chelate - nonaqueous solvent system are suggested

  18. Strategy and structure in interaction: What determines the boundaries of the firm?

    OpenAIRE

    Staffan Canback; Phillip Samouel; David Price

    2003-01-01

    This paper analyzes empirically the boundaries of the firm based on Williamson's perspective on what determines firm size. It uses firm performance (risk-adjusted profitability and growth) as dependent variable; and firm organization, diseconomies of scale (atmospheric consequences, bureaucratic insularity, incentive limits, and communication distortion), economies of scale, and asset specificity as independent variables in a structural equation model. Data were collected from the 784 largest...

  19. Structure determination of cyclo pentane terpene derivatives by crossed NMR and MS techniques

    Energy Technology Data Exchange (ETDEWEB)

    Pianet, I.; Bourgeois, G. [Bordeaux-1 Univ., 33 - Talence (France); Dolatkhani, M.; Cramail, H.; Deffieux, A. [Centre National de la Recherche Scientifique (CNRS), 33 - Talence (France)

    1995-10-01

    3 of the 4 stereoisomers of the 1-isopropenyl 2,3-dimethylcyclopentane, obtained from the cracking of 3,7-dimethylocta-1,6-diene, were purified and characterized. Dihedral angles, between the protons of the substituted carbons, have been determined by molecular modelling. Analysis of the NMR and mass spectra allowed us to access to the structure of the different isomers. (authors). 6 refs., 2 tabs.

  20. Determination of localized magnetic moments in Fe-Cr-Al alloys and the electron structure

    International Nuclear Information System (INIS)

    Blau, W.

    1977-01-01

    The localized magnetic moments of Fe and Cr are determined by combination of saturation magnetization measurements and magnetic diffuse scattering. Power series characterizing the interactions between the different kinds of atoms in the alloys are chosen to describe the concentration dependence of the magnetic moments. The different terms are discussed on the basis of band structure models valid for dilute alloys taking into account their modification by impurity interactions. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

    Cornaby, Sterling [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Szebenyi, Doletha M. E. [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Smilgies, Detlef-M. [CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Schuller, David J.; Gillilan, Richard; Hao, Quan [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Bilderback, Donald H., E-mail: dhb2@cornell.edu [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States)

    2010-01-01

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

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

    International Nuclear Information System (INIS)

    Cornaby, Sterling; Szebenyi, Doletha M. E.; Smilgies, Detlef-M.; Schuller, David J.; Gillilan, Richard; Hao, Quan; Bilderback, Donald H.

    2010-01-01

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

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

    Science.gov (United States)

    Piwowarski, Jakub P; Kiss, Anna K

    2013-01-01

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

  4. Crystallographic Orientation Determination of Hexagonal Structure Crystals by Laser Ultrasonic Technique

    International Nuclear Information System (INIS)

    Li, W; Coulson, J; Marrow, P; Smith, R J; Clark, M; Sharples, S D; Lainé, S J

    2016-01-01

    Spatially resolved acoustic spectroscopy (SRAS) is a laser ultrasonic technique that shows qualitative contrast between grains of different orientation, illustrating the sensitivity of acoustic waves to the material structure. The technique has been improved significantly on determining the full orientation of multigrain cubic metals, by comparing the measured surface acoustic wave (SAW) velocity to a pre-calculated model. In this paper we demonstrate the ability of this technique to determine the orientation of hexagonal structure crystals, such as magnesium and titanium based alloys. Because of the isotropy of the SAW velocity on the basal plane (0001) of hexagonal crystals, the slowness surface is shown as a circle. As the plane moves from (0001) towards (112-bar0) or towards (101-bar0), the slowness surface gradually turns into an oval. These acoustic properties increase the difficulty in orientation determination. The orientation results of a grade 1 commercially pure titanium by SRAS is presented, with comparison with electron backscattered diffraction (EBSD) results. Due to the nature of SAWs on hexagonal structure crystals, only the results of Euler angles 1 and 2 are discussed. The error between SRAS and EBSD is also investigated. (paper)

  5. Moessbauer determination of magnetic structure of Fe3BO6 crystal

    International Nuclear Information System (INIS)

    Kovalenko, P.P.; Labushkin, V.G.; Ovsepyan, A.K.; Sarkisov, Eh.R.; Smirnov, E.V.; Prokopov, A.R.; Seleznev, V.N.

    1984-01-01

    The magnetic structure of a Fe 3 BO 6 crystal belonging to space group Dsub(2h)sup(16)(Psub(nma)) is determined by the Moessbauer γ-radiation diffraction. The bragg reflection (700) of Moessbauer 14.4 keV γ-quanta from the Fe 3 BO 6 monocrystal has been studied experimentally. A high sensitivity of the interference of γ-quantum diffraction scattering on Fe nuclei being in crystallographically non-equivalent 8d- and 4s-positions to the type of magnetic ordering in the crystal is used for determination of the magnetic structure. Agreement of the experimental results with the theoretical calculations, conducted for types of magnetic ordering resolved by the symmetry of the crystal, permitted to reliably determine the magnetic structure of this compound. The results obtained confirm the data of neutrondiffraction studies on magnetic ordering in Fe 3 BO 6 . Advantages of the Moessbauer-diffraction study, as compared to the magnetic neutrondiffraction method, in particular, for investigation of crystals, in which the hyperfine magnetic fields on Fe nuclei have different values, are revealed and discussed in detail

  6. Moessbauer determination of magnetic structure of Fe/sub 3/BO/sub 6/ crystal

    Energy Technology Data Exchange (ETDEWEB)

    Kovalenko, P.P.; Labushkin, V.G.; Ovsepyan, A.K.; Sarkisov, Eh.R.; Smirnov, E.V.; Prokopov, A.R.; Seleznev, V.N.

    1984-10-01

    The magnetic structure of a Fe/sub 3/BO/sub 6/ crystal belonging to space group Dsub(2h)sup(16)(Psub(nma)) is determined by the Moessbauer ..gamma..-radiation diffraction. The bragg reflection (700) of Moessbauer 14.4 keV ..gamma..-quanta from the Fe/sub 3/BO/sub 6/ monocrystal has been studied experimentally. A high sensitivity of the interference of ..gamma..-quantum diffraction scattering on Fe nuclei being in crystallographically non-equivalent 8d- and 4s-positions to the type of magnetic ordering in the crystal is used for determination of the magnetic structure. Agreement of the experimental results with the theoretical calculations, conducted for types of magnetic ordering resolved by the symmetry of the crystal, permitted to reliably determine the magnetic structure of this compound. The results obtained confirm the data of neutrondiffraction studies on magnetic ordering in Fe/sub 3/BO/sub 6/. Advantages of the Moessbauer-diffraction study, as compared to the magnetic neutrondiffraction method, in particular, for investigation of crystals, in which the hyperfine magnetic fields on Fe nuclei have different values, are revealed and discussed in detail.

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

    Energy Technology Data Exchange (ETDEWEB)

    Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G. (Purdue)

    2012-03-15

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

  8. Comparative study for methods to determine the seismic response of NPP structures

    International Nuclear Information System (INIS)

    Varpasuo, P.

    1995-01-01

    There are many different important problem areas in evaluating the seismic response of structures. In this study the effort is concentrated on three of these areas. The first task is the mathematical formulation of earthquake excitation. The random vibration theory is taken as the tool in this task. The second area of interest in this study is the soil-structure interaction analysis. The approach of impedance functions is chosen and the focal point of interest is the significance of frequency dependent impedance functions. The third area of interest is the methods to determine the structural response. The following three methods were tested: the mode superposition time history method; the complex frequency response method; the response spectrum method. The comparison was made with the aid of MSC/NASTRAN code. The three methods gave for outer containment building response results which were in good agreement with each other. (author). 4 refs., 5 figs

  9. The importance of bulk density determination in gravity data processing for structure interpretation

    Science.gov (United States)

    Wildan, D.; Akbar, A. M.; Novranza, K. M. S.; Sobirin, R.; Permadi, A. N.; Supriyanto

    2017-07-01

    Gravity method use rock density variation for determining subsurface lithology and geological structure. In the "green area" where measurement of rock density has not been done, an attemp to find density is usually performed by calculating using Parasnis method, or by using using the average of rock density in the earth's crust (2,67 gr/cm3) or by using theoritical value of dominant rock density in the survey area (2,90 gr/cm3). Those three values of densities are applied to gravity data analysis in the hilly "X" area. And we have compared all together in order to observed which value has represented the structure better. The result showed that the higher value of rock density, the more obvious structure in the Bouguer anomaly profile. It is due to the contrast of maximum and minimum value of Bouguer anomaly that will affect the exageration in distance vs Bouguer anomaly graphic.

  10. Structure determination of LpxD from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii

    International Nuclear Information System (INIS)

    Badger, John; Chie-Leon, Barbara; Logan, Cheyenne; Sridhar, Vandana; Sankaran, Banumathi; Zwart, Peter H.; Nienaber, Vicki

    2012-01-01

    Crystal structures of the protein LpxD from A. baumannii were solved in apo forms that are suitable for structure-based antibacterial drug discovery. Acinetobacter baumannii is a Gram-negative bacterium that is resistant to many currently available antibiotics. The protein LpxD is a component of the biosynthetic pathway for lipopolysaccharides in the outer membrane of this bacterium and is a potential target for new antibacterial agents. This paper describes the structure determination of apo forms of LpxD in space groups P2 1 and P4 3 22. These crystals contained six and three copies of the protein molecule in the asymmetric unit and diffracted to 2.8 and 2.7 Å resolution, respectively. A comparison of the multiple protein copies in the asymmetric units of these crystals reveals a common protein conformation and a conformation in which the relative orientation between the two major domains in the protein is altered

  11. Structural Orders of Wheat Starch Do Not Determine the In Vitro Enzymatic Digestibility.

    Science.gov (United States)

    Wang, Shujun; Wang, Shaokang; Liu, Lu; Wang, Shuo; Copeland, Les

    2017-03-01

    In this study, we elucidated the underlying mechanisms that are responsible for the rate-limiting step for wheat starch digestion. Wheat starch samples with a degree of gelatinization (DG) ranging from 0 to 100% were prepared. As DG increased, the ordered structures of the starch were disrupted increasingly. In contrast, almost all of the increase in the rate and extent of in vitro enzymatic digestion coincided with a DG of only 6% and a minor loss of structural order. As DG increased beyond 6%, digestibility of the starch increased only slightly. We propose that the access and binding of enzymes to starch is greatly increased with only a small DG, which is followed by the simultaneous hydrolysis of crystalline and amorphous areas in gelatinized starch. In vitro enzymatic digestibility of starch was determined predominantly by enzyme binding to starch rather than the ordered structures of starch.

  12. An Analytical Technique to Determine the Potential for Moisture Accumulation in Deactivated Structures

    International Nuclear Information System (INIS)

    MINICHAN, RL

    2004-01-01

    This paper describes an analytical technique developed to predict an order of magnitude volume of moisture accumulation in massive structures after deactivation. This work was done to support deactivation of a Department of Energy nuclear materials processing facility. The structure is a four-story, concrete building with a rectangular footprint that is approximately 250m long by 37m wide by 22m high. Its walls are 1.2m thick. The building will be supplied with unconditioned ventilation air after deactivation. The objective of the work was to provide a cost effective engineering evaluation to determine if the un-conditioned ventilation air would result in condensate accumulating inside the building under study. The analysis described is a simple representation of a complex problem. The modeling method is discussed in sufficient detail to allow its application to the study of similar structures

  13. Low-energy electron diffraction experiment, theory and surface structure determination

    CERN Document Server

    Hove, Michel A; Chan, Chi-Ming

    1986-01-01

    Surface crystallography plays the same fundamental role in surface science which bulk crystallography has played so successfully in solid-state physics and chemistry. The atomic-scale structure is one of the most important aspects in the understanding of the behavior of surfaces in such widely diverse fields as heterogeneous catalysis, microelectronics, adhesion, lubrication, cor­ rosion, coatings, and solid-solid and solid-liquid interfaces. Low-Energy Electron Diffraction or LEED has become the prime tech­ nique used to determine atomic locations at surfaces. On one hand, LEED has yielded the most numerous and complete structural results to date (almost 200 structures), while on the other, LEED has been regarded as the "technique to beat" by a variety of other surface crystallographic methods, such as photoemission, SEXAFS, ion scattering and atomic diffraction. Although these other approaches have had impressive successes, LEED has remained the most productive technique and has shown the most versatility...

  14. IRMA iterative relaxation matrix approach for NMR structure determination application to DNA fragments

    International Nuclear Information System (INIS)

    Koning, M.M.G.

    1990-01-01

    The subject of this thesis is the structure determination of DNA molecules in solution with the use of NMR. For this purpose a new relaxation matrix approach is introduced. The emphasis is on the interpretation of nuclear Overhauser effects (NOEs) in terms of proton-proton distances and related three dimensional structures. The DNA molecules studied are obligonucleotides, unmodifief as well as modified molecules bu UV radiation. From comparison with unmodified molecules it turned out that UV irradiation scarcely influences the helical structure of the DNA string. At one place of the string a nucleotide is rotated towards the high-ANTI conformation which results in a slight unwinding of the DNA string but sufficient for blocking of the normal reading of genetic information. (H.W.). 456 refs.; 50 figs.; 30 tabs

  15. The method of intersecting spheres for determination of coordination numbers of atoms in crystal structures

    International Nuclear Information System (INIS)

    Serezhkin, V.N.; Buslaev, Yu.A.; Mikhajlov, Yu.N.

    1997-01-01

    New method for determination of coordination numbers (CN) of atoms in crystal structures, based on the model of interatomic interaction, within the frames whereof each atom is approximated by two spheres with the common center in the atom nuclei, is proposed. One of the spheres specifies conditionally isolated (chemically unbound) atom and its radius is a constant, which for atoms of the given chemical sort in the structure of any compound is equal to quasi-orbital Sleiter radius. The sphere of the other radius specifies chemically bound atom and coincides with the sphere, the volume whereof is equal to the volume of the Voronoj-Dirichlet polyhedron of the corresponding atom in the structure of the concrete crystal. Using a series of examples, workability of the given method for CN determination of atoms in structures of both simple substances and chemical compounds (alkali, transition metals, U, Th). Good agreement of the obtained results with the generally accepted CN s of atoms for the considered crystals is noted and a number of principal advantages of the new method, as compared to classical one of the CNs evaluation, is demonstrated

  16. Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

    International Nuclear Information System (INIS)

    Makino, Debora Lika; Conti, Elena

    2013-01-01

    The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented

  17. Determining Complex Structures using Docking Method with Single Particle Scattering Data

    Directory of Open Access Journals (Sweden)

    Haiguang Liu

    2017-04-01

    Full Text Available Protein complexes are critical for many molecular functions. Due to intrinsic flexibility and dynamics of complexes, their structures are more difficult to determine using conventional experimental methods, in contrast to individual subunits. One of the major challenges is the crystallization of protein complexes. Using X-ray free electron lasers (XFELs, it is possible to collect scattering signals from non-crystalline protein complexes, but data interpretation is more difficult because of unknown orientations. Here, we propose a hybrid approach to determine protein complex structures by combining XFEL single particle scattering data with computational docking methods. Using simulations data, we demonstrate that a small set of single particle scattering data collected at random orientations can be used to distinguish the native complex structure from the decoys generated using docking algorithms. The results also indicate that a small set of single particle scattering data is superior to spherically averaged intensity profile in distinguishing complex structures. Given the fact that XFEL experimental data are difficult to acquire and at low abundance, this hybrid approach should find wide applications in data interpretations.

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

    Science.gov (United States)

    Vajravijayan, S; Nandhagopal, N; Gunasekaran, K

    2017-12-01

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

  19. Structure of a 13-fold superhelix (almost determined from first principles

    Directory of Open Access Journals (Sweden)

    Guillaume A. Schoch

    2015-03-01

    Full Text Available Nuclear hormone receptors are cytoplasm-based transcription factors that bind a ligand, translate to the nucleus and initiate gene transcription in complex with a co-activator such as TIF2 (transcriptional intermediary factor 2. For structural studies the co-activator is usually mimicked by a peptide of circa 13 residues, which for the largest part forms an α-helix when bound to the receptor. The aim was to co-crystallize the glucocorticoid receptor in complex with a ligand and the TIF2 co-activator peptide. The 1.82 Å resolution diffraction data obtained from the crystal could not be phased by molecular replacement using the known receptor structures. HPLC analysis of the crystals revealed the absence of the receptor and indicated that only the co-activator peptide was present. The self-rotation function displayed 13-fold rotational symmetry, which initiated an exhaustive but unsuccessful molecular-replacement approach using motifs of 13-fold symmetry such as α- and β-barrels in various geometries. The structure was ultimately determined by using a single α-helix and the software ARCIMBOLDO, which assembles fragments placed by PHASER before using them as seeds for density modification model building in SHELXE. Systematic variation of the helix length revealed upper and lower size limits for successful structure determination. A beautiful but unanticipated structure was obtained that forms superhelices with left-handed twist throughout the crystal, stabilized by ligand interactions. Together with the increasing diversity of structural elements in the Protein Data Bank the results from TIF2 confirm the potential of fragment-based molecular replacement to significantly accelerate the phasing step for native diffraction data at around 2 Å resolution.

  20. Synthesis and atomic structure determination of Al8V5 gamma-brass

    International Nuclear Information System (INIS)

    Mizutani, Uichiro

    2006-01-01

    Many structurally complex compounds like quasicrystals and their approximants are known to be stabilized at a particular electron per atom ratio e/a, regardless of constituent elements involved. This has been often referred to as the Hume-Rothery electron concentration rule. We consider the understanding of the Hume-Rothery stabilization mechanism to be best deepened by performing both ab initio LMTO-ASA and FLAPW band calculations for the complex compound whose atomic structure is experimentally determined. Admittedly, however, a computing time increases rapidly beyond practical level with increasing the number of atoms in a unit cell. Among various candidates, we chose a series of gamma-brasses containing 52 atoms in a unit cell by taking a full advantage of the facts that it exists in as many as 24 binary alloy systems and that its unit cell is just in size to be handled even in more time-consuming FLAPW method. We have so far studied the stability mechanism of Cu 5 Zn 8 and Cu 9 Al 4 , both being regarded as its prototype, and TM 2 Zn 11 gamma-brasses containing late transition elements TM=Fe, Co, Ni and Pd. In the present work, we chose the gamma-brass consisting of early transition metal element V and trivalent element Al. An almost single phase Al 8 V 5 gamma-brass was ultimately synthesized by overcoming metallurgical difficulties encountered. Its atomic structure was determined by using the Brandon model as a starting structure in the Rietveld structure analysis for powdered diffraction spectra taken at the beam line BL02B2 of 8 GeV synchrotron radiation facility, SPring-8, Japan. The atomic structure suitable for band calculations was then proposed by eliminating quenched-in chemical disorder, i.e., partial mixing of Al and V atoms at given sites with minimum sacrifice. (author)

  1. PREFACE: Structure and dynamics determined by neutron and x-ray scattering Structure and dynamics determined by neutron and x-ray scattering

    Science.gov (United States)

    Müller-Buschbaum, Peter

    2011-06-01

    Neutron and x-ray scattering have emerged as powerful methods for the determination of structure and dynamics. Driven by emerging new, powerful neutron and synchrotron radiation sources, the continuous development of new instrumentation and novel scattering techniques gives rise to exciting possibilities. For example, in situ observations become possible via a high neutron or x-ray flux at the sample and, as a consequence, morphological transitions with small time constants can be detected. This special issue covers a broad range of different materials from soft to hard condensed matter. Hence, different material classes such as colloids, polymers, alloys, oxides and metals are addressed. The issue is dedicated to the 60th birthday of Professor Winfried Petry, scientific director of the Research Neutron Source Heinz Maier-Leibnitz (FRM-II), Germany, advisor at the physics department for the Bayerische Elite-Akademie, chair person of the Arbeitsgemeinschaft Metall- und Materialphysik of the German Physical Society (DPG) and a member of the professional council of the German Science Foundation (Deutsche Forschungsgemeinschaft, DFG). We would like to acknowledge and thank all contributors for their submissions, which made this special issue possible in the first place. Moreover, we would like to thank the staff at IOP Publishing for helping us with the administrative aspects and for coordinating the refereeing process, and Valeria Lauter for the beautiful cover artwork. Finally, to the readers, we hope that you find this special issue a valuable resource that provides insights into the present possibilities of neutron and x-ray scattering as powerful tools for the investigation of structure and dynamics. Structure and dynamics determined by neutron and x-ray scattering contents In situ studies of mass transport in liquid alloys by means of neutron radiography F Kargl, M Engelhardt, F Yang, H Weis, P Schmakat, B Schillinger, A Griesche and A Meyer Magnetic spin

  2. Three-dimensional solution structure of Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.

    Science.gov (United States)

    Cai, M; Gong, Y; Kao, J L; Krishnamoorthi, R

    1995-04-18

    The solution structure of Cucurbita maxima trypsin inhibitor-V (CMTI-V), which is also a specific inhibitor of the blood coagulation protein, factor XIIa, was determined by 1H NMR spectroscopy in combination with a distance-geometry and simulated annealing algorithm. Sequence-specific resonance assignments were made for all the main-chain and most of the side-chain hydrogens. Stereospecific assignments were also made for some of the beta-, gamma-, delta-, and epsilon-hydrogens and valine methyl hydrogens. The ring conformations of all six prolines in the inhibitor were determined on the basis of 1H-1H vicinal coupling constant patterns; most of the proline ring hydrogens were stereospecifically assigned on the basis of vicinal coupling constant and intraresidue nuclear Overhauser effect (NOE) patterns. Distance constraints were determined on the basis of NOEs between pairs of hydrogens. Dihedral angle constraints were determined from estimates of scalar coupling constants and intraresidue NOEs. On the basis of 727 interproton distance and 111 torsion angle constraints, which included backbone phi angles and side-chain chi 1, chi 2, chi 3, and chi 4 angles, 22 structures were calculated by a distance geometry algorithm and refined by energy minimization and simulated annealing methods. Both main-chain and side-chain atoms are well-defined, except for a loop region, two terminal residues, and some side-chain atoms located on the molecular surface. The average root mean squared deviation in the position for equivalent atoms between the 22 individual structures and the mean structure obtained by averaging their coordinates is 0.58 +/- 0.06 A for the main-chain atoms and 1.01 +/- 0.07 A for all the non-hydrogen atoms of residues 3-40 and 49-67. These structures were compared to the X-ray crystallographic structure of another protein of the same inhibitor family-chymotrypsin inhibitor-2 from barley seeds [CI-2; McPhalen, C. A., & James, M. N. G. (1987) Biochemistry 26

  3. Atomic Resolution Structures of Human Bufaviruses Determined by Cryo-Electron Microscopy

    Directory of Open Access Journals (Sweden)

    Maria Ilyas

    2018-01-01

    Full Text Available Bufavirus strain 1 (BuV1, a member of the Protoparvovirus genus of the Parvoviridae, was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 Å, respectively. The BuVs, 65–73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core β-barrel (βB-βI, α-helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses.

