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Sample records for previously determined structures

  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. Long- term effects of previous experience determine nutrient discrimination abilities in birds

    Directory of Open Access Journals (Sweden)

    Spitzer Kathrin

    2008-02-01

    Full Text Available Abstract Background Foraging behaviour is an essential ecological process linking different trophic levels. A central assumption of foraging theory is that food selection maximises the fitness of the consumer. It remains unknown, however, whether animals use innate or learned behaviour to discriminate food rewards. While many studies demonstrated that previous experience is a strong determinant of complex food choices such as diet mixing, the response to simple nutritional stimuli, such as sugar concentrations, is often believed to be innate. Results Here we show that previous experience determines the ability to track changes in sugar composition in same-aged individuals of a short-lived migratory songbird, the garden warbler (Sylvia borin. Although birds received identical foods for seven months prior to the experiment, wild-caught birds achieved higher sugar intake rates than hand-raised birds when confronted with alternative, differently coloured, novel food types. Hand-raised and wild birds did not differ in their initial colour selection or overall food intake, but wild birds were quicker to adjust food choice to varying sugar intake. Conclusion Over a period of at least seven months, broader previous experience translates into a higher plasticity of food choice leading to higher nutrient intake. Our results thus highlight the need to address previous long-term experience in foraging experiments. Furthermore, they show that hand-raised animals are often poor surrogates for testing the foraging behaviour of wild animals.

  5. 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

  6. Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays

    Directory of Open Access Journals (Sweden)

    Aramburu Ander

    2010-11-01

    Full Text Available Abstract Background Exon arrays provide a way to measure the expression of different isoforms of genes in an organism. Most of the procedures to deal with these arrays are focused on gene expression or on exon expression. Although the only biological analytes that can be properly assigned a concentration are transcripts, there are very few algorithms that focus on them. The reason is that previously developed summarization methods do not work well if applied to transcripts. In addition, gene structure prediction, i.e., the correspondence between probes and novel isoforms, is a field which is still unexplored. Results We have modified and adapted a previous algorithm to take advantage of the special characteristics of the Affymetrix exon arrays. The structure and concentration of transcripts -some of them possibly unknown- in microarray experiments were predicted using this algorithm. Simulations showed that the suggested modifications improved both specificity (SP and sensitivity (ST of the predictions. The algorithm was also applied to different real datasets showing its effectiveness and the concordance with PCR validated results. Conclusions The proposed algorithm shows a substantial improvement in the performance over the previous version. This improvement is mainly due to the exploitation of the redundancy of the Affymetrix exon arrays. An R-Package of SPACE with the updated algorithms have been developed and is freely available.

  7. 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

  8. Determinants of Capital Structure of UK Companies

    OpenAIRE

    Huang, Xu

    2013-01-01

    This paper aims to examine the determinants of capital structure of the UK companies and to provide some up-to-date empirical evidence for previous literatures. The sample of this study involves all non-financial companies listed on the FTSE350 Index during the time period from 2003 to 2012. The analysis of variance and panel data regression models are performed to test what factors may affect the UK companies’ financing decisions. In each model, three different measures of financial leverage...

  9. Analysis on Population Level Reveals Trappability of Wild Rodents Is Determined by Previous Trap Occupant.

    Directory of Open Access Journals (Sweden)

    Marc J Brouard

    Full Text Available Live trapping is central to the study of small mammals. Thus, any bias needs to be understood and accounted for in subsequent analyses to ensure accurate population estimates. One rarely considered bias is the behavioural response of individuals to the trap, in particular the olfactory cues left behind by previous occupants (PO. We used a data set of 8,115 trap nights spanning 17 separate trapping sessions between August 2002 and November 2013 in Wytham Woods, Oxfordshire, UK to examine if the decision to enter a trap was affected by the PO, if this was detectable in traditional Capture-Mark-Recapture trapping data (i.e., individuals not uniquely marked, and if it was possible for this effect to bias the population estimates obtained. Data were collected on Apodemus sylvaticus, Myodes glareolus, and Microtus agrestis. Three Generalised Linear Models revealed a significant tendency for the three species to enter traps with same-species PO. With, for example, A. sylvaticus 9.1 times more likely to enter a same species PO trap compared to one that contained a M. agrestis in the grassland during the nocturnal period. Simulation highlighted that, when all other factors are equal, the species with the highest PO effect will have the highest capture rate and therefore return more accurate population estimates. Despite the large dataset, certain species-, sex-, and/ or age-combinations were under-represented, and thus no effects of any additional individual-specific characteristics could be evaluated. Uniquely marking individuals would allow for the PO effect to be disentangled from other biases such as trap-shyness and spatial heterogeneity, but may not be possible in all cases and will depend on the aims of the study and the resources available.

  10. 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)

  11. Counting the Homeless: A Previously Incalculable Tuberculosis Risk and Its Social Determinants

    Science.gov (United States)

    Teeter, Larry D.; Musser, James M.; Graviss, Edward A.

    2013-01-01

    Tuberculosis (TB) surveillance among the homeless is not supported by the political will necessary for TB elimination. We merged the first stakeholder-accepted enumeration of homeless persons with existing surveillance data to assess TB risk among the homeless in Houston, Texas. The average incidence per 100 000 was 411 among homeless and 9.5 among housed persons. The homeless were more likely than the housed to be US-born, clustered, and in a larger-sized cluster. Multivariate analysis revealed that TB rates among the homeless were driven not by comorbidities but by social determinants. Homeless patients were hospitalized more days than the housed and required more follow-up time. Reporting of TB rates for populations with known health disparities could help reframe TB prevention and better target limited funds. PMID:23488504

  12. 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.

  13. Structural determinants of arrestin functions.

    Science.gov (United States)

    Gurevich, Vsevolod V; Gurevich, Eugenia V

    2013-01-01

    Arrestins are a small protein family with only four members in mammals. Arrestins demonstrate an amazing versatility, interacting with hundreds of different G protein-coupled receptor (GPCR) subtypes, numerous nonreceptor signaling proteins, and components of the internalization machinery, as well as cytoskeletal elements, including regular microtubules and centrosomes. Here, we focus on the structural determinants that mediate various arrestin functions. The receptor-binding elements in arrestins were mapped fairly comprehensively, which set the stage for the construction of mutants targeting particular GPCRs. The elements engaged by other binding partners are only now being elucidated and in most cases we have more questions than answers. Interestingly, even very limited and imprecise identification of structural requirements for the interaction with very few other proteins has enabled the development of signaling-biased arrestin mutants. More comprehensive understanding of the structural underpinning of different arrestin functions will pave the way for the construction of arrestins that can link the receptor we want to the signaling pathway of our choosing. Copyright © 2013 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Narihiro, Takashi; Tamaki, Hideyuki; Akiba, Aya; Takasaki, Kazuto; Nakano, Koichiro; Kamagata, Yoichi; Hanada, Satoshi; Maji, Taizo

    2014-01-01

    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.

  15. 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.

  16. 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

  17. 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

  18. Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland.

    Science.gov (United States)

    Pedreschi, Debbi; Kelly-Quinn, Mary; Caffrey, Joe; O'Grady, Martin; Mariani, Stefano; Phillimore, Albert

    2014-03-01

    We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Ireland, Britain and continental Europe. A total of 752 pike ( Esox lucius ) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two 'waves', the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies for this species.

  19. Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland

    Science.gov (United States)

    Pedreschi, Debbi; Kelly-Quinn, Mary; Caffrey, Joe; O’Grady, Martin; Mariani, Stefano; Phillimore, Albert

    2014-01-01

    Aim We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Location Ireland, Britain and continental Europe. Methods A total of 752 pike (Esox lucius) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Results Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Main conclusions Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two ‘waves’, the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies

  20. 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.

  1. 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

  2. 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...

  3. 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.

  4. Structure determination from powder diffraction data.

    Science.gov (United States)

    David, W I F; Shankland, K

    2008-01-01

    Advances made over the past decade in structure determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal structures, new methods are required to make the solution of inorganic crystal structures more routine. The use of complementary techniques such as NMR to assist structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of structure determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal structures over the next decade are assessed.

  5. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure......In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... 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...

  6. 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

  7. The Structure of Treponema pallidum Tp0624 Reveals a Modular Assembly of Divergently Functionalized and Previously Uncharacterized Domains.

    Science.gov (United States)

    Parker, Michelle L; Houston, Simon; Wetherell, Charmaine; Cameron, Caroline E; Boulanger, Martin J

    2016-01-01

    Treponema pallidum subspecies pallidum is the causative agent of syphilis, a chronic, multistage, systemic infection that remains a major global health concern. The molecular mechanisms underlying T. pallidum pathogenesis are incompletely understood, partially due to the phylogenetic divergence of T. pallidum. One aspect of T. pallidum that differentiates it from conventional Gram-negative bacteria, and is believed to play an important role in pathogenesis, is its unusual cell envelope ultrastructure; in particular, the T. pallidum peptidoglycan layer is chemically distinct, thinner and more distal to the outer membrane. Established functional roles for peptidoglycan include contributing to the structural integrity of the cell envelope and stabilization of the flagellar motor complex, which are typically mediated by the OmpA domain-containing family of proteins. To gain insight into the molecular mechanisms that govern peptidoglycan binding and cell envelope biogenesis in T. pallidum we report here the structural characterization of the putative OmpA-like domain-containing protein, Tp0624. Analysis of the 1.70 Å resolution Tp0624 crystal structure reveals a multi-modular architecture comprised of three distinct domains including a C-terminal divergent OmpA-like domain, which we show is unable to bind the conventional peptidoglycan component diaminopimelic acid, and a previously uncharacterized tandem domain unit. Intriguingly, bioinformatic analysis indicates that the three domains together are found in all orthologs from pathogenic treponemes, but are not observed together in genera outside Treponema. These findings provide the first structural insight into a multi-modular treponemal protein containing an OmpA-like domain and its potential role in peptidoglycan coordination and stabilization of the T. pallidum cell envelope.

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

    African Journals Online (AJOL)

    Journal of. Family Psychotherapy, 1:29-38. Science achievement determinants: factorial structure of family variables. Elias Oupa Mashile. Faculty of Education ... children themselves have about such involvement and support. Most researchers only ascribe a few of these variables to familial influence in their studies. Also ...

  9. Determinants of the detrital arthropod community structure

    DEFF Research Database (Denmark)

    Lessard, J.P.; Sackett, Tara E.; Reynolds, William N.

    2011-01-01

    in the determinants of community structure. In this study, we first examined the relative importance of environmental gradients, microclimate, and food resources in driving spatial variation in the structure of detrital communities in forests of the southeastern USA. Then, in order to assess whether the determinants...... of detrital community structure varied along a climatic gradient, we manipulated resource availability and microclimatic conditions at 15 sites along a well-studied elevational gradient. We found that arthropod abundance and richness generally declined with increasing elevation, though the shape...... manipulative experiments along environmental gradients can help tease apart the relative importance and detect the interactive effects of local-scale factors and broad-scale climatic variation in shaping communities...

  10. 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

  11. 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.

    1999-01-01

    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 a dose of 200 Gy completely prevented it. Diapausing larvae were more susceptible to irradiation than 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 days old larvae and it continues to accumulate throughout the larvae 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)

  12. 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)

  13. 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.

  14. 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 ...

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

    Science.gov (United States)

    Reynaud, Yann; Zheng, Chao; Wu, Guihui; Sun, Qun; Rastogi, Nalin

    2017-01-01

    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). PMID:28166309

  16. 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.

  17. Protein structure determination using metagenome sequence data.

    Science.gov (United States)

    Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A; Kim, David E; Kamisetty, Hetunandan; Kyrpides, Nikos C; Baker, David

    2017-01-20

    Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost. Copyright © 2017, American Association for the Advancement of Science.

  18. Structural definition by antibody engineering of an idiotypic determinant.

    Science.gov (United States)

    Sollazzo, M; Castiglia, D; Billetta, R; Tramontano, A; Zanetti, M

    1990-05-01

    Using computer-aided techniques for predicting molecular structure, we constructed an atomic model of the variable domain of a murine anti-thyroglobulin antibody whose immunodominant idiotypic determinant (Id62) was mapped by site-directed mutagenesis and immunochemical analysis. We previously showed that under experimental conditions this idiotype activates anti-idiotypic B cells and T cells, and modulates the response to thyroglobulin in mice. Because idiotype interactions are considered of physiological importance for immune regulation, we studied this idiotype as a model to understand the relationship between function and structure. To determine the contribution of heavy- and light-chain variable domains to the idiotype structure, we constructed chimeric expression vectors and introduced them into the (non-secreting) P3X63Ag8.653 myeloma cell line. Mutants of the heavy-chain variable domain were obtained by site-directed mutagenesis and transfected into the murine (lambda 1) light-chain producer J558L cell line. The expressed proteins were purified from culture supernatants of transfected cells and characterized. We provide evidence that the third hypervariable loop (D region) of the heavy-chain variable domain is the structural correlate of the idiotypic determinant of this autoantibody and is independent from the nature of the associated light chain. Substitution of residues of the first and second complementarity-determining regions do not affect idiotype expression. The results described here are discussed in relation to our understanding, at a molecular level, of the interaction of idiotopes with B- and T-cell compartments.

  19. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L

    2000-01-01

    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  20. Structural Determinants of Juvenile Offenses in School.

    Science.gov (United States)

    Kowalski, Gregory S.; And Others

    1983-01-01

    Using multiple regression techniques, evaluates the relative contributions of community structure, school structure, and crime prevention efforts to delinquency in public schools. Finds that distance from central business district, school size, and region are of predictive value, when crimes against persons, property, and perceived crime are…

  1. The utility of clinical care pathways in determining perinatal outcomes for women with one previous caesarean section; a retrospective service evaluation

    Directory of Open Access Journals (Sweden)

    Karuga Robinson N

    2010-10-01

    Full Text Available Abstract Background The rising rates of primary caesarean section have resulted in a larger obstetric population with scarred uteri. Subsequent pregnancies in these women are risk-prone and may complicate. Besides ensuring standardised management, care pathways could be used to evaluate for perinatal outcomes in these high risk pregnancies. We aim to demonstrate the use of a care pathway for vaginal birth after caesarean section as a service evaluation tool to determine perinatal outcomes. Methods A retrospective service evaluation by review of delivery case notes and records was undertaken at the Aga Khan University Hospital, Nairobi, Kenya between January 2008 and December 2009 Women with ≥2 previous caesarean sections, previous classical caesarean section, multiple gestation, breech presentation, severe pre-eclampsia, transverse lie, placenta praevia, conditions requiring induction of labour and incomplete records were excluded. Outcome measures included the proportion of eligible women who opted for test of scar (ToS, success rate of vaginal birth after caesarean section (VBAC; proportion on women opting for elective repeat caesarean section (ERCS and their perinatal outcomes. Results A total of 215 women with one previous caesarean section were followed up using a standard care pathway. The median parity (minimum-maximum was 1.01234. The other demographic characteristics were comparable. Only 44.6% of eligible mothers opted to have a ToS. The success rate for VBAC was 49.4% with the commonest (31.8% reason for failure being protracted active phase of labour. Maternal morbidity was comparable for the failed and successful VBAC group. The incidence of hemorrhage was 2.3% and 4.4% for the successful and failed VBAC groups respectively. The proportion of babies with acidotic arterial PH ( Conclusions Besides ensuring standardised management, care pathways could be objective audit and service evaluation tools for determining perinatal outcomes.

  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. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-09-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  4. 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.

  5. 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.

  6. 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.

  7. 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

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

    African Journals Online (AJOL)

    At a time of continuous economic uncertainty and a highly competitive labour market, it is crucial for undergraduates to be more pro-active about their future careers. This study investigates the structural influence of career guidance activities on university students' employability in Nigeria. Data was collected from 600 ...

  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. Electron Diffraction Determination of Nanoscale Structures

    Energy Technology Data Exchange (ETDEWEB)

    Parks, Joel H

    2013-03-01

    Dominant research results on adsorption on gold clusters are reviewed, including adsorption of H{sub 2}O and O{sub 2} on gold cluster cations and anions, kinetics of CO adsorption to middle sized gold cluster cations, adsorption of CO on Au{sub n}{sup +} with induced changes in structure, and H{sub 2}O enhancement of CO adsorption.

  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. determination of verticality of reservoir engineering structure

    African Journals Online (AJOL)

    user

    recent TLS, digital cameras have been integrated into the instruments which further enhance the beauty and utilization of the instrument. Another possible combination is the determination of the scanner position and orientation with GNSS, which allows the user to transform data to the desired coordinate system with the.

  13. [Determination of in vitro susceptibility of Candida species to amphotericin B by E-test and previously proposed MIC breakpoints on two different media].

    Science.gov (United States)

    Alp, Sehnaz; Sancak, Banu; Arikan, Sevtap

    2008-04-01

    Although much work has concentrated on defining a reliable and reproducible method for determining in vitro susceptibility of Candida species to amphotericin B, there still has been limitations of the proposed techniques. In this study, amphotericin B minimal inhibitory concentrations (MIC) and susceptibility categories of 212 Candida strains (57 C. glabrata, 53 C. lusitaniae, 51 C. krusei and 51 C. tropicalis) were determined by E-test on RPMI agar (RPG) and antibiotic medium 3 agar (AM3) both supplemented with 2% glucose. The results were interpreted according to the proposed MIC breakpoints (> or = 0.38 microg/ml on RPG, >1 microg/ml on AM3) and discrepancies between susceptibility categories were investigated. While all Candida strains included in the study were determined to be susceptible on AM3 by amphotericin B E-test at 48h, 36.3% of the isolates were classified as resistant on RPG at 48 hours. On RPG, C. krusei strains showed the highest resistance rate (94.1% at 48 h), followed by C. tropicalis (35.3% at 48 h) and C. glabrata (17.5% at 48h). At 48h of incubation, 98.1% of C. lusitaniae isolates were found to be susceptible on RPG. The categorical agreement rates between the results obtained on two media and for C. lusitaniae and C. glabrata were 98.1% and 82.5% at 48 hours. For C. tropicalis and C. krusei, the rates of agreement were 64.7% and 5.9% at 48 hours. Conclusively, according to the previously proposed MIC breakpoints for amphotericin B E-test on RPG and AM3, discrepancies between susceptibility categories of Candida species were of remarkable significance.

  14. Magnetic Structure Determinations at NBS/NIST.

    Science.gov (United States)

    Lynn, J W; Borchers, J A; Huang, Q; Santoro, A; Erwin, R W

    2001-01-01

    Magnetic neutron scattering plays a central role in determining and understanding the microscopic properties of a vast variety of magnetic systems, from the fundamental nature, symmetry, and dynamics of magnetically ordered materials to elucidating the magnetic characteristics essential in technological applications. From the early days of neutron scattering measurements at NBS/NIST, magnetic diffraction studies have been a central theme involving many universities, industrial and government labs from around the United States and worldwide. Such measurements have been used to determine the spatial arrangement and directions of the atomic magnetic moments, the atomic magnetization density of the individual atoms in the material, and the value of the ordered moments as a function of thermodynamic parameters such as temperature, pressure, and applied magnetic field. These types of measurements have been carried out on single crystals, powders, thin films, and artificially grown multilayers, and often the information collected can be obtained by no other experimental technique. This article presents, in an historical perspective, a few examples of work carried out at the NIST Center for Neutron Research (NCNR), and discusses the key role that the Center can expect to play in future magnetism research.

  15. 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.

  16. Semiconductors with structurally determined vacancies PAC studies

    CERN Document Server

    Dietrich, M; Kortus, J; Unterricker, S; Deicher, M; Burchard, A; Magerle, R

    1999-01-01

    Ternary semiconductors of type Square Operator A/sup II/B/sub 2//sup III/C/sub 4//sup VI/ with an ordered array of vacancies were investigated by PAC. Thereby the six probes /sup 111m/Cd, /sup 117/Cd (/sup 117/In), /sup 111/In(/sup 111/Cd), /sup 111/Ag(/sup 111/Cd), /sup 77/Br(/sup 77/Se) and /sup 77/Kr(/sup 77/Br) were applied. The positions of the different probes are determined and the corresponding electric field gradients by the WIEN 95 code calculated. By /sup 111/Ag(/sup 111/Cd)-probes the vacancies could be substituted. The electronic charge density distributions are discussed. At elevated temperatures the substances show order- disorder transitions. As compared to the X-ray diffraction patterns the beginning of disorder is observed by PAC at distinctly lower temperatures. (7 refs).

  17. 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

  18. 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....

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

    Indian Academy of Sciences (India)

    Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination ...

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

    Indian Academy of Sciences (India)

    Unknown

    Structure determination at room temperature and phase transition studies above Tc in ABi4Ti4O15 (A = Ba, Sr or Pb). G NALINI and T N GURU ROW*. Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India. MS received 9 May 2002. Abstract. The room temperature structure of three ...

  1. 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 .

  2. Automating the determination of 3D protein structure

    Energy Technology Data Exchange (ETDEWEB)

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  3. 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.

  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. 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.

  6. NMRFAM-SDF: a protein structure determination framework

    International Nuclear Information System (INIS)

    Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C.; Cornilescu, Gabriel; Assadi-Porter, Fariba M.; Westler, William M.; Eghbalnia, Hamid R.; Markley, John L.

    2015-01-01

    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR—from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website ( http://nmrfam.wisc.edu/software.htm http://nmrfam.wisc.edu/software.htm )

  7. NMRFAM-SDF: a protein structure determination framework

    Energy Technology Data Exchange (ETDEWEB)

    Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C.; Cornilescu, Gabriel; Assadi-Porter, Fariba M.; Westler, William M.; Eghbalnia, Hamid R.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)

    2015-08-15

    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR—from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website ( http://nmrfam.wisc.edu/software.htm http://nmrfam.wisc.edu/software.htm )

  8. 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 ...

  9. Isolation, Characterization and X-ray Structure Determination of the ...

    African Journals Online (AJOL)

    NICO

    2014-12-20

    Dec 20, 2014 ... varied both sterically and electronically. On the other hand, the aminothiazole ring system is a useful structural element in medicinal chemistry.5 We have reported substituted pyrazolones with various amino thiazoles and their molecular structures were determined.6 The ligands can exist in three tautomeric.

  10. Determination of conduction and valence band electronic structure ...

    Indian Academy of Sciences (India)

    Abstract. Electronic structures of rutile and anatase polymorph of TiO2 were determined by resonant inelas- tic X-ray scattering measurements and FEFF9.0 calculations. Difference between crystalline structures led to shifts in the rutile Ti d-band to lower energy with respect to anatase, i.e., decrease in band gap. Anatase ...

  11. The determinants of financial structure in the algerian enterprises: A ...

    African Journals Online (AJOL)

    The results of our research indicate that the Algerian SMEs and large companies have almost the same determinants of financial structure, i.e. the debt rate, the rate of sustainable growth and profitability. The undercapitalization of SMEs has negative repercussions on their financial structure and, consequently, on their ...

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

    African Journals Online (AJOL)

    Determination of Velocity And Acceleration of Structural Deformation Using Kalman Filter Technique. ... This paper outlines the procedure of geodetic monitoring system of circular oil storage tanks and presents the analysis of the resulted observations to determine the values of their deformation. At the Forcados Tank Farm, ...

  14. A topology-constrained distance network algorithm for protein structure determination from NOESY data.

    Science.gov (United States)

    Huang, Yuanpeng Janet; Tejero, Roberto; Powers, Robert; Montelione, Gaetano T

    2006-03-15

    This article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-constrained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology-constrained distance network analysis algorithm and iteratively generates structures using the three-dimensional (3D) protein structure calculation programs XPLOR/CNS or DYANA. The minimum input for AutoStructure includes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D-NOESY cross peaks. AutoStructure can also analyze homodimeric proteins when X-filtered NOESY experiments are available. The quality of input data and final 3D structures is evaluated using recall, precision, and F-measure (RPF) scores, a statistical measure of goodness of fit with the input data. AutoStructure has been tested on three protein NMR data sets for which high-quality structures have previously been solved by an expert, and yields comparable high-quality distance constraint lists and 3D protein structures in hours. We also compare several protein structures determined using AutoStructure with corresponding homologous proteins determined with other independent methods. The program has been used in more than two dozen protein structure determinations, several of which have already been published. (c) 2005 Wiley-Liss, Inc.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. Three-dimensional structure determination from a single view.

    Science.gov (United States)

    Raines, Kevin S; Salha, Sara; Sandberg, Richard L; Jiang, Huaidong; Rodríguez, Jose A; Fahimian, Benjamin P; Kapteyn, Henry C; Du, Jincheng; Miao, Jianwei

    2010-01-14

    The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for three-dimensional (3D) structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography, or by scanning a series of thin sections through the sample, as in confocal microscopy. Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning 'curved' and graphein meaning 'writing'), which under certain circumstances enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is in principle determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 A resolution, and a single poliovirus at 2-3 nm resolution, from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we also provide a preliminary demonstration that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. With further development, this approach of obtaining complete 3D structure information from a single view could find broad applications in the physical and life sciences.

  2. 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.

  3. 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.

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

    International Nuclear Information System (INIS)

    Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S.

    2013-01-01

    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.

  5. Influence of 12 weeks of jogging on magnetic resonance-determined left ventricular characteristics in previously sedentary subjects free of cardiovascular disease.

    Science.gov (United States)

    Sipola, Petri; Heikkinen, Jari; Laaksonen, David E; Kettunen, Raimo

    2009-02-15

    Hypertrophy of the left ventricle is a diagnostic dilemma in subjects who engage in regular endurance exercise. We studied prospectively whether endurance training in previously sedentary young and middle-aged men and women can alter left ventricular (LV) characteristics. We recruited 33 healthy young and middle-aged subjects (18 women, 15 men, ages 21 to 59 years) to undergo 12 weeks of home-based brisk walking and jogging at a target heart rate > or =120 beats/min for > or =30 minutes 3 times a week. LV characteristics were measured by cine magnetic resonance imaging. Training intensity as estimated by heart rate correlated positively with the increase in LV myocardial area (r = 0.51, p = 0.005) in the 28 men and women completing the study. In the 13 men and women who trained with heart rate of > or =120 beats/min, LV myocardial area was larger after than before training (17.7 +/- 2.9 vs 16.8 +/- 2.8 cm(2), p <0.05). Moreover, in these subjects LV myocardial area increased more (5.5 +/- 9.0% vs -3.0 +/- 5.0%) than in the 15 men and women who trained at a lower intensity (p <0.05). LV end-systolic and end-diastolic area and ejection fraction did not change significantly. In conclusion, moderate-to-vigorous endurance training at moderate volumes does not influence LV end-diastolic volume or ejection fraction, but has a minor influence on LV hypertrophy in previously sedentary young and middle-aged men and women.

  6. 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.

  7. 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)

  8. 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.

  9. 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.

  10. Structure determination of drug target proteins by neutron crystallography

    International Nuclear Information System (INIS)

    Tamada, Taro; Adachi, Motoyasu

    2010-01-01

    High resolution X-ray crystallography provides information for most of the atoms comprising the proteins, with the exception of hydrogen atoms. Whereas, neutron crystallography, which is a powerful technique for locating hydrogen atoms, enables us to obtain accurate atomic positions within proteins. Neutron diffraction data can provide information of the location of hydrogen atoms to the structural information determined by X-ray crystallography. Here, we show the recent results of the structural determination of drug-target proteins, porcine pancreatic elastase and human immuno-deficiency virus type-1 protease by both X-ray and neutron diffraction. The structure of porcine pancreatic elastase with its potent inhibitor was determined to 0.094 nm resolution by X-ray diffraction and 0.165 nm resolution by neutron diffraction. The structure of HIV-PR with its potent inhibitor was also determined to 0.093 nm resolution by X-ray diffraction and 0.19 nm resolution by neutron diffraction. The ionization state and the location of hydrogen atoms of the catalytic residue in these enzymes were determined by neutron diffraction. Furthermore, collaborative use of both X-ray and neutron crystallography to identify the location of ambiguous hydrogen atoms will be shown. (author)

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

    DEFF Research Database (Denmark)

    Olsson, Simon; Boomsma, Wouter; Frellsen, Jes

    2011-01-01

    rigorous approach was developed which treats structure determination as a problem of Bayesian inference. In this case, the forcefields are brought in as a prior distribution in the form of a Boltzmann factor. Due to high computational cost, the approach has been only sparsely applied in practice. Here, we...

  12. 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

  13. 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…

  14. 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...

  15. 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)

  16. 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.

  17. 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

  18. Age determination and age structure of a striped fieldmouse ...

    African Journals Online (AJOL)

    Thereafter, the only reliable technique of age determination Involves a visual evaluation of the degree of molar tooth wear. Five wear classes are described and used to assess the age of 780 R. pumilio collected during a five-year period. The annual cycles of population age structure and size were dependent on seasonal ...

  19. 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.

  20. 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.

  1. 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...

  2. 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.

  3. 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.

  4. 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, E-mail: chatake@rri.kyoto-u.ac.jp [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.

  5. 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...

  6. 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.

  7. 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

  8. PREVIOUS SECOND TRIMESTER ABORTION

    African Journals Online (AJOL)

    PNLC

    PREVIOUS SECOND TRIMESTER ABORTION: A risk factor for third trimester uterine rupture in three ... for accurate diagnosis of uterine rupture. KEY WORDS: Induced second trimester abortion - Previous uterine surgery - Uterine rupture. ..... scarred uterus during second trimester misoprostol- induced labour for a missed ...