  4. Structural and biochemical characterization of the cell fate determining nucleotidyltransferase fold protein MAB21L1.

    Science.gov (United States)

    de Oliveira Mann, Carina C; Kiefersauer, Reiner; Witte, Gregor; Hopfner, Karl-Peter

    2016-06-08

    The exceptionally conserved metazoan MAB21 proteins are implicated in cell fate decisions and share considerable sequence homology with the cyclic GMP-AMP synthase. cGAS is the major innate immune sensor for cytosolic DNA and produces the second messenger 2'-5', 3'-5' cyclic GMP-AMP. Little is known about the structure and biochemical function of other proteins of the cGAS-MAB21 subfamily, such as MAB21L1, MAB21L2 and MAB21L3. We have determined the crystal structure of human full-length MAB21L1. Our analysis reveals high structural conservation between MAB21L1 and cGAS but also uncovers important differences. Although monomeric in solution, MAB21L1 forms a highly symmetric double-pentameric oligomer in the crystal, raising the possibility that oligomerization could be a feature of MAB21L1. In the crystal, MAB21L1 is in an inactive conformation requiring a conformational change - similar to cGAS - to develop any nucleotidyltransferase activity. Co-crystallization with NTP identified a putative ligand binding site of MAB21 proteins that corresponds to the DNA binding site of cGAS. Finally, we offer a structure-based explanation for the effects of MAB21L2 mutations in patients with eye malformations. The underlying residues participate in fold-stabilizing interaction networks and mutations destabilize the protein. In summary, we provide a first structural framework for MAB21 proteins.

  5. Synthesis and Structure Determination of Large-Pore Zeolite SCM-14.

    Science.gov (United States)

    Luo, Yi; Smeets, Stef; Peng, Fei; Etman, Ahmed S; Wang, Zhendong; Sun, Junliang; Yang, Weimin

    2017-11-27

    SCM-14 (Sinopec Composite Material No. 14), a new stable germanosilicate zeolite with a 12×8×8-ring channel system, was synthesized using commercially available 4-pyrrolidinopyridine as organic structure-directing agents (OSDAs) in fluoride medium. The framework structure of SCM-14 was determined using rotation electron diffraction (RED), and refined against synchrotron X-ray powder diffraction (SXPD) data for both as-made and calcined materials. The framework structure of SCM-14 is closely related to that of three known zeolites: mordenite (MOR), GUS-1 (GON), and IM-16 (UOS). SCM-14 has the same projection as that of mordenite and GUS-1 when viewed along the 12-ring channels, and possesses two more straight 8-ring channels running perpendicular to the 12-ring channels. The structure of SCM-14 can be constructed by either the same layers as that of GUS-1 or the same columns as that of IM-16. Based on their structural relationship, three topologically reasonable hypothetical zeolites were predicted. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Quasiparticle band structure of rocksalt-CdO determined using maximally localized Wannier functions.

    Science.gov (United States)

    Dixit, H; Lamoen, D; Partoens, B

    2013-01-23

    CdO in the rocksalt structure is an indirect band gap semiconductor. Thus, in order to determine its band gap one needs to calculate the complete band structure. However, in practice, the exact evaluation of the quasiparticle band structure for the large number of k-points which constitute the different symmetry lines in the Brillouin zone can be an extremely demanding task compared to the standard density functional theory (DFT) calculation. In this paper we report the full quasiparticle band structure of CdO using a plane-wave pseudopotential approach. In order to reduce the computational effort and time, we make use of maximally localized Wannier functions (MLWFs). The MLWFs offer a highly accurate method for interpolation of the DFT or GW band structure from a coarse k-point mesh in the irreducible Brillouin zone, resulting in a much reduced computational effort. The present paper discusses the technical details of the scheme along with the results obtained for the quasiparticle band gap and the electron effective mass.

  7. Structure determination of butylone as a new psychoactive substance using chiroptical and vibrational spectroscopies.

    Science.gov (United States)

    Spálovská, Dita; Králík, František; Kohout, Michal; Jurásek, Bronislav; Habartová, Lucie; Kuchař, Martin; Setnička, Vladimír

    2018-05-01

    Recently, there has been a worldwide substantial increase in the consumption of new psychoactive substances (NPS), compounds that mimic the structure of illicit drugs, such as amphetamines or ecstasy. The producers try to avoid the law by a slight modification of illicit structures, thereby developing dozens of temporarily legal NPS every year. The current trends in the detection and monitoring of such substances demand a fast and reliable analysis. Molecular spectroscopy represents a highly effective tool for the identification of NPS and chiroptical methods can provide further information on their 3D structure, which is the key for the determination of their biological activity. We present the first systematic study of NPS, specifically butylone, combining chiroptical and vibrational spectroscopies with ab initio calculations. According to density functional theory calculations, 6 stable lowest energy conformers of butylone were found and their molecular structure was described. For each conformer, the relative abundance based on the Boltzmann distribution was estimated, their population weighted spectra predicted and compared to the experimental results. Very good agreement between the experimental and the simulated spectra was achieved, which allowed not only the assignment of the absolute configuration, but also a precise description of the molecular structure. © 2018 Wiley Periodicals, Inc.

  8. The effects of temperature and diet on age grading and population age structure determination in Drosophila.

    Science.gov (United States)

    Aw, Wen C; Ballard, J William O

    2013-10-01

    The age structure of natural population is of interest in physiological, life history and ecological studies but it is often difficult to determine. One methodological problem is that samples may need to be invasively sampled preventing subsequent taxonomic curation. A second problem is that it can be very expensive to accurately determine the age structure of given population because large sample sizes are often necessary. In this study, we test the effects of temperature (17 °C, 23 °C and 26 °C) and diet (standard cornmeal and low calorie diet) on the accuracy of the non-invasive, inexpensive and high throughput near-infrared spectroscopy (NIRS) technique to determine the age of Drosophila flies. Composite and simplified calibration models were developed for each sex. Independent sets for each temperature and diet treatments with flies not involved in calibration model were then used to validate the accuracy of the calibration models. The composite NIRS calibration model was generated by including flies reared under all temperatures and diets. This approach permits rapid age measurement and age structure determination in large population of flies as less than or equal to 9 days, or more than 9 days old with 85-97% and 64-99% accuracy, respectively. The simplified calibration models were generated by including flies reared at 23 °C on standard diet. Low accuracy rates were observed when simplified calibration models were used to identify (a) Drosophila reared at 17 °C and 26 °C and (b) 23 °C with low calorie diet. These results strongly suggest that appropriate calibration models need to be developed in the laboratory before this technique can be reliably used in field. These calibration models should include the major environmental variables that change across space and time in the particular natural population to be studied. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Interpopulation Variation in Contour Feather Structure Is Environmentally Determined in Great Tits

    Science.gov (United States)

    Broggi, Juli; Gamero, Anna; Hohtola, Esa; Orell, Markku; Nilsson, Jan-Åke

    2011-01-01

    Background The plumage of birds is important for flying, insulation and social communication. Contour feathers cover most of the avian body and among other functions they provide a critical insulation layer against heat loss. Feather structure and composition are known to vary among individuals, which in turn determines variation in the insulation properties of the feather. However, the extent and the proximate mechanisms underlying this variation remain unexplored. Methodology/Principal Findings We analyzed contour feather structure from two different great tit populations adapted to different winter regimes, one northern population in Oulu (Finland) and one southern population in Lund (Sweden). Great tits from the two populations differed significantly in feather structure. Birds from the northern population had a denser plumage but consisting of shorter feathers with a smaller proportion containing plumulaceous barbs, compared with conspecifics from the southern population. However, differences disappeared when birds originating from the two populations were raised and moulted in identical conditions in a common-garden experiment located in Oulu, under ad libitum nutritional conditions. All birds raised in the aviaries, including adult foster parents moulting in the same captive conditions, developed a similar feather structure. These feathers were different from that of wild birds in Oulu but similar to wild birds in Lund, the latter moulting in more benign conditions than those of Oulu. Conclusions/Significance Wild populations exposed to different conditions develop contour feather differences either due to plastic responses or constraints. Environmental conditions, such as nutrient availability during feather growth play a crucial role in determining such differences in plumage structure among populations. PMID:21949798

  10. Coulomb-explosion technique for determining geometrical structures of molecular ions

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1981-01-01

    Traditional experimental techniques (e.g. studies on photon absorption or emission) for determining the sterochemical structures of neutral molecules are extremeley difficult to apply to molecular ions because of problems in obtaining a sufficient spatial density of the ions to be studied. Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the sterochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2+ , HeH + , CH + , NH + , OH + , N 2+ , O 2+ , etc.) with an accuracy of approx. 0.01 A. H 3+ has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2+ , N 2 O + , C 3 H 3+ , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2+ ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 --- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means

  11. Interpopulation variation in contour feather structure is environmentally determined in great tits.

    Directory of Open Access Journals (Sweden)

    Juli Broggi

    Full Text Available The plumage of birds is important for flying, insulation and social communication. Contour feathers cover most of the avian body and among other functions they provide a critical insulation layer against heat loss. Feather structure and composition are known to vary among individuals, which in turn determines variation in the insulation properties of the feather. However, the extent and the proximate mechanisms underlying this variation remain unexplored.We analyzed contour feather structure from two different great tit populations adapted to different winter regimes, one northern population in Oulu (Finland and one southern population in Lund (Sweden. Great tits from the two populations differed significantly in feather structure. Birds from the northern population had a denser plumage but consisting of shorter feathers with a smaller proportion containing plumulaceous barbs, compared with conspecifics from the southern population. However, differences disappeared when birds originating from the two populations were raised and moulted in identical conditions in a common-garden experiment located in Oulu, under ad libitum nutritional conditions. All birds raised in the aviaries, including adult foster parents moulting in the same captive conditions, developed a similar feather structure. These feathers were different from that of wild birds in Oulu but similar to wild birds in Lund, the latter moulting in more benign conditions than those of Oulu.Wild populations exposed to different conditions develop contour feather differences either due to plastic responses or constraints. Environmental conditions, such as nutrient availability during feather growth play a crucial role in determining such differences in plumage structure among populations.

  12. Structure determination of feline calicivirus virus-like particles in the context of a pseudo-octahedral arrangement.

    Directory of Open Access Journals (Sweden)

    Wim P Burmeister

    Full Text Available The vesivirus feline calicivirus (FCV is a positive strand RNA virus encapsidated by an icosahedral T=3 shell formed by the viral VP1 protein. Upon its expression in the insect cell - baculovirus system in the context of vaccine development, two types of virus-like particles (VLPs were formed, a majority built of 60 subunits (T=1 and a minority probably built of 180 subunits (T=3. The structure of the small particles was determined by x-ray crystallography at 0.8 nm resolution helped by cryo-electron microscopy in order to understand their formation. Cubic crystals belonged to space group P213. Their self-rotation function showed the presence of an octahedral pseudo-symmetry similar to the one described previously by Agerbandje and co-workers for human parvovirus VLPs. The crystal structure could be solved starting from the published VP1 structure in the context of the T=3 viral capsid. In contrast to viral capsids, where the capsomers are interlocked by the exchange of the N-terminal arm (NTA domain, this domain is disordered in the T=1 capsid of the VLPs. Furthermore it is prone to proteolytic cleavage. The relative orientation of P (protrusion and S (shell domains is alerted so as to fit VP1 to the smaller T=1 particle whereas the intermolecular contacts around 2-fold, 3-fold and 5-fold axes are conserved. By consequence the surface of the VLP is very similar compared to the viral capsid and suggests a similar antigenicity. The knowledge of the structure of the VLPs will help to improve their stability, in respect to a use for vaccination.

  13. Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Kuszewski, John J.; Thottungal, Robin Augustine [National Institutes of Health, Imaging Sciences Laboratory, Center for Information Technology (United States); Clore, G. Marius [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: mariusc@mail.nih.gov; Schwieters, Charles D. [National Institutes of Health, Imaging Sciences Laboratory, Center for Information Technology (United States)], E-mail: Charles.Schwieters@nih.gov

    2008-08-15

    We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258-6273). The improved protocol includes extensive analysis of input spectral data to create a low-resolution contact map of residues expected to be close in space. This map is used to obtain reasonable initial guesses of NOE assignment likelihoods which are refined during subsequent structure calculations. Information in the contact map about which residues are predicted to not be close in space is applied via conservative repulsive distance restraints which are used in early phases of the structure calculations. In comparison with the previous protocol, the new protocol requires significantly less computation time. We show results of running the new PASD protocol on six proteins and demonstrate that useful assignment and structural information is extracted on proteins of more than 220 residues. We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined.

  14. Rain water drop impact as a laboratory methodology to determinate the soils structural stability

    International Nuclear Information System (INIS)

    Arias, Dora M; Amezquita E

    1999-01-01

    To avoid degradation, it is necessary to have (sufficiently) sensitive parameter to the use actions, so that it is possible to determine what negative changes are happening and to take the soil management measures that avoid the degradation. One of the main causes of degradation in the areas of hillside of Colombia is the erosion, which begins with the impact of the drop of rainwater on the bare soil. For this research samples of an oxic dystropepts were taken at two depths (0-2.5 and 2.5-5 cm) to studying the susceptibility of its structure, to the impact of the drop falling from 2000 mm high. The samples were subjected to drop impact, in a special assembly apparatus that generated drops falling on samples that were 2-m below rotating in a rotations apparatus of generation of drops. As the time of impact advanced, the changes in the hydraulic conductivity were determined. This as parameter was used as an indicator appraiser of the structural resistance of the soils. The results show that the used methodology was sensitive to the situations of use of the soils. The initial hydraulic conductivity was higher in the production systems less intervened (natural forest, leucaena, with mulch, without mulch) and smaller in la those ones most intervened (monocrops of corn, bean, yuca), showing that human intervention has promotes a decay in the stability of soil structure

  15. Determination of material constants of vertically aligned carbon nanotube structures in compressions

    International Nuclear Information System (INIS)

    Li, Yupeng; Kang, Junmo; Choi, Jae-Boong; Nam, Jae-Do; Suhr, Jonghwan

    2015-01-01

    Different chemical vapour deposition (CVD) fabrication conditions lead to a wide range of variation in the microstructure and morphologies of carbon nanotubes (CNTs), which actually determine the compressive mechanical properties of CNTs. However, the underlying relationship between the structure/morphology and mechanical properties of CNTs is not fully understood. In this study, we characterized and compared the structural and morphological properties of three kinds of vertically aligned carbon nanotube (VACNT) arrays from different CVD fabrication methods and performed monotonic compressive tests for each VACNT array. The compressive stress–strain responses and plastic deformation were first compared and analyzed with nanotube buckling behaviours. To quantify the compressive properties of the VACNT arrays, a strain density energy function was used to determine their intrinsic material constants. Then, the structural and morphological effects on the quantified material constants of the VACNTs were statistically investigated and analogized to cellular materials with an open-cell model. The statistical analysis shows that density, defect degree, and the moment of inertia of the CNTs are key factors in the improvement of the compressive mechanical properties of VACNT arrays. This approach could allow a model-driven CNT synthesis for engineering their mechanical behaviours. (paper)

  16. Precession technique and electron diffractometry as new tools for crystal structure analysis and chemical bonding determination

    International Nuclear Information System (INIS)

    Avilov, A.; Kuligin, K.; Nicolopoulos, S.; Nickolskiy, M.; Boulahya, K.; Portillo, J.; Lepeshov, G.; Sobolev, B.; Collette, J.P.; Martin, N.; Robins, A.C.; Fischione, P.

    2007-01-01

    We have developed a new fast electron diffractometer working with high dynamic range and linearity for crystal structure determinations. Electron diffraction (ED) patterns can be scanned serially in front of a Faraday cage detector; the total measurement time for several hundred ED reflections can be tens of seconds having high statistical accuracy for all measured intensities (1-2%). This new tool can be installed to any type of TEM without any column modification and is linked to a specially developed electron beam precession 'Spinning Star' system. Precession of the electron beam (Vincent-Midgley technique) reduces dynamical effects allowing also use of accurate intensities for crystal structure analysis. We describe the technical characteristics of this new tool together with the first experimental results. Accurate measurement of electron diffraction intensities by electron diffractometer opens new possibilities not only for revealing unknown structures, but also for electrostatic potential determination and chemical bonding investigation. As an example, we present detailed atomic bonding information of CaF 2 as revealed for the first time by precise electron diffractometry

  17. Structural determinants for protein adsorption/non-adsorption to silica surface

    International Nuclear Information System (INIS)

    Mathe, Christelle; Devineau, Stephanie; Aude, Jean-Christophe; Lagniel, Gilles; Chedin, Stephane; Legros, Veronique; Mathon, Marie-Helene; Renault, Jean-Philippe; Pin, Serge; Boulard, Yves; Labarre, Jean

    2013-01-01

    The understanding of the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest in both fundamental research and applications such as nano-technology. However, despite intense research, the mechanisms and the structural determinants of protein/surface interactions are still unclear. We developed a strategy consisting in identifying, in a mixture of hundreds of soluble proteins, those proteins that are adsorbed on the surface and those that are not. If the two protein subsets are large enough, their statistical comparative analysis must reveal the physicochemical determinants relevant for adsorption versus non-adsorption. This methodology was tested with silica nanoparticles. We found that the adsorbed proteins contain a higher number of charged amino acids, particularly arginine, which is consistent with involvement of this basic amino acid in electrostatic interactions with silica. The analysis also identified a marked bias toward low aromatic amino acid content (phenylalanine, tryptophan, tyrosine and histidine) in adsorbed proteins. Structural analyses and molecular dynamics simulations of proteins from the two groups indicate that non-adsorbed proteins have twice as many p-p interactions and higher structural rigidity. The data are consistent with the notion that adsorption is correlated with the flexibility of the protein and with its ability to spread on the surface. Our findings led us to propose a refined model of protein adsorption. (authors)

  18. Structure re-determination and superconductivity observation of bulk 1T MoS{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Yuqiang; He, Jianqiao; Bu, Kejun [State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai (China); University of Chinese Academy of Sciences, Beijing (China); State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing (China); Pan, Jie; Wang, Dong; Che, Xiangli; Zhao, Wei; Lin, Tianquan [State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai (China); Luo, Ruichun; Liu, Pan [State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai (China); Mu, Gang; Zhang, Hui [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai (China); Huang, Fuqiang [State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai (China); State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing (China)

    2018-01-26

    2H MoS{sub 2} has been intensively studied because of its layer-dependent electronic structures and novel physical properties. Though the metastable 1T MoS{sub 2} with a [MoS{sub 6}] octahedron was observed over the microscopic area, the true crystal structure of 1T phase has not been strictly determined. Moreover, the true physical properties have not been demonstrated from experiments owing to the challenge for the preparation of pure 1T MoS{sub 2} crystals. 1T MoS{sub 2} single crystals were successfully synthesized and the crystal structure of 1T MoS{sub 2} re-determined from single-crystal X-ray diffraction. 1T MoS{sub 2} crystallizes in the space group P anti 3m1 with a cell of a=b=3.190(3) Aa and c=5.945(6) Aa. The individual MoS{sub 2} layer consists of MoS{sub 6} octahedra sharing edges with each other. More surprisingly, the bulk 1T MoS{sub 2} crystals undergo a superconducting transition of T{sub c}=4 K, which is the first observation of superconductivity in pure 1T MoS{sub 2} phase. (copyright 2018 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. Determining the Thickness and the Sub-Structure Details of the Magnetopause from MMS Data

    Science.gov (United States)

    Manuzzo, R.; Belmont, G.; Rezeau, L.

    2017-12-01

    The magnetopause thickness, like its mean location, is a notion that can have different meanings depending which parameters are considered (magnetic field or plasma properties). In any case, all the determinations have been done, up to now, considering the magnetopause boundary as a structure strictly stationary and 1D (or with a simple curvature). These determinations have shown to be very sensitive to the accuracy of the normal direction, because it affects the projection of the quantities of interest in studying geometrical sensitive phenomena such as the magnetic reconnection. Furthermore, the 1D stationary assumptions are likely to be rarely verified at the real magnetopause. The high quality measurements of MMS and their high time resolution now allow investigating the magnetopause structure in its more delicate features and with an unequal spatio-temporal accuracy. We make use here of the MDD tool developed by [Shi et al., 2005], which gives the dimensionality of the gradients from the four-point measurements of MMS and allows estimating the direction of the local normal when defined. Extending this method to various quantities, we can draw their profiles as functions of a physical abscissa (length instead of time) along a sensible normal. This procedure allows answering quantitatively the questions concerning the locations and the thicknesses of the different sub-structures encountered inside the "global magnetopause" [Rezeau, 2017, paper submitted to JGR-Space Physics].

  20. Structural determinants for protein adsorption/non-adsorption to silica surface.

    Directory of Open Access Journals (Sweden)

    Christelle Mathé

    Full Text Available The understanding of the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest in both fundamental research and applications such as nanotechnology. However, despite intense research, the mechanisms and the structural determinants of protein/surface interactions are still unclear. We developed a strategy consisting in identifying, in a mixture of hundreds of soluble proteins, those proteins that are adsorbed on the surface and those that are not. If the two protein subsets are large enough, their statistical comparative analysis must reveal the physicochemical determinants relevant for adsorption versus non-adsorption. This methodology was tested with silica nanoparticles. We found that the adsorbed proteins contain a higher number of charged amino acids, particularly arginine, which is consistent with involvement of this basic amino acid in electrostatic interactions with silica. The analysis also identified a marked bias toward low aromatic amino acid content (phenylalanine, tryptophan, tyrosine and histidine in adsorbed proteins. Structural analyses and molecular dynamics simulations of proteins from the two groups indicate that non-adsorbed proteins have twice as many π-π interactions and higher structural rigidity. The data are consistent with the notion that adsorption is correlated with the flexibility of the protein and with its ability to spread on the surface. Our findings led us to propose a refined model of protein adsorption.