  9. REAL STRUCTURE AND RESIDUAL STRESSES IN ADVANCED WELDS DETERMINED BY X-RAY AND NEUTRON DIFFRACTION

    Directory of Open Access Journals (Sweden)

    Karel Trojan

    2017-07-01

    Full Text Available The paper outlines the capability of X-ray diffraction (XRD for evaluation of real structure changes and residual stresses (RS on cross-section of advanced thick welds due to the welding of ferromagnetic plates. The results of neutron diffraction describe a three-dimensional state of RS and also verify previous assumptions of RS redistribution as a result of the surface preparation for determination 2D maps measured by XRD.

  10. 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

  11. 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

  12. Determination of the nucleon structure using the weak neutral current

    International Nuclear Information System (INIS)

    Bogert, D.; Burnstein, R.; Fisk, R.

    1985-07-01

    An experimental determination of the neutral current structure functions of the nucleon is obtained by measuring the ratio of the neutral current x distribution to the charged current x distribution. The analysis is based on deep inelastic neutrino nucleon scattering data gathered in a massive fine-grained neutrino detector exposed to a narrow band neutrino beam at Fermilab. 12 refs., 2 figs., 2 tabs

  13. 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.)

  14. Determining the Structure of Higgs Couplings at the LHC

    CERN Document Server

    Plehn, Tilman; Zeppenfeld, Dieter

    2002-01-01

    Higgs boson production via weak boson fusion at the CERN Large Hadron Collider has the capability to determine the dominant CP nature of a Higgs boson, via the tensor structure of its coupling to weak bosons. This information is contained in the azimuthal angle distribution of the two outgoing forward tagging jets. The technique is independent of both the Higgs boson mass and the observed decay channel.

  15. 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......, indicating that they are important for biofilm initiation. Their enzymatic degradation, in an established biofilm, caused dispersal, showing that these proteins are critical for structural integrity. A combination of antibiotics with hECM degrading enzymes did not improve the treatment outcome. We conclude...... 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...

  16. Local magnetic structure determination using polarized neutron holography

    Science.gov (United States)

    Szakál, Alex; Markó, Márton; Cser, László

    2015-05-01

    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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yingang, E-mail: fengyg@qibebt.ac.cn [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Song, Xiaxia [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Lin, Jinzhong [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Xuan, Jinsong [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Cui, Qiu [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Wang, Jinfeng [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

    2014-07-18

    Highlights: • The archaea-specific ribosomal protein L46a has no homology to known proteins. • Three dimensional structure and backbone dynamics of L46a were determined by NMR. • The structure of L46a represents a novel protein fold. • A potential rRNA-binding surface on L46a was identified. • The potential position of L46a on the ribosome was proposed. - Abstract: Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae.

  2. 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.

  3. The Phenix software for automated determination of macromolecular structures.

    Science.gov (United States)

    Adams, Paul D; Afonine, Pavel V; Bunkóczi, Gábor; Chen, Vincent B; Echols, Nathaniel; Headd, Jeffrey J; Hung, Li-Wei; Jain, Swati; Kapral, Gary J; Grosse Kunstleve, Ralf W; McCoy, Airlie J; Moriarty, Nigel W; Oeffner, Robert D; Read, Randy J; Richardson, David C; Richardson, Jane S; Terwilliger, Thomas C; Zwart, Peter H

    2011-09-01

    X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. 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

  5. Total structure determination of thiolate-protected Au38 nanoparticles.

    Science.gov (United States)

    Qian, Huifeng; Eckenhoff, William T; Zhu, Yan; Pintauer, Tomislav; Jin, Rongchao

    2010-06-23

    We report the total structure of Au(38)(SC(2)H(4)Ph)(24) nanoparticles determined by single crystal X-ray crystallography. This nanoparticle is based upon a face-fused Au(23) biicosahedral core, which is further capped by three monomeric Au(SR)(2) staples at the waist of the Au(23) rod and six dimeric staples with three on the top icosahedron and other three on the bottom icosahedron. The six Au(2)(SR)(3) staples are arranged in a staggered configuration, and the Au(38)S(24) framework has a C(3) rotation axis.

  6. 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

  7. Heparin's solution structure determined by small-angle neutron scattering.

    Science.gov (United States)

    Rubinson, Kenneth A; Chen, Yin; Cress, Brady F; Zhang, Fuming; Linhardt, Robert J

    2016-12-01

    Heparin is a linear, anionic polysaccharide that is widely used as a clinical anticoagulant. Despite its discovery 100 years ago in 1916, the solution structure of heparin remains unknown. The solution shape of heparin has not previously been examined in water under a range of concentrations, and here is done so in D2 O solution using small-angle neutron scattering (SANS). Solutions of 10 kDa heparin-in the millimolar concentration range-were probed with SANS. Our results show that when sodium concentrations are equivalent to the polyelectrolyte's charge or up to a few hundred millimoles higher, the molecular structure of heparin is compact and the shape could be well modeled by a cylinder with a length three to four times its diameter. In the presence of molar concentrations of sodium, the molecule becomes extended to nearly its full length estimated from reported X-ray measurements on stretched fibers. This stretched form is not found in the presence of molar concentrations of potassium ions. In this high-potassium environment, the heparin molecules have the same shape as when its charges were mostly protonated at pD ≈ 0.5, that is, they are compact and approximately half the length of the extended molecules. © 2016 Wiley Periodicals, Inc.

  8. 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.

  9. Structural Determinants of Workforce Participation after Retirement in Poland.

    Science.gov (United States)

    Oleksiyenko, Olena; Życzyńska-Ciołek, Danuta

    2018-01-01

    In this paper, we aim to analyse selected structural determinants of workforce participation after retirement in Poland. By structural determinants we mean characteristics of one's socio-economic position that (a) result from the interplay of social conditions (mechanisms of power, differentiated access to resources) and individual agency, and (b) restrict or facilitate individuals' choices. We conceptualise workforce participation as engaging in either part- or full-time paid employment despite receiving the old-age pension. Our general hypothesis is that working in older age is not only a matter of motivation or psychological traits but also a complex interplay of structural characteristics, accumulated by individuals during their life course. In the paper, we test a number of hypotheses about the role of specific components of socio-economic status (SES), i.e. occupational prestige, education, and wealth, for workforce participation among retirees. We argue that, in case of retirees, the prestige of the last job before retirement is a more reliable measure of the social position than education. Hence, we conduct a more detailed analysis of the role of occupational prestige for the chances of being employed after retirement. The analysis was based on data gathered in the years 2013-2014 within the sixth wave of the Polish Panel Survey POLPAN (www.polpan.org). We extracted a subsample of retirees from this dataset and used logistic regression to test the hypotheses described above. We found that both occupational prestige of the last job before retirement and educational attainments are strong predictors of being in paid work after retirement, however the impact of occupational prestige varies across the groups with the lowest and higher level of retirement pension. We also found that there are horizontal differences in the occupational structure of the chances for workforce participation after retirement and additionally found that being a farm owner increases

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

    Science.gov (United States)

    Pacakova, B; Kubickova, S; Salas, G; Mantlikova, A R; Marciello, M; Morales, M P; Niznansky, D; Vejpravova, J

    2017-04-20

    This work aims to emphasize that the magnetic response of single-domain magnetic nanoparticles (NPs) is driven by the NPs' internal structure, and the NP size dependencies of magnetic properties are overestimated. The relationship between the degree of the NPs' crystallinity and magnetic response is unambiguously demonstrated in eight samples of uniform maghemite/magnetite NPs and corroborated with the results obtained for about 20 samples of spinel ferrite NPs with different degrees of crystallinity. The NP samples were prepared by the thermal decomposition of an organic iron precursor subjected to varying reaction conditions, yielding variations in the NP size, shape and relative crystallinity. We characterized the samples by using several complementary methods, such as powder X-ray diffraction (PXRD), transmission electron microscopy (TEM), high resolution TEM (HR-TEM) and Mössbauer spectroscopy (MS). We evaluated the NPs' relative crystallinity by comparing the NP sizes determined from TEM and PXRD and further inspecting the NPs' internal structure and relative crystallinity by using HR-TEM. The results of the structural characterization were put in the context of the NPs' magnetic response. In this work, the highest saturation magnetization (M s ) was measured for the smallest but well-crystalline NPs, while the larger NPs exhibiting worse crystallinity revealed a lower M s . Our results clearly demonstrate that the NP crystallinity level that is mirrored in the internal spin order drives the specific magnetic response of the single-domain NPs.

  11. 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

  12. Annular dark field transmission electron microscopy for protein structure determination.

    Science.gov (United States)

    Koeck, Philip J B

    2016-02-01

    Recently annular dark field (ADF) transmission electron microscopy (TEM) has been advocated as a means of recording images of biological specimens with better signal to noise ratio (SNR) than regular bright field images. I investigate whether and how such images could be used to determine the three-dimensional structure of proteins given that an ADF aperture with a suitable pass-band can be manufactured and used in practice. I develop an approximate theory of ADF-TEM image formation for weak amplitude and phase objects and test this theory using computer simulations. I also test whether these simulated images can be used to calculate a three-dimensional model of the protein using standard software and discuss problems and possible ways to overcome these. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Determination of partial structure factors of disordered alloys

    International Nuclear Information System (INIS)

    Andonov, P.

    1993-01-01

    Often, isotopic substitution method in neutron diffraction or the differential anomalous X-ray scattering, cannot be applied; ancient results obtained from approximate methods are presented for three binary alloys: liquid Pd-Si (Si-Si contribution neglected in X-ray diffraction and assumed in neutron diffraction), liquid Cd-Zn (partial functions assumed independent of the concentration), amorphous Mg-Zn (correct CSRO determination but unsuccessful attempt of the three radiations method due to a structural evolution under the electron beam); accuracy and validity limits are recalled. The example of the ternary LiNbO 3 melt is considered: two diffraction experiments from X-rays and neutrons, in conjunction with the SAXS and the crystalline distribution, made it possible to describe a local order reduced to the first neighbours. 3 figs., 12 refs

  14. Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Rory N.; Chumbler, Nicole M.; Rutherford, Stacey A.; Farrow, Melissa A.; Friedman, David B.; Spiller, Ben; Lacy, D. Borden (Vanderbilt)

    2012-03-28

    The principle virulence factors in Clostridium difficile pathogenesis are TcdA and TcdB, homologous glucosyltransferases capable of inactivating small GTPases within the host cell. We present crystal structures of the TcdA glucosyltransferase domain in the presence and absence of the co-substrate UDP-glucose. Although the enzymatic core is similar to that of TcdB, the proposed GTPase-binding surface differs significantly. We show that TcdA is comparable with TcdB in its modification of Rho family substrates and that, unlike TcdB, TcdA is also capable of modifying Rap family GTPases both in vitro and in cells. The glucosyltransferase activities of both toxins are reduced in the context of the holotoxin but can be restored with autoproteolytic activation and glucosyltransferase domain release. These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell.

  15. 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

  16. 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)

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Structural Determinants of Youth Bullying and Fighting in 79 Countries.

    Science.gov (United States)

    Elgar, Frank J; McKinnon, Britt; Walsh, Sophie D; Freeman, John; D Donnelly, Peter; de Matos, Margarida Gaspar; Gariepy, Genevieve; Aleman-Diaz, Aixa Y; Pickett, William; Molcho, Michal; Currie, Candace

    2015-12-01

    The prevention of youth violence is a public health priority in many countries. We examined the prevalence of bullying victimization and physical fighting in youths in 79 high- and low-income countries and the relations between structural determinants of adolescent health (country wealth, income inequality, and government spending on education) and international differences in youth violence. Cross-sectional surveys were administered in schools between 2003 and 2011. These surveys provided national prevalence rates of bullying victimization (n = 334,736) and four or more episodes of physical fighting in the past year (n = 342,312) in eligible and consenting 11-16 year olds. Contextual measures included per capita income, income inequality, and government expenditures on education. We used meta-regression to examine relations between country characteristics and youth violence. Approximately 30% of adolescents reported bullying victimization and 10.7% of males and 2.7% of females were involved in frequent physical fighting. More youth were exposed to violence in African and Eastern Mediterranean countries than in Europe and Asia. Violence directly related to country wealth; a 1 standard deviation increase in per capita income corresponded to less bullying (-3.9% in males and -4.2% in females) and less fighting (-2.9% in males and -1.0% in females). Income inequality and education spending modified the relation between country wealth and fighting; where inequality was high, country wealth related more closely to fighting if education spending was also high. Country wealth is a robust determinant of youth violence. Fighting in affluent but economically unequal countries might be reduced through increased government spending on education. Copyright © 2015 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

  2. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    Science.gov (United States)

    Nandhakumar, N.; Smith, Philip W.

    1993-12-01

    In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. Structure determination of bisacetylenic oxylipins in carrots (Daucus carota L.) and enantioselective synthesis of falcarindiol.

    Science.gov (United States)

    Schmiech, Ludger; Alayrac, Carole; Witulski, Bernhard; Hofmann, Thomas

    2009-11-25

    Although bisacetylenic oxylipins have been demonstrated to exhibit diverse biological activities, the chemical structures of many representatives of this class of phytochemicals still remain elusive. As carrots play an important role in our daily diet and are known as a source of bisacetylenes, an extract made from Daucus carota L. was screened for bisacetylenic oxylipins, and, after isolation, their structures were determined by means of LC-MS and 1D/2D NMR spectroscopy. Besides the previously reported falcarinol, falcarindiol, and falcarindiol 3-acetate, nine additional bisacetylenes were identified, among which six derivatives are reported for the first time in literature and three compounds were previously not identified in carrots. To determine the absolute stereochemistry of falcarindiol in carrots, the (3R,8R)-, (3R,8S)-, (3S,8R)-, and (3S,8S)-stereoisomers of falcarindiol were synthesized according to a novel 10-step total synthesis involving a Cadiot-Chodkiewicz cross-coupling reaction of (S)- and (R)-trimethylsilanyl-4-dodecen-1-yn-3-ol and (R)- and (S)-5-bromo-1-penten-4-yn-3-ol, respectively. Comparative chiral HPLC analysis of the synthetic stereoisomers with the isolated phytochemical led to the unequivocal assignment of the (Z)-(3R,8S)-configuration for falcarindiol in carrot extracts from Daucus carota L.

  8. Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data.

    Science.gov (United States)

    Ginn, Helen M; Messerschmidt, Marc; Ji, Xiaoyun; Zhang, Hanwen; Axford, Danny; Gildea, Richard J; Winter, Graeme; Brewster, Aaron S; Hattne, Johan; Wagner, Armin; Grimes, Jonathan M; Evans, Gwyndaf; Sauter, Nicholas K; Sutton, Geoff; Stuart, David I

    2015-03-09

    The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and protein core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.

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

    Indian Academy of Sciences (India)

    Unknown

    displacement of Bi atoms along the 'a' axis might be responsible for ferroelectricity in these compounds. The high temperature X-ray data above Tc indicate no structural transition for A = Ba and Pb while A = Sr transforms to the tetragonal structure. Keywords. ab initio structure; powder XRD; Rietveld refinement; Aurivillius ...

  10. Fuel material neutron crystallography texture and structure determinations (1960)

    International Nuclear Information System (INIS)

    Laniesse, J.; Englander, M.; Meriel, P.

    1960-01-01

    The method here described has the advantage over the classic X-ray diffraction method of giving fuller and quicker information about the texture of a built polycrystalline aggregate of U metal, and of following more easily the evolution of its crystalline structure during the allotropic transformation. It uses a thermal neutron beam coming out of the Saclay CEN reactor EL3, monochromatized at λ = 1,143 ± 0,030 Angstrom, and directed after collimation, perpendicularly to the fiber axis of an optimized dimensioned cylindrical specimen. The scattered neutron beam is collected into a BF3 counter which is able to describe in a horizontal plane containing the neutron beam axis, a circle 130 cm in radius centered on the specimen. In testing at room temperature a specimen which is entirely free from residual or parasite texture, the reference spectral lines of pure U alpha phase are determined by means of a recording meter and a counting device. The same method gives the spectral distribution of the U beta phase by using, instead of pure uranium, a metastable solid solution containing a minimum concentration of some metallic impurities (Cr or Si). These spectra are then compared with the calculated ones and the X-ray diffraction ones. After choosing a certain number of given diffraction lines, it was possible to check qualitatively and semi-quantitatively the evolution of eventual predominant orientations versus mechanical and/or thermal treatments. By following the intensity of a 'mixed' spectrum line suitably placed within the lines of the α and β spectra, it was possible to determine the kinetic of the β → α transformation at temperature where frequency and counting rates are adequate. By way of examples, the paper illustrates results obtained with a 600 deg. C extruded pure U rod (reduction in area = 6 ,4) , and with a four times beta-water quenched α extruded specimen. It also shows the equation giving the time for the β → α transformation at 333 deg. K

  11. 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

  12. 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.

  13. Application of energy derivative method to determine the structural components' contribution on the deceleration in crashes.

    Science.gov (United States)

    Nagasaka, Kei; Mizuno, Koji; Thomson, Robert

    2018-03-26

    For occupant protection, it is important to understand how a car's deceleration-time history in crashes can be designed using efficient of energy absorption by a car body's structure. In a previous paper, the authors proposed an energy derivative method to determine each structural component's contribution on the longitudinal deceleration of a car passenger compartment in crashes. In this study, this method was extended to two dimensions in order to analyze various crash test conditions. The contribution of each structure estimated from the energy derivative method was compared to that from a conventional finite element (FE) analysis method using cross-sectional forces. A two-dimensional energy derivative method was established. A simple FE model with a structural column connected to a rigid body was used to confirm the validity of this method and to compare with the result of cross-sectional forces determined using conventional analysis. Applying this method to a full-width frontal impact simulation of a car FE model, the contribution and the cross-sectional forces of the front rails were compared. In addition, this method was applied to a pedestrian headform FE simulation in order to determine the influence of the structural and inertia forces of the hood structures on the deceleration of the headform undergoing planar motion. In an oblique impact of the simple column and rigid body model, the sum of the contributions of each part agrees with the rigid body deceleration, which indicates the validity of two-dimensional energy derivative method. Using the energy derivative method, it was observed that each part of the column contributes to the deceleration of the rigid body by collapsing in the sequence from front to rear whereas the cross-section force at the rear of the column cannot detect the continuous collapse. In the full-width impact of a car, the contributions of the front rails estimated in the energy derivative method was smaller than that using the

  14. 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.

  15. 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

  16. 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.

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

    Indian Academy of Sciences (India)

    Unknown

    Powder data is especially useful to deduce accurate cell parameters. Rietveld's refinement procedure1,2 has revolutionized the application of powder X-ray diffraction by resulting in a large number of structures being refined in the last decade. If a suitable starting model is available, it has become routine to refine structures ...

  18. 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.

  19. Structural Determination of a Transcribing RNA Polymerase II Complex

    Science.gov (United States)

    2000-05-01

    were previously detected only at radio wavelengths using ’ Consejo Superior de Investigaciones Cientlficas, In- interferometric techniques. We have...detected with the Infrared Space Obser- stituto de Estructura de Ia Materia, Departamento Fisica Molecular, Serrano 121, 28006 Madrid, Spain. vatory

  20. Environmental filtering determines metacommunity structure in wetland microcrustaceans.

    Science.gov (United States)

    Gascón, Stéphanie; Arranz, Ignasi; Cañedo-Argüelles, Miguel; Nebra, Alfonso; Ruhí, Albert; Rieradevall, Maria; Caiola, Nuno; Sala, Jordi; Ibàñez, Carles; Quintana, Xavier D; Boix, Dani

    2016-05-01

    Metacommunity approaches are becoming popular when analyzing factors driving species distribution at the regional scale. However, until the popularization of the variation partitioning technique it was difficult to assess the main drivers of the observed patterns (spatial or environmental). Here we propose a new framework linking the emergence of different metacommunity structures (e.g., nested, Gleasonian, Clementsian) to spatial and environmental filters. This is a novel approach that provides a more profound analysis of how both drivers could lead to similar metacommunity structures. We tested this framework on 110 sites covering a strong environmental gradient (i.e., microcrustacean assemblages organized along a salinity gradient, from freshwater to brackish water wetlands). First we identified the metacommunity structure that better fitted these microcrustacean assemblages. Then, we used hierarchical variation partitioning to quantify the relative influences of environmental filters and the distance among wetlands on the identified structure. Our results showed that under strong environmental filtering metacommunity structures were non-random. We also noted that even passive dispersers, that are supposed to be poorly spatially filtered, showed spatial signals at a large geographical scale. However, some difficulties arose when inferring biotic interactions at finer-scale spatial signals. Overall, our study shows the potential of elements of metacommunity structure combined with variation partition techniques to detect environmental drivers and broadscale patterns of metacommunity structure, and that some caution is needed when interpreting finer-scale spatial signals.

  1. Nodal Structure of Unconventional Superconductors Determined by Thermal Conductivity

    International Nuclear Information System (INIS)

    Matsuda, Y.; Izawa, K.

    2003-01-01

    The superconducting gap structure, especially the direction of the nodes, is an unresolved issue in most of unconventional superconductors. Recently it has been demonstrated that the thermal conductivity κ is a powerful tool for probing the nodal structure. Here measuring κ in H rotating within the basal plane, we discuss the nodal structure of the unconventional superconductors, spin-triplet Sr 2 RuO 4 , heavy fermion CeCoIn 5 , organic κ -(BEDT-TTF) 2 Cu(NCS) 2 , and borocarbide YNi 2 B 2 C. (author)

  2. Novel test structures for temperature budget determination during wafer processing

    NARCIS (Netherlands)

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

    2010-01-01

    Temperature is a crucial parameter in many planar technology processing steps. However, the determination of the actual temperature history at the device side of the substrate is not straightforward. We present a novel method for determining the temperature history of the process side of silicon

  3. Determining wildlife use of wildlife crossing structures under different scenarios.

    Science.gov (United States)

    2012-05-01

    This research evaluated Utahs wildlife crossing structures to help UDOT and the Utah Division of Wildlife Resources assess crossing efficacy. In this study, remote motion-sensed cameras were used at 14 designated wildlife crossing culverts and bri...

  4. Structural Determinants of Cadherin-23 Function in Hearing and Deafness

    Energy Technology Data Exchange (ETDEWEB)

    Sotomayor, Marcos; Weihofen, Wilhelm A.; Gaudet, Rachelle; Corey, David P. (Harvard-Med); (Harvard)

    2010-06-21

    The hair-cell tip link, a fine filament directly conveying force to mechanosensitive transduction channels, is composed of two proteins, protocadherin-15 and cadherin-23, whose mutation causes deafness. However, their molecular structure, elasticity, and deafness-related structural defects are unknown. We present crystal structures of the first and second extracellular cadherin repeats of cadherin-23. Overall, structures show typical cadherin folds, but reveal an elongated N terminus that precludes classical cadherin interactions and contributes to an N-terminal Ca{sup 2+}-binding site. The deafness mutation D101G, in the linker region between the repeats, causes a slight bend between repeats and decreases Ca{sup 2+} affinity. Molecular dynamics simulations suggest that cadherin-23 repeats are stiff and that either removing Ca{sup 2+} or mutating Ca{sup 2+}-binding residues reduces rigidity and unfolding strength. The structures define an uncharacterized cadherin family and, with simulations, suggest mechanisms underlying inherited deafness and how cadherin-23 may bind with itself and with protocadherin-15 to form the tip link.

  5. Determination of conduction and valence band electronic structure ...

    Indian Academy of Sciences (India)

    insufficient to study in-depth unoccupied states of investigated materials because it overlooks the shallow traps. Keywords. Photo-catalysis; high-resolution RIXS; electronic structure. 1. Introduction. Photocatalysis is an emerging field that offers poten- tial to address some of the energy and waste manage- ment challenges.

  6. Synthesis, crystal structure determination of two-dimensional ...

    Indian Academy of Sciences (India)

    The structure consists of 4-c uninodal net where Point symbol for Ag (I) ion and net is (44.62) with sql type topology. X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, twothird times more close contacts are obtained. The fingerprint plots demonstrate that ...

  7. 5 THE DETERMINANTS OF FINANCIAL STRUCTURE IN THE ...

    African Journals Online (AJOL)

    comparative study between SMEs and large companies to verify the existence of a size effect ..... d. F level, tolerance, or VIN insufficient for further computation. ..... Thus, the logic of the pecking order may not be compatible with the specificity of. Algerian SMEs. The relationship between financial structure and liquidity has a.

  8. Determination of verticality of reservoir engineering structure from ...

    African Journals Online (AJOL)

    Terrestrial laser scanners (TLS) are used nowadays as Geomatics instruments for various applications. One of these applications is 3D survey and management of oil and gas facilities and other engineering structures. This recent attention is due to the fact that laser scanner has the ability to generate massive amounts of ...

  9. The determination of turbulent structures in the atmospheric surface layer

    NARCIS (Netherlands)

    Schols, J.L.J.

    1984-01-01

    The turbulent flow in the atmospheric surface layer (ASL) contains turbulent structures, which are defined as spatially coherent, organized flow motions. 'Organized' means that characteristic patterns, observed at a point in space, occur almost simultaneously in more than one turbulence signal and

  10. Structural Determinants of Intergroup Association: Interracial Marriage and Crime.

    Science.gov (United States)

    South, Scott J.; Messner, Steven F.

    1986-01-01

    Using data from a sample of 25 U. S. metropolitan cities, this study investigates the relationship between interracial marriage and violent interracial crime. Results show a positive relationship, one which was predicted by Blau's macrosociological theory of social structure. (Author/JDH)

  11. 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.

  12. 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…

  13. 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

  14. Novel test structures for dedicated temperature budget determination

    NARCIS (Netherlands)

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

    2012-01-01

    We present a novel method for determining the temperature budget of the process side of silicon substrates and chips, based on well-known silicide formation reactions of metal–Si systems and (four-point probe) resistance measurements. In this paper, we focus on the Pd–Si system that is most

  15. Structural Determinants of Oligomerization of the Aquaporin-4 Channel*

    Science.gov (United States)

    Kitchen, Philip; Conner, Matthew T.; Bill, Roslyn M.; Conner, Alex C.

    2016-01-01

    The aquaporin (AQP) family of integral membrane protein channels mediate cellular water and solute flow. Although qualitative and quantitative differences in channel permeability, selectivity, subcellular localization, and trafficking responses have been observed for different members of the AQP family, the signature homotetrameric quaternary structure is conserved. Using a variety of biophysical techniques, we show that mutations to an intracellular loop (loop D) of human AQP4 reduce oligomerization. Non-tetrameric AQP4 mutants are unable to relocalize to the plasma membrane in response to changes in extracellular tonicity, despite equivalent constitutive surface expression levels and water permeability to wild-type AQP4. A network of AQP4 loop D hydrogen bonding interactions, identified using molecular dynamics simulations and based on a comparative mutagenic analysis of AQPs 1, 3, and 4, suggest that loop D interactions may provide a general structural framework for tetrameric assembly within the AQP family. PMID:26786101

  16. Structural Determinants of Oligomerization of the Aquaporin-4 Channel.

    Science.gov (United States)

    Kitchen, Philip; Conner, Matthew T; Bill, Roslyn M; Conner, Alex C

    2016-03-25

    The aquaporin (AQP) family of integral membrane protein channels mediate cellular water and solute flow. Although qualitative and quantitative differences in channel permeability, selectivity, subcellular localization, and trafficking responses have been observed for different members of the AQP family, the signature homotetrameric quaternary structure is conserved. Using a variety of biophysical techniques, we show that mutations to an intracellular loop (loop D) of human AQP4 reduce oligomerization. Non-tetrameric AQP4 mutants are unable to relocalize to the plasma membrane in response to changes in extracellular tonicity, despite equivalent constitutive surface expression levels and water permeability to wild-type AQP4. A network of AQP4 loop D hydrogen bonding interactions, identified using molecular dynamics simulations and based on a comparative mutagenic analysis of AQPs 1, 3, and 4, suggest that loop D interactions may provide a general structural framework for tetrameric assembly within the AQP family. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. 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...

  18. 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

  19. Simplified Light Plane Determination during Structured Light Scanning

    OpenAIRE

    Pribanić, Tomislav; Cifrić, Ivan; Cifrek, Mario; Goldberger, Goran; Peharec, Stanislav

    2006-01-01

    Structured light illumination is a widely spread approach for 3D shape reconstruction. Scanning the scene of interest with hard edge stripe via video projector is a very common implementation. During the scanning light planes are being projected across the space and their positions in time are needed to triangulate 3D position of some point. Traditionally, light plane equation is readily obtained in case of calibrated video projector. This paper presents a method where light plane positions a...

  20. 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...... to a mechanism-inspired inhibitor that illuminates substrate binding and catalytic function of the enzyme. Key features that distinguish iridoid synthase from its close homolog progesterone 5β-reductase are highlighted....

  1. 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)

  2. 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.

  3. 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...

  4. [Cultural structures that determine suffering among various populations].

    Science.gov (United States)

    Pagés Larraya, F

    1986-09-01

    The cross-cultural consideration of our Psychiatric Epidemiology Program outlined the profile of the madman and his discourse as both mirror and enigma of his cultural community. This enigma occurs as a result of the suffering, the violence and the slyness inherent to creativity, in the sense that his own accomplishments are inexorably questionable because of the ubiquitous presence of the tragic and das Unheimliche. The madman "malgré soi" becomes a perfect interpreter of the cultural crisis and is a real key to his deepest structural interpretation. Therefore, we uphold a "tragic erasmism" and from then on discuss the hermeneutics of Nietzsche, Freud and Heidegger.

  5. 3D structure determination of protein using TEM single particle analysis.

    Science.gov (United States)

    Sato, Chikara; Mio, Kazuhiro; Kawata, Masaaki; Ogura, Toshihiko

    2014-11-01

    -type. Signal peptide peptidase (SPP) is an atypical aspartic protease that hydrolyzes peptide bonds within the transmembrane domain of substrates and is implicated in several biological and pathological functions. The structure of human SPP was determined by SPA at a resolution of 22 Å [8]. SPP forms a slender, bullet-shaped homotetramer with dimensions of 85 x 85 x 130 Å. The SPP complex has four concaves on the rhombus-like sides, connected to a large chamber inside the molecule. For the tetrameric assembly, the N-terminal region of SPP was found to be sufficient. Moreover, when N-terminal region was overexpressed, the formation of the endogenous SPP tetramer was inhibited, which suppressed the proteolytic activity within cells. From these data, the N-terminal region is considered to work as the structural scaffold.Transmembrane (TM) translocation of newly synthesized secretion proteins and membrane proteins are carried out by a Sec translocon protein complex. The polypeptide-conducting pore is formed by the SecYEG-SecA complex in bacteria, and the membrane protein SecDF is necessary for the efficient transport of proteins. However the molecular mechanism how SecDF realized efficient transport is not clear. A previous X-ray structural study of the whole protein and subdomain suggest that SecDF has at least two conformational variants, which could reflect molecular dynamics of this protein. To confirm this hypothesis, we analyzed the 3D structure of SecDF using dark field STEM electron tomography and single particle reconstruction. We determined two different whole SecDF protein structures which well explains the X-ray data. From these data, we would like to propose the possible molecular mechanism of SecDF during polypeptide translocation. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. 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...

  7. Determinants of the mouse ultrasonic vocal structure and repertoire.

    Science.gov (United States)

    Heckman, Jesse; McGuinness, Brigit; Celikel, Tansu; Englitz, Bernhard

    2016-06-01

    Mouse ultrasonic vocalizations (USV) exhibit a high degree of complexity as demonstrated in recent years. A multitude of factors have been identified to influence USVs on the spectrotemporal as well as structural - e.g. syntactic - level. A synthesis of the various studies that attributes semantics to USV properties or sequences is still lacking. Presently, we address the factors modulating the composition of USVs, specifically age, gender, genetic background (including the targeted FoxP2 mutagenesis), behavioral state and individuality. It emerges that the different factors share a set of common influences, e.g. vocalization rate and frequency range are universally modulated across independent variables described; however, distinct influences exist for sequential structure (different effects for age, behavioral state and genetic background) or vocal repertoire (age). Recently, USV research has seen important advances based on the quantitative maturation of methods on multiple levels of vocalization. Adoption of these methods to address the natural statistics of USV will ultimately benefit several related research areas, e.g. neurolinguistics, neurodevelopmental disorders, multisensory and sensorimotor research. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Structural biomechanics determine spectral purity of bush-cricket calls.

    Science.gov (United States)

    Chivers, Benedict D; Jonsson, Thorin; Soulsbury, Carl D; Montealegre-Z, Fernando

    2017-11-01

    Bush-crickets (Orthoptera: Tettigoniidae) generate sound using tegminal stridulation. Signalling effectiveness is affected by the widely varying acoustic parameters of temporal pattern, frequency and spectral purity (tonality). During stridulation, frequency multiplication occurs as a scraper on one wing scrapes across a file of sclerotized teeth on the other. The frequency with which these tooth-scraper interactions occur, along with radiating wing cell resonant properties, dictates both frequency and tonality in the call. Bush-cricket species produce calls ranging from resonant, tonal calls through to non-resonant, broadband signals. The differences are believed to result from differences in file tooth arrangement and wing radiators, but a systematic test of the structural causes of broadband or tonal calls is lacking. Using phylogenetically controlled structural equation models, we show that parameters of file tooth density and file length are the best-fitting predictors of tonality across 40 bush-cricket species. Features of file morphology constrain the production of spectrally pure signals, but systematic distribution of teeth alone does not explain pure-tone sound production in this family. © 2017 The Authors.

  9. A clustering algorithm for determining community structure in complex networks

    Science.gov (United States)

    Jin, Hong; Yu, Wei; Li, ShiJun

    2018-02-01

    Clustering algorithms are attractive for the task of community detection in complex networks. DENCLUE is a representative density based clustering algorithm which has a firm mathematical basis and good clustering properties allowing for arbitrarily shaped clusters in high dimensional datasets. However, this method cannot be directly applied to community discovering due to its inability to deal with network data. Moreover, it requires a careful selection of the density parameter and the noise threshold. To solve these issues, a new community detection method is proposed in this paper. First, we use a spectral analysis technique to map the network data into a low dimensional Euclidean Space which can preserve node structural characteristics. Then, DENCLUE is applied to detect the communities in the network. A mathematical method named Sheather-Jones plug-in is chosen to select the density parameter which can describe the intrinsic clustering structure accurately. Moreover, every node on the network is meaningful so there were no noise nodes as a result the noise threshold can be ignored. We test our algorithm on both benchmark and real-life networks, and the results demonstrate the effectiveness of our algorithm over other popularity density based clustering algorithms adopted to community detection.

  10. Molecular Determinants of Staphylococcal Biofilm Dispersal and Structuring

    Directory of Open Access Journals (Sweden)

    Katherine Y Le

    2014-11-01

    Full Text Available Staphylococci are frequently implicated in human infections, and continue to pose a therapeutic dilemma due to their ability to form deeply seated microbial communities, known as biofilms, on the surfaces of implanted medical devices and host tissues. Biofilm development has been proposed to occur in three stages: 1 attachment, 2 proliferation/structuring, and 3 detachment/dispersal. Although research within the last several decades has implicated multiple molecules in the roles as effectors of staphylococcal biofilm proliferation/structuring and detachment/dispersal, to date, only phenol soluble modulins (PSMs have been consistently demonstrated to serve in this role under both in-vitro and in-vivo settings. PSMs are regulated directly through a density-dependent manner by the accessory gene regulator (Agr system. They disrupt the non-covalent forces holding the biofilm extracellular matrix together, which is necessary for the formation of channels, a process essential for the delivery of nutrients to deeper biofilm layers, and for dispersal/dissemination of clusters of biofilm to distal organs in acute infection. Given their relevance in both acute and chronic biofilm-associated infections, the Agr system and the psm genes hold promise as potential therapeutic targets.

  11. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation will utilize self learning neural network technology to determine the structure of osteoporosis, immune system disease, and excess radiation...

  12. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose a dual objective innovation that has valuable NASA applicability and tremendous commercial potential. The first innovation is the structure determination...

  13. Structure and Interactions of a Dimeric Variant of sHIP, a Novel Virulence Determinant of Streptococcus pyogenes

    DEFF Research Database (Denmark)

    Diehl, Carl; Wisniewska, Magdalena; Frick, Inga-Maria

    2016-01-01

    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 s......HIP, 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...

  14. Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate

    Science.gov (United States)

    Khoshouei, Maryam; Radjainia, Mazdak; Baumeister, Wolfgang; Danev, Radostin

    2017-01-01

    With the advent of direct electron detectors, the perspectives of cryo-electron microscopy (cryo-EM) have changed in a profound way. These cameras are superior to previous detectors in coping with the intrinsically low contrast and beam-induced motion of radiation-sensitive organic materials embedded in amorphous ice, and hence they have enabled the structure determination of many macromolecular assemblies to atomic or near-atomic resolution. Nevertheless, there are still limitations and one of them is the size of the target structure. Here, we report the use of a Volta phase plate in determining the structure of human haemoglobin (64 kDa) at 3.2 Å. Our results demonstrate that this method can be applied to complexes that are significantly smaller than those previously studied by conventional defocus-based approaches. Cryo-EM is now close to becoming a fast and cost-effective alternative to crystallography for high-resolution protein structure determination. PMID:28665412

  15. 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.

  16. Interevent relationships and judgment under uncertainty: structure determines strategy.

    Science.gov (United States)

    Sanfey, Alan G; Hastie, Reid

    2002-09-01

    A fundamental empirical question regarding judgments about events is whether experienced absolute frequencies or relative frequencies are relied on when the likelihood of a particular occurrence is judged. The present research explicates the conditions under which people rely on remembered raw absolute frequencies versus on inferred relative frequencies or proportions when making predictions. Participants saw opinion poll results for candidates prior to an election and, on the basis of these, made judgments concerning the likelihood of each candidate's winning this election. Certain candidates demonstrated a high absolute frequency of winning in the polls, whereas other candidates had high relative win frequencies. The results indicated that adults are cognitively flexible with regard to the inputs used in this judgment. Certain stimulus event configurations induced reasoning by way of absolute frequencies, whereas other configurations elicited judgments based on relative frequencies. More specifically, as the relational complexity of the event structure increased and more inferences were required to make predictions, the tendency to rely on absolute, as opposed to relative, frequencies also increased.

  17. FINITE VOLUME METHOD FOR DETERMINING THE NATURAL CHARACTERISTICS OF STRUCTURES

    Directory of Open Access Journals (Sweden)

    N. FALLAH

    2013-02-01

    Full Text Available In this paper a finite volume based formulation is developed to calculate the structural natural characteristics including the natural frequencies and the critical buckling loads of slender beam/beam-columns in which the shear effects are taken into account. For natural frequency calculations, both shear effects and rotational inertia effects are considered. In this finite volume based approach, the equilibrium equations of control volumes are expressed and used with the boundary conditions to obtain the eigenvalue equation in the standard format. Then, the natural characteristics of beam/beam-columns are obtained by solving the eigenvalue equations. The formulation is tested on a number of benchmark problems. Accordingly, the proposed formulation has been found to accurately predict the natural frequencies and the critical buckling loads of the test problems. Also, the formulation is tested for the very thin and thick beams. It is found that the formulation is also able to analyze the thin beams in which no shear locks is observed.

  18. Determination of population structure and stock composition of chum salmon (Oncorhynchus keta) in Russia determined with microsatellites

    OpenAIRE

    Beacham, Terry D.; Varnavskaya, Nataly V.; Le, Khai D.; Wetklo, Michael H.

    2008-01-01

    Variation at 14 microsatellite loci was examined in 34 chum salmon (Oncorhynchus keta) populations from Russia and evaluated for its use in the determination of population structure and stock composition in simulated mixed-stock fishery samples. The genetic differentiation index (Fst) over all populations and loci was 0.017, and individual locus values ranged from 0.003 to 0.054. Regional population structure was observed, and populations from Primorye, Sakhalin Island, and northeast Ru...

  19. Structural determinants of an insect beta-N-Acetyl-D-hexosaminidase specialized as a chitinolytic enzyme.

    Science.gov (United States)

    Liu, Tian; Zhang, Haitao; Liu, Fengyi; Wu, Qingyue; Shen, Xu; Yang, Qing

    2011-02-11

    β-N-acetyl-D-hexosaminidase has been postulated to have a specialized function. However, the structural basis of this specialization is not yet established. OfHex1, the enzyme from the Asian corn borer Ostrinia furnacalis (one of the most destructive pests) has previously been reported to function merely in chitin degradation. Here the vital role of OfHex1 during the pupation of O. furnacalis was revealed by RNA interference, and the crystal structures of OfHex1 and OfHex1 complexed with TMG-chitotriomycin were determined at 2.1 Å. The mechanism of selective inhibition by TMG-chitotriomycin was related to the existence of the +1 subsite at the active pocket of OfHex1 and a key residue, Trp(490), at this site. Mutation of Trp(490) to Ala led to a 2,277-fold decrease in sensitivity toward TMG-chitotriomycin as well as an 18-fold decrease in binding affinity for the substrate (GlcNAc)(2). Although the overall topology of the catalytic domain of OfHex1 shows a high similarity with the human and bacterial enzymes, OfHex1 is distinguished from these enzymes by large conformational changes linked to an "open-close" mechanism at the entrance of the active site, which is characterized by the "lid" residue, Trp(448). Mutation of Trp(448) to Ala or Phe resulted in a more than 1,000-fold loss in enzyme activity, due mainly to the effect on k(cat). The current work has increased our understanding of the structure-function relationship of OfHex1, shedding light on the structural basis that accounts for the specialized function of β-N-acetyl-D-hexosaminidase as well as making the development of species-specific pesticides a likely reality.

  20. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    Science.gov (United States)

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  1. Placental complications after a previous cesarean section

    OpenAIRE

    Milošević Jelena; Lilić Vekoslav; Tasić Marija; Radović-Janošević Dragana; Stefanović Milan; Antić Vladimir

    2009-01-01

    Introduction The incidence of cesarean section has been rising in the past 50 years. With the increased number of cesarean sections, the number of pregnancies with the previous cesarean section rises as well. The aim of this study was to establish the influence of the previous cesarean section on the development of placental complications: placenta previa, placental abruption and placenta accreta, as well as to determine the influence of the number of previous cesarean sections on the complic...

  2. 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

  3. Valence-band structure of cubic CdS as determined by angle-resolved photoemission

    Science.gov (United States)

    Stampfl, A. P. J.; Hofmann, Ph.; Schaff, O.; Bradshaw, A. M.

    1997-04-01

    The valence-band structure of cubic CdS along the Γ-Σ-X direction and at all high-symmetry points has been experimentally determined using angle-resolved photoemission and compared to two local density approximation (LDA) calculations as well as to a recent quasiparticle calculation. The Cd 4d level was found to be semibandlike with an energy dispersion of up to 1 eV. The energy difference between the experimental and our calculated linear-muffin-tin orbital (LMTO) LDA energies falls, as expected, along a line of positive gradient. The quasiparticle calculation by Pollmann and co-workers fits the experimental values somewhat better than the LMTO calculation, although a difference of ~1.0 eV was still found to occur for the Cd 4d band. The self-interaction and relaxation-corrected pseudopotential LDA results by the same group give the best fit to within ~+/-0.5 eV for nearly all critical energies measured. Comparison with previously reported photoemission results on the wurtzite structure shows that energies at equivalent symmetry points agree within experimental error.

  4. Structural determinants of bacterial lytic polysaccharide monooxygenase functionality.

    Science.gov (United States)

    Forsberg, Zarah; Bissaro, Bastien; Gullesen, Jonathan; Dalhus, Bjørn; Vaaje-Kolstad, Gustav; Eijsink, Vincent G H

    2018-01-26

    Bacterial lytic polysaccharide monooxygenases (LPMO10s) use redox chemistry to cleave glycosidic bonds in the two foremost recalcitrant polysaccharides found in nature, namely cellulose and chitin. Analysis of correlated mutations revealed that the substrate-binding and copper-containing surface of LPMO10s composes a network of co-evolved residues and interactions, whose roles in LPMO functionality are unclear. Here, we mutated a subset of these correlated residues in a newly characterized C1/C4-oxidizing LPMO10 from Micromonospora aurantiaca ( Ma LPMO10B) to the corresponding residues in strictly C1-oxidizing LPMO10s. We found that surface properties near the catalytic copper, i.e. side chains likely to be involved in substrate positioning, are major determinants of the C1:C4 ratio. Several Ma LPMO10B mutants almost completely lost C4-oxidizing activity while maintaining C1-oxidizing activity. These mutants also lost chitin-oxidizing activity, which is typically observed for C1/C4-oxidizing, but not for C1-oxidizing, cellulose-active LPMO10s. Selective loss in C1-oxidizing activity was not observed. Additional mutational experiments disclosed that neither truncation of the Ma LPMO10B family 2 carbohydrate-binding module nor mutations altering access to the solvent-exposed axial copper coordination site significantly change the C1:C4 ratio. Importantly, several of the mutations that altered interactions with the substrate exhibited reduced stability. This effect could be explained by productive substrate binding that protects LPMOs from oxidative self-inactivation. We discuss these stability issues in view of recent findings on LPMO catalysis, such as the involvement of H 2 O 2 Our results show that residues on the substrate-binding surface of LPMOs have co-evolved to optimize several of the interconnected properties: substrate binding and specificity, oxidative regioselectivity, catalytic efficiency, and stability. © 2018 by The American Society for Biochemistry

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

    Energy Technology Data Exchange (ETDEWEB)

    Sun, X. H.; Akahori, Takuya; Anderson, C. S.; Farnes, J. S.; O’Sullivan, S. P. [Sydney Institute for Astronomy, School of Physics, The University of Sydney, NSW 2006 (Australia); Rudnick, L.; O’Brien, T. [Minnesota Institute for Astrophysics, School of Physics and Astronomy, University of Minnesota, 116 Church Street SE, Minneapolis, MN 55455 (United States); Bell, M. R. [Max Planck Institute for Astrophysics, Karl-Schwarzschild-Str. 1, D-85748 Garching (Germany); Bray, J. D.; Scaife, A. M. M. [Department of Physics and Astronomy, University of Southampton, Highfield, Southampton SO17 1BJ (United Kingdom); Ideguchi, S.; Kumazaki, K. [University of Nagoya, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan); Stepanov, R. [Institute of Continuous Media Mechanics, Korolyov str. 1, 614061 Perm (Russian Federation); Stil, J.; Wolleben, M. [Department of Physics and Astronomy, University of Calgary, 2500 University Drive NW, Calgary AB T2 N 1N4 (Canada); Takahashi, K. [University of Kumamoto, 2–39-1, Kurokami, Kumamoto 860-8555 (Japan); Weeren, R. J. van, E-mail: x.sun@physics.usyd.edu.au, E-mail: larry@umn.edu [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States)

    2015-02-01

    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{sub wtd}, (2) the separation Δϕ of two Faraday components, and (3) the reduced chi-squared χ{sub r}{sup 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{sub 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

  6. 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

  7. New improvements in automatic structure elucidation using the LSD (Logic for Structure Determination) and the SISTEMAT expert systems.

    Science.gov (United States)

    Plainchont, Bertrand; Nuzillard, Jean-Marc; Rodrigues, Gilberto V; Ferreira, Marcelo J P; Scotti, Marcus T; Emerenciano, Vicente P

    2010-05-01

    This article describes the integration of the LSD (Logic for Structure Determination) and SISTEMAT expert systems that were both designed for the computer-assisted structure elucidation of small organic molecules. A first step has been achieved towards the linking of the SISTEMAT database with the LSD structure generator. The skeletal descriptions found by the SISTEMAT programs are now easily transferred to LSD as substructural constraints. Examples of the synergy between these expert systems are given for recently reported natural products.

  8. 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...

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. Niche heterogeneity determines bacterial community structure in the termite gut (Reticulitermes santonensis).

    Science.gov (United States)

    Yang, Hong; Schmitt-Wagner, Dirk; Stingl, Ulrich; Brune, Andreas

    2005-07-01

    Differences in microenvironment and interactions of microorganisms within and across habitat boundaries should influence structure and diversity of the microbial communities within an ecosystem. We tested this hypothesis using the well characterized gut tract of the European subterranean termite Reticulitermes santonensis as a model. By cloning and sequencing analysis and molecular fingerprinting (terminal restriction fragment length polymorphism), we characterized the bacterial microbiota in the major intestinal habitats - the midgut, the wall of the hindgut paunch, the hindgut fluid and the intestinal protozoa. The bacterial community was very diverse (> 200 ribotypes) and comprised representatives of several phyla, including Firmicutes (mainly clostridia, streptococci and Mycoplasmatales-related clones), Bacteroidetes, Spirochaetes and a number of Proteobacteria, all of which were unevenly distributed among the four habitats. The largest group of clones fell into the so-called Termite group 1 (TG-1) phylum, which has no cultivated representatives. The majority of the TG-1 clones were associated with the protozoa and formed two phylogenetically distinct clusters, which consisted exclusively of clones previously retrieved from the gut of this and other Reticulitermes species. Also the other clones represented lineages of microorganisms that were exclusively recovered from the intestinal tract of termites. The termite specificity of these lineages was underscored by the finding that the closest relatives of the bacterial clones obtained from R. santonensis were usually derived also from the most closely related termites. Overall, differences in diversity between the different gut habitats and the uneven distribution of individual phylotypes support conclusively that niche heterogeneity is a strong determinant of the structure and spatial organization of the microbial community in the termite gut.

  17. Solving the Phase Problem in Crystal Structure Determination: A Simple Introduction to Direct Methods.

    Science.gov (United States)

    Schenk, H.

    1979-01-01

    Presents a simple way to introduce Direct Methods program systems to solve phase problems in x-ray crystal structure determination. It is intended for the undergraduate chemistry student laboratory. (Author/SA)

  18. 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

  19. 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.

  20. The Role of Conformational Entropy in the Determination of Structural-Kinetic Relationships for Helix-Coil Transitions

    Directory of Open Access Journals (Sweden)

    Joseph F. Rudzinski

    2018-02-01

    Full Text Available Coarse-grained molecular simulation models can provide significant insight into the complex behavior of protein systems, but suffer from an inherently distorted description of dynamical properties. We recently demonstrated that, for a heptapeptide of alanine residues, the structural and kinetic properties of a simulation model are linked in a rather simple way, given a certain level of physics present in the model. In this work, we extend these findings to a longer peptide, for which the representation of configuration space in terms of a full enumeration of sequences of helical/coil states along the peptide backbone is impractical. We verify the structural-kinetic relationships by scanning the parameter space of a simple native-biased model and then employ a distinct transferable model to validate and generalize the conclusions. Our results further demonstrate the validity of the previous findings, while clarifying the role of conformational entropy in the determination of the structural-kinetic relationships. More specifically, while the global, long timescale kinetic properties of a particular class of models with varying energetic parameters but approximately fixed conformational entropy are determined by the overarching structural features of the ensemble, a shift in these kinetic observables occurs for models with a distinct representation of steric interactions. At the same time, the relationship between structure and more local, faster kinetic properties is not affected by varying the conformational entropy of the model.

  1. Developed approach to determine the seismic vulnerability of reinforced concrete structures

    Directory of Open Access Journals (Sweden)

    Mahmoud Serraye

    2018-01-01

    Full Text Available Several evaluation methods of the seismic vulnerability have been developed around the world. Which are very use ful from humanitarian and socioeconomic point of view. Generally these methods use knowledge obtained from previous earthquakes and they are basing on seismic intensity scales and on buildings direct observation. But the macroseismic intensity expresses the consequences of the seism, and not its physical characteristics of the structures. Contrary to this type of methods, an approach based on a nonlinear analysis (Push-Over method is proposed in this work. It consists in modeling the excitation of the earthquake by a response spectrum and building's behavior by capacity curves. These capacity curves are obtained from numerical modeling performed by Opensees software. The superposition of the two curves, response spectra and capacity curve, makes it possible to determine the performance point and consequently to deduce the state of expected damage. To estimate the probability of damage of a building at a given level of solicitation (defined by Sd, we excites a group of buildings characterized by different parameters related to the geometry of the building and those are related to the materials used (concrete, steel by seismic solicitation (Response spectrum - RPA 99. The performance point for each building is determined by a procedure defined in FEMA 440. We classifies the buildings according to the position of performance point on their curve which defines a damage state of ds (Mild, Moderate, Important or Ruin according to the damage levels of Risk-UE. A statistical analysis is then made for each class to build the fragility curves.

  2. 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

  3. Structure determination and analysis of a bacterial chymotrypsin from Cellulomonas bogoriensis.

    Science.gov (United States)

    Shaw, A; Saldajeno, M L; Kolkman, M A B; Jones, B E; Bott, R

    2007-04-01

    The crystal structure of a secreted chymotrypsin from the alkaliphile Cellulomonas bogoriensis has been determined using data to 1.78 A resolution and refined to a crystallographic R factor of 0.167. The crystal structure reveals a large P1 substrate-specificity pocket, as expected for chymotrypsins. The structure is compared with close structural homologues. This comparison does not reveal clear reasons for the alkali tolerance of the enzyme, but the greater compactness of the structure and lowered hydrogen bonding may play a role.

  4. 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.

  5. 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...

  6. Life history determines genetic structure and evolutionary potential of host–parasite interactions

    OpenAIRE

    Barrett, Luke G.; Thrall, Peter H.; Burdon, Jeremy J.; Linde, Celeste C.

    2008-01-01

    Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the f...

  7. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference.

    Science.gov (United States)

    MacCallum, Justin L; Perez, Alberto; Dill, Ken A

    2015-06-02

    More than 100,000 protein structures are now known at atomic detail. However, far more are not yet known, particularly among large or complex proteins. Often, experimental information is only semireliable because it is uncertain, limited, or confusing in important ways. Some experiments give sparse information, some give ambiguous or nonspecific information, and others give uncertain information-where some is right, some is wrong, but we don't know which. We describe a method called Modeling Employing Limited Data (MELD) that can harness such problematic information in a physics-based, Bayesian framework for improved structure determination. We apply MELD to eight proteins of known structure for which such problematic structural data are available, including a sparse NMR dataset, two ambiguous EPR datasets, and four uncertain datasets taken from sequence evolution data. MELD gives excellent structures, indicating its promise for experimental biomolecule structure determination where only semireliable data are available.

  8. Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers

    NARCIS (Netherlands)

    Periole, Xavier; Knepp, Adam M.; Sakmar, Thomas P.; Marrink, Siewert J.; Huber, Thomas

    2012-01-01

    The G protein-coupled receptor (GPCR) rhodopsin self-assembles into supramolecular structures in native bilayers, but the structural determinants of receptor oligomerization are not known. We carried out multiple self-assembly coarse-grained molecular dynamics (CGMD) simulations of model membranes

  9. Class of continuous timelike curves determines the topology of spacetime. [Causal, topological, differential, and conformal structure

    Energy Technology Data Exchange (ETDEWEB)

    Malament, D.B.

    1977-07-01

    The title assertion is proven, and two corollaries are established. First, the topology of every past and future distinguishing spacetime is determined by its causal structure. Second, in every spacetime the path topology of Hawking, King, and McCarthy codes topological, differential, and conformal structure.

  10. 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…

  11. 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...... taken at tilted positions, can be transformed to the real macroscopic orientation of the planar structures with estimated error of about +/- 2 degrees. (C) 1998 Elsevier Science B.V. All rights reserved....

  12. Polymorph identification and crystal structure determination by a combined crystal structure prediction and transmission electron microscopy approach.

    Science.gov (United States)

    Eddleston, Mark D; Hejczyk, Katarzyna E; Bithell, Erica G; Day, Graeme M; Jones, William

    2013-06-10

    Electron diffraction offers advantages over X-ray based methods for crystal structure determination because it can be applied to sub-micron sized crystallites, and picogram quantities of material. For molecular organic species, however, crystal structure determination with electron diffraction is hindered by rapid crystal deterioration in the electron beam, limiting the amount of diffraction data that can be collected, and by the effect of dynamical scattering on reflection intensities. Automated electron diffraction tomography provides one possible solution. We demonstrate here, however, an alternative approach in which a set of putative crystal structures of the compound of interest is generated by crystal structure prediction methods and electron diffraction is used to determine which of these putative structures is experimentally observed. This approach enables the advantages of electron diffraction to be exploited, while avoiding the need to obtain large amounts of diffraction data or accurate reflection intensities. We demonstrate the application of the methodology to the pharmaceutical compounds paracetamol, scyllo-inositol and theophylline. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. 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

  14. 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

  15. 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

  16. 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

  17. Automated Protein NMR Structure Determination Using Wavelet De-noised NOESY Spectra

    International Nuclear Information System (INIS)

    Dancea, Felician; Guenther, Ulrich

    2005-01-01

    A major time-consuming step of protein NMR structure determination is the generation of reliable NOESY cross peak lists which usually requires a significant amount of manual interaction. Here we present a new algorithm for automated peak picking involving wavelet de-noised NOESY spectra in a process where the identification of peaks is coupled to automated structure determination. The core of this method is the generation of incremental peak lists by applying different wavelet de-noising procedures which yield peak lists of a different noise content. In combination with additional filters which probe the consistency of the peak lists, good convergence of the NOESY-based automated structure determination could be achieved. These algorithms were implemented in the context of the ARIA software for automated NOE assignment and structure determination and were validated for a polysulfide-sulfur transferase protein of known structure. The procedures presented here should be commonly applicable for efficient protein NMR structure determination and automated NMR peak picking

  18. Applicability study of the structure-factor phase method for determining the polarity of binary semiconductors.

    Science.gov (United States)

    Cao, Jiefeng; Guo, Chao; Zou, Huamin

    2013-12-01

    The structure-factor phase method of convergent-beam electron diffraction (CBED) has been widely applied as an effective tool in determining the polarity of binary compound materials, for example, the typical sphalerite material, GaAs. However, its validity on other polar materials is still unknown. In this paper we extensively investigated its potential applicability onto 11 AB-type semiconductors by dynamical simulations of CBED. Two key factors during the simulation, the difference between A and B atomic numbers and the sample thickness, are discussed in detail. It was found that this method is efficient to determine the polarity for a sphalerite structure under certain conditions, and, reversely, limited to determine the polarity for a wurtzite structure even though it is very similar to the sphalerite structure.

  19. Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints

    Science.gov (United States)

    Alber, Frank; Chait, Brian T.; Rout, Michael P.; Sali, Andrej

    To understand the cell, we need to determine the structures of macromolecular assemblies, many of which consist of tens to hundreds of components. A great variety of experimental data can be used to characterize the assemblies at several levels of resolution, from atomic structures to component configurations. To maximize completeness, resolution, accuracy, precision and efficiency of the structure determination, a computational approach is needed that can use spatial information from a variety of experimental methods. We propose such an approach, defined by its three main components: a hierarchical representation of the assembly, a scoring function consisting of spatial restraints derived from experimental data, and an optimization method that generates structures consistent with the data. We illustrate the approach by determining the configuration of the 456 proteins in the nuclear pore complex from Baker's yeast.

  20. [Determination of hemagglutination inhibiting antibodies against influenza virus A/Port Chalmers/1/73 in samples from the Roman population (1962-1974). Relation of antibody titers to those obtained against previous influenza A strains].