  1. METHODOLOGY FOR DETERMINATION OF SOUND INSULATION OF APARTMENTS’ ENCLOSING STRUCTURES TO MEET NOISE PROTECTION REQUIREMENTS

    Directory of Open Access Journals (Sweden)

    Giyasov Botir Iminzhonovich

    2017-10-01

    Full Text Available Subject: an important task in the design of internal enclosing structures of apartments is the establishment of their required soundproofing ability. At present, there is no reliable method for determining the required sound insulation and in this regard internal enclosures are designed without proper justification for noise protection. Research objectives: development of a technique for determining the required sound insulation of apartment’s internal enclosures to ensure an acceptable noise regime in the apartments’ rooms under the action of intra-apartment noise sources. Materials and methods: the methodology was developed on the basis of a statistical method for noise calculation in the apartments, treated as systems of acoustically coupled proportionate rooms, and with the help of a computer program that implements this method. Results: the technique makes it possible to generate, with the use of computer technologies, a targeted selection of internal enclosures of the apartment to meet their soundproofing requirements. Conclusions: the technique proposed in the article can be used at the design stage of apartments when determining the required soundproofing of partitions and doors. Using this technique, it is possible to harmonize the sound insulation ratio of individual elements among themselves and thereby guarantee a selection of internal structures for their acoustic and economic efficiency.

  2. Structure and interactions of a dimeric variant of sHIP, a novel virulence determinant of Streptococcus pyogenes

    Directory of Open Access Journals (Sweden)

    Carl eDiehl

    2016-02-01

    Full Text Available Streptococcus pyogenes is one of the most significant bacterial pathogens in the human population mostly causing superficial and uncomplicated infections (pharyngitis and impetigo but also invasive and life-threatening disease. We have previously identified a virulence determinant, protein sHIP, which is secreted at higher levels by an invasive compared to a non-invasive strain of S. pyogenes. The present work presents a further characterization of the structural and functional properties of this bacterial protein. Biophysical and structural studies have shown that protein sHIP forms stable tetramers both in the crystal and in solution. The tetramers are composed of four helix-loop-helix motifs with the loop regions connecting the helices displaying a high degree of flexibility. Owing to interactions at the tetramer interface, the observed tetramer can be described as a dimer of dimers. We identified three residues at the tetramer interface (Leu84, Leu88, Tyr95, which due to largely non-polar side-chains, could be important determinants for protein oligomerization. Based on these observations, we produced a sHIP variant in which these residues were mutated to alanines. Biophysical experiments clearly indicated that the sHIP mutant appear only as dimers in solution confirming the importance of the interfacial residues for protein oligomerisation. Furthermore, we could show that the sHIP mutant interacts with intact histidine-rich glycoprotein (HRG and the histidine-rich repeats in HRG, and inhibits their antibacterial activity to the same or even higher extent as compared to the wild type protein sHIP. We determined the crystal structure of the sHIP mutant, which, as a result of the high quality of the data, allowed us to improve the existing structural model of the protein. Finally, by employing NMR spectroscopy in solution, we generated a model for the complex between the sHIP mutant and an HRG-derived heparin-binding peptide, providing further

  3. Determinants

    Directory of Open Access Journals (Sweden)

    N. Ntui Asundep

    2013-12-01

    Nineteen percent of the women experienced an adverse pregnancy outcome. For 49% of the women, cost influenced their antenatal attendance. Cost was associated with increased likelihood of a woman experiencing an adverse outcome (adjusted OR = 2.15; 95% CI = 1.16–3.99; p = 0.016. Also, women with >5 births had an increased likelihood of an adverse outcome compared with women with single deliveries (adjusted OR = 3.77; 95% CI = 1.50–9.53; p = 0.005. The prevalence of adverse outcomes was lower than previously reported (44.6 versus 19%. Cost and distance were associated with adverse outcomes after adjusting for confounders. Cost and distance could be minimized through a wider application of the Ghana National Health Insurance Scheme.

  4. Structural determination of Bi-doped magnetite multifunctional nanoparticles for contrast imaging.

    Science.gov (United States)

    Laguna-Marco, M A; Piquer, C; Roca, A G; Boada, R; Andrés-Vergés, M; Veintemillas-Verdaguer, S; Serna, C J; Iadecola, A; Chaboy, J

    2014-09-14

    To determine with precision how Bi atoms are distributed in Bi-doped iron oxide nanoparticles their structural characterization has been carried out by X-ray absorption spectroscopy (XAS) recorded at the K edge of Fe and at the L3 edge of Bi. The inorganic nanoparticles are nominally hybrid structures integrating an iron oxide core and a bismuth oxide shell. Fe K-edge XAS indicates the formation of a structurally ordered, non-stoichiometric magnetite (Fe3-δO4) phase for all the nanoparticles. The XAS spectra show that, in the samples synthesized by precipitation in aqueous media and laser pyrolysis, the Bi atoms neither enter into the iron oxide spinel lattice nor form any other mixed Bi-Fe oxides. No modification of the local structure around the Fe atoms induced by the Bi atoms is observed at the Fe K edge. In addition, contrary to expectations, our results indicate that the Bi atoms do not form a well-defined Bi oxide structure. The XAS study at the Bi L3 edge indicates that the environment around Bi atoms is highly disordered and only a first oxygen coordination shell is observed. Indefinite [BiO6-x(OH)x] units (isolated or aggregated forming tiny amorphous clusters) bonded through hydroxyl bridges to the nanoparticle, rather than a well defined Bi2O3 shell, surround the nanoparticle. On the other hand, the XAS study indicates that, in the samples synthesized by thermal decomposition, the Bi atoms are embedded in a longer range ordered structure showing the first and second neighbors.

  5. Structural features of nitroaromatics that determine mutagenic activity in Salmonella typhimurium

    International Nuclear Information System (INIS)

    Vance, W.A.; Levin, D.E.

    1984-01-01

    Seventeen structurally homologous nitroaromatics were tested for direct-acting mutagenic potency in nine strains of Salmonella typhimurium. The following four structural features were determined to have a strong influence on mutagenic activity: physical dimensions of the aromatic rings, isomeric position of the nitro group, conformation of the nitro group with respect to the plane of the aromatic rings, and ability to resonance-stabilize the utimate electrophile. Progressive addition of five- and six-membered rings to a nitrobenzene nucleus demonstrated that mutagenic activity was a direct function of size. Nitroaromatics with a nitro group oriented along the long axis of symmetry of the molecule were more potent mutagens that those with the nitro group oriented along the short axis. These results are discussed in light of the insertion-denaturation model for intercalation of certain DNA adducts. Finally, structural features that contribute to resonance stabilization of the reactive nitrenium ion enhance mutagenic potency. The predictive value of these structure-activity relationships should permit a first approximation in the assessment of mutagenic potency of nitroaromatics

  6. Using an electrostatic accelerator to determine the stereochemical structures of molecular ions

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1980-01-01

    Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the stereochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2 + , HeH + , CH + , NH + , OH + , N 2 + , O 2 + , etc.) with an accuracy of approx. 0.01 A. H 3 + has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2 + , N 2 O + , C 3 H 3 + , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2 + ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 +- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means

  7. Procedure and reference standard to determine the structural resolution in coordinate metrology

    Science.gov (United States)

    Illemann, Jens; Bartscher, Markus; Jusko, Otto; Härtig, Frank; Neuschaefer-Rube, Ulrich; Wendt, Klaus

    2014-06-01

    A new procedure and reference standards for specifying the structural resolution in coordinate metrology traceable to the SI unit the metre are proposed. With the definition of the structural resolution, a significant gap will be closed to complete ‘acceptance and verification tests’ of the coordinate measuring systems (CMSs) which are specified in the ISO 10360 series dealing with tactile sensors, optical sensors, and x-ray computed tomography measurement systems (CTs). The proposed new procedure uses reference standards with circular rounded edges. The idea is to measure the radius of curvature on a calibrated round edge structure. From the deviation between the measured and the calibrated radius, an analogue Gaussian broadening of the measurement system is determined. This value is a well-defined and easy-to-apply measure to define the structural resolution for dimensional measurements. It is applicable to CMSs which are based on different sensing principles, e.g. tactile, optical and CT systems. On the other hand, it has a physical meaning similar to the classical optical point-spread function. It makes it possible to predict which smallest details the CMS is capable of measuring reliably for an arbitrary object shape. The theoretical background of the new procedure is given, an appropriate reference standard is described and comparative, quantitative measurement data of CMSs featuring different sensors are shown.

  8. Corporate life cycle as determinant of capital structure in companies of Czech automotive industry

    Directory of Open Access Journals (Sweden)

    Pavlína Pinková

    2012-01-01

    Full Text Available The issue of capital structure choice belongs to fundamental strategic financial decisions. A variety of potential determinants was suggested by theoreticians; however, the corporate life cycle was considered of peripheral importance, and thus the relationship between corporate life stages and capital structure was investigated only exceptionally. Both concepts were in the meantime developed separately. Recently, it has appeared that the aforementioned relation has become a subject of increased interest of the researches as a way to better understanding of how the corporate funding is changing in the course of time. The main objective of this paper is to investigate the impact of corporate life cycle on the capital structure of companies. For the purpose of the article quantitative research is used. The sample consists of fifty companies belonging to NACE division 29, manufacture of motor vehicles, trailers and semi-trailers. The data come from financial statements of the chosen companies and mostly cover a period since their start-up till year 2010. First, the method based on cash flow patterns is applied for the identification of firm’s life cycle. Next, the methods of descriptive statistics and the hypothesis test about a population proportion are used. The paper explores the relationship between capital structure and corporate life cycle. The empirical study is performed to support theoretical findings.

  9. A general centroid determination methodology, with application to multilayer dielectric structures and thermally stimulated current measurements

    International Nuclear Information System (INIS)

    Miller, S.L.; Fleetwood, D.M.; McWhorter, P.J.; Reber, R.A. Jr.; Murray, J.R.

    1993-01-01

    A general methodology is developed to experimentally characterize the spatial distribution of occupied traps in dielectric films on a semiconductor. The effects of parasitics such as leakage, charge transport through more than one interface, and interface trap charge are quantitatively addressed. Charge transport with contributions from multiple charge species is rigorously treated. The methodology is independent of the charge transport mechanism(s), and is directly applicable to multilayer dielectric structures. The centroid capacitance, rather than the centroid itself, is introduced as the fundamental quantity that permits the generic analysis of multilayer structures. In particular, the form of many equations describing stacked dielectric structures becomes independent of the number of layers comprising the stack if they are expressed in terms of the centroid capacitance and/or the flatband voltage. The experimental methodology is illustrated with an application using thermally stimulated current (TSC) measurements. The centroid of changes (via thermal emission) in the amount of trapped charge was determined for two different samples of a triple-layer dielectric structure. A direct consequence of the TSC analyses is the rigorous proof that changes in interface trap charge can contribute, though typically not significantly, to thermally stimulated current

  10. Aggregate size and structure determination of nanomaterials in physiological media: importance of dynamic evolution

    Science.gov (United States)

    Afrooz, A. R. M. Nabiul; Hussain, Saber M.; Saleh, Navid B.

    2014-12-01

    Most in vitro nanotoxicological assays are performed after 24 h exposure. However, in determining size and shape effect of nanoparticles in toxicity assays, initial characterization data are generally used to describe experimental outcome. The dynamic size and structure of aggregates are typically ignored in these studies. This brief communication reports dynamic evolution of aggregation characteristics of gold nanoparticles. The study finds that gradual increase in aggregate size of gold nanospheres (AuNS) occurs up to 6 h duration; beyond this time period, the aggregation process deviates from gradual to a more abrupt behavior as large networks are formed. Results of the study also show that aggregated clusters possess unique structural conformation depending on nominal diameter of the nanoparticles. The differences in fractal dimensions of the AuNS samples likely occurred due to geometric differences, causing larger packing propensities for smaller sized particles. Both such observations can have profound influence on dosimetry for in vitro nanotoxicity analyses.

  11. Robust determination of the superconducting gap sign structure via quasiparticle interference

    Energy Technology Data Exchange (ETDEWEB)

    Altenfeld, Dustin [Institut fuer Theoretische Physik III, Ruhr-Universitaet Bochum, D-44801 Bochum (Germany); Hirschfeld, Peter [Department of Physics, University of Florida, Gainesville, Florida 32611 (United States); Eremin, Ilya [Institut fuer Theoretische Physik III, Ruhr-Universitaet Bochum, D-44801 Bochum (Germany); Kazan Federal University, Kazan 420008 (Russian Federation); Mazin, Igor [Naval Research Laboratory, Code 6393, Washington, DC 20375 (United States)

    2016-07-01

    Using an electronic theory, we present a qualitative description to identify sign changes of the superconducting order parameter via quasiparticle interference (QPI) measurement in Fe-based superconductors (FeSc). In particular, we point out that the temperature dependence of the momentum-integrated QPI data can be used to differentiate between s{sub +-} and s{sub ++} states in a system with typical iron pnictide Fermi surface. We show that the signed symmetrized and antisymmetrized QPI maps are useful to obtain a characteristic signature of a gap sign change or lack thereof, starting from two-band model up to ab initio based band structure calculation. We further suggest this method as a robust way of the determination of the superconducting gap sign structure in experiment and discuss its application to the LiFeAs compounds.

  12. Structural and enzymatic characterization of a host-specificity determinant from Salmonella

    Energy Technology Data Exchange (ETDEWEB)

    Kohler, Amanda C. [Rockefeller University, New York, NY 10065 (United States); Spanò, Stefania; Galán, Jorge E. [Yale University School of Medicine, New Haven, CT 06536 (United States); Stebbins, C. Erec, E-mail: stebbins@rockefeller.edu [Rockefeller University, New York, NY 10065 (United States)

    2014-02-01

    The Salmonella effector protein GtgE functions as a cysteine protease to cleave a subset of the Rab-family GTPases and to prevent delivery of antimicrobial agents to the Salmonella-containing vacuole. GtgE is an effector protein from Salmonella Typhimurium that modulates trafficking of the Salmonella-containing vacuole. It exerts its function by cleaving the Rab-family GTPases Rab29, Rab32 and Rab38, thereby preventing the delivery of antimicrobial factors to the bacteria-containing vacuole. Here, the crystal structure of GtgE at 1.65 Å resolution is presented, and structure-based mutagenesis and in vivo infection assays are used to identify its catalytic triad. A panel of cysteine protease inhibitors were examined and it was determined that N-ethylmaleimide, antipain and chymostatin inhibit GtgE activity in vitro. These findings provide the basis for the development of novel therapeutic strategies to combat Salmonella infections.

  13. Algorithm based on the Thomson problem for determination of equilibrium structures of metal nanoclusters

    Science.gov (United States)

    Arias, E.; Florez, E.; Pérez-Torres, J. F.

    2017-06-01

    A new algorithm for the determination of equilibrium structures suitable for metal nanoclusters is proposed. The algorithm performs a stochastic search of the minima associated with the nuclear potential energy function restricted to a sphere (similar to the Thomson problem), in order to guess configurations of the nuclear positions. Subsequently, the guessed configurations are further optimized driven by the total energy function using the conventional gradient descent method. This methodology is equivalent to using the valence shell electron pair repulsion model in guessing initial configurations in the traditional molecular quantum chemistry. The framework is illustrated in several clusters of increasing complexity: Cu7, Cu9, and Cu11 as benchmark systems, and Cu38 and Ni9 as novel systems. New equilibrium structures for Cu9, Cu11, Cu38, and Ni9 are reported.

  14. Structured Additive Quantile Regression for Assessing the Determinants of Childhood Anemia in Rwanda.

    Science.gov (United States)

    Habyarimana, Faustin; Zewotir, Temesgen; Ramroop, Shaun

    2017-06-17

    Childhood anemia is among the most significant health problems faced by public health departments in developing countries. This study aims at assessing the determinants and possible spatial effects associated with childhood anemia in Rwanda. The 2014/2015 Rwanda Demographic and Health Survey (RDHS) data was used. The analysis was done using the structured spatial additive quantile regression model. The findings of this study revealed that the child's age; the duration of breastfeeding; gender of the child; the nutritional status of the child (whether underweight and/or wasting); whether the child had a fever; had a cough in the two weeks prior to the survey or not; whether the child received vitamin A supplementation in the six weeks before the survey or not; the household wealth index; literacy of the mother; mother's anemia status; mother's age at the birth are all significant factors associated with childhood anemia in Rwanda. Furthermore, significant structured spatial location effects on childhood anemia was found.

  15. Structure determination from small crystals of two aluminophosphates, CrAPO-14 and SAPO-43

    International Nuclear Information System (INIS)

    Helliwell, M.; Kaucic, V.; Cheetham, G.M.T.; Harding, M.M.; Kariuki, B.M.; Rizkallah, P.J.

    1993-01-01

    Small single crystals, ca 10 5 μm 3 , of two aluminophosphates have been used to determine their structures. Both compounds were synthesized with the aim of incorporating chromium into the framework, and for CrAPO-14 the X-ray diffraction results show that this has been achieved. For CrAPO-14, Al 3.96 Cr 0.04 (PO 4 ) 4 (OH).C 3 H 10 N.H 2 O, data recorded on a Rigaku AFC-5R diffractometer (Cu Kα) and, independently, on an Enraf-Nonius FAST diffractometer (Mo Kα), showed the structure to be like that of GaPO-14; aluminium atoms occupy four-, five- and six-coordinated sites, and 4-5% of the aluminium in the six-coordinate site is replaced by chromium. For SAPO-43, Al 2 (PO 4 ) 2 (C 3 H 10 N), data were recorded independently on the AFC-5R (Cu Kα) and on a FAST diffractometer with synchrotron radiation of wavelength 0.895 A; the structure is like that of gismondin, but replacement of Al by Cr to a significant extent could not be established. Framework Al, P and O atoms are located with e.s.d.'s of 0.001-0.005 A, template atoms with e.s.d.'s of ca 0.01 A in CrAPO-14, and larger e.s.d.'s in SAPO-43 where there is disorder in the template-molecule position. In all these respects the two independent determinations for each structure are in agreement. The effectiveness of the different methods of intensity-data collection is compared. (orig.)

  16. Raphide crystal structure in agave tequilana determined by x-ray originating from synchrotron radiation

    International Nuclear Information System (INIS)

    Tadokoro, Makoto; Ozawa, Yoshiki; Mitsumi, Minoru; Toriumi, Kohshiro; Ogura, Tetsuya

    2005-01-01

    The first single crystal structure of small natural raphides in an agave plant is completely determined using an intense X-ray originating from a synchrotron radiation. The SEM image shows that the tip of the crystal is approximately hundreds of nanometer in width sharply grow to stick to the tissue of herbivorous vermin. Furthermore, the crystal develops cracks that propagate at an inclination of approximately 45deg towards the direction of crystal growth such that the crystal easily splits into small pieces in the tissue. (author)

  17. Determination of structural and spectroscopic parameters of 4-hydroxyantipyrine, using DFT method

    International Nuclear Information System (INIS)

    Catikkas, B.; Aktan, E.

    2010-01-01

    In this study, structural and vibrational parameters were calculated. First of all, conformational analysis of 4-hydroxyantipyrine was carried out in gas phase. Then, the geometric parameters (bond length, bond angle and tortion angle) of the most stable conformer were calculated and the Infrared and Raman frequencies of fundamental modes were determined. Calculations were made by using DFT B3LYP/6-311+G(d,p) method implemented the Gaussian 03 program. Afterwards, vibrational assignments of the title molecule were calculated by using Scaled Quantum Mechanical (SQM) analysis. In conclusion, calculated values were compared with corresponding experimental results.

  18. Parameter studies to determine sensitivity of slug impact loads to properties of core surrounding structures

    International Nuclear Information System (INIS)

    Gvildys, J.

    1985-01-01

    A sensitivity study of the HCDA slug impact response of fast reactor primary containment to properties of core surrounding structures was performed. Parameters such as the strength of the radial shield material, mass, void, and compressibility properties of the gas plenum material, mass of core material, and mass and compressibility properties of the coolant were used as variables to determine the magnitude of the slug impact loads. The response of the reactor primary containment and the partition of energy were also given. A study was also performed using water as coolant to study the difference in slug impact loads

  19. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    Science.gov (United States)

    Xie, Jianming [San Diego, CA; Wang, Lei [San Diego, CA; Wu, Ning [Boston, MA; Schultz, Peter G [La Jolla, CA

    2008-07-15

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  20. The cytoskeleton in cell-autonomous immunity: structural determinants of host defence

    Science.gov (United States)

    Mostowy, Serge; Shenoy, Avinash R.

    2016-01-01

    Host cells use antimicrobial proteins, pathogen-restrictive compartmentalization and cell death in their defence against intracellular pathogens. Recent work has revealed that four components of the cytoskeleton — actin, microtubules, intermediate filaments and septins, which are well known for their roles in cell division, shape and movement — have important functions in innate immunity and cellular self-defence. Investigations using cellular and animal models have shown that these cytoskeletal proteins are crucial for sensing bacteria and for mobilizing effector mechanisms to eliminate them. In this Review, we highlight the emerging roles of the cytoskeleton as a structural determinant of cell-autonomous host defence. PMID:26292640

  1. Seismic transmission tomography: determination of the elastic properties of building structures (some examples

    Directory of Open Access Journals (Sweden)

    E. Cardarelli

    2000-06-01

    Full Text Available This paper is a general review on seismic transmission tomography considering data acquisition and processing. Some questions on linear and non linear inversions are tackled, and advice given on the choice of the best damping factor. Taking into account prediction matrices we show that it is possible to point out the best distribution of sensors and shot points in terms of resolution and stability of system. Then two examples in which seismic tomography was used are described concerning the determination of elastic characteristics of building structures.

  2. Strain-Based Damage Determination Using Finite Element Analysis for Structural Health Management

    Science.gov (United States)

    Hochhalter, Jacob D.; Krishnamurthy, Thiagaraja; Aguilo, Miguel A.

    2016-01-01

    A damage determination method is presented that relies on in-service strain sensor measurements. The method employs a gradient-based optimization procedure combined with the finite element method for solution to the forward problem. It is demonstrated that strains, measured at a limited number of sensors, can be used to accurately determine the location, size, and orientation of damage. Numerical examples are presented to demonstrate the general procedure. This work is motivated by the need to provide structural health management systems with a real-time damage characterization. The damage cases investigated herein are characteristic of point-source damage, which can attain critical size during flight. The procedure described can be used to provide prognosis tools with the current damage configuration.