    Science.gov (United States)

    Castagnari, L; Delia, S; Russo, V; Sebastiani, A

    1975-01-01

    The h.i.a. titer has been determined against the strain of the A/Port Chalmers/1/73 influenza virus in 805 serum samples obtained in Rome from as many adults during six distinct periods between spring 1962 and summer-autumn 1974.

  1. 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.

  2. 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.

  3. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.

    Science.gov (United States)

    Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

    2013-11-01

    The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. © 2013 FEBS.

  4. 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.

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

    Science.gov (United States)

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

    2016-06-01

    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.

  6. 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.

  7. INTRODUCTION Previous reports have documented a high ...

    African Journals Online (AJOL)

    pregnancy if they were married, educated, had dental insurance, previously used dental services when not pregnant, or had knowledge about the possible connection between oral health and pregnancy outcome8. The purpose of this study was to explore the factors determining good oral hygiene among pregnant women ...

  8. Determination of partial structure factors by reverse Monte Carlo modelling—a test of the method

    Science.gov (United States)

    Gruner, S.; Akinlade, O.; Hoyer, W.

    2006-05-01

    The reverse Monte Carlo modelling technique is commonly applied for the analysis of the atomic structure of liquid and amorphous substances. In particular, partial structure factors of multi-component alloys can be determined using this method. In the present study we use the example of the liquid Ni33Ge67 alloy to investigate the impact of different input data on the result of RMC modelling. It was found that even two experimental structure factors might be sufficient to obtain reliable partial structure factors if the contrast between them is high enough.

  9. Role of electrostatic interactions in determining the G-quadruplex structures

    Science.gov (United States)

    Lee, Jinkeong; Im, Haeri; Chong, Song-Ho; Ham, Sihyun

    2018-02-01

    We investigate the energetics of the antiparallel, hybrid and parallel type G-quadruplex structures of the human telomere DNA sequence. We find that both the conformational energy and solvation free energy of these structures are roughly inversely proportional to their radii of gyration. We rationalize this finding in terms of the dominance of the electrostatic contributions. We also show that the solvation free energy is more significant than the conformational energy in determining the G-quadruplex structures, which is in contrast to the canonical B-DNA structures. Our work will contribute to an understanding of the molecular mechanisms dictating various G-quadruplex topologies.

  10. Determining Orientational Structure of Diamondoid Thiols Attached to Silver Using Near Edge X-ray Absorption Fine Structure Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Willey, T M; Lee, J I; Fabbri, J D; Wang, D; Nielsen, M; Randel, J C; Schreiner, P R; Fokin, A A; Tkachenko, B A; Fokina, N A; Dahl, J P; Carlson, R K; Terminello, L J; Melosh, N A; van Buuren, T

    2008-10-07

    Near-edge x-ray absorption fine structure spectroscopy (NEXAFS) is a powerful tool for determination of molecular orientation in self-assembled monolayers and other surface-attached molecules. A general framework for using NEXAFS to simultaneously determine molecular tilt and twist of rigid molecules attached to surfaces is presented. This framework is applied to self-assembled monolayers of higher diamondoid, hydrocarbon molecules with cubic-diamond-cage structures. Diamondoid monolayers chemisorbed on metal substrates are known to exhibit interesting electronic and surface properties. This work compares molecular orientation in monolayers prepared on silver substrates using two different thiol positional isomers of [121]tetramantane, and thiols derived from two different pentamantane structural isomers, [1212]pentamantane and [1(2,3)4]pentamantane. The observed differences in monolayer structure demonstrate the utility and limitations of NEXAFS spectroscopy and the framework. The results also demonstrate the ability to control diamondoid assembly, in particular the molecular orientational structure, providing a flexible platform for the modification of surface properties with this exciting new class of nanodiamond materials.

  11. 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)

  12. 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)

  13. 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.

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

    Science.gov (United States)

    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.

  15. 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

  16. Clinical significance of previously cryptic copy number alterations and loss of heterozygosity in pediatric acute myeloid leukemia and myelodysplastic syndrome determined using combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray analyses.

    Science.gov (United States)

    Koh, Kyung-Nam; Lee, Jin Ok; Seo, Eul Ju; Lee, Seong Wook; Suh, Jin Kyung; Im, Ho Joon; Seo, Jong Jin

    2014-07-01

    The combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray (CGH+SNP microarray) platform can simultaneously detect copy number alterations (CNA) and copy-neutral loss of heterozygosity (LOH). Eighteen children with acute myeloid leukemia (AML) (n=15) or myelodysplastic syndrome (MDS) (n=3) were studied using CGH+SNP microarray to evaluate the clinical significance of submicroscopic chromosomal aberrations. CGH+SNP microarray revealed CNAs at 14 regions in 9 patients, while metaphase cytogenetic (MC) analysis detected CNAs in 11 regions in 8 patients. Using CGH+SNP microarray, LOHs>10 Mb involving terminal regions or the whole chromosome were detected in 3 of 18 patients (17%). CGH+SNP microarray revealed cryptic LOHs with or without CNAs in 3 of 5 patients with normal karyotypes. CGH+SNP microarray detected additional cryptic CNAs (n=2) and LOHs (n=5) in 6 of 13 patients with abnormal MC. In total, 9 patients demonstrated additional aberrations, including CNAs (n=3) and/or LOHs (n=8). Three of 15 patients with AML and terminal LOH>10 Mb demonstrated a significantly inferior relapse-free survival rate (P=0.041). This study demonstrates that CGH+SNP microarray can simultaneously detect previously cryptic CNAs and LOH, which may demonstrate prognostic implications.

  17. 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

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

    Directory of Open Access Journals (Sweden)

    Krzyżek Robert

    2017-12-01

    Full Text Available 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

  19. 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

  20. Single-particle structure determination by correlations of snapshot X-ray diffraction patterns

    Science.gov (United States)

    Starodub, D.; Aquila, A.; Bajt, S.; Barthelmess, M.; Barty, A.; Bostedt, C.; Bozek, J. D.; Coppola, N.; Doak, R. B.; Epp, S. W.; Erk, B.; Foucar, L.; Gumprecht, L.; Hampton, C. Y.; Hartmann, A.; Hartmann, R.; Holl, P.; Kassemeyer, S.; Kimmel, N.; Laksmono, H.; Liang, M.; Loh, N. D.; Lomb, L.; Martin, A. V.; Nass, K.; Reich, C.; Rolles, D.; Rudek, B.; Rudenko, A.; Schulz, J.; Shoeman, R. L.; Sierra, R. G.; Soltau, H.; Steinbrener, J.; Stellato, F.; Stern, S.; Weidenspointner, G.; Frank, M.; Ullrich, J.; Strüder, L.; Schlichting, I.; Chapman, H. N.; Spence, J. C. H.; Bogan, M. J.

    2012-12-01

    Diffractive imaging with free-electron lasers allows structure determination from ensembles of weakly scattering identical nanoparticles. The ultra-short, ultra-bright X-ray pulses provide snapshots of the randomly oriented particles frozen in time, and terminate before the onset of structural damage. As signal strength diminishes for small particles, the synthesis of a three-dimensional diffraction volume requires simultaneous involvement of all data. Here we report the first application of a three-dimensional spatial frequency correlation analysis to carry out this synthesis from noisy single-particle femtosecond X-ray diffraction patterns of nearly identical samples in random and unknown orientations, collected at the Linac Coherent Light Source. Our demonstration uses unsupported test particles created via aerosol self-assembly, and composed of two polystyrene spheres of equal diameter. The correlation analysis avoids the need for orientation determination entirely. This method may be applied to the structural determination of biological macromolecules in solution.

  1. 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.

  2. 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)

  3. Life history determines genetic structure and evolutionary potential of host-parasite interactions.

    Science.gov (United States)

    Barrett, Luke G; Thrall, Peter H; Burdon, Jeremy J; Linde, Celeste C

    2008-12-01

    Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns.

  4. A comparison of the copper sensitivity of two economically important saltwater mussel species and a review of previously reported copper toxicity data for mussels: important implications for determining future ambient copper saltwater criteria in the USA.

    Science.gov (United States)

    Arnold, W Ray; Cotsifas, Jeffrey S; Smith, D Scott; Le Page, Steven; Gruenthal, Kristen M

    2009-12-01

    Saltwater bivalves of the genus Mytilus are among the most copper sensitive taxa listed in both the current and recently proposed U.S. EPA ambient saltwater copper criteria documents. The copper saltwater quality criteria are somewhat unique in that the criteria were set specifically to protect Mytilus. However, there is considerable uncertainty in the reported taxonomy of Mytilus species in the criteria database and it has recently been demonstrated the copper toxicity to M. galloprovincialis is dependent on the organic matter content of the test water. A review of the toxicity and biogeography literature was conducted to rationalize the existing criteria database. Elimination of some data is suggested due to the uncertainty of test organism genotype. Moreover, due to the lack of reported dissolved organic matter content of the test waters in tests included in the criteria database, it is impossible to determine if the difference in species mean acute values reported in the criteria documents for Mytilus was due to differences in water chemistry or differences in species sensitivity. Experiments were designed and conducted with M. galloprovincialis and M. edulis (genetically confirmed) to determine if copper toxicity is a function of organic matter content for these two species and if there is a significant difference in species copper sensitivity. Results showed that copper toxicity is a function of organic matter concentration for both species and copper sensitivity of each species was statistically similar. Results support the normalization of the saltwater copper criteria database with respect to dissolved organic matter when developing ambient saltwater copper criteria. The USEPA toxicity database would benefit from future testing of M. trossulus and M. californianus.

  5. Structure determination of contaminant proteins using the MarathonMR procedure.

    Science.gov (United States)

    Hatti, Kaushik; Biswas, Ansuman; Chaudhary, Santosh; Dadireddy, Venkatareddy; Sekar, Kanagaraj; Srinivasan, Narayanaswamy; Murthy, Mathur R N

    2017-03-01

    In the recent decades, essential steps of protein structure determination such as phasing by multiple isomorphous replacement and multi wave length anomalous dispersion, molecular replacement, refinement of the structure determined and its validation have been fully automated. Several computer program suites that execute all these steps as a pipeline operation have been made available. In spite of these great advances, determination of a protein structure may turn out to be a challenging task for a variety of reasons. It might be difficult to obtain multiple isomorphous replacement or multi wave length anomalous dispersion data or the crystal may have defects such as twinning or pseudo translation. Apart from these usual difficulties, more frequent difficulties have been encountered in recent years because of the large number of projects handled by structural biologists. These new difficulties usually result from contamination of the protein of interest by other proteins or presence of proteins from pathogenic organisms that could withstand the antibiotics used to prevent bacterial contamination. It could also be a result of poor book keeping. Recently, we have developed a procedure called MarathonMR that has the power to resolve some of these problems automatically. In this communication, we describe how the MarathonMR was used to determine four different protein structures that had remained elusive for several years. We describe the plausible reasons for the difficulties encountered in determining these structures and point out that the method presented here could be a validation tool for protein structures deposited in the protein data bank. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Habitat Heterogeneity Determines Climate Impact on Zooplankton Community Structure and Dynamics

    OpenAIRE

    Otto, Saskia A.; Diekmann, Rabea; Flinkman, Juha; Kornilovs, Georgs; Möllmann, Christian

    2014-01-01

    Understanding and predicting species distribution in space and time and consequently community structure and dynamics is an important issue in ecology, and particularly in climate change research. A crucial factor determining the composition and dynamics of animal populations is habitat heterogeneity, i.e., the number of structural elements in a given locality. In the marine pelagic environment habitat heterogeneity is represented by the distribution of physical oceanographic parameters such ...

  7. 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.

  8. 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...

  9. 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.

  10. 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

  11. Present and future of membrane protein structure determination by electron crystallography.

    Science.gov (United States)

    Ubarretxena-Belandia, Iban; Stokes, David L

    2010-01-01

    Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This chapter describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins. Copyright © 2010 Elsevier Inc. All rights reserved.

  12. 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.

  13. 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.)

  14. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data

    Energy Technology Data Exchange (ETDEWEB)

    Bunkóczi, Gábor; McCoy, Airlie J.; Echols, Nathaniel; Grosse-Kunstleve, Ralf W.; Adams, Paul D.; Holton, James M.; Read, Randy J.; Terwilliger, Thomas C.

    2014-12-22

    We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-06-30

    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 P1 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.

  16. Determination of magnetic structure of substance based on neutron diffraction experiment data

    International Nuclear Information System (INIS)

    Men'shikov, A.Z.; Vokhmyanin, A.P.; Dorofeev, Yu.A.

    1997-01-01

    The technique based on the experimental neutron diffraction data is developed for determination of the magnetic structure in solid solutions with the high symmetry. The theoretical junction of the elastic magnetic neutron scattering is considered. The examples of definition of magnetic structures of alloys Fe(Pd 1-x Pt) 3 , Fe(Pt 1-x Au) 3 , (Mn 1-x Fe x )Pt, (Fe 1-x Mn x )Pt by means of the proposed method are presented. The neutron diffraction images obtained with the resolution equal to 10 -2 are used for the recognition of the magnetic structures of these alloys [ru

  17. Determination of the optical model of the MOS structure with spectroscopic ellipsometry

    Science.gov (United States)

    Kudla, Andrzej; Brzezinska, Danuta; Wagner, Thomas; Sawicki, Zbigniew

    1997-04-01

    The internal photo injection phenomena in a semitransparent gate metal-oxide-semiconductor (MOS) structure were described among others by the Przewlocki formula. This formula describes the dependence between external voltage applied to the gate to get zero photoelectric current and the light absorption in both electrodes. To study optical properties of the MOS structure, ellipsometric measurements and calculations for the Al-SiO2-Si system were done using J.A. Woolam spectroscopic ellipsometer VASE. The optical model of this structure was determined and used to calculate the dependence of the voltage on the light wavelength (lambda) in Przewlocki's formula.

  18. Direct methods determination of the Si(111)-(6x6)Au surface structure

    DEFF Research Database (Denmark)

    Grozea, D.; Landree, E.; Marks, L.D.

    1998-01-01

    The atomic structure of the Au 6 x 6 on Si(111) phase has been determined using direct methods and surface X-ray diffraction data. This surface structure is very complicated, with 14 independent gold atoms, relaxations in 24 independent silicon sites and three partially occupied gold sites. In one...... the gold structures in the coverage range 0.8-1.5 monolayers as pseudo-glasses with strong short-range order but varying degrees of long-range order. (C) 1998 Elsevier Science B.V. All rights reserved....

  19. The Resource Approach to Determining the Competitiveness of Integrated Business Structures

    Directory of Open Access Journals (Sweden)

    Kosata Inna A.

    2015-03-01

    Full Text Available Solving problems of increasing the competitiveness of domestic integrated business structures under the current conditions of increasing impact of the global financial and economic crisis is inextricably linked to the effective use of available resources by business entities. This raises the need for creating new approaches to assessing the conditions, justification of characteristics , definition of the goals and directions of the integration processes, forms of cooperation between economic entities, assessing the degree of integration, establishing the functioning of integrated business structures at different stages of the life cycle and assessing their competitiveness. In the article the resource approach to determining the competitiveness of integrated business structures has been developed

  20. 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

  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 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.

  2. 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.

  3. Structure determination of biological macromolecules by NMR in solution: impact in biomedical research

    International Nuclear Information System (INIS)

    Wuethrich, K.

    1995-01-01

    Three-dimensional protein structures have a key role in biological and biomedical research, both as a basis for investigating correlations between molecular structure and physiological functions in natural systems, and as a platform for protein design and protein engineering. Although in this article little consideration was given to compounds other than peptides and proteins, the same applies to other biological macromolecules, in particular nucleic acids and their interactions with effector molecules and drugs. Eight years ago NMR spectroscopy in solution was introduced as a second method for structure determination of biopolymers, besides X-ray diffraction in protein crystals. In the meantime more than 200 NMR solution structures of proteins, nucleic acids, and complexes of drugs with molecules of these two classes of compounds have been determined, which is an important contribution toward easing the bottleneck in protein engineering and drug design caused by the scarcity of data on 3D structures. More importantly, perhaps, the structural data collected by NMR in solution complement the information obtained from crystallography, in particular by additional characterization of dynamic molecular properties. Combined use of information from the two techniques can therefore establish a more reliable structural foundation for modern biomedical research. In the present report this is illustrated with the cyclophilin-cyclosporin A system, which is of keen interest in the biomedical field. (author). 54 refs., 7 figs., 1 tab

  4. Uterine rupture without previous caesarean delivery

    DEFF Research Database (Denmark)

    Thisted, Dorthe L. A.; H. Mortensen, Laust; Krebs, Lone

    2015-01-01

    OBJECTIVE: To determine incidence and patient characteristics of women with uterine rupture during singleton births at term without a previous caesarean delivery. STUDY DESIGN: Population based cohort study. Women with term singleton birth, no record of previous caesarean delivery and planned...... vaginal delivery (n=611,803) were identified in the Danish Medical Birth Registry (1997-2008). Medical records from women recorded with uterine rupture during labour were reviewed to ascertain events of complete uterine rupture. Relative Risk (RR) and adjusted Relative Risk Ratio (aRR) of complete uterine...... rupture with 95% confidence intervals (95% CI) were ascertained according to characteristics of the women and of the delivery. RESULTS: We identified 20 cases with complete uterine rupture. The incidence of complete uterine rupture among women without previous caesarean delivery was about 3...

  5. Solution structure and molecular determinants of hemoglobin binding of the first NEAT domain of IsdB in Staphylococcus aureus.

    Science.gov (United States)

    Fonner, Brittany A; Tripet, Brian P; Eilers, Brian J; Stanisich, Jessica; Sullivan-Springhetti, Rose K; Moore, Rebecca; Liu, Mengyao; Lei, Benfang; Copié, Valérie

    2014-06-24

    The human pathogen Staphylococcus aureus acquires heme iron from hemoglobin (Hb) via the action of a series of iron-regulated surface determinant (Isd) proteins. The cell wall anchored IsdB protein is recognized as the predominant Hb receptor, and is comprised of two NEAr transporter (NEAT) domains that act in concert to bind, extract, and transfer heme from Hb to downstream Isd proteins. Structural details of the NEAT 2 domain of IsdB have been investigated, but the molecular coordination between NEAT 2 and NEAT 1 to extract heme from hemoglobin has yet to be characterized. To obtain a more complete understanding of IsdB structure and function, we have solved the 3D solution structure of the NEAT 1 domain of IsdB (IsdB(N1)) spanning residues 125-272 of the full-length protein by NMR. The structure reveals a canonical NEAT domain fold and has particular structural similarity to the NEAT 1 and NEAT 2 domains of IsdH, which also interact with Hb. IsdB(N1) is also comprised of a short N-terminal helix, which has not been previously observed in other NEAT domain structures. Interestingly, the Hb binding region (loop 2 of IsdB(N1)) is disordered in solution. Analysis of Hb binding demonstrates that IsdB(N1) can bind metHb weakly and the affinity of this interaction is further increased by the presence of IsdB linker domain. IsdB(N1) loop 2 variants reveal that phenylalanine 164 (F164) of IsdB is necessary for Hb binding and rapid heme transfer from metHb to IsdB. Together, these findings provide a structural role for IsdB(N1) in enhancing the rate of extraction of metHb heme by the IsdB NEAT 2 domain.

  6. 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

  7. First-principles structure determination of interface materials: The NixInAs nickelides

    Science.gov (United States)

    Schusteritsch, Georg; Hepplestone, Steven P.; Pickard, Chris J.

    2015-08-01

    We present here a first-principles study of the ternary compounds formed by Ni, In, and As, a material of great importance for self-aligned metallic contacts in next-generation InAs-based MOS transistors. The approach we outline is general and can be applied to study the crystal structure and properties of a host of other new interface compounds. Using the ab initio random structure searching approach we find the previously unknown low-energy structures of NixInAs and assess their stability with respect to the known binary compounds of Ni, In, and As. Guided by experiments, we focus on Ni3InAs and find a rich energy landscape for this stoichiometry. We consider the five lowest-energy structures, with space groups P m m n , P b c m , P 21/m , C m c m , and R 3 ¯ . The five low-energy structures for Ni3InAs are all found to be metallic and nonmagnetic. By comparison to previously published TEM results we identify the crystal structure observed in experiments to be C m c m Ni3InAs . We calculate the work function for C m c m Ni3InAs and, according to the Schottky-Mott model, expect the material to form an Ohmic contact with InAs. We further explicitly consider the interface between C m c m Ni3InAs and InAs and find it to be Ohmic with an n -type Schottky barrier height of -0.55 eV .

  8. 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

  9. 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

  10. 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

  11. 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 ...

  12. Synthesis and crystal structure determination of YCo Fe O 3 (= 0 ...

    Indian Academy of Sciences (India)

    The results on synthesis, crystal structure determination and calculation of crystallochemical parameters of YCo1−FeO3 ( = 0, 0.33, 0.5, 0.67 and 1) perovskites are presented in this work. The compounds within this series were synthesized by solution combustion method using two different fuels: urea and citric acid.

  13. 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 ...

  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. 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 has...

  16. Requirements on paramagnetic relaxation enhancement data for membrane protein structure determination by NMR.

    Science.gov (United States)

    Gottstein, Daniel; Reckel, Sina; Dötsch, Volker; Güntert, Peter

    2012-06-06

    Nuclear magnetic resonance (NMR) structure calculations of the α-helical integral membrane proteins DsbB, GlpG, and halorhodopsin show that distance restraints from paramagnetic relaxation enhancement (PRE) can provide sufficient structural information to determine their structure with an accuracy of about 1.5 Å in the absence of other long-range conformational restraints. Our systematic study with simulated NMR data shows that about one spin label per transmembrane helix is necessary for obtaining enough PRE distance restraints to exclude wrong topologies, such as pseudo mirror images, if only limited other NMR restraints are available. Consequently, an experimentally realistic amount of PRE data enables α-helical membrane protein structure determinations that would not be feasible with the very limited amount of conventional NOESY data normally available for these systems. These findings are in line with our recent first de novo NMR structure determination of a heptahelical integral membrane protein, proteorhodopsin, that relied extensively on PRE data. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    Midtgaard, Søren Roi; Darwish, Tamim A; Pedersen, Martin Cramer; Huda, Pie; Larsen, Andreas Haahr; Jensen, Grethe Vestergaard; Kynde, Søren Andreas Røssell; Skar-Gislinge, Nicholas; Nielsen, Agnieszka Janina Zygadlo; Olesen, Claus; Blaise, Mickael; Dorosz, Jerzy Józef; Thorsen, Thor Seneca; Venskutonytė, Raminta; Krintel, Christian; Møller, Jesper V; Frielinghaus, Henrich; Gilbert, Elliot Paul; Martel, Anne; Kastrup, Jette Sandholm; Jensen, Poul Erik; Nissen, Poul; Arleth, Lise

    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 scattering length difference between hydrogen and deuterium. Individual hydrogen/deuterium levels of the detergent head and tail groups were achieved such that the formed micelles became effectively invisible in heavy water (D 2 O) when investigated by neutrons. This way, only the signal from the membrane protein remained in the SANS data. We demonstrate that the method is not only generally applicable on five very different membrane proteins but also reveals subtle structural details about the sarco/endoplasmatic reticulum Ca 2+ ATPase (SERCA). In all, the synthesis of isotope-substituted detergents makes solution structure determination of membrane proteins by SANS and subsequent data analysis available to nonspecialists. © 2017 Federation of European Biochemical Societies.

  18. The use of a redox indicator to determine corrosiveness of wastewater towards metal structures

    Directory of Open Access Journals (Sweden)

    Butko Denis

    2017-01-01

    Full Text Available Corrosion damages of metal structures of wastewater treatment facilities affect the work process parameters and operation safety. The analysis of the factors causing corrosion of metal elements and the assessment of corrosion resistance of the steel grades St08ps, St3sp and St5sp during the treatment stages, including the chlorine treatment, were conducted based on the data obtained from the Rostov-on-Don aeration plant. The article search techniques to determine the corrosiveness of water towards the metal structures. It is established that in this case it is advantageous to use redox indicator systems (rH2, which is calculated on the basis of field measurements of redox potential (ORP of water. Based on the conducted studies, the correlation dependence for determining the corrosion rate of the steel grades St08ps and St5sp was suggested and statistically assessed for the aeration plant structures.

  19. 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)

  20. 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.

  1. 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.

  2. 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.

  3. Experimental and theoretical aspects of ab initio structure determination using powder diffraction techniques

    International Nuclear Information System (INIS)

    David, W.I.F.; Johnson, M.W.; Wilson, C.C.

    1988-01-01

    Neutron powder diffraction has, over the past two decades, developed into a powerful technique for the refinement of moderately complex crystal structures. The advent of a new generation of ultra-high resolution X-ray and neutron powder diffractometers, however, not only permits the refinement of more complex materials but also opens up new areas of research. Perhaps the most exciting development in powder diffraction techniques associated with high resolution is the ab initio determination of crystal structures. This has until recently been possible, in a routine way, only by single crystal studies. The compression of three dimensions of diffraction data to the one dimension of a powder diffraction pattern leads to an unavoidable loss of information. For many, but not all, crystal symmetries high resolution minimises this loss thus allowing the intensities of a sufficient number of resolved Bragg reflections from moderately complex materials to be extracted for use in structure solution by direct methods of phase determination and by Patterson methods. Recent structure determination using the high resolution powder diffractometer, HRPD, at ISIS will be presented. The inherent limitations resulting from crystal and instrumental resolution are discussed along with maximum entropy techniques that seek to optimise the information content of a powder diffraction pattern. (author) 36 refs., 1 fig., 3 tabs

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

    International Nuclear Information System (INIS)

    Huang, Yuanpeng Janet; Mao, Binchen; Xu, Fei; Montelione, Gaetano T.

    2015-01-01

    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 15 N– 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

  5. The economic, institutional, and political determinants of public health delivery system structures.

    Science.gov (United States)

    Ingram, Richard C; Scutchfield, F Douglas; Mays, Glen P; Bhandari, Michelyn W

    2012-01-01

    A typology of local public health systems was recently introduced, and a large degree of structural transformation over time was discovered in the systems analyzed. We present a qualitative exploration of the factors that determine variation and change in the seven structural configurations that comprise the local public health delivery system typology. We applied a 10-item semistructured telephone interview protocol to representatives from the local health agency in two randomly selected systems from each configuration--one that had maintained configuration over time and one that had changed configuration over time. We assessed the interviews for patterns of variation between the configurations. Four key determinants of structural change emerged: availability of financial resources, interorganizational relationships, public health agency organization, and political relationships. Systems that had changed were more likely to experience strengthened partnerships between public health agencies and other community organizations and enjoy support from policy makers, while stable systems were more likely to be characterized by strong partnerships between public health agencies and other governmental bodies and less supportive relationships with policy makers. This research provides information regarding the determinants of system change, and may help public health leaders to better prepare for the impacts of change in the areas discussed. It may also help those who are seeking to implement change to determine the contextual factors that need to be in place before change can happen, or how best to implement change in the face of contextual factors that are beyond their control.

  6. 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.

  7. 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

  8. 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

    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.

  9. Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data

    Science.gov (United States)

    Nilges, Michael

    2016-01-01

    Chromosome conformation capture (3C) techniques have revealed many fascinating insights into the spatial organization of genomes. 3C methods typically provide information about chromosomal contacts in a large population of cells, which makes it difficult to draw conclusions about the three-dimensional organization of genomes in individual cells. Recently it became possible to study single cells with Hi-C, a genome-wide 3C variant, demonstrating a high cell-to-cell variability of genome organization. In principle, restraint-based modeling should allow us to infer the 3D structure of chromosomes from single-cell contact data, but suffers from the sparsity and low resolution of chromosomal contacts. To address these challenges, we adapt the Bayesian Inferential Structure Determination (ISD) framework, originally developed for NMR structure determination of proteins, to infer statistical ensembles of chromosome structures from single-cell data. Using ISD, we are able to compute structural error bars and estimate model parameters, thereby eliminating potential bias imposed by ad hoc parameter choices. We apply and compare different models for representing the chromatin fiber and for incorporating singe-cell contact information. Finally, we extend our approach to the analysis of diploid chromosome data. PMID:28027298

  10. 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.

  11. 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.

  12. Economic development of the Republic of Serbia determined by the sectoral structure of the economy

    Directory of Open Access Journals (Sweden)

    Vladimir Micic

    2017-05-01

    Full Text Available Experience and good practice show that, in order to achieve economic growth and development, changes in the economic structure need to be made. They have an influence on the relative share, place and role of certain activities in the economy and they are the driver of sustainable economic development. Efficient structural changes are related to the capability of an economy to create more propulsive economic activities. The subject matter of the research in this paper is the determination of the degree of the determination of the economic development of the Republic of Serbia by the sectoral structure of the economy. The research goal is to indicate the adequacy of the size of and contribution of the sectors to the creation of gross value added and the total employment, i.e. the influence of the size, intensity and directions of changes between the sectors on the economic development. The research results are indicative of the fact that the achieved level of the development and low growth rate of the economy of the Republic of Serbia are the consequence of insufficiently comprehensive and intensive changes, changes that are late and are not stable. The future development of the economy will directly depend on the speed of changes and the creation of a modern sectional economic structure, especially the development of a propulsive manufacturing structure or “4.0 industries”.

  13. Discovering affordances that determine the spatial structure of reach-to-grasp movements.

    Science.gov (United States)

    Mon-Williams, Mark; Bingham, Geoffrey P

    2011-05-01

    Extensive research has identified the affordances used to guide actions, as originally conceived by Gibson (Perceiving, acting, and knowing: towards an ecological psychology. Erlbaum, Hillsdale, 1977; The ecological approach to visual perception. Erlbaum, Hillsdale, 1979/1986). We sought to discover the object affordance properties that determine the spatial structure of reach-to-grasp movements--movements that entail both collision avoidance and targeting. First, we constructed objects that presented a significant collision hazard and varied properties relevant to targeting, namely, object width and size of contact surface. Participants reached-to-grasp objects at three speeds (slow, normal, and fast). In Experiment 1, we explored a "stop" task where participants grasped the objects without moving them. In Experiment 2, we studied "fly-through" movements where the objects were lifted. We discovered the object affordance properties that produced covariance in the spatial structure of reaches-to-grasp. Maximum grasp aperture (MGA) reflected affordances determined by collision avoidance. Terminal grasp aperture (TGA)--when the hand stops moving but prior to finger contact--reflected affordances relevant to targeting accuracy. A model with a single free parameter predicted the prehensile spatial structure and provided a functional affordance-based account of that structure. In Experiment 3, we investigated a "slam" task where participants reached-to-grasp flat rectangular objects on a tabletop. The affordance structure of this task was found to eliminate the collision risk and thus reduced safety margins in MGA and TGA to zero for larger objects. The results emphasize the role of affordances in determining the structure and scaling of reach-to-grasp actions. Finally, we report evidence supporting the opposition vector as an appropriate unit of analysis in the study of grasping and a unit of action that maps directly to affordance properties.

  14. 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

  15. Structure of drug-target proteins determined by both X-ray and neutron diffraction

    International Nuclear Information System (INIS)

    Kuroki, Ryota

    2009-01-01

    Crystallography enables us to obtain accurate atomic positions within proteins. High resolution X-ray crystallography provides information for most of the atoms comprising a protein, with the exception of hydrogens. Neutron diffraction data can provide information of the location of hydrogen atoms to the structural information determined by X-ray crystallography. Here, we show the recent of the structural determination of drug-target proteins, porcine pancreatic elastase (PPE) and human immuno-deficiency virus type-1 protease (HIV-PR) by both X-ray and neutron diffraction. The structure of porcine pancreatic elastase with its potent inhibitor (FR13080) was determined to 0.94A resolution by X-ray diffraction and 1.75 A resolution by neutron diffraction. It was found that there are two characteristic hydrogen bonding interactions in which hydrogen atoms were confirmed. One is located between a catalytic aspartate and histidine, another is involved in the inhibitor recognition site. The structure of HIV-PR with its potent inhibitor (KNI-272) was also determined to 0.93 A resolution by X-ray diffraction and 2.3 A resolution by neutron diffraction. The ionization state of the catalytic residues were clarified to show that Asp125 is protonated and Asp25 is deprotonated. The ionization state and the location of hydrogen atoms of the catalytic residue in HIV-PR were firstly determined by neutron diffraction. Furthermore, collaborative use of both X-ray and neutron to identify the location of ambiguous hydrogen atoms will be shown. (author)

  16. Determination of Partial Structure Factors of Molten Eutectic Ni33Ge67

    Science.gov (United States)

    Halm, Th.; Hoyer, W.; Neumann, H.; Bellissent, R.

    1993-03-01

    Using isotopic substitution and X-ray scattering, different weighted structure factors were measured and combined in order to calculate partial structure factors. Although we got an overdetermined system of equations, the solution of this problem was difficult due to the small value of the determinant. From the partial pair correlation functions and the radial concentration correlation function a splitting of the first coordination shell is obvious. The dip in SNi-Ge and the corresponding peak in SNi-Ni indicate some degree of charge transfer in the melt.

  17. Structure Re-determination and Superconductivity Observation of Bulk 1T MoS2

    OpenAIRE

    Fang, Yuqiang; Pan, Jie; He, Jianqiao; Luo, Ruichun; Wang, Dong; Che, Xiangli; Bu, Kejun; Zhao, Wei; Liu, Pan; Mu, Gang; Zhang, Hui; Lin, Tianquan; Huang, Fuqiang

    2017-01-01

    2H MoS2 has been intensively studied because of layer-dependent electronic structures and novel physical properties. Though the metastable 1T MoS2 with the [MoS6] octahedron was observed from the microscopic area, the true crystal structure of 1T phase has not been determined strictly. Moreover, the true physical properties have not been demonstrated from experiments due to the challenge for the preparation of pure 1T MoS2 crystals. Here, we successfully synthesized the 1T MoS2 single crystal...

  18. 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.

  19. A Dynamic Analysis of Capital Structure Determinants. Empirical Results for Romanian Capital Market

    Directory of Open Access Journals (Sweden)

    Mihaela Dragota

    2008-04-01

    Full Text Available The analysis of capital structure and its determinants represents an useful approach for the Romanian and foreign investors and for the companies, at the same time. The main conclusion for capital structure analysis was that Romanian listed companies sustained their assets, in this order, on equity, commercial debt and, finally, on financial debt. The four variables used in the regression model are significant. The pecking order theory seemed to be more appropriate for the Romanian capital market, but the signalling theory was not entirely rejected.

  20. Towards the Structure Determination of a Modulated Protein Crystal: The Semicrystalline State of Profilin:Actin

    Science.gov (United States)

    Borgstahl, G.; Lovelace, J.; Snell, E. H.; Bellamy, H.

    2003-01-01

    One of the remaining challenges to structural biology is the solution of modulated structures. While small molecule crystallographers have championed this type of structure, to date, no modulated macromolecular structures have been determined. Modulation of the molecular structures within the crystal can produce satellite reflections or a superlattice of reflections in reciprocal space. We have developed the data collection methods and strategies that are needed to collect and analyze these data. If the macromolecule's crystal lattice is composed of physiologically relevant packing contacts, structural changes induced under physiological conditions can cause distortion relevant to the function and biophysical processes of the molecule making up the crystal. By careful measurement of the distortion, and the corresponding three-dimensional structure of the distorted molecule, we will visualize the motion and mechanism of the biological macromolecule(s). We have measured the modulated diffraction pattern produced by the semicrystalline state of profilin:actin crystals using highly parallel and highly monochromatic synchrotron radiation coupled with fine phi slicing (0.001-0.010 degrees) for structure determination. These crystals present these crystals present a unique opportunity to address an important question in structural biology. The modulation is believed to be due to the formation of actin helical filaments from the actin beta ribbon upon the pH-induced dissociation of profilin. To date, the filamentous state of actin has resisted crystallization and no detailed structures are available. The semicrystalline state profilin:actin crystals provides a unique opportunity to understand the many conformational states of actin. This knowledge is essential for understanding the dynamics underlying shape changes and motility of eukaryotic cells. Many essential processes, such as cytokinesis, phagocytosis, and cellular migration depend upon the capacity of the actin

  1. 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.

  2. Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.

    Science.gov (United States)

    Finer-Moore, J S; Kossiakoff, A A; Hurley, J H; Earnest, T; Stroud, R M

    1992-03-01

    The solvent structure in orthorhombic crystals of bovine trypsin has been independently determined by X-ray diffraction to 1.35 A resolution and by neutron diffraction to 2.1 A resolution. A consensus model of the water molecule positions was obtained using oxygen positions identified in the electron density map determined by X-ray diffraction, which were verified by comparison to D2O-H2O difference neutron scattering density. Six of 184 water molecules in the X-ray structure, all with B-factors greater than 50 A2, were found to be spurious after comparison with neutron results. Roughly two-thirds of the water of hydration expected from thermodynamic data for proteins was localized by neutron diffraction; approximately one-half of the water of hydration was located by X-ray diffraction. Polar regions of the protein are well hydrated, and significant D2O-H2O difference density is seen for a small number of water molecules in a second shell of hydration. Hydrogen bond lengths and angles calculated from unconstrained refinement of water positions are distributed about values typically seen in small molecule structures. Solvent models found in seven other bovine trypsin and trypsinogen and rat trypsin structures determined by X-ray diffraction were compared. Internal water molecules are well conserved in all trypsin structures including anionic rat trypsin, which is 65% homologous to bovine trypsin. Of the 22 conserved waters in trypsin, 19 were also found in trypsinogen, suggesting that they are located in regions of the apoprotein that are structurally conserved in the transition to the mature protein. Seven waters were displaced upon activation of trypsinogen. Water structure at crystal contacts is not generally conserved in different crystal forms. Three groups of integral structural water molecules are highly conserved in all solvent structures, including a spline of water molecules inserted between two beta-strands, which may resemble an intermediate in the

  3. Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling.

    Science.gov (United States)

    Harrer, Nadine; Schindler, Christina E M; Bruetzel, Linda K; Forné, Ignasi; Ludwigsen, Johanna; Imhof, Axel; Zacharias, Martin; Lipfert, Jan; Mueller-Planitz, Felix

    2018-02-06

    Chromatin remodeling factors assume critical roles by regulating access to nucleosomal DNA. To determine the architecture of the Drosophila ISWI remodeling enzyme, we developed an integrative structural approach that combines protein cross-linking, mass spectrometry, small-angle X-ray scattering, and computational modeling. The resulting structural model shows the ATPase module in a resting state with both ATPase lobes twisted against each other, providing support for a conformation that was recently trapped by crystallography. The autoinhibiting NegC region does not protrude from the ATPase module as suggested previously. The regulatory NTR domain is located near both ATPase lobes. The full-length enzyme is flexible and can adopt a compact structure in solution with the C-terminal HSS domain packing against the ATPase module. Our data imply a series of conformational changes upon activation of the enzyme and illustrate how the NTR, NegC, and HSS domains contribute to regulation of the ATPase module. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Secondary structure determination by NMR spectroscopy of an immunoglobulin-like domain from the giant muscle protein titin.

    Science.gov (United States)

    Pfuhl, M; Gautel, M; Politou, A S; Joseph, C; Pastore, A

    1995-07-01

    We present the complete 15N and 1H NMR assignment and the secondary structure of an immunoglobulin-like domain from the giant muscle protein titin. The assignment was obtained using homonuclear and 15N heteronuclear 2D and 3D experiments. The complementarity of 3D TOCSY-NOESY and 3D 15N NOESY-HSQC experiments, using WATERGATE for water suppression, allowed an efficient assignment of otherwise ambiguous cross peaks and was helpful in overcoming poor TOCSY transfer for some amino acids. The secondary structure is derived from specific NOEs between backbone alpha- and amide protons, secondary chemical shifts of alpha-protons and chemical exchange for the backbone amide protons. It consists of eight beta-strands, forming two beta-sheets with four strands each, similar to the classical beta-sandwich of the immunoglobulin superfamily, as previously predicted by sequence analysis. Two of the beta-strands are connected by type II beta-turns; the first beta-strand forms a beta-bulge. The whole topology is very similar to the only intracellular immunoglobulin-like domain for which a structure has been determined so far, i.e., telokin.

  5. 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 ...

  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. 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.

  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. Research on determination of operating posture of a complicated opto-mechanical structure

    Science.gov (United States)

    Su, Ruifeng; Zhu, Mingzhi; Chen, Xiaojuan; Wu, Wenkai; Huang, Zhan; Wang, Baoxu

    2016-10-01

    Operating posture of complicated opto-mechanical structures critically matter gravity-induced distortion of the structure, and further affect optical performance. With the aim to solve this problem, determination of operating postures of a supporting system of a KDP crystal is studied. A concept of key stiffness component is firstly proposed in this paper, as far as the authors are concerned, taking advantage of which gravity-induced distortion of the supporting system is analyzed, as well as the rotation of the KDP crystal that is cased by the distortion of the supporting system. Furthermore, effects of operating postures of the supporting system on the distortion of the supporting system and the rotation of the KDP crystal are investigated. It is demonstrated that key stiffness component is of great insignificance to distortion of the supporting system, and it could function as a guidance in determination of operating posture of the supporting system.

  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. X-ray structure determination of fully hydrated L alpha phase dipalmitoylphosphatidylcholine bilayers.

    Science.gov (United States)

    Nagle, J F; Zhang, R; Tristram-Nagle, S; Sun, W; Petrache, H I; Suter, R M

    1996-03-01

    Bilayer form factors obtained from x-ray scattering data taken with high instrumental resolution are reported for multilamellar vesicles of L alpha phase lipid bilayers of dipalmitoylphosphatidylcholine at 50 degrees C under varying osmotic pressure. Artifacts in the magnitudes of the form factors due to liquid crystalline fluctuations have been eliminated by using modified Caillé theory. The Caillé fluctuation parameter eta 1 increases systematically with increasing lamellar D spacing and this explains why some higher order peaks are unobservable for the larger D spacings. The corrected form factors fall on one smooth continuous transform F(q); this shows that the bilayer does not change shape as D decreases from 67.2 A (fully hydrated) to 60.9 A. The distance between headgroup peaks is obtained from Fourier reconstruction of samples with four orders of diffraction and from electron density models that use 38 independent form factors. By combining these results with previous gel phase results, area AF per lipid molecule and other structural quantities are obtained for the fluid L alpha phase. Comparison with results that we derived from previous neutron diffraction data is excellent, and we conclude from diffraction studies that AF = 62.9 +/- 1.3 A2, which is in excellent agreement with a previous estimate from NMR data.

  12. 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

  13. 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.

  14. 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

  15. 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...

  16. Xplor-NIH for molecular structure determination from NMR and other data sources.

    Science.gov (United States)

    Schwieters, Charles D; Bermejo, Guillermo A; Clore, G Marius

    2018-01-01

    Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. Here, some of Xplor-NIH's most useful data-associated energy terms are reviewed, including newer alternative options for using residual dipolar coupling data in structure calculations. Further, we discuss new developments in the implementation of strict symmetry for the calculation of symmetric homo-oligomers, and in the representation of the system as an ensemble of structures to account for motional effects. Finally, the different available force fields are presented, among other Xplor-NIH capabilities. © 2017 This article is a U.S. Government work and is in the public domain in the USA.

  17. Determining the Structure of Biomaterials Interfaces using Synchrotron-based X-ray Diffraction

    Energy Technology Data Exchange (ETDEWEB)

    McBride, M

    2002-01-24

    The purpose of this project is to explore the feasibility of using surface X-ray diffraction (SXRD) to determine the structure of biomineral surfaces in electrolyte solutions and of the adsorbed layer of acidic amino acids that are believed to play a central role in the control of biomineral formation and function. The work is a critical component in the development of an integrated picture of the physical and chemical basis for deposition and dissolution at solid-liquid interfaces in biological systems, and brings a new and very powerful surface-sensitive capability to LLNL. We have chosen as our model systems calcium carbonate and calcium phosphate in aspartic and glutamic acid-bearing solutions. The calcium compounds are ubiquitous among biomineral structures, both those that are beneficial such as bones and teeth, and those that are pathological such as kidney stones, while the two acidic amino acids--both as simple and poly-amino acids--are the dominant constituents of protein mixtures implicated in the control of biomineralization. The goals of the work are: (1) to determine the surface structure of pure calcium phosphate and calcium carbonate surfaces in aqueous solution using SXRD; (2) to determine how those surfaces are modified by the presence of aspartic and glutamic acid, both as the simple amino acids and as poly-aspartate and poly-glutamate and (3) to model the interactions of acidic amino acids with calcite.

  18. 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

  19. 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

  20. 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.

  1. A systematic review of the main factors that determine agility in sport using structural equation modeling

    Directory of Open Access Journals (Sweden)

    Hojka Vladimir

    2016-09-01

    Full Text Available While tests of basic motor abilities such as speed, maximum strength or endurance are well recognized, testing of complex motor functions such as agility remains unresolved in current literature. Therefore, the aim of this review was to evaluate which main factor or factor structures quantitatively determine agility. In methodological detail, this review focused on research that explained or described the relationships between latent variables in a factorial model of agility using approaches such as principal component analysis, factor analysis and structural equation modeling. Four research studies met the defined inclusion criteria. No quantitative empirical research was found that tried to verify the quality of the whole suggested model of the main factors determining agility through the use of a structural equation modeling (SEM approach or a confirmatory factor analysis. From the whole structure of agility, only change of direction speed (CODS and some of its subtests were appropriately analyzed. The combination of common CODS tests is reliable and useful to estimate performance in sub-elite athletes; however, for elite athletes, CODS tests must be specific to the needs of a particular sport discipline. Sprinting and jumping tests are stronger factors for CODS than explosive strength and maximum strength tests. The authors suggest the need to verify the agility factorial model by a second generation data analysis technique such as SEM.

  2. 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.

  3. A systematic review of the main factors that determine agility in sport using structural equation modeling.

    Science.gov (United States)

    Hojka, Vladimir; Stastny, Petr; Rehak, Tomas; Gołas, Artur; Mostowik, Aleksandra; Zawart, Marek; Musálek, Martin

    2016-09-01

    While tests of basic motor abilities such as speed, maximum strength or endurance are well recognized, testing of complex motor functions such as agility remains unresolved in current literature. Therefore, the aim of this review was to evaluate which main factor or factor structures quantitatively determine agility. In methodological detail, this review focused on research that explained or described the relationships between latent variables in a factorial model of agility using approaches such as principal component analysis, factor analysis and structural equation modeling. Four research studies met the defined inclusion criteria. No quantitative empirical research was found that tried to verify the quality of the whole suggested model of the main factors determining agility through the use of a structural equation modeling (SEM) approach or a confirmatory factor analysis. From the whole structure of agility, only change of direction speed (CODS) and some of its subtests were appropriately analyzed. The combination of common CODS tests is reliable and useful to estimate performance in sub-elite athletes; however, for elite athletes, CODS tests must be specific to the needs of a particular sport discipline. Sprinting and jumping tests are stronger factors for CODS than explosive strength and maximum strength tests. The authors suggest the need to verify the agility factorial model by a second generation data analysis technique such as SEM.

  4. 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.

  5. Determinants of the Effectiveness of Capital Structure Management at Ukrainian Listed Power-Producing Companies

    Directory of Open Access Journals (Sweden)

    Mastiuk Dmytro O.

    2017-07-01

    Full Text Available This article is concerned with a theoretical and practical study on determinants of the effectiveness of capital structure management. The basic theories on the formation and management of the capital structure were allocated; other researches related to studying the capital structure of enterprises was considered. The author considers 19 independent variables of diverse effect level (micro, meso and macro levels and one dependent variable – economically added value, which was selected as an indicator of the effectiveness of capital structure management. The studied period is 14 years from 2003 to 2016 and is based on five listed power-producing companies. Eight key determinants of the effectiveness of capital management were defined. The highest positive impact among certain factors is the rate by the National Bank of Ukraine and profitability, while the strongest negative influences are the levels of competition in the market and of inflation. On results of the study, a series of recommendations for selected power-producing equity companies in Ukraine have been proposed, with the aim of reducing negative influences and enhancing positive effects through the development and selection of financial strategies.

  6. Determining Complex Structures using Docking Method with Single Particle Scattering Data.

    Science.gov (United States)

    Wang, Hongxiao; Liu, Haiguang

    2017-01-01

    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.

  7. Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Makino, Debora Lika, E-mail: dmakino@biochem.mpg.de; Conti, Elena [Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany)

    2013-11-01

    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.

  8. Quantitative structure determination of nanostructured materials using the atomic pair distribution function analysis

    Science.gov (United States)

    Masadeh, Ahmad Salah

    The employed experimental method in this Ph.D. dissertation research is the atomic pair distribution function (PDF) technique specializing in high real space resolution local structure determination. The PDF is obtained via Fourier transform from powder total scattering data including the important local structural information in the diffuse scattering intensities underneath, and in-between, the Bragg peaks. Having long been used to study liquids and amorphous materials, the PDF technique has been recently successfully applied to highly crystalline materials owing to the advances in modern X-ray and neutron sources and computing power. The conventional XRD experiments probe for the presence of periodic structure which are reflected in the Bragg peaks. Local structural deviations or disorder mainly affect the diffuse scattering background. In order to have information about both long-range order and local structure disorder, a technique that takes both Bragg and diffuse scattering need to be used, such as the atomic pair distribution function (PDF) technique. This Ph.D. work introduces a PDF based methodology to quantitatively study nanostructure materials in general. The introduced methodology have been applied to a size-dependent structural study on CdSe nanoparticles (NPs). Quantitative structural information about structure, crystallinity level, core size, NP size, and inhomogeneous internal strain in the studied NPs have been obtained. This method is generally applicable to the characterization of the nano-scale solid, many of which may exhibit complex disorder and strain. The introduced methodology have been also applied on technologically important system, ultra-small CdSe NPs.

  9. Amperometric Determination of Bismuth Using Gallacetophenone Phenylhydrazone with the Structural Elucidation of Complex

    Directory of Open Access Journals (Sweden)

    D. Venkataramana Reddy

    2010-01-01

    Full Text Available Gallacetophenone phenylhydrazone (GPPH has been used as an analytical reagent for amperometric determination of bismuth. Bismuth is quantitatively determined by GPPH at pH 3.0-6.0. After studying the polarographic behaviour of GPPH and bismuth(III at dropping mercury electrode (DME, applied potential was fixed at -0.4v vs. saturated calomel electrode (SCE. The method was applied for the determination of bismuth in wood’s alloy. The composition of the complex corresponds to the formula Bi(C14 H14 O3 N22. The structure of the complex was arrived from the micro analytical data of the solid complex, thermogravimetric and differential thermal analysis curves and also from the infrared spectra of the complex.

  10. 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

  11. Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies.

    Science.gov (United States)

    Kaufmann, Kristian W; Dawson, Eric S; Henry, L Keith; Field, Julie R; Blakely, Randy D; Meiler, Jens

    2009-02-15

    To identify potential determinants of substrate selectivity in serotonin (5-HT) transporters (SERT), models of human and Drosophila serotonin transporters (hSERT, dSERT) were built based on the leucine transporter (LeuT(Aa)) structure reported by Yamashita et al. (Nature 2005;437:215-223), PBDID 2A65. Although the overall amino acid identity between SERTs and the LeuT(Aa) is only 17%, it increases to above 50% in the first shell of the putative 5-HT binding site, allowing de novo computational docking of tryptamine derivatives in atomic detail. Comparison of hSERT and dSERT complexed with substrates pinpoints likely structural determinants for substrate binding. Forgoing the use of experimental transport and binding data of tryptamine derivatives for construction of these models enables us to critically assess and validate their predictive power: A single 5-HT binding mode was identified that retains the amine placement observed in the LeuT(Aa) structure, matches site-directed mutagenesis and substituted cysteine accessibility method (SCAM) data, complies with support vector machine derived relations activity relations, and predicts computational binding energies for 5-HT analogs with a significant correlation coefficient (R = 0.72). This binding mode places 5-HT deep in the binding pocket of the SERT with the 5-position near residue hSERT A169/dSERT D164 in transmembrane helix 3, the indole nitrogen next to residue Y176/Y171, and the ethylamine tail under residues F335/F327 and S336/S328 within 4 A of residue D98. Our studies identify a number of potential contacts whose contribution to substrate binding and transport was previously unsuspected. (c) 2008 Wiley-Liss, Inc.

  12. 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.

  13. 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

    2018-02-09

    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.

  14. Direct Determination of Atomic Structure and Magnetic Coupling of Magnetite Twin Boundaries.

    Science.gov (United States)

    Chen, Chunlin; Li, Hongping; Seki, Takehito; Yin, Deqiang; Sanchez-Santolino, Gabriel; Inoue, Kazutoshi; Shibata, Naoya; Ikuhara, Yuichi

    2018-03-27

    Clarifying how the atomic structure of interfaces/boundaries in materials affects the magnetic coupling nature across them is of significant academic value and will facilitate the development of state-of-the-art magnetic devices. Here, by combining atomic-resolution transmission electron microscopy, atomistic spin-polarized first-principles calculations, and differential phase contrast imaging, we conduct a systematic investigation of the atomic and electronic structures of individual Fe 3 O 4 twin boundaries (TBs) and determine their concomitant magnetic couplings. We demonstrate that the magnetic coupling across the Fe 3 O 4 TBs can be either antiferromagnetic or ferromagnetic, which directly depends on the TB atomic core structures and resultant electronic structures within a few atomic layers. Revealing the one-to-one correspondence between local atomic structures and magnetic properties of individual grain boundaries will shed light on in-depth understanding of many interesting magnetic behaviors of widely used polycrystalline magnetic materials, which will surely promote the development of advanced magnetic materials and devices.

  15. 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.

  16. Near-atomic structure of Japanese encephalitis virus reveals critical determinants of virulence and stability.

    Science.gov (United States)

    Wang, Xiangxi; Li, Shi-Hua; Zhu, Ling; Nian, Qing-Gong; Yuan, Shuai; Gao, Qiang; Hu, Zhongyu; Ye, Qing; Li, Xiao-Feng; Xie, Dong-Yang; Shaw, Neil; Wang, Junzhi; Walter, Thomas S; Huiskonen, Juha T; Fry, Elizabeth E; Qin, Cheng-Feng; Stuart, David I; Rao, Zihe

    2017-04-26

    Although several different flaviviruses may cause encephalitis, Japanese encephalitis virus is the most significant, being responsible for thousands of deaths each year in Asia. The structural and molecular basis of this encephalitis is not fully understood. Here, we report the cryo-electron microscopy structure of mature Japanese encephalitis virus at near-atomic resolution, which reveals an unusual "hole" on the surface, surrounded by five encephalitic-specific motifs implicated in receptor binding. Glu138 of E, which is highly conserved in encephalitic flaviviruses, maps onto one of these motifs and is essential for binding to neuroblastoma cells, with the E138K mutation abrogating the neurovirulence and neuroinvasiveness of Japanese encephalitis virus in mice. We also identify structural elements modulating viral stability, notably Gln264 of E, which, when replaced by His264 strengthens a hydrogen-bonding network, leading to a more stable virus. These studies unveil determinants of neurovirulence and stability in Japanese encephalitis virus, opening up new avenues for therapeutic interventions against neurotropic flaviviruses.Japanese encephalitis virus (JEV) is a Flavivirus responsible for thousands of deaths every year for which there are no specific anti-virals. Here, Wang et al. report the cryo-EM structure of mature JEV at near-atomic resolution and identify structural elements that modulate stability and virulence.

  17. Structural determinants of the catalytic inhibition of human topoisomerase IIα by salicylate analogs and salicylate-based drugs.

    Science.gov (United States)

    Bau, Jason T; Kurz, Ebba U

    2014-06-15

    We previously identified salicylate as a novel catalytic inhibitor of human DNA topoisomerase II (topo II; EC 5.99.1.3) that preferentially targets the alpha isoform by interfering with topo II-mediated DNA cleavage. Many pharmaceuticals and compounds found in foods are salicylate-based. We have now investigated whether these are also catalytic inhibitors of topo II and the structural determinants modulating these effects. We have determined that a number of hydroxylated benzoic acids attenuate doxorubicin-induced DNA damage signaling mediated by the ATM protein kinase and inhibit topo II decatenation activity in vitro with varying potencies. Based on the chemical structures of these and other derivatives, we identified unique properties influencing topo II inhibition, including the importance of substitutions at the 2'- and 5'-positions. We extended our findings to a number of salicylate-based pharmaceuticals including sulfasalazine and diflunisal and found that both were effective at attenuating doxorubicin-induced DNA damage signaling, topo II DNA decatenation and they blocked stabilization of doxorubicin-induced topo II cleavable complexes in cells. In a manner similar to salicylate, we determined that these agents inhibit topo II-mediated DNA cleavage. This was accompanied by a concomitant decrease in topo II-mediated ATP-hydrolysis. Taken together, these findings reveal a novel function for the broader class of salicylate-related compounds and highlight the need for additional studies into whether they may impact the efficacy of chemotherapy regimens that include topo II poisons. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. 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.

  19. Ultrafast colorimetric determination of predominant protein structure evolution with gold nanoplasmonic particles

    Science.gov (United States)

    Kim, Hye Young; Choi, Inhee

    2016-01-01

    The intracellular and extracellular accumulation of disordered proteins and aggregated proteins occurs in many protein conformational diseases, such as aging-related neurodegeneration and alcoholic liver diseases. However, the conventional methods to study protein structural changes are limited for the rapid detection and monitoring of protein aggregation because of long incubation times (i.e., usually several days), complicated sample pretreatment steps, and expensive instrumentation. Here, we describe an ultrafast colorimetric method for the real-time monitoring of protein structure evolution and the determination of predominant structures via nanoparticle-assisted protein aggregation. During the aggregation process, nanoparticles act as nucleation cores, which form networks depending on the structures of the protein aggregates, and accelerate the kinetics of the protein aggregation. Simultaneously, these nanoparticles exhibit colorimetric responses according to their embedded shapes (e.g., fibrillar and amorphous) on the protein aggregates. We observed distinct spectral shifts and concomitant colorimetric responses of concentration- and type-dependent protein aggregation with the naked eye within a few minutes (drugs for protein conformational diseases.The intracellular and extracellular accumulation of disordered proteins and aggregated proteins occurs in many protein conformational diseases, such as aging-related neurodegeneration and alcoholic liver diseases. However, the conventional methods to study protein structural changes are limited for the rapid detection and monitoring of protein aggregation because of long incubation times (i.e., usually several days), complicated sample pretreatment steps, and expensive instrumentation. Here, we describe an ultrafast colorimetric method for the real-time monitoring of protein structure evolution and the determination of predominant structures via nanoparticle-assisted protein aggregation. During the aggregation

  20. 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

  1. 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.

  2. [Placental complications after a previous cesarean section].