  3. Model for determining stresses in the structure of a fast reactor fuel assembly

    International Nuclear Information System (INIS)

    Kervevan, J.-J.

    1974-01-01

    Deformations in a reactor core are due to two metallurgical phenomena, swelling of the steel under irradiation and irradiation creep when the structure is under stress. The first step is to determine the deformation of each sub-assembly supposed free, subjected to a neutron flux or temperature gradient, and the second is to study the interactions amongst most of the sub-assemblies. Under the influence of the deformations the interaction value will change with time, and this development must be determined. Calculation methods were developed for the purpose. A number of computing codes already exist and it is necessary to complete them, modify them if necessary, create new ones as the case arises and form a coherent whole [fr

  4. Determination of the maximum-depth to potential field sources by a maximum structural index method

    Science.gov (United States)

    Fedi, M.; Florio, G.

    2013-01-01

    A simple and fast determination of the limiting depth to the sources may represent a significant help to the data interpretation. To this end we explore the possibility of determining those source parameters shared by all the classes of models fitting the data. One approach is to determine the maximum depth-to-source compatible with the measured data, by using for example the well-known Bott-Smith rules. These rules involve only the knowledge of the field and its horizontal gradient maxima, and are independent from the density contrast. Thanks to the direct relationship between structural index and depth to sources we work out a simple and fast strategy to obtain the maximum depth by using the semi-automated methods, such as Euler deconvolution or depth-from-extreme-points method (DEXP). The proposed method consists in estimating the maximum depth as the one obtained for the highest allowable value of the structural index (Nmax). Nmax may be easily determined, since it depends only on the dimensionality of the problem (2D/3D) and on the nature of the analyzed field (e.g., gravity field or magnetic field). We tested our approach on synthetic models against the results obtained by the classical Bott-Smith formulas and the results are in fact very similar, confirming the validity of this method. However, while Bott-Smith formulas are restricted to the gravity field only, our method is applicable also to the magnetic field and to any derivative of the gravity and magnetic field. Our method yields a useful criterion to assess the source model based on the (∂f/∂x)max/fmax ratio. The usefulness of the method in real cases is demonstrated for a salt wall in the Mississippi basin, where the estimation of the maximum depth agrees with the seismic information.

  5. Structure of Csd3 from Helicobacter pylori, a cell shape-determining metallopeptidase

    International Nuclear Information System (INIS)

    An, Doo Ri; Kim, Hyoun Sook; Kim, Jieun; Im, Ha Na; Yoon, Hye Jin; Yoon, Ji Young; Jang, Jun Young; Hesek, Dusan; Lee, Mijoon; Mobashery, Shahriar; Kim, Soon-Jong; Lee, Byung Il; Suh, Se Won

    2015-01-01

    H. pylori Csd3 (HP0506), together with other peptidoglycan hydrolases, plays an important role in determining cell shape. Its crystal structure in the latent state is reported. Helicobacter pylori is associated with various gastrointestinal diseases such as gastritis, ulcers and gastric cancer. Its colonization of the human gastric mucosa requires high motility, which depends on its helical cell shape. Seven cell shape-determining genes (csd1, csd2, csd3/hdpA, ccmA, csd4, csd5 and csd6) have been identified in H. pylori. Their proteins play key roles in determining the cell shape through modifications of the cell-wall peptidoglycan by the alteration of cross-linking or by the trimming of peptidoglycan muropeptides. Among them, Csd3 (also known as HdpA) is a bifunctional enzyme. Its d, d-endopeptidase activity cleaves the d-Ala 4 -mDAP 3 peptide bond between cross-linked muramyl tetrapeptides and pentapeptides. It is also a d, d-carboxypeptidase that cleaves off the terminal d-Ala 5 from the muramyl pentapeptide. Here, the crystal structure of this protein has been determined, revealing the organization of its three domains in a latent and inactive state. The N-terminal domain 1 and the core of domain 2 share the same fold despite a very low level of sequence identity, and their surface-charge distributions are different. The C-terminal LytM domain contains the catalytic site with a Zn 2+ ion, like the similar domains of other M23 metallopeptidases. Domain 1 occludes the active site of the LytM domain. The core of domain 2 is held against the LytM domain by the C-terminal tail region that protrudes from the LytM domain

  6. Structure of Csd3 from Helicobacter pylori, a cell shape-determining metallopeptidase

    Energy Technology Data Exchange (ETDEWEB)

    An, Doo Ri [Seoul National University, Seoul 151-742 (Korea, Republic of); Kim, Hyoun Sook [Seoul National University, Seoul 151-742 (Korea, Republic of); Seoul National University, Seoul 151 742 (Korea, Republic of); Kim, Jieun; Im, Ha Na; Yoon, Hye Jin; Yoon, Ji Young; Jang, Jun Young [Seoul National University, Seoul 151-742 (Korea, Republic of); Hesek, Dusan; Lee, Mijoon; Mobashery, Shahriar [University of Notre Dame, Notre Dame, IN 46556 (United States); Kim, Soon-Jong [Mokpo National University, Chonnam 534-729 (Korea, Republic of); Lee, Byung Il [National Cancer Center, Gyeonggi 410-769 (Korea, Republic of); Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Seoul National University, Seoul 151-742 (Korea, Republic of); Seoul National University, Seoul 151-742 (Korea, Republic of)

    2015-03-01

    H. pylori Csd3 (HP0506), together with other peptidoglycan hydrolases, plays an important role in determining cell shape. Its crystal structure in the latent state is reported. Helicobacter pylori is associated with various gastrointestinal diseases such as gastritis, ulcers and gastric cancer. Its colonization of the human gastric mucosa requires high motility, which depends on its helical cell shape. Seven cell shape-determining genes (csd1, csd2, csd3/hdpA, ccmA, csd4, csd5 and csd6) have been identified in H. pylori. Their proteins play key roles in determining the cell shape through modifications of the cell-wall peptidoglycan by the alteration of cross-linking or by the trimming of peptidoglycan muropeptides. Among them, Csd3 (also known as HdpA) is a bifunctional enzyme. Its d, d-endopeptidase activity cleaves the d-Ala{sup 4}-mDAP{sup 3} peptide bond between cross-linked muramyl tetrapeptides and pentapeptides. It is also a d, d-carboxypeptidase that cleaves off the terminal d-Ala{sup 5} from the muramyl pentapeptide. Here, the crystal structure of this protein has been determined, revealing the organization of its three domains in a latent and inactive state. The N-terminal domain 1 and the core of domain 2 share the same fold despite a very low level of sequence identity, and their surface-charge distributions are different. The C-terminal LytM domain contains the catalytic site with a Zn{sup 2+} ion, like the similar domains of other M23 metallopeptidases. Domain 1 occludes the active site of the LytM domain. The core of domain 2 is held against the LytM domain by the C-terminal tail region that protrudes from the LytM domain.

  7. Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR.

    Science.gov (United States)

    Tyson, Jess; Armour, John A L

    2012-12-11

    Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in) regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

  8. Determination of the structure of thiol-specific antioxidant (Tsa 2) of Saccharomyces cerevisiae

    International Nuclear Information System (INIS)

    Breyer, C.A.; Oliveira, M.A.

    2012-01-01

    Full text: The peroxiredoxin (Prx), is a group of antioxidant proteins that have been widely studied for its role in the decomposition of several species of peroxides such as hydrogen peroxide, peroxynitrite and organic hydroperoxides using two highly reactive cysteines, named cysteine peroxidatic (Cys P ) and resolve cysteine (Cys R ), present in the active site. In Saccharomyces cerevisiae were identified five Prx isoforms, three cytosolic (Tsa1, Tsa2 and Ahp1), a mitochondrial (mTPx) and a nu- clear one (nTPx). Tsa1 and Tsa2 are homodimers that in heat shock or oxidative stress form complex structures of high molecular-weight with chaperone function. These proteins are very similar (86% identity and 96% similarity) but despite this structural similarity it has been shown that they present different functions: Tsa1 is mainly involved in the response to oxidative stress while Tsa2 is involved in signal transduction. Tsa1 was already crystallized and a structural model was generated, but Tsa2 structural studies were not performed. The research goal is the determination of the structure of Tsa2. The initial screening experiments of crystallization using the kits CS1 and CS2 (Hampton Research) showed favorable results when the conditions were 0,1M sodium acetate trihydrate pH 4.6 and 8% polyethylene glycol 4000. To improve our results the crystallization condition is been refined using variations of pH and concentration of polyethylene glycol 4000. We believe that the results of this study may contribute significantly to the understanding of the formation of over oxidized forms and cellular functions of Tsa2. (author)

  9. Ab initio structure determination and refinement of a scorpion protein toxin.

    Science.gov (United States)

    Smith, G D; Blessing, R H; Ealick, S E; Fontecilla-Camps, J C; Hauptman, H A; Housset, D; Langs, D A; Miller, R

    1997-09-01

    The structure of toxin II from the scorpion Androctonus australis Hector has been determined ab initio by direct methods using SnB at 0.96 A resolution. For the purpose of this structure redetermination, undertaken as a test of the minimal function and the SnB program, the identity and sequence of the protein was withheld from part of the research team. A single solution obtained from 1 619 random atom trials was clearly revealed by the bimodal distribution of the final value of the minimal function associated with each individual trial. Five peptide fragments were identified from a conservative analysis of the initial E-map, and following several refinement cycles with X-PLOR, a model was built of the complete structure. At the end of the X-PLOR refinement, the sequence was compared with the published sequence and 57 of the 64 residues had been correctly identified. Two errors in sequence resulted from side chains with similar size while the rest of the errors were a result of severe disorder or high thermal motion in the side chains. Given the amino-acid sequence, it is estimated that the initial E-map could have produced a model containing 99% of all main-chain and 81% of side-chain atoms. The structure refinement was completed with PROFFT, including the contributions of protein H atoms, and converged at a residual of 0.158 for 30 609 data with F >or= 2sigma(F) in the resolution range 8.0-0.964 A. The final model consisted of 518 non-H protein atoms (36 disordered), 407 H atoms, and 129 water molecules (43 with occupancies less than unity). This total of 647 non-H atoms represents the largest light-atom structure solved to date.

  10. Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR

    Directory of Open Access Journals (Sweden)

    Tyson Jess

    2012-12-01

    Full Text Available Abstract Background Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. Results In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. Conclusion This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

  11. First-principles determination of the ground-state structure of Mg(BH4)(2)

    DEFF Research Database (Denmark)

    Caputo, R.; Tekin, Adem; Sikora, W.

    2009-01-01

    The ground-state structure of magnesium tetrahydroborate, Mg(BH4)(2), is still under debate. The experimentally and theoretically proposed structures mismatch, and even among the computationally determined structures a disagreement still exists. The main debated question is related to the lattice...

  12. Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups.

    Science.gov (United States)

    Coia, Valentina; Capocasa, Marco; Anagnostou, Paolo; Pascali, Vincenzo; Scarnicci, Francesca; Boschi, Ilaria; Battaggia, Cinzia; Crivellaro, Federica; Ferri, Gianmarco; Alù, Milena; Brisighelli, Francesca; Busby, George B J; Capelli, Cristian; Maixner, Frank; Cipollini, Giovanna; Viazzo, Pier Paolo; Zink, Albert; Destro Bisol, Giovanni

    2013-01-01

    Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of "local ethnicity" on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood

  13. Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups.

    Directory of Open Access Journals (Sweden)

    Valentina Coia

    Full Text Available Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of "local ethnicity" on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet

  14. Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

    Science.gov (United States)

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

    2012-01-01

    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

  15. The Determinants of Capital Structure: an Empirical Study of Omani Listed Industrial Companies

    Directory of Open Access Journals (Sweden)

    Mawih Al Ani

    2015-06-01

    Full Text Available This study investigates five determinants of capital structure (leverage in three subsectors of the Omani Industrial companies (food, construction and chemical listed on Muscat Securities Market for the period 2008–2012. According to available information and literature review, the determinants are profitability measured by return on assets (ROA, risk measured by the standard deviation of return on assets, the size of the company measured by the natural logarithm of total assets, rate of growth measured by the market-book value ratio (P/E and assets tangibility measured by fixed assets to total assets ratio. The capital structure or leverage is measured by total debt ratio. In the industrial sector as whole; the findings of the study indicate that there is a statistically positive association between risk and tangibility and leverage. Also, there is a statistically negative association between growth rate and profitability and leverage, while there is no association with size. Regression analysis indicates that size, tangibility and risk have a statistically significant effect on leverage.

  16. Climate Effects and Feedback Structure Determining Weed Population Dynamics in a Long-Term Experiment

    Science.gov (United States)

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

    2012-01-01

    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements. PMID:22272362

  17. Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

    Directory of Open Access Journals (Sweden)

    Mauricio Lima

    Full Text Available Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors. Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

  18. Direct determination of triplet phases and enantiomorphs of non-centrosymmetric structures. Pt. 2

    International Nuclear Information System (INIS)

    Huemmer, K.; Weckert, E.; Bondza, H.

    1989-01-01

    Direct measurements of triplet phase relationships for non-centrosymmetric light-atom organic structures with medium-size unit cells are reported. The phase information can be extracted from the three-beam profiles of a Renninger ψ-scan experiment. The measurements were carried out with a special ψ-circle diffractometer installed on a rotating Cu-anode generator. The incident-beam divergence is reduced to 0.02 0 . The experimental results confirm the theoretical considerations of paper I of this work. As triplet phases of ±90 0 can be distinguished, the absolute structure can be determined unambiguously. The measurements show that the triplet-phase-dependent interference effects may be superposed on phase-independent Umweganregung or Aufhellung effects. By a comparison of the ψ-scan profiles of two centrosymmetrically related three-beam cases, the triplet phases of which have opposite signs, it is possible to evaluate the phase-independent effects and to determine the value of the triplet phase with an accuracy of at least 90 0 . (orig.)

  19. Determinants of capital structure: An empirical study of companies from selected post-transition economies

    Directory of Open Access Journals (Sweden)

    Sasho Arsov

    2016-06-01

    Full Text Available The goal of this paper is to examine if there are any determinants that systematically influence the capital structure of the companies in the Balkan countries and to determine if any of the existing capital structure theories are relevant in their case. We apply a panel regression on a sample consisting of the largest and most frequently traded joint-stock companies from four countries. The results show that the larger companies and those with higher fixed asset investments exhibit higher leverage, while the more profitable companies and those with more tangible assets use less debt financing. Other variables, such as the concentration of company ownership, the riskiness of its operating profits and the effective tax rates have not been found statistically significant. These results, supported by the robustness tests, have confirmed our expectation that the managers in these countries do not set specific target leverage ratios, but instead follow a particular order in the selection of the sources of financing. In other words, the companies behave in accordance with the pecking order theory, which is a confirmation of our initial hypothesis. The governments of these countries should put more effort on stimulating the use of other sources of financing to relieve the possible excessive company dependence on the banking sector.

  20. Crystal structure determination and thermal behavior upon melting of p-synephrine

    Energy Technology Data Exchange (ETDEWEB)

    Rosa, Frédéric [Unité de Technologies Chimiques et Biologiques pour la Santé, U1022 INSERM, UMR8258 CNRS, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue de l' Observatoire, 75006 Paris (France); Négrier, Philippe [Laboratoire Ondes et Matière d' Aquitaine, Université de Bordeaux, UMR CNRS 5798, 351 cours de la Libération, 33 405 Talence Cedex (France); Corvis, Yohann [Unité de Technologies Chimiques et Biologiques pour la Santé, U1022 INSERM, UMR8258 CNRS, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue de l' Observatoire, 75006 Paris (France); Espeau, Philippe, E-mail: philippe.espeau@parisdescartes.fr [Unité de Technologies Chimiques et Biologiques pour la Santé, U1022 INSERM, UMR8258 CNRS, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue de l' Observatoire, 75006 Paris (France)

    2016-05-20

    Highlights: • The refinement of the crystal structure is achieved from X-ray powder diffraction. • P-Synephrine is revealed to be a racemic compound. • Degradation during melting can be bypassed using high DSC scan rates. • The temperature and enthalpy of melting are then proposed for this compound. - Abstract: The crystal structure of p-synephrine was solved from a high-resolution X-ray powder diffraction pattern optimized by energy-minimization calculations using the Dreiding force field. The title compound crystallizes in a monoclinic system (space group P2{sub 1}/c, Z = 4, with a = 8.8504(11) Å, b = 12.1166(15) Å, c = 9.7820(11) Å, β = 122.551(2)°, V = 884.21(19) Å{sup 3} and d = 1.256 g cm{sup −3}). Since p-synephrine degrades upon melting, its melting data were determined from DSC experiments carried out as a function of the heating rate. This method allowed determining a melting temperature and enthalpy equal to 199.8 ± 1.3 °C and 57 ± 3 kJ mol{sup −1}, respectively.

  1. One-photon mass-analyzed threshold ionization (MATI) spectroscopy of pyridine: Determination of accurate ionization energy and cationic structure

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Yu Ran; Kang, Do Won; Kim, Hong Lae, E-mail: chkwon@kangwon.ac.kr, E-mail: hlkim@kangwon.ac.kr; Kwon, Chan Ho, E-mail: chkwon@kangwon.ac.kr, E-mail: hlkim@kangwon.ac.kr [Department of Chemistry and Institute for Molecular Science and Fusion Technology, College of Natural Sciences, Kangwon National University, Chuncheon 200-701 (Korea, Republic of)

    2014-11-07

    Ionization energies and cationic structures of pyridine were intensively investigated utilizing one-photon mass-analyzed threshold ionization (MATI) spectroscopy with vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The present one-photon high-resolution MATI spectrum of pyridine demonstrated a much finer and richer vibrational structure than that of the previously reported two-photon MATI spectrum. From the MATI spectrum and photoionization efficiency curve, the accurate ionization energy of the ionic ground state of pyridine was confidently determined to be 73 570 ± 6 cm{sup −1} (9.1215 ± 0.0007 eV). The observed spectrum was almost completely assigned by utilizing Franck-Condon factors and vibrational frequencies calculated through adjustments of the geometrical parameters of cationic pyridine at the B3LYP/cc-pVTZ level. A unique feature unveiled through rigorous analysis was the prominent progression of the 10 vibrational mode, which corresponds to in-plane ring bending, and the combination of other totally symmetric fundamentals with the ring bending overtones, which contribute to the geometrical change upon ionization. Notably, the remaining peaks originate from the upper electronic state ({sup 2}A{sub 2}), as predicted by high-resolution photoelectron spectroscopy studies and symmetry-adapted cluster configuration interaction calculations. Based on the quantitatively good agreement between the experimental and calculated results, it was concluded that upon ionization the pyridine cation in the ground electronic state should have a planar structure of C{sub 2v} symmetry through the C-N axis.

  2. 15N-Labelling and structure determination of adamantylated azolo-azines in solution

    Directory of Open Access Journals (Sweden)

    Sergey L. Deev

    2017-11-01

    Full Text Available Determining the accurate chemical structures of synthesized compounds is essential for biomedical studies and computer-assisted drug design. The unequivocal determination of N-adamantylation or N-arylation site(s in nitrogen-rich heterocycles, characterized by a low density of hydrogen atoms, using NMR methods at natural isotopic abundance is difficult. In these compounds, the heterocyclic moiety is covalently attached to the carbon atom of the substituent group that has no bound hydrogen atoms, and the connection between the two moieties of the compound cannot always be established via conventional 1H-1H and 1H-13C NMR correlation experiments (COSY and HMBC, respectively or nuclear Overhauser effect spectroscopy (NOESY or ROESY. The selective incorporation of 15N-labelled atoms in different positions of the heterocyclic core allowed for the use of 1H-15N (JHN and 13C-15N (JCN coupling constants for the structure determinations of N-alkylated nitrogen-containing heterocycles in solution. This method was tested on the N-adamantylated products in a series of azolo-1,2,4-triazines and 1,2,4-triazolo[1,5-a]pyrimidine. The syntheses of adamantylated azolo-azines were based on the interactions of azolo-azines and 1-adamatanol in TFA solution. For azolo-1,2,4-triazinones, the formation of mixtures of N-adamantyl derivatives was observed. The JHN and JCN values were measured using amplitude-modulated 1D 1H spin-echo experiments with the selective inversion of the 15N nuclei and line-shape analysis in the 1D 13С spectra acquired with selective 15N decoupling, respectively. Additional spin–spin interactions were detected in the 15N-HMBC spectra. NMR data and DFT (density functional theory calculations permitted to suggest a possible mechanism of isomerization for the adamantylated products of the azolo-1,2,4-triazines. The combined analysis of the JHN and JCN couplings in 15N-labelled compounds provides an efficient method for the structure

  3. Determining the Structure of an Unliganded and Fully Glycosylated SIV gp120 Envelope Glycoprotein

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Bing; Vogan, Erik M.; Gong, Haiyun; Skehel, John J.; Wiley, Don C.; Harrison, Stephen C. (Harvard-Med); (NIMR)

    2010-07-13

    HIV/SIV envelope glycoproteins mediate the first steps in viral infection. They are trimers of a membrane-anchored polypeptide chain, cleaved into two fragments known as gp120 and gp41. The structure of HIV gp120 bound with receptor (CD4) has been known for some time. We have now determined the structure of a fully glycosylated SIV gp120 envelope glycoprotein in an unliganded conformation by X-ray crystallography at 4.0 {angstrom} resolution. We describe here our experimental and computational approaches, which may be relevant to other resolution-limited crystallographic problems. Key issues were attention to details of beam geometry mandated by small, weakly diffracting crystals, and choice of strategies for phase improvement, starting with two isomorphous derivatives and including multicrystal averaging. We validated the structure by analyzing composite omit maps, averaged among three distinct crystal lattices, and by calculating model-based, SeMet anomalous difference maps. There are at least four ordered sugars on many of the thirteen oligosaccharides.