    Science.gov (United States)

    Milosević, Jelena; Lilić, Vekoslav; Tasić, Marija; Radović-Janosević, Dragana; Stefanović, Milan; Antić, Vladimir

    2009-01-01

    The incidence of cesarean section has been rising in the past 50 years. With the increased number of cesarean sections, the number of pregnancies with the previous cesarean section rises as well. The aim of this study was to establish the influence of the previous cesarean section on the development of placental complications: placenta previa, placental abruption and placenta accreta, as well as to determine the influence of the number of previous cesarean sections on the complication development. The research was conducted at the Clinic of Gynecology and Obstetrics in Nis covering 10-year-period (from 1995 to 2005) with 32358 deliveries, 1280 deliveries after a previous cesarean section, 131 cases of placenta previa and 118 cases of placental abruption. The experimental groups was presented by the cases of placenta previa or placental abruption with prior cesarean section in obstetrics history, opposite to the control group having the same conditions but without a cesarean section in medical history. The incidence of placenta previa in the control group was 0.33%, opposite to the 1.86% incidence after one cesarean section (pcesarean sections and as high as 14.28% after three cesarean sections in obstetric history. Placental abruption was recorded as placental complication in 0.33% pregnancies in the control group, while its incidence was 1.02% after one cesarean section (pcesarean sections. The difference in the incidence of intrapartal hysterectomy between the group with prior cesarean section (0.86%) and without it (0.006%) shows a high statistical significance (pcesarean section is an important risk factor for the development of placental complications.

  3. 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

  4. 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)

  5. 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].

  6. 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.

  7. 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

  8. 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.

  9. Crystal structure of NAD+-dependent Peptoniphilus asaccharolyticus glutamate dehydrogenase reveals determinants of cofactor specificity.

    Science.gov (United States)

    Oliveira, Tânia; Panjikar, Santosh; Carrigan, John B; Hamza, Muaawia; Sharkey, Michael A; Engel, Paul C; Khan, Amir R

    2012-02-01

    Glutamate dehydrogenases (EC 1.4.1.2-4) catalyse the oxidative deamination of l-glutamate to α-ketoglutarate using NAD(P) as a cofactor. The bacterial enzymes are hexamers and each polypeptide consists of an N-terminal substrate-binding (Domain I) followed by a C-terminal cofactor-binding segment (Domain II). The reaction takes place at the junction of the two domains, which move as rigid bodies and are presumed to narrow the cleft during catalysis. Distinct signature sequences in the nucleotide-binding domain have been linked to NAD(+) vs. NADP(+) specificity, but they are not unambiguous predictors of cofactor preferences. Here, we have determined the crystal structure of NAD(+)-specific Peptoniphilus asaccharolyticus glutamate dehydrogenase in the apo state. The poor quality of native crystals was resolved by derivatization with selenomethionine, and the structure was solved by single-wavelength anomalous diffraction methods. The structure reveals an open catalytic cleft in the absence of substrate and cofactor. Modeling of NAD(+) in Domain II suggests that a hydrophobic pocket and polar residues contribute to nucleotide specificity. Mutagenesis and isothermal titration calorimetry studies of a critical glutamate at the P7 position of the core fingerprint confirms its role in NAD(+) binding. Finally, the cofactor binding site is compared with bacterial and mammalian enzymes to understand how the amino acid sequences and three-dimensional structures may distinguish between NAD(+) vs. NADP(+) recognition. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. 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.

  11. Deflection determination of concrete structures considering nonlinearity based on long-gauge strain sensors

    Science.gov (United States)

    Hong, Wan; Lv, Kui; Li, Bing; Jiang, Yuchen; Hu, Xiamin; Qu, Qizhong

    2017-10-01

    Deflection determination of concrete structures using distributed long-gauge strain sensors is investigated in this paper. Firstly, the relationship between deflection and distributed long-gauge strain of concrete beams is presented, and the method is independent of external load and takes account of structural nonlinearity. The deflection distribution along the span of a beam-like structure can be predicted from strain response for the whole process of loading (elastic stage, concrete cracking stage and steel yielding stage). Secondly, experiment of a reinforced concrete beam has been conducted to verify the accuracy of the method. Experimental results show that the relative error between the estimated and actual deflection can be controlled within about 5% while the error can reach up to about 70% if structural nonlinearity is not considered. Finally, the influence of error of material parameters and sensor gauge length on deflection estimation has been analyzed. The error of concrete compression strength has a limited influence on deflection prediction while the contribution of tensile concrete should be considered before concrete cracking. The error of area of tensile bars will affect the deflection accuracy after concrete cracking.

  12. Tutorial for Collecting and Processing Images of Composite Structures to Determine the Fiber Volume Fraction

    Science.gov (United States)

    Conklin, Lindsey

    2017-01-01

    Fiber-reinforced composite structures have become more common in aerospace components due to their light weight and structural efficiency. In general, the strength and stiffness of a composite structure are directly related to the fiber volume fraction, which is defined as the fraction of fiber volume to total volume of the composite. The most common method to measure the fiber volume fraction is acid digestion, which is a useful method when the total weight of the composite, the fiber weight, and the total weight can easily be obtained. However, acid digestion is a destructive test, so the material will no longer be available for additional characterization. Acid digestion can also be difficult to machine out specific components of a composite structure with complex geometries. These disadvantages of acid digestion led the author to develop a method to calculate the fiber volume fraction. The developed method uses optical microscopy to calculate the fiber area fraction based on images of the cross section of the composite. The fiber area fraction and fiber volume fraction are understood to be the same, based on the assumption that the shape and size of the fibers are consistent in the depth of the composite. This tutorial explains the developed method for optically determining fiber area fraction performed at NASA Langley Research Center.

  13. 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

  14. A high-resolution structure of a DNA-chromomycin-Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance.

    Science.gov (United States)

    Gochin, M

    2000-04-15

    The drug chromomycin-A(3) binds to the minor groove of DNA and requires a divalent metal ion for complex formation. (1)H, (31)P and (13)C pseudocontact shifts occurring in the presence of a tightly bound divalent cobalt ion in the complex between d(TTGGCCAA)(2) and chromomycin-A(3) have been used to determine the structure of the complex. The accuracy of the structure was verified by validation with nuclear Overhauser enhancements (NOEs) and J-coupling constants not used in the structure calculation. The final structure was determined to 0.7 A resolution. The structure was compared with a structure obtained in an earlier study using NOEs, in order to assess the accuracy of NOEs in giving global structural information for a DNA complex. Although some basic features of the structures agreed, they differed substantially in the fine structural details and in the DNA axis curvature generated by the drug. The distortion of base-pair planarity that was observed in the NOE structure was not seen in our structure. Differences in drug orientation and hydrogen bonding also occurred. The curvature and elongation of the DNA that was obtained previously was not found to occur in our study. The use of pseudocontact shifts has enabled us to obtain a high-precision global structure of the chromomycin-DNA complex, which provides an accurate template on which to consider targeting minor groove binding drugs. The effect of such binding is not propagated far along the helix but is restricted to a local kink in the axis that reverts to its original direction within four base pairs.

  15. Structural and enzymatic characterization of a host-specificity determinant from Salmonella

    International Nuclear Information System (INIS)

    Kohler, Amanda C.; Spanò, Stefania; Galán, Jorge E.; Stebbins, C. Erec

    2014-01-01

    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

  16. Determination of the structure of Langmuir-Blodgett monolayers by infrared dichroism

    International Nuclear Information System (INIS)

    Chollet, Pierre-Alain

    1982-01-01

    We show that the study of absorption and reflexion infrared dichroism is a suitable tool for the determination of the crystallographic structure and of the molecules orientation in Langmuir-Blodgett multilayers. Their thickness range is comprised between 30 and 2000 angstroms. We have worked up a theoretical model which allows a quantitative interpretation of the absorption of thin anisotropic crystals. Two kind of multilayers are studied: one built of a saturated aliphatic acid and the other one with an ethylenic acid. These layers are composed of adjoining crystallites which are oriented on the substrate during the transfer process. The crystallisation propagates in a direction perpendicular to the layers in the case of the saturated acid, while ethylenic acid monolayers are constituted of a superimposition of two-dimensional smectic structures. Using reflexion experiments on metallic substrates we show that the molecules in the very first layers are oriented in a direction perpendicular to the substrate. (author) [fr

  17. 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.

  18. 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.

  19. Structure determination of Pt-coated Au dumbbells via fluctuation X-ray scattering.

    Science.gov (United States)

    Chen, Gang; Modestino, Miguel A; Poon, Billy K; Schirotzek, André; Marchesini, Stefano; Segalman, Rachel A; Hexemer, Alexander; Zwart, Peter H

    2012-09-01

    A fluctuation X-ray scattering experiment has been carried out on platinum-coated gold nanoparticles randomly oriented on a substrate. A complete algorithm for determining the electron density of an individual particle from diffraction patterns of many particles randomly oriented about a single axis is demonstrated. This algorithm operates on angular correlations among the measured intensity distributions and recovers the angular correlation functions of a single particle from measured diffraction patterns. Taking advantage of the cylindrical symmetry of the nanoparticles, a cylindrical slice model is proposed to reconstruct the structure of the nanoparticles by fitting the experimental ring angular auto-correlation and small-angle scattering data obtained from many scattering patterns. The physical meaning of the refined structure is discussed in terms of their statistical distributions of the shape and electron density profile.

  20. 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...... scattering length difference between hydrogen and deuterium. Individual hydrogen/deuterium levels of the detergent head and tail groups were achieved such that the formed micelles became effectively invisible in heavy water (D2 O) when investigated by neutrons. This way, only the signal from the membrane...... protein remained in the SANS data. We demonstrate that the method is not only generally applicable on five very different membrane proteins but also reveals subtle structural details about the sarco/endoplasmatic reticulum Ca2+ ATPase (SERCA). In all, the synthesis of isotope-substituted detergents makes...

  1. SOLVATION STRUCTURE DETERMINATION OF Ni2+ ION IN WATER BY MEANS OF MONTE CARLO METHOD

    Directory of Open Access Journals (Sweden)

    Tutik Arindah

    2010-06-01

    Full Text Available Determination of solvation structure of Ni2+ ion in water has been achieved using Monte Carlo method using canonic assemble (NVT constant. Simulation of a Ni2+ ion in 215 H2O molecules has been done under NVT condition (298.15 K. The results showed that number of H2O molecules surround Ni2+ ion were 8 molecules in first shell and 17 molecules in second shell, interaction energy of Ni2+-H2O in first shell was -68.7 kcal/mol and in second shell was -9.8 kcal/mol, and there were two angles of O-Ni2+-O, i.e. 74o and 142o. According to those results, the solvation structure of Ni2+ ion in water was cubic antisymetric.   Keywords: Water simulation, Monte Carlo simulation

  2. A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions.

    Science.gov (United States)

    Conte, Matthew A; Gammerdinger, William J; Bartie, Kerry L; Penman, David J; Kocher, Thomas D

    2017-05-02

    Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these fish. In this study, we developed a significantly improved assembly of the tilapia genome using the latest genome sequencing methods and show how it improves the characterization of two sex determination regions in two tilapia species. A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing. Dozens of candidate de novo assemblies were generated and an optimal assembly (contig NG50 of 3.3Mbp) was selected using principal component analysis of likelihood scores calculated from several paired-end sequencing libraries. Comparison of the new assembly to the previous O. niloticus genome assembly reveals that recently duplicated portions of the genome are now well represented. The overall number of genes in the new assembly increased by 27.3%, including a 67% increase in pseudogenes. The new tilapia genome assembly correctly represents two recent vasa gene duplication events that have been verified with BAC sequencing. At total of 146Mbp of additional transposable element sequence are now assembled, a large proportion of which are recent insertions. Large centromeric satellite repeats are assembled and annotated in cichlid fish for the first time. Finally, the new assembly identifies the long-range structure of both a ~9Mbp XY sex determination region on LG1 in O. niloticus, and a ~50Mbp WZ sex determination region on LG3 in the related species O. aureus. This study highlights the use of long read sequencing to correctly assemble recent duplications and to characterize repeat-filled regions of the genome. The study serves as an example of the need for high quality genome assemblies and provides a framework for identifying sex determining genes in tilapia and related fish species.

  3. Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage ${\\Phi}$6 Major Capsid Protein

    Energy Technology Data Exchange (ETDEWEB)

    Nemecek, Daniel [Masaryk Univ., Brno (Czech Republic); Plevka, Pavel [Masaryk Univ., Brno (Czech Republic); Boura, Evzen [Czech Academy of Sciences, Prague (Czech Republic). Inst. of Organic Chemistry and Biochemistry

    2013-11-29

    Bacteriophage ${\\Phi}$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of ${\\Phi}$6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the ${\\Phi}$6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.

  4. Interactions between Intracellular Domains as Key Determinants of the Quaternary Structure and Function of Receptor Heteromers*

    Science.gov (United States)

    Navarro, Gemma; Ferré, Sergi; Cordomi, Arnau; Moreno, Estefania; Mallol, Josefa; Casadó, Vicent; Cortés, Antoni; Hoffmann, Hanne; Ortiz, Jordi; Canela, Enric I.; Lluís, Carme; Pardo, Leonardo; Franco, Rafael; Woods, Amina S.

    2010-01-01

    G protein-coupled receptor (GPCR) heteromers are macromolecular complexes with unique functional properties different from those of its individual protomers. Little is known about what determines the quaternary structure of GPCR heteromers resulting in their unique functional properties. In this study, using resonance energy transfer techniques in experiments with mutated receptors, we provide for the first time clear evidence for a key role of intracellular domains in the determination of the quaternary structure of GPCR heteromers between adenosine A2A, cannabinoid CB1, and dopamine D2 receptors. In these interactions, arginine-rich epitopes form salt bridges with phosphorylated serine or threonine residues from CK1/2 consensus sites. Each receptor (A2A, CB1, and D2) was found to include two evolutionarily conserved intracellular domains to establish selective electrostatic interactions with intracellular domains of the other two receptors, indicating that these particular electrostatic interactions constitute a general mechanism for receptor heteromerization. Mutation experiments indicated that the interactions of the intracellular domains of the CB1 receptor with A2A and D2 receptors are fundamental for the correct formation of the quaternary structure needed for the function (MAPK signaling) of the A2A-CB1-D2 receptor heteromers. Analysis of MAPK signaling in striatal slices of CB1 receptor KO mice and wild-type littermates supported the existence of A1-CB1-D2 receptor heteromer in the brain. These findings allowed us to propose the first molecular model of the quaternary structure of a receptor heteromultimer. PMID:20562103

  5. Effective Computational Strategies for Determining Structures of Carcinogen-Damaged DNA

    Science.gov (United States)

    Broyde, S.; Hingerty, B. E.

    1999-05-01

    To determine three-dimensional conformations of DNA damaged by environmental chemical carcinogens, effective molecular mechanics search techniques have been developed to deal with the large system sizes and computational demands. First, extensive surveys of the potential energy surface are carried out by energy minimization. These search strategies rely on (1) using the reduced variable domain of torsion-angle (rather than Cartesian) space, (2) building larger units (about 12 base pairs) on the basis of structures of small modified subunits, and (3) employing penalty functions to search for selected hydrogen bonding patterns and to incorporate interproton distance bounds when available from experimental high-resolution nuclear magnetic resonance (NMR) studies. Second, molecular dynamics simulations with solvent can subsequently be employed to probe conformational features in the presence of polymerase enzyme responsible for DNA replication, using structures computed in the energy minimization searches as initial coordinates. A key structure-function relationship involving mirror-image molecules with very differing experimentally determined tumorigenic potencies has been deduced: the members of the pairs align oppositely when bound to DNA, making it likely that their treatment by replication and repair enzymes differ. This opposite orientation phenomenon, first predicted computationally (Singh et al., 1991), has been observed in experimental high-resolution NMR studies combined with our molecular mechanics computations in a number of different examples and has recently been confirmed experimentally in other laboratories as well (reviewed in Geacintov et al., 1997). Elucidation of this conformational feature has paved the way to uncovering the structural origin underlying very different biological outcomes stemming from chemically identical but mirror-image molecules.

  6. Ultra-small-angle neutron scattering: large-scale structure determination from a bird's eye view

    International Nuclear Information System (INIS)

    Rehma, A.; Brûlé, A.; Freund, A.; Kennedy, S.

    2012-01-01

    Both natural and synthetic materials science and engineering rely increasingly on detailed knowledge of the microstructure and interactions in soft and hard materials. Contemporary research areas in biology and the life sciences, e.g., include membrane biophysics, drug-delivery systems and pharmacology, denial and medical composites, biomaterials, fillings and implants in each of these areas large length scale measurements become necessary as model biological systems begin to approach the complexity of natural systems Porosity (void structure) and particle size need to be understood so that the processes of agglomeration and water transport can be quantified in materials such as cements, oil bearing rooks, and pewit pigments Complex fluids, containing structures and complexes in the nanometre and much larger length scales, have widely varying physical properties and are extensively used in food, cosmetic/personal care, pharmaceuticals and drug-delivery, and mining industries. In these length-scales are some of the organisational features that dictate the bulk rheological and stability properties of solutions. At ANSTO a new ultra-small-angle neutron scattering (USANS) instrument, Kookaburra (currently) under construction with an expected transition to operation in mid-2013), will advance large-scale structure determination in the size range of 0.1-10 µm. Based on the well-established Bonse-Hart method. Kookaburra will individually operate at two different wavelengths to optimally accommodate weakly and strongly scattering samples at one sample position. This contribution will present specifics of Kookaburra and also discuss a practical application of the USANS technique in polymer science. Both its versatility and estimated neutron flux suggest that this state-.of-the-art instrument will generate a major impact in the field of large-scale structure determination.

  7. 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)

  8. 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

  9. A simple structural power method for determining the vibratory strength of machinery sources

    DEFF Research Database (Denmark)

    Ohlrich, Mogens

    1998-01-01

    A new simple characterisation of the vibrational source strength of multi-terminal machinery is formulated in terms of a total terminal source power. This single power spectrum is determined from a summation of pairs of mean square velocities and point mobilities of the machine feet. The method...... is tested experimentally for two practical source-receiver configurations. The results clearly demonstrate the simplicity of the method and its high potential for engineering evaluation of machinery source strength and for coarse prediction of power transmission to supporting structures. In principle...

  10. Functional Identification and Structure Determination of Two Novel Prolidases from cog1228 in the Amidohydrolase Superfamily

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, Dao Feng; Patskovsky, Yury; Xu, Chengfu; Fedorov, Alexander A.; Fedorov, Elena V.; Sisco, Abby A.; Sauder, J. Michael; Burley, Stephen K.; Almo, Steven C.; Raushel, Frank M. (Einstein); (TAM); (Lilly)

    2010-12-07

    Two uncharacterized enzymes from the amidohydrolase superfamily belonging to cog1228 were cloned, expressed, and purified to homogeneity. The two proteins, Sgx9260c (gi|44242006) and Sgx9260b (gi|44479596), were derived from environmental DNA samples originating from the Sargasso Sea. The catalytic function and substrate profiles for Sgx9260c and Sgx9260b were determined using a comprehensive library of dipeptides and N-acyl derivative of L-amino acids. Sgx9260c catalyzes the hydrolysis of Gly-L-Pro, L-Ala-L-Pro, and N-acyl derivatives of L-Pro. The best substrate identified to date is N-acetyl-L-Pro with a value of k{sub cat}/K{sub m} of 3 x 10{sup 5} M{sup -1} s{sup -1}. Sgx9260b catalyzes the hydrolysis of L-hydrophobic L-Pro dipeptides and N-acyl derivatives of L-Pro. The best substrate identified to date is N-propionyl-L-Pro with a value of k{sub cat}/K{sub m} of 1 x 10{sup 5} M{sup -1} s{sup -1}. Three-dimensional structures of both proteins were determined by X-ray diffraction methods (PDB codes 3MKV and 3FEQ). These proteins fold as distorted ({beta}/{alpha})8-barrels with two divalent cations in the active site. The structure of Sgx9260c was also determined as a complex with the N-methylphosphonate derivative of L-Pro (PDB code 3N2C). In this structure the phosphonate moiety bridges the binuclear metal center, and one oxygen atom interacts with His-140. The {alpha}-carboxylate of the inhibitor interacts with Tyr-231. The proline side chain occupies a small substrate binding cavity formed by residues contributed from the loop that follows {beta}-strand 7 within the ({beta}/{alpha})8-barrel. A total of 38 other proteins from cog1228 are predicted to have the same substrate profile based on conservation of the substrate binding residues. The structure of an evolutionarily related protein, Cc2672 from Caulobacter crecentus, was determined as a complex with the N-methylphosphonate derivative of L-arginine (PDB code 3MTW).

  11. 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.

  12. Determination of the structure of a new tetragonal U2FeAl20 phase

    International Nuclear Information System (INIS)

    Meshi, L.; Munitz, A.; Talianker, M.

    2008-01-01

    The atomic structure of a new ternary U 2 FeAl 20 phase appearing in the Al-rich corner of a U-Fe-Al system was solved using electron crystallography and X-ray powder diffraction techniques (XRD). The positions of U atoms were determined from crystallographically processed high-resolution electron microscopy (HRTEM) images. These positions were used as a starting set for determining the coordinates of Fe and Al atoms by difference-Fourier synthesis technique. The U 2 FeAl 20 phase is tetragonal and belongs to the I4-bar 2m space group. Its unit cell contains 80 Al, 4 Fe, and 8 U atoms. The lattice parameters obtained after Rietveld refinement are: a = 12.4138 A, c = 10.3014 A. The reliability factors characterizing the Rietveld refinement procedure are: R p = 8.65%, R wp = 11.2% and R b = 5.93%

  13. Determination of assurance сoefficient by supporting structures fatigue of car bodies during transportation by the railway ferries

    Directory of Open Access Journals (Sweden)

    A. A. Lovskaya

    2014-12-01

    Full Text Available Purpose. To determine assurance coefficient by supporting structures fatigue of car bodies during transportation by the railway ferries. Methodology. The operating conditions of cars in international railway-water communication have been investigated in previous works for the solution of this problem. To solve the problem there were conducted researches of dynamic features of car bodies transporting by the railway ferries in conditions of the sea storm. A mathematical model of car bodies movement was made up and accelerations acting on them in placements on the decks were determined. During determination of accelerations the actual meteorological characteristics of the Black Sea during a storm were taken into account. The assurance coefficient fatigue by supporting structures of car bodies by the railway ferries was determined and it was found that under regular loading of the car body n ≈ 2,0 . It is higher than the admissible value. Findings. Comparison of obtained acceleration values with the accelerations acting on car bodies when operating on main-line routes showed that they have exceeded the acceleration specified in the regulations approximately on 40%. It proves the need of accounting the loads acting on car bodies during transportations by the railway ferries when designing new generation cars. Originality. There was proposed a mathematical model of car bodies movement by the railway ferries in the conditions of sea storm. It gives the possibility of determining the accelerations of car bodies placed on the decker rail ferries taking into account the hydrometeorology characteristics. Practical value. The results of researches can be used when designing new generation cars to provide their strength during the combination of railway and water transportation. It gives an opportunity to develop measures as to the adaptation of cars bodies to the interaction with the fastenings of railway ferries by means of equipping their bearing

  14. 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

  15. 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.

  16. Determination of households fish consumption structure and purchase behaviors in urban areas of Van

    Directory of Open Access Journals (Sweden)

    Mustafa Terin

    2016-08-01

    Full Text Available This study has been carried out to determine the household fish consumption structure and purchase behaviors in urban areas of Van Province. The main data of this study has been compiled through questionnaires from 260 households. In the analysis of the data, frequency tables, chi-square independence test were used and the relationships between the quantity of fish consumption of the households and some socio–demographic categorical variables have been examined through f and t tests. It has been determined that 89.2 % of the participating households consume fish while 10.8 % do not. Nearly a third (35.7 % of the households that do not consume fish do so for the smell of the fish. 84.1 % of the households consume fish in winter. 87.2 % consume fresh fish while 40 % consume fish by frying. Mostly preferred fish are anchovy, trout and tarek respectively. It has been determined that the amounts of fish consumption per month per household and per person are 6.3 kg and 1.4 kg respectively. It has also been determined that households with children, employed head and owning the house consume more fish than those households without children, unemployed head and tenants.Keywords: Fish consumption, socio-demographic factors, consumer preferences, consumer analysis, Van

  17. Determination of a complex crystal structure in the absence of single crystals: analysis of powder X-ray diffraction data, guided by solid-state NMR and periodic DFT calculations, reveals a new 2'-deoxyguanosine structural motif.

    Science.gov (United States)

    Hughes, Colan E; Reddy, G N Manjunatha; Masiero, Stefano; Brown, Steven P; Williams, P Andrew; Harris, Kenneth D M

    2017-05-01

    Derivatives of guanine exhibit diverse supramolecular chemistry, with a variety of distinct hydrogen-bonding motifs reported in the solid state, including ribbons and quartets, which resemble the G-quadruplex found in nucleic acids with sequences rich in guanine. Reflecting this diversity, the solid-state structural properties of 3',5'-bis- O -decanoyl-2'-deoxyguanosine, reported in this paper, reveal a hydrogen-bonded guanine ribbon motif that has not been observed previously for 2'-deoxyguanosine derivatives. In this case, structure determination was carried out directly from powder XRD data, representing one of the most challenging organic molecular structures (a 90-atom molecule) that has been solved to date by this technique. While specific challenges were encountered in the structure determination process, a successful outcome was achieved by augmenting the powder XRD analysis with information derived from solid-state NMR data and with dispersion-corrected periodic DFT calculations for structure optimization. The synergy of experimental and computational methodologies demonstrated in the present work is likely to be an essential feature of strategies to further expand the application of powder XRD as a technique for structure determination of organic molecular materials of even greater complexity in the future.

  18. 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.

  19. Determination of the structure of thiol-specific antioxidant (Tsa 2) of Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Breyer, C.A. [Universidade Federal de Sao Carlos (UFSCar), SP (Brazil); Oliveira, M.A. [Universidade Estadual Paulista Julio de Mesquita Fillho (UNESP), Assis, SP (Brazil)

    2012-07-01

    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{sub P} ) and resolve cysteine (Cys{sub 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)

  20. 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.

  1. 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

  2. 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

  3. 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

  4. Soils and fire jointly determine vegetation structure in an African savanna.

    Science.gov (United States)

    Staver, A Carla; Botha, Judith; Hedin, Lars

    2017-12-01

    Savanna vegetation is variable, and predicting how water, nutrients, and chronic disturbances interact to determine vegetation structure in savannas represents a challenge. Here, we examined in situ interactions among rainfall, soils, grasses, fire, and elephants that determine tree layer responses to resource gradients in Kruger National Park in South Africa, using 363 long-term monitoring sites throughout the park. Grass biomass increased with rainfall and on nutrient-rich clay soils. Fire frequency, too, increased with rainfall. Conversely, tree density was greater on sandier soils, where water infiltrates more readily, and in areas where the maximum interval between fires was longer, irrespective of average fire frequency. Elephant density responded positively to tree density, but did not contribute significantly to decreasing tree density. Savanna vegetation structure was reasonably predictable, via a combination of rainfall (favoring grasses), soil (sandy soils favoring trees), and fire (limiting trees until a longer interval between fires allows them to establish). Explicit consideration of bottom-up and top-down interactions may thus contribute to a predictive understanding of savanna vegetation heterogeneity. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  5. Structural properties governing drug-plasma protein binding determined by high-performance liquid chromatography method.

    Science.gov (United States)

    Kamble, Sharad; Loadman, Paul; Abraham, Michael H; Liu, Xiangli

    2018-02-05

    The high-performance liquid chromatography (HPLC) method employing stationary phases immobilized with plasma proteins was used for this study to investigate the structural properties governing drug-plasma protein binding. A set of 65 compounds with a broad range of structural diversity (in terms of volume, hydrogen-bonding, polarity and electrostatic force) were selected for this purpose. The Abraham linear free energy relationship (LFER) analyses of the retention factors on the immobilized HSA (human serum albumin) and AGP (α 1 -acid glycoprotein) stationary phases showed that McGowan's characteristic molecular volume (V), dipolarity/polarizability (S) and hydrogen bond basicity (B) are the three significant molecular descriptors of solutes determining the interaction with immobilized plasma proteins, whereas excess molar refraction (E) is less important and hydrogen bond acidity (A) is not of statistical significance in both systems, for electrically neutral compounds. It was shown that ionised acids, as carboxylate anions, bind very strongly to the immobilized HSA stationary phase and that ionised bases, as cations bind strongly to the AGP stationary phase. This is the first time that the effect of ionised species on plasma protein binding has been determined quantitatively; the increased binding of acids to HSA is due almost entirely to acids in their ionised form. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. 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.)

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Determining Three Dimension Q - Attenuation Structure beneath Kyushu Island, Japan exerting Waveform - Spectra of Microearthquakes

    Science.gov (United States)

    Parithusta, R.; Matsumoto, S.; Shimizu, H.

    2007-12-01

    Examining the anelastic structure in the uppermost mantle and the crust continues to be a significant problem in seismology. In particular, the observation of attenuation heterogeneities around subduction zones and active fault has implication for the dynamic oceanic lithosphere and asthenosphere. Seismic attenuation can be estimated by extracting the amplitude-frequency information contained in seismic waveforms and it provides an important insight into the nature of heterogeneities structure and composition of the earth's interior. The study area at Kyushu Island, in South Part of Japan is characterized by subduction from Philippine Sea Slab and Eurasian Plate; volcanic front seen in islands arcs runs through the central part of Kyushu Island. Futagawa- Hinagu Fault zone, which is one of the active faults in Japan, lies in the middle of Kyushu, in which the seismic activity of shallow earthquakes is high. The fault is furrow from southwest of Aso volcano until Yatsushiro city, with the type of right-lateral strike slip. For investigating the 3D wave attenuation Q structure of the crust and the upper mantle in Kyushu Island, we examined the seismic wave spectra for micro earthquakes (Magnitude 2.5 - 4.5) observed at seismic stations by Kyushu Univ., JMA, and Hi-net. In this study selected waveform were used for spectral analysis concerning strong lateral heterogeneities, to estimate Q values by the spectral decay of the spectrum. Used for estimating path attenuation, we obtained the best result with amplitude spectra determined for a 128 - sample window around seismic-wave arrivals and having signal-to-noise ratio greater than 2 over the continuous frequency range. Solving for Q structure, an inversion program were developed with referring Tsumura, 2000.,by given a set of path attenuation, source parameter, site response and velocity model, the Q structure can be distinguished the difference between fore-arc zone and back arc zone around Kyushu Island, especially

  14. Mars deep internal structure determination using Phobos tide measurement strategy with the SEIS/InSight experiment

    Science.gov (United States)

    Pou, Laurent; Mimoun, David; Garcia, Raphaël; Lognonné, Philippe; Banerdt, William Bruce; Karatekin, Özgür; Dehant, Véronique; Zhu, Ping

    2016-04-01

    The Insight NASA Discovery mission, led by the Jet Propulsion Laboratory, will deploy in 2018 a very broadband seismometer on the Mars surface, SEIS (Seismic Experiment for Interior Structure). It is a hybrid 3-axes instrument, which encloses 3 very broadband oblique sensors and 3 short period sensors. The sensor assembly and its wind and thermal shield will by deployed on the Mars surface from the Phoenix-like spacecraft by a robotic arm (IDS). The acquisition system will be hosted in the spacecraft warm electronics box, and connected to the deployed sensor assembly by a tether. The SEIS experiment is provided by CNES, the French Space Agency that makes the coordination of a wide consortium including IPGP of Paris, ETH of Zürich, the Jet Propulsion Laboratory of Pasadena, MPS of Göttingen, Imperial College of London, and ISAE from Toulouse. One of the mission goals is to determine the deep internal structure of Mars in order to improve our models on the formation and evolution of telluric planets. In particular, the SEIS experiment aims at assessing the state (solid or liquid) of the planet core together with its size. This will be possible using the Phobos tide, a solid tide on Mars induced by one of its natural satellite, Phobos. As it orbits the planet, Phobos creates a small displacement of the Martian surface which will be measured to determine the absolute amplitude of one of the tide main harmonics which depends on Mars internal structure through the gravimetric factor γ2 (a combination of the gravitational and displacement Love numbers) at a frequency range around 50 μHz. Since Phobos orbital properties are already well-known, comparing these measurements with existing proposed models of Mars allows us to refine the previous estimations of the Mars core state and diameter. Reliable assessment of the core state will be possible if the Phobos tide absolute amplitude is measured with a precision of 2.5 10-11 m/s2 at 50μHz, making noise determination and

  15. 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.

  16. 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.

  17. 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.

  18. Structural determinants for activity and specificity of the bacterial toxin LlpA.

    Directory of Open Access Journals (Sweden)

    Maarten G K Ghequire

    2013-02-01

    Full Text Available Lectin-like bacteriotoxic proteins, identified in several plant-associated bacteria, are able to selectively kill closely related species, including several phytopathogens, such as Pseudomonas syringae and Xanthomonas species, but so far their mode of action remains unrevealed. The crystal structure of LlpABW, the prototype lectin-like bacteriocin from Pseudomonas putida, reveals an architecture of two monocot mannose-binding lectin (MMBL domains and a C-terminal β-hairpin extension. The C-terminal MMBL domain (C-domain adopts a fold very similar to MMBL domains from plant lectins and contains a binding site for mannose and oligomannosides. Mutational analysis indicates that an intact sugar-binding pocket in this domain is crucial for bactericidal activity. The N-terminal MMBL domain (N-domain adopts the same fold but is structurally more divergent and lacks a functional mannose-binding site. Differential activity of engineered N/C-domain chimers derived from two LlpA homologues with different killing spectra, disclosed that the N-domain determines target specificity. Apparently this bacteriocin is assembled from two structurally similar domains that evolved separately towards dedicated functions in target recognition and bacteriotoxicity.

  19. 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.

  20. 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.

  1. Chromatin structure and replication origins: determinants of chromosome replication and nuclear organization.

    Science.gov (United States)

    Smith, Owen K; Aladjem, Mirit I

    2014-10-09

    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. Published by Elsevier Ltd.

  2. Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant.

    Science.gov (United States)

    Bowen, Jennifer L; Kearns, Patrick J; Byrnes, Jarrett E K; Wigginton, Sara; Allen, Warwick J; Greenwood, Michael; Tran, Khang; Yu, Jennifer; Cronin, James T; Meyerson, Laura A

    2017-09-05

    Plant-microbe interactions play crucial roles in species invasions but are rarely investigated at the intraspecific level. Here, we study these interactions in three lineages of a globally distributed plant, Phragmites australis. We use field surveys and a common garden experiment to analyze bacterial communities in the rhizosphere of P. australis stands from native, introduced, and Gulf lineages to determine lineage-specific controls on rhizosphere bacteria. We show that within-lineage bacterial communities are similar, but are distinct among lineages, which is consistent with our results in a complementary common garden experiment. Introduced P. australis rhizosphere bacterial communities have lower abundances of pathways involved in antimicrobial biosynthesis and degradation, suggesting a lower exposure to enemy attack than native and Gulf lineages. However, lineage and not rhizosphere bacterial communities dictate individual plant growth in the common garden experiment. We conclude that lineage is crucial for determination of both rhizosphere bacterial communities and plant fitness.Environmental factors often outweigh host heritable factors in structuring host-associated microbiomes. Here, Bowen et al. show that host lineage is crucial for determination of rhizosphere bacterial communities in Phragmites australis, a globally distributed invasive plant.

  3. 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.

  4. 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

  5. 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.

  6. Volta phase plate data collection facilitates image processing and cryo-EM structure determination.

    Science.gov (United States)

    von Loeffelholz, Ottilie; Papai, Gabor; Danev, Radostin; Myasnikov, Alexander G; Natchiar, S Kundhavai; Hazemann, Isabelle; Ménétret, Jean-François; Klaholz, Bruno P

    2018-01-11

    A current bottleneck in structure determination of macromolecular complexes by cryo electron microscopy (cryo-EM) is the large amount of data needed to obtain high-resolution 3D reconstructions, including through sorting into different conformations and compositions with advanced image processing. Additionally, it may be difficult to visualize small ligands that bind in sub-stoichiometric levels. Volta phase plates (VPP) introduce a phase shift in the contrast transfer and drastically increase the contrast of the recorded low-dose cryo-EM images while preserving high frequency information. Here we present a comparative study to address the behavior of different data sets during image processing and quantify important parameters during structure refinement. The automated data collection was done from the same human ribosome sample either as a conventional defocus range dataset or with a Volta phase plate close to focus (cfVPP) or with a small defocus (dfVPP). The analysis of image processing parameters shows that dfVPP data behave more robustly during cryo-EM structure refinement because particle alignments, Euler angle assignments and 2D & 3D classifications behave more stably and converge faster. In particular, less particle images are required to reach the same resolution in the 3D reconstructions. Finally, we find that defocus range data collection is also applicable to VPP. This study shows that data processing and cryo-EM map interpretation, including atomic model refinement, are facilitated significantly by performing VPP cryo-EM, which will have an important impact on structural biology. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. 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

  8. Structure Determination of Ornithine-Linked Cisplatin by Infrared Multiple Photon Dissociation Action Spectroscopy

    Science.gov (United States)

    He, Chenchen; Kimutai, Bett; Hamlow, Lucas; Roy, Harrison; Nei, Y.-W.; Bao, Xun; Gao, Juehan; Martens, Jonathan K.; Berden, Giel; Oomens, Jos; Maitre, Philippe; Steinmetz, Vincent; McNary, Christopher P.; Armentrout, Peter B.; Chow, C. S.; Rodgers, M. T.

    2016-06-01

    Cisplatin [(NH_3)_2PtCl_2], 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 with guanine as its major target. Amino acid-linked cisplatin derivatives are being investigated as alternatives for cisplatin that may exhibit altered binding selectivity such as that found for ornithine-linked cisplatin (Ornplatin, [(Orn)PtCl_2]), which exhibits a preference for adenine over guanine in RNA. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and complementary electronic structure calculations are performed on a series of Ornplatin complexes to elucidate the nature of binding of the Orn amino acid to the Pt center and how that binding is influenced by the local environment. The complexes examined in the work include: [(Orn-H)PtCl_2]-, [(Orn)PtCl]+, [(Orn)Pt(H_2O)Cl]+, and [(Orn)PtCl_2+Na]+. In contrast to that found previously for the glycine-linked cisplatin complex (Glyplatin), which binds via the backbone amino and carboxylate groups, binding of Orn in these complexes is found to involve both the backbone and sidechain amino groups. Extensive broadening of the IRMPD spectrum for the [(Orn)Pt(H_2O)Cl]+ complex suggests that either multiple structures are contributing to the measured spectrum or strong intra-molecular hydrogen-binding interactions are present. The results for Ornplatin lead to an interesting discussion about the differences in selectivity and reactivity versus cisplatin.

  9. 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.

  10. 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

  11. 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)

  12. Socialist and postsocialist land-use legacies determine farm woodland composition and structure

    DEFF Research Database (Denmark)

    Plieninger, Tobias; Schaich, H.

    2014-01-01

    European agroecosystems host a variety of farm woodlands that act as primary determinants of biodiversity and ecosystem services. While woodland areas have been in decline worldwide, they have regionally increased, for example, in Eastern Germany. This study performs a quantitative and spatially...... of variability. Percentages of nonnative (7 %) and coniferous (10 %) individuals are low. The findings suggest that socialist and postsocialist farmland and forest policies translated into distinct land-use legacies in the newly established farm woodlands, which differ considerably from the composition...... and structure of presocialist woodlands. We argue that forest conservation planning should actively consider land-use legacies, which are of particular relevance in the landscapes of Central and Eastern Europe, as these have undergone multiple, abrupt, and severe land-use transitions....

  13. 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.

  14. 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

  15. Synthesis, growth, structure determination and optical properties of chalcone derivative single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Karthi, S., E-mail: girijaeaswaradas@gmail.com; Girija, E. K., E-mail: girijaeaswaradas@gmail.com [Department of Physics, Periyar University, Salem - 636011 (India)

    2014-04-24

    Acquiring large nonlinear optical (NLO) efficient organic material is essential for the development of optoelectronics and photonic devices. Chalcone is the donor - Π - acceptor - Π - donor (D-Π-A-Π-D) type conjugated molecule with appreciable hyperpolarizability of potential interest in NLO applications. The addition of vinyl and electron donor groups in the chalcone molecule may enhance the second harmonic generation (SHG) efficiency. Here we report the synthesis, crystal growth and characterization of a chalcone derivative 1-(4-methylphenyl)-5-(4-methoxyphenyl)-penta-2,4-dien-1-one (MPMPP). The MPMPP crystal was grown by slow evaporation solution growth technique from acetone. The grown crystal structure was studied by single crystal X-ray diffraction. The SHG efficiency of the grown crystal was determined by Kurtz and Perry method.

  16. 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.

  17. ALGORITMA PARALLEL SUPERVISED PNN STRUCTURE DETERMINATION DAN IMPLEMENTASI BERBASIS MESSAGE PASSING INTERFACE

    Directory of Open Access Journals (Sweden)

    Heru Suhartanto

    2012-05-01

    Full Text Available Probabilistic Neural Network (PNN adalah salah satu tipe jaringan neural yang umum digunakan untuk memecahkan permasalahan klasifikasi pola. Di samping struktur jaringan dan metode pelatihan yang sederhana, PNN memiliki kelemahan utama yaitu dalam menentukan struktur jaringan yang terdiri dari penentuan nilai parameter smoothing dan jumlah neuron yang digunakan pada lapisan pola. Dengan adanya kelemahan ini, beberapa peneliti mengajukan algoritma Supervised PNN Structure Determination (SPNN dengan tujuan untuk mempermudah penentuan struktur PNN. Akan tetapi dalam implementasi iteratif yang telah dilaporkan, SPNN masih memerlukan waktu komputasi yang cukup lama untuk menentukan struktur PNN yang baik. Makalah ini menjelaskan usaha perbaikan kinerja waktu proses implementasi SPNN dengan memperhatikan bagian-bagian proses yang independent serta memodifikasi algoritmanya untuk dapat diterapkan pemrosesan secara paralel. Hasil eksperimen menunjukkan percepatan yang cukup berarti.

  18. Quantitative 3D determination of self-assembled structures on nanoparticles using small angle neutron scattering.

    Science.gov (United States)

    Luo, Zhi; Marson, Domenico; Ong, Quy K; Loiudice, Anna; Kohlbrecher, Joachim; Radulescu, Aurel; Krause-Heuer, Anwen; Darwish, Tamim; Balog, Sandor; Buonsanti, Raffaella; Svergun, Dmitri I; Posocco, Paola; Stellacci, Francesco

    2018-04-09

    The ligand shell (LS) determines a number of nanoparticles' properties. Nanoparticles' cores can be accurately characterized; yet the structure of the LS, when composed of mixture of molecules, can be described only qualitatively (e.g., patchy, Janus, and random). Here we show that quantitative description of the LS' morphology of monodisperse nanoparticles can be obtained using small-angle neutron scattering (SANS), measured at multiple contrasts, achieved by either ligand or solvent deuteration. Three-dimensional models of the nanoparticles' core and LS are generated using an ab initio reconstruction method. Characteristic length scales extracted from the models are compared with simulations. We also characterize the evolution of the LS upon thermal annealing, and investigate the LS morphology of mixed-ligand copper and silver nanoparticles as well as gold nanoparticles coated with ternary mixtures. Our results suggest that SANS combined with multiphase modeling is a versatile approach for the characterization of nanoparticles' LS.

  19. 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.

  20. 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

  1. Structural Determination of Ruthenium Complexes Containing Bi-Dentate Pyrrole-Ketone Ligands.

    Science.gov (United States)

    Tsai, Ya-Wen; Chen, Yun-Fan; Li, Yong-Jie; Chen, Kuan-Hung; Lin, Chia-Her; Huang, Jui-Hsien

    2018-01-13

    A series of ruthenium compounds containing a pyrrole-ketone bidentate ligand, 2-(2'-methoxybenzoyl)pyrrole ( 1 ), have been synthesized and characterized. Reacting 1 with [(η⁶-cymene)RuCl₂]₂ and RuHCl(CO)(PPh₃)₃ generated Ru(η⁶-cymene)[C₄H₃N-2-(CO-C₆H₄-2-OMe)]Cl ( 2 ) and {RuCl(CO)(PPh₃)₂[C₄H₃N-2-(COC₆H₄-2-OMe)]} ( 3 ), respectively, in moderate yields. Successively reacting 2 with sodium cyanate and sodium azide gave {Ru(η⁶-cymene)[C₄H₃N-2-(CO-C₆H₄-2-OMe)]X} ( 4 , X=OCN; 5 , X=N₃) with the elimination of sodium chloride. Compounds 2 - 5 were all characterized by ¹H and 13 C-NMR spectra and their structures were also determined by X-ray single crystallography.

  2. Determination of surface structure of cleaved (001) USb2 single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Shao-ping [Los Alamos National Laboratory; Hawley, Marilyn [Los Alamos National Laboratory; Bauer, Eric D [Los Alamos National Laboratory; Stockum, Phil B [STANFORD UNIV; Manoharan, Hari C [STANFORD UNIV

    2009-01-01

    We have achieved what we believe to be the first atomic resolution STM images for a uranium compound taken at room temperature. The a, b, and c lattice parameters in the images confirm that the USb{sub 2} crystals cleave on the (001) basal plane as expected. The a and b dimensions were equal, with the atoms arranged in a cubic pattern. Our calculations indicate a symmetric cut between Sb planes to be the most favorable cleavage plane and U atoms to be responsible for most of the DOS measured by STM. Some strange features associated with vacancies were observed in the STM win be discussed in conjunction with ab initio calculations. The purpose of this work is to demonstrate the power of scanning tunneling microscopy (STM) techniques combined with a theoretical underpinning to determine the surface atomic structure and properties of actinide materials, such as the quasi 2-dimensional uranium dipnictide USb{sub 2} single crystal, thereby contributing to the understanding of their surface structural and electronic properties. The members of this interesting UX{sub 2} (X=P, As, Sb, Bi) series of compounds display dual localized and itinerant 5f electron behavior within the same compound due to the hybridization of the 5f orbitals with the conduction band. With the exception of UO{sub 2}, which has to be studied at elevated temperature to generate enough carriers for STM imaging, STM techniques have not been applied successfully to the characterization of the surface atomic structure of any other single crystal actinide compound, to the best of our knowledge. However, STM has been used to a limited extent for the study of some cerium compounds. STM probes electronic properties at the atomic level and can directly provide information about the local density of filled and empty states (LDOS) states simultaneously. A STM topograph provides the local atomic arrangement and spacing of the atoms on the surface, local defect structures (e.g. steps, vacancies, and kink sites

  3. Molecular structure of caffeine as determined by gas electron diffraction aided by theoretical calculations

    Science.gov (United States)

    Egawa, Toru; Kamiya, Akemi; Takeuchi, Hiroshi; Konaka, Shigehiro

    2006-12-01

    The molecular structure of caffeine (3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione) was determined by means of gas electron diffraction. The nozzle temperature was 185 °C. The results of MP2 and B3LYP calculations with the 6-31G ∗∗ basis set were used as supporting information. These calculations predicted that caffeine has only one conformer and some of the methyl groups perform low frequency internal rotation. The electron diffraction data were analyzed on this basis. The determined structural parameters ( rg and ∠ α) of caffeine are as follows: = 1.382(3) Å; r(C dbnd C) = 1.382(←) Å; r(C sbnd C) = 1.446(18) Å; r(C dbnd N) = 1.297(11) Å; = 1.459(13) Å; = 1.206(5) Å; = 1.085(11) Å; ∠N 1sbnd C 2sbnd N 3 = 116.5(11)°; ∠N 3sbnd C 4dbnd C 5 = 121. 5(13)°; ∠C 4dbnd C 5sbnd C 6 = 122.9(10)°; ∠C 4dbnd C 5sbnd N 7 = 104.7(14)°; ∠N 9-C 4=C 5 = 111.6(10)°; = 108.5(28)°. Angle brackets denote average values; parenthesized values are the estimated limits of error (3 σ) referring to the last significant digit; left arrow in parentheses means that this parameter is bound to the preceding one.

  4. Substrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of small subunit residues

    Energy Technology Data Exchange (ETDEWEB)

    Jeyakanthan, Jeyaraman [National Synchrotron Radiation Research Center; Drevland, Randy [University of Texas, Austin; Gayathri, Dasara [University of Madras; Velmurugan, Devadasan [University of Madras; Shinkai, Akeo [SPring8/JASRI, Mikazuki, Hyogo and RIKEN, Japan; Kuramitsu, Seiki [SPring8/JASRI, Mikazuki, Hyogo and RIKEN, Japan; Yokoyama, Shigeyuki [University of Tokyo, Tokyo, Japan; Graham, David E [ORNL

    2010-01-01

    The aconitase family of hydro-lyase enzymes includes three classes of proteins that catalyze the isomerization of -hydroxyacids to -hydroxyacids. Besides aconitase, isopropylmalate isomerase (IPMI) proteins specifically catalyze the isomerization of , -dicarboxylates with hydrophobic -chain groups, and homoaconitase (HACN) proteins catalyze the isomerization of tricarboxylates with variable chain length -carboxylate groups. These enzymes stereospecific hydro-lyase activities make them attractive catalysts to produce diastereomers from unsaturated precursors. However, sequence similarity and convergent evolution among these proteins leads to widespread misannotation and uncertainty about gene function. To find the substrate specificity determinants of homologous IPMI and HACN proteins from Methanocaldococcus jannaschii, the small-subunit HACN protein (MJ1271) was crystallized for X-ray diffraction. The structural model showed characteristic residues in a flexible loop region between 2 and 3 that distinguish HACN from IPMI and aconitase proteins. Site-directed mutagenesis of MJ1271 produced loop-region variant proteins that were reconstituted with wild-type MJ1003 large-subunit protein. The heteromers formed promiscuous hydro-lyases with reduced activity but broader substrate specificity. Both R26K and R26V variants formed relatively efficient IPMI enzymes, while the T27A variant had uniformly lower specificity constants for both IPMI and HACN substrates. The R26V T27Y variant resembles the MJ1277 IPMI small subunit in its flexible loop sequence, but demonstrated the broad substrate specificity of the R26V variant. These mutations may reverse the evolution of HACN activity from an ancestral IPMI gene, demonstrating the evolutionary potential for promiscuity in hydro-lyase enzymes. Understanding these specificity determinants enables the functional reannotation of paralogous HACN and IPMI genes in numerous genome sequences. These structural and kinetic results will

  5. Resonance assignment and secondary structure determination and stability of the recombinant human uteroglobin with heteronuclear multidimensional NMR

    Energy Technology Data Exchange (ETDEWEB)

    Carlomagno, Teresa [University of Naples ' Federico II' , Department of Chemistry (Italy); Mantile, Giuditta [Section on Developmental Genetics, Heritable Disorders Branch (United States); Bazzo, Renzo [IRBM P. Angeletti, Spa. (Italy); Miele, Lucio [Section on Developmental Genetics, Heritable Disorders Branch (United States); Paolillo, Livio [University of Naples ' Federico II' , Department of Chemistry (Italy); Mukherjee, Anil B. [Section on Developmental Genetics, Heritable Disorders Branch (United States); Barbato, Gaetano [IRBM P. Angeletti, Spa. (Italy)

    1997-01-15

    Human uteroglobin (h-UG) or Clara cell 10kDa (cc10kDa) is a steroid-dependent, 17 kDahomodimeric, secretory protein with potent anti-inflammatory/immunomodulatory properties. However, the exact physiological role still remains to be determined. It has been hypothesised that its activity is exerted through the binding of a specific target represented by a small molecule (still unknown), and that the binding is regulated by the formation/disruption of two cysteine bonds. The binding properties of the reduced UG have been proved in vitro for several different molecules, but no in vivo data are available to date. However, binding has been observed between reduced rabbit UG and a protein of an apparent molecular mass of 90 kDa and, more recently, we found an h-UG-binding protein (putative receptor), of an apparent molecular mass of 190 kDa, on the surface of several cell types. The recognition involves oxidised h-UG. These findings pose the problem of the relevance of the oxidation state in the recognition process. To determine the solution structure of the oxidised h-UG, we produced wild-type as well as uniformly 15N- and 15N/13C-labelled samples of the recombinant protein. The assignments of the 1H, 15N and 13C resonances are presented,based on a series of homonuclear 2D and 3D and heteronuclear 2D and 3D double and triple resonance NMR experiments. Our results indicate that h-UG is an extremely stable protein under a wide range of temperatures and pH conditions. The secondary structure in solution is in general agreement with previously reported crystal structures of rabbit UG, suggesting that cc10kDa and h-UG are indeed the same protein. Small local differences found in the N-and C-terminal helices seem to support the hypothesis that flexibility involves these residues;moreover, it possibly accounts for the residual binding properties observed when the protein is in the oxidised state.

  6. 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.

  7. Rates of induced abortion in Denmark according to age, previous births and previous abortions

    Directory of Open Access Journals (Sweden)

    Marie-Louise H. Hansen

    2009-11-01

    Full Text Available Background: Whereas the effects of various socio-demographic determinants on a woman's risk of having an abortion are relatively well-documented, less attention has been given to the effect of previous abortions and births. Objective: To study the effect of previous abortions and births on Danish women's risk of an abortion, in addition to a number of demographic and personal characteristics. Data and methods: From the Fertility of Women and Couples Dataset we obtained data on the number of live births and induced abortions by year (1981-2001, age (16-39, county of residence and marital status. Logistic regression analysis was used to estimate the influence of the explanatory variables on the probability of having an abortion in a relevant year. Main findings and conclusion: A woman's risk of having an abortion increases with the number of previous births and previous abortions. Some interactions were was found in the way a woman's risk of abortion varies with calendar year, age and parity. The risk of an abortion for women with no children decreases while the risk of an abortion for women with children increases over time. Furthermore, the risk of an abortion decreases with age, but relatively more so for women with children compared to childless women. Trends for teenagers are discussed in a separate section.

  8. A new supramolecular chromium(III) complex: Synthesis, structural determination, optical study, magnetic and antibacterial activity

    Science.gov (United States)

    Dridi, Rihab; Dhieb, Cyrine; Cherni, Saoussen Namouchi; Boudjada, Nassira Chniba; Sadfi Zouaoui, Najla; Zid, Mohamed Faouzi

    2018-01-01

    A new chromium (III) complex 1,5-Naphthyridine Trans-diaquadioxalatochromate (III) dihydrate, had been synthesized by self-assembly of chromium (III) nitrate with oxalic acid and 1,5-Naphthyridine. The complex was characterized by X-ray diffraction, Fourier Transform Infrared spectroscopy, thermogravimetric analysis and UV-Visible spectroscopy. The crystal morphology was carried out using Bravais-Friedel-Donnay-Harker (BFDH) model. Single crystal X-Ray structure determination revealed that the complex posses two crystallographically independent Cr(III) centers. Each Cr(III) has a distorted octahedron geometry involving two axial O atoms from two water molecules and four equatorial O atoms from two oxalate dianions forming trans-[Cr(C2O4)2(H2O)2]- complex anions. The charge compensation is accomplished by the incorporation of 1,5-Naphthyridine cations. Connection between these entities is ensured by means of strong hydrogen bonds giving rise to 3D supramolecular architecture. Hirshfeld surface analysis and the related 2D fingerprint plots were used for decoding plausible intermolecular interactions in the crystal packing. The magnetic properties of the complex had been investigated and discussed in the context of its structure. The antimicrobial activity was evaluated by disc diffusion method highlighting an antagonistic effect of the synthesized complex against Gram-positive and Gram-negative species.

  9. 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.

  10. Determinants of the Capital Structure of Small and Medium Sized Brazilian Enterprises

    Directory of Open Access Journals (Sweden)

    Denis Forte

    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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. Diet is the primary determinant of bacterial community structure in the guts of higher termites.

    Science.gov (United States)

    Mikaelyan, Aram; Dietrich, Carsten; Köhler, Tim; Poulsen, Michael; Sillam-Dussès, David; Brune, Andreas

    2015-10-01

    The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches. © 2015 John Wiley & Sons Ltd.

  17. Myosin head orientation: a structural determinant for the Frank-Starling relationship

    Energy Technology Data Exchange (ETDEWEB)

    Farman, Gerrie P.; Gore, David; Allen, Edward; Schoenfelt, Kelly; Irving, Thomas C.; de Tombe, Pieter P. (IIT); (UIC)

    2011-09-06

    The cellular mechanism underlying the Frank-Starling law of the heart is myofilament length-dependent activation. The mechanism(s) whereby sarcomeres detect changes in length and translate this into increased sensitivity to activating calcium has been elusive. Small-angle X-ray diffraction studies have revealed that the intact myofilament lattice undergoes numerous structural changes upon an increase in sarcomere length (SL): lattice spacing and the I{sub 1,1}/I{sub 1,0} intensity ratio decreases, whereas the M3 meridional reflection intensity (I{sub M3}) increases, concomitant with increases in diastolic and systolic force. Using a short ({approx}10 ms) X-ray exposure just before electrical stimulation, we were able to obtain detailed structural information regarding the effects of external osmotic compression (with mannitol) and obtain SL on thin intact electrically stimulated isolated rat right ventricular trabeculae. We show that over the same incremental increases in SL, the relative changes in systolic force track more closely to the relative changes in myosin head orientation (as reported by IM3) than to the relative changes in lattice spacing. We conclude that myosin head orientation before activation determines myocardial sarcomere activation levels and that this may be the dominant mechanism for length-dependent activation.

  18. 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.

  19. Crystal structure of magnesium dichloride decahydrate determined by X-ray and neutron diffraction under high pressure.

    Science.gov (United States)

    Komatsu, Kazuki; Shinozaki, Ayako; Machida, Shinichi; Matsubayashi, Takuto; Watanabe, Mao; Kagi, Hiroyuki; Sano-Furukawa, Asami; Hattori, Takanori

    2015-02-01

    Magnesium dichloride decahydrate (MgCl2·10H2O) and its deuterated counterpart (MgCl2·10D2O) are identified for the first time by in-situ powder synchrotron X-ray and spallation neutron diffraction. These substances are crystallized from a previously unidentified nanocrystalline compound, which originates from an amorphous state at low temperature. A combination of a recently developed autoindexing procedure and the charge-flipping method reveals that the crystal structure of MgCl2·10H2O consists of an ABCABC··· sequence of Mg(H2O)6 octahedra. The Cl(-) anions and remaining water molecules unconnected to the Mg(2+) cations bind the octahedra, similar to other water-rich magnesium dichloride hydrates. The D positions in MgCl2·10D2O, determined by the difference Fourier methods using the neutron powder diffraction patterns at 2.5 GPa, show the features such as bifurcated hydrogen bonds and tetrahedrally coordinated O atoms, which were not found in other forms of magnesium chloride hydrates.

  20. 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.