  4. NMR strategies to support medicinal chemistry workflows for primary structure determination.

    Science.gov (United States)

    Oguadinma, Paul; Bilodeau, Francois; LaPlante, Steven R

    2017-01-15

    Central to drug discovery is the correct characterization of the primary structures of compounds. In general, medicinal chemists make great synthetic and characterization efforts to deliver the intended compounds. However, there are occasions which incorrect compounds are presented, such as those reported for Bosutinib and TIC10. This may be due to a variety of reasons such as uncontrolled reaction schemes, reliance on limited characterization techniques (LC-MS and/or 1D 1H NMR spectra), or even the lack of availability or knowledge of characterization strategies. Here, we present practical NMR approaches that support medicinal chemist workflows for addressing compound characterization issues and allow for reliable primary structure determinations. These strategies serve to differentiate between regioisomers and geometric isomers, distinguish between N- versus O-alkyl analogues, and identify rotamers and atropisomers. Overall, awareness and application of these available NMR methods (e.g. HMBC/HSQC, ROESY and VT experiments, to name only a few) should help practicing chemists to reveal chemical phenomena and avoid mis-assignment of the primary structures of compounds. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Firm, Country and Macroeconomic Determinants of Capital Structure: Evidence from Turkish Banking Sector

    Directory of Open Access Journals (Sweden)

    Nuri Baltacı

    2014-03-01

    Full Text Available This study explores the significance of firm-specific, country, and macroeconomic factors in explaining variation in leverage using a sample of banks from Turkish banking sector. The analysis is based on quarterly firm-level data from Turkish banking sector in 2002–2012. We aims to contribute to the empirical capital structure literature in the following ways. Our first contribution comes from assessing the importance of firm-specific factors, country-level factors and industrial factors for capital structure decisions in Turkish banking sector. Second, we employ appropriate and advanced dynamic panel data estimators, Blundell and Bond’s (1998 generalized methods of moment’s estimators (GMM System. We find that leverage is significantly and positively associated with average industry leverage, firm size and GDP growth. We find also that leverage is significantly and negatively associated with tangibility, profitability, inflation and financial risk. The regression results for leverage are both theoretically and empirically plausible for banks in Turkey. Moreover, tangibility, profitability and GDP growth are consistent with the predictions of the pecking order theory, while firm size is consistent with the predictions of the trade-off theory. Our findings suggest that the capital structures of financial and non-financial firms are ultimately determined by the same drivers.

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

    Science.gov (United States)

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

    2013-12-05

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

  7. Mapping the Zambian prison health system: An analysis of key structural determinants.

    Science.gov (United States)

    Topp, Stephanie M; Moonga, Clement N; Luo, Nkandu; Kaingu, Michael; Chileshe, Chisela; Magwende, George; Henostroza, German

    2017-07-01

    Health and health service access in Zambian prisons are in a state of 'chronic emergency'. This study aimed to identify major structural barriers to strengthening the prison health systems. A case-based analysis drew on key informant interviews (n = 7), memos generated during workshops (n = 4) document review and investigator experience. Structural determinants were defined as national or macro-level contextual and material factors directly or indirectly influencing prison health services. The analysis revealed that despite an favourable legal framework, four major and intersecting structural factors undermined the Zambian prison health system. Lack of health financing was a central and underlying challenge. Weak health governance due to an undermanned prisons health directorate impeded planning, inter-sectoral coordination, and recruitment and retention of human resources for health. Outdated prison infrastructure simultaneously contributed to high rates of preventable disease related to overcrowding and lack of basic hygiene. These findings flag the need for policy and administrative reform to establish strong mechanisms for domestic prison health financing and enable proactive prison health governance, planning and coordination.

  8. Determinants of capital structure: An empirical study on Vietnamese listed firms

    Directory of Open Access Journals (Sweden)

    Le Trung Thanh

    2017-05-01

    Full Text Available This paper aims to explore the capital structure of listed Vietnamese companies in an updated context of financial development (the recent situation of domestic equity and debt capital market. By applying Random Effect model for panel data, we analyze 05 firm-specific and 01 country-specific determinants of capital structure based on the data set of 228 firms listed on Ho Chi Minh Stock Exchange during the period 2010 – 2014. The results indicated that The Pecking Order theory better explains the financing behaviors of Vietnamese listed firms. Accordingly, although in recent years, Vietnam’s equity market and corporate debt capital market have evolved considerably, the capital structure of Vietnamese companies are still dominated by the use of short-term financing sources. High-growth firms or large-sized firms still rely heavily on external debt rather than equity issuance while State-owned enterprises (SOE are reported to have positive association with the use of long-term financing sources. This study proposed some recommendations to the policymakers in two dimensions: improving the efficiency and role of capital markets to mitigate the reliance on short-term funds and ensuring that bank finance is allocated on a commercial basis.

  9. Structural determinants for selective recognition of peptide ligands for endothelin receptor subtypes ETA and ETB.

    Science.gov (United States)

    Lättig, Jens; Oksche, Alexander; Beyermann, Michael; Rosenthal, Walter; Krause, Gerd

    2009-07-01

    The molecular basis for recognition of peptide ligands endothelin-1, -2 and -3 in endothelin receptors is poorly understood. Especially the origin of ligand selectivity for ET(A) or ET(B) is not clearly resolved. We derived sequence-structure-function relationships of peptides and receptors from mutational data and homology modeling. Our major findings are the dissection of peptide ligands into four epitopes and the delineation of four complementary structural portions on receptor side explaining ligand recognition in both endothelin receptor subtypes. In addition, structural determinants for ligand selectivity could be described. As a result, we could improve the selectivity of BQ3020 about 10-fold by a single amino acid substitution, validating our hypothesis for ligand selectivity caused by different entrances to the receptors' transmembrane binding sites. A narrow tunnel shape in ET(A) is restrictive for a selected group of peptide ligands' N-termini, whereas a broad funnel-shaped entrance in ET(B) accepts a variety of different shapes and properties of ligands.

  10. Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Takeda, Mitsuhiro [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan); Ono, Akira M.; Terauchi, Tsutomu [SAIL Technologies Co., Inc. (Japan); Kainosho, Masatsune, E-mail: kainosho@nmr.chem.metro-u.ac.j [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan)

    2010-01-15

    The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines ({epsilon}- and {zeta}-SAIL Phe) and tyrosine ({epsilon}-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized {delta}-SAIL Phe and {delta}-SAIL Tyr, which allow us to observe and assign {delta}-{sup 13}C/{sup 1}H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the {delta}-, {epsilon}- or {zeta}-{sup 13}C/{sup 1}H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the {delta}-, {epsilon}-, and {zeta}-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly {sup 13}C, {sup 15}N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of {zeta}-SAIL Phe and {epsilon}-SAIL Tyr would be practically the best choice for protein structural determinations.

  11. Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination.

    Science.gov (United States)

    Takeda, Mitsuhiro; Ono, Akira M; Terauchi, Tsutomu; Kainosho, Masatsune

    2010-01-01

    The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines (epsilon- and zeta-SAIL Phe) and tyrosine (epsilon-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized delta-SAIL Phe and delta-SAIL Tyr, which allow us to observe and assign delta-(13)C/(1)H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the delta-, epsilon- or zeta-(13)C/(1)H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the delta-, epsilon-, and zeta-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly (13)C, (15)N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of zeta-SAIL Phe and epsilon-SAIL Tyr would be practically the best choice for protein structural determinations.

  12. Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination

    International Nuclear Information System (INIS)

    Takeda, Mitsuhiro; Ono, Akira M.; Terauchi, Tsutomu; Kainosho, Masatsune

    2010-01-01

    The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines (ε- and ζ-SAIL Phe) and tyrosine (ε-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized δ-SAIL Phe and δ-SAIL Tyr, which allow us to observe and assign δ- 13 C/ 1 H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the δ-, ε- or ζ- 13 C/ 1 H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the δ-, ε-, and ζ-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly 13 C, 15 N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of ζ-SAIL Phe and ε-SAIL Tyr would be practically the best choice for protein structural determinations.

  13. Determining

    Directory of Open Access Journals (Sweden)

    Bahram Andarzian

    2015-06-01

    Full Text Available Wheat production in the south of Khuzestan, Iran is constrained by heat stress for late sowing dates. For optimization of yield, sowing at the appropriate time to fit the cultivar maturity length and growing season is critical. Crop models could be used to determine optimum sowing window for a locality. The objectives of this study were to evaluate the Cropping System Model (CSM-CERES-Wheat for its ability to simulate growth, development, grain yield of wheat in the tropical regions of Iran, and to study the impact of different sowing dates on wheat performance. The genetic coefficients of cultivar Chamran were calibrated for the CSM-CERES-Wheat model and crop model performance was evaluated with experimental data. Wheat cultivar Chamran was sown on different dates, ranging from 5 November to 9 January during 5 years of field experiments that were conducted in the Khuzestan province, Iran, under full and deficit irrigation conditions. The model was run for 8 sowing dates starting on 25 October and repeated every 10 days until 5 January using long-term historical weather data from the Ahvaz, Behbehan, Dezful and Izeh locations. The seasonal analysis program of DSSAT was used to determine the optimum sowing window for different locations as well. Evaluation with the experimental data showed that performance of the model was reasonable as indicated by fairly accurate simulation of crop phenology, biomass accumulation and grain yield against measured data. The normalized RMSE were 3%, 2%, 11.8%, and 3.4% for anthesis date, maturity date, grain yield and biomass, respectively. Optimum sowing window was different among locations. It was opened and closed on 5 November and 5 December for Ahvaz; 5 November and 15 December for Behbehan and Dezful;and 1 November and 15 December for Izeh, respectively. CERES-Wheat model could be used as a tool to evaluate the effect of sowing date on wheat performance in Khuzestan conditions. Further model evaluations

  14. Determination of the object surface function by structured light: application to the study of spinal deformities

    International Nuclear Information System (INIS)

    Buendia, M.; Salvador, R.; Cibrian, R.; Sotoca, J.M.; Laguia, M.

    1999-01-01

    The projection of structured light is a technique frequently used to determine the surface shape of an object. In this paper, a new procedure is described that efficiently resolves the correspondence between the knots of the projected grid and those obtained on the object when the projection is made. The method is based on the use of three images of the projected grid. In two of them the grid is projected over a flat surface placed, respectively, before and behind the object; both images are used for calibration. In the third image the grid is projected over the object. It is not reliant on accurate determination of the camera and projector pair relative to the grid and object. Once the method is calibrated, we can obtain the surface function by just analysing the projected grid on the object. The procedure is especially suitable for the study of objects without discontinuities or large depth gradients. It can be employed for determining, in a non-invasive way, the patient's back surface function. Symmetry differences permit a quantitative diagnosis of spinal deformities such as scoliosis. (author)

  15. Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

    Science.gov (United States)

    Smith, Owen K.; Aladjem, Mirit I.

    2014-01-01

    The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome’s three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication. PMID:24905010

  16. Application Of The Work Breakdown Structure In Determining Cost Buffers In Construction Schedules

    Directory of Open Access Journals (Sweden)

    Połoński M.

    2015-03-01

    Full Text Available The paper presents methods of determining the location of cost buffers and corresponding contingency costs in the CPM schedule based on its work breakdown structure. Application of correctly located cost buffers with appropriately established reserve costs is justified by the common overrunning of scheduled costs in construction projects. Interpolated cost buffers (CB as separate tasks have been combined with relevant summary tasks by the start–to–start (SS relationship, whereas the time of their execution has been dynamically connected with the time of accomplishment of particular summary tasks using the “paste connection” option. Besides cost buffers linked with the group of tasks assigned to summary tasks, a definition of the cost buffer for the entire project (PCB has been proposed, i.e. as one initial task of the entire project. Contingency costs corresponding to these buffers, depending on the data that the planner has at his disposal, can be determined using different methods, but always depend on the costs of all tasks protected by each buffer. The paper presents an exemplary schedule for a facility and the method of determining locations and cost for buffers CB and PCB, as well as their influence on the course of the curve illustrating the budgeted cost of work scheduled (BCWS. The proposed solution has been adjusted and presented with consideration of the possibilities created by the scheduling software MS Project, though its general assumptions may be implemented with application of other similar specialist tools.

  17. Improving the chances of successful protein structure determination with a random forest classifier

    Energy Technology Data Exchange (ETDEWEB)

    Jahandideh, Samad [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92307 (United States); Joint Center for Structural Genomics, (United States); Jaroszewski, Lukasz; Godzik, Adam, E-mail: adam@burnham.org [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92307 (United States); Joint Center for Structural Genomics, (United States); University of California, San Diego, La Jolla, California (United States)

    2014-03-01

    Using an extended set of protein features calculated separately for protein surface and interior, a new version of XtalPred based on a random forest classifier achieves a significant improvement in predicting the success of structure determination from the primary amino-acid sequence. Obtaining diffraction quality crystals remains one of the major bottlenecks in structural biology. The ability to predict the chances of crystallization from the amino-acid sequence of the protein can, at least partly, address this problem by allowing a crystallographer to select homologs that are more likely to succeed and/or to modify the sequence of the target to avoid features that are detrimental to successful crystallization. In 2007, the now widely used XtalPred algorithm [Slabinski et al. (2007 ▶), Protein Sci.16, 2472–2482] was developed. XtalPred classifies proteins into five ‘crystallization classes’ based on a simple statistical analysis of the physicochemical features of a protein. Here, towards the same goal, advanced machine-learning methods are applied and, in addition, the predictive potential of additional protein features such as predicted surface ruggedness, hydrophobicity, side-chain entropy of surface residues and amino-acid composition of the predicted protein surface are tested. The new XtalPred-RF (random forest) achieves significant improvement of the prediction of crystallization success over the original XtalPred. To illustrate this, XtalPred-RF was tested by revisiting target selection from 271 Pfam families targeted by the Joint Center for Structural Genomics (JCSG) in PSI-2, and it was estimated that the number of targets entered into the protein-production and crystallization pipeline could have been reduced by 30% without lowering the number of families for which the first structures were solved. The prediction improvement depends on the subset of targets used as a testing set and reaches 100% (i.e. twofold) for the top class of predicted

  18. A Multimodal Approach for Determining Brain Networks by Jointly Modeling Functional and Structural Connectivity

    Directory of Open Access Journals (Sweden)

    Wenqiong eXue

    2015-02-01

    Full Text Available Recent innovations in neuroimaging technology have provided opportunities for researchers to investigate connectivity in the human brain by examining the anatomical circuitry as well as functional relationships between brain regions. Existing statistical approaches for connectivity generally examine resting-state or task-related functional connectivity (FC between brain regions or separately examine structural linkages. As a means to determine brain networks, we present a unified Bayesian framework for analyzing FC utilizing the knowledge of associated structural connections, which extends an approach by Patel et al.(2006a that considers only functional data. We introduce an FC measure that rests upon assessments of functional coherence between regional brain activity identified from functional magnetic resonance imaging (fMRI data. Our structural connectivity (SC information is drawn from diffusion tensor imaging (DTI data, which is used to quantify probabilities of SC between brain regions. We formulate a prior distribution for FC that depends upon the probability of SC between brain regions, with this dependence adhering to structural-functional links revealed by our fMRI and DTI data. We further characterize the functional hierarchy of functionally connected brain regions by defining an ascendancy measure that compares the marginal probabilities of elevated activity between regions. In addition, we describe topological properties of the network, which is composed of connected region pairs, by performing graph theoretic analyses. We demonstrate the use of our Bayesian model using fMRI and DTI data from a study of auditory processing. We further illustrate the advantages of our method by comparisons to methods that only incorporate functional information.

  19. Silicon Σ13(5 0 1) grain boundary interface structure determined by bicrystal Bragg rod X-ray scattering

    International Nuclear Information System (INIS)

    Howes, P.B.; Rhead, S.; Roy, M.; Nicklin, C.L.; Rawle, J.L.; Norris, C.A.

    2013-01-01

    The atomic structure of the silicon Σ13(5 0 1) symmetric tilt grain boundary interface has been determined using Bragg rod X-ray scattering. In contrast to conventional structural studies of grain boundary structure using transmission electron microscopy, this approach allows the non-destructive measurement of macroscopic samples. The interface was found to have a single structure that is fully fourfold coordinated. X-ray diffraction data were measured at Beamline I07 at the Diamond Light Source

  20. Structural determinants for binding to angiotensin converting enzyme 2 (ACE2 and angiotensin receptors

    Directory of Open Access Journals (Sweden)

    Daniel eClayton

    2015-01-01

    Full Text Available Angiotensin converting enzyme 2 (ACE2 is a zinc carboxypeptidase involved in the renin angiotensin system (RAS and inactivates the potent vasopressive peptide angiotensin II (Ang II by removing the C-terminal phenylalanine residue to yield Ang1-7. This conversion inactivates the vasoconstrictive action of Ang II and yields a peptide that acts as a vasodilatory molecule at the Mas receptor and potentially other receptors. Given the growing complexity of RAS and level of cross-talk between ligands and their corresponding enzymes and receptors, the design of molecules with selectivity for the major RAS binding partners to control cardiovascular tone is an on-going challenge. In previous studies we used single β-amino acid substitutions to modulate the structure of Ang II and its selectivity for ACE2, AT1R and angiotensin type 2 (AT2R receptor. We showed that modification at the C-terminus of Ang II generally resulted in more pronounced changes to secondary structure and ligand binding, and here we further explore this region for the potential to modulate ligand specificity. In this study, 1 a library of forty-seven peptides derived from the C-terminal tetra-peptide sequence (-IHPF of Ang II was synthesised and assessed for ACE2 binding, 2 the terminal group requirements for high affinity ACE2 binding were explored by and N- and C-terminal modification, 3 high affinity ACE2 binding chimeric AngII analogues were then synthesized and assessed, 4 the structure of the full-length Ang II analogues were assessed by circular dichroism, and 5 the Ang II analogues were assessed for AT1R/AT2R selectivity by cell-based assays. Studies on the C-terminus of Ang II demonstrated varied specificity at different residue positions for ACE2 binding and four Ang II chimeric peptides were identified as selective ligands for the AT2 receptor. Overall, these results provide insight into the residue and structural requirements for ACE2 binding and angiotensin receptor

  1. Theoriebedingte Wörterbuchform-probleme und wörterbuchformbedingte Benutzerprobleme I. Ein Beitrag zur Wörterbuchkritik und zur Erweiterung der Theorie der Wörterbuchform Theory-determined Dictionary Structure Problems and Dictionary Structure Determined User Problems I. A Contribution to Dictionary Criticism and the Theory of Dictionary Structures.

    Directory of Open Access Journals (Sweden)

    Herbert Ernst Wiegand

    2012-01-01

    rterbuchartikel; theoriebedingtes Wörterbuchformproblem; wörterbuchformbedingtes Benutzerproblem; Wortfamilienfenster; zweifach komplexer Wörterbuchartikel

    The empirical domain of the subject matter of dictionary research changes, among others, due to the publication of new dictionaries. A noticeable trend seems to be the increasing occurrence of more new elements regarding dictionary structures in the front matter, central list and back matter. This makes dictionary structure more complex. For the theory of dictionary structures this leads to theory-determined dictionary structure problems: If the theory wants to take cognizance of the new developments it has to be expanded and becomes increasingly complex. If it is expanded one can recognise, in the light of the theory, the strengths and weaknesses of the new structural elements. This leads to dictionary criticism. The weaknesses, especially, lead to dictionary structure-determined user problems. In this first part of the contribution theory-determined article structure problems are treated that result from an investigation of an article type not previously examined, i.e. the complex dictionary articles in which two or more structurally identical words belonging to two or more part of speech classes are lexicographically treated. The theory-determined article structure problems prevail because there are no structural concept for articles of this type, no systematic terminology, no typology and partially no means and methods of presentation. The problems are thereby solved that the theory of dictionary structures is systematically expanded and the heuristics extended to provide for the missing elements.

    Keywords: article sequence with window; article structure scheme; article window; basic complex dictionary article; complex article structural image; complex dictionary article; dictionary structure determined user problem; noun-verb-adjective article; partial article; partial article external

  2. Structure Determination of Cisplatin-Amino Acid Analogues by Infrared Multiple Photon Dissociation Action Spectroscopy

    Science.gov (United States)

    He, Chenchen; Bao, Xun; Zhu, Yanlong; Strobehn, Stephen; Kimutai, Bett; Nei, Y.-W.; Chow, C. S.; Rodgers, M. T.; Gao, Juehan; Oomens, J.

    2015-06-01

    To gain a better understanding of the binding mechanism and assist in the optimization of relevant drug and chemical probe design, both experimental and theoretical studies were performed on a series of amino acid-linked cisplatin derivatives, including glycine-, lysine-, and ornithine-linked cisplatin, Gplatin, Kplatin, and Oplatin, respectively. Cisplatin, the first FDA-approved platinum-based anticancer drug, has been widely used in cancer chemotherapy. Its pharmacological mechanism has been identified as its ability to coordinate to genomic DNA, and guanine is its major target. In previous reports, cisplatin was successfully utilized as a chemical probe to detect solvent accessible sites in ribosomal RNA (rRNA). Among the amino-acid-linked cisplatin derivatives, Oplatin exhibits preference for adenine over guanine. The mechanism behind its different selectivity compared to cisplatin may relate to its potential of forming a hydrogen bond between the carboxylate group in Pt (II) complex and the 6-amino moiety of adenosine stabilizes A-Oplatin products. Tandem mass spectrometry analysis also indicates that different coordination sites of Oplatin on adenosine affect glycosidic bond stability. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on all three amino acid-linked cisplatin to characterize their structures. An extensive theoretical study has been performed on Gplatin to guide the selection of the most effective theory and basis set based on its geometric information. The results for Gplatin provide the foundation for characterization of the more complex amino acid-linked cisplatin derivatives, Oplatin and Kplatin. Structural and energetic information elucidated for these compounds, particularly Oplatin reveal the reason for its alternative selectivity compared to cisplatin.

  3. Beyond Cassie equation: Local structure of heterogeneous surfaces determines the contact angles of microdroplets

    Science.gov (United States)

    Zhang, Bo; Wang, Jianjun; Liu, Zhiping; Zhang, Xianren

    2014-01-01

    The application of Cassie equation to microscopic droplets is recently under intense debate because the microdroplet dimension is often of the same order of magnitude as the characteristic size of substrate heterogeneities, and the mechanism to describe the contact angle of microdroplets is not clear. By representing real surfaces statistically as an ensemble of patterned surfaces with randomly or regularly distributed heterogeneities (patches), lattice Boltzmann simulations here show that the contact angle of microdroplets has a wide distribution, either continuous or discrete, depending on the patch size. The origin of multiple contact angles observed is ascribed to the contact line pinning effect induced by substrate heterogeneities. We demonstrate that the local feature of substrate structure near the contact line determines the range of contact angles that can be stabilized, while the certain contact angle observed is closely related to the contact line width. PMID:25059292

  4. Quantitative methodology to extract regional magnetotelluric impedances and determine the dimension of the conductivity structure

    Energy Technology Data Exchange (ETDEWEB)

    Groom, R [PetRos EiKon Incorporated, Ontario (Canada); Kurtz, R; Jones, A; Boerner, D [Geological Survey of Canada, Ontario (Canada)

    1996-05-01

    This paper describes a systematic method for determining the appropriate dimensionality of magnetotelluric (MT) data from a site, and illustrates the application of this method to analyze both synthetic data and real data. Additionally, it describes the extraction of regional impedance responses from multiple sites. This method was examined extensively with synthetic data, and proven to be successful. It was demonstrated for two neighboring sites that the analysis methodology can be extremely useful in unraveling the bulk regional response when hidden by strong three-dimensional effects. Although there may still be some uncertainties remaining in the true levels for the regional responses for stations LIT000 and LITW02, the analysis has provided models which not only fit the data but are consistent for neighboring sites. It was suggested from these data that the stations are seeing significantly different structures. 12 refs.

  5. Determination of the sterile release rate for stopping growing age-structured populations

    International Nuclear Information System (INIS)

    Barclay, Hugh John

    2016-01-01

    A freely-growing age-structured population was modelled for growth and control by sterile male releases. Equilibrium populations yield critical sterile male release rates that would hold the population at equilibrium. It is shown here that these rates may be different from the release rates required to stop a growing population and bring it to an equilibrium. A computer simulation was constructed of this population and a parameter sensitivity analysis graphed the effects on the required sterile male release rate of fertility, mating delay in adult females, net juvenile survivorship, three adult survivorship curves, the time spent in the juvenile stages, and total life span. The adult survivorship curves had the greatest effect on the required sterile release rate for population elimination. The required release rate was also determined for Ceratitis capitata (Wiedemann) using survivorship and fertility data from a laboratory strain. The concepts of over-flooding ratio and release ratio were discussed and quantified for the cases above. (author)

  6. Physical mechanism determining the radial electric field and its radial structure in a toroidal plasma

    International Nuclear Information System (INIS)

    Ida, Katsumi; Miura, Yukitoshi; Itoh, Sanae

    1994-10-01

    Radial structures of plasma rotation and radial electric field are experimentally studied in tokamak, heliotron/torsatron and stellarator devices. The perpendicular and parallel viscosities are measured. The parallel viscosity, which is dominant in determining the toroidal velocity in heliotron/torsatron and stellarator devices, is found to be neoclassical. On the other hand, the perpendicular viscosity, which is dominant in dictating the toroidal rotation in tokamaks, is anomalous. Even without external momentum input, both a plasma rotation and a radial electric field exist in tokamaks and heliotrons/torsatrons. The observed profiles of the radial electric field do not agree with the theoretical prediction based on neoclassical transport. This is mainly due to the existence of anomalous perpendicular viscosity. The shear of the radial electric field improves particle and heat transport both in bulk and edge plasma regimes of tokamaks. (author) 95 refs

  7. A hybrid computation method for determining fluctuations of temperature in branched structures

    International Nuclear Information System (INIS)

    Czomber, L.

    1982-01-01

    A hybrid computation method for determining temperature fluctuations at discrete points of slab like geometries is developed on the basis of a new formulation of the finite difference method. For this purpose, a new finite difference method is combined with an exact solution of the heat equation within the range of values of the Laplace transformation. Whereas the exact solution can be applied to arbitraryly large ranges, the finite difference formulation is given for structural ranges which need finer discretization. The boundary conditions of the exact solution are substituted by finite difference terms for the boundary residual flow or an internal heat source, depending on the problem. The resulting system of conditional equations contains only the node parameters of the finite difference method. (orig.) [de

  8. Relating Topological Determinants of Complex Networks to Their Spectral Properties: Structural and Dynamical Effects

    Science.gov (United States)

    Castellano, Claudio; Pastor-Satorras, Romualdo

    2017-10-01

    The largest eigenvalue of a network's adjacency matrix and its associated principal eigenvector are key elements for determining the topological structure and the properties of dynamical processes mediated by it. We present a physically grounded expression relating the value of the largest eigenvalue of a given network to the largest eigenvalue of two network subgraphs, considered as isolated: the hub with its immediate neighbors and the densely connected set of nodes with maximum K -core index. We validate this formula by showing that it predicts, with good accuracy, the largest eigenvalue of a large set of synthetic and real-world topologies. We also present evidence of the consequences of these findings for broad classes of dynamics taking place on the networks. As a by-product, we reveal that the spectral properties of heterogeneous networks built according to the linear preferential attachment model are qualitatively different from those of their static counterparts.

  9. Isolation and crystal structure determination of piperazine dicarbamate obtained from a direct reaction

    Energy Technology Data Exchange (ETDEWEB)

    Sim, Jae Ung; Jo, Eun Hee; Jhon, Young Ho; Paek, Kyung Soo; Kim, Ja Heon [Dept. of Chemistry, Soongsil University, Seoul (Korea, Republic of); Jang Se Gyu; Shim, Jae Goo; Jang, Kyung Ryong [Korea Future Technology Research Laboratory, Korea Electric Power Research Institute (KEPRI), Daejeon (Korea, Republic of)

    2016-11-15

    Separation of CO{sub 2} in the flue gas emitted from coal-fired power plants is the first technological step toward reducing the CO{sub 2} concentration in atmosphere, and eventually for mitigating the global climate change. We could isolate the PZ-dicarbamate, where two CO{sub 2} molecules are bonded to each secondary amine group, through CO{sub 2} absorption by PZ in methanol, and determined its crystal structure by X-ray crystallography. The PZ-dicarbamate as a salt with piperazinium allowed further analyses such as TGA and NMR measurements, which gave information on the fate of the salt. In particular, the salt can be used as a standard sample exhibiting 100% CO{sub 2} loading in a PZ molecule.

  10. Structure determination of the neutral exopolysaccharide produced by Lactobacillus delbrueckii subsp. bulgaricus OLL1073R-1.

    Science.gov (United States)

    Van Calsteren, Marie-Rose; Gagnon, Fleur; Nishimura, Junko; Makino, Seiya

    2015-09-02

    The neutral exopolysaccharide (NPS) of Lactobacillus delbrueckii subsp. bulgaricus strain OLL1073R-1 was purified and characterized. The molecular mass was 5.0×10(6) g/mol. Sugar and absolute configuration analyses gave the following composition: d-Glc, 1; d-Gal, 1.5. The NPS was also submitted to periodate oxidation followed by borohydride reduction and Smith degradation. Sugar and methylation analyses, (1)H and (13)C nuclear magnetic resonance, and mass spectrometry of the NPS or of its specifically modified products allowed determining the repeating unit sequence: {2)Glc(α1-3)Glc(β1-3)[Gal(β1-4)]Gal(β1-4)Gal(α1-}n. The structure is compared to that of exopolysaccharides produced by other Lactobacillus bulgaricus strains. Copyright © 2015. Published by Elsevier Ltd.

  11. Neutral axis determination of full size concrete structures using coda wave measurements

    Science.gov (United States)

    Jiang, Hanwan; Zhan, Hanyu; Zhuang, Chenxu; Jiang, Ruinian

    2018-03-01

    Coda waves experiencing multiple scattering behaviors are sensitive to weak changes occurring in media. In this paper, a typical four-point bending test with varied external loads is conducted on a 30-meter T-beam that is removed from a bridge after being in service for 15 years, and the coda wave signals are collected with a couple of sources-receivers pairs. Then the observed coda waves at different loads are compared to calculate their relative velocity variations, which are utilized as the parameter to distinct the compression and tensile zones as well as determine the neutral axis position. Without any prior knowledge of the concrete beam, the estimated axis position agrees well with the associated strain gage measurement results, and the zones bearing stress and tension behaviors are indicated. The presented work offers significant potential for Non-Destructive Testing and Evaluation of full-size concrete structures in future work.

  12. Can low energy experiments supply the effective information to determine the inner structure of hadrons

    International Nuclear Information System (INIS)

    Sawada, Tetsuo

    1980-01-01

    It is explained that the low energy experiments with high precision are important sources of information to determine the inner structure of hadrons. For such purpose, the magnetic monopole model of hadron due to Schwinger is reviewed. Appearance of the strong van der Waals force between hadrons is one of the most important consequences of such a model. A technique, which enables us to separate the effect of such a long range force from that of the short range force arising from the exchanges of pions, is introduced. Present status of the related experiments are summarized, and the experiments necessary to confirm the existence of the strong van der Waals force in a clear-cut way are explained. Possible impacts to the hadron physics, when the existence of such a long range force is confirmed, are discussed. (author)

  13. Determination of structure and properties of molecular crystals from first principles.

    Science.gov (United States)

    Szalewicz, Krzysztof

    2014-11-18

    CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be

  14. Experimental determination of neutron capture cross sections of fast reactor structure materials integrated in intermediate energy spectra. Vol. 2: description of experimental structure

    International Nuclear Information System (INIS)

    Tassan, S.

    1978-01-01

    A selection of technical documents is given concerning the experimental determination of the neutron capture cross-sections of fast reactor structural materials (Fe, Cr, Ni...) integrated over the intermediate energy spectra. The experimental structure project and modifications of the reactor RB2 for this experiment, together with criticality and safety calculations, are presented

  15. Structural determinants of hydration, mechanics and fluid flow in freeze-dried collagen scaffolds.

    Science.gov (United States)

    Offeddu, G S; Ashworth, J C; Cameron, R E; Oyen, M L

    2016-09-01

    Freeze-dried scaffolds provide regeneration templates for a wide range of tissues, due to their flexibility in physical and biological properties. Control of structure is crucial for tuning such properties, and therefore scaffold functionality. However, the common approach of modeling these scaffolds as open-cell foams does not fully account for their structural complexity. Here, the validity of the open-cell model is examined across a range of physical characteristics, rigorously linking morphology to hydration and mechanical properties. Collagen scaffolds with systematic changes in relative density were characterized using Scanning Electron Microscopy, X-ray Micro-Computed Tomography and spherical indentation analyzed in a time-dependent poroelastic framework. Morphologically, all scaffolds were mid-way between the open- and closed-cell models, approaching the closed-cell model as relative density increased. Although pore size remained constant, transport pathway diameter decreased. Larger collagen fractions also produced greater volume swelling on hydration, although the change in pore diameter was constant, and relatively small at ∼6%. Mechanically, the dry and hydrated scaffold moduli varied quadratically with relative density, as expected of open-cell materials. However, the increasing pore wall closure was found to determine the time-dependent nature of the hydrated scaffold response, with a decrease in permeability producing increasingly elastic rather than viscoelastic behavior. These results demonstrate that characterizing the deviation from the open-cell model is vital to gain a full understanding of scaffold biophysical properties, and provide a template for structural studies of other freeze-dried biomaterials. Freeze-dried collagen sponges are three-dimensional microporous scaffolds that have been used for a number of exploratory tissue engineering applications. The characterization of the structure-properties relationships of these scaffolds is

  16. Structural determinants of NH3 and NH4+ transport by mouse Rhbg, a renal Rh glycoprotein.

    Science.gov (United States)

    Abdulnour-Nakhoul, Solange; Le, Trang; Rabon, Edd; Hamm, L Lee; Nakhoul, Nazih L

    2016-12-01

    Renal Rhbg is localized to the basolateral membrane of intercalated cells and is involved in NH 3 /NH 4 + transport. The structure of Rhbg is not yet resolved; however, a high-resolution crystal structure of AmtB, a bacterial homolog of Rh, has been determined. We aligned the sequence of Rhbg to that of AmtB and identified important sites of Rhbg that may affect transport. Our analysis positioned three conserved amino acids, histidine 183 (H183), histidine 342 (H342), and tryptophan 230 (W230), within the hydrophobic pore where they presumably serve to control NH 3 transport. A fourth residue, phenylalanine 128 (F128) was positioned at the upper vestibule, presumably contributing to recruitment of NH 4 + We generated three mutations each of H183, H342, W230, and F128 and expressed them in frog oocytes. Immunolabeling showed that W230 and F128 mutants were localized to the cell membrane, whereas H183 and H342 staining was diffuse and mostly intracellular. To determine function, we compared measurements of NH 3 /NH 4 + and methyl amine (MA)/methyl ammonium (MA + )-induced currents, intracellular pH, and surface pH (pHs) among oocytes expressing the mutants, Rhbg, or injected with H 2 O. In H183 and W230 mutants, NH 4 + -induced current and intracellular acidification were inhibited compared with that of Rhbg, and MA-induced intracellular alkalinization was completely absent. Expression of H183A or W230A mutants inhibited NH 3 /NH 4 + - and MA/MA + -induced decrease in pHs to the level observed in H 2 O-injected oocytes. Mutations of F128 did not significantly affect transport of NH 3 or NH 4 + These data demonstrated that mutating H183 or W230 caused loss of function but not F128. H183 and H342 may affect membrane expression of the transporter.

  17. Determining the depth of certain gravity sources without a priori specification of their structural index

    Science.gov (United States)

    Zhou, Shuai; Huang, Danian

    2015-11-01

    We have developed a new method for the interpretation of gravity tensor data based on the generalized Tilt-depth method. Cooper (2011, 2012) extended the magnetic Tilt-depth method to gravity data. We take the gradient-ratio method of Cooper (2011, 2012) and modify it so that the source type does not need to be specified a priori. We develop the new method by generalizing the Tilt-depth method for depth estimation for different types of source bodies. The new technique uses only the three vertical tensor components of the full gravity tensor data observed or calculated at different height plane to estimate the depth of the buried bodies without a priori specification of their structural index. For severely noise-corrupted data, our method utilizes different upward continuation height data, which can effectively reduce the influence of noise. Theoretical simulations of the gravity source model with and without noise illustrate the ability of the method to provide source depth information. Additionally, the simulations demonstrate that the new method is simple, computationally fast and accurate. Finally, we apply the method using the gravity data acquired over the Humble Salt Dome in the USA as an example. The results show a good correspondence to the previous drilling and seismic interpretation results.

  18. Determinants of the Capital Structure of Small and Medium Sized Brazilian Enterprises

    Directory of Open Access Journals (Sweden)

    Wilson Toshiro Nakamura

    2013-07-01

    Full Text Available This research investigates the determinants of the capital structure of small and medium enterprises (SMEs using a unique database that includes over 19,000 Brazilian firms and spans 13 years of data. The econometric analysis employs the System Generalized Method of Moments estimator (GMM-Sys and two strong results emerge: (a profitability is negatively related to leverage, and (b asset growth is positively related to leverage. Both results are consistent with the pecking order theory of capital structure and suggest that SMEs tend to finance their expansion with debt only after exhausting their internal resources. Additionally, we find weaker evidence for the following: (a size is positively related to leverage, which can be interpreted as evidence that larger firms have more access to credit markets; (b riskier SMEs tend to be less financially leveraged, consistent with the bankruptcy cost arguments from trade-off theories; and (c the age of the firm is negatively related to financial leverage, suggesting that older SMEs may be slightly more conservative in their financing choices. Finally, the magnitude of the coefficient of lagged leverage shows the high persistence of this variable and is compatible with the hypothesis that SMEs adjust their debt/equity ratio towards a target value, although at a low speed.

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

    Science.gov (United States)

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

    2014-06-01

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

  20. Determining the drivers of population structure in a highly urbanized landscape to inform conservation planning.

    Science.gov (United States)

    Thomassen, Henri A; Harrigan, Ryan J; Semple Delaney, Kathleen; Riley, Seth P D; Serieys, Laurel E K; Pease, Katherine; Wayne, Robert K; Smith, Thomas B

    2018-02-01

    Understanding the environmental contributors to population structure is of paramount importance for conservation in urbanized environments. We used spatially explicit models to determine genetic population structure under current and future environmental conditions across a highly fragmented, human-dominated environment in Southern California to assess the effects of natural ecological variation and urbanization. We focused on 7 common species with diverse habitat requirements, home-range sizes, and dispersal abilities. We quantified the relative roles of potential barriers, including natural environmental characteristics and an anthropogenic barrier created by a major highway, in shaping genetic variation. The ability to predict genetic variation in our models differed among species: 11-81% of intraspecific genetic variation was explained by environmental variables. Although an anthropogenically induced barrier (a major highway) severely restricted gene flow and movement at broad scales for some species, genetic variation seemed to be primarily driven by natural environmental heterogeneity at a local level. Our results show how assessing environmentally associated variation for multiple species under current and future climate conditions can help identify priority regions for maximizing population persistence under environmental change in urbanized regions. © 2017 Society for Conservation Biology.

  1. Aggregate size and structure determination of nanomaterials in physiological media: importance of dynamic evolution

    International Nuclear Information System (INIS)

    Afrooz, A. R. M. Nabiul; Hussain, Saber M.; Saleh, Navid B.

    2014-01-01

    Most in vitro nanotoxicological assays are performed after 24 h exposure. However, in determining size and shape effect of nanoparticles in toxicity assays, initial characterization data are generally used to describe experimental outcome. The dynamic size and structure of aggregates are typically ignored in these studies. This brief communication reports dynamic evolution of aggregation characteristics of gold nanoparticles. The study finds that gradual increase in aggregate size of gold nanospheres (AuNS) occurs up to 6 h duration; beyond this time period, the aggregation process deviates from gradual to a more abrupt behavior as large networks are formed. Results of the study also show that aggregated clusters possess unique structural conformation depending on nominal diameter of the nanoparticles. The differences in fractal dimensions of the AuNS samples likely occurred due to geometric differences, causing larger packing propensities for smaller sized particles. Both such observations can have profound influence on dosimetry for in vitro nanotoxicity analyses.Graphical Abstract

  2. Applications of Tandem Mass Spectrometry in the Structure Determination of Permethylated Sialic Acid-containing Oligosaccharides

    International Nuclear Information System (INIS)

    Yoo, Eun Sun; Yoon, In Mo

    2005-01-01

    Sets of sialic acid-containing trisaccharides having different internal and terminal linkages have been synthesized to develop a sensitive method for analysis of the reducing terminal linkage positions. The trisaccharides, sialyl(α 2-3)Gal(β 1-3)GalNAc and sialyl(α 2-3)Gal(β 1-X)GlcNAc where X=3, 4 and 6, were synthesized and examined using electrospray ionization (ESI)-collision induced dissociation (CID) tandem mass spectrometry (MS/MS). The compounds chosen for this study are related to terminal groups likely to be found on polylactosamine-like glycoproteins and glycolipids which occur on the surface of mammalian cells. The purpose of this study is to develop tandem mass spectrometral methods to determine detailed carbohydrate structures on permethylated or partially methylated oligosaccharides for future applications on biologically active glycoconjugates and to exploit a faster method of synthesizing a series of structural isomeric oligosaccharides to be used for further mass spectrometry and instrumental analysis

  3. Evaluating multiple determinants of the structure of plant-animal mutualistic networks.

    Science.gov (United States)

    Vázquez, Diego P; Chacoff, Natacha P; Cagnolo, Luciano

    2009-08-01

    The structure of mutualistic networks is likely to result from the simultaneous influence of neutrality and the constraints imposed by complementarity in species phenotypes, phenologies, spatial distributions, phylogenetic relationships, and sampling artifacts. We develop a conceptual and methodological framework to evaluate the relative contributions of these potential determinants. Applying this approach to the analysis of a plant-pollinator network, we show that information on relative abundance and phenology suffices to predict several aggregate network properties (connectance, nestedness, interaction evenness, and interaction asymmetry). However, such information falls short of predicting the detailed network structure (the frequency of pairwise interactions), leaving a large amount of variation unexplained. Taken together, our results suggest that both relative species abundance and complementarity in spatiotemporal distribution contribute substantially to generate observed network patters, but that this information is by no means sufficient to predict the occurrence and frequency of pairwise interactions. Future studies could use our methodological framework to evaluate the generality of our findings in a representative sample of study systems with contrasting ecological conditions.

  4. Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities.

    Science.gov (United States)

    López-García, Álvaro; Varela-Cervero, Sara; Vasar, Martti; Öpik, Maarja; Barea, José M; Azcón-Aguilar, Concepción

    2017-12-01

    Functional diversity in ecosystems has traditionally been studied using aboveground plant traits. Despite the known effect of plant traits on the microbial community composition, their effects on the microbial functional diversity are only starting to be assessed. In this study, the phylogenetic structure of arbuscular mycorrhizal (AM) fungal communities associated with plant species differing in life cycle and growth form, that is, plant life forms, was determined to unravel the effect of plant traits on the functional diversity of this fungal group. The results of the 454 pyrosequencing showed that the AM fungal community composition differed across plant life forms and this effect was dependent on the soil collection date. Plants with ruderal characteristics tended to associate with phylogenetically clustered AM fungal communities. By contrast, plants with resource-conservative traits associated with phylogenetically overdispersed AM fungal communities. Additionally, the soil collected in different seasons yielded AM fungal communities with different phylogenetic dispersion. In summary, we found that the phylogenetic structure, and hence the functional diversity, of AM fungal communities is dependent on plant traits. This finding adds value to the use of plant traits for the evaluation of belowground ecosystem diversity, functions and processes. © 2017 John Wiley & Sons Ltd.

  5. Structured Additive Quantile Regression for Assessing the Determinants of Childhood Anemia in Rwanda

    Directory of Open Access Journals (Sweden)

    Faustin Habyarimana

    2017-06-01

    Full Text Available Childhood anemia is among the most significant health problems faced by public health departments in developing countries. This study aims at assessing the determinants and possible spatial effects associated with childhood anemia in Rwanda. The 2014/2015 Rwanda Demographic and Health Survey (RDHS data was used. The analysis was done using the structured spatial additive quantile regression model. The findings of this study revealed that the child’s age; the duration of breastfeeding; gender of the child; the nutritional status of the child (whether underweight and/or wasting; whether the child had a fever; had a cough in the two weeks prior to the survey or not; whether the child received vitamin A supplementation in the six weeks before the survey or not; the household wealth index; literacy of the mother; mother’s anemia status; mother’s age at the birth are all significant factors associated with childhood anemia in Rwanda. Furthermore, significant structured spatial location effects on childhood anemia was found.

  6. Near-Atomic Resolution Structure of a Plant Geminivirus Determined by Electron Cryomicroscopy.

    Science.gov (United States)

    Hipp, Katharina; Grimm, Clemens; Jeske, Holger; Böttcher, Bettina

    2017-08-01

    African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure. The tip of the pentameric capsomer is sealed by a plug formed by a turn region harboring the evolutionary conserved residue Y193. Basic amino acid residues inside the capsid form a positively charged pocket next to the five-fold axis of the capsomer suitable for binding DNA. Within this pocket, density most likely corresponding to DNA was resolved. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Aggregate size and structure determination of nanomaterials in physiological media: importance of dynamic evolution

    Energy Technology Data Exchange (ETDEWEB)

    Afrooz, A. R. M. Nabiul [The University of Texas, Civil, Architectural and Environmental Engineering (United States); Hussain, Saber M. [Wright-Patterson AFB, Human Effectiveness Directorate, 711th Human Performance Wing, Air Force Research Laboratory (United States); Saleh, Navid B., E-mail: navid.saleh@utexas.edu [The University of Texas, Civil, Architectural and Environmental Engineering (United States)

    2014-12-15

    Most in vitro nanotoxicological assays are performed after 24 h exposure. However, in determining size and shape effect of nanoparticles in toxicity assays, initial characterization data are generally used to describe experimental outcome. The dynamic size and structure of aggregates are typically ignored in these studies. This brief communication reports dynamic evolution of aggregation characteristics of gold nanoparticles. The study finds that gradual increase in aggregate size of gold nanospheres (AuNS) occurs up to 6 h duration; beyond this time period, the aggregation process deviates from gradual to a more abrupt behavior as large networks are formed. Results of the study also show that aggregated clusters possess unique structural conformation depending on nominal diameter of the nanoparticles. The differences in fractal dimensions of the AuNS samples likely occurred due to geometric differences, causing larger packing propensities for smaller sized particles. Both such observations can have profound influence on dosimetry for in vitro nanotoxicity analyses.Graphical Abstract.

  8. Review of Structural Social Determinants of Health in Early Childhood Development

    Directory of Open Access Journals (Sweden)

    Firoozeh Sajedi

    2015-09-01

    Full Text Available Development is a dynamic and continuous phenomenon  that is under the influence of various factors forming a complicated multidimensional system together. Any impairment in these factors can lead to impaired development in children, which is one of the most common problems in children. Therefore, this study provides a brief overview of these factors and the way they affect early childhood development. A brief review was performed in databases including Google scholar, PUBMED, Proquest, SID, Magiran, Iranmedex, Irandoc with following keywords: child  development, income, occupation, education, employment, boy, girl,  gender, sex, social class, Race and Ethnicity. All of article was reviewed then categorized based on WHO model. Among the papers reviewed, most of the studies were about employment, education, and income and most of them investigated these risk factors in terms of socioeconomic status. Structural factors of social determinants of health had a close relationship with each other, and they  had affected development through each other. Given that, only few studies on structural factors, except for socioeconomic factors, have been conducted and little attention has been paid to the way these factors affect child development, further studies in this area are required to propose a model in order to better understand the interaction between these factors.

  9. Structural determinants of PIP(2) regulation of inward rectifier K(ATP) channels.

    Science.gov (United States)

    Shyng, S L; Cukras, C A; Harwood, J; Nichols, C G

    2000-11-01

    Phosphatidylinositol 4,5-bisphosphate (PIP(2)) activates K(ATP) and other inward rectifier (Kir) channels. To determine residues important for PIP(2) regulation, we have systematically mutated each positive charge in the COOH terminus of Kir6.2 to alanine. The effects of these mutations on channel function were examined using (86)Rb efflux assays on intact cells and inside-out patch-clamp methods. Both methods identify essentially the same basic residues in two narrow regions (176-222 and 301-314) in the COOH terminus that are important for the maintenance of channel function and interaction with PIP(2). Only one residue (R201A) simultaneously affected ATP and PIP(2) sensitivity, which is consistent with the notion that these ligands, while functionally competitive, are unlikely to bind to identical sites. Strikingly, none of 13 basic residues in the terminal portion (residues 315-390) of the COOH terminus affected channel function when neutralized. The data help to define the structural requirements for PIP(2) sensitivity of K(ATP) channels. Moreover, the regions and residues defined in this study parallel those uncovered in recent studies of PIP(2) sensitivity in other inward rectifier channels, indicating a common structural basis for PIP(2) regulation.

  10. Determination of the Magnetic Structure of Complex anti-Perovskite Fluorides by Neutron Diffraction

    Science.gov (United States)

    Felder, Justin; Yeon, Jeongho; Zur Loye, Hans-Conrad

    An unusual family of anti-perovskite fluorides consisting of complex ions as the A, B, and X building units has been synthesized as single crystals. This family of anti-perovskites provides a unique framework to probe the magnetic properties of transition metals. Presented here is the Fe endmember of the family: [Cu(H2O)4]3[FeF6]2. The iron member exhibits complex magnetic behavior at low temperatures, which has been probed by magnetometry and neutron diffraction experiments. Presented here are the results from the anisotropic magnetometry study as well as the magnetic spin structure as determined by neutron diffraction experiments. The materials presented here represent an interesting class of perovskites that are as-yet unexplored. Given the wide range of properties possible in perovskites and related structures, it is reasonable to expect that further exploration of these materials will reveal many interesting attributes; both chemical and physical. United States Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, Award DE-SC0008664.

  11. Fuzzy Reasoning to More Accurately Determine Void Areas on Optical Micrographs of Composite Structures

    Science.gov (United States)

    Dominquez, Jesus A.; Tate, Lanetra C.; Wright, M. Clara; Caraccio, Anne

    2013-01-01

    Accomplishing the best-performing composite matrix (resin) requires that not only the processing method but also the cure cycle generate low-void-content structures. If voids are present, the performance of the composite matrix will be significantly reduced. This is usually noticed by significant reductions in matrix-dominated properties, such as compression and shear strength. Voids in composite materials are areas that are absent of the composite components: matrix and fibers. The characteristics of the voids and their accurate estimation are critical to determine for high performance composite structures. One widely used method of performing void analysis on a composite structure sample is acquiring optical micrographs or Scanning Electron Microscope (SEM) images of lateral sides of the sample and retrieving the void areas within the micrographs/images using an image analysis technique. Segmentation for the retrieval and subsequent computation of void areas within the micrographs/images is challenging as the gray-scaled values of the void areas are close to the gray-scaled values of the matrix leading to the need of manually performing the segmentation based on the histogram of the micrographs/images to retrieve the void areas. The use of an algorithm developed by NASA and based on Fuzzy Reasoning (FR) proved to overcome the difficulty of suitably differentiate void and matrix image areas with similar gray-scaled values leading not only to a more accurate estimation of void areas on composite matrix micrographs but also to a faster void analysis process as the algorithm is fully autonomous.

  12. Latest Developments in Data Analysis and Structure Determination and Refinement: Software for Chemical Crystallography

    International Nuclear Information System (INIS)

    Dix, I.; Adam, M.; Jacob, H. F.; Roter, A.

    2003-01-01

    The introduction of a two-dimensional CCD X-ray detector nearly 10 years ago by Bruker started a revolution in chemical crystallography. Since then, crystallographers can accomplish a complete data collection even of small and poorly scattering crystals in a few hours instead of days. The launch of the kappa geometry by Nonius a few years ago beforehand equally revolutionized the field of single crystal diffractometry. Currently Bruker Nonius has far more than 500 CCD systems installed. The latest development of Bruker Nonius, the X8 APEX, is the powerful combination of both: the APEX CCD detector and the unique Kappa four-circle goniometer. The APEX 4K CCD detector provides the utmost sensitivity, while the Kappa four-circle goniometer offers a very open geometry, granting all the flexibility to align any crystallographic axis. This provides a more efficient data collection for axial photographs to investigate e.g. diffuse scattering or incommensurate structures. Even the crystal-detector distance is computer-controlled for precise and superior data collection. The X8 APEX software suite gives a whole new look to the CCD users interface. It not only has improved data collection abilities, but also guides the chemist or mineralogist through gathering the raw crystal data to producing the final crystal structure. It provides context-dependent menus, which are well-known from business software packages such as Outlook. The tools for unit cell determination, views into reciprocal space, optimisation of the data collection strategy, data integration, scaling and correcting (SADABS) as well as tools for structure solving and refining (SHELXTL package) will be presented. Low temperature work has become an essential tool for challenging samples. The Bruker Nonius Kryo-Flex cryogenic device makes chemical crystallography at low temperatures a routine method in your laboratory. Of course, the Kryo-Flex is fully controlled by the new graphical user interface of the X8 APEX

  13. Determinants of phubbing, which is the sum of many virtual addictions: a structural equation model.

    Science.gov (United States)

    Karadağ, Engin; Tosuntaş, Şule Betül; Erzen, Evren; Duru, Pinar; Bostan, Nalan; Şahin, Berrak Mizrak; Çulha, İlkay; Babadağ, Burcu

    2015-06-01

    Phubbing can be described as an individual looking at his or her mobile phone during a conversation with other individuals, dealing with the mobile phone and escaping from interpersonal communication. In this research, determinants of phubbing behavior were investigated; in addition, the effects of gender, smart phone ownership and social media membership were tested as moderators. To examine the cause-effect relations among the variables of the theoretical model, the research employs a correlational design. Participants were 409 university students who were selected via random sampling. Phubbing was obtained via the scales featuring mobile phone addiction, SMS addiction, internet addiction, social media addiction and game addiction. The obtained data were analyzed using a correlation analysis, multiple linear regression analysis and structural equation model. The results showed that the most important determinants of phubbing behavior are mobile phone, SMS, social media and internet addictions. Although the findings show that the highest correlation value explaining phubbing is a mobile phone addiction, the other correlation values reflect a dependency on the phone. There is an increasing tendency towards mobile phone use, and this tendency prepares the basis of phubbing.

  14. Subsurface Structure Determination of Geotermal Area in Siogung-ogung Samosir District by Using Magnetic Method

    Science.gov (United States)

    Tampubolon, Togi; Hutahaean, Juniar; Siregar, Suryani N. J.

    2018-03-01

    Underwater research often uses geomagnets. It is one of the geophysical methods for measuring magnetic field variations. This research was done to identify how the subsurface rock structure is and determine kinds of rock based on its susceptibility value in Siogung-ogung geothermal area, Pangururan, Samosir District. The tool measurement of total magnetic field called Proton Precission Magnetometer, positioning using Global Position System, and north axis determination using geological compass. Data collection was done randomly with total 51 measuring points obtained. Data analysis started with International geomagnetics Reference Field correction to obtain the total magnetic field anomaly. Then, the data analysis of total magnetic anomaly was done by using surfer program 12. To get a magnetic anomaly cross section used Magdc For Windows program. Magnetic measurement results indicated that the variation of magnetic field strength in each point with the lowest magnetic intensity value of 41785.67 nano tesla. The highest magnetic intensity value is 43140, 33. From the results of qualitative interpretation, the magnetic anomaly value is at -200.92 to 1154.45 whereas the quantitative interpretive results of model show the existence of degradation and andesitic rocks, with the value of susceptibility

  15. Determinants of Phubbing, Which is the Sum of Many Virtual Addictions: A Structural Equation Model

    Science.gov (United States)

    Karadağ, Engi̇n; Tosuntaş, Şule Betül; Erzen, Evren; Duru, Pinar; Bostan, Nalan; Şahi̇n, Berrak Mizrak; Çulha, İLKAY; Babadağ, Burcu

    2015-01-01

    Background and Aims Phubbing can be described as an individual looking at his or her mobile phone during a conversation with other individuals, dealing with the mobile phone and escaping from interpersonal communication. In this research, determinants of phubbing behavior were investigated; in addition, the effects of gender, smart phone ownership and social media membership were tested as moderators. Methods To examine the cause–effect relations among the variables of the theoretical model, the research employs a correlational design. Participants were 409 university students who were selected via random sampling. Phubbing was obtained via the scales featuring mobile phone addiction, SMS addiction, internet addiction, social media addiction and game addiction. The obtained data were analyzed using a correlation analysis, multiple linear regression analysis and structural equation model. Results The results showed that the most important determinants of phubbing behavior are mobile phone, SMS, social media and internet addictions. Discussion Although the findings show that the highest correlation value explaining phubbing is a mobile phone addiction, the other correlation values reflect a dependency on the phone. Conclusions There is an increasing tendency towards mobile phone use, and this tendency prepares the basis of phubbing. PMID:26014669

  16. Testing a continuum structure of self-determined motivation: A meta-analysis.

    Science.gov (United States)

    Howard, Joshua L; Gagné, Marylène; Bureau, Julien S

    2017-12-01

    Self-determination theory proposes a multidimensional representation of motivation comprised of several factors said to fall along a continuum of relative autonomy. The current meta-analysis examined the relationships between these motivation factors in order to demonstrate how reliably they conformed to a predictable continuum-like pattern. Based on data from 486 samples representing over 205,000 participants who completed 1 of 13 validated motivation scales, the results largely supported a continuum-like structure of motivation and indicate that self-determination is central in explaining human motivation. Further examination of heterogeneity indicated that while regulations were predictably ordered across domains and scales, the exact distance between subscales varied across samples in a way that was not explainable by a set of moderators. Results did not support the inclusion of integrated regulation or the 3 subscales of intrinsic motivation (i.e., intrinsic motivation to know, to experience stimulation, and to achieve) due to excessively high interfactor correlations and overlapping confidence intervals. Recommendations for scale refinements and the scoring of motivation are provided. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  17. Factors Affecting the Structural Features of Dairy Farming Organizations in Yalova: Determining the Breeding Activities

    Directory of Open Access Journals (Sweden)

    Galip BAKIR

    2014-03-01

    Full Text Available This research has been performed to determine dairy farms’ breeders’ social conditions, presence of animals, care, milk production, happiness with animal farming, problems and situation of being organized in Yalova. The data that obtained from 324 randomly chosen dairy farms around the city by the means of the survey comprised the material of research. The obtained data has been analyzed in SPSS package program by taking animal numbers, age and educational background of breeders as factors affecting the structural condition of farm. In the analysis of race distribution it was determined that breeders having primary education preferred to use crossbred animals, whereas breeders having secondary, high school and higher education tended to use culture breeds. For determining the heat in animals, breeders who have primary school education take bellowing and mounting of animals into consideration. All breeders at any education level considered the 15-18 months of age as age at fist insemination for heifers. As the age of breeders increased, contrary to education level, the ratio for 15-18 month age criterion decreased. In the farms producing less than 10 kg milk the ratio of farmers having primary school education is 68.9%. This ratio is 8.5% for high school and higher graduates. 61.2% of breeders who have middle school education level obtain 11-20 kg milk yield in their farms. While 48.6% of breeders who have less than 5 animals obtain 10 kg milk yield, as the number of animals rises, this rate declined to 23.1%. In the farms having less than 5 animals the proportion of obtaining 10-21 kg milk yield is 48.4%. As the animals numbers increased this proportion increased up to 63.5%.

  18. A new method to determine large scale structure from the luminosity distance

    International Nuclear Information System (INIS)

    Romano, Antonio Enea; Chiang, Hsu-Wen; Chen, Pisin

    2014-01-01

    The luminosity distance can be used to determine the properties of large scale structure around the observer. To this purpose we develop a new inversion method to map luminosity distance to a Lemaitre–Tolman–Bondi (LTB) metric based on the use of the exact analytical solution for Einstein equations. The main advantages of this approach are an improved numerical accuracy and stability, an exact analytical setting of the initial conditions for the differential equations which need to be solved and the validity for any sign of the functions determining the LTB geometry. Given the fully analytical form of the differential equations, this method also simplifies the calculation of the red-shift expansion around the apparent horizon point where the numerical solution becomes unstable. We test the method by inverting the supernovae Ia luminosity distance function corresponding to the best fit ΛCDM model. We find that only a limited range of initial conditions is compatible with observations, or a transition from red to blue-shift can occur at relatively low red-shift. Despite LTB solutions without a cosmological constant have been shown not to be compatible with all different set of available observational data, those studies normally fit data assuming a special functional ansatz for the inhomogeneity profile, which often depend only on few parameters. Inversion methods on the contrary are able to fully explore the freedom in fixing the functions which determine a LTB solution. Another important possible application is not about LTB solutions as cosmological models, but rather as tools to study the effects on the observations made by a generic observer located in an inhomogeneous region of the Universe where a fully non perturbative treatment involving exact solutions of Einstein equations is required. (paper)

  19. Isolation, structural determination, synthesis and quantitative determination of impurities in Intron-A, leached from a silicone tubing.

    Science.gov (United States)

    Chan, Tze-Ming; Pramanik, Birendra; Aslanian, Robert; Gullo, Vincent; Patel, Mahesh; Cronin, Bart; Boyce, Chris; McCormick, Kevin; Berlin, Mike; Zhu, Xiaohong; Buevich, Alexei; Heimark, Larry; Bartner, Peter; Chen, Guodong; Pu, Haiyan; Hegde, Vinod

    2009-02-20

    Investigation of unexpected levels of impurities in Intron product has revealed the presence of low levels of impurities leached from the silicone tubing (Rehau RAU-SIK) on the Bosch filling line. In order to investigate the effect of these compounds (1a, 1b and 2) on humans, they were isolated identified and synthesized. They were extracted from the tubing by stirring in Intron placebo at room temperature for 72 h and were enriched on a reverse phase CHP-20P column, eluting with gradient aqueous ACN and were separated by HPLC. Structural elucidation of 1a, 1b and 2 by MS and NMR studies demonstrated them to be halogenated biphenyl carboxylic acids. The structures were confirmed by independent synthesis. Levels of extractable impurities in first filled vials of actual production are estimated to be in the range of 0.01-0.55 microg/vial for each leached impurity. Potential toxicity of these extractables does not represent a risk for patients under the conditions of clinical use.

  20. Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Sundlov, Jesse A.; Gulick, Andrew M., E-mail: gulick@hwi.buffalo.edu [University at Buffalo, 700 Ellicott Street, Buffalo, NY 14203 (United States)

    2013-08-01

    The structure of the functional interaction of NRPS adenylation and carrier protein domains, trapped with a mechanism-based inhibitor, is described. Crystals exhibit translational non-crystallographic symmetry, which challenged structure determination and refinement. The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic activity or that play a role in iron acquisition. Understanding the structural mechanisms that govern the domain interactions has been a long-standing goal. During NRPS synthesis, amino-acid substrates are loaded onto integrated carrier protein domains through the activity of NRPS adenylation domains. The structures of two adenylation domain–carrier protein domain complexes have recently been determined in an effort that required the use of a mechanism-based inhibitor to trap the domain interaction. Here, the continued analysis of these proteins is presented, including a higher resolution structure of an engineered di-domain protein containing the EntE adenylation domain fused with the carrier protein domain of its partner EntB. The protein crystallized in a novel space group in which molecular replacement and refinement were challenged by noncrystallographic pseudo-translational symmetry. The structure determination and how the molecular packing impacted the diffraction intensities are reported. Importantly, the structure illustrates that in this new crystal form the functional interface between the adenylation domain and the carrier protein domain remains the same as that observed previously. At a resolution that allows inclusion of water molecules, additional interactions are observed between the two protein domains and between the protein and its ligands. In particular, a highly solvated region that surrounds the carrier protein cofactor is described.

  1. Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry

    International Nuclear Information System (INIS)

    Sundlov, Jesse A.; Gulick, Andrew M.

    2013-01-01

    The structure of the functional interaction of NRPS adenylation and carrier protein domains, trapped with a mechanism-based inhibitor, is described. Crystals exhibit translational non-crystallographic symmetry, which challenged structure determination and refinement. The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic activity or that play a role in iron acquisition. Understanding the structural mechanisms that govern the domain interactions has been a long-standing goal. During NRPS synthesis, amino-acid substrates are loaded onto integrated carrier protein domains through the activity of NRPS adenylation domains. The structures of two adenylation domain–carrier protein domain complexes have recently been determined in an effort that required the use of a mechanism-based inhibitor to trap the domain interaction. Here, the continued analysis of these proteins is presented, including a higher resolution structure of an engineered di-domain protein containing the EntE adenylation domain fused with the carrier protein domain of its partner EntB. The protein crystallized in a novel space group in which molecular replacement and refinement were challenged by noncrystallographic pseudo-translational symmetry. The structure determination and how the molecular packing impacted the diffraction intensities are reported. Importantly, the structure illustrates that in this new crystal form the functional interface between the adenylation domain and the carrier protein domain remains the same as that observed previously. At a resolution that allows inclusion of water molecules, additional interactions are observed between the two protein domains and between the protein and its ligands. In particular, a highly solvated region that surrounds the carrier protein cofactor is described

  2. Methodology of determining soil structure in important groundwater areas: case studies in Kauvonkangas, Finnish Lapland

    Science.gov (United States)

    Kupila, Juho

    2016-04-01

    Finland is fully self-sufficient in clean groundwater and even has a capacity of exportation. There are approx. 6000 groundwater areas with a total yield of 5.4 million m3/day. Currently only 10% of this groundwater resource is in use. For the efficient and safe exploitation of these areas in the future, detailed modeling of soil structure is an important method in groundwater surveys. 3D -models improve the general knowledge of linkage between land use planning and groundwater protection. Results can be used as a base information in water supply service development and when performing the measures needed in case of environmental accidents. Also, when creating the groundwater flow models the collected information is utilized and is usually the main data source. Geological Survey of Finland has carried out soil structure studies in co-operation with authorities, municipalities and the local water suppliers. The main objectives of these projects are to determine the geological structure of groundwater area for estimating the validity of the present exclusion area, the quantity of ground water volume and recharge capability and possible risks to the groundwater. Research areas are usually under an active water supply service. Kauvonkangas groundwater area is located in the municipality of Tervola, in Southern part of Finnish Lapland. Extent of the area is 7.9 km2 and it is an important water source for the local and nearby population centers. There are two active water supply companies in the area. Field studies in the project will include general geological and hydrological mapping, soil drilling with observation pipe installation, test pumping and water sampling. Geophysical measures will play a key-role, including ground penetrating radar (GPR) and gravimetric measurements. Studies will be carried out in spring and summer 2016. The main results will be the models of the bedrock and groundwater level and main characteristics of the soil layers in the area. Results

  3. Creation and structure determination of an artificial protein with three complete sequence repeats

    Energy Technology Data Exchange (ETDEWEB)

    Adachi, Motoyasu, E-mail: adachi.motoyasu@jaea.go.jp; Shimizu, Rumi; Kuroki, Ryota [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Blaber, Michael [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Florida State University, Tallahassee, FL 32306-4300 (United States)

    2013-11-01

    An artificial protein with three complete sequence repeats was created and the structure was determined by X-ray crystallography. The structure showed threefold symmetry even though there is an amino- and carboxy-terminal. The artificial protein with threefold symmetry may be useful as a scaffold to capture small materials with C3 symmetry. Symfoil-4P is a de novo protein exhibiting the threefold symmetrical β-trefoil fold designed based on the human acidic fibroblast growth factor. First three asparagine–glycine sequences of Symfoil-4P are replaced with glutamine–glycine (Symfoil-QG) or serine–glycine (Symfoil-SG) sequences protecting from deamidation, and His-Symfoil-II was prepared by introducing a protease digestion site into Symfoil-QG so that Symfoil-II has three complete repeats after removal of the N-terminal histidine tag. The Symfoil-QG and SG and His-Symfoil-II proteins were expressed in Eschericha coli as soluble protein, and purified by nickel affinity chromatography. Symfoil-II was further purified by anion-exchange chromatography after removing the HisTag by proteolysis. Both Symfoil-QG and Symfoil-II were crystallized in 0.1 M Tris-HCl buffer (pH 7.0) containing 1.8 M ammonium sulfate as precipitant at 293 K; several crystal forms were observed for Symfoil-QG and II. The maximum diffraction of Symfoil-QG and II crystals were 1.5 and 1.1 Å resolution, respectively. The Symfoil-II without histidine tag diffracted better than Symfoil-QG with N-terminal histidine tag. Although the crystal packing of Symfoil-II is slightly different from Symfoil-QG and other crystals of Symfoil derivatives having the N-terminal histidine tag, the refined crystal structure of Symfoil-II showed pseudo-threefold symmetry as expected from other Symfoils. Since the removal of the unstructured N-terminal histidine tag did not affect the threefold structure of Symfoil, the improvement of diffraction quality of Symfoil-II may be caused by molecular characteristics of

  4. State of the art in the determination of the fine structure constant: test of Quantum Electrodynamics and determination of h/mu

    International Nuclear Information System (INIS)

    Bouchendira, Rym; Clade, Pierre; Nez, Francois; Biraben, Francois; Guellati-Khelifa, Saida

    2013-01-01

    The fine structure constant α has a particular status in physics. Its precise determination is required to test the quantum electrodynamics (QED) theory. The constant α is also a keystone for the determination of other fundamental physical constants, especially the ones involved in the framework of the future International System of units. This paper presents Paris experiment, where the fine structure constant is determined by measuring the recoil velocity of a rubidium atom when it absorbs a photon. The impact of the recent improvement of QED calculations of the electron moment anomaly and the recent measurement of the cesium atom recoil at Berkeley will be discussed. The opportunity to provide a precise value of the ratio h/m u between the Planck constant and the atomic mass constant will be investigated. (copyright 2013 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  5. How taxonomic diversity, community structure, and sample size determine the reliability of higher taxon surrogates.

    Science.gov (United States)

    Neeson, Thomas M; Van Rijn, Itai; Mandelik, Yael

    2013-07-01

    Ecologists and paleontologists often rely on higher taxon surrogates instead of complete inventories of biological diversity. Despite their intrinsic appeal, the performance of these surrogates has been markedly inconsistent across empirical studies, to the extent that there is no consensus on appropriate taxonomic resolution (i.e., whether genus- or family-level categories are more appropriate) or their overall usefulness. A framework linking the reliability of higher taxon surrogates to biogeographic setting would allow for the interpretation of previously published work and provide some needed guidance regarding the actual application of these surrogates in biodiversity assessments, conservation planning, and the interpretation of the fossil record. We developed a mathematical model to show how taxonomic diversity, community structure, and sampling effort together affect three measures of higher taxon performance: the correlation between species and higher taxon richness, the relative shapes and asymptotes of species and higher taxon accumulation curves, and the efficiency of higher taxa in a complementarity-based reserve-selection algorithm. In our model, higher taxon surrogates performed well in communities in which a few common species were most abundant, and less well in communities with many equally abundant species. Furthermore, higher taxon surrogates performed well when there was a small mean and variance in the number of species per higher taxa. We also show that empirically measured species-higher-taxon correlations can be partly spurious (i.e., a mathematical artifact), except when the species accumulation curve has reached an asymptote. This particular result is of considerable practical interest given the widespread use of rapid survey methods in biodiversity assessment and the application of higher taxon methods to taxa in which species accumulation curves rarely reach an asymptote, e.g., insects.

  6. Protein fiber linear dichroism for structure determination and kinetics in a low-volume, low-wavelength couette flow cell

    OpenAIRE

    Dafforn, Tim; Rajendra, Jacindra; Halsall, David J.; Serpell, Louise C.; Rodger, Alison

    2004-01-01

    High-resolution structure determination of soluble globular proteins relies heavily on x-ray crystallography techniques. Such an approach is often ineffective for investigations into the structure of fibrous proteins as these proteins generally do not crystallize. Thus investigations into fibrous protein structure have relied on less direct methods such as x-ray fiber diffraction and circular dichroism. Ultraviolet linear dichroism has the potential to provide additional information on the st...

  7. Application of the crystalline structure determination method by X-ray diffraction to natural products and organic compounds

    International Nuclear Information System (INIS)

    Vencato, I.

    1984-01-01

    The structures of two natural compounds, a synthetic phosphate and a copper complexe were determined and the structure of another copper complex was refined. The reflection intensities were measured with a CAD-4 automatic diffractometer. The structures were solved by direct methods using either MULTAN-80 or the Patterson function and were refined by the least squares method, with a full matrix. (E.G.) [pt

  8. Determination of contact maps in proteins: A combination of structural and chemical approaches

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl [Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw (Poland); Gómez-Sicilia, Àngel [Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), Av. Doctor Arce, 37, 28002 Madrid (Spain); Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), C/Faraday 9, 28049 Cantoblanco (Madrid) (Spain)

    2015-12-28

    Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones — a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.

  9. [Geopolitical development inequalities in gender in Spain 1980-2005: a structural determinant of health].

    Science.gov (United States)

    Carrasco-Portiño, Mercedes; Ruiz Cantero, María Teresa; Fernández Sáez, José; Clemente Gómez, Vicente; Roca Pérez, Victoria

    2010-01-01

    Gender is a structural health determinant. This study analyses the changes in gender development inequalities in Spain and its regions (1980-2005). Ecological study of the evolution of Gender Development Index and its components (Education, Income, Life Expectancy at Birth) by sex in Spain and its regions (1980-2005). Information Source: Gender Development Index (1980-2005) from the Human Capital Report, plus construction ad hoc of the Gender Development Index 2005 following the same methodology of Human Capital Report. National Statistics Institute, Active Population Survey, Municipal Register, Ministry of Education, Universities Council, EUROSTAT, and Wage Structure Survey. Spanish Gender Development Index 2005:0,903 and 1980:0,810. The range between regions under Spanish Gender Development Index was 3 times higher in 1980 (DifferenceC.Valenciana-Extremadura:0,068) than in 2005 (DifferenceAsturias-Extremadura:0,023). The regions above the Spanish Gender Development Index did not vary much. The three components (Education, Income, Life Expectancy at Birth) of the Gender Development Index improved from 1980 to 2005. The Spanish Education Index of men was higher than this value in women until 1985; later this index becomes higher in women than in men. The Spanish Income Index of women in 2005 (0,814) is inferior to that of men 25 years before (1980:0,867). Despite the improvement of the gender development happened in Spain between 1980 and 2005, the inter-regional inequalities between north-south persist. In 2005, women have more education level than men. However, the Spanish income media in women in 2005 are inferior to the media of the men in 1980.

  10. Structure determination and functional analysis of a chromate reductase from Gluconacetobacter hansenii.

    Directory of Open Access Journals (Sweden)

    Hongjun Jin

    Full Text Available Environmental protection through biological mechanisms that aid in the reductive immobilization of toxic metals (e.g., chromate and uranyl has been identified to involve specific NADH-dependent flavoproteins that promote cell viability. To understand the enzyme mechanisms responsible for metal reduction, the enzyme kinetics of a putative chromate reductase from Gluconacetobacter hansenii (Gh-ChrR was measured and the crystal structure of the protein determined at 2.25 Å resolution. Gh-ChrR catalyzes the NADH-dependent reduction of chromate, ferricyanide, and uranyl anions under aerobic conditions. Kinetic measurements indicate that NADH acts as a substrate inhibitor; catalysis requires chromate binding prior to NADH association. The crystal structure of Gh-ChrR shows the protein is a homotetramer with one bound flavin mononucleotide (FMN per subunit. A bound anion is visualized proximal to the FMN at the interface between adjacent subunits within a cationic pocket, which is positioned at an optimal distance for hydride transfer. Site-directed substitutions of residues proposed to involve in both NADH and metal anion binding (N85A or R101A result in 90-95% reductions in enzyme efficiencies for NADH-dependent chromate reduction. In comparison site-directed substitution of a residue (S118A participating in the coordination of FMN in the active site results in only modest (50% reductions in catalytic efficiencies, consistent with the presence of a multitude of side chains that position the FMN in the active site. The proposed proximity relationships between metal anion binding site and enzyme cofactors is discussed in terms of rational design principles for the use of enzymes in chromate and uranyl bioremediation.

  11. Determinants of Functional and Structural Properties of Large Arteries in Healthy Individuals

    Energy Technology Data Exchange (ETDEWEB)

    Tolezani, Elaine Cristina; Costa-Hong, Valéria, E-mail: hong.valeria@gmail.com; Correia, Gustavo; Mansur, Alfredo José; Drager, Luciano Ferreira; Bortolotto, Luiz Aparecido [Instituto do Coração, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP (Brazil)

    2014-11-15

    Changes in the properties of large arteries correlate with higher cardiovascular risk. Recent guidelines have included the assessment of those properties to detect subclinical disease. Establishing reference values for the assessment methods as well as determinants of the arterial parameters and their correlations in healthy individuals is important to stratify patients. To assess, in healthy adults, the distribution of the values of pulse wave velocity, diameter, intima-media thickness and relative distensibility of the carotid artery, in addition to assessing the demographic and clinical determinants of those parameters and their correlations. This study evaluated 210 individuals (54% women; mean age, 44 ± 13 years) with no evidence of cardiovascular disease. The carotid-femoral pulse wave velocity was measured with a Complior{sup ®} device. The functional and structural properties of the carotid artery were assessed by using radiofrequency ultrasound. The means of the following parameters were: pulse wave velocity, 8.7 ± 1.5 m/s; diameter, 6,707.9 ± 861.6 μm; intima-media thickness, 601 ± 131 μm; relative distensibility, 5.3 ± 2.1%. No significant difference related to sex or ethnicity was observed. On multiple linear logistic regression, the factors independently related to the vascular parameters were: pulse wave velocity, to age (p < 0.01) and triglycerides (p = 0.02); intima-media thickness, to age (p < 0.01); diameter, to creatinine (p = 0.03) and age (p = 0.02); relative distensibility, to age (p < 0.01) and systolic and diastolic blood pressures (p = 0.02 and p = 0.01, respectively). Pulse wave velocity showed a positive correlation with intima media thickness (p < 0.01) and with relative distensibility (p < 0.01), while diameter showed a positive correlation with distensibility (p = 0.03). In healthy individuals, age was the major factor related to aortic stiffness, while age and diastolic blood pressure related to the carotid functional measure

  12. Determinants of Functional and Structural Properties of Large Arteries in Healthy Individuals

    International Nuclear Information System (INIS)

    Tolezani, Elaine Cristina; Costa-Hong, Valéria; Correia, Gustavo; Mansur, Alfredo José; Drager, Luciano Ferreira; Bortolotto, Luiz Aparecido

    2014-01-01

    Changes in the properties of large arteries correlate with higher cardiovascular risk. Recent guidelines have included the assessment of those properties to detect subclinical disease. Establishing reference values for the assessment methods as well as determinants of the arterial parameters and their correlations in healthy individuals is important to stratify patients. To assess, in healthy adults, the distribution of the values of pulse wave velocity, diameter, intima-media thickness and relative distensibility of the carotid artery, in addition to assessing the demographic and clinical determinants of those parameters and their correlations. This study evaluated 210 individuals (54% women; mean age, 44 ± 13 years) with no evidence of cardiovascular disease. The carotid-femoral pulse wave velocity was measured with a Complior ® device. The functional and structural properties of the carotid artery were assessed by using radiofrequency ultrasound. The means of the following parameters were: pulse wave velocity, 8.7 ± 1.5 m/s; diameter, 6,707.9 ± 861.6 μm; intima-media thickness, 601 ± 131 μm; relative distensibility, 5.3 ± 2.1%. No significant difference related to sex or ethnicity was observed. On multiple linear logistic regression, the factors independently related to the vascular parameters were: pulse wave velocity, to age (p < 0.01) and triglycerides (p = 0.02); intima-media thickness, to age (p < 0.01); diameter, to creatinine (p = 0.03) and age (p = 0.02); relative distensibility, to age (p < 0.01) and systolic and diastolic blood pressures (p = 0.02 and p = 0.01, respectively). Pulse wave velocity showed a positive correlation with intima media thickness (p < 0.01) and with relative distensibility (p < 0.01), while diameter showed a positive correlation with distensibility (p = 0.03). In healthy individuals, age was the major factor related to aortic stiffness, while age and diastolic blood pressure related to the carotid functional measure. The

  13. Determinants of Functional and Structural Properties of Large Arteries in Healthy Individuals

    Directory of Open Access Journals (Sweden)

    Elaine Cristina Tolezani

    2014-11-01

    Full Text Available Background: Changes in the properties of large arteries correlate with higher cardiovascular risk. Recent guidelines have included the assessment of those properties to detect subclinical disease. Establishing reference values for the assessment methods as well as determinants of the arterial parameters and their correlations in healthy individuals is important to stratify patients. Objective: To assess, in healthy adults, the distribution of the values of pulse wave velocity, diameter, intima-media thickness and relative distensibility of the carotid artery, in addition to assessing the demographic and clinical determinants of those parameters and their correlations. Methods: This study evaluated 210 individuals (54% women; mean age, 44 ± 13 years with no evidence of cardiovascular disease. The carotid-femoral pulse wave velocity was measured with a Complior® device. The functional and structural properties of the carotid artery were assessed by using radiofrequency ultrasound. Results: The means of the following parameters were: pulse wave velocity, 8.7 ± 1.5 m/s; diameter, 6,707.9 ± 861.6 μm; intima-media thickness, 601 ± 131 μm; relative distensibility, 5.3 ± 2.1%. No significant difference related to sex or ethnicity was observed. On multiple linear logistic regression, the factors independently related to the vascular parameters were: pulse wave velocity, to age (p < 0.01 and triglycerides (p = 0.02; intima-media thickness, to age (p < 0.01; diameter, to creatinine (p = 0.03 and age (p = 0.02; relative distensibility, to age (p < 0.01 and systolic and diastolic blood pressures (p = 0.02 and p = 0.01, respectively. Pulse wave velocity showed a positive correlation with intima media thickness (p < 0.01 and with relative distensibility (p < 0.01, while diameter showed a positive correlation with distensibility (p = 0.03. Conclusion: In healthy individuals, age was the major factor related to aortic stiffness, while age and diastolic

  14. Optimum conditions for the determination of ionization potentials, appearance potentials and fine structure in ionization efficiency curves using edd technique

    International Nuclear Information System (INIS)

    Selim, Ezzat T.; El-Kholy, S.B.; Zahran, Nagwa F.

    1978-01-01

    The optimum conditions for determining ionization potentials as well as fine structure in electron impact ionization efficiency curves are studied using energy distribution difference technique. Applying these conditions to Ar + , Kr + , CO + 2 and N + from N 2 , very good agreement is obtained when compared with results determined by other techniques including UV spectroscopy. The merits and limitation of the technique are also discussed

  15. Structure of antigenetic determinants in the amino-terminal region of bovine fibrinogen Aα chain

    International Nuclear Information System (INIS)

    Tanswell, P.; Reiter, H.; Timpl, R.

    1978-01-01

    A radioimmunoassay was developed for peptide F-CB1α from the amino of bovine fibrinogen Aα chain, isolated after reduction and carboxymethylation of the multichain disulfide-linked cyanogen bromide peptide F-CB1. Seven out of twelve different rabbit antisera produced against fibrinogen, peptide F-CB1 or Aα chain showed distinct binding to 125 I-labelled F-CB1α. Thrombin cleavage of F-CB1α yielded two fragments: fibrinopeptide A (residues 1-19) and the carboxy-terminal fragment Th2 (residues 20-54). Antisera could be classified into three groups according to whether they recognized antigenic determinants on fibrinopeptide A, on peptide Th2 or as they showed diminished reactions with both fragments. Only little or no cross-reaction was observed with the amino-terminal cyanogen bromide peptides of Bβ and γ chain. Proteolytic fragments of fibrinopeptide A were isolated and tested for inhibitory activity with two antisera. One antiserum contained anitbodies binding selectively to the amino-terminal sequence (residues 4-11) and did not cross-react with human fibrinopeptide A. Another antiserum showed a specific binding restricted to the carboxy-terminal sequence (residues 11-18) and cross-reacted completely with human fibrinopeptide A. These results correlate well with the primary structures of the two fibrinopeptides. The antigenic activity of the peptide fragment Th2 was localized on a 15-residue tryptic peptide derived from the central portion of the sequence. These and further data indicate that at least six different antigenic determinants are present in peptide F-CB1α. (orig.) 891 AJ [de

  16. Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy

    International Nuclear Information System (INIS)

    Bonwell, E.; Fisher, T.; Fritz, A.; Wetzel, D.

    2008-01-01

    substantial variance in this feature and its determination allows the prediction of relative quality for breadmaking to be taken into consideration for subsequent steps in the wheat breeding process. Data treatments include deconvolution, modeling of the individual resulting bands that contribute to the amide I band to enable measurement of the relative amounts of both forms. Results with specimens representing multiple crop years of hard winter wheat breeding are reported. It is evident that a range is available for the breeder to choose from, that allows including this protein molecular structural attribute in the selection process.

  17. Determining the structural relaxation times deep in the glassy state of the pharmaceutical Telmisartan

    Energy Technology Data Exchange (ETDEWEB)

    Adrjanowicz, K; Paluch, M [Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland); Ngai, K L [Naval Research Laboratory, Washington, DC 20375-5320 (United States)

    2010-03-31

    By using the dielectric relaxation method proposed recently by Casalini and Roland (2009 Phys. Rev. Lett. 102 035701), we were able to determine the structural alpha-relaxation times deep in the glassy state of the pharmaceutical, Telmisartan. Normally, deep in the glassy state tau{sub a}lpha is so long that it cannot be measured but tau{sub b}eta, which is usually much shorter, can be directly determined. The method basically takes advantage of the connection between the alpha-relaxation and the secondary beta-relaxation of the Johari-Goldstein kind, including a relation between their relaxation times tau{sub a}lpha and tau{sub b}eta, respectively. Thus, tau{sub a}lpha of Telmisartan were determined by monitoring the change of the dielectric beta-loss, epsilon'', with physical aging time at temperatures well below the vitrification temperature. The values of tau{sub a}lpha were compared with those expected by the coupling model (CM). Unequivocal comparison cannot be made in the case of Telmisartan because its beta-loss peak is extremely broad, and the CM predicts only an order of magnitude agreement between the primitive relaxation frequency and the beta-peak frequency. We also made an attempt to analyze all isothermal and aging susceptibility data after transformation into the electric modulus representation. The tau{sub a}lpha found in the glass state by using the method of Casalini and Roland in the modulus representation are similar to those obtained in the susceptibility representation. However, it is remarkable that the stretching parameter beta{sub KWWM} = 0.51 in the electric modulus representation gives more precise fits to the aging data than in the susceptibility representation with beta{sub KWW} = 0.61. Our results suggest that the electric modulus representation may be useful as an alternative to analyze aging data, especially in the case of highly polar glassformers having a large ratio of low frequency and high frequency dielectric

  18. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    Directory of Open Access Journals (Sweden)

    Lees Jonathan G

    2008-01-01

    Full Text Available Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  19. Determination of ICRF antenna fields in the vicinity of a 3-D Faraday shield structure

    Energy Technology Data Exchange (ETDEWEB)

    Ryan, P M; Rothe, K E; Whealton, J H; Shepard, T D [Oak Ridge National Lab., TN (USA)

    1990-04-01

    A three-dimensional (3-D) magnetostatic analysis developed at Oak Ridge National Laboratory has been used to calculate the electromagnetic transmission properties of representative Faraday shield designs. The analysis uses the long-wavelength approximation to obtain a 3-D Laplace solution for the magnetic scalar potential over one poloidal period of the Faraday shield, from which the complete magnetic field distribution may be obtained. Once the magnetic field distributions in the presence and absence of a Faraday shield are known, the flux transmission coefficient can be found, as well as any change in the distributed inductance of the current strap. The distrbuted capacitance of the strap can be found from an analogous 3-D electrostatic calculation, enabling the phase velocity of the slow-wave structure to be determined. Power dissipation in the shield may be estimated by equating the surface current on a perfect conductor with the surface magnetic field and using this surface current in conjunction with the finite conductivities of the shield materials to obtain the power distribution due to eddy current heating. (orig.).

  20. A procedure for the radioimmunochemical determination of antigens with different structures

    International Nuclear Information System (INIS)

    Galoci, J.; Machan, V.

    1990-01-01

    To a solution of a specific antibody, its antigen labelled with iodine 125, and of the unknown sample is added animal (e.g., goat) antibody against rabbit immunoglobulin immobilized on modified microcrystalline cellulose; always the same quantities are applied always for the same time. After incubation for 1 hr at 20 degC, the immunochemical complex formed is centrifuged and its radioactivity is measured, and the amount of the antigen in sample is determined by comparison with standards. The procedure is applicable to antigens with any structure. Assets of the separating system include a very good stability in solution, a low value of nonspecific bonding and a low sedimentation velocity of the particles used. The procedure is well suited to the quantitation of antigens present in very low concentrations in blood serum, urine, milk, and extracts from tissues or animal feed. In a modification of the procedure, the animal antibody against rabbit immunoglobulin is immobilized on the surface of modified cellulose particles 5 to 15 μm in size exhibiting a very low sedimentation velocity, activated with 1,1-carbonyldiimidazole. (M.D.)