  1. Elephants, fire, and frost can determine community structure and composition in Kalahari Woodlands.

    Science.gov (United States)

    Holdo, Ricardo M

    2007-03-01

    Fire, elephants, and frost are important disturbance factors in many African savannas, but the relative magnitude of their effects on vegetation and their interactions have not been quantified. Understanding how disturbance shapes savanna structure and composition is critical for predicting changes in tree cover and for formulating management and conservation policy. A simulation model was used to investigate how the disturbance regime determines vegetation structure and composition in a mixed Kalahari sand woodland savanna in western Zimbabwe. The model consisted of submodels for tree growth, tree damage caused by disturbance, mortality, and recruitment that were parameterized from field data collected over a two-year period. The model predicts that, under the current disturbance regime, tree basal area in the study area will decline by two-thirds over the next two decades and become dominated by species unpalatable to elephants. Changes in the disturbance regime are predicted to greatly modify vegetation structure and community composition. Elephants are the primary drivers of woodland change in this community at present-day population densities, and their impacts are exacerbated by the effects of fire and frost. Frost, in particular, does not play an important role when acting independently but appears to be a key secondary factor in the presence of elephants and/or fire. Unlike fire and frost, which cannot suppress the woodland phase on their own in this ecosystem, elephants can independently drive the vegetation to the scrub phase. The results suggest that elephant and fire management may be critical for the persistence of certain woodland communities within dry-season elephant habitats in the eastern Kalahari, particularly those dominated by Brachystegia spiciformis and other palatable species.

  2. 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.

  3. 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

  4. 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).

  5. 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

  6. Method of determining the extent to which a nickel structure has been attached by a fluorine-containing gas

    Science.gov (United States)

    Brusie, James P.

    2004-07-13

    The method of determining the extent to which a nickel structure has been attacked by a halogen containing gas to which it has been exposed which comprises preparing a quantity of water substantially free from dissolved oxygen, passing ammonia gas through a cuprammonium solution to produce ammonia substantially free from oxygen, dissolving said oxygen-free ammonia in said water to produce a saturated aqueous ammonia solution free from uncombined oxygen, treating at least a portion of said nickel structure of predetermined weight with said solution to dissolve nickel compounds from the surface of said structure without dissolving an appreciable amount of said nickel and analyzing the resulting solution to determine the quantity of said nickel compounds that was associated with said said portion of said structure to determine the proportion of combined nickel in said nickel structure.

  7. Method of Determining the Extent to which a Nickel Structure has been Attached by a Fluorine-Containing Gas

    Energy Technology Data Exchange (ETDEWEB)

    Brusie, James P.

    2004-07-13

    The method of determining the extent to which a nickel structure has been attacked by a halogen containing gas to which it has been exposed which comprises preparing a quantity of water substantially free from dissolved oxygen, passing ammonia gas through a cuprammonium solution to produce ammonia substantially free from oxygen, dissolving said oxygen-free ammonia in said water to produce a saturated aqueous ammonia solution free from uncombined oxygen, treating at least a portion of said nickel structure of predetermined weight with said solution to dissolve nickel compounds from the surface of said structure without dissolving an appreciable amount of said nickel and analyzing the resulting solution to determine the quantity of said nickel compounds that was associated with said said portion of said structure to determine the proportion of combined nickel in said nickel structure.

  8. Method of determining the speed of sheet washout for design of structures on slopes

    Directory of Open Access Journals (Sweden)

    Volodina Lyudmila Aleksandrovna

    2014-09-01

    Full Text Available The authors present the study of sheet washout of soil relevant in the framework of the stability of structures, retaining walls and trays over them, pillars of stairs, power lines and other structures on the slopes. Flushing speed can be approximately defined using phytoindicational way, determining the depth of erosion of the soil near perennial plants, the roots of which are naked. This approach to determining the rate of sheet erosion has been used by many scientists. The techniques offered in their works were created to improve the agricultural use of the lands for the territories of Central Asia. In order to protect the structures in natural areas of Moscow, the authors suggested their methods. It is assumed that the beginning of the erosion process in the measuring point coincides with the beginning of tree growth. At this point its root neck was at the level of the earth. Thus, for the rate of erosion we accepted the height position of root neck of the tree. The measurement should be horizontal to the tree in connection with the retention of soil by the tree and "hill" formation on the top side of the tree and rich soil washout from the bottom side. The average annual rate of erosion can be calculated by determining the age of the tree and by measuring the excess of root neck above the surface of the slope. The age of the tree may be determined by the correlation of age with a diameter of a tree, measured at height of 1.3 m above the ground level. The average annual increase in the diameter of a tree can be defined on the stumps, available in the study area. When calculating the age of trees to clarify the diameters, it is recommended to make allowance for the thickness of the crust. It was noted that the study of the process of sheet washout should be made in condition of stability of influencing factors: climate, topography, geology, soils, vegetation and human activities. In order to validate the approach, the slopes of ravines in the

  9. 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

  10. Membrane Protein Structure Determination Using Crystallography and Lipidic Mesophases - Recent Advances and Successes

    Science.gov (United States)

    Caffrey, Martin; Li, Dianfan; Dukkipati, Abhiram

    2012-01-01

    The crystal structure of the β2-adrenergic receptor in complex with an agonist and its cognate G protein has just recently been solved. It is now possible to explore in molecular detail the means by which this paradigmatic transmembrane receptor binds agonist, communicates the impulse or signalling event across the membrane and sets in motion a series of G protein-directed intracellular responses. The structure was determined using crystals of the ternary complex grown in a rationally designed lipidic mesophase by the so-called in meso method. The method is proving to be particularly useful in the G protein-coupled receptor field where the structures of thirteen distinct receptor types have been solved in the past five years. In addition to receptors, the method has proven useful with a wide variety of integral membrane protein classes that include bacterial and eukaryotic rhodopsins, a light harvesting complex II (LHII), photosynthetic reaction centers, cytochrome oxidases, β-barrels, an exchanger, and an integral membrane peptide. This attests to the versatility and range of the method and supports the view that the in meso method should be included in the arsenal of the serious membrane structural biologist. For this to happen however, the reluctance in adopting it attributable, in part, to the anticipated difficulties associated with handling the sticky, viscous cubic mesophase in which crystals grow must be overcome. Harvesting and collecting diffraction data with the mesophase-grown crystals is also viewed with some trepidation. It is acknowledged that there are challenges associated with the method. Over the years, we have endeavored to establish how the method works at a molecular level and to make it user-friendly. To these ends, tools for handling the mesophase in the pico- to nano-liter volume range have been developed for highly efficient crystallization screening in manual and robotic modes. Methods have been implemented for evaluating the functional

  11. 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

  12. Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy : A molecular dynamics simulation study

    NARCIS (Netherlands)

    Fan, H; Mark, AE

    2003-01-01

    The relative stability of protein structures determined by either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy has been investigated by using molecular dynamics simulation techniques. Published structures of 34 proteins containing between 50 and 100 residues have been

  13. Short-range structure in (partially) crystalline potato starch determined with attenuated total reflectance Fourier-transform IR spectroscopy

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Soest, J.J.G. van; Tournois, H.; Wit, D. de

    1995-01-01

    A fast and direct method, based on infrared spectroscopy, for quantitative determination of starch short-range structure has been developed. The IR spectrum of starch is sensitive to changes in short-range structure in the C—C and C—O stretching region at 1300-800 cm−1. The IR absorbance band at

  14. NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

    OpenAIRE

    Jang, Richard; Wang, Yan; Xue, Zhidong; Zhang, Yang

    2015-01-01

    NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates...

  15. Free energy determinants of secondary structure formation: I. alpha-Helices.

    Science.gov (United States)

    Yang, A S; Honig, B

    1995-09-22

    The Zimm-Bragg parameters s and sigma are calculated for the helix-coil transition of poly-L-alanine. The theoretical approach involves evaluating gas phase conformational energies for both coil and helical states using the CHARMM potential function and accounting for solvation effects with various continuum solvation models. Conformational free energies are then incorporated into a formalism developed by Go et al. for the calculation of s and sigma. Calculated values for both s and sigma as well as the enthalpy change associated with helix formation are in good agreement with experimental data when the Finite Difference Poisson-Boltzmann (FDPB) method is used to treat solvent effects. The driving force for the helix-coil transition is analyzed in terms of individual free energy components. Hydrogen bond formation is found to contribute little to helix stability because the internal hydrogen bonding energy is largely canceled by the large free energy cost associated with removing polar groups from water. The entropic cost associated with fixing backbone dihedral angles in the helical conformation is found to be approximately 7 e.u./residue (about 2 kcal/mol at room temperature). The major driving force favoring helix formation can be associated with interactions including enhanced van der Waals interactions in the close-packed helix conformation and the hydrophobic effect. These contribute about 2 kcal/mol favoring the helical state. The differences in helical propensities between alanine and glycine are attributed primarily to hydrophobic and packing interactions involving the C beta with a smaller contribution arising from increased conformational freedom for glycine in the coil state. The description of helix formation presented here is consistent with previous conclusions regarding tertiary structure formation which suggest that hydrophobic and close-packed interactions provide stability while hydrogen bond formation constitutes a structural constraint imposed

  16. 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.

  17. Structural Determinants of Oligomerization of !1-Pyrroline-5-Carboxylate Dehydrogenase: Identification of a Hexamerization Hot Spot

    Science.gov (United States)

    Luo, Min; Singh, Ranjan K.; Tanner, John J.

    2013-01-01

    The aldehyde dehydrogenase (ALDH) superfamily member !1-pyrroline-5-carboxylate dehydrogenase (P5CDH) catalyzes the NAD+-dependent oxidation of glutamate semialdehyde to glutamate, which is the final step of proline catabolism. Defects in P5CDH activity lead to the metabolic disorder type II hyperprolinemia, P5CDH is essential for virulence of the fungal pathogen Cryptococcus neoformans, and bacterial P5CDHs have been targeted for vaccine development. Although the enzyme oligomeric state is known to be important for ALDH function, the oligomerization of P5CDH has remained relatively unstudied. Here we determine the oligomeric states and quaternary structures of four bacterial P5CDHs using a combination of small-angle X-ray scattering, X-ray crystallography, and dynamic light scattering. The P5CDHs from Thermus thermophilus and Deinococcus radiodurans form trimer-of-dimers hexamers in solution, which is the first observation of a hexameric ALDH in solution. In contrast, two Bacillus P5CDHs form dimers in solution but do not assemble into a higher order oligomer. Site-directed mutagenesis was used to identify a hexamerization hot spot that is centered on an arginine residue in the NAD+-binding domain. Mutation of this critical Arg residue to Ala in either of the hexameric enzymes prevents hexamer formation in solution. Paradoxically, the dimeric Arg-to-Ala T. thermophilus mutant enzyme packs as a hexamer in the crystal state, which illustrates the challenges associated with predicting the biological assembly in solution from crystal structures. The observation of different oligomeric states among P5CDHs suggests potential differences in cooperativity and protein-protein interactions. PMID:23747974

  18. 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.

  19. 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

  20. 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

  1. Determination of structural water by neutron protein crystallography: an analysis of the carbon monoxide myoglobin water structure

    International Nuclear Information System (INIS)

    Schoenborn, B.P.; Hanson, J.C.

    1979-01-01

    An ideal technique for studying the water structure of proteins using neutron crystallography is discussed. The advantages of using deuterons (D 2 O) instead of hydrogen (H 2 O) are explained. The results of an early unrefined met myoglobin neutron analysis are presented. More recent high resolution x-ray analysis of met myoglobin and refined neutron analysis of carbon monoxide myoglobin water structure were compared. Neutron maps were included

  2. Population Structure and Properties of Candida albicans, as Determined by Multilocus Sequence Typing†

    Science.gov (United States)

    Tavanti, Arianna; Davidson, Amanda D.; Fordyce, Mark J.; Gow, Neil A. R.; Maiden, Martin C. J.; Odds, Frank C.

    2005-01-01

    We submitted a panel of 416 isolates of Candida albicans from separate sources to multilocus sequence typing (MLST). The data generated determined a population structure in which four major clades of closely related isolates were delineated, together with eight minor clades comprising five or more isolates. By Fisher's exact test, a statistically significant association was found between particular clades and the anatomical source, geographical source, ABC genotype, decade of isolation, and homozygosity versus heterozygosity at the mating type-like locus (MTL) of the isolates in the clade. However, these associations may have been influenced by confounding variables, since in a univariate analysis of variance, only the clade associations with ABC type and anatomical source emerged as statistically significant, providing the first indication of possible differences between C. albicans strain type clades and their propensity to infect or colonize different anatomical locations. There were no significant differences between clades with respect to distributions of isolates resistant to fluconazole, itraconazole, or flucytosine. However, the majority of flucytosine-resistant isolates belonged to clade 1, and these isolates, but not flucytosine-resistant isolates in other clades, bore a unique mutation in the FUR1 gene that probably accounts for their resistance. A significantly higher proportion of isolates resistant to fluconazole, itraconazole, and flucytosine were homozygous at the MTL, suggesting that antifungal pressure may trigger a common mechanism that leads both to resistance and to MTL homozygosity. The utility of MLST for determining clade assignments of clinical isolates will form the basis for strain selection for future research into C. albicans virulence. PMID:16272493

  3. 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.

  4. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations.

    Science.gov (United States)

    Lees, Jonathan G; Janes, Robert W

    2008-01-15

    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. 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. Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  5. 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.

  6. 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

  7. Structural determinants of Arabidopsis thaliana Hyponastic leaves 1 function in vivo.

    Directory of Open Access Journals (Sweden)

    Paula Burdisso

    Full Text Available MicroRNAs have turned out to be important regulators of gene expression. These molecules originate from longer transcripts that are processed by ribonuclease III (RNAse III enzymes. Dicer proteins are essential RNAse III enzymes that are involved in the generation of microRNAs (miRNAs and other small RNAs. The correct function of Dicer relies on the participation of accessory dsRNA binding proteins, the exact function of which is not well-understood so far. In plants, the double stranded RNA binding protein Hyponastic Leaves 1 (HYL1 helps Dicer Like protein (DCL1 to achieve an efficient and precise excision of the miRNAs from their primary precursors. Here we dissected the regions of HYL1 that are essential for its function in Arabidopsis thaliana plant model. We generated mutant forms of the protein that retain their structure but affect its RNA-binding properties. The mutant versions of HYL1 were studied both in vitro and in vivo, and we were able to identify essential aminoacids/residues for its activity. Remarkably, mutation and even ablation of one of the purportedly main RNA binding determinants does not give rise to any major disturbances in the function of the protein. We studied the function of the mutant forms in vivo, establishing a direct correlation between affinity for the pri-miRNA precursors and protein activity.

  8. Determining the resolution of scanning microwave impedance microscopy using atomic-precision buried donor structures

    Science.gov (United States)

    Scrymgeour, D. A.; Baca, A.; Fishgrab, K.; Simonson, R. J.; Marshall, M.; Bussmann, E.; Nakakura, C. Y.; Anderson, M.; Misra, S.

    2017-11-01

    To quantify the resolution limits of scanning microwave impedance microscopy (sMIM), we created scanning tunneling microscope (STM)-patterned donor nanostructures in silicon composed of 10 nm lines of highly conductive silicon buried under a protective top cap of silicon, and imaged them with sMIM. This dopant pattern is an ideal test of the resolution and sensitivity of the sMIM technique, as it is made with nm-resolution and offers minimal complications from topography convolution. It has been determined that typical sMIM tips can resolve lines down to ∼80 nm spacing, while resolution is independent of tip geometry as extreme tip wear does not change the resolving power, contrary to traditional scanning capacitance microscopy (SCM). Going forward, sMIM is an ideal technique for qualifying buried patterned devices, potentially allowing for quantitative post-fabrication characterization of donor structures, which may be an important tool for the study of atomic-scale transistors and state of the art quantum computation schemes.

  9. Cation distribution in NiZn-ferrite films determined using x-ray absorption fine structure

    Science.gov (United States)

    Harris, V. G.; Koon, N. C.; Williams, C. M.; Zhang, Q.; Abe, M.

    1996-04-01

    We have applied extended x-ray absorption fine structure (EXAFS) spectroscopy to study the cation distribution in a series of spin-sprayed NiZn-ferrite films, Ni0.15ZnyFe2.85-yO4 (y=0.16, 0.23, 0.40, 0.60). The Ni, Zn, and Fe EXAFS were collected from each sample and analyzed to Fourier transforms. Samples of Ni-ferrite, Zn-ferrite, and magnetite were similarly studied as empirical standards. These standards, together with EXAFS data generated from the theoretical EXAFS FEFF codes, allowed the correlation of features in the Fourier transforms with specific lattice sites in the spinel unit cell. We find that the Ni ions reside mostly on the octahedral (B) sites whereas the Zn ions are predominantly on the tetrahedral (A) sites. The Fe ions reside on both A and B sites in a ratio determined by the ratio of Zn/Fe. The addition of Zn displaces a larger fraction of Fe cations onto the B sites serving to increase the net magnetization. The fraction of A site Ni ions is measured to increase peaking at ≊25% for y=0.6. At higher Zn concentrations (y≥0.5) the lattice experiences local distortions around the Zn sites causing a decrease in the superexchange resulting in a decrease in the net magnetization.

  10. 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.)

  11. Microwave-assisted stereospecific synthesis of novel tetrahydropyran adenine isonucleosides and crystal structures determination

    Science.gov (United States)

    Silva, Fábio P. L.; Cirqueira, Marilia L.; Martins, Felipe T.; Vasconcellos, Mário L. A. A.

    2013-11-01

    We describe in this article stereospecific syntheses for new isonucleosides analogs of adenine 5-7 from tosyl derivatives 2-4 accessing by microwave irradiations (50-80%). The adenine reacts entirely at the N(9) position. Compounds 2-4 were prepared in two steps from the corresponding alcohols 1, 8 and 9 (81-92%). These tetrahydropyrans alcohols 1, 8 and 9 are achiral (Meso compounds) and were prepared in two steps with complete control of 2,4,6-cis relative configuration by Prins cyclization reaction (60-63%) preceded by the Barbier reaction between allyl bromide with benzaldehyde, 4-fluorobenzaldehyde and 2-naphthaldehyde respectively under Lewis acid conditions (96-98%). The configurations and preferential conformations of 5-7 were determined by crystal structure of 6. These novel isonucleosides 5-7 present in silico potentiality to act as GPCR ligand, kinase inhibitor and enzyme inhibitor, evaluated by Molinspiration program, consistent with the expected antiviral and anticancer bioactivities.

  12. Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia.

    Science.gov (United States)

    Gomes, Newton C M; Flocco, Cecilia G; Costa, Rodrigo; Junca, Howard; Vilchez, Ramiro; Pieper, Dietmar H; Krögerrecklenfort, Ellen; Paranhos, Rodolfo; Mendonça-Hagler, Leda C S; Smalla, Kornelia

    2010-11-01

    In this study, the combination of culture enrichments and molecular tools was used to identify bacterial guilds, plasmids and functional genes potentially important in the process of petroleum hydrocarbon (PH) decontamination in mangrove microniches (rhizospheres and bulk sediment). In addition, we aimed to recover PH-degrading consortia (PHDC) for future use in remediation strategies. The PHDC were enriched with petroleum from rhizosphere and bulk sediment samples taken from a mangrove chronically polluted with oil hydrocarbons. Southern blot hybridization (SBH) assays of PCR amplicons from environmental DNA before enrichments resulted in weak positive signals for the functional gene types targeted, suggesting that PH-degrading genotypes and plasmids were in low abundance in the rhizosphere and bulk sediments. However, after enrichment, these genes were detected and strong microniche-dependent differences in the abundance and composition of hydrocarbonoclastic bacterial populations, plasmids (IncP-1α, IncP-1β, IncP-7 and IncP-9) and functional genes (naphthalene, extradiol and intradiol dioxygenases) were revealed by in-depth molecular analyses [PCR-denaturing gradient gel electrophoresis and hybridization (SBH and microarray)]. Our results suggest that, despite the low abundance of PH-degrading genes and plasmids in the environmental samples, the original bacterial composition of the mangrove microniches determined the structural and functional diversity of the PHDC enriched. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  13. Structural Inheritance of the Actin Cytoskeletal Organization Determines the Body Axis in Regenerating Hydra.

    Science.gov (United States)

    Livshits, Anton; Shani-Zerbib, Lital; Maroudas-Sacks, Yonit; Braun, Erez; Keren, Kinneret

    2017-02-07

    Understanding how mechanics complement bio-signaling in defining patterns during morphogenesis is an outstanding challenge. Here, we utilize the multicellular polyp Hydra to investigate the role of the actomyosin cytoskeleton in morphogenesis. We find that the supra-cellular actin fiber organization is inherited from the parent Hydra and determines the body axis in regenerating tissue segments. This form of structural inheritance is non-trivial because of the tissue folding and dynamic actin reorganization involved. We further show that the emergence of multiple body axes can be traced to discrepancies in actin fiber alignment at early stages of the regeneration process. Mechanical constraints induced by anchoring regenerating Hydra on stiff wires suppressed the emergence of multiple body axes, highlighting the importance of mechanical feedbacks in defining and stabilizing the body axis. Together, these results constitute an important step toward the development of an integrated view of morphogenesis that incorporates mechanics. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  14. Structure of Nanoporous Biocarbon for Hydrogen Storage as Determined by Small Angle X-Ray Scattering

    Science.gov (United States)

    Wood, Mikael; Burress, J.; Pobst, J.; Carter, S.; Pfeifer, P.; Wexler, C.; Shah, P.; Suppes, G.

    2008-03-01

    As a member of the Alliance for Collaborative Research in Alternative Fuel Technology (ALL-CRAFT) our research group studies the properties of nanoporous biocarbon, produced from waste corn cob, with the goal of achieving the Department of Energy's gravimetric and volumetric standards for both hydrogen and methane gas storage. Small Angle X-Ray Scattering (SAXS) is a valuable tool in our investigation of the geometry of the pore space in our carbon samples. In this talk, we will compare the experimental SAXS data with theoretical results for various pore geometries to determine which pore models are consistent with experiment. Using data from nitrogen adsorption isotherms, along with SAXS, yields significant structural information about the pore space. This analysis should allow us to fully optimize our production process and to achieve the DOE's target storage capacities. This work supported by: 1. National Science Foundation (PFI-0438469) 2. U.S. Department of Education (P200A040038) 3. U.S. Department of Energy (DE-AC02-06CH11357) 4. University of Missouri (RB-06-040) 5. U.S. Department of Defense (N00164-07-P-1306) 6. U.S. Department of Energy (DE-FG02-07ER46411)

  15. Structural Determination of Ruthenium Complexes Containing Bi-Dentate Pyrrole-Ketone Ligands

    Directory of Open Access Journals (Sweden)

    Ya-Wen Tsai

    2018-01-01

    Full Text Available A series of ruthenium compounds containing a pyrrole-ketone bidentate ligand, 2-(2′-methoxybenzoylpyrrole (1, have been synthesized and characterized. Reacting 1 with [(η6-cymeneRuCl2]2 and RuHCl(CO(PPh33 generated Ru(η6-cymene[C4H3N-2-(CO-C6H4-2-OMe]Cl (2 and {RuCl(CO(PPh32[C4H3N-2-(COC6H4-2-OMe]} (3, respectively, in moderate yields. Successively reacting 2 with sodium cyanate and sodium azide gave {Ru(η6-cymene[C4H3N-2-(CO-C6H4-2-OMe]X} (4, X=OCN; 5, X=N3 with the elimination of sodium chloride. Compounds 2–5 were all characterized by 1H and 13C-NMR spectra and their structures were also determined by X-ray single crystallography.

  16. The crystal structures of the tryparedoxin-tryparedoxin peroxidase couple unveil the structural determinants of Leishmania detoxification pathway.

    Directory of Open Access Journals (Sweden)

    Annarita Fiorillo

    Full Text Available Leishmaniasis is a neglected disease caused by Leishmania, an intracellular protozoan parasite which possesses a unique thiol metabolism based on trypanothione. Trypanothione is used as a source of electrons by the tryparedoxin/tryparedoxin peroxidase system (TXN/TXNPx to reduce the hydroperoxides produced by macrophages during infection. This detoxification pathway is not only unique to the parasite but is also essential for its survival; therefore, it constitutes a most attractive drug target. Several forms of TXNPx, with very high sequence identity to one another, have been found in Leishmania strains, one of which has been used as a component of a potential anti-leishmanial polyprotein vaccine. The structures of cytosolic TXN and TXNPx from L. major (LmTXN and LmTXNPx offer a unique opportunity to study peroxide reduction in Leishmania parasites at a molecular level, and may provide new tools for multienzyme inhibition-based drug discovery. Structural analyses bring out key structural features to elucidate LmTXN and LmTXNPx function. LmTXN displays an unusual N-terminal α-helix which allows the formation of a stable domain-swapped dimer. In LmTXNPx, crystallized in reducing condition, both the locally unfolded (LU and fully folded (FF conformations, typical of the oxidized and reduced protein respectively, are populated. The structural analysis presented here points to a high flexibility of the loop that includes the peroxidatic cysteine which facilitates Cys52 to form an inter-chain disulfide bond with the resolving cysteine (Cys173, thereby preventing over-oxidation which would inactivate the enzyme. Analysis of the electrostatic surface potentials of both LmTXN and LmTXNPx unveils the structural elements at the basis of functionally relevant interaction between the two proteins. Finally, the structural analysis of TXNPx allows us to identify the position of the epitopes that make the protein antigenic and therefore potentially suitable

  17. A study on determinants of risk perception and attitude structures concerning nuclear power technology

    International Nuclear Information System (INIS)

    Tsuchida, Shoji; Kitada, Atsuko; Ato, Kazunori

    2000-01-01

    attitude structures, in order to manage the risks of mega-technologies, especially the risk of nuclear technology. Social surveys on people's attitudes toward nuclear power plants carried out in Japan showed that cognition of necessity and safety of them and fear of them had strong effects on the attitudes, and that the female had more negative attitudes than the male, and that people on administrative positions by occupation had most affirmative attitudes. However, there are few social survey researches that focus on the people's tendencies to zero-risk perception or comparative-risk perception to clarify the nature and determinants of attitude structures toward nuclear power technology. In this presentation we try to point out the factors which should be considered to manage the risks of mega-technologies in the social decision making processes by describing the survey data of zero-risk perception, comparative-risk perception, and over-sensibility to hazards relating to the attitude structures toward nuclear power technology. (author)

  18. Relationships between grade determining properties of Spanish scots and laricio pine structural timber

    Directory of Open Access Journals (Sweden)

    Fernández-Golfín, J. I.

    2003-06-01

    Full Text Available In a. sample made up of 3312 boards of scots pine (pinus sylvestris and 3318 boards of laricio pine pinus nigra Van Saltzmannii, both of Spanish provenance, and ranging in size from 100x40x2500 mm to 200x70x4500 mm, previously tested in accordance with the procedure set forth in UNE EN 408 standard, the relationships between the grade determining properties considered in the UNE EN 338 standard (bending strength, global and local modulus of elasticity in bending, density are studied. In addition to these variables, the modulus of elasticity was also considered, calculated by means of the measuring of the transmission speed of an ultrasonic pulse generated by a Sylvatest device. The global modulus of elasticity calculated by measuring the deformation at the neutral axis seems to be the best predictor of the ultimate bending strength, while the local modulus of elasticity proves to be difficult to obtain, and has a lower predictive quality, and so its elimination is suggested. The need to consider one single testing procedure to determine the global modulus of elasticity is also analyzed, along with the convenience of carrying out further studies regarding the use of ultrasonic techniques in order to predict the modulus of elasticity, due to the fact that the systems available are not sufficiently precise.

    En una muestra compuesta por 3.312 piezas de madera aserrada de pino laricio (pimis nigra y 3.318 piezas de pino silvestre (pinus sylvestris de procedencia española y con dimensiones que varían entre 100x40x2.500 mm y 200x70x4.500 mm, previamente ensayada a flexión de acuerdo con el procedimiento descrito en la norma UNE EN 408, se analizan las relaciones existentes entre las propiedades indicadoras establecidas en la norma UNE EN 338 (resistencia última a flexión, módulos de elasticidad global y local en flexión, densidad. Adicionalmente a estas variables se determinó también el módulo de elasticidad obtenido mediante la medici

  19. Zero in on Key Open Problems in Automated NMR Protein Structure Determination

    KAUST Repository

    Abbas, Ahmed

    2015-11-12

    Nuclear magnetic resonance (NMR) is one of the main approaches for protein struc- ture determination. The biggest advantage of this approach is that it can determine the three-dimensional structure of the protein in the solution phase. Thus, the natural dynamics of the protein can be studied. However, NMR protein structure determina- tion is an expertise intensive and time-consuming process. If the structure determi- nation process can be accelerated or even automated by computational methods, that will significantly advance the structural biology field. Our goal in this dissertation is to propose highly efficient and error tolerant methods that can work well on real and noisy data sets of NMR. Our first contribution in this dissertation is the development of a novel peak pick- ing method (WaVPeak). First, WaVPeak denoises the NMR spectra using wavelet smoothing. A brute force method is then used to identify all the candidate peaks. Af- ter that, the volume of each candidate peak is estimated. Finally, the peaks are sorted according to their volumes. WaVPeak is tested on the same benchmark data set that was used to test the state-of-the-art method, PICKY. WaVPeak shows significantly better performance than PICKY in terms of recall and precision. Our second contribution is to propose an automatic method to select peaks pro- duced by peak picking methods. This automatic method is used to overcome the limitations of fixed number-based methods. Our method is based on the Benjamini- Hochberg (B-H) algorithm. The method is used with both WaVPeak and PICKY to automatically select the number of peaks to return from out of hundreds of candidate peaks. The volume (in WaVPeak) and the intensity (in PICKY) are converted into p-values. Peaks that have p-values below some certain threshold are selected. Ex- perimental results show that the new method is better than the fixed number-based method in terms of recall. To improve precision, we tried to eliminate false peaks using

  20. CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO

    International Nuclear Information System (INIS)

    Guerry, Paul; Duong, Viet Dung; Herrmann, Torsten

    2015-01-01

    UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved—including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO–ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